90% seizure reduction. Only 1 patient was not effectively treated (<50% seizure reduction). Eighty-eight percent of parents reported improvement in behavioral functioning. Shorter duration of epilepsy prior to surgery was a significant predictor of surgical outcome. CONCLUSIONS: Patients with Lennox-Gastaut syndrome symptomatic to hypothalamic hamartomas have better postsurgical outcome due to other etiologies compared with cryptogenic and symptomatic Lennox-Gastaut syndrome patients. However, compared with overall hypothalamic hamartomas postsurgical outcomes, this cohort was less favorable. Earlier surgery may lead to better outcomes.","corpus_id":44510867,"score":0},{"doc_id":"25011392","title":"Ketogenic diet in patients with Lennox-Gastaut syndrome.","abstract":"PURPOSE: The ketogenic diet (KD) has been used as an alternative to antiepileptic drugs (AEDs) for patients with refractory epilepsy. Lennox-Gastaut syndrome (LGS) belongs to the group of epileptic encephalopathies that often prove refractory to AED treatment. In this prospective study we assess the efficacy and tolerability of the KD in patients with LGS. METHODS: Between March 1, 1990 and April 1, 2013, 61 patients who met diagnostic criteria of LGS were seen at our department. Twenty of them were placed on the KD and followed for a minimum of 16 months. RESULTS: The children had previously received a mean of 6.5 different AEDs and were on a mean of 2.5 AEDs when the diet was started. Eighteen months after initiating the diet, fifteen of the initial patients (75%) remained on the diet; three patients (15%) were seizure free, three (15%) had a 75-99% decrease in seizures, two (10%) had a 50-74% decrease in seizures, and the remaining seven children (35%) had a <50% decrease in seizures. Three seizure-free patients were tapered off the diet after remaining seizure free. In the three patients who had a 75-99% decrease in seizures AEDs were reduced. CONCLUSION: The KD is an effective and well-tolerated treatment option for patients with LGS, not only for those with cryptogenic, but also for those with structural LGS. The diet should be considered early in the course of this syndrome.","corpus_id":17045191,"score":0},{"doc_id":"25575287","title":"Acute behavioral crises in psychiatric inpatients with autism spectrum disorder (ASD): recognition of concomitant medical or non-ASD psychiatric conditions predicts enhanced improvement.","abstract":"During adolescence, some individuals with autism spectrum disorder (ASD) engage in severe challenging behaviors, such as aggression, self-injury, disruption, agitation and tantrums. We aimed to assess risk factors associated with very acute behavioral crises in adolescents with ASD admitted to a dedicated neurobehavioral unit. We included retrospectively in 2008 and 2009 29 adolescents and young adults with ASD hospitalized for severe challenging behaviors and proposed a guideline (Perisse et al., 2010) that we applied prospectively for 29 patients recruited for the same indications between 2010 and 2012. In total, 58 patients were admitted (n=70 hospitalizations, mean age=15.66 (±4.07) years, 76% male). We systematically collected data describing socio-demographic characteristics, clinical variables (severity, presence of language, cognitive level), comorbid organic conditions, etiologic diagnosis of the episode, and treatments. We explored predictors of Global Assessment Functioning Scale (GAFS) score and duration of hospitalization at discharge. All but 2 patients exhibited severe autistic symptoms and intellectual disability (ID), and two-thirds had no functional verbal language. During the inpatient stay (mean=84.3 (±94.9) days), patients doubled on average their GAFS scores (mean=17.66 (±9.05) at admission vs. mean=31.4 (±9.48) at discharge). Most common etiologies for acute behavioral crises were organic causes [n=20 (28%), including epilepsy: n=10 (14%) and painful medical conditions: n=10 (14%)], environmental causes [n=17 (25%) including lack of treatment: n=11 (16%) and adjustment disorder: n=6 (9%)], and non-ASD psychiatric condition [n=33 (48%) including catatonia: n=5 (7%), major depressive episode: n=6 (9%), bipolar disorder: n=4 (6%), schizophrenia: n=6 (9%), other/unknown diagnosis: n=12 (17%)]. We found no influence of age, gender, socio-economic status, migration, level of ID, or history of seizure on improvement of GAFS score at discharge. Severity of autism at admission was the only negative predictor (p<.001). Painful medical conditions (p=.04), non-ASD psychiatric diagnoses (p=.001), prior usage of specialized ASD care programs (p=.004), functional language (p=.007), as well as a higher number of challenging behaviors upon admission (p=.001) were associated with higher GAFS scores at discharge. Clinical severity at admission, based on the number of challenging behaviors (r=.35, p=.003) and GAFS score (r=-.32, p=.008) was correlated with a longer inpatient stay. Longer hospitalization was however correlated (r=.27, p=.03) with higher GAFS score at discharge even after adjustment for confounding factors. Challenging behaviors among adolescents with ASD may stem from diverse risk factors, including environmental problems, comorbid acute psychiatric conditions, or somatic illness such as epilepsy or acute pain. The management of these behavioral challenges requires a unified, multidisciplinary approach.","corpus_id":7486089,"score":0},{"doc_id":"26167208","title":"Relationship of Lennox-Gastaut syndrome with perinatal event: A cross-sectional study.","abstract":"INTRODUCTION: About one-half of children with Lennox-Gastaut syndrome (LGS) have history of birth hypoxia or other perinatal event but the knowledge about clinical, radiological profile and severity of epilepsy in these children as compared to those without a perinatal event is not known. MATERIALS AND METHODS: Thirty-one children with LGS were enrolled in this study and divided into two groups: One group with the perinatal event and other group without evidence of the perinatal event. We hypothesized that LGS with the perinatal event will have an early age of onset of LGS, more motor deficits and abnormal brain magnetic resonance imaging (MRI) and more severe epilepsy. RESULTS: There were 17 children in the perinatal event group and 14 in the other group. The mean age of onset of illness was significantly earlier in the perinatal event group (P < 0.05). More children in the perinatal event group had delayed milestones (P < 0.05), had higher seizure frequency (P < 0.05) however; there was no significant difference in number of anti-epileptic drugs consumed, motor deficits or MRI abnormalities. CONCLUSION: LGS children with the perinatal event have more severe epilepsy with early onset of disease and delayed milestones. History of perinatal insult in these children may help in predicting prognosis in LGS.","corpus_id":22850987,"score":0},{"doc_id":"26245776","title":"Clobazam and Aggression-Related Adverse Events in Pediatric Patients With Lennox-Gastaut Syndrome.","abstract":"BACKGROUND: Lennox-Gastaut syndrome is an intractable epileptic encephalopathy marked by frequent drop seizures. Most patients develop moderate intellectual disability and behavioral problems, including hyperactivity, aggressiveness, insecurity, and autistic features. Treatment with benzodiazepines, including clobazam, may increase aggression/behavioral problems in patients with Lennox-Gastaut syndrome. Post hoc analyses of data from the OV-1012 trial assessed the potential for behavioral effects with clobazam treatment in pediatric (2 to 18 years) patients with Lennox-Gastaut syndrome. METHODS: OV-1012 was a phase 3, randomized, double-blind, parallel-group trial comprising a 4-week baseline period, 3-week titration period, and a 12-week maintenance period. Data from 194 patients were analyzed for a history of aggression/behavioral problems, occurrence of aggression-related adverse events, and by assessment of potential drug-related effects on four behavior domains of the Child Behavior Checklist. RESULTS: Twenty-nine aggression-related adverse events were reported for 27 (13.9%) patients. Similar percentages of clobazam-treated patients with and without a history of aggressive behavior experienced an aggression-related adverse event (16.7% versus 15.5%, respectively). In the medium- and high-dosage clobazam groups, onset of aggression-related adverse effects occurred within the 3-week titration period with 63.2% resolving by the end of the study. Aggression-related adverse event onset and resolution were similar for the low-dosage clobazam and placebo groups. Analysis of baseline to postbaseline T scores for the behavior domains of the Child Behavior Checklist indicated no significant differences between clobazam and placebo. CONCLUSIONS: Post hoc analyses indicate that the overall rate of aggression with clobazam treatment was low and dosage dependent. Clobazam treatment was effective in reducing drop seizures regardless of aggression experience.","corpus_id":207349934,"score":0},{"doc_id":"26808205","title":"Pontine and cerebral atrophy in Lennox-Gastaut syndrome.","abstract":"OBJECTIVES: Lennox-Gastaut syndrome (LGS) is a severe epilepsy of childhood onset associated with intellectual disability and multiple seizure types. Characteristic interictal electrographic discharges include generalized paroxysmal fast activity and slow spike and wave, which we have previously shown recruit widespread areas of association cortex. We wished to determine whether patients with Lennox-Gastaut syndrome (LGS) have changes in cerebral volumes that match this pattern of cortical recruitment. METHODS: High resolution T1 weighted structural MRI was collected from 10 patients with LGS and 10 age and sex matched controls. Voxel-based morphometry (VBM) was used to compare tissue volumes across the whole brain (grey matter, white matter and CSF) and pontine volume between patients and controls, as well as to identify other regions of maximal tissue loss. RESULTS: LGS patients showed a significant decrease in whole brain volume compared to controls. Cortical atrophy was prominent in the mesial frontal region and bilateral anterior temporal poles. White matter atrophy was widespread and included peri-central and premotor regions. Atrophy was prominent in the pons, particularly in the region of the reticular formation. Grey matter atrophy trended to progress with age. SIGNIFICANCE: Grey and white matter atrophy are a feature of Lennox-Gastaut syndrome. Grey matter atrophy is apparent in the mesial frontal lobe suggesting this region may be an important node in the epilepsy network of LGS. Atrophy maximal in the pons and cerebellum mimics the patterns of seizure spread that has been previously observed during tonic seizures. This supports the idea that the pons is a key part of the epilepsy network in LGS.","corpus_id":24616061,"score":0},{"doc_id":"27665735","title":"The molecular and phenotypic spectrum of IQSEC2-related epilepsy.","abstract":"OBJECTIVE: IQSEC2 is an X-linked gene associated with intellectual disability (ID) and epilepsy. Herein we characterize the epilepsy/epileptic encephalopathy of patients with IQSEC2 pathogenic variants. METHODS: Forty-eight patients with IQSEC2 variants were identified worldwide through Medline search. Two patients were recruited from our early onset epileptic encephalopathy cohort and one patient from personal communication. The 18 patients who have epilepsy in addition to ID are the subject of this study. Information regarding the 18 patients was ascertained by questionnaire provided to the treating clinicians. RESULTS: Six affected individuals had an inherited IQSEC2 variant and 12 had a de novo one (male-to-female ratio, 12:6). The pathogenic variant types were as follows: missense (8), nonsense (5), frameshift (1), intragenic duplications (2), translocation (1), and insertion (1). An epileptic encephalopathy was diagnosed in 9 (50%) of 18 patients. Seizure onset ranged from 8 months to 4 years; seizure types included spasms, atonic, myoclonic, tonic, absence, focal seizures, and generalized tonic-clonic (GTC) seizures. The electroclinical syndromes could be defined in five patients: late-onset epileptic spasms (three) and Lennox-Gastaut or Lennox-Gastaut-like syndrome (two). Seizures were pharmacoresistant in all affected individuals with epileptic encephalopathy. The epilepsy in the other nine patients had a variable age at onset from infancy to 18 years; seizure types included GTC and absence seizures in the hereditary cases and GTC and focal seizures in de novo cases. Seizures were responsive to medical treatment in most cases. All 18 patients had moderate to profound intellectual disability. Developmental regression, autistic features, hypotonia, strabismus, and white matter changes on brain magnetic resonance imaging (MRI) were prominent features. SIGNIFICANCE: The phenotypic spectrum of IQSEC2 disorders includes epilepsy and epileptic encephalopathy. Epileptic encephalopathy is a main clinical feature in sporadic cases. IQSEC2 should be evaluated in both male and female patients with an epileptic encephalopathy.","corpus_id":24916469,"score":0},{"doc_id":"28471101","title":"Ophthalmologic Features of Lennox-Gastaut Syndrome.","abstract":"PURPOSE: To describe the characteristics and frequency of ophthalmologic findings in patients with Lennox-Gastaut syndrome (LGS). METHODS: The medical records of patients diagnosed with LGS at Seoul National University Children's Hospital from January 2004 to August 2014 were retrospectively reviewed. The records of 34 patients (mean age ± standard deviation, 2.66 ± 3.51 years; male, 58.8%) were reviewed. The primary measure was the incidence of ophthalmologic manifestations. RESULTS: Of the 34 patients, 88.2% had at least one ocular abnormality. Refractive error (52.9%) was the most frequently observed ophthalmologic manifestation in patients with LGS, followed by strabismus (32.4%), cortical visual impairment (23.5%), and retinopathy of prematurity (8.8%). Among these cases, seven patients had exotropia and three had esotropia. CONCLUSIONS: LGS is a childhood-onset epileptic encephalopathy with variable ophthalmologic manifestations, the most frequent being refractive errors. Patients with suspected LGS should be examined regularly because ophthalmological features can change during their disease course.","corpus_id":28671096,"score":0},{"doc_id":"28957735","title":"Inattention and hyperactivity/impulsivity among children with attention-deficit/hyperactivity-disorder, autism spectrum disorder, and intellectual disability.","abstract":"BACKGROUND: Attention-Deficit/Hyperactivity Disorder (ADHD), Autism Spectrum Disorder (ASD), and Intellectual Disability (ID) are common co-occurring neurodevelopmental disorders; however, limited research exists regarding the presentation and severity of overlapping symptomology, particularly inattention and hyperactivity/impulsivity, when a child is diagnosed with one of more of these neurodevelopmental disorders. AIMS: As difficulties with inattention and hyperactivity/impulsivity are symptoms frequently associated with these disorders, the current study aims to determine the differences in the severity of inattention and hyperactivity/impulsivity in children diagnosed with ADHD, ASD, ID, and co-occurring diagnosis of ADHD/ID, ASD/ADHD, and ASD/ID. METHODS AND PROCEDURES: Participants in the current study included 113 children between the ages of 6 and 11 who were diagnosed with ADHD, ASD, ID, ADHD/ID, ASD/ADHD, or ASD/ID. Two MANOVA analyses were used to compare these groups witih respsect to symptom (i.e., inattention, hyperactivity/impulsivity) severity. OUTCOMES AND RESULTS: Results indicated that the majority of diagnostic groups experienced elevated levels of both inattention and hyperactivity/impulsivity. However, results yielded differences in inattention and hyperactivity/impulsivity severity. In addition, differences in measure sensitivity across behavioral instruments was found. CONCLUSIONS AND IMPLICATIONS: Children with neurodevelopmental disorders often exhibit inattention and hyperactivity/impulsivity, particularly those with ADHD, ASD, ASD/ADHD, and ADHD/ID; therefore, differential diagnosis may be complicated due to similarities in ADHD symptom severity. However, intellectual abilities may be an important consideration for practitioners in the differential diagnosis process as children with ID and ASD/ID exhibited significantly less inattention and hyperactive/impulsive behaviors. Additionally, the use of multiple behavior rating measures in conjunction with other assessment procedures may help practitioners determine the most appropriate diagnosis.","corpus_id":46309266,"score":0}],"string":"[\n {\n \"doc_id\": \"21620773\",\n \"title\": \"Autism in Dravet syndrome: prevalence, features, and relationship to the clinical characteristics of epilepsy and mental retardation.\",\n \"abstract\": \"Autism is a pervasive developmental disorder that frequently co-occurs with epilepsy. Dravet syndrome is a severe epileptic encephalopathy associated with psychomotor developmental delay. Autism in Dravet syndrome, however, has rarely been studied. In this study, the prevalence and features of autism in patients with Dravet syndrome, their potential association with mental retardation, and the clinical characteristics of epilepsy were investigated. Clinical data of 37 patients with Dravet syndrome were collected, and evaluations of autism and mental retardation were performed. Nine patients (24.3%) met the criteria for autism. All patients with autism showed speech delay, no emotional reciprocity, and narrow interests, whereas 89.3, 46.4, and 39.9% of patients without autism had speech delay, short temper, and narrow interests, respectively. Mental retardation was observed in 94.6% of patients with Dravet syndrome, with more frequent severe or profound mental retardation in those with autism. The clinical features of epilepsy did not statistically differ between the patients with autism and the patients without autism.\",\n \"corpus_id\": 25596753,\n \"score\": 2\n },\n {\n \"doc_id\": \"28186331\",\n \"title\": \"Adult motor phenotype differentiates Dravet syndrome from Lennox-Gastaut syndrome and links SCN1A to early onset parkinsonian features.\",\n \"abstract\": \"Distinguishing adult patients with Lennox-Gastaut syndrome from those with Dravet syndrome is challenging. We have previously reported that patients with Dravet syndrome present a very peculiar motor phenotype. Here we sought to confirm that this association was not linked to the chronic use of antiepileptic drugs or the many lifetime seizures. To this aim, we studied 14 adult patients with Lennox-Gastaut syndrome and 14 adults with Dravet syndrome because both conditions share similar seizure severity. We found that antecollis and parkinsonian gait were significantly more common in the Dravet group, thus suggesting that these features are part of the Dravet syndrome adult phenotype.\",\n \"corpus_id\": 28914053,\n \"score\": 2\n },\n {\n \"doc_id\": \"19588340\",\n \"title\": \"Treatment of Lennox-Gastaut syndrome.\",\n \"abstract\": \"BACKGROUND: The Lennox-Gastaut syndrome is an age-specific disorder, characterised by epileptic seizures, a characteristic electroencephalogram (EEG), psychomotor delay and behaviour disorders. It occurs more frequently in males and onset is usually before the age of eight, with a peak between three and five years. Late cases occurring in adolescence and early adulthood have rarely been reported. Language is frequently affected, with both slowness in ideation and expression in addition to difficulties of motor dysfunction. Severe behavioural disorders (for example hyperactivity, aggressiveness and autistic tendencies) and personality disorders are nearly always present. There is also a tendency for psychosis to develop with time. The long-term prognosis is poor; although the epilepsy often improves, complete seizure freedom is rare and conversely the mental and psychiatric disorders tend to worsen with time. OBJECTIVES: To compare the effects of pharmaceutical therapies used to treat Lennox-Gastaut syndrome in terms of control of seizures and adverse effects. Many people who suffer from this syndrome will already be receiving other antiepileptic medications at the time of their entry into a trial. However, for the purpose of this review we will only consider the effect of the single therapeutic agent being trialed (often as add-on therapy). SEARCH STRATEGY: We searched the Cochrane Epilepsy Group's Specialized Register (February 2009), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 1, 2009), and MEDLINE (1950 to January 2009). We also searched EMBASE (1980 to March 2003). We imposed no language restrictions. We searched the ISRCTN register for ongoing trials and in addition, we contacted pharmaceutical companies and colleagues in the field to seek any unpublished or ongoing studies. SELECTION CRITERIA: All randomised controlled trials (RCTs) of the administration of drug therapy to patients with Lennox-Gastaut syndrome. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data. Analysis included assessing study quality, as well as statistical analysis of the effects on overall seizure rates and effects on specific seizure types (e.g. drop attacks), adverse effects and mortality. MAIN RESULTS: We found seven RCTs, but were unable to perform any meta-analysis, because each trial looked at different populations, different therapies and considered different outcomes. AUTHORS' CONCLUSIONS: The optimum treatment for Lennox-Gastaut syndrome remains uncertain and no study to date has shown any one drug to be highly efficacious; rufinamide, lamotrigine, topiramate and felbamate may be helpful as add-on therapy. Until further research has been undertaken, clinicians will need to continue to consider each patient individually, taking into account the potential benefit of each therapy weighed against the risk of adverse effects.\",\n \"corpus_id\": 205168993,\n \"score\": 1\n },\n {\n \"doc_id\": \"19589458\",\n \"title\": \"Factors influencing the evolution of West syndrome to Lennox-Gastaut syndrome.\",\n \"abstract\": \"This study examines factors influencing the evolution of West syndrome to Lennox-Gastaut syndrome. The study population comprised 98 patients diagnosed with West syndrome and monitored for at least 3 years. During follow-up, West syndrome evolved to Lennox-Gastaut syndrome in 48 of the 98 patients. Etiology analysis indicated that West syndrome was cryptogenic in 36 patients (36.7%) and symptomatic in 62 (63.3%). West syndrome was managed with antiepileptic drugs in 31 patients, ketogenic diets in 33 patients, hormonal therapy with prednisolone in 45 patients and with adrenocorticotropic hormone in 15 patients, epileptic surgery in 3 patients, and either no treatment or only herbal medication in 4 patients. The risk of developing Lennox-Gastaut syndrome was significantly lower in patients who were placed on a ketogenic diet, given prednisolone or adrenocorticotropic hormone, or treated with a combination of these two therapies (bivariate logistic regression analysis, P < 0.05). There was no relationship between the development of Lennox-Gastaut syndrome and age at West syndrome onset or disease etiology. In conclusion, a ketogenic diet and hormonal therapy may play key roles in preventing encephalopathy in patients with West syndrome.\",\n \"corpus_id\": 207347888,\n \"score\": 1\n },\n {\n \"doc_id\": \"19737795\",\n \"title\": \"Autism spectrum disorders in young children: effect of changes in diagnostic practices.\",\n \"abstract\": \"BACKGROUND: It is unclear whether the increase in autism over the past two decades is a real increase or due to changes in diagnosis and ascertainment of autism spectrum disorders (ASDs), which include autism, Asperger syndrome and pervasive developmental disorder not otherwise specified (PDD-NOS). The aim of this study was to examine the trends in ASD over time in Western Australia (WA) and the possible effects and contribution of changes in diagnostic criteria, age at diagnosis, eligibility for service provision based on ASD diagnoses and changes in diagnostic practices. METHODS: A population-based study was conducted among the cohort of children born in WA between 1983 and 1999 and diagnosed with ASD between the age of 2 and 8 years up to December 31, 2004. The trend in ASD diagnosis over the study period was assessed by investigating birth cohort and period effects, and examining whether these were modified by age of diagnosis. ASD diagnosis corresponding with changes in diagnostic criteria, funding and service provision over time were also investigated. A subgroup analysis of children aged <or=5 years was also conducted to examine trends in the incidence and age of diagnosis of ASD and intellectual disability (ID) and to investigate the role of changes in diagnostic practices. RESULTS: The overall prevalence of ASD among children born between 1983 and 1999 and diagnosed by age 8 was 30 per 10,000 births with the prevalence of autism comprising 21 per 10,000 births. The prevalence of ASD increased by 11.9% per annum, from 8 cases per 10,000 births in 1983 to 46 cases per 10,000 births in 1999. The annual incidence of ASD, based on newly diagnosed ASD cases in each year from 1985 to 2002, increased over the study period. The increase in incidence of ASD appeared to coincide with changes in diagnostic criteria and availability of funding and services in WA, particularly for children aged <5 years. The age-specific rates of autism and PDD-NOS increased over time and the median age of diagnosis for autism decreased from 4 to 3 years of age throughout the 1990s. For children aged <or=5 years the incidence of ASD diagnosis increased significantly from 1992, with an average annual increase of 22%. Similar findings were found for autism. In the corresponding years the incidence of diagnosis of severe ID fell by 10% per annum and mild-moderate ID increased by 3% per annum. CONCLUSIONS: The rise in incidence of all types of ASDs by year of diagnosis appears to be related to changes in diagnostic and service provision practices in WA. In children aged <or=5 years, diagnosis of severe ID decreased, but mild-moderate ID increased during the study period. A true increase in ASD cannot be ruled out.\",\n \"corpus_id\": 5569035,\n \"score\": 1\n },\n {\n \"doc_id\": \"19782004\",\n \"title\": \"SCN1A mutation screening in adult patients with Lennox-Gastaut syndrome features.\",\n \"abstract\": \"Mutations in the SCN1A gene have been identified in a variety of epilepsy phenotypes, from severe encephalopathies such as Dravet syndrome to milder familial forms such as generalized epilepsy with febrile seizures plus. In a previous study, an SCN1A mutation was also identified in a patient with Lennox-Gastaut syndrome (LGS), and the aim of our study was to investigate the importance of mutations in the SCN1A gene in Norwegian patients with clinical features of LGS. We screened 22 adult patients for SCN1A mutations by direct sequencing of DNA and for micro-rearrangements with multiplex ligation-dependent probe amplification. In one patient a mutation was found, which demonstrates a clinical overlap between LGS and Dravet syndrome. This finding emphasizes the significance of SCN1A mutations also in epileptic disorders with features of LGS, particularly in the myoclonic variant of the disorder.\",\n \"corpus_id\": 35833269,\n \"score\": 1\n },\n {\n \"doc_id\": \"20533249\",\n \"title\": \"[Lennox-Gastaut syndrome in Spain: a descriptive retrospective epidemiological study].\",\n \"abstract\": \"Síndrome de Lennox-Gastaut en España: estudio epidemiológico retrospectivo y descriptivo. INTRODUCTION: Lennox-Gastaut syndrome (LGS) is one of the most severe epileptic syndromes in childhood. It is characterised by the presence of several types of seizures, a characteristic electroencephalographic trace and its frequent association with mental retardation. There are no accurate data on the epidemiology of LGS in Spain. AIM: To describe the epidemiological profile of LGS in Spain. PATIENTS AND METHODS: We conducted a retrospective epidemiological study of a series of 331 patients with LGS from 50 Spanish hospitals. Patients were considered to be cases of LGS if they had at least two of the three types of seizures that characterise LGS (axial tonic seizures, atypical absences and atonic seizures) and displayed slow diffuse intercritical spike-wave activity (lower than 3 Hz) in the electroencephalogram in wakefulness. RESULTS: The mean age of the patients was 18.2 +/- 13.5 years. Of the total sample, 62% were males and 97% had cognitive retardation. And 54% of cases had a symptomatic aetiology. The most frequent types of seizures were axial tonic (89%), followed by the atypical absent type (84%) and atonic seizures (69%). In all, 99% of patients were treated with polytherapy, the most commonly used drugs being valproic acid, lamotrigine and topiramate. CONCLUSIONS: The results of the study are in line with those from previous analyses carried out in populations with similar characteristics. The high percentage of LGS patients with cognitive retardation in this epileptic encephalopathy results in important family and social repercussions.\",\n \"corpus_id\": 7315038,\n \"score\": 1\n },\n {\n \"doc_id\": \"20563296\",\n \"title\": \"Comparisons between individuals with autism spectrum disorders and individuals with Down syndrome in adulthood.\",\n \"abstract\": \"Differences between 70 adults with autism spectrum disorders and intellectual disability and 70 age-matched adults with Down syndrome were examined on variables indicative of independence in adult life. Adults with autism spectrum disorder had less residential independence and social contact with friends, had more limited functional abilities and literacy, exhibited more behavior problems, had more unmet service needs, and received fewer services as compared to adults with Down syndrome. Reflecting these differences, adults with autism spectrum disorder were less likely to be classified as having high or moderate levels of independence in adult life as compared to adults with Down syndrome. Predictors of independence in adult life differed for adults with autism spectrum disorder as compared with adults who have Down syndrome. Implications for service delivery are discussed.\",\n \"corpus_id\": 31892051,\n \"score\": 1\n },\n {\n \"doc_id\": \"21233883\",\n \"title\": \"[Lennox-Gastaut syndrome--course and treatment].\",\n \"abstract\": \"Lennox-Gastauts syndrom--forløp og behandling. BACKGROUND: Lennox-Gastaut syndrome (LGS) is a severe epileptic encephalopathy, which starts in childhood with various seizure types. The children develop cognitive impairment and a typical EEG pattern. The aim of this article is to describe the clinical presentation of LGS, with particular emphasis on the course in adulthood. MATERIAL AND METHODS: The article is based on literature (up to November 2009) identified through a non-systematic search in PubMed and our own clinical experience. RESULTS: There are cases with unknown etiology and symptomatic cases with a wide spectrum of etiologies. While children with LGS have a high frequency of generalized seizures, seizure activity tends to decrease somewhat in adulthood and the seizures may become more focal. The prognosis is usually poor. The adult patient with LGS is clearly affected by global encephalopathy and is typically characterized by bluntness, apathy, progressive cognitive failure and motoric deficits. Valproate has been the first-line treatment for many years, but newer antiepileptic drugs; such as lamotrigine, topiramate and rufinamide, have shown efficacy as add-on therapy. Overtreatment with antiepileptic drugs is common. INTERPRETATION: For optimal treatment, a specialist should follow LGS patients at all ages. New treatment options with milder side effects may improve the quality of life for these patients.\",\n \"corpus_id\": 27217100,\n \"score\": 1\n },\n {\n \"doc_id\": \"21341220\",\n \"title\": \"[Development of Lennox-Gastaut syndrome in adulthood].\",\n \"abstract\": \"Evolucion del sindrome de Lennox-Gastaut en la edad adulta. INTRODUCTION: Lennox-Gastaut syndrome (LGS) is an epileptic encephalopathy that starts in childhood and has an unknown pathophysiological mechanism. Studies on the progress of LGS reveal a poor prognosis. PATIENTS AND METHODS: A retrospective study of 1629 patients with epilepsy was conducted. Patients included in the study were those with an age of onset during childhood, tonic seizures and atypical absences (who might also suffer from other types of seizures); electroencephalogram (EEG) showing generalised slow spike-wave and generalised fast activity; mental retardation and a follow-up time of at least 10 years. RESULTS: The sample consisted of 12 patients, 9 of whom were males. Follow-up time: 20 years. Onset of seizures: 3 years. Cryptogenic LGS: 67%; symptomatic: 33%. Frequency of the seizures at onset: daily (83.3%) or weekly (16.7%). Types of seizures: tonic and atypical absences (100%); drop-attacks (83%); generalised tonic-clonic (75%); myoclonias (41.7%); partial (8.3%) and pseudo-epileptic (8.3%). EEG with slow background activity, generalised slow spike-wave and generalised fast activity: 100%. Fifty percent of the patients had at least one epileptic status. They used an average of 7.5 different antiepileptic drugs. At the end of the follow-up 33% were suffering from seizures on a daily basis; 17% were weekly and 42% monthly. A total of 8.3% were free from seizures. All of them were following combination therapy: 17% in bitherapy and 83% with an average of 3.8 drugs (range: 3-5). A total of 92% suffered from severe or very severe mental retardation. Fifty percent required neuroleptic drugs due to behavioural disorders. CONCLUSIONS: Despite the fact that the diagnosis of LGS is serious, we observed a decrease in the number of seizures after several years of development, although the antiepileptic combination therapy remains constant. The mental retardation and behavioural disorders lead to a poor functional prognosis.\",\n \"corpus_id\": 23607702,\n \"score\": 1\n },\n {\n \"doc_id\": \"21351810\",\n \"title\": \"Management of seizures in Lennox-Gastaut syndrome.\",\n \"abstract\": \"Lennox-Gastaut syndrome is an epilepsy syndrome that begins in childhood (between 1 and 8 years of age), worsens during latency and persists frequently into adulthood, is refractory to antiepileptic medications, and results in cognitive decline and behavioral problems in affected individuals. Seizure types consist primarily of axial tonic, atonic, and atypical absence; nocturnal tonic seizures are the most common seizure pattern in this population, but often are not one of the initial seizure patterns. Some patients also have myoclonic seizures; this seizure pattern is less frequent than the three preceding types. Although there are some cases that are cryptogenic, most are symptomatic, arising during prenatal and perinatal periods from intrauterine infections, and vascular insults to the brain. Examples of causes of Lennox-Gastaut syndrome include migrational abnormalities of the brain, late effects of CNS infections, certain genetic disorders such as tuberous sclerosis, and inherited metabolic disorders. The difficulty early in the course of Lennox-Gastaut syndrome is distinguishing this diagnosis from severe myoclonic epilepsy of infancy (Dravet syndrome) or from myoclonic-astatic epilepsy (Doose syndrome), as the seizure patterns in these three syndromes may overlap at the onset. EEG is a helpful diagnostic tool in the diagnosis of Lennox-Gastaut syndrome, usually demonstrating high voltage, bifrontal 1.5-2.5 Hz spike and wave complexes interictally, and attenuation with paroxysmal fast activity (10-13 Hz) during the ictal phase. Treatment options for Lennox-Gastaut syndrome have been less than optimal. In recent years, several drugs have been tested and approved for the treatment of this syndrome; these include felbamate, lamotrigine, topiramate, and rufinamide. The long-term outcome does not appear to be any better with the newer antiepileptic drugs than when using earlier prescribed antiepileptic drugs or polytherapy. Treatment options other than antiepileptic drugs include a ketogenic diet, vagus nerve stimulation, and corpus callosotomy. Long-term outcome of these patients relative to seizure control and cognition is poor. Most develop moderate intellectual disability within a few years of onset of the syndrome. Many develop behavioral problems with inattention, hyperactivity, and aggression.\",\n \"corpus_id\": 23335844,\n \"score\": 1\n },\n {\n \"doc_id\": \"21669558\",\n \"title\": \"All children who experience epileptic falls do not necessarily have Lennox-Gastaut syndrome... but many do.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe, chronic, epileptic encephalopathy, primarily with childhood onset, which is characterised by a triad of features: multiple seizure types, including tonic seizures that may appear late in the course of the disorder; abnormal EEG features with slow spike-wave discharges; and cognitive impairment. Recognition of LGS is problematic, since the seizure types and EEG features that characterise it are not pathognomonic and often change over time. Furthermore, although seizures associated with LGS may occur de novo, the appearance of core LGS seizures may be preceded by prolonged periods of other seizure types, including myoclonic seizures, partial seizures, or infantile spasms. This has led some authors to postulate that a continuum between LGS and other types of childhood epilepsy may exist. Accurate diagnosis requires careful assessment of both clinical and EEG features, in order to distinguish LGS from other childhood epilepsy syndromes, such as atypical benign partial epilepsy of childhood, Dravet syndrome or epilepsies with predominantly myoclonic-astatic seizures. Since there is no biological marker that can be used to confirm diagnosis of LGS and because of the multiple aetiologies that could lead to its development, early referral to a specialist team may prove to be crucial for facilitating both diagnosis and management. Such an approach ensures that patients receive the appropriate treatment at the correct time, providing the best opportunity for the clinical course and overall prognosis to be improved. Effective management of LGS requires regular reappraisal of the evolving symptoms and features, and adjustment of the treatment accordingly.\",\n \"corpus_id\": 1156266,\n \"score\": 1\n },\n {\n \"doc_id\": \"21790560\",\n \"title\": \"Definition and natural history of Lennox-Gastaut syndrome.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a rare epileptic encephalopathy with a peak age of onset of 3-5 years of age. Reported prevalence rates for LGS vary widely from 1-10% of all childhood epilepsies. Incidence rates are much lower. LGS is characterized by intractable, multiple, generalized seizure types and an interictal electroencephalogram showing bursts of slow spike-and-wave, paroxysmal bursts of generalized polyspikes, and a slow background. All patients have tonic seizures during sleep that may be subtle, and nearly all have treatment-resistant, lifelong epilepsy. Cognitive stagnation and behavioral problems are seen in almost all patients and lead to a life of dependency. The differential diagnosis includes other symptomatic generalized epilepsies and pseudo-Lennox syndrome. Misdiagnosis is common. Children and adults with LGS have an enormous impact on their families, and efforts to improve the quality of life for these patients are complex.\",\n \"corpus_id\": 30931205,\n \"score\": 1\n },\n {\n \"doc_id\": \"21883598\",\n \"title\": \"Autism spectrum disorder in Down syndrome: cluster analysis of Aberrant Behaviour Checklist data supports diagnosis.\",\n \"abstract\": \"BACKGROUND: The diagnostic validity of autism spectrum disorder (ASD) based on Diagnostic and Statistical Manual of Mental Disorders (DSM) has been challenged in Down syndrome (DS), because of the high prevalence of cognitive impairments in this population. Therefore, we attempted to validate DSM-based diagnoses via an unbiased categorisation of participants with a DSM-independent behavioural instrument. METHODS: Based on scores on the Aberrant Behaviour Checklist - Community, we performed sequential factor (four DS-relevant factors: Autism-Like Behaviour, Disruptive Behaviour, Hyperactivity, Self-Injury) and cluster analyses on a 293-participant paediatric DS clinic cohort. The four resulting clusters were compared with DSM-delineated groups: DS + ASD, DS + None (no DSM diagnosis), DS + DBD (disruptive behaviour disorder) and DS + SMD (stereotypic movement disorder), the latter two as comparison groups. RESULTS: Two clusters were identified with DS + ASD: Cluster 1 (35.1%) with higher disruptive behaviour and Cluster 4 (48.2%) with more severe autistic behaviour and higher percentage of late onset ASD. The majority of participants in DS + None (71.9%) and DS + DBD (87.5%) were classified into Cluster 2 and 3, respectively, while participants in DS + SMD were relatively evenly distributed throughout the four clusters. CONCLUSIONS: Our unbiased, DSM-independent analyses, using a rating scale specifically designed for individuals with severe intellectual disability, demonstrated that DSM-based criteria of ASD are applicable to DS individuals despite their cognitive impairments. Two DS + ASD clusters were identified and supported the existence of at least two subtypes of ASD in DS, which deserve further characterisation. Despite the prominence of stereotypic behaviour in DS, the SMD diagnosis was not identified by cluster analysis, suggesting that high-level stereotypy is distributed throughout DS. Further supporting DSM diagnoses, typically behaving DS participants were easily distinguished as a group from those with maladaptive behaviours.\",\n \"corpus_id\": 205339081,\n \"score\": 1\n },\n {\n \"doc_id\": \"22738402\",\n \"title\": \"High-functioning autism spectrum disorder and fragile X syndrome: report of two affected sisters.\",\n \"abstract\": \"BACKGROUND: Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability (ID), as well as the most frequent monogenic cause of autism spectrum disorder (ASD). Men with FXS exhibit ID, often associated with autistics features, whereas women heterozygous for the full mutation are typically less severely affected; about half have a normal or borderline intelligence quotient (IQ). Previous findings have shown a strong association between ID and ASD in both men and women with FXS. We describe here the case of two sisters with ASD and FXS but without ID. One of the sisters presented with high-functioning autism, the other one with pervasive developmental disorder not otherwise specified and low normal IQ. METHODS: The methylation status of the mutated FMR1 alleles was examined by Southern blot and methylation-sensitive polymerase chain reaction. The X-chromosome inactivation was determined by analyzing the methylation status of the androgen receptor at Xq12. RESULTS: Both sisters carried a full mutation in the FMR1 gene, with complete methylation and random X chromosome inactivation. We present the phenotype of the two sisters and other family members. CONCLUSIONS: These findings suggest that autistic behaviors and cognitive impairment can manifest as independent traits in FXS. Mutations in FMR1, known to cause syndromic autism, may also contribute to the etiology of high-functioning, non-syndromic ASD, particularly in women. Thus, screening for FXS in patients with ASD should not be limited to those with comorbid ID.\",\n \"corpus_id\": 6000786,\n \"score\": 1\n },\n {\n \"doc_id\": \"22921514\",\n \"title\": \"Lennox-Gastaut syndrome in south Iran: electro-clinical manifestations.\",\n \"abstract\": \"PURPOSE: Lennox-Gastaut syndrome (LGS) is an uncommon epileptic encephalopathy. In this study, we tried to determine the clinical and EEG characteristics of patients with LGS in south Iran. METHODS: In this retrospective study, all patients with a clinical diagnosis of LGS were recruited at the outpatient epilepsy clinic at Shiraz University of Medical Sciences from 2008 through 2012. Age, gender, age at seizure onset, seizure type(s), epilepsy risk factors, EEG and imaging findings of all patients were registered routinely. RESULTS: During the study period, 2500 patients with epilepsy were registered at our epilepsy clinic. One-hundred and thirty-five patients (5.4%) were diagnosed as having LGS. Age of onset (mean±standard deviation) was 3.2±3.8 years. In 14 (10.4%) patients, age of onset was above 8 years. Eighty-three patients (61.5%) were male and 52 (38.5%) were female. The most common seizure type was tonic, followed by generalized tonic-clonic and myoclonic seizures. The most common EEG finding was slow spike-wave complexes. The most common abnormal MRI finding was brain atrophy. CONCLUSION: LGS is an uncommon epileptic encephalopathy characterized by multiple seizure types, a specific electroencephalographic pattern and psychomotor retardation, beginning in childhood. However, variants of this classical triad including atypical EEG findings, normal psychomotor function, and late-onset disease could be seen in some patients. These atypical findings in a patient with typical history for LGS should not deter from the correct diagnosis. The mainstay for making a correct syndromic diagnosis is a detailed clinical history.\",\n \"corpus_id\": 283375,\n \"score\": 1\n },\n {\n \"doc_id\": \"23415449\",\n \"title\": \"Copy number variants in adult patients with Lennox-Gastaut syndrome features.\",\n \"abstract\": \"PURPOSE: Lennox-Gastaut syndrome (LGS) is a severe epileptic encephalopathy with complex etiology. To explore possible genetic predispositions and causes of LGS, we have searched for copy number variants (CNVs). METHODS: We studied 21 patients with LGS or LGS-like epilepsy for CNVs using whole-genome array comparative genomic hybridization (aCGH). KEY FINDINGS: Eight patients (38%) carried rare CNVs that might contribute to their phenotype. The pathogenicity could be questioned in some of them, but in four patients (19%) a causative role was considered highly probable. Three had CNVs and clinical features consistent with known genetic syndromes: 22q13.3 deletion, 2q23.1 deletion, and MECP2 duplication. SIGNIFICANCE: There is a high frequency of rare CNVs in adult patients with LGS-like epilepsy. The phenotypes of these background disorders may be obscured by the effects of intractable seizures and massive antiepileptic drug treatment. Previously, syndromic disorders were primarily identified by their clinical features; however, a genome wide approach with identification of the genotype might shed light on the phenotype.\",\n \"corpus_id\": 6221643,\n \"score\": 1\n },\n {\n \"doc_id\": \"23450537\",\n \"title\": \"Treatment of Lennox-Gastaut syndrome.\",\n \"abstract\": \"BACKGROUND: The Lennox-Gastaut syndrome (LGS) is an age-specific disorder, characterised by epileptic seizures, a characteristic electroencephalogram (EEG), psychomotor delay and behavioural disorder. It occurs more frequently in males and onset is usually before the age of eight years, with a peak between three and five years of age. Late cases occurring in adolescence and early adulthood have rarely been reported. Language is frequently affected, with both slowness in ideation and expression in addition to difficulties of motor dysfunction. Severe behavioural disorders (e.g. hyperactivity, aggressiveness and autistic tendencies) and personality disorders are nearly always present. There is also a tendency for psychosis to develop with time. The long-term prognosis is poor; although the epilepsy often improves, complete seizure freedom is rare and conversely the mental and psychiatric disorders tend to worsen with time. OBJECTIVES: To compare the effects of pharmaceutical therapies used to treat LGS in terms of control of seizures and adverse effects. Many people who suffer from this syndrome will already be receiving other antiepileptic medications at the time of their entry into a trial. However, for the purpose of this review we will only consider the effect of the single therapeutic agent being trialled (often as add-on therapy). SEARCH METHODS: We searched the Cochrane Epilepsy Group's Specialized Register (18 October 2012), the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library Issue 10 of 12, 2012) and MEDLINE (1946 to October week 2, 2012). We also searched EMBASE (1980 to March 2003). We imposed no language restrictions. We searched the International Standard Randomised Controlled Trial Number (ISRCTN) register (18 October 2012) for ongoing trials and in addition, we contacted pharmaceutical companies and colleagues in the field to seek any unpublished or ongoing studies. SELECTION CRITERIA: All randomised controlled trials (RCTs) of the administration of drug therapy to patients with LGS. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data. Analysis included assessing study quality, as well as statistical analysis of the effects on overall seizure rates and effects on specific seizure types (e.g. drop attacks), adverse effects and mortality. MAIN RESULTS: We found nine RCTs, but were unable to perform any meta-analysis, because each trial looked at different populations, different therapies and considered different outcomes. AUTHORS' CONCLUSIONS: The optimum treatment for LGS remains uncertain and no study to date has shown any one drug to be highly efficacious; rufinamide, lamotrigine, topiramate and felbamate may be helpful as add-on therapy, clobazam may be helpful for drop seizures. Until further research has been undertaken, clinicians will need to continue to consider each patient individually, taking into account the potential benefit of each therapy weighed against the risk of adverse effects.\",\n \"corpus_id\": 205169001,\n \"score\": 1\n },\n {\n \"doc_id\": \"23650212\",\n \"title\": \"Autism spectrum disorders: the quest for genetic syndromes.\",\n \"abstract\": \"Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disabilities with various etiologies, but with a heritability estimate of more than 90%. Although the strong correlation between autism and genetic factors has been long established, the exact genetic background of ASD remains unclear. A number of genetic syndromes manifest ASD at higher than expected frequencies compared to the general population. These syndromes account for more than 10% of all ASD cases and include tuberous sclerosis, fragile X, Down, neurofibromatosis, Angelman, Prader-Willi, Williams, Duchenne, etc. Clinicians are increasingly required to recognize genetic disorders in individuals with ASD, in terms of providing proper care and prognosis to the patient, as well as genetic counseling to the family. Vice versa, it is equally essential to identify ASD in patients with genetic syndromes, in order to ensure correct management and appropriate educational placement. During investigation of genetic syndromes, a number of issues emerge: impact of intellectual disability in ASD diagnoses, identification of autistic subphenotypes and differences from idiopathic autism, validity of assessment tools designed for idiopathic autism, possible mechanisms for the association with ASD, etc. Findings from the study of genetic syndromes are incorporated into the ongoing research on autism etiology and pathogenesis; different syndromes converge upon common biological backgrounds (such as disrupted molecular pathways and brain circuitries), which probably account for their comorbidity with autism. This review paper critically examines the prevalence and characteristics of the main genetic syndromes, as well as the possible mechanisms for their association with ASD.\",\n \"corpus_id\": 25874745,\n \"score\": 1\n },\n {\n \"doc_id\": \"23737708\",\n \"title\": \"Coexisting disorders and problems in preschool children with autism spectrum disorders.\",\n \"abstract\": \"OBJECTIVES: To analyze cooccurring disorders and problems in a representative group of 198 preschool children with autism spectrum disorders (ASD) who had had interventions at a specialized habilitation center. METHODS: Parents and children were seen by a research team. Data were based on parental interviews, pediatric assessments, and tests of the child. Information on autistic symptoms, general cognitive function, speech and language, motor function, epilepsy, vision, hearing, activity level, behavior, and sleep was collected. RESULTS: Three ASD categories were used: (1) autistic disorder (AD), (2) autistic-like condition (ALC) or Asperger syndrome, and (3) one group with autistic symptoms/traits but not entirely all its criteria met for ASD. Children with autism had a mean of 3.2 coexisting disorders or problems, the ALC/Asperger group had a mean of 1.6, and children with autistic traits had a mean of 1.6. The most common disorder/problems in the total group pertained to language problems (78%), intellectual disability (ID) (49%), below average motor function (37%), and severe hyperactivity/ADHD (33%). CONCLUSIONS: The results accord with the concept of early symptomatic syndromes eliciting neurodevelopmental clinical examination (ESSENCE), and highlight the need of considering ASD in a broad perspective taking also other cooccurring developmental disorders into account.\",\n \"corpus_id\": 2699520,\n \"score\": 1\n },\n {\n \"doc_id\": \"24116958\",\n \"title\": \"Lennox-Gastaut syndrome of unknown cause: phenotypic characteristics of patients in the Epilepsy Phenome/Genome Project.\",\n \"abstract\": \"PURPOSE: Lennox-Gastaut syndrome (LGS) is a devastating childhood-onset epilepsy syndrome. The cause is unknown in 25% of cases. Little has been described about the specific clinical or electroencephalography (EEG) features of LGS of unknown or genetic cause (LGS(u)). The Epilepsy Phenome/Genome Project (EPGP) aims to characterize LGS(u) by phenotypic analysis of patients with LGS(u) and their parents. METHODS: One hundred thirty-five patients with LGS with no known etiology and their parents were enrolled from 19 EPGP centers in the United States and Australia. Clinical data from medical records, standardized questionnaires, imaging, and EEG were collected with use of online informatics systems developed for EPGP. KEY FINDINGS: LGS(u) in the EPGP cohort had a broad range of onset of epilepsy from 1 to 13 years, was male predominant (p < 0.0002), and was associated with normal development prior to seizure onset in 59.2% of patients. Despite the diagnosis, almost half of the adult patients with LGS(u) completed secondary school. Parents were cognitively normal. All subjects had EEG recordings with generalized epileptiform abnormalities with a spike wave frequency range of 1-5 Hz (median 2 Hz), whereas 8.1% of subjects had EEG studies with a normal posterior dominant rhythm. Almost 12% of patients evolved from West syndrome. SIGNIFICANCE: LGS(u) has distinctive characteristics including a broad age range of onset, male predominance, and often normal development prior to the onset of seizures. Cognitive achievements such as completion of secondary school were possible in half of adult patients. Our phenotypic description of LGS(u) coupled with future genetic studies will advance our understanding of this epilepsy syndrome.\",\n \"corpus_id\": 14802355,\n \"score\": 1\n },\n {\n \"doc_id\": \"24225340\",\n \"title\": \"Encephalopathy in children with Dravet syndrome is not a pure consequence of epilepsy.\",\n \"abstract\": \"BACKGROUND: Dravet syndrome (DS) is currently considered as an epileptic encephalopathy, a condition in which epilepsy causes deterioration or developmental delay but preliminary data suggested that cognitive course may worsen independently from epilepsy. Our objective was to prospectively analyze the neuropsychological features in a large cohort of DS patients and its relationships with epilepsy and SCN1A mutation. METHODS: 81 examinations were performed in 67 patients with typical DS (9m-24y, 15 longitudinally studied) using Brunet-Lezine (developmental/intelligence quotient [DQ/IQ] and DQ sub-scores), Achenbach, Conners, and a semi-quantitative psychomotor score (SQPS). We studied the correlation between DQ/IQ/SQPS and age, epilepsy characteristics, and whether patients presented SCN1A mutation. RESULTS: DQ/IQ significantly decreased with age (r = -.53, p < .001), from normal before 2y (mean 80, range 64-105) to low after 3y (mean 48, range 30-69), with hyperactivity and attention disorders hampering learning abilities especially up to 6y. However, raw (not age-adjusted) DQ sub-scores increased with age during the first decade, showing that there is no regression. We did not find any significant correlation between DQ/IQ at last evaluation and epilepsy data, i.e. first seizure (age, type, duration, fever), seizures during the course (type, fever sensitivity), status epilepticus (age of onset, number, fever), photosensitivity, and treatment, except for myoclonus and focal seizures which were associated with a lower QD/IQ after 3y. SCN1A mutated patients (n = 58) seemed to exhibit worse psychomotor course than non-mutated ones (n = 9) (severe SQPS in 26% vs 0%), although their epilepsy tended to be less severe (tonic seizures in 12% vs 44% [p = 0.04], first status epilepticus before 6 m in 26% vs 67% [p = .02], mean number of SE 2.5 vs 4.5 [p = .09]). DQ sub-scores were dissociated throughout the whole course: from onset hand-eye coordination was significantly lower than language, posture and sociability (p < .01). Dissociation seemed to be more frequent in mutated than in non-mutated patients (motor SQPS was normal for in 77% vs 44% [p = 0.017] whereas language SQPS was normal for 47% vs 100%). CONCLUSIONS: Although psychomotor/cognitive delay declines with age, there is no regression. In addition, encephalopathy is not a pure consequence of epilepsy but SCN1A mutation seems to play an additional, direct role.\",\n \"corpus_id\": 6300017,\n \"score\": 1\n },\n {\n \"doc_id\": \"24614520\",\n \"title\": \"CHD2 mutations in Lennox-Gastaut syndrome.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is an epileptic encephalopathy with a heterogeneous etiology. In this study, we aimed to explore the role of CHD2 in LGS, as CHD2 mutations have been described recently in various epileptic encephalopathies. We have previously identified one patient with a large deletion affecting the CHD2 gene in a group of 22 patients with LGS or LGS-like epilepsy. In the remaining 17 patients without known etiology, Sanger sequencing revealed a de novo 1-bp duplication in the CHD2 gene in another patient. This mutation leads to a frameshift and, consequently, a premature stop codon 49bp downstream of the mutation. The patient had prominent myoclonic seizures and photosensitivity, thus, sharing phenotypic features with previously reported patients with CHD2-related epilepsy. In our original material of 22 patients with LGS features, we have now found two (9%) with mutations in the CHD2 gene. Our findings suggest that CHD2 mutations are important in the etiological spectrum of LGS.\",\n \"corpus_id\": 140207920,\n \"score\": 1\n },\n {\n \"doc_id\": \"24665294\",\n \"title\": \"Sodium Channel Gene Mutations in Children with GEFS+ and Dravet Syndrome: A Cross Sectional Study.\",\n \"abstract\": \"OBJECTIVE: Dravet syndrome or severe myoclonic epilepsy of infancy (SMEI) is a baleful epileptic encephalopathy that begins in the first year of life. This syndrome specified by febrile seizures followed by intractable epilepsy, disturbed psychomotor development, and ataxia. Clinical similarities between Dravet syndrome and generalized epilepsy with febrile seizure plus (GEFS+) includes occurrence of febrile seizures and joint molecular genetic etiology. Shared features of these two diseases support the idea that these two disorders represent a severity spectrum of the same illness. Nowadays, more than 60 heterozygous pattern SCN1A mutations, which many are de novo mutations, have been detected in Dravet syndrome. MATERIALS & METHODS: From May 2008 to August 2012, 35 patients who referred to Pediatric Neurology Clinic of Mofid Children Hospital in Tehran were enrolled in this study. Entrance criterion of this study was having equal or more than four criteria for Dravet syndrome. We compared clinical features and genetic findings of the patients diagnosed as Dravet syndrome or GEFS+. RESULTS: 35 patients (15 girls and 20 boys) underwent genetic testing. Mean age of them was 7.7 years (a range of 13 months to 15 years). Three criteria that were best evident in SCN1A mutation positive patients are as follows: \\\"Normal development before the onset of seizures, onset of seizure before age of one year, and psychomotor retardation after onset of seizures. Our genetic testing showed that 1 of 3 (33.3%) patients with clinical Dravet syndrome and 3 of 20 (15%) patients that diagnosed as GEFS+, had SCN1A mutation. CONCLUSION: In this study, normal development before seizure onset, seizures beginning before age of one year and psychomotor retardation after age of two years are the most significant criteria in SCN1A mutation positive patients.\",\n \"corpus_id\": 22330440,\n \"score\": 1\n },\n {\n \"doc_id\": \"24902608\",\n \"title\": \"Lennox-Gastaut syndrome and phenotype: secondary network epilepsies.\",\n \"abstract\": \"OBJECTIVE: Lennox-Gastaut syndrome (LGS) is a severe epilepsy phenotype with characteristic electroclinical features despite diverse etiologies. We previously found common cerebral networks involved during slow spike-and-wave (SSW) and generalized paroxysmal fast activity (PFA), characteristic interictal discharges. Some patients have a Lennox-Gastaut-like phenotype and cortical lesions. We wished to explore the interaction between cerebral networks and lesions in this group. METHODS: 3 Tesla electroencephalography-functional magnetic resonance imaging (EEG-fMRI) on six subjects with Lennox-Gastaut phenotype and a structural lesion. Timings of SSW and PFA events were used in an event-related fMRI analysis, and to estimate the time course of the hemodynamic response from key regions. RESULTS: (1) PFA-robust fMRI signal increases were observed in frontal and parietal association cortical areas, thalamus, and pons, with simultaneous increases in both \\\"attention\\\" and resting-state (default mode) networks, a highly unusual pattern. ( 2) SSW showed mixed increased and decreased fMRI activity, with preevent increases in association cortex and thalamus, and then prominent postevent reduction. There was decreased fMRI activity in primary cortical areas. ( 3) Lesion-variable fMRI increases were observed during PFA and SSW discharges. Three subjects who proceeded to lesionectomy are >1 year seizure-free. SIGNIFICANCE: We conceptualize Lennox-Gastaut phenotype as a being a network epilepsy, where key cerebral networks become autonomously unstable. Epileptiform activity in Lennox-Gastaut phenotype, and by implication in LGS, appears to be amplified and expressed through association cortical areas, possibly because the attention and default-mode networks are widely interconnected, fundamental brain networks. Seizure freedom in the subjects who proceeded to lesionectomy suggests that cortical lesions are able to establish and maintain this abnormal unstable network behavior. LGS may be considered a secondary network epilepsy because the unifying epileptic manifestations of the disorder, including PFA and SSW, reflect network dysfunction, rather than the specific initiating process.\",\n \"corpus_id\": 25576134,\n \"score\": 1\n },\n {\n \"doc_id\": \"25266269\",\n \"title\": \"A case of Lennox-Gastaut syndrome in a patient with FOXG1-related disorder.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a drug-resistant epileptic encephalopathy of childhood with a heterogeneous etiology. Recently, genome-wide association studies have led to the identification of new de novo mutations associated with this epileptic syndrome. Herein, we report an 8-year-old child with intellectual disability, severe postnatal microcephaly, Rett-like features, and LGS, carrying a de novo missense mutation in the forkhead box G1 (FOXG1) gene. This gene is responsible for FOXG1 syndrome, characterized by severe postnatal microcephaly, moderate postnatal growth deficiency, mental retardation with poor social interaction, stereotyped behavior and dyskinesias, absent language, sleep disorders, and epilepsy. Nonspecific epilepsy syndromes have been associated with this genetic disorder. Thus, we hypothesize that FOXG1 might be a new candidate gene in the etiology of LGS and suggest screening for this gene in cases of LGS with concomitant microcephaly and clinical features overlapping with Rett syndrome.\",\n \"corpus_id\": 205116547,\n \"score\": 1\n },\n {\n \"doc_id\": \"25284032\",\n \"title\": \"Lennox-Gastaut syndrome: a consensus approach to differential diagnosis.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe epileptic encephalopathy that shares many features and characteristics of other treatment-resistant childhood epilepsies. Accurate and early diagnosis is essential to both prognosis and overall patient management. However, accurate diagnosis of LGS can be clinically challenging. This article summarizes key characteristics of LGS and areas of overlap with other childhood epilepsies. Drawing upon input from a committee of established LGS experts convened in June 2012 in Chicago, Illinois, the authors highlight key diagnostic tests for making the differential diagnosis and propose a diagnostic scheme for people with suspected LGS.\",\n \"corpus_id\": 27913979,\n \"score\": 1\n },\n {\n \"doc_id\": \"25400619\",\n \"title\": \"Conceptualizing lennox-gastaut syndrome as a secondary network epilepsy.\",\n \"abstract\": \"Lennox-Gastaut Syndrome (LGS) is a category of severe, disabling epilepsy, characterized by frequent, treatment-resistant seizures, and cognitive impairment. Electroencephalography (EEG) shows characteristic generalized epileptic activity that is similar in those with lesional, genetic, or unknown causes, suggesting a common underlying mechanism. The condition typically begins in young children, leaving many severely disabled with recurring seizures throughout their adult life. Scalp EEG of the tonic seizures of LGS is characterized by a diffuse high-voltage slow transient evolving into generalized low-voltage fast activity, likely reflecting sustained fast neuronal firing over a wide cortical area. The typical interictal discharges (runs of slow spike-and-wave and bursts of generalized paroxysmal fast activity) also have a \\\"generalized\\\" electrical field, suggesting widespread cortical involvement. Recent brain mapping studies have begun to reveal which cortical and subcortical regions are active during these \\\"generalized\\\" discharges. In this critical review, we examine findings from neuroimaging studies of LGS and place these in the context of the electrical and clinical features of the syndrome. We suggest that LGS can be conceptualized as \\\"secondary network epilepsy,\\\" where the epileptic activity is expressed through large-scale brain networks, particularly the attention and default-mode networks. Cortical lesions, when present, appear to chronically interact with these networks to produce network instability rather than triggering each individual epileptic discharge. LGS can be considered as \\\"secondary\\\" network epilepsy because the epileptic manifestations of the disorder reflect the networks being driven, rather than the specific initiating process. In this review, we begin with a summation of the clinical manifestations of LGS and what this has revealed about the underlying etiology of the condition. We then undertake a systematic review of the functional neuroimaging literature in LGS, which leads us to conclude that LGS can best be conceptualized as \\\"secondary network epilepsy.\\\"\",\n \"corpus_id\": 9068254,\n \"score\": 1\n },\n {\n \"doc_id\": \"25599987\",\n \"title\": \"Clinical characteristics of children and young adults with co-occurring autism spectrum disorder and epilepsy.\",\n \"abstract\": \"The association between autism spectrum disorder (ASD) and epilepsy has been described for decades, and yet we still lack the full understanding of this relationship both clinically and at the pathophysiologic level. This review evaluates the available data in the literature pertaining to the clinical characteristics of patients with autism spectrum disorder who develop epilepsy and, conversely, patients with epilepsy who develop autism spectrum disorder. Many studies demonstrate an increased risk of epilepsy in individuals with ASD, but rates vary widely. This variability is likely secondary to the different study methods employed, including the study population and definitions of the disorders. Established risk factors for an increased risk of epilepsy in patients with ASD include intellectual disability and female gender. There is some evidence of an increased risk of epilepsy associated with other factors such as ASD etiology (syndromic), severity of autistic features, developmental regression, and family history. No one epilepsy syndrome or seizure type has been associated, although focal or localization-related seizures are often reported. The age at seizure onset can vary from infancy to adulthood with some evidence of a bimodal age distribution. The severity and intractability of epilepsy in populations with ASD have not been well studied, and there is very little investigation of the role that epilepsy plays in the autism behavioral phenotype. There is evidence of abnormal EEGs (especially epileptiform abnormalities) in children with ASD even in the absence of clinical seizures, but very little is known about this phenomenon and what it means. The development of autism spectrum disorder in patients with epilepsy is less well studied, but there is evidence that the ASD risk is greater in those with epilepsy than in the general population. One of the risk factors is intellectual disability, and there is some evidence that the presence of a particular seizure type, infantile spasms, may increase risk, but some of the data are conflicting. We believe that one of the reasons that so little is known about this phenomenon is the lack of cross talk between researchers and clinicians alike in the two fields. We conclude that large systematic studies that employ strict ascertainment of samples using standardized definitions of both disorders, validated data collection tools, and appropriate longitudinal follow-up are needed to better shed light on certain clinical aspects of the comorbidity of ASD and epilepsy. Ideally, we could provide the optimal diagnostic and treatment services to these patients in a multidisciplinary setting with both epilepsy and neurobehavioral specialists. This article is part of a Special Issue entitled \\\"Autism and Epilepsy\\\".\",\n \"corpus_id\": 27472345,\n \"score\": 1\n },\n {\n \"doc_id\": \"25935511\",\n \"title\": \"Perceived efficacy of cannabidiol-enriched cannabis extracts for treatment of pediatric epilepsy: A potential role for infantile spasms and Lennox-Gastaut syndrome.\",\n \"abstract\": \"There is a great need for safe and effective therapies for treatment of infantile spasms (IS) and Lennox-Gastaut syndrome (LGS). Based on anecdotal reports and limited experience in an open-label trial, cannabidiol (CBD) has received tremendous attention as a potential treatment for pediatric epilepsy, especially Dravet syndrome. However, there is scant evidence of specific utility for treatment of IS and LGS. We sought to document the experiences of children with IS and/or LGS who have been treated with CBD-enriched cannabis preparations. We conducted a brief online survey of parents who administered CBD-enriched cannabis preparations for the treatment of their children's epilepsy. We specifically recruited parents of children with IS and LGS and focused on perceived efficacy, dosage, and tolerability. Survey respondents included 117 parents of children with epilepsy (including 53 with IS or LGS) who had administered CBD products to their children. Perceived efficacy and tolerability were similar across etiologic subgroups. Eighty-five percent of all parents reported a reduction in seizure frequency, and 14% reported complete seizure freedom. Epilepsy was characterized as highly refractory with median latency from epilepsy onset to CBD initiation of five years, during which the patient's seizures failed to improve after a median of eight antiseizure medication trials. The median duration and the median dosage of CBD exposure were 6.8 months and 4.3mg/kg/day, respectively. Reported side effects were far less common during CBD exposure, with the exception of increased appetite (30%). A high proportion of respondents reported improvement in sleep (53%), alertness (71%), and mood (63%) during CBD therapy. Although this study suggests a potential role for CBD in the treatment of refractory childhood epilepsy including IS and LGS, it does not represent compelling evidence of efficacy or safety. From a methodological standpoint, this study is extraordinarily vulnerable to participation bias and limited by lack of blinded outcome ascertainment. Appropriately controlled clinical trials are essential to establish efficacy and safety.\",\n \"corpus_id\": 19931966,\n \"score\": 1\n },\n {\n \"doc_id\": \"26093133\",\n \"title\": \"[Hypokalemia in Lennox-Gastaut syndrome].\",\n \"abstract\": \"Ipopotassiemia in sindrome di Lennox-Gastaut. The Lennox-Gastaut Syndrome (LGS) is a childhood epileptic encephalopathy. Incidence: 1/1.000.000/year, prevalence: 15/100.000. LGS covers 5-10% of epileptic patients and 1-2% of childhood epilepsies. Also referred to as cryptogenic or symptomatic generalized epilepsy. LGS is characterized by: multiple seizures (atypical absences, axial tonic seizures and sudden atonic or myoclonic falls), diffuse slow cryptic EEG waves when awake (<3 Hz), fast rhythmic peaks (10 Hz) during sleep, mental retardation and personality disorders. The LGS is not responding to treatment. Some new drugs have proven to be effective in controlling the disease (Felbamate, Lamotrigine, Topiramate, Levetiracetam). The mortality rate is about 5%; only rarely death is due to epilepsy, which is usually caused by stroke or epileptic episodes. Here we describe the case of a 45-year-old female patient with LGS, severe hypokalemia, mental retardation and focal seizures. Normal renal function: creatinine 0.9 mg/dl, urea 26 mg/dl, creatinine clearance 96 ml/min, serum potassium levels to the minimum: 3.5 mEq/L. This level of potassium, however, had been achieved with the assumption of 8 oral tablets/day of potassium chloride. Osmotic diuresis, use of diuretics, Bartter, Gitelman (normal urinary calcium and magnesium) and pseudo-Bartter syndromes were all excluded whereas aldosteronism was found. Our findings lead to hypokalemia related to assumption of topiramate and hyperaldosteronism. Reduction in drug intake was not effective due to the increased seizures, so the drug was maintained, along with potassium supplementation. In conclusion, the patient has been diagnosed with hypokalemia and iatrogenic hyperaldosteronism, rare in our outpatient practice.\",\n \"corpus_id\": 21079911,\n \"score\": 1\n },\n {\n \"doc_id\": \"26945476\",\n \"title\": \"Abnormal cognitive network interactions in Lennox-Gastaut syndrome: A potential mechanism of epileptic encephalopathy.\",\n \"abstract\": \"OBJECTIVE: In patients with Lennox-Gastaut syndrome (LGS), recurrent epileptic activity is thought to contribute to impaired cognition (epileptic encephalopathy). Using concurrent electroencephalography-functional magnetic resonance imaging (EEG-fMRI), we recently showed that epileptiform discharges in LGS recruit large-scale networks that normally support key cognitive processes. In LGS, given that epileptic activity engages cognitive networks, and cognition is pervasively impaired, we hypothesized that cognitive network interactions in LGS are persistently abnormal. METHODS: We studied 15 LGS patients (mean age ± 1 standard deviation [SD] = 28.7 ± 10.6 years) and 17 healthy controls (mean age ± 1 SD = 27.6 ± 6.6 years) using task-free EEG-fMRI. Four networks of interest (default-mode, dorsal attention, executive control, and anterior salience) were defined using group-level independent components analysis (ICA). Functional connectivity within and between networks was determined for each subject, and then LGS network interactions were compared to network behavior in the control group. To test whether group differences were present in periods without scalp-detectable epileptiform discharges (i.e., persistent), we separately assessed discharge-affected and discharge-unaffected epochs in six patients with sufficient data for this analysis. RESULTS: In LGS, cognitive networks showed (1) reduced within-network integration, including weaker connectivity within the default-mode network, and (2) impaired between-network segregation, including stronger connectivity between the default-mode and dorsal attention networks. Abnormal interactions were present during fMRI periods with and without discharges, indicating that impaired network behavior may endure during periods without scalp-detectable epileptic activity. SIGNIFICANCE: In LGS, cognitive network interactions are persistently abnormal. Given that cognition typically worsens with the onset of LGS, and may improve after seizure control, our findings are consistent with the hypothesis that the epileptic process in LGS may initiate and perhaps sustain abnormal network behavior. We propose that epileptic encephalopathy may be a consequence of persistently disrupted cognitive network interactions.\",\n \"corpus_id\": 1156175,\n \"score\": 1\n },\n {\n \"doc_id\": \"27179713\",\n \"title\": \"Autism spectrum disorder phenotype and intellectual disability in females with epilepsy and PCDH-19 mutations.\",\n \"abstract\": \"INTRODUCTION: Autism features and various degrees of cognitive deficit are reported in patients with PCDH-19 mutations and epilepsy. Autism spectrum disorder (ASD) and, often, cognitive profile are usually assessed clinically. We studied autism phenotype and cognitive outcome in a series of patients using standardized tools for development and ASD. We aimed to describe the phenotype of ASD in this series and to understand whether ASD is strictly linked to intellectual disability (ID) or is present as a comorbidity. METHODS: Eight females aged 5 to 17years old with PCDH-19 mutations and epilepsy were recruited. For ASD diagnosis, the Autism Diagnostic Interview - Revised (ADI-R) and the Autism Diagnosis Observation Schedule (ADOS) were administered. Patients underwent a neuropsychological examination with tests measuring global intellectual efficiency (WPPSI-III and WISC-IV), language, and executive and social cognition abilities. Parental adaptive behavioral questionnaires were also obtained (VABS, CBCL, and BRIEF). RESULTS: Six out of eight patients presented with ASD and ID. Two patients had neither ASD nor ID, and both had the latest age of onset for their epilepsy. All cognitive functions were deficient, but theory-of-mind abilities compared to other cognitive features were even impaired. Features of ASD lacked major repetitive and stereotyped behaviors and show some differences with the classical ASD features related to ID. CONCLUSION: Our results show a large spectrum of ID and a very high rate of ASD in patients with epilepsy and PCDH-19 mutations. Autism spectrum disorder seems to be a genuine comorbidity, more than a consequence of ID. It highlights the importance of standardized psychiatric and cognitive evaluation in order to establish a tailored rehabilitation program.\",\n \"corpus_id\": 3866765,\n \"score\": 1\n },\n {\n \"doc_id\": \"27350381\",\n \"title\": \"The effect of epilepsy on autistic symptom severity assessed by the social responsiveness scale in children with autism spectrum disorder.\",\n \"abstract\": \"BACKGROUND: As the prevalence of autism spectrum disorders in people with epilepsy ranges from 15 to 47 % (Clarke et al. in Epilepsia 46:1970-1977, 2005), it is speculated that there is a special relationship between the two disorders, yet there has been a lack of systematic studies comparing the behavioral phenotype between autistic individuals and autistic individuals with epilepsy. This study aims to investigate how the co-occurrence of epilepsy and Autism Spectrum Disorder (ASD) affects autistic characteristics assessed by the Social Responsiveness Scale (SRS), which has been used as a measure of autism symptoms in previous studies. In this research we referred to all individuals with Autism or Autistic Disorder as individuals with ASD. METHODS: We reviewed the complete medical records of 182 participants who presented to a single tertiary care referral center from January 1, 2013 to July 28, 2015, and subsequently received complete child and adolescent psychiatric assessments. Of the 182 participants, 22 were diagnosed with Autism Spectrum Disorder and epilepsy. Types of epilepsy observed in these individuals included complex partial seizure, generalized tonic-clonic seizure, or infantile spasm. Using 'Propensity Score Matching' we selected 44 children, diagnosed with only Autism Spectrum Disorder, whose age, gender, and intelligence quotient (IQ) were closely matched with the 22 children diagnosed with Autism Spectrum Disorder and epilepsy. Social functioning of participants was assessed by the social responsiveness scale, which consists of five categories: social awareness, social cognition, social communication, social motivation, and autistic mannerisms. Bivariate analyses were conducted to compare the ASD participants with epilepsy group with the ASD-only group on demographic and clinical characteristics. Chi square and t test p values were calculated when appropriate. RESULTS: There was no significant difference in age (p = 0.172), gender (p > 0.999), IQ (FSIQ, p = 0.139; VIQ, p = 0.114; PIQ, p = 0.295) between the two groups. ASD participants with epilepsy were significantly more impaired than ASD participants on some measures of social functioning such as social awareness (p = 0.03) and social communication (p = 0.027). ASD participants with epilepsy also scored significantly higher on total SRS t-score than ASD participants (p = 0.023). CONCLUSIONS: Understanding the relationship between ASD and epilepsy is critical for appropriate management (e.g. social skills training, seizure control) of ASD participants with co-occurring epilepsy. Results of this study suggest that mechanisms involved in producing epilepsy may play a role in producing or augmenting autistic features such as poor social functioning. Prospective study with larger sample sizes is warranted to further explore this association.\",\n \"corpus_id\": 16089106,\n \"score\": 1\n },\n {\n \"doc_id\": \"27859447\",\n \"title\": \"The co-occurrence of Down syndrome and autism spectrum disorder: is it because of additional genetic variations?\",\n \"abstract\": \"Individuals with Down syndrome (DS) are diagnosed with autism spectrum disorder (ASD) at a significantly higher frequency than the typical population. The differentiation of ASD symptoms from those of severe intellectual disability presents diagnostic challenges, which have led to more refined methods in the clinical evaluation of ASD in DS. These improved phenotypic characterization methods not only provide better diagnosis of ASD in DS, but may also be useful in elucidating the etiology of the increased prevalence of ASD in DS. Because all individuals with the classic presentation of DS have trisomy 21, it is possible that those with co-occurring DS and ASD may have additional genetic variants which can act as modifiers of the phenotype, leading to the development of ASD. © 2016 John Wiley & Sons, Ltd.\",\n \"corpus_id\": 31826863,\n \"score\": 1\n },\n {\n \"doc_id\": \"27994367\",\n \"title\": \"Brainstem dysfunction in patients with late-onset Lennox-Gastaut syndrome: Voxel-based morphometry and tract-based spatial statistics study.\",\n \"abstract\": \"BACKGROUND: There have been a few reports of patients who developed Lennox-Gastaut syndrome (LGS) in the second decades of their life. OBJECTIVES: The aim of this study was to investigate electroclinical presentation in patients with late-onset LGS. In addition, we evaluated structural abnormalities of the brain, which may give some clue about the common pathogenic pathway in LGS. MATERIALS AND METHODS: We enrolled the patients with late-onset LGS. We collected electroclinical characteristics of the patients and evaluated structural abnormalities using voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) analysis. RESULTS: The three subjects were diagnosed with late-onset LGS. The patients have no mental retardation and normal background activities on electroencephalography (EEG), and they had generalized paroxysmal fast activities on EEG, especially during sleep. The TBSS analysis revealed that fractional anisotropy values in the patients were significantly reduced in the white matter of brainstem compared with normal controls. However, VBM analysis did not show any significant difference between the patients and normal controls. CONCLUSIONS: Patients with late-onset LGS have different clinical and EEG characteristics from those with early-onset LGS. In addition, we demonstrated that brainstem dysfunction might contribute to the pathogenesis of late-onset LGS.\",\n \"corpus_id\": 6191192,\n \"score\": 1\n },\n {\n \"doc_id\": \"28292045\",\n \"title\": \"Prevalence and comorbidities of autism among children referred to the outpatient clinics for neurodevelopmental disorders.\",\n \"abstract\": \"INTRODUCTION: Autism spectrum disorders (ASD) is a neurodevelopmental disorder that has been rarely diagnosed in Sub-Saharan Africa. Although a proportion of children do present features of ASD in the Democratic Republic of Congo (DRC), little is known about it prevalence. Often, the co-morbidities constitute the upfront symptoms and therefore may it recognition and management difficult, aggravating as such the prognosis. The present study therefore aimed at studying the clinical profile of autism spectrum disorder (ASD) and the associated morbidities among children and adolescents in outpatient clinics in Kinshasa, the Democratic Republic of Congo. METHODS: We conducted a cross sectional study in the three outpatients centers receiving patients referred for neurodevelopmental disorders in Kinshasa, DRC, from June 2008 to June 2010. A total of 450 subjects aged from 1-18 years old were referred and included in the study. The clinical diagnosis for ASD was made using the DSM-IV-R and the ADIR. Co-morbidities were identified using DSM-IV-R criteria together with an extensive clinical interview and observation. All patients were subject to an intellectual quotient evaluation and an electroencephalogram reporting. RESULTS: Of the 450 subjects referred, 120 (29.3%) received the diagnosis of ASD, with boys outnumbering girls (OR 3:1. The mean age was 7.9 years (SD 3.4) (p< 0.001). Intellectual disability (75.83 %) and epilepsy (72.50%) were the main co-morbidities significantly associated with autism (p< 0.001). It was also found that co-morbidities were most frequent in subjects with an IQ<70 (p=0.05). CONCLUSION: ASD is frequent among patients referred for neurodevelopmental disorders in the three outpatients' centers for neurodevelopmental disorders in Kinshasa. Males seem to be more affected than female. The main co-morbidities were epilepsy and intellectual disabilities. Our findings suggest that it is important to screen for ASD and co-morbidities among all subjects referred for neurodevelopmental disorders and to undertake survey on ASD in various structures of rejected children from the society in Kinshasa DRC. This will help to identify and manage ASD and associated co-morbidities at an early stage for a better prognosis.\",\n \"corpus_id\": 17602784,\n \"score\": 1\n },\n {\n \"doc_id\": \"28346953\",\n \"title\": \"Lennox-Gastaut Syndrome: A State of the Art Review.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe age-dependent epileptic encephalopathy usually with onset between 1 and 8 years of age. Functional neuroimaging studies recently introduced the concept of Lennox-Gastaut as \\\"secondary network epilepsy\\\" resulting from dysfunctions of a complex system involving both cortical and subcortical structures (default-mode network, corticoreticular connections, and thalamus). These dysfunctions are produced by different disorders including hypoxic-ischemic encephalopathies, meningoencephalitis, cortical malformations, neurocutaneous disorders, or tumors. The list of etiologies was expanded to pathogenic copy number variants at whole-genome array comparative genomic hybridization associated with late-onset cases or pathogenic mutations involving genes, such as GABRB3, ALG13, SCN8A, STXBP1, DNM1, FOXG1, or CHD2. Various clinical trials demonstrated the usefulness of different drugs (including rufinamide, clobazam, lamotrigine, topiramate, or felbamate), ketogenic diet, resective surgery, corpus callosotomy, and vagus nerve stimulation in the treatment of epileptic manifestations. The outcome of LGS often remains disappointing regarding seizure control or cognitive functioning. The realization of animal models, which are still lacking, and the full comprehension of molecular mechanisms involved in epileptogenesis and cognitive impairment would give a relevant support to further improvements in therapeutic strategies for LGS patients.\",\n \"corpus_id\": 3849215,\n \"score\": 1\n },\n {\n \"doc_id\": \"28479797\",\n \"title\": \"Lennox-Gastaut Syndrome: A Prospective Follow-up Study.\",\n \"abstract\": \"OBJECTIVES: Lennox-Gastaut syndrome is a catastrophic epileptic encephalopathy. In Lennox-Gastaut syndrome, seizures are resistant to pharmacological treatment. In this prospective study, we evaluated the clinical features, neuroimaging, and response to treatment. MATERIALS AND METHODS: Forty-three consecutive newly diagnosed patients of Lennox-Gastaut syndrome were enrolled in the study. Baseline clinical assessment included seizure semiology, seizure frequency, electroencephalography, and neuroimaging. Patients were treated with combinations of preferred antiepileptic drugs (sodium valproate [VPA], clobazam [CLB], levetiracetam [LVT], lamotrigine [LMT], and topiramate [TPM]). Patients were followed for 6 months. The outcome was assessed using modified Barthel index. RESULTS: Tonic and generalized tonic-clonic forms were the most common seizures types. Features suggestive of hypoxic-ischemic encephalopathy (37.2%) were most frequent neuroimaging abnormality. Neuroimaging was normal in 32.6% of patients. With a combination valproic acid (VPA), CLB, and LVT, in 81.4% of patients, we were able to achieve >50% reduction in seizure frequency. Eleven (25.58%) patients showed an improvement in the baseline disability status. CONCLUSIONS: A combination of VPA, CLB, and LVT is an appropriate treatment regimen for patients with Lennox-Gastaut syndrome.\",\n \"corpus_id\": 30643538,\n \"score\": 1\n },\n {\n \"doc_id\": \"28609734\",\n \"title\": \"Assessment of treatment patterns and healthcare costs associated with probable Lennox-Gastaut syndrome.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a chronic and severe form of epilepsy characterized by intractable seizures, cognitive impairment, and abnormal electroencephalogram findings with slow spike-wave complexes. It typically presents before age 8, but symptoms continue into adulthood and require lifelong treatment associated with significant clinical burden. Data on LGS-associated healthcare utilization and costs are limited. In this study we use a claims-based LGS classifier based on random forest methodology to identify patients with probable LGS from the a Medicaid multi-state database and assess its prevalence across the age spectrum, healthcare utilization, treatment patterns, costs, and comorbid conditions. The classifier identified patients with probable LGS across all ages, with up to 8% of 10-year-old patients with epilepsy identified as having probable LGS. The prevalence of probable LGS was lower in older age cohorts, indicating that it may be under-recognized in older patients. Our analysis showed that probable LGS is associated with considerably higher total healthcare and medical costs than non-LGS patients. The costs were generally consistent between age cohorts, suggesting that the cost burden extends beyond childhood and has a lifelong impact. Analysis of treatment patterns suggest that while the majority of probable LGS patients in this study received widest-spectrum AEDs, a considerable proportion did not and therefore may have been inadequately treated. Further, usage of clobazam and rufinamide was decreased in older compared to younger patient cohorts, indicating that older patient cohorts are less likely to be receiving optimum treatment for LGS. These findings indicate the need for increased clinical attention to LGS beyond pediatric years, with a focus on optimization of treatment for LGS patients of all ages with widest-spectrum AEDs. Timely recognition and adequate treatment of LGS are likely to result in improved outcomes and less costly management of this condition.\",\n \"corpus_id\": 4410708,\n \"score\": 1\n },\n {\n \"doc_id\": \"28689466\",\n \"title\": \"Early Diagnosis and Treatment of Lennox-Gastaut Syndrome.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe form of childhood-onset epilepsy associated with high morbidity and mortality. The peak period for manifestations of Lennox-Gastaut syndrome is between ages 3 and 5 years, a time of critical brain development and corresponding vulnerability to the electroclinical dysfunction arising from Lennox-Gastaut syndrome. Diagnosis is based on a triad of symptoms: multiple seizure types, cognitive impairment, and slow spike-and-wave pattern on electroencephalography. In practice, Lennox-Gastaut syndrome presentation is diverse, and there may be a delay between initial symptoms and emergence of the full triad of clinical features. Additionally, differential diagnosis is complicated by the resemblance of Lennox-Gastaut syndrome to other forms of epilepsy and by the need for varied diagnostic techniques requiring specific clinical skills. Because diagnosis is complex and early intervention may lead to improved outcomes, clinicians should consider treatment when Lennox-Gastaut syndrome symptoms are present, even in the absence of a formal diagnosis.\",\n \"corpus_id\": 33699237,\n \"score\": 1\n },\n {\n \"doc_id\": \"29085326\",\n \"title\": \"Expert Opinion on the Management of Lennox-Gastaut Syndrome: Treatment Algorithms and Practical Considerations.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe epileptic and developmental encephalopathy that is associated with a high rate of morbidity and mortality. It is characterized by multiple seizure types, abnormal electroencephalographic features, and intellectual disability. Although intellectual disability and associated behavioral problems are characteristic of LGS, they are not necessarily present at its outset and are therefore not part of its diagnostic criteria. LGS is typically treated with a variety of pharmacological and non-pharmacological therapies, often in combination. Management and treatment decisions can be challenging, due to the multiple seizure types and comorbidities associated with the condition. A panel of five epileptologists met to discuss consensus recommendations for LGS management, based on the latest available evidence from literature review and clinical experience. Treatment algorithms were formulated. Current evidence favors the continued use of sodium valproate (VPA) as the first-line treatment for patients with newly diagnosed de novo LGS. If VPA is ineffective alone, evidence supports lamotrigine, or subsequently rufinamide, as adjunctive therapy. If seizure control remains inadequate, the choice of next adjunctive antiepileptic drug (AED) should be discussed with the patient/parent/caregiver/clinical team, as current evidence is limited. Non-pharmacological therapies, including resective surgery, the ketogenic diet, vagus nerve stimulation, and callosotomy, should be considered for use alongside AED therapy from the outset of treatment. For patients with LGS that has evolved from another type of epilepsy who are already being treated with an AED other than VPA, VPA therapy should be considered if not trialed previously. Thereafter, the approach for a de novo patient should be followed. Where possible, no more than two AEDs should be used concomitantly. Patients with established LGS should undergo review by a neurologist specialized in epilepsy on at least an annual basis, including a thorough reassessment of their diagnosis and treatment plan. Clinicians should always be vigilant to the possibility of treatable etiologies and alert to the possibility that a patient's diagnosis may change, since the seizure types and electroencephalographic features that characterize LGS evolve over time. To date, available treatments are unlikely to lead to seizure remission in the majority of patients and therefore the primary focus of treatment should always be optimization of learning, behavioral management, and overall quality of life.\",\n \"corpus_id\": 6408047,\n \"score\": 1\n },\n {\n \"doc_id\": \"29119560\",\n \"title\": \"Prevalence and risk factors for autism spectrum disorder in epilepsy: a systematic review and meta-analysis.\",\n \"abstract\": \"AIM: To assess the prevalence and risk factors for autism spectrum disorder (ASD) in epilepsy, and to better understand the relationship and comorbidity between these disorders. METHOD: PsychINFO and PubMed were searched for articles published in the past 15 years that examined the prevalence of ASD in individuals with epilepsy. RESULTS: A total of 19 studies were found with a pooled ASD prevalence of 6.3% in epilepsy. When divided by type, the risks of ASD for general epilepsy, infantile spasms, focal seizures, and Dravet syndrome were 4.7%, 19.9%, 41.9%, and 47.4% respectively. Studies with populations under 18 years showed a 13.2 times greater risk of ASD than study populations over 18 years, and samples with most (>50%) individuals with intellectual disability showed a greater risk 4.9 times higher than study populations with a minority of individuals with intellectual disability. The main risk factors for ASD reported in the 19 studies included presence of intellectual disability, sex, age, and symptomatic aetiology of epilepsy. INTERPRETATION: Current research supports a high prevalence of ASD in epilepsy. This study helps to define the clinical profile of patients with epilepsy who are at risk for ASD, which may help clinicians in early screening and diagnosis of ASD in this population. WHAT THIS PAPER ADDS: Critical evaluation of previous studies examining the prevalence of autism spectrum disorder (ASD) in individuals with epilepsy. A meta-analysis of 19 studies showed a pooled ASD prevalence of 6.3% in individuals with epilepsy. Studies that included a majority of individuals with intellectual disability or younger population age had a higher prevalence of autism. Risk factors reported in studies included presence of intellectual disability, sex, age, and symptomatic epilepsy origin.\",\n \"corpus_id\": 13654554,\n \"score\": 1\n },\n {\n \"doc_id\": \"29124439\",\n \"title\": \"Lennox-Gastaut syndrome: a comprehensive review.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is considered an epileptic encephalopathy and is defined by a triad of multiple drug-resistant seizure types, a specific EEG pattern showing bursts of slow spike-wave complexes or generalized paroxysmal fast activity, and intellectual disability. The prevalence of LGS is estimated between 1 and 2% of all patients with epilepsy. The etiology of LGS is often divided into two groups: identifiable (genetic-structural-metabolic) in 65 to 75% of the patients and LGS of unknown cause in others. Lennox-Gastaut syndrome may be considered as secondary network epilepsy. The seizures in LGS are usually drug-resistant, and complete seizure control with resolution of intellectual and psychosocial dysfunction is often not achievable. Reduction in frequency of the most incapacitating seizures (e.g., drop attacks and tonic-clonic seizures) should be the major objective. Valproate, lamotrigine, and topiramate are considered to be the first-line drugs by many experts. Other effective antiepileptic drugs include levetiracetam, clobazam, rufinamide, and zonisamide. The ketogenic diet is an effective and well-tolerated treatment option. For patients with drug resistance, a further therapeutic option is surgical intervention. Corpus callosotomy is a palliative surgical procedure that aims at controlling the most injurious seizures. Finally, vagus nerve stimulation offers reasonable seizure improvement. The long-term outcome for patients with LGS is generally poor. This syndrome is often associated with long-term adverse effects on intellectual development, social functioning, and independent living.\",\n \"corpus_id\": 4243468,\n \"score\": 1\n },\n {\n \"doc_id\": \"29126048\",\n \"title\": \"Lennox-Gastaut syndrome in adulthood: Long-term clinical follow-up of 38 patients and analysis of their recorded seizures.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a severe epileptic encephalopathy with childhood onset that usually continues through adolescence and into adulthood. In the long term, patients with this condition still have intractable seizures, intellectual disability, behavioral problems, and physical comorbidities. The aim of this study was to describe the clinical and EEG characteristics of a group of adults with Lennox-Gastaut syndrome. We identified 38 (22 females, 16 males) patients with LGS older than age 18years at their last evaluation, with mean age of 43.3±10.6years. Median follow-up was 14.4years (range: 2-40). All of our patients had 3 or more seizure types during their clinical history. The most prevalent seizure types at follow-up were atypical absences (28/38), tonic (28/38), generalized tonic-clonic (17/38), focal (11/38), and myoclonic seizures (9/38). All patients had drug-resistant seizures. Besides epilepsy, intellectual disability and behavioral problems were prominent features. Surprisingly, paroxysmal nonepileptic seizures were reported in 3 patients. Our observations confirm the poor outcome of Lennox-Gastaut syndrome through adulthood, regardless of age at seizure onset, etiology, and history of previous West syndrome.\",\n \"corpus_id\": 10877067,\n \"score\": 1\n },\n {\n \"doc_id\": \"29249509\",\n \"title\": \"What is the Relationship Between Autism Spectrum Disorders and Epilepsy?\",\n \"abstract\": \"The association of epilepsy and autism spectrum disorders (ASD) is best understood by examining the relationship between social cognition, nonsocial cognition, and epilepsy. The relationship between ASD and epilepsy is bidirectional and is strongly linked to intellectual disability (ID). The risk of developing ASD in children with epilepsy is highest in children with early onset seizures, with a high prevalence in children with infantile spasms. The risk of developing epilepsy in children first diagnosed with ASD is highest in those with ID. The prevalence of seizures in ASD increases with age. When epilepsy and ASD coexist, they share common pathophysiological mechanisms. In epilepsy with and without ID, social-cognitive deficits are an important determinant of neurodevelopmental outcomes. Early recognition of social deficits is an important aspect of the comprehensive management of children with epilepsy. Treating the seizures in individuals with epilepsy and ASD is crucial but interventions that address social-cognitive deficits are necessary to maximize neurodevelopmental outcomes.\",\n \"corpus_id\": 28462962,\n \"score\": 1\n },\n {\n \"doc_id\": \"19898669\",\n \"title\": \"Update on the management of Lennox-Gastaut syndrome with a focus on rufinamide.\",\n \"abstract\": \"OBJECTIVE: This review summarizes the treatment of Lennox-Gastaut syndrome, an intractable epileptic encephalopathy of early childhood. In particular, the review focuses on rufinamide, a recently released anticonvulsant medication with reported effectiveness in this epilepsy syndrome. METHODS: A systematic literature search (PubMed) was performed to review the existing literature pertaining to the treatment of Lennox-Gastaut syndrome as well as studies involving rufinamide as an anticonvulsant medication. RESULTS: The published literature to date documents a beneficial effect of rufinamide on children over 4 years old with Lennox-Gastaut syndrome. Studies indicate a significant decrease in tonic and atonic seizure frequency as well as total seizure frequency compared to placebo-treated children. Rufinamide appears to be well tolerated and a safe medication, somnolence and vomiting being the most common side effects. CONCLUSIONS: Rufinamide is a promising adjunctive therapy for Lennox-Gastaut syndrome, an intractable childhood epilepsy. To ensure its optimal effectiveness, clinicians must be familiar with the medication's clinical response profile and potential for adverse effects.\",\n \"corpus_id\": 3953855,\n \"score\": 0\n },\n {\n \"doc_id\": \"20957124\",\n \"title\": \"Treating Lennox-Gastaut syndrome in epileptic pediatric patients with third-generation rufinamide.\",\n \"abstract\": \"Lennox-Gastaut syndrome (LGS) is a rare but debilitating pediatric epileptic encephalopathy characterized by multiple intractable seizure types. Treatment of LGS is challenging because of the small number of antiepileptic drugs (AEDs) which are effective for this syndrome, as well as the need for polytherapy in the majority of patients. This review focuses on the treatment of LGS with rufinamide, a recently approved third-generation AED with reported efficacy as adjunctive therapy for LGS. All relevant papers identified through a PubMed search on the treatment of LGS with rufinamide were reviewed. To date, the literature suggests improvements in seizure frequency for pediatric patients with LGS on rufinamide. Rufinamide appears to be especially effective for atonic or drop attack seizures. Rufinamide also displays a favorable adverse event profile compared with the older anticonvulsants, as well as a minimal number of drug interactions, making it a promising option for the adjunctive treatment of seizures associated with LGS.\",\n \"corpus_id\": 14148583,\n \"score\": 0\n },\n {\n \"doc_id\": \"21348771\",\n \"title\": \"Rufinamide for the treatment of Lennox-Gastaut syndrome.\",\n \"abstract\": \"INTRODUCTION: Lennox-Gastaut syndrome (LGS) is a severe treatment-resistant childhood-onset epilepsy. This review examines the role of the new drug rufinamide for the treatment of LGS. AREAS COVERED: MEDLINE and Google Scholar searches were undertaken. The pharmaceutical company was contacted for the latest information. LGS is characterized by the triad of diffuse slow spike-wave discharges in the electroencephalogram (EEG), learning disability (mental retardation) and frequent generalized seizures of multiple types, usually including tonic, atonic and atypical absence seizures. Felbamate, lamotrigine and topiramate have resulted in significant reductions in some seizure types, but no treatment has achieved acceptable seizure control in most patients. In a pivotal randomized, double-blind, placebo-controlled trial, the new drug rufinamide achieved significant improvements in seizure control in previously resistant subjects when added to up to three concomitant antiepileptic drugs. Open studies including patients with LGS have also demonstrated efficacy. These trials and a large open trial in adults and adolescents with partial seizures have revealed no serious adverse effects so far. The most common adverse events were fatigue/somnolence and vomiting. Rufinamide is of value in decreasing seizure frequency in LGS, but seizure freedom is seldom achieved. Although no serious adverse effects have been identified, the limited data available at present allow no firm conclusions to be drawn with regard to safety. EXPERT OPINION: The data support a role for rufinamide in treating LGS. However, more efforts are required to provide antiepileptic drugs for this treatment-resistant epilepsy syndrome. Rufinamide might also be of value in treating other forms of epilepsy.\",\n \"corpus_id\": 37713175,\n \"score\": 0\n },\n {\n \"doc_id\": \"21792306\",\n \"title\": \"Update on rufinamide in childhood epilepsy.\",\n \"abstract\": \"Rufinamide is an orally active, structurally novel compound (1-[(2,6-difluorophenil1) methyl1]-1 hydro 1,2,3-triazole-4 carboxamide), which is structurally distinct from other anticonvulsant drugs. It was granted orphan drug status for the adjunctive treatment of Lennox-Gastaut syndrome (LGS) in the United States in 2004, and released for use in Europe in 2007. In January 2009, rufinamide was approved by the United States Food and Drug Administration for treatment of LGS in children 4 years of age and older. It is also approved for adjunctive treatment for partial seizures in adults and adolescents. Rufinamide's efficacy mainly against atonic/tonic seizures in patients with LGS seems nowadays indubitable and has been confirmed both in randomized controlled trial and in open label extension studies. More recently, rufinamide was evaluated for the adjunctive treatment of childhood-onset epileptic encephalopathies and epileptic syndromes other than LGS, including epileptic spasms, multifocal epileptic encephalopathy with spasm/tonic seizures, myoclonic-astatic epilepsy, Dravet syndrome and malignant migrating partial seizures in infancy. This review updates the existing literature data on the efficacy and safety/tolerability of rufinamide in childhood-onset epilepsy syndromes.\",\n \"corpus_id\": 9078765,\n \"score\": 0\n },\n {\n \"doc_id\": \"22576075\",\n \"title\": \"Late-onset Lennox-Gastaut syndrome as a phenotype of 15q11.1q13.3 duplication.\",\n \"abstract\": \"The clinical symptoms associated with chromosome 15q duplication syndrome manifest through a heterogeneous group of symptoms characterised by hypotonia, delay in motor skills and language development, cognitive and learning disabilities, autism spectrum disorder and refractory epilepsy. The late development of Lennox-Gastaut syndrome in patients with 15q11q13 duplication is a possibility that physicians should be aware of. We report the case of a 27-year-old man with a neurodevelopmental syndrome due to a 15q duplication, with intellectual disability, psychiatric disturbances, and an epileptic phenotype diagnosed as late-onset Lennox-Gastaut syndrome.\",\n \"corpus_id\": 15886692,\n \"score\": 0\n },\n {\n \"doc_id\": \"23827423\",\n \"title\": \"Lennox-Gastaut syndrome symptomatic to hypothalamic hamartoma: evolution and long-term outcome following surgery.\",\n \"abstract\": \"BACKGROUND: Lennox-Gastaut syndrome is a catastrophic childhood cryptogenic or symptomatic epilepsy. Hypothalamic hamartomas cause refractory epilepsy often consistent with Lennox-Gastaut syndrome. METHODS: Children with Lennox-Gastaut syndrome were defined by a triad of multiple generalized seizure types, slow spike-and-wave on EEG, and mental retardation. RESULTS: Twenty-one of 159 hypothalamic hamartoma patients (14%) met the diagnostic criteria of Lennox-Gastaut syndrome. The median age of patients at epilepsy onset was 0.9 years (range, birth to 9 years). Six of the 21 patients (28%) had preceding infantile spasms. All patients underwent different surgical approaches, including endoscopic, transcallosal, orbitozygomatic resections, and radiosurgery treatment. Five of the 21 (24%) were seizure free with an additional 9 (42%) having at least >90% seizure reduction. Only 1 patient was not effectively treated (<50% seizure reduction). Eighty-eight percent of parents reported improvement in behavioral functioning. Shorter duration of epilepsy prior to surgery was a significant predictor of surgical outcome. CONCLUSIONS: Patients with Lennox-Gastaut syndrome symptomatic to hypothalamic hamartomas have better postsurgical outcome due to other etiologies compared with cryptogenic and symptomatic Lennox-Gastaut syndrome patients. However, compared with overall hypothalamic hamartomas postsurgical outcomes, this cohort was less favorable. Earlier surgery may lead to better outcomes.\",\n \"corpus_id\": 44510867,\n \"score\": 0\n },\n {\n \"doc_id\": \"25011392\",\n \"title\": \"Ketogenic diet in patients with Lennox-Gastaut syndrome.\",\n \"abstract\": \"PURPOSE: The ketogenic diet (KD) has been used as an alternative to antiepileptic drugs (AEDs) for patients with refractory epilepsy. Lennox-Gastaut syndrome (LGS) belongs to the group of epileptic encephalopathies that often prove refractory to AED treatment. In this prospective study we assess the efficacy and tolerability of the KD in patients with LGS. METHODS: Between March 1, 1990 and April 1, 2013, 61 patients who met diagnostic criteria of LGS were seen at our department. Twenty of them were placed on the KD and followed for a minimum of 16 months. RESULTS: The children had previously received a mean of 6.5 different AEDs and were on a mean of 2.5 AEDs when the diet was started. Eighteen months after initiating the diet, fifteen of the initial patients (75%) remained on the diet; three patients (15%) were seizure free, three (15%) had a 75-99% decrease in seizures, two (10%) had a 50-74% decrease in seizures, and the remaining seven children (35%) had a <50% decrease in seizures. Three seizure-free patients were tapered off the diet after remaining seizure free. In the three patients who had a 75-99% decrease in seizures AEDs were reduced. CONCLUSION: The KD is an effective and well-tolerated treatment option for patients with LGS, not only for those with cryptogenic, but also for those with structural LGS. The diet should be considered early in the course of this syndrome.\",\n \"corpus_id\": 17045191,\n \"score\": 0\n },\n {\n \"doc_id\": \"25575287\",\n \"title\": \"Acute behavioral crises in psychiatric inpatients with autism spectrum disorder (ASD): recognition of concomitant medical or non-ASD psychiatric conditions predicts enhanced improvement.\",\n \"abstract\": \"During adolescence, some individuals with autism spectrum disorder (ASD) engage in severe challenging behaviors, such as aggression, self-injury, disruption, agitation and tantrums. We aimed to assess risk factors associated with very acute behavioral crises in adolescents with ASD admitted to a dedicated neurobehavioral unit. We included retrospectively in 2008 and 2009 29 adolescents and young adults with ASD hospitalized for severe challenging behaviors and proposed a guideline (Perisse et al., 2010) that we applied prospectively for 29 patients recruited for the same indications between 2010 and 2012. In total, 58 patients were admitted (n=70 hospitalizations, mean age=15.66 (±4.07) years, 76% male). We systematically collected data describing socio-demographic characteristics, clinical variables (severity, presence of language, cognitive level), comorbid organic conditions, etiologic diagnosis of the episode, and treatments. We explored predictors of Global Assessment Functioning Scale (GAFS) score and duration of hospitalization at discharge. All but 2 patients exhibited severe autistic symptoms and intellectual disability (ID), and two-thirds had no functional verbal language. During the inpatient stay (mean=84.3 (±94.9) days), patients doubled on average their GAFS scores (mean=17.66 (±9.05) at admission vs. mean=31.4 (±9.48) at discharge). Most common etiologies for acute behavioral crises were organic causes [n=20 (28%), including epilepsy: n=10 (14%) and painful medical conditions: n=10 (14%)], environmental causes [n=17 (25%) including lack of treatment: n=11 (16%) and adjustment disorder: n=6 (9%)], and non-ASD psychiatric condition [n=33 (48%) including catatonia: n=5 (7%), major depressive episode: n=6 (9%), bipolar disorder: n=4 (6%), schizophrenia: n=6 (9%), other/unknown diagnosis: n=12 (17%)]. We found no influence of age, gender, socio-economic status, migration, level of ID, or history of seizure on improvement of GAFS score at discharge. Severity of autism at admission was the only negative predictor (p<.001). Painful medical conditions (p=.04), non-ASD psychiatric diagnoses (p=.001), prior usage of specialized ASD care programs (p=.004), functional language (p=.007), as well as a higher number of challenging behaviors upon admission (p=.001) were associated with higher GAFS scores at discharge. Clinical severity at admission, based on the number of challenging behaviors (r=.35, p=.003) and GAFS score (r=-.32, p=.008) was correlated with a longer inpatient stay. Longer hospitalization was however correlated (r=.27, p=.03) with higher GAFS score at discharge even after adjustment for confounding factors. Challenging behaviors among adolescents with ASD may stem from diverse risk factors, including environmental problems, comorbid acute psychiatric conditions, or somatic illness such as epilepsy or acute pain. The management of these behavioral challenges requires a unified, multidisciplinary approach.\",\n \"corpus_id\": 7486089,\n \"score\": 0\n },\n {\n \"doc_id\": \"26167208\",\n \"title\": \"Relationship of Lennox-Gastaut syndrome with perinatal event: A cross-sectional study.\",\n \"abstract\": \"INTRODUCTION: About one-half of children with Lennox-Gastaut syndrome (LGS) have history of birth hypoxia or other perinatal event but the knowledge about clinical, radiological profile and severity of epilepsy in these children as compared to those without a perinatal event is not known. MATERIALS AND METHODS: Thirty-one children with LGS were enrolled in this study and divided into two groups: One group with the perinatal event and other group without evidence of the perinatal event. We hypothesized that LGS with the perinatal event will have an early age of onset of LGS, more motor deficits and abnormal brain magnetic resonance imaging (MRI) and more severe epilepsy. RESULTS: There were 17 children in the perinatal event group and 14 in the other group. The mean age of onset of illness was significantly earlier in the perinatal event group (P < 0.05). More children in the perinatal event group had delayed milestones (P < 0.05), had higher seizure frequency (P < 0.05) however; there was no significant difference in number of anti-epileptic drugs consumed, motor deficits or MRI abnormalities. CONCLUSION: LGS children with the perinatal event have more severe epilepsy with early onset of disease and delayed milestones. History of perinatal insult in these children may help in predicting prognosis in LGS.\",\n \"corpus_id\": 22850987,\n \"score\": 0\n },\n {\n \"doc_id\": \"26245776\",\n \"title\": \"Clobazam and Aggression-Related Adverse Events in Pediatric Patients With Lennox-Gastaut Syndrome.\",\n \"abstract\": \"BACKGROUND: Lennox-Gastaut syndrome is an intractable epileptic encephalopathy marked by frequent drop seizures. Most patients develop moderate intellectual disability and behavioral problems, including hyperactivity, aggressiveness, insecurity, and autistic features. Treatment with benzodiazepines, including clobazam, may increase aggression/behavioral problems in patients with Lennox-Gastaut syndrome. Post hoc analyses of data from the OV-1012 trial assessed the potential for behavioral effects with clobazam treatment in pediatric (2 to 18 years) patients with Lennox-Gastaut syndrome. METHODS: OV-1012 was a phase 3, randomized, double-blind, parallel-group trial comprising a 4-week baseline period, 3-week titration period, and a 12-week maintenance period. Data from 194 patients were analyzed for a history of aggression/behavioral problems, occurrence of aggression-related adverse events, and by assessment of potential drug-related effects on four behavior domains of the Child Behavior Checklist. RESULTS: Twenty-nine aggression-related adverse events were reported for 27 (13.9%) patients. Similar percentages of clobazam-treated patients with and without a history of aggressive behavior experienced an aggression-related adverse event (16.7% versus 15.5%, respectively). In the medium- and high-dosage clobazam groups, onset of aggression-related adverse effects occurred within the 3-week titration period with 63.2% resolving by the end of the study. Aggression-related adverse event onset and resolution were similar for the low-dosage clobazam and placebo groups. Analysis of baseline to postbaseline T scores for the behavior domains of the Child Behavior Checklist indicated no significant differences between clobazam and placebo. CONCLUSIONS: Post hoc analyses indicate that the overall rate of aggression with clobazam treatment was low and dosage dependent. Clobazam treatment was effective in reducing drop seizures regardless of aggression experience.\",\n \"corpus_id\": 207349934,\n \"score\": 0\n },\n {\n \"doc_id\": \"26808205\",\n \"title\": \"Pontine and cerebral atrophy in Lennox-Gastaut syndrome.\",\n \"abstract\": \"OBJECTIVES: Lennox-Gastaut syndrome (LGS) is a severe epilepsy of childhood onset associated with intellectual disability and multiple seizure types. Characteristic interictal electrographic discharges include generalized paroxysmal fast activity and slow spike and wave, which we have previously shown recruit widespread areas of association cortex. We wished to determine whether patients with Lennox-Gastaut syndrome (LGS) have changes in cerebral volumes that match this pattern of cortical recruitment. METHODS: High resolution T1 weighted structural MRI was collected from 10 patients with LGS and 10 age and sex matched controls. Voxel-based morphometry (VBM) was used to compare tissue volumes across the whole brain (grey matter, white matter and CSF) and pontine volume between patients and controls, as well as to identify other regions of maximal tissue loss. RESULTS: LGS patients showed a significant decrease in whole brain volume compared to controls. Cortical atrophy was prominent in the mesial frontal region and bilateral anterior temporal poles. White matter atrophy was widespread and included peri-central and premotor regions. Atrophy was prominent in the pons, particularly in the region of the reticular formation. Grey matter atrophy trended to progress with age. SIGNIFICANCE: Grey and white matter atrophy are a feature of Lennox-Gastaut syndrome. Grey matter atrophy is apparent in the mesial frontal lobe suggesting this region may be an important node in the epilepsy network of LGS. Atrophy maximal in the pons and cerebellum mimics the patterns of seizure spread that has been previously observed during tonic seizures. This supports the idea that the pons is a key part of the epilepsy network in LGS.\",\n \"corpus_id\": 24616061,\n \"score\": 0\n },\n {\n \"doc_id\": \"27665735\",\n \"title\": \"The molecular and phenotypic spectrum of IQSEC2-related epilepsy.\",\n \"abstract\": \"OBJECTIVE: IQSEC2 is an X-linked gene associated with intellectual disability (ID) and epilepsy. Herein we characterize the epilepsy/epileptic encephalopathy of patients with IQSEC2 pathogenic variants. METHODS: Forty-eight patients with IQSEC2 variants were identified worldwide through Medline search. Two patients were recruited from our early onset epileptic encephalopathy cohort and one patient from personal communication. The 18 patients who have epilepsy in addition to ID are the subject of this study. Information regarding the 18 patients was ascertained by questionnaire provided to the treating clinicians. RESULTS: Six affected individuals had an inherited IQSEC2 variant and 12 had a de novo one (male-to-female ratio, 12:6). The pathogenic variant types were as follows: missense (8), nonsense (5), frameshift (1), intragenic duplications (2), translocation (1), and insertion (1). An epileptic encephalopathy was diagnosed in 9 (50%) of 18 patients. Seizure onset ranged from 8 months to 4 years; seizure types included spasms, atonic, myoclonic, tonic, absence, focal seizures, and generalized tonic-clonic (GTC) seizures. The electroclinical syndromes could be defined in five patients: late-onset epileptic spasms (three) and Lennox-Gastaut or Lennox-Gastaut-like syndrome (two). Seizures were pharmacoresistant in all affected individuals with epileptic encephalopathy. The epilepsy in the other nine patients had a variable age at onset from infancy to 18 years; seizure types included GTC and absence seizures in the hereditary cases and GTC and focal seizures in de novo cases. Seizures were responsive to medical treatment in most cases. All 18 patients had moderate to profound intellectual disability. Developmental regression, autistic features, hypotonia, strabismus, and white matter changes on brain magnetic resonance imaging (MRI) were prominent features. SIGNIFICANCE: The phenotypic spectrum of IQSEC2 disorders includes epilepsy and epileptic encephalopathy. Epileptic encephalopathy is a main clinical feature in sporadic cases. IQSEC2 should be evaluated in both male and female patients with an epileptic encephalopathy.\",\n \"corpus_id\": 24916469,\n \"score\": 0\n },\n {\n \"doc_id\": \"28471101\",\n \"title\": \"Ophthalmologic Features of Lennox-Gastaut Syndrome.\",\n \"abstract\": \"PURPOSE: To describe the characteristics and frequency of ophthalmologic findings in patients with Lennox-Gastaut syndrome (LGS). METHODS: The medical records of patients diagnosed with LGS at Seoul National University Children's Hospital from January 2004 to August 2014 were retrospectively reviewed. The records of 34 patients (mean age ± standard deviation, 2.66 ± 3.51 years; male, 58.8%) were reviewed. The primary measure was the incidence of ophthalmologic manifestations. RESULTS: Of the 34 patients, 88.2% had at least one ocular abnormality. Refractive error (52.9%) was the most frequently observed ophthalmologic manifestation in patients with LGS, followed by strabismus (32.4%), cortical visual impairment (23.5%), and retinopathy of prematurity (8.8%). Among these cases, seven patients had exotropia and three had esotropia. CONCLUSIONS: LGS is a childhood-onset epileptic encephalopathy with variable ophthalmologic manifestations, the most frequent being refractive errors. Patients with suspected LGS should be examined regularly because ophthalmological features can change during their disease course.\",\n \"corpus_id\": 28671096,\n \"score\": 0\n },\n {\n \"doc_id\": \"28957735\",\n \"title\": \"Inattention and hyperactivity/impulsivity among children with attention-deficit/hyperactivity-disorder, autism spectrum disorder, and intellectual disability.\",\n \"abstract\": \"BACKGROUND: Attention-Deficit/Hyperactivity Disorder (ADHD), Autism Spectrum Disorder (ASD), and Intellectual Disability (ID) are common co-occurring neurodevelopmental disorders; however, limited research exists regarding the presentation and severity of overlapping symptomology, particularly inattention and hyperactivity/impulsivity, when a child is diagnosed with one of more of these neurodevelopmental disorders. AIMS: As difficulties with inattention and hyperactivity/impulsivity are symptoms frequently associated with these disorders, the current study aims to determine the differences in the severity of inattention and hyperactivity/impulsivity in children diagnosed with ADHD, ASD, ID, and co-occurring diagnosis of ADHD/ID, ASD/ADHD, and ASD/ID. METHODS AND PROCEDURES: Participants in the current study included 113 children between the ages of 6 and 11 who were diagnosed with ADHD, ASD, ID, ADHD/ID, ASD/ADHD, or ASD/ID. Two MANOVA analyses were used to compare these groups witih respsect to symptom (i.e., inattention, hyperactivity/impulsivity) severity. OUTCOMES AND RESULTS: Results indicated that the majority of diagnostic groups experienced elevated levels of both inattention and hyperactivity/impulsivity. However, results yielded differences in inattention and hyperactivity/impulsivity severity. In addition, differences in measure sensitivity across behavioral instruments was found. CONCLUSIONS AND IMPLICATIONS: Children with neurodevelopmental disorders often exhibit inattention and hyperactivity/impulsivity, particularly those with ADHD, ASD, ASD/ADHD, and ADHD/ID; therefore, differential diagnosis may be complicated due to similarities in ADHD symptom severity. However, intellectual abilities may be an important consideration for practitioners in the differential diagnosis process as children with ID and ASD/ID exhibited significantly less inattention and hyperactive/impulsive behaviors. Additionally, the use of multiple behavior rating measures in conjunction with other assessment procedures may help practitioners determine the most appropriate diagnosis.\",\n \"corpus_id\": 46309266,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":47,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29691445\",\n \"title\": \"Propagation of Disturbances in AC Electricity Grids.\",\n \"abstract\": \"The energy transition towards high shares of renewable energy will affect the stability of electricity grids in many ways. Here, we aim to study its impact on propagation of disturbances by solving nonlinear swing equations describing coupled rotating masses of synchronous generators and motors on different grid topologies. We consider a tree, a square grid and as a real grid topology, the german transmission grid. We identify ranges of parameters with different transient dynamics: the disturbance decays exponentially in time, superimposed by oscillations with the fast decay rate of a single node, or with a smaller decay rate without oscillations. Most remarkably, as the grid inertia is lowered, nodes may become correlated, slowing down the propagation from ballistic to diffusive motion, decaying with a power law in time. Applying linear response theory we show that tree grids have a spectral gap leading to exponential relaxation as protected by topology and independent on grid size. Meshed grids are found to have a spectral gap which decreases with increasing grid size, leading to slow power law relaxation and collective diffusive propagation of disturbances. We conclude by discussing consequences if no measures are undertaken to preserve the grid inertia in the energy transition.\",\n \"corpus_id\": 13962974\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19282548","title":"A novel visualization technique for electric power grid analytics.","abstract":"The application of information visualization holds tremendous promise for the electric power industry, but its potential has so far not been sufficiently exploited by the visualization community. Prior work on visualizing electric power systems has been limited to depicting raw or processed information on top of a geographic layout. Little effort has been devoted to visualizing the physics of the power grids, which ultimately determines the condition and stability of the electricity infrastructure. Based on this assessment, we developed a novel visualization system prototype, GreenGrid, to explore the planning and monitoring of the North American Electricity Infrastructure. The paper discusses the rationale underlying the GreenGrid design, describes its implementation and performance details, and assesses its strengths and weaknesses against the current geographic-based power grid visualization. We also present a case study using GreenGrid to analyze the information collected moments before the last major electric blackout in the Western United States and Canada, and a usability study to evaluate the practical significance of our design in simulated real-life situations. Our result indicates that many of the disturbance characteristics can be readily identified with the proper form of visualization.","corpus_id":445873,"score":2},{"doc_id":"19905395","title":"Message passing for optimization and control of a power grid: model of a distribution system with redundancy.","abstract":"We use a power grid model with M generators and N consumption units to optimize the grid and its control. Each consumer demand is drawn from a predefined finite-size-support distribution, thus simulating the instantaneous load fluctuations. Each generator has a maximum power capability. A generator is not overloaded if the sum of the loads of consumers connected to a generator does not exceed its maximum production. In the standard grid each consumer is connected only to its designated generator, while we consider a more general organization of the grid allowing each consumer to select one generator depending on the load from a predefined consumer dependent and sufficiently small set of generators which can all serve the load. The model grid is interconnected in a graph with loops, drawn from an ensemble of random bipartite graphs, while each allowed configuration of loaded links represent a set of graph covering trees. Losses, the reactive character of the grid and the transmission-level connections between generators (and many other details relevant to realistic power grid) are ignored in this proof-of-principles study. We focus on the asymptotic limit, N-->infinity and N/M-->D=O(1)>1 , and we show that the interconnects allow significant expansion of the parameter domains for which the probability of a generator overload is asymptotically zero. Our construction explores the formal relation between the problem of grid optimization and the modern theory of sparse graphical models. We also design heuristic algorithms that achieve the asymptotically optimal selection of loaded links. We conclude discussing the ability of this approach to include other effects such as a more realistic modeling of the power grid and related optimization and control algorithms.","corpus_id":12662045,"score":2},{"doc_id":"20409486","title":"Protein collective motions coupled to ligand migration in myoglobin.","abstract":"Ligand migration processes inside myoglobin and protein dynamics coupled to the migration were theoretically investigated with molecular dynamics simulations. Based on a linear response theory, we identified protein motions coupled to the transient migration of ligand, carbon monoxide (CO), through channels. The result indicates that the coupled protein motions involve collective motions extended over the entire protein correlated with local gating motions at the channels. Protein motions, coupled to opening of a channel from the distal pocket to a neighboring xenon site, were found to share the collective motion with experimentally observed protein motions coupled to a doming motion of the heme Fe atom upon photodissociation of the ligand. Analysis based on generalized Langevin dynamics elucidated slow and diffusive features of the protein response motions. Remarkably small transmission coefficients for rates of the CO migrations through myoglobin were found, suggesting that the CO migration dynamics are characterized as motions governed by the protein dynamics involving the collective motions, rather than as thermally activated transitions across energy barriers of well-structured channels.","corpus_id":21036471,"score":2},{"doc_id":"21893072","title":"Exponential transient propagating oscillations in a ring of spiking neurons with unidirectional slow inhibitory synaptic coupling.","abstract":"Transient oscillations in a ring of spiking neuron models unidirectionally coupled with slow inhibitory synapses are studied. There are stable spatially fixed steady firing-resting states and unstable symmetric propagating firing-resting states. In transients, firing-resting patterns rotate in the direction of coupling (propagating oscillations), the duration of which increases exponentially with the number of neurons (exponential transients). Further, the duration of randomly generated transient propagating oscillations is distributed in a power law form and spatiotemporal noise of intermediate strength sustains propagating oscillations. These properties agree with those of transient propagating waves in a ring of sigmoidal neuron models.","corpus_id":26944422,"score":2},{"doc_id":"22096188","title":"Electrical energy storage for the grid: a battery of choices.","abstract":"The increasing interest in energy storage for the grid can be attributed to multiple factors, including the capital costs of managing peak demands, the investments needed for grid reliability, and the integration of renewable energy sources. Although existing energy storage is dominated by pumped hydroelectric, there is the recognition that battery systems can offer a number of high-value opportunities, provided that lower costs can be obtained. The battery systems reviewed here include sodium-sulfur batteries that are commercially available for grid applications, redox-flow batteries that offer low cost, and lithium-ion batteries whose development for commercial electronics and electric vehicles is being applied to grid storage.","corpus_id":206536979,"score":2},{"doc_id":"22346628","title":"A grid-based distributed event detection scheme for wireless sensor networks.","abstract":"This paper presents a grid-based distributed event detection scheme for wireless sensor networks. The network is divided into square-shaped grids of predefined grid size, where sensor nodes in each grid form a cluster with a cluster head. Event detection at each grid alone based on the readings of its member nodes is limited in event detection performance, especially for a small event region compared to the grid size. To improve the performance, each grid is further divided into 2 × 2 sub-grids of equal size. The decision on an event is made by finding a square region of 2 × 2 sub-grids, not necessarily in the same grid, that passed a predefined threshold. This process is conducted at each cluster head in a distributed manner by inter-cluster communications. Event detection is initiated when a cluster head receives an alarm from its member nodes. The cluster-head communicates with its neighboring cluster heads to exchange the number of nodes reporting an alarm. The threshold for event detection can be dynamically adjusted to reflect the number of sensor nodes in a grid and event size, if known. High event detection accuracy is achieved with a relatively low threshold without sacrificing false alarm rate by filtering most errors due to transient faults and isolating nodes with permanent faults. Experimental results show that the proposed scheme can achieve high detection accuracy, while maintaining low false alarm rate.","corpus_id":1652331,"score":2},{"doc_id":"22587093","title":"Wave propagation in random granular chains.","abstract":"The influence of randomness on wave propagation in one-dimensional chains of spherical granular media is investigated. The interaction between the elastic spheres is modeled using the classical Hertzian contact law. Randomness is introduced in the discrete model using random distributions of particle mass, Young's modulus, or radius. Of particular interest in this study is the quantification of the attenuation in the amplitude of the impulse associated with various levels of randomness: two distinct regimes of decay are observed, characterized by an exponential or a power law, respectively. The responses are normalized to represent a vast array of material parameters and impact conditions. The virial theorem is applied to investigate the transfer from potential to kinetic energy components in the system for different levels of randomness. The level of attenuation in the two decay regimes is compared for the three different sources of randomness and it is found that randomness in radius leads to the maximum rate of decay in the exponential regime of wave propagation.","corpus_id":11500332,"score":2},{"doc_id":"22712907","title":"Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method.","abstract":"The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required per wavelength for accurate simulations. The model is based on coupled first-order acoustic equations valid for nonlinear wave propagation in heterogeneous media with power law absorption. These are derived from the equations of fluid mechanics and include a pressure-density relation that incorporates the effects of nonlinearity, power law absorption, and medium heterogeneities. The additional terms accounting for convective nonlinearity and power law absorption are expressed as spatial gradients making them efficient to numerically encode. The governing equations are then discretized using a k-space pseudospectral technique in which the spatial gradients are computed using the Fourier-collocation method. This increases the accuracy of the gradient calculation and thus relaxes the requirement for dense computational grids compared to conventional finite difference methods. The accuracy and utility of the developed model is demonstrated via several numerical experiments, including the 3D simulation of the beam pattern from a clinical ultrasound probe.","corpus_id":23453034,"score":2},{"doc_id":"23006269","title":"Self-organized synchronization in decentralized power grids.","abstract":"Robust synchronization (phase locking) of power plants and consumers centrally underlies the stable operation of electric power grids. Despite current attempts to control large-scale networks, even their uncontrolled collective dynamics is not fully understood. Here we analyze conditions enabling self-organized synchronization in oscillator networks that serve as coarse-scale models for power grids, focusing on decentralizing power sources. Intriguingly, we find that whereas more decentralized grids become more sensitive to dynamical perturbations, they simultaneously become more robust to topological failures. Decentralizing power sources may thus facilitate the onset of synchronization in modern power grids.","corpus_id":11209846,"score":2},{"doc_id":"23319658","title":"Synchronization in complex oscillator networks and smart grids.","abstract":"The emergence of synchronization in a network of coupled oscillators is a fascinating topic in various scientific disciplines. A widely adopted model of a coupled oscillator network is characterized by a population of heterogeneous phase oscillators, a graph describing the interaction among them, and diffusive and sinusoidal coupling. It is known that a strongly coupled and sufficiently homogeneous network synchronizes, but the exact threshold from incoherence to synchrony is unknown. Here, we present a unique, concise, and closed-form condition for synchronization of the fully nonlinear, nonequilibrium, and dynamic network. Our synchronization condition can be stated elegantly in terms of the network topology and parameters or equivalently in terms of an intuitive, linear, and static auxiliary system. Our results significantly improve upon the existing conditions advocated thus far, they are provably exact for various interesting network topologies and parameters; they are statistically correct for almost all networks; and they can be applied equally to synchronization phenomena arising in physics and biology as well as in engineered oscillator networks, such as electrical power networks. We illustrate the validity, the accuracy, and the practical applicability of our results in complex network scenarios and in smart grid applications.","corpus_id":4849531,"score":2},{"doc_id":"23848724","title":"Hysteresis, phase transitions, and dangerous transients in electrical power distribution systems.","abstract":"The majority of dynamical studies in power systems focus on the high-voltage transmission grids where models consider large generators interacting with crude aggregations of individual small loads. However, new phenomena have been observed indicating that the spatial distribution of collective, nonlinear contribution of these small loads in the low-voltage distribution grid is crucial to the outcome of these dynamical transients. To elucidate the phenomenon, we study the dynamics of voltage and power flows in a spatially extended distribution feeder (circuit) connecting many asynchronous induction motors and discover that this relatively simple 1+1 (space+time) dimensional system exhibits a plethora of nontrivial spatiotemporal effects, some of which may be dangerous for power system stability. Long-range motor-motor interactions mediated by circuit voltage and electrical power flows result in coexistence and segregation of spatially extended phases defined by individual motor states, a \"normal\" state where the motors' mechanical (rotation) frequency is slightly smaller than the nominal frequency of the basic ac flows and a \"stalled\" state where the mechanical frequency is small. Transitions between the two states can be initiated by a perturbation of the voltage or base frequency at the head of the distribution feeder. Such behavior is typical of first-order phase transitions in physics, and this 1+1 dimensional model shows many other properties of a first-order phase transition with the spatial distribution of the motors' mechanical frequency playing the role of the order parameter. In particular, we observe (a) propagation of the phase-transition front with the constant speed (in very long feeders) and (b) hysteresis in transitions between the normal and stalled (or partially stalled) phases.","corpus_id":20671263,"score":2},{"doc_id":"24081270","title":"Modeling nonlinear wave propagation on nonuniform grids using a mapped k-space pseudospectral method.","abstract":"Simulating the propagation of nonlinear ultrasound waves is computationally difficult because of the dense grids needed to capture high-frequency harmonics. Here, a mapped k-space pseudospectral method is presented which allows the use of nonuniform grid spacings. This enables grid points to be clustered around steep regions of the wave field. Compared with using a uniform grid, this significantly reduces the total number of grid points needed for accurate simulations. Two methods for selecting a suitable nonuniform grid mapping are discussed.","corpus_id":26812474,"score":2},{"doc_id":"24200162","title":"Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.","abstract":"In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes.","corpus_id":12263838,"score":2},{"doc_id":"24424239","title":"Abruptness of cascade failures in power grids.","abstract":"Electric power-systems are one of the most important critical infrastructures. In recent years, they have been exposed to extreme stress due to the increasing demand, the introduction of distributed renewable energy sources, and the development of extensive interconnections. We investigate the phenomenon of abrupt breakdown of an electric power-system under two scenarios: load growth (mimicking the ever-increasing customer demand) and power fluctuations (mimicking the effects of renewable sources). Our results on real, realistic and synthetic networks indicate that increasing the system size causes breakdowns to become more abrupt; in fact, mapping the system to a solvable statistical-physics model indicates the occurrence of a first order transition in the large size limit. Such an enhancement for the systemic risk failures (black-outs) with increasing network size is an effect that should be considered in the current projects aiming to integrate national power-grids into \"super-grids\".","corpus_id":15643227,"score":2},{"doc_id":"24697385","title":"Impact of network topology on synchrony of oscillatory power grids.","abstract":"Replacing conventional power sources by renewable sources in current power grids drastically alters their structure and functionality. In particular, power generation in the resulting grid will be far more decentralized, with a distinctly different topology. Here, we analyze the impact of grid topologies on spontaneous synchronization, considering regular, random, and small-world topologies and focusing on the influence of decentralization. We model the consumers and sources of the power grid as second order oscillators. First, we analyze the global dynamics of the simplest non-trivial (two-node) network that exhibit a synchronous (normal operation) state, a limit cycle (power outage), and coexistence of both. Second, we estimate stability thresholds for the collective dynamics of small network motifs, in particular, star-like networks and regular grid motifs. For larger networks, we numerically investigate decentralization scenarios finding that decentralization itself may support power grids in exhibiting a stable state for lower transmission line capacities. Decentralization may thus be beneficial for power grids, regardless of the details of their resulting topology. Regular grids show a specific sharper transition not found for random or small-world grids.","corpus_id":18677972,"score":2},{"doc_id":"24807951","title":"Artificial neural networks for control of a grid-connected rectifier/inverter under disturbance, dynamic and power converter switching conditions.","abstract":"Three-phase grid-connected converters are widely used in renewable and electric power system applications. Traditionally, grid-connected converters are controlled with standard decoupled d-q vector control mechanisms. However, recent studies indicate that such mechanisms show limitations in their applicability to dynamic systems. This paper investigates how to mitigate such restrictions using a neural network to control a grid-connected rectifier/inverter. The neural network implements a dynamic programming algorithm and is trained by using back-propagation through time. To enhance performance and stability under disturbance, additional strategies are adopted, including the use of integrals of error signals to the network inputs and the introduction of grid disturbance voltage to the outputs of a well-trained network. The performance of the neural-network controller is studied under typical vector control conditions and compared against conventional vector control methods, which demonstrates that the neural vector control strategy proposed in this paper is effective. Even in dynamic and power converter switching environments, the neural vector controller shows strong ability to trace rapidly changing reference commands, tolerate system disturbances, and satisfy control requirements for a faulted power system.","corpus_id":-1,"score":2},{"doc_id":"24910217","title":"How dead ends undermine power grid stability.","abstract":"The cheapest and thus widespread way to add new generators to a high-voltage power grid is by a simple tree-like connection scheme. However, it is not entirely clear how such locally cost-minimizing connection schemes affect overall system performance, in particular the stability against blackouts. Here we investigate how local patterns in the network topology influence a power grid's ability to withstand blackout-prone large perturbations. Employing basin stability, a nonlinear concept, we find in numerical simulations of artificially generated power grids that tree-like connection schemes--so-called dead ends and dead trees--strongly diminish stability. A case study of the Northern European power system confirms this result and demonstrates that the inverse is also true: repairing dead ends by addition of a few transmission lines substantially enhances stability. This may indicate a topological design principle for future power grids: avoid dead ends.","corpus_id":38044866,"score":2},{"doc_id":"25243201","title":"Global renewable energy-based electricity generation and smart grid system for energy security.","abstract":"Energy is an indispensable factor for the economic growth and development of a country. Energy consumption is rapidly increasing worldwide. To fulfill this energy demand, alternative energy sources and efficient utilization are being explored. Various sources of renewable energy and their efficient utilization are comprehensively reviewed and presented in this paper. Also the trend in research and development for the technological advancement of energy utilization and smart grid system for future energy security is presented. Results show that renewable energy resources are becoming more prevalent as more electricity generation becomes necessary and could provide half of the total energy demands by 2050. To satisfy the future energy demand, the smart grid system can be used as an efficient system for energy security. The smart grid also delivers significant environmental benefits by conservation and renewable generation integration.","corpus_id":16901025,"score":2},{"doc_id":"25833596","title":"Decoupling of relaxation and diffusion in random pinning glass-forming liquids.","abstract":"We investigate numerically the relaxation and diffusion dynamics in three-dimensional Kob-Andersen glass-forming liquids in which part of the particles are randomly chosen and pinned permanently. We find that both the relaxation dynamics and diffusion dynamics slow down as increasing the pinning concentration (cpin) at fixed temperatures that we study. For higher temperature and lower cpin, the α relaxation time τ and the diffusion coefficient D have the scaling relationship D ∼ τ(-1). However, this coupling behavior breaks down if cpin is further increased, and the scaling relationship is replaced by D ∼ τ(-ν) with ν < 1. At temperatures around the onset temperature of the bulk system, a transition from ν ∼ 0.75 to ν ∼ 0.61 with increasing cpin is found. However, at lower temperatures, ν ∼ 0.67 holds in the whole studied cpin range. By fitting the relaxation time as a function of cpin with Vogel-Fulcher-Tamman equation, we find that the change of scaling exponent ν is accompanied with the change of fragility parameter K at higher temperatures. However, at lower temperatures, pinning particles have little effect on the system's qualitative properties. Moreover, we investigate three measures of heterogeneity of dynamics and find that the relaxation and the diffusion motion of particles show different responses to the pinned particles, which may lead to the slower relaxation than diffusion and the decoupling of relaxation and diffusion. The string-like motion is found to saturate at the mode-coupling theory (MCT) crossover point, which indicates that other relaxation modes may exist below the MCT transition point.","corpus_id":20605582,"score":2},{"doc_id":"25897178","title":"Semi-implicit Integration Factor Methods on Sparse Grids for High-Dimensional Systems.","abstract":"Numerical methods for partial differential equations in high-dimensional spaces are often limited by the curse of dimensionality. Though the sparse grid technique, based on a one-dimensional hierarchical basis through tensor products, is popular for handling challenges such as those associated with spatial discretization, the stability conditions on time step size due to temporal discretization, such as those associated with high-order derivatives in space and stiff reactions, remain. Here, we incorporate the sparse grids with the implicit integration factor method (IIF) that is advantageous in terms of stability conditions for systems containing stiff reactions and diffusions. We combine IIF, in which the reaction is treated implicitly and the diffusion is treated explicitly and exactly, with various sparse grid techniques based on the finite element and finite difference methods and a multi-level combination approach. The overall method is found to be efficient in terms of both storage and computational time for solving a wide range of PDEs in high dimensions. In particular, the IIF with the sparse grid combination technique is flexible and effective in solving systems that may include cross-derivatives and non-constant diffusion coefficients. Extensive numerical simulations in both linear and nonlinear systems in high dimensions, along with applications of diffusive logistic equations and Fokker-Planck equations, demonstrate the accuracy, efficiency, and robustness of the new methods, indicating potential broad applications of the sparse grid-based integration factor method.","corpus_id":23511617,"score":2},{"doc_id":"26610212","title":"Computational Investigation of Wave Packet Scattering in the Complex Plane: Propagation on a Grid.","abstract":"The time-dependent scattering of a wave packet from a Gaussian barrier is investigated computationally in the complex z-plane. The initial wave packet and the potential energy are obtained through analytic continuation from functions specified on the real-axis. The wave packet is then propagated on the two-dimensional grid. For a low initial wave packet energy, the time evolution is followed by plotting the following functions: |ψ(z,t)|, real(ψ(z,t)), and the quantum momentum function (QMF), p(z,t). In the reflected packet, an important role is played by ripples (quasi-nodes) forming above the real axis. As these quasi-nodes move down across the real axis, they are 'detected' as 'interference oscillations' in the density. In contrast, the component of the packet below the real axis makes a significant contribution to the transmitted packet. Vector maps of the QMF show hyperbolic flow around quasi-nodes and counterclockwise circular flow around transient stagnation points, where the QMF vanishes. However, when the Pólya vector field (defined by P(z,t) = p*(z,t)) is plotted, circular counterclockwise flow is obtained near the quasi-nodes. The real and imaginary parts of the quantum action function S(z,t) are plotted and the vorticity, defined by the curl of the Pólya field, is used to pinpoint regions of nonanalyticity in the QMF.","corpus_id":317374,"score":2},{"doc_id":"26735210","title":"Cultured Construction: Global Evidence of the Impact of National Values on Renewable Electricity Infrastructure Choice.","abstract":"Renewable electricity is an important tool in the fight against climate change, but globally these technologies are still in the early stages of diffusion. To contribute to our understanding of the factors driving this diffusion, I study relationships between national values (measured by Hofstede's cultural dimensions) and renewable electricity adoption at the national level. Existing data for 66 nations (representing an equal number of developed and developing economies) are used to fuel the analysis. Somewhat dependent on limited available data on controls for grid reliability and the cost of electricity, I discover that three of Hofstede's dimensions (high uncertainty avoidance, low masculinity-femininity, and high individualism-collectivism) have significant exponential relationships with renewable electricity adoption. The dimension of uncertainty avoidance appears particularly appropriate for practical application. Projects or organizations implementing renewable electricity policy, designs, or construction should particularly attend to this cultural dimension. In particular, as the data imply that renewable technologies are being used to manage risk in electricity supply, geographies with unreliable grids are particularly likely to be open to renewable electricity technologies.","corpus_id":29809187,"score":2},{"doc_id":"27078359","title":"Linear stability and the Braess paradox in coupled-oscillator networks and electric power grids.","abstract":"We investigate the influence that adding a new coupling has on the linear stability of the synchronous state in coupled-oscillator networks. Using a simple model, we show that, depending on its location, the new coupling can lead to enhanced or reduced stability. We extend these results to electric power grids where a new line can lead to four different scenarios corresponding to enhanced or reduced grid stability as well as increased or decreased power flows. Our analysis shows that the Braess paradox may occur in any complex coupled system, where the synchronous state may be weakened and sometimes even destroyed by additional couplings.","corpus_id":28708004,"score":2},{"doc_id":"27176235","title":"Superdiffusion, large-scale synchronization, and topological defects.","abstract":"We study an ensemble of random walkers carrying internal noisy phase oscillators which are synchronized among the walkers by local interactions. Due to individual mobility, the interaction partners of every walker change randomly, hereby introducing an additional, independent source of fluctuations, thus constituting the intrinsic nonequilibrium nature of the temporal dynamics. We employ this paradigmatic model system to discuss how the emergence of order is affected by the motion of individual entities. In particular, we consider both normal diffusive motion and superdiffusion. A non-Hamiltonian field theory including multiplicative noise terms is derived which describes the nonequilibrium dynamics at the macroscale. This theory reveals a defect-mediated transition from incoherence to quasi-long-range order for normal diffusion of oscillators in two dimensions, implying a power-law dependence of all synchronization properties on system size. In contrast, superdiffusive transport suppresses the emergence of topological defects, thereby inducing a continuous synchronization transition to long-range order in two dimensions. These results are consistent with particle-based simulations.","corpus_id":3822974,"score":2},{"doc_id":"27225708","title":"Enhancing synchronization stability in a multi-area power grid.","abstract":"Maintaining a synchronous state of generators is of central importance to the normal operation of power grids, in which many networks are generally interconnected. In order to understand the condition under which the stability can be optimized, it is important to relate network stability with feedback control strategies as well as network structure. Here, we present a stability analysis on a multi-area power grid by relating it with several control strategies and topological design of network structure. We clarify the minimal feedback gain in the self-feedback control, and build the optimal communication network for the local and global control strategies. Finally, we consider relationship between the interconnection pattern and the synchronization stability; by optimizing the network interlinks, the obtained network shows better synchronization stability than the original network does, in particular, at a high power demand. Our analysis shows that interlinks between spatially distant nodes will improve the synchronization stability. The results seem unfeasible to be implemented in real systems but provide a potential guide for the design of stable power systems.","corpus_id":4337483,"score":2},{"doc_id":"27415291","title":"Building blocks of the basin stability of power grids.","abstract":"Given a power grid and a transmission (coupling) strength, basin stability is a measure of synchronization stability for individual nodes. Earlier studies have focused on the basin stability's dependence of the position of the nodes in the network for single values of transmission strength. Basin stability grows from zero to one as transmission strength increases, but often in a complex, nonmonotonous way. In this study, we investigate the entire functional form of the basin stability's dependence on transmission strength. To be able to perform a systematic analysis, we restrict ourselves to small networks. We scan all isomorphically distinct networks with an equal number of power producers and consumers of six nodes or less. We find that the shapes of the basin stability fall into a few, rather well-defined classes, that could be characterized by the number of edges and the betweenness of the nodes, whereas other network positional quantities matter less.","corpus_id":10494188,"score":2},{"doc_id":"27575148","title":"Long-range response in ac electricity grids.","abstract":"Local changes in the topology of electricity grids can cause overloads far away from the disturbance [D. Witthaut and M. Timme, Eur. Phys. J. B 86, 377 (2013)EPJBFY1434-602810.1140/epjb/e2013-40469-4], making the prediction of the robustness against changes in the topology-for example, caused by power outages or grid extensions-a challenging task. The impact of single-line additions on the long-range response of dc electricity grids has recently been studied [D. Labavić, R. Suciu, H. Meyer-Ortmanns, and S. Kettemann, Eur. Phys. J.: Spec. Top. 223, 2517 (2014)1951-635510.1140/epjst/e2014-02273-0]. By solving the real part of the static ac load flow equations, we conduct a similar investigation for ac grids. In a regular two-dimensional grid graph with cyclic boundary conditions, we find a power law decay for the change of power flow as a function of distance to the disturbance over a wide range of distances. The power exponent increases and saturates for large system sizes. By applying the same analysis to the German transmission grid topology, we show that also in real-world topologies a long-ranged response can be found.","corpus_id":15438738,"score":2},{"doc_id":"27713509","title":"Islanding the power grid on the transmission level: less connections for more security.","abstract":"Islanding is known as a management procedure of the power system that is implemented at the distribution level to preserve sensible loads from outages and to guarantee the continuity in electricity supply, when a high amount of distributed generation occurs. In this paper we study islanding on the level of the transmission grid and shall show that it is a suitable measure to enhance energy security and grid resilience. We consider the German and Italian transmission grids. We remove links either randomly to mimic random failure events, or according to a topological characteristic, their so-called betweenness centrality, to mimic an intentional attack and test whether the resulting fragments are self-sustainable. We test this option via the tool of optimized DC power flow equations. When transmission lines are removed according to their betweenness centrality, the resulting islands have a higher chance of being dynamically self-sustainable than for a random removal. Less connections may even increase the grid's stability. These facts should be taken into account in the design of future power grids.","corpus_id":9936023,"score":2},{"doc_id":"27739704","title":"Cascading failures in ac electricity grids.","abstract":"Sudden failure of a single transmission element in a power grid can induce a domino effect of cascading failures, which can lead to the isolation of a large number of consumers or even to the failure of the entire grid. Here we present results of the simulation of cascading failures in power grids, using an alternating current (AC) model. We first apply this model to a regular square grid topology. For a random placement of consumers and generators on the grid, the probability to find more than a certain number of unsupplied consumers decays as a power law and obeys a scaling law with respect to system size. Varying the transmitted power threshold above which a transmission line fails does not seem to change the power-law exponent q≈1.6. Furthermore, we study the influence of the placement of generators and consumers on the number of affected consumers and demonstrate that large clusters of generators and consumers are especially vulnerable to cascading failures. As a real-world topology, we consider the German high-voltage transmission grid. Applying the dynamic AC model and considering a random placement of consumers, we find that the probability to disconnect more than a certain number of consumers depends strongly on the threshold. For large thresholds the decay is clearly exponential, while for small ones the decay is slow, indicating a power-law decay.","corpus_id":5054954,"score":2},{"doc_id":"27781449","title":"Control and prediction for blackouts caused by frequency collapse in smart grids.","abstract":"The electric power system is one of the cornerstones of modern society. One of its most serious malfunctions is the blackout, a catastrophic event that may disrupt a substantial portion of the system, playing havoc to human life and causing great economic losses. Thus, understanding the mechanisms leading to blackouts and creating a reliable and resilient power grid has been a major issue, attracting the attention of scientists, engineers, and stakeholders. In this paper, we study the blackout problem in power grids by considering a practical phase-oscillator model. This model allows one to simultaneously consider different types of power sources (e.g., traditional AC power plants and renewable power sources connected by DC/AC inverters) and different types of loads (e.g., consumers connected to distribution networks and consumers directly connected to power plants). We propose two new control strategies based on our model, one for traditional power grids and another one for smart grids. The control strategies show the efficient function of the fast-response energy storage systems in preventing and predicting blackouts in smart grids. This work provides innovative ideas which help us to build up a robuster and more economic smart power system.","corpus_id":26000359,"score":2},{"doc_id":"28085307","title":"Delocalization of disturbances and the stability of ac electricity grids.","abstract":"In order to study how local disturbances affect the ac grid stability, we start from nonlinear power balance equations and map them to complex linear wave equations. Having obtained stationary solutions with phases φ_{i} at generator and consumer nodes i, we next study the dynamics of deviations. Starting with an initially localized perturbation, it is found to spread in a periodic grid diffusively throughout the grid. We find the parametric dependence of diffusion constant D. We apply the same solution strategy to general grid topologies and analyze their stability against local perturbations. The perturbation remains either localized or becomes delocalized, depending on grid topology, power capacity, and distribution of consumers and generator power P_{i}. Delocalization is found to increase the lifetime of perturbations and thereby their influence on grid stability, whereas localization results in an exponentially fast decay of perturbations at all grid sites. These results may therefore lead to new strategies to control the stability of electricity grids.","corpus_id":41090271,"score":2},{"doc_id":"28147501","title":"Synchronization of cyclic power grids: Equilibria and stability of the synchronous state.","abstract":"Synchronization is essential for the proper functioning of power grids; we investigate the synchronous states and their stability for cyclic power grids. We calculate the number of stable equilibria and investigate both the linear and nonlinear stabilities of the synchronous state. The linear stability analysis shows that the stability of the state, determined by the smallest nonzero eigenvalue, is inversely proportional to the size of the network. We use the energy barrier to measure the nonlinear stability and calculate it by comparing the potential energy of the type-1 saddles with that of the stable synchronous state. We find that the energy barrier depends on the network size (N) in a more complicated fashion compared to the linear stability. In particular, when the generators and consumers are evenly distributed in an alternating way, the energy barrier decreases to a constant when N approaches infinity. For a heterogeneous distribution of generators and consumers, the energy barrier decreases with N. The more heterogeneous the distribution is, the stronger the energy barrier depends on N. Finally, we find that by comparing situations with equal line loads in cyclic and tree networks, tree networks exhibit reduced stability. This difference disappears in the limit of N→∞. This finding corroborates previous results reported in the literature and suggests that cyclic (sub)networks may be applied to enhance power transfer while maintaining stable synchronous operation.","corpus_id":12007948,"score":2},{"doc_id":"28364771","title":"Smoothing effect for spatially distributed renewable resources and its impact on power grid robustness.","abstract":"In this paper, we show that spatial correlation of renewable energy outputs greatly influences the robustness of the power grids against large fluctuations of the effective power. First, we evaluate the spatial correlation among renewable energy outputs. We find that the spatial correlation of renewable energy outputs depends on the locations, while the influence of the spatial correlation of renewable energy outputs on power grids is not well known. Thus, second, by employing the topology of the power grid in eastern Japan, we analyze the robustness of the power grid with spatial correlation of renewable energy outputs. The analysis is performed by using a realistic differential-algebraic equations model. The results show that the spatial correlation of the energy resources strongly degrades the robustness of the power grid. Our results suggest that we should consider the spatial correlation of the renewable energy outputs when estimating the stability of power grids.","corpus_id":205218927,"score":2},{"doc_id":"28912454","title":"Resilience of electricity grids against transmission line overloads under wind power injection at different nodes.","abstract":"A steadily increasing fraction of renewable energy sources for electricity production requires a better understanding of how stochastic power generation affects the stability of electricity grids. Here, we assess the resilience of an IEEE test grid against single transmission line overloads under wind power injection based on the dc power flow equations and a quasi-static grid response to wind fluctuations. Thereby we focus on the mutual influence of wind power generation at different nodes. We find that overload probabilities vary strongly between different pairs of nodes and become highly affected by spatial correlations of wind fluctuations. An unexpected behaviour is uncovered: for a large number of node pairs, increasing wind power injection at one node can increase the power threshold at the other node with respect to line overloads in the grid. We find that this seemingly paradoxical behaviour is related to the topological distance of the overloaded line from the shortest path connecting the wind nodes. In the considered test grid, it occurs for all node pairs, where the overloaded line belongs to the shortest path.","corpus_id":22241441,"score":2},{"doc_id":"29289040","title":"Stability of synchrony against local intermittent fluctuations in tree-like power grids.","abstract":"90% of all Renewable Energy Power in Germany is installed in tree-like distribution grids. Intermittent power fluctuations from such sources introduce new dynamics into the lower grid layers. At the same time, distributed resources will have to contribute to stabilize the grid against these fluctuations in the future. In this paper, we model a system of distributed resources as oscillators on a tree-like, lossy power grid and its ability to withstand desynchronization from localized intermittent renewable infeed. We find a remarkable interplay of the network structure and the position of the node at which the fluctuations are fed in. An important precondition for our findings is the presence of losses in distribution grids. Then, the most network central node splits the network into branches with different influence on network stability. Troublemakers, i.e., nodes at which fluctuations are especially exciting the grid, tend to be downstream branches with high net power outflow. For low coupling strength, we also find branches of nodes vulnerable to fluctuations anywhere in the network. These network regions can be predicted at high confidence using an eigenvector based network measure taking the turbulent nature of perturbations into account. While we focus here on tree-like networks, the observed effects also appear, albeit less pronounced, for weakly meshed grids. On the other hand, the observed effects disappear for lossless power grids often studied in the complex system literature.","corpus_id":24033472,"score":2},{"doc_id":"29401941","title":"Optical coherence grids and their propagation characteristics.","abstract":"A novel class of partially coherent light sources termed optical coherence grids (OCGs) are introduced that can yield stable optical grids in the far field. The optical grids, of which the light distributes in a network of straight lines crossing each other to form a series of hollow cages, can be seen as a better controlled optical lattice. Propagation properties of OCG beams in free space, including spectral density, transverse coherence, and M2 factor, are investigated in detail. It is interesting that a periodic grid pattern is produced at a distance and remains stable on further propagation, and we stress that the structure of far-field optical grids can be flexibly tuned by modulating the correlation parameters of the source. In addition, by performing convolution of degree of coherence, we also propose perfect optical coherence grids (POCG). The far-field grid pattern of POCG is in a fully controllable fashion. This work is expected to find applications in cooling atoms, trapping microscopic particles, or assembling cells, etc.","corpus_id":46765572,"score":2},{"doc_id":"19045156","title":"Inertial effects in the nonlinear transient relaxation of rigid rodlike molecules in a strong dc electric field.","abstract":"A method of calculation of nonlinear transient responses of an assembly of noninteracting polar linear molecules due to sudden changes in a strong external dc electric field is presented. The infinite hierarchy of differential-recurrence relations for the decay functions describing the relaxation of the system is derived by averaging the underlying inertial Langevin equation. The solution of this hierarchy is obtained in terms of matrix continued fractions. The integral relaxation time and the spectrum of the electric polarization for various nonlinear transient responses (step-on, step-off, and rapidly rotating field) are calculated for typical values of the model parameters. The nonlinear transient responses exhibit pronounced nonlinear effects due to the strong dc field. Analytical equations for the quantities of interest are presented in the overdamped limit. Furthermore, the linear response relaxation function and linear dynamic susceptibility are obtained as a particular case of a general nonlinear theory.","corpus_id":17756942,"score":1},{"doc_id":"20462247","title":"Electric response of nonspherical and spherical silica particle dispersions to ac electric field.","abstract":"For the purpose of revealing unique aspects of the electrical double layer (EDL) around nonspherical particles, we focus on a silica square platelike particle with well-defined shape, i.e., H-ilerite. Impedance measurements for suspensions of silica spherical and square platelike particles are performed to examine ion concentration polarization and its relaxation in their EDLs under ac electric fields that are high enough to orient H-ilerite to electric fields and form pearl chains of particles. For a silica spherical particle, the relaxation frequency of ion concentration polarization in EDL around the particles is independent of applied electric field strength and the volume fraction of the particles in suspension. The conductance ratios of silica particle suspension to its supernatant show a good linear relation against the volume fraction independently of applied electric field strength. For H-ilerite, at low electric field strength where there is neither electric orientation nor pearl chain formation, the conductance ratio also shows a linear relation against the volume fraction. The slope of the conductance ratio to the volume fraction increases and the relaxation frequency decreases as applied electric field strength increases. In addition, two linear relations with different slopes, where the slope becomes steep at higher volume fractions, appear in the plots of the conductance ratio against the volume fraction. Such a unique response of H-ilerite suspension to electric field can be explained by the electric orientation of H-ilerite accompanying pearl chain formation.","corpus_id":38684454,"score":1},{"doc_id":"20866296","title":"Lattice splitting under intermittent flows.","abstract":"We study the splitting of regular square lattices subject to stochastic intermittent flows. Various flow patterns are produced by different groupings of the nodes, based on their random alternation between two possible states. The resulting flows on the lattices decrease with the number of groups according to a power law. By Monte Carlo simulations we reveal how the time span until the occurrence of a splitting depends on the flow patterns. Increasing the flow fluctuation frequency shortens this time span, which reaches a minimum before rising again due to inertia effects incorporated in the model. The size of the largest connected component after the splitting is rather independent of the flow fluctuation frequency but slightly decreases with the link capacities. Our findings carry important implications for real-world networks, such as electric power grids with a large share of renewable intermittent energy sources.","corpus_id":10461064,"score":1},{"doc_id":"21247206","title":"Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.","abstract":"To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the frequency fluctuation is small. Thus, we observed a distinct difference between the classical and quantum mechanically calculated multidimensional spectra in the slow modulation case where spectral diffusion plays a role. This fact indicates that one may not reproduce the experimentally obtained multidimensional spectrum for high-frequency vibrational modes based on classical molecular dynamics simulations if the modulation that arises from surrounding molecules is weak and slow. A practical way to overcome the difference between the classical and quantum simulations was discussed.","corpus_id":25212051,"score":1},{"doc_id":"21599168","title":"Time-dependent correlations in a supercooled liquid from nonlinear fluctuating hydrodynamics.","abstract":"We solve numerically the equations of nonlinear fluctuating hydrodynamics (NFH). A coarse graining of the density field is applied at each time step to avoid instabilities which otherwise plague the algorithm at long times. The equilibrium correlation of the density fluctuations at different times obtained directly from the solutions of the NFH equations are shown here to be in quantitative agreement with corresponding molecular dynamics simulation data. Low-order perturbative treatment of the these NFH equations obtains the mode coupling model. The latter has been widely studied for understanding the slow dynamics characteristic of the supercooled state. A crucial aspect of this theory is a rounded version of a possible ergodic-nonergodic transition in the supercooled liquid at a temperature T(c) between melting point T(m) and the glass transition temperature T(g). In the present work we demonstrate numerically the role of strongly coupled density fluctuations in giving rise to slow dynamics and how the 1/ρ nonlinearity in the NFH equations of motion is essential in restoring the ergodic behavior in the liquid. The relaxation data indicate that at moderate supercooling near T(c), the time temperature superposition holds. The relaxation gets increasingly stretched with increased supercooling. The relaxation time τ shows an initial power-law divergence approaching a transition temperature T(c) generally identified as the mode coupling temperature. From the direct solutions we obtain a value for T(c) much lower than that typically estimated from solution of low-order integral equations of mode coupling theory. This is in agreement with the trend seen in computer simulations.","corpus_id":46218076,"score":1},{"doc_id":"22060330","title":"Relaxation properties in a diffusive model of k-mers with constrained movements on a triangular lattice.","abstract":"We study the relaxation process in a two-dimensional lattice gas model, based on the concept of geometrical frustration. In this model the particles are k-mers that can both randomly translate and rotate on the planar triangular lattice. In the absence of rotation, the diffusion of hard-core particles in crossed single-file systems is investigated. We monitor, for different densities, several quantities: mean-square displacement, the self-part of the van Hove correlation function, and the self-intermediate scattering function. We observe a considerable slowing of diffusion on a long-time scale when suppressing the rotational motion of k-mers; our system is subdiffusive at intermediate times between the initial transient and the long-time diffusive regime. We show that the self-part of the van Hove correlation function exhibits, as a function of particle displacement, a stretched exponential decay at intermediate times. The self-intermediate scattering function (SISF), displaying slower than exponential relaxation, suggests the existence of heterogeneous dynamics. For each value of density, the SISF is well described by the Kohlrausch-Williams-Watts law; the characteristic timescale τ(q(n)) is found to decrease with the wave vector q(n) according to a simple power law. Furthermore, the slowing of the dynamics with density ρ(0) is consistent with the scaling law 1/τ(q(n);ρ(0))∝(ρ(c)-ρ(0))(ϰ), with the same exponent ϰ=3.34±0.12 for all wave vectors q(n). The density ρ(c) is approximately equal to the closest packing limit, θ(CPL)≲1, for dimers on the two-dimensional triangular lattice. The self-diffusion coefficient D(s) scales with the same power-law exponent and critical density.","corpus_id":35126432,"score":1},{"doc_id":"22277723","title":"Quasi-elastic neutron scattering studies of the slow dynamics of supercooled and glassy aspirin.","abstract":"Aspirin, also known as acetylsalicylic acid (ASA), is not only a wonderful drug, but also a good glass former. Therefore, it serves as an important molecular system to study the near-arrest and arrested phenomena. In this paper, a high-resolution quasi-elastic neutron scattering (QENS) technique is used to investigate the slow dynamics of supercooled liquid and glassy aspirin from 410 down to 350 K. The measured QENS spectra can be analyzed with a stretched exponential model. We find that (i) the stretched exponent β(Q) is independent of the wavevector transfer Q in the measured Q range and (ii) the structural relaxation time τ(Q) follows a power-law dependence on Q. Consequently, the Q-independent structural relaxation time τ(0) can be extracted for each temperature to characterize the slow dynamics of aspirin. The temperature dependence of τ(0) can be fitted with the mode-coupling power law, the Vogel-Fulcher-Tammann equation and a universal equation for fragile glass forming liquids recently proposed by Tokuyama in the measured temperature range. The calculated dynamic response function χ(T)(Q, t) using the experimentally determined self-intermediate scattering function of the hydrogen atoms of aspirin shows direct evidence of the enhanced dynamic fluctuations as the aspirin is increasingly supercooled, in agreement with the fixed-time mean squared displacement ⟨x(2)⟩ and the non-Gaussian parameter α(2) extracted from the elastic scattering.","corpus_id":206038716,"score":1},{"doc_id":"22475003","title":"Wind power electricity: the bigger the turbine, the greener the electricity?","abstract":"Wind energy is a fast-growing and promising renewable energy source. The investment costs of wind turbines have decreased over the years, making wind energy economically competitive to conventionally produced electricity. Size scaling in the form of a power law, experience curves and progress rates are used to estimate the cost development of ever-larger turbines. In life cycle assessment, scaling and progress rates are seldom applied to estimate the environmental impacts of wind energy. This study quantifies whether the trend toward larger turbines affects the environmental profile of the generated electricity. Previously published life cycle inventories were combined with an engineering-based scaling approach as well as European wind power statistics. The results showed that the larger the turbine is, the greener the electricity becomes. This effect was caused by pure size effects of the turbine (micro level) as well as learning and experience with the technology over time (macro level). The environmental progress rate was 86%, indicating that for every cumulative production doubling, the global warming potential per kWh was reduced by 14%. The parameters, hub height and rotor diameter were identified as Environmental Key Performance Indicators that can be used to estimate the environmental impacts for a generic turbine.","corpus_id":28942884,"score":1},{"doc_id":"22755699","title":"High-ratio grid considerations in mobile chest radiography.","abstract":"PURPOSE: Grids are often not used in mobile chest radiography, and when used, they have a low ratio and are often inaccurately aligned. Recently, a mobile radiography automatic grid alignment system (MRAGA) was developed that accurately and automatically aligns the focal spot with the grid. The objective of this study is to investigate high-ratio grid tradeoffs in mobile chest radiography at fixed patient dose when the focal spot lies on the focal axis of the grid. METHODS: The chest phantoms (medium and large) used in this study were modifications of the ANSI (American National Standards Institute) chest phantom and consisted of layers of Lucite™, aluminum, and air. For the large chest phantom, the amount of Lucite and aluminum was increased by 50% over the medium phantom. Further modifications included a mediastinum insert and the addition of contrast targets in the lung and mediastinum regions. Five high-ratio grids were evaluated and compared to the nongrid results at x-ray tube potentials of 80, 90, 100, and 110 kVp for both phantoms. The grids investigated were from two manufacturers: 12:1 and 15:1 aluminum interspace grids from one and 10:1, 13:1, and 15:1 fiber interspace grids from another. MRAGA was employed to align the focal spot with the grid. All exposures for a given kVp and phantom size were made using the same current-time product (CTP). The phantom images were acquired using computed radiography, and contrast-to-noise ratios (CNR) and CNR improvement factors (k(CNR)) were determined from the resultant images. The noise in the targets and the contrast between the targets and their backgrounds were calculated using a local detrending correction, and the CNR was calculated as the ratio of the target contrast to the background noise. k(CNR) was defined as the ratio of the CNR imaged with the grid divided by the CNR imaged without a grid. RESULTS: The CNR values obtained with a high-ratio grid were 4%-65% higher than those obtained without a grid at the same phantom dose. The improvement was greater for the large chest phantom than the medium chest phantom and greater for the mediastinum targets than for the lung targets. In general, the fiber interspace grids performed better than the aluminum interspace grids. In the lung, k(CNR) for both types of grids exhibited little dependence on kVp or grid ratio. In the mediastinum, k(CNR) decreased 4%-10% with increasing kVp, and varied up to 5.3% with grid ratio. CONCLUSIONS: When the focal spot is accurately aligned with the grid, the use of a high-ratio grid in mobile chest radiography improves image quality with no increase in dose to the phantom. For the grids studied, the performance of the fiber interspace grids was superior to the performance of the aluminum interspace grids, with the fiber interspace 13:1 grid producing the best overall results for the medium chest phantom and the fiber interspace 15:1 producing the best overall results for the large chest phantom.","corpus_id":19777062,"score":1},{"doc_id":"22975242","title":"An exact analytical solution for the evolution of a dipole-dipole interacting system under spherical diffusion in magnetic resonance experiments.","abstract":"A model system consisting of an isotropic ensemble of spin pairs, where dipole-dipole interaction is assumed to be effective only within each pair, is considered. The ideal segment connecting the spins in a couple has a fixed length but is free to rotate following a diffusion dynamics. This allows the free induction decay (FID) to be derived non-perturbatively by solving the appropriate Dyson equation associated to the problem. Motional narrowing can be described analytically in terms of only two parameters, i.e. the coupling constant of the interaction hamiltonian, b, and the orientational diffusion coefficient D. Salient features of the transverse correlation function thus obtained are discussed, and a comparison with numerical simulations performed with the software SPINEVOLUTION is presented. Interpreting b and D as effective parameters describing multiple interactions of a single spin with its neighbors in a real system, the analysis of published experimental data on poly(ethyl acrylate) has been carried out. It is found that for temperatures higher than and not too close to the glass transition, the results are the same as those found within the Anderson-Weiss approach by assuming a single time exponential decay of the average dipole-dipole interaction. On the other hand, as D tends to zero, FID oscillations characteristic of a rigid lattice show up.","corpus_id":41915762,"score":1},{"doc_id":"23004950","title":"Nonequilibrium Kondo model: crossover from weak to strong coupling.","abstract":"We analyze the nonequilibrium Kondo model at finite voltage and temperature by using a new formulation of the real-time renormalization group method with the Laplace variable as the flow parameter. We evaluate the energy-dependent spin relaxation rate and nonlinear conductance, and derive an approximate form for the universal line shape for the latter in the whole crossover regime from weak to strong coupling. The results are shown to agree well with exact methods in equilibrium, Fermi-liquid theory, weak-coupling expansions, and recent experiments. For the transient spin dynamics we find a universal exponential decay in the long-time limit along with a truncation-dependent pre-exponential power law. For multichannel models a pure power-law decay typical for non-Fermi-liquid behavior is predicted.","corpus_id":24820432,"score":1},{"doc_id":"23421210","title":"Intercellular synchronization of coupled smooth muscle cells via Ca2+ propagation.","abstract":"The propagation of Ca2+ wave through gap junction in smooth muscle cell is studied as a function of electrical coupling parameter (g) modulated by Ca2+ level in the cell. The range of activation time of Ca2+ propagation with amplitude is found to increase as increase in electrical coupling parameter g, which is identified by increase in critical time of activation, T(F) as a function of g. Then identical Ca2+ oscillators are allowed to interact via electrical and diffusive coupling of Ca2+ ions diffused through gap junctions, and rate of intercellular synchronization among them is studied. The phase diagrams in (T(F) - g) and (T(F) - epsilon) parameter spaces separate oscillation death and damped oscillations regimes which correspond to deactivated and activated regimes of Ca2+ level. The effect of on T(F) is significantly very slow, however it enhances the rate of synchronization among the coupled oscillators. The increase in g comparatively slows down the rate of synchronization of the coupled oscillators as shown in the phase diagram in (epsilon - g) parameter space which separates desynchronized and synchronized regimes.","corpus_id":7156273,"score":1},{"doc_id":"24229173","title":"Manifestation of random first-order transition theory in Wigner glasses.","abstract":"We use Brownian dynamics simulations of a binary mixture of highly charged spherical colloidal particles to test some of the predictions of the random first-order transition (RFOT) theory [Phys. Rev. Lett. 58, 2091 (1987); Phys. Rev. A 40, 1045 (1989)]. In accord with mode-coupling theory and RFOT, we find that as the volume fraction of the colloidal particles ϕ approaches the dynamical transition value ϕ(A), three measures of dynamics show an effective ergodic to nonergodic transition. First, there is a dramatic slowing down of diffusion, with the translational diffusion constant decaying as a power law as ϕ→ϕ(A)(-). Second, the energy metric, a measure of ergodicity breaking in classical many-body systems, shows that the system becomes effectively nonergodic as ϕ(A) is approached. Finally, the time t(*), at which the four-point dynamical susceptibility achieves a maximum, also increases as a power law near ϕ(A). Remarkably, the translational diffusion coefficients, ergodic diffusion coefficient, and (t(*))(-) all vanish as (ϕ(-1)-ϕ(A)(-1))(γ) with both ϕ(A)(≈0.1) and γ being the roughly the same for all three quantities. Above ϕ(A), transport involves crossing free energy barriers. In this regime, the density-density correlation function decays as a stretched exponential [exp-(t/τ(α))(β)] with β≈0.45. The ϕ dependence of the relaxation time τ(α) could be fit using the Vogel-Tamman-Fulcher law with the ideal glass transition at ϕ(K)≈0.47. By using a local entropy measure, we show that the law of large numbers is not obeyed above ϕ(A), and gives rise to subsample to subsample fluctuations in all physical observables. We propose that dynamical heterogeneity is a consequence of violation of law of large numbers.","corpus_id":50610,"score":1},{"doc_id":"24521155","title":"Length scales and structural dynamics in nematogen pseudonematic domains measured with 2D IR vibrational echoes and optical Kerr effect experiments.","abstract":"Nematogen liquids in the isotropic phase are macroscopically homogeneous but on multinanometer length scales have pseudonematic domains with correlation lengths that grow as the isotropic to nematic phase transition temperature (TNI) is approached from above. Orientational relaxation of nematogens in the isotropic phase manifests as two fast power laws and a slow exponential decay when measured by optical heterodyne detected optical Kerr effect (OHD-OKE) experiments. The long time exponential relaxation is associated with complete randomization of pseudonematic domains. We examine the effect of local orientational correlation on spectral diffusion (structural evolution) experienced by a vibrational probe molecule within the pseudonematic domains of 4-cyano-4'-pentylbiphenyl (5CB) using two-dimensional infrared (2D IR) vibrational echo spectroscopy. The addition of low concentration 4-pentyl-4'-thiocyanobiphenyl (5SCB) as a long-lived vibrational probe to 5CB is shown to lower TNI of the sample slightly, but the fast power law dynamics and exponential decays observed by OHD-OKE spectroscopy are unchanged. We compare the complete orientational relaxation and spectral diffusion for samples of 5SCB in 5CB to 5SCB in 4-pentylbiphenyl (5B) at four temperatures above TNI. 5B has a molecular structure similar to 5CB but is not a nematogen. At all but the lowest temperature, the spectral diffusion in 5CB and 5B is described well as a triexponential decay with very similar time constants. The results demonstrate that the presence of local orientational order at temperatures well above TNI does not affect the spectral diffusion (structural evolution) within pseudonematic domains when the correlation lengths are short. However, when the temperature of the sample is held very close to TNI, the spectral diffusion in 5CB slows dramatically while that in 5B does not. It is only as the correlation length becomes very long that its presence impacts the spectral diffusion (structural fluctuations) sensed by the vibrational probes located in pseudonematic domains. The orientational relaxation is modeled with schematic mode coupling theory (MCT). Fitting with MCT provides density and orientational correlation functions. The density correlation decays are similar for 5B and 5CB, but the orientational correlation decays are much slower for 5CB. Additionally, the time dependence of the spectral diffusion in 5CB is strikingly similar to that of the density correlation function decay, while the orientational correlation function decay is far too slow to contribute to the spectral diffusion. Therefore, density fluctuations are likely the source of spectral diffusion at temperatures at least 5 K above TNI.","corpus_id":207613368,"score":1},{"doc_id":"25243214","title":"Smart grid as a service: a discussion on design issues.","abstract":"Smart grid allows the integration of distributed renewable energy resources into the conventional electricity distribution power grid such that the goals of reduction in power cost and in environment pollution can be met through an intelligent and efficient matching between power generators and power loads. Currently, this rapidly developing infrastructure is not as \"smart\" as it should be because of the lack of a flexible, scalable, and adaptive structure. As a solution, this work proposes smart grid as a service (SGaaS), which not only allows a smart grid to be composed out of basic services, but also allows power users to choose between different services based on their own requirements. The two important issues of service-level agreements and composition of services are also addressed in this work. Finally, we give the details of how SGaaS can be implemented using a FIPA-compliant JADE multiagent system.","corpus_id":5110603,"score":1},{"doc_id":"25353889","title":"Oscillating-grid experiments in water and superfluid helium.","abstract":"Passing a fluid through a grid is a well-known mechanism used to study the properties of turbulence. Oscillating a horizontal grid vertically in a tank has also been used extensively and is considered to be a source of almost homogenous isotropic turbulence. When the oscillating grid is turned on a turbulent flow is induced. A front translates into the experimental tank, behind which the flow is highly turbulent. Long predicted that the growth of such a front would grow diffusively as the square root of time (i.e., d ∼ sqrt[t]) and Dickinson and Long presented experimental evidence for the diffusive result at a low mesh Reynolds number of 555. This paper revisits these experiments and attempts a set of two models for the advancing front in both square and round tanks. We do not observe significant differences between runs in square and round tanks. The experiments in water reach mesh Reynolds numbers of order 30000. Using some data from superfluid helium experiments we are able to explore mesh Reynolds numbers to about 43000. We find the power law for the advancing front decreases weakly with the mesh Reynolds number. Using a very long tank we find that the turbulent front stops completely at a certain depth and attempt a simple explanation for that behavior. We study the propagation of the turbulent front into tubes of different diameters inserted into the main tank. We show that these tubes exclude wavelengths much larger than the tube diameter. We explore the variation of the position of the steady-state boundary H on tube diameter D and find that H = cD with c ∼ 2. We suggest this may be explained by saturation of the energy-containing length scale ℓ(e). We also report on the effect of plugging up just one hole of the grid. Finally, we recall some earlier oscillating grid experiments in superfluid (4)He in the light of the present results.","corpus_id":21914497,"score":1},{"doc_id":"25481151","title":"Interface initiation and propagation in liquid demixing with electric fields.","abstract":"We investigate the dynamics of liquid-liquid phase separation confined in a charged concentric cylindrical geometry. Two main time scales characterize the non-equilibrium interface behavior: (1) the lag time t(L) for forming an interface, and (2) the relaxation time to equilibrium. We find that t(L) increases as parameters (temperature, bulk composition, and surface charge) approach the electrostatic spinodal line in the phase diagram. Close to this line, t(L) is proportional to a renormalized bulk concentration with an exponent of -1.16 ± 0.03. The relaxation of the interface to equilibrium can be divided into three phases: early, intermediate (power-law), and late (exponential). During power-law relaxation, the location of the rescaled interface is proportional to time with an exponent of -0.94 ± 0.04. Exponential relaxation occurs as a consequence of finite-size effects, and the associated time constant decreases with decreasing system size (with a power-law scaling), decreasing concentration, and increasing surface charge. The time constant also decreases with increasing (decreasing) temperature when the concentration is below (above) the critical concentration.","corpus_id":28175571,"score":1},{"doc_id":"25737231","title":"Biological electric fields and rate equations for biophotons.","abstract":"Biophoton intensities depend upon the squared modulus of the electric field. Hence, we first make some general estimates about the inherent electric fields within various biosystems. Generally, these intensities do not follow a simple exponential decay law. After a brief discussion on the inapplicability of a linear rate equation that leads to strict exponential decay, we study other, nonlinear rate equations that have been successfully used for biosystems along with their physical origins when available.","corpus_id":8818415,"score":1},{"doc_id":"26277149","title":"An itinerant oscillator model with cage inertia for mesorheological granular experiments.","abstract":"Recent experiments with a rotating probe immersed in weakly fluidized granular materials show a complex behavior on a wide range of time scales. Viscous-like relaxation at high frequency is accompanied by an almost harmonic dynamical trapping at intermediate times, with possibly anomalous long time behavior in the form of super-diffusion. Inspired by the itinerant oscillator model for diffusion in molecular liquids, and other models with coupled thermostats acting at different time scales, here we discuss a new model able to account for fast viscous relaxation, dynamical trapping, and super-diffusion at long times. The main difference with respect to liquids is a non-negligible cage inertia for the surrounding (granular) fluid, which allows it to sustain a slow but persistent motion for long times. The computed velocity power density spectra and mean-squared displacement qualitatively reproduce the experimental findings. We also discuss the linear response to external perturbations and the tail of the distribution of persistency time, which is associated with superdiffusion, and whose cut-off time is determined by cage inertia.","corpus_id":11640888,"score":1},{"doc_id":"26631463","title":"Can Neural Activity Propagate by Endogenous Electrical Field?","abstract":"UNLABELLED: It is widely accepted that synaptic transmissions and gap junctions are the major governing mechanisms for signal traveling in the neural system. Yet, a group of neural waves, either physiological or pathological, share the same speed of ∼0.1 m/s without synaptic transmission or gap junctions, and this speed is not consistent with axonal conduction or ionic diffusion. The only explanation left is an electrical field effect. We tested the hypothesis that endogenous electric fields are sufficient to explain the propagation with in silico and in vitro experiments. Simulation results show that field effects alone can indeed mediate propagation across layers of neurons with speeds of 0.12 ± 0.09 m/s with pathological kinetics, and 0.11 ± 0.03 m/s with physiologic kinetics, both generating weak field amplitudes of ∼2-6 mV/mm. Further, the model predicted that propagation speed values are inversely proportional to the cell-to-cell distances, but do not significantly change with extracellular resistivity, membrane capacitance, or membrane resistance. In vitro recordings in mice hippocampi produced similar speeds (0.10 ± 0.03 m/s) and field amplitudes (2.5-5 mV/mm), and by applying a blocking field, the propagation speed was greatly reduced. Finally, osmolarity experiments confirmed the model's prediction that cell-to-cell distance inversely affects propagation speed. Together, these results show that despite their weak amplitude, electric fields can be solely responsible for spike propagation at ∼0.1 m/s. This phenomenon could be important to explain the slow propagation of epileptic activity and other normal propagations at similar speeds. SIGNIFICANCE STATEMENT: Neural activity (waves or spikes) can propagate using well documented mechanisms such as synaptic transmission, gap junctions, or diffusion. However, the purpose of this paper is to provide an explanation for experimental data showing that neural signals can propagate by means other than synaptic transmission, gap junction, or diffusion. The results indicate that electric fields (ephaptic effects) are capable of mediating propagation of self-regenerating neural waves. This novel mechanism coupling cell-by-volume conduction could be involved in other types of propagating neural signals, such as slow-wave sleep, sharp hippocampal waves, theta waves, or seizures.","corpus_id":14502452,"score":1},{"doc_id":"27517161","title":"Nonlinear physics of electrical wave propagation in the heart: a review.","abstract":"The beating of the heart is a synchronized contraction of muscle cells (myocytes) that is triggered by a periodic sequence of electrical waves (action potentials) originating in the sino-atrial node and propagating over the atria and the ventricles. Cardiac arrhythmias like atrial and ventricular fibrillation (AF,VF) or ventricular tachycardia (VT) are caused by disruptions and instabilities of these electrical excitations, that lead to the emergence of rotating waves (VT) and turbulent wave patterns (AF,VF). Numerous simulation and experimental studies during the last 20 years have addressed these topics. In this review we focus on the nonlinear dynamics of wave propagation in the heart with an emphasis on the theory of pulses, spirals and scroll waves and their instabilities in excitable media with applications to cardiac modeling. After an introduction into electrophysiological models for action potential propagation, the modeling and analysis of spatiotemporal alternans, spiral and scroll meandering, spiral breakup and scroll wave instabilities like negative line tension and sproing are reviewed in depth and discussed with emphasis on their impact for cardiac arrhythmias.","corpus_id":4432898,"score":1},{"doc_id":"28297930","title":"Analysis of spontaneous oscillations for a three-state power-stroke model.","abstract":"Our study considers the mechanism of the spontaneous oscillations of molecular motors that are driven by the power stroke principle by applying linear stability analysis around the stationary solution. By representing the coupling equation of microscopic molecular motor dynamics and mesoscopic sarcomeric dynamics by a rank-1 updated matrix system, we derived the analytical representations of the eigenmodes of the Jacobian matrix that cause the oscillation. Based on these analytical representations, we successfully derived the essential conditions for the oscillation in terms of the rate constants of the power stroke and the reversal stroke transitions of the molecular motor. Unlike the two-state model, in which the dependence of the detachment rates on the motor coordinates or the applied forces on the motors plays a key role for the oscillation, our three-state power stroke model demonstrates that the dependence of the rate constants of the power and reversal strokes on the strains in the elastic elements in the motor molecules plays a key role, where these rate constants are rationally determined from the free energy available for the power stroke, the stiffness of the elastic element in the molecular motor, and the working stroke size. By applying the experimentally confirmed values to the free energy, the stiffness, and the working stroke size, our numerical model reproduces well the experimentally observed oscillatory behavior. Furthermore, our analysis shows that two eigenmodes with real positive eigenvalues characterize the oscillatory behavior, where the eigenmode with the larger eigenvalue indicates the transient of the system of the quick sarcomeric lengthening induced by the collective reversal strokes, and the smaller eigenvalue correlates with the speed of sarcomeric shortening, which is much slower than lengthening. Applying the perturbation analyses with primal physical parameters, we find that these two real eigenvalues occur on two branches derived from a merge point of a pair of complex-conjugate eigenvalues generated by Hopf bifurcation.","corpus_id":43545932,"score":1},{"doc_id":"28863584","title":"Nonlinear wave propagation in porous materials based on the Biot theory.","abstract":"Nonlinearity must be considered with some porous granular media because of the large deformation under seismic waves. In this study, the propagation of nonlinear waves in porous media is studied based on the Biot theory and the governing equations are obtained by the Lagrangian formulation. Three new nonlinear parameters are introduced to consider the coupled nonlinearity between the solid and fluid components in porous media. It is shown that an additional nonlinear wave with a double frequency is generated by the coupling effect of linear fast and slow waves. When only a shear wave is applied at the source, no double-frequency nonlinear wave is predicted and three nonlinear longitudinal waves are generated. On the basis of the practical case studies, the effect of strong nonlinearity is computed under the influence of a one-dimensional single longitudinal wave source and a single shear wave source.","corpus_id":321641,"score":1},{"doc_id":"29319842","title":"Quantitative evaluation of potential irradiation geometries for carbon-ion beam grid therapy.","abstract":"PURPOSE: Radiotherapy using grids containing cm-wide beam elements has been carried out sporadically for more than a century. During the past two decades, preclinical research on radiotherapy with grids containing small beam elements, 25 μm-0.7 mm wide, has been performed. Grid therapy with larger beam elements is technically easier to implement, but the normal tissue tolerance to the treatment is decreasing. In this work, a new approach in grid therapy, based on irradiations with grids containing narrow carbon-ion beam elements was evaluated dosimetrically. The aim formulated for the suggested treatment was to obtain a uniform target dose combined with well-defined grids in the irradiated normal tissue. The gain, obtained by crossfiring the carbon-ion beam grids over a simulated target volume, was quantitatively evaluated. METHODS: The dose distributions produced by narrow rectangular carbon-ion beams in a water phantom were simulated with the PHITS Monte Carlo code. The beam-element height was set to 2.0 cm in the simulations, while the widths varied from 0.5 to 10.0 mm. A spread-out Bragg peak (SOBP) was then created for each beam element in the grid, to cover the target volume with dose in the depth direction. The dose distributions produced by the beam-grid irradiations were thereafter constructed by adding the dose profiles simulated for single beam elements. The variation of the valley-to-peak dose ratio (VPDR) with depth in water was thereafter evaluated. The separation of the beam elements inside the grids were determined for different irradiation geometries with a selection criterion. RESULTS: The simulated carbon-ion beams remained narrow down to the depths of the Bragg peaks. With the formulated selection criterion, a beam-element separation which was close to the beam-element width was found optimal for grids containing 3.0-mm-wide beam elements, while a separation which was considerably larger than the beam-element width was found advantageous for grids containing 0.5-mm-wide beam elements. With the single-grid irradiation setup, the VPDRs were close to 1.0 already at a distance of several cm from the target. The valley doses given to the normal tissue at 0.5 cm distance from the target volume could be limited to less than 10% of the mean target dose if a crossfiring setup with four interlaced grids was used. CONCLUSIONS: The dose distributions produced by grids containing 0.5- and 3.0-mm wide beam elements had characteristics which could be useful for grid therapy. Grids containing mm-wide carbon-ion beam elements could be advantageous due to the technical ease with which these beams can be produced and delivered, despite the reduced threshold doses observed for early and late responding normal tissue for beams of millimeter width, compared to submillimetric beams. The treatment simulations showed that nearly homogeneous dose distributions could be created inside the target volumes, combined with low valley doses in the normal tissue located close to the target volume, if the carbon-ion beam grids were crossfired in an interlaced manner with optimally selected beam-element separations. The formulated selection criterion was found useful for the quantitative evaluation of the dose distributions produced by the different irradiation setups.","corpus_id":3880187,"score":0}],"string":"[\n {\n \"doc_id\": \"19282548\",\n \"title\": \"A novel visualization technique for electric power grid analytics.\",\n \"abstract\": \"The application of information visualization holds tremendous promise for the electric power industry, but its potential has so far not been sufficiently exploited by the visualization community. Prior work on visualizing electric power systems has been limited to depicting raw or processed information on top of a geographic layout. Little effort has been devoted to visualizing the physics of the power grids, which ultimately determines the condition and stability of the electricity infrastructure. Based on this assessment, we developed a novel visualization system prototype, GreenGrid, to explore the planning and monitoring of the North American Electricity Infrastructure. The paper discusses the rationale underlying the GreenGrid design, describes its implementation and performance details, and assesses its strengths and weaknesses against the current geographic-based power grid visualization. We also present a case study using GreenGrid to analyze the information collected moments before the last major electric blackout in the Western United States and Canada, and a usability study to evaluate the practical significance of our design in simulated real-life situations. Our result indicates that many of the disturbance characteristics can be readily identified with the proper form of visualization.\",\n \"corpus_id\": 445873,\n \"score\": 2\n },\n {\n \"doc_id\": \"19905395\",\n \"title\": \"Message passing for optimization and control of a power grid: model of a distribution system with redundancy.\",\n \"abstract\": \"We use a power grid model with M generators and N consumption units to optimize the grid and its control. Each consumer demand is drawn from a predefined finite-size-support distribution, thus simulating the instantaneous load fluctuations. Each generator has a maximum power capability. A generator is not overloaded if the sum of the loads of consumers connected to a generator does not exceed its maximum production. In the standard grid each consumer is connected only to its designated generator, while we consider a more general organization of the grid allowing each consumer to select one generator depending on the load from a predefined consumer dependent and sufficiently small set of generators which can all serve the load. The model grid is interconnected in a graph with loops, drawn from an ensemble of random bipartite graphs, while each allowed configuration of loaded links represent a set of graph covering trees. Losses, the reactive character of the grid and the transmission-level connections between generators (and many other details relevant to realistic power grid) are ignored in this proof-of-principles study. We focus on the asymptotic limit, N-->infinity and N/M-->D=O(1)>1 , and we show that the interconnects allow significant expansion of the parameter domains for which the probability of a generator overload is asymptotically zero. Our construction explores the formal relation between the problem of grid optimization and the modern theory of sparse graphical models. We also design heuristic algorithms that achieve the asymptotically optimal selection of loaded links. We conclude discussing the ability of this approach to include other effects such as a more realistic modeling of the power grid and related optimization and control algorithms.\",\n \"corpus_id\": 12662045,\n \"score\": 2\n },\n {\n \"doc_id\": \"20409486\",\n \"title\": \"Protein collective motions coupled to ligand migration in myoglobin.\",\n \"abstract\": \"Ligand migration processes inside myoglobin and protein dynamics coupled to the migration were theoretically investigated with molecular dynamics simulations. Based on a linear response theory, we identified protein motions coupled to the transient migration of ligand, carbon monoxide (CO), through channels. The result indicates that the coupled protein motions involve collective motions extended over the entire protein correlated with local gating motions at the channels. Protein motions, coupled to opening of a channel from the distal pocket to a neighboring xenon site, were found to share the collective motion with experimentally observed protein motions coupled to a doming motion of the heme Fe atom upon photodissociation of the ligand. Analysis based on generalized Langevin dynamics elucidated slow and diffusive features of the protein response motions. Remarkably small transmission coefficients for rates of the CO migrations through myoglobin were found, suggesting that the CO migration dynamics are characterized as motions governed by the protein dynamics involving the collective motions, rather than as thermally activated transitions across energy barriers of well-structured channels.\",\n \"corpus_id\": 21036471,\n \"score\": 2\n },\n {\n \"doc_id\": \"21893072\",\n \"title\": \"Exponential transient propagating oscillations in a ring of spiking neurons with unidirectional slow inhibitory synaptic coupling.\",\n \"abstract\": \"Transient oscillations in a ring of spiking neuron models unidirectionally coupled with slow inhibitory synapses are studied. There are stable spatially fixed steady firing-resting states and unstable symmetric propagating firing-resting states. In transients, firing-resting patterns rotate in the direction of coupling (propagating oscillations), the duration of which increases exponentially with the number of neurons (exponential transients). Further, the duration of randomly generated transient propagating oscillations is distributed in a power law form and spatiotemporal noise of intermediate strength sustains propagating oscillations. These properties agree with those of transient propagating waves in a ring of sigmoidal neuron models.\",\n \"corpus_id\": 26944422,\n \"score\": 2\n },\n {\n \"doc_id\": \"22096188\",\n \"title\": \"Electrical energy storage for the grid: a battery of choices.\",\n \"abstract\": \"The increasing interest in energy storage for the grid can be attributed to multiple factors, including the capital costs of managing peak demands, the investments needed for grid reliability, and the integration of renewable energy sources. Although existing energy storage is dominated by pumped hydroelectric, there is the recognition that battery systems can offer a number of high-value opportunities, provided that lower costs can be obtained. The battery systems reviewed here include sodium-sulfur batteries that are commercially available for grid applications, redox-flow batteries that offer low cost, and lithium-ion batteries whose development for commercial electronics and electric vehicles is being applied to grid storage.\",\n \"corpus_id\": 206536979,\n \"score\": 2\n },\n {\n \"doc_id\": \"22346628\",\n \"title\": \"A grid-based distributed event detection scheme for wireless sensor networks.\",\n \"abstract\": \"This paper presents a grid-based distributed event detection scheme for wireless sensor networks. The network is divided into square-shaped grids of predefined grid size, where sensor nodes in each grid form a cluster with a cluster head. Event detection at each grid alone based on the readings of its member nodes is limited in event detection performance, especially for a small event region compared to the grid size. To improve the performance, each grid is further divided into 2 × 2 sub-grids of equal size. The decision on an event is made by finding a square region of 2 × 2 sub-grids, not necessarily in the same grid, that passed a predefined threshold. This process is conducted at each cluster head in a distributed manner by inter-cluster communications. Event detection is initiated when a cluster head receives an alarm from its member nodes. The cluster-head communicates with its neighboring cluster heads to exchange the number of nodes reporting an alarm. The threshold for event detection can be dynamically adjusted to reflect the number of sensor nodes in a grid and event size, if known. High event detection accuracy is achieved with a relatively low threshold without sacrificing false alarm rate by filtering most errors due to transient faults and isolating nodes with permanent faults. Experimental results show that the proposed scheme can achieve high detection accuracy, while maintaining low false alarm rate.\",\n \"corpus_id\": 1652331,\n \"score\": 2\n },\n {\n \"doc_id\": \"22587093\",\n \"title\": \"Wave propagation in random granular chains.\",\n \"abstract\": \"The influence of randomness on wave propagation in one-dimensional chains of spherical granular media is investigated. The interaction between the elastic spheres is modeled using the classical Hertzian contact law. Randomness is introduced in the discrete model using random distributions of particle mass, Young's modulus, or radius. Of particular interest in this study is the quantification of the attenuation in the amplitude of the impulse associated with various levels of randomness: two distinct regimes of decay are observed, characterized by an exponential or a power law, respectively. The responses are normalized to represent a vast array of material parameters and impact conditions. The virial theorem is applied to investigate the transfer from potential to kinetic energy components in the system for different levels of randomness. The level of attenuation in the two decay regimes is compared for the three different sources of randomness and it is found that randomness in radius leads to the maximum rate of decay in the exponential regime of wave propagation.\",\n \"corpus_id\": 11500332,\n \"score\": 2\n },\n {\n \"doc_id\": \"22712907\",\n \"title\": \"Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method.\",\n \"abstract\": \"The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required per wavelength for accurate simulations. The model is based on coupled first-order acoustic equations valid for nonlinear wave propagation in heterogeneous media with power law absorption. These are derived from the equations of fluid mechanics and include a pressure-density relation that incorporates the effects of nonlinearity, power law absorption, and medium heterogeneities. The additional terms accounting for convective nonlinearity and power law absorption are expressed as spatial gradients making them efficient to numerically encode. The governing equations are then discretized using a k-space pseudospectral technique in which the spatial gradients are computed using the Fourier-collocation method. This increases the accuracy of the gradient calculation and thus relaxes the requirement for dense computational grids compared to conventional finite difference methods. The accuracy and utility of the developed model is demonstrated via several numerical experiments, including the 3D simulation of the beam pattern from a clinical ultrasound probe.\",\n \"corpus_id\": 23453034,\n \"score\": 2\n },\n {\n \"doc_id\": \"23006269\",\n \"title\": \"Self-organized synchronization in decentralized power grids.\",\n \"abstract\": \"Robust synchronization (phase locking) of power plants and consumers centrally underlies the stable operation of electric power grids. Despite current attempts to control large-scale networks, even their uncontrolled collective dynamics is not fully understood. Here we analyze conditions enabling self-organized synchronization in oscillator networks that serve as coarse-scale models for power grids, focusing on decentralizing power sources. Intriguingly, we find that whereas more decentralized grids become more sensitive to dynamical perturbations, they simultaneously become more robust to topological failures. Decentralizing power sources may thus facilitate the onset of synchronization in modern power grids.\",\n \"corpus_id\": 11209846,\n \"score\": 2\n },\n {\n \"doc_id\": \"23319658\",\n \"title\": \"Synchronization in complex oscillator networks and smart grids.\",\n \"abstract\": \"The emergence of synchronization in a network of coupled oscillators is a fascinating topic in various scientific disciplines. A widely adopted model of a coupled oscillator network is characterized by a population of heterogeneous phase oscillators, a graph describing the interaction among them, and diffusive and sinusoidal coupling. It is known that a strongly coupled and sufficiently homogeneous network synchronizes, but the exact threshold from incoherence to synchrony is unknown. Here, we present a unique, concise, and closed-form condition for synchronization of the fully nonlinear, nonequilibrium, and dynamic network. Our synchronization condition can be stated elegantly in terms of the network topology and parameters or equivalently in terms of an intuitive, linear, and static auxiliary system. Our results significantly improve upon the existing conditions advocated thus far, they are provably exact for various interesting network topologies and parameters; they are statistically correct for almost all networks; and they can be applied equally to synchronization phenomena arising in physics and biology as well as in engineered oscillator networks, such as electrical power networks. We illustrate the validity, the accuracy, and the practical applicability of our results in complex network scenarios and in smart grid applications.\",\n \"corpus_id\": 4849531,\n \"score\": 2\n },\n {\n \"doc_id\": \"23848724\",\n \"title\": \"Hysteresis, phase transitions, and dangerous transients in electrical power distribution systems.\",\n \"abstract\": \"The majority of dynamical studies in power systems focus on the high-voltage transmission grids where models consider large generators interacting with crude aggregations of individual small loads. However, new phenomena have been observed indicating that the spatial distribution of collective, nonlinear contribution of these small loads in the low-voltage distribution grid is crucial to the outcome of these dynamical transients. To elucidate the phenomenon, we study the dynamics of voltage and power flows in a spatially extended distribution feeder (circuit) connecting many asynchronous induction motors and discover that this relatively simple 1+1 (space+time) dimensional system exhibits a plethora of nontrivial spatiotemporal effects, some of which may be dangerous for power system stability. Long-range motor-motor interactions mediated by circuit voltage and electrical power flows result in coexistence and segregation of spatially extended phases defined by individual motor states, a \\\"normal\\\" state where the motors' mechanical (rotation) frequency is slightly smaller than the nominal frequency of the basic ac flows and a \\\"stalled\\\" state where the mechanical frequency is small. Transitions between the two states can be initiated by a perturbation of the voltage or base frequency at the head of the distribution feeder. Such behavior is typical of first-order phase transitions in physics, and this 1+1 dimensional model shows many other properties of a first-order phase transition with the spatial distribution of the motors' mechanical frequency playing the role of the order parameter. In particular, we observe (a) propagation of the phase-transition front with the constant speed (in very long feeders) and (b) hysteresis in transitions between the normal and stalled (or partially stalled) phases.\",\n \"corpus_id\": 20671263,\n \"score\": 2\n },\n {\n \"doc_id\": \"24081270\",\n \"title\": \"Modeling nonlinear wave propagation on nonuniform grids using a mapped k-space pseudospectral method.\",\n \"abstract\": \"Simulating the propagation of nonlinear ultrasound waves is computationally difficult because of the dense grids needed to capture high-frequency harmonics. Here, a mapped k-space pseudospectral method is presented which allows the use of nonuniform grid spacings. This enables grid points to be clustered around steep regions of the wave field. Compared with using a uniform grid, this significantly reduces the total number of grid points needed for accurate simulations. Two methods for selecting a suitable nonuniform grid mapping are discussed.\",\n \"corpus_id\": 26812474,\n \"score\": 2\n },\n {\n \"doc_id\": \"24200162\",\n \"title\": \"Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.\",\n \"abstract\": \"In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes.\",\n \"corpus_id\": 12263838,\n \"score\": 2\n },\n {\n \"doc_id\": \"24424239\",\n \"title\": \"Abruptness of cascade failures in power grids.\",\n \"abstract\": \"Electric power-systems are one of the most important critical infrastructures. In recent years, they have been exposed to extreme stress due to the increasing demand, the introduction of distributed renewable energy sources, and the development of extensive interconnections. We investigate the phenomenon of abrupt breakdown of an electric power-system under two scenarios: load growth (mimicking the ever-increasing customer demand) and power fluctuations (mimicking the effects of renewable sources). Our results on real, realistic and synthetic networks indicate that increasing the system size causes breakdowns to become more abrupt; in fact, mapping the system to a solvable statistical-physics model indicates the occurrence of a first order transition in the large size limit. Such an enhancement for the systemic risk failures (black-outs) with increasing network size is an effect that should be considered in the current projects aiming to integrate national power-grids into \\\"super-grids\\\".\",\n \"corpus_id\": 15643227,\n \"score\": 2\n },\n {\n \"doc_id\": \"24697385\",\n \"title\": \"Impact of network topology on synchrony of oscillatory power grids.\",\n \"abstract\": \"Replacing conventional power sources by renewable sources in current power grids drastically alters their structure and functionality. In particular, power generation in the resulting grid will be far more decentralized, with a distinctly different topology. Here, we analyze the impact of grid topologies on spontaneous synchronization, considering regular, random, and small-world topologies and focusing on the influence of decentralization. We model the consumers and sources of the power grid as second order oscillators. First, we analyze the global dynamics of the simplest non-trivial (two-node) network that exhibit a synchronous (normal operation) state, a limit cycle (power outage), and coexistence of both. Second, we estimate stability thresholds for the collective dynamics of small network motifs, in particular, star-like networks and regular grid motifs. For larger networks, we numerically investigate decentralization scenarios finding that decentralization itself may support power grids in exhibiting a stable state for lower transmission line capacities. Decentralization may thus be beneficial for power grids, regardless of the details of their resulting topology. Regular grids show a specific sharper transition not found for random or small-world grids.\",\n \"corpus_id\": 18677972,\n \"score\": 2\n },\n {\n \"doc_id\": \"24807951\",\n \"title\": \"Artificial neural networks for control of a grid-connected rectifier/inverter under disturbance, dynamic and power converter switching conditions.\",\n \"abstract\": \"Three-phase grid-connected converters are widely used in renewable and electric power system applications. Traditionally, grid-connected converters are controlled with standard decoupled d-q vector control mechanisms. However, recent studies indicate that such mechanisms show limitations in their applicability to dynamic systems. This paper investigates how to mitigate such restrictions using a neural network to control a grid-connected rectifier/inverter. The neural network implements a dynamic programming algorithm and is trained by using back-propagation through time. To enhance performance and stability under disturbance, additional strategies are adopted, including the use of integrals of error signals to the network inputs and the introduction of grid disturbance voltage to the outputs of a well-trained network. The performance of the neural-network controller is studied under typical vector control conditions and compared against conventional vector control methods, which demonstrates that the neural vector control strategy proposed in this paper is effective. Even in dynamic and power converter switching environments, the neural vector controller shows strong ability to trace rapidly changing reference commands, tolerate system disturbances, and satisfy control requirements for a faulted power system.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"24910217\",\n \"title\": \"How dead ends undermine power grid stability.\",\n \"abstract\": \"The cheapest and thus widespread way to add new generators to a high-voltage power grid is by a simple tree-like connection scheme. However, it is not entirely clear how such locally cost-minimizing connection schemes affect overall system performance, in particular the stability against blackouts. Here we investigate how local patterns in the network topology influence a power grid's ability to withstand blackout-prone large perturbations. Employing basin stability, a nonlinear concept, we find in numerical simulations of artificially generated power grids that tree-like connection schemes--so-called dead ends and dead trees--strongly diminish stability. A case study of the Northern European power system confirms this result and demonstrates that the inverse is also true: repairing dead ends by addition of a few transmission lines substantially enhances stability. This may indicate a topological design principle for future power grids: avoid dead ends.\",\n \"corpus_id\": 38044866,\n \"score\": 2\n },\n {\n \"doc_id\": \"25243201\",\n \"title\": \"Global renewable energy-based electricity generation and smart grid system for energy security.\",\n \"abstract\": \"Energy is an indispensable factor for the economic growth and development of a country. Energy consumption is rapidly increasing worldwide. To fulfill this energy demand, alternative energy sources and efficient utilization are being explored. Various sources of renewable energy and their efficient utilization are comprehensively reviewed and presented in this paper. Also the trend in research and development for the technological advancement of energy utilization and smart grid system for future energy security is presented. Results show that renewable energy resources are becoming more prevalent as more electricity generation becomes necessary and could provide half of the total energy demands by 2050. To satisfy the future energy demand, the smart grid system can be used as an efficient system for energy security. The smart grid also delivers significant environmental benefits by conservation and renewable generation integration.\",\n \"corpus_id\": 16901025,\n \"score\": 2\n },\n {\n \"doc_id\": \"25833596\",\n \"title\": \"Decoupling of relaxation and diffusion in random pinning glass-forming liquids.\",\n \"abstract\": \"We investigate numerically the relaxation and diffusion dynamics in three-dimensional Kob-Andersen glass-forming liquids in which part of the particles are randomly chosen and pinned permanently. We find that both the relaxation dynamics and diffusion dynamics slow down as increasing the pinning concentration (cpin) at fixed temperatures that we study. For higher temperature and lower cpin, the α relaxation time τ and the diffusion coefficient D have the scaling relationship D ∼ τ(-1). However, this coupling behavior breaks down if cpin is further increased, and the scaling relationship is replaced by D ∼ τ(-ν) with ν < 1. At temperatures around the onset temperature of the bulk system, a transition from ν ∼ 0.75 to ν ∼ 0.61 with increasing cpin is found. However, at lower temperatures, ν ∼ 0.67 holds in the whole studied cpin range. By fitting the relaxation time as a function of cpin with Vogel-Fulcher-Tamman equation, we find that the change of scaling exponent ν is accompanied with the change of fragility parameter K at higher temperatures. However, at lower temperatures, pinning particles have little effect on the system's qualitative properties. Moreover, we investigate three measures of heterogeneity of dynamics and find that the relaxation and the diffusion motion of particles show different responses to the pinned particles, which may lead to the slower relaxation than diffusion and the decoupling of relaxation and diffusion. The string-like motion is found to saturate at the mode-coupling theory (MCT) crossover point, which indicates that other relaxation modes may exist below the MCT transition point.\",\n \"corpus_id\": 20605582,\n \"score\": 2\n },\n {\n \"doc_id\": \"25897178\",\n \"title\": \"Semi-implicit Integration Factor Methods on Sparse Grids for High-Dimensional Systems.\",\n \"abstract\": \"Numerical methods for partial differential equations in high-dimensional spaces are often limited by the curse of dimensionality. Though the sparse grid technique, based on a one-dimensional hierarchical basis through tensor products, is popular for handling challenges such as those associated with spatial discretization, the stability conditions on time step size due to temporal discretization, such as those associated with high-order derivatives in space and stiff reactions, remain. Here, we incorporate the sparse grids with the implicit integration factor method (IIF) that is advantageous in terms of stability conditions for systems containing stiff reactions and diffusions. We combine IIF, in which the reaction is treated implicitly and the diffusion is treated explicitly and exactly, with various sparse grid techniques based on the finite element and finite difference methods and a multi-level combination approach. The overall method is found to be efficient in terms of both storage and computational time for solving a wide range of PDEs in high dimensions. In particular, the IIF with the sparse grid combination technique is flexible and effective in solving systems that may include cross-derivatives and non-constant diffusion coefficients. Extensive numerical simulations in both linear and nonlinear systems in high dimensions, along with applications of diffusive logistic equations and Fokker-Planck equations, demonstrate the accuracy, efficiency, and robustness of the new methods, indicating potential broad applications of the sparse grid-based integration factor method.\",\n \"corpus_id\": 23511617,\n \"score\": 2\n },\n {\n \"doc_id\": \"26610212\",\n \"title\": \"Computational Investigation of Wave Packet Scattering in the Complex Plane: Propagation on a Grid.\",\n \"abstract\": \"The time-dependent scattering of a wave packet from a Gaussian barrier is investigated computationally in the complex z-plane. The initial wave packet and the potential energy are obtained through analytic continuation from functions specified on the real-axis. The wave packet is then propagated on the two-dimensional grid. For a low initial wave packet energy, the time evolution is followed by plotting the following functions: |ψ(z,t)|, real(ψ(z,t)), and the quantum momentum function (QMF), p(z,t). In the reflected packet, an important role is played by ripples (quasi-nodes) forming above the real axis. As these quasi-nodes move down across the real axis, they are 'detected' as 'interference oscillations' in the density. In contrast, the component of the packet below the real axis makes a significant contribution to the transmitted packet. Vector maps of the QMF show hyperbolic flow around quasi-nodes and counterclockwise circular flow around transient stagnation points, where the QMF vanishes. However, when the Pólya vector field (defined by P(z,t) = p*(z,t)) is plotted, circular counterclockwise flow is obtained near the quasi-nodes. The real and imaginary parts of the quantum action function S(z,t) are plotted and the vorticity, defined by the curl of the Pólya field, is used to pinpoint regions of nonanalyticity in the QMF.\",\n \"corpus_id\": 317374,\n \"score\": 2\n },\n {\n \"doc_id\": \"26735210\",\n \"title\": \"Cultured Construction: Global Evidence of the Impact of National Values on Renewable Electricity Infrastructure Choice.\",\n \"abstract\": \"Renewable electricity is an important tool in the fight against climate change, but globally these technologies are still in the early stages of diffusion. To contribute to our understanding of the factors driving this diffusion, I study relationships between national values (measured by Hofstede's cultural dimensions) and renewable electricity adoption at the national level. Existing data for 66 nations (representing an equal number of developed and developing economies) are used to fuel the analysis. Somewhat dependent on limited available data on controls for grid reliability and the cost of electricity, I discover that three of Hofstede's dimensions (high uncertainty avoidance, low masculinity-femininity, and high individualism-collectivism) have significant exponential relationships with renewable electricity adoption. The dimension of uncertainty avoidance appears particularly appropriate for practical application. Projects or organizations implementing renewable electricity policy, designs, or construction should particularly attend to this cultural dimension. In particular, as the data imply that renewable technologies are being used to manage risk in electricity supply, geographies with unreliable grids are particularly likely to be open to renewable electricity technologies.\",\n \"corpus_id\": 29809187,\n \"score\": 2\n },\n {\n \"doc_id\": \"27078359\",\n \"title\": \"Linear stability and the Braess paradox in coupled-oscillator networks and electric power grids.\",\n \"abstract\": \"We investigate the influence that adding a new coupling has on the linear stability of the synchronous state in coupled-oscillator networks. Using a simple model, we show that, depending on its location, the new coupling can lead to enhanced or reduced stability. We extend these results to electric power grids where a new line can lead to four different scenarios corresponding to enhanced or reduced grid stability as well as increased or decreased power flows. Our analysis shows that the Braess paradox may occur in any complex coupled system, where the synchronous state may be weakened and sometimes even destroyed by additional couplings.\",\n \"corpus_id\": 28708004,\n \"score\": 2\n },\n {\n \"doc_id\": \"27176235\",\n \"title\": \"Superdiffusion, large-scale synchronization, and topological defects.\",\n \"abstract\": \"We study an ensemble of random walkers carrying internal noisy phase oscillators which are synchronized among the walkers by local interactions. Due to individual mobility, the interaction partners of every walker change randomly, hereby introducing an additional, independent source of fluctuations, thus constituting the intrinsic nonequilibrium nature of the temporal dynamics. We employ this paradigmatic model system to discuss how the emergence of order is affected by the motion of individual entities. In particular, we consider both normal diffusive motion and superdiffusion. A non-Hamiltonian field theory including multiplicative noise terms is derived which describes the nonequilibrium dynamics at the macroscale. This theory reveals a defect-mediated transition from incoherence to quasi-long-range order for normal diffusion of oscillators in two dimensions, implying a power-law dependence of all synchronization properties on system size. In contrast, superdiffusive transport suppresses the emergence of topological defects, thereby inducing a continuous synchronization transition to long-range order in two dimensions. These results are consistent with particle-based simulations.\",\n \"corpus_id\": 3822974,\n \"score\": 2\n },\n {\n \"doc_id\": \"27225708\",\n \"title\": \"Enhancing synchronization stability in a multi-area power grid.\",\n \"abstract\": \"Maintaining a synchronous state of generators is of central importance to the normal operation of power grids, in which many networks are generally interconnected. In order to understand the condition under which the stability can be optimized, it is important to relate network stability with feedback control strategies as well as network structure. Here, we present a stability analysis on a multi-area power grid by relating it with several control strategies and topological design of network structure. We clarify the minimal feedback gain in the self-feedback control, and build the optimal communication network for the local and global control strategies. Finally, we consider relationship between the interconnection pattern and the synchronization stability; by optimizing the network interlinks, the obtained network shows better synchronization stability than the original network does, in particular, at a high power demand. Our analysis shows that interlinks between spatially distant nodes will improve the synchronization stability. The results seem unfeasible to be implemented in real systems but provide a potential guide for the design of stable power systems.\",\n \"corpus_id\": 4337483,\n \"score\": 2\n },\n {\n \"doc_id\": \"27415291\",\n \"title\": \"Building blocks of the basin stability of power grids.\",\n \"abstract\": \"Given a power grid and a transmission (coupling) strength, basin stability is a measure of synchronization stability for individual nodes. Earlier studies have focused on the basin stability's dependence of the position of the nodes in the network for single values of transmission strength. Basin stability grows from zero to one as transmission strength increases, but often in a complex, nonmonotonous way. In this study, we investigate the entire functional form of the basin stability's dependence on transmission strength. To be able to perform a systematic analysis, we restrict ourselves to small networks. We scan all isomorphically distinct networks with an equal number of power producers and consumers of six nodes or less. We find that the shapes of the basin stability fall into a few, rather well-defined classes, that could be characterized by the number of edges and the betweenness of the nodes, whereas other network positional quantities matter less.\",\n \"corpus_id\": 10494188,\n \"score\": 2\n },\n {\n \"doc_id\": \"27575148\",\n \"title\": \"Long-range response in ac electricity grids.\",\n \"abstract\": \"Local changes in the topology of electricity grids can cause overloads far away from the disturbance [D. Witthaut and M. Timme, Eur. Phys. J. B 86, 377 (2013)EPJBFY1434-602810.1140/epjb/e2013-40469-4], making the prediction of the robustness against changes in the topology-for example, caused by power outages or grid extensions-a challenging task. The impact of single-line additions on the long-range response of dc electricity grids has recently been studied [D. Labavić, R. Suciu, H. Meyer-Ortmanns, and S. Kettemann, Eur. Phys. J.: Spec. Top. 223, 2517 (2014)1951-635510.1140/epjst/e2014-02273-0]. By solving the real part of the static ac load flow equations, we conduct a similar investigation for ac grids. In a regular two-dimensional grid graph with cyclic boundary conditions, we find a power law decay for the change of power flow as a function of distance to the disturbance over a wide range of distances. The power exponent increases and saturates for large system sizes. By applying the same analysis to the German transmission grid topology, we show that also in real-world topologies a long-ranged response can be found.\",\n \"corpus_id\": 15438738,\n \"score\": 2\n },\n {\n \"doc_id\": \"27713509\",\n \"title\": \"Islanding the power grid on the transmission level: less connections for more security.\",\n \"abstract\": \"Islanding is known as a management procedure of the power system that is implemented at the distribution level to preserve sensible loads from outages and to guarantee the continuity in electricity supply, when a high amount of distributed generation occurs. In this paper we study islanding on the level of the transmission grid and shall show that it is a suitable measure to enhance energy security and grid resilience. We consider the German and Italian transmission grids. We remove links either randomly to mimic random failure events, or according to a topological characteristic, their so-called betweenness centrality, to mimic an intentional attack and test whether the resulting fragments are self-sustainable. We test this option via the tool of optimized DC power flow equations. When transmission lines are removed according to their betweenness centrality, the resulting islands have a higher chance of being dynamically self-sustainable than for a random removal. Less connections may even increase the grid's stability. These facts should be taken into account in the design of future power grids.\",\n \"corpus_id\": 9936023,\n \"score\": 2\n },\n {\n \"doc_id\": \"27739704\",\n \"title\": \"Cascading failures in ac electricity grids.\",\n \"abstract\": \"Sudden failure of a single transmission element in a power grid can induce a domino effect of cascading failures, which can lead to the isolation of a large number of consumers or even to the failure of the entire grid. Here we present results of the simulation of cascading failures in power grids, using an alternating current (AC) model. We first apply this model to a regular square grid topology. For a random placement of consumers and generators on the grid, the probability to find more than a certain number of unsupplied consumers decays as a power law and obeys a scaling law with respect to system size. Varying the transmitted power threshold above which a transmission line fails does not seem to change the power-law exponent q≈1.6. Furthermore, we study the influence of the placement of generators and consumers on the number of affected consumers and demonstrate that large clusters of generators and consumers are especially vulnerable to cascading failures. As a real-world topology, we consider the German high-voltage transmission grid. Applying the dynamic AC model and considering a random placement of consumers, we find that the probability to disconnect more than a certain number of consumers depends strongly on the threshold. For large thresholds the decay is clearly exponential, while for small ones the decay is slow, indicating a power-law decay.\",\n \"corpus_id\": 5054954,\n \"score\": 2\n },\n {\n \"doc_id\": \"27781449\",\n \"title\": \"Control and prediction for blackouts caused by frequency collapse in smart grids.\",\n \"abstract\": \"The electric power system is one of the cornerstones of modern society. One of its most serious malfunctions is the blackout, a catastrophic event that may disrupt a substantial portion of the system, playing havoc to human life and causing great economic losses. Thus, understanding the mechanisms leading to blackouts and creating a reliable and resilient power grid has been a major issue, attracting the attention of scientists, engineers, and stakeholders. In this paper, we study the blackout problem in power grids by considering a practical phase-oscillator model. This model allows one to simultaneously consider different types of power sources (e.g., traditional AC power plants and renewable power sources connected by DC/AC inverters) and different types of loads (e.g., consumers connected to distribution networks and consumers directly connected to power plants). We propose two new control strategies based on our model, one for traditional power grids and another one for smart grids. The control strategies show the efficient function of the fast-response energy storage systems in preventing and predicting blackouts in smart grids. This work provides innovative ideas which help us to build up a robuster and more economic smart power system.\",\n \"corpus_id\": 26000359,\n \"score\": 2\n },\n {\n \"doc_id\": \"28085307\",\n \"title\": \"Delocalization of disturbances and the stability of ac electricity grids.\",\n \"abstract\": \"In order to study how local disturbances affect the ac grid stability, we start from nonlinear power balance equations and map them to complex linear wave equations. Having obtained stationary solutions with phases φ_{i} at generator and consumer nodes i, we next study the dynamics of deviations. Starting with an initially localized perturbation, it is found to spread in a periodic grid diffusively throughout the grid. We find the parametric dependence of diffusion constant D. We apply the same solution strategy to general grid topologies and analyze their stability against local perturbations. The perturbation remains either localized or becomes delocalized, depending on grid topology, power capacity, and distribution of consumers and generator power P_{i}. Delocalization is found to increase the lifetime of perturbations and thereby their influence on grid stability, whereas localization results in an exponentially fast decay of perturbations at all grid sites. These results may therefore lead to new strategies to control the stability of electricity grids.\",\n \"corpus_id\": 41090271,\n \"score\": 2\n },\n {\n \"doc_id\": \"28147501\",\n \"title\": \"Synchronization of cyclic power grids: Equilibria and stability of the synchronous state.\",\n \"abstract\": \"Synchronization is essential for the proper functioning of power grids; we investigate the synchronous states and their stability for cyclic power grids. We calculate the number of stable equilibria and investigate both the linear and nonlinear stabilities of the synchronous state. The linear stability analysis shows that the stability of the state, determined by the smallest nonzero eigenvalue, is inversely proportional to the size of the network. We use the energy barrier to measure the nonlinear stability and calculate it by comparing the potential energy of the type-1 saddles with that of the stable synchronous state. We find that the energy barrier depends on the network size (N) in a more complicated fashion compared to the linear stability. In particular, when the generators and consumers are evenly distributed in an alternating way, the energy barrier decreases to a constant when N approaches infinity. For a heterogeneous distribution of generators and consumers, the energy barrier decreases with N. The more heterogeneous the distribution is, the stronger the energy barrier depends on N. Finally, we find that by comparing situations with equal line loads in cyclic and tree networks, tree networks exhibit reduced stability. This difference disappears in the limit of N→∞. This finding corroborates previous results reported in the literature and suggests that cyclic (sub)networks may be applied to enhance power transfer while maintaining stable synchronous operation.\",\n \"corpus_id\": 12007948,\n \"score\": 2\n },\n {\n \"doc_id\": \"28364771\",\n \"title\": \"Smoothing effect for spatially distributed renewable resources and its impact on power grid robustness.\",\n \"abstract\": \"In this paper, we show that spatial correlation of renewable energy outputs greatly influences the robustness of the power grids against large fluctuations of the effective power. First, we evaluate the spatial correlation among renewable energy outputs. We find that the spatial correlation of renewable energy outputs depends on the locations, while the influence of the spatial correlation of renewable energy outputs on power grids is not well known. Thus, second, by employing the topology of the power grid in eastern Japan, we analyze the robustness of the power grid with spatial correlation of renewable energy outputs. The analysis is performed by using a realistic differential-algebraic equations model. The results show that the spatial correlation of the energy resources strongly degrades the robustness of the power grid. Our results suggest that we should consider the spatial correlation of the renewable energy outputs when estimating the stability of power grids.\",\n \"corpus_id\": 205218927,\n \"score\": 2\n },\n {\n \"doc_id\": \"28912454\",\n \"title\": \"Resilience of electricity grids against transmission line overloads under wind power injection at different nodes.\",\n \"abstract\": \"A steadily increasing fraction of renewable energy sources for electricity production requires a better understanding of how stochastic power generation affects the stability of electricity grids. Here, we assess the resilience of an IEEE test grid against single transmission line overloads under wind power injection based on the dc power flow equations and a quasi-static grid response to wind fluctuations. Thereby we focus on the mutual influence of wind power generation at different nodes. We find that overload probabilities vary strongly between different pairs of nodes and become highly affected by spatial correlations of wind fluctuations. An unexpected behaviour is uncovered: for a large number of node pairs, increasing wind power injection at one node can increase the power threshold at the other node with respect to line overloads in the grid. We find that this seemingly paradoxical behaviour is related to the topological distance of the overloaded line from the shortest path connecting the wind nodes. In the considered test grid, it occurs for all node pairs, where the overloaded line belongs to the shortest path.\",\n \"corpus_id\": 22241441,\n \"score\": 2\n },\n {\n \"doc_id\": \"29289040\",\n \"title\": \"Stability of synchrony against local intermittent fluctuations in tree-like power grids.\",\n \"abstract\": \"90% of all Renewable Energy Power in Germany is installed in tree-like distribution grids. Intermittent power fluctuations from such sources introduce new dynamics into the lower grid layers. At the same time, distributed resources will have to contribute to stabilize the grid against these fluctuations in the future. In this paper, we model a system of distributed resources as oscillators on a tree-like, lossy power grid and its ability to withstand desynchronization from localized intermittent renewable infeed. We find a remarkable interplay of the network structure and the position of the node at which the fluctuations are fed in. An important precondition for our findings is the presence of losses in distribution grids. Then, the most network central node splits the network into branches with different influence on network stability. Troublemakers, i.e., nodes at which fluctuations are especially exciting the grid, tend to be downstream branches with high net power outflow. For low coupling strength, we also find branches of nodes vulnerable to fluctuations anywhere in the network. These network regions can be predicted at high confidence using an eigenvector based network measure taking the turbulent nature of perturbations into account. While we focus here on tree-like networks, the observed effects also appear, albeit less pronounced, for weakly meshed grids. On the other hand, the observed effects disappear for lossless power grids often studied in the complex system literature.\",\n \"corpus_id\": 24033472,\n \"score\": 2\n },\n {\n \"doc_id\": \"29401941\",\n \"title\": \"Optical coherence grids and their propagation characteristics.\",\n \"abstract\": \"A novel class of partially coherent light sources termed optical coherence grids (OCGs) are introduced that can yield stable optical grids in the far field. The optical grids, of which the light distributes in a network of straight lines crossing each other to form a series of hollow cages, can be seen as a better controlled optical lattice. Propagation properties of OCG beams in free space, including spectral density, transverse coherence, and M2 factor, are investigated in detail. It is interesting that a periodic grid pattern is produced at a distance and remains stable on further propagation, and we stress that the structure of far-field optical grids can be flexibly tuned by modulating the correlation parameters of the source. In addition, by performing convolution of degree of coherence, we also propose perfect optical coherence grids (POCG). The far-field grid pattern of POCG is in a fully controllable fashion. This work is expected to find applications in cooling atoms, trapping microscopic particles, or assembling cells, etc.\",\n \"corpus_id\": 46765572,\n \"score\": 2\n },\n {\n \"doc_id\": \"19045156\",\n \"title\": \"Inertial effects in the nonlinear transient relaxation of rigid rodlike molecules in a strong dc electric field.\",\n \"abstract\": \"A method of calculation of nonlinear transient responses of an assembly of noninteracting polar linear molecules due to sudden changes in a strong external dc electric field is presented. The infinite hierarchy of differential-recurrence relations for the decay functions describing the relaxation of the system is derived by averaging the underlying inertial Langevin equation. The solution of this hierarchy is obtained in terms of matrix continued fractions. The integral relaxation time and the spectrum of the electric polarization for various nonlinear transient responses (step-on, step-off, and rapidly rotating field) are calculated for typical values of the model parameters. The nonlinear transient responses exhibit pronounced nonlinear effects due to the strong dc field. Analytical equations for the quantities of interest are presented in the overdamped limit. Furthermore, the linear response relaxation function and linear dynamic susceptibility are obtained as a particular case of a general nonlinear theory.\",\n \"corpus_id\": 17756942,\n \"score\": 1\n },\n {\n \"doc_id\": \"20462247\",\n \"title\": \"Electric response of nonspherical and spherical silica particle dispersions to ac electric field.\",\n \"abstract\": \"For the purpose of revealing unique aspects of the electrical double layer (EDL) around nonspherical particles, we focus on a silica square platelike particle with well-defined shape, i.e., H-ilerite. Impedance measurements for suspensions of silica spherical and square platelike particles are performed to examine ion concentration polarization and its relaxation in their EDLs under ac electric fields that are high enough to orient H-ilerite to electric fields and form pearl chains of particles. For a silica spherical particle, the relaxation frequency of ion concentration polarization in EDL around the particles is independent of applied electric field strength and the volume fraction of the particles in suspension. The conductance ratios of silica particle suspension to its supernatant show a good linear relation against the volume fraction independently of applied electric field strength. For H-ilerite, at low electric field strength where there is neither electric orientation nor pearl chain formation, the conductance ratio also shows a linear relation against the volume fraction. The slope of the conductance ratio to the volume fraction increases and the relaxation frequency decreases as applied electric field strength increases. In addition, two linear relations with different slopes, where the slope becomes steep at higher volume fractions, appear in the plots of the conductance ratio against the volume fraction. Such a unique response of H-ilerite suspension to electric field can be explained by the electric orientation of H-ilerite accompanying pearl chain formation.\",\n \"corpus_id\": 38684454,\n \"score\": 1\n },\n {\n \"doc_id\": \"20866296\",\n \"title\": \"Lattice splitting under intermittent flows.\",\n \"abstract\": \"We study the splitting of regular square lattices subject to stochastic intermittent flows. Various flow patterns are produced by different groupings of the nodes, based on their random alternation between two possible states. The resulting flows on the lattices decrease with the number of groups according to a power law. By Monte Carlo simulations we reveal how the time span until the occurrence of a splitting depends on the flow patterns. Increasing the flow fluctuation frequency shortens this time span, which reaches a minimum before rising again due to inertia effects incorporated in the model. The size of the largest connected component after the splitting is rather independent of the flow fluctuation frequency but slightly decreases with the link capacities. Our findings carry important implications for real-world networks, such as electric power grids with a large share of renewable intermittent energy sources.\",\n \"corpus_id\": 10461064,\n \"score\": 1\n },\n {\n \"doc_id\": \"21247206\",\n \"title\": \"Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.\",\n \"abstract\": \"To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the frequency fluctuation is small. Thus, we observed a distinct difference between the classical and quantum mechanically calculated multidimensional spectra in the slow modulation case where spectral diffusion plays a role. This fact indicates that one may not reproduce the experimentally obtained multidimensional spectrum for high-frequency vibrational modes based on classical molecular dynamics simulations if the modulation that arises from surrounding molecules is weak and slow. A practical way to overcome the difference between the classical and quantum simulations was discussed.\",\n \"corpus_id\": 25212051,\n \"score\": 1\n },\n {\n \"doc_id\": \"21599168\",\n \"title\": \"Time-dependent correlations in a supercooled liquid from nonlinear fluctuating hydrodynamics.\",\n \"abstract\": \"We solve numerically the equations of nonlinear fluctuating hydrodynamics (NFH). A coarse graining of the density field is applied at each time step to avoid instabilities which otherwise plague the algorithm at long times. The equilibrium correlation of the density fluctuations at different times obtained directly from the solutions of the NFH equations are shown here to be in quantitative agreement with corresponding molecular dynamics simulation data. Low-order perturbative treatment of the these NFH equations obtains the mode coupling model. The latter has been widely studied for understanding the slow dynamics characteristic of the supercooled state. A crucial aspect of this theory is a rounded version of a possible ergodic-nonergodic transition in the supercooled liquid at a temperature T(c) between melting point T(m) and the glass transition temperature T(g). In the present work we demonstrate numerically the role of strongly coupled density fluctuations in giving rise to slow dynamics and how the 1/ρ nonlinearity in the NFH equations of motion is essential in restoring the ergodic behavior in the liquid. The relaxation data indicate that at moderate supercooling near T(c), the time temperature superposition holds. The relaxation gets increasingly stretched with increased supercooling. The relaxation time τ shows an initial power-law divergence approaching a transition temperature T(c) generally identified as the mode coupling temperature. From the direct solutions we obtain a value for T(c) much lower than that typically estimated from solution of low-order integral equations of mode coupling theory. This is in agreement with the trend seen in computer simulations.\",\n \"corpus_id\": 46218076,\n \"score\": 1\n },\n {\n \"doc_id\": \"22060330\",\n \"title\": \"Relaxation properties in a diffusive model of k-mers with constrained movements on a triangular lattice.\",\n \"abstract\": \"We study the relaxation process in a two-dimensional lattice gas model, based on the concept of geometrical frustration. In this model the particles are k-mers that can both randomly translate and rotate on the planar triangular lattice. In the absence of rotation, the diffusion of hard-core particles in crossed single-file systems is investigated. We monitor, for different densities, several quantities: mean-square displacement, the self-part of the van Hove correlation function, and the self-intermediate scattering function. We observe a considerable slowing of diffusion on a long-time scale when suppressing the rotational motion of k-mers; our system is subdiffusive at intermediate times between the initial transient and the long-time diffusive regime. We show that the self-part of the van Hove correlation function exhibits, as a function of particle displacement, a stretched exponential decay at intermediate times. The self-intermediate scattering function (SISF), displaying slower than exponential relaxation, suggests the existence of heterogeneous dynamics. For each value of density, the SISF is well described by the Kohlrausch-Williams-Watts law; the characteristic timescale τ(q(n)) is found to decrease with the wave vector q(n) according to a simple power law. Furthermore, the slowing of the dynamics with density ρ(0) is consistent with the scaling law 1/τ(q(n);ρ(0))∝(ρ(c)-ρ(0))(ϰ), with the same exponent ϰ=3.34±0.12 for all wave vectors q(n). The density ρ(c) is approximately equal to the closest packing limit, θ(CPL)≲1, for dimers on the two-dimensional triangular lattice. The self-diffusion coefficient D(s) scales with the same power-law exponent and critical density.\",\n \"corpus_id\": 35126432,\n \"score\": 1\n },\n {\n \"doc_id\": \"22277723\",\n \"title\": \"Quasi-elastic neutron scattering studies of the slow dynamics of supercooled and glassy aspirin.\",\n \"abstract\": \"Aspirin, also known as acetylsalicylic acid (ASA), is not only a wonderful drug, but also a good glass former. Therefore, it serves as an important molecular system to study the near-arrest and arrested phenomena. In this paper, a high-resolution quasi-elastic neutron scattering (QENS) technique is used to investigate the slow dynamics of supercooled liquid and glassy aspirin from 410 down to 350 K. The measured QENS spectra can be analyzed with a stretched exponential model. We find that (i) the stretched exponent β(Q) is independent of the wavevector transfer Q in the measured Q range and (ii) the structural relaxation time τ(Q) follows a power-law dependence on Q. Consequently, the Q-independent structural relaxation time τ(0) can be extracted for each temperature to characterize the slow dynamics of aspirin. The temperature dependence of τ(0) can be fitted with the mode-coupling power law, the Vogel-Fulcher-Tammann equation and a universal equation for fragile glass forming liquids recently proposed by Tokuyama in the measured temperature range. The calculated dynamic response function χ(T)(Q, t) using the experimentally determined self-intermediate scattering function of the hydrogen atoms of aspirin shows direct evidence of the enhanced dynamic fluctuations as the aspirin is increasingly supercooled, in agreement with the fixed-time mean squared displacement ⟨x(2)⟩ and the non-Gaussian parameter α(2) extracted from the elastic scattering.\",\n \"corpus_id\": 206038716,\n \"score\": 1\n },\n {\n \"doc_id\": \"22475003\",\n \"title\": \"Wind power electricity: the bigger the turbine, the greener the electricity?\",\n \"abstract\": \"Wind energy is a fast-growing and promising renewable energy source. The investment costs of wind turbines have decreased over the years, making wind energy economically competitive to conventionally produced electricity. Size scaling in the form of a power law, experience curves and progress rates are used to estimate the cost development of ever-larger turbines. In life cycle assessment, scaling and progress rates are seldom applied to estimate the environmental impacts of wind energy. This study quantifies whether the trend toward larger turbines affects the environmental profile of the generated electricity. Previously published life cycle inventories were combined with an engineering-based scaling approach as well as European wind power statistics. The results showed that the larger the turbine is, the greener the electricity becomes. This effect was caused by pure size effects of the turbine (micro level) as well as learning and experience with the technology over time (macro level). The environmental progress rate was 86%, indicating that for every cumulative production doubling, the global warming potential per kWh was reduced by 14%. The parameters, hub height and rotor diameter were identified as Environmental Key Performance Indicators that can be used to estimate the environmental impacts for a generic turbine.\",\n \"corpus_id\": 28942884,\n \"score\": 1\n },\n {\n \"doc_id\": \"22755699\",\n \"title\": \"High-ratio grid considerations in mobile chest radiography.\",\n \"abstract\": \"PURPOSE: Grids are often not used in mobile chest radiography, and when used, they have a low ratio and are often inaccurately aligned. Recently, a mobile radiography automatic grid alignment system (MRAGA) was developed that accurately and automatically aligns the focal spot with the grid. The objective of this study is to investigate high-ratio grid tradeoffs in mobile chest radiography at fixed patient dose when the focal spot lies on the focal axis of the grid. METHODS: The chest phantoms (medium and large) used in this study were modifications of the ANSI (American National Standards Institute) chest phantom and consisted of layers of Lucite™, aluminum, and air. For the large chest phantom, the amount of Lucite and aluminum was increased by 50% over the medium phantom. Further modifications included a mediastinum insert and the addition of contrast targets in the lung and mediastinum regions. Five high-ratio grids were evaluated and compared to the nongrid results at x-ray tube potentials of 80, 90, 100, and 110 kVp for both phantoms. The grids investigated were from two manufacturers: 12:1 and 15:1 aluminum interspace grids from one and 10:1, 13:1, and 15:1 fiber interspace grids from another. MRAGA was employed to align the focal spot with the grid. All exposures for a given kVp and phantom size were made using the same current-time product (CTP). The phantom images were acquired using computed radiography, and contrast-to-noise ratios (CNR) and CNR improvement factors (k(CNR)) were determined from the resultant images. The noise in the targets and the contrast between the targets and their backgrounds were calculated using a local detrending correction, and the CNR was calculated as the ratio of the target contrast to the background noise. k(CNR) was defined as the ratio of the CNR imaged with the grid divided by the CNR imaged without a grid. RESULTS: The CNR values obtained with a high-ratio grid were 4%-65% higher than those obtained without a grid at the same phantom dose. The improvement was greater for the large chest phantom than the medium chest phantom and greater for the mediastinum targets than for the lung targets. In general, the fiber interspace grids performed better than the aluminum interspace grids. In the lung, k(CNR) for both types of grids exhibited little dependence on kVp or grid ratio. In the mediastinum, k(CNR) decreased 4%-10% with increasing kVp, and varied up to 5.3% with grid ratio. CONCLUSIONS: When the focal spot is accurately aligned with the grid, the use of a high-ratio grid in mobile chest radiography improves image quality with no increase in dose to the phantom. For the grids studied, the performance of the fiber interspace grids was superior to the performance of the aluminum interspace grids, with the fiber interspace 13:1 grid producing the best overall results for the medium chest phantom and the fiber interspace 15:1 producing the best overall results for the large chest phantom.\",\n \"corpus_id\": 19777062,\n \"score\": 1\n },\n {\n \"doc_id\": \"22975242\",\n \"title\": \"An exact analytical solution for the evolution of a dipole-dipole interacting system under spherical diffusion in magnetic resonance experiments.\",\n \"abstract\": \"A model system consisting of an isotropic ensemble of spin pairs, where dipole-dipole interaction is assumed to be effective only within each pair, is considered. The ideal segment connecting the spins in a couple has a fixed length but is free to rotate following a diffusion dynamics. This allows the free induction decay (FID) to be derived non-perturbatively by solving the appropriate Dyson equation associated to the problem. Motional narrowing can be described analytically in terms of only two parameters, i.e. the coupling constant of the interaction hamiltonian, b, and the orientational diffusion coefficient D. Salient features of the transverse correlation function thus obtained are discussed, and a comparison with numerical simulations performed with the software SPINEVOLUTION is presented. Interpreting b and D as effective parameters describing multiple interactions of a single spin with its neighbors in a real system, the analysis of published experimental data on poly(ethyl acrylate) has been carried out. It is found that for temperatures higher than and not too close to the glass transition, the results are the same as those found within the Anderson-Weiss approach by assuming a single time exponential decay of the average dipole-dipole interaction. On the other hand, as D tends to zero, FID oscillations characteristic of a rigid lattice show up.\",\n \"corpus_id\": 41915762,\n \"score\": 1\n },\n {\n \"doc_id\": \"23004950\",\n \"title\": \"Nonequilibrium Kondo model: crossover from weak to strong coupling.\",\n \"abstract\": \"We analyze the nonequilibrium Kondo model at finite voltage and temperature by using a new formulation of the real-time renormalization group method with the Laplace variable as the flow parameter. We evaluate the energy-dependent spin relaxation rate and nonlinear conductance, and derive an approximate form for the universal line shape for the latter in the whole crossover regime from weak to strong coupling. The results are shown to agree well with exact methods in equilibrium, Fermi-liquid theory, weak-coupling expansions, and recent experiments. For the transient spin dynamics we find a universal exponential decay in the long-time limit along with a truncation-dependent pre-exponential power law. For multichannel models a pure power-law decay typical for non-Fermi-liquid behavior is predicted.\",\n \"corpus_id\": 24820432,\n \"score\": 1\n },\n {\n \"doc_id\": \"23421210\",\n \"title\": \"Intercellular synchronization of coupled smooth muscle cells via Ca2+ propagation.\",\n \"abstract\": \"The propagation of Ca2+ wave through gap junction in smooth muscle cell is studied as a function of electrical coupling parameter (g) modulated by Ca2+ level in the cell. The range of activation time of Ca2+ propagation with amplitude is found to increase as increase in electrical coupling parameter g, which is identified by increase in critical time of activation, T(F) as a function of g. Then identical Ca2+ oscillators are allowed to interact via electrical and diffusive coupling of Ca2+ ions diffused through gap junctions, and rate of intercellular synchronization among them is studied. The phase diagrams in (T(F) - g) and (T(F) - epsilon) parameter spaces separate oscillation death and damped oscillations regimes which correspond to deactivated and activated regimes of Ca2+ level. The effect of on T(F) is significantly very slow, however it enhances the rate of synchronization among the coupled oscillators. The increase in g comparatively slows down the rate of synchronization of the coupled oscillators as shown in the phase diagram in (epsilon - g) parameter space which separates desynchronized and synchronized regimes.\",\n \"corpus_id\": 7156273,\n \"score\": 1\n },\n {\n \"doc_id\": \"24229173\",\n \"title\": \"Manifestation of random first-order transition theory in Wigner glasses.\",\n \"abstract\": \"We use Brownian dynamics simulations of a binary mixture of highly charged spherical colloidal particles to test some of the predictions of the random first-order transition (RFOT) theory [Phys. Rev. Lett. 58, 2091 (1987); Phys. Rev. A 40, 1045 (1989)]. In accord with mode-coupling theory and RFOT, we find that as the volume fraction of the colloidal particles ϕ approaches the dynamical transition value ϕ(A), three measures of dynamics show an effective ergodic to nonergodic transition. First, there is a dramatic slowing down of diffusion, with the translational diffusion constant decaying as a power law as ϕ→ϕ(A)(-). Second, the energy metric, a measure of ergodicity breaking in classical many-body systems, shows that the system becomes effectively nonergodic as ϕ(A) is approached. Finally, the time t(*), at which the four-point dynamical susceptibility achieves a maximum, also increases as a power law near ϕ(A). Remarkably, the translational diffusion coefficients, ergodic diffusion coefficient, and (t(*))(-) all vanish as (ϕ(-1)-ϕ(A)(-1))(γ) with both ϕ(A)(≈0.1) and γ being the roughly the same for all three quantities. Above ϕ(A), transport involves crossing free energy barriers. In this regime, the density-density correlation function decays as a stretched exponential [exp-(t/τ(α))(β)] with β≈0.45. The ϕ dependence of the relaxation time τ(α) could be fit using the Vogel-Tamman-Fulcher law with the ideal glass transition at ϕ(K)≈0.47. By using a local entropy measure, we show that the law of large numbers is not obeyed above ϕ(A), and gives rise to subsample to subsample fluctuations in all physical observables. We propose that dynamical heterogeneity is a consequence of violation of law of large numbers.\",\n \"corpus_id\": 50610,\n \"score\": 1\n },\n {\n \"doc_id\": \"24521155\",\n \"title\": \"Length scales and structural dynamics in nematogen pseudonematic domains measured with 2D IR vibrational echoes and optical Kerr effect experiments.\",\n \"abstract\": \"Nematogen liquids in the isotropic phase are macroscopically homogeneous but on multinanometer length scales have pseudonematic domains with correlation lengths that grow as the isotropic to nematic phase transition temperature (TNI) is approached from above. Orientational relaxation of nematogens in the isotropic phase manifests as two fast power laws and a slow exponential decay when measured by optical heterodyne detected optical Kerr effect (OHD-OKE) experiments. The long time exponential relaxation is associated with complete randomization of pseudonematic domains. We examine the effect of local orientational correlation on spectral diffusion (structural evolution) experienced by a vibrational probe molecule within the pseudonematic domains of 4-cyano-4'-pentylbiphenyl (5CB) using two-dimensional infrared (2D IR) vibrational echo spectroscopy. The addition of low concentration 4-pentyl-4'-thiocyanobiphenyl (5SCB) as a long-lived vibrational probe to 5CB is shown to lower TNI of the sample slightly, but the fast power law dynamics and exponential decays observed by OHD-OKE spectroscopy are unchanged. We compare the complete orientational relaxation and spectral diffusion for samples of 5SCB in 5CB to 5SCB in 4-pentylbiphenyl (5B) at four temperatures above TNI. 5B has a molecular structure similar to 5CB but is not a nematogen. At all but the lowest temperature, the spectral diffusion in 5CB and 5B is described well as a triexponential decay with very similar time constants. The results demonstrate that the presence of local orientational order at temperatures well above TNI does not affect the spectral diffusion (structural evolution) within pseudonematic domains when the correlation lengths are short. However, when the temperature of the sample is held very close to TNI, the spectral diffusion in 5CB slows dramatically while that in 5B does not. It is only as the correlation length becomes very long that its presence impacts the spectral diffusion (structural fluctuations) sensed by the vibrational probes located in pseudonematic domains. The orientational relaxation is modeled with schematic mode coupling theory (MCT). Fitting with MCT provides density and orientational correlation functions. The density correlation decays are similar for 5B and 5CB, but the orientational correlation decays are much slower for 5CB. Additionally, the time dependence of the spectral diffusion in 5CB is strikingly similar to that of the density correlation function decay, while the orientational correlation function decay is far too slow to contribute to the spectral diffusion. Therefore, density fluctuations are likely the source of spectral diffusion at temperatures at least 5 K above TNI.\",\n \"corpus_id\": 207613368,\n \"score\": 1\n },\n {\n \"doc_id\": \"25243214\",\n \"title\": \"Smart grid as a service: a discussion on design issues.\",\n \"abstract\": \"Smart grid allows the integration of distributed renewable energy resources into the conventional electricity distribution power grid such that the goals of reduction in power cost and in environment pollution can be met through an intelligent and efficient matching between power generators and power loads. Currently, this rapidly developing infrastructure is not as \\\"smart\\\" as it should be because of the lack of a flexible, scalable, and adaptive structure. As a solution, this work proposes smart grid as a service (SGaaS), which not only allows a smart grid to be composed out of basic services, but also allows power users to choose between different services based on their own requirements. The two important issues of service-level agreements and composition of services are also addressed in this work. Finally, we give the details of how SGaaS can be implemented using a FIPA-compliant JADE multiagent system.\",\n \"corpus_id\": 5110603,\n \"score\": 1\n },\n {\n \"doc_id\": \"25353889\",\n \"title\": \"Oscillating-grid experiments in water and superfluid helium.\",\n \"abstract\": \"Passing a fluid through a grid is a well-known mechanism used to study the properties of turbulence. Oscillating a horizontal grid vertically in a tank has also been used extensively and is considered to be a source of almost homogenous isotropic turbulence. When the oscillating grid is turned on a turbulent flow is induced. A front translates into the experimental tank, behind which the flow is highly turbulent. Long predicted that the growth of such a front would grow diffusively as the square root of time (i.e., d ∼ sqrt[t]) and Dickinson and Long presented experimental evidence for the diffusive result at a low mesh Reynolds number of 555. This paper revisits these experiments and attempts a set of two models for the advancing front in both square and round tanks. We do not observe significant differences between runs in square and round tanks. The experiments in water reach mesh Reynolds numbers of order 30000. Using some data from superfluid helium experiments we are able to explore mesh Reynolds numbers to about 43000. We find the power law for the advancing front decreases weakly with the mesh Reynolds number. Using a very long tank we find that the turbulent front stops completely at a certain depth and attempt a simple explanation for that behavior. We study the propagation of the turbulent front into tubes of different diameters inserted into the main tank. We show that these tubes exclude wavelengths much larger than the tube diameter. We explore the variation of the position of the steady-state boundary H on tube diameter D and find that H = cD with c ∼ 2. We suggest this may be explained by saturation of the energy-containing length scale ℓ(e). We also report on the effect of plugging up just one hole of the grid. Finally, we recall some earlier oscillating grid experiments in superfluid (4)He in the light of the present results.\",\n \"corpus_id\": 21914497,\n \"score\": 1\n },\n {\n \"doc_id\": \"25481151\",\n \"title\": \"Interface initiation and propagation in liquid demixing with electric fields.\",\n \"abstract\": \"We investigate the dynamics of liquid-liquid phase separation confined in a charged concentric cylindrical geometry. Two main time scales characterize the non-equilibrium interface behavior: (1) the lag time t(L) for forming an interface, and (2) the relaxation time to equilibrium. We find that t(L) increases as parameters (temperature, bulk composition, and surface charge) approach the electrostatic spinodal line in the phase diagram. Close to this line, t(L) is proportional to a renormalized bulk concentration with an exponent of -1.16 ± 0.03. The relaxation of the interface to equilibrium can be divided into three phases: early, intermediate (power-law), and late (exponential). During power-law relaxation, the location of the rescaled interface is proportional to time with an exponent of -0.94 ± 0.04. Exponential relaxation occurs as a consequence of finite-size effects, and the associated time constant decreases with decreasing system size (with a power-law scaling), decreasing concentration, and increasing surface charge. The time constant also decreases with increasing (decreasing) temperature when the concentration is below (above) the critical concentration.\",\n \"corpus_id\": 28175571,\n \"score\": 1\n },\n {\n \"doc_id\": \"25737231\",\n \"title\": \"Biological electric fields and rate equations for biophotons.\",\n \"abstract\": \"Biophoton intensities depend upon the squared modulus of the electric field. Hence, we first make some general estimates about the inherent electric fields within various biosystems. Generally, these intensities do not follow a simple exponential decay law. After a brief discussion on the inapplicability of a linear rate equation that leads to strict exponential decay, we study other, nonlinear rate equations that have been successfully used for biosystems along with their physical origins when available.\",\n \"corpus_id\": 8818415,\n \"score\": 1\n },\n {\n \"doc_id\": \"26277149\",\n \"title\": \"An itinerant oscillator model with cage inertia for mesorheological granular experiments.\",\n \"abstract\": \"Recent experiments with a rotating probe immersed in weakly fluidized granular materials show a complex behavior on a wide range of time scales. Viscous-like relaxation at high frequency is accompanied by an almost harmonic dynamical trapping at intermediate times, with possibly anomalous long time behavior in the form of super-diffusion. Inspired by the itinerant oscillator model for diffusion in molecular liquids, and other models with coupled thermostats acting at different time scales, here we discuss a new model able to account for fast viscous relaxation, dynamical trapping, and super-diffusion at long times. The main difference with respect to liquids is a non-negligible cage inertia for the surrounding (granular) fluid, which allows it to sustain a slow but persistent motion for long times. The computed velocity power density spectra and mean-squared displacement qualitatively reproduce the experimental findings. We also discuss the linear response to external perturbations and the tail of the distribution of persistency time, which is associated with superdiffusion, and whose cut-off time is determined by cage inertia.\",\n \"corpus_id\": 11640888,\n \"score\": 1\n },\n {\n \"doc_id\": \"26631463\",\n \"title\": \"Can Neural Activity Propagate by Endogenous Electrical Field?\",\n \"abstract\": \"UNLABELLED: It is widely accepted that synaptic transmissions and gap junctions are the major governing mechanisms for signal traveling in the neural system. Yet, a group of neural waves, either physiological or pathological, share the same speed of ∼0.1 m/s without synaptic transmission or gap junctions, and this speed is not consistent with axonal conduction or ionic diffusion. The only explanation left is an electrical field effect. We tested the hypothesis that endogenous electric fields are sufficient to explain the propagation with in silico and in vitro experiments. Simulation results show that field effects alone can indeed mediate propagation across layers of neurons with speeds of 0.12 ± 0.09 m/s with pathological kinetics, and 0.11 ± 0.03 m/s with physiologic kinetics, both generating weak field amplitudes of ∼2-6 mV/mm. Further, the model predicted that propagation speed values are inversely proportional to the cell-to-cell distances, but do not significantly change with extracellular resistivity, membrane capacitance, or membrane resistance. In vitro recordings in mice hippocampi produced similar speeds (0.10 ± 0.03 m/s) and field amplitudes (2.5-5 mV/mm), and by applying a blocking field, the propagation speed was greatly reduced. Finally, osmolarity experiments confirmed the model's prediction that cell-to-cell distance inversely affects propagation speed. Together, these results show that despite their weak amplitude, electric fields can be solely responsible for spike propagation at ∼0.1 m/s. This phenomenon could be important to explain the slow propagation of epileptic activity and other normal propagations at similar speeds. SIGNIFICANCE STATEMENT: Neural activity (waves or spikes) can propagate using well documented mechanisms such as synaptic transmission, gap junctions, or diffusion. However, the purpose of this paper is to provide an explanation for experimental data showing that neural signals can propagate by means other than synaptic transmission, gap junction, or diffusion. The results indicate that electric fields (ephaptic effects) are capable of mediating propagation of self-regenerating neural waves. This novel mechanism coupling cell-by-volume conduction could be involved in other types of propagating neural signals, such as slow-wave sleep, sharp hippocampal waves, theta waves, or seizures.\",\n \"corpus_id\": 14502452,\n \"score\": 1\n },\n {\n \"doc_id\": \"27517161\",\n \"title\": \"Nonlinear physics of electrical wave propagation in the heart: a review.\",\n \"abstract\": \"The beating of the heart is a synchronized contraction of muscle cells (myocytes) that is triggered by a periodic sequence of electrical waves (action potentials) originating in the sino-atrial node and propagating over the atria and the ventricles. Cardiac arrhythmias like atrial and ventricular fibrillation (AF,VF) or ventricular tachycardia (VT) are caused by disruptions and instabilities of these electrical excitations, that lead to the emergence of rotating waves (VT) and turbulent wave patterns (AF,VF). Numerous simulation and experimental studies during the last 20 years have addressed these topics. In this review we focus on the nonlinear dynamics of wave propagation in the heart with an emphasis on the theory of pulses, spirals and scroll waves and their instabilities in excitable media with applications to cardiac modeling. After an introduction into electrophysiological models for action potential propagation, the modeling and analysis of spatiotemporal alternans, spiral and scroll meandering, spiral breakup and scroll wave instabilities like negative line tension and sproing are reviewed in depth and discussed with emphasis on their impact for cardiac arrhythmias.\",\n \"corpus_id\": 4432898,\n \"score\": 1\n },\n {\n \"doc_id\": \"28297930\",\n \"title\": \"Analysis of spontaneous oscillations for a three-state power-stroke model.\",\n \"abstract\": \"Our study considers the mechanism of the spontaneous oscillations of molecular motors that are driven by the power stroke principle by applying linear stability analysis around the stationary solution. By representing the coupling equation of microscopic molecular motor dynamics and mesoscopic sarcomeric dynamics by a rank-1 updated matrix system, we derived the analytical representations of the eigenmodes of the Jacobian matrix that cause the oscillation. Based on these analytical representations, we successfully derived the essential conditions for the oscillation in terms of the rate constants of the power stroke and the reversal stroke transitions of the molecular motor. Unlike the two-state model, in which the dependence of the detachment rates on the motor coordinates or the applied forces on the motors plays a key role for the oscillation, our three-state power stroke model demonstrates that the dependence of the rate constants of the power and reversal strokes on the strains in the elastic elements in the motor molecules plays a key role, where these rate constants are rationally determined from the free energy available for the power stroke, the stiffness of the elastic element in the molecular motor, and the working stroke size. By applying the experimentally confirmed values to the free energy, the stiffness, and the working stroke size, our numerical model reproduces well the experimentally observed oscillatory behavior. Furthermore, our analysis shows that two eigenmodes with real positive eigenvalues characterize the oscillatory behavior, where the eigenmode with the larger eigenvalue indicates the transient of the system of the quick sarcomeric lengthening induced by the collective reversal strokes, and the smaller eigenvalue correlates with the speed of sarcomeric shortening, which is much slower than lengthening. Applying the perturbation analyses with primal physical parameters, we find that these two real eigenvalues occur on two branches derived from a merge point of a pair of complex-conjugate eigenvalues generated by Hopf bifurcation.\",\n \"corpus_id\": 43545932,\n \"score\": 1\n },\n {\n \"doc_id\": \"28863584\",\n \"title\": \"Nonlinear wave propagation in porous materials based on the Biot theory.\",\n \"abstract\": \"Nonlinearity must be considered with some porous granular media because of the large deformation under seismic waves. In this study, the propagation of nonlinear waves in porous media is studied based on the Biot theory and the governing equations are obtained by the Lagrangian formulation. Three new nonlinear parameters are introduced to consider the coupled nonlinearity between the solid and fluid components in porous media. It is shown that an additional nonlinear wave with a double frequency is generated by the coupling effect of linear fast and slow waves. When only a shear wave is applied at the source, no double-frequency nonlinear wave is predicted and three nonlinear longitudinal waves are generated. On the basis of the practical case studies, the effect of strong nonlinearity is computed under the influence of a one-dimensional single longitudinal wave source and a single shear wave source.\",\n \"corpus_id\": 321641,\n \"score\": 1\n },\n {\n \"doc_id\": \"29319842\",\n \"title\": \"Quantitative evaluation of potential irradiation geometries for carbon-ion beam grid therapy.\",\n \"abstract\": \"PURPOSE: Radiotherapy using grids containing cm-wide beam elements has been carried out sporadically for more than a century. During the past two decades, preclinical research on radiotherapy with grids containing small beam elements, 25 μm-0.7 mm wide, has been performed. Grid therapy with larger beam elements is technically easier to implement, but the normal tissue tolerance to the treatment is decreasing. In this work, a new approach in grid therapy, based on irradiations with grids containing narrow carbon-ion beam elements was evaluated dosimetrically. The aim formulated for the suggested treatment was to obtain a uniform target dose combined with well-defined grids in the irradiated normal tissue. The gain, obtained by crossfiring the carbon-ion beam grids over a simulated target volume, was quantitatively evaluated. METHODS: The dose distributions produced by narrow rectangular carbon-ion beams in a water phantom were simulated with the PHITS Monte Carlo code. The beam-element height was set to 2.0 cm in the simulations, while the widths varied from 0.5 to 10.0 mm. A spread-out Bragg peak (SOBP) was then created for each beam element in the grid, to cover the target volume with dose in the depth direction. The dose distributions produced by the beam-grid irradiations were thereafter constructed by adding the dose profiles simulated for single beam elements. The variation of the valley-to-peak dose ratio (VPDR) with depth in water was thereafter evaluated. The separation of the beam elements inside the grids were determined for different irradiation geometries with a selection criterion. RESULTS: The simulated carbon-ion beams remained narrow down to the depths of the Bragg peaks. With the formulated selection criterion, a beam-element separation which was close to the beam-element width was found optimal for grids containing 3.0-mm-wide beam elements, while a separation which was considerably larger than the beam-element width was found advantageous for grids containing 0.5-mm-wide beam elements. With the single-grid irradiation setup, the VPDRs were close to 1.0 already at a distance of several cm from the target. The valley doses given to the normal tissue at 0.5 cm distance from the target volume could be limited to less than 10% of the mean target dose if a crossfiring setup with four interlaced grids was used. CONCLUSIONS: The dose distributions produced by grids containing 0.5- and 3.0-mm wide beam elements had characteristics which could be useful for grid therapy. Grids containing mm-wide carbon-ion beam elements could be advantageous due to the technical ease with which these beams can be produced and delivered, despite the reduced threshold doses observed for early and late responding normal tissue for beams of millimeter width, compared to submillimetric beams. The treatment simulations showed that nearly homogeneous dose distributions could be created inside the target volumes, combined with low valley doses in the normal tissue located close to the target volume, if the carbon-ion beam grids were crossfired in an interlaced manner with optimally selected beam-element separations. The formulated selection criterion was found useful for the quantitative evaluation of the dose distributions produced by the different irradiation setups.\",\n \"corpus_id\": 3880187,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":48,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29690519\",\n \"title\": \"Thermocatalytic Behavior of Manganese (IV) Oxide as Nanoporous Material on the Dissociation of a Gas Mixture Containing Hydrogen Peroxide.\",\n \"abstract\": \"In this article, we present an overview on the thermocatalytic reaction of hydrogen peroxide (H 2 O 2 ) gas on a manganese (IV) oxide (MnO 2 ) catalytic structure. The principle of operation and manufacturing techniques are introduced for a calorimetric H 2 O 2 gas sensor based on porous MnO 2 . Results from surface analyses by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) of the catalytic material provide indication of the H 2 O 2 dissociation reaction schemes. The correlation between theory and the experiments is documented in numerical models of the catalytic reaction. The aim of the numerical models is to provide further information on the reaction kinetics and performance enhancement of the porous MnO 2 catalyst.\",\n \"corpus_id\": 13838421\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19136141","title":"Hydrogen peroxide decomposition on manganese oxide (pyrolusite): kinetics, intermediates, and mechanism.","abstract":"The objective of this study is the kinetic interpretation of hydrogen peroxide decomposition on manganese oxide (pyrolusite) and the explanation of the reaction mechanism including the hydroperoxide/superoxide anion. The decomposition of hydrogen peroxide on manganese oxide at pH 7 was represented by a pseudo first-order model. The maximum value of the observed first-order rates constants (k(obs)) was 0.741 min(-1) at 11.8 of [H(2)O(2)]/[triple bond MnO(2)] when [H(2)O(2)]/[triple bond MnO(2)] were ranged from 58.8 to 3.92. The pseudo first-order rate constants (kMnO(2)) approximated as the average value of 0.025 (min mM)(-1) with a standard deviation of 0.003 at [H(2)O(2)]/[triple bond MnO(2)] ranged from 39.2 to 11.8. When [H(2)O(2)]/[triple bond MnO(2)] was 3.92, the rate constants (kMnO(2)) was 0.061 (min mM)(-1) as maximum. Oxygen production showed that the initial rates increased with decreasing [H(2)O(2)]/[triple bond MnO(2)] and the total amounts of oxygen was slightly less than the stoichiometric value (0.5) in most experiments. However, oxygen was produced at more than 0.5 in low [H(2)O(2)]/[triple bond MnO(2)] (i.e. 3.92 and 9.79). The relative production of hydroperoxide/superoxide anion implied that the production increased with low [H(2)O(2)]/[triple bond MnO(2)], and the existence of anions suggested that the mechanism includes propagation reactions with intermediates such as hydroperoxide/superoxide anion in solution. In addition, both [H(2)O(2)] decomposition and the production of anion were accelerated in alkaline solution. Manganese ion dissolved into solution was negligible in neutral and alkaline conditions, but it greatly increased in acidic conditions.","corpus_id":26095579,"score":2},{"doc_id":"20638494","title":"A highly sensitive hydrogen peroxide amperometric sensor based on MnO2-modified vertically aligned multiwalled carbon nanotubes.","abstract":"In this report, a highly sensitive amperometric sensor based on MnO(2)-modified vertically aligned multiwalled carbon nanotubes (MnO(2)/VACNTs) for determination of hydrogen peroxide (H(2)O(2)) was fabricated by electrodeposition. The morphology of the nanocomposite was characterized by scanning electron microscopy, energy-dispersive X-ray spectrometer and X-ray diffraction. Cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy were applied to investigate the electrochemical properties of the MnO(2)/VACNTs nanocomposite electrode. The mechanism for the electrochemical reaction of H(2)O(2) at the MnO(2)/VACNTs nanocomposite electrode was also discussed. In borate buffer (pH 7.8, 0.20 M), the MnO(2)/VACNTs nanocomposite electrode exhibits a linear dependence (R=0.998) on the concentration of H(2)O(2) from 1.2 x 10(-6)M to 1.8 x 10(-3)M, a high sensitivity of 1.08 x 10(6) microA M(-1) cm(-2) and a detection limit of 8.0 x 10(-7) M (signal/noise=3). Meanwhile, the MnO(2)/VACNTs nanocomposite electrode is also highly resistant towards typical inorganic salts and some biomolecules such as acetic acid, citric acid, uric acid and D-(+)-glucose, etc. In addition, the sensor based on the MnO(2)/VACNTs nanocomposite electrode was applied for the determination of trace of H(2)O(2) in milk with high accuracy, demonstrating its potential for practical application.","corpus_id":205208011,"score":2},{"doc_id":"20875556","title":"A novel nonenzymatic hydrogen peroxide sensor based on MnO2/graphene oxide nanocomposite.","abstract":"A new electrocatalyst, MnO(2)/graphene oxide hybrid nanostructure was successfully synthesized for the nonenzymatic detection of H(2)O(2). The morphological characterization was examined by scanning electron microscopy and transmission electron microscopy. The MnO(2)/graphene oxide based electrodes showed high electrochemical activity for the detection of H(2)O(2) in alkaline medium. The nonenzymatic biosensors displayed good performance along with low working potential, high sensitivity, low detection limit, and long-term stability, which could be attributed to the high surface area of graphene oxide providing for the deposition of MnO(2) nanoparticles. These results demonstrate that this new nanocomposite with the high surface area and electrocatalytic activity offers great promise for new class of nanostructured electrode for nonenzymatic biosensor and energy conversion applications.","corpus_id":11499318,"score":2},{"doc_id":"21229179","title":"Pitfalls in the characterization of nanoporous and nanosized materials.","abstract":"With the advent of highly sophisticated analytical tools, numerous physical methods are nowadays available for comprehensive characterization of inorganic matter and, as special cases, of porous and nanosized materials. Intelligent experimental setup and correct evaluation of the experimental data can provide helpful insights into the chemical and physical properties of such materials. However, scanning of literature reports shows that in many cases evaluation and interpretation of experimental data are erroneous. As a result, the description of a new material can be useless or even worse, misleading. Wrong evaluation is even more critical if mechanistic theories are based on such data. Characterization of porous and/or nanosized materials is mainly performed by gas adsorption, X-ray powder diffraction, electron microscopy and surface spectroscopy. For correct interpretation of experimental data one should be aware of certain pitfalls. The present paper summarizes prominent faults and may show how they can be avoided. It is supposed to provide some hand-on knowledge on correct analysis of materials. Addressed are primarily non-experts and researchers being new to the field of characterization of inorganic nanosized or nanoporous materials.","corpus_id":22847911,"score":2},{"doc_id":"26592586","title":"A novel nonenzymatic amperometric hydrogen peroxide sensor based on CuO@Cu2O nanowires embedded into poly(vinyl alcohol).","abstract":"A new, very simple, rapid and inexpensive nonenzymatic amperometric sensor for hydrogen peroxide (H2O2) detection is proposed. It is based on the immobilization of cupric/cuprous oxide core shell nanowires (CuO@Cu2O-NWs) in a poly(vinyl alcohol) (PVA) matrix directly drop casted on a glassy carbon electrode surface to make a CuO@Cu2O core shell like NWs PVA embedded (CuO@Cu2O-NWs/PVA) sensor. CuO nanowires with mean diameters of 120-170nm and length in the range 2-5μm were grown by a simple catalyst-free thermal oxidation process based on resistive heating of pure copper wires at ambient conditions. The oxidation process of the copper wire surface led to the formation of a three layered structure: a thick Cu2O bottom layer, a CuO thin intermediate layer and CuO nanowires. CuO nanowires were carefully scratched from Cu2O layer with a sharp knife, dispersed into ethanol and sonicated. Then, the NWs were embedded in PVA matrix. The morphological and spectroscopic characterization of synthesized CuO-NWs and CuO@Cu2O-NWs/PVA were performed by transmission electron microscopy (TEM), selected area diffraction pattern (SAD), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) analysis. Moreover a complete electrochemical characterization of these new CuO@Cu2O-NWs/PVA modified glassy carbon electrodes was performed by Cyclic Voltammetry (CV) and Cronoamperometry (CA) in phosphate buffer (pH=7; I=0.2) to investigate the sensing properties of this material against H2O2. The electrochemical performances of proposed sensors as high sensitivity, fast response, reproducibility and selectivity make them suitable for the quantitative determination of hydrogen peroxide substrate in batch analysis.","corpus_id":23399705,"score":2},{"doc_id":"20131606","title":"Remediation of sulfidic wastewater by catalytic oxidation with hydrogen peroxide.","abstract":"Oxidation of sulfide in aqueous solution by hydrogen peroxide was investigated in the presence of hydrated ferric oxide catalyst. The ferric oxide catalyst was synthesized by sol gel technique from ferric chloride and ammonia. The synthesized catalyst was characterized by Fourier transform infrared spectroscopy, X-Ray diffraction analysis, scanning electrom microscope and energy dispersive X-ray analysis. The catalyst was quite effective in oxidizing the sulfide by hydrogen peroxide. The effects of sulfide concentration, catalyst loading, H2O2 dosing and temperature on the kinetics of sulfide oxidation were investigated. Kinetic equations and activation energies for the catalytic oxidation reaction were calculated based on the experimental results.","corpus_id":10179383,"score":1},{"doc_id":"21507410","title":"Porous magnetic manganese oxide nanostructures: synthesis and their application in water treatment.","abstract":"Magnetic manganese oxide nanostructures are fabricated at room temperature by mixing a KMnO(4) solution and oleic acid capped Fe(3)O(4) particles. Oleic acid molecules capped Fe(3)O(4) particles are oxidized by potassium permanganate (KMnO(4)) in an aqueous solution to produce porous magnetic manganese oxide nanostructures. The synthesis technique can be extended to other MnO(x) structures with composition of different nanocrystals, such as quantum dots, noble metal crystals which may have important applications as catalysts, adsorbents, electrodes and advanced materials in many scientific disciplines. Transmission electron microscopy, energy-dispersive X-ray spectroscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray powder diffraction, Fourier transform infrared spectroscopy, and nitrogen adsorption-desorption measurements are employed to characterize the structures. As an adsorbent in water treatment, the nanostructures possess a large adsorption capability and high organic pollutant removal rates due to the large surface area and pore volume. The nanostructures are recyclable as their adsorption capability can be recovered by combustion. Furthermore, the strong magnetism exhibited by the structures provides an easy and efficient separation means in wastewater treatment under an external magnetic field.","corpus_id":13704751,"score":1},{"doc_id":"21817483","title":"Two-dimensional manganese oxide nanolayers on Pd(100): the surface phase diagram.","abstract":"Two-dimensional manganese oxide layers have been grown on Pd(100) and have been characterized by means of scanning tunnelling microscopy, low energy electron diffraction and x-ray photoelectron spectroscopy (XPS). The complex surface phase diagram of MnO(x) on Pd(100) is reported, where nine different novel Mn oxide phases have been detected as a function of the chemical potential of oxygen μ(O). Three regions of the chemical potential of oxygen can be identified, in which structurally related oxide phases are formed, often in coexistence at the surface. The different regions of μ(O) are reflected in the oxidation states of the respective Mn oxide nanolayers as revealed by the Mn 2p and O 1s XPS binding energies. The MnO(x) nanolayers form two-dimensional wetting layers and it is speculated that they mediate the epitaxial growth of MnO on Pd(100) by providing structurally graded interfaces.","corpus_id":21321142,"score":1},{"doc_id":"22413904","title":"Manganese oxides with rod-, wire-, tube-, and flower-like morphologies: highly effective catalysts for the removal of toluene.","abstract":"Nanosized rod-like, wire-like, and tubular α-MnO(2) and flower-like spherical Mn(2)O(3) have been prepared via the hydrothermal method and the CCl(4) solution method, respectively. The physicochemical properties of the materials were characterized using numerous analytical techniques. The catalytic activities of the catalysts were evaluated for toluene oxidation. It is shown that α-MnO(2) nanorods, nanowires, and nanotubes with a surface area of 45-83 m(2)/g were tetragonal in crystal structure, whereas flower-like spherical Mn(2)O(3) with a surface area of 162 m(2)/g was of cubic crystal structure. There were the presence of surface Mn ions in multiple oxidation states (e.g., Mn(3+), Mn(4+), or even Mn(2+)) and the formation of surface oxygen vacancies. The oxygen adspecies concentration and low-temperature reducibility decreased in the order of rod-like α-MnO(2) > tube-like α-MnO(2) > flower-like Mn(2)O(3) > wire-like α-MnO(2), in good agreement with the sequence of the catalytic performance of these samples. The best-performing rod-like α-MnO(2) catalyst could effectively catalyze the total oxidation of toluene at lower temperatures (T(50%) = 210 °C and T(90%) = 225 °C at space velocity = 20,000 mL/(g h)). It is concluded that the excellent catalytic performance of α-MnO(2) nanorods might be associated with the high oxygen adspecies concentration and good low-temperature reducibility. We are sure that such one-dimensional well-defined morphological manganese oxides are promising materials for the catalytic elimination of air pollutants.","corpus_id":34503295,"score":1},{"doc_id":"24054675","title":"Te oxide nanowires as advanced materials for amperometric nonenzymatic hydrogen peroxide sensing.","abstract":"A new nonenzymatic platinum Te oxide nanowires modified electrode (Pt/TeO2-NWs) for amperometric detection of hydrogen peroxide (H2O2) is proposed. The modified electrode has been developed by direct drop casting, with TeO2 nanowires (TeO2-NWs), synthesized by thermal evaporation of Te(0) in an oxygen atmosphere. The morphological and spectroscopic characterization of the TeO2-NWs as synthesized on Pt foil was performed by scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis. XPS and XRD analyses are especially involved to gain information on the chemical environment of TeO2-NWs in contact with Pt surface. Moreover electrochemical characterization of these new modified Pt/TeO2-NWs modified electrodes was performed by Cyclic Voltammetry (CV) and Cronoamperometry (CA) in phosphate buffer (pH=7; I=0.2) to investigate the sensing properties of this material against H2O2. The proposed sensor exhibits a wide linear and dynamic range from 2 µM to 16 mM (R(2)=0.9998) and the detection limit is estimated to be 0.6 µM (S/N=3). Moreover, this sensor shows a rapid amperometric response time of less than 5s and possessed good reproducibility. These results indicate that Pt/TeO2-NWs composite is suitable to be used as material for sensing applications.","corpus_id":34526200,"score":1},{"doc_id":"26109374","title":"Sewage-sludge-derived carbonaceous materials for catalytic wet hydrogen peroxide oxidation of m-cresol in batch and continuous reactors.","abstract":"In this study, four sewage-sludge-derived carbonaceous materials (SWs) were evaluated for their catalytic wet hydrogen peroxide oxidation (CWPO) performance of m-cresol in batch reactor and continuous reactor, respectively. The SWs were produced by carbonization (SW); carbonization with the addition of CaO (CaO-SW); HNO3 pretreatment (HNO3-SW) and steam activation (Activated-SW). The properties of SW catalysts were assessed by thermogravimetric analysis, Brunauer-Emmett-Teller, Fourier Transform Infrared Spectroscopy, X-ray Fluorescence, Scanning electron microscopy, energy dispersive X-ray analysis and zeta potential. The results showed that SW treated by HNO3 (HNO3-SW) had a high conversion of m-cresol in batch reactor and continuous reactor, respectively. Under the conditions of batch reaction (Cm-cresol = 100 mg L(-1), CH2O2 = 15.7 mmol L(-1), initial pH=7.0, 0.5 g L(-1) catalyst, 80°C, 180 min adsorption and 210 min oxidation), the conversion of m-cresol reached 100% and total organic carbon removal was 67.1%. It had a high catalytic activity and stability on the treatment of m-cresol in CWPO for more than 1100 h. Furthermore, a possible reaction mechanism for the oxidation of m-cresol to 2-methyl-p-benzoquinone by CWPO was proposed.","corpus_id":21598655,"score":1},{"doc_id":"29175960","title":"Silver-palladium catalysts for the direct synthesis of hydrogen peroxide.","abstract":"A series of bimetallic silver-palladium catalysts supported on titania were prepared by wet impregnation and assessed for the direct synthesis of hydrogen peroxide, and its subsequent side reactions. The addition of silver to a palladium catalyst was found to significantly decrease hydrogen peroxide productivity and hydrogenation, but crucially increase the rate of decomposition. The decomposition product, which is predominantly hydroxyl radicals, can be used to decrease bacterial colonies. The interaction between silver and palladium was characterized using scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and temperature programmed reduction (TPR). The results of the TPR and XPS indicated the formation of a silver-palladium alloy. The optimal 1% Ag-4% Pd/TiO2 bimetallic catalyst was able to produce approximately 200 ppm of H2O2 in 30 min. The findings demonstrate that AgPd/TiO2 catalysts are active for the synthesis of hydrogen peroxide and its subsequent decomposition to reactive oxygen species. The catalysts are promising for use in wastewater treatment as they combine the disinfectant properties of silver, hydrogen peroxide production and subsequent decomposition. This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.","corpus_id":4663319,"score":1},{"doc_id":"18459091","title":"Gas storage in nanoporous materials.","abstract":"Gas storage in solids is becoming an ever more important technology, with applications and potential applications ranging from energy and the environment all the way to biology and medicine. Very highly porous materials, such as zeolites, carbon materials, polymers, and metal-organic frameworks, offer a wide variety of chemical composition and structural architectures that are suitable for the adsorption and storage of many different gases, including hydrogen, methane, nitric oxide, and carbon dioxide. However, the challenges associated with designing materials to have sufficient adsorption capacity, controllable delivery rates, suitable lifetimes, and recharging characteristics are not trivial in many instances. The different chemistry associated with the various gases of interest makes it necessary to carefully match the properties of the porous material to the required application.","corpus_id":31145843,"score":0},{"doc_id":"18786680","title":"Synthesis, characterization, and catalytic activity of cryptomelane nanomaterials produced with industrial manganese sulfate.","abstract":"Industrial manganese sulfate from manganese mines has been utilized to synthesize cryptomelane in a simple and feasible route. K-birnessite precursor was prepared by air oxidation of the mixture of MnSO4 and KOH solutions under alkaline conditions, and then transformed to cryptomelane under a heating process. The effects of OH- concentration, airflow rate, liquid reaction temperature, stirring rate, liquid reaction time, washing condition, calcination time, and temperature were investigated. X-ray diffraction (XRD), scanning electron microscopy (SEM), and high-resolution transmission electron microscopy (HRTEM) revealed that cryptomelane prepared under optimal conditions had a tetragonal symmetry and the particles were mostly in short lathy form with sizes of 20-30 nm. The average pore size and BET surface area of cryptomelane examined by N2 adsorption methods were 24.15 nm and 32.21 m2/g, respectively. X-ray photoelectron spectroscopy (XPS) studies demonstrated that the average oxidation state of manganese in cryptomelane was about 3.9 in comparison with prephase K-birnessite of 3.4. The synthesized cryptomelane sample showed improved catalytic activity for decomposition of hydrogen peroxide as compared with natural cryptomelane, but lower than those synthesized with hydrothermal and sol-gel methods. The results of this investigation will provide fundamental information for developing a large-scale production process for transforming manganese sulfate to cryptomelane.","corpus_id":35572913,"score":0},{"doc_id":"19082020","title":"Hydrogen-rich boron-containing materials for hydrogen storage.","abstract":"Hydrogen-rich boron-containing compounds have received extensive attention as potential hydrogen storage media for vehicular applications. The past years have seen significant progresses in material discovery, material composition/structure tailoring, catalyst identification and regeneration chemistry, which give rise to state-of-the-art hydrogen storage materials/technologies. Lithium tetrahydroborate-related materials exhibit the hitherto highest reversible hydrogen capacity via solid-gas reactions. Catalytic hydrolysis of sodium tetrahydroborate offers an on-demand hydrogen generation system for vehicular applications. Ammonia borane-related materials exhibit a satisfactory combination of material properties that are suited for on-board hydrogen sources, coupled with significant advances in spent fuels regeneration. This Perspective discusses the current progresses of these representative reversible or irreversible material systems, aiming at providing an outline of the forefront of hydrogen storage materials/technologies for transportation applications.","corpus_id":205713742,"score":0},{"doc_id":"19178167","title":"Green decomposition of organic dyes using octahedral molecular sieve manganese oxide catalysts.","abstract":"The catalytic degradation of organic dye (methylene blue, MB) has been studied using green oxidation methods (tertiary-butyl hydrogen peroxide, TBHP, as the oxidant with several doped mixed-valent and regular manganese oxide catalysts in water) at room and higher temperatures. These catalysts belong to a class of porous manganese oxides known as octahedral molecular sieves (OMS). The most active catalysts were those of Mo(6+)- and V(5+)-doped OMS. Rates of reaction were found to be first-order with respect to the dye. TBHP has been found to enhance the MB decomposition, whereas H(2)O(2) does not. Reactions were studied at pH 3-11. The optimum pH for these reactions was pH 3. Dye-decomposing activity was proportional to the amount of catalyst used, and a significant increase in catalytic activity was observed with increasing temperature. X-ray diffraction (XRD), energy dispersive spectroscopy (EDX), and thermogravimetric analysis (TGA) studies showed that no changes in the catalyst structure occurred after the dye-degradation reaction. The products as analyzed by electrospray ionization mass spectrometry (ESI-MS) showed that MB was successively decomposed through different intermediate species.","corpus_id":5886164,"score":0},{"doc_id":"19778036","title":"Bacteriogenic manganese oxides.","abstract":"Microorganisms control the redox cycling of manganese in the natural environment. Although the homogeneous oxidation of Mn(II) to form manganese oxide minerals is slow, solid MnO(2) is the stable form of manganese in the oxygenated portion of the biosphere. Diverse bacteria and fungi have evolved the ability to catalyze this process, producing the manganese oxides found in soils and sediments. Other bacteria have evolved to utilize MnO(2) as a terminal electron acceptor in respiration. This Account summarizes the properties of Mn oxides produced by bacteria (bacteriogenic MnO(2)) and our current thinking about the biochemical mechanisms of bacterial Mn(II) oxidation. According to X-ray absorption spectroscopy and X-ray scattering studies, the MnO(2) produced by bacteria consists of stacked hexagonal sheets of MnO(6) octahedra, but these particles are extremely small and have numerous structural defects, particularly cation vacancies. The defects provide coordination sites for binding exogenous metal ions, which can be adsorbed to a high loading. As a result, bacterial production of MnO(2) influences the bioavailability of these metals in the natural environment. Because of its high surface area and oxidizing power, bacteriogenic MnO(2) efficiently degrades biologically recalcitrant organic molecules to lower-molecular-mass compounds, spurring interest in using these properties in the bioremediation of xenobiotic organic compounds. Finally, bacteriogenic MnO(2) is reduced to soluble Mn(II) rapidly in the presence of exogenous ligands or sunlight. It can therefore help to regulate the bioavailability of Mn(II), which is known to protect organisms from superoxide radicals and is required to assemble the water-splitting complex in photosynthetic organisms. Bioinorganic chemists and microbiologists have long been interested in the biochemical mechanism of Mn(IV) oxide production. The reaction requires a two-electron oxidation of Mn(II), but genetic and biochemical evidence for several bacteria implicate multicopper oxidases (MCOs), which are only known to engage one-electron transfers from substrate to O(2). In experiments with the exosporium of a Mn(II)-oxidizing Bacillus species, we could trap the one-electron oxidation product, Mn(III), as a pyrophosphate complex in an oxygen-dependent reaction inhibited by azide, consistent with MCO catalysis. The Mn(III) pyrophosphate complex can further act as a substrate, reacting in the presence of the exosporium to produce Mn(IV) oxide. Although this process appears to be unprecedented in biology, it is reminiscent of the oxidation of Fe(II) to form Fe(2)O(3) in the ferritin iron storage protein. However, it includes a critical additional step of Mn(III) oxidation or disproportionation. We shall continue to investigate this biochemically unique process with purified enzymes.","corpus_id":206829100,"score":0},{"doc_id":"20067294","title":"Mesoporous MnO2/carbon aerogel composites as promising electrode materials for high-performance supercapacitors.","abstract":"MnO(2) as one of the most promising candidates for electrochemical supercapacitors has attracted much attention because of its superior electrochemical performance, low cost, and environmentally benign nature. In this Letter, we explored a novel route to prepare mesoporous MnO(2)/carbon aerogel composites by electrochemical deposition assisted by gas bubbles. The products were characterized by energy-dispersive spectrometry (EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The MnO(2) deposits are found to have high purity and have a mesoporous structure that will optimize the electronic and ionic conductivity to minimize the total resistance of the system and thereby maximize the performance characteristics of this material for use in supercapacitor electrodes. The results of nitrogen adsorption-desorption experiments and electrochemical measurements showed that these obtained mesoporous MnO(2)/carbon aerogel composites had a large specific surface area (120 m(2)/g), uniform pore-size distribution (around 5 nm), high specific capacitance (515.5 F/g), and good stability over 1000 cycles, which give these composites potential application as high-performance supercapacitor electrode materials.","corpus_id":7988690,"score":0},{"doc_id":"20449456","title":"Comparative study of the catalytic activity of [Mn(II)(bpy)2Cl2] and [Mn2(III/IV)(mu-O)2(bpy)4](ClO4)3 in the H2O2 induced oxidation of organic dyes in carbonate buffered aqueous solution.","abstract":"The kinetics of the hydrogen peroxide induced oxidative degradation of the azo dye Orange II in aqueous carbonate buffered solution were studied for the oxo-bridged [Mn(2)(III/IV)(mu-O)(2)(bpy)(4)](ClO(4))(3) complex and its mononuclear analogue [Mn(II)(bpy)(2)Cl(2)] as catalysts to reveal the underlying reaction mechanism and reactive intermediates participating in the catalytic cycle. Both catalysts show identical oxidative reactivity when used at equimolar manganese concentration. If a simple Mn(II) salt and a 1 : 2 concentration of bipyridine are added to the substrate and oxidant containing reaction mixture, the same oxidative reactivity as found for both readily prepared catalysts was observed for several investigated substrates. This demonstrates the in situ accessibility of a reactive intermediate and its precursor complex. The crucial role of bicarbonate as co-catalyst was studied. The distinct dependence of the observed rate constant for the oxidation reaction on the total carbonate concentration can be accounted for in terms of in situ generation of peroxycarbonate. EPR and rapid scan UV/Vis measurements of the reaction of hydrogen peroxide in carbonate buffered solution with [Mn(2)(III/IV)(mu-O)(2)(bpy)(4)](ClO(4))(3) and [Mn(II)(bpy)(2)Cl(2)], revealed for both catalysts the presence of monomeric Mn(II) and Mn(IV)-oxo species as the main intermediates. The proposed reaction mechanism involves two-electron oxidation of a mononuclear Mn(II) precursor complex to a high-valent Mn(IV)=O intermediate as catalytically active species. Differences in the activity of in situ prepared catalyst precursors of different metal to ligand ratios are reported. The 1 : 2 complex was found to be the catalytically more active precursor for the oxidation of the selected substrates, whereas the 1 : 3 complex rather catalyzed the disproportion of hydrogen peroxide.","corpus_id":34050042,"score":0},{"doc_id":"21138016","title":"Hydrothermal-reduction synthesis of manganese oxide nanomaterials for electrochemical supercapacitors.","abstract":"In the present work, amorphous manganese oxide nanomaterials have been synthesized by a common hydrothermal method based on the redox reaction between MnO4(-) and Fe(2+) under an acidic condition. The synthesized MnO2 samples were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and electrochemical studies. XRD results showed that amorphous manganese oxide phase was obtained. XPS quantitative analysis revealed that the atomic ratio of Mn to Fe was 3.5 in the MnO2 samples. TEM images showed the porous structure of the samples. Electrochemical properties of the MnO2 electrodes were studied using cyclic voltammetry and galvanostatic charge-discharge cycling in 1 M Na2SO4 aqueous electrolyte, which showed excellent pseudocapacitance properties. A specific capacitance of 192 Fg(-1) at a current density of 0.5 Ag(-1) was obtained at the potential window from -0.1 to 0.9 V (vs. SCE).","corpus_id":22023474,"score":0},{"doc_id":"21258687","title":"The structure and catalytic activity of anatase and rutile titania supported manganese oxide catalysts for selective catalytic reduction of NO by NH3.","abstract":"The structure and catalytic properties of anatase and rutile supported manganese oxide catalysts prepared by impregnation method have been studied by using X-ray diffraction (XRD), laser Raman spectroscopy (LRS), X-ray photoelectron spectroscopy (XPS), H(2) temperature-programmed reduction (H(2)-TPR) and BET surface area measurements combined with activity testing of selective catalytic reduction (SCR) of NO by NH(3). It has been shown that the manganese oxide loadings on the two TiO(2) supports exert great influences on the SCR activity. For the rutile supported manganese oxide catalysts, increasing manganese oxide loading leads to the increase of reducibility of dispersed manganese oxide species and the rate constant k, which reaches a maximum around 9.6 × 10(-6) mol g(Mn)(-1) s(-1) at 0.5 mmol Mn per 100 m(2) TiO(2). When the manganese oxide loading is beyond this value, the existence of amorphous MnO(x) multiple layers will certainly reduce the ratio of manganese oxide species exposed on the surface and the reducibility of dispersed manganese oxide species, resulting in the rapid decrease of rate constant k. The LRS and XPS results have revealed that for the anatase supported manganese oxide catalysts manganese oxide species exist in Mn(+4) as a major species with Mn(+3) species and partially undecomposed Mn-nitrate as the minor species. Under the SCR reaction conditions, Mn(+3) species on anatase are oxidized to Mn(+4) species, inserting in the surface of anatase and promoting the anatase-to-rutile transformation in the surface layers of the anatase support. Since these Mn(4+) cations are actually dispersed on the support with a rutile shell-anatase core structure and its concentration is very near to that of MnO(x)/TiO(2) (R) catalyst, the relation between the rate constant k and the MnO(x) loading on the anatase support is similar to that on the rutile support, and that the rate constant k values for anatase and rutile supported manganese oxide catalysts are very close at the same MnO(x) loading.","corpus_id":21173218,"score":0},{"doc_id":"21380431","title":"Epoxidation of alkenes and oxidation of alcohols with hydrogen peroxide catalyzed by a manganese(V) nitrido complex.","abstract":"The manganese(V) nitrido complex (PPh(4))(2)[Mn(N)(CN)(4)] is an active catalyst for alkene epoxidation and alcohol oxidation using H(2)O(2) as an oxidant. The catalytic oxidation is greatly enhanced by the addition of just one equivalent of acetic acid. The oxidation of ethene by this system has been studied computationally by the DFT method.","corpus_id":20825316,"score":0},{"doc_id":"21966674","title":"Oxidative desulfurization of dibenzothiophene with hydrogen peroxide catalyzed by selenium(IV)-containing peroxotungstate.","abstract":"With stoichiometric H(2)O(2) as oxidant, dibenzothiophene (DBT) is oxidized to its corresponding sulfone with high efficiency, catalyzed by a sub-valence heteronuclear peroxotungstate, [C(18)H(37)N(CH(3))(3)](4)[H(2)Se(IV)(3)W(6)O(34)], under mild biphase conditions and the catalyst shows remarkable selectivity of catalytic oxidation towards DBT, cinnamyl alcohol and quinoline.","corpus_id":43220431,"score":0},{"doc_id":"22040038","title":"Application of XPS and solution chemistry analyses to investigate soluble manganese removal by MnO(x)(s)-coated media.","abstract":"X-ray photoelectron spectroscopy (XPS) was applied to investigate Mn(II) removal by MnO(x)(s)-coated media under experimental conditions similar to the engineered environment of drinking water treatment plants in the absence and presence of chlorine. Macroscopic and spectroscopic results suggest that Mn(II) removal at pH 6.3 and pH 7.2 in the absence of chlorine was mainly due to adsorption onto the MnO(x)(s) surface coating, while removal in the presence of chlorine was due to a combination of initial surface adsorption followed by subsequent surface-catalyzed oxidation. However, Mn(III) was identified by XPS analyses of the Mn 3p photoline for experiments performed in the absence of chlorine at pH 6.3 and pH 7.2, suggesting that surface-catalyzed Mn oxidation also occurred at these conditions. Results obtained at pH 8.2 at 8 and 0.5 mg·L(-1) dissolved oxygen in the absence of chlorine suggest that Mn(II) removal was mainly due to initial adsorption followed by surface-catalyzed oxidation. XPS analyses suggest that Mn(IV) was the predominant species in experiments operated in the presence of chlorine. This study confirms that the use of chlorine combined with the catalytic action of MnO(x)(s) oxides is effective for Mn(II) removal from drinking water filtration systems.","corpus_id":23766823,"score":0},{"doc_id":"22309023","title":"Impact of interactions between metal oxides to oxidative reactivity of manganese dioxide.","abstract":"Manganese oxides typically exist as mixtures with other metal oxides in soil-water environments; however, information is only available on their redox activity as single oxides. To bridge this gap, we examined three binary oxide mixtures containing MnO(2) and a secondary metal oxide (Al(2)O(3), SiO(2) or TiO(2)). The goal was to understand how these secondary oxides affect the oxidative reactivity of MnO(2). SEM images suggest significant heteroaggregation between Al(2)O(3) and MnO(2) and to a lesser extent between SiO(2)/TiO(2) and MnO(2). Using triclosan and chlorophene as probe compounds, pseudofirst-order kinetic results showed that Al(2)O(3) had the strongest inhibitory effect on MnO(2) reactivity, followed by SiO(2) and then TiO(2). Al(3+) ion or soluble SiO(2) had comparable inhibitory effects as Al(2)O(3) or SiO(2), indicating the dominant inhibitory mechanism was surface complexation/precipitation of Al/Si species on MnO(2) surfaces. TiO(2) inhibited MnO(2) reactivity only when a limited amount of triclosan was present. Due to strong adsorption and slow desorption of triclosan by TiO(2), precursor-complex formation between triclosan and MnO(2) was much slower and likely became the new rate-limiting step (as opposed to electron transfer in all other cases). These mechanisms can also explain the observed adsorption behavior of triclosan by the binary oxide mixtures and single oxides.","corpus_id":7911746,"score":0},{"doc_id":"22341981","title":"Effect of precursor and preparation method on manganese based activated carbon sorbents for removing H2S from hot coal gas.","abstract":"Activated carbon (AC) supported manganese oxide sorbents were prepared by the supercritical water impregnation (SCWI) using two different precursor of Mn(NO(3))(2) (SCW(N)) and Mn(Ac)(2)·4H(2)O (SCW(A)). Their capacities of removing H(2)S from coal gas were evaluated and compared to the sorbents prepared by the pore volume impregnation (PVI) method. The structure and composition of different sorbents were characterized by XRD, SEM, TEM, XPS and XANES techniques. It is found that the precursor of active component plays the crucial role and SCW(N) sorbents show much better sulfidation performance than the SCW(A) sorbents. This is because the Mn(3)O(4) active phase of the SCW(N) sorbents are well dispersed on the AC support, while the Mn(2)SiO(4)-like species in the SCW(A) sorbent can be formed and seriously aggregated. The SCW(N) sorbents with 2.80% and 5.60% manganese are favorable for the sulfidation reaction, since the Mn species are better dispersed on the SCW(N) sorbents than those on the PV(N) sorbents and results in the better sulfidation performance of the SCW(N) sorbents. As the Mn content increases to 11.20%, the metal oxide particles on AC supports aggregate seriously, which leads to poorer sulfidation performance of the SCW(N)11.20% sorbents than that of the PV(N)11.20% sorbents.","corpus_id":11495435,"score":0},{"doc_id":"22579460","title":"Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion.","abstract":"The aim of this work was to study combustion of toluene (1000ppm) over MnO(2) modified with different supports. α-Al(2)O(3) and γ-Al(2)O(3) obtained from Boehmite, γ-Al(2)O(3) (commercial), SiO(2), TiO(2) and ZrO(2) were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO(2) was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO(2)/α-Al(2)O(3)(B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289°C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity.","corpus_id":37497640,"score":0},{"doc_id":"22592889","title":"One-step sonochemical synthesis of a graphene oxide-manganese oxide nanocomposite for catalytic glycolysis of poly(ethylene terephthalate).","abstract":"Ultrasound-assisted synthesis of a graphene oxide (GO)-manganese oxide nanocomposite (GO-Mn(3)O(4)) was conducted without further modification of GO or employing secondary materials. With the GO nanoplate as a support, potassium permanganate oxidizes the carbon atoms in the GO support and gets reduced to Mn(3)O(4). An intensive ultrasound method could reduce the number of reaction steps and temperature, enhance the reaction rate and furthermore achieve a Mn(3)O(4) phase. The composite was characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and thermogravimetric analysis (TGA). The coverage and crystallinity of Mn(3)O(4) were controlled by changing the ratio of permanganate to GO dispersion. The synthesized nanocomposite was used as a catalyst for poly(ethylene terephthalate) (PET) depolymerization into its monomer, bis(2-hydroxylethyl) terephthalate (BHET). The highest monomer yield of 96.4% was obtained with the nanocomposite containing the lowest amount of Mn(3)O(4), while PET glycolysis with the Mn(3)O(4) without GO yielded 82.7% BHET.","corpus_id":9789438,"score":0},{"doc_id":"22723249","title":"Degradation of ciprofloxacin by cryptomelane-type manganese(III/IV) oxides.","abstract":"The objective of this study is to investigate and understand the oxidizing properties of a manganese oxide, specifically synthetic cryptomelane (KMn(8)O(16)) and its derivatives, in aqueous solution. Ciprofloxacin (CIP), a commonly used fluoroquinolone antibiotic, was used as the probe. Synthetic cryptomelane, known as octahedral molecular sieves (OMS-2), was synthesized, and its derivatives were prepared by adding transition metal oxides, V(2)O(5) or MoO(3), as dopants during synthesis. The solids were characterized by x-ray powder diffraction (XRD), SEM-energy-dispersive spectrometry (SEM-EDX), x-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectra (FTIR), Raman spectra, and N(2)-Brunauer-Emmett-Teller method. Degradation of CIP by different doped OMS-2 was carried out. Process conditions were optimized using response surface methodology (RSM). XRD patterns indicated the crystal phase of regular and doped OMS-2 as the cryptomelane type. Presence of the dopants in doped cryptomelane was confirmed by SEM-EDX and XPS. FTIR and Raman results suggested that the dopants were substituted into the framework in place of manganese. SEM images, XRD analysis, and surface area analysis of doped OMS-2 indicated decreased particle size, decreased crystallinity, and increased surface area compared to regular OMS-2. Higher oxidizing reactivity of doped OMS-2 was also observed with increased CIP removal rates from aqueous solution. The enhancement of reactivity may be due to the increase of surface areas. Nine percent Mo/OMS-2, the most effective oxidant of all synthesized derivatives, was selected for optimization study. Favorable treatment conditions were obtained using RSM at pH 3 with molar ratio [9 % Mo/OMS-2]/[CIP] ≥ 50. Under such conditions, more than 90 % CIP can be removed in 30 min. The degradation kinetics was modeled by a modified first order rate with introduction of a retardation factor-α (R (2) > 0.98). Analysis of degradation products indicated that oxidation takes place mainly on the piperazine ring of CIP.","corpus_id":7246185,"score":0},{"doc_id":"22806229","title":"Nano-sized manganese oxide: a proposed catalyst for water oxidation in the reaction of some manganese complexes and cerium(IV) ammonium nitrate.","abstract":"According to UV-visible spectroscopy, X-ray diffraction spectrometry, dynamic light scattering, Fourier transform infrared spectroscopy, electron paramagnetic resonance spectroscopy, transmission electron microscopy, scanning electron microscopy and X-ray photoelectron spectroscopy, nano-sized manganese oxides are proposed as active catalysts for water oxidation in the reaction of some manganese complexes and cerium(IV) ammonium nitrate.","corpus_id":13332578,"score":0},{"doc_id":"22948163","title":"Glucose-promoted Zn-based metal-organic framework/graphene oxide composites for hydrogen sulfide removal.","abstract":"Zinc-based metal-organic frameworks/graphene oxide (MOF-5/GO) composites were synthesized via the solvothermal method. The materials were characterized by scanning electron microscopy (SEM), nitrogen adsorption, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS), and their performances for hydrogen sulfide (H(2)S) removal were evaluated by dynamic testing at room temperature. The composites exhibit microporous structure with a small amount of mesopores, and the structure is highly dependent on the amount of GO loaded. The surface area and pore volume first increase and then decrease with increasing GO, reaching the maximum value when the GO ratio is 5.25%. The composites exhibit high adsorption capacities for H(2)S, with the maximum uptakes reaching up to 130.1 mg/g. Although the loading of GO makes a contribution to the enhancement of dispersive force in the porous structure, it leads to the crystal distortion of MOF-5. The introduction of glucose can restrain this distortion to maintain the structure stability. A good match between GO and glucose have a well synergy effect to develop the porous structure, resulting in the highest H(2)S adsorption capacity.","corpus_id":20582109,"score":0},{"doc_id":"23050871","title":"Chromium(III) oxidation by three poorly-crystalline manganese(IV) oxides. 1. Chromium(III)-oxidizing capacity.","abstract":"The Cr(III)-oxidizing capacity of three layered poorly crystalline Mn(IV)O(2) phases, i.e. δ-MnO(2), Random Stacked Birnessite (RSB), and Acid Birnessite (AB), was determined in real-time and in situ, using Quick X-ray Absorption Fine Structure Spectroscopy (Q-XAFS). The results obtained with this technique, which allows the measurement of the total amount of Cr(VI) produced in the system, indicated that the Cr(III) oxidation reaction had ceased between 30 min and 1 h under most experimental conditions. However, this cessation was not observed with a traditional batch technique, which only allows the measurement of Cr(VI) present in solution and thus neglects the amount of Cr(VI) that may be sorbed to Mn(IV)O(2). This study also demonstrated that the Mn(IV)O(2) phase oxidizing the highest amount of Cr(III), which is positively charged in solution, was the mineral featuring the most negatively charged surface. Also, the results indicated that the presence of Mn(II) and/or Mn(III) impurities inside the Mn(IV)O(2) structure could enhance the mineral's capacity to oxidize Cr(III). The information provided in this study will be useful in predicting the capabilities of naturally occurring Mn oxide minerals, which are similar to the three synthetic Mn(IV)O(2) investigated, to oxidize Cr(III) to toxic and mobile Cr(VI) in the soil of contaminated sites.","corpus_id":206960974,"score":0},{"doc_id":"23143326","title":"Preparation of materials in the presence of hydrogen peroxide: from discrete or \"zero-dimensional\" objects to bulk materials.","abstract":"Based on selected examples from the literature, this perspective aims to provide a short overview of synthetic methods using hydrogen peroxide and/or peroxidic species for the elaboration of discrete or zero-dimensional species, as well as mono-, bi- and tri-dimensional materials. There are several advantages in using peroxidic species: no foreign ion or organic ligand is introduced in the reaction medium, they are relatively cheap compared to costly alkoxides, for example, and in certain favorable cases these methods allow the selective formation of a given oxide polymorph. The materials prepared are used in several important technological applications such as electrochromism, gas sensing and electrochemistry but, in this review, special emphasis is placed on oxidation catalysis. Indeed, the deposition of peroxo species on or into oxide supports generally leads to catalytic materials that display higher activities related to a better dispersion of the active metal species in the host matrix. This review also focuses on the use of hydrogen peroxide for the recycling of toxic metal-containing spent materials such as those found in batteries for portable electronic devices.","corpus_id":205820362,"score":0},{"doc_id":"23249159","title":"Hole doping in Al-containing nickel oxide materials to improve electrochromic performance.","abstract":"Electrochromic materials exhibit switchable optical properties that can find applications in various fields, including smart windows, nonemissive displays, and semiconductors. High-performing nickel oxide electrochromic materials have been realized by controlling the material composition and tuning the nanostructural morphology. Post-treatment techniques could represent efficient and cost-effective approaches for performance enhancement. Herein, we report on a post-processing ozone technique that improves the electrochromic performance of an aluminum-containing nickel oxide material in lithium-ion electrolytes. The resulting materials were studied using X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible-near-infrared (UV-vis-NIR) spectroscopy, and X-ray absorption spectroscopy (XAS). It was observed that ozone exposure increased the Ni oxidation state by introducing hole states in the NiO(6) octahedral unit. In addition, ozone exposure gives rise to higher-performing aluminum-containing nickel oxide films, relative to nickel oxide containing both Al and Li, in terms of switching kinetics, bleached-state transparency, and optical modulation. The improved performance is attributed to the decreased crystallinity and increased nickel oxidation state in aluminum-containing nickel oxide electrochromic films. The present study provides an alternative route to improve electrochromic performance for nickel oxide materials.","corpus_id":35402783,"score":0},{"doc_id":"23286528","title":"Unique properties of ceria nanoparticles supported on metals: novel inverse ceria/copper catalysts for CO oxidation and the water-gas shift reaction.","abstract":"Oxides play a central role in important industrial processes, including applications such as the production of renewable energy, remediation of environmental pollutants, and the synthesis of fine chemicals. They were originally used as catalyst supports and were thought to be chemically inert, but now they are used to build catalysts tailored toward improved selectivity and activity in chemical reactions. Many studies have compared the morphological, electronic, and chemical properties of oxide materials with those of unoxidized metals. Researchers know much less about the properties of oxides at the nanoscale, which display distinct behavior from their bulk counterparts. More is known about metal nanoparticles. Inverse-model catalysts, composed of oxide nanoparticles supported on metal or oxide substrates instead of the reverse (oxides supporting metal nanoparticles), are excellent tools for systematically testing the properties of novel catalytic oxide materials. Inverse models are prepared in situ and can be studied with a variety of surface science tools (e.g. scanning tunneling microscopy, X-ray photoemission spectroscopy, ultraviolet photoemission spectroscopy, low-energy electron microscopy) and theoretical tools (e.g. density functional theory). Meanwhile, their catalytic activity can be tested simultaneously in a reactor. This approach makes it possible to identify specific functions or structures that affect catalyst performance or reaction selectivity. Insights gained from these tests help to tailor powder systems, with the primary objective of rational design (experimental and theoretical) of catalysts for specific chemical reactions. This Account describes the properties of inverse catalysts composed of CeOx nanoparticles supported on Cu(111) or CuOx/Cu(111) as determined through the methods described above. Ceria is an important material for redox chemistry because of its interchangeable oxidation states (Ce⁴⁺ and Ce³⁺). Cu(111), meanwhile, is a standard catalyst for reactions such as CO oxidation and the water-gas shift (WGS). This metal serves as an ideal replacement for other noble metals that are neither abundant nor cost effective. To prepare the inverse system we deposited nanoparticles (2-20 nm) of cerium oxide onto the Cu(111) surface. During this process, the Cu(111) surface grows an oxide layer that is characteristic of Cu₂O (Cu¹⁺). This oxide can influence the growth of ceria nanoparticles. Evidence suggests triangular-shaped CeO₂(111) grows on Cu₂O(111) surfaces while rectangular CeO₂(100) grows on Cu₄O₃(111) surfaces. We used the CeOx/Cu₂O/Cu(111) inverse system to study two catalytic processes: the WGS (CO + H₂O → CO₂ + H₂) and CO oxidation (2CO + O₂ → 2CO₂). We discovered that the addition of small amounts of ceria nanoparticles can activate the Cu(111) surface and achieve remarkable enhancement of catalytic activity in the investigated reactions. In the case of the WGS, the CeOx nanoparticle facilitated this process by acting at the interface with Cu to dissociate water. In the CO oxidation case, an enhancement in the dissociation of O₂ by the nanoparticles was a key factor. The strong interaction between CeOx nanoparticles and Cu(111) when preoxidized and reduced in CO resulted in a massive surface reconstruction of the copper substrate with the introduction of microterraces that covered 25-35% of the surface. This constitutes a new mechanism for surface reconstruction not observed before. These microterraces helped to facilitate a further enhancement of activity towards the WGS by opening an additional channel for the dissociation of water. In summary, inverse catalysts of CeOx/Cu(111) and CeO₂/Cu₂O/Cu(111) demonstrate the versatility of a model system to obtain insightful knowledge of catalytic processes. These systems will continue to offer a unique opportunity to probe key catalytic components and elucidate the relationship between structure and reactivity of novel materials and reactions in the future.","corpus_id":9873971,"score":0},{"doc_id":"23660768","title":"In situ/operando studies for the production of hydrogen through the water-gas shift on metal oxide catalysts.","abstract":"In this perspective article, we show how a series of in situ techniques {X-ray diffraction (XRD), pair-distribution-function analysis (PDF), X-ray absorption fine structure (XAFS), environmental transmission electron microscopy (ETEM), infrared spectroscopy (IR), ambient-pressure X-ray photoelectron spectroscopy (AP-XPS)} can be combined to perform detailed studies of the structural, electronic and chemical properties of metal oxide catalysts used for the production of hydrogen through the water-gas shift reaction (WGS, CO + H2O → H2 + CO2). Under reaction conditions most WGS catalysts undergo chemical transformations that drastically modify their composition with respect to that obtained during the synthesis process. Experiments of time-resolved in situ XRD, XAFS, and PDF indicate that the active phase of catalysts which combine Cu, Au or Pt with oxides such as ZnO, CeO2, TiO2, CeOx/TiO2 and Fe2O3 essentially involves nanoparticles of the reduced noble metals. The oxide support undergoes partial reduction and is not a simple spectator, facilitating the dissociation of water and in some cases modifying the chemical properties of the supported metal. Therefore, to optimize the performance of these catalysts one must take into consideration the properties of the metal and oxide phases. IR and AP-XPS have been used to study the reaction mechanism for the WGS on metal oxide catalysts. Data of IR spectroscopy indicate that formate species are not necessarily involved in the main reaction path for the water-gas shift on Cu-, Au- and Pt-based catalysts. Thus, a pure redox mechanism or associative mechanisms that involve either carbonate-like (CO3, HCO3) or carboxyl (HOCO) species should be considered. In the last two decades, there have been tremendous advances in our ability to study catalytic materials under reaction conditions and we are moving towards the major goal of fully understanding how the active sites for the production of hydrogen through the WGS actually work.","corpus_id":1101507,"score":0},{"doc_id":"23928911","title":"Low-temperature selective catalytic reduction of NO with NH₃ over nanoflaky MnOx on carbon nanotubes in situ prepared via a chemical bath deposition route.","abstract":"Nanoflaky MnO(x) on carbon nanotubes (nf-MnO(x)@CNTs) was in situ synthesized by a facile chemical bath deposition route for low-temperature selective catalytic reduction (SCR) of NO with NH₃. This catalyst was mainly characterized by the techniques of X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), N₂ adsorption-desorption analysis, X-ray photoelectron spectroscopy (XPS), H₂ temperature-programmed reduction (H₂-TPR) and NH₃ temperature-programmed desorption (NH₃-TPD). The SEM, TEM, XRD results and N₂ adsorption-desorption analysis indicated that the CNTs were surrounded by nanoflaky MnO(x) and the obtained catalyst exhibited a large surface area as well. Compared with the MnO(x)/CNT and MnO(x)/TiO₂ catalysts prepared by an impregnation method, the nf-MnO(x)@CNTs presented better NH₃-SCR activity at low temperature and a more extensive operating temperature window. The XPS results showed that a higher atomic concentration of Mn(4+) and more chemisorbed oxygen species existed on the surface of CNTs for nf-MnO(x)@CNTs. The H₂-TPR and NH₃-TPD results demonstrated that the nf-MnO(x)@CNTs possessed stronger reducing ability, more acid sites and stronger acid strength than the other two catalysts. Based on the above mentioned favourable properties, the nf-MnO(x)@CNT catalyst has an excellent performance in the low-temperature SCR of NO to N₂ with NH₃. In addition, the nf-MnO(x)@CNT catalyst also presented favourable stability and H₂O resistance.","corpus_id":205869110,"score":0},{"doc_id":"23980657","title":"H2 dissociation over NbO: the first step toward hydrogenation of Mg.","abstract":"Niobium-based oxide nanoparticles have proven to be catalytically effective toward hydrogenation of Mg where H2 dissociation over the niobium-oxides is considered to be a crucial reaction step. However, the role of niobium oxides toward H2 dissociation still remains unclear as to what atomic configurations are responsible for the catalytic activity. H2 dissociation over different surface planes of Nb, NbO, and Nb2O5 as well as small NbO clusters is performed by using a density functional theory. The calculations reveal that H2 dissociation, adsorption energy, and the bond type between H and surfaces (clusters) depend on the atomic configurations of Nb and O. In particular, H2 adsorption on NbO(111) is enhanced by O atoms without forming O-H bond where the bond type of H and surface is found to be an electron pairing. Thus, NbO(111) could not only be a effective catalyst but also potentially prevent the formation of MgO during the hydrogenation of Mg. The results should be helpful in developing and tailoring the efficient catalyst toward H2 dissociation and hydrogenation of Mg.","corpus_id":30558372,"score":0},{"doc_id":"24196690","title":"Redox preparation of mixed-valence cobalt manganese oxide nanostructured materials: highly efficient noble metal-free electrocatalysts for sensing hydrogen peroxide.","abstract":"High-performance hydrogen peroxide sensors provide valuable signals of biological interactions, disorders, and developing of diseases. Low-cost metal oxides are promising alternatives but suffer from low conductivity and sensing activity. Multi-component metal oxides are excellent candidates to accomplish these challenges, but the composition inhomogeneity is difficult to manage with conventional material preparation. We demonstrated redox preparation strategies to successfully synthesize highly homogeneous, noble metal-free H2O2 sensors of spinel nanostructured cobalt manganese oxides with enhanced conductivity, multiple mixed-valence features, and efficient H2O2 sensing activities. The designed redox reactions accompanied with material nucleation/formation are the key factors for compositional homogeneity. High conductivity (1.5 × 10(-2) S cm(-1)) and H2O2 sensing activity (12 times higher than commercial Co3O4) were achieved due to the homogeneous multiple mixed-valence systems of Co(ii)/(iii) and Mn(iii)/(iv). A wide linear detection range (from 0.1 to 25 mM) with a detection limit of 15 μM was observed. Manganese species assist the formation of large surface area nanostructures, enhancing the H2O2 reduction activities, and inhibit the sensing interference. The material controls of hierarchical nanostructures, elemental compositions, porosity, and electrochemical performances are highly associated with the reaction temperatures. The temperature-dependent properties and nanostructure formation mechanisms based on a reaction rate competition are proposed.","corpus_id":21201187,"score":0},{"doc_id":"25011608","title":"Freestanding 3D mesoporous Co₃O₄@carbon foam nanostructures for ethanol gas sensing.","abstract":"Metal oxide materials have been widely used as gas-sensing platforms, and their sensing performances are largely dependent on the morphology and surface structure. Here, freestanding flower-like Co3O4 nanostructures supported on three-dimensional (3D) carbon foam (Co3O4@CF) were successfully synthesized by a facile and low-cost hydrothermal route and annealing procedure. The morphology and structure of the nanocomposites were studied by X-ray diffraction, X-ray photoelectron spectroscopy, energy-dispersive spectroscopy, and scanning electron microscopy (SEM). The SEM characterizations showed that the skeleton of the porous carbon foam was fully covered by flower-like Co3O4 nanostructures. Moreover, each Co3O4 nanoflower is composed of densely packed nanoneedles with a length of ~10 μm, which can largely enhance the surface area (about 286.117 m(2)/g) for ethanol sensing. Gas sensor based on the as-synthesized 3D Co3O4@CF nanostructures was fabricated to study the sensing performance for ethanol at a temperature range from 180 to 360 °C. Due to the 3D porous structure and the improvement in sensing surface/interface, the Co3O4@CF nanostructure exhibited enhanced sensing performance for ethanol detection with low resistance, fast response and recovery time, high sensitivity, and limit of detection as low as 15 ppm at 320 °C. The present study shows that such novel 3D metal oxide/carbon hybrid nanostructures are promising platforms for gas sensing.","corpus_id":36445973,"score":0},{"doc_id":"25043803","title":"Nickel oxide thin film from electrodeposited nickel sulfide thin film: peroxide sensing and photo-decomposition of phenol.","abstract":"A novel non-enzymatic peroxide sensor has been constructed by using nickel oxide (NiO) thin films as sensing material, which were prepared by a two-step process: (i) electrodeposition of nickel sulfide (NiS) and (ii) thermal air oxidation of as-deposited NiS to NiO. The resultant material is highly porous and comprises interconnected nanofibers. UV-Vis spectroscopy, FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and field-emission scanning electron microscopy (FESEM) were used for a complete characterization of nanostructured NiO thin films. Cyclic voltammetry study shows that NiO/ITO electrode facilitates the oxidation of hydrogen peroxide and exhibits excellent catalytic activity towards its sensing. The amperometric study of NiO/ITO was carried out to determine the sensitivity, linear range, detection limit of the proposed sensor. The sensor exhibits prominent electrocatalytic activity toward the oxidation of H2O2 with a wide linear range and a low detection limit. The possible use of the synthesized NiO thin films as an effective photocatalyst for the decomposition of phenol is also discussed.","corpus_id":262546729,"score":0},{"doc_id":"25127389","title":"Graphene oxide as an effective catalyst for wet air oxidation of phenol.","abstract":"The graphene oxide (GO) and chemically reduced graphene oxides, used as catalysts in absence of any metals, were investigated in the catalytic wet air oxidation (CWAO) of phenol in a batch reactor. The characterization of the materials was measured with scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman, fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The carbon materials exhibited good phenol and total organic compounds (TOC) removals in the CWAO of phenol. The GO had the highest catalytic activity, total phenol removal was achieved after 40 min, and ca. 84% TOC removal was obtained after 120 min at reaction temperature of 155°C, total pressure of 2.5 MPa and catalyst loading of 0.2 gL(-1).","corpus_id":8825252,"score":0},{"doc_id":"25140618","title":"Tremendous effect of the morphology of birnessite-type manganese oxide nanostructures on catalytic activity.","abstract":"The octahedral layered birnessite-type manganese oxide (OL-1) with the morphologies of nanoflowers, nanowires, and nanosheets were prepared and characterized with X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric/differential scanning calorimetry (TG/DSC), Brunnauer-Emmett-Teller (BET), inductively coupled plasma (ICP), and X-ray photoelectron spectroscopy (XPS). The OL-1 nanoflowers possess the highest concentration of oxygen vacancies or Mn(3+), followed by the OL-1 nanowires and nanosheets. The result of catalytic tests shows that the OL-1 nanoflowers exhibit a tremendous enhancement in the catalytic activity for benzene oxidation as compared to the OL-1 nanowires and nanosheets. Compared to the OL-1 nanosheets, the OL-1 nanoflowers demonstrate an enormous decrease (ΔT(50) = 274 °C; ΔT(90) > 248 °C) in reaction temperatures T50 and T90 (corresponding to 50 and 90% benzene conversion, respectively) for benzene oxidation. The origin of the tremendous effect of morphology on the catalytic activity for the nanostructured OL-1 catalysts is experimentally and theoretically studied via CO temperature-programmed reduction (CO-TPR) and density functional theory (DFT) calculation. The tremendous catalytic enhancement of the OL-1 nanoflowers compared to the OL-1 nanowires and nanosheets is attributed to their highest surface area as well as their highest lattice oxygen reactivity due to their higher concentration of oxygen vacancies or Mn(3+), thus tremendously improving the catalytic activity for the benzene oxidation.","corpus_id":1634678,"score":0},{"doc_id":"25599521","title":"Quantitative depth profiling of Ce(3+) in Pt/CeO2 by in situ high-energy XPS in a hydrogen atmosphere.","abstract":"The redox property of ceria is a key factor in the catalytic activity of ceria-based catalysts. The oxidation state of well-defined ceria nanocubes in gas environments was analysed in situ by a novel combination of near-ambient pressure X-ray Photoelectron Spectroscopy (XPS) and high-energy XPS at a synchrotron X-ray source. In situ high-energy XPS is a promising new tool to determine the electronic structure of matter under defined conditions. The aim was to quantitatively determine the degree of cerium reduction in a nano-structured ceria-supported platinum catalyst as a function of the gas environment. To obtain a non-destructive depth profile at near-ambient pressure, in situ high-energy XPS analysis was performed by varying the kinetic energy of photoelectrons from 1 to 5 keV, and, thus, the probing depth. In ceria nanocubes doped with platinum, oxygen vacancies formed only in the uppermost layers of ceria in an atmosphere of 1 mbar hydrogen and 403 K. For pristine ceria nanocubes, no change in the cerium oxidation state in various hydrogen or oxygen atmospheres was observed as a function of probing depth. In the absence of platinum, hydrogen does not dissociate and, thus, does not lead to reduction of ceria.","corpus_id":5392191,"score":0},{"doc_id":"25852349","title":"Vanadia supported on nickel manganese oxide nanocatalysts for the catalytic oxidation of aromatic alcohols.","abstract":"Vanadia nanoparticles supported on nickel manganese mixed oxides were synthesized by co-precipitation method. The catalytic properties of these materials were investigated for the oxidation of benzyl alcohol using molecular oxygen as oxidant. It was observed that the calcination temperature and the size of particles play an important role in the catalytic process. The catalyst was evaluated for its oxidation property against aliphatic and aromatic alcohols, which was found to display selectivity towards aromatic alcohols. The samples were characterized by employing scanning electron microscopy, transmission electron microscopy, X-ray diffraction, Brunauer-Emmett-Teller analysis, thermogravimetric analysis, and X-ray photoelectron spectroscopy.","corpus_id":17386989,"score":0},{"doc_id":"25913679","title":"Sulfate radicals induced from peroxymonosulfate by cobalt manganese oxides (Co(x)Mn(3-x)O4) for Fenton-Like reaction in water.","abstract":"A series of CoxMn3-xO4 particles as Fenton-like solid catalysts were synthesized, and their catalytic performance in oxidative degradation of organic dye compounds in water was investigated. The surface morphology and structure of the CoxMn3-xO4 catalysts were characterized by field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), powder X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The results showed that, as an oxide composite of Co and Mn elements, CoMn2O4 showed much stronger catalytic activity in peroxymonosulfate (PMS) oxidation than Co3O4, Mn2O3, and their physical mixture. Typically, the uses of 0.02 g/dm(3) CoMn2O4 and 0.2 g/dm(3) PMS yielded a nearly complete removal of Rhodamine B (0.03 g/dm(3)) in 80 min at 25 °C. The efficiency of Rhodamine B decomposition increased with increasing temperature (15-55 °C), but decreased with the increase of fulvic acid concentration (0-0.08 g/dm(3)). Furthermore, CoMn2O4 could maintain its catalytic activity in the repeated batch experiments. Moreover, HO· and SO4(·-) radicals participating in the process were evidenced using quenching experiments, and a rational mechanism was proposed. PMS oxidation with CoMn2O4 is an efficient technique for remediation of organic contaminants in wastewater.","corpus_id":25983226,"score":0},{"doc_id":"25924339","title":"Development of Ni-Mo/Al2O3 catalyst for reverse water gas shift (RWGS) reaction.","abstract":"In the present study, Mo/Al2O3 catalyst was prepared using impregnation method. Then it was promoted with Ni ions to produce Ni-Mo/Al2O3 catalyst. The structures of the catalysts were studied using X-ray diffraction (XRD), Energy dispersive X-ray (EDAX), Brunauer-Emmett-Teller (BET), X-ray photoelectron spectroscopy (XPS), CO chemisorption, temperature programmed reduction of hydrogen (H2-TPR) and scanning electron microscope (SEM) techniques. Catalytic performances of the two catalysts were investigated in a fixed-bed reactor for RWGS reaction. The results indicated that addition of nickel promoter to Mo/Al2O3 catalyst enhances its activity. It is reasonable for the electron deficient state of the Ni species and existence of NiMoO4 phase to possess high activity in RWGS reaction. Stability test of Ni-Mo/Al2O3 catalyst was carried out in a fixed bed reactor and a high CO2 conversion for 60 h time on stream was demonstrated. This study introduces a new catalyst, Ni-Mo/Al2O3, with high activity and stability for RWGS reaction.","corpus_id":25989381,"score":0},{"doc_id":"25924399","title":"Study on the electrochemical behavior of nanostructure S-doping manganese oxide as a novel supercapacitor material.","abstract":"A nanostructure S-doping manganese oxide (MnO(x)S(y)) amorphous powder was prepared by a homogeneous coprecipitation method for supercapacitor application. The structure and surface morphology of the as-prepared MnO(x)S(y) powder were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), elemental analysis and X-ray photoelectron spectroscopy (XPS). The as-prepared nanostructure S-doping manganese oxide powder was confirmed with a chemical composition of MnO1.26S0.23 by elemental analysis, in which the average oxidation state of manganese is about 3.1. The supercapacitive behavior of the as-prepared MnO1.26S0.23 was studied by means of cyclic voltammetry (CV) and constant current charge-discharge cycling (CD) experiments in 1 mol L(-1) Na2SO4 electrolyte. A maximum specific capacitance of 181 F g(-1) was obtained for MnO1.26S0.23. Furthermore, the specific capacitance remained 97.3% of the original value after 500 cycles. The superior capacitive behavior and better cycling stability indicate that the amorphous nanostructure MnO(x)S(y) maybe a promising electrode material for electrochemical capacitors.","corpus_id":29429264,"score":0},{"doc_id":"26370819","title":"Oxidation of elemental mercury by modified spent TiO2-based SCR-DeNOx catalysts in simulated coal-fired flue gas.","abstract":"In order to reduce the costs, the recycle of spent TiO2-based SCR-DeNOx catalysts were employed as a potential catalytic support material for elemental mercury (Hg(0)) oxidation in simulated coal-fired flue gas. The catalytic mechanism for simultaneous removal of Hg(0) and NO was also investigated. The catalysts were characterized by Brunauer-Emmett-Teller (BET), scanning electron microscope (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) method. Results indicated that spent TiO2-based SCR-DeNOx catalyst supported Ce-Mn mixed oxides catalyst (CeMn/SCR1) was highly active for Hg(0) oxidation at low temperatures. The Ce1.00Mn/SCR1 performed the best catalytic activities, and approximately 92.80 % mercury oxidation efficiency was obtained at 150 °C. The inhibition effect of NH3 on Hg(0) oxidation was confirmed in that NH3 consumed the surface oxygen. Moreover, H2O inhibited Hg(0) oxidation while SO2 had a promotional effect with the aid of O2. The XPS results illustrated that the surface oxygen was responsible for Hg(0) oxidation and NO conversion. Besides, the Hg(0) oxidation and NO conversion were thought to be aided by synergistic effect between the manganese and cerium oxides.","corpus_id":5455710,"score":0},{"doc_id":"26433477","title":"A trimodal porous carbon as an effective catalyst for hydrogen production by methane decomposition.","abstract":"A new type of porous carbon with an interconnected trimodal pore system is synthesized by a nanocasting method using nanoparticulated bimodal micro-mesoporous silica particles as the template. The synthesized template and carbon material are characterized using transmission electron microscopy (TEM), field emission electron scanning microscopy (FESEM) and nitrogen adsorption-desorption test. The synthesized carbon material has an extremely high surface area, a large pore volume and an interconnected pore structure, which could provide abundant active sites and space for chemical reactions and minimize the diffusion resistance of the reactants. The resulting carbon is used as the catalyst for hydrogen production by the thermal decomposition of methane. The catalytic results show that the as-synthesized carbon in this study produces much higher methane conversion and hydrogen yield than the commercial carbon materials.","corpus_id":8862437,"score":0},{"doc_id":"26784198","title":"Studies of Reduced Graphene Oxide and Graphite Oxide in the Aspect of Their Possible Application in Gas Sensors.","abstract":"The paper presents the results of investigations on resistance structures based on graphite oxide (GRO) and graphene oxide (rGO). The subject matter of the investigations was thaw the sensitivity of the tested structures was affected by hydrogen, nitrogen dioxide and carbon dioxide. The experiments were performed at a temperature range from 30 °C to 150 °C in two carrier gases: nitrogen and synthetic air. The measurements were also aimed at characterization of the graphite oxide and graphene oxide. In our measurements we used (among others) techniques such as: Atomic Force Microscopy (AFM); Scanning Electron Microscopy (SEM); Raman Spectroscopy (RS); Fourier Transform Infrared Spectroscopy (FT-IR) and X-ray Photoelectron Microscopy (XPS). The data resulting from the characterizations of graphite oxide and graphene oxide have made it possible to interpret the obtained results from the point of view of physicochemical changes occurring in these structures.","corpus_id":7271967,"score":0},{"doc_id":"27042821","title":"Supercapacitive properties of nanoporous oxide layer formed on 304 type stainless steel.","abstract":"The nanoporous oxide layer is formed on the surface of 304 type stainless steel (SS) by chemical oxidation method. The characterization of the oxide layer is carried out using X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), contact angle and energy-dispersive X-ray spectroscopy (EDS) techniques. The supercapacitive properties of oxide layer are studied using cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy techniques.","corpus_id":28419427,"score":0},{"doc_id":"27333408","title":"Insights into the solar light driven thermocatalytic oxidation of VOCs over tunnel structured manganese oxides.","abstract":"Different tunnel structured manganese oxides (1*1, 2*2, and 3*3) have been synthesized via a facile hydrothermal strategy. The three catalysts exhibit high photothermal performance, resulting in a considerable increase of temperature above the light-off temperature for VOC oxidation. On this point, aerobic oxidation reactions of propane and propylene under simulated sunlight and infrared light irradiation were selected as probe reactions to explore their light driven thermocatalytic activity. Furthermore, the light-off curves of the manganese oxides for propane and propylene were carefully investigated, which clearly explained the possibility of combining both the efficient photothermal effect and excellent thermocatalytic activity of the manganese oxides. Results show that the catalytic effects follow the order of 1*1 < 3*3 < 2*2. 2*2 exhibited the best catalytic properties due to better low-temperature reducibility, suitable tunnel structure and the presence of more Mn(4+). This work suggests new applications for traditional catalysts with intense photoabsorption and provides insights into the overall utilization of solar energy.","corpus_id":206018186,"score":0},{"doc_id":"27423769","title":"Integrated ternary nanocomposite of TiO2/NiO/reduced graphene oxide as a visible light photocatalyst for efficient degradation of o-chlorophenol.","abstract":"This study investigated a novel approach for the synthesis of an integrated ternary nanocomposite which could act as a good photo-catalyst under visible light irradiation for the removal of organic pollutants from aqueous environments. The photo-catalyst included nickel oxide (NiO) as a dopant, and reduced graphene oxide (RGO) as a good carbon basal support for enhancement of the photo-catalytic activity of TiO2. Under irradiation with visible light, the ternary nanocomposite (TiO2/NiO-RGO) system generates e(-)/h(+) pairs, and then reacts with H2O and O2(-) molecules to produce oxy-radicals which can be used for the mineralization of o-chlorophenol from aqueous solution. The characteristic of all photo-catalysts were investigated by UV-Vis analysis, with surface area and pore size measurements by Brunauer-Emmett-Teller (BET), crystallinity by X-ray diffraction (XRD), elemental composition by X-ray photoelectron spectroscopy (XPS), and morphology by scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX). The functional groups were measured by Fourier transform infrared (FT-IR) spectroscopy before and after o-chlorophenol degradation. TiO2/NiO-RGO was capable of achieving 88.4% photo-degradation of 100 mg/L o-chlorophenol (100 mL) within 8 h with addition of 0.01% H2O2 under visible light irradiation at pH 6.5. The photo-degradation followed a pseudo-first-order reaction. The TiO2/NiO-RGO nanocomposite retained its high removal efficiency, even after four photo-catalytic cycles.","corpus_id":9678145,"score":0},{"doc_id":"28210734","title":"Ceria-based model catalysts: fundamental studies on the importance of the metal-ceria interface in CO oxidation, the water-gas shift, CO2 hydrogenation, and methane and alcohol reforming.","abstract":"Model metal/ceria and ceria/metal catalysts have been shown to be excellent systems for studying fundamental phenomena linked to the operation of technical catalysts. In the last fifteen years, many combinations of well-defined systems involving different kinds of metals and ceria have been prepared and characterized using the modern techniques of surface science. So far most of the catalytic studies have been centered on a few reactions: CO oxidation, the hydrogenation of CO2, and the production of hydrogen through the water-gas shift reaction and the reforming of methane or alcohols. Using model catalysts it has been possible to examine in detail correlations between the structural, electronic and catalytic properties of ceria-metal interfaces. In situ techniques (X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, infrared spectroscopy, scanning tunneling microscopy) have been combined to study the morphological changes under reaction conditions and investigate the evolution of active phases involved in the cleavage of C-O, C-H and C-C bonds. Several studies with model ceria catalysts have shown the importance of strong metal-support interactions. In general, a substantial body of knowledge has been acquired and concepts have been developed for a more rational approach to the design of novel technical catalysts containing ceria.","corpus_id":3743836,"score":0},{"doc_id":"28344278","title":"Investigation of MnO₂ and Ordered Mesoporous Carbon Composites as Electrocatalysts for Li-O₂ Battery Applications.","abstract":"The electrocatalytic activities of the MnO₂/C composites are examined in Li-O₂ cells as the cathode catalysts. Hierarchically mesoporous carbon-supported manganese oxide (MnO₂/C) composites are prepared using a combination of soft template and hydrothermal methods. The composites are characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, small angle X-ray scattering, The Brunauer-Emmett-Teller (BET) measurements, galvanostatic charge-discharge methods, and rotating ring-disk electrode (RRDE) measurements. The electrochemical tests indicate that the MnO₂/C composites have excellent catalytic activity towards oxygen reduction reactions (ORRs) due to the larger surface area of ordered mesoporous carbon and higher catalytic activity of MnO₂. The O₂ solubility, diffusion rates of O₂ and O₂(•-) coefficients (DO₂ and DO(-)₂), the rate constant (kf) for producing O₂(•-), and the propylene carbonate (PC)-electrolyte decomposition rate constant (k) of the MnO₂/C material were measured by RRDE experiments in the 0.1 M TBAPF₆/PC electrolyte. The values of kf and k for MnO₂/C are 4.29 × 10(-2) cm·s(-1) and 2.6 s(-1), respectively. The results indicate that the MnO₂/C cathode catalyst has higher electrocatalytic activity for the first step of ORR to produce O₂(•-) and achieves a faster PC-electrolyte decomposition rate.","corpus_id":14794338,"score":0},{"doc_id":"28892795","title":"Uniform dispersion of cobalt nanoparticles over nonporous TiO2 with low activation energy for magnesium sulfate recovery in a novel magnesia-based desulfurization process.","abstract":"The forced oxidation of magnesium sulfite (MgSO3) aims to not only reclaim the by-product in the magnesia desulfurization, but also lower the risk of secondary pollution. The non-porous titanium dioxide nanoparticle was used as a support to prepare the cobalt catalyst (Co-TiO2) in order to expedite the oxidation rate. This fabricated Co-TiO2 was characterized by inductively coupled plasma optical emission spectroscopy (ICP-OES), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), and energy dispersive spectroscopy (EDS) to figure out its catalytic mechanism. The results revealed that the cobalt nanoparticles were uniformly dispersed on the surface of the TiO2 in forms of Co3O4 and Co2O3. The kinetics of the MgSO3 oxidation catalyzed by the prepared Co-TiO2 was investigated in a bubbling tank reactor, indicating that the oxidation rate was dependent on the catalyst concentration, oxygen partial pressure, pH value, and the reaction temperature. Compared with the reported porous catalyst (Co-CNTs), the activation energy with the Co-TiO2 (17.29kJmol-1) decreased by 50.9%, resulting in a good catalytic performance in sulfite oxidation. The findings will help advance the industrial application of the novel magnesia desulfurization process.","corpus_id":44831843,"score":0},{"doc_id":"28895018","title":"Promotional effect of rare earth-doped manganese oxides supported on activated semi-coke for selective catalytic reduction of NO with NH3.","abstract":"A composite catalyst for the selective catalytic reduction (SCR) of NOx with NH3 is investigated, in which the rare earth (RE, including La, Ce, Pr, and Nd) is doped into manganese oxides supported on activated semi-coke (MnOx/ASC) via hydrothermal method at the molar ratio of Mn:RE = 1:5. It is evidenced that the addition of RE at a rather low molar ratio can enhance the catalytic activity of MnOx/ASC. The catalyst with a Mn:Ce molar ratio of 10:1 yields an over 90% NOx removal efficiency in the temperature range of 150-250 °C. An approximate 100% NO conversion and 95% N2 selectivity are achieved at about 200 °C. The catalysts are characterized by N2 physisorption, X-ray powder diffraction (XRD), scanning electron microscope (SEM), hydrogen temperature-programmed reduction (H2-TPR) and X-ray photoelectron spectroscopy (XPS). The results indicated that the Ce additive is conducive to the NOx adsorption and then accelerates the SCR reaction due to the formation of more chemisorbed oxygen (Oβ), which is favored during the oxidation of NH3 and NO. Moreover, the in situ diffused reflectance infrared Fourier transform spectroscopy (DRIFTS) results confirm that the Ce additive on MnOx/ASC catalyst could provide more active Brønsted acid sites, which eventually contributes to the SCR reaction. The generation of ad-NH4+ and nitrite species is proved to play the crucial role in the promotional effect of RE addition.","corpus_id":30338472,"score":0},{"doc_id":"29111664","title":"Oxygen Plasma-Treated Graphene Oxide Surface Functionalization for Sensitivity Enhancement of Thin-Film Piezoelectric Acoustic Gas Sensors.","abstract":"In this work, we presented a thin-film piezoelectric acoustic gas sensor with enhanced sensitivity by a surface modification strategy of oxygen plasma treated graphene oxide (GO) functionalization. By exposing to ammonia vapor (NH3) of various concentrations at controlled temperature and humidity, the characteristics of the GO-coated acoustic sensor were investigated, that is, sensitivity, linearity, response, and recovery time. Oxygen plasma treatment of the GO-coated sensor further enhanced the sensitivity compared with the freshly prepared GO-coated sensor. The mechanism of oxygen plasma treatment effect on the GO-coated sensor was discussed based on characterizations of X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, scanning electron microscope (SEM), and precise weighing of the acoustic sensor. It was found that the oxygen plasma treatment introduces numerous defects to GO flakes, which are uniformly distributed across the GO surface, providing more gas molecule binding sites.","corpus_id":206462433,"score":0},{"doc_id":"29163900","title":"Manganese complex-catalyzed oxidation and oxidative kinetic resolution of secondary alcohols by hydrogen peroxide.","abstract":"The highly efficient catalytic oxidation and oxidative kinetic resolution (OKR) of secondary alcohols has been achieved using a synthetic manganese catalyst with low loading and hydrogen peroxide as an environmentally benign oxidant in the presence of a small amount of sulfuric acid as an additive. The product yields were high (up to 93%) for alcohol oxidation and the enantioselectivity was excellent (>90% ee) for the OKR of secondary alcohols. Mechanistic studies revealed that alcohol oxidation occurs via hydrogen atom (H-atom) abstraction from an α-CH bond of the alcohol substrate and a two-electron process by an electrophilic Mn-oxo species. Density functional theory calculations revealed the difference in reaction energy barriers for H-atom abstraction from the α-CH bonds of R- and S-enantiomers by a chiral high-valent manganese-oxo complex, supporting the experimental result from the OKR of secondary alcohols.","corpus_id":-1,"score":0}],"string":"[\n {\n \"doc_id\": \"19136141\",\n \"title\": \"Hydrogen peroxide decomposition on manganese oxide (pyrolusite): kinetics, intermediates, and mechanism.\",\n \"abstract\": \"The objective of this study is the kinetic interpretation of hydrogen peroxide decomposition on manganese oxide (pyrolusite) and the explanation of the reaction mechanism including the hydroperoxide/superoxide anion. The decomposition of hydrogen peroxide on manganese oxide at pH 7 was represented by a pseudo first-order model. The maximum value of the observed first-order rates constants (k(obs)) was 0.741 min(-1) at 11.8 of [H(2)O(2)]/[triple bond MnO(2)] when [H(2)O(2)]/[triple bond MnO(2)] were ranged from 58.8 to 3.92. The pseudo first-order rate constants (kMnO(2)) approximated as the average value of 0.025 (min mM)(-1) with a standard deviation of 0.003 at [H(2)O(2)]/[triple bond MnO(2)] ranged from 39.2 to 11.8. When [H(2)O(2)]/[triple bond MnO(2)] was 3.92, the rate constants (kMnO(2)) was 0.061 (min mM)(-1) as maximum. Oxygen production showed that the initial rates increased with decreasing [H(2)O(2)]/[triple bond MnO(2)] and the total amounts of oxygen was slightly less than the stoichiometric value (0.5) in most experiments. However, oxygen was produced at more than 0.5 in low [H(2)O(2)]/[triple bond MnO(2)] (i.e. 3.92 and 9.79). The relative production of hydroperoxide/superoxide anion implied that the production increased with low [H(2)O(2)]/[triple bond MnO(2)], and the existence of anions suggested that the mechanism includes propagation reactions with intermediates such as hydroperoxide/superoxide anion in solution. In addition, both [H(2)O(2)] decomposition and the production of anion were accelerated in alkaline solution. Manganese ion dissolved into solution was negligible in neutral and alkaline conditions, but it greatly increased in acidic conditions.\",\n \"corpus_id\": 26095579,\n \"score\": 2\n },\n {\n \"doc_id\": \"20638494\",\n \"title\": \"A highly sensitive hydrogen peroxide amperometric sensor based on MnO2-modified vertically aligned multiwalled carbon nanotubes.\",\n \"abstract\": \"In this report, a highly sensitive amperometric sensor based on MnO(2)-modified vertically aligned multiwalled carbon nanotubes (MnO(2)/VACNTs) for determination of hydrogen peroxide (H(2)O(2)) was fabricated by electrodeposition. The morphology of the nanocomposite was characterized by scanning electron microscopy, energy-dispersive X-ray spectrometer and X-ray diffraction. Cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy were applied to investigate the electrochemical properties of the MnO(2)/VACNTs nanocomposite electrode. The mechanism for the electrochemical reaction of H(2)O(2) at the MnO(2)/VACNTs nanocomposite electrode was also discussed. In borate buffer (pH 7.8, 0.20 M), the MnO(2)/VACNTs nanocomposite electrode exhibits a linear dependence (R=0.998) on the concentration of H(2)O(2) from 1.2 x 10(-6)M to 1.8 x 10(-3)M, a high sensitivity of 1.08 x 10(6) microA M(-1) cm(-2) and a detection limit of 8.0 x 10(-7) M (signal/noise=3). Meanwhile, the MnO(2)/VACNTs nanocomposite electrode is also highly resistant towards typical inorganic salts and some biomolecules such as acetic acid, citric acid, uric acid and D-(+)-glucose, etc. In addition, the sensor based on the MnO(2)/VACNTs nanocomposite electrode was applied for the determination of trace of H(2)O(2) in milk with high accuracy, demonstrating its potential for practical application.\",\n \"corpus_id\": 205208011,\n \"score\": 2\n },\n {\n \"doc_id\": \"20875556\",\n \"title\": \"A novel nonenzymatic hydrogen peroxide sensor based on MnO2/graphene oxide nanocomposite.\",\n \"abstract\": \"A new electrocatalyst, MnO(2)/graphene oxide hybrid nanostructure was successfully synthesized for the nonenzymatic detection of H(2)O(2). The morphological characterization was examined by scanning electron microscopy and transmission electron microscopy. The MnO(2)/graphene oxide based electrodes showed high electrochemical activity for the detection of H(2)O(2) in alkaline medium. The nonenzymatic biosensors displayed good performance along with low working potential, high sensitivity, low detection limit, and long-term stability, which could be attributed to the high surface area of graphene oxide providing for the deposition of MnO(2) nanoparticles. These results demonstrate that this new nanocomposite with the high surface area and electrocatalytic activity offers great promise for new class of nanostructured electrode for nonenzymatic biosensor and energy conversion applications.\",\n \"corpus_id\": 11499318,\n \"score\": 2\n },\n {\n \"doc_id\": \"21229179\",\n \"title\": \"Pitfalls in the characterization of nanoporous and nanosized materials.\",\n \"abstract\": \"With the advent of highly sophisticated analytical tools, numerous physical methods are nowadays available for comprehensive characterization of inorganic matter and, as special cases, of porous and nanosized materials. Intelligent experimental setup and correct evaluation of the experimental data can provide helpful insights into the chemical and physical properties of such materials. However, scanning of literature reports shows that in many cases evaluation and interpretation of experimental data are erroneous. As a result, the description of a new material can be useless or even worse, misleading. Wrong evaluation is even more critical if mechanistic theories are based on such data. Characterization of porous and/or nanosized materials is mainly performed by gas adsorption, X-ray powder diffraction, electron microscopy and surface spectroscopy. For correct interpretation of experimental data one should be aware of certain pitfalls. The present paper summarizes prominent faults and may show how they can be avoided. It is supposed to provide some hand-on knowledge on correct analysis of materials. Addressed are primarily non-experts and researchers being new to the field of characterization of inorganic nanosized or nanoporous materials.\",\n \"corpus_id\": 22847911,\n \"score\": 2\n },\n {\n \"doc_id\": \"26592586\",\n \"title\": \"A novel nonenzymatic amperometric hydrogen peroxide sensor based on CuO@Cu2O nanowires embedded into poly(vinyl alcohol).\",\n \"abstract\": \"A new, very simple, rapid and inexpensive nonenzymatic amperometric sensor for hydrogen peroxide (H2O2) detection is proposed. It is based on the immobilization of cupric/cuprous oxide core shell nanowires (CuO@Cu2O-NWs) in a poly(vinyl alcohol) (PVA) matrix directly drop casted on a glassy carbon electrode surface to make a CuO@Cu2O core shell like NWs PVA embedded (CuO@Cu2O-NWs/PVA) sensor. CuO nanowires with mean diameters of 120-170nm and length in the range 2-5μm were grown by a simple catalyst-free thermal oxidation process based on resistive heating of pure copper wires at ambient conditions. The oxidation process of the copper wire surface led to the formation of a three layered structure: a thick Cu2O bottom layer, a CuO thin intermediate layer and CuO nanowires. CuO nanowires were carefully scratched from Cu2O layer with a sharp knife, dispersed into ethanol and sonicated. Then, the NWs were embedded in PVA matrix. The morphological and spectroscopic characterization of synthesized CuO-NWs and CuO@Cu2O-NWs/PVA were performed by transmission electron microscopy (TEM), selected area diffraction pattern (SAD), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) analysis. Moreover a complete electrochemical characterization of these new CuO@Cu2O-NWs/PVA modified glassy carbon electrodes was performed by Cyclic Voltammetry (CV) and Cronoamperometry (CA) in phosphate buffer (pH=7; I=0.2) to investigate the sensing properties of this material against H2O2. The electrochemical performances of proposed sensors as high sensitivity, fast response, reproducibility and selectivity make them suitable for the quantitative determination of hydrogen peroxide substrate in batch analysis.\",\n \"corpus_id\": 23399705,\n \"score\": 2\n },\n {\n \"doc_id\": \"20131606\",\n \"title\": \"Remediation of sulfidic wastewater by catalytic oxidation with hydrogen peroxide.\",\n \"abstract\": \"Oxidation of sulfide in aqueous solution by hydrogen peroxide was investigated in the presence of hydrated ferric oxide catalyst. The ferric oxide catalyst was synthesized by sol gel technique from ferric chloride and ammonia. The synthesized catalyst was characterized by Fourier transform infrared spectroscopy, X-Ray diffraction analysis, scanning electrom microscope and energy dispersive X-ray analysis. The catalyst was quite effective in oxidizing the sulfide by hydrogen peroxide. The effects of sulfide concentration, catalyst loading, H2O2 dosing and temperature on the kinetics of sulfide oxidation were investigated. Kinetic equations and activation energies for the catalytic oxidation reaction were calculated based on the experimental results.\",\n \"corpus_id\": 10179383,\n \"score\": 1\n },\n {\n \"doc_id\": \"21507410\",\n \"title\": \"Porous magnetic manganese oxide nanostructures: synthesis and their application in water treatment.\",\n \"abstract\": \"Magnetic manganese oxide nanostructures are fabricated at room temperature by mixing a KMnO(4) solution and oleic acid capped Fe(3)O(4) particles. Oleic acid molecules capped Fe(3)O(4) particles are oxidized by potassium permanganate (KMnO(4)) in an aqueous solution to produce porous magnetic manganese oxide nanostructures. The synthesis technique can be extended to other MnO(x) structures with composition of different nanocrystals, such as quantum dots, noble metal crystals which may have important applications as catalysts, adsorbents, electrodes and advanced materials in many scientific disciplines. Transmission electron microscopy, energy-dispersive X-ray spectroscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray powder diffraction, Fourier transform infrared spectroscopy, and nitrogen adsorption-desorption measurements are employed to characterize the structures. As an adsorbent in water treatment, the nanostructures possess a large adsorption capability and high organic pollutant removal rates due to the large surface area and pore volume. The nanostructures are recyclable as their adsorption capability can be recovered by combustion. Furthermore, the strong magnetism exhibited by the structures provides an easy and efficient separation means in wastewater treatment under an external magnetic field.\",\n \"corpus_id\": 13704751,\n \"score\": 1\n },\n {\n \"doc_id\": \"21817483\",\n \"title\": \"Two-dimensional manganese oxide nanolayers on Pd(100): the surface phase diagram.\",\n \"abstract\": \"Two-dimensional manganese oxide layers have been grown on Pd(100) and have been characterized by means of scanning tunnelling microscopy, low energy electron diffraction and x-ray photoelectron spectroscopy (XPS). The complex surface phase diagram of MnO(x) on Pd(100) is reported, where nine different novel Mn oxide phases have been detected as a function of the chemical potential of oxygen μ(O). Three regions of the chemical potential of oxygen can be identified, in which structurally related oxide phases are formed, often in coexistence at the surface. The different regions of μ(O) are reflected in the oxidation states of the respective Mn oxide nanolayers as revealed by the Mn 2p and O 1s XPS binding energies. The MnO(x) nanolayers form two-dimensional wetting layers and it is speculated that they mediate the epitaxial growth of MnO on Pd(100) by providing structurally graded interfaces.\",\n \"corpus_id\": 21321142,\n \"score\": 1\n },\n {\n \"doc_id\": \"22413904\",\n \"title\": \"Manganese oxides with rod-, wire-, tube-, and flower-like morphologies: highly effective catalysts for the removal of toluene.\",\n \"abstract\": \"Nanosized rod-like, wire-like, and tubular α-MnO(2) and flower-like spherical Mn(2)O(3) have been prepared via the hydrothermal method and the CCl(4) solution method, respectively. The physicochemical properties of the materials were characterized using numerous analytical techniques. The catalytic activities of the catalysts were evaluated for toluene oxidation. It is shown that α-MnO(2) nanorods, nanowires, and nanotubes with a surface area of 45-83 m(2)/g were tetragonal in crystal structure, whereas flower-like spherical Mn(2)O(3) with a surface area of 162 m(2)/g was of cubic crystal structure. There were the presence of surface Mn ions in multiple oxidation states (e.g., Mn(3+), Mn(4+), or even Mn(2+)) and the formation of surface oxygen vacancies. The oxygen adspecies concentration and low-temperature reducibility decreased in the order of rod-like α-MnO(2) > tube-like α-MnO(2) > flower-like Mn(2)O(3) > wire-like α-MnO(2), in good agreement with the sequence of the catalytic performance of these samples. The best-performing rod-like α-MnO(2) catalyst could effectively catalyze the total oxidation of toluene at lower temperatures (T(50%) = 210 °C and T(90%) = 225 °C at space velocity = 20,000 mL/(g h)). It is concluded that the excellent catalytic performance of α-MnO(2) nanorods might be associated with the high oxygen adspecies concentration and good low-temperature reducibility. We are sure that such one-dimensional well-defined morphological manganese oxides are promising materials for the catalytic elimination of air pollutants.\",\n \"corpus_id\": 34503295,\n \"score\": 1\n },\n {\n \"doc_id\": \"24054675\",\n \"title\": \"Te oxide nanowires as advanced materials for amperometric nonenzymatic hydrogen peroxide sensing.\",\n \"abstract\": \"A new nonenzymatic platinum Te oxide nanowires modified electrode (Pt/TeO2-NWs) for amperometric detection of hydrogen peroxide (H2O2) is proposed. The modified electrode has been developed by direct drop casting, with TeO2 nanowires (TeO2-NWs), synthesized by thermal evaporation of Te(0) in an oxygen atmosphere. The morphological and spectroscopic characterization of the TeO2-NWs as synthesized on Pt foil was performed by scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis. XPS and XRD analyses are especially involved to gain information on the chemical environment of TeO2-NWs in contact with Pt surface. Moreover electrochemical characterization of these new modified Pt/TeO2-NWs modified electrodes was performed by Cyclic Voltammetry (CV) and Cronoamperometry (CA) in phosphate buffer (pH=7; I=0.2) to investigate the sensing properties of this material against H2O2. The proposed sensor exhibits a wide linear and dynamic range from 2 µM to 16 mM (R(2)=0.9998) and the detection limit is estimated to be 0.6 µM (S/N=3). Moreover, this sensor shows a rapid amperometric response time of less than 5s and possessed good reproducibility. These results indicate that Pt/TeO2-NWs composite is suitable to be used as material for sensing applications.\",\n \"corpus_id\": 34526200,\n \"score\": 1\n },\n {\n \"doc_id\": \"26109374\",\n \"title\": \"Sewage-sludge-derived carbonaceous materials for catalytic wet hydrogen peroxide oxidation of m-cresol in batch and continuous reactors.\",\n \"abstract\": \"In this study, four sewage-sludge-derived carbonaceous materials (SWs) were evaluated for their catalytic wet hydrogen peroxide oxidation (CWPO) performance of m-cresol in batch reactor and continuous reactor, respectively. The SWs were produced by carbonization (SW); carbonization with the addition of CaO (CaO-SW); HNO3 pretreatment (HNO3-SW) and steam activation (Activated-SW). The properties of SW catalysts were assessed by thermogravimetric analysis, Brunauer-Emmett-Teller, Fourier Transform Infrared Spectroscopy, X-ray Fluorescence, Scanning electron microscopy, energy dispersive X-ray analysis and zeta potential. The results showed that SW treated by HNO3 (HNO3-SW) had a high conversion of m-cresol in batch reactor and continuous reactor, respectively. Under the conditions of batch reaction (Cm-cresol = 100 mg L(-1), CH2O2 = 15.7 mmol L(-1), initial pH=7.0, 0.5 g L(-1) catalyst, 80°C, 180 min adsorption and 210 min oxidation), the conversion of m-cresol reached 100% and total organic carbon removal was 67.1%. It had a high catalytic activity and stability on the treatment of m-cresol in CWPO for more than 1100 h. Furthermore, a possible reaction mechanism for the oxidation of m-cresol to 2-methyl-p-benzoquinone by CWPO was proposed.\",\n \"corpus_id\": 21598655,\n \"score\": 1\n },\n {\n \"doc_id\": \"29175960\",\n \"title\": \"Silver-palladium catalysts for the direct synthesis of hydrogen peroxide.\",\n \"abstract\": \"A series of bimetallic silver-palladium catalysts supported on titania were prepared by wet impregnation and assessed for the direct synthesis of hydrogen peroxide, and its subsequent side reactions. The addition of silver to a palladium catalyst was found to significantly decrease hydrogen peroxide productivity and hydrogenation, but crucially increase the rate of decomposition. The decomposition product, which is predominantly hydroxyl radicals, can be used to decrease bacterial colonies. The interaction between silver and palladium was characterized using scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and temperature programmed reduction (TPR). The results of the TPR and XPS indicated the formation of a silver-palladium alloy. The optimal 1% Ag-4% Pd/TiO2 bimetallic catalyst was able to produce approximately 200 ppm of H2O2 in 30 min. The findings demonstrate that AgPd/TiO2 catalysts are active for the synthesis of hydrogen peroxide and its subsequent decomposition to reactive oxygen species. The catalysts are promising for use in wastewater treatment as they combine the disinfectant properties of silver, hydrogen peroxide production and subsequent decomposition. This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.\",\n \"corpus_id\": 4663319,\n \"score\": 1\n },\n {\n \"doc_id\": \"18459091\",\n \"title\": \"Gas storage in nanoporous materials.\",\n \"abstract\": \"Gas storage in solids is becoming an ever more important technology, with applications and potential applications ranging from energy and the environment all the way to biology and medicine. Very highly porous materials, such as zeolites, carbon materials, polymers, and metal-organic frameworks, offer a wide variety of chemical composition and structural architectures that are suitable for the adsorption and storage of many different gases, including hydrogen, methane, nitric oxide, and carbon dioxide. However, the challenges associated with designing materials to have sufficient adsorption capacity, controllable delivery rates, suitable lifetimes, and recharging characteristics are not trivial in many instances. The different chemistry associated with the various gases of interest makes it necessary to carefully match the properties of the porous material to the required application.\",\n \"corpus_id\": 31145843,\n \"score\": 0\n },\n {\n \"doc_id\": \"18786680\",\n \"title\": \"Synthesis, characterization, and catalytic activity of cryptomelane nanomaterials produced with industrial manganese sulfate.\",\n \"abstract\": \"Industrial manganese sulfate from manganese mines has been utilized to synthesize cryptomelane in a simple and feasible route. K-birnessite precursor was prepared by air oxidation of the mixture of MnSO4 and KOH solutions under alkaline conditions, and then transformed to cryptomelane under a heating process. The effects of OH- concentration, airflow rate, liquid reaction temperature, stirring rate, liquid reaction time, washing condition, calcination time, and temperature were investigated. X-ray diffraction (XRD), scanning electron microscopy (SEM), and high-resolution transmission electron microscopy (HRTEM) revealed that cryptomelane prepared under optimal conditions had a tetragonal symmetry and the particles were mostly in short lathy form with sizes of 20-30 nm. The average pore size and BET surface area of cryptomelane examined by N2 adsorption methods were 24.15 nm and 32.21 m2/g, respectively. X-ray photoelectron spectroscopy (XPS) studies demonstrated that the average oxidation state of manganese in cryptomelane was about 3.9 in comparison with prephase K-birnessite of 3.4. The synthesized cryptomelane sample showed improved catalytic activity for decomposition of hydrogen peroxide as compared with natural cryptomelane, but lower than those synthesized with hydrothermal and sol-gel methods. The results of this investigation will provide fundamental information for developing a large-scale production process for transforming manganese sulfate to cryptomelane.\",\n \"corpus_id\": 35572913,\n \"score\": 0\n },\n {\n \"doc_id\": \"19082020\",\n \"title\": \"Hydrogen-rich boron-containing materials for hydrogen storage.\",\n \"abstract\": \"Hydrogen-rich boron-containing compounds have received extensive attention as potential hydrogen storage media for vehicular applications. The past years have seen significant progresses in material discovery, material composition/structure tailoring, catalyst identification and regeneration chemistry, which give rise to state-of-the-art hydrogen storage materials/technologies. Lithium tetrahydroborate-related materials exhibit the hitherto highest reversible hydrogen capacity via solid-gas reactions. Catalytic hydrolysis of sodium tetrahydroborate offers an on-demand hydrogen generation system for vehicular applications. Ammonia borane-related materials exhibit a satisfactory combination of material properties that are suited for on-board hydrogen sources, coupled with significant advances in spent fuels regeneration. This Perspective discusses the current progresses of these representative reversible or irreversible material systems, aiming at providing an outline of the forefront of hydrogen storage materials/technologies for transportation applications.\",\n \"corpus_id\": 205713742,\n \"score\": 0\n },\n {\n \"doc_id\": \"19178167\",\n \"title\": \"Green decomposition of organic dyes using octahedral molecular sieve manganese oxide catalysts.\",\n \"abstract\": \"The catalytic degradation of organic dye (methylene blue, MB) has been studied using green oxidation methods (tertiary-butyl hydrogen peroxide, TBHP, as the oxidant with several doped mixed-valent and regular manganese oxide catalysts in water) at room and higher temperatures. These catalysts belong to a class of porous manganese oxides known as octahedral molecular sieves (OMS). The most active catalysts were those of Mo(6+)- and V(5+)-doped OMS. Rates of reaction were found to be first-order with respect to the dye. TBHP has been found to enhance the MB decomposition, whereas H(2)O(2) does not. Reactions were studied at pH 3-11. The optimum pH for these reactions was pH 3. Dye-decomposing activity was proportional to the amount of catalyst used, and a significant increase in catalytic activity was observed with increasing temperature. X-ray diffraction (XRD), energy dispersive spectroscopy (EDX), and thermogravimetric analysis (TGA) studies showed that no changes in the catalyst structure occurred after the dye-degradation reaction. The products as analyzed by electrospray ionization mass spectrometry (ESI-MS) showed that MB was successively decomposed through different intermediate species.\",\n \"corpus_id\": 5886164,\n \"score\": 0\n },\n {\n \"doc_id\": \"19778036\",\n \"title\": \"Bacteriogenic manganese oxides.\",\n \"abstract\": \"Microorganisms control the redox cycling of manganese in the natural environment. Although the homogeneous oxidation of Mn(II) to form manganese oxide minerals is slow, solid MnO(2) is the stable form of manganese in the oxygenated portion of the biosphere. Diverse bacteria and fungi have evolved the ability to catalyze this process, producing the manganese oxides found in soils and sediments. Other bacteria have evolved to utilize MnO(2) as a terminal electron acceptor in respiration. This Account summarizes the properties of Mn oxides produced by bacteria (bacteriogenic MnO(2)) and our current thinking about the biochemical mechanisms of bacterial Mn(II) oxidation. According to X-ray absorption spectroscopy and X-ray scattering studies, the MnO(2) produced by bacteria consists of stacked hexagonal sheets of MnO(6) octahedra, but these particles are extremely small and have numerous structural defects, particularly cation vacancies. The defects provide coordination sites for binding exogenous metal ions, which can be adsorbed to a high loading. As a result, bacterial production of MnO(2) influences the bioavailability of these metals in the natural environment. Because of its high surface area and oxidizing power, bacteriogenic MnO(2) efficiently degrades biologically recalcitrant organic molecules to lower-molecular-mass compounds, spurring interest in using these properties in the bioremediation of xenobiotic organic compounds. Finally, bacteriogenic MnO(2) is reduced to soluble Mn(II) rapidly in the presence of exogenous ligands or sunlight. It can therefore help to regulate the bioavailability of Mn(II), which is known to protect organisms from superoxide radicals and is required to assemble the water-splitting complex in photosynthetic organisms. Bioinorganic chemists and microbiologists have long been interested in the biochemical mechanism of Mn(IV) oxide production. The reaction requires a two-electron oxidation of Mn(II), but genetic and biochemical evidence for several bacteria implicate multicopper oxidases (MCOs), which are only known to engage one-electron transfers from substrate to O(2). In experiments with the exosporium of a Mn(II)-oxidizing Bacillus species, we could trap the one-electron oxidation product, Mn(III), as a pyrophosphate complex in an oxygen-dependent reaction inhibited by azide, consistent with MCO catalysis. The Mn(III) pyrophosphate complex can further act as a substrate, reacting in the presence of the exosporium to produce Mn(IV) oxide. Although this process appears to be unprecedented in biology, it is reminiscent of the oxidation of Fe(II) to form Fe(2)O(3) in the ferritin iron storage protein. However, it includes a critical additional step of Mn(III) oxidation or disproportionation. We shall continue to investigate this biochemically unique process with purified enzymes.\",\n \"corpus_id\": 206829100,\n \"score\": 0\n },\n {\n \"doc_id\": \"20067294\",\n \"title\": \"Mesoporous MnO2/carbon aerogel composites as promising electrode materials for high-performance supercapacitors.\",\n \"abstract\": \"MnO(2) as one of the most promising candidates for electrochemical supercapacitors has attracted much attention because of its superior electrochemical performance, low cost, and environmentally benign nature. In this Letter, we explored a novel route to prepare mesoporous MnO(2)/carbon aerogel composites by electrochemical deposition assisted by gas bubbles. The products were characterized by energy-dispersive spectrometry (EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The MnO(2) deposits are found to have high purity and have a mesoporous structure that will optimize the electronic and ionic conductivity to minimize the total resistance of the system and thereby maximize the performance characteristics of this material for use in supercapacitor electrodes. The results of nitrogen adsorption-desorption experiments and electrochemical measurements showed that these obtained mesoporous MnO(2)/carbon aerogel composites had a large specific surface area (120 m(2)/g), uniform pore-size distribution (around 5 nm), high specific capacitance (515.5 F/g), and good stability over 1000 cycles, which give these composites potential application as high-performance supercapacitor electrode materials.\",\n \"corpus_id\": 7988690,\n \"score\": 0\n },\n {\n \"doc_id\": \"20449456\",\n \"title\": \"Comparative study of the catalytic activity of [Mn(II)(bpy)2Cl2] and [Mn2(III/IV)(mu-O)2(bpy)4](ClO4)3 in the H2O2 induced oxidation of organic dyes in carbonate buffered aqueous solution.\",\n \"abstract\": \"The kinetics of the hydrogen peroxide induced oxidative degradation of the azo dye Orange II in aqueous carbonate buffered solution were studied for the oxo-bridged [Mn(2)(III/IV)(mu-O)(2)(bpy)(4)](ClO(4))(3) complex and its mononuclear analogue [Mn(II)(bpy)(2)Cl(2)] as catalysts to reveal the underlying reaction mechanism and reactive intermediates participating in the catalytic cycle. Both catalysts show identical oxidative reactivity when used at equimolar manganese concentration. If a simple Mn(II) salt and a 1 : 2 concentration of bipyridine are added to the substrate and oxidant containing reaction mixture, the same oxidative reactivity as found for both readily prepared catalysts was observed for several investigated substrates. This demonstrates the in situ accessibility of a reactive intermediate and its precursor complex. The crucial role of bicarbonate as co-catalyst was studied. The distinct dependence of the observed rate constant for the oxidation reaction on the total carbonate concentration can be accounted for in terms of in situ generation of peroxycarbonate. EPR and rapid scan UV/Vis measurements of the reaction of hydrogen peroxide in carbonate buffered solution with [Mn(2)(III/IV)(mu-O)(2)(bpy)(4)](ClO(4))(3) and [Mn(II)(bpy)(2)Cl(2)], revealed for both catalysts the presence of monomeric Mn(II) and Mn(IV)-oxo species as the main intermediates. The proposed reaction mechanism involves two-electron oxidation of a mononuclear Mn(II) precursor complex to a high-valent Mn(IV)=O intermediate as catalytically active species. Differences in the activity of in situ prepared catalyst precursors of different metal to ligand ratios are reported. The 1 : 2 complex was found to be the catalytically more active precursor for the oxidation of the selected substrates, whereas the 1 : 3 complex rather catalyzed the disproportion of hydrogen peroxide.\",\n \"corpus_id\": 34050042,\n \"score\": 0\n },\n {\n \"doc_id\": \"21138016\",\n \"title\": \"Hydrothermal-reduction synthesis of manganese oxide nanomaterials for electrochemical supercapacitors.\",\n \"abstract\": \"In the present work, amorphous manganese oxide nanomaterials have been synthesized by a common hydrothermal method based on the redox reaction between MnO4(-) and Fe(2+) under an acidic condition. The synthesized MnO2 samples were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and electrochemical studies. XRD results showed that amorphous manganese oxide phase was obtained. XPS quantitative analysis revealed that the atomic ratio of Mn to Fe was 3.5 in the MnO2 samples. TEM images showed the porous structure of the samples. Electrochemical properties of the MnO2 electrodes were studied using cyclic voltammetry and galvanostatic charge-discharge cycling in 1 M Na2SO4 aqueous electrolyte, which showed excellent pseudocapacitance properties. A specific capacitance of 192 Fg(-1) at a current density of 0.5 Ag(-1) was obtained at the potential window from -0.1 to 0.9 V (vs. SCE).\",\n \"corpus_id\": 22023474,\n \"score\": 0\n },\n {\n \"doc_id\": \"21258687\",\n \"title\": \"The structure and catalytic activity of anatase and rutile titania supported manganese oxide catalysts for selective catalytic reduction of NO by NH3.\",\n \"abstract\": \"The structure and catalytic properties of anatase and rutile supported manganese oxide catalysts prepared by impregnation method have been studied by using X-ray diffraction (XRD), laser Raman spectroscopy (LRS), X-ray photoelectron spectroscopy (XPS), H(2) temperature-programmed reduction (H(2)-TPR) and BET surface area measurements combined with activity testing of selective catalytic reduction (SCR) of NO by NH(3). It has been shown that the manganese oxide loadings on the two TiO(2) supports exert great influences on the SCR activity. For the rutile supported manganese oxide catalysts, increasing manganese oxide loading leads to the increase of reducibility of dispersed manganese oxide species and the rate constant k, which reaches a maximum around 9.6 × 10(-6) mol g(Mn)(-1) s(-1) at 0.5 mmol Mn per 100 m(2) TiO(2). When the manganese oxide loading is beyond this value, the existence of amorphous MnO(x) multiple layers will certainly reduce the ratio of manganese oxide species exposed on the surface and the reducibility of dispersed manganese oxide species, resulting in the rapid decrease of rate constant k. The LRS and XPS results have revealed that for the anatase supported manganese oxide catalysts manganese oxide species exist in Mn(+4) as a major species with Mn(+3) species and partially undecomposed Mn-nitrate as the minor species. Under the SCR reaction conditions, Mn(+3) species on anatase are oxidized to Mn(+4) species, inserting in the surface of anatase and promoting the anatase-to-rutile transformation in the surface layers of the anatase support. Since these Mn(4+) cations are actually dispersed on the support with a rutile shell-anatase core structure and its concentration is very near to that of MnO(x)/TiO(2) (R) catalyst, the relation between the rate constant k and the MnO(x) loading on the anatase support is similar to that on the rutile support, and that the rate constant k values for anatase and rutile supported manganese oxide catalysts are very close at the same MnO(x) loading.\",\n \"corpus_id\": 21173218,\n \"score\": 0\n },\n {\n \"doc_id\": \"21380431\",\n \"title\": \"Epoxidation of alkenes and oxidation of alcohols with hydrogen peroxide catalyzed by a manganese(V) nitrido complex.\",\n \"abstract\": \"The manganese(V) nitrido complex (PPh(4))(2)[Mn(N)(CN)(4)] is an active catalyst for alkene epoxidation and alcohol oxidation using H(2)O(2) as an oxidant. The catalytic oxidation is greatly enhanced by the addition of just one equivalent of acetic acid. The oxidation of ethene by this system has been studied computationally by the DFT method.\",\n \"corpus_id\": 20825316,\n \"score\": 0\n },\n {\n \"doc_id\": \"21966674\",\n \"title\": \"Oxidative desulfurization of dibenzothiophene with hydrogen peroxide catalyzed by selenium(IV)-containing peroxotungstate.\",\n \"abstract\": \"With stoichiometric H(2)O(2) as oxidant, dibenzothiophene (DBT) is oxidized to its corresponding sulfone with high efficiency, catalyzed by a sub-valence heteronuclear peroxotungstate, [C(18)H(37)N(CH(3))(3)](4)[H(2)Se(IV)(3)W(6)O(34)], under mild biphase conditions and the catalyst shows remarkable selectivity of catalytic oxidation towards DBT, cinnamyl alcohol and quinoline.\",\n \"corpus_id\": 43220431,\n \"score\": 0\n },\n {\n \"doc_id\": \"22040038\",\n \"title\": \"Application of XPS and solution chemistry analyses to investigate soluble manganese removal by MnO(x)(s)-coated media.\",\n \"abstract\": \"X-ray photoelectron spectroscopy (XPS) was applied to investigate Mn(II) removal by MnO(x)(s)-coated media under experimental conditions similar to the engineered environment of drinking water treatment plants in the absence and presence of chlorine. Macroscopic and spectroscopic results suggest that Mn(II) removal at pH 6.3 and pH 7.2 in the absence of chlorine was mainly due to adsorption onto the MnO(x)(s) surface coating, while removal in the presence of chlorine was due to a combination of initial surface adsorption followed by subsequent surface-catalyzed oxidation. However, Mn(III) was identified by XPS analyses of the Mn 3p photoline for experiments performed in the absence of chlorine at pH 6.3 and pH 7.2, suggesting that surface-catalyzed Mn oxidation also occurred at these conditions. Results obtained at pH 8.2 at 8 and 0.5 mg·L(-1) dissolved oxygen in the absence of chlorine suggest that Mn(II) removal was mainly due to initial adsorption followed by surface-catalyzed oxidation. XPS analyses suggest that Mn(IV) was the predominant species in experiments operated in the presence of chlorine. This study confirms that the use of chlorine combined with the catalytic action of MnO(x)(s) oxides is effective for Mn(II) removal from drinking water filtration systems.\",\n \"corpus_id\": 23766823,\n \"score\": 0\n },\n {\n \"doc_id\": \"22309023\",\n \"title\": \"Impact of interactions between metal oxides to oxidative reactivity of manganese dioxide.\",\n \"abstract\": \"Manganese oxides typically exist as mixtures with other metal oxides in soil-water environments; however, information is only available on their redox activity as single oxides. To bridge this gap, we examined three binary oxide mixtures containing MnO(2) and a secondary metal oxide (Al(2)O(3), SiO(2) or TiO(2)). The goal was to understand how these secondary oxides affect the oxidative reactivity of MnO(2). SEM images suggest significant heteroaggregation between Al(2)O(3) and MnO(2) and to a lesser extent between SiO(2)/TiO(2) and MnO(2). Using triclosan and chlorophene as probe compounds, pseudofirst-order kinetic results showed that Al(2)O(3) had the strongest inhibitory effect on MnO(2) reactivity, followed by SiO(2) and then TiO(2). Al(3+) ion or soluble SiO(2) had comparable inhibitory effects as Al(2)O(3) or SiO(2), indicating the dominant inhibitory mechanism was surface complexation/precipitation of Al/Si species on MnO(2) surfaces. TiO(2) inhibited MnO(2) reactivity only when a limited amount of triclosan was present. Due to strong adsorption and slow desorption of triclosan by TiO(2), precursor-complex formation between triclosan and MnO(2) was much slower and likely became the new rate-limiting step (as opposed to electron transfer in all other cases). These mechanisms can also explain the observed adsorption behavior of triclosan by the binary oxide mixtures and single oxides.\",\n \"corpus_id\": 7911746,\n \"score\": 0\n },\n {\n \"doc_id\": \"22341981\",\n \"title\": \"Effect of precursor and preparation method on manganese based activated carbon sorbents for removing H2S from hot coal gas.\",\n \"abstract\": \"Activated carbon (AC) supported manganese oxide sorbents were prepared by the supercritical water impregnation (SCWI) using two different precursor of Mn(NO(3))(2) (SCW(N)) and Mn(Ac)(2)·4H(2)O (SCW(A)). Their capacities of removing H(2)S from coal gas were evaluated and compared to the sorbents prepared by the pore volume impregnation (PVI) method. The structure and composition of different sorbents were characterized by XRD, SEM, TEM, XPS and XANES techniques. It is found that the precursor of active component plays the crucial role and SCW(N) sorbents show much better sulfidation performance than the SCW(A) sorbents. This is because the Mn(3)O(4) active phase of the SCW(N) sorbents are well dispersed on the AC support, while the Mn(2)SiO(4)-like species in the SCW(A) sorbent can be formed and seriously aggregated. The SCW(N) sorbents with 2.80% and 5.60% manganese are favorable for the sulfidation reaction, since the Mn species are better dispersed on the SCW(N) sorbents than those on the PV(N) sorbents and results in the better sulfidation performance of the SCW(N) sorbents. As the Mn content increases to 11.20%, the metal oxide particles on AC supports aggregate seriously, which leads to poorer sulfidation performance of the SCW(N)11.20% sorbents than that of the PV(N)11.20% sorbents.\",\n \"corpus_id\": 11495435,\n \"score\": 0\n },\n {\n \"doc_id\": \"22579460\",\n \"title\": \"Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion.\",\n \"abstract\": \"The aim of this work was to study combustion of toluene (1000ppm) over MnO(2) modified with different supports. α-Al(2)O(3) and γ-Al(2)O(3) obtained from Boehmite, γ-Al(2)O(3) (commercial), SiO(2), TiO(2) and ZrO(2) were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO(2) was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO(2)/α-Al(2)O(3)(B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289°C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity.\",\n \"corpus_id\": 37497640,\n \"score\": 0\n },\n {\n \"doc_id\": \"22592889\",\n \"title\": \"One-step sonochemical synthesis of a graphene oxide-manganese oxide nanocomposite for catalytic glycolysis of poly(ethylene terephthalate).\",\n \"abstract\": \"Ultrasound-assisted synthesis of a graphene oxide (GO)-manganese oxide nanocomposite (GO-Mn(3)O(4)) was conducted without further modification of GO or employing secondary materials. With the GO nanoplate as a support, potassium permanganate oxidizes the carbon atoms in the GO support and gets reduced to Mn(3)O(4). An intensive ultrasound method could reduce the number of reaction steps and temperature, enhance the reaction rate and furthermore achieve a Mn(3)O(4) phase. The composite was characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and thermogravimetric analysis (TGA). The coverage and crystallinity of Mn(3)O(4) were controlled by changing the ratio of permanganate to GO dispersion. The synthesized nanocomposite was used as a catalyst for poly(ethylene terephthalate) (PET) depolymerization into its monomer, bis(2-hydroxylethyl) terephthalate (BHET). The highest monomer yield of 96.4% was obtained with the nanocomposite containing the lowest amount of Mn(3)O(4), while PET glycolysis with the Mn(3)O(4) without GO yielded 82.7% BHET.\",\n \"corpus_id\": 9789438,\n \"score\": 0\n },\n {\n \"doc_id\": \"22723249\",\n \"title\": \"Degradation of ciprofloxacin by cryptomelane-type manganese(III/IV) oxides.\",\n \"abstract\": \"The objective of this study is to investigate and understand the oxidizing properties of a manganese oxide, specifically synthetic cryptomelane (KMn(8)O(16)) and its derivatives, in aqueous solution. Ciprofloxacin (CIP), a commonly used fluoroquinolone antibiotic, was used as the probe. Synthetic cryptomelane, known as octahedral molecular sieves (OMS-2), was synthesized, and its derivatives were prepared by adding transition metal oxides, V(2)O(5) or MoO(3), as dopants during synthesis. The solids were characterized by x-ray powder diffraction (XRD), SEM-energy-dispersive spectrometry (SEM-EDX), x-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectra (FTIR), Raman spectra, and N(2)-Brunauer-Emmett-Teller method. Degradation of CIP by different doped OMS-2 was carried out. Process conditions were optimized using response surface methodology (RSM). XRD patterns indicated the crystal phase of regular and doped OMS-2 as the cryptomelane type. Presence of the dopants in doped cryptomelane was confirmed by SEM-EDX and XPS. FTIR and Raman results suggested that the dopants were substituted into the framework in place of manganese. SEM images, XRD analysis, and surface area analysis of doped OMS-2 indicated decreased particle size, decreased crystallinity, and increased surface area compared to regular OMS-2. Higher oxidizing reactivity of doped OMS-2 was also observed with increased CIP removal rates from aqueous solution. The enhancement of reactivity may be due to the increase of surface areas. Nine percent Mo/OMS-2, the most effective oxidant of all synthesized derivatives, was selected for optimization study. Favorable treatment conditions were obtained using RSM at pH 3 with molar ratio [9 % Mo/OMS-2]/[CIP] ≥ 50. Under such conditions, more than 90 % CIP can be removed in 30 min. The degradation kinetics was modeled by a modified first order rate with introduction of a retardation factor-α (R (2) > 0.98). Analysis of degradation products indicated that oxidation takes place mainly on the piperazine ring of CIP.\",\n \"corpus_id\": 7246185,\n \"score\": 0\n },\n {\n \"doc_id\": \"22806229\",\n \"title\": \"Nano-sized manganese oxide: a proposed catalyst for water oxidation in the reaction of some manganese complexes and cerium(IV) ammonium nitrate.\",\n \"abstract\": \"According to UV-visible spectroscopy, X-ray diffraction spectrometry, dynamic light scattering, Fourier transform infrared spectroscopy, electron paramagnetic resonance spectroscopy, transmission electron microscopy, scanning electron microscopy and X-ray photoelectron spectroscopy, nano-sized manganese oxides are proposed as active catalysts for water oxidation in the reaction of some manganese complexes and cerium(IV) ammonium nitrate.\",\n \"corpus_id\": 13332578,\n \"score\": 0\n },\n {\n \"doc_id\": \"22948163\",\n \"title\": \"Glucose-promoted Zn-based metal-organic framework/graphene oxide composites for hydrogen sulfide removal.\",\n \"abstract\": \"Zinc-based metal-organic frameworks/graphene oxide (MOF-5/GO) composites were synthesized via the solvothermal method. The materials were characterized by scanning electron microscopy (SEM), nitrogen adsorption, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS), and their performances for hydrogen sulfide (H(2)S) removal were evaluated by dynamic testing at room temperature. The composites exhibit microporous structure with a small amount of mesopores, and the structure is highly dependent on the amount of GO loaded. The surface area and pore volume first increase and then decrease with increasing GO, reaching the maximum value when the GO ratio is 5.25%. The composites exhibit high adsorption capacities for H(2)S, with the maximum uptakes reaching up to 130.1 mg/g. Although the loading of GO makes a contribution to the enhancement of dispersive force in the porous structure, it leads to the crystal distortion of MOF-5. The introduction of glucose can restrain this distortion to maintain the structure stability. A good match between GO and glucose have a well synergy effect to develop the porous structure, resulting in the highest H(2)S adsorption capacity.\",\n \"corpus_id\": 20582109,\n \"score\": 0\n },\n {\n \"doc_id\": \"23050871\",\n \"title\": \"Chromium(III) oxidation by three poorly-crystalline manganese(IV) oxides. 1. Chromium(III)-oxidizing capacity.\",\n \"abstract\": \"The Cr(III)-oxidizing capacity of three layered poorly crystalline Mn(IV)O(2) phases, i.e. δ-MnO(2), Random Stacked Birnessite (RSB), and Acid Birnessite (AB), was determined in real-time and in situ, using Quick X-ray Absorption Fine Structure Spectroscopy (Q-XAFS). The results obtained with this technique, which allows the measurement of the total amount of Cr(VI) produced in the system, indicated that the Cr(III) oxidation reaction had ceased between 30 min and 1 h under most experimental conditions. However, this cessation was not observed with a traditional batch technique, which only allows the measurement of Cr(VI) present in solution and thus neglects the amount of Cr(VI) that may be sorbed to Mn(IV)O(2). This study also demonstrated that the Mn(IV)O(2) phase oxidizing the highest amount of Cr(III), which is positively charged in solution, was the mineral featuring the most negatively charged surface. Also, the results indicated that the presence of Mn(II) and/or Mn(III) impurities inside the Mn(IV)O(2) structure could enhance the mineral's capacity to oxidize Cr(III). The information provided in this study will be useful in predicting the capabilities of naturally occurring Mn oxide minerals, which are similar to the three synthetic Mn(IV)O(2) investigated, to oxidize Cr(III) to toxic and mobile Cr(VI) in the soil of contaminated sites.\",\n \"corpus_id\": 206960974,\n \"score\": 0\n },\n {\n \"doc_id\": \"23143326\",\n \"title\": \"Preparation of materials in the presence of hydrogen peroxide: from discrete or \\\"zero-dimensional\\\" objects to bulk materials.\",\n \"abstract\": \"Based on selected examples from the literature, this perspective aims to provide a short overview of synthetic methods using hydrogen peroxide and/or peroxidic species for the elaboration of discrete or zero-dimensional species, as well as mono-, bi- and tri-dimensional materials. There are several advantages in using peroxidic species: no foreign ion or organic ligand is introduced in the reaction medium, they are relatively cheap compared to costly alkoxides, for example, and in certain favorable cases these methods allow the selective formation of a given oxide polymorph. The materials prepared are used in several important technological applications such as electrochromism, gas sensing and electrochemistry but, in this review, special emphasis is placed on oxidation catalysis. Indeed, the deposition of peroxo species on or into oxide supports generally leads to catalytic materials that display higher activities related to a better dispersion of the active metal species in the host matrix. This review also focuses on the use of hydrogen peroxide for the recycling of toxic metal-containing spent materials such as those found in batteries for portable electronic devices.\",\n \"corpus_id\": 205820362,\n \"score\": 0\n },\n {\n \"doc_id\": \"23249159\",\n \"title\": \"Hole doping in Al-containing nickel oxide materials to improve electrochromic performance.\",\n \"abstract\": \"Electrochromic materials exhibit switchable optical properties that can find applications in various fields, including smart windows, nonemissive displays, and semiconductors. High-performing nickel oxide electrochromic materials have been realized by controlling the material composition and tuning the nanostructural morphology. Post-treatment techniques could represent efficient and cost-effective approaches for performance enhancement. Herein, we report on a post-processing ozone technique that improves the electrochromic performance of an aluminum-containing nickel oxide material in lithium-ion electrolytes. The resulting materials were studied using X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible-near-infrared (UV-vis-NIR) spectroscopy, and X-ray absorption spectroscopy (XAS). It was observed that ozone exposure increased the Ni oxidation state by introducing hole states in the NiO(6) octahedral unit. In addition, ozone exposure gives rise to higher-performing aluminum-containing nickel oxide films, relative to nickel oxide containing both Al and Li, in terms of switching kinetics, bleached-state transparency, and optical modulation. The improved performance is attributed to the decreased crystallinity and increased nickel oxidation state in aluminum-containing nickel oxide electrochromic films. The present study provides an alternative route to improve electrochromic performance for nickel oxide materials.\",\n \"corpus_id\": 35402783,\n \"score\": 0\n },\n {\n \"doc_id\": \"23286528\",\n \"title\": \"Unique properties of ceria nanoparticles supported on metals: novel inverse ceria/copper catalysts for CO oxidation and the water-gas shift reaction.\",\n \"abstract\": \"Oxides play a central role in important industrial processes, including applications such as the production of renewable energy, remediation of environmental pollutants, and the synthesis of fine chemicals. They were originally used as catalyst supports and were thought to be chemically inert, but now they are used to build catalysts tailored toward improved selectivity and activity in chemical reactions. Many studies have compared the morphological, electronic, and chemical properties of oxide materials with those of unoxidized metals. Researchers know much less about the properties of oxides at the nanoscale, which display distinct behavior from their bulk counterparts. More is known about metal nanoparticles. Inverse-model catalysts, composed of oxide nanoparticles supported on metal or oxide substrates instead of the reverse (oxides supporting metal nanoparticles), are excellent tools for systematically testing the properties of novel catalytic oxide materials. Inverse models are prepared in situ and can be studied with a variety of surface science tools (e.g. scanning tunneling microscopy, X-ray photoemission spectroscopy, ultraviolet photoemission spectroscopy, low-energy electron microscopy) and theoretical tools (e.g. density functional theory). Meanwhile, their catalytic activity can be tested simultaneously in a reactor. This approach makes it possible to identify specific functions or structures that affect catalyst performance or reaction selectivity. Insights gained from these tests help to tailor powder systems, with the primary objective of rational design (experimental and theoretical) of catalysts for specific chemical reactions. This Account describes the properties of inverse catalysts composed of CeOx nanoparticles supported on Cu(111) or CuOx/Cu(111) as determined through the methods described above. Ceria is an important material for redox chemistry because of its interchangeable oxidation states (Ce⁴⁺ and Ce³⁺). Cu(111), meanwhile, is a standard catalyst for reactions such as CO oxidation and the water-gas shift (WGS). This metal serves as an ideal replacement for other noble metals that are neither abundant nor cost effective. To prepare the inverse system we deposited nanoparticles (2-20 nm) of cerium oxide onto the Cu(111) surface. During this process, the Cu(111) surface grows an oxide layer that is characteristic of Cu₂O (Cu¹⁺). This oxide can influence the growth of ceria nanoparticles. Evidence suggests triangular-shaped CeO₂(111) grows on Cu₂O(111) surfaces while rectangular CeO₂(100) grows on Cu₄O₃(111) surfaces. We used the CeOx/Cu₂O/Cu(111) inverse system to study two catalytic processes: the WGS (CO + H₂O → CO₂ + H₂) and CO oxidation (2CO + O₂ → 2CO₂). We discovered that the addition of small amounts of ceria nanoparticles can activate the Cu(111) surface and achieve remarkable enhancement of catalytic activity in the investigated reactions. In the case of the WGS, the CeOx nanoparticle facilitated this process by acting at the interface with Cu to dissociate water. In the CO oxidation case, an enhancement in the dissociation of O₂ by the nanoparticles was a key factor. The strong interaction between CeOx nanoparticles and Cu(111) when preoxidized and reduced in CO resulted in a massive surface reconstruction of the copper substrate with the introduction of microterraces that covered 25-35% of the surface. This constitutes a new mechanism for surface reconstruction not observed before. These microterraces helped to facilitate a further enhancement of activity towards the WGS by opening an additional channel for the dissociation of water. In summary, inverse catalysts of CeOx/Cu(111) and CeO₂/Cu₂O/Cu(111) demonstrate the versatility of a model system to obtain insightful knowledge of catalytic processes. These systems will continue to offer a unique opportunity to probe key catalytic components and elucidate the relationship between structure and reactivity of novel materials and reactions in the future.\",\n \"corpus_id\": 9873971,\n \"score\": 0\n },\n {\n \"doc_id\": \"23660768\",\n \"title\": \"In situ/operando studies for the production of hydrogen through the water-gas shift on metal oxide catalysts.\",\n \"abstract\": \"In this perspective article, we show how a series of in situ techniques {X-ray diffraction (XRD), pair-distribution-function analysis (PDF), X-ray absorption fine structure (XAFS), environmental transmission electron microscopy (ETEM), infrared spectroscopy (IR), ambient-pressure X-ray photoelectron spectroscopy (AP-XPS)} can be combined to perform detailed studies of the structural, electronic and chemical properties of metal oxide catalysts used for the production of hydrogen through the water-gas shift reaction (WGS, CO + H2O → H2 + CO2). Under reaction conditions most WGS catalysts undergo chemical transformations that drastically modify their composition with respect to that obtained during the synthesis process. Experiments of time-resolved in situ XRD, XAFS, and PDF indicate that the active phase of catalysts which combine Cu, Au or Pt with oxides such as ZnO, CeO2, TiO2, CeOx/TiO2 and Fe2O3 essentially involves nanoparticles of the reduced noble metals. The oxide support undergoes partial reduction and is not a simple spectator, facilitating the dissociation of water and in some cases modifying the chemical properties of the supported metal. Therefore, to optimize the performance of these catalysts one must take into consideration the properties of the metal and oxide phases. IR and AP-XPS have been used to study the reaction mechanism for the WGS on metal oxide catalysts. Data of IR spectroscopy indicate that formate species are not necessarily involved in the main reaction path for the water-gas shift on Cu-, Au- and Pt-based catalysts. Thus, a pure redox mechanism or associative mechanisms that involve either carbonate-like (CO3, HCO3) or carboxyl (HOCO) species should be considered. In the last two decades, there have been tremendous advances in our ability to study catalytic materials under reaction conditions and we are moving towards the major goal of fully understanding how the active sites for the production of hydrogen through the WGS actually work.\",\n \"corpus_id\": 1101507,\n \"score\": 0\n },\n {\n \"doc_id\": \"23928911\",\n \"title\": \"Low-temperature selective catalytic reduction of NO with NH₃ over nanoflaky MnOx on carbon nanotubes in situ prepared via a chemical bath deposition route.\",\n \"abstract\": \"Nanoflaky MnO(x) on carbon nanotubes (nf-MnO(x)@CNTs) was in situ synthesized by a facile chemical bath deposition route for low-temperature selective catalytic reduction (SCR) of NO with NH₃. This catalyst was mainly characterized by the techniques of X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), N₂ adsorption-desorption analysis, X-ray photoelectron spectroscopy (XPS), H₂ temperature-programmed reduction (H₂-TPR) and NH₃ temperature-programmed desorption (NH₃-TPD). The SEM, TEM, XRD results and N₂ adsorption-desorption analysis indicated that the CNTs were surrounded by nanoflaky MnO(x) and the obtained catalyst exhibited a large surface area as well. Compared with the MnO(x)/CNT and MnO(x)/TiO₂ catalysts prepared by an impregnation method, the nf-MnO(x)@CNTs presented better NH₃-SCR activity at low temperature and a more extensive operating temperature window. The XPS results showed that a higher atomic concentration of Mn(4+) and more chemisorbed oxygen species existed on the surface of CNTs for nf-MnO(x)@CNTs. The H₂-TPR and NH₃-TPD results demonstrated that the nf-MnO(x)@CNTs possessed stronger reducing ability, more acid sites and stronger acid strength than the other two catalysts. Based on the above mentioned favourable properties, the nf-MnO(x)@CNT catalyst has an excellent performance in the low-temperature SCR of NO to N₂ with NH₃. In addition, the nf-MnO(x)@CNT catalyst also presented favourable stability and H₂O resistance.\",\n \"corpus_id\": 205869110,\n \"score\": 0\n },\n {\n \"doc_id\": \"23980657\",\n \"title\": \"H2 dissociation over NbO: the first step toward hydrogenation of Mg.\",\n \"abstract\": \"Niobium-based oxide nanoparticles have proven to be catalytically effective toward hydrogenation of Mg where H2 dissociation over the niobium-oxides is considered to be a crucial reaction step. However, the role of niobium oxides toward H2 dissociation still remains unclear as to what atomic configurations are responsible for the catalytic activity. H2 dissociation over different surface planes of Nb, NbO, and Nb2O5 as well as small NbO clusters is performed by using a density functional theory. The calculations reveal that H2 dissociation, adsorption energy, and the bond type between H and surfaces (clusters) depend on the atomic configurations of Nb and O. In particular, H2 adsorption on NbO(111) is enhanced by O atoms without forming O-H bond where the bond type of H and surface is found to be an electron pairing. Thus, NbO(111) could not only be a effective catalyst but also potentially prevent the formation of MgO during the hydrogenation of Mg. The results should be helpful in developing and tailoring the efficient catalyst toward H2 dissociation and hydrogenation of Mg.\",\n \"corpus_id\": 30558372,\n \"score\": 0\n },\n {\n \"doc_id\": \"24196690\",\n \"title\": \"Redox preparation of mixed-valence cobalt manganese oxide nanostructured materials: highly efficient noble metal-free electrocatalysts for sensing hydrogen peroxide.\",\n \"abstract\": \"High-performance hydrogen peroxide sensors provide valuable signals of biological interactions, disorders, and developing of diseases. Low-cost metal oxides are promising alternatives but suffer from low conductivity and sensing activity. Multi-component metal oxides are excellent candidates to accomplish these challenges, but the composition inhomogeneity is difficult to manage with conventional material preparation. We demonstrated redox preparation strategies to successfully synthesize highly homogeneous, noble metal-free H2O2 sensors of spinel nanostructured cobalt manganese oxides with enhanced conductivity, multiple mixed-valence features, and efficient H2O2 sensing activities. The designed redox reactions accompanied with material nucleation/formation are the key factors for compositional homogeneity. High conductivity (1.5 × 10(-2) S cm(-1)) and H2O2 sensing activity (12 times higher than commercial Co3O4) were achieved due to the homogeneous multiple mixed-valence systems of Co(ii)/(iii) and Mn(iii)/(iv). A wide linear detection range (from 0.1 to 25 mM) with a detection limit of 15 μM was observed. Manganese species assist the formation of large surface area nanostructures, enhancing the H2O2 reduction activities, and inhibit the sensing interference. The material controls of hierarchical nanostructures, elemental compositions, porosity, and electrochemical performances are highly associated with the reaction temperatures. The temperature-dependent properties and nanostructure formation mechanisms based on a reaction rate competition are proposed.\",\n \"corpus_id\": 21201187,\n \"score\": 0\n },\n {\n \"doc_id\": \"25011608\",\n \"title\": \"Freestanding 3D mesoporous Co₃O₄@carbon foam nanostructures for ethanol gas sensing.\",\n \"abstract\": \"Metal oxide materials have been widely used as gas-sensing platforms, and their sensing performances are largely dependent on the morphology and surface structure. Here, freestanding flower-like Co3O4 nanostructures supported on three-dimensional (3D) carbon foam (Co3O4@CF) were successfully synthesized by a facile and low-cost hydrothermal route and annealing procedure. The morphology and structure of the nanocomposites were studied by X-ray diffraction, X-ray photoelectron spectroscopy, energy-dispersive spectroscopy, and scanning electron microscopy (SEM). The SEM characterizations showed that the skeleton of the porous carbon foam was fully covered by flower-like Co3O4 nanostructures. Moreover, each Co3O4 nanoflower is composed of densely packed nanoneedles with a length of ~10 μm, which can largely enhance the surface area (about 286.117 m(2)/g) for ethanol sensing. Gas sensor based on the as-synthesized 3D Co3O4@CF nanostructures was fabricated to study the sensing performance for ethanol at a temperature range from 180 to 360 °C. Due to the 3D porous structure and the improvement in sensing surface/interface, the Co3O4@CF nanostructure exhibited enhanced sensing performance for ethanol detection with low resistance, fast response and recovery time, high sensitivity, and limit of detection as low as 15 ppm at 320 °C. The present study shows that such novel 3D metal oxide/carbon hybrid nanostructures are promising platforms for gas sensing.\",\n \"corpus_id\": 36445973,\n \"score\": 0\n },\n {\n \"doc_id\": \"25043803\",\n \"title\": \"Nickel oxide thin film from electrodeposited nickel sulfide thin film: peroxide sensing and photo-decomposition of phenol.\",\n \"abstract\": \"A novel non-enzymatic peroxide sensor has been constructed by using nickel oxide (NiO) thin films as sensing material, which were prepared by a two-step process: (i) electrodeposition of nickel sulfide (NiS) and (ii) thermal air oxidation of as-deposited NiS to NiO. The resultant material is highly porous and comprises interconnected nanofibers. UV-Vis spectroscopy, FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and field-emission scanning electron microscopy (FESEM) were used for a complete characterization of nanostructured NiO thin films. Cyclic voltammetry study shows that NiO/ITO electrode facilitates the oxidation of hydrogen peroxide and exhibits excellent catalytic activity towards its sensing. The amperometric study of NiO/ITO was carried out to determine the sensitivity, linear range, detection limit of the proposed sensor. The sensor exhibits prominent electrocatalytic activity toward the oxidation of H2O2 with a wide linear range and a low detection limit. The possible use of the synthesized NiO thin films as an effective photocatalyst for the decomposition of phenol is also discussed.\",\n \"corpus_id\": 262546729,\n \"score\": 0\n },\n {\n \"doc_id\": \"25127389\",\n \"title\": \"Graphene oxide as an effective catalyst for wet air oxidation of phenol.\",\n \"abstract\": \"The graphene oxide (GO) and chemically reduced graphene oxides, used as catalysts in absence of any metals, were investigated in the catalytic wet air oxidation (CWAO) of phenol in a batch reactor. The characterization of the materials was measured with scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman, fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The carbon materials exhibited good phenol and total organic compounds (TOC) removals in the CWAO of phenol. The GO had the highest catalytic activity, total phenol removal was achieved after 40 min, and ca. 84% TOC removal was obtained after 120 min at reaction temperature of 155°C, total pressure of 2.5 MPa and catalyst loading of 0.2 gL(-1).\",\n \"corpus_id\": 8825252,\n \"score\": 0\n },\n {\n \"doc_id\": \"25140618\",\n \"title\": \"Tremendous effect of the morphology of birnessite-type manganese oxide nanostructures on catalytic activity.\",\n \"abstract\": \"The octahedral layered birnessite-type manganese oxide (OL-1) with the morphologies of nanoflowers, nanowires, and nanosheets were prepared and characterized with X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric/differential scanning calorimetry (TG/DSC), Brunnauer-Emmett-Teller (BET), inductively coupled plasma (ICP), and X-ray photoelectron spectroscopy (XPS). The OL-1 nanoflowers possess the highest concentration of oxygen vacancies or Mn(3+), followed by the OL-1 nanowires and nanosheets. The result of catalytic tests shows that the OL-1 nanoflowers exhibit a tremendous enhancement in the catalytic activity for benzene oxidation as compared to the OL-1 nanowires and nanosheets. Compared to the OL-1 nanosheets, the OL-1 nanoflowers demonstrate an enormous decrease (ΔT(50) = 274 °C; ΔT(90) > 248 °C) in reaction temperatures T50 and T90 (corresponding to 50 and 90% benzene conversion, respectively) for benzene oxidation. The origin of the tremendous effect of morphology on the catalytic activity for the nanostructured OL-1 catalysts is experimentally and theoretically studied via CO temperature-programmed reduction (CO-TPR) and density functional theory (DFT) calculation. The tremendous catalytic enhancement of the OL-1 nanoflowers compared to the OL-1 nanowires and nanosheets is attributed to their highest surface area as well as their highest lattice oxygen reactivity due to their higher concentration of oxygen vacancies or Mn(3+), thus tremendously improving the catalytic activity for the benzene oxidation.\",\n \"corpus_id\": 1634678,\n \"score\": 0\n },\n {\n \"doc_id\": \"25599521\",\n \"title\": \"Quantitative depth profiling of Ce(3+) in Pt/CeO2 by in situ high-energy XPS in a hydrogen atmosphere.\",\n \"abstract\": \"The redox property of ceria is a key factor in the catalytic activity of ceria-based catalysts. The oxidation state of well-defined ceria nanocubes in gas environments was analysed in situ by a novel combination of near-ambient pressure X-ray Photoelectron Spectroscopy (XPS) and high-energy XPS at a synchrotron X-ray source. In situ high-energy XPS is a promising new tool to determine the electronic structure of matter under defined conditions. The aim was to quantitatively determine the degree of cerium reduction in a nano-structured ceria-supported platinum catalyst as a function of the gas environment. To obtain a non-destructive depth profile at near-ambient pressure, in situ high-energy XPS analysis was performed by varying the kinetic energy of photoelectrons from 1 to 5 keV, and, thus, the probing depth. In ceria nanocubes doped with platinum, oxygen vacancies formed only in the uppermost layers of ceria in an atmosphere of 1 mbar hydrogen and 403 K. For pristine ceria nanocubes, no change in the cerium oxidation state in various hydrogen or oxygen atmospheres was observed as a function of probing depth. In the absence of platinum, hydrogen does not dissociate and, thus, does not lead to reduction of ceria.\",\n \"corpus_id\": 5392191,\n \"score\": 0\n },\n {\n \"doc_id\": \"25852349\",\n \"title\": \"Vanadia supported on nickel manganese oxide nanocatalysts for the catalytic oxidation of aromatic alcohols.\",\n \"abstract\": \"Vanadia nanoparticles supported on nickel manganese mixed oxides were synthesized by co-precipitation method. The catalytic properties of these materials were investigated for the oxidation of benzyl alcohol using molecular oxygen as oxidant. It was observed that the calcination temperature and the size of particles play an important role in the catalytic process. The catalyst was evaluated for its oxidation property against aliphatic and aromatic alcohols, which was found to display selectivity towards aromatic alcohols. The samples were characterized by employing scanning electron microscopy, transmission electron microscopy, X-ray diffraction, Brunauer-Emmett-Teller analysis, thermogravimetric analysis, and X-ray photoelectron spectroscopy.\",\n \"corpus_id\": 17386989,\n \"score\": 0\n },\n {\n \"doc_id\": \"25913679\",\n \"title\": \"Sulfate radicals induced from peroxymonosulfate by cobalt manganese oxides (Co(x)Mn(3-x)O4) for Fenton-Like reaction in water.\",\n \"abstract\": \"A series of CoxMn3-xO4 particles as Fenton-like solid catalysts were synthesized, and their catalytic performance in oxidative degradation of organic dye compounds in water was investigated. The surface morphology and structure of the CoxMn3-xO4 catalysts were characterized by field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), powder X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The results showed that, as an oxide composite of Co and Mn elements, CoMn2O4 showed much stronger catalytic activity in peroxymonosulfate (PMS) oxidation than Co3O4, Mn2O3, and their physical mixture. Typically, the uses of 0.02 g/dm(3) CoMn2O4 and 0.2 g/dm(3) PMS yielded a nearly complete removal of Rhodamine B (0.03 g/dm(3)) in 80 min at 25 °C. The efficiency of Rhodamine B decomposition increased with increasing temperature (15-55 °C), but decreased with the increase of fulvic acid concentration (0-0.08 g/dm(3)). Furthermore, CoMn2O4 could maintain its catalytic activity in the repeated batch experiments. Moreover, HO· and SO4(·-) radicals participating in the process were evidenced using quenching experiments, and a rational mechanism was proposed. PMS oxidation with CoMn2O4 is an efficient technique for remediation of organic contaminants in wastewater.\",\n \"corpus_id\": 25983226,\n \"score\": 0\n },\n {\n \"doc_id\": \"25924339\",\n \"title\": \"Development of Ni-Mo/Al2O3 catalyst for reverse water gas shift (RWGS) reaction.\",\n \"abstract\": \"In the present study, Mo/Al2O3 catalyst was prepared using impregnation method. Then it was promoted with Ni ions to produce Ni-Mo/Al2O3 catalyst. The structures of the catalysts were studied using X-ray diffraction (XRD), Energy dispersive X-ray (EDAX), Brunauer-Emmett-Teller (BET), X-ray photoelectron spectroscopy (XPS), CO chemisorption, temperature programmed reduction of hydrogen (H2-TPR) and scanning electron microscope (SEM) techniques. Catalytic performances of the two catalysts were investigated in a fixed-bed reactor for RWGS reaction. The results indicated that addition of nickel promoter to Mo/Al2O3 catalyst enhances its activity. It is reasonable for the electron deficient state of the Ni species and existence of NiMoO4 phase to possess high activity in RWGS reaction. Stability test of Ni-Mo/Al2O3 catalyst was carried out in a fixed bed reactor and a high CO2 conversion for 60 h time on stream was demonstrated. This study introduces a new catalyst, Ni-Mo/Al2O3, with high activity and stability for RWGS reaction.\",\n \"corpus_id\": 25989381,\n \"score\": 0\n },\n {\n \"doc_id\": \"25924399\",\n \"title\": \"Study on the electrochemical behavior of nanostructure S-doping manganese oxide as a novel supercapacitor material.\",\n \"abstract\": \"A nanostructure S-doping manganese oxide (MnO(x)S(y)) amorphous powder was prepared by a homogeneous coprecipitation method for supercapacitor application. The structure and surface morphology of the as-prepared MnO(x)S(y) powder were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), elemental analysis and X-ray photoelectron spectroscopy (XPS). The as-prepared nanostructure S-doping manganese oxide powder was confirmed with a chemical composition of MnO1.26S0.23 by elemental analysis, in which the average oxidation state of manganese is about 3.1. The supercapacitive behavior of the as-prepared MnO1.26S0.23 was studied by means of cyclic voltammetry (CV) and constant current charge-discharge cycling (CD) experiments in 1 mol L(-1) Na2SO4 electrolyte. A maximum specific capacitance of 181 F g(-1) was obtained for MnO1.26S0.23. Furthermore, the specific capacitance remained 97.3% of the original value after 500 cycles. The superior capacitive behavior and better cycling stability indicate that the amorphous nanostructure MnO(x)S(y) maybe a promising electrode material for electrochemical capacitors.\",\n \"corpus_id\": 29429264,\n \"score\": 0\n },\n {\n \"doc_id\": \"26370819\",\n \"title\": \"Oxidation of elemental mercury by modified spent TiO2-based SCR-DeNOx catalysts in simulated coal-fired flue gas.\",\n \"abstract\": \"In order to reduce the costs, the recycle of spent TiO2-based SCR-DeNOx catalysts were employed as a potential catalytic support material for elemental mercury (Hg(0)) oxidation in simulated coal-fired flue gas. The catalytic mechanism for simultaneous removal of Hg(0) and NO was also investigated. The catalysts were characterized by Brunauer-Emmett-Teller (BET), scanning electron microscope (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) method. Results indicated that spent TiO2-based SCR-DeNOx catalyst supported Ce-Mn mixed oxides catalyst (CeMn/SCR1) was highly active for Hg(0) oxidation at low temperatures. The Ce1.00Mn/SCR1 performed the best catalytic activities, and approximately 92.80 % mercury oxidation efficiency was obtained at 150 °C. The inhibition effect of NH3 on Hg(0) oxidation was confirmed in that NH3 consumed the surface oxygen. Moreover, H2O inhibited Hg(0) oxidation while SO2 had a promotional effect with the aid of O2. The XPS results illustrated that the surface oxygen was responsible for Hg(0) oxidation and NO conversion. Besides, the Hg(0) oxidation and NO conversion were thought to be aided by synergistic effect between the manganese and cerium oxides.\",\n \"corpus_id\": 5455710,\n \"score\": 0\n },\n {\n \"doc_id\": \"26433477\",\n \"title\": \"A trimodal porous carbon as an effective catalyst for hydrogen production by methane decomposition.\",\n \"abstract\": \"A new type of porous carbon with an interconnected trimodal pore system is synthesized by a nanocasting method using nanoparticulated bimodal micro-mesoporous silica particles as the template. The synthesized template and carbon material are characterized using transmission electron microscopy (TEM), field emission electron scanning microscopy (FESEM) and nitrogen adsorption-desorption test. The synthesized carbon material has an extremely high surface area, a large pore volume and an interconnected pore structure, which could provide abundant active sites and space for chemical reactions and minimize the diffusion resistance of the reactants. The resulting carbon is used as the catalyst for hydrogen production by the thermal decomposition of methane. The catalytic results show that the as-synthesized carbon in this study produces much higher methane conversion and hydrogen yield than the commercial carbon materials.\",\n \"corpus_id\": 8862437,\n \"score\": 0\n },\n {\n \"doc_id\": \"26784198\",\n \"title\": \"Studies of Reduced Graphene Oxide and Graphite Oxide in the Aspect of Their Possible Application in Gas Sensors.\",\n \"abstract\": \"The paper presents the results of investigations on resistance structures based on graphite oxide (GRO) and graphene oxide (rGO). The subject matter of the investigations was thaw the sensitivity of the tested structures was affected by hydrogen, nitrogen dioxide and carbon dioxide. The experiments were performed at a temperature range from 30 °C to 150 °C in two carrier gases: nitrogen and synthetic air. The measurements were also aimed at characterization of the graphite oxide and graphene oxide. In our measurements we used (among others) techniques such as: Atomic Force Microscopy (AFM); Scanning Electron Microscopy (SEM); Raman Spectroscopy (RS); Fourier Transform Infrared Spectroscopy (FT-IR) and X-ray Photoelectron Microscopy (XPS). The data resulting from the characterizations of graphite oxide and graphene oxide have made it possible to interpret the obtained results from the point of view of physicochemical changes occurring in these structures.\",\n \"corpus_id\": 7271967,\n \"score\": 0\n },\n {\n \"doc_id\": \"27042821\",\n \"title\": \"Supercapacitive properties of nanoporous oxide layer formed on 304 type stainless steel.\",\n \"abstract\": \"The nanoporous oxide layer is formed on the surface of 304 type stainless steel (SS) by chemical oxidation method. The characterization of the oxide layer is carried out using X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), contact angle and energy-dispersive X-ray spectroscopy (EDS) techniques. The supercapacitive properties of oxide layer are studied using cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy techniques.\",\n \"corpus_id\": 28419427,\n \"score\": 0\n },\n {\n \"doc_id\": \"27333408\",\n \"title\": \"Insights into the solar light driven thermocatalytic oxidation of VOCs over tunnel structured manganese oxides.\",\n \"abstract\": \"Different tunnel structured manganese oxides (1*1, 2*2, and 3*3) have been synthesized via a facile hydrothermal strategy. The three catalysts exhibit high photothermal performance, resulting in a considerable increase of temperature above the light-off temperature for VOC oxidation. On this point, aerobic oxidation reactions of propane and propylene under simulated sunlight and infrared light irradiation were selected as probe reactions to explore their light driven thermocatalytic activity. Furthermore, the light-off curves of the manganese oxides for propane and propylene were carefully investigated, which clearly explained the possibility of combining both the efficient photothermal effect and excellent thermocatalytic activity of the manganese oxides. Results show that the catalytic effects follow the order of 1*1 < 3*3 < 2*2. 2*2 exhibited the best catalytic properties due to better low-temperature reducibility, suitable tunnel structure and the presence of more Mn(4+). This work suggests new applications for traditional catalysts with intense photoabsorption and provides insights into the overall utilization of solar energy.\",\n \"corpus_id\": 206018186,\n \"score\": 0\n },\n {\n \"doc_id\": \"27423769\",\n \"title\": \"Integrated ternary nanocomposite of TiO2/NiO/reduced graphene oxide as a visible light photocatalyst for efficient degradation of o-chlorophenol.\",\n \"abstract\": \"This study investigated a novel approach for the synthesis of an integrated ternary nanocomposite which could act as a good photo-catalyst under visible light irradiation for the removal of organic pollutants from aqueous environments. The photo-catalyst included nickel oxide (NiO) as a dopant, and reduced graphene oxide (RGO) as a good carbon basal support for enhancement of the photo-catalytic activity of TiO2. Under irradiation with visible light, the ternary nanocomposite (TiO2/NiO-RGO) system generates e(-)/h(+) pairs, and then reacts with H2O and O2(-) molecules to produce oxy-radicals which can be used for the mineralization of o-chlorophenol from aqueous solution. The characteristic of all photo-catalysts were investigated by UV-Vis analysis, with surface area and pore size measurements by Brunauer-Emmett-Teller (BET), crystallinity by X-ray diffraction (XRD), elemental composition by X-ray photoelectron spectroscopy (XPS), and morphology by scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX). The functional groups were measured by Fourier transform infrared (FT-IR) spectroscopy before and after o-chlorophenol degradation. TiO2/NiO-RGO was capable of achieving 88.4% photo-degradation of 100 mg/L o-chlorophenol (100 mL) within 8 h with addition of 0.01% H2O2 under visible light irradiation at pH 6.5. The photo-degradation followed a pseudo-first-order reaction. The TiO2/NiO-RGO nanocomposite retained its high removal efficiency, even after four photo-catalytic cycles.\",\n \"corpus_id\": 9678145,\n \"score\": 0\n },\n {\n \"doc_id\": \"28210734\",\n \"title\": \"Ceria-based model catalysts: fundamental studies on the importance of the metal-ceria interface in CO oxidation, the water-gas shift, CO2 hydrogenation, and methane and alcohol reforming.\",\n \"abstract\": \"Model metal/ceria and ceria/metal catalysts have been shown to be excellent systems for studying fundamental phenomena linked to the operation of technical catalysts. In the last fifteen years, many combinations of well-defined systems involving different kinds of metals and ceria have been prepared and characterized using the modern techniques of surface science. So far most of the catalytic studies have been centered on a few reactions: CO oxidation, the hydrogenation of CO2, and the production of hydrogen through the water-gas shift reaction and the reforming of methane or alcohols. Using model catalysts it has been possible to examine in detail correlations between the structural, electronic and catalytic properties of ceria-metal interfaces. In situ techniques (X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, infrared spectroscopy, scanning tunneling microscopy) have been combined to study the morphological changes under reaction conditions and investigate the evolution of active phases involved in the cleavage of C-O, C-H and C-C bonds. Several studies with model ceria catalysts have shown the importance of strong metal-support interactions. In general, a substantial body of knowledge has been acquired and concepts have been developed for a more rational approach to the design of novel technical catalysts containing ceria.\",\n \"corpus_id\": 3743836,\n \"score\": 0\n },\n {\n \"doc_id\": \"28344278\",\n \"title\": \"Investigation of MnO₂ and Ordered Mesoporous Carbon Composites as Electrocatalysts for Li-O₂ Battery Applications.\",\n \"abstract\": \"The electrocatalytic activities of the MnO₂/C composites are examined in Li-O₂ cells as the cathode catalysts. Hierarchically mesoporous carbon-supported manganese oxide (MnO₂/C) composites are prepared using a combination of soft template and hydrothermal methods. The composites are characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, small angle X-ray scattering, The Brunauer-Emmett-Teller (BET) measurements, galvanostatic charge-discharge methods, and rotating ring-disk electrode (RRDE) measurements. The electrochemical tests indicate that the MnO₂/C composites have excellent catalytic activity towards oxygen reduction reactions (ORRs) due to the larger surface area of ordered mesoporous carbon and higher catalytic activity of MnO₂. The O₂ solubility, diffusion rates of O₂ and O₂(•-) coefficients (DO₂ and DO(-)₂), the rate constant (kf) for producing O₂(•-), and the propylene carbonate (PC)-electrolyte decomposition rate constant (k) of the MnO₂/C material were measured by RRDE experiments in the 0.1 M TBAPF₆/PC electrolyte. The values of kf and k for MnO₂/C are 4.29 × 10(-2) cm·s(-1) and 2.6 s(-1), respectively. The results indicate that the MnO₂/C cathode catalyst has higher electrocatalytic activity for the first step of ORR to produce O₂(•-) and achieves a faster PC-electrolyte decomposition rate.\",\n \"corpus_id\": 14794338,\n \"score\": 0\n },\n {\n \"doc_id\": \"28892795\",\n \"title\": \"Uniform dispersion of cobalt nanoparticles over nonporous TiO2 with low activation energy for magnesium sulfate recovery in a novel magnesia-based desulfurization process.\",\n \"abstract\": \"The forced oxidation of magnesium sulfite (MgSO3) aims to not only reclaim the by-product in the magnesia desulfurization, but also lower the risk of secondary pollution. The non-porous titanium dioxide nanoparticle was used as a support to prepare the cobalt catalyst (Co-TiO2) in order to expedite the oxidation rate. This fabricated Co-TiO2 was characterized by inductively coupled plasma optical emission spectroscopy (ICP-OES), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), and energy dispersive spectroscopy (EDS) to figure out its catalytic mechanism. The results revealed that the cobalt nanoparticles were uniformly dispersed on the surface of the TiO2 in forms of Co3O4 and Co2O3. The kinetics of the MgSO3 oxidation catalyzed by the prepared Co-TiO2 was investigated in a bubbling tank reactor, indicating that the oxidation rate was dependent on the catalyst concentration, oxygen partial pressure, pH value, and the reaction temperature. Compared with the reported porous catalyst (Co-CNTs), the activation energy with the Co-TiO2 (17.29kJmol-1) decreased by 50.9%, resulting in a good catalytic performance in sulfite oxidation. The findings will help advance the industrial application of the novel magnesia desulfurization process.\",\n \"corpus_id\": 44831843,\n \"score\": 0\n },\n {\n \"doc_id\": \"28895018\",\n \"title\": \"Promotional effect of rare earth-doped manganese oxides supported on activated semi-coke for selective catalytic reduction of NO with NH3.\",\n \"abstract\": \"A composite catalyst for the selective catalytic reduction (SCR) of NOx with NH3 is investigated, in which the rare earth (RE, including La, Ce, Pr, and Nd) is doped into manganese oxides supported on activated semi-coke (MnOx/ASC) via hydrothermal method at the molar ratio of Mn:RE = 1:5. It is evidenced that the addition of RE at a rather low molar ratio can enhance the catalytic activity of MnOx/ASC. The catalyst with a Mn:Ce molar ratio of 10:1 yields an over 90% NOx removal efficiency in the temperature range of 150-250 °C. An approximate 100% NO conversion and 95% N2 selectivity are achieved at about 200 °C. The catalysts are characterized by N2 physisorption, X-ray powder diffraction (XRD), scanning electron microscope (SEM), hydrogen temperature-programmed reduction (H2-TPR) and X-ray photoelectron spectroscopy (XPS). The results indicated that the Ce additive is conducive to the NOx adsorption and then accelerates the SCR reaction due to the formation of more chemisorbed oxygen (Oβ), which is favored during the oxidation of NH3 and NO. Moreover, the in situ diffused reflectance infrared Fourier transform spectroscopy (DRIFTS) results confirm that the Ce additive on MnOx/ASC catalyst could provide more active Brønsted acid sites, which eventually contributes to the SCR reaction. The generation of ad-NH4+ and nitrite species is proved to play the crucial role in the promotional effect of RE addition.\",\n \"corpus_id\": 30338472,\n \"score\": 0\n },\n {\n \"doc_id\": \"29111664\",\n \"title\": \"Oxygen Plasma-Treated Graphene Oxide Surface Functionalization for Sensitivity Enhancement of Thin-Film Piezoelectric Acoustic Gas Sensors.\",\n \"abstract\": \"In this work, we presented a thin-film piezoelectric acoustic gas sensor with enhanced sensitivity by a surface modification strategy of oxygen plasma treated graphene oxide (GO) functionalization. By exposing to ammonia vapor (NH3) of various concentrations at controlled temperature and humidity, the characteristics of the GO-coated acoustic sensor were investigated, that is, sensitivity, linearity, response, and recovery time. Oxygen plasma treatment of the GO-coated sensor further enhanced the sensitivity compared with the freshly prepared GO-coated sensor. The mechanism of oxygen plasma treatment effect on the GO-coated sensor was discussed based on characterizations of X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, scanning electron microscope (SEM), and precise weighing of the acoustic sensor. It was found that the oxygen plasma treatment introduces numerous defects to GO flakes, which are uniformly distributed across the GO surface, providing more gas molecule binding sites.\",\n \"corpus_id\": 206462433,\n \"score\": 0\n },\n {\n \"doc_id\": \"29163900\",\n \"title\": \"Manganese complex-catalyzed oxidation and oxidative kinetic resolution of secondary alcohols by hydrogen peroxide.\",\n \"abstract\": \"The highly efficient catalytic oxidation and oxidative kinetic resolution (OKR) of secondary alcohols has been achieved using a synthetic manganese catalyst with low loading and hydrogen peroxide as an environmentally benign oxidant in the presence of a small amount of sulfuric acid as an additive. The product yields were high (up to 93%) for alcohol oxidation and the enantioselectivity was excellent (>90% ee) for the OKR of secondary alcohols. Mechanistic studies revealed that alcohol oxidation occurs via hydrogen atom (H-atom) abstraction from an α-CH bond of the alcohol substrate and a two-electron process by an electrophilic Mn-oxo species. Density functional theory calculations revealed the difference in reaction energy barriers for H-atom abstraction from the α-CH bonds of R- and S-enantiomers by a chiral high-valent manganese-oxo complex, supporting the experimental result from the OKR of secondary alcohols.\",\n \"corpus_id\": -1,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":49,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29670409\",\n \"title\": \"Safinamide: an add-on treatment for managing Parkinson's disease.\",\n \"abstract\": \"Heterogeneous expression of neurotransmitter deficits results from onset and progression of Parkinson's disease. Intervals, characterized by reappearance of motor and associated certain nonmotor symptoms, determine the end of good tolerability and efficacy of oral levodopa therapy. These \\\"OFF\\\" states result from levodopa pharmacokinetics and disease progression-related deterioration of the central buffering capacity for fluctuations of dopamine levels. This review discusses safinamide as an add-on therapeutic agent in orally levodopa-treated patients with \\\"OFF\\\" phenomena. Safinamide provided beneficial effects on \\\"OFF\\\" symptoms in pivotal trials with doses of 50 or 100 mg once daily. Safinamide reversibly inhibits mono-amine oxidase B and declines abnormal glutamate release by modulation of potassium- and sodium ion channels. An ideal candidate for combination with safinamide is opicapone. This inhibitor of peripheral catechol-O-methyltransferase supports continuous brain delivery of levodopa and, thus, the continuous dopaminergic stimulation concept. Both compounds with their once-daily application and good tolerability may complement each other by reduction of necessary oral levodopa intakes and \\\"OFF\\\" times. Thus, a promising, future option will be combination of safinamide and opicapone in one formulation. It will reduce adherence issues and may complement levodopa treatment. It will probably cause less nausea and edema than a dopamine agonist/levodopa regimen.\",\n \"corpus_id\": 4947530\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"23673910","title":"Pharmacokinetic considerations for the use of levodopa in the treatment of Parkinson disease: focus on levodopa/carbidopa/entacapone for treatment of levodopa-associated motor complications.","abstract":"Parkinson disease (PD) is a progressive, disabling, neurodegenerative disorder characterized by both motor and nonmotor symptoms. Monoamine oxidase B inhibitors, dopamine agonists, N-methyl-D-aspartate antagonists and levodopa (LD), with its various formulations and administration modes, mainly improve the motor symptoms in PD, which are thought to be related to decreased dopamine levels in the brain. Of these therapeutic drug options, LD represents the most effective and best tolerated compound when it is administered several times a day. Pharmacokinetic trials of oral LD/dopa decarboxylase inhibitor (DDCI) formulations with and without the catechol-O-methyltransferase inhibitor, entacapone, showed that repeated administration with entacapone causes an increase in both the maximum concentration (Cmax) and time to Cmax (Tmax) of LD. In addition, gastrointestinal motility may also impact plasma LD behavior. These peripheral components of LD metabolism contribute to the onset of motor complications, which are predominantly associated with LD/DDCI owing to its short plasma half-life. The increase in Tmax is related to a slower increase in plasma LD concentrations after repeated LD/DDCI intake, which may also increase the risk of wearing off. An elevation in Cmax after reiterated LD intake increases the risk of peak-dose dyskinesia. Therefore, it may be useful to start with higher doses of LD formulations in the morning and then to titrate with different LD doses during the day according to the individual patient's motor behavior, which is particularly characterized by the onset of motor complications, such as off periods and dyskinesia, in more advanced stages of PD.","corpus_id":37581901,"score":2},{"doc_id":"24053341","title":"Current status of safinamide for the drug portfolio of Parkinson's disease therapy.","abstract":"Parkinson's disease (PD) is characterized by a slowly ongoing neuronal death. This alters dopaminergic and glutamatergic neurotransmission and causes a wide variety of motor and non-motor features. Safinamide has a unique pharmacological profile, which combines modulation of dopamine metabolism by reversible, highly specific monoamine oxidase-B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and of glutamate release induced by abnormal neuronal activity. Therefore, safinamide represents an ideal candidate for the treatment of PD. This compound asks for one time daily intake only within an optimum dose range between 50 and 100 mg. In clinical trials, safinamide was well tolerated and safe, improved motor behavior even in combination with dopamine agonist only, ameliorated levodopa-associated motor complications. Safinamide has the potential to become an important compound for the therapy of PD, since its symptomatic efficacy appears to be superior to available monoamine oxidase-B inhibitors or N-methyl-d-aspartate receptor antagonists like amantadine, according to available trial outcomes.","corpus_id":207193329,"score":2},{"doc_id":"24323641","title":"Randomized trial of safinamide add-on to levodopa in Parkinson's disease with motor fluctuations.","abstract":"Levodopa is effective for the motor symptoms of Parkinson's disease (PD), but is associated with motor fluctuations and dyskinesia. Many patients require add-on therapy to improve motor fluctuations without exacerbating dyskinesia. The objective of this Phase III, multicenter, double-blind, placebo-controlled, parallel-group study was to evaluate the efficacy and safety of safinamide, an α-aminoamide with dopaminergic and nondopaminergic mechanisms, as add-on to l-dopa in the treatment of patients with PD and motor fluctuations. Patients were randomized to oral safinamide 100 mg/day (n = 224), 50 mg/day (n = 223), or placebo (n = 222) for 24 weeks. The primary endpoint was total on time with no or nontroublesome dyskinesia (assessed using the Hauser patient diaries). Secondary endpoints included off time, Unified Parkinson's Disease Rating Scale (UPDRS) Part III (motor) scores, and Clinical Global Impression-Change (CGI-C). At week 24, mean ± SD increases in total on time with no or nontroublesome dyskinesia were 1.36 ± 2.625 hours for safinamide 100 mg/day, 1.37 ± 2.745 hours for safinamide 50 mg/day, and 0.97 ± 2.375 hours for placebo. Least squares means differences in both safinamide groups were significantly higher versus placebo. Improvements in off time, UPDRS Part III, and CGI-C were significantly greater in both safinamide groups versus placebo. There were no significant between-group differences for incidences of treatment-emergent adverse events (TEAEs) or TEAEs leading to discontinuation. The addition of safinamide 50 mg/day or 100 mg/day to l-dopa in patients with PD and motor fluctuations significantly increased total on time with no or nontroublesome dyskinesia, decreased off time, and improved parkinsonism, indicating that safinamide improves motor symptoms and parkinsonism without worsening dyskinesia.","corpus_id":18182887,"score":2},{"doc_id":"24650154","title":"Safinamide for the treatment of Parkinson's disease.","abstract":"INTRODUCTION: Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta. Non-dopaminergic neurotransmitter systems are also involved in its pathomechanism. The aim of the treatment is to improve the dopamine-deficient state and to alleviate the motor and the non-motor symptoms. Safinamide is an α-aminoamide derivative with a combined, dopaminergic and non-dopaminergic mode of action. Phase III clinical trials with safinamide, as add-on therapy to a dopamine agonist (DAA) and to levodopa (LD) in early and advanced stage PD, respectively, demonstrated an improvement of the motor symptoms. AREAS COVERED: The review discusses the pharmacokinetic and pharmacodynamic properties of safinamide and provides an overview of the clinical trials conducted with safinamide in PD. A literature search was made in PubMed for safinamide, safinamide pharmacokinetics, PD treatment and monoamine oxidase-B inhibitors, and in PubMed and on the ClinicalTrials.gov site for clinical trials with safinamide in PD. EXPERT OPINION: The place of safinamide in the therapy of PD is yet to be determined. However, the authors believe that safinamide is a valuable drug in the treatment of PD treatment with favorable pharmacokinetic and side-effect profiles. Data so far suggest that it can be used beneficially as add-on therapy both to DAAs in early PD and to LD in the later stages of the disease.","corpus_id":23200408,"score":2},{"doc_id":"25559423","title":"Catechol-O-methyltransferase inhibitors in Parkinson's disease.","abstract":"Inhibitors of catechol-O-methyltransferase (COMT) are commonly used as an adjunct to levodopa in patients with Parkinson's disease (PD) for the amelioration of wearing-off symptoms. This narrative review aims to discuss the role of COMT inhibitors on peripheral levodopa metabolism and continuous brain delivery of levodopa, and to describe their metabolic properties. Oral application of levodopa formulations with a dopa decarboxylase inhibitor (DDI) results in fluctuating levodopa plasma concentrations, predominantly due to the short half-life of levodopa and its slowing of gastric emptying. Following transport across the blood-brain barrier and its metabolic conversion to dopamine, these peripheral 'ups and downs' of levodopa are reflected in fluctuating dopamine levels in the synaptic cleft between presynaptic and postsynaptic dopaminergic neurons of the nigrostriatal system. As a result, pulsatile postsynaptic dopaminergic stimulation takes place and results in the occurrence of motor complications, such as wearing-off and dyskinesia. More continuous plasma behaviour was observed after the combination of levodopa/DDI formulations with COMT inhibitors. These compounds also weaken a levodopa/DDI-related homocysteine increase, as biomarker for an impaired methylation capacity, which is involved in an elevated oxidative stress exposure. These findings favour the concept of chronic levodopa/DDI application with concomitant inhibition of COMT and monoamine oxidase, since deamination of dopamine via this enzyme also generates free radicals. This triple combination is suggested as standard levodopa application in patients with PD who need levodopa, if they will tolerate it.","corpus_id":33939261,"score":2},{"doc_id":"26725544","title":"Opicapone as an adjunct to levodopa in patients with Parkinson's disease and end-of-dose motor fluctuations: a randomised, double-blind, controlled trial.","abstract":"BACKGROUND: Opicapone is a novel, once-daily, potent third-generation catechol-O-methyltransferase inhibitor. We aimed to assess the safety and efficacy of opicapone as an adjunct to levodopa compared with placebo or entacapone in patients with Parkinson's disease and motor fluctuations. METHODS: We did a randomised, double-blind, placebo-controlled and active-controlled trial of opicapone as an adjunct to levodopa in patients with Parkinson's disease with end-of-dose motor fluctuations. Patients aged 30-83 years were enrolled at 106 specialist centres across 19 European countries and Russia and were randomly assigned (1:1:1:1:1) by a proprietary computer-generated sequence to oral treatment with opicapone (5 mg, 25 mg, or 50 mg once daily), placebo, or entacapone (200 mg with every levodopa intake) for 14-15 weeks. Patients and investigators (ie, outcome assessors) were masked to treatment allocation. The primary endpoint was the change from baseline to end of study treatment in absolute time in the off state, as assessed by daily paper patient diaries; the primary analysis followed a hierarchical procedure for each opicapone dose in which superiority compared with placebo in the full analysis set was first tested and then, if positive, non-inferiority to entacapone was tested in the per-protocol set with a margin of 30 min. This trial is registered with EudraCT, 2010-021860-13, and ClinicalTrials.gov, NCT01568073. FINDINGS: Between March 31, 2011, and Nov 30, 2013, of 679 patients screened, 600 were randomly assigned. 590 patients were included in the full analysis set (120 in the placebo group, 120 in the entacapone group, 119 in the opicapone 5 mg group, 116 in the opicapone 25 mg group, and 115 in the opicapone 50 mg group) and 537 in the per-protocol set (112 in the placebo group, 104 in the entacapone group, 110 in the opicapone 5 mg group, 105 in the opicapone 25 mg group, and 106 in the opicapone 50 mg group). The mean change in time in the off state was -56·0 min (SE 13·4; 95% CI -82·3 to -29·7) for placebo, -96·3 min (13·4; -122·6 to -70·0) for entacapone, -91·3 min (13·5; -117·7 to -64·8) for opicapone 5 mg, -85·9 min (13·7; -112·8 to -59·1) for opicapone 25 mg, and -116·8 min (14·0; -144·2 to -89·4) for opicapone 50 mg. Treatment with opicapone 50 mg was superior to placebo (mean difference in change from baseline -60·8 min, 95% CI -97·2 to -24·4; p=0·0015) and non-inferior to entacapone (-26·2 min, -63·8 to 11·4; p=0·0051). Treatment with opicapone 5 mg (p=0·056) or 25 mg (p=0·080) was not significantly different from treatment with placebo. Treatment-emergent adverse events were reported in 60 (50%) of 121 patients in the placebo group, 69 (57%) of 122 in the entacapone group, 63 (52%) of 122 in the opicapone 5 mg group, 65 (55%) of 119 in the opicapone 25 mg group, and 62 (54%) of 115 in the opicapone 50 mg group. The most common adverse events were dyskinesia (in five patients in the placebo group, ten in the entacapone group, 17 in the opicapone 5 mg group, nine in the opicapone 25 mg group, and 18 in the opicapone 50 mg group), insomnia (in one, seven, two, seven, and seven patients, respectively), and constipation (in three, five, four, none, and seven patients, respectively). Serious adverse events were reported in six patients in the placebo group, eight in the entacapone group, four each in the opicapone 5 mg and opicapone 50 mg groups, and one in the opicapone 25 mg group. INTERPRETATION: The addition of opicapone 50 mg to levodopa treatment in patients with Parkinson's disease and end-of-dose motor fluctuations could enable a simplified drug regimen that allows physicians to individually tailor the existing levodopa daily regimen, by potentially reducing the total daily levodopa dose, increasing the dosing interval, and ultimately reducing the number of intakes, thereby maximising its benefit. FUNDING: BIAL.","corpus_id":28714513,"score":2},{"doc_id":"26744740","title":"Safinamide for symptoms of Parkinson's disease.","abstract":"Chronic and slow progression of neuronal death in Parkinson's disease is responsible for an altered neurotransmission of various biogenic amines, such as dopamine. Therefore, an individually different pronounced heterogeneity of motor and nonmotor symptoms characterizes each Parkinson's disease patient. Ideal candidates for the balance of these neurotransmitter deficits are compounds like safinamide with broad mechanisms of action such as reversible monoamine oxidase type B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and of glutamate release. Safinamide is administered one time daily with oral doses ranging from 50 to 100 mg. Safinamide was well tolerated and safe, ameliorated motor symptoms when combined with dopamine agonist only or additional levodopa in clinical trials. Safinamide is a novel instrument for the drug therapy of Parkinson's disease with better safety and tolerability particularly concerning diarrhea than inhibitors of catechol-O-methyltransferase, like entacapone, according to an indirect comparison within a meta-analysis with entacapone.","corpus_id":39866671,"score":2},{"doc_id":"26889632","title":"Safinamide as Add-On Therapy to Levodopa in Mid- to Late-Stage Parkinson's Disease Fluctuating Patients: Post hoc Analyses of Studies 016 and SETTLE.","abstract":"BACKGROUND: Studies 016 and SETTLE showed that safinamide was safe and effective as adjunct therapy in patients with advanced Parkinson's disease (PD) and motor fluctuations. The addition of safinamide to a stable dose of levodopa alone or with other antiparkinsonian medications significantly increased ON time with no/non-troublesome dyskinesia, decreased OFF time and improved Parkinson's symptoms. OBJECTIVE: To evaluate the clinical effects of safinamide 100 mg/day on motor fluctuations and cardinal Parkinson's symptoms in specific patient subgroups using pooled data from Studies 016 and SETTLE. METHODS: Both studies were double blind, placebo-controlled, randomized, phase 3 trials which enrolled patients with mid- to late-stage PD experiencing motor fluctuations while receiving optimized and stable doses of levodopa, alone or with other dopaminergic treatments. The present post-hoc analyses assessed the change from baseline in ON time (with no or non-troublesome dyskinesia) and OFF time in subgroups of patients who were receiving only levodopa at baseline, who were classified as \"mild fluctuators\" (daily OFF time ≤4 h), and who were receiving concomitant dopaminergic therapy, with or without amantadine, and the effects of safinamide versus placebo on individual cardinal PD symptoms during ON time. RESULTS: Safinamide significantly increased mean ON time (with no or non-troublesome dyskinesia) and reduced mean OFF time when used as first adjunct therapy in levodopa-treated patients and patients with mild motor fluctuations. Mean daily ON time (with no or non-troublesome dyskinesia) and OFF time were favorably changed, compared with placebo, to similar extents regardless of whether patients were receiving concomitant dopamine agonists, catechol-O-methyltransferase inhibitors and amantadine. Additionally, safinamide improved bradykinesia, rigidity, tremor and gait. CONCLUSIONS: Safinamide was a safe and effective first adjunct therapy in levodopa-treated patients and improved 4/5 cardinal symptoms of PD while providing benefits to mild and non-mild fluctuators and patients receiving other concomitant dopaminergic therapies.","corpus_id":16293044,"score":2},{"doc_id":"27536120","title":"Emerging approaches in Parkinson's disease - adjunctive role of safinamide.","abstract":"Ongoing neuronal death in Parkinson's disease (PD) causes an altered neurotransmission of various biogenic amines, particularly dopamine. As these changes do not follow a distinct pattern, they vary individually, and are differently pronounced. As a result, a heterogeneous onset of motor and nonmotor features occurs in each patient with PD during the whole course of the disease. PD actually describes a set of distinct diseases that manifest themselves in clinical syndromes with certain similarities but also great differences. This clinical picture responds to drugs with a broad spectrum of modes of actions better than to compounds with an exclusive focus on specific receptor subtypes. Therefore, safinamide is an ideal candidate for treatment of patients with PD, since its pharmacological profile includes reversible monoamine oxidase-B inhibition, blockade of voltage-dependent sodium channels, modulation of calcium channels, and inhibition of glutamate release. Safinamide is applied only once daily. Its oral dose ranges from 50 to 100 mg. Safinamide was well tolerated and safe in the clinical development program that demonstrated the amelioration of motor symptoms and OFF phenomena by safinamide when combined with dopamine agonists or levodopa. In the real world of maintenance of patients with PD, effects of safinamide application resemble therapy with classical monoamine oxidase inhibitors or amantadine in combination with other dopamine-substituting drugs. Safinamide is becoming increasingly available in the EU despite complex approval and pricing scenarios.","corpus_id":7752034,"score":2},{"doc_id":"27665574","title":"Clinical Pharmacokinetics and Pharmacodynamics of Safinamide.","abstract":"The symptoms of Parkinson's disease (PD) reflect disruptions of a number of brain neurotransmitter systems of varying type and degree. Pharmacological agents with multiple neurochemical mechanisms of action are therefore promising candidates for countering these problems and providing comprehensive symptomatic relief for patients. The pharmacological profile of safinamide includes reversible monoamine oxidase B inhibition, blockage of voltage-dependent Na(+) channels, modulation of Ca(2+) channels, and inhibition of glutamate release. Safinamide is administered once daily at oral doses of 50-100 mg; it is well-tolerated and safe. Clinical trials have found that it ameliorates motor symptoms when added to established levodopa or single dopamine receptor agonist therapy. The future role of safinamide in PD may be that it enables a reduction in the dosage of dopamine replacement therapies, thereby reducing the adverse effects associated with these treatments. The clinical convenience (once-daily administration), safety, and tolerability of safinamide are better than those of dopamine receptor agonists. The introduction of safinamide reflects a change of approach to drug development for anti-parkinsonian agents in that its broad spectrum of action corresponds to the multiple heterogeneous alterations of brain neurochemistry in PD, rather than being targeted at a single receptor type or neurochemical process. Safinamide is a promising new instrument for the effective symptomatic therapy of PD.","corpus_id":22265280,"score":2},{"doc_id":"27942720","title":"Assessment of Safety and Efficacy of Safinamide as a Levodopa Adjunct in Patients With Parkinson Disease and Motor Fluctuations: A Randomized Clinical Trial.","abstract":"Importance: Although levodopa remains the most effective oral pharmacotherapy for Parkinson disease (PD), its use is often limited by wearing off effect and dyskinesias. Management of such complications continues to be a significant challenge. Objective: To investigate the efficacy and safety of safinamide (an oral aminoamide derivative with dopaminergic and nondopaminergic actions) in levodopa-treated patients with motor fluctuations. Design, Setting, and Participants: From March 5, 2009, through February 23, 2012, patients from academic PD care centers were randomized (1:1 ratio) to receive double-blind adjunctive safinamide or placebo for 24 weeks. All patients had idiopathic PD with \"off\" time (time when medication effect has worn off and parkinsonian features, including bradykinesia and rigidity, return) of greater than 1.5 hours per day (excluding morning akinesia). Their pharmacotherapy included oral levodopa plus benserazide or carbidopa in a regimen that had been stable for 4 weeks or longer. During screening, each patient's regimen was optimized to minimize motor fluctuations. Study eligibility required that after 4 weeks of optimized treatment, the patients still have more than 1.5 hours per day of off time. Adverse events caused the premature study discontinuation of 12 individuals (4.4%) in the safinamide group and 10 individuals (3.6%) in the placebo group. Interventions: Patients took safinamide or placebo as 1 tablet daily with breakfast. If no tolerability issues arose by day 14, the starting dose, 50 mg, was increased to 100 mg. Main Outcomes and Measures: The prespecified primary outcome was each treatment group's mean change from baseline to week 24 (or last \"on\" treatment value) in daily \"on\" time (relief of parkinsonian motor features) without troublesome dyskinesia, as assessed from diary data. Results: At 119 centers, 549 patients were randomized (mean [SD] age, 61.9 [9.0] years; 334 male [60.8%] and 371 white [67.6%]): 274 to safinamide and 275 to placebo. Among them, 245 (89.4%) receiving safinamide and 241 (87.6%) receiving placebo completed the study. Mean (SD) change in daily on time without troublesome dyskinesia was +1.42 (2.80) hours for safinamide, from a baseline of 9.30 (2.41) hours, vs +0.57 (2.47) hours for placebo, from a baseline of 9.06 (2.50) hours (least-squares mean difference, 0.96 hour; 95% CI, 0.56-1.37 hours; P < .001, analysis of covariance). The most frequently reported adverse event was dyskinesia (in 40 [14.6%] vs 15 [5.5%] and as a severe event in 5 [1.8%] vs 1 [0.4%]). Conclusions and Relevance: The outcomes of this trial support safinamide as an effective adjunct to levodopa in patients with PD and motor fluctuations to improve on time without troublesome dyskinesia and reduce wearing off. Trial Registration: clinicaltrials.gov Identifier NCT00627640.","corpus_id":33773319,"score":2},{"doc_id":"28537214","title":"Pharmacokinetic drug evaluation of safinamide mesylate for the treatment of mid-to-late stage Parkinson's disease.","abstract":"INTRODUCTION: Patients with Parkinson's disease suffer from a heterogeneous expression of neurotransmitter deficits. They cause an individual variable expression of motor and non-motor symptoms. Thus, drugs with various mechanisms of actions are suitable to counteract these disease related neurotransmitter alterations. Areas covered: This invited review suggests safinamide as an ideal compound for therapy of Parkinson's disease, as its pharmacological profile includes reversible monoamine oxidase B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and abnormal glutamate release. Safinamide may provide benefits effects on non-motor symptoms in addition to the demonstrated amelioration of motor impairment in levodopa treated patients with Parkinson's disease. Safinamide was well tolerated and safe when administered in dose of 50 or 100 mg daily in pivotal trials. Expert opinion: Clinical handling, safety and tolerability of Safinamide are better than of dopamine agonists or levodopa. Safinamide supplements the existing armamentarium of drugs for Parkinson's disease. Safinamide will help to reduce dosing of levodopa but also of dopamine agonists during long term treatment in patients with Parkinson's disease.","corpus_id":41398809,"score":2},{"doc_id":"29569037","title":"Monoamine oxidase-B inhibitors in the treatment of Parkinson's disease: clinical-pharmacological aspects.","abstract":"This invited narrative review emphasizes the role of MAO-B inhibition in the drug portfolio for dopamine substitution in patients with Parkinson's disease. Neuronal and glial MAO-B inhibition contributes to more stable levels of dopamine and other biogenic amines in the synaptic cleft. Accordingly, symptomatic effects of MAO-B inhibition for a limited amelioration of impaired motor behaviour and wearing-off phenomena in patients with Parkinson's disease are well proven, even when MAO-B inhibitors are only applied together with dopamine agonists. Delay of disease progression by MAO-B inhibition is under debate despite positive experimental findings. This discussion does not consider, that levodopa, respectively, dopamine agonists, are substrates, respectively, inhibitors of the ABCB1 (P-gp, MDR1, and CD243) transporter system. It supports toxin efflux over the blood-brain barrier. ABCB1 transporters have a limited capacity. MAO-B inhibitors do not weaken it. Treatment with MAO-B inhibitors is advantageous as it enables sparing of dopamine agonist and levodopa dosing.","corpus_id":4275601,"score":2},{"doc_id":"18549347","title":"An expert opinion on safinamide in Parkinson's disease.","abstract":"BACKGROUND: Dopamine replacement therapies (levodopa, dopamine receptor agonists, anticholinergics, monoamine oxidase B inhibitors, and catechol-O-methyltransferase inhibitors) remain the cornerstones of therapeutic interventions for Parkinson's disease (PD). Despite the treatment options for PD symptoms, a cure remains elusive. An optimal treatment would be one that combined relief in both motor and nonmotor symptoms with neuroprotective properties. Safinamide is an investigational drug for PD currently in development as add-on therapy to both dopamine agonists and levodopa. Safinamide is a unique molecule with a novel mode of action, targeting both dopaminergic and glutaminergic systems, and potentially provides motor symptom control. Preliminary results from experimental models suggest potential neuroprotective effects. Studies on the potential effects on nonmotor symptoms are ongoing. OBJECTIVE: To review the mechanism of action and pharmacokinetics, and to evaluate the available clinical safety and efficacy results of safinamide. METHODS: A search of the electronic database MEDLINE (PubMed, no time limits) was performed on 14 December 2007. The full text of all citations was obtained for review. Furthermore, two abstracts on safinamide published as proceedings of a European conference were reviewed. RESULTS/CONCLUSION: Safinamide is a promising investigational drug for PD with a novel mode of action. Early reports confirm the potential efficacy of safinamide in PD. Further studies on potential effects on cognition and neuroprotection are needed.","corpus_id":25856669,"score":1},{"doc_id":"20816270","title":"Management of motor complications in Parkinson disease: current and emerging therapies.","abstract":"Motor fluctuations and dyskinesias are common motor complications that manifest within the first few years from the initiation of therapy in patients with Parkinson disease. These complications negatively affect the quality of life and represent an important source of disability. A growing number of therapeutic options including treatments aimed at prolonging the efficacy of levodopa (eg, selective monoamine oxidase-B inhibitors and catechol-O-methyltransferase inhibitors), administration of longer-acting dopamine agonists (eg, rotigotine, sustained-release ropinirole), and continuous administration of intraduodenal levodopa exist or will soon become available. Patients who maintain a good response to levodopa but continue to experience disabling motor complications despite the best medical management may benefit from a regimen of subcutaneous apomorphine, ideally delivered by a subcutaneous pump, or deep-brain stimulation of the subthalamic nucleus or internal portion of the pallidum. Emerging therapies for motor complications are expected to further enhance continuous (physiologic) delivery of dopaminergic drugs and extend the reach of therapies beyond the dopaminergic system to influence not only the motor but also the vast range of nonmotor complications of this multisystemic disease.","corpus_id":24970145,"score":1},{"doc_id":"22133327","title":"Monoamine oxidase B inhibitors for the treatment of Parkinson's disease: a review of symptomatic and potential disease-modifying effects.","abstract":"Parkinson's disease is a disorder characterized pathologically by progressive neurodegeneration of the dopaminergic cells of the nigrostriatal pathway. Although the resulting dopamine deficiency is the cause of the typical motor features of Parkinson's disease (bradykinesia, rigidity, tremor), additional non-motor symptoms appear at various timepoints and are the result of non-dopamine nerve degeneration. Monoamine oxidase B (MAO-B) inhibitors are used in the symptomatic treatment of Parkinson's disease as they increase synaptic dopamine by blocking its degradation. Two MAO-B inhibitors, selegiline and rasagiline, are currently licensed in Europe and North America for the symptomatic improvement of early Parkinson's disease and to reduce off-time in patients with more advanced Parkinson's disease and motor fluctuations related to levodopa. A third MAO-B inhibitor (safinamide), which also combines additional non-dopaminergic properties of potential benefit to Parkinson's disease, is currently under development in phase III clinical trials as adjuvant therapy to either a dopamine agonist or levodopa. MAO-B inhibitors have also been studied extensively for possible neuroprotective or disease-modifying actions. There is considerable laboratory evidence that MAO-B inhibitors do exert some neuroprotective properties, at least in the Parkinson's disease models currently available. However, these models have significant limitations and caution is required in assuming that such results may easily be extrapolated to clinical trials. Rasagiline 1 mg/day has been shown to provide improved motor control in terms of Unified Parkinson's Disease Rating Scale (UPDRS) score at 18 months in those patients with early disease who began the drug 9 months before a second group. There are a number of possible explanations for this effect that may include a disease-modifying action; however, the US FDA recently declined an application for the licence of rasagiline to be extended to cover disease modification.","corpus_id":39302397,"score":1},{"doc_id":"22967035","title":"Long-term efficacy and safety of safinamide as add-on therapy in early Parkinson's disease.","abstract":"BACKGROUND AND PURPOSE: Safinamide is an α-aminoamide with both dopaminergic and non-dopaminergic mechanisms of action in Phase III clinical development as a once-daily add-on to dopamine agonist (DA) therapy for early Parkinson's disease (PD). METHODS: Study 017 was a 12-month, randomized, double-blind, placebo-controlled pre-planned extension study to the previously reported Study 015. Patients received safinamide 100 or 200 mg/day or placebo added to a single DA in early PD. The primary efficacy endpoint was the time from baseline (Study 015 randomization) to 'intervention', defined as increase in DA dose; addition of another DA, levodopa or other PD treatment; or discontinuation due to lack of efficacy. Safinamide groups were pooled for the primary efficacy endpoint analysis; post hoc analyses were performed on each separate dose group. RESULTS: Of the 269 patients randomized in Study 015, 227 (84%) enrolled in Study 017 and 187/227 (82%) patients completed the extension study. Median time to intervention was 559 and 466 days in the pooled safinamide and placebo groups, respectively (log-rank test; P = 0.3342). In post hoc analyses, patients receiving safinamide 100 mg/day experienced a significantly lower rate of intervention compared with placebo (25% vs. 51%, respectively) and a delay in median time to intervention of 9 days (P < 0.05; 240- to 540-day analysis). CONCLUSIONS: The pooled data from the safinamide groups failed to reach statistical significance for the primary endpoint of median time from baseline to additional drug intervention. Post hoc analyses indicate that safinamide 100 mg/day may be effective as add-on treatment to DA in PD.","corpus_id":1793815,"score":1},{"doc_id":"23917951","title":"Non-dopaminergic treatments for motor control in Parkinson's disease.","abstract":"The pathological processes underlying Parkinson's disease (PD) involve more than dopamine cell loss within the midbrain. These non-dopaminergic neurotransmitters include noradrenergic, serotonergic, glutamatergic, and cholinergic systems within cortical, brainstem and basal ganglia regions. Several non-dopaminergic treatments are now in clinical use to treat motor symptoms of PD, or are being evaluated as potential therapies. Agents for symptomatic monotherapy and as adjunct to dopaminergic therapies for motor symptoms include adenosine A2A antagonists and the mixed monoamine-B inhibitor (MAO-BI) and glutamate release agent safinamide. The largest area of potential use for non-dopaminergic drugs is as add-on therapy for motor fluctuations. Thus adenosine A2A antagonists, safinamide, and the antiepileptic agent zonisamide can extend the duration of action of levodopa. To reduce levodopa-induced dyskinesia, drugs that target overactive glutamatergic neurotransmission can be used, and include the non-selective N-methyl D-aspartate antagonist amantadine. More recently, selective metabotropic glutamate receptor (mGluR₅) antagonists are being evaluated in phase II randomized controlled trials. Serotonergic agents acting as 5-HT2A/2C antagonists, such as the atypical antipsychotic clozapine, may also reduce dyskinesia. 5-HT1A agonists theoretically can reduce dyskinesia, but in practice, may also worsen PD motor symptoms, and so clinical applicability has not yet been shown. Noradrenergic α2A antagonism using fipamezole can potentially reduce dyskinesia. Several non-dopaminergic agents have also been investigated to reduce non-levodopa-responsive motor symptoms such as gait and tremor. Thus the cholinesterase inhibitor donepezil showed mild benefit in gait, while the predominantly noradrenergic re-uptake inhibitor methylphenidate had conflicting results in advanced PD subjects. Tremor in PD may respond to muscarinic M4 cholinergic antagonists (anticholinergics), but tolerability is often poor. Alternatives include β-adrenergic antagonists such as propranolol. Other options include 5-HT2A antagonists, and drugs that have mixed binding properties involving serotonin and acetylcholine, such as clozapine and the antidepressant mirtazapine, can be effective in reducing PD tremor. Many other non-dopaminergic agents are in preclinical and phase I/II early stages of study, and the reader is directed to recent reviews. While levodopa remains the most effective agent to treat motor symptoms in PD, the overall approach to using non-dopaminergic drugs in PD is to reduce reliance on levodopa and to target non-levodopa-responsive symptoms.","corpus_id":9849241,"score":1},{"doc_id":"24323838","title":"Continuous drug delivery in Parkinson's disease.","abstract":"Development of motor and non-motor complications during the course of Parkinson's disease (PD) is a major challenge for therapeutic management. At advanced disease stages, patients frequently fluctuate between PD symptoms-such as bradykinesia-and dyskinesias, in response to fluctuations in drug concentrations. Continuous subcutaneous infusion of the dopamine agonist apomorphine or intestinal infusion of levodopa reduce such fluctuations in both pharmacokinetics and motor function. This is the basis for the concept of continuous drug delivery in PD, and the more theoretical concept of continuous dopaminergic stimulation. These expressions are sometimes used to describe a treatment that is more continuous in its pharmacokinetic profile or that produces more sustained effects, compared with immediate-release levodopa, i.e. not only pump treatments. For example, sustained-release formulations of levodopa or dopamine agonists, transdermal delivery of rotigotine, and addition of catechol-O-methyltransferase inhibitors or monoamine oxidase-B inhibitors have been developed with the aim to provide more continuous drug concentrations, sustained benefits and minimized side effects. Progress has been made, but there are still knowledge gaps regarding how these treatment alternatives can be optimally used. New treatments are currently being developed to provide the continuous drug delivery that is known to successfully alleviate motor and non-motor complications. Hopefully, although not yet proven, these new methods may also prevent or postpone some of the late-stage complications.","corpus_id":5790880,"score":1},{"doc_id":"25044402","title":"Two-year, randomized, controlled study of safinamide as add-on to levodopa in mid to late Parkinson's disease.","abstract":"In a 6-month double-blind, placebo-controlled study of Parkinson's disease patients with motor fluctuations, safinamide 50 and 100 mg/d significantly increased ON-time without increasing dyskinesia. Further long-term safinamide use in these patients was evaluated over an additional 18 months. Patients continued on their randomized placebo, 50, or 100 mg/d safinamide. The primary endpoint was change in Dyskinesia Rating Scale total score during ON-time over 24 months. Other efficacy endpoints included change in ON-time without troublesome dyskinesia, changes in individual diary categories, depressive symptoms, and quality of life measures. Change in Dyskinesia Rating Scale was not significantly different in safinamide versus placebo groups, despite decreased mean total Dyskinesia Rating Scale with safinamide compared with an almost unchanged score in placebo. Ad hoc subgroup analysis of moderate to severe dyskinetic patients at baseline (36% of patients) showed a decrease with safinamide 100 mg/d compared with placebo (P = 0.0317). Improvements in motor function, activities of daily living, depressive symptoms, clinical status, and quality of life at 6 months remained significant at 24 months. Adverse events and discontinuation rates were similar with safinamide and placebo. This 2-year, controlled study of add-on safinamide in mid-to-late Parkinson's disease with motor fluctuations, although not demonstrating an overall difference in dyskinesias between patients and controls, showed improvement in dyskinesia in patients at least moderately dyskinetic at baseline. The study additionally demonstrated significant clinical benefits in ON-time (without troublesome dyskinesia), OFF-time, activities of daily living, motor symptoms, quality of life, and symptoms of depression.","corpus_id":11110615,"score":1},{"doc_id":"25300164","title":"Safinamide for the treatment of Parkinson's disease.","abstract":"Parkinson's disease (PD) is a neurodegenerative disease caused by a complex interaction of loss of dopaminergic and non-dopaminergic neurotransmitter systems. Drugs acting on the dopaminergic pathways are the mainstay of treatment for motor symptoms today. Safinamide (NW-1015) is a novel drug with multiple actions. It is a monoamine oxidase B inhibitor and improves dopaminergic transmission. In addition, it has antiglutamatergic effects and can thus reduce dyskinesias, which is a side effect limiting most dopaminergic therapy. In Phase III trials, safinamide has been found to be a useful adjunctive to dopamine agonists in early PD and has been shown to increase time without increasing troublesome dyskinesias when used as an adjunct to levodopa in patients with advanced PD. A possible neuroprotective role in inhibiting PD disease progression is envisaged and warrants future studies.","corpus_id":207207979,"score":1},{"doc_id":"25649051","title":"Effect of opicapone on levodopa pharmacokinetics, catechol-O-methyltransferase activity and motor fluctuations in patients with Parkinson's disease.","abstract":"BACKGROUND AND PURPOSE: Opicapone (OPC) is a novel third generation catechol-O-methyltransferase (COMT) inhibitor that enhances levodopa availability. This study investigated the effects of OPC in comparison with placebo on levodopa pharmacokinetics, tolerability and safety, COMT activity and motor response to levodopa in Parkinson's disease (PD) patients with motor fluctuations. METHODS: This was a randomized, multicentre, double-blind and placebo-controlled study in four parallel groups of PD patients treated with standard-release 100/25 mg levodopa/carbidopa or levodopa/benserazide and with motor fluctuations (wearing-OFF phenomenon). Subjects were sequentially assigned to be administered, once-daily, up to 28 days (maintenance phase), placebo (n = 10) or 5 (n = 10), 15 (n = 10) and 30 mg (n = 10) OPC. Two levodopa tests were performed, one at baseline and another following the maintenance phase. Subjects kept a diary to record motor fluctuations (ON/OFF periods) throughout the study. RESULTS: In relation to placebo, levodopa exposure (AUC0-6) increased 24.7%, 53.9% and 65.6% following 5, 15 and 30 mg OPC, respectively. Maximum COMT inhibition (Emax) ranged from 52% (5 mg OPC) to 80% (30 mg OPC). The study was not designed to detect any significant differences in motor performance, but the exploratory analysis performed shows improvement in various motor outcomes, including a dose-dependent change in absolute OFF time corresponding to a percentage decrease of 4.16% (P > 0.05), 29.55% (P > 0.05) and 32.71% (P < 0.05) with 5, 15 and 30 mg OPC, respectively. Treatments were generally well tolerated and safe. CONCLUSIONS: OPC is a promising new COMT inhibitor that significantly decreased COMT activity, increased systemic exposure to levodopa and improved motor response.","corpus_id":205111356,"score":1},{"doc_id":"26406127","title":"Long-Term Effects of Safinamide on Dyskinesia in Mid- to Late-Stage Parkinson's Disease: A Post-Hoc Analysis.","abstract":"BACKGROUND: Safinamide is a novel α-aminoamide with dopaminergic and non-dopaminergic properties developed as adjunctive therapy for patients with PD. Results from a 24-month double-blind controlled study suggested that as add-on to levodopa (and other PD medications) the benefits of safinamide on dyskinesia may be related to severity of dyskinesia at baseline. OBJECTIVE: This post-hoc analysis further characterized the effects of safinamide on dyskinesia in mid- to late-stage PD patients. METHODS: Patients were stratified by the presence or absence of dyskinesia at baseline, and by whether or not the dose of levodopa had been changed during the 24-month treatment period. Differences between safinamide and placebo were evaluated using the Wilcoxon rank-sum test. RESULTS: For the overall treated population (with or without baseline dyskinesia), safinamide 100 mg/day significantly improved the dyskinesia rating scale score, compared with placebo, in the subgroup of patients with no change in levodopa dose (p = 0.0488). For patients with baseline dyskinesia, improvements over placebo were also significant (p = 0.0153) in patients with or without changes in levodopa dose, and nearly significant (p = 0.0546) in patients with no change in levodopa dose, suggesting that these improvements were not due to levodopa dose reductions. CONCLUSIONS: While no statistically significant difference in mean DRS scores was seen between safinamide and placebo in the original study population, the present post-hoc analysis helps to provide a meaningful interpretation of the long-term effects of safinamide on dyskinesia. These results may be related to safinamide state- and use-dependent inhibition of sodium channels and stimulated glutamate release, and are unlikely due to reduced dopaminergic stimulation.","corpus_id":14914773,"score":1},{"doc_id":"26587996","title":"Clinical pharmacology review of safinamide for the treatment of Parkinson's disease.","abstract":"Safinamide (Xadago™) is an oral α-aminoamide derivative marketed for the treatment of Parkinson's disease (PD). The drug has both dopaminergic properties, namely highly selective and reversible inhibition of monoamine oxidase B, and nondopamimetic properties, namely selective sodium channel blockade and calcium channel modulation, with consequent inhibition of excessive glutamate release. In 2014, safinamide was approved in the European Economic Area, as \"an add-on therapy to stable dose levodopa, alone or in combination with other PD therapies in mid- to late-stage-fluctuating PD patients.\" In addition, evidence has been provided for safinamide in the treatment of motor symptoms in early PD patients. This article summarizes the pharmacological properties, development program, clinical indications for PD treatment, stratified according to several disease's stages and the safety profile of safinamide. A meta-analysis of the most frequent adverse events among Phase III trials has been also performed.","corpus_id":36717221,"score":1},{"doc_id":"26917951","title":"Adjuvant therapies for Parkinson's disease: critical evaluation of safinamide.","abstract":"Safinamide (SAF) is a new drug developed for the treatment of Parkinson's disease (PD). It is a benzylamino derivative with multiple mechanisms of action and antiparkinsonian, anticonvulsant, and neuroprotective properties. SAF inhibits monoamine oxidase B and dopamine reuptake and glutamate release, blocks voltage-dependent sodium channels, and modulates calcium channels. Although the antiparkinsonian effect can be ascribed in part to the inhibition of the monoamine oxidase B, which is complete at 50 mg, the enhanced benefit seen at the 100 mg dose is probably due to nondopaminergic mechanisms. SAF will represent an important option for patients with both early and advanced PD. In early PD patients, the addition of SAF to dopamine agonists may be an effective treatment strategy to improve motor function, prolong the use of dopamine agonists, and/or delay the introduction of levodopa. In advanced parkinsonian patients, SAF has been demonstrated to significantly increase on time with no, or nontroublesome dyskinesias. All studies performed have demonstrated its efficacy in benefiting both short-term and long-term quality-of-life outcomes in both early and advanced PD patients. SAF has been investigated in long-term (24 months), double-blind, placebo-controlled studies, where it showed a very good safety profile. SAF has not been studied in de novo PD patients, and its potential positive effect on dyskinesia deserves further dedicated studies.","corpus_id":5582957,"score":1},{"doc_id":"27186120","title":"Investigational agents in the treatment of Parkinson's disease: focus on safinamide.","abstract":"The authors review management issues in Parkinson's disease (PD) and provide an overview of the current pharmacological management strategies, with a specific focus on safinamide. Current therapeutic management of PD largely involves strategies to optimize the replacement of deficient dopamine, using levodopa, dopamine agonists, and inhibitors of dopamine-metabolizing enzymes. Currently under investigation for use in the treatment of PD, safinamide has multiple modes of action including monoamine oxidase B inhibition. It is well absorbed orally, has a long plasma half-life, and does not have liver enzyme-inducing or liver enzyme-inhibiting activity. Peak plasma concentration occurs 2-4 hours after single oral doses. Safinamide as monotherapy and as an adjunct to dopamine agonists improves Unified Parkinson's Disease Rating Scale motor scores. One randomized, placebo-controlled trial involving 168 patients given a median safinamide dose of 70 mg/day (range 40-90 mg/day) significantly increased the proportion of responders - defined as patients improving their Unified Parkinson's Disease Rating Scale motor scores by 30% or more from baseline - after 3 months (37.5% for safinamide versus 21.4% for placebo; P < 0.05). Safinamide increased \"on\" time with no or minor dyskinesia compared with the placebo in another trial, but dyskinesia severity was not reduced. Safinamide was well tolerated, with an adverse effect profile similar to that of the placebo. Further Phase III trial data for safinamide efficacy is awaited, and will be of interest in a comparison with other developments in PD therapeutics: modified formulations of available compounds, new drug classes such as adenosine receptor antagonists, and gene-based therapies.","corpus_id":1281866,"score":1},{"doc_id":"28110399","title":"Safinamide: A Review in Parkinson's Disease.","abstract":"Safinamide (Xadago(®)) is an orally active, selective, reversible monoamine oxidase-B inhibitor with both dopaminergic and non-dopaminergic (glutamatergic) properties. In the EU, safinamide is approved for the treatment of mid- to late-stage fluctuating Parkinson's disease (PD) as add-on therapy to a stable dose of levodopa alone or in combination with other PD medications. Safinamide 50-100 mg/day administered as a fixed or flexible dose significantly increased daily 'on' time without dyskinesia (primary endpoint) in patients with mid- to late-stage PD with motor fluctuations in 24-week, placebo-controlled clinical trials. Other outcomes, including motor function, overall clinical status and health-related quality of life, were also generally improved with safinamide. Furthermore, in an 18-month extension of one study, although dyskinesia (primary endpoint) was not significantly improved with safinamide relative to placebo, treatment benefits in other outcomes were generally sustained over 24 months of treatment. Safinamide was generally well tolerated in clinical trials; dyskinesia was the most common adverse event. Although further studies are needed, including comparative and long-term studies, current evidence indicates that safinamide extends the treatment options available for use as add-on therapy to levodopa and other PD medications in patients with mid- to late-stage PD experiencing motor fluctuations.","corpus_id":23485955,"score":1},{"doc_id":"28504022","title":"Safinamide for the treatment of Parkinson's disease.","abstract":"INTRODUCTION: The major unmet needs in the medical treatment of Parkinson disease (PD) are reduction of motor side effects from dopaminergic drugs, management of non-motor symptoms and disease modification. Areas covered: Motor fluctuations and OFF periods are a significant determinant of quality of life in PD and reducing their duration and severity can significantly improve motor function. This aim may be partly facilitated by the development of effective adjunctive drugs for dopamine replacement. Safinamide (Xadago), which is a first generation anticonvulsant, has pharmacological properties which are of interest in the context of neurodegenerative diseases, leading to research into its potential as an adjunct to levodopa in PD. Expert opinion: Although its mechanism has not been fully defined, safinamide provides enhanced symptom control of motor function in advanced PD and improves quality of life.","corpus_id":418489,"score":1},{"doc_id":"28580819","title":"Opicapone for the management of end-of-dose motor fluctuations in patients with Parkinson's disease treated with L-DOPA.","abstract":"INTRODUCTION: Opicapone is a third generation, highly potent and effective catechol O‑methyltransferase (COMT) inhibitor that optimizes the pharmacokinetics and bioavailability of L-DOPA therapy. Areas covered: In this review, the authors describe the preclinical and clinical development of opicapone. In PD patients with motor fluctuations, once daily opicapone administration was well-tolerated and consistently reduced OFF-time and increased ON-time without increasing the frequency of troublesome dyskinesia, and these benefits were maintained over at least a year of continued open-label therapy. Expert commentary: With its convenient once-daily regimen, adjunct opicapone should be considered as an effective option for use in L-DOPA treated PD patients experiencing motor fluctuations.","corpus_id":37748591,"score":1},{"doc_id":"28777756","title":"Long-Term Effects of Safinamide on Mood Fluctuations in Parkinson's Disease.","abstract":"BACKGROUND: Mood disorders are very frequent in Parkinson's Disease (PD), and their effective treatment is still a major unresolved issue: growing evidence suggests that glutamatergic system dysfunction is directly involved. Safinamide is a drug with an innovative mechanism of action, dopaminergic and non-dopaminergic, that includes the reversible inhibition of the monoamine oxidase-B (MAO-B) enzyme and the modulation of excessive glutamate release through the use- and state-dependent blockade of the sodium channels. OBJECTIVE: To investigate the effects of safinamide on mood over two-year treatment in PD patients with motor fluctuations. METHODS: This was a post-hoc analysis of the data from studies 016 and 018. The analysis focused on outcomes related to mood, namely: scores of the \"Emotional well-being\" domain of the Parkinson's Disease Questionnaire (PDQ-39), scores of the GRID Hamilton Rating Scale for Depression (GRID-HAMD) and the proportion of patients reporting depression as an adverse event over the entire treatment period. RESULTS: Safinamide, compared to placebo, significantly improved the PDQ-39 \"Emotional well-being\" domain after6-months (p = 0.0067) and 2 years (p = 0.0006), as well as the GRID-HAMD (p = 0.0408 after 6 months and p = 0.0027 after 2 years). Significantly fewer patients in the safinamide group, compared to placebo, experienced depression as adverse event (p = 0.0444 after 6 months and p = 0.0057 after 2 years). CONCLUSION: The favorable effect of safinamide on mood may be explained by the improvement in wearing off and by its modulation of glutamatergic hyperactivity and reversible MAO-B inhibition. Prospective studies are warranted to investigate this potential benefit.","corpus_id":3687749,"score":1},{"doc_id":"29441484","title":"Real life evaluation of safinamide effectiveness in Parkinson's disease.","abstract":"In this retrospective study, we evaluated both efficacy and effectiveness of safinamide 50 and 100 mg in the treatment of motor fluctuations and disabling dyskinesias in a cohort of patients with idiopathic Parkinson's disease (PD). Ninety-one PD patients were evaluated during the first year of commercialization of the drug, both prior to starting safinamide and at the last available follow-up. Evaluations were based on the Unified Parkinson's Disease Scale part III (UPDRS III), Hoehn & Yahr (HY), Unified Dyskinesia Rating Scale (UDysRS) walking and balance item 9 score, daily time spent in OFF and in ON with disabling dyskinesias (1 week diary), mean daily dose of levodopa (LD), dopamine-agonists (DA), catechol-O-methyl transferase inhibitor (COMT-I), monoamine oxidase B inhibitor (MAOB-I), and their LD equivalent dose (LEDD). Eight patients withdrew safinamide within the first month for minor side effects. At the follow-up evaluation, after a mean time with safinamide of 7.5 months ± 3.4, all patients showed a significant improvement of all the scale scores, except for HY, and of the daily dosages of the drugs and the LEDD. The same results were shown by PD patients treated with safinamide 50 mg and patients who started safinamide without switching from a previous MAOBI. PD patients with safinamide 100 mg and patients who started safinamide switching from a previous MAOBI significantly improved in time spent in OFF and LEDD. In conclusion, safinamide is safe and effective in improving motor complications in patients with idiopathic PD and can be considered a useful levodopa sparing strategy.","corpus_id":4703400,"score":1},{"doc_id":"29760163","title":"▼ Safinamide for Parkinson's disease.","abstract":"▼ Safinamide (Xadago - Zambon S.p. A) is a monoamine-oxidase B (MAO-B) inhibitor licensed as add-on therapy for people with idiopathic Parkinson's disease who are experiencing motor fluctuations with levodopa.1 Currently there is no cure for Parkinson's disease and drugs are used to reduce motor symptoms and improve daily activities.2,3 Here, we review the evidence for this MAO-B inhibitor.","corpus_id":46890111,"score":1},{"doc_id":"18042245","title":"Constant dopaminergic stimulation by transdermal delivery of dopaminergic drugs: a new treatment paradigm in Parkinson's disease.","abstract":"Current dopaminergic therapies for the treatment of Parkinson's disease are associated with the development of long-term motor complications. Abnormal pulsatile stimulation of dopamine receptors is thought to underlie the development of motor complications. There is thus a need for therapies that mimic the normal physiological state more closely by resulting in constant dopaminergic stimulation (CDS). Several studies support the hypothesis that CDS can reverse levodopa-induced motor complications. Other potential benefits of CDS include alleviating nocturnal disturbances, minimizing daytime sleepiness, avoiding priming for motor fluctuations and dyskinesia, preventing the development of gastrointestinal dysfunction and reducing the risk of developing psychosis or behavioural disturbances. Continuous infusion of dopaminergic therapies is impractical for the routine treatment of large numbers of patients. Although catechol-O-methyltransferase inhibitors or sustained-release preparations of levodopa may be beneficial, they do not entirely eliminate pulsatile stimulation of dopamine receptors. A new dopamine agonist (rotigotine), delivered over 24 h by a once-daily transdermal patch, has been investigated in several clinical trials. Continuous delivery of rotigotine has been shown to provide 'true' CDS in animal models. The potential of true CDS therapy to prevent or reduce long-term motor and non-motor complications requires investigation in appropriately designed clinical trials.","corpus_id":25280693,"score":0},{"doc_id":"19589043","title":"Levodopa/carbidopa/entacapone in Parkinson's disease.","abstract":"Levodopa is the most efficacious agent for the treatment of motor features of Parkinson's disease but its chronic use is associated with the development of motor complications. Mounting evidence indicates the short half-life of levodopa and resultant pulsatile stimulation of striatal dopamine receptors leads to wearing off, motor fluctuations and dyskinesias. Longer acting dopaminergic agents, such as dopamine agonists, are less likely to cause motor fluctuations and dyskinesias but are not as efficacious for control of motor symptoms. Therefore, there is interest in exploring ways to deliver levodopa in a more continuous fashion, in an effort to maintain benefit through the day and reduce the development of motor fluctuations and dyskinesias. A dopa decarboxylase inhibitor (DDCI), such as carbidopa or benserazide, is administered with levodopa to attenuate its peripheral conversion to dopamine, reduce nausea and increase central bioavailability. When levodopa is administered with a DDCI, its main route of peripheral metabolism is via catechol-O-methyl transferase (COMT). A COMT inhibitor can be added to the combination of levodopa and a DDCI to further extend the levodopa peripheral half-life and increase central bioavailability. Stalevo is a combination tablet comprised of levodopa, carbidopa, and the COMT inhibitor entacapone. It is available in fixed-dose combinations of levodopa/carbidopa/entacapone, 50/12.5/200, 75/18.75/200, 100/25/200, 125/31.25/200, 150/37.5/200 and 200/50/200 mg. Stalevo is currently approved for use in Parkinson's disease patients with end-of-dose wearing off.","corpus_id":31790179,"score":0},{"doc_id":"19821381","title":"Monoamine oxidase B inhibitors versus other dopaminergic agents in early Parkinson's disease.","abstract":"BACKGROUND: It has been postulated that monoamine oxidase B (MAO-B) inhibitors alter disease progression in Parkinson's disease (PD) but trials have produced conflicting results. OBJECTIVES: To assess the effectiveness and safety of long-term use of MAO-B inhibitors compared with other dopaminergic agents in early PD. SEARCH STRATEGY: We searched several electronic databases including: the Cochrane Central Register of Controlled Trials (The Cochrane Library Issue 1, 2009), MEDLINE (January 1950 to February 2009) and EMBASE (January 1980 to February 2009). We also handsearched neurology and movement disorders conference proceedings, checked reference lists of relevant studies and contacted other researchers. SELECTION CRITERIA: We included all randomised controlled trials that compared a MAO-B inhibitor with other dopaminergic agents (presently levodopa or dopamine agonists) in patients with early PD, where treatment and follow up lasted at least one year. DATA COLLECTION AND ANALYSIS: Two reviewers independently selected trials for inclusion, assessed the methodological quality, and extracted the data. Additional data were provided by the original authors. Random-effects models were used to analyse results, where appropriate. MAIN RESULTS: Only two eligible trials were included (593 patients), both of reasonable quality although one was unblinded. Both trials compared selegiline with a dopamine agonist, whilst one also compared selegiline with levodopa. MAO-B inhibitors were not associated with a significant increase or decrease in deaths compared with levodopa (odds ratio (OR) 0.96; 95% confidence interval (CI) 0.52 to 1.76) or dopamine agonists (OR 1.30; 95% CI 0.69 to 2.45). Those receiving MAO-B inhibitors were more likely to require add-on therapy during follow-up than those receiving levodopa (OR 12.02; 95% CI 6.78 to 21.31) or dopamine agonist (OR 2.00; 95% CI 1.05 to 3.81). There was a reduction in motor fluctuations with MAO-B inhibitors compared with levodopa (OR 0.55; 95% CI 0.32 to 0.94) but not dopamine agonists (OR 1.15; 95% CI 0.65 to 2.05). Withdrawals due to adverse events were less common with MAO-B inhibitors than with dopamine agonists (OR 0.11; 95% CI 0.01 to 0.99). AUTHORS' CONCLUSIONS: MAO-B inhibitors are one option for the early treatment of PD although they have weaker symptomatic effects than levodopa and dopamine agonists. They may reduce the rate of motor fluctuations compared with initial levodopa therapy and may have fewer significant adverse effects than the older agonists but data are too few to provide reliable conclusions.","corpus_id":205184450,"score":0},{"doc_id":"19951137","title":"Current strategies in the treatment of Parkinson's disease and a personalized approach to management.","abstract":"Parkinson's disease is a progressive, neurodegenerative disorder affecting millions of people worldwide. Given the aging population, the prevalence of the disease is expected to increase substantially. The mainstay of treatment has been dopamine replacement therapy with carbidopa, levodopa, dopamine agonists, monoamine oxidase type B inhibitors, catechol-O-methyltransferase inhibitors and amantadine. Nonmotor features, such as cognitive impairment, mood disorders, autonomic dysfunction, gastrointestinal and genitourinary dysfunction, have a substantial impact on Parkinson's disease patients and their quality of life. This review will provide an overview on medications currently available for management of both motor and nonmotor symptoms of Parkinson's disease. Focus will be placed on recent and evolving studies evaluating symptomatic and neuroprotective effects of medications, and how such studies may impact the future management of Parkinson's disease.","corpus_id":11126160,"score":0},{"doc_id":"20707760","title":"Safinamide in the treatment of Parkinson's disease.","abstract":"IMPORTANCE OF THE FIELD: Current therapy for Parkinson's disease (PD) is primarily directed at reversing the motor symptoms that are the consequence of dopamine deficiency and includes levodopa, dopamine agonists and monoamine oxidase (MAO) B inhibitors. New drugs offering both dopaminergic and non-dopaminergic actions could offer a significant advantage. AREAS COVERED IN THIS REVIEW: This review surveys the current treatment strategies for PD. Defining unmet needs and how a new compound - safinamide, which has both dopaminergic and non-dopaminergic actions - might address these. WHAT THE READER WILL GAIN: The reader will gain an understanding of safinamide and its mechanisms of action, including reversible MAOB inhibition and reduced dopamine reuptake with antiglutamatergic effects, and how it may potentially provide improvement of PD motor symptoms with an antidyskinetic effect through its effect on glutamate release. The clinical trial profile of safinamide is reviewed. Early results are promising in terms of improved motor function and reduced 'OFF' time. Additional Phase III trials are now in progress for this adjunctive indication. Finally, the reader will understand the potential role for safinamide in the selection and sequencing of drugs for PD. TAKE HOME MESSAGE: safinamide combines both dopaminergic and non-dopaminergic actions that may add a new dimension to PD treatment options as an adjunct to current drugs. Its efficacy is under active evaluation in Phase III clinical trials.","corpus_id":45746856,"score":0},{"doc_id":"21255197","title":"Drugs and drug delivery in PD: optimizing control of symptoms with pramipexole prolonged-release.","abstract":"Intermittent or pulsatile dopamine-receptor stimulation is postulated to induce plastic changes in motor systems that are responsible for the development of motor fluctuations and dyskinesia, complicating long-term levodopa therapy of Parkinson's disease (PD). Continuous dopamine stimulation (CDS) is a concept that refers to the hypothesis that more continuous dopamine-receptor stimulation will reduce the risk of motor complications, particularly dyskinesias, and may also treat established dyskinesias. In line with this hypothesis, the intermittent administration of dopaminergic agents with short half-lives induce motor complications in animal models, whilst the continuous administration of the same compounds via mini-pumps substantially reduces such symptoms. Continuous drug delivery (CDD) strategies are therefore explored in clinical trials to prevent or manage motor complications. The early use of a dopamine agonist reduces the risk of motor fluctuations compared with levodopa. Conversely, the early combination of the catechol-O-methyltransferase inhibitor entacapone with levodopa has failed to demonstrate a comparable advantage. Outcomes of uncontrolled long-term studies of PD patients with motor complications treated for several months with subcutaneous continuous infusion of apomorphine or intraduodenal levodopa are compatible with CDS. New once-daily prolonged-release formulations of dopamine agonists have demonstrated antiparkinsonian efficacy in randomized trials conducted in early as well as advanced patients with PD. Once-daily administration is convenient and may improve compliance. Other theoretical advantages in terms of efficacy or tolerability deserve further exploration.","corpus_id":205582694,"score":0},{"doc_id":"22691758","title":"Therapies in Parkinson's disease.","abstract":"PURPOSE OF REVIEW: This review examines currently available therapeutic strategies for Parkinson's disease, emphasizing evidence-based data as well as a patient-centered approach to the treatment of motor and nonmotor symptoms. RECENT FINDINGS: Although clinical trials of disease-modifying approaches have been thus far disappointing, steady advances are being made in the symptomatic treatment of Parkinson's disease. In this review, we focus on recent studies with monoamine oxidase type B inhibitors (selegiline and rasagiline), coenzyme Q10, creatine, and exercise in early Parkinson's disease. We also discuss the relative merits and disadvantages of delaying the initiation of levodopa therapy, the role of dopamine agonists, particularly ropinirole and pramipexole, and management of motor and behavioral complications, such as fluctuations, dyskinesias and impulse-control disorders. Novel formulations and delivery approaches for conventional and new drugs are also discussed. Finally, we review recent studies of surgical treatments of Parkinson's disease, such as deep brain stimulation. SUMMARY: Numerous clinical trials have provided evidence that health-related quality of life can be substantially improved with early diagnosis and institution of exercise and other physical measures, appropriate timing of dopaminergic therapy, and strategies to delay and treat levodopa-related motor complications and nonmotor Parkinson's disease-related symptoms.","corpus_id":6997872,"score":0},{"doc_id":"22772874","title":"Emerging therapies for Parkinson's disease.","abstract":"PURPOSE OF REVIEW: The experimental therapeutics of Parkinson's disease are reviewed, highlighting the current pipeline of emerging therapeutic approaches. RECENT FINDINGS: This review includes novel approaches to dopaminergic drug delivery such as intraintestinal infusions or new extended-release formulations of levodopa and also intrapulmonary delivery of apomorphine as well as novel dopaminergic agents like the monoamine oxidase-B inhibitor safinamide or novel catechol-O-methyl transferase inhibitors. An even greater number of ongoing clinical trials assess the efficacy and safety of nondopaminergic approaches to enhance motor control or reduce motor complications like fluctuations and dyskinesias. These include adenosine A2A antagonists, α-adrenergic and serotonergic agonists as well as drugs acting on the glutamatergic system. Gene-based or cell-based intrastriatal delivery of therapeutic principles that enhance striatal dopaminergic transmission directly or via the stimulation of trophic activity has also reached phase II clinical development with encouraging results in some studies. Finally, a wide spectrum of agents with a potential for slowing disease progression is currently tested. SUMMARY: A variety of medical and nonmedical interventions in different phases of clinical development provide an interesting and promising portfolio of emerging therapies for Parkinson's disease.","corpus_id":32540153,"score":0},{"doc_id":"24756517","title":"Pharmacological treatment of Parkinson disease: a review.","abstract":"IMPORTANCE: Parkinson disease is the second most common neurodegenerative disease worldwide. Although no available therapies alter the underlying neurodegenerative process, symptomatic therapies can improve patient quality of life. OBJECTIVE: To provide an evidence-based review of the initial pharmacological management of the classic motor symptoms of Parkinson disease; describe management of medication-related motor complications (such as motor fluctuations and dyskinesia), and other medication adverse effects (nausea, psychosis, and impulse control disorders and related behaviors); and discuss the management of selected nonmotor symptoms of Parkinson disease, including rapid eye movement sleep behavior disorder, cognitive impairment, depression, orthostatic hypotension, and sialorrhea. EVIDENCE REVIEW: References were identified using searches of PubMed between January 1985 and February 2014 for English-language human studies and the full database of the Cochrane Library. The classification of studies by quality (classes I-IV) was assessed using the levels of evidence guidelines from the American Academy of Neurology and the highest-quality data for each topic. RESULTS: Although levodopa is the most effective medication available for treating the motor symptoms of Parkinson disease, in certain instances (eg, mild symptoms, tremor as the only or most prominent symptom, aged <60 years) other medications (eg, monoamine oxidase type B inhibitors [MAOBIs], amantadine, anticholinergics, β-blockers, or dopamine agonists) may be initiated first to avoid levodopa-related motor complications. Motor fluctuations may be managed by modifying the levodopa dosing regimen or by adding several other medications, such as MAOBIs, catechol-O-methyltransferase inhibitors, or dopamine agonists. Impulse control disorders are typically managed by reducing or withdrawing dopaminergic medication, particularly dopamine agonists. Evidence-based management of some nonmotor symptoms is limited by a paucity of high-quality positive studies. CONCLUSIONS AND RELEVANCE: Strong evidence supports using levodopa and dopamine agonists for motor symptoms at all stages of Parkinson disease. Dopamine agonists and drugs that block dopamine metabolism are effective for motor fluctuations and clozapine is effective for hallucinations. Cholinesterase inhibitors may improve symptoms of dementia and antidepressants and pramipexole may improve depression. Evidence supporting other therapies for motor and nonmotor features is less well established.","corpus_id":205058847,"score":0},{"doc_id":"24950010","title":"Treatment of early Parkinson's disease.","abstract":"PURPOSE OF REVIEW: This review summarizes currently available treatment options and treatment strategies, investigational treatments, and the importance of exercise for early Parkinson's disease. RECENT FINDINGS: The available treatment options for early Parkinson's disease have changed little in the past decade and include carbidopa/levodopa, dopamine agonists, and monoamine oxidase type B (MAO-B) inhibitors. However, we discuss changes in treatment strategies, including dosing and the use of combination therapy used in an attempt to reduce or delay the appearance of motor complications and other adverse events. We will also review several investigational treatments that have shown promise for the treatment of early Parkinson's disease, including a new extended release formulation of carbidopa/levodopa (IPX066), safinamide which inhibits MAO-B, dopamine uptake and glutamate and pardoprunox which is a 5HT-1A agonist and a partial dopamine agonist. Finally, we discuss recent studies focusing on exercise as an important component in the management of early Parkinson's disease. SUMMARY: Advances in the management of early Parkinson's disease include evolving treatment strategies, new investigational treatments, and earlier implementation of various forms of exercise.","corpus_id":52861149,"score":0},{"doc_id":"25711470","title":"1-[2-(4-Benzyloxyphenoxy)Ethyl]Imidazole inhibits monoamine oxidase B and protects against neuronal loss and behavioral impairment in rodent models of Parkinson's disease.","abstract":"Monoamine oxidase B (MAO-B) is well known as a therapeutic target for Parkinson's disease (PD). MAO-B inhibitors retain antiparkinsonism abilities to improve motor function and prevent neuronal loss by decreasing dopamine metabolism and oxidative stress in the brain. From the study to find novel antiparkinsonism drugs that can inhibit MAO-B activity, neuronal loss, and behavioral deficits in the mouse model of PD, we identified that 1-[2-(4-benzyloxyphenoxy)ethyl]imidazole (BPEI) or safinamide strongly and selectively inhibited MAO-B activities in a dose-dependent manner (IC50 of BPEI and safinamide for MAO-B were 0.016 and 0.0021 µM and for MAO-A were 70.0 and 370 µM, respectively). In ex vivo studies after an administration (30 mg/kg, i.p.) of BPEI or safinamide to normal mice, the MAO-B activity in the brain was reduced by up to 90.6% or 82.4% at 1.0 hr. BPEI (20 mg/kg, i.p.) or safinamide (20 mg/kg, i.p.) significantly reversed the behavioral impairments, dopamine levels in the striatum, and neuronal loss in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice compared with the MPTP-alone-treated group. In the 6-hydroxydopamine-induced PD rat model, behavioral improvement by levodopa sparing activity was observed in the BPEI- or safinamide-treated (20 mg/kg, i.p.) rats. Moreover, BPEI revealed additional curative activities for nonmotor symptoms of PD such as pain, anxiety, epilepsy, and depression in rodent disease models. Therefore, BPEI has broad therapeutic potential for treating motor symptoms via strong and selective inhibitory effects on MAO-B, with additional benefits for comorbid symptoms in PD.","corpus_id":28927174,"score":0},{"doc_id":"26293004","title":"New treatments for levodopa-induced motor complications.","abstract":"Levodopa (l-dopa)-induced motor complications, including motor fluctuations and dyskinesia, affect almost all patients with Parkinson's disease (PD) at some point during the disease course, with relevant implications in global health status. Various dopaminergic and nondopaminergic pharmacological approaches as well as more invasive strategies including devices and functional surgery are available to manage such complications. In spite of undisputable improvements during the last decades, many patients remain significantly disabled, and a fully satisfying management of l-dopa-induced motor complications is still an important unmet need of PD therapy. This article reviews the recent trial results published from 2013 to April 2015 about pharmacological and nonpharmacological interventions to treat motor complications. Randomized controlled trials conducted in patients suffering from already established complications showed that new levodopa (l-dopa) formulations such as intrajejunal l-dopa-carbidopa infusion and bilayered extended-release l-dopa-carbidopa (IPX066) can improve motor fluctuations. Positive results were also obtained with a new monoamine oxidase B (MAO-B) inhibitor (safinamide) and a catechol-O-methyltransferase COMT inhibitor (opicapone). Pilot data suggest that new formulations of dopamine agonists (inhaled apomorphine) are also of potential interest. The development of novel nondopaminergic adenosine A2A antagonists (istradefylline, preladenant, and tozadenant) to treat motor fluctuations showed conflicting results in phase 2 and phase 3 trials. For dyskinesia, trials with new amantadine extended-release formulations confirmed the interest of the glutamatergic N-methyl-d-aspartate (NMDA) antagonist approach. Positive pilot antidyskinetic effects were also recently reported using serotonin agents such as eltoprazine and glutamate mGluR5 modulators such as mavoglurant. However, the translation to clinical practice of such innovative concepts remains challenging, because subsequent phase 2 trials conducted to confirm the antidyskynetic effects of mavoglurant failed, leading to the interruption of the development of this compound for this indication.","corpus_id":19682541,"score":0},{"doc_id":"26293352","title":"Modern treatment in Parkinson's disease, a personal approach.","abstract":"There are many guidelines available concerning the treatment of Parkinson's disease. Most of these advocate treating young-onset patients with a dopamine agonist and older patients with levodopa. The rationale behind this recommendation has its origins in the side effects associated with each of these drug classes: whilst levodopa leads to dyskinesia, which may not be relevant for patients with a limited life-expectancy, dopamine agonists have a much longer plasma half life which probably leads to more continuous dopamine receptor stimulation and thus decreases the occurrence and severity of dyskinesia. However, the side effects associated with the use of dopamine agonists, such as sleepiness, orthostatic problems, hallucinations and impulse control disorders are a drawback. In this overview, the hypothesis will be put forward that perhaps such a strict distinction is no longer needed. A new idea may be the early combination of levodopa with a dopamine agonist which would provide good clinical efficacy and, because of the relatively low doses involved, would reduce the side effects associated with both substances. MAO-B inhibitors may be a good option for early treatment and especially for patients who experience first motor fluctuations. Similarly, and particularly if a wearing-off symptom is present, COMT inhibitors smoothen and prolong the action of levodopa. More invasive escalation therapy comes into play when patients reach the advanced stages with problems of insufficient motor control, such as bradykinesia, rigidity and resting tremor, combined with on-time dyskinesia. The use of all oral and invasive treatment has to be individualized to gain a good motor and non-motor control and especially a good quality of life.","corpus_id":25992055,"score":0},{"doc_id":"26300398","title":"Neuroprotection by safinamide in the 6-hydroxydopamine model of Parkinson's disease.","abstract":"AIMS: Current therapies in Parkinson's disease mainly treat symptoms rather than provide effective neuroprotection. We examined the effects of safinamide (monoamine oxidase B and sodium channel blocker) on microglial activation and the degeneration of dopaminergic neurons in a rat model of PD in vivo, and on microglia in vitro. METHODS: Rats received unilateral stereotaxic injection of 6-hydroxydopamine into the medial forebrain bundle on day 0: The contralateral side served as control. Safinamide or vehicle was delivered from days 0 or 1, for 7 days, via sub-cutaneous mini-pumps. RESULTS: In vehicle-treated rats 6-hydroxydopamine caused a significant increase in the number of activated MHC-II(+) microglia compared with the contralateral side, and only 50% of the dopaminergic neurons survived in the ipsilateral SNc. In contrast, rats treated daily with safinamide 50 and 150 mg/ml (on day 0 or 1) exhibited a significantly reduced number of activated microglia (55% reduction at 150 mg/ml) and a significant protection of dopaminergic neurons (80% of neurons survived) (P < 0.001) compared with vehicle-treated controls. Rasagiline, a monoamine oxidase B inhibitor, and lamotrigine, a sodium channel blocking drug, also protected dopaminergic neurons, indicating that safinamide may act by either or both mechanisms. Safinamide also reduced the activation of microglial cells in response to lipopolysaccharide exposure in vitro. CONCLUSION: Safinamide therapy suppresses microglial activation and protects dopaminergic neurons from degeneration in the 6-hydroxydopamine model of PD, suggesting that the drug not only treats symptoms but also provides neuroprotection.","corpus_id":23711043,"score":0},{"doc_id":"26849427","title":"The safety and efficacy of safinamide mesylate for the treatment of Parkinson's disease.","abstract":"Safinamide (brand name Xadago®, Zambon S.p. A) is a third-generation reversible MAO-B inhibitor, which also blocks sodium voltage-sensitive channels and modulates stimulated release of glutamate. Safinamide was recently licensed by EMA for the treatment of PD as add-on therapy to a stable dose of levodopa alone or in combination with other PD medicinal products in mid-to advanced-stage fluctuating patients. It is also under review by the US FDA. Studies in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys and 6OHDA-lesioned rats suggest antiparkinsonian efficacy and antidyskinesic effects. Randomized, double-blind, placebo-controlled trials have shown efficacy for the treatment of motor symptoms in stable PD patients on dopamine agonists and in fluctuating PD patients on levodopa. Significant improvement in daily ON time was also observed in the latter. This effect was maintained for at least 2 years in double-blind conditions and, interestingly, without significant worsening of dyskinesia. Clinical studies have not detected any specific safety issue other than those already known with MAO-B inhibitors.","corpus_id":37787896,"score":0},{"doc_id":"27498199","title":"Opicapone: A Review in Parkinson's Disease.","abstract":"Oral opicapone (Ongentys(®)), a potent, third-generation, long-acting, peripheral catechol-O-methyltransferase (COMT) inhibitor, is approved as adjunctive treatment to levodopa (L-Dopa)/dopa-decarboxylase inhibitor (DDCI) therapy in adults with Parkinson's disease (PD) and end-of-dose motor fluctuations who cannot be stabilized on those combinations. In 14- to 15-week, double-blind, multinational trials and in 1-year, open-label extension studies in this patient population, opicapone was an effective and generally well tolerated adjunctive therapy to L-Dopa plus a DDCI and other PD therapy. During the double-blind phase, adjunctive opicapone 50 mg once daily provided significantly greater improvements in motor fluctuations than placebo, with these improvements noninferior to those with entacapone. These beneficial improvements in motor fluctuations with opicapone were maintained in patients who continued adjunctive opicapone during the extension studies, with patients who switched from placebo or entacapone to opicapone experiencing significant improvements in motor fluctuations during this year. No new unexpected safety concerns were identified after ≈1.4 years' treatment with opicapone, with no serious cases of hepatotoxicity reported in clinical trials. With its convenient once-daily regimen, oral opicapone is an emerging COMT inhibitor option for use as adjunctive therapy to L-Dopa/DDCI therapy in adults with PD and end-of dose motor fluctuations who cannot be stabilized on those combinations.","corpus_id":5787752,"score":0},{"doc_id":"27577098","title":"Current and experimental treatments of Parkinson disease: A guide for neuroscientists.","abstract":"Over a period of more than 50 years, the symptomatic treatment of the motor symptoms of Parkinson disease (PD) has been optimized using pharmacotherapy, deep brain stimulation, and physiotherapy. The arsenal of pharmacotherapies includes L-Dopa, several dopamine agonists, inhibitors of monoamine oxidase (MAO)-B and catechol-o-methyltransferase (COMT), and amantadine. In the later course of the disease, motor complications occur, at which stage different oral formulations of L-Dopa or dopamine agonists with long half-life, a transdermal application or parenteral pumps for continuous drug supply can be subscribed. Alternatively, the patient is offered deep brain stimulation of the subthalamic nucleus (STN) or the internal part of the globus pallidus (GPi). For a more efficacious treatment of motor complications, new formulations of L-Dopa, dopamine agonists, and amantadine as well as new MAO-B and COMT inhibitors are currently tested in clinical trials, and some of them already yielding positive results in phase 3 trials. In addition, non-dopaminergic agents have been tested in the early clinical phase for the treatment of motor fluctuations and dyskinesia, including adenosine A2A antagonists (istradefylline, preladenant, and tozadenant) and modulators of the metabolic glutamate receptor 5 (mGluR5 - mavoglurant) and serotonin (eltoprazine) receptors. Recent clinical trials testing coenzyme Q10, the dopamine agonist pramipexole, creatine monohydrate, pioglitazone, or AAV-mediated gene therapy aimed at increasing expression of neurturin, did not prove efficacious. Treatment with nicotine, caffeine, inosine (a precursor of urate), and isradipine (a dihydropyridine calcium channel blocker), as well as active and passive immunization against α-synuclein and inhibitors or modulators of α-synuclein-aggregation are currently studied in clinical trials. However, to date, no disease-modifying treatment is available. We here review the current status of treatment options for motor and non-motor symptoms, and discuss current investigative strategies for disease modification. This review provides basic insights, mainly addressing basic scientists and non-specialists. It stresses the need to intensify therapeutic PD research and points out reasons why the translation of basic research to disease-modifying therapies has been unsuccessful so far. The symptomatic treatment of the motor symptoms of Parkinson disease (PD) has been constantly optimized using pharmacotherapy (L-Dopa, several dopamine agonists, inhibitors of monoamine oxidase (MAO)-B and catechol-o-methyltransferase (COMT), and amantadine), deep brain stimulation, and physiotherapy. For a more efficacious treatment of motor complications, new formulations of L-Dopa, dopamine agonists, and amantadine as well as new MAO-B and COMT inhibitors are currently tested in clinical trials. Non-dopaminergic agents have been tested in the early clinical phase for the treatment of motor fluctuations and dyskinesia. Recent clinical trials testing coenzyme Q10, the dopamine agonist pramipexole, creatine monohydrate, pioglitazone, or AAV-mediated gene therapy aimed at increasing expression of neurturin, did not prove efficacious. Treatment with nicotine, caffeine, and isradipine - a dihydropyridine calcium channel blocker - as well as active and passive immunization against α-synuclein and inhibitors of α-synuclein-aggregation are currently studied in clinical trials. However, to date, no disease-modifying treatment is available for PD. We here review the current status of treatment options and investigative strategies for both motor and non-motor symptoms. This review stresses the need to intensify therapeutic PD research and points out reasons why the translation of basic research to disease-modifying therapies has been unsuccessful so far. This article is part of a special issue on Parkinson disease.","corpus_id":30497369,"score":0},{"doc_id":"27599671","title":"Clinical pharmacology review of opicapone for the treatment of Parkinson's disease.","abstract":"Two catechol-O-methyl transferase inhibitors are currently used as add-on therapy to levodopa for the amelioration of end-of-dose motor fluctuations in Parkinson's disease patients: entacapone, which has moderate efficacy and requires multiple dosing, and tolcapone, which has a poor safety profile. Opicapone (OPC) is a novel, long-acting, peripherally selective, once daily, third-generation catechol-O-methyl transferase inhibitor. Two Phase III clinical trials demonstrated OPC efficacy in reducing OFF-time by an average of about 60 min daily compared with placebo, without increasing ON-time with troublesome dyskinesias, with a good drug safety profile. In June 2016, the European Commission granted a marketing authorization valid throughout the European Union for OPC, indicated as adjunctive of levodopa decarboxylase inhibitors in adult patients with Parkinson's disease and end-of-dose motor fluctuations.","corpus_id":3492185,"score":0},{"doc_id":"28123288","title":"Spotlight on opicapone as an adjunct to levodopa in Parkinson's disease: design, development and potential place in therapy.","abstract":"Parkinson's disease (PD) is a progressive, chronic, neurodegenerative disease characterized by rigidity, tremor, bradykinesia and postural instability secondary to dopaminergic deficit in the nigrostriatal system. Currently, disease-modifying therapies are not available, and levodopa (LD) treatment remains the gold standard for controlling motor and nonmotor symptoms of the disease. LD is extensively and rapidly metabolized by peripheral enzymes, namely, aromatic amino acid decarboxylase and catechol-O-methyltransferase (COMT). To increase the bioavailability of LD, COMT inhibitors are frequently used in clinical settings. Opicapone is a novel COMT inhibitor that has been recently approved by the European Medicines Agency as an adjunctive therapy to combinations of LD and aromatic amino acid decarboxylase inhibitor in adult PD patients with end-of-dose motor fluctuations. We aimed to review the biochemical properties of opicapone, summarize its preclinical and clinical trials and discuss its future potential role in the treatment of PD.","corpus_id":3088229,"score":0},{"doc_id":"28124620","title":"Monoamine Oxidase B Inhibitors in Parkinson's Disease.","abstract":"BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder with a prevalence increasing with age. Oxidative stress and glutamate toxicity are involved in its pathomechanism. There are still many unmet needs of PD patients, including the alleviation of motor fluctuations and dyskinesias, and the development of therapies with neuroprotective potential. OBJECTIVE: To give an overview of the pharmacological properties, the efficacy and safety of the monoamine oxidase B (MAO-B) inhibitors in the treatment of PD, with special focus on the results of randomized clinical trials. METHOD: A literature search was conducted in PubMed for 'PD treatment', 'MAO-B inhibitors', 'selegiline', 'rasagiline', 'safinamide' and 'clinical trials' with 'MAO-B inhibitors' in 'Parkinson' disease'. RESULTS: MAO-B inhibitors have a favorable pharmacokinetic profile, improve the dopamine deficient state and may have neuroprotective properties. Safinamide exhibits an anti-glutamatergic effect as well. When applied as monotherapy, MAO-B inhibitors provide a modest, but significant improvement of motor function and delay the need for levodopa. Rasagiline and safinamide were proven safe and effective when added to a dopamine agonist in early PD. As add-on to levodopa, MAO-B inhibitors significantly reduced off-time and were comparable in efficacy to COMT inhibitors. Improvements were achieved as regards certain non-motor symptoms as well. CONCLUSION: Due to the efficacy shown in clinical trials and their favorable side-effect profile, MAO-B inhibitors are valuable drugs in the treatment of PD. They are recommended as monotherapy in the early stages of the disease and as add-on therapy to levodopa in advanced PD.","corpus_id":4928424,"score":0},{"doc_id":"28234566","title":"Opicapone for the treatment of Parkinson's disease.","abstract":"INTRODUCTION: Parkinson's disease (PD) is a progressive neurodegenerative disease. The currently available treatment options only have a symptomatic effect. With disease progression almost all antiparkinsonian pharmacological classes are tried, but the gold standard of pharmacological management is still L-dopa. Various strategies can be used to raise the dopaminergic tone. Catechol-O-methyltransferase (COMT) inhibitors attain this goal by decreasing L-dopa peripheral metabolism. Areas covered: Opicapone (Ongentys®) is a new COMT inhibitor developed to fulfill the need for more potent, safer and longer acting COMT inhibitors. This review puts into context opicapone's indications, its chemical and preclinical data, the pharmacodynamics and pharmacokinetic characteristics, and the efficacy and safety results delivered by clinical trials. Expert opinion: Opicapone is an efficacious COMT inhibitor. Its proprieties make it adequate for a once-a-day oral dose regimen. It has proved to reduce the off-time and to increase the on-time without troublesome dyskinesias in PD patients with motor fluctuations. The reported adverse events suggest an overall safe and well-tolerated profile. The most common adverse events were dyskinesia, and there were no issues of concern for hepatotoxicity, severe diarrhoea or chromaturia. Further evidence is still needed to conclude how it compares with other drugs for the treatment of motor fluctuations.","corpus_id":5251815,"score":0},{"doc_id":"28511252","title":"Diagnosis and Management of Parkinson's Disease.","abstract":"Despite numerous efforts to identify specific and sensitive biomarkers, the diagnosis of Parkinson's disease (PD) is still based on clinical criteria that include the presence of a combination of cardinal motor features (tremor, rigidity, bradykinesia, and postural instability), other motor features (including freezing of gait and abnormal postures), and numerous nonmotor features. In addition, the presence of atypical features may suggest an alternative diagnosis. Levodopa therapy remains the gold standard in the management of motor features of PD. New formulations of levodopa and novel delivery systems are currently being evaluated and gradually introduced in clinical practice in an attempt to prevent or treat levodopa-related motor complications. Dopamine agonists also play an important role as monotherapy in mild or adjunctive therapy in moderately advanced disease. As the disease progresses and patients develop complications from levodopa therapy, specifically motor fluctuations and dyskinesias, deep brain stimulation becomes an alternative therapeutic option. Clinical trials of experimental therapeutics are currently fueling the PD therapeutic pipeline.","corpus_id":398250,"score":0},{"doc_id":"29018297","title":"Xadago (Safinamide): A Monoamine Oxidase B Inhibitor for the Adjunct Treatment of Motor Symptoms in Parkinson's Disease.","abstract":"Xadago (safinamide), a monoamine oxidase B inhibitor for the adjunct treatment of motor symptoms in Parkinson's disease.","corpus_id":22895774,"score":0},{"doc_id":"29130466","title":"[Safinamide from daily clinical practice: first clinical steps].","abstract":"Safinamida desde la practica clinica diaria: primeros pasos clinicos. INTRODUCTION: The management of motor complications in Parkinson's disease (PD) is still limited. Safinamide, a new drug that has MAO-B inhibition and antiglutamatergic effects through inhibition of sodium channels, has shown efficacy for the treatment of fluctuations at doses of 50-100 mg/day. PATIENTS AND METHODS: From daily clinical practice, we describe the efficacy and tolerability of safinamide at three months in PD patients with motor complications. Efficacy was assessed by the Clinical Global Impression of Change scale and change in 'off' time during the daytime. All reported adverse events were recorded. RESULTS: Fifty patients were recruited. 57.4% reported to be much better or moderately better at three months, improving both motor and non-motor fluctuations. Significant decrease of 0.9 ± 0.6 h/day was achieved at three months. In 13 patients (27.6%), levodopa equivalent daily dose was reduced in 132 mg/day. In patients with dyskinesias, safinamide 100 mg/day was better for controlling fluctuations and dyskinesias. 19% of patients had mild adverse events. Seven patients stopped treatment after development of confusional syndrome. CONCLUSIONS: The dopaminergic and non-dopaminergic action of safinamide exerts a good control of motor fluctuations. In patients with fluctuations and dyskinesias the dose of 100 mg/day of safinamide is preferred. Tolerability was good, except for patients older than 75 years or in advanced stages of the disease.","corpus_id":27208131,"score":0},{"doc_id":"29339106","title":"Safinamide: a new hope for Parkinson's disease?","abstract":"The loss of dopaminergic neurons (DAn) and reduced dopamine (DA) production underlies the reasoning behind the gold standard treatment for Parkinson's disease (PD) using levodopa (L-DOPA). Recently licensed by the European Medicine Agency (EMA) and US Food and Drug Administration (FDA), safinamide [a monoamine oxidase B (MOA-B) inhibitor] is an alternative to L-DOPA; as we discuss here, it enhances dopaminergic transmission with decreased secondary effects compared with L-DOPA. In addition, nondopaminergic actions (neuroprotective effects) have been reported, with safinamide inhibiting glutamate release and sodium/calcium channels, reducing the excitotoxic input to dopaminergic neuronal death. Effects of safinamide have been correlated with the amelioration of non-motor symptoms (NMS), although these remain under discussion. Overall, safinamide can be considered to have potential antidyskinetic and neuroprotective effects and future trials and/or studies should be performed to provide further evidence for its potential as an anti-PD drug.","corpus_id":3885257,"score":0},{"doc_id":"29542008","title":"Long-term Efficacy of Safinamide on Parkinson's Disease Chronic Pain.","abstract":"INTRODUCTION: Chronic pain is an important yet overlooked non-motor symptom of Parkinson's disease (PD), caused by an imbalance of the dopaminergic and glutamatergic systems. Safinamide has a multimodal mechanism of action, dopaminergic (reversible MAO-B inhibition) and non-dopaminergic (modulation of the abnormal glutamate release), that might be beneficial for both motor and non-motor symptoms. OBJECTIVES: To investigate the long-term (2-year) efficacy of safinamide on PD chronic pain and to confirm the positive effects observed after 6 months of treatment. METHODS: This is a post hoc analysis of the data from the 2-year study 018, focused on the reduction of concomitant pain treatments and on the scores of pain-related items of the Parkinson's disease quality of life questionnaire (PDQ-39). RESULTS: Safinamide, compared with placebo, significantly improved the PDQ-39 items 37 (\"painful cramps or spasm,\" p = 0.0074) and 39 (\"unpleasantly hot or cold,\" p = 0.0209) and significantly reduced the number of concomitant pain treatments by 26.2% (p = 0.005). A significantly greater proportion of patients in the safinamide group was not using pain drugs after 2 years of treatment (p = 0.0478). CONCLUSIONS: The positive effects of safinamide on PD chronic pain were maintained in the long term. Further investigations are desirable to confirm their clinical relevance. FUNDING: Zambon SpA.","corpus_id":5006485,"score":0},{"doc_id":"29570862","title":"Medical and surgical management of advanced Parkinson's disease.","abstract":"Advanced Parkinson's disease is characterized by the presence of motor fluctuations, various degree of dyskinesia, and disability with functional impact on activities of daily living and independence. Therapeutic management aims to extend levodopa benefit while minimizing motor complications and includes, in selected cases, the implementation of drug infusion and surgical techniques. In milder forms of motor complications, these can often be controlled with manipulation of levodopa dose and the introduction of supplemental therapies such as catechol-O-methyl transferase inhibitors, monoamine oxidase B inhibitors, and dopamine agonists including apomorphine. Clinical experience and evidence from published studies indicate that when these agents cannot satisfactorily control motor complications, patients should be assessed and considered for device-aided therapies. This review article summarizes some of the newer available therapeutic opportunities such as use of enzyme inhibitors like opicapone and safinamide, adenosine A2A receptor antagonists, apomorphine and levodopa/carbidopa intestinal gel infusion, deep brain stimulation including the role of closed-loop and adaptive stimulation, and MRI-guided focused ultrasound. © 2018 International Parkinson and Movement Disorder Society.","corpus_id":206250568,"score":0},{"doc_id":"29614697","title":"Are There Benefits in Adding Catechol-O Methyltransferase Inhibitors in the Pharmacotherapy of Parkinson's Disease Patients? A Systematic Review.","abstract":"BACKGROUND: A qualified consensus suggests that a combination of levodopa with a peripherally acting dopa decarboxylase inhibitor continues to present the gold standard treatment of Parkinson's disease (PD). However, as the disease progresses the therapeutic window of levodopa becomes narrowed. Pharmacological strategies for motor fluctuations are focused on providing less pulsatile and more continuous dopaminergic stimulation. Peripheral catechol-O-methyltransferase (COMT) inhibition improves the bioavailability of levodopa and results in a prolonged response. OBJECTIVE: The primary aim of this study was to investigate the efficacy and safety of the two available COMT inhibitors; entacapone and tolcapone and the recently introduced opicapone. METHODS: Electronic databases were systematically searched for original studies published within the last 37 years. In addition, lists of identified studies, reviews and their references were examined. RESULTS: Twelve studies fulfilled the inclusion criteria. 3701 patients with PD were included in this systematic review. CONCLUSIONS: Adjuvant treatment of PD patients experiencing motor fluctuations with entacapone resulted in improvement of motor function and was well tolerated. Therefore, entacapone presented an acceptable benefit to risk ratio. Tolcapone appeared to result in a greater therapeutic effect. However, this was not consistent across all motor variables and studies, and thus would not support its use, given the current onerous monitoring that is required. Opicapone was not associated with adverse reactions in a phase III trial but did not present a greater efficacy than entacapone, and thus further studies are required in order to illustrate its cost effectiveness.","corpus_id":4595585,"score":0}],"string":"[\n {\n \"doc_id\": \"23673910\",\n \"title\": \"Pharmacokinetic considerations for the use of levodopa in the treatment of Parkinson disease: focus on levodopa/carbidopa/entacapone for treatment of levodopa-associated motor complications.\",\n \"abstract\": \"Parkinson disease (PD) is a progressive, disabling, neurodegenerative disorder characterized by both motor and nonmotor symptoms. Monoamine oxidase B inhibitors, dopamine agonists, N-methyl-D-aspartate antagonists and levodopa (LD), with its various formulations and administration modes, mainly improve the motor symptoms in PD, which are thought to be related to decreased dopamine levels in the brain. Of these therapeutic drug options, LD represents the most effective and best tolerated compound when it is administered several times a day. Pharmacokinetic trials of oral LD/dopa decarboxylase inhibitor (DDCI) formulations with and without the catechol-O-methyltransferase inhibitor, entacapone, showed that repeated administration with entacapone causes an increase in both the maximum concentration (Cmax) and time to Cmax (Tmax) of LD. In addition, gastrointestinal motility may also impact plasma LD behavior. These peripheral components of LD metabolism contribute to the onset of motor complications, which are predominantly associated with LD/DDCI owing to its short plasma half-life. The increase in Tmax is related to a slower increase in plasma LD concentrations after repeated LD/DDCI intake, which may also increase the risk of wearing off. An elevation in Cmax after reiterated LD intake increases the risk of peak-dose dyskinesia. Therefore, it may be useful to start with higher doses of LD formulations in the morning and then to titrate with different LD doses during the day according to the individual patient's motor behavior, which is particularly characterized by the onset of motor complications, such as off periods and dyskinesia, in more advanced stages of PD.\",\n \"corpus_id\": 37581901,\n \"score\": 2\n },\n {\n \"doc_id\": \"24053341\",\n \"title\": \"Current status of safinamide for the drug portfolio of Parkinson's disease therapy.\",\n \"abstract\": \"Parkinson's disease (PD) is characterized by a slowly ongoing neuronal death. This alters dopaminergic and glutamatergic neurotransmission and causes a wide variety of motor and non-motor features. Safinamide has a unique pharmacological profile, which combines modulation of dopamine metabolism by reversible, highly specific monoamine oxidase-B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and of glutamate release induced by abnormal neuronal activity. Therefore, safinamide represents an ideal candidate for the treatment of PD. This compound asks for one time daily intake only within an optimum dose range between 50 and 100 mg. In clinical trials, safinamide was well tolerated and safe, improved motor behavior even in combination with dopamine agonist only, ameliorated levodopa-associated motor complications. Safinamide has the potential to become an important compound for the therapy of PD, since its symptomatic efficacy appears to be superior to available monoamine oxidase-B inhibitors or N-methyl-d-aspartate receptor antagonists like amantadine, according to available trial outcomes.\",\n \"corpus_id\": 207193329,\n \"score\": 2\n },\n {\n \"doc_id\": \"24323641\",\n \"title\": \"Randomized trial of safinamide add-on to levodopa in Parkinson's disease with motor fluctuations.\",\n \"abstract\": \"Levodopa is effective for the motor symptoms of Parkinson's disease (PD), but is associated with motor fluctuations and dyskinesia. Many patients require add-on therapy to improve motor fluctuations without exacerbating dyskinesia. The objective of this Phase III, multicenter, double-blind, placebo-controlled, parallel-group study was to evaluate the efficacy and safety of safinamide, an α-aminoamide with dopaminergic and nondopaminergic mechanisms, as add-on to l-dopa in the treatment of patients with PD and motor fluctuations. Patients were randomized to oral safinamide 100 mg/day (n = 224), 50 mg/day (n = 223), or placebo (n = 222) for 24 weeks. The primary endpoint was total on time with no or nontroublesome dyskinesia (assessed using the Hauser patient diaries). Secondary endpoints included off time, Unified Parkinson's Disease Rating Scale (UPDRS) Part III (motor) scores, and Clinical Global Impression-Change (CGI-C). At week 24, mean ± SD increases in total on time with no or nontroublesome dyskinesia were 1.36 ± 2.625 hours for safinamide 100 mg/day, 1.37 ± 2.745 hours for safinamide 50 mg/day, and 0.97 ± 2.375 hours for placebo. Least squares means differences in both safinamide groups were significantly higher versus placebo. Improvements in off time, UPDRS Part III, and CGI-C were significantly greater in both safinamide groups versus placebo. There were no significant between-group differences for incidences of treatment-emergent adverse events (TEAEs) or TEAEs leading to discontinuation. The addition of safinamide 50 mg/day or 100 mg/day to l-dopa in patients with PD and motor fluctuations significantly increased total on time with no or nontroublesome dyskinesia, decreased off time, and improved parkinsonism, indicating that safinamide improves motor symptoms and parkinsonism without worsening dyskinesia.\",\n \"corpus_id\": 18182887,\n \"score\": 2\n },\n {\n \"doc_id\": \"24650154\",\n \"title\": \"Safinamide for the treatment of Parkinson's disease.\",\n \"abstract\": \"INTRODUCTION: Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta. Non-dopaminergic neurotransmitter systems are also involved in its pathomechanism. The aim of the treatment is to improve the dopamine-deficient state and to alleviate the motor and the non-motor symptoms. Safinamide is an α-aminoamide derivative with a combined, dopaminergic and non-dopaminergic mode of action. Phase III clinical trials with safinamide, as add-on therapy to a dopamine agonist (DAA) and to levodopa (LD) in early and advanced stage PD, respectively, demonstrated an improvement of the motor symptoms. AREAS COVERED: The review discusses the pharmacokinetic and pharmacodynamic properties of safinamide and provides an overview of the clinical trials conducted with safinamide in PD. A literature search was made in PubMed for safinamide, safinamide pharmacokinetics, PD treatment and monoamine oxidase-B inhibitors, and in PubMed and on the ClinicalTrials.gov site for clinical trials with safinamide in PD. EXPERT OPINION: The place of safinamide in the therapy of PD is yet to be determined. However, the authors believe that safinamide is a valuable drug in the treatment of PD treatment with favorable pharmacokinetic and side-effect profiles. Data so far suggest that it can be used beneficially as add-on therapy both to DAAs in early PD and to LD in the later stages of the disease.\",\n \"corpus_id\": 23200408,\n \"score\": 2\n },\n {\n \"doc_id\": \"25559423\",\n \"title\": \"Catechol-O-methyltransferase inhibitors in Parkinson's disease.\",\n \"abstract\": \"Inhibitors of catechol-O-methyltransferase (COMT) are commonly used as an adjunct to levodopa in patients with Parkinson's disease (PD) for the amelioration of wearing-off symptoms. This narrative review aims to discuss the role of COMT inhibitors on peripheral levodopa metabolism and continuous brain delivery of levodopa, and to describe their metabolic properties. Oral application of levodopa formulations with a dopa decarboxylase inhibitor (DDI) results in fluctuating levodopa plasma concentrations, predominantly due to the short half-life of levodopa and its slowing of gastric emptying. Following transport across the blood-brain barrier and its metabolic conversion to dopamine, these peripheral 'ups and downs' of levodopa are reflected in fluctuating dopamine levels in the synaptic cleft between presynaptic and postsynaptic dopaminergic neurons of the nigrostriatal system. As a result, pulsatile postsynaptic dopaminergic stimulation takes place and results in the occurrence of motor complications, such as wearing-off and dyskinesia. More continuous plasma behaviour was observed after the combination of levodopa/DDI formulations with COMT inhibitors. These compounds also weaken a levodopa/DDI-related homocysteine increase, as biomarker for an impaired methylation capacity, which is involved in an elevated oxidative stress exposure. These findings favour the concept of chronic levodopa/DDI application with concomitant inhibition of COMT and monoamine oxidase, since deamination of dopamine via this enzyme also generates free radicals. This triple combination is suggested as standard levodopa application in patients with PD who need levodopa, if they will tolerate it.\",\n \"corpus_id\": 33939261,\n \"score\": 2\n },\n {\n \"doc_id\": \"26725544\",\n \"title\": \"Opicapone as an adjunct to levodopa in patients with Parkinson's disease and end-of-dose motor fluctuations: a randomised, double-blind, controlled trial.\",\n \"abstract\": \"BACKGROUND: Opicapone is a novel, once-daily, potent third-generation catechol-O-methyltransferase inhibitor. We aimed to assess the safety and efficacy of opicapone as an adjunct to levodopa compared with placebo or entacapone in patients with Parkinson's disease and motor fluctuations. METHODS: We did a randomised, double-blind, placebo-controlled and active-controlled trial of opicapone as an adjunct to levodopa in patients with Parkinson's disease with end-of-dose motor fluctuations. Patients aged 30-83 years were enrolled at 106 specialist centres across 19 European countries and Russia and were randomly assigned (1:1:1:1:1) by a proprietary computer-generated sequence to oral treatment with opicapone (5 mg, 25 mg, or 50 mg once daily), placebo, or entacapone (200 mg with every levodopa intake) for 14-15 weeks. Patients and investigators (ie, outcome assessors) were masked to treatment allocation. The primary endpoint was the change from baseline to end of study treatment in absolute time in the off state, as assessed by daily paper patient diaries; the primary analysis followed a hierarchical procedure for each opicapone dose in which superiority compared with placebo in the full analysis set was first tested and then, if positive, non-inferiority to entacapone was tested in the per-protocol set with a margin of 30 min. This trial is registered with EudraCT, 2010-021860-13, and ClinicalTrials.gov, NCT01568073. FINDINGS: Between March 31, 2011, and Nov 30, 2013, of 679 patients screened, 600 were randomly assigned. 590 patients were included in the full analysis set (120 in the placebo group, 120 in the entacapone group, 119 in the opicapone 5 mg group, 116 in the opicapone 25 mg group, and 115 in the opicapone 50 mg group) and 537 in the per-protocol set (112 in the placebo group, 104 in the entacapone group, 110 in the opicapone 5 mg group, 105 in the opicapone 25 mg group, and 106 in the opicapone 50 mg group). The mean change in time in the off state was -56·0 min (SE 13·4; 95% CI -82·3 to -29·7) for placebo, -96·3 min (13·4; -122·6 to -70·0) for entacapone, -91·3 min (13·5; -117·7 to -64·8) for opicapone 5 mg, -85·9 min (13·7; -112·8 to -59·1) for opicapone 25 mg, and -116·8 min (14·0; -144·2 to -89·4) for opicapone 50 mg. Treatment with opicapone 50 mg was superior to placebo (mean difference in change from baseline -60·8 min, 95% CI -97·2 to -24·4; p=0·0015) and non-inferior to entacapone (-26·2 min, -63·8 to 11·4; p=0·0051). Treatment with opicapone 5 mg (p=0·056) or 25 mg (p=0·080) was not significantly different from treatment with placebo. Treatment-emergent adverse events were reported in 60 (50%) of 121 patients in the placebo group, 69 (57%) of 122 in the entacapone group, 63 (52%) of 122 in the opicapone 5 mg group, 65 (55%) of 119 in the opicapone 25 mg group, and 62 (54%) of 115 in the opicapone 50 mg group. The most common adverse events were dyskinesia (in five patients in the placebo group, ten in the entacapone group, 17 in the opicapone 5 mg group, nine in the opicapone 25 mg group, and 18 in the opicapone 50 mg group), insomnia (in one, seven, two, seven, and seven patients, respectively), and constipation (in three, five, four, none, and seven patients, respectively). Serious adverse events were reported in six patients in the placebo group, eight in the entacapone group, four each in the opicapone 5 mg and opicapone 50 mg groups, and one in the opicapone 25 mg group. INTERPRETATION: The addition of opicapone 50 mg to levodopa treatment in patients with Parkinson's disease and end-of-dose motor fluctuations could enable a simplified drug regimen that allows physicians to individually tailor the existing levodopa daily regimen, by potentially reducing the total daily levodopa dose, increasing the dosing interval, and ultimately reducing the number of intakes, thereby maximising its benefit. FUNDING: BIAL.\",\n \"corpus_id\": 28714513,\n \"score\": 2\n },\n {\n \"doc_id\": \"26744740\",\n \"title\": \"Safinamide for symptoms of Parkinson's disease.\",\n \"abstract\": \"Chronic and slow progression of neuronal death in Parkinson's disease is responsible for an altered neurotransmission of various biogenic amines, such as dopamine. Therefore, an individually different pronounced heterogeneity of motor and nonmotor symptoms characterizes each Parkinson's disease patient. Ideal candidates for the balance of these neurotransmitter deficits are compounds like safinamide with broad mechanisms of action such as reversible monoamine oxidase type B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and of glutamate release. Safinamide is administered one time daily with oral doses ranging from 50 to 100 mg. Safinamide was well tolerated and safe, ameliorated motor symptoms when combined with dopamine agonist only or additional levodopa in clinical trials. Safinamide is a novel instrument for the drug therapy of Parkinson's disease with better safety and tolerability particularly concerning diarrhea than inhibitors of catechol-O-methyltransferase, like entacapone, according to an indirect comparison within a meta-analysis with entacapone.\",\n \"corpus_id\": 39866671,\n \"score\": 2\n },\n {\n \"doc_id\": \"26889632\",\n \"title\": \"Safinamide as Add-On Therapy to Levodopa in Mid- to Late-Stage Parkinson's Disease Fluctuating Patients: Post hoc Analyses of Studies 016 and SETTLE.\",\n \"abstract\": \"BACKGROUND: Studies 016 and SETTLE showed that safinamide was safe and effective as adjunct therapy in patients with advanced Parkinson's disease (PD) and motor fluctuations. The addition of safinamide to a stable dose of levodopa alone or with other antiparkinsonian medications significantly increased ON time with no/non-troublesome dyskinesia, decreased OFF time and improved Parkinson's symptoms. OBJECTIVE: To evaluate the clinical effects of safinamide 100 mg/day on motor fluctuations and cardinal Parkinson's symptoms in specific patient subgroups using pooled data from Studies 016 and SETTLE. METHODS: Both studies were double blind, placebo-controlled, randomized, phase 3 trials which enrolled patients with mid- to late-stage PD experiencing motor fluctuations while receiving optimized and stable doses of levodopa, alone or with other dopaminergic treatments. The present post-hoc analyses assessed the change from baseline in ON time (with no or non-troublesome dyskinesia) and OFF time in subgroups of patients who were receiving only levodopa at baseline, who were classified as \\\"mild fluctuators\\\" (daily OFF time ≤4 h), and who were receiving concomitant dopaminergic therapy, with or without amantadine, and the effects of safinamide versus placebo on individual cardinal PD symptoms during ON time. RESULTS: Safinamide significantly increased mean ON time (with no or non-troublesome dyskinesia) and reduced mean OFF time when used as first adjunct therapy in levodopa-treated patients and patients with mild motor fluctuations. Mean daily ON time (with no or non-troublesome dyskinesia) and OFF time were favorably changed, compared with placebo, to similar extents regardless of whether patients were receiving concomitant dopamine agonists, catechol-O-methyltransferase inhibitors and amantadine. Additionally, safinamide improved bradykinesia, rigidity, tremor and gait. CONCLUSIONS: Safinamide was a safe and effective first adjunct therapy in levodopa-treated patients and improved 4/5 cardinal symptoms of PD while providing benefits to mild and non-mild fluctuators and patients receiving other concomitant dopaminergic therapies.\",\n \"corpus_id\": 16293044,\n \"score\": 2\n },\n {\n \"doc_id\": \"27536120\",\n \"title\": \"Emerging approaches in Parkinson's disease - adjunctive role of safinamide.\",\n \"abstract\": \"Ongoing neuronal death in Parkinson's disease (PD) causes an altered neurotransmission of various biogenic amines, particularly dopamine. As these changes do not follow a distinct pattern, they vary individually, and are differently pronounced. As a result, a heterogeneous onset of motor and nonmotor features occurs in each patient with PD during the whole course of the disease. PD actually describes a set of distinct diseases that manifest themselves in clinical syndromes with certain similarities but also great differences. This clinical picture responds to drugs with a broad spectrum of modes of actions better than to compounds with an exclusive focus on specific receptor subtypes. Therefore, safinamide is an ideal candidate for treatment of patients with PD, since its pharmacological profile includes reversible monoamine oxidase-B inhibition, blockade of voltage-dependent sodium channels, modulation of calcium channels, and inhibition of glutamate release. Safinamide is applied only once daily. Its oral dose ranges from 50 to 100 mg. Safinamide was well tolerated and safe in the clinical development program that demonstrated the amelioration of motor symptoms and OFF phenomena by safinamide when combined with dopamine agonists or levodopa. In the real world of maintenance of patients with PD, effects of safinamide application resemble therapy with classical monoamine oxidase inhibitors or amantadine in combination with other dopamine-substituting drugs. Safinamide is becoming increasingly available in the EU despite complex approval and pricing scenarios.\",\n \"corpus_id\": 7752034,\n \"score\": 2\n },\n {\n \"doc_id\": \"27665574\",\n \"title\": \"Clinical Pharmacokinetics and Pharmacodynamics of Safinamide.\",\n \"abstract\": \"The symptoms of Parkinson's disease (PD) reflect disruptions of a number of brain neurotransmitter systems of varying type and degree. Pharmacological agents with multiple neurochemical mechanisms of action are therefore promising candidates for countering these problems and providing comprehensive symptomatic relief for patients. The pharmacological profile of safinamide includes reversible monoamine oxidase B inhibition, blockage of voltage-dependent Na(+) channels, modulation of Ca(2+) channels, and inhibition of glutamate release. Safinamide is administered once daily at oral doses of 50-100 mg; it is well-tolerated and safe. Clinical trials have found that it ameliorates motor symptoms when added to established levodopa or single dopamine receptor agonist therapy. The future role of safinamide in PD may be that it enables a reduction in the dosage of dopamine replacement therapies, thereby reducing the adverse effects associated with these treatments. The clinical convenience (once-daily administration), safety, and tolerability of safinamide are better than those of dopamine receptor agonists. The introduction of safinamide reflects a change of approach to drug development for anti-parkinsonian agents in that its broad spectrum of action corresponds to the multiple heterogeneous alterations of brain neurochemistry in PD, rather than being targeted at a single receptor type or neurochemical process. Safinamide is a promising new instrument for the effective symptomatic therapy of PD.\",\n \"corpus_id\": 22265280,\n \"score\": 2\n },\n {\n \"doc_id\": \"27942720\",\n \"title\": \"Assessment of Safety and Efficacy of Safinamide as a Levodopa Adjunct in Patients With Parkinson Disease and Motor Fluctuations: A Randomized Clinical Trial.\",\n \"abstract\": \"Importance: Although levodopa remains the most effective oral pharmacotherapy for Parkinson disease (PD), its use is often limited by wearing off effect and dyskinesias. Management of such complications continues to be a significant challenge. Objective: To investigate the efficacy and safety of safinamide (an oral aminoamide derivative with dopaminergic and nondopaminergic actions) in levodopa-treated patients with motor fluctuations. Design, Setting, and Participants: From March 5, 2009, through February 23, 2012, patients from academic PD care centers were randomized (1:1 ratio) to receive double-blind adjunctive safinamide or placebo for 24 weeks. All patients had idiopathic PD with \\\"off\\\" time (time when medication effect has worn off and parkinsonian features, including bradykinesia and rigidity, return) of greater than 1.5 hours per day (excluding morning akinesia). Their pharmacotherapy included oral levodopa plus benserazide or carbidopa in a regimen that had been stable for 4 weeks or longer. During screening, each patient's regimen was optimized to minimize motor fluctuations. Study eligibility required that after 4 weeks of optimized treatment, the patients still have more than 1.5 hours per day of off time. Adverse events caused the premature study discontinuation of 12 individuals (4.4%) in the safinamide group and 10 individuals (3.6%) in the placebo group. Interventions: Patients took safinamide or placebo as 1 tablet daily with breakfast. If no tolerability issues arose by day 14, the starting dose, 50 mg, was increased to 100 mg. Main Outcomes and Measures: The prespecified primary outcome was each treatment group's mean change from baseline to week 24 (or last \\\"on\\\" treatment value) in daily \\\"on\\\" time (relief of parkinsonian motor features) without troublesome dyskinesia, as assessed from diary data. Results: At 119 centers, 549 patients were randomized (mean [SD] age, 61.9 [9.0] years; 334 male [60.8%] and 371 white [67.6%]): 274 to safinamide and 275 to placebo. Among them, 245 (89.4%) receiving safinamide and 241 (87.6%) receiving placebo completed the study. Mean (SD) change in daily on time without troublesome dyskinesia was +1.42 (2.80) hours for safinamide, from a baseline of 9.30 (2.41) hours, vs +0.57 (2.47) hours for placebo, from a baseline of 9.06 (2.50) hours (least-squares mean difference, 0.96 hour; 95% CI, 0.56-1.37 hours; P < .001, analysis of covariance). The most frequently reported adverse event was dyskinesia (in 40 [14.6%] vs 15 [5.5%] and as a severe event in 5 [1.8%] vs 1 [0.4%]). Conclusions and Relevance: The outcomes of this trial support safinamide as an effective adjunct to levodopa in patients with PD and motor fluctuations to improve on time without troublesome dyskinesia and reduce wearing off. Trial Registration: clinicaltrials.gov Identifier NCT00627640.\",\n \"corpus_id\": 33773319,\n \"score\": 2\n },\n {\n \"doc_id\": \"28537214\",\n \"title\": \"Pharmacokinetic drug evaluation of safinamide mesylate for the treatment of mid-to-late stage Parkinson's disease.\",\n \"abstract\": \"INTRODUCTION: Patients with Parkinson's disease suffer from a heterogeneous expression of neurotransmitter deficits. They cause an individual variable expression of motor and non-motor symptoms. Thus, drugs with various mechanisms of actions are suitable to counteract these disease related neurotransmitter alterations. Areas covered: This invited review suggests safinamide as an ideal compound for therapy of Parkinson's disease, as its pharmacological profile includes reversible monoamine oxidase B inhibition, blockage of voltage-dependent sodium channels, modulation of calcium channels and abnormal glutamate release. Safinamide may provide benefits effects on non-motor symptoms in addition to the demonstrated amelioration of motor impairment in levodopa treated patients with Parkinson's disease. Safinamide was well tolerated and safe when administered in dose of 50 or 100 mg daily in pivotal trials. Expert opinion: Clinical handling, safety and tolerability of Safinamide are better than of dopamine agonists or levodopa. Safinamide supplements the existing armamentarium of drugs for Parkinson's disease. Safinamide will help to reduce dosing of levodopa but also of dopamine agonists during long term treatment in patients with Parkinson's disease.\",\n \"corpus_id\": 41398809,\n \"score\": 2\n },\n {\n \"doc_id\": \"29569037\",\n \"title\": \"Monoamine oxidase-B inhibitors in the treatment of Parkinson's disease: clinical-pharmacological aspects.\",\n \"abstract\": \"This invited narrative review emphasizes the role of MAO-B inhibition in the drug portfolio for dopamine substitution in patients with Parkinson's disease. Neuronal and glial MAO-B inhibition contributes to more stable levels of dopamine and other biogenic amines in the synaptic cleft. Accordingly, symptomatic effects of MAO-B inhibition for a limited amelioration of impaired motor behaviour and wearing-off phenomena in patients with Parkinson's disease are well proven, even when MAO-B inhibitors are only applied together with dopamine agonists. Delay of disease progression by MAO-B inhibition is under debate despite positive experimental findings. This discussion does not consider, that levodopa, respectively, dopamine agonists, are substrates, respectively, inhibitors of the ABCB1 (P-gp, MDR1, and CD243) transporter system. It supports toxin efflux over the blood-brain barrier. ABCB1 transporters have a limited capacity. MAO-B inhibitors do not weaken it. Treatment with MAO-B inhibitors is advantageous as it enables sparing of dopamine agonist and levodopa dosing.\",\n \"corpus_id\": 4275601,\n \"score\": 2\n },\n {\n \"doc_id\": \"18549347\",\n \"title\": \"An expert opinion on safinamide in Parkinson's disease.\",\n \"abstract\": \"BACKGROUND: Dopamine replacement therapies (levodopa, dopamine receptor agonists, anticholinergics, monoamine oxidase B inhibitors, and catechol-O-methyltransferase inhibitors) remain the cornerstones of therapeutic interventions for Parkinson's disease (PD). Despite the treatment options for PD symptoms, a cure remains elusive. An optimal treatment would be one that combined relief in both motor and nonmotor symptoms with neuroprotective properties. Safinamide is an investigational drug for PD currently in development as add-on therapy to both dopamine agonists and levodopa. Safinamide is a unique molecule with a novel mode of action, targeting both dopaminergic and glutaminergic systems, and potentially provides motor symptom control. Preliminary results from experimental models suggest potential neuroprotective effects. Studies on the potential effects on nonmotor symptoms are ongoing. OBJECTIVE: To review the mechanism of action and pharmacokinetics, and to evaluate the available clinical safety and efficacy results of safinamide. METHODS: A search of the electronic database MEDLINE (PubMed, no time limits) was performed on 14 December 2007. The full text of all citations was obtained for review. Furthermore, two abstracts on safinamide published as proceedings of a European conference were reviewed. RESULTS/CONCLUSION: Safinamide is a promising investigational drug for PD with a novel mode of action. Early reports confirm the potential efficacy of safinamide in PD. Further studies on potential effects on cognition and neuroprotection are needed.\",\n \"corpus_id\": 25856669,\n \"score\": 1\n },\n {\n \"doc_id\": \"20816270\",\n \"title\": \"Management of motor complications in Parkinson disease: current and emerging therapies.\",\n \"abstract\": \"Motor fluctuations and dyskinesias are common motor complications that manifest within the first few years from the initiation of therapy in patients with Parkinson disease. These complications negatively affect the quality of life and represent an important source of disability. A growing number of therapeutic options including treatments aimed at prolonging the efficacy of levodopa (eg, selective monoamine oxidase-B inhibitors and catechol-O-methyltransferase inhibitors), administration of longer-acting dopamine agonists (eg, rotigotine, sustained-release ropinirole), and continuous administration of intraduodenal levodopa exist or will soon become available. Patients who maintain a good response to levodopa but continue to experience disabling motor complications despite the best medical management may benefit from a regimen of subcutaneous apomorphine, ideally delivered by a subcutaneous pump, or deep-brain stimulation of the subthalamic nucleus or internal portion of the pallidum. Emerging therapies for motor complications are expected to further enhance continuous (physiologic) delivery of dopaminergic drugs and extend the reach of therapies beyond the dopaminergic system to influence not only the motor but also the vast range of nonmotor complications of this multisystemic disease.\",\n \"corpus_id\": 24970145,\n \"score\": 1\n },\n {\n \"doc_id\": \"22133327\",\n \"title\": \"Monoamine oxidase B inhibitors for the treatment of Parkinson's disease: a review of symptomatic and potential disease-modifying effects.\",\n \"abstract\": \"Parkinson's disease is a disorder characterized pathologically by progressive neurodegeneration of the dopaminergic cells of the nigrostriatal pathway. Although the resulting dopamine deficiency is the cause of the typical motor features of Parkinson's disease (bradykinesia, rigidity, tremor), additional non-motor symptoms appear at various timepoints and are the result of non-dopamine nerve degeneration. Monoamine oxidase B (MAO-B) inhibitors are used in the symptomatic treatment of Parkinson's disease as they increase synaptic dopamine by blocking its degradation. Two MAO-B inhibitors, selegiline and rasagiline, are currently licensed in Europe and North America for the symptomatic improvement of early Parkinson's disease and to reduce off-time in patients with more advanced Parkinson's disease and motor fluctuations related to levodopa. A third MAO-B inhibitor (safinamide), which also combines additional non-dopaminergic properties of potential benefit to Parkinson's disease, is currently under development in phase III clinical trials as adjuvant therapy to either a dopamine agonist or levodopa. MAO-B inhibitors have also been studied extensively for possible neuroprotective or disease-modifying actions. There is considerable laboratory evidence that MAO-B inhibitors do exert some neuroprotective properties, at least in the Parkinson's disease models currently available. However, these models have significant limitations and caution is required in assuming that such results may easily be extrapolated to clinical trials. Rasagiline 1 mg/day has been shown to provide improved motor control in terms of Unified Parkinson's Disease Rating Scale (UPDRS) score at 18 months in those patients with early disease who began the drug 9 months before a second group. There are a number of possible explanations for this effect that may include a disease-modifying action; however, the US FDA recently declined an application for the licence of rasagiline to be extended to cover disease modification.\",\n \"corpus_id\": 39302397,\n \"score\": 1\n },\n {\n \"doc_id\": \"22967035\",\n \"title\": \"Long-term efficacy and safety of safinamide as add-on therapy in early Parkinson's disease.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: Safinamide is an α-aminoamide with both dopaminergic and non-dopaminergic mechanisms of action in Phase III clinical development as a once-daily add-on to dopamine agonist (DA) therapy for early Parkinson's disease (PD). METHODS: Study 017 was a 12-month, randomized, double-blind, placebo-controlled pre-planned extension study to the previously reported Study 015. Patients received safinamide 100 or 200 mg/day or placebo added to a single DA in early PD. The primary efficacy endpoint was the time from baseline (Study 015 randomization) to 'intervention', defined as increase in DA dose; addition of another DA, levodopa or other PD treatment; or discontinuation due to lack of efficacy. Safinamide groups were pooled for the primary efficacy endpoint analysis; post hoc analyses were performed on each separate dose group. RESULTS: Of the 269 patients randomized in Study 015, 227 (84%) enrolled in Study 017 and 187/227 (82%) patients completed the extension study. Median time to intervention was 559 and 466 days in the pooled safinamide and placebo groups, respectively (log-rank test; P = 0.3342). In post hoc analyses, patients receiving safinamide 100 mg/day experienced a significantly lower rate of intervention compared with placebo (25% vs. 51%, respectively) and a delay in median time to intervention of 9 days (P < 0.05; 240- to 540-day analysis). CONCLUSIONS: The pooled data from the safinamide groups failed to reach statistical significance for the primary endpoint of median time from baseline to additional drug intervention. Post hoc analyses indicate that safinamide 100 mg/day may be effective as add-on treatment to DA in PD.\",\n \"corpus_id\": 1793815,\n \"score\": 1\n },\n {\n \"doc_id\": \"23917951\",\n \"title\": \"Non-dopaminergic treatments for motor control in Parkinson's disease.\",\n \"abstract\": \"The pathological processes underlying Parkinson's disease (PD) involve more than dopamine cell loss within the midbrain. These non-dopaminergic neurotransmitters include noradrenergic, serotonergic, glutamatergic, and cholinergic systems within cortical, brainstem and basal ganglia regions. Several non-dopaminergic treatments are now in clinical use to treat motor symptoms of PD, or are being evaluated as potential therapies. Agents for symptomatic monotherapy and as adjunct to dopaminergic therapies for motor symptoms include adenosine A2A antagonists and the mixed monoamine-B inhibitor (MAO-BI) and glutamate release agent safinamide. The largest area of potential use for non-dopaminergic drugs is as add-on therapy for motor fluctuations. Thus adenosine A2A antagonists, safinamide, and the antiepileptic agent zonisamide can extend the duration of action of levodopa. To reduce levodopa-induced dyskinesia, drugs that target overactive glutamatergic neurotransmission can be used, and include the non-selective N-methyl D-aspartate antagonist amantadine. More recently, selective metabotropic glutamate receptor (mGluR₅) antagonists are being evaluated in phase II randomized controlled trials. Serotonergic agents acting as 5-HT2A/2C antagonists, such as the atypical antipsychotic clozapine, may also reduce dyskinesia. 5-HT1A agonists theoretically can reduce dyskinesia, but in practice, may also worsen PD motor symptoms, and so clinical applicability has not yet been shown. Noradrenergic α2A antagonism using fipamezole can potentially reduce dyskinesia. Several non-dopaminergic agents have also been investigated to reduce non-levodopa-responsive motor symptoms such as gait and tremor. Thus the cholinesterase inhibitor donepezil showed mild benefit in gait, while the predominantly noradrenergic re-uptake inhibitor methylphenidate had conflicting results in advanced PD subjects. Tremor in PD may respond to muscarinic M4 cholinergic antagonists (anticholinergics), but tolerability is often poor. Alternatives include β-adrenergic antagonists such as propranolol. Other options include 5-HT2A antagonists, and drugs that have mixed binding properties involving serotonin and acetylcholine, such as clozapine and the antidepressant mirtazapine, can be effective in reducing PD tremor. Many other non-dopaminergic agents are in preclinical and phase I/II early stages of study, and the reader is directed to recent reviews. While levodopa remains the most effective agent to treat motor symptoms in PD, the overall approach to using non-dopaminergic drugs in PD is to reduce reliance on levodopa and to target non-levodopa-responsive symptoms.\",\n \"corpus_id\": 9849241,\n \"score\": 1\n },\n {\n \"doc_id\": \"24323838\",\n \"title\": \"Continuous drug delivery in Parkinson's disease.\",\n \"abstract\": \"Development of motor and non-motor complications during the course of Parkinson's disease (PD) is a major challenge for therapeutic management. At advanced disease stages, patients frequently fluctuate between PD symptoms-such as bradykinesia-and dyskinesias, in response to fluctuations in drug concentrations. Continuous subcutaneous infusion of the dopamine agonist apomorphine or intestinal infusion of levodopa reduce such fluctuations in both pharmacokinetics and motor function. This is the basis for the concept of continuous drug delivery in PD, and the more theoretical concept of continuous dopaminergic stimulation. These expressions are sometimes used to describe a treatment that is more continuous in its pharmacokinetic profile or that produces more sustained effects, compared with immediate-release levodopa, i.e. not only pump treatments. For example, sustained-release formulations of levodopa or dopamine agonists, transdermal delivery of rotigotine, and addition of catechol-O-methyltransferase inhibitors or monoamine oxidase-B inhibitors have been developed with the aim to provide more continuous drug concentrations, sustained benefits and minimized side effects. Progress has been made, but there are still knowledge gaps regarding how these treatment alternatives can be optimally used. New treatments are currently being developed to provide the continuous drug delivery that is known to successfully alleviate motor and non-motor complications. Hopefully, although not yet proven, these new methods may also prevent or postpone some of the late-stage complications.\",\n \"corpus_id\": 5790880,\n \"score\": 1\n },\n {\n \"doc_id\": \"25044402\",\n \"title\": \"Two-year, randomized, controlled study of safinamide as add-on to levodopa in mid to late Parkinson's disease.\",\n \"abstract\": \"In a 6-month double-blind, placebo-controlled study of Parkinson's disease patients with motor fluctuations, safinamide 50 and 100 mg/d significantly increased ON-time without increasing dyskinesia. Further long-term safinamide use in these patients was evaluated over an additional 18 months. Patients continued on their randomized placebo, 50, or 100 mg/d safinamide. The primary endpoint was change in Dyskinesia Rating Scale total score during ON-time over 24 months. Other efficacy endpoints included change in ON-time without troublesome dyskinesia, changes in individual diary categories, depressive symptoms, and quality of life measures. Change in Dyskinesia Rating Scale was not significantly different in safinamide versus placebo groups, despite decreased mean total Dyskinesia Rating Scale with safinamide compared with an almost unchanged score in placebo. Ad hoc subgroup analysis of moderate to severe dyskinetic patients at baseline (36% of patients) showed a decrease with safinamide 100 mg/d compared with placebo (P = 0.0317). Improvements in motor function, activities of daily living, depressive symptoms, clinical status, and quality of life at 6 months remained significant at 24 months. Adverse events and discontinuation rates were similar with safinamide and placebo. This 2-year, controlled study of add-on safinamide in mid-to-late Parkinson's disease with motor fluctuations, although not demonstrating an overall difference in dyskinesias between patients and controls, showed improvement in dyskinesia in patients at least moderately dyskinetic at baseline. The study additionally demonstrated significant clinical benefits in ON-time (without troublesome dyskinesia), OFF-time, activities of daily living, motor symptoms, quality of life, and symptoms of depression.\",\n \"corpus_id\": 11110615,\n \"score\": 1\n },\n {\n \"doc_id\": \"25300164\",\n \"title\": \"Safinamide for the treatment of Parkinson's disease.\",\n \"abstract\": \"Parkinson's disease (PD) is a neurodegenerative disease caused by a complex interaction of loss of dopaminergic and non-dopaminergic neurotransmitter systems. Drugs acting on the dopaminergic pathways are the mainstay of treatment for motor symptoms today. Safinamide (NW-1015) is a novel drug with multiple actions. It is a monoamine oxidase B inhibitor and improves dopaminergic transmission. In addition, it has antiglutamatergic effects and can thus reduce dyskinesias, which is a side effect limiting most dopaminergic therapy. In Phase III trials, safinamide has been found to be a useful adjunctive to dopamine agonists in early PD and has been shown to increase time without increasing troublesome dyskinesias when used as an adjunct to levodopa in patients with advanced PD. A possible neuroprotective role in inhibiting PD disease progression is envisaged and warrants future studies.\",\n \"corpus_id\": 207207979,\n \"score\": 1\n },\n {\n \"doc_id\": \"25649051\",\n \"title\": \"Effect of opicapone on levodopa pharmacokinetics, catechol-O-methyltransferase activity and motor fluctuations in patients with Parkinson's disease.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: Opicapone (OPC) is a novel third generation catechol-O-methyltransferase (COMT) inhibitor that enhances levodopa availability. This study investigated the effects of OPC in comparison with placebo on levodopa pharmacokinetics, tolerability and safety, COMT activity and motor response to levodopa in Parkinson's disease (PD) patients with motor fluctuations. METHODS: This was a randomized, multicentre, double-blind and placebo-controlled study in four parallel groups of PD patients treated with standard-release 100/25 mg levodopa/carbidopa or levodopa/benserazide and with motor fluctuations (wearing-OFF phenomenon). Subjects were sequentially assigned to be administered, once-daily, up to 28 days (maintenance phase), placebo (n = 10) or 5 (n = 10), 15 (n = 10) and 30 mg (n = 10) OPC. Two levodopa tests were performed, one at baseline and another following the maintenance phase. Subjects kept a diary to record motor fluctuations (ON/OFF periods) throughout the study. RESULTS: In relation to placebo, levodopa exposure (AUC0-6) increased 24.7%, 53.9% and 65.6% following 5, 15 and 30 mg OPC, respectively. Maximum COMT inhibition (Emax) ranged from 52% (5 mg OPC) to 80% (30 mg OPC). The study was not designed to detect any significant differences in motor performance, but the exploratory analysis performed shows improvement in various motor outcomes, including a dose-dependent change in absolute OFF time corresponding to a percentage decrease of 4.16% (P > 0.05), 29.55% (P > 0.05) and 32.71% (P < 0.05) with 5, 15 and 30 mg OPC, respectively. Treatments were generally well tolerated and safe. CONCLUSIONS: OPC is a promising new COMT inhibitor that significantly decreased COMT activity, increased systemic exposure to levodopa and improved motor response.\",\n \"corpus_id\": 205111356,\n \"score\": 1\n },\n {\n \"doc_id\": \"26406127\",\n \"title\": \"Long-Term Effects of Safinamide on Dyskinesia in Mid- to Late-Stage Parkinson's Disease: A Post-Hoc Analysis.\",\n \"abstract\": \"BACKGROUND: Safinamide is a novel α-aminoamide with dopaminergic and non-dopaminergic properties developed as adjunctive therapy for patients with PD. Results from a 24-month double-blind controlled study suggested that as add-on to levodopa (and other PD medications) the benefits of safinamide on dyskinesia may be related to severity of dyskinesia at baseline. OBJECTIVE: This post-hoc analysis further characterized the effects of safinamide on dyskinesia in mid- to late-stage PD patients. METHODS: Patients were stratified by the presence or absence of dyskinesia at baseline, and by whether or not the dose of levodopa had been changed during the 24-month treatment period. Differences between safinamide and placebo were evaluated using the Wilcoxon rank-sum test. RESULTS: For the overall treated population (with or without baseline dyskinesia), safinamide 100 mg/day significantly improved the dyskinesia rating scale score, compared with placebo, in the subgroup of patients with no change in levodopa dose (p = 0.0488). For patients with baseline dyskinesia, improvements over placebo were also significant (p = 0.0153) in patients with or without changes in levodopa dose, and nearly significant (p = 0.0546) in patients with no change in levodopa dose, suggesting that these improvements were not due to levodopa dose reductions. CONCLUSIONS: While no statistically significant difference in mean DRS scores was seen between safinamide and placebo in the original study population, the present post-hoc analysis helps to provide a meaningful interpretation of the long-term effects of safinamide on dyskinesia. These results may be related to safinamide state- and use-dependent inhibition of sodium channels and stimulated glutamate release, and are unlikely due to reduced dopaminergic stimulation.\",\n \"corpus_id\": 14914773,\n \"score\": 1\n },\n {\n \"doc_id\": \"26587996\",\n \"title\": \"Clinical pharmacology review of safinamide for the treatment of Parkinson's disease.\",\n \"abstract\": \"Safinamide (Xadago™) is an oral α-aminoamide derivative marketed for the treatment of Parkinson's disease (PD). The drug has both dopaminergic properties, namely highly selective and reversible inhibition of monoamine oxidase B, and nondopamimetic properties, namely selective sodium channel blockade and calcium channel modulation, with consequent inhibition of excessive glutamate release. In 2014, safinamide was approved in the European Economic Area, as \\\"an add-on therapy to stable dose levodopa, alone or in combination with other PD therapies in mid- to late-stage-fluctuating PD patients.\\\" In addition, evidence has been provided for safinamide in the treatment of motor symptoms in early PD patients. This article summarizes the pharmacological properties, development program, clinical indications for PD treatment, stratified according to several disease's stages and the safety profile of safinamide. A meta-analysis of the most frequent adverse events among Phase III trials has been also performed.\",\n \"corpus_id\": 36717221,\n \"score\": 1\n },\n {\n \"doc_id\": \"26917951\",\n \"title\": \"Adjuvant therapies for Parkinson's disease: critical evaluation of safinamide.\",\n \"abstract\": \"Safinamide (SAF) is a new drug developed for the treatment of Parkinson's disease (PD). It is a benzylamino derivative with multiple mechanisms of action and antiparkinsonian, anticonvulsant, and neuroprotective properties. SAF inhibits monoamine oxidase B and dopamine reuptake and glutamate release, blocks voltage-dependent sodium channels, and modulates calcium channels. Although the antiparkinsonian effect can be ascribed in part to the inhibition of the monoamine oxidase B, which is complete at 50 mg, the enhanced benefit seen at the 100 mg dose is probably due to nondopaminergic mechanisms. SAF will represent an important option for patients with both early and advanced PD. In early PD patients, the addition of SAF to dopamine agonists may be an effective treatment strategy to improve motor function, prolong the use of dopamine agonists, and/or delay the introduction of levodopa. In advanced parkinsonian patients, SAF has been demonstrated to significantly increase on time with no, or nontroublesome dyskinesias. All studies performed have demonstrated its efficacy in benefiting both short-term and long-term quality-of-life outcomes in both early and advanced PD patients. SAF has been investigated in long-term (24 months), double-blind, placebo-controlled studies, where it showed a very good safety profile. SAF has not been studied in de novo PD patients, and its potential positive effect on dyskinesia deserves further dedicated studies.\",\n \"corpus_id\": 5582957,\n \"score\": 1\n },\n {\n \"doc_id\": \"27186120\",\n \"title\": \"Investigational agents in the treatment of Parkinson's disease: focus on safinamide.\",\n \"abstract\": \"The authors review management issues in Parkinson's disease (PD) and provide an overview of the current pharmacological management strategies, with a specific focus on safinamide. Current therapeutic management of PD largely involves strategies to optimize the replacement of deficient dopamine, using levodopa, dopamine agonists, and inhibitors of dopamine-metabolizing enzymes. Currently under investigation for use in the treatment of PD, safinamide has multiple modes of action including monoamine oxidase B inhibition. It is well absorbed orally, has a long plasma half-life, and does not have liver enzyme-inducing or liver enzyme-inhibiting activity. Peak plasma concentration occurs 2-4 hours after single oral doses. Safinamide as monotherapy and as an adjunct to dopamine agonists improves Unified Parkinson's Disease Rating Scale motor scores. One randomized, placebo-controlled trial involving 168 patients given a median safinamide dose of 70 mg/day (range 40-90 mg/day) significantly increased the proportion of responders - defined as patients improving their Unified Parkinson's Disease Rating Scale motor scores by 30% or more from baseline - after 3 months (37.5% for safinamide versus 21.4% for placebo; P < 0.05). Safinamide increased \\\"on\\\" time with no or minor dyskinesia compared with the placebo in another trial, but dyskinesia severity was not reduced. Safinamide was well tolerated, with an adverse effect profile similar to that of the placebo. Further Phase III trial data for safinamide efficacy is awaited, and will be of interest in a comparison with other developments in PD therapeutics: modified formulations of available compounds, new drug classes such as adenosine receptor antagonists, and gene-based therapies.\",\n \"corpus_id\": 1281866,\n \"score\": 1\n },\n {\n \"doc_id\": \"28110399\",\n \"title\": \"Safinamide: A Review in Parkinson's Disease.\",\n \"abstract\": \"Safinamide (Xadago(®)) is an orally active, selective, reversible monoamine oxidase-B inhibitor with both dopaminergic and non-dopaminergic (glutamatergic) properties. In the EU, safinamide is approved for the treatment of mid- to late-stage fluctuating Parkinson's disease (PD) as add-on therapy to a stable dose of levodopa alone or in combination with other PD medications. Safinamide 50-100 mg/day administered as a fixed or flexible dose significantly increased daily 'on' time without dyskinesia (primary endpoint) in patients with mid- to late-stage PD with motor fluctuations in 24-week, placebo-controlled clinical trials. Other outcomes, including motor function, overall clinical status and health-related quality of life, were also generally improved with safinamide. Furthermore, in an 18-month extension of one study, although dyskinesia (primary endpoint) was not significantly improved with safinamide relative to placebo, treatment benefits in other outcomes were generally sustained over 24 months of treatment. Safinamide was generally well tolerated in clinical trials; dyskinesia was the most common adverse event. Although further studies are needed, including comparative and long-term studies, current evidence indicates that safinamide extends the treatment options available for use as add-on therapy to levodopa and other PD medications in patients with mid- to late-stage PD experiencing motor fluctuations.\",\n \"corpus_id\": 23485955,\n \"score\": 1\n },\n {\n \"doc_id\": \"28504022\",\n \"title\": \"Safinamide for the treatment of Parkinson's disease.\",\n \"abstract\": \"INTRODUCTION: The major unmet needs in the medical treatment of Parkinson disease (PD) are reduction of motor side effects from dopaminergic drugs, management of non-motor symptoms and disease modification. Areas covered: Motor fluctuations and OFF periods are a significant determinant of quality of life in PD and reducing their duration and severity can significantly improve motor function. This aim may be partly facilitated by the development of effective adjunctive drugs for dopamine replacement. Safinamide (Xadago), which is a first generation anticonvulsant, has pharmacological properties which are of interest in the context of neurodegenerative diseases, leading to research into its potential as an adjunct to levodopa in PD. Expert opinion: Although its mechanism has not been fully defined, safinamide provides enhanced symptom control of motor function in advanced PD and improves quality of life.\",\n \"corpus_id\": 418489,\n \"score\": 1\n },\n {\n \"doc_id\": \"28580819\",\n \"title\": \"Opicapone for the management of end-of-dose motor fluctuations in patients with Parkinson's disease treated with L-DOPA.\",\n \"abstract\": \"INTRODUCTION: Opicapone is a third generation, highly potent and effective catechol O‑methyltransferase (COMT) inhibitor that optimizes the pharmacokinetics and bioavailability of L-DOPA therapy. Areas covered: In this review, the authors describe the preclinical and clinical development of opicapone. In PD patients with motor fluctuations, once daily opicapone administration was well-tolerated and consistently reduced OFF-time and increased ON-time without increasing the frequency of troublesome dyskinesia, and these benefits were maintained over at least a year of continued open-label therapy. Expert commentary: With its convenient once-daily regimen, adjunct opicapone should be considered as an effective option for use in L-DOPA treated PD patients experiencing motor fluctuations.\",\n \"corpus_id\": 37748591,\n \"score\": 1\n },\n {\n \"doc_id\": \"28777756\",\n \"title\": \"Long-Term Effects of Safinamide on Mood Fluctuations in Parkinson's Disease.\",\n \"abstract\": \"BACKGROUND: Mood disorders are very frequent in Parkinson's Disease (PD), and their effective treatment is still a major unresolved issue: growing evidence suggests that glutamatergic system dysfunction is directly involved. Safinamide is a drug with an innovative mechanism of action, dopaminergic and non-dopaminergic, that includes the reversible inhibition of the monoamine oxidase-B (MAO-B) enzyme and the modulation of excessive glutamate release through the use- and state-dependent blockade of the sodium channels. OBJECTIVE: To investigate the effects of safinamide on mood over two-year treatment in PD patients with motor fluctuations. METHODS: This was a post-hoc analysis of the data from studies 016 and 018. The analysis focused on outcomes related to mood, namely: scores of the \\\"Emotional well-being\\\" domain of the Parkinson's Disease Questionnaire (PDQ-39), scores of the GRID Hamilton Rating Scale for Depression (GRID-HAMD) and the proportion of patients reporting depression as an adverse event over the entire treatment period. RESULTS: Safinamide, compared to placebo, significantly improved the PDQ-39 \\\"Emotional well-being\\\" domain after6-months (p = 0.0067) and 2 years (p = 0.0006), as well as the GRID-HAMD (p = 0.0408 after 6 months and p = 0.0027 after 2 years). Significantly fewer patients in the safinamide group, compared to placebo, experienced depression as adverse event (p = 0.0444 after 6 months and p = 0.0057 after 2 years). CONCLUSION: The favorable effect of safinamide on mood may be explained by the improvement in wearing off and by its modulation of glutamatergic hyperactivity and reversible MAO-B inhibition. Prospective studies are warranted to investigate this potential benefit.\",\n \"corpus_id\": 3687749,\n \"score\": 1\n },\n {\n \"doc_id\": \"29441484\",\n \"title\": \"Real life evaluation of safinamide effectiveness in Parkinson's disease.\",\n \"abstract\": \"In this retrospective study, we evaluated both efficacy and effectiveness of safinamide 50 and 100 mg in the treatment of motor fluctuations and disabling dyskinesias in a cohort of patients with idiopathic Parkinson's disease (PD). Ninety-one PD patients were evaluated during the first year of commercialization of the drug, both prior to starting safinamide and at the last available follow-up. Evaluations were based on the Unified Parkinson's Disease Scale part III (UPDRS III), Hoehn & Yahr (HY), Unified Dyskinesia Rating Scale (UDysRS) walking and balance item 9 score, daily time spent in OFF and in ON with disabling dyskinesias (1 week diary), mean daily dose of levodopa (LD), dopamine-agonists (DA), catechol-O-methyl transferase inhibitor (COMT-I), monoamine oxidase B inhibitor (MAOB-I), and their LD equivalent dose (LEDD). Eight patients withdrew safinamide within the first month for minor side effects. At the follow-up evaluation, after a mean time with safinamide of 7.5 months ± 3.4, all patients showed a significant improvement of all the scale scores, except for HY, and of the daily dosages of the drugs and the LEDD. The same results were shown by PD patients treated with safinamide 50 mg and patients who started safinamide without switching from a previous MAOBI. PD patients with safinamide 100 mg and patients who started safinamide switching from a previous MAOBI significantly improved in time spent in OFF and LEDD. In conclusion, safinamide is safe and effective in improving motor complications in patients with idiopathic PD and can be considered a useful levodopa sparing strategy.\",\n \"corpus_id\": 4703400,\n \"score\": 1\n },\n {\n \"doc_id\": \"29760163\",\n \"title\": \"▼ Safinamide for Parkinson's disease.\",\n \"abstract\": \"▼ Safinamide (Xadago - Zambon S.p. A) is a monoamine-oxidase B (MAO-B) inhibitor licensed as add-on therapy for people with idiopathic Parkinson's disease who are experiencing motor fluctuations with levodopa.1 Currently there is no cure for Parkinson's disease and drugs are used to reduce motor symptoms and improve daily activities.2,3 Here, we review the evidence for this MAO-B inhibitor.\",\n \"corpus_id\": 46890111,\n \"score\": 1\n },\n {\n \"doc_id\": \"18042245\",\n \"title\": \"Constant dopaminergic stimulation by transdermal delivery of dopaminergic drugs: a new treatment paradigm in Parkinson's disease.\",\n \"abstract\": \"Current dopaminergic therapies for the treatment of Parkinson's disease are associated with the development of long-term motor complications. Abnormal pulsatile stimulation of dopamine receptors is thought to underlie the development of motor complications. There is thus a need for therapies that mimic the normal physiological state more closely by resulting in constant dopaminergic stimulation (CDS). Several studies support the hypothesis that CDS can reverse levodopa-induced motor complications. Other potential benefits of CDS include alleviating nocturnal disturbances, minimizing daytime sleepiness, avoiding priming for motor fluctuations and dyskinesia, preventing the development of gastrointestinal dysfunction and reducing the risk of developing psychosis or behavioural disturbances. Continuous infusion of dopaminergic therapies is impractical for the routine treatment of large numbers of patients. Although catechol-O-methyltransferase inhibitors or sustained-release preparations of levodopa may be beneficial, they do not entirely eliminate pulsatile stimulation of dopamine receptors. A new dopamine agonist (rotigotine), delivered over 24 h by a once-daily transdermal patch, has been investigated in several clinical trials. Continuous delivery of rotigotine has been shown to provide 'true' CDS in animal models. The potential of true CDS therapy to prevent or reduce long-term motor and non-motor complications requires investigation in appropriately designed clinical trials.\",\n \"corpus_id\": 25280693,\n \"score\": 0\n },\n {\n \"doc_id\": \"19589043\",\n \"title\": \"Levodopa/carbidopa/entacapone in Parkinson's disease.\",\n \"abstract\": \"Levodopa is the most efficacious agent for the treatment of motor features of Parkinson's disease but its chronic use is associated with the development of motor complications. Mounting evidence indicates the short half-life of levodopa and resultant pulsatile stimulation of striatal dopamine receptors leads to wearing off, motor fluctuations and dyskinesias. Longer acting dopaminergic agents, such as dopamine agonists, are less likely to cause motor fluctuations and dyskinesias but are not as efficacious for control of motor symptoms. Therefore, there is interest in exploring ways to deliver levodopa in a more continuous fashion, in an effort to maintain benefit through the day and reduce the development of motor fluctuations and dyskinesias. A dopa decarboxylase inhibitor (DDCI), such as carbidopa or benserazide, is administered with levodopa to attenuate its peripheral conversion to dopamine, reduce nausea and increase central bioavailability. When levodopa is administered with a DDCI, its main route of peripheral metabolism is via catechol-O-methyl transferase (COMT). A COMT inhibitor can be added to the combination of levodopa and a DDCI to further extend the levodopa peripheral half-life and increase central bioavailability. Stalevo is a combination tablet comprised of levodopa, carbidopa, and the COMT inhibitor entacapone. It is available in fixed-dose combinations of levodopa/carbidopa/entacapone, 50/12.5/200, 75/18.75/200, 100/25/200, 125/31.25/200, 150/37.5/200 and 200/50/200 mg. Stalevo is currently approved for use in Parkinson's disease patients with end-of-dose wearing off.\",\n \"corpus_id\": 31790179,\n \"score\": 0\n },\n {\n \"doc_id\": \"19821381\",\n \"title\": \"Monoamine oxidase B inhibitors versus other dopaminergic agents in early Parkinson's disease.\",\n \"abstract\": \"BACKGROUND: It has been postulated that monoamine oxidase B (MAO-B) inhibitors alter disease progression in Parkinson's disease (PD) but trials have produced conflicting results. OBJECTIVES: To assess the effectiveness and safety of long-term use of MAO-B inhibitors compared with other dopaminergic agents in early PD. SEARCH STRATEGY: We searched several electronic databases including: the Cochrane Central Register of Controlled Trials (The Cochrane Library Issue 1, 2009), MEDLINE (January 1950 to February 2009) and EMBASE (January 1980 to February 2009). We also handsearched neurology and movement disorders conference proceedings, checked reference lists of relevant studies and contacted other researchers. SELECTION CRITERIA: We included all randomised controlled trials that compared a MAO-B inhibitor with other dopaminergic agents (presently levodopa or dopamine agonists) in patients with early PD, where treatment and follow up lasted at least one year. DATA COLLECTION AND ANALYSIS: Two reviewers independently selected trials for inclusion, assessed the methodological quality, and extracted the data. Additional data were provided by the original authors. Random-effects models were used to analyse results, where appropriate. MAIN RESULTS: Only two eligible trials were included (593 patients), both of reasonable quality although one was unblinded. Both trials compared selegiline with a dopamine agonist, whilst one also compared selegiline with levodopa. MAO-B inhibitors were not associated with a significant increase or decrease in deaths compared with levodopa (odds ratio (OR) 0.96; 95% confidence interval (CI) 0.52 to 1.76) or dopamine agonists (OR 1.30; 95% CI 0.69 to 2.45). Those receiving MAO-B inhibitors were more likely to require add-on therapy during follow-up than those receiving levodopa (OR 12.02; 95% CI 6.78 to 21.31) or dopamine agonist (OR 2.00; 95% CI 1.05 to 3.81). There was a reduction in motor fluctuations with MAO-B inhibitors compared with levodopa (OR 0.55; 95% CI 0.32 to 0.94) but not dopamine agonists (OR 1.15; 95% CI 0.65 to 2.05). Withdrawals due to adverse events were less common with MAO-B inhibitors than with dopamine agonists (OR 0.11; 95% CI 0.01 to 0.99). AUTHORS' CONCLUSIONS: MAO-B inhibitors are one option for the early treatment of PD although they have weaker symptomatic effects than levodopa and dopamine agonists. They may reduce the rate of motor fluctuations compared with initial levodopa therapy and may have fewer significant adverse effects than the older agonists but data are too few to provide reliable conclusions.\",\n \"corpus_id\": 205184450,\n \"score\": 0\n },\n {\n \"doc_id\": \"19951137\",\n \"title\": \"Current strategies in the treatment of Parkinson's disease and a personalized approach to management.\",\n \"abstract\": \"Parkinson's disease is a progressive, neurodegenerative disorder affecting millions of people worldwide. Given the aging population, the prevalence of the disease is expected to increase substantially. The mainstay of treatment has been dopamine replacement therapy with carbidopa, levodopa, dopamine agonists, monoamine oxidase type B inhibitors, catechol-O-methyltransferase inhibitors and amantadine. Nonmotor features, such as cognitive impairment, mood disorders, autonomic dysfunction, gastrointestinal and genitourinary dysfunction, have a substantial impact on Parkinson's disease patients and their quality of life. This review will provide an overview on medications currently available for management of both motor and nonmotor symptoms of Parkinson's disease. Focus will be placed on recent and evolving studies evaluating symptomatic and neuroprotective effects of medications, and how such studies may impact the future management of Parkinson's disease.\",\n \"corpus_id\": 11126160,\n \"score\": 0\n },\n {\n \"doc_id\": \"20707760\",\n \"title\": \"Safinamide in the treatment of Parkinson's disease.\",\n \"abstract\": \"IMPORTANCE OF THE FIELD: Current therapy for Parkinson's disease (PD) is primarily directed at reversing the motor symptoms that are the consequence of dopamine deficiency and includes levodopa, dopamine agonists and monoamine oxidase (MAO) B inhibitors. New drugs offering both dopaminergic and non-dopaminergic actions could offer a significant advantage. AREAS COVERED IN THIS REVIEW: This review surveys the current treatment strategies for PD. Defining unmet needs and how a new compound - safinamide, which has both dopaminergic and non-dopaminergic actions - might address these. WHAT THE READER WILL GAIN: The reader will gain an understanding of safinamide and its mechanisms of action, including reversible MAOB inhibition and reduced dopamine reuptake with antiglutamatergic effects, and how it may potentially provide improvement of PD motor symptoms with an antidyskinetic effect through its effect on glutamate release. The clinical trial profile of safinamide is reviewed. Early results are promising in terms of improved motor function and reduced 'OFF' time. Additional Phase III trials are now in progress for this adjunctive indication. Finally, the reader will understand the potential role for safinamide in the selection and sequencing of drugs for PD. TAKE HOME MESSAGE: safinamide combines both dopaminergic and non-dopaminergic actions that may add a new dimension to PD treatment options as an adjunct to current drugs. Its efficacy is under active evaluation in Phase III clinical trials.\",\n \"corpus_id\": 45746856,\n \"score\": 0\n },\n {\n \"doc_id\": \"21255197\",\n \"title\": \"Drugs and drug delivery in PD: optimizing control of symptoms with pramipexole prolonged-release.\",\n \"abstract\": \"Intermittent or pulsatile dopamine-receptor stimulation is postulated to induce plastic changes in motor systems that are responsible for the development of motor fluctuations and dyskinesia, complicating long-term levodopa therapy of Parkinson's disease (PD). Continuous dopamine stimulation (CDS) is a concept that refers to the hypothesis that more continuous dopamine-receptor stimulation will reduce the risk of motor complications, particularly dyskinesias, and may also treat established dyskinesias. In line with this hypothesis, the intermittent administration of dopaminergic agents with short half-lives induce motor complications in animal models, whilst the continuous administration of the same compounds via mini-pumps substantially reduces such symptoms. Continuous drug delivery (CDD) strategies are therefore explored in clinical trials to prevent or manage motor complications. The early use of a dopamine agonist reduces the risk of motor fluctuations compared with levodopa. Conversely, the early combination of the catechol-O-methyltransferase inhibitor entacapone with levodopa has failed to demonstrate a comparable advantage. Outcomes of uncontrolled long-term studies of PD patients with motor complications treated for several months with subcutaneous continuous infusion of apomorphine or intraduodenal levodopa are compatible with CDS. New once-daily prolonged-release formulations of dopamine agonists have demonstrated antiparkinsonian efficacy in randomized trials conducted in early as well as advanced patients with PD. Once-daily administration is convenient and may improve compliance. Other theoretical advantages in terms of efficacy or tolerability deserve further exploration.\",\n \"corpus_id\": 205582694,\n \"score\": 0\n },\n {\n \"doc_id\": \"22691758\",\n \"title\": \"Therapies in Parkinson's disease.\",\n \"abstract\": \"PURPOSE OF REVIEW: This review examines currently available therapeutic strategies for Parkinson's disease, emphasizing evidence-based data as well as a patient-centered approach to the treatment of motor and nonmotor symptoms. RECENT FINDINGS: Although clinical trials of disease-modifying approaches have been thus far disappointing, steady advances are being made in the symptomatic treatment of Parkinson's disease. In this review, we focus on recent studies with monoamine oxidase type B inhibitors (selegiline and rasagiline), coenzyme Q10, creatine, and exercise in early Parkinson's disease. We also discuss the relative merits and disadvantages of delaying the initiation of levodopa therapy, the role of dopamine agonists, particularly ropinirole and pramipexole, and management of motor and behavioral complications, such as fluctuations, dyskinesias and impulse-control disorders. Novel formulations and delivery approaches for conventional and new drugs are also discussed. Finally, we review recent studies of surgical treatments of Parkinson's disease, such as deep brain stimulation. SUMMARY: Numerous clinical trials have provided evidence that health-related quality of life can be substantially improved with early diagnosis and institution of exercise and other physical measures, appropriate timing of dopaminergic therapy, and strategies to delay and treat levodopa-related motor complications and nonmotor Parkinson's disease-related symptoms.\",\n \"corpus_id\": 6997872,\n \"score\": 0\n },\n {\n \"doc_id\": \"22772874\",\n \"title\": \"Emerging therapies for Parkinson's disease.\",\n \"abstract\": \"PURPOSE OF REVIEW: The experimental therapeutics of Parkinson's disease are reviewed, highlighting the current pipeline of emerging therapeutic approaches. RECENT FINDINGS: This review includes novel approaches to dopaminergic drug delivery such as intraintestinal infusions or new extended-release formulations of levodopa and also intrapulmonary delivery of apomorphine as well as novel dopaminergic agents like the monoamine oxidase-B inhibitor safinamide or novel catechol-O-methyl transferase inhibitors. An even greater number of ongoing clinical trials assess the efficacy and safety of nondopaminergic approaches to enhance motor control or reduce motor complications like fluctuations and dyskinesias. These include adenosine A2A antagonists, α-adrenergic and serotonergic agonists as well as drugs acting on the glutamatergic system. Gene-based or cell-based intrastriatal delivery of therapeutic principles that enhance striatal dopaminergic transmission directly or via the stimulation of trophic activity has also reached phase II clinical development with encouraging results in some studies. Finally, a wide spectrum of agents with a potential for slowing disease progression is currently tested. SUMMARY: A variety of medical and nonmedical interventions in different phases of clinical development provide an interesting and promising portfolio of emerging therapies for Parkinson's disease.\",\n \"corpus_id\": 32540153,\n \"score\": 0\n },\n {\n \"doc_id\": \"24756517\",\n \"title\": \"Pharmacological treatment of Parkinson disease: a review.\",\n \"abstract\": \"IMPORTANCE: Parkinson disease is the second most common neurodegenerative disease worldwide. Although no available therapies alter the underlying neurodegenerative process, symptomatic therapies can improve patient quality of life. OBJECTIVE: To provide an evidence-based review of the initial pharmacological management of the classic motor symptoms of Parkinson disease; describe management of medication-related motor complications (such as motor fluctuations and dyskinesia), and other medication adverse effects (nausea, psychosis, and impulse control disorders and related behaviors); and discuss the management of selected nonmotor symptoms of Parkinson disease, including rapid eye movement sleep behavior disorder, cognitive impairment, depression, orthostatic hypotension, and sialorrhea. EVIDENCE REVIEW: References were identified using searches of PubMed between January 1985 and February 2014 for English-language human studies and the full database of the Cochrane Library. The classification of studies by quality (classes I-IV) was assessed using the levels of evidence guidelines from the American Academy of Neurology and the highest-quality data for each topic. RESULTS: Although levodopa is the most effective medication available for treating the motor symptoms of Parkinson disease, in certain instances (eg, mild symptoms, tremor as the only or most prominent symptom, aged <60 years) other medications (eg, monoamine oxidase type B inhibitors [MAOBIs], amantadine, anticholinergics, β-blockers, or dopamine agonists) may be initiated first to avoid levodopa-related motor complications. Motor fluctuations may be managed by modifying the levodopa dosing regimen or by adding several other medications, such as MAOBIs, catechol-O-methyltransferase inhibitors, or dopamine agonists. Impulse control disorders are typically managed by reducing or withdrawing dopaminergic medication, particularly dopamine agonists. Evidence-based management of some nonmotor symptoms is limited by a paucity of high-quality positive studies. CONCLUSIONS AND RELEVANCE: Strong evidence supports using levodopa and dopamine agonists for motor symptoms at all stages of Parkinson disease. Dopamine agonists and drugs that block dopamine metabolism are effective for motor fluctuations and clozapine is effective for hallucinations. Cholinesterase inhibitors may improve symptoms of dementia and antidepressants and pramipexole may improve depression. Evidence supporting other therapies for motor and nonmotor features is less well established.\",\n \"corpus_id\": 205058847,\n \"score\": 0\n },\n {\n \"doc_id\": \"24950010\",\n \"title\": \"Treatment of early Parkinson's disease.\",\n \"abstract\": \"PURPOSE OF REVIEW: This review summarizes currently available treatment options and treatment strategies, investigational treatments, and the importance of exercise for early Parkinson's disease. RECENT FINDINGS: The available treatment options for early Parkinson's disease have changed little in the past decade and include carbidopa/levodopa, dopamine agonists, and monoamine oxidase type B (MAO-B) inhibitors. However, we discuss changes in treatment strategies, including dosing and the use of combination therapy used in an attempt to reduce or delay the appearance of motor complications and other adverse events. We will also review several investigational treatments that have shown promise for the treatment of early Parkinson's disease, including a new extended release formulation of carbidopa/levodopa (IPX066), safinamide which inhibits MAO-B, dopamine uptake and glutamate and pardoprunox which is a 5HT-1A agonist and a partial dopamine agonist. Finally, we discuss recent studies focusing on exercise as an important component in the management of early Parkinson's disease. SUMMARY: Advances in the management of early Parkinson's disease include evolving treatment strategies, new investigational treatments, and earlier implementation of various forms of exercise.\",\n \"corpus_id\": 52861149,\n \"score\": 0\n },\n {\n \"doc_id\": \"25711470\",\n \"title\": \"1-[2-(4-Benzyloxyphenoxy)Ethyl]Imidazole inhibits monoamine oxidase B and protects against neuronal loss and behavioral impairment in rodent models of Parkinson's disease.\",\n \"abstract\": \"Monoamine oxidase B (MAO-B) is well known as a therapeutic target for Parkinson's disease (PD). MAO-B inhibitors retain antiparkinsonism abilities to improve motor function and prevent neuronal loss by decreasing dopamine metabolism and oxidative stress in the brain. From the study to find novel antiparkinsonism drugs that can inhibit MAO-B activity, neuronal loss, and behavioral deficits in the mouse model of PD, we identified that 1-[2-(4-benzyloxyphenoxy)ethyl]imidazole (BPEI) or safinamide strongly and selectively inhibited MAO-B activities in a dose-dependent manner (IC50 of BPEI and safinamide for MAO-B were 0.016 and 0.0021 µM and for MAO-A were 70.0 and 370 µM, respectively). In ex vivo studies after an administration (30 mg/kg, i.p.) of BPEI or safinamide to normal mice, the MAO-B activity in the brain was reduced by up to 90.6% or 82.4% at 1.0 hr. BPEI (20 mg/kg, i.p.) or safinamide (20 mg/kg, i.p.) significantly reversed the behavioral impairments, dopamine levels in the striatum, and neuronal loss in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice compared with the MPTP-alone-treated group. In the 6-hydroxydopamine-induced PD rat model, behavioral improvement by levodopa sparing activity was observed in the BPEI- or safinamide-treated (20 mg/kg, i.p.) rats. Moreover, BPEI revealed additional curative activities for nonmotor symptoms of PD such as pain, anxiety, epilepsy, and depression in rodent disease models. Therefore, BPEI has broad therapeutic potential for treating motor symptoms via strong and selective inhibitory effects on MAO-B, with additional benefits for comorbid symptoms in PD.\",\n \"corpus_id\": 28927174,\n \"score\": 0\n },\n {\n \"doc_id\": \"26293004\",\n \"title\": \"New treatments for levodopa-induced motor complications.\",\n \"abstract\": \"Levodopa (l-dopa)-induced motor complications, including motor fluctuations and dyskinesia, affect almost all patients with Parkinson's disease (PD) at some point during the disease course, with relevant implications in global health status. Various dopaminergic and nondopaminergic pharmacological approaches as well as more invasive strategies including devices and functional surgery are available to manage such complications. In spite of undisputable improvements during the last decades, many patients remain significantly disabled, and a fully satisfying management of l-dopa-induced motor complications is still an important unmet need of PD therapy. This article reviews the recent trial results published from 2013 to April 2015 about pharmacological and nonpharmacological interventions to treat motor complications. Randomized controlled trials conducted in patients suffering from already established complications showed that new levodopa (l-dopa) formulations such as intrajejunal l-dopa-carbidopa infusion and bilayered extended-release l-dopa-carbidopa (IPX066) can improve motor fluctuations. Positive results were also obtained with a new monoamine oxidase B (MAO-B) inhibitor (safinamide) and a catechol-O-methyltransferase COMT inhibitor (opicapone). Pilot data suggest that new formulations of dopamine agonists (inhaled apomorphine) are also of potential interest. The development of novel nondopaminergic adenosine A2A antagonists (istradefylline, preladenant, and tozadenant) to treat motor fluctuations showed conflicting results in phase 2 and phase 3 trials. For dyskinesia, trials with new amantadine extended-release formulations confirmed the interest of the glutamatergic N-methyl-d-aspartate (NMDA) antagonist approach. Positive pilot antidyskinetic effects were also recently reported using serotonin agents such as eltoprazine and glutamate mGluR5 modulators such as mavoglurant. However, the translation to clinical practice of such innovative concepts remains challenging, because subsequent phase 2 trials conducted to confirm the antidyskynetic effects of mavoglurant failed, leading to the interruption of the development of this compound for this indication.\",\n \"corpus_id\": 19682541,\n \"score\": 0\n },\n {\n \"doc_id\": \"26293352\",\n \"title\": \"Modern treatment in Parkinson's disease, a personal approach.\",\n \"abstract\": \"There are many guidelines available concerning the treatment of Parkinson's disease. Most of these advocate treating young-onset patients with a dopamine agonist and older patients with levodopa. The rationale behind this recommendation has its origins in the side effects associated with each of these drug classes: whilst levodopa leads to dyskinesia, which may not be relevant for patients with a limited life-expectancy, dopamine agonists have a much longer plasma half life which probably leads to more continuous dopamine receptor stimulation and thus decreases the occurrence and severity of dyskinesia. However, the side effects associated with the use of dopamine agonists, such as sleepiness, orthostatic problems, hallucinations and impulse control disorders are a drawback. In this overview, the hypothesis will be put forward that perhaps such a strict distinction is no longer needed. A new idea may be the early combination of levodopa with a dopamine agonist which would provide good clinical efficacy and, because of the relatively low doses involved, would reduce the side effects associated with both substances. MAO-B inhibitors may be a good option for early treatment and especially for patients who experience first motor fluctuations. Similarly, and particularly if a wearing-off symptom is present, COMT inhibitors smoothen and prolong the action of levodopa. More invasive escalation therapy comes into play when patients reach the advanced stages with problems of insufficient motor control, such as bradykinesia, rigidity and resting tremor, combined with on-time dyskinesia. The use of all oral and invasive treatment has to be individualized to gain a good motor and non-motor control and especially a good quality of life.\",\n \"corpus_id\": 25992055,\n \"score\": 0\n },\n {\n \"doc_id\": \"26300398\",\n \"title\": \"Neuroprotection by safinamide in the 6-hydroxydopamine model of Parkinson's disease.\",\n \"abstract\": \"AIMS: Current therapies in Parkinson's disease mainly treat symptoms rather than provide effective neuroprotection. We examined the effects of safinamide (monoamine oxidase B and sodium channel blocker) on microglial activation and the degeneration of dopaminergic neurons in a rat model of PD in vivo, and on microglia in vitro. METHODS: Rats received unilateral stereotaxic injection of 6-hydroxydopamine into the medial forebrain bundle on day 0: The contralateral side served as control. Safinamide or vehicle was delivered from days 0 or 1, for 7 days, via sub-cutaneous mini-pumps. RESULTS: In vehicle-treated rats 6-hydroxydopamine caused a significant increase in the number of activated MHC-II(+) microglia compared with the contralateral side, and only 50% of the dopaminergic neurons survived in the ipsilateral SNc. In contrast, rats treated daily with safinamide 50 and 150 mg/ml (on day 0 or 1) exhibited a significantly reduced number of activated microglia (55% reduction at 150 mg/ml) and a significant protection of dopaminergic neurons (80% of neurons survived) (P < 0.001) compared with vehicle-treated controls. Rasagiline, a monoamine oxidase B inhibitor, and lamotrigine, a sodium channel blocking drug, also protected dopaminergic neurons, indicating that safinamide may act by either or both mechanisms. Safinamide also reduced the activation of microglial cells in response to lipopolysaccharide exposure in vitro. CONCLUSION: Safinamide therapy suppresses microglial activation and protects dopaminergic neurons from degeneration in the 6-hydroxydopamine model of PD, suggesting that the drug not only treats symptoms but also provides neuroprotection.\",\n \"corpus_id\": 23711043,\n \"score\": 0\n },\n {\n \"doc_id\": \"26849427\",\n \"title\": \"The safety and efficacy of safinamide mesylate for the treatment of Parkinson's disease.\",\n \"abstract\": \"Safinamide (brand name Xadago®, Zambon S.p. A) is a third-generation reversible MAO-B inhibitor, which also blocks sodium voltage-sensitive channels and modulates stimulated release of glutamate. Safinamide was recently licensed by EMA for the treatment of PD as add-on therapy to a stable dose of levodopa alone or in combination with other PD medicinal products in mid-to advanced-stage fluctuating patients. It is also under review by the US FDA. Studies in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys and 6OHDA-lesioned rats suggest antiparkinsonian efficacy and antidyskinesic effects. Randomized, double-blind, placebo-controlled trials have shown efficacy for the treatment of motor symptoms in stable PD patients on dopamine agonists and in fluctuating PD patients on levodopa. Significant improvement in daily ON time was also observed in the latter. This effect was maintained for at least 2 years in double-blind conditions and, interestingly, without significant worsening of dyskinesia. Clinical studies have not detected any specific safety issue other than those already known with MAO-B inhibitors.\",\n \"corpus_id\": 37787896,\n \"score\": 0\n },\n {\n \"doc_id\": \"27498199\",\n \"title\": \"Opicapone: A Review in Parkinson's Disease.\",\n \"abstract\": \"Oral opicapone (Ongentys(®)), a potent, third-generation, long-acting, peripheral catechol-O-methyltransferase (COMT) inhibitor, is approved as adjunctive treatment to levodopa (L-Dopa)/dopa-decarboxylase inhibitor (DDCI) therapy in adults with Parkinson's disease (PD) and end-of-dose motor fluctuations who cannot be stabilized on those combinations. In 14- to 15-week, double-blind, multinational trials and in 1-year, open-label extension studies in this patient population, opicapone was an effective and generally well tolerated adjunctive therapy to L-Dopa plus a DDCI and other PD therapy. During the double-blind phase, adjunctive opicapone 50 mg once daily provided significantly greater improvements in motor fluctuations than placebo, with these improvements noninferior to those with entacapone. These beneficial improvements in motor fluctuations with opicapone were maintained in patients who continued adjunctive opicapone during the extension studies, with patients who switched from placebo or entacapone to opicapone experiencing significant improvements in motor fluctuations during this year. No new unexpected safety concerns were identified after ≈1.4 years' treatment with opicapone, with no serious cases of hepatotoxicity reported in clinical trials. With its convenient once-daily regimen, oral opicapone is an emerging COMT inhibitor option for use as adjunctive therapy to L-Dopa/DDCI therapy in adults with PD and end-of dose motor fluctuations who cannot be stabilized on those combinations.\",\n \"corpus_id\": 5787752,\n \"score\": 0\n },\n {\n \"doc_id\": \"27577098\",\n \"title\": \"Current and experimental treatments of Parkinson disease: A guide for neuroscientists.\",\n \"abstract\": \"Over a period of more than 50 years, the symptomatic treatment of the motor symptoms of Parkinson disease (PD) has been optimized using pharmacotherapy, deep brain stimulation, and physiotherapy. The arsenal of pharmacotherapies includes L-Dopa, several dopamine agonists, inhibitors of monoamine oxidase (MAO)-B and catechol-o-methyltransferase (COMT), and amantadine. In the later course of the disease, motor complications occur, at which stage different oral formulations of L-Dopa or dopamine agonists with long half-life, a transdermal application or parenteral pumps for continuous drug supply can be subscribed. Alternatively, the patient is offered deep brain stimulation of the subthalamic nucleus (STN) or the internal part of the globus pallidus (GPi). For a more efficacious treatment of motor complications, new formulations of L-Dopa, dopamine agonists, and amantadine as well as new MAO-B and COMT inhibitors are currently tested in clinical trials, and some of them already yielding positive results in phase 3 trials. In addition, non-dopaminergic agents have been tested in the early clinical phase for the treatment of motor fluctuations and dyskinesia, including adenosine A2A antagonists (istradefylline, preladenant, and tozadenant) and modulators of the metabolic glutamate receptor 5 (mGluR5 - mavoglurant) and serotonin (eltoprazine) receptors. Recent clinical trials testing coenzyme Q10, the dopamine agonist pramipexole, creatine monohydrate, pioglitazone, or AAV-mediated gene therapy aimed at increasing expression of neurturin, did not prove efficacious. Treatment with nicotine, caffeine, inosine (a precursor of urate), and isradipine (a dihydropyridine calcium channel blocker), as well as active and passive immunization against α-synuclein and inhibitors or modulators of α-synuclein-aggregation are currently studied in clinical trials. However, to date, no disease-modifying treatment is available. We here review the current status of treatment options for motor and non-motor symptoms, and discuss current investigative strategies for disease modification. This review provides basic insights, mainly addressing basic scientists and non-specialists. It stresses the need to intensify therapeutic PD research and points out reasons why the translation of basic research to disease-modifying therapies has been unsuccessful so far. The symptomatic treatment of the motor symptoms of Parkinson disease (PD) has been constantly optimized using pharmacotherapy (L-Dopa, several dopamine agonists, inhibitors of monoamine oxidase (MAO)-B and catechol-o-methyltransferase (COMT), and amantadine), deep brain stimulation, and physiotherapy. For a more efficacious treatment of motor complications, new formulations of L-Dopa, dopamine agonists, and amantadine as well as new MAO-B and COMT inhibitors are currently tested in clinical trials. Non-dopaminergic agents have been tested in the early clinical phase for the treatment of motor fluctuations and dyskinesia. Recent clinical trials testing coenzyme Q10, the dopamine agonist pramipexole, creatine monohydrate, pioglitazone, or AAV-mediated gene therapy aimed at increasing expression of neurturin, did not prove efficacious. Treatment with nicotine, caffeine, and isradipine - a dihydropyridine calcium channel blocker - as well as active and passive immunization against α-synuclein and inhibitors of α-synuclein-aggregation are currently studied in clinical trials. However, to date, no disease-modifying treatment is available for PD. We here review the current status of treatment options and investigative strategies for both motor and non-motor symptoms. This review stresses the need to intensify therapeutic PD research and points out reasons why the translation of basic research to disease-modifying therapies has been unsuccessful so far. This article is part of a special issue on Parkinson disease.\",\n \"corpus_id\": 30497369,\n \"score\": 0\n },\n {\n \"doc_id\": \"27599671\",\n \"title\": \"Clinical pharmacology review of opicapone for the treatment of Parkinson's disease.\",\n \"abstract\": \"Two catechol-O-methyl transferase inhibitors are currently used as add-on therapy to levodopa for the amelioration of end-of-dose motor fluctuations in Parkinson's disease patients: entacapone, which has moderate efficacy and requires multiple dosing, and tolcapone, which has a poor safety profile. Opicapone (OPC) is a novel, long-acting, peripherally selective, once daily, third-generation catechol-O-methyl transferase inhibitor. Two Phase III clinical trials demonstrated OPC efficacy in reducing OFF-time by an average of about 60 min daily compared with placebo, without increasing ON-time with troublesome dyskinesias, with a good drug safety profile. In June 2016, the European Commission granted a marketing authorization valid throughout the European Union for OPC, indicated as adjunctive of levodopa decarboxylase inhibitors in adult patients with Parkinson's disease and end-of-dose motor fluctuations.\",\n \"corpus_id\": 3492185,\n \"score\": 0\n },\n {\n \"doc_id\": \"28123288\",\n \"title\": \"Spotlight on opicapone as an adjunct to levodopa in Parkinson's disease: design, development and potential place in therapy.\",\n \"abstract\": \"Parkinson's disease (PD) is a progressive, chronic, neurodegenerative disease characterized by rigidity, tremor, bradykinesia and postural instability secondary to dopaminergic deficit in the nigrostriatal system. Currently, disease-modifying therapies are not available, and levodopa (LD) treatment remains the gold standard for controlling motor and nonmotor symptoms of the disease. LD is extensively and rapidly metabolized by peripheral enzymes, namely, aromatic amino acid decarboxylase and catechol-O-methyltransferase (COMT). To increase the bioavailability of LD, COMT inhibitors are frequently used in clinical settings. Opicapone is a novel COMT inhibitor that has been recently approved by the European Medicines Agency as an adjunctive therapy to combinations of LD and aromatic amino acid decarboxylase inhibitor in adult PD patients with end-of-dose motor fluctuations. We aimed to review the biochemical properties of opicapone, summarize its preclinical and clinical trials and discuss its future potential role in the treatment of PD.\",\n \"corpus_id\": 3088229,\n \"score\": 0\n },\n {\n \"doc_id\": \"28124620\",\n \"title\": \"Monoamine Oxidase B Inhibitors in Parkinson's Disease.\",\n \"abstract\": \"BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder with a prevalence increasing with age. Oxidative stress and glutamate toxicity are involved in its pathomechanism. There are still many unmet needs of PD patients, including the alleviation of motor fluctuations and dyskinesias, and the development of therapies with neuroprotective potential. OBJECTIVE: To give an overview of the pharmacological properties, the efficacy and safety of the monoamine oxidase B (MAO-B) inhibitors in the treatment of PD, with special focus on the results of randomized clinical trials. METHOD: A literature search was conducted in PubMed for 'PD treatment', 'MAO-B inhibitors', 'selegiline', 'rasagiline', 'safinamide' and 'clinical trials' with 'MAO-B inhibitors' in 'Parkinson' disease'. RESULTS: MAO-B inhibitors have a favorable pharmacokinetic profile, improve the dopamine deficient state and may have neuroprotective properties. Safinamide exhibits an anti-glutamatergic effect as well. When applied as monotherapy, MAO-B inhibitors provide a modest, but significant improvement of motor function and delay the need for levodopa. Rasagiline and safinamide were proven safe and effective when added to a dopamine agonist in early PD. As add-on to levodopa, MAO-B inhibitors significantly reduced off-time and were comparable in efficacy to COMT inhibitors. Improvements were achieved as regards certain non-motor symptoms as well. CONCLUSION: Due to the efficacy shown in clinical trials and their favorable side-effect profile, MAO-B inhibitors are valuable drugs in the treatment of PD. They are recommended as monotherapy in the early stages of the disease and as add-on therapy to levodopa in advanced PD.\",\n \"corpus_id\": 4928424,\n \"score\": 0\n },\n {\n \"doc_id\": \"28234566\",\n \"title\": \"Opicapone for the treatment of Parkinson's disease.\",\n \"abstract\": \"INTRODUCTION: Parkinson's disease (PD) is a progressive neurodegenerative disease. The currently available treatment options only have a symptomatic effect. With disease progression almost all antiparkinsonian pharmacological classes are tried, but the gold standard of pharmacological management is still L-dopa. Various strategies can be used to raise the dopaminergic tone. Catechol-O-methyltransferase (COMT) inhibitors attain this goal by decreasing L-dopa peripheral metabolism. Areas covered: Opicapone (Ongentys®) is a new COMT inhibitor developed to fulfill the need for more potent, safer and longer acting COMT inhibitors. This review puts into context opicapone's indications, its chemical and preclinical data, the pharmacodynamics and pharmacokinetic characteristics, and the efficacy and safety results delivered by clinical trials. Expert opinion: Opicapone is an efficacious COMT inhibitor. Its proprieties make it adequate for a once-a-day oral dose regimen. It has proved to reduce the off-time and to increase the on-time without troublesome dyskinesias in PD patients with motor fluctuations. The reported adverse events suggest an overall safe and well-tolerated profile. The most common adverse events were dyskinesia, and there were no issues of concern for hepatotoxicity, severe diarrhoea or chromaturia. Further evidence is still needed to conclude how it compares with other drugs for the treatment of motor fluctuations.\",\n \"corpus_id\": 5251815,\n \"score\": 0\n },\n {\n \"doc_id\": \"28511252\",\n \"title\": \"Diagnosis and Management of Parkinson's Disease.\",\n \"abstract\": \"Despite numerous efforts to identify specific and sensitive biomarkers, the diagnosis of Parkinson's disease (PD) is still based on clinical criteria that include the presence of a combination of cardinal motor features (tremor, rigidity, bradykinesia, and postural instability), other motor features (including freezing of gait and abnormal postures), and numerous nonmotor features. In addition, the presence of atypical features may suggest an alternative diagnosis. Levodopa therapy remains the gold standard in the management of motor features of PD. New formulations of levodopa and novel delivery systems are currently being evaluated and gradually introduced in clinical practice in an attempt to prevent or treat levodopa-related motor complications. Dopamine agonists also play an important role as monotherapy in mild or adjunctive therapy in moderately advanced disease. As the disease progresses and patients develop complications from levodopa therapy, specifically motor fluctuations and dyskinesias, deep brain stimulation becomes an alternative therapeutic option. Clinical trials of experimental therapeutics are currently fueling the PD therapeutic pipeline.\",\n \"corpus_id\": 398250,\n \"score\": 0\n },\n {\n \"doc_id\": \"29018297\",\n \"title\": \"Xadago (Safinamide): A Monoamine Oxidase B Inhibitor for the Adjunct Treatment of Motor Symptoms in Parkinson's Disease.\",\n \"abstract\": \"Xadago (safinamide), a monoamine oxidase B inhibitor for the adjunct treatment of motor symptoms in Parkinson's disease.\",\n \"corpus_id\": 22895774,\n \"score\": 0\n },\n {\n \"doc_id\": \"29130466\",\n \"title\": \"[Safinamide from daily clinical practice: first clinical steps].\",\n \"abstract\": \"Safinamida desde la practica clinica diaria: primeros pasos clinicos. INTRODUCTION: The management of motor complications in Parkinson's disease (PD) is still limited. Safinamide, a new drug that has MAO-B inhibition and antiglutamatergic effects through inhibition of sodium channels, has shown efficacy for the treatment of fluctuations at doses of 50-100 mg/day. PATIENTS AND METHODS: From daily clinical practice, we describe the efficacy and tolerability of safinamide at three months in PD patients with motor complications. Efficacy was assessed by the Clinical Global Impression of Change scale and change in 'off' time during the daytime. All reported adverse events were recorded. RESULTS: Fifty patients were recruited. 57.4% reported to be much better or moderately better at three months, improving both motor and non-motor fluctuations. Significant decrease of 0.9 ± 0.6 h/day was achieved at three months. In 13 patients (27.6%), levodopa equivalent daily dose was reduced in 132 mg/day. In patients with dyskinesias, safinamide 100 mg/day was better for controlling fluctuations and dyskinesias. 19% of patients had mild adverse events. Seven patients stopped treatment after development of confusional syndrome. CONCLUSIONS: The dopaminergic and non-dopaminergic action of safinamide exerts a good control of motor fluctuations. In patients with fluctuations and dyskinesias the dose of 100 mg/day of safinamide is preferred. Tolerability was good, except for patients older than 75 years or in advanced stages of the disease.\",\n \"corpus_id\": 27208131,\n \"score\": 0\n },\n {\n \"doc_id\": \"29339106\",\n \"title\": \"Safinamide: a new hope for Parkinson's disease?\",\n \"abstract\": \"The loss of dopaminergic neurons (DAn) and reduced dopamine (DA) production underlies the reasoning behind the gold standard treatment for Parkinson's disease (PD) using levodopa (L-DOPA). Recently licensed by the European Medicine Agency (EMA) and US Food and Drug Administration (FDA), safinamide [a monoamine oxidase B (MOA-B) inhibitor] is an alternative to L-DOPA; as we discuss here, it enhances dopaminergic transmission with decreased secondary effects compared with L-DOPA. In addition, nondopaminergic actions (neuroprotective effects) have been reported, with safinamide inhibiting glutamate release and sodium/calcium channels, reducing the excitotoxic input to dopaminergic neuronal death. Effects of safinamide have been correlated with the amelioration of non-motor symptoms (NMS), although these remain under discussion. Overall, safinamide can be considered to have potential antidyskinetic and neuroprotective effects and future trials and/or studies should be performed to provide further evidence for its potential as an anti-PD drug.\",\n \"corpus_id\": 3885257,\n \"score\": 0\n },\n {\n \"doc_id\": \"29542008\",\n \"title\": \"Long-term Efficacy of Safinamide on Parkinson's Disease Chronic Pain.\",\n \"abstract\": \"INTRODUCTION: Chronic pain is an important yet overlooked non-motor symptom of Parkinson's disease (PD), caused by an imbalance of the dopaminergic and glutamatergic systems. Safinamide has a multimodal mechanism of action, dopaminergic (reversible MAO-B inhibition) and non-dopaminergic (modulation of the abnormal glutamate release), that might be beneficial for both motor and non-motor symptoms. OBJECTIVES: To investigate the long-term (2-year) efficacy of safinamide on PD chronic pain and to confirm the positive effects observed after 6 months of treatment. METHODS: This is a post hoc analysis of the data from the 2-year study 018, focused on the reduction of concomitant pain treatments and on the scores of pain-related items of the Parkinson's disease quality of life questionnaire (PDQ-39). RESULTS: Safinamide, compared with placebo, significantly improved the PDQ-39 items 37 (\\\"painful cramps or spasm,\\\" p = 0.0074) and 39 (\\\"unpleasantly hot or cold,\\\" p = 0.0209) and significantly reduced the number of concomitant pain treatments by 26.2% (p = 0.005). A significantly greater proportion of patients in the safinamide group was not using pain drugs after 2 years of treatment (p = 0.0478). CONCLUSIONS: The positive effects of safinamide on PD chronic pain were maintained in the long term. Further investigations are desirable to confirm their clinical relevance. FUNDING: Zambon SpA.\",\n \"corpus_id\": 5006485,\n \"score\": 0\n },\n {\n \"doc_id\": \"29570862\",\n \"title\": \"Medical and surgical management of advanced Parkinson's disease.\",\n \"abstract\": \"Advanced Parkinson's disease is characterized by the presence of motor fluctuations, various degree of dyskinesia, and disability with functional impact on activities of daily living and independence. Therapeutic management aims to extend levodopa benefit while minimizing motor complications and includes, in selected cases, the implementation of drug infusion and surgical techniques. In milder forms of motor complications, these can often be controlled with manipulation of levodopa dose and the introduction of supplemental therapies such as catechol-O-methyl transferase inhibitors, monoamine oxidase B inhibitors, and dopamine agonists including apomorphine. Clinical experience and evidence from published studies indicate that when these agents cannot satisfactorily control motor complications, patients should be assessed and considered for device-aided therapies. This review article summarizes some of the newer available therapeutic opportunities such as use of enzyme inhibitors like opicapone and safinamide, adenosine A2A receptor antagonists, apomorphine and levodopa/carbidopa intestinal gel infusion, deep brain stimulation including the role of closed-loop and adaptive stimulation, and MRI-guided focused ultrasound. © 2018 International Parkinson and Movement Disorder Society.\",\n \"corpus_id\": 206250568,\n \"score\": 0\n },\n {\n \"doc_id\": \"29614697\",\n \"title\": \"Are There Benefits in Adding Catechol-O Methyltransferase Inhibitors in the Pharmacotherapy of Parkinson's Disease Patients? A Systematic Review.\",\n \"abstract\": \"BACKGROUND: A qualified consensus suggests that a combination of levodopa with a peripherally acting dopa decarboxylase inhibitor continues to present the gold standard treatment of Parkinson's disease (PD). However, as the disease progresses the therapeutic window of levodopa becomes narrowed. Pharmacological strategies for motor fluctuations are focused on providing less pulsatile and more continuous dopaminergic stimulation. Peripheral catechol-O-methyltransferase (COMT) inhibition improves the bioavailability of levodopa and results in a prolonged response. OBJECTIVE: The primary aim of this study was to investigate the efficacy and safety of the two available COMT inhibitors; entacapone and tolcapone and the recently introduced opicapone. METHODS: Electronic databases were systematically searched for original studies published within the last 37 years. In addition, lists of identified studies, reviews and their references were examined. RESULTS: Twelve studies fulfilled the inclusion criteria. 3701 patients with PD were included in this systematic review. CONCLUSIONS: Adjuvant treatment of PD patients experiencing motor fluctuations with entacapone resulted in improvement of motor function and was well tolerated. Therefore, entacapone presented an acceptable benefit to risk ratio. Tolcapone appeared to result in a greater therapeutic effect. However, this was not consistent across all motor variables and studies, and thus would not support its use, given the current onerous monitoring that is required. Opicapone was not associated with adverse reactions in a phase III trial but did not present a greater efficacy than entacapone, and thus further studies are required in order to illustrate its cost effectiveness.\",\n \"corpus_id\": 4595585,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":50,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29614051\",\n \"title\": \"The Effect of Seasonal Floods on Health: Analysis of Six Years of National Health Data and Flood Maps.\",\n \"abstract\": \"There is limited knowledge on the effect of seasonal flooding on health over time. We quantified the short- and long-term effects of floods on selected health indicators at public healthcare facilities in 11 districts in Cambodia, a flood-prone setting. Counts of inpatient discharge diagnoses and outpatient consultations for diarrhea, acute respiratory infections, skin infections, injuries, noncommunicable diseases and vector-borne diseases were retrieved from public healthcare facilities for each month between January 2008 and December 2013. Flood water was mapped by month, in square kilometers, from satellite data. Poisson regression models with three lag months were constructed for the health problems in each district, controlled for seasonality and long-term trends. During times of flooding and three months after, there were small to moderate increases in visits to healthcare facilities for skin infections, acute respiratory infections, and diarrhea, while no association was seen at one to two months. The associations were small to moderate, and a few of our results were significant. We observed increases in care seeking for diarrhea, skin infections, and acute respiratory infections following floods, but the associations are uncertain. Additional research on previous exposure to flooding, using community- and facility-based data, would help identify expected health risks after floods in flood-prone settings.\",\n \"corpus_id\": 4594102\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20586021","title":"Health impacts of floods.","abstract":"INTRODUCTION: Floods are the most common hazard to cause disasters and have led to extensive morbidity and mortality throughout the world. The impact of floods on the human community is related directly to the location and topography of the area, as well as human demographics and characteristics of the built environment. OBJECTIVES: The aim of this study is to identify the health impacts of disasters and the underlying causes of health impacts associated with floods. A conceptual framework is developed that may assist with the development of a rational and comprehensive approach to prevention, mitigation, and management. METHODS: This study involved an extensive literature review that located >500 references, which were analyzed to identify common themes, findings, and expert views. The findings then were distilled into common themes. RESULTS: The health impacts of floods are wide ranging, and depend on a number of factors. However, the health impacts of a particular flood are specific to the particular context. The immediate health impacts of floods include drowning, injuries, hypothermia, and animal bites. Health risks also are associated with the evacuation of patients, loss of health workers, and loss of health infrastructure including essential drugs and supplies. In the medium-term, infected wounds, complications of injury, poisoning, poor mental health, communicable diseases, and starvation are indirect effects of flooding. In the long-term, chronic disease, disability, poor mental health, and poverty-related diseases including malnutrition are the potential legacy. CONCLUSIONS: This article proposes a structured approach to the classification of the health impacts of floods and a conceptual framework that demonstrates the relationships between floods and the direct and indirect health consequences.","corpus_id":6702725,"score":2},{"doc_id":"21288358","title":"Long-term effects of flooding on mortality in England and Wales, 1994-2005: controlled interrupted time-series analysis.","abstract":"BACKGROUND: Limited evidence suggests that being flooded may increase mortality and morbidity among affected householders not just at the time of the flood but for months afterwards. The objective of this study is to explore the methods for quantifying such long-term health effects of flooding by analysis of routine mortality registrations in England and Wales. METHODS: Mortality data, geo-referenced by postcode of residence, were linked to a national database of flood events for 1994 to 2005. The ratio of mortality in the post-flood year to that in the pre-flood year within flooded postcodes was compared with that in non-flooded boundary areas (within 5 km of a flood). Further analyses compared the observed number of flood-area deaths in the year after flooding with the number expected from analysis of mortality trends stratified by region, age-group, sex, deprivation group and urban-rural status. RESULTS: Among the 319 recorded floods, there were 771 deaths in the year before flooding and 693 deaths in the year after (post-/pre-flood ratio of 0.90, 95% CI 0.82, 1.00). This ratio did not vary substantially by age, sex, population density or deprivation. A similar post-flood 'deficit' of deaths was suggested by the analyses based on observed/expected deaths. CONCLUSIONS: The observed post-flood 'deficit' of deaths is counter-intuitive and difficult to interpret because of the possible influence of population displacement caused by flooding. The bias that might arise from such displacement remains unquantified but has important implications for future studies that use place of residence as a marker of exposure.","corpus_id":7551088,"score":2},{"doc_id":"21866222","title":"Impacts of flood on health: epidemiologic evidence from Hanoi, Vietnam.","abstract":"BACKGROUND: Vietnam is one of the most disaster-prone countries in the world. The country suffers from many kinds of natural disasters, of which the most common and serious one is flooding. Long and heavy rainfall during the last days of October and the first week of November 2008 resulted in a devastating flood unseen for over three decades in the capital city of Hanoi. It caused a substantial health impact on residents in and around the city and compromised the capacity of local health services. OBJECTIVE: The aim of this study is to ascertain the vulnerability and health impacts of the devastating flood in Hanoi by identifying the differences in mortality, injuries, and morbidity patterns (dengue, pink eye, dermatitis, psychological problems, and hypertension) between flood affected and non-affected households. DESIGN: A cross-sectional study was carried out involving 871 households in four selected communes (two heavily flood affected and two comparatively less affected) from two severely flooded districts of Hanoi. Participants were interviewed and information collected on the social, economic, and health impacts of the devastation within 1 month after the flood. RESULTS: The self-reported number of deaths and injuries reported in this study within 1 month after the heavy rainfall were a bit higher in severely affected communes as compared to that of the less affected communes of our study. The findings showed higher incidences of dengue fever, pink eye, dermatitis, and psychological problems in communes severely affected by flood as compared to that of the controlled communes. CONCLUSIONS: For people in flood prone areas (at risk for flooding), flood prevention and mitigation strategies need to be seriously thought through and acted upon, as these people are exposed to greater health problems such as psychological issues and communicable diseases such as pink eye or dermatitis.","corpus_id":26599167,"score":2},{"doc_id":"22082995","title":"Health effects of flooding in rural Bangladesh.","abstract":"BACKGROUND: There is little information available on nontraumatic health risks as the result of floods, and on the factors that determine vulnerability to them (especially in low-income settings). We estimated the pattern of mortality, diarrhea, and acute respiratory infection following the 2004 floods in rural Bangladesh. METHODS: We conducted controlled interrupted time-series analysis of adverse health outcomes, from 2001 to 2007, in a cohort of 211,000 residents of the Matlab region classified as flooded or nonflooded in 2004. Ratios of mortality, diarrhea, and acute respiratory infection rates in flooded compared with nonflooded areas were calculated by week for mortality and diarrhea, and by month for acute respiratory infection. We controlled for baseline differences as well as normal seasonal patterns in the flooded and nonflooded areas. Variations in flood-related health risks were examined by age, income level, drinking-water source, latrine type, and service area. RESULTS: After fully controlling for pre-flood rate differences and for seasonality, there was no clear evidence of excesses in mortality or diarrhea risk during or after flooding. For acute respiratory infection, we found no evidence of excess risk during the flood itself but a moderate increase in risk during the 6 months after the flood (relative risk = 1.25 [95% confidence interval = 1.06-1.47]) and the subsequent 18 months. CONCLUSIONS: We found little evidence of increased risk of diarrhea or mortality following the floods, but evidence of a moderate elevation in risk of acute respiratory infection during the 2 years after flooding. The discrepancies between our results and the apparent excesses for mortality and diarrhea reported in other situations, using less- controlled estimates, emphasize the importance of stringent confounder control.","corpus_id":31349784,"score":2},{"doc_id":"22750033","title":"Floods and human health: a systematic review.","abstract":"Floods are the most common type of disaster globally, responsible for almost 53,000 deaths in the last decade alone (23:1 low- versus high-income countries). This review assessed recent epidemiological evidence on the impacts of floods on human health. Published articles (2004-2011) on the quantitative relationship between floods and health were systematically reviewed. 35 relevant epidemiological studies were identified. Health outcomes were categorized into short- and long-term and were found to depend on the flood characteristics and people's vulnerability. It was found that long-term health effects are currently not well understood. Mortality rates were found to increase by up to 50% in the first year post-flood. After floods, it was found there is an increased risk of disease outbreaks such as hepatitis E, gastrointestinal disease and leptospirosis, particularly in areas with poor hygiene and displaced populations. Psychological distress in survivors (prevalence 8.6% to 53% two years post-flood) can also exacerbate their physical illness. There is a need for effective policies to reduce and prevent flood-related morbidity and mortality. Such steps are contingent upon the improved understanding of potential health impacts of floods. Global trends in urbanization, burden of disease, malnutrition and maternal and child health must be better reflected in flood preparedness and mitigation programs.","corpus_id":22576348,"score":2},{"doc_id":"23569839","title":"Infectious diseases in the aftermath of monsoon flooding in Pakistan.","abstract":"Pakistan is ranked 9th in terms of flood-affected countries worldwide. In the summer of 2010, the northern province of Khyber-Pakhtunkhwa received more than 312 mm of rain in a 56 hour period. This resulted in over 1 600 deaths across the region. In addition, over 14 million people were directly affected by this record-breaking deluge. Flood affected regions serve as ideal breeding grounds for pathogens, leading to the spread of diseases. The poor standards of hygiene in camps set up for individuals displaced by the floods also contribute to this. It is essential that those involved in relief efforts are aware of the epidemiology of diseases that have historically seen a sudden upsurge after natural disasters. Keeping this in mind, we conducted a simple review of literature. An extensive literature search was conducted using the PubMed data base and online search engines. Articles published in the last 20 years were considered along with some historical articles where a background was required. Seven major diseases were identified to increase substantially in the aftermath of natural disasters. They were then classified into acute and sub-acute settings. Diarrhea, skin & eye infections and leptospirosis were identified in the acute setting while malaria, leishmaniasis, respiratory infections and hepatitis were identified in the sub-acute setting.","corpus_id":42611917,"score":2},{"doc_id":"23762291","title":"Quantitative analysis of burden of infectious diarrhea associated with floods in northwest of anhui province, china: a mixed method evaluation.","abstract":"BACKGROUND: Persistent and heavy rainfall in the upper and middle Huaihe River of China brought about severe floods during the end of June and July 2007. However, there has been no assessment on the association between the floods and infectious diarrhea. This study aimed to quantify the impact of the floods in 2007 on the burden of disease due to infectious diarrhea in northwest of Anhui Province. METHODS: A time-stratified case-crossover analysis was firstly conducted to examine the relationship between daily cases of infectious diarrhea and the 2007 floods in Fuyang and Bozhou of Anhui Province. Odds ratios (ORs) of the flood risk were quantified by conditional logistic regression. The years lived with disability (YLDs) of infectious diarrhea attributable to floods were then estimated based on the WHO framework of the calculating potential impact fraction in the Burden of Disease study. RESULTS: A total of 197 infectious diarrheas were notified during the exposure and control periods in the two study areas. The strongest effect was shown with a 2-day lag in Fuyang and a 5-day lag in Bozhou. Multivariable analysis showed that floods were significantly associated with an increased risk of the number cases of infectious diarrhea (OR = 3.175, 95%CI: 1.126-8.954 in Fuyang; OR = 6.754, 95%CI: 1.954-23.344 in Bozhou). Attributable YLD per 1000 of infectious diarrhea resulting from the floods was 0.0081 in Fuyang and 0.0209 in Bozhou. CONCLUSIONS: Our findings confirm that floods have significantly increased the risks of infectious diarrhea in the study areas. In addition, prolonged moderate flood may cause more burdens of infectious diarrheas than severe flood with a shorter duration. More attention should be paid to particular vulnerable groups, including younger children and elderly, in developing public health preparation and intervention programs. Findings have significant implications for developing strategies to prevent and reduce health impact of floods.","corpus_id":14485419,"score":2},{"doc_id":"24073902","title":"Flood-related skin diseases: a literature review.","abstract":"Flood is one of the most common natural disasters, which commonly occurs in all parts of the world. The effects of the disasters considerably become enormous problems to overall public health systems. Flood-related skin diseases are a portion of these consequences presenting with cutaneous manifestations and/or signs of systemic illnesses. We conducted a systematic literature review of research publications relating to flooding and skin diseases. The purpose of this review was to provide dermatologists as well as general practitioners with comprehensive conditions of flood-related skin diseases and suggested treatments. Moreover, we categorized these flood-related diseases into four groups comprising inflammatory skin diseases, skin infections, traumatic skin diseases, and other miscellaneous skin diseases in a bid to implement early interventions and educate, prevent, and efficaciously handle those skin diseases under such a catastrophic situation so that better treatment outcomes and prevention of further complications could be ultimately achieved and accomplished.","corpus_id":20986687,"score":2},{"doc_id":"24625900","title":"[Climate changes, floods, and health consequences].","abstract":"Cambiamenti climatici, alluvioni e impatto sulla salute. In the European Region, floods are the most common natural disaster, causing extensive damage and disruption. In Italy, it has been estimated that over 68% of municipalities are at high hydrogeological risk and with the recent intense rainfall events local populations have been facing severe disruptions. The health consequences of floods are wide ranging and are dependent upon the vulnerability of the environment and the local population. Health effects can be a direct or indirect consequence of flooding. The immediate health impacts of floods include drowning, heart attacks, injuries and hypothermia. The indirect effects include, injuries and infections, water-borne infectious disease, mental health problems, respiratory disease and allergies in both the medium and long term after a flood. Future efforts should be addressed to integrate health preparedness and prevention measures into emergency flood plans and hydrological warning systems.","corpus_id":10403883,"score":2},{"doc_id":"25098726","title":"Impacts of floods on dysentery in Xinxiang city, China, during 2004-2010: a time-series Poisson analysis.","abstract":"BACKGROUND: Xinxiang, a city in Henan Province, suffered from frequent floods due to persistent and heavy precipitation from 2004 to 2010. In the same period, dysentery was a common public health problem in Xinxiang, with the proportion of reported cases being the third highest among all the notified infectious diseases. OBJECTIVES: We focused on dysentery disease consequences of different degrees of floods and examined the association between floods and the morbidity of dysentery on the basis of longitudinal data during the study period. DESIGN: A time-series Poisson regression model was conducted to examine the relationship between 10 times different degrees of floods and the monthly morbidity of dysentery from 2004 to 2010 in Xinxiang. Relative risks (RRs) of moderate and severe floods on the morbidity of dysentery were calculated in this paper. In addition, we estimated the attributable contributions of moderate and severe floods to the morbidity of dysentery. RESULTS: A total of 7591 cases of dysentery were notified in Xinxiang during the study period. The effect of floods on dysentery was shown with a 0-month lag. Regression analysis showed that the risk of moderate and severe floods on the morbidity of dysentery was 1.55 (95% CI: 1.42-1.670) and 1.74 (95% CI: 1.56-1.94), respectively. The attributable risk proportions (ARPs) of moderate and severe floods to the morbidity of dysentery were 35.53 and 42.48%, respectively. CONCLUSIONS: This study confirms that floods have significantly increased the risk of dysentery in the study area. In addition, severe floods have a higher proportional contribution to the morbidity of dysentery than moderate floods. Public health action should be taken to avoid and control a potential risk of dysentery epidemics after floods.","corpus_id":7536430,"score":2},{"doc_id":"25282279","title":"Association between annual river flood pulse and paediatric hospital admissions in the Mekong Delta area.","abstract":"The Mekong Delta is the most vulnerable region to extreme climate and hydrological conditions however the association between these conditions and children's health has been little studied. We examine the association between annual river flood pulse and paediatric hospital admissions in a Vietnam Mekong Delta city. Daily paediatric hospital admissions (PHA) were collected from the City Paediatric Hospital, and daily river water level (RWL) and meteorological data were retrieved from the Southern Regional Hydro-Meteorological Centre from 2008 to 2011. We evaluated the association between annual river flood pulse (>=90th percentile of RWL) and PHA using the Poisson distributed lag model, controlling for temperature, relative humidity, day of week, seasonal and long-term trends. The seasonal pattern of PHA was examined using harmonic and polynomial regression models. The cumulative risk ratios estimated for a 15-day period following an extreme RWL was 1.26 (95%CI, 1.2-1.38) for all age groups, 1.27 (95%CI, 1.23-1.30) for under five-years and 1.15 (95%CI, 1.07-1.20) for school-aged children, 1.24 (95%CI, 1.21-1.27) for all-causes, 1.18 (95%CI, 1.12-1.21) for communicable infection, 1.66 (95%CI, 1.57-1.74) for respiratory infection and 1.06 (95%CI, 1.01-1.1) for other diseases. The peak PHA risk is in the September-October period corresponding to the highest RWL, and the PHA-RWL association was modified by temperature. An increase in PHA is significantly associated with annual river flood, and the pattern of PHA is seasonally correspondent to the RWL. These findings combined with projected changes in climate conditions suggest important implications of climate change for human health in the Mekong Delta region.","corpus_id":18685357,"score":2},{"doc_id":"25329916","title":"Flooding and emergency room visits for gastrointestinal illness in Massachusetts: a case-crossover study.","abstract":"INTRODUCTION: Floods and other severe weather events are anticipated to increase as a result of global climate change. Floods can lead to outbreaks of gastroenteritis and other infectious diseases due to disruption of sewage and water infrastructure and impacts on sanitation and hygiene. Floods have also been indirectly associated with outbreaks through population displacement and crowding. METHODS: We conducted a case-crossover study to investigate the association between flooding and emergency room visits for gastrointestinal illness (ER-GI) in Massachusetts for the years 2003 through 2007. We obtained ER-GI visits from the State of Massachusetts and records of floods from the National Oceanic and Atmospheric Association's Storm Events Database. ER-GI visits were considered exposed if a flood occurred in the town of residence within three hazard periods of the visit: 0-4 days; 5-9 days; and 10-14 days. A time-stratified bi-directional design was used for control selection, matching on day of the week with two weeks lead or lag time from the ER-GI visit. Fixed effect logistic regression models were used to estimate the risk of ER-GI visits following the flood. RESULTS AND CONCLUSIONS: A total of 270,457 ER-GI visits and 129 floods occurred in Massachusetts over the study period. Across all counties, flooding was associated with an increased risk for ER-GI in the 0-4 day period after flooding (Odds Ratio: 1.08; 95% Confidence Interval: 1.03-1.12); but not the 5-9 days (Odds Ratio: 0.995; 95% Confidence Interval: 0.955-1.04) or the 10-14 days after (Odds Ratio: 0.966, 95% Confidence Interval: 0.927-1.01). Similar results were observed for different definitions of ER-GI. The effect differed across counties, suggesting local differences in the risk and impact of flooding. Statewide, across the study period, an estimated 7% of ER-GI visits in the 0-4 days after a flood event were attributable to flooding.","corpus_id":6722447,"score":2},{"doc_id":"25546280","title":"Water-borne diseases and extreme weather events in Cambodia: review of impacts and implications of climate change.","abstract":"Cambodia is prone to extreme weather events, especially floods, droughts and typhoons. Climate change is predicted to increase the frequency and intensity of such events. The Cambodian population is highly vulnerable to the impacts of these events due to poverty; malnutrition; agricultural dependence; settlements in flood-prone areas, and public health, governance and technological limitations. Yet little is known about the health impacts of extreme weather events in Cambodia. Given the extremely low adaptive capacity of the population, this is a crucial knowledge gap. A literature review of the health impacts of floods, droughts and typhoons in Cambodia was conducted, with regional and global information reviewed where Cambodia-specific literature was lacking. Water-borne diseases are of particular concern in Cambodia, in the face of extreme weather events and climate change, due to, inter alia, a high pre-existing burden of diseases such as diarrhoeal illness and a lack of improved sanitation infrastructure in rural areas. A time-series analysis under quasi-Poisson distribution was used to evaluate the association between floods and diarrhoeal disease incidence in Cambodian children between 2001 and 2012 in 16 Cambodian provinces. Floods were significantly associated with increased diarrhoeal disease in two provinces, while the analysis conducted suggested a possible protective effect from toilets and piped water. Addressing the specific, local pre-existing vulnerabilities is vital to promoting population health resilience and strengthening adaptive capacity to extreme weather events and climate change in Cambodia.","corpus_id":22563372,"score":2},{"doc_id":"26090609","title":"Flooding and Clostridium difficile Infection: A Case-Crossover Analysis.","abstract":"Clostridium difficile is a bacterium that can spread by water. It often causes acute gastrointestinal illness in older adults who are hospitalized and/or receiving antibiotics; however, community-associated infections affecting otherwise healthy individuals have become more commonly reported. A case-crossover study was used to assess emergency room (ER) and outpatient visits for C. difficile infection following flood events in Massachusetts from 2003 through 2007. Exposure status was based on whether or not a flood occurred prior to the case/control date during the following risk periods: 0-6 days, 7-13 days, 14-20 days, and 21-27 days. Fixed-effects logistic regression was used to estimate the risk of diagnosis with C. difficile infection following a flood. There were 129 flood events and 1575 diagnoses of C. difficile infection. Among working age adults (19-64 years), ER and outpatient visits for C. difficile infection were elevated during the 7-13 days following a flood (Odds Ratio, OR = 1.69; 95% Confidence Interval, CI: 0.84, 3.37). This association was more substantial among males (OR = 3.21; 95% CI: 1.01-10.19). Associations during other risk periods were not observed (p < 0.05). Although we were unable to differentiate community-associated versus nosocomial infections, a potential increase in C. difficile infections should be considered as more flooding is projected due to climate change.","corpus_id":23708504,"score":2},{"doc_id":"26159354","title":"The Infectious and Noninfectious Dermatological Consequences of Flooding: A Field Manual for the Responding Provider.","abstract":"Meteorological data show that disastrous floods are increasingly frequent and more severe in recent years, perhaps due to climatic changes such as global warming. During and after a flood disaster, traumatic injuries, communicable diseases, chemical exposures, malnutrition, decreased access to care, and even mental health disorders dramatically increase, and many of these have dermatological manifestations. Numerous case reports document typical and atypical cutaneous infections, percutaneous trauma, immersion injuries, noninfectious contact exposures, exposure to wildlife, and exacerbation of underlying skin diseases after such disasters as the 2004 Asian tsunami, Hurricane Katrina in 2005, and the 2010 Pakistan floods. This review attempts to provide a basic field manual of sorts to providers who are engaged in care after a flooding event, with particular focus on the infectious consequences. Bacterial pathogens such as Staphylococcus and Streptococcus are still common causes of skin infections after floods, with atypical bacteria also greatly increased. Vibrio vulnificus is classically associated with exposure to saltwater or brackish water. It may present as necrotizing fasciitis with hemorrhagic bullae, and treatment consists of doxycycline or a quinolone, plus a third-generation cephalosporin and surgical debridement. Atypical mycobacterial infections typically produce indolent cutaneous infections, possibly showing sporotrichoid spread. A unique nontuberculous infection called spam has recently been identified in Satowan Pacific Islanders; combination antibiotic therapy is recommended. Aeromonas infection is typically associated with freshwater exposure and, like Vibrio infections, immunocompromised or cirrhotic patients are at highest risk for severe disease, such as necrotizing fasciitis and sepsis. Various antibiotics can be used to treat Aeromonas infections. Melioidosis is seen mainly in Southeast Asia and Australia, particularly in rice farmers, and can remain latent for many years before presenting as the host's immunocompetence wanes. It can present with a variety of skin findings or as a nonspecific febrile illness, and preferred treatment consists of ceftazidime or a carbapenem with trimethoprim/sulfamethoxazole (TMP/SMX) for 2 weeks, then continuing TMP/SMX for at least 3 months. Leptospirosis is a waterborne zoonosis that is often prevalent after heavy rains or flooding. Different forms exist, including Fort Bragg fever, which produces a distinctive erythematous papular rash on the shins. Doxycycline is often sufficient; however, volume and potassium repletion may be necessary if renal involvement exists. Chromobacterium violaceum infection may occur after open skin is exposed to stagnant or muddy water. Cultured colonies produce a unique violacein pigment, and treatment typically consists of a carbapenem. Both typical and atypical fungal infections are increased in the flooding disaster scenario, such as dermatophytosis, chromoblastomycosis, blastomycosis, and mucormycosis. Appropriate antifungals should be used. In addition, land inundated with water expands the habitat for parasites and/or vectors, thus increased vigilance for regional parasitic infections is necessary after a flood. Lastly, noninfectious consequences of a flooding disaster are also common and include miliaria, immersion foot syndromes, irritant and allergic contact dermatitis, traumatic wounds and animal bites, and arthropod assault, as well as exacerbation of existing skin conditions such as atopic dermatitis, psoriasis, and alopecia areata due to increased stress or nonavailability of daily medications.","corpus_id":35243897,"score":2},{"doc_id":"26861372","title":"Flood-Exposure is Associated with Higher Prevalence of Child Undernutrition in Rural Eastern India.","abstract":"BACKGROUND: Child undernutrition and flooding are highly prevalent public health issues in Asia, yet epidemiological studies investigating this association are lacking. METHODS: To investigate to what extent floods exacerbate poor nutritional status in children and identify most vulnerable groups, we conducted a population-based survey of children aged 6-59 months inhabiting flooded and non-flooded communities of the Jagatsinghpur district, Odisha (India), one year after large floods in 2008. Anthropometric measurements on 879 children and child, parental and household level variables were collected through face-to-face interviews in September 2009. The association between flooding and the prevalence of wasting, stunting and underweight was examined using weighted multivariate logistic regression for children inhabiting communities exposed solely to floods in 2008 and those communities repeatedly flooded (2006 and 2008) controlling for parental education and other relevant variables. We examined the influence of age on this association. Propensity score matching was conducted to test the robustness of our findings. RESULTS: The prevalence of wasting among children flooded in 2006 and 2008 was 51.6%, 41.4% in those flooded only in 2008, and 21.2% in children inhabiting non-flooded communities. Adjusting by confounders, the increased prevalence relative to non-flooded children in the exposed groups were 2.30 (adjusted prevalence ratio (aPR); 95% CI: 1.86, 2.85) and 1.94 (95% CI: 1.43, 2.63), respectively. Among repeatedly flooded communities, cases of severe wasting in children were 3.37 times more prevalent than for children inhabiting in those non-flooded (95% CI: 2.34, 4.86) and nearly twice more prevalent relative to those flooded only once. Those children younger than one year during previous floods in 2006 showed the largest difference in prevalence of wasting compared to their non-flooded counterparts (aPR: 4.01; 95% CI: 1.51, 10.63). RESULTS were robust to alternative adjusted models and in propensity score matching analyses. For similar analyses, no significant associations were found for child stunting, and more moderate effects were observed in the case of child underweight. CONCLUSIONS: Particularly in low-resource or subsistence-farming rural settings, long-lasting nutritional response in the aftermath of floods should be seriously considered to counteract the long-term nutritional effects on children, particularly infants, and include their mothers on whom they are dependent. The systematic monitoring of nutritional status in these groups might help to tailor efficient responses in each particular context.","corpus_id":11499747,"score":2},{"doc_id":"27171415","title":"Risk of Flood-Related Diseases of Eyes, Skin and Gastrointestinal Tract in Taiwan: A Retrospective Cohort Study.","abstract":"Floods are known to cause serious environmental damage and health impacts. Studies on flood-related diseases have been primarily on individual events, and limited evidence could be drawn on potential health impacts from floods using large population data. This study used reimbursement records of one million people of the Taiwan National Health Insurance program to compare incident diseases of the eyes, skin and gastrointestinal (GI) tract associated with floods. Incidence rates for the selected diseases were calculated according to outpatient/emergency visit data. The incidence rates were evaluated by flood status: in 10 days before floods, during floods and within 10 days after the floods receded. Outpatient/emergency visit rates for the eye, skin and GI tract diseases were highest after floods and lowest during floods. Results from multivariate Poisson regression analyses showed that, when compared with the incidence in 10 days before floods, the incidence rate ratios (IRR) of diseases within 10 days after floods were 1.15 (95% confidence interval (CI) = 1.10-1.20) for eyes, 1.08 (95% C.I. = 1.05-1.10) for skin, and 1.11 (95% CI = 1.08-1.14) for GI tract, after controlling for covariates. All risks increased with ambient temperature. V-shaped trends were found between age and eye diseases, and between age and GI tract diseases. In contrast, the risk of skin diseases increased with age. In conclusion, more diseases of eyes, skin and GI tract could be diagnosed after the flood.","corpus_id":6240652,"score":2},{"doc_id":"27174415","title":"Projections of hepatitis A virus infection associated with flood events by 2020 and 2030 in Anhui Province, China.","abstract":"Assessing and responding to health risk of climate change is important because of its impact on the natural and societal ecosystems. More frequent and severe flood events will occur in China due to climate change. Given that population is projected to increase, more people will be vulnerable to flood events, which may lead to an increased incidence of HAV infection in the future. This population-based study is going to project the future health burden of HAV infection associated with flood events in Huai River Basin of China. The study area covered four cities of Anhui province in China, where flood events were frequent. Time-series adjusted Poisson regression model was developed to quantify the risks of flood events on HAV infection based on the number of daily cases during summer seasons from 2005 to 2010, controlling for other meteorological variables. Projections of HAV infection in 2020 and 2030 were estimated based on the scenarios of flood events and demographic data. Poisson regression model suggested that compared with the periods without flood events, the risks of severe flood events for HAV infection were significant (OR = 1.28, 95 % CI 1.05-1.55), while risks were not significant from moderate flood events (OR = 1.16, 95 % CI 0.72-1.87) and mild flood events (OR = 1.14, 95 % CI 0.87-1.48). Using the 2010 baseline data and the flood event scenarios (one severe flood event), increased incidence of HAV infection were estimated to be between 0.126/10(5) and 0.127/10(5) for 2020. Similarly, the increased HAV infection incidence for 2030 was projected to be between 0.382/10(5) and 0.399/10(5). Our study has, for the first time, quantified the increased incidence of HAV infection that will result from flood events in Anhui, China, in 2020 and 2030. The results have implications for public health preparation for developing public health responses to reduce HAV infection during future flood events.","corpus_id":7724237,"score":2},{"doc_id":"27312685","title":"Short-term impacts of floods on enteric infectious disease in Qingdao, China, 2005-2011.","abstract":"The current study aimed to examine the relationship between floods and the three enteric infectious diseases, namely bacillary dysentery (BD), hand-foot-mouth disease (HFMD) and other infectious diarrhoea (OID) in Qingdao, China. Relative risks (RRs) and 95% confidence intervals (CIs) of floods on BD, HFMD and OID were calculated using a quasi-Poisson generalized linear model, adjusting for daily average temperature, daily average relative humidity, and seasonal and long-term temporal trends. Two separate models within two different periods were designed. Model 1 for the summer period showed that floods were positively associated with BD for 4- to 12-day lags, with the greatest effects for 7-day (RR 1·41, 95% CI 1·22-1·62) and 11-day (RR 1·42, 95% CI 1·22-1·64) lags. Similar findings were found in model 2 for the whole study period for 5- to 12-day lags. However, HFMD and OID were not significantly associated with floods in both models. Results from this study will provide insight into the health risks associated with floods and may help inform public health precautionary measures for such disasters.","corpus_id":19186183,"score":2},{"doc_id":"28606191","title":"No Calm After the Storm: A Systematic Review of Human Health Following Flood and Storm Disasters.","abstract":"Introduction How the burden of disease varies during different phases after floods and after storms is essential in order to guide a medical response, but it has not been well-described. The objective of this review was to elucidate the health problems following flood and storm disasters. METHODS: A literature search of the databases Medline (US National Library of Medicine, National Institutes of Health; Bethesda, Maryland USA); Cinahl (EBSCO Information Services; Ipswich, Massachusetts USA); Global Health (EBSCO Information Services; Ipswich, Massachusetts USA); Web of Science Core Collection (Thomson Reuters; New York, New York USA); Embase (Elsevier; Amsterdam, Netherlands); and PubMed (National Center for Biotechnology Information, National Institutes of Health; Bethesda, Maryland USA) was conducted in June 2015 for English-language research articles on morbidity or mortality and flood or storm disasters. Articles on mental health, interventions, and rescue or health care workers were excluded. Data were extracted from articles that met the eligibility criteria and analyzed by narrative synthesis. RESULTS: The review included 113 studies. Poisonings, wounds, gastrointestinal infections, and skin or soft tissue infections all increased after storms. Gastrointestinal infections were more frequent after floods. Leptospirosis and diabetes-related complications increased after both. The majority of changes occurred within four weeks of floods or storms. CONCLUSION: Health changes differently after floods and after storms. There is a lack of data on the health effects of floods alone, long-term changes in health, and the strength of the association between disasters and health problems. This review highlights areas of consideration for medical response and the need for high-quality, systematic research in this area. Saulnier DD , Brolin Ribacke K , von Schreeb J . No calm after the storm: a systematic review of human health following flood and storm disasters. Prehosp Disaster Med. 2017;32(5):1-12.","corpus_id":13147929,"score":2},{"doc_id":"29339262","title":"The long-term physical and psychological health impacts of flooding: A systematic mapping.","abstract":"BACKGROUND: Flooding has caused significant and wide ranging long-term health impacts for affected populations. However, until now, the long-term health outcomes, epidemiological trends and specific impact factors of flooding had not been identified. In this study, the relevant literature was systematically mapped to create the first synthesis of the evidence of the long-term health impacts of flooding. METHODS: The systematic mapping method was used to collect and categorize all the relevant literature. A study was included if it had a description or measurement of health impacts over six months after flooding. The search was limited to peer reviewed articles and grey literature written in English, published from 1996 to 2016. RESULTS: A total of 56 critical articles were extracted for the final map, including 5 qualitative and 51 quantitative studies. Most long-term studies investigated the psychological impacts of flooding, including PTSD, depression, anxiety, psychiatric disorders, sleep disorder and suicide. Others investigated the physiological impacts, including health-related quality of life, acute myocardial infarction, chronic diseases, and malnutrition. Social support was proved to be protective factors that can improve health outcomes in the long-term after flooding. To date, there have been relatively few reviews had focused on the long-term health impacts of flooding. This study coded and catalogued the existing evidence across a wide range of variables and described the long-term health consequences within a conceptual map. DISCUSSION AND CONCLUSIONS: Although there was no boundary between the short-term and the long-term impacts of flooding, the identified health outcomes in this systematic mapping could be used to define long-term health impacts. The studies showed that the prevalence of psychological diseases had a reversed increasing trend occurred even in the long-term in relatively poor post-flooding environments. Further cohort or longitudinal research focused on disability, chronic diseases, relocation population, and social interventions after flooding, are urgently required.","corpus_id":3862968,"score":2},{"doc_id":"29734967","title":"Floods Increase the Risks of Hand-Foot-Mouth Disease in Qingdao, China, 2009-2013: A Quantitative Analysis.","abstract":"BACKGROUND: We aimed to quantify the impact of few times floods on hand-foot-mouth disease (HFMD) in Qingdao during 2009-2013. METHODS: The Spearman correlation test was applied to examine the lagged effects of floods on monthly morbidity of HFMD during study period in Qingdao. We further quantified the effects of 5 flood events on the morbidity of HFMD using the time-series Poisson regression controlling for climatic factors, seasonality, and lagged effects among different populations. RESULTS: A total of 55,920 cases of HFMD were reported in the study region over the study period. The relative risks of floods on the morbidity of HFMD among the total population, males, females, under 1-2 years old, and 3-5 years old were 1.178, 1.165, 1.198, 1.338, and 1.245, respectively. CONCLUSIONS: This study has, for the first time, provided the positive evidence of the impact of floods on HFMD. It demonstrates that floods can significantly increase the risk of HFMD during study period. Additionally, among the different populations, the risks were higher among children under 1-5 years old. ( Disaster Med Public Health Preparedness. 2018;12:723-729).","corpus_id":13682854,"score":2},{"doc_id":"22435044","title":"Prepared to react? Assessing the functional capacity of the primary health care system in rural Orissa, India to respond to the devastating flood of September 2008.","abstract":"BACKGROUND: Early detection of an impending flood and the availability of countermeasures to deal with it can significantly reduce its health impacts. In developing countries like India, public primary health care facilities are frontline organizations that deal with disasters particularly in rural settings. For developing robust counter reacting systems evaluating preparedness capacities within existing systems becomes necessary. OBJECTIVE: The objective of the study is to assess the functional capacity of the primary health care system in Jagatsinghpur district of rural Orissa in India to respond to the devastating flood of September 2008. METHODS: An onsite survey was conducted in all 29 primary and secondary facilities in five rural blocks (administrative units) of Jagatsinghpur district in Orissa state. A pre-tested structured questionnaire was administered face to face in the facilities. The data was entered, processed and analyzed using STATA(®) 10. RESULTS: Data from our primary survey clearly shows that the healthcare facilities are ill prepared to handle the flood despite being faced by them annually. Basic utilities like electricity backup and essential medical supplies are lacking during floods. Lack of human resources along with missing standard operating procedures; pre-identified communication and incident command systems; effective leadership; and weak financial structures are the main hindering factors in mounting an adequate response to the floods. CONCLUSION: The 2008 flood challenged the primary curative and preventive health care services in Jagatsinghpur. Simple steps like developing facility specific preparedness plans which detail out standard operating procedures during floods and identify clear lines of command will go a long way in strengthening the response to future floods. Performance critiques provided by the grass roots workers, like this one, should be used for institutional learning and effective preparedness planning. Additionally each facility should maintain contingency funds for emergency response along with local vendor agreements to ensure stock supplies during floods. The facilities should ensure that baseline public health standards for health care delivery identified by the Government are met in non-flood periods in order to improve the response during floods. Building strong public primary health care systems is a development challenge. The recovery phases of disasters should be seen as an opportunity to expand and improve services and facilities.","corpus_id":12538378,"score":1},{"doc_id":"23994865","title":"High temperature as a risk factor for infectious diarrhea in Shanghai, China.","abstract":"BACKGROUND: Recent studies indicate that ambient temperature could be a risk factor for infectious diarrhea, but evidence for such a relation is limited in China. METHODS: We investigated the short-term association between daily temperature and physician-diagnosed infectious diarrhea during 2008-2010 in Shanghai, China. We adopted a time-series approach to analyze the data and a quasi-Poisson regression model with a natural spline-smoothing function to adjust for long-term and seasonal trends, as well as other time-varying covariates. RESULTS: There was a significant association between temperature and outpatient visits for diarrhea. A 1°C increase in the 6-day moving average of temperature was associated with a 2.68% (95% CI: 1.83%, 3.52%) increase in outpatient visits for diarrhea. We did not find a significant association between rainfall and infectious diarrhea. CONCLUSIONS: High temperature might be a risk factor for infectious diarrhea in Shanghai. Public health programs should focus on preventing diarrhea related to high temperature among city residents.","corpus_id":17545497,"score":1},{"doc_id":"24336027","title":"Factors increasing vulnerability to health effects before, during and after floods.","abstract":"Identifying the risk factors for morbidity and mortality effects pre-, during and post-flood may aid the appropriate targeting of flood-related adverse health prevention strategies. We conducted a systematic PubMed search to identify studies examining risk factors for health effects of precipitation-related floods, among Organisation for Economic Co-Operation and Development (OECD) member countries. Research identifying flood-related morbidity and mortality risk factors is limited and primarily examines demographic characteristics such as age and gender. During floods, females, elderly and children appear to be at greater risk of psychological and physical health effects, while males between 10 to 29 years may be at greater risk of mortality. Post-flood, those over 65 years and males are at increased risk of physical health effects, while females appear at greater risk of psychological health effects. Other risk factors include previous flood experiences, greater flood depth or flood trauma, existing illnesses, medication interruption, and low education or socio-economic status. Tailoring messages to high-risk groups may increase their effectiveness. Target populations differ for morbidity and mortality effects, and differ pre-, during, and post-flood. Additional research is required to identify the risk factors associated with pre- and post-flood mortality and post-flood morbidity, preferably using prospective cohort studies.","corpus_id":5249566,"score":1},{"doc_id":"25511879","title":"Primary healthcare system capacities for responding to storm and flood-related health problems: a case study from a rural district in central Vietnam.","abstract":"BACKGROUND: As a tropical depression in the East Sea, Vietnam is greatly affected by climate change and natural disasters. Knowledge of the current capacity of the primary healthcare system in Vietnam to respond to health issues associated with storms and floods is very important for policy making in the country. However, there has been little scientific research in this area. OBJECTIVE: This research was to assess primary healthcare system capacities in a rural district in central Vietnam to respond to such health issues. DESIGN: This was a cross-sectional descriptive study using quantitative and qualitative approaches. Quantitative methods used self-administered questionnaires. Qualitative methods (in-depth interviews and focus groups discussions) were used to broaden understanding of the quantitative material and to get additional information on actions taken. RESULTS: 1) Service delivery: Medical emergency services, especially surgical operations and referral systems, were not always available during the storm and flood seasons. 2) Governance: District emergency plans focus largely on disaster response rather than prevention. The plans did not clearly define the role of primary healthcare and had no clear information on the coordination mechanism among different sectors and organizations. 3) Financing: The budget for prevention and control of flood and storm activities was limited and had no specific items for healthcare activities. Only a little additional funding was available, but the procedures to get this funding were usually time-consuming. 4) Human resources: Medical rescue teams were established, but there were no epidemiologists or environmental health specialists to take care of epidemiological issues. Training on prevention and control of climate change and disaster-related health issues did not meet actual needs. 5) Information and research: Data that can be used for planning and management (including population and epidemiological data) were largely lacking. The district lacked a disease early-warning system. 6) Medical products and technology: Emergency treatment protocols were not available in every studied health facility. CONCLUSIONS: The primary care system capacity in rural Vietnam is inadequate for responding to storm and flood-related health problems in terms of preventive and treatment healthcare. Developing clear facility preparedness plans, which detail standard operating procedures during floods and identify specific job descriptions, would strengthen responses to future floods. Health facilities should have contingency funds available for emergency response in the event of storms and floods. Health facilities should ensure that standard protocols exist in order to improve responses in the event of floods. Introduction of a computerized health information system would accelerate information and data processing. National and local policies need to be strengthened and developed in a way that transfers into action in local rural communities.","corpus_id":23692386,"score":1},{"doc_id":"25633112","title":"Health Vulnerability of Households in Flooded Communities and Their Adaptation Measures: Case Study in Northeastern Thailand.","abstract":"Floods adversely affect community well-being and health. This study aims to assess the present health vulnerability of households to floods in a rural flood-prone area of northeastern Thailand, as well as their adaptation measures. The participants were the representatives of 312 randomly selected households, and data were collected using an interview questionnaire. Health vulnerability was assessed in terms of flood exposure, flood sensitivity, and flood adaptive capacity. The data were analyzed with descriptive statistics. The results showed that 47.1% of the households had a low level of health vulnerability to flooding, while in 21.2% the level was high. Households had been adapting themselves to cope with the health impacts from flood. Their coping practices included special arrangements for the protection of property, food management, the provision of water supply and waste disposal, the elimination of sources of vector-borne diseases, family health care, the protection of family livelihood, and communication and transportation.","corpus_id":13058641,"score":1},{"doc_id":"25813771","title":"The impact of flooding on people living with HIV: a case study from the Ohangwena Region, Namibia.","abstract":"BACKGROUND: Floods are a disaster situation for all affected populations and especially for vulnerable groups within communities such as children, orphans, women, and people with chronic diseases such as HIV and AIDS. They need functioning health care, sanitation and hygiene, safe water, and healthy food supply, and are critically dependent on their social care and support networks. A study carried out in the Ohangwena region, Namibia, where HIV prevalence is high and extensive flooding frequently occurs, aims to provide a deeper understanding of the impact that flooding has on people living with HIV (PLWHIV) as well as on HIV service providers in the region. DESIGN: The qualitative research applying grounded theory included semi-structured interviews with PLWHIV, focus group discussions with HIV service providers, and a national feedback meeting. The findings were interpreted using the sustainable livelihoods framework, the natural hazard research approach, and health behaviour theories. RESULTS: The study reveals that flooding poses major problems to PLWHIV in terms of their everyday lives, affecting livelihoods, work, income, and living conditions. The factors threatening them under normal conditions - poverty, malnutrition, unsafe water, sanitation and hygiene, limited access to health facilities, a weak health status, and stigma - are intensified by flood-related breakdown of infrastructure, insecurity, malnutrition, and diseases evolving over the course of a flood. A potential dual risk exists for their health: the increased risk both of infection and disease due to the inaccessibility of health services and antiretroviral treatment. A HIV and Flooding Framework was developed to display the results. CONCLUSIONS: This study demonstrates that vulnerabilities and health risks of PLWHIV will increase in a disaster situation like flooding if access to HIV prevention, treatment, care and support are not addressed and ensured. The findings and the HIV and Flooding Framework are not specific to Ohangwena and can be transferred to any flood-affected region that has a high HIV prevalence and relies mainly on subsistence agriculture. They serve as a model case for analysing vulnerabilities related to health and health service provision under disaster conditions. The impact will vary according to the physical, geographical, climatological, social, and behavioural characteristics of the region and the people affected. In the Ohangwena region, a disaster risk management mechanism is already in place which addresses people with HIV during flooding. However, preparedness could be improved further by applying the HIV and Flooding Framework.","corpus_id":54518141,"score":1},{"doc_id":"25860572","title":"Flooding and mental health: a systematic mapping review.","abstract":"BACKGROUND: Floods are the most common type of global natural disaster. Floods have a negative impact on mental health. Comprehensive evaluation and review of the literature are lacking. OBJECTIVE: To systematically map and review available scientific evidence on mental health impacts of floods caused by extended periods of heavy rain in river catchments. METHODS: We performed a systematic mapping review of published scientific literature in five languages for mixed studies on floods and mental health. PUBMED and Web of Science were searched to identify all relevant articles from 1994 to May 2014 (no restrictions). RESULTS: The electronic search strategy identified 1331 potentially relevant papers. Finally, 83 papers met the inclusion criteria. Four broad areas are identified: i) the main mental health disorders-post-traumatic stress disorder, depression and anxiety; ii] the factors associated with mental health among those affected by floods; iii) the narratives associated with flooding, which focuses on the long-term impacts of flooding on mental health as a consequence of the secondary stressors; and iv) the management actions identified. The quantitative and qualitative studies have consistent findings. However, very few studies have used mixed methods to quantify the size of the mental health burden as well as exploration of in-depth narratives. Methodological limitations include control of potential confounders and short-term follow up. LIMITATIONS: Floods following extreme events were excluded from our review. CONCLUSIONS: Although the level of exposure to floods has been systematically associated with mental health problems, the paucity of longitudinal studies and lack of confounding controls precludes strong conclusions. IMPLICATIONS: We recommend that future research in this area include mixed-method studies that are purposefully designed, using more rigorous methods. Studies should also focus on vulnerable groups and include analyses of policy and practical responses.","corpus_id":5011009,"score":1},{"doc_id":"25909883","title":"An exploration of factors affecting the long term psychological impact and deterioration of mental health in flooded households.","abstract":"The long term psychological effect of the distress and trauma caused by the memory of damage and losses associated with flooding of communities remains an under researched impact of flooding. This is particularly important for communities that are likely to be repeatedly flooded where levels of mental health disorder will damage long term resilience to future flooding. There are a variety of factors that affect the prevalence of mental health disorders in the aftermath of flooding including pre-existing mental health, socio-economic factors and flood severity. However previous research has tended to focus on the short term impacts immediately following the flood event and much less focus has been given to the longer terms effects of flooding. Understanding of factors affecting the longer term mental health outcomes for flooded households is critical in order to support communities in improving social resilience. Hence, the aim of this study was to explore the characteristics associated with psychological distress and mental health deterioration over the longer term. The research examined responses from a postal survey of households flooded during the 2007 flood event across England. Descriptive statistics, correlation analysis and binomial logistic regression were applied to data representing household characteristics, flood event characteristics and post-flood stressors and coping strategies. These factors were related to reported measures of stress, anxiety, depression and mental health deterioration. The results showed that household income, depth of flooding; having to move out during reinstatement and mitigating actions are related to the prevalence of psycho-social symptoms in previously flooded households. In particular relocation and household income were the most predictive factors. The practical implication of these findings for recovery after flooding are: to consider the preferences of households in terms of the need to move out during restorative building works and the financial resource constraints that may lead to severe mental hardship. In addition the findings suggest that support with installing mitigation measures may lead to improved mental health outcomes for communities at risk.","corpus_id":6246722,"score":1},{"doc_id":"26552993","title":"Flood Risk, Flood Mitigation, and Location Choice: Evaluating the National Flood Insurance Program's Community Rating System.","abstract":"Climate change is expected to worsen the negative effects of natural disasters like floods. The negative impacts, however, can be mitigated by individuals' adjustments through migration and relocation behaviors. Previous literature has identified flood risk as one significant driver in relocation decisions, but no prior study examines the effect of the National Flood Insurance Program's voluntary program-the Community Rating System (CRS)-on residential location choice. This article fills this gap and tests the hypothesis that flood risk and the CRS-creditable flood control activities affect residential location choices. We employ a two-stage sorting model to empirically estimate the effects. In the first stage, individuals' risk perception and preference heterogeneity for the CRS activities are considered, while mean effects of flood risk and the CRS activities are estimated in the second stage. We then estimate heterogeneous marginal willingness to pay (WTP) for the CRS activities by category. Results show that age, ethnicity and race, educational attainment, and prior exposure to risk explain risk perception. We find significant values for the CRS-creditable mitigation activities, which provides empirical evidence for the benefits associated with the program. The marginal WTP for an additional credit point earned for public information activities, including hazard disclosure, is found to be the highest. Results also suggest that water amenities dominate flood risk. Thus, high amenity values may increase exposure to flood risk, and flood mitigation projects should be strategized in coastal regions accordingly.","corpus_id":10061071,"score":1},{"doc_id":"26639744","title":"A 9-year Trend in the Prevalence of Allergic Disease Based on National Health Insurance Data.","abstract":"OBJECTIVES: To investigate trends in the prevalence of allergic disease over a 9-year period. METHODS: Using National Health Insurance Service (NHIS) data, the annual number of patients with allergic disease was obtained for each regional subdivisions (small cities, counties, and districts) from 2003 to 2011. Annual populations for each sub-region were obtained and used to calculate the standardized prevalence. To compare prevalence within the study period, data was standardized spatially and temporally. For standardization, demographic data was used to obtain the registered population and demographic structure for 2010, which was used to perform direct standardization of previous years. In addition, a geographic information system (GIS) was used to visualize prevalence for individual sub-regions, and allergic diseases were categorized into five groups according to prevalence. RESULTS: The nationwide outpatient prevalence of allergic rhinitis increased approximately 2.3-fold, from 1.27% in 2003 to 2.97% in 2013, while inpatient prevalence also increased approximately 2.4-fold,. The outpatient prevalence of asthma increased 1.2-fold, and inpatient prevalence increased 1.3-fold. The outpatient prevalence of atopic dermatitis decreased approximately 12%, and inpatient prevalence decreased 5%. CONCLUSIONS: There was a large difference between prevalence estimated from actual treatment data and prevalence based on patients' self-reported data, particularly for allergic rhinitis. Prevalence must continually be calculated and trends should be analyzed for the efficient management of allergic diseases. To this end, prevalence studies using NHIS claims data may be useful.","corpus_id":24614754,"score":1},{"doc_id":"28129410","title":"Self-Reported and FEMA Flood Exposure Assessment after Hurricane Sandy: Association with Mental Health Outcomes.","abstract":"Hurricane Sandy caused extensive physical and economic damage; the long-term mental health consequences are unknown. Flooding is a central component of hurricane exposure, influencing mental health through multiple pathways that unfold over months after flooding recedes. Here we assess the concordance in self-reported and Federal Emergency Management (FEMA) flood exposure after Hurricane Sandy and determine the associations between flooding and anxiety, depression, and post-traumatic stress disorder (PTSD). Self-reported flood data and mental health symptoms were obtained through validated questionnaires from New York City and Long Island residents (N = 1231) following Sandy. Self-reported flood data was compared to FEMA data obtained from the FEMA Modeling Task Force Hurricane Sandy Impact Analysis. Multivariable logistic regressions were performed to determine the relationship between flooding exposure and mental health outcomes. There were significant discrepancies between self-reported and FEMA flood exposure data. Self-reported dichotomous flooding was positively associated with anxiety (ORadj: 1.5 [95% CI: 1.1-1.9]), depression (ORadj: 1.7 [1.3-2.2]), and PTSD (ORadj: 2.5 [1.8-3.4]), while self-reported continuous flooding was associated with depression (ORadj: 1.1 [1.01-1.12]) and PTSD (ORadj: 1.2 [1.1-1.2]). Models with FEMA dichotomous flooding (ORadj: 2.1 [1.5-2.8]) or FEMA continuous flooding (ORadj: 1.1 [1.1-1.2]) were only significantly associated with PTSD. Associations between mental health and flooding vary according to type of flood exposure measure utilized. Future hurricane preparedness and recovery efforts must integrate micro and macro-level flood exposures in order to accurately determine flood exposure risk during storms and realize the long-term importance of flooding on these three mental health symptoms.","corpus_id":16200299,"score":1},{"doc_id":"28129752","title":"The English national cohort study of flooding and health: cross-sectional analysis of mental health outcomes at year one.","abstract":"BACKGROUND: In winter 2013/14 there was widespread flooding in England. Previous studies have described an increased prevalence of psychological morbidity six months after flooding. Disruption to essential services may increase morbidity however there have been no studies examining whether those experiencing disruption but not directly flooded are affected. The National Study of Flooding and Health was established in order to investigate the longer-term impact of flooding and related disruptions on mental health and wellbeing. METHODS: In year one we conducted a cross sectional analysis of people living in neighbourhoods affected by flooding between 1 December 2013 and 31 March 2014. 8761 households were invited to participate. Participants were categorised according to exposure as flooded, disrupted by flooding or unaffected. We used validated instruments to screen for probable psychological morbidity, the Patient Health Questionnaire (PHQ 2), Generalised Anxiety Disorder scale (GAD-2) and Post Traumatic Stress Disorder (PTSD) checklist (PCL-6). We calculated prevalence and odds ratios for each outcome by exposure group relative to unaffected participants, adjusting for confounders. RESULTS: 2126 people (23%) responded. The prevalence of psychological morbidity was elevated amongst flooded participants ([n = 622] depression 20.1%, anxiety 28.3%, PTSD 36.2%) and disrupted participants ([n = 1099] depression 9.6%, anxiety 10.7% PTSD 15.2%). Flooding was associated with higher odds of all outcomes (adjusted odds ratios (aORs), 95% CIs for depression 5.91 (3.91-10.99), anxiety 6.50 (3.77-11.24), PTSD 7.19 (4.33-11.93)). Flooded participants who reported domestic utilities disruption had higher odds of all outcomes than other flooded participants, (aORs, depression 6.19 (3.30-11.59), anxiety 6.64 (3.84-11.48), PTSD 7.27 (4.39-12.03) aORs without such disruption, depression, 3.14 (1.17-8.39), anxiety 3.45 (1.45-8.22), PTSD 2.90 (1.25-6.73)). Increased floodwater depth was significantly associated with higher odds of each outcome. Disruption without flooding was associated with borderline higher odds of anxiety (aOR 1.61 (0.94-2.77)) and higher odds of PTSD 2.06 (1.27-3.35)) compared with unaffected participants. Disruption to health/social care and work/education was also associated with higher odds of psychological morbidity. CONCLUSIONS: This study provides an insight into the impact of flooding on mental health, suggesting that the impacts of flooding are large, prolonged and extend beyond just those whose homes are flooded.","corpus_id":2386660,"score":1},{"doc_id":"29396332","title":"Association between floods and infectious diarrhea and their effect modifiers in Hunan province, China: A two-stage model.","abstract":"BACKGROUND: Understanding the potential links between floods and infectious diarrhea is important under the context of climate change. However, little is known about the risk of infectious diarrhea after floods and what factors could modify these effects in China. OBJECTIVES: This study aims to quantitatively examine the relationship between floods and infectious diarrhea and their effect modifiers. METHODS: Weekly number of infectious diarrhea cases from 2004 to 2011 during flood season in Hunan province were supplied by the National Notifiable Disease Surveillance System. Flood and meteorological data over the same period were obtained. A two-stage model was used to estimate a provincial average association and their effect modifiers between floods and infectious diarrhea, accounting for other confounders. RESULTS: A total of 134,571 cases of infectious diarrhea were notified from 2004 to 2011. After controlling for seasonality, long-term trends, and meteorological factors, floods were significantly associated with infectious diarrhea in the provincial level with a cumulative RR of 1.22 (95% CI: 1.05, 1.43) with a lagged effect of 0-1 week. Geographic locations and economic levels were identified as effect modifiers, with a higher impact of floods on infectious diarrhea in the western and regions with a low economic level of Hunan. CONCLUSIONS: Our study provides strong evidence of a positive association between floods and infectious diarrhea in the study area. Local control strategies for public health should be taken in time to prevent and reduce the risk of infectious diarrhea after floods, especially for the vulnerable regions identified.","corpus_id":3836850,"score":1},{"doc_id":"29514665","title":"The English National Cohort Study of Flooding and Health: the change in the prevalence of psychological morbidity at year two.","abstract":"BACKGROUND: The longer term impact of flooding on health is poorly understood. In 2015, following widespread flooding in the UK during winter 2013/14, Public Health England launched the English National Study of Flooding and Health. The study identified a higher prevalence of probable psychological morbidity one year after exposure to flooding. We now report findings after two years. METHODS: In year two (2016), a self-assessment questionnaire including flooding-related exposures and validated instruments to screen for probable anxiety, depression and post-traumatic stress disorder (PTSD) was sent to all participants who consented to further follow-up. Participants exposure status was categorised according to responses in year one; we assessed for exposure to new episodes of flooding and continuing flood-related problems in respondents homes. We calculated the prevalence and odds ratio for each outcome by exposure group relative to unaffected participants, adjusting for confounders. We used the McNemar test to assess change in outcomes between year one and year two. RESULTS: In year two, 1064 (70%) people responded. The prevalence of probable psychological morbidity remained elevated amongst flooded participants [n = 339] (depression 10.6%, anxiety 13.6%, PTSD 24.5%) and disrupted participants [n = 512] (depression 4.1%, anxiety 6.4%, PTSD 8.9%), although these rates were reduced compared to year one. A greater reduction in anxiety 7.6% (95% confidence interval [CI] 4.6-9.9) was seen than depression 3.8% (95% CI 1.5-6.1) and PTSD: 6.6% (95% CI 3.9-9.2). Exposure to flooding was associated with a higher odds of anxiety (adjusted odds ratio [aOR] 5.2 95%, 95% CI 1.7-16.3) and depression (aOR 8.7, 95% CI 1.9-39.8) but not PTSD. Exposure to disruption caused by flooding was not significantly associated with probable psychological morbidity. Persistent damage in the home as a consequence of the original flooding event was reported by 119 participants (14%). The odds of probable psychological morbidity amongst flooded participants who reported persistent damage, compared with those who were unaffected, were significantly higher than the same comparison amongst flooded participants who did not report persistent damage. CONCLUSIONS: This study shows a continuance of probable psychological morbidity at least two years following exposure to flooding. Commissioners and providers of health and social care services should be aware that the increased need in populations may be prolonged. Efforts to resolve persistent damage to homes may reduce the risk of probable psychological morbidity.","corpus_id":3847537,"score":1},{"doc_id":"18633629","title":"[Documentation of outpatient treatment of Paget's disease in Westphalia-Lippe. Descriptive analysis of statutory health insurance data for the year 2005].","abstract":"Dokumentation der ambulanten Morbus-Paget-Behandlung am Beispiel der Region Westfalen-Lippe: Deskriptive Analyse der Abrechnungsdaten gesetzlich Krankenversicherter für das Jahr 2005. GOAL: Inpatient health care data are often used as a source of information for health reporting in Germany, despite the fact that a lot of diseases are predominantly treated in the outpatient sector. This study provides a first overview of the outpatient care situation in relation to Paget's disease. METHOD: Outpatient care data from the Association of Statutory Health Insurance Physicians constituted the database for a descriptive analysis, capturing the state of medical care for the rare rheumatic illness Paget's disease (Osteodystrophia deformans) in the region of East Westphalia-Lippe in 2005. RESULTS: While the health report of North Rhine-Westphalia documents a total of 56 cases of M. Paget discharged from hospital for the year 2003, 166 patients suffering from Paget's disease consulted an practice-based physician in 2005 in the district of Detmold alone. The latter figure corresponds to 8.0 treated patients per 100.000 inhabitants. The treatment rates of men and women are comparable. The probability of treatment increases with advancing age. On average, patients with Paget's disease are 65.6 years old (SD=15.4 years). Almost 90% of the diagnoses of Paget's disease are classified as M88.9 according to ICD 10; more exact localisations are provided only for relatively few cases. Nearly a quarter of the cases (24.1%) are treated by general practitioners and internists. Anaesthetists treated 17.5% of the patients and orthopaedists 16.9%. In addition, ophthalmologists treat a considerable proportion of cases (12.0%). CONCLUSION: Consistent with the rareness of Paget's disease, the treatment data are as low as expected. However, the results show that routinely collected health care data allow insights into morbidity structures within the outpatient sector. It follows that for statutory health insurants (approximately 90% of the population) there should be an extension of health reporting to diseases that are mainly treated in outpatient settings.","corpus_id":26070253,"score":0},{"doc_id":"19017311","title":"Trends observed during a decade of paediatric sick visits to peripheral health facilities in rural western Kenya, 1997-2006.","abstract":"OBJECTIVES: To assess whether longitudinal surveillance in peripheral health facilities could document trends in disease burden, healthcare practice and utilization resulting from large-scale public health interventions made in the decade 1997-2006. METHODS: Data were collected from sick child visits (SCVs) among children <5 years attending 14 outpatient facilities in Asembo, rural western Kenya, during 1997-2006. Changes in proportions, and counts and rates were evaluated using chi-square and Poisson regression respectively. RESULTS: During the decade, 64 394 SCVs were made, yielding an average rate of 0.70 SCVs per child-year. The annual number of SCVs stayed constant during 1997-2003, then increased by 74% between 2003 and 2006 (P < 0.01). The time between symptom onset and SCV shortened from 5.6 days in 1997 to 4.4 days in 2006 (P < 0.01). Malaria and upper respiratory tract infection (URTI) were most commonly diagnosed (69% and 36% of SCVs respectively). Between 2003 and 2006, the proportion of SCVs with a malaria diagnosis fell from 77% to 48%, although the rate of malaria SCVs did not. URTI visits increased in 2004-2006. The most frequently prescribed antimalarials changed three times, lagging 1-2 years behind changes in national policy. Treatment of pneumonia with antibiotics varied by year, ranging from 19% to 89%. CONCLUSION: Surveillance of paediatric SCVs at peripheral health facilities was useful in documenting the timing and penetration of changes in national policies and clinical patterns of drug use for common infections. The surveillance data suggested that improved access to care, rather than disease burden changes, likely led to greater healthcare utilization after 2003.","corpus_id":11609915,"score":0},{"doc_id":"19278754","title":"National point prevalence of Clostridium difficile in US health care facility inpatients, 2008.","abstract":"BACKGROUND: Recent published estimates of Clostridium difficile infection (CDI) incidence have been based on small numbers of hospitals or national hospital discharge data. These data suggest that CDI incidence is increasing. METHODS: We conducted a point prevalence survey of C difficile in inpatients at US health care facilities. The survey was developed, received Institutional Review Board approval, and was then distributed to all Association for Professionals in Infection Control and Epidemiology, Inc (APIC) members. They were asked to complete the survey on 1 day between May 7 and August 29, 2008, reporting the number of inpatients with CDI or colonization and facility-specific information. RESULTS: Personnel at 648 hospitals completed the survey; this represents approximately 12.5% of all US acute care facilities. All but 3 states and the District of Columbia were represented (mean, 14 facilities per state; range, 2-43). Eighty-two percent reported that their CDI rate had not decreased in the past 3 years. Respondents reported 1443 C difficile-colonized/infected patients among 110,550 inpatients; the overall C difficile prevalence rate was 13.1 per 1000 inpatients (94.4% infection). Detailed data were provided on 1062 (73.6%) patients. Of these, 55.5% were female, 69.2% were >60 years of age, 67.6% had selected comorbid conditions, 79% had received antimicrobials within 30 days, and 94.4% were detected by enzyme immunoassay. The majority of patients (54.4%) were diagnosed < or =48 hours of hospitalization, but 35% had been admitted to a long-term care facility within 30 days, and 47% had been hospitalized within 90 days; 73% met Centers for Disease Control and Prevention criteria for health care-associated CDI. Most facilities (>90%) used contact isolation for CDI patients. Bleach was used for environmental disinfection more commonly during CDI outbreaks than during nonoutbreak periods. CONCLUSION: Our survey documents a higher C difficile prevalence rate than previous estimates using different methodologies. The majority of inpatient CDI appears to be health care associated. Given that not all patients with diarrhea are tested for CDI and that most facilities use enzyme immunoassays with limited sensitivity to detect C difficile, these are minimum estimates of the US health care facility C difficile burden.","corpus_id":20008678,"score":0},{"doc_id":"20209226","title":"[Association between particulate matter from biomass burning and respiratory diseases in the southern region of the Brazilian Amazon].","abstract":"Associação entre material particulado de queimadas e doenças respiratórias na região sul da Amazônia brasileira. OBJECTIVE: To investigate the short-term effects of exposure to particulate matter from biomass burning in the Amazon on the daily demand for outpatient care due to respiratory diseases in children and the elderly. METHODS: Epidemiologic study with ecologic time series design. Daily consultation records were obtained from the 14 primary health care clinics in the municipality of Alta Floresta, state of Mato Grosso, in the southern region of the Brazilian Amazon, between January 2004 and December 2005. Information on the daily levels of fine particulate matter was made available by the Brazilian National Institute for Spatial Research. To control for confounding factors (situations in which a non-causal association between exposure and disease is observed due to a third variable), variables related to time trends, seasonality, temperature, relative humidity, rainfall, and calendar effects (such as occurrence of holidays and weekends) were included in the model. Poisson regression with generalized additive models was used. RESULTS: A 10 microg/m3 increase in the level of exposure to particulate matter was associated with increases of 2.9% and 2.6% in outpatient consultations due to respiratory diseases in children on the 6th and 7th days following exposure. Significant associations were not observed for elderly individuals. CONCLUSIONS: The results suggest that the levels of particulate matter from biomass burning in the Amazon are associated with adverse effects on the respiratory health of children.","corpus_id":9557115,"score":0},{"doc_id":"20813066","title":"Development of temporal modelling for forecasting and prediction of malaria infections using time-series and ARIMAX analyses: a case study in endemic districts of Bhutan.","abstract":"BACKGROUND: Malaria still remains a public health problem in some districts of Bhutan despite marked reduction of cases in last few years. To strengthen the country's prevention and control measures, this study was carried out to develop forecasting and prediction models of malaria incidence in the endemic districts of Bhutan using time series and ARIMAX. METHODS: This study was carried out retrospectively using the monthly reported malaria cases from the health centres to Vector-borne Disease Control Programme (VDCP) and the meteorological data from Meteorological Unit, Department of Energy, Ministry of Economic Affairs. Time series analysis was performed on monthly malaria cases, from 1994 to 2008, in seven malaria endemic districts. The time series models derived from a multiplicative seasonal autoregressive integrated moving average (ARIMA) was deployed to identify the best model using data from 1994 to 2006. The best-fit model was selected for each individual district and for the overall endemic area was developed and the monthly cases from January to December 2009 and 2010 were forecasted. In developing the prediction model, the monthly reported malaria cases and the meteorological factors from 1996 to 2008 of the seven districts were analysed. The method of ARIMAX modelling was employed to determine predictors of malaria of the subsequent month. RESULTS: It was found that the ARIMA (p, d, q) (P, D, Q)s model (p and P representing the auto regressive and seasonal autoregressive; d and D representing the non-seasonal differences and seasonal differencing; and q and Q the moving average parameters and seasonal moving average parameters, respectively and s representing the length of the seasonal period) for the overall endemic districts was (2,1,1)(0,1,1)12; the modelling data from each district revealed two most common ARIMA models including (2,1,1)(0,1,1)12 and (1,1,1)(0,1,1)12. The forecasted monthly malaria cases from January to December 2009 and 2010 varied from 15 to 82 cases in 2009 and 67 to 149 cases in 2010, where population in 2009 was 285,375 and the expected population of 2010 to be 289,085. The ARIMAX model of monthly cases and climatic factors showed considerable variations among the different districts. In general, the mean maximum temperature lagged at one month was a strong positive predictor of an increased malaria cases for four districts. The monthly number of cases of the previous month was also a significant predictor in one district, whereas no variable could predict malaria cases for two districts. CONCLUSIONS: The ARIMA models of time-series analysis were useful in forecasting the number of cases in the endemic areas of Bhutan. There was no consistency in the predictors of malaria cases when using ARIMAX model with selected lag times and climatic predictors. The ARIMA forecasting models could be employed for planning and managing malaria prevention and control programme in Bhutan.","corpus_id":2172504,"score":0},{"doc_id":"20825976","title":"Short-term effect of fine particulate matter (PM 2.5) on daily mortality due to diseases of the circulatory system in Madrid (Spain).","abstract":"INTRODUCTION: Owing to their small size, fine particles, i.e., those having a diameter ≤ 2.5 μm (PM(2.5)), have a high alveolar penetration capacity, thereby triggering a local inflammatory process with circulatory repercussion. Despite being linked to respiratory and cardiovascular morbidities, there is limited evidence of an association between this type of particulate matter and short-term increases in mortality. OBJECTIVE: The aim of this study was to analyse and quantify the short-term impact of PM(2.5) on daily mortality due to diseases of the circulatory system, registered in Madrid from 1 January 2003 to 31 December 2005. METHODS: An ecological longitudinal time-series study was conducted, with risks being quantified by means of Poisson regression models. As a dependent variable, we took daily mortality registered in Madrid from 1 January 2003 to 31 December 2005, attributed to all diseases of the circulatory system as classified under heads I00-I99 of the International Classification of Diseases-10th revision (ICD-10) and broken down as follows: I21, acute myocardial infarction (AMI); I20, I22-I25, other ischemic heart diseases; and I60-I69, cerebrovascular diseases. The independent variable was daily mean PM(2.5) concentration. The other variables controlled for were: chemical pollution (PM(10), O(3), SO(2), NO(2) and NO(x)); acoustic and biotic pollution; influenza; minimum and maximum temperatures; seasonalities; trend; and autocorrelation of the series. RESULTS: A linear relationship was observed between PM(2.5) levels and mortality due to diseases of the circulatory system. For every increase of 10 μg/m(3) in daily mean PM(2.5) concentration, the relative risks (RR) were as follows: for overall circulatory mortality, associations were established at lags 2 and 6, with RR of 1.022 (1.005-1.039) and 1.025 (1.007-1.043) respectively; and for AMI mortality, there was an association at lag 6, with an RR of 1.066 (1.032-1.100). The corresponding attributable risks percent (AR%) were 2.16%, 2.47% and 6.21% respectively. No statistically significant association was found with other ischemic heart diseases or with cerebrovascular diseases. CONCLUSION: PM(2.5) concentrations are an important risk factor for daily circulatory-cause mortality in Madrid. From a public health point of view, the planning and implementation of specific measures targeted at reducing these levels constitute a pressing need.","corpus_id":37343666,"score":0},{"doc_id":"21845165","title":"Assessment of vulnerability to extreme flash floods in design storms.","abstract":"There has been an increase in the occurrence of sudden local flooding of great volume and short duration caused by heavy or excessive rainfall intensity over a small area, which presents the greatest potential danger threat to the natural environment, human life, public health and property, etc. Such flash floods have rapid runoff and debris flow that rises quickly with little or no advance warning to prevent flood damage. This study develops a flash flood index through the average of the same scale relative severity factors quantifying characteristics of hydrographs generated from a rainfall-runoff model for the long-term observed rainfall data in a small ungauged study basin, and presents regression equations between rainfall characteristics and the flash flood index. The aim of this study is to develop flash flood index-duration-frequency relation curves by combining the rainfall intensity-duration-frequency relation and the flash flood index from probability rainfall data in order to evaluate vulnerability to extreme flash floods in design storms. This study is an initial effort to quantify the flash flood severity of design storms for both existing and planned flood control facilities to cope with residual flood risks due to extreme flash floods that have ocurred frequently in recent years.","corpus_id":7559952,"score":0},{"doc_id":"22529923","title":"Acute and chronic effects of particles on hospital admissions in New-England.","abstract":"BACKGROUND: Many studies have reported significant associations between exposure to PM(2.5) and hospital admissions, but all have focused on the effects of short-term exposure. In addition all these studies have relied on a limited number of PM(2.5) monitors in their study regions, which introduces exposure error, and excludes rural and suburban populations from locations in which monitors are not available, reducing generalizability and potentially creating selection bias. METHODS: Using our novel prediction models for exposure combining land use regression with physical measurements (satellite aerosol optical depth) we investigated both the long and short term effects of PM(2.5) exposures on hospital admissions across New-England for all residents aged 65 and older. We performed separate Poisson regression analysis for each admission type: all respiratory, cardiovascular disease (CVD), stroke and diabetes. Daily admission counts in each zip code were regressed against long and short-term PM(2.5) exposure, temperature, socio-economic data and a spline of time to control for seasonal trends in baseline risk. RESULTS: We observed associations between both short-term and long-term exposure to PM(2.5) and hospitalization for all of the outcomes examined. In example, for respiratory diseases, for every 10-µg/m(3) increase in short-term PM(2.5) exposure there is a 0.70 percent increase in admissions (CI = 0.35 to 0.52) while concurrently for every 10-µg/m(3) increase in long-term PM(2.5) exposure there is a 4.22 percent increase in admissions (CI = 1.06 to 4.75). CONCLUSIONS: As with mortality studies, chronic exposure to particles is associated with substantially larger increases in hospital admissions than acute exposure and both can be detected simultaneously using our exposure models.","corpus_id":443855,"score":0},{"doc_id":"22690208","title":"Estimation of the relative severity of floods in small ungauged catchments for preliminary observations on flash flood preparedness: a case study in Korea.","abstract":"An increase in the occurrence of sudden local flooding of great volume and short duration has caused significant danger and loss of life and property in Korea as well as many other parts of the World. Since such floods usually accompanied by rapid runoff and debris flow rise quite quickly with little or no advance warning to prevent flood damage, this study presents a new flash flood indexing methodology to promptly provide preliminary observations regarding emergency preparedness and response to flash flood disasters in small ungauged catchments. Flood runoff hydrographs are generated from a rainfall-runoff model for the annual maximum rainfall series of long-term observed data in the two selected small ungauged catchments. The relative flood severity factors quantifying characteristics of flood runoff hydrographs are standardized by the highest recorded maximum value, and then averaged to obtain the flash flood index only for flash flood events in each study catchment. It is expected that the regression equations between the proposed flash flood index and rainfall characteristics can provide the basis database of the preliminary information for forecasting the local flood severity in order to facilitate flash flood preparedness in small ungauged catchments.","corpus_id":12693087,"score":0},{"doc_id":"22849236","title":"Effects of short-term exposure to air pollution on hospital admissions of young children for acute lower respiratory infections in Ho Chi Minh City, Vietnam.","abstract":"There is emerging evidence, largely from studies in Europe and North America, that economic deprivation increases the magnitude of morbidity and mortality related to air pollution. Two major reasons why this may be true are that the poor experience higher levels of exposure to air pollution, and they are more vulnerable to its effects--in other words, due to poorer nutrition, less access to medical care, and other factors, they experience more health impact per unit of exposure. The relations among health, air pollution, and poverty are likely to have important implications for public health and social policy, especially in areas such as the developing countries of Asia where air pollution levels are high and many live in poverty. The aims of this study were to estimate the effect of exposure to air pollution on hospital admissions of young children for acute lower respiratory infection (ALRI*) and to explore whether such effects differed between poor children and other children. ALRI, which comprises pneumonia and bronchiolitis, is the largest single cause of mortality among young children worldwide and is responsible for a substantial burden of disease among young children in developing countries. To the best of our knowledge, this is the first study of the health effects of air pollution in Ho Chi Minh City (HCMC), Vietnam. For these reasons, the results of this study have the potential to make an important contribution to the growing literature on the health effects of air pollution in Asia. The study focused on the short-term effects of daily average exposure to air pollutants on hospital admissions of children less than 5 years of age for ALRI, defined as pneumonia or bronchiolitis, in HCMC during 2003, 2004, and 2005. Admissions data were obtained from computerized records of Children's Hospital 1 and Children's Hospital 2 (CH1 and CH2) in HCMC. Nearly all children hospitalized for respiratory illnesses in the city are admitted to one of these two pediatric hospitals. Daily citywide 24-hour average concentrations of particulate matter (PM) < or =10 microm in aerodynamic diameter (PM10), nitrogen dioxide (NO2), and sulfur dioxide (SO2) and 8-hour maximum average concentrations of ozone (O3) were estimated from the HCMC Environmental Protection Agency (HEPA) ambient air quality monitoring network. Daily meteorologic information including temperature and relative humidity were collected from KTTV NB, the Southern Regional Hydro-Meteorological Center. An individual-level indicator of socioeconomic position (SEP) was based on the degree to which the patient was exempt from payment according to hospital financial records. A group-level indicator of SEP was based on estimates of poverty prevalence in the districts of HCMC in 2004, obtained from a poverty mapping project of the Institute of Economic Research in HCMC, in collaboration with the General Statistics Office of Vietnam and the World Bank. Poverty prevalence was defined using the poverty line set by the People's Committee of HCMC of 6 million Vietnamese dong (VND) annual income. Quartiles of district-level poverty prevalence were created based on poverty prevalence estimates for each district. Analyses were conducted using both time-series and case-crossover approaches. In the absence of measurement error, confounding, and other sources of bias, the two approaches were expected to provide estimates that differed only with regard to precision. For the time-series analyses, the unit of observation was daily counts of hospital admissions for ALRI. Poisson regression with smoothing functions for meteorologic variables and variables for seasonal and long-term trends was used. Case-crossover analyses were conducted using time-stratified selection of controls. Control days were every 7th day from the date of admission within the same month as admission. Large seasonal differences were observed in pollutant levels and hospital admission patterns during the investigation period for HCMC. Of the 15,717 ALRI admissions occurring within the study period, 60% occurred in the rainy season (May through October), with a peak in these admissions during July and August of each year. Average daily concentrations for PM10, O3, NO2, and SO2 were 73, 75, 22, and 22 microg/m3, respectively, with higher pollutant concentrations observed in the dry season (November through April) compared with the rainy season. As the time between onset of illness and hospital admission was thought to range from 1 to 6 days, it was not possible to specify a priori a single-day lag. We assessed results for single-day lags from lag 0 to lag 10, but emphasize results for an average of lag 1-6, since this best reflects the case reference period. Results were robust to differences in temperature lags with lag 0 and the average lag (1-6 days); results for lag 0 for temperature are presented. Results differed markedly when analyses were stratified by season, rather than simply adjusted for season. ALRI admissions were generally positively associated with ambient levels of PM10, NO2, and SO2 during the dry season (November-April), but not the rainy season (May-October). Positive associations between O3 and ALRI admissions were not observed in either season. We do not believe that exposure to air pollution could reduce the risk of ALRI in the rainy season and infer that these results could be driven by residual confounding present within the rainy season. The much lower correlation between NO2 and PM10 levels during the rainy season provides further evidence that these pollutants may not be accurate indicators of exposure to air pollution from combustion processes in the rainy season. Results were generally consistent across time-series and case-crossover analyses. In the dry season, risks for ALRI hospital admissions with average pollutant lag (1-6 days) were highest for NO2 and SO2 in the single-pollutant case-crossover analyses, with excess risks of 8.50% (95% CI, 0.80-16.79) and 5.85% (95% CI, 0.44-11.55) observed, respectively. NO2 and SO2 effects remained higher than PM10 effects in both the single-pollutant and two-pollutant models. The two-pollutant model indicated that NO2 confounded the PM10 and SO2 effects. For example, PM10 was weakly associated with an excess risk in the dry season of 1.25% (95% CI, -0.55 to 3.09); after adjusting for SO2 and O3, the risk estimate was reduced but remained elevated, with much wider confidence intervals; after adjusting for NO2, an excess risk was no longer observed. Though the effects seem to be driven by NO2, the statistical limitations of adequately addressing collinearity, given the high correlation between PM10 and NO2 (r = 0.78), limited our ability to clearly distinguish between PM10 and NO2 effects. In the rainy season, negative associations between PM10 and ALRI admissions were observed. No association with O3 was observed in the single-pollutant model, but O3 exposure was negatively associated with ALRI admissions in the two-pollutant model. There was little evidence of an association between NO2 and ALRI admissions. The single-pollutant estimate from the case-crossover analysis suggested a negative association between NO2 and ALRI admissions, but this effect was no longer apparent after adjustment for other pollutants. Although associations between SO2 and ALRI admissions were not observed in the rainy season, point estimates for the case-crossover analyses suggested negative associations, while time-series (Poisson regression) analyses suggested positive associations--an exception to the general consistency between case-crossover and time-series results. Results were robust to differences in seasonal classification. Inclusion of rainfall as a continuous variable and the seasonal reclassification of selected series of data did not influence results. No clear evidence of station-specific effects could be observed, since results for the different monitoring stations had overlapping confidence intervals. In the dry season, increased concentrations of NO2 and SO2 were associated with increased hospital admissions of young children for ALRI in HCMC. PM10 could also be associated with increased hospital admissions in the dry season, but the high correlation of 0.78 between PM10 and NO2 levels limits our ability to distinguish between PM10 and NO2 effects. Nevertheless, the results support the presence of an association between combustion-source pollution and increased ALRI admissions. There also appears to be evidence of uncontrolled negative confounding within the rainy season, with higher incidence of ALRI and lower pollutant concentrations overall. Exploratory analyses made using limited historical and regional data on monthly prevalence of respiratory syncytial virus (RSV) suggest that an unmeasured, time-varying confounder (RSV, in this case) could have, in an observational study like this one, created enough bias to reverse the observed effect estimates of pollutants in the rainy season. In addition, with virtually no RSV incidence in the dry season, these findings also lend some credibility to the notion that RSV could influence results primarily in the rainy season. Analyses were not able to identify differential effects by individual-level indicators of SEP, mainly due to the small number of children classified as poor based on information in the hospitals' financial records. Analyses assessing differences in effect by district-level indicator of SEP did not indicate a clear trend in risk across SEP quartiles, but there did appear to be a slightly higher risk among the residents of districts with the highest quartile of SEP. As these are the districts within the urban center of HCMC, results could be indicative of increased exposures for residents living within the city center. ( ABSTRACT TRUNCATED)","corpus_id":42144452,"score":0},{"doc_id":"23114861","title":"The burden of maternal health care expenditure in India: multilevel analysis of national data.","abstract":"To quantify the economic burden of maternal health care services on Indian households and examine the levels of expenditure incurred in public and private health care institutions at the national, state and community levels. Cross-sectional population data from the 2004 National Sample Survey Organisation were used, which considered 9,643 households for the analysis where at least one woman received maternal health care services during the year preceding the survey. Multilevel linear regression techniques were used to estimate the effect of household, cluster and state characteristics on the proportion of maternal health care expenditures over total household expenditures. Over 80 % of households reported paying for maternal health care services, with those using private care facilities paying almost 4 times more than those using public facilities. Multilevel analyses show evidence of high burden of maternal health care expenditures, which varied significantly across states according to the level of health care utilisation, and with considerable heterogeneity at the household and community levels. Maternal health care services in India are offered free at the point of delivery, yet many families face significant out-of-pocket expenditures. The recent governmental policy interventions to encourage institutional births by providing nominal financial assistance is a welcome step but this might not help to compensate mothers for other indirect expenditures, especially those living in rural areas and poorer communities who are increasingly seeking care in private facilities.","corpus_id":24907122,"score":0},{"doc_id":"24343621","title":"Can routinely collected national data on childhood morbidity and mortality from diarrhea be used to monitor health impact of rotavirus vaccination in Africa? Examination of pre-vaccine baseline data from Rwanda.","abstract":"BACKGROUND: As rotavirus vaccine is introduced into routine childhood immunization programs in Africa, understanding its impact on diarrheal disease burden is important. The objective of this analysis was to determine whether routinely collected health information on national diarrhea hospitalizations, in-hospital deaths and outpatient visits would be useful to monitor rotavirus vaccine impact. METHODS: We analyzed data for all-cause, nonbloody diarrheal disease among children <5 years of age from the routine health management information system (HMIS) in Rwanda from January 2008 through December 2011. We described trends in absolute numbers of inpatient admissions, in-hospital deaths and outpatient visits by year, age and setting. RESULTS: All-cause, nonbloody diarrheal hospitalizations and outpatient visits among children <5 years of age in Rwanda from 2008 to 2011 peaked during the June to August dry season, coinciding with the rotavirus season. The bulk of the diarrheal disease burden occurred in children <1 year of age. Health centers provided many care to children with diarrhea including 60-72% of hospitalizations and 97-99% of outpatient visits. Many in-hospital diarrheal deaths (84%) occurred in district hospitals. DISCUSSION: Given the stable and consistent trends and the prominent seasonality consistent with that of rotavirus, HMIS data should provide a useful baseline to monitor rotavirus vaccine impact on the overall diarrheal disease burden in Rwanda. Active, sentinel surveillance for rotavirus diarrhea will help interpret changes in diarrheal disease trends following vaccine introduction. Other countries planning rotavirus vaccine introduction should explore the availability and quality of their HMIS data.","corpus_id":205688700,"score":0},{"doc_id":"25849769","title":"The air quality health index and emergency department visits for urticaria in Windsor, Canada.","abstract":"Ambient air pollution exposure has been associated with several health conditions, limited not only to respiratory and cardiovascular systems but also to cutaneous tissues. However, few epidemiological studies examined pollution exposure on skin problems. Basically, the common mechanism by which pollution may affect skin physiology is by induction of oxidative stress and inflammation. Urticaria is among the skin pathologies that have been associated with pollution. Based on the combined effects of three ambient air pollutants, ozone (O₃), nitrogen dioxide (NO₂), and fine particulate matter (PM) with a median aerodynamic diameter of less than 2.5 μm (PM(2.5)), on mortality, the Air Quality Health Index (AQHI) in Canada was developed. The aim of this study was to examine the associations of short-term changes in AQHI with emergency department (ED) visits for urticaria in Windsor-area hospitals in Canada. Diagnosed ED visits were retrieved from the National Ambulatory Care Reporting System (NACRS). A time-stratified case-crossover design was applied to 2905 ED visits (males = 1215; females = 1690) for urticaria from April 2004 through December 2010. Odds ratios (OR) and their corresponding 95% confidence intervals (95%CI) for ED visits associated with increase by one unit of risk index were calculated employing conditional logistic regression. Positive and significant results were observed between AQHI levels and OR for ED visits for urticaria in Windsor for lags 2 and 3 days. A distributed lag nonlinear model technique was applied to daily counts of ED visits for lags 0 to 10 and significant results were obtained from lag 2 to lag 5 and for lag 9. These findings demonstrated associations between ambient air pollution and urticarial confirming that air pollution affects skin conditions.","corpus_id":38878944,"score":0},{"doc_id":"26020627","title":"Predicting unprecedented dengue outbreak using imported cases and climatic factors in Guangzhou, 2014.","abstract":"INTRODUCTION: Dengue is endemic in more than 100 countries, mainly in tropical and subtropical regions, and the incidence has increased 30-fold in the past 50 years. The situation of dengue in China has become more and more severe, with an unprecedented dengue outbreak hitting south China in 2014. Building a dengue early warning system is therefore urgent and necessary for timely and effective response. METHODOLOGY AND PRINCIPAL FINDINGS: In the study we developed a time series Poisson multivariate regression model using imported dengue cases, local minimum temperature and accumulative precipitation to predict the dengue occurrence in four districts of Guangzhou, China. The time series data were decomposed into seasonal, trend and remainder components using a seasonal-trend decomposition procedure based on loess (STL). The time lag of climatic factors included in the model was chosen based on Spearman correlation analysis. Autocorrelation, seasonality and long-term trend were controlled in the model. A best model was selected and validated using Generalized Cross Validation (GCV) score and residual test. The data from March 2006 to December 2012 were used to develop the model while the data from January 2013 to September 2014 were employed to validate the model. Time series Poisson model showed that imported cases in the previous month, minimum temperature in the previous month and accumulative precipitation with three month lags could project the dengue outbreaks occurred in 2013 and 2014 after controlling the autocorrelation, seasonality and long-term trend. CONCLUSIONS: Together with the sole transmission vector Aedes albopictus, imported cases, monthly minimum temperature and monthly accumulative precipitation may be used to develop a low-cost effective early warning system.","corpus_id":11245866,"score":0},{"doc_id":"26369521","title":"\"Know What to Do If You Encounter a Flash Flood\": Mental Models Analysis for Improving Flash Flood Risk Communication and Public Decision Making.","abstract":"Understanding how people view flash flood risks can help improve risk communication, ultimately improving outcomes. This article analyzes data from 26 mental models interviews about flash floods with members of the public in Boulder, Colorado, to understand their perspectives on flash flood risks and mitigation. The analysis includes a comparison between public and professional perspectives by referencing a companion mental models study of Boulder-area professionals. A mental models approach can help to diagnose what people already know about flash flood risks and responses, as well as any critical gaps in their knowledge that might be addressed through improved risk communication. A few public interviewees mentioned most of the key concepts discussed by professionals as important for flash flood warning decision making. However, most interviewees exhibited some incomplete understandings and misconceptions about aspects of flash flood development and exposure, effects, or mitigation that may lead to ineffective warning decisions when a flash flood threatens. These include important misunderstandings about the rapid evolution of flash floods, the speed of water in flash floods, the locations and times that pose the greatest flash flood risk in Boulder, the value of situational awareness and environmental cues, and the most appropriate responses when a flash flood threatens. The findings point to recommendations for ways to improve risk communication, over the long term and when an event threatens, to help people quickly recognize and understand threats, obtain needed information, and make informed decisions in complex, rapidly evolving extreme weather events such as flash floods.","corpus_id":26670560,"score":0},{"doc_id":"26752641","title":"The Mexican Cycle of Suicide: A National Analysis of Seasonality, 2000-2013.","abstract":"INTRODUCTION: Suicide is a complex and multifactorial phenomenon with growing importance to public health. An increase in its occurrence has been observed in Mexico over the past 10 years. The present article analyzes the secular trend in suicide at the national level between the years 2000 and 2013. MATERIALS AND METHODS: All suicides during the study period (n = 64,298, of which 82.11% were men) were characterized using a spectral decomposition of the time series and a wavelet analysis to evaluate the effect of seasonal changes, type of area (urban versus rural) and sex. RESULTS: A seasonal pattern was observed with statistically significant cycles every 12 months, where peaks were identified in May but only for men in urban zones as of the year 2007. In addition, specific days of the year were found to have a higher frequency of suicides, which coincided with holidays (New Year, Mother's Day, Mexican Independence Day and Christmas). CONCLUSION: A wavelet analysis can be used to decompose complex time series. To the best of our knowledge, this is the first application of this technique to the study of suicides in developing countries. This analysis enabled identifying a seasonal pattern among urban men in Mexico. The identification of seasonal patterns can help to create primary prevention strategies, increase the dissemination of crisis intervention strategies and promote mental health. These strategies could be emphasized during specific periods of the year and directed towards profiles with a higher risk.","corpus_id":20759792,"score":0},{"doc_id":"27111734","title":"Combining Healthcare-Based and Participatory Approaches to Surveillance: Trends in Diarrheal and Respiratory Conditions Collected by a Mobile Phone System by Community Health Workers in Rural Nepal.","abstract":"BACKGROUND: Surveillance systems are increasingly relying upon community-based or crowd-sourced data to complement traditional facilities-based data sources. Data collected by community health workers during the routine course of care could combine the early warning power of community-based data collection with the predictability and diagnostic regularity of facility data. These data could inform public health responses to epidemics and spatially-clustered endemic diseases. Here, we analyze data collected on a daily basis by community health workers during the routine course of clinical care in rural Nepal. We evaluate if such community-based surveillance systems can capture temporal trends in diarrheal diseases and acute respiratory infections. METHODS: During the course of their clinical activities from January to December 2013, community health workers recorded healthcare encounters using mobile phones. In parallel, we accessed condition-specific admissions from 2011-2013 in the hospital from which the community health program was based. We compared diarrhea and acute respiratory infection rates from both the hospital and the community, and assigned three categories of local disease activity (low, medium, and high) to each week in each village cluster with categories determined by tertiles. We compared condition-specific mean hospital rates across categories using ANOVA to assess concordance between hospital and community-collected data. RESULTS: There were 2,710 cases of diarrhea and 373 cases of acute respiratory infection reported by community health workers during the one-year study period. At the hospital, the average weekly incidence of diarrhea and acute respiratory infections over the three-year period was 1.8 and 3.9 cases respectively per 1,000 people in each village cluster. In the community, the average weekly rate of diarrhea and acute respiratory infections was 2.7 and 0.5 cases respectively per 1,000 people. Both diarrhea and acute respiratory infections exhibited significant differences between the three categories of disease rate burden (diarrhea p = 0.009, acute respiratory infection p = 0.001) when comparing community health worker-collected rates to hospital rates. CONCLUSION: Community-level data on diarrhea and acute respiratory infections modestly correlated with hospital data for the same condition in each village each week. Our experience suggests that community health worker-collected data on mobile phones may be a feasible adjunct to other community- and healthcare-related data sources for surveillance of such conditions. Such systems are vitally needed in resource-limited settings like rural Nepal.","corpus_id":6059743,"score":0},{"doc_id":"27686765","title":"[Impact of PM2.5 on daily outpatient numbers for respiratory diseases in Shenzhen, China].","abstract":"Objective: To assess the association between the concentration of the air pollutant PM2.5 and daily outpatient visits for respiratory disease. Methods: All records of daily outpatient visits to three hospitals in Shenzhen from January 1 to December 31, 2013 were collected. Daily air pollution monitoring and meteorology data from the same period were also collected in Shenzhen. The data were analyzed using a semiparametric generalized additive model with Poisson distribution of time series analysis controlling for long-term and seasonal trends, flu, DOW, public holidays, and meteorological factors. The excess risk(ER)of respiratory disease and its 95% CI value were calculated, along with the incremental increase of 10 μg/m(3) in PM2.5 concentration. Results: Number of outpatient visits for respiratory diseases totaled 1 428 672(daily range: 1 790-5 228). The annual average PM2.5 concentration was 40.2 μg/m(3)(daily range: 7.2-137.1 μg/m(3)). The lag1 factor had the most significant impact on the lag effect. We estimated that a 10 μ g/m(3) increase in day-before PM2.5 concentration was associated with a 1.809%(95% CI: 1.709%-1.909%)ER of visits for respiratory disease. After controlling for other pollutants(NO2, CO, and O3), the effect remained stable. When NO2, CO, and O3 were introduced separately, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of daily outpatient visits for respiratory disease was 1.814%(95% CI: 1.706%-1.923%), 2.780%(95% CI: 2.668%-2.892%), and 1.513%(95% CI: 1.403%-1.624%), respectively. With simultaneous control of NO2 and O3, NO2 and CO, and CO and O3, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of respiratory disease was 1.369%(95% CI: 1.242%-1.497%), 2.709%(95% CI: 2.590%-2.828%), and 2.577%(95% CI: 2.452%-2.702%), respectively. With simultaneous control of NO2, CO, and O3, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of respiratory disease was 2.370%(95% CI: 2.231%-2.509%). Conclusions: PM2.5 can increase the risk of outpatient visits for respiratory disease in Shenzhen.","corpus_id":20269834,"score":0},{"doc_id":"27782160","title":"Global-scale river flood vulnerability in the last 50 years.","abstract":"The impacts of flooding are expected to rise due to population increases, economic growth and climate change. Hence, understanding the physical and spatiotemporal characteristics of risk drivers (hazard, exposure and vulnerability) is required to develop effective flood mitigation measures. Here, the long-term trend in flood vulnerability was analysed globally, calculated from the ratio of the reported flood loss or damage to the modelled flood exposure using a global river and inundation model. A previous study showed decreasing global flood vulnerability over a shorter period using different disaster data. The long-term analysis demonstrated for the first time that flood vulnerability to economic losses in upper-middle, lower-middle and low-income countries shows an inverted U-shape, as a result of the balance between economic growth and various historical socioeconomic efforts to reduce damage, leading to non-significant upward or downward trends. We also show that the flood-exposed population is affected by historical changes in population distribution, with changes in flood vulnerability of up to 48.9%. Both increasing and decreasing trends in flood vulnerability were observed in different countries, implying that population growth scenarios considering spatial distribution changes could affect flood risk projections.","corpus_id":4853675,"score":0},{"doc_id":"28458242","title":"Short-term effects of ambient air pollution on pediatric outpatient visits for respiratory diseases in Yichang city, China.","abstract":"Previous studies have suggested that short-term exposure to ambient air pollution was associated with pediatric hospital admissions and emergency room visits for certain respiratory diseases; however, there is limited evidence on the association between short-term air pollution exposure and pediatric outpatient visits. Our aim was to quantitatively assess the short-term effects of ambient air pollution on pediatric outpatient visits for respiratory diseases. We conducted a time-series study in Yichang city, China between Jan 1, 2014 and Dec 31, 2015. Daily counts of pediatric respiratory outpatient visits were collected from 3 large hospitals, and then linked with air pollution data from 5 air quality monitoring stations by date. We used generalized additive Poisson models to conduct linear and nonlinear exposure-response analyses between air pollutant exposures and pediatric respiratory outpatient visits, adjusting for seasonality, day of week, public holiday, temperature, and relative humidity. Each interquartile range (IQR) increase in PM2.5 (lag 0), PM10 (lag 0), NO2 (lag 0), CO (lag 0), and O3 (lag 4) concentrations was significantly associated with a 1.91% (95% CI: 0.60%, 3.23%), 2.46% (1.09%, 3.85%), 1.88% (0.49%, 3.29%), 2.00% (0.43%, 3.59%), and 1.91% (0.45%, 3.39%) increase of pediatric respiratory outpatient visits, respectively. Similarly, the nonlinear exposure-response analyses showed monotonic increases of pediatric respiratory outpatient visits by increasing air pollutant exposures, though the associations for NO2 and CO attenuated at higher concentrations. These associations were unlikely modified by season. We did not observe significant association for SO2 exposure. Our results suggest that short-term exposures to PM2.5, PM10, NO2, CO, and O3 may account for increased risk of pediatric outpatient visits for respiratory diseases, and emphasize the needs for reduction of air pollutant exposures for children.","corpus_id":37414954,"score":0},{"doc_id":"29121954","title":"Temporal variation in confirmed diagnosis of fever-related malarial cases among children under-5 years by community health workers and in health facilities between years 2013 and 2015 in Siaya County, Kenya.","abstract":"BACKGROUND: Malaria case management continues to experience dynamic changes. Building community capacity is instrumental in both prevention and treatment of malaria. The World Health Organization (WHO) recommends utilization of well-trained and supervised community health workers (CHWs) to reduce the burden of malaria deaths among children under-5 years of age in Africa. Longitudinally-tracked information on utilization of CHWs by communities in terms of trends in diagnosis of malaria in children under-5 years of age is essential in influencing national and local malaria control policies and strategies. METHODS: A desktop review was carried out of a database consisting of confirmed uncomplicated malaria cases in 10 villages using CHWs and out-patient departments of 10 health facilities in children under-five for the period of 3 years between January 2013 and December 2015. Analyses of association between the diagnosed cases and satellite-based rainfall, village and time (months and years) were carried out using a Poisson regression model. RESULTS: Analysis of malaria diagnoses made by CHWs showed the following trends: (i) the incidence of reported documented malaria-positive fever cases increased with time (2013-2015) and the difference over the years was statistically significant (P < 0.001), (ii) specific village was significantly associated (P < 0.001) with reporting malaria-positive fever cases, (iii) the long-term monthly sequence starting from highest to lowest incidence of reported malaria-positive fever cases was July, May and June, March, August, April, September, November, and February, October and, finally, January, and the difference in reported malaria-positives between the months was statistically significant (P = 0.001) and (iv) none of the tested rainfall regimes (current, lagged or cumulative) was associated with reported malaria-positive fever cases during the 3-year period (P > 0.1). Looking at the number of diagnoses made at the health facilities, (i) The number of reported malaria-positive fever cases decreased with time (2013-2015) and the difference among the years was not statistically significant (P = 0.399), (ii) The long-term monthly sequence starting from highest to lowest number of reported malaria-positive fever cases was July, June, May, April, January, August, March, February, September, November, October and December, and the difference between the months was statistically significant (P < 0.001). CONCLUSIONS: CHWs have the potential to play a major role in diagnosing and treating malaria, thereby decreasing under-five children mortality. Temporally, the risk of diagnosing malaria seems predictable and this may present opportunities for policy-targeted malaria preparedness and control. The findings are expected to support policy actions that may scale-up community health services in remote rural settings.","corpus_id":21292417,"score":0},{"doc_id":"29440305","title":"Exposure to traffic-related air pollution and acute bronchitis in children: season and age as modifiers.","abstract":"BACKGROUND: Acute bronchitis (AB) is one of the principal causes of childhood morbidity. Increasing number of studies has shown that air pollution is an important environmental contributor of respiratory disease. However, evidence so far is scarce regarding the effects of air pollution on childhood AB, and it also remains unclear how the risk of AB will change by season and age. METHODS: Data on hospital visits for AB in children, air pollution and meteorological factors from 1 January 2015 to 31 December 2016 were collected in Hefei, China. Time-series analysis was applied to assess the short-term effects of traffic-related air pollution on childhood AB outpatient visits. A Poisson generalised linear regression model combined with a distributed lag non-linear model was used to estimate the relationships, controlling for long-term trends, seasonal patterns, meteorological factors and other possible confounders. RESULTS: We found that an IQR increase in concentrations of nitrogen dioxide, particulate matter <2.5 µm and carbon monoxide significantly increased the daily hospital visits for childhood AB with 4-day cumulative effect estimates (relative risks: 1.03, 95% CI 1.01 to 1.05; 1.09, 95% CI 1.07 to 1.11; 1.07, 95% CI 1.05 to 1.09). Notably, the risk estimates during the cold season are pronounced; however, no significant association was observed during the warm season. Interestingly, children aged 6-14 years were more vulnerable to air pollutants than children aged less than 1 year and within 1-5 years. However, no gender difference was observed. CONCLUSION: A significant association of traffic-related air pollution and increased department visits for childhood AB was observed, notably in school-age children and during the cold season.","corpus_id":46778515,"score":0},{"doc_id":"29482552","title":"Short-term effects of ambient fine particulate matter pollution on hospital visits for chronic obstructive pulmonary disease in Beijing, China.","abstract":"BACKGROUND: Little is known about the effect of ambient fine particulate matter (PM2.5) on chronic obstructive pulmonary disease (COPD) in China. The objective of this study was to explore the short-term effects of PM2.5 on outpatient and inpatient visits for COPD in Beijing, China. METHODS: A total of 3,503,313 outpatient visits and 126,982 inpatient visits for COPD between January 1, 2010, and June 30, 2012, were identified from the Beijing Medical Claim Data for Employees. A generalized additive Poisson model was applied to estimate the percentage change with 95% confidence interval (CI) in hospital visits for COPD in relation to an interquartile range (IQR) (90.8 μg/m3) increase in PM2.5 concentrations. RESULTS: Short-term exposure to PM2.5 was significantly associated with increased use of COPD-related health services. There were clear exposure-response associations of PM2.5 with COPD outpatient and inpatient visits. An IQR increase in the concurrent day PM2.5 concentrations was significantly associated with a 2.38% (95% CI, 2.22%-2.53%) and 6.03% (95% CI, 5.19%-6.87%) increase in daily outpatient visits and inpatient visits, respectively. Elderly people were more sensitive to the adverse effects. The estimated risk was higher during the warm season compared to the cool season. CONCLUSIONS: Short-term exposure to PM2.5 was associated with increased risk of hospital visits for COPD. Our findings contributed to the limited evidence concerning the effects of ambient PM2.5 on COPD morbidity in developing countries.","corpus_id":3571414,"score":0},{"doc_id":"29751419","title":"Mapping flood susceptibility in mountainous areas on a national scale in China.","abstract":"Mountainous terrain covers nearly half of China and is susceptible to floods, which can lead to substantial losses of human life and property. Historical flooding records from government bulletins and newspapers, the only available information regarding floods that have occurred in some mountainous areas, are valuable for understanding flood disaster mechanisms in these regions. In this study, the flood susceptibility in mountainous regions in China was mapped based on historical flooding records from 1949 to 2000. A Random Forest (RF) model, which can handle large datasets through factor contribution analysis, was chosen to characterize the relationships between flooding occurrences and twelve geographic, meteorological, and hydrological explanatory factors. The results indicate that the RF model can effectively identify flood-prone areas and has advantages over artificial neural network (ANN) and support vector machine (SVM) methods. Among these explanatory factors, the geographic factors (elevation, longitude and drainage density) are the most important predictors of flooding in China's mountainous areas, whereas the hydrological factors (relative elevation and curve number) are the least important. Two independent datasets of historical flooding events from the Bulletin of Flood and Drought Disasters in China (2006-2014) alongside news reports and yearbooks (2008-2014) were collected and chosen to validate the capability of the RF model. The validation results confirm that the RF model can identify the flood susceptibility with satisfactory accuracy. This study proposes a preliminary flood susceptibility map of mountainous areas in China and provides a reference for predicting and mitigating potentially disastrous flooding events.","corpus_id":21659876,"score":0}],"string":"[\n {\n \"doc_id\": \"20586021\",\n \"title\": \"Health impacts of floods.\",\n \"abstract\": \"INTRODUCTION: Floods are the most common hazard to cause disasters and have led to extensive morbidity and mortality throughout the world. The impact of floods on the human community is related directly to the location and topography of the area, as well as human demographics and characteristics of the built environment. OBJECTIVES: The aim of this study is to identify the health impacts of disasters and the underlying causes of health impacts associated with floods. A conceptual framework is developed that may assist with the development of a rational and comprehensive approach to prevention, mitigation, and management. METHODS: This study involved an extensive literature review that located >500 references, which were analyzed to identify common themes, findings, and expert views. The findings then were distilled into common themes. RESULTS: The health impacts of floods are wide ranging, and depend on a number of factors. However, the health impacts of a particular flood are specific to the particular context. The immediate health impacts of floods include drowning, injuries, hypothermia, and animal bites. Health risks also are associated with the evacuation of patients, loss of health workers, and loss of health infrastructure including essential drugs and supplies. In the medium-term, infected wounds, complications of injury, poisoning, poor mental health, communicable diseases, and starvation are indirect effects of flooding. In the long-term, chronic disease, disability, poor mental health, and poverty-related diseases including malnutrition are the potential legacy. CONCLUSIONS: This article proposes a structured approach to the classification of the health impacts of floods and a conceptual framework that demonstrates the relationships between floods and the direct and indirect health consequences.\",\n \"corpus_id\": 6702725,\n \"score\": 2\n },\n {\n \"doc_id\": \"21288358\",\n \"title\": \"Long-term effects of flooding on mortality in England and Wales, 1994-2005: controlled interrupted time-series analysis.\",\n \"abstract\": \"BACKGROUND: Limited evidence suggests that being flooded may increase mortality and morbidity among affected householders not just at the time of the flood but for months afterwards. The objective of this study is to explore the methods for quantifying such long-term health effects of flooding by analysis of routine mortality registrations in England and Wales. METHODS: Mortality data, geo-referenced by postcode of residence, were linked to a national database of flood events for 1994 to 2005. The ratio of mortality in the post-flood year to that in the pre-flood year within flooded postcodes was compared with that in non-flooded boundary areas (within 5 km of a flood). Further analyses compared the observed number of flood-area deaths in the year after flooding with the number expected from analysis of mortality trends stratified by region, age-group, sex, deprivation group and urban-rural status. RESULTS: Among the 319 recorded floods, there were 771 deaths in the year before flooding and 693 deaths in the year after (post-/pre-flood ratio of 0.90, 95% CI 0.82, 1.00). This ratio did not vary substantially by age, sex, population density or deprivation. A similar post-flood 'deficit' of deaths was suggested by the analyses based on observed/expected deaths. CONCLUSIONS: The observed post-flood 'deficit' of deaths is counter-intuitive and difficult to interpret because of the possible influence of population displacement caused by flooding. The bias that might arise from such displacement remains unquantified but has important implications for future studies that use place of residence as a marker of exposure.\",\n \"corpus_id\": 7551088,\n \"score\": 2\n },\n {\n \"doc_id\": \"21866222\",\n \"title\": \"Impacts of flood on health: epidemiologic evidence from Hanoi, Vietnam.\",\n \"abstract\": \"BACKGROUND: Vietnam is one of the most disaster-prone countries in the world. The country suffers from many kinds of natural disasters, of which the most common and serious one is flooding. Long and heavy rainfall during the last days of October and the first week of November 2008 resulted in a devastating flood unseen for over three decades in the capital city of Hanoi. It caused a substantial health impact on residents in and around the city and compromised the capacity of local health services. OBJECTIVE: The aim of this study is to ascertain the vulnerability and health impacts of the devastating flood in Hanoi by identifying the differences in mortality, injuries, and morbidity patterns (dengue, pink eye, dermatitis, psychological problems, and hypertension) between flood affected and non-affected households. DESIGN: A cross-sectional study was carried out involving 871 households in four selected communes (two heavily flood affected and two comparatively less affected) from two severely flooded districts of Hanoi. Participants were interviewed and information collected on the social, economic, and health impacts of the devastation within 1 month after the flood. RESULTS: The self-reported number of deaths and injuries reported in this study within 1 month after the heavy rainfall were a bit higher in severely affected communes as compared to that of the less affected communes of our study. The findings showed higher incidences of dengue fever, pink eye, dermatitis, and psychological problems in communes severely affected by flood as compared to that of the controlled communes. CONCLUSIONS: For people in flood prone areas (at risk for flooding), flood prevention and mitigation strategies need to be seriously thought through and acted upon, as these people are exposed to greater health problems such as psychological issues and communicable diseases such as pink eye or dermatitis.\",\n \"corpus_id\": 26599167,\n \"score\": 2\n },\n {\n \"doc_id\": \"22082995\",\n \"title\": \"Health effects of flooding in rural Bangladesh.\",\n \"abstract\": \"BACKGROUND: There is little information available on nontraumatic health risks as the result of floods, and on the factors that determine vulnerability to them (especially in low-income settings). We estimated the pattern of mortality, diarrhea, and acute respiratory infection following the 2004 floods in rural Bangladesh. METHODS: We conducted controlled interrupted time-series analysis of adverse health outcomes, from 2001 to 2007, in a cohort of 211,000 residents of the Matlab region classified as flooded or nonflooded in 2004. Ratios of mortality, diarrhea, and acute respiratory infection rates in flooded compared with nonflooded areas were calculated by week for mortality and diarrhea, and by month for acute respiratory infection. We controlled for baseline differences as well as normal seasonal patterns in the flooded and nonflooded areas. Variations in flood-related health risks were examined by age, income level, drinking-water source, latrine type, and service area. RESULTS: After fully controlling for pre-flood rate differences and for seasonality, there was no clear evidence of excesses in mortality or diarrhea risk during or after flooding. For acute respiratory infection, we found no evidence of excess risk during the flood itself but a moderate increase in risk during the 6 months after the flood (relative risk = 1.25 [95% confidence interval = 1.06-1.47]) and the subsequent 18 months. CONCLUSIONS: We found little evidence of increased risk of diarrhea or mortality following the floods, but evidence of a moderate elevation in risk of acute respiratory infection during the 2 years after flooding. The discrepancies between our results and the apparent excesses for mortality and diarrhea reported in other situations, using less- controlled estimates, emphasize the importance of stringent confounder control.\",\n \"corpus_id\": 31349784,\n \"score\": 2\n },\n {\n \"doc_id\": \"22750033\",\n \"title\": \"Floods and human health: a systematic review.\",\n \"abstract\": \"Floods are the most common type of disaster globally, responsible for almost 53,000 deaths in the last decade alone (23:1 low- versus high-income countries). This review assessed recent epidemiological evidence on the impacts of floods on human health. Published articles (2004-2011) on the quantitative relationship between floods and health were systematically reviewed. 35 relevant epidemiological studies were identified. Health outcomes were categorized into short- and long-term and were found to depend on the flood characteristics and people's vulnerability. It was found that long-term health effects are currently not well understood. Mortality rates were found to increase by up to 50% in the first year post-flood. After floods, it was found there is an increased risk of disease outbreaks such as hepatitis E, gastrointestinal disease and leptospirosis, particularly in areas with poor hygiene and displaced populations. Psychological distress in survivors (prevalence 8.6% to 53% two years post-flood) can also exacerbate their physical illness. There is a need for effective policies to reduce and prevent flood-related morbidity and mortality. Such steps are contingent upon the improved understanding of potential health impacts of floods. Global trends in urbanization, burden of disease, malnutrition and maternal and child health must be better reflected in flood preparedness and mitigation programs.\",\n \"corpus_id\": 22576348,\n \"score\": 2\n },\n {\n \"doc_id\": \"23569839\",\n \"title\": \"Infectious diseases in the aftermath of monsoon flooding in Pakistan.\",\n \"abstract\": \"Pakistan is ranked 9th in terms of flood-affected countries worldwide. In the summer of 2010, the northern province of Khyber-Pakhtunkhwa received more than 312 mm of rain in a 56 hour period. This resulted in over 1 600 deaths across the region. In addition, over 14 million people were directly affected by this record-breaking deluge. Flood affected regions serve as ideal breeding grounds for pathogens, leading to the spread of diseases. The poor standards of hygiene in camps set up for individuals displaced by the floods also contribute to this. It is essential that those involved in relief efforts are aware of the epidemiology of diseases that have historically seen a sudden upsurge after natural disasters. Keeping this in mind, we conducted a simple review of literature. An extensive literature search was conducted using the PubMed data base and online search engines. Articles published in the last 20 years were considered along with some historical articles where a background was required. Seven major diseases were identified to increase substantially in the aftermath of natural disasters. They were then classified into acute and sub-acute settings. Diarrhea, skin & eye infections and leptospirosis were identified in the acute setting while malaria, leishmaniasis, respiratory infections and hepatitis were identified in the sub-acute setting.\",\n \"corpus_id\": 42611917,\n \"score\": 2\n },\n {\n \"doc_id\": \"23762291\",\n \"title\": \"Quantitative analysis of burden of infectious diarrhea associated with floods in northwest of anhui province, china: a mixed method evaluation.\",\n \"abstract\": \"BACKGROUND: Persistent and heavy rainfall in the upper and middle Huaihe River of China brought about severe floods during the end of June and July 2007. However, there has been no assessment on the association between the floods and infectious diarrhea. This study aimed to quantify the impact of the floods in 2007 on the burden of disease due to infectious diarrhea in northwest of Anhui Province. METHODS: A time-stratified case-crossover analysis was firstly conducted to examine the relationship between daily cases of infectious diarrhea and the 2007 floods in Fuyang and Bozhou of Anhui Province. Odds ratios (ORs) of the flood risk were quantified by conditional logistic regression. The years lived with disability (YLDs) of infectious diarrhea attributable to floods were then estimated based on the WHO framework of the calculating potential impact fraction in the Burden of Disease study. RESULTS: A total of 197 infectious diarrheas were notified during the exposure and control periods in the two study areas. The strongest effect was shown with a 2-day lag in Fuyang and a 5-day lag in Bozhou. Multivariable analysis showed that floods were significantly associated with an increased risk of the number cases of infectious diarrhea (OR = 3.175, 95%CI: 1.126-8.954 in Fuyang; OR = 6.754, 95%CI: 1.954-23.344 in Bozhou). Attributable YLD per 1000 of infectious diarrhea resulting from the floods was 0.0081 in Fuyang and 0.0209 in Bozhou. CONCLUSIONS: Our findings confirm that floods have significantly increased the risks of infectious diarrhea in the study areas. In addition, prolonged moderate flood may cause more burdens of infectious diarrheas than severe flood with a shorter duration. More attention should be paid to particular vulnerable groups, including younger children and elderly, in developing public health preparation and intervention programs. Findings have significant implications for developing strategies to prevent and reduce health impact of floods.\",\n \"corpus_id\": 14485419,\n \"score\": 2\n },\n {\n \"doc_id\": \"24073902\",\n \"title\": \"Flood-related skin diseases: a literature review.\",\n \"abstract\": \"Flood is one of the most common natural disasters, which commonly occurs in all parts of the world. The effects of the disasters considerably become enormous problems to overall public health systems. Flood-related skin diseases are a portion of these consequences presenting with cutaneous manifestations and/or signs of systemic illnesses. We conducted a systematic literature review of research publications relating to flooding and skin diseases. The purpose of this review was to provide dermatologists as well as general practitioners with comprehensive conditions of flood-related skin diseases and suggested treatments. Moreover, we categorized these flood-related diseases into four groups comprising inflammatory skin diseases, skin infections, traumatic skin diseases, and other miscellaneous skin diseases in a bid to implement early interventions and educate, prevent, and efficaciously handle those skin diseases under such a catastrophic situation so that better treatment outcomes and prevention of further complications could be ultimately achieved and accomplished.\",\n \"corpus_id\": 20986687,\n \"score\": 2\n },\n {\n \"doc_id\": \"24625900\",\n \"title\": \"[Climate changes, floods, and health consequences].\",\n \"abstract\": \"Cambiamenti climatici, alluvioni e impatto sulla salute. In the European Region, floods are the most common natural disaster, causing extensive damage and disruption. In Italy, it has been estimated that over 68% of municipalities are at high hydrogeological risk and with the recent intense rainfall events local populations have been facing severe disruptions. The health consequences of floods are wide ranging and are dependent upon the vulnerability of the environment and the local population. Health effects can be a direct or indirect consequence of flooding. The immediate health impacts of floods include drowning, heart attacks, injuries and hypothermia. The indirect effects include, injuries and infections, water-borne infectious disease, mental health problems, respiratory disease and allergies in both the medium and long term after a flood. Future efforts should be addressed to integrate health preparedness and prevention measures into emergency flood plans and hydrological warning systems.\",\n \"corpus_id\": 10403883,\n \"score\": 2\n },\n {\n \"doc_id\": \"25098726\",\n \"title\": \"Impacts of floods on dysentery in Xinxiang city, China, during 2004-2010: a time-series Poisson analysis.\",\n \"abstract\": \"BACKGROUND: Xinxiang, a city in Henan Province, suffered from frequent floods due to persistent and heavy precipitation from 2004 to 2010. In the same period, dysentery was a common public health problem in Xinxiang, with the proportion of reported cases being the third highest among all the notified infectious diseases. OBJECTIVES: We focused on dysentery disease consequences of different degrees of floods and examined the association between floods and the morbidity of dysentery on the basis of longitudinal data during the study period. DESIGN: A time-series Poisson regression model was conducted to examine the relationship between 10 times different degrees of floods and the monthly morbidity of dysentery from 2004 to 2010 in Xinxiang. Relative risks (RRs) of moderate and severe floods on the morbidity of dysentery were calculated in this paper. In addition, we estimated the attributable contributions of moderate and severe floods to the morbidity of dysentery. RESULTS: A total of 7591 cases of dysentery were notified in Xinxiang during the study period. The effect of floods on dysentery was shown with a 0-month lag. Regression analysis showed that the risk of moderate and severe floods on the morbidity of dysentery was 1.55 (95% CI: 1.42-1.670) and 1.74 (95% CI: 1.56-1.94), respectively. The attributable risk proportions (ARPs) of moderate and severe floods to the morbidity of dysentery were 35.53 and 42.48%, respectively. CONCLUSIONS: This study confirms that floods have significantly increased the risk of dysentery in the study area. In addition, severe floods have a higher proportional contribution to the morbidity of dysentery than moderate floods. Public health action should be taken to avoid and control a potential risk of dysentery epidemics after floods.\",\n \"corpus_id\": 7536430,\n \"score\": 2\n },\n {\n \"doc_id\": \"25282279\",\n \"title\": \"Association between annual river flood pulse and paediatric hospital admissions in the Mekong Delta area.\",\n \"abstract\": \"The Mekong Delta is the most vulnerable region to extreme climate and hydrological conditions however the association between these conditions and children's health has been little studied. We examine the association between annual river flood pulse and paediatric hospital admissions in a Vietnam Mekong Delta city. Daily paediatric hospital admissions (PHA) were collected from the City Paediatric Hospital, and daily river water level (RWL) and meteorological data were retrieved from the Southern Regional Hydro-Meteorological Centre from 2008 to 2011. We evaluated the association between annual river flood pulse (>=90th percentile of RWL) and PHA using the Poisson distributed lag model, controlling for temperature, relative humidity, day of week, seasonal and long-term trends. The seasonal pattern of PHA was examined using harmonic and polynomial regression models. The cumulative risk ratios estimated for a 15-day period following an extreme RWL was 1.26 (95%CI, 1.2-1.38) for all age groups, 1.27 (95%CI, 1.23-1.30) for under five-years and 1.15 (95%CI, 1.07-1.20) for school-aged children, 1.24 (95%CI, 1.21-1.27) for all-causes, 1.18 (95%CI, 1.12-1.21) for communicable infection, 1.66 (95%CI, 1.57-1.74) for respiratory infection and 1.06 (95%CI, 1.01-1.1) for other diseases. The peak PHA risk is in the September-October period corresponding to the highest RWL, and the PHA-RWL association was modified by temperature. An increase in PHA is significantly associated with annual river flood, and the pattern of PHA is seasonally correspondent to the RWL. These findings combined with projected changes in climate conditions suggest important implications of climate change for human health in the Mekong Delta region.\",\n \"corpus_id\": 18685357,\n \"score\": 2\n },\n {\n \"doc_id\": \"25329916\",\n \"title\": \"Flooding and emergency room visits for gastrointestinal illness in Massachusetts: a case-crossover study.\",\n \"abstract\": \"INTRODUCTION: Floods and other severe weather events are anticipated to increase as a result of global climate change. Floods can lead to outbreaks of gastroenteritis and other infectious diseases due to disruption of sewage and water infrastructure and impacts on sanitation and hygiene. Floods have also been indirectly associated with outbreaks through population displacement and crowding. METHODS: We conducted a case-crossover study to investigate the association between flooding and emergency room visits for gastrointestinal illness (ER-GI) in Massachusetts for the years 2003 through 2007. We obtained ER-GI visits from the State of Massachusetts and records of floods from the National Oceanic and Atmospheric Association's Storm Events Database. ER-GI visits were considered exposed if a flood occurred in the town of residence within three hazard periods of the visit: 0-4 days; 5-9 days; and 10-14 days. A time-stratified bi-directional design was used for control selection, matching on day of the week with two weeks lead or lag time from the ER-GI visit. Fixed effect logistic regression models were used to estimate the risk of ER-GI visits following the flood. RESULTS AND CONCLUSIONS: A total of 270,457 ER-GI visits and 129 floods occurred in Massachusetts over the study period. Across all counties, flooding was associated with an increased risk for ER-GI in the 0-4 day period after flooding (Odds Ratio: 1.08; 95% Confidence Interval: 1.03-1.12); but not the 5-9 days (Odds Ratio: 0.995; 95% Confidence Interval: 0.955-1.04) or the 10-14 days after (Odds Ratio: 0.966, 95% Confidence Interval: 0.927-1.01). Similar results were observed for different definitions of ER-GI. The effect differed across counties, suggesting local differences in the risk and impact of flooding. Statewide, across the study period, an estimated 7% of ER-GI visits in the 0-4 days after a flood event were attributable to flooding.\",\n \"corpus_id\": 6722447,\n \"score\": 2\n },\n {\n \"doc_id\": \"25546280\",\n \"title\": \"Water-borne diseases and extreme weather events in Cambodia: review of impacts and implications of climate change.\",\n \"abstract\": \"Cambodia is prone to extreme weather events, especially floods, droughts and typhoons. Climate change is predicted to increase the frequency and intensity of such events. The Cambodian population is highly vulnerable to the impacts of these events due to poverty; malnutrition; agricultural dependence; settlements in flood-prone areas, and public health, governance and technological limitations. Yet little is known about the health impacts of extreme weather events in Cambodia. Given the extremely low adaptive capacity of the population, this is a crucial knowledge gap. A literature review of the health impacts of floods, droughts and typhoons in Cambodia was conducted, with regional and global information reviewed where Cambodia-specific literature was lacking. Water-borne diseases are of particular concern in Cambodia, in the face of extreme weather events and climate change, due to, inter alia, a high pre-existing burden of diseases such as diarrhoeal illness and a lack of improved sanitation infrastructure in rural areas. A time-series analysis under quasi-Poisson distribution was used to evaluate the association between floods and diarrhoeal disease incidence in Cambodian children between 2001 and 2012 in 16 Cambodian provinces. Floods were significantly associated with increased diarrhoeal disease in two provinces, while the analysis conducted suggested a possible protective effect from toilets and piped water. Addressing the specific, local pre-existing vulnerabilities is vital to promoting population health resilience and strengthening adaptive capacity to extreme weather events and climate change in Cambodia.\",\n \"corpus_id\": 22563372,\n \"score\": 2\n },\n {\n \"doc_id\": \"26090609\",\n \"title\": \"Flooding and Clostridium difficile Infection: A Case-Crossover Analysis.\",\n \"abstract\": \"Clostridium difficile is a bacterium that can spread by water. It often causes acute gastrointestinal illness in older adults who are hospitalized and/or receiving antibiotics; however, community-associated infections affecting otherwise healthy individuals have become more commonly reported. A case-crossover study was used to assess emergency room (ER) and outpatient visits for C. difficile infection following flood events in Massachusetts from 2003 through 2007. Exposure status was based on whether or not a flood occurred prior to the case/control date during the following risk periods: 0-6 days, 7-13 days, 14-20 days, and 21-27 days. Fixed-effects logistic regression was used to estimate the risk of diagnosis with C. difficile infection following a flood. There were 129 flood events and 1575 diagnoses of C. difficile infection. Among working age adults (19-64 years), ER and outpatient visits for C. difficile infection were elevated during the 7-13 days following a flood (Odds Ratio, OR = 1.69; 95% Confidence Interval, CI: 0.84, 3.37). This association was more substantial among males (OR = 3.21; 95% CI: 1.01-10.19). Associations during other risk periods were not observed (p < 0.05). Although we were unable to differentiate community-associated versus nosocomial infections, a potential increase in C. difficile infections should be considered as more flooding is projected due to climate change.\",\n \"corpus_id\": 23708504,\n \"score\": 2\n },\n {\n \"doc_id\": \"26159354\",\n \"title\": \"The Infectious and Noninfectious Dermatological Consequences of Flooding: A Field Manual for the Responding Provider.\",\n \"abstract\": \"Meteorological data show that disastrous floods are increasingly frequent and more severe in recent years, perhaps due to climatic changes such as global warming. During and after a flood disaster, traumatic injuries, communicable diseases, chemical exposures, malnutrition, decreased access to care, and even mental health disorders dramatically increase, and many of these have dermatological manifestations. Numerous case reports document typical and atypical cutaneous infections, percutaneous trauma, immersion injuries, noninfectious contact exposures, exposure to wildlife, and exacerbation of underlying skin diseases after such disasters as the 2004 Asian tsunami, Hurricane Katrina in 2005, and the 2010 Pakistan floods. This review attempts to provide a basic field manual of sorts to providers who are engaged in care after a flooding event, with particular focus on the infectious consequences. Bacterial pathogens such as Staphylococcus and Streptococcus are still common causes of skin infections after floods, with atypical bacteria also greatly increased. Vibrio vulnificus is classically associated with exposure to saltwater or brackish water. It may present as necrotizing fasciitis with hemorrhagic bullae, and treatment consists of doxycycline or a quinolone, plus a third-generation cephalosporin and surgical debridement. Atypical mycobacterial infections typically produce indolent cutaneous infections, possibly showing sporotrichoid spread. A unique nontuberculous infection called spam has recently been identified in Satowan Pacific Islanders; combination antibiotic therapy is recommended. Aeromonas infection is typically associated with freshwater exposure and, like Vibrio infections, immunocompromised or cirrhotic patients are at highest risk for severe disease, such as necrotizing fasciitis and sepsis. Various antibiotics can be used to treat Aeromonas infections. Melioidosis is seen mainly in Southeast Asia and Australia, particularly in rice farmers, and can remain latent for many years before presenting as the host's immunocompetence wanes. It can present with a variety of skin findings or as a nonspecific febrile illness, and preferred treatment consists of ceftazidime or a carbapenem with trimethoprim/sulfamethoxazole (TMP/SMX) for 2 weeks, then continuing TMP/SMX for at least 3 months. Leptospirosis is a waterborne zoonosis that is often prevalent after heavy rains or flooding. Different forms exist, including Fort Bragg fever, which produces a distinctive erythematous papular rash on the shins. Doxycycline is often sufficient; however, volume and potassium repletion may be necessary if renal involvement exists. Chromobacterium violaceum infection may occur after open skin is exposed to stagnant or muddy water. Cultured colonies produce a unique violacein pigment, and treatment typically consists of a carbapenem. Both typical and atypical fungal infections are increased in the flooding disaster scenario, such as dermatophytosis, chromoblastomycosis, blastomycosis, and mucormycosis. Appropriate antifungals should be used. In addition, land inundated with water expands the habitat for parasites and/or vectors, thus increased vigilance for regional parasitic infections is necessary after a flood. Lastly, noninfectious consequences of a flooding disaster are also common and include miliaria, immersion foot syndromes, irritant and allergic contact dermatitis, traumatic wounds and animal bites, and arthropod assault, as well as exacerbation of existing skin conditions such as atopic dermatitis, psoriasis, and alopecia areata due to increased stress or nonavailability of daily medications.\",\n \"corpus_id\": 35243897,\n \"score\": 2\n },\n {\n \"doc_id\": \"26861372\",\n \"title\": \"Flood-Exposure is Associated with Higher Prevalence of Child Undernutrition in Rural Eastern India.\",\n \"abstract\": \"BACKGROUND: Child undernutrition and flooding are highly prevalent public health issues in Asia, yet epidemiological studies investigating this association are lacking. METHODS: To investigate to what extent floods exacerbate poor nutritional status in children and identify most vulnerable groups, we conducted a population-based survey of children aged 6-59 months inhabiting flooded and non-flooded communities of the Jagatsinghpur district, Odisha (India), one year after large floods in 2008. Anthropometric measurements on 879 children and child, parental and household level variables were collected through face-to-face interviews in September 2009. The association between flooding and the prevalence of wasting, stunting and underweight was examined using weighted multivariate logistic regression for children inhabiting communities exposed solely to floods in 2008 and those communities repeatedly flooded (2006 and 2008) controlling for parental education and other relevant variables. We examined the influence of age on this association. Propensity score matching was conducted to test the robustness of our findings. RESULTS: The prevalence of wasting among children flooded in 2006 and 2008 was 51.6%, 41.4% in those flooded only in 2008, and 21.2% in children inhabiting non-flooded communities. Adjusting by confounders, the increased prevalence relative to non-flooded children in the exposed groups were 2.30 (adjusted prevalence ratio (aPR); 95% CI: 1.86, 2.85) and 1.94 (95% CI: 1.43, 2.63), respectively. Among repeatedly flooded communities, cases of severe wasting in children were 3.37 times more prevalent than for children inhabiting in those non-flooded (95% CI: 2.34, 4.86) and nearly twice more prevalent relative to those flooded only once. Those children younger than one year during previous floods in 2006 showed the largest difference in prevalence of wasting compared to their non-flooded counterparts (aPR: 4.01; 95% CI: 1.51, 10.63). RESULTS were robust to alternative adjusted models and in propensity score matching analyses. For similar analyses, no significant associations were found for child stunting, and more moderate effects were observed in the case of child underweight. CONCLUSIONS: Particularly in low-resource or subsistence-farming rural settings, long-lasting nutritional response in the aftermath of floods should be seriously considered to counteract the long-term nutritional effects on children, particularly infants, and include their mothers on whom they are dependent. The systematic monitoring of nutritional status in these groups might help to tailor efficient responses in each particular context.\",\n \"corpus_id\": 11499747,\n \"score\": 2\n },\n {\n \"doc_id\": \"27171415\",\n \"title\": \"Risk of Flood-Related Diseases of Eyes, Skin and Gastrointestinal Tract in Taiwan: A Retrospective Cohort Study.\",\n \"abstract\": \"Floods are known to cause serious environmental damage and health impacts. Studies on flood-related diseases have been primarily on individual events, and limited evidence could be drawn on potential health impacts from floods using large population data. This study used reimbursement records of one million people of the Taiwan National Health Insurance program to compare incident diseases of the eyes, skin and gastrointestinal (GI) tract associated with floods. Incidence rates for the selected diseases were calculated according to outpatient/emergency visit data. The incidence rates were evaluated by flood status: in 10 days before floods, during floods and within 10 days after the floods receded. Outpatient/emergency visit rates for the eye, skin and GI tract diseases were highest after floods and lowest during floods. Results from multivariate Poisson regression analyses showed that, when compared with the incidence in 10 days before floods, the incidence rate ratios (IRR) of diseases within 10 days after floods were 1.15 (95% confidence interval (CI) = 1.10-1.20) for eyes, 1.08 (95% C.I. = 1.05-1.10) for skin, and 1.11 (95% CI = 1.08-1.14) for GI tract, after controlling for covariates. All risks increased with ambient temperature. V-shaped trends were found between age and eye diseases, and between age and GI tract diseases. In contrast, the risk of skin diseases increased with age. In conclusion, more diseases of eyes, skin and GI tract could be diagnosed after the flood.\",\n \"corpus_id\": 6240652,\n \"score\": 2\n },\n {\n \"doc_id\": \"27174415\",\n \"title\": \"Projections of hepatitis A virus infection associated with flood events by 2020 and 2030 in Anhui Province, China.\",\n \"abstract\": \"Assessing and responding to health risk of climate change is important because of its impact on the natural and societal ecosystems. More frequent and severe flood events will occur in China due to climate change. Given that population is projected to increase, more people will be vulnerable to flood events, which may lead to an increased incidence of HAV infection in the future. This population-based study is going to project the future health burden of HAV infection associated with flood events in Huai River Basin of China. The study area covered four cities of Anhui province in China, where flood events were frequent. Time-series adjusted Poisson regression model was developed to quantify the risks of flood events on HAV infection based on the number of daily cases during summer seasons from 2005 to 2010, controlling for other meteorological variables. Projections of HAV infection in 2020 and 2030 were estimated based on the scenarios of flood events and demographic data. Poisson regression model suggested that compared with the periods without flood events, the risks of severe flood events for HAV infection were significant (OR = 1.28, 95 % CI 1.05-1.55), while risks were not significant from moderate flood events (OR = 1.16, 95 % CI 0.72-1.87) and mild flood events (OR = 1.14, 95 % CI 0.87-1.48). Using the 2010 baseline data and the flood event scenarios (one severe flood event), increased incidence of HAV infection were estimated to be between 0.126/10(5) and 0.127/10(5) for 2020. Similarly, the increased HAV infection incidence for 2030 was projected to be between 0.382/10(5) and 0.399/10(5). Our study has, for the first time, quantified the increased incidence of HAV infection that will result from flood events in Anhui, China, in 2020 and 2030. The results have implications for public health preparation for developing public health responses to reduce HAV infection during future flood events.\",\n \"corpus_id\": 7724237,\n \"score\": 2\n },\n {\n \"doc_id\": \"27312685\",\n \"title\": \"Short-term impacts of floods on enteric infectious disease in Qingdao, China, 2005-2011.\",\n \"abstract\": \"The current study aimed to examine the relationship between floods and the three enteric infectious diseases, namely bacillary dysentery (BD), hand-foot-mouth disease (HFMD) and other infectious diarrhoea (OID) in Qingdao, China. Relative risks (RRs) and 95% confidence intervals (CIs) of floods on BD, HFMD and OID were calculated using a quasi-Poisson generalized linear model, adjusting for daily average temperature, daily average relative humidity, and seasonal and long-term temporal trends. Two separate models within two different periods were designed. Model 1 for the summer period showed that floods were positively associated with BD for 4- to 12-day lags, with the greatest effects for 7-day (RR 1·41, 95% CI 1·22-1·62) and 11-day (RR 1·42, 95% CI 1·22-1·64) lags. Similar findings were found in model 2 for the whole study period for 5- to 12-day lags. However, HFMD and OID were not significantly associated with floods in both models. Results from this study will provide insight into the health risks associated with floods and may help inform public health precautionary measures for such disasters.\",\n \"corpus_id\": 19186183,\n \"score\": 2\n },\n {\n \"doc_id\": \"28606191\",\n \"title\": \"No Calm After the Storm: A Systematic Review of Human Health Following Flood and Storm Disasters.\",\n \"abstract\": \"Introduction How the burden of disease varies during different phases after floods and after storms is essential in order to guide a medical response, but it has not been well-described. The objective of this review was to elucidate the health problems following flood and storm disasters. METHODS: A literature search of the databases Medline (US National Library of Medicine, National Institutes of Health; Bethesda, Maryland USA); Cinahl (EBSCO Information Services; Ipswich, Massachusetts USA); Global Health (EBSCO Information Services; Ipswich, Massachusetts USA); Web of Science Core Collection (Thomson Reuters; New York, New York USA); Embase (Elsevier; Amsterdam, Netherlands); and PubMed (National Center for Biotechnology Information, National Institutes of Health; Bethesda, Maryland USA) was conducted in June 2015 for English-language research articles on morbidity or mortality and flood or storm disasters. Articles on mental health, interventions, and rescue or health care workers were excluded. Data were extracted from articles that met the eligibility criteria and analyzed by narrative synthesis. RESULTS: The review included 113 studies. Poisonings, wounds, gastrointestinal infections, and skin or soft tissue infections all increased after storms. Gastrointestinal infections were more frequent after floods. Leptospirosis and diabetes-related complications increased after both. The majority of changes occurred within four weeks of floods or storms. CONCLUSION: Health changes differently after floods and after storms. There is a lack of data on the health effects of floods alone, long-term changes in health, and the strength of the association between disasters and health problems. This review highlights areas of consideration for medical response and the need for high-quality, systematic research in this area. Saulnier DD , Brolin Ribacke K , von Schreeb J . No calm after the storm: a systematic review of human health following flood and storm disasters. Prehosp Disaster Med. 2017;32(5):1-12.\",\n \"corpus_id\": 13147929,\n \"score\": 2\n },\n {\n \"doc_id\": \"29339262\",\n \"title\": \"The long-term physical and psychological health impacts of flooding: A systematic mapping.\",\n \"abstract\": \"BACKGROUND: Flooding has caused significant and wide ranging long-term health impacts for affected populations. However, until now, the long-term health outcomes, epidemiological trends and specific impact factors of flooding had not been identified. In this study, the relevant literature was systematically mapped to create the first synthesis of the evidence of the long-term health impacts of flooding. METHODS: The systematic mapping method was used to collect and categorize all the relevant literature. A study was included if it had a description or measurement of health impacts over six months after flooding. The search was limited to peer reviewed articles and grey literature written in English, published from 1996 to 2016. RESULTS: A total of 56 critical articles were extracted for the final map, including 5 qualitative and 51 quantitative studies. Most long-term studies investigated the psychological impacts of flooding, including PTSD, depression, anxiety, psychiatric disorders, sleep disorder and suicide. Others investigated the physiological impacts, including health-related quality of life, acute myocardial infarction, chronic diseases, and malnutrition. Social support was proved to be protective factors that can improve health outcomes in the long-term after flooding. To date, there have been relatively few reviews had focused on the long-term health impacts of flooding. This study coded and catalogued the existing evidence across a wide range of variables and described the long-term health consequences within a conceptual map. DISCUSSION AND CONCLUSIONS: Although there was no boundary between the short-term and the long-term impacts of flooding, the identified health outcomes in this systematic mapping could be used to define long-term health impacts. The studies showed that the prevalence of psychological diseases had a reversed increasing trend occurred even in the long-term in relatively poor post-flooding environments. Further cohort or longitudinal research focused on disability, chronic diseases, relocation population, and social interventions after flooding, are urgently required.\",\n \"corpus_id\": 3862968,\n \"score\": 2\n },\n {\n \"doc_id\": \"29734967\",\n \"title\": \"Floods Increase the Risks of Hand-Foot-Mouth Disease in Qingdao, China, 2009-2013: A Quantitative Analysis.\",\n \"abstract\": \"BACKGROUND: We aimed to quantify the impact of few times floods on hand-foot-mouth disease (HFMD) in Qingdao during 2009-2013. METHODS: The Spearman correlation test was applied to examine the lagged effects of floods on monthly morbidity of HFMD during study period in Qingdao. We further quantified the effects of 5 flood events on the morbidity of HFMD using the time-series Poisson regression controlling for climatic factors, seasonality, and lagged effects among different populations. RESULTS: A total of 55,920 cases of HFMD were reported in the study region over the study period. The relative risks of floods on the morbidity of HFMD among the total population, males, females, under 1-2 years old, and 3-5 years old were 1.178, 1.165, 1.198, 1.338, and 1.245, respectively. CONCLUSIONS: This study has, for the first time, provided the positive evidence of the impact of floods on HFMD. It demonstrates that floods can significantly increase the risk of HFMD during study period. Additionally, among the different populations, the risks were higher among children under 1-5 years old. ( Disaster Med Public Health Preparedness. 2018;12:723-729).\",\n \"corpus_id\": 13682854,\n \"score\": 2\n },\n {\n \"doc_id\": \"22435044\",\n \"title\": \"Prepared to react? Assessing the functional capacity of the primary health care system in rural Orissa, India to respond to the devastating flood of September 2008.\",\n \"abstract\": \"BACKGROUND: Early detection of an impending flood and the availability of countermeasures to deal with it can significantly reduce its health impacts. In developing countries like India, public primary health care facilities are frontline organizations that deal with disasters particularly in rural settings. For developing robust counter reacting systems evaluating preparedness capacities within existing systems becomes necessary. OBJECTIVE: The objective of the study is to assess the functional capacity of the primary health care system in Jagatsinghpur district of rural Orissa in India to respond to the devastating flood of September 2008. METHODS: An onsite survey was conducted in all 29 primary and secondary facilities in five rural blocks (administrative units) of Jagatsinghpur district in Orissa state. A pre-tested structured questionnaire was administered face to face in the facilities. The data was entered, processed and analyzed using STATA(®) 10. RESULTS: Data from our primary survey clearly shows that the healthcare facilities are ill prepared to handle the flood despite being faced by them annually. Basic utilities like electricity backup and essential medical supplies are lacking during floods. Lack of human resources along with missing standard operating procedures; pre-identified communication and incident command systems; effective leadership; and weak financial structures are the main hindering factors in mounting an adequate response to the floods. CONCLUSION: The 2008 flood challenged the primary curative and preventive health care services in Jagatsinghpur. Simple steps like developing facility specific preparedness plans which detail out standard operating procedures during floods and identify clear lines of command will go a long way in strengthening the response to future floods. Performance critiques provided by the grass roots workers, like this one, should be used for institutional learning and effective preparedness planning. Additionally each facility should maintain contingency funds for emergency response along with local vendor agreements to ensure stock supplies during floods. The facilities should ensure that baseline public health standards for health care delivery identified by the Government are met in non-flood periods in order to improve the response during floods. Building strong public primary health care systems is a development challenge. The recovery phases of disasters should be seen as an opportunity to expand and improve services and facilities.\",\n \"corpus_id\": 12538378,\n \"score\": 1\n },\n {\n \"doc_id\": \"23994865\",\n \"title\": \"High temperature as a risk factor for infectious diarrhea in Shanghai, China.\",\n \"abstract\": \"BACKGROUND: Recent studies indicate that ambient temperature could be a risk factor for infectious diarrhea, but evidence for such a relation is limited in China. METHODS: We investigated the short-term association between daily temperature and physician-diagnosed infectious diarrhea during 2008-2010 in Shanghai, China. We adopted a time-series approach to analyze the data and a quasi-Poisson regression model with a natural spline-smoothing function to adjust for long-term and seasonal trends, as well as other time-varying covariates. RESULTS: There was a significant association between temperature and outpatient visits for diarrhea. A 1°C increase in the 6-day moving average of temperature was associated with a 2.68% (95% CI: 1.83%, 3.52%) increase in outpatient visits for diarrhea. We did not find a significant association between rainfall and infectious diarrhea. CONCLUSIONS: High temperature might be a risk factor for infectious diarrhea in Shanghai. Public health programs should focus on preventing diarrhea related to high temperature among city residents.\",\n \"corpus_id\": 17545497,\n \"score\": 1\n },\n {\n \"doc_id\": \"24336027\",\n \"title\": \"Factors increasing vulnerability to health effects before, during and after floods.\",\n \"abstract\": \"Identifying the risk factors for morbidity and mortality effects pre-, during and post-flood may aid the appropriate targeting of flood-related adverse health prevention strategies. We conducted a systematic PubMed search to identify studies examining risk factors for health effects of precipitation-related floods, among Organisation for Economic Co-Operation and Development (OECD) member countries. Research identifying flood-related morbidity and mortality risk factors is limited and primarily examines demographic characteristics such as age and gender. During floods, females, elderly and children appear to be at greater risk of psychological and physical health effects, while males between 10 to 29 years may be at greater risk of mortality. Post-flood, those over 65 years and males are at increased risk of physical health effects, while females appear at greater risk of psychological health effects. Other risk factors include previous flood experiences, greater flood depth or flood trauma, existing illnesses, medication interruption, and low education or socio-economic status. Tailoring messages to high-risk groups may increase their effectiveness. Target populations differ for morbidity and mortality effects, and differ pre-, during, and post-flood. Additional research is required to identify the risk factors associated with pre- and post-flood mortality and post-flood morbidity, preferably using prospective cohort studies.\",\n \"corpus_id\": 5249566,\n \"score\": 1\n },\n {\n \"doc_id\": \"25511879\",\n \"title\": \"Primary healthcare system capacities for responding to storm and flood-related health problems: a case study from a rural district in central Vietnam.\",\n \"abstract\": \"BACKGROUND: As a tropical depression in the East Sea, Vietnam is greatly affected by climate change and natural disasters. Knowledge of the current capacity of the primary healthcare system in Vietnam to respond to health issues associated with storms and floods is very important for policy making in the country. However, there has been little scientific research in this area. OBJECTIVE: This research was to assess primary healthcare system capacities in a rural district in central Vietnam to respond to such health issues. DESIGN: This was a cross-sectional descriptive study using quantitative and qualitative approaches. Quantitative methods used self-administered questionnaires. Qualitative methods (in-depth interviews and focus groups discussions) were used to broaden understanding of the quantitative material and to get additional information on actions taken. RESULTS: 1) Service delivery: Medical emergency services, especially surgical operations and referral systems, were not always available during the storm and flood seasons. 2) Governance: District emergency plans focus largely on disaster response rather than prevention. The plans did not clearly define the role of primary healthcare and had no clear information on the coordination mechanism among different sectors and organizations. 3) Financing: The budget for prevention and control of flood and storm activities was limited and had no specific items for healthcare activities. Only a little additional funding was available, but the procedures to get this funding were usually time-consuming. 4) Human resources: Medical rescue teams were established, but there were no epidemiologists or environmental health specialists to take care of epidemiological issues. Training on prevention and control of climate change and disaster-related health issues did not meet actual needs. 5) Information and research: Data that can be used for planning and management (including population and epidemiological data) were largely lacking. The district lacked a disease early-warning system. 6) Medical products and technology: Emergency treatment protocols were not available in every studied health facility. CONCLUSIONS: The primary care system capacity in rural Vietnam is inadequate for responding to storm and flood-related health problems in terms of preventive and treatment healthcare. Developing clear facility preparedness plans, which detail standard operating procedures during floods and identify specific job descriptions, would strengthen responses to future floods. Health facilities should have contingency funds available for emergency response in the event of storms and floods. Health facilities should ensure that standard protocols exist in order to improve responses in the event of floods. Introduction of a computerized health information system would accelerate information and data processing. National and local policies need to be strengthened and developed in a way that transfers into action in local rural communities.\",\n \"corpus_id\": 23692386,\n \"score\": 1\n },\n {\n \"doc_id\": \"25633112\",\n \"title\": \"Health Vulnerability of Households in Flooded Communities and Their Adaptation Measures: Case Study in Northeastern Thailand.\",\n \"abstract\": \"Floods adversely affect community well-being and health. This study aims to assess the present health vulnerability of households to floods in a rural flood-prone area of northeastern Thailand, as well as their adaptation measures. The participants were the representatives of 312 randomly selected households, and data were collected using an interview questionnaire. Health vulnerability was assessed in terms of flood exposure, flood sensitivity, and flood adaptive capacity. The data were analyzed with descriptive statistics. The results showed that 47.1% of the households had a low level of health vulnerability to flooding, while in 21.2% the level was high. Households had been adapting themselves to cope with the health impacts from flood. Their coping practices included special arrangements for the protection of property, food management, the provision of water supply and waste disposal, the elimination of sources of vector-borne diseases, family health care, the protection of family livelihood, and communication and transportation.\",\n \"corpus_id\": 13058641,\n \"score\": 1\n },\n {\n \"doc_id\": \"25813771\",\n \"title\": \"The impact of flooding on people living with HIV: a case study from the Ohangwena Region, Namibia.\",\n \"abstract\": \"BACKGROUND: Floods are a disaster situation for all affected populations and especially for vulnerable groups within communities such as children, orphans, women, and people with chronic diseases such as HIV and AIDS. They need functioning health care, sanitation and hygiene, safe water, and healthy food supply, and are critically dependent on their social care and support networks. A study carried out in the Ohangwena region, Namibia, where HIV prevalence is high and extensive flooding frequently occurs, aims to provide a deeper understanding of the impact that flooding has on people living with HIV (PLWHIV) as well as on HIV service providers in the region. DESIGN: The qualitative research applying grounded theory included semi-structured interviews with PLWHIV, focus group discussions with HIV service providers, and a national feedback meeting. The findings were interpreted using the sustainable livelihoods framework, the natural hazard research approach, and health behaviour theories. RESULTS: The study reveals that flooding poses major problems to PLWHIV in terms of their everyday lives, affecting livelihoods, work, income, and living conditions. The factors threatening them under normal conditions - poverty, malnutrition, unsafe water, sanitation and hygiene, limited access to health facilities, a weak health status, and stigma - are intensified by flood-related breakdown of infrastructure, insecurity, malnutrition, and diseases evolving over the course of a flood. A potential dual risk exists for their health: the increased risk both of infection and disease due to the inaccessibility of health services and antiretroviral treatment. A HIV and Flooding Framework was developed to display the results. CONCLUSIONS: This study demonstrates that vulnerabilities and health risks of PLWHIV will increase in a disaster situation like flooding if access to HIV prevention, treatment, care and support are not addressed and ensured. The findings and the HIV and Flooding Framework are not specific to Ohangwena and can be transferred to any flood-affected region that has a high HIV prevalence and relies mainly on subsistence agriculture. They serve as a model case for analysing vulnerabilities related to health and health service provision under disaster conditions. The impact will vary according to the physical, geographical, climatological, social, and behavioural characteristics of the region and the people affected. In the Ohangwena region, a disaster risk management mechanism is already in place which addresses people with HIV during flooding. However, preparedness could be improved further by applying the HIV and Flooding Framework.\",\n \"corpus_id\": 54518141,\n \"score\": 1\n },\n {\n \"doc_id\": \"25860572\",\n \"title\": \"Flooding and mental health: a systematic mapping review.\",\n \"abstract\": \"BACKGROUND: Floods are the most common type of global natural disaster. Floods have a negative impact on mental health. Comprehensive evaluation and review of the literature are lacking. OBJECTIVE: To systematically map and review available scientific evidence on mental health impacts of floods caused by extended periods of heavy rain in river catchments. METHODS: We performed a systematic mapping review of published scientific literature in five languages for mixed studies on floods and mental health. PUBMED and Web of Science were searched to identify all relevant articles from 1994 to May 2014 (no restrictions). RESULTS: The electronic search strategy identified 1331 potentially relevant papers. Finally, 83 papers met the inclusion criteria. Four broad areas are identified: i) the main mental health disorders-post-traumatic stress disorder, depression and anxiety; ii] the factors associated with mental health among those affected by floods; iii) the narratives associated with flooding, which focuses on the long-term impacts of flooding on mental health as a consequence of the secondary stressors; and iv) the management actions identified. The quantitative and qualitative studies have consistent findings. However, very few studies have used mixed methods to quantify the size of the mental health burden as well as exploration of in-depth narratives. Methodological limitations include control of potential confounders and short-term follow up. LIMITATIONS: Floods following extreme events were excluded from our review. CONCLUSIONS: Although the level of exposure to floods has been systematically associated with mental health problems, the paucity of longitudinal studies and lack of confounding controls precludes strong conclusions. IMPLICATIONS: We recommend that future research in this area include mixed-method studies that are purposefully designed, using more rigorous methods. Studies should also focus on vulnerable groups and include analyses of policy and practical responses.\",\n \"corpus_id\": 5011009,\n \"score\": 1\n },\n {\n \"doc_id\": \"25909883\",\n \"title\": \"An exploration of factors affecting the long term psychological impact and deterioration of mental health in flooded households.\",\n \"abstract\": \"The long term psychological effect of the distress and trauma caused by the memory of damage and losses associated with flooding of communities remains an under researched impact of flooding. This is particularly important for communities that are likely to be repeatedly flooded where levels of mental health disorder will damage long term resilience to future flooding. There are a variety of factors that affect the prevalence of mental health disorders in the aftermath of flooding including pre-existing mental health, socio-economic factors and flood severity. However previous research has tended to focus on the short term impacts immediately following the flood event and much less focus has been given to the longer terms effects of flooding. Understanding of factors affecting the longer term mental health outcomes for flooded households is critical in order to support communities in improving social resilience. Hence, the aim of this study was to explore the characteristics associated with psychological distress and mental health deterioration over the longer term. The research examined responses from a postal survey of households flooded during the 2007 flood event across England. Descriptive statistics, correlation analysis and binomial logistic regression were applied to data representing household characteristics, flood event characteristics and post-flood stressors and coping strategies. These factors were related to reported measures of stress, anxiety, depression and mental health deterioration. The results showed that household income, depth of flooding; having to move out during reinstatement and mitigating actions are related to the prevalence of psycho-social symptoms in previously flooded households. In particular relocation and household income were the most predictive factors. The practical implication of these findings for recovery after flooding are: to consider the preferences of households in terms of the need to move out during restorative building works and the financial resource constraints that may lead to severe mental hardship. In addition the findings suggest that support with installing mitigation measures may lead to improved mental health outcomes for communities at risk.\",\n \"corpus_id\": 6246722,\n \"score\": 1\n },\n {\n \"doc_id\": \"26552993\",\n \"title\": \"Flood Risk, Flood Mitigation, and Location Choice: Evaluating the National Flood Insurance Program's Community Rating System.\",\n \"abstract\": \"Climate change is expected to worsen the negative effects of natural disasters like floods. The negative impacts, however, can be mitigated by individuals' adjustments through migration and relocation behaviors. Previous literature has identified flood risk as one significant driver in relocation decisions, but no prior study examines the effect of the National Flood Insurance Program's voluntary program-the Community Rating System (CRS)-on residential location choice. This article fills this gap and tests the hypothesis that flood risk and the CRS-creditable flood control activities affect residential location choices. We employ a two-stage sorting model to empirically estimate the effects. In the first stage, individuals' risk perception and preference heterogeneity for the CRS activities are considered, while mean effects of flood risk and the CRS activities are estimated in the second stage. We then estimate heterogeneous marginal willingness to pay (WTP) for the CRS activities by category. Results show that age, ethnicity and race, educational attainment, and prior exposure to risk explain risk perception. We find significant values for the CRS-creditable mitigation activities, which provides empirical evidence for the benefits associated with the program. The marginal WTP for an additional credit point earned for public information activities, including hazard disclosure, is found to be the highest. Results also suggest that water amenities dominate flood risk. Thus, high amenity values may increase exposure to flood risk, and flood mitigation projects should be strategized in coastal regions accordingly.\",\n \"corpus_id\": 10061071,\n \"score\": 1\n },\n {\n \"doc_id\": \"26639744\",\n \"title\": \"A 9-year Trend in the Prevalence of Allergic Disease Based on National Health Insurance Data.\",\n \"abstract\": \"OBJECTIVES: To investigate trends in the prevalence of allergic disease over a 9-year period. METHODS: Using National Health Insurance Service (NHIS) data, the annual number of patients with allergic disease was obtained for each regional subdivisions (small cities, counties, and districts) from 2003 to 2011. Annual populations for each sub-region were obtained and used to calculate the standardized prevalence. To compare prevalence within the study period, data was standardized spatially and temporally. For standardization, demographic data was used to obtain the registered population and demographic structure for 2010, which was used to perform direct standardization of previous years. In addition, a geographic information system (GIS) was used to visualize prevalence for individual sub-regions, and allergic diseases were categorized into five groups according to prevalence. RESULTS: The nationwide outpatient prevalence of allergic rhinitis increased approximately 2.3-fold, from 1.27% in 2003 to 2.97% in 2013, while inpatient prevalence also increased approximately 2.4-fold,. The outpatient prevalence of asthma increased 1.2-fold, and inpatient prevalence increased 1.3-fold. The outpatient prevalence of atopic dermatitis decreased approximately 12%, and inpatient prevalence decreased 5%. CONCLUSIONS: There was a large difference between prevalence estimated from actual treatment data and prevalence based on patients' self-reported data, particularly for allergic rhinitis. Prevalence must continually be calculated and trends should be analyzed for the efficient management of allergic diseases. To this end, prevalence studies using NHIS claims data may be useful.\",\n \"corpus_id\": 24614754,\n \"score\": 1\n },\n {\n \"doc_id\": \"28129410\",\n \"title\": \"Self-Reported and FEMA Flood Exposure Assessment after Hurricane Sandy: Association with Mental Health Outcomes.\",\n \"abstract\": \"Hurricane Sandy caused extensive physical and economic damage; the long-term mental health consequences are unknown. Flooding is a central component of hurricane exposure, influencing mental health through multiple pathways that unfold over months after flooding recedes. Here we assess the concordance in self-reported and Federal Emergency Management (FEMA) flood exposure after Hurricane Sandy and determine the associations between flooding and anxiety, depression, and post-traumatic stress disorder (PTSD). Self-reported flood data and mental health symptoms were obtained through validated questionnaires from New York City and Long Island residents (N = 1231) following Sandy. Self-reported flood data was compared to FEMA data obtained from the FEMA Modeling Task Force Hurricane Sandy Impact Analysis. Multivariable logistic regressions were performed to determine the relationship between flooding exposure and mental health outcomes. There were significant discrepancies between self-reported and FEMA flood exposure data. Self-reported dichotomous flooding was positively associated with anxiety (ORadj: 1.5 [95% CI: 1.1-1.9]), depression (ORadj: 1.7 [1.3-2.2]), and PTSD (ORadj: 2.5 [1.8-3.4]), while self-reported continuous flooding was associated with depression (ORadj: 1.1 [1.01-1.12]) and PTSD (ORadj: 1.2 [1.1-1.2]). Models with FEMA dichotomous flooding (ORadj: 2.1 [1.5-2.8]) or FEMA continuous flooding (ORadj: 1.1 [1.1-1.2]) were only significantly associated with PTSD. Associations between mental health and flooding vary according to type of flood exposure measure utilized. Future hurricane preparedness and recovery efforts must integrate micro and macro-level flood exposures in order to accurately determine flood exposure risk during storms and realize the long-term importance of flooding on these three mental health symptoms.\",\n \"corpus_id\": 16200299,\n \"score\": 1\n },\n {\n \"doc_id\": \"28129752\",\n \"title\": \"The English national cohort study of flooding and health: cross-sectional analysis of mental health outcomes at year one.\",\n \"abstract\": \"BACKGROUND: In winter 2013/14 there was widespread flooding in England. Previous studies have described an increased prevalence of psychological morbidity six months after flooding. Disruption to essential services may increase morbidity however there have been no studies examining whether those experiencing disruption but not directly flooded are affected. The National Study of Flooding and Health was established in order to investigate the longer-term impact of flooding and related disruptions on mental health and wellbeing. METHODS: In year one we conducted a cross sectional analysis of people living in neighbourhoods affected by flooding between 1 December 2013 and 31 March 2014. 8761 households were invited to participate. Participants were categorised according to exposure as flooded, disrupted by flooding or unaffected. We used validated instruments to screen for probable psychological morbidity, the Patient Health Questionnaire (PHQ 2), Generalised Anxiety Disorder scale (GAD-2) and Post Traumatic Stress Disorder (PTSD) checklist (PCL-6). We calculated prevalence and odds ratios for each outcome by exposure group relative to unaffected participants, adjusting for confounders. RESULTS: 2126 people (23%) responded. The prevalence of psychological morbidity was elevated amongst flooded participants ([n = 622] depression 20.1%, anxiety 28.3%, PTSD 36.2%) and disrupted participants ([n = 1099] depression 9.6%, anxiety 10.7% PTSD 15.2%). Flooding was associated with higher odds of all outcomes (adjusted odds ratios (aORs), 95% CIs for depression 5.91 (3.91-10.99), anxiety 6.50 (3.77-11.24), PTSD 7.19 (4.33-11.93)). Flooded participants who reported domestic utilities disruption had higher odds of all outcomes than other flooded participants, (aORs, depression 6.19 (3.30-11.59), anxiety 6.64 (3.84-11.48), PTSD 7.27 (4.39-12.03) aORs without such disruption, depression, 3.14 (1.17-8.39), anxiety 3.45 (1.45-8.22), PTSD 2.90 (1.25-6.73)). Increased floodwater depth was significantly associated with higher odds of each outcome. Disruption without flooding was associated with borderline higher odds of anxiety (aOR 1.61 (0.94-2.77)) and higher odds of PTSD 2.06 (1.27-3.35)) compared with unaffected participants. Disruption to health/social care and work/education was also associated with higher odds of psychological morbidity. CONCLUSIONS: This study provides an insight into the impact of flooding on mental health, suggesting that the impacts of flooding are large, prolonged and extend beyond just those whose homes are flooded.\",\n \"corpus_id\": 2386660,\n \"score\": 1\n },\n {\n \"doc_id\": \"29396332\",\n \"title\": \"Association between floods and infectious diarrhea and their effect modifiers in Hunan province, China: A two-stage model.\",\n \"abstract\": \"BACKGROUND: Understanding the potential links between floods and infectious diarrhea is important under the context of climate change. However, little is known about the risk of infectious diarrhea after floods and what factors could modify these effects in China. OBJECTIVES: This study aims to quantitatively examine the relationship between floods and infectious diarrhea and their effect modifiers. METHODS: Weekly number of infectious diarrhea cases from 2004 to 2011 during flood season in Hunan province were supplied by the National Notifiable Disease Surveillance System. Flood and meteorological data over the same period were obtained. A two-stage model was used to estimate a provincial average association and their effect modifiers between floods and infectious diarrhea, accounting for other confounders. RESULTS: A total of 134,571 cases of infectious diarrhea were notified from 2004 to 2011. After controlling for seasonality, long-term trends, and meteorological factors, floods were significantly associated with infectious diarrhea in the provincial level with a cumulative RR of 1.22 (95% CI: 1.05, 1.43) with a lagged effect of 0-1 week. Geographic locations and economic levels were identified as effect modifiers, with a higher impact of floods on infectious diarrhea in the western and regions with a low economic level of Hunan. CONCLUSIONS: Our study provides strong evidence of a positive association between floods and infectious diarrhea in the study area. Local control strategies for public health should be taken in time to prevent and reduce the risk of infectious diarrhea after floods, especially for the vulnerable regions identified.\",\n \"corpus_id\": 3836850,\n \"score\": 1\n },\n {\n \"doc_id\": \"29514665\",\n \"title\": \"The English National Cohort Study of Flooding and Health: the change in the prevalence of psychological morbidity at year two.\",\n \"abstract\": \"BACKGROUND: The longer term impact of flooding on health is poorly understood. In 2015, following widespread flooding in the UK during winter 2013/14, Public Health England launched the English National Study of Flooding and Health. The study identified a higher prevalence of probable psychological morbidity one year after exposure to flooding. We now report findings after two years. METHODS: In year two (2016), a self-assessment questionnaire including flooding-related exposures and validated instruments to screen for probable anxiety, depression and post-traumatic stress disorder (PTSD) was sent to all participants who consented to further follow-up. Participants exposure status was categorised according to responses in year one; we assessed for exposure to new episodes of flooding and continuing flood-related problems in respondents homes. We calculated the prevalence and odds ratio for each outcome by exposure group relative to unaffected participants, adjusting for confounders. We used the McNemar test to assess change in outcomes between year one and year two. RESULTS: In year two, 1064 (70%) people responded. The prevalence of probable psychological morbidity remained elevated amongst flooded participants [n = 339] (depression 10.6%, anxiety 13.6%, PTSD 24.5%) and disrupted participants [n = 512] (depression 4.1%, anxiety 6.4%, PTSD 8.9%), although these rates were reduced compared to year one. A greater reduction in anxiety 7.6% (95% confidence interval [CI] 4.6-9.9) was seen than depression 3.8% (95% CI 1.5-6.1) and PTSD: 6.6% (95% CI 3.9-9.2). Exposure to flooding was associated with a higher odds of anxiety (adjusted odds ratio [aOR] 5.2 95%, 95% CI 1.7-16.3) and depression (aOR 8.7, 95% CI 1.9-39.8) but not PTSD. Exposure to disruption caused by flooding was not significantly associated with probable psychological morbidity. Persistent damage in the home as a consequence of the original flooding event was reported by 119 participants (14%). The odds of probable psychological morbidity amongst flooded participants who reported persistent damage, compared with those who were unaffected, were significantly higher than the same comparison amongst flooded participants who did not report persistent damage. CONCLUSIONS: This study shows a continuance of probable psychological morbidity at least two years following exposure to flooding. Commissioners and providers of health and social care services should be aware that the increased need in populations may be prolonged. Efforts to resolve persistent damage to homes may reduce the risk of probable psychological morbidity.\",\n \"corpus_id\": 3847537,\n \"score\": 1\n },\n {\n \"doc_id\": \"18633629\",\n \"title\": \"[Documentation of outpatient treatment of Paget's disease in Westphalia-Lippe. Descriptive analysis of statutory health insurance data for the year 2005].\",\n \"abstract\": \"Dokumentation der ambulanten Morbus-Paget-Behandlung am Beispiel der Region Westfalen-Lippe: Deskriptive Analyse der Abrechnungsdaten gesetzlich Krankenversicherter für das Jahr 2005. GOAL: Inpatient health care data are often used as a source of information for health reporting in Germany, despite the fact that a lot of diseases are predominantly treated in the outpatient sector. This study provides a first overview of the outpatient care situation in relation to Paget's disease. METHOD: Outpatient care data from the Association of Statutory Health Insurance Physicians constituted the database for a descriptive analysis, capturing the state of medical care for the rare rheumatic illness Paget's disease (Osteodystrophia deformans) in the region of East Westphalia-Lippe in 2005. RESULTS: While the health report of North Rhine-Westphalia documents a total of 56 cases of M. Paget discharged from hospital for the year 2003, 166 patients suffering from Paget's disease consulted an practice-based physician in 2005 in the district of Detmold alone. The latter figure corresponds to 8.0 treated patients per 100.000 inhabitants. The treatment rates of men and women are comparable. The probability of treatment increases with advancing age. On average, patients with Paget's disease are 65.6 years old (SD=15.4 years). Almost 90% of the diagnoses of Paget's disease are classified as M88.9 according to ICD 10; more exact localisations are provided only for relatively few cases. Nearly a quarter of the cases (24.1%) are treated by general practitioners and internists. Anaesthetists treated 17.5% of the patients and orthopaedists 16.9%. In addition, ophthalmologists treat a considerable proportion of cases (12.0%). CONCLUSION: Consistent with the rareness of Paget's disease, the treatment data are as low as expected. However, the results show that routinely collected health care data allow insights into morbidity structures within the outpatient sector. It follows that for statutory health insurants (approximately 90% of the population) there should be an extension of health reporting to diseases that are mainly treated in outpatient settings.\",\n \"corpus_id\": 26070253,\n \"score\": 0\n },\n {\n \"doc_id\": \"19017311\",\n \"title\": \"Trends observed during a decade of paediatric sick visits to peripheral health facilities in rural western Kenya, 1997-2006.\",\n \"abstract\": \"OBJECTIVES: To assess whether longitudinal surveillance in peripheral health facilities could document trends in disease burden, healthcare practice and utilization resulting from large-scale public health interventions made in the decade 1997-2006. METHODS: Data were collected from sick child visits (SCVs) among children <5 years attending 14 outpatient facilities in Asembo, rural western Kenya, during 1997-2006. Changes in proportions, and counts and rates were evaluated using chi-square and Poisson regression respectively. RESULTS: During the decade, 64 394 SCVs were made, yielding an average rate of 0.70 SCVs per child-year. The annual number of SCVs stayed constant during 1997-2003, then increased by 74% between 2003 and 2006 (P < 0.01). The time between symptom onset and SCV shortened from 5.6 days in 1997 to 4.4 days in 2006 (P < 0.01). Malaria and upper respiratory tract infection (URTI) were most commonly diagnosed (69% and 36% of SCVs respectively). Between 2003 and 2006, the proportion of SCVs with a malaria diagnosis fell from 77% to 48%, although the rate of malaria SCVs did not. URTI visits increased in 2004-2006. The most frequently prescribed antimalarials changed three times, lagging 1-2 years behind changes in national policy. Treatment of pneumonia with antibiotics varied by year, ranging from 19% to 89%. CONCLUSION: Surveillance of paediatric SCVs at peripheral health facilities was useful in documenting the timing and penetration of changes in national policies and clinical patterns of drug use for common infections. The surveillance data suggested that improved access to care, rather than disease burden changes, likely led to greater healthcare utilization after 2003.\",\n \"corpus_id\": 11609915,\n \"score\": 0\n },\n {\n \"doc_id\": \"19278754\",\n \"title\": \"National point prevalence of Clostridium difficile in US health care facility inpatients, 2008.\",\n \"abstract\": \"BACKGROUND: Recent published estimates of Clostridium difficile infection (CDI) incidence have been based on small numbers of hospitals or national hospital discharge data. These data suggest that CDI incidence is increasing. METHODS: We conducted a point prevalence survey of C difficile in inpatients at US health care facilities. The survey was developed, received Institutional Review Board approval, and was then distributed to all Association for Professionals in Infection Control and Epidemiology, Inc (APIC) members. They were asked to complete the survey on 1 day between May 7 and August 29, 2008, reporting the number of inpatients with CDI or colonization and facility-specific information. RESULTS: Personnel at 648 hospitals completed the survey; this represents approximately 12.5% of all US acute care facilities. All but 3 states and the District of Columbia were represented (mean, 14 facilities per state; range, 2-43). Eighty-two percent reported that their CDI rate had not decreased in the past 3 years. Respondents reported 1443 C difficile-colonized/infected patients among 110,550 inpatients; the overall C difficile prevalence rate was 13.1 per 1000 inpatients (94.4% infection). Detailed data were provided on 1062 (73.6%) patients. Of these, 55.5% were female, 69.2% were >60 years of age, 67.6% had selected comorbid conditions, 79% had received antimicrobials within 30 days, and 94.4% were detected by enzyme immunoassay. The majority of patients (54.4%) were diagnosed < or =48 hours of hospitalization, but 35% had been admitted to a long-term care facility within 30 days, and 47% had been hospitalized within 90 days; 73% met Centers for Disease Control and Prevention criteria for health care-associated CDI. Most facilities (>90%) used contact isolation for CDI patients. Bleach was used for environmental disinfection more commonly during CDI outbreaks than during nonoutbreak periods. CONCLUSION: Our survey documents a higher C difficile prevalence rate than previous estimates using different methodologies. The majority of inpatient CDI appears to be health care associated. Given that not all patients with diarrhea are tested for CDI and that most facilities use enzyme immunoassays with limited sensitivity to detect C difficile, these are minimum estimates of the US health care facility C difficile burden.\",\n \"corpus_id\": 20008678,\n \"score\": 0\n },\n {\n \"doc_id\": \"20209226\",\n \"title\": \"[Association between particulate matter from biomass burning and respiratory diseases in the southern region of the Brazilian Amazon].\",\n \"abstract\": \"Associação entre material particulado de queimadas e doenças respiratórias na região sul da Amazônia brasileira. OBJECTIVE: To investigate the short-term effects of exposure to particulate matter from biomass burning in the Amazon on the daily demand for outpatient care due to respiratory diseases in children and the elderly. METHODS: Epidemiologic study with ecologic time series design. Daily consultation records were obtained from the 14 primary health care clinics in the municipality of Alta Floresta, state of Mato Grosso, in the southern region of the Brazilian Amazon, between January 2004 and December 2005. Information on the daily levels of fine particulate matter was made available by the Brazilian National Institute for Spatial Research. To control for confounding factors (situations in which a non-causal association between exposure and disease is observed due to a third variable), variables related to time trends, seasonality, temperature, relative humidity, rainfall, and calendar effects (such as occurrence of holidays and weekends) were included in the model. Poisson regression with generalized additive models was used. RESULTS: A 10 microg/m3 increase in the level of exposure to particulate matter was associated with increases of 2.9% and 2.6% in outpatient consultations due to respiratory diseases in children on the 6th and 7th days following exposure. Significant associations were not observed for elderly individuals. CONCLUSIONS: The results suggest that the levels of particulate matter from biomass burning in the Amazon are associated with adverse effects on the respiratory health of children.\",\n \"corpus_id\": 9557115,\n \"score\": 0\n },\n {\n \"doc_id\": \"20813066\",\n \"title\": \"Development of temporal modelling for forecasting and prediction of malaria infections using time-series and ARIMAX analyses: a case study in endemic districts of Bhutan.\",\n \"abstract\": \"BACKGROUND: Malaria still remains a public health problem in some districts of Bhutan despite marked reduction of cases in last few years. To strengthen the country's prevention and control measures, this study was carried out to develop forecasting and prediction models of malaria incidence in the endemic districts of Bhutan using time series and ARIMAX. METHODS: This study was carried out retrospectively using the monthly reported malaria cases from the health centres to Vector-borne Disease Control Programme (VDCP) and the meteorological data from Meteorological Unit, Department of Energy, Ministry of Economic Affairs. Time series analysis was performed on monthly malaria cases, from 1994 to 2008, in seven malaria endemic districts. The time series models derived from a multiplicative seasonal autoregressive integrated moving average (ARIMA) was deployed to identify the best model using data from 1994 to 2006. The best-fit model was selected for each individual district and for the overall endemic area was developed and the monthly cases from January to December 2009 and 2010 were forecasted. In developing the prediction model, the monthly reported malaria cases and the meteorological factors from 1996 to 2008 of the seven districts were analysed. The method of ARIMAX modelling was employed to determine predictors of malaria of the subsequent month. RESULTS: It was found that the ARIMA (p, d, q) (P, D, Q)s model (p and P representing the auto regressive and seasonal autoregressive; d and D representing the non-seasonal differences and seasonal differencing; and q and Q the moving average parameters and seasonal moving average parameters, respectively and s representing the length of the seasonal period) for the overall endemic districts was (2,1,1)(0,1,1)12; the modelling data from each district revealed two most common ARIMA models including (2,1,1)(0,1,1)12 and (1,1,1)(0,1,1)12. The forecasted monthly malaria cases from January to December 2009 and 2010 varied from 15 to 82 cases in 2009 and 67 to 149 cases in 2010, where population in 2009 was 285,375 and the expected population of 2010 to be 289,085. The ARIMAX model of monthly cases and climatic factors showed considerable variations among the different districts. In general, the mean maximum temperature lagged at one month was a strong positive predictor of an increased malaria cases for four districts. The monthly number of cases of the previous month was also a significant predictor in one district, whereas no variable could predict malaria cases for two districts. CONCLUSIONS: The ARIMA models of time-series analysis were useful in forecasting the number of cases in the endemic areas of Bhutan. There was no consistency in the predictors of malaria cases when using ARIMAX model with selected lag times and climatic predictors. The ARIMA forecasting models could be employed for planning and managing malaria prevention and control programme in Bhutan.\",\n \"corpus_id\": 2172504,\n \"score\": 0\n },\n {\n \"doc_id\": \"20825976\",\n \"title\": \"Short-term effect of fine particulate matter (PM 2.5) on daily mortality due to diseases of the circulatory system in Madrid (Spain).\",\n \"abstract\": \"INTRODUCTION: Owing to their small size, fine particles, i.e., those having a diameter ≤ 2.5 μm (PM(2.5)), have a high alveolar penetration capacity, thereby triggering a local inflammatory process with circulatory repercussion. Despite being linked to respiratory and cardiovascular morbidities, there is limited evidence of an association between this type of particulate matter and short-term increases in mortality. OBJECTIVE: The aim of this study was to analyse and quantify the short-term impact of PM(2.5) on daily mortality due to diseases of the circulatory system, registered in Madrid from 1 January 2003 to 31 December 2005. METHODS: An ecological longitudinal time-series study was conducted, with risks being quantified by means of Poisson regression models. As a dependent variable, we took daily mortality registered in Madrid from 1 January 2003 to 31 December 2005, attributed to all diseases of the circulatory system as classified under heads I00-I99 of the International Classification of Diseases-10th revision (ICD-10) and broken down as follows: I21, acute myocardial infarction (AMI); I20, I22-I25, other ischemic heart diseases; and I60-I69, cerebrovascular diseases. The independent variable was daily mean PM(2.5) concentration. The other variables controlled for were: chemical pollution (PM(10), O(3), SO(2), NO(2) and NO(x)); acoustic and biotic pollution; influenza; minimum and maximum temperatures; seasonalities; trend; and autocorrelation of the series. RESULTS: A linear relationship was observed between PM(2.5) levels and mortality due to diseases of the circulatory system. For every increase of 10 μg/m(3) in daily mean PM(2.5) concentration, the relative risks (RR) were as follows: for overall circulatory mortality, associations were established at lags 2 and 6, with RR of 1.022 (1.005-1.039) and 1.025 (1.007-1.043) respectively; and for AMI mortality, there was an association at lag 6, with an RR of 1.066 (1.032-1.100). The corresponding attributable risks percent (AR%) were 2.16%, 2.47% and 6.21% respectively. No statistically significant association was found with other ischemic heart diseases or with cerebrovascular diseases. CONCLUSION: PM(2.5) concentrations are an important risk factor for daily circulatory-cause mortality in Madrid. From a public health point of view, the planning and implementation of specific measures targeted at reducing these levels constitute a pressing need.\",\n \"corpus_id\": 37343666,\n \"score\": 0\n },\n {\n \"doc_id\": \"21845165\",\n \"title\": \"Assessment of vulnerability to extreme flash floods in design storms.\",\n \"abstract\": \"There has been an increase in the occurrence of sudden local flooding of great volume and short duration caused by heavy or excessive rainfall intensity over a small area, which presents the greatest potential danger threat to the natural environment, human life, public health and property, etc. Such flash floods have rapid runoff and debris flow that rises quickly with little or no advance warning to prevent flood damage. This study develops a flash flood index through the average of the same scale relative severity factors quantifying characteristics of hydrographs generated from a rainfall-runoff model for the long-term observed rainfall data in a small ungauged study basin, and presents regression equations between rainfall characteristics and the flash flood index. The aim of this study is to develop flash flood index-duration-frequency relation curves by combining the rainfall intensity-duration-frequency relation and the flash flood index from probability rainfall data in order to evaluate vulnerability to extreme flash floods in design storms. This study is an initial effort to quantify the flash flood severity of design storms for both existing and planned flood control facilities to cope with residual flood risks due to extreme flash floods that have ocurred frequently in recent years.\",\n \"corpus_id\": 7559952,\n \"score\": 0\n },\n {\n \"doc_id\": \"22529923\",\n \"title\": \"Acute and chronic effects of particles on hospital admissions in New-England.\",\n \"abstract\": \"BACKGROUND: Many studies have reported significant associations between exposure to PM(2.5) and hospital admissions, but all have focused on the effects of short-term exposure. In addition all these studies have relied on a limited number of PM(2.5) monitors in their study regions, which introduces exposure error, and excludes rural and suburban populations from locations in which monitors are not available, reducing generalizability and potentially creating selection bias. METHODS: Using our novel prediction models for exposure combining land use regression with physical measurements (satellite aerosol optical depth) we investigated both the long and short term effects of PM(2.5) exposures on hospital admissions across New-England for all residents aged 65 and older. We performed separate Poisson regression analysis for each admission type: all respiratory, cardiovascular disease (CVD), stroke and diabetes. Daily admission counts in each zip code were regressed against long and short-term PM(2.5) exposure, temperature, socio-economic data and a spline of time to control for seasonal trends in baseline risk. RESULTS: We observed associations between both short-term and long-term exposure to PM(2.5) and hospitalization for all of the outcomes examined. In example, for respiratory diseases, for every 10-µg/m(3) increase in short-term PM(2.5) exposure there is a 0.70 percent increase in admissions (CI = 0.35 to 0.52) while concurrently for every 10-µg/m(3) increase in long-term PM(2.5) exposure there is a 4.22 percent increase in admissions (CI = 1.06 to 4.75). CONCLUSIONS: As with mortality studies, chronic exposure to particles is associated with substantially larger increases in hospital admissions than acute exposure and both can be detected simultaneously using our exposure models.\",\n \"corpus_id\": 443855,\n \"score\": 0\n },\n {\n \"doc_id\": \"22690208\",\n \"title\": \"Estimation of the relative severity of floods in small ungauged catchments for preliminary observations on flash flood preparedness: a case study in Korea.\",\n \"abstract\": \"An increase in the occurrence of sudden local flooding of great volume and short duration has caused significant danger and loss of life and property in Korea as well as many other parts of the World. Since such floods usually accompanied by rapid runoff and debris flow rise quite quickly with little or no advance warning to prevent flood damage, this study presents a new flash flood indexing methodology to promptly provide preliminary observations regarding emergency preparedness and response to flash flood disasters in small ungauged catchments. Flood runoff hydrographs are generated from a rainfall-runoff model for the annual maximum rainfall series of long-term observed data in the two selected small ungauged catchments. The relative flood severity factors quantifying characteristics of flood runoff hydrographs are standardized by the highest recorded maximum value, and then averaged to obtain the flash flood index only for flash flood events in each study catchment. It is expected that the regression equations between the proposed flash flood index and rainfall characteristics can provide the basis database of the preliminary information for forecasting the local flood severity in order to facilitate flash flood preparedness in small ungauged catchments.\",\n \"corpus_id\": 12693087,\n \"score\": 0\n },\n {\n \"doc_id\": \"22849236\",\n \"title\": \"Effects of short-term exposure to air pollution on hospital admissions of young children for acute lower respiratory infections in Ho Chi Minh City, Vietnam.\",\n \"abstract\": \"There is emerging evidence, largely from studies in Europe and North America, that economic deprivation increases the magnitude of morbidity and mortality related to air pollution. Two major reasons why this may be true are that the poor experience higher levels of exposure to air pollution, and they are more vulnerable to its effects--in other words, due to poorer nutrition, less access to medical care, and other factors, they experience more health impact per unit of exposure. The relations among health, air pollution, and poverty are likely to have important implications for public health and social policy, especially in areas such as the developing countries of Asia where air pollution levels are high and many live in poverty. The aims of this study were to estimate the effect of exposure to air pollution on hospital admissions of young children for acute lower respiratory infection (ALRI*) and to explore whether such effects differed between poor children and other children. ALRI, which comprises pneumonia and bronchiolitis, is the largest single cause of mortality among young children worldwide and is responsible for a substantial burden of disease among young children in developing countries. To the best of our knowledge, this is the first study of the health effects of air pollution in Ho Chi Minh City (HCMC), Vietnam. For these reasons, the results of this study have the potential to make an important contribution to the growing literature on the health effects of air pollution in Asia. The study focused on the short-term effects of daily average exposure to air pollutants on hospital admissions of children less than 5 years of age for ALRI, defined as pneumonia or bronchiolitis, in HCMC during 2003, 2004, and 2005. Admissions data were obtained from computerized records of Children's Hospital 1 and Children's Hospital 2 (CH1 and CH2) in HCMC. Nearly all children hospitalized for respiratory illnesses in the city are admitted to one of these two pediatric hospitals. Daily citywide 24-hour average concentrations of particulate matter (PM) < or =10 microm in aerodynamic diameter (PM10), nitrogen dioxide (NO2), and sulfur dioxide (SO2) and 8-hour maximum average concentrations of ozone (O3) were estimated from the HCMC Environmental Protection Agency (HEPA) ambient air quality monitoring network. Daily meteorologic information including temperature and relative humidity were collected from KTTV NB, the Southern Regional Hydro-Meteorological Center. An individual-level indicator of socioeconomic position (SEP) was based on the degree to which the patient was exempt from payment according to hospital financial records. A group-level indicator of SEP was based on estimates of poverty prevalence in the districts of HCMC in 2004, obtained from a poverty mapping project of the Institute of Economic Research in HCMC, in collaboration with the General Statistics Office of Vietnam and the World Bank. Poverty prevalence was defined using the poverty line set by the People's Committee of HCMC of 6 million Vietnamese dong (VND) annual income. Quartiles of district-level poverty prevalence were created based on poverty prevalence estimates for each district. Analyses were conducted using both time-series and case-crossover approaches. In the absence of measurement error, confounding, and other sources of bias, the two approaches were expected to provide estimates that differed only with regard to precision. For the time-series analyses, the unit of observation was daily counts of hospital admissions for ALRI. Poisson regression with smoothing functions for meteorologic variables and variables for seasonal and long-term trends was used. Case-crossover analyses were conducted using time-stratified selection of controls. Control days were every 7th day from the date of admission within the same month as admission. Large seasonal differences were observed in pollutant levels and hospital admission patterns during the investigation period for HCMC. Of the 15,717 ALRI admissions occurring within the study period, 60% occurred in the rainy season (May through October), with a peak in these admissions during July and August of each year. Average daily concentrations for PM10, O3, NO2, and SO2 were 73, 75, 22, and 22 microg/m3, respectively, with higher pollutant concentrations observed in the dry season (November through April) compared with the rainy season. As the time between onset of illness and hospital admission was thought to range from 1 to 6 days, it was not possible to specify a priori a single-day lag. We assessed results for single-day lags from lag 0 to lag 10, but emphasize results for an average of lag 1-6, since this best reflects the case reference period. Results were robust to differences in temperature lags with lag 0 and the average lag (1-6 days); results for lag 0 for temperature are presented. Results differed markedly when analyses were stratified by season, rather than simply adjusted for season. ALRI admissions were generally positively associated with ambient levels of PM10, NO2, and SO2 during the dry season (November-April), but not the rainy season (May-October). Positive associations between O3 and ALRI admissions were not observed in either season. We do not believe that exposure to air pollution could reduce the risk of ALRI in the rainy season and infer that these results could be driven by residual confounding present within the rainy season. The much lower correlation between NO2 and PM10 levels during the rainy season provides further evidence that these pollutants may not be accurate indicators of exposure to air pollution from combustion processes in the rainy season. Results were generally consistent across time-series and case-crossover analyses. In the dry season, risks for ALRI hospital admissions with average pollutant lag (1-6 days) were highest for NO2 and SO2 in the single-pollutant case-crossover analyses, with excess risks of 8.50% (95% CI, 0.80-16.79) and 5.85% (95% CI, 0.44-11.55) observed, respectively. NO2 and SO2 effects remained higher than PM10 effects in both the single-pollutant and two-pollutant models. The two-pollutant model indicated that NO2 confounded the PM10 and SO2 effects. For example, PM10 was weakly associated with an excess risk in the dry season of 1.25% (95% CI, -0.55 to 3.09); after adjusting for SO2 and O3, the risk estimate was reduced but remained elevated, with much wider confidence intervals; after adjusting for NO2, an excess risk was no longer observed. Though the effects seem to be driven by NO2, the statistical limitations of adequately addressing collinearity, given the high correlation between PM10 and NO2 (r = 0.78), limited our ability to clearly distinguish between PM10 and NO2 effects. In the rainy season, negative associations between PM10 and ALRI admissions were observed. No association with O3 was observed in the single-pollutant model, but O3 exposure was negatively associated with ALRI admissions in the two-pollutant model. There was little evidence of an association between NO2 and ALRI admissions. The single-pollutant estimate from the case-crossover analysis suggested a negative association between NO2 and ALRI admissions, but this effect was no longer apparent after adjustment for other pollutants. Although associations between SO2 and ALRI admissions were not observed in the rainy season, point estimates for the case-crossover analyses suggested negative associations, while time-series (Poisson regression) analyses suggested positive associations--an exception to the general consistency between case-crossover and time-series results. Results were robust to differences in seasonal classification. Inclusion of rainfall as a continuous variable and the seasonal reclassification of selected series of data did not influence results. No clear evidence of station-specific effects could be observed, since results for the different monitoring stations had overlapping confidence intervals. In the dry season, increased concentrations of NO2 and SO2 were associated with increased hospital admissions of young children for ALRI in HCMC. PM10 could also be associated with increased hospital admissions in the dry season, but the high correlation of 0.78 between PM10 and NO2 levels limits our ability to distinguish between PM10 and NO2 effects. Nevertheless, the results support the presence of an association between combustion-source pollution and increased ALRI admissions. There also appears to be evidence of uncontrolled negative confounding within the rainy season, with higher incidence of ALRI and lower pollutant concentrations overall. Exploratory analyses made using limited historical and regional data on monthly prevalence of respiratory syncytial virus (RSV) suggest that an unmeasured, time-varying confounder (RSV, in this case) could have, in an observational study like this one, created enough bias to reverse the observed effect estimates of pollutants in the rainy season. In addition, with virtually no RSV incidence in the dry season, these findings also lend some credibility to the notion that RSV could influence results primarily in the rainy season. Analyses were not able to identify differential effects by individual-level indicators of SEP, mainly due to the small number of children classified as poor based on information in the hospitals' financial records. Analyses assessing differences in effect by district-level indicator of SEP did not indicate a clear trend in risk across SEP quartiles, but there did appear to be a slightly higher risk among the residents of districts with the highest quartile of SEP. As these are the districts within the urban center of HCMC, results could be indicative of increased exposures for residents living within the city center. ( ABSTRACT TRUNCATED)\",\n \"corpus_id\": 42144452,\n \"score\": 0\n },\n {\n \"doc_id\": \"23114861\",\n \"title\": \"The burden of maternal health care expenditure in India: multilevel analysis of national data.\",\n \"abstract\": \"To quantify the economic burden of maternal health care services on Indian households and examine the levels of expenditure incurred in public and private health care institutions at the national, state and community levels. Cross-sectional population data from the 2004 National Sample Survey Organisation were used, which considered 9,643 households for the analysis where at least one woman received maternal health care services during the year preceding the survey. Multilevel linear regression techniques were used to estimate the effect of household, cluster and state characteristics on the proportion of maternal health care expenditures over total household expenditures. Over 80 % of households reported paying for maternal health care services, with those using private care facilities paying almost 4 times more than those using public facilities. Multilevel analyses show evidence of high burden of maternal health care expenditures, which varied significantly across states according to the level of health care utilisation, and with considerable heterogeneity at the household and community levels. Maternal health care services in India are offered free at the point of delivery, yet many families face significant out-of-pocket expenditures. The recent governmental policy interventions to encourage institutional births by providing nominal financial assistance is a welcome step but this might not help to compensate mothers for other indirect expenditures, especially those living in rural areas and poorer communities who are increasingly seeking care in private facilities.\",\n \"corpus_id\": 24907122,\n \"score\": 0\n },\n {\n \"doc_id\": \"24343621\",\n \"title\": \"Can routinely collected national data on childhood morbidity and mortality from diarrhea be used to monitor health impact of rotavirus vaccination in Africa? Examination of pre-vaccine baseline data from Rwanda.\",\n \"abstract\": \"BACKGROUND: As rotavirus vaccine is introduced into routine childhood immunization programs in Africa, understanding its impact on diarrheal disease burden is important. The objective of this analysis was to determine whether routinely collected health information on national diarrhea hospitalizations, in-hospital deaths and outpatient visits would be useful to monitor rotavirus vaccine impact. METHODS: We analyzed data for all-cause, nonbloody diarrheal disease among children <5 years of age from the routine health management information system (HMIS) in Rwanda from January 2008 through December 2011. We described trends in absolute numbers of inpatient admissions, in-hospital deaths and outpatient visits by year, age and setting. RESULTS: All-cause, nonbloody diarrheal hospitalizations and outpatient visits among children <5 years of age in Rwanda from 2008 to 2011 peaked during the June to August dry season, coinciding with the rotavirus season. The bulk of the diarrheal disease burden occurred in children <1 year of age. Health centers provided many care to children with diarrhea including 60-72% of hospitalizations and 97-99% of outpatient visits. Many in-hospital diarrheal deaths (84%) occurred in district hospitals. DISCUSSION: Given the stable and consistent trends and the prominent seasonality consistent with that of rotavirus, HMIS data should provide a useful baseline to monitor rotavirus vaccine impact on the overall diarrheal disease burden in Rwanda. Active, sentinel surveillance for rotavirus diarrhea will help interpret changes in diarrheal disease trends following vaccine introduction. Other countries planning rotavirus vaccine introduction should explore the availability and quality of their HMIS data.\",\n \"corpus_id\": 205688700,\n \"score\": 0\n },\n {\n \"doc_id\": \"25849769\",\n \"title\": \"The air quality health index and emergency department visits for urticaria in Windsor, Canada.\",\n \"abstract\": \"Ambient air pollution exposure has been associated with several health conditions, limited not only to respiratory and cardiovascular systems but also to cutaneous tissues. However, few epidemiological studies examined pollution exposure on skin problems. Basically, the common mechanism by which pollution may affect skin physiology is by induction of oxidative stress and inflammation. Urticaria is among the skin pathologies that have been associated with pollution. Based on the combined effects of three ambient air pollutants, ozone (O₃), nitrogen dioxide (NO₂), and fine particulate matter (PM) with a median aerodynamic diameter of less than 2.5 μm (PM(2.5)), on mortality, the Air Quality Health Index (AQHI) in Canada was developed. The aim of this study was to examine the associations of short-term changes in AQHI with emergency department (ED) visits for urticaria in Windsor-area hospitals in Canada. Diagnosed ED visits were retrieved from the National Ambulatory Care Reporting System (NACRS). A time-stratified case-crossover design was applied to 2905 ED visits (males = 1215; females = 1690) for urticaria from April 2004 through December 2010. Odds ratios (OR) and their corresponding 95% confidence intervals (95%CI) for ED visits associated with increase by one unit of risk index were calculated employing conditional logistic regression. Positive and significant results were observed between AQHI levels and OR for ED visits for urticaria in Windsor for lags 2 and 3 days. A distributed lag nonlinear model technique was applied to daily counts of ED visits for lags 0 to 10 and significant results were obtained from lag 2 to lag 5 and for lag 9. These findings demonstrated associations between ambient air pollution and urticarial confirming that air pollution affects skin conditions.\",\n \"corpus_id\": 38878944,\n \"score\": 0\n },\n {\n \"doc_id\": \"26020627\",\n \"title\": \"Predicting unprecedented dengue outbreak using imported cases and climatic factors in Guangzhou, 2014.\",\n \"abstract\": \"INTRODUCTION: Dengue is endemic in more than 100 countries, mainly in tropical and subtropical regions, and the incidence has increased 30-fold in the past 50 years. The situation of dengue in China has become more and more severe, with an unprecedented dengue outbreak hitting south China in 2014. Building a dengue early warning system is therefore urgent and necessary for timely and effective response. METHODOLOGY AND PRINCIPAL FINDINGS: In the study we developed a time series Poisson multivariate regression model using imported dengue cases, local minimum temperature and accumulative precipitation to predict the dengue occurrence in four districts of Guangzhou, China. The time series data were decomposed into seasonal, trend and remainder components using a seasonal-trend decomposition procedure based on loess (STL). The time lag of climatic factors included in the model was chosen based on Spearman correlation analysis. Autocorrelation, seasonality and long-term trend were controlled in the model. A best model was selected and validated using Generalized Cross Validation (GCV) score and residual test. The data from March 2006 to December 2012 were used to develop the model while the data from January 2013 to September 2014 were employed to validate the model. Time series Poisson model showed that imported cases in the previous month, minimum temperature in the previous month and accumulative precipitation with three month lags could project the dengue outbreaks occurred in 2013 and 2014 after controlling the autocorrelation, seasonality and long-term trend. CONCLUSIONS: Together with the sole transmission vector Aedes albopictus, imported cases, monthly minimum temperature and monthly accumulative precipitation may be used to develop a low-cost effective early warning system.\",\n \"corpus_id\": 11245866,\n \"score\": 0\n },\n {\n \"doc_id\": \"26369521\",\n \"title\": \"\\\"Know What to Do If You Encounter a Flash Flood\\\": Mental Models Analysis for Improving Flash Flood Risk Communication and Public Decision Making.\",\n \"abstract\": \"Understanding how people view flash flood risks can help improve risk communication, ultimately improving outcomes. This article analyzes data from 26 mental models interviews about flash floods with members of the public in Boulder, Colorado, to understand their perspectives on flash flood risks and mitigation. The analysis includes a comparison between public and professional perspectives by referencing a companion mental models study of Boulder-area professionals. A mental models approach can help to diagnose what people already know about flash flood risks and responses, as well as any critical gaps in their knowledge that might be addressed through improved risk communication. A few public interviewees mentioned most of the key concepts discussed by professionals as important for flash flood warning decision making. However, most interviewees exhibited some incomplete understandings and misconceptions about aspects of flash flood development and exposure, effects, or mitigation that may lead to ineffective warning decisions when a flash flood threatens. These include important misunderstandings about the rapid evolution of flash floods, the speed of water in flash floods, the locations and times that pose the greatest flash flood risk in Boulder, the value of situational awareness and environmental cues, and the most appropriate responses when a flash flood threatens. The findings point to recommendations for ways to improve risk communication, over the long term and when an event threatens, to help people quickly recognize and understand threats, obtain needed information, and make informed decisions in complex, rapidly evolving extreme weather events such as flash floods.\",\n \"corpus_id\": 26670560,\n \"score\": 0\n },\n {\n \"doc_id\": \"26752641\",\n \"title\": \"The Mexican Cycle of Suicide: A National Analysis of Seasonality, 2000-2013.\",\n \"abstract\": \"INTRODUCTION: Suicide is a complex and multifactorial phenomenon with growing importance to public health. An increase in its occurrence has been observed in Mexico over the past 10 years. The present article analyzes the secular trend in suicide at the national level between the years 2000 and 2013. MATERIALS AND METHODS: All suicides during the study period (n = 64,298, of which 82.11% were men) were characterized using a spectral decomposition of the time series and a wavelet analysis to evaluate the effect of seasonal changes, type of area (urban versus rural) and sex. RESULTS: A seasonal pattern was observed with statistically significant cycles every 12 months, where peaks were identified in May but only for men in urban zones as of the year 2007. In addition, specific days of the year were found to have a higher frequency of suicides, which coincided with holidays (New Year, Mother's Day, Mexican Independence Day and Christmas). CONCLUSION: A wavelet analysis can be used to decompose complex time series. To the best of our knowledge, this is the first application of this technique to the study of suicides in developing countries. This analysis enabled identifying a seasonal pattern among urban men in Mexico. The identification of seasonal patterns can help to create primary prevention strategies, increase the dissemination of crisis intervention strategies and promote mental health. These strategies could be emphasized during specific periods of the year and directed towards profiles with a higher risk.\",\n \"corpus_id\": 20759792,\n \"score\": 0\n },\n {\n \"doc_id\": \"27111734\",\n \"title\": \"Combining Healthcare-Based and Participatory Approaches to Surveillance: Trends in Diarrheal and Respiratory Conditions Collected by a Mobile Phone System by Community Health Workers in Rural Nepal.\",\n \"abstract\": \"BACKGROUND: Surveillance systems are increasingly relying upon community-based or crowd-sourced data to complement traditional facilities-based data sources. Data collected by community health workers during the routine course of care could combine the early warning power of community-based data collection with the predictability and diagnostic regularity of facility data. These data could inform public health responses to epidemics and spatially-clustered endemic diseases. Here, we analyze data collected on a daily basis by community health workers during the routine course of clinical care in rural Nepal. We evaluate if such community-based surveillance systems can capture temporal trends in diarrheal diseases and acute respiratory infections. METHODS: During the course of their clinical activities from January to December 2013, community health workers recorded healthcare encounters using mobile phones. In parallel, we accessed condition-specific admissions from 2011-2013 in the hospital from which the community health program was based. We compared diarrhea and acute respiratory infection rates from both the hospital and the community, and assigned three categories of local disease activity (low, medium, and high) to each week in each village cluster with categories determined by tertiles. We compared condition-specific mean hospital rates across categories using ANOVA to assess concordance between hospital and community-collected data. RESULTS: There were 2,710 cases of diarrhea and 373 cases of acute respiratory infection reported by community health workers during the one-year study period. At the hospital, the average weekly incidence of diarrhea and acute respiratory infections over the three-year period was 1.8 and 3.9 cases respectively per 1,000 people in each village cluster. In the community, the average weekly rate of diarrhea and acute respiratory infections was 2.7 and 0.5 cases respectively per 1,000 people. Both diarrhea and acute respiratory infections exhibited significant differences between the three categories of disease rate burden (diarrhea p = 0.009, acute respiratory infection p = 0.001) when comparing community health worker-collected rates to hospital rates. CONCLUSION: Community-level data on diarrhea and acute respiratory infections modestly correlated with hospital data for the same condition in each village each week. Our experience suggests that community health worker-collected data on mobile phones may be a feasible adjunct to other community- and healthcare-related data sources for surveillance of such conditions. Such systems are vitally needed in resource-limited settings like rural Nepal.\",\n \"corpus_id\": 6059743,\n \"score\": 0\n },\n {\n \"doc_id\": \"27686765\",\n \"title\": \"[Impact of PM2.5 on daily outpatient numbers for respiratory diseases in Shenzhen, China].\",\n \"abstract\": \"Objective: To assess the association between the concentration of the air pollutant PM2.5 and daily outpatient visits for respiratory disease. Methods: All records of daily outpatient visits to three hospitals in Shenzhen from January 1 to December 31, 2013 were collected. Daily air pollution monitoring and meteorology data from the same period were also collected in Shenzhen. The data were analyzed using a semiparametric generalized additive model with Poisson distribution of time series analysis controlling for long-term and seasonal trends, flu, DOW, public holidays, and meteorological factors. The excess risk(ER)of respiratory disease and its 95% CI value were calculated, along with the incremental increase of 10 μg/m(3) in PM2.5 concentration. Results: Number of outpatient visits for respiratory diseases totaled 1 428 672(daily range: 1 790-5 228). The annual average PM2.5 concentration was 40.2 μg/m(3)(daily range: 7.2-137.1 μg/m(3)). The lag1 factor had the most significant impact on the lag effect. We estimated that a 10 μ g/m(3) increase in day-before PM2.5 concentration was associated with a 1.809%(95% CI: 1.709%-1.909%)ER of visits for respiratory disease. After controlling for other pollutants(NO2, CO, and O3), the effect remained stable. When NO2, CO, and O3 were introduced separately, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of daily outpatient visits for respiratory disease was 1.814%(95% CI: 1.706%-1.923%), 2.780%(95% CI: 2.668%-2.892%), and 1.513%(95% CI: 1.403%-1.624%), respectively. With simultaneous control of NO2 and O3, NO2 and CO, and CO and O3, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of respiratory disease was 1.369%(95% CI: 1.242%-1.497%), 2.709%(95% CI: 2.590%-2.828%), and 2.577%(95% CI: 2.452%-2.702%), respectively. With simultaneous control of NO2, CO, and O3, for every 10 μg/m(3) rise in PM2.5 concentration, the excess risk of respiratory disease was 2.370%(95% CI: 2.231%-2.509%). Conclusions: PM2.5 can increase the risk of outpatient visits for respiratory disease in Shenzhen.\",\n \"corpus_id\": 20269834,\n \"score\": 0\n },\n {\n \"doc_id\": \"27782160\",\n \"title\": \"Global-scale river flood vulnerability in the last 50 years.\",\n \"abstract\": \"The impacts of flooding are expected to rise due to population increases, economic growth and climate change. Hence, understanding the physical and spatiotemporal characteristics of risk drivers (hazard, exposure and vulnerability) is required to develop effective flood mitigation measures. Here, the long-term trend in flood vulnerability was analysed globally, calculated from the ratio of the reported flood loss or damage to the modelled flood exposure using a global river and inundation model. A previous study showed decreasing global flood vulnerability over a shorter period using different disaster data. The long-term analysis demonstrated for the first time that flood vulnerability to economic losses in upper-middle, lower-middle and low-income countries shows an inverted U-shape, as a result of the balance between economic growth and various historical socioeconomic efforts to reduce damage, leading to non-significant upward or downward trends. We also show that the flood-exposed population is affected by historical changes in population distribution, with changes in flood vulnerability of up to 48.9%. Both increasing and decreasing trends in flood vulnerability were observed in different countries, implying that population growth scenarios considering spatial distribution changes could affect flood risk projections.\",\n \"corpus_id\": 4853675,\n \"score\": 0\n },\n {\n \"doc_id\": \"28458242\",\n \"title\": \"Short-term effects of ambient air pollution on pediatric outpatient visits for respiratory diseases in Yichang city, China.\",\n \"abstract\": \"Previous studies have suggested that short-term exposure to ambient air pollution was associated with pediatric hospital admissions and emergency room visits for certain respiratory diseases; however, there is limited evidence on the association between short-term air pollution exposure and pediatric outpatient visits. Our aim was to quantitatively assess the short-term effects of ambient air pollution on pediatric outpatient visits for respiratory diseases. We conducted a time-series study in Yichang city, China between Jan 1, 2014 and Dec 31, 2015. Daily counts of pediatric respiratory outpatient visits were collected from 3 large hospitals, and then linked with air pollution data from 5 air quality monitoring stations by date. We used generalized additive Poisson models to conduct linear and nonlinear exposure-response analyses between air pollutant exposures and pediatric respiratory outpatient visits, adjusting for seasonality, day of week, public holiday, temperature, and relative humidity. Each interquartile range (IQR) increase in PM2.5 (lag 0), PM10 (lag 0), NO2 (lag 0), CO (lag 0), and O3 (lag 4) concentrations was significantly associated with a 1.91% (95% CI: 0.60%, 3.23%), 2.46% (1.09%, 3.85%), 1.88% (0.49%, 3.29%), 2.00% (0.43%, 3.59%), and 1.91% (0.45%, 3.39%) increase of pediatric respiratory outpatient visits, respectively. Similarly, the nonlinear exposure-response analyses showed monotonic increases of pediatric respiratory outpatient visits by increasing air pollutant exposures, though the associations for NO2 and CO attenuated at higher concentrations. These associations were unlikely modified by season. We did not observe significant association for SO2 exposure. Our results suggest that short-term exposures to PM2.5, PM10, NO2, CO, and O3 may account for increased risk of pediatric outpatient visits for respiratory diseases, and emphasize the needs for reduction of air pollutant exposures for children.\",\n \"corpus_id\": 37414954,\n \"score\": 0\n },\n {\n \"doc_id\": \"29121954\",\n \"title\": \"Temporal variation in confirmed diagnosis of fever-related malarial cases among children under-5 years by community health workers and in health facilities between years 2013 and 2015 in Siaya County, Kenya.\",\n \"abstract\": \"BACKGROUND: Malaria case management continues to experience dynamic changes. Building community capacity is instrumental in both prevention and treatment of malaria. The World Health Organization (WHO) recommends utilization of well-trained and supervised community health workers (CHWs) to reduce the burden of malaria deaths among children under-5 years of age in Africa. Longitudinally-tracked information on utilization of CHWs by communities in terms of trends in diagnosis of malaria in children under-5 years of age is essential in influencing national and local malaria control policies and strategies. METHODS: A desktop review was carried out of a database consisting of confirmed uncomplicated malaria cases in 10 villages using CHWs and out-patient departments of 10 health facilities in children under-five for the period of 3 years between January 2013 and December 2015. Analyses of association between the diagnosed cases and satellite-based rainfall, village and time (months and years) were carried out using a Poisson regression model. RESULTS: Analysis of malaria diagnoses made by CHWs showed the following trends: (i) the incidence of reported documented malaria-positive fever cases increased with time (2013-2015) and the difference over the years was statistically significant (P < 0.001), (ii) specific village was significantly associated (P < 0.001) with reporting malaria-positive fever cases, (iii) the long-term monthly sequence starting from highest to lowest incidence of reported malaria-positive fever cases was July, May and June, March, August, April, September, November, and February, October and, finally, January, and the difference in reported malaria-positives between the months was statistically significant (P = 0.001) and (iv) none of the tested rainfall regimes (current, lagged or cumulative) was associated with reported malaria-positive fever cases during the 3-year period (P > 0.1). Looking at the number of diagnoses made at the health facilities, (i) The number of reported malaria-positive fever cases decreased with time (2013-2015) and the difference among the years was not statistically significant (P = 0.399), (ii) The long-term monthly sequence starting from highest to lowest number of reported malaria-positive fever cases was July, June, May, April, January, August, March, February, September, November, October and December, and the difference between the months was statistically significant (P < 0.001). CONCLUSIONS: CHWs have the potential to play a major role in diagnosing and treating malaria, thereby decreasing under-five children mortality. Temporally, the risk of diagnosing malaria seems predictable and this may present opportunities for policy-targeted malaria preparedness and control. The findings are expected to support policy actions that may scale-up community health services in remote rural settings.\",\n \"corpus_id\": 21292417,\n \"score\": 0\n },\n {\n \"doc_id\": \"29440305\",\n \"title\": \"Exposure to traffic-related air pollution and acute bronchitis in children: season and age as modifiers.\",\n \"abstract\": \"BACKGROUND: Acute bronchitis (AB) is one of the principal causes of childhood morbidity. Increasing number of studies has shown that air pollution is an important environmental contributor of respiratory disease. However, evidence so far is scarce regarding the effects of air pollution on childhood AB, and it also remains unclear how the risk of AB will change by season and age. METHODS: Data on hospital visits for AB in children, air pollution and meteorological factors from 1 January 2015 to 31 December 2016 were collected in Hefei, China. Time-series analysis was applied to assess the short-term effects of traffic-related air pollution on childhood AB outpatient visits. A Poisson generalised linear regression model combined with a distributed lag non-linear model was used to estimate the relationships, controlling for long-term trends, seasonal patterns, meteorological factors and other possible confounders. RESULTS: We found that an IQR increase in concentrations of nitrogen dioxide, particulate matter <2.5 µm and carbon monoxide significantly increased the daily hospital visits for childhood AB with 4-day cumulative effect estimates (relative risks: 1.03, 95% CI 1.01 to 1.05; 1.09, 95% CI 1.07 to 1.11; 1.07, 95% CI 1.05 to 1.09). Notably, the risk estimates during the cold season are pronounced; however, no significant association was observed during the warm season. Interestingly, children aged 6-14 years were more vulnerable to air pollutants than children aged less than 1 year and within 1-5 years. However, no gender difference was observed. CONCLUSION: A significant association of traffic-related air pollution and increased department visits for childhood AB was observed, notably in school-age children and during the cold season.\",\n \"corpus_id\": 46778515,\n \"score\": 0\n },\n {\n \"doc_id\": \"29482552\",\n \"title\": \"Short-term effects of ambient fine particulate matter pollution on hospital visits for chronic obstructive pulmonary disease in Beijing, China.\",\n \"abstract\": \"BACKGROUND: Little is known about the effect of ambient fine particulate matter (PM2.5) on chronic obstructive pulmonary disease (COPD) in China. The objective of this study was to explore the short-term effects of PM2.5 on outpatient and inpatient visits for COPD in Beijing, China. METHODS: A total of 3,503,313 outpatient visits and 126,982 inpatient visits for COPD between January 1, 2010, and June 30, 2012, were identified from the Beijing Medical Claim Data for Employees. A generalized additive Poisson model was applied to estimate the percentage change with 95% confidence interval (CI) in hospital visits for COPD in relation to an interquartile range (IQR) (90.8 μg/m3) increase in PM2.5 concentrations. RESULTS: Short-term exposure to PM2.5 was significantly associated with increased use of COPD-related health services. There were clear exposure-response associations of PM2.5 with COPD outpatient and inpatient visits. An IQR increase in the concurrent day PM2.5 concentrations was significantly associated with a 2.38% (95% CI, 2.22%-2.53%) and 6.03% (95% CI, 5.19%-6.87%) increase in daily outpatient visits and inpatient visits, respectively. Elderly people were more sensitive to the adverse effects. The estimated risk was higher during the warm season compared to the cool season. CONCLUSIONS: Short-term exposure to PM2.5 was associated with increased risk of hospital visits for COPD. Our findings contributed to the limited evidence concerning the effects of ambient PM2.5 on COPD morbidity in developing countries.\",\n \"corpus_id\": 3571414,\n \"score\": 0\n },\n {\n \"doc_id\": \"29751419\",\n \"title\": \"Mapping flood susceptibility in mountainous areas on a national scale in China.\",\n \"abstract\": \"Mountainous terrain covers nearly half of China and is susceptible to floods, which can lead to substantial losses of human life and property. Historical flooding records from government bulletins and newspapers, the only available information regarding floods that have occurred in some mountainous areas, are valuable for understanding flood disaster mechanisms in these regions. In this study, the flood susceptibility in mountainous regions in China was mapped based on historical flooding records from 1949 to 2000. A Random Forest (RF) model, which can handle large datasets through factor contribution analysis, was chosen to characterize the relationships between flooding occurrences and twelve geographic, meteorological, and hydrological explanatory factors. The results indicate that the RF model can effectively identify flood-prone areas and has advantages over artificial neural network (ANN) and support vector machine (SVM) methods. Among these explanatory factors, the geographic factors (elevation, longitude and drainage density) are the most important predictors of flooding in China's mountainous areas, whereas the hydrological factors (relative elevation and curve number) are the least important. Two independent datasets of historical flooding events from the Bulletin of Flood and Drought Disasters in China (2006-2014) alongside news reports and yearbooks (2008-2014) were collected and chosen to validate the capability of the RF model. The validation results confirm that the RF model can identify the flood susceptibility with satisfactory accuracy. This study proposes a preliminary flood susceptibility map of mountainous areas in China and provides a reference for predicting and mitigating potentially disastrous flooding events.\",\n \"corpus_id\": 21659876,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":51,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29686383\",\n \"title\": \"The IL-33-PIN1-IRAK-M axis is critical for type 2 immunity in IL-33-induced allergic airway inflammation.\",\n \"abstract\": \"Interleukin 33 (IL-33) is among the earliest-released cytokines in response to allergens that orchestrate type 2 immunity. The prolyl cis-trans isomerase PIN1 is known to induce cytokines for eosinophil survival and activation by stabilizing cytokines mRNAs, but the function of PIN1 in upstream signaling pathways in asthma is unknown. Here we show that interleukin receptor associated kinase M (IRAK-M) is a PIN1 target critical for IL-33 signaling in allergic asthma. NMR analysis and docking simulations suggest that PIN1 might regulate IRAK-M conformation and function in IL-33 signaling. Upon IL-33-induced airway inflammation, PIN1 is activated for binding with and isomerization of IRAK-M, resulting in IRAK-M nuclear translocation and induction of selected proinflammatory genes in dendritic cells. Thus, the IL-33-PIN1-IRAK-M is an axis critical for dendritic cell activation, type 2 immunity and IL-33 induced airway inflammation.\",\n \"corpus_id\": 5078958\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18188456","title":"Pin1 regulates TGF-beta1 production by activated human and murine eosinophils and contributes to allergic lung fibrosis.","abstract":"Eosinophilic inflammation is a cornerstone of chronic asthma that often culminates in subepithelial fibrosis with variable airway obstruction. Pulmonary eosinophils (Eos) are a predominant source of TGF-beta1, which drives fibroblast proliferation and extracellular matrix deposition. We investigated the regulation of TGF-beta1 and show here that the peptidyl-prolyl isomerase (PPIase) Pin1 promoted the stability of TGF-beta1 mRNA in human Eos. In addition, Pin1 regulated cytokine production by both in vitro and in vivo activated human Eos. We found that Pin1 interacted with both PKC-alpha and protein phosphatase 2A, which together control Pin1 isomerase activity. Pharmacologic blockade of Pin1 in a rat asthma model selectively reduced eosinophilic pulmonary inflammation, TGF-beta1 and collagen expression, and airway remodeling. Furthermore, chronically challenged Pin1(-/-) mice showed reduced peribronchiolar collagen deposition compared with wild-type controls. These data suggest that pharmacologic suppression of Pin1 may be a novel therapeutic option to prevent airway fibrosis in individuals with chronic asthma.","corpus_id":207693447,"score":2},{"doc_id":"18802081","title":"IL-33 induces antigen-specific IL-5+ T cells and promotes allergic-induced airway inflammation independent of IL-4.","abstract":"Type 2 cytokines (IL-4, IL-5, and IL-13) play a pivotal role in helminthic infection and allergic disorders. CD4(+) T cells which produce type 2 cytokines can be generated via IL-4-dependent and -independent pathways. Although the IL-4-dependent pathway is well documented, factors that drive IL-4-independent Th2 cell differentiation remain obscure. We report here that the new cytokine IL-33, in the presence of Ag, polarizes murine and human naive CD4(+) T cells into a population of T cells which produce mainly IL-5 but not IL-4. This polarization requires IL-1R-related molecule and MyD88 but not IL-4 or STAT6. The IL-33-induced T cell differentiation is also dependent on the phosphorylation of MAPKs and NF-kappaB but not the induction of GATA3 or T-bet. In vivo, ST2(-/-) mice developed attenuated airway inflammation and IL-5 production in a murine model of asthma. Conversely, IL-33 administration induced the IL-5-producing T cells and exacerbated allergen-induced airway inflammation in wild-type as well as IL-4(-/-) mice. Finally, adoptive transfer of IL-33-polarized IL-5(+)IL-4(-)T cells triggered airway inflammation in naive IL-4(-/-) mice. Thus, we demonstrate here that, in the presence of Ag, IL-33 induces IL-5-producing T cells and promotes airway inflammation independent of IL-4.","corpus_id":33713359,"score":2},{"doc_id":"19996739","title":"Signaling pathways critical for allergic airway inflammation.","abstract":"PURPOSE OF REVIEW: Activated mast cells, basophils, and CD4 helper T cells have critical roles in allergic inflammation. Therefore, devising ways to specifically inhibit these cells will likely be useful for controlling allergic inflammation. We summarize recent findings regarding the role of mast cells and basophils in allergic responses and the regulation of signaling pathways downstream of the IgE receptor, the chief inducer of mast cell and basophil activation. We also highlight studies addressing the roles of the protein tyrosine kinases Zap-70 and Itk in immune system development and in the regulation of CD4 helper T cell responses. RECENT FINDINGS: Recent work has demonstrated that mast cell function is unexpectedly diverse and that basophils have a more prominent role in Th2-type immune responses than previously appreciated. Biochemical analysis of the IgE receptor signaling pathway has led to insights regarding the roles of phosphatases and other enzymes in this process. Studies of Zap-70 and Itk have helped to define the potential outcomes and complications of inhibiting these enzymes in order to suppress allergic inflammation. SUMMARY: Analysis of genetically engineered mice and biochemical studies continue to help unravel the molecular pathways that drive allergic inflammatory reactions. The knowledge acquired may lead to novel approaches for suppressing allergic inflammation.","corpus_id":31147422,"score":2},{"doc_id":"20029461","title":"Intracellular signaling mechanisms regulating the activation of human eosinophils by the novel Th2 cytokine IL-33: implications for allergic inflammation.","abstract":"The novel interleukin (IL)-1 family cytokine IL-33 has been shown to activate T helper 2 (Th2) lymphocytes, mast cells and basophils to produce an array of proinflammatory cytokines, as well as to mediate blood eosinophilia, IgE secretion and hypertrophy of airway epithelium in mice. In the present study, we characterized the activation of human eosinophils by IL-33, and investigated the underlying intracellular signaling mechanisms. IL-33 markedly enhanced eosinophil survival and upregulated cell surface expression of the adhesion molecule intercellular adhesion molecule (ICAM)-1 on eosinophils, but it suppressed that of ICAM-3 and L-selectin. In addition, IL-33 mediates significant release of the proinflammatory cytokine IL-6 and the chemokines CXCL8 and CCL2. We found that IL-33-mediated enhancement of survival, induction of adhesion molecules, and release of cytokines and chemokines were differentially regulated by activation of the nuclear factor (NF)-kappaB, p38 mitogen-activated protein kinase (MAPK) and extracellular signal-regulated kinase (ERK) pathways. Furthermore, we compared the above IL-33 activities with two structurally and functionally related cytokines, IL-1beta and IL-18. IL-1beta, but not IL-18, markedly upregulated cell surface expression of ICAM-1. IL-1beta and IL-18 also significantly enhanced eosinophil survival, and induced the release of IL-6 and chemokines CXCL8 and CCL2 via the activation of the NF-kappaB, p38 MAPK and ERK pathways. Synergistic effects on the release of IL-6 were also observed in combined treatment with IL-1beta, IL-18 and IL-33. Taken together, our findings provide insight into IL-33-mediated activation of eosinophils via differential intracellular signaling cascades in the immunopathogenesis of allergic inflammation.","corpus_id":25497766,"score":2},{"doc_id":"20357831","title":"Cytokine gene-modulated dendritic cells protect against allergic airway inflammation by inducing IL-10(+)IFN-gamma(+)CD4(+) T cells.","abstract":"Asthma is characterized by allergen-induced airway inflammation orchestrated by Th2 cells. Dendritic cells (DCs) were found to efficiently prime naive T-helper cells. Thus, modification of DC function may be used as an ideal tool to treat allergic asthma by changing CD4(+) T-cell differentiation or suppressing Th2 development. In this study, we examined whether a DC-based vaccine can be applied to DCs modified with interleukin (IL)-10- and IL-12-expressing adenoviruses to prevent ovalbumin (OVA)-induced asthma in mice. Herein, we show that these modified DCs efficiently moderated the characteristics of asthma, including expressions of OVA-specific antibodies, airway hyperresponsiveness, eosinophilic airway inflammation, and Th2 cytokines production. Additionally, IL-10 and IL-12 gene-modified DCs enhanced the development of both T-helper type 1 (Th1) and IL-10(+)IFN-gamma(+) (interferon-gamma) double-positive T cells in vivo. In vitro-generated OVA-specific IL-10(+)IFN-gamma(+)CD4(+) T cells inhibited the proliferation of naive CD4(+) T cells, and this suppressive effect was a cell contact-dependent mechanism. Furthermore, we showed that combined cytokine-modulated DCs could alleviate established allergic airway inflammation. Taken together, these results suggest that IL-10 and IL-12 gene-modulated DCs are effective in suppressing asthmatic airway inflammation through both immune deviation and immune suppression and are a potential therapeutic approach for asthma.","corpus_id":20661600,"score":2},{"doc_id":"20425513","title":"Pathogenesis of allergic airway inflammation.","abstract":"Advances have been made in defining the mechanisms for the control of allergic airway inflammation in response to inhaled antigens. Several genes, including ADAM33, DPP10, PHF11, GPRA, TIM-1, PDE4D, OPN3, and ORMDL3, have been implicated in the pathogenesis and susceptibility to atopy and asthma. Growing evidence associates asthma with a systemic propensity for allergic T-helper type 2 cytokines. Disordered coagulation and fibrinolysis also exacerbate asthma symptoms. Balance among functionally distinct dendritic cell subsets contributes to the outcome of T-cell-mediated immunity. Allergen-specific T-regulatory cells play a pivotal role in the development of tolerance to allergens and immune suppression. The major emphasis on immunotherapy for asthma during the past decade has been to direct the immune response to a type 1 response, or immune tolerance. In this review, we discuss the current information on the pathogenesis of allergic airway inflammation and potential immunotherapy, which could be beneficial in the treatment of airway inflammation, allergy, and asthma.","corpus_id":7754748,"score":2},{"doc_id":"20599782","title":"The interleukin-1 receptor-associated kinases: critical regulators of innate immune signalling.","abstract":"The interleukin receptor-associated kinase (IRAK) family are involved in regulating Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways. TLRs are pattern recognition receptors of the innate immune response that are responsible for sensing pathogens and initiating immunity, while IL-1 is one of the key cytokines that mediates inflammation. As such, IL-1/TLR signalling pathways and the IRAK family are critical in anti-pathogen responses, inflammation and autoimmunity. The family comprises of four members, IRAK-1, IRAK-2, IRAK-M (IRAK-3) and IRAK-4, and has a role in both positive and negative regulation of signal transduction. While it was once thought that the family displayed some redundancy, each member of the family is emerging as a distinct and vital contributor to IL-1/TLR signalling mechanisms. Knockout mouse studies have explored the relative contribution of each of the IRAKs in IL-1/TLR signalling, while the recent generation of kinase-inactive knock-in IRAK-4 mice have revealed which of IRAK-4 functions require its kinase activity. IRAK-2, previously thought of as a pseudokinase, has recently been proposed to have kinase activity that is essential for TLR signalling. Not surprisingly given their critical role in IL-1/TLR signalling, the IRAK family members have been implicated in certain disease models including human immunodeficiencies. Thus the potential targeting of these essential protein kinases therapeutically is also discussed.","corpus_id":22566434,"score":2},{"doc_id":"21461246","title":"IL-33 and Airway Inflammation.","abstract":"Interleukin-33 (IL-33) is the 11th member of IL-1 cytokine family which includes IL-1 and IL-18. Unlike IL-1β and IL-18, IL-33 is suggested to function as an alarmin that is released upon endothelial or epithelial cell damage and may not enhance acquired immune responses through activation of inflammasome. ST2, a IL-33 receptor component, is preferentially expressed by T-helper type (Th) 2 cells, mast cells, eosinophils and basophils, compared to Th1 cells, Th17 cells and neutrophils. Thus, IL-33 profoundly enhances allergic inflammation through increased expression of proallergic cytokines and chemokines. Indeed, IL-33 and its receptor genes are recognized as the most susceptible genes for asthma by several recent genomewide association studies. It has also recently been shown that IL-33 plays a crucial role in innate eosinophilic airway inflammation rather than acquired immune responses such as IgE production. As such, IL-33 provides a unique therapeutic way for asthma, i.e., ameliorating innate airway inflammation.","corpus_id":9260626,"score":2},{"doc_id":"21469105","title":"IL-33-activated dendritic cells are critical for allergic airway inflammation.","abstract":"IL-33, a new member of the IL-1 family cytokine, is involved in Th2-type responses in a wide range of diseases and signals through the ST2 receptor expressed on many immune cells. Since the effects of IL-33 on DCs remain controversial, we investigated the ability of IL-33 to modulate DC functions in vitro and in vivo. Here, we report that IL-33 activates myeloid DCs to produce IL-6, IL-1b, TNF, CCL17 and to express high levels of CD40, CD80 OX40L and CCR7. Importantly, IL-33-activated DCs prime naive lymphocytes to produce the Th2 cytokines IL-5 and IL-13, but not IL-4. In vivo, IL-33 exposure induces DC recruitment and activation in the lung. Using an OVA-induced allergic lung inflammation model, we demonstrate that the reduced airway inflammation in ST2-deficient mice correlates with the failure in DC activation and migration to the draining LN. Finally, we show that adoptive transfer of IL-33-activated DCs exacerbates lung inflammation in a DC-driven model of allergic airway inflammation. These data demonstrate for the first time that IL-33 activates DCs during antigen presentation and thereby drives a Th2-type response in allergic lung inflammation.","corpus_id":1822987,"score":2},{"doc_id":"21624504","title":"The active contribution of Toll-like receptors to allergic airway inflammation.","abstract":"Epithelia lining the respiratory tract represent a major portal of entry for microorganisms and allergens and are equipped with innate and adaptive immune signaling receptors for host protection. These include Toll-like receptors (TLRs) that recognize microbial components and evoke diverse responses in cells of the respiratory system. TLR stimulation by microorganism-derived molecules activates antigen presenting cells, control T helper (Th) 1, Th2, and Th17 immune cell differentiation, cytokine production by mast cells, and activation of eosinophils. It is clear that TLR are involved in the pathophysiology of allergic airway diseases such as asthma. Dendritic cells (DCs), a kind of antigen presenting cells, which play a key role in the induction of allergic airway inflammation, are privileged targets for pathogen associated molecular patterns (PAMPs). During the allergic responses, engagement of TLRs on DCs determines the Th2 polarization of the T cells. TLR signaling in mast cells increases the release of IL-5, and TLR activation of airway epithelial cells forces the generation of proallergic Th2 type of cytokines. Although these responses aim to protect the host, they may also result in inflammatory tissue damage in the airway. Under certain conditions, stimulation of TLRs, in particular, TLR9, may reduce Th2-dependent allergic inflammation by induction of Th1 responses. Therefore, understanding the complex regulatory roles of TLRs in the pathogenesis of allergic airway inflammation should facilitate the development of preventive and therapeutic measures for asthmatic patients.","corpus_id":30335225,"score":2},{"doc_id":"24446582","title":"Blockade of IL-33/ST2 ameliorates airway inflammation in a murine model of allergic asthma.","abstract":"OBJECTIVE: Interleukin (IL)-33 is involved in the development of lung inflammation by inducing or amplifying Th2 type-mediated responses in various animal models of allergic asthma. The ST2 gene is a member of the IL-1 receptor family, producing a transmembrane form (ST2L) and a soluble secreted form (sST2). sST2 has been shown to block this IL-33/ST2 signaling pathway. This study aimed to investigate whether anti-IL-33 and sST2 reduced airway inflammation in a murine model of asthma. METHODS: BALB/c mice were sensitized and challenged with ovalbumin (OVA), and the effect of sST2 and anti-IL-33 antibody on airway inflammation and airway hyperresponsiveness (AHR) was evaluated. Furthermore, we measured changes in various cytokines in the bronchoalveolar lavage (BAL) fluid when treated with sST2 or anti-IL-33. RESULTS: We observed that anti-IL-33 antibody and sST2 exert a negative regulation on OVA-mediated allergic airway inflammation. Both treatments reduced total cell counts and eosinophil counts in BAL fluid and AHR to methacholine. The Th2 cytokines, such as IL-4, IL-5, and IL-13 in BAL fluid were also significantly decreased after both treatments. However, there were no changes in the level of TGF- ß1 and IL-10 after each treatment. CONCLUSIONS: These results suggest that anti-IL-33 as well as sST2 have therapeutic potential for allergic asthma through inhibition of Th2 cytokine production.","corpus_id":22974724,"score":2},{"doc_id":"24487979","title":"IL-25 promotes Th2 immunity responses in airway inflammation of asthmatic mice via activation of dendritic cells.","abstract":"Allergic asthma occurs as a consequence of inappropriate immunologic inflammation to allergens and characterized by Th2 adaptive immune response. Recent studies indicated that interleukin (IL)-25, a member of the IL-17 cytokine family, had been implicated in inducing Th2 cell-dependent inflammation in airway epithelium and IL-25-deficient mice exhibit impaired Th2 immunity responses; however, how these cytokines influence innate immune responses remains poorly understood. In this study, we used ovalbumin (OVA) sensitization and challenge to induce the murine asthmatic model and confirmed by histological analysis of lung tissues and serum levels of total and OVA-specific immunoglobulin (Ig)-E. The expression of IL-25 was detected by quantitative real-time PCR and immunohistochemistry, respectively, and the dendritic cells (DCs) activation was detected by levels of CD80 and CD86 in bronchoalveolar lavage fluid (BALF) by flow cytometry. The mice sensitized and challenged with OVA showed high expression of IL-25 in both mRNA and protein levels in lungs. We detected the expression of CD80 and CD86 in BALF was also increased. A tight correlation between IL-25 mRNA and other Th2 cells producing cytokines such as IL-4, IL-5, and IL-13 in BALF was identified. Furthermore, when the asthmatic mice were treated with inhaled corticosteroids, the inflammatory cells infiltration and the inflammatory cytokines secretion were significantly decreased. In this study, we show that IL-25 promoted the accumulation of co-stimulatory molecules of CD80 and CD86 on DCs and then induced the differentiation of prime naive CD4(+) T cells to become proinflammatory Th2 cells and promoted Th2 cytokine responses in OVA-induced airway inflammation. The ability of IL-25 to promote the activation and differentiation of DCs population was identified as a link between the IL-17 cytokine family and the innate immune response and suggested a previously unrecognized innate immune pathway that promotes Th2 cytokine responses in asthmatic airway inflammation. Inhaled corticosteroids might be capable of inhibiting the promotion of IL-25 and present a promising strategy for the treatment of asthma.","corpus_id":21571675,"score":2},{"doc_id":"25479317","title":"The paradigm of cytokine networks in allergic airway inflammation.","abstract":"PURPOSE OF REVIEW: Cytokines are immunomodulatory proteins important in cell signaling. Complex interactions of innate and adaptive immune cells, as well as structural cells and their cytokines, play crucial roles in regulating allergic airway inflammation. Here, we summarize current knowledge about the potential roles of known and newly identified helper T cells and epithelial cell-derived cytokines [interleukin (IL)-9, IL-17, IL-22, IL-25, and IL-33] in allergic rhinitis and asthma. RECENT FINDINGS: Although T-helper (Th)2 cells were considered to be the main orchestrators of allergic airway inflammation, recent studies have revealed the potential interaction of other helper T cells and their cytokines in this process. Th17 cells may have a role in allergic rhinitis and asthma, and chronic rhinosinusitis with nasal polyps. An IL-9-producing subset called Th9 cells, Th22 cells which primarily secrete IL-22, IL-13, tumor necrosis factor-α, Th25 cells via producing IL-25 and epithelial cell-derived thymic stromal lymphopoietin, IL-33, IL-31, and IL-25 are believed to be important for the initiation of allergic reactions and inducing airway inflammation. SUMMARY: A new paradigm of an interplay of cytokines is important in allergic rhinitis and asthma in orchestrating the allergic inflammatory response. Potential therapeutic applications emerging from the roles of these cytokines are promising, but need further research.","corpus_id":3281721,"score":2},{"doc_id":"25878673","title":"Therapeutic potential of anti-IL-6 therapies for granulocytic airway inflammation in asthma.","abstract":"BACKGROUND: Determining the cellular and molecular phenotypes of inflammation in asthma can identify patient populations that may best benefit from targeted therapies. Although elevated IL-6 and polymorphisms in IL-6 signalling are associated with lung dysfunction in asthma, it remains unknown if elevated IL-6 levels are associated with a specific cellular inflammatory phenotype, and how IL-6 blockade might impact such inflammatory responses. METHODS: Patients undergoing exacerbations of asthma were phenotyped according to their airway inflammatory characteristics (normal cell count, eosinophilic, neutrophilic, mixed granulocytic), sputum cytokine profiles, and lung function. Mice were exposed to the common allergen, house dust-mite (HDM), in the presence or absence of endogenous IL-6. The intensity and nature of lung inflammation, and levels of pro-granulocytic cytokines and chemokines under these conditions were analyzed. RESULTS: Elevated IL-6 was associated with a lower FEV1 in patients with mixed eosinophilic-neutrophilic bronchitis. In mice, allergen exposure increased lung IL-6 and IL-6 was produced by dendritic cells and alveolar macrophages. Loss-of-function of IL-6 signalling (knockout or antibody-mediated neutralization) abrogated elevations of eosinophil and neutrophil recruiting cytokines/chemokines and allergen-induced airway inflammation in mice. CONCLUSIONS: We demonstrate the association of pleiotropic cellular airway inflammation with IL-6 using human and animal data. These data suggest that exacerbations of asthma, particularly those with a combined eosinophilic and neutrophilic bronchitis, may respond to therapies targeting the IL-6 pathway and therefore, provide a rational basis for initiation of clinical trials to evaluate this.","corpus_id":8376496,"score":2},{"doc_id":"26232935","title":"Critical role of IL-6 in dendritic cell-induced allergic inflammation of asthma.","abstract":"UNLABELLED: Interleukin (IL)-6 plays important roles in autoimmunity and inflammation and is essential for T helper (Th) 2 and Th17 differentiation. However, whether it is involved in the development and function of dendritic cells (DCs) during allergen-induced airway inflammation and airway hyper-reactivity (AHR) remains undefined. In this study, Dermatophagoides pteronyssinus (Der p)-induced airway inflammation and AHR were studied in IL-6 knockout (KO) mice. Der p-loaded bone marrow-derived DCs (BMDCs) from IL-6 KO mice were used to assaying their ability to induce airway inflammation in naïve wild-type mice. Our results showed that IL-6 KO mice showed reduced AHR, significant decreases in inflammatory cell recruitment and Th2 and Th17 cytokine production in the airways, and lowered Der p-specific immunoglobulin G1 after Der p exposure. Further exploration of BMDCs from IL-6 KO mice revealed decreased activity of phagocytosis and reduced expression of MHC class II and CD86 after Der p stimulation. Adoptive transfer of Der p-loaded BMDCs from IL-6 KO mice also showed a functional defect in their inability to induce Th2 and Th17 immune responses and trigger airway inflammation and AHR in recipient mice. Finally, in allergic asthmatics, DCs that differentiated from monocytes treated with anti-IL-6 receptor antibody (tocilizumab) had poor capacity for eliciting Th2 polarization as compared to DCs generated from monocytes without antibody treatment. In conclusion, IL-6 signaling in DCs is essential for their uptake of allergens, maturation, and initiation of Th2/Th17-mediated airway inflammation and AHR in asthma, thus providing a new potential target for treating allergic asthma. KEY MESSAGES: IL-6 signaling is important for DCs to take up allergens and to initiate Th2/Th17-mediated airway inflammation. DCs from allergic asthmatics treated with anti-IL-6 receptor antibody had poor capacity for eliciting Th2 polarization. Anti-IL-6 treatment may provide a new potential target for treating allergic asthma.","corpus_id":17019620,"score":2},{"doc_id":"28665693","title":"Critical Role of IRAK-M in Regulating Antigen-induced Airway Inflammation.","abstract":"Asthma is an airway epithelium disorder involving allergic lung inflammation. IRAK-M is a negative regulator of Toll-like receptor (TLR) signaling on airway epithelial cells and macrophages and known to limit overproduction of cytokines during the inflammatory process. However, the direct role of IRAK-M on asthma pathogenesis is unclear. In the present study, we found significant elevation of IRAK-M expression in mouse lungs following ovalbumin (OVA) exposure. Compared to wild type (WT) mice, IRAK-M knockout (KO) mice responded to OVA challenge with significantly worse infiltration of airway inflammatory cells, greater airway responsiveness, higher proinflammatory cytokine levels in lung homogenates, and more prominent Th2 and Th17 deviation. OVA exposure also induced higher activities of dendritic cells (DCs) and macrophages from IRAK-M KO mouse lungs. Furthermore, adoptive transfer of either IRAK-M KO bone marrow derived-DCs or -macrophages into WT mice aggravated OVA-induced airway inflammation. In vitro experiments showed that IRAK-M KO naïve CD4+ T cells were more prone to differentiate to Th17, but not Tregs. Consistently, activation of IκBζ was significantly increased in absence of IRAK-M to facilitate Th17 polarization. These findings suggest that IRAK-M plays a crucial role in the regulation of allergic airway inflammation through modifying the function of airway epithelia, DCs, macrophages and differentiation of naïve CD4+ T cell. Modulation of IRAK-M may provide a novel target to control asthma.","corpus_id":207718594,"score":2},{"doc_id":"28951634","title":"Effect of IRAK-M on Airway Inflammation Induced by Cigarette Smoking.","abstract":"BACKGROUND: IRAK-M, negatively regulating Toll-like receptor, is shown the dual properties in the varied disease contexts. We studied the effect of IRAK-M deficiency on cigarette smoking- (CS-) induced airway inflammation under acute or subacute conditions in a mouse model. METHODS: A number of cellular and molecular techniques were used to detect the differences between IRAK-M knockout (KO) and wild type (WT) mice exposed to 3-day or 7-week CS. RESULTS: Airway inflammation was comparable between IRAK-M KO and WT mice under 3-day CS exposure. Upon short-term CS exposure and lipopolysaccharide (LPS) inhalation, IRAK-M KO mice demonstrated worse airway inflammation, significantly higher percentage of Th17 cells and concentrations of proinflammatory cytokines in the lungs, and significantly elevated expression of costimulatory molecules CD40 and CD86 by lung dendritic cells (DCs) or macrophages. Conversely, 7-week CS exposed IRAK-M KO mice demonstrated significantly attenuated airway inflammation, significantly lower concentrations of proinflammatory cytokines in the lungs, significantly increased percentage of Tregs, and lower expression of CD11b and CD86 by lung DCs or macrophages. CONCLUSIONS: IRAK-M plays distinctive effect on CS-induced airway inflammation, and influences Treg/Th17 balance and expression of costimulatory molecules by DCs and macrophages, depending on duration and intensity of stimulus.","corpus_id":21161981,"score":2},{"doc_id":"29556000","title":"Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33.","abstract":"Allergic inflammation has crucial roles in allergic diseases such as asthma. It is therefore important to understand why and how the immune system responds to allergens. Here we found that full-length interleukin 33 (IL-33FL), an alarmin cytokine with critical roles in type 2 immunity and asthma, functioned as a protease sensor that detected proteolytic activities associated with various environmental allergens across four kingdoms, including fungi, house dust mites, bacteria and pollens. When exposed to allergen proteases, IL-33FL was rapidly cleaved in its central 'sensor' domain, which led to activation of the production of type 2 cytokines in group 2 innate lymphoid cells. Preventing cleavage of IL-33FL reduced allergic airway inflammation. Our findings reveal a molecular mechanism for the rapid induction of allergic type 2 inflammation following allergen exposure, with important implications for allergic diseases.","corpus_id":4015423,"score":2},{"doc_id":"18178860","title":"The IL-3/IL-5/GM-CSF common receptor plays a pivotal role in the regulation of Th2 immunity and allergic airway inflammation.","abstract":"The eosinophil is a central effector cell in allergic asthma. Differentiation and function of eosinophils are regulated by the CD4 Th2 cytokines IL-3, IL-5, and GM-CSF, which all signal through a common beta receptor subunit (betac). Recent therapeutic approaches targeting IL-5 alone have not ablated tissue accumulation of eosinophils and have had limited effects on disease progression, suggesting important roles for IL-3 and GM-CSF. By using a mouse model of allergic airways inflammation, we show that allergen-induced expansion and accumulation of eosinophils in the lung are abolished in betac-deficient (betac-/-) mice. Moreover, betac deficiency resulted in inhibition of hallmark features of asthma, including airways hypersensitivity, mucus hypersecretion, and production of Ag-specific IgE. Surprisingly, we also identified a critical role for this receptor in regulating type 2 immunity. Th2 cells in the lung of allergen-challenged betac-/- mice were limited in their ability to proliferate, produce cytokines, and migrate to effector sites, which was attributed to reduced numbers of myeloid dendritic cells in the lung compartment. Thus, the betac plays a critical role in allergen-induced eosinophil expansion and infiltration and is pivotal in regulating molecules that promote both early and late phases of allergic inflammation, representing a novel target for therapy.","corpus_id":11571451,"score":1},{"doc_id":"19155487","title":"Potential contribution of IL-7 to allergen-induced eosinophilic airway inflammation in asthma.","abstract":"The primary function of IL-7 is to promote maturation and survival of T cells. Through microarray expression analysis, we previously observed that human blood eosinophils express mRNA for IL-7R alpha (CD127) and its common gamma chain (CD132). The purpose of this study was to determine whether eosinophils have functional IL-7 receptors and to assess the potential contribution of IL-7 to eosinophilic airway inflammation by evaluating its presence in bronchoalveolar lavage (BAL) fluid of subjects with atopic asthma before and after segmental bronchoprovocation with allergen. Immunoblot analysis revealed that CD127 is present in highly purified human blood eosinophils. Furthermore, eosinophils responded to IL-7 with phosphorylation of STAT5, up-regulation of the activation marker CD69, and prolonged survival. Neutralization of GM-CSF but not IL-5 significantly blunted these functional responses, suggesting that IL-7 mediates its effects by promoting eosinophil release of autologous GM-CSF. Notably, the suppressive effect of anti-GM-CSF on STAT5 phosphorylation occurred within 10 min of eosinophil exposure to IL-7. Thus, IL-7 likely activates eosinophil release of preformed rather than newly synthesized GM-CSF. The biological relevance of IL-7 to eosinophilia in vivo was implicated in a study of airway allergen challenge in patients with allergic asthma. IL-7 concentrations in BAL fluid increased significantly 48 h after segmental allergen challenge and were highly correlated with BAL eosinophils (r = 0.7, p < 0.001). In conclusion, the airway response to allergen is associated with the generation of IL-7, which may contribute to airway inflammation by promoting enhanced eosinophil activation and survival. Activation of eosinophils is a novel function for IL-7.","corpus_id":17422887,"score":1},{"doc_id":"19181383","title":"The kinase activities of interleukin-1 receptor associated kinase (IRAK)-1 and 4 are redundant in the control of inflammatory cytokine expression in human cells.","abstract":"IRAK-1 and IRAK-4 are protein kinases that mediate signaling by Toll/IL1/Plant R (TIR) domain-containing receptors including the IL-1, IL-18, and Toll-like receptors (TLRs). Although well studied in mouse systems, the mechanism by which they function in human systems is less clear. To extend our knowledge of how these proteins regulate inflammatory signaling in human cells, we genetically and pharmacologically manipulated IRAK-1 and IRAK-4 kinase activities in vitro. Ablation of IRAK-4 expression in human umbilical vein endothelial cells (HUVEC) with siRNA suppressed IL-1beta induced IL-6 and IL-8 production whereas IRAK-1 siRNA suppressed TNFalpha induced but not IL-1beta induced cytokine production. Complementation of IRAK-4-depleted cells with a kinase-inactive allele restored IL-1beta induced cytokine gene expression suggesting that the IRAK-4 kinase activity is dispensable relative to its scaffolding function. Consistent with this finding, an IRAK-4 selective kinase inhibitor (RO6245) that inhibited IRAK-1 degradation failed to block IL-1beta induced cytokine production. In contrast, an inhibitor of both IRAK-1 and IRAK-4 (RO0884) reduced IL-1beta induced p38 MAP kinase, c-Jun N-terminal kinase activation, and IL-6 production in HUVEC. RO0884 also antagonized IL-1beta, TNFalpha, and TLR-mediated cytokine production in human fibroblast-like synoviocytes and peripheral blood mononuclear cells. Therefore in human cells the non-kinase functions of IRAK-4 are essential, whereas the kinase activity of IRAK-4 appears redundant with that of IRAK-1. Pharmacologic inhibition of both kinases appears necessary to block pro-inflammatory cytokine production.","corpus_id":23928452,"score":1},{"doc_id":"19299500","title":"Pulmonary suppressor of cytokine signaling-1 induced by IL-13 regulates allergic asthma phenotype.","abstract":"RATIONALE: Th2 cytokines play an important role in allergic diseases. These cytokines activate signal transduction pathways, including Janus kinase/signal transducer and activator of transcription (STAT) signaling. Although the suppressor of cytokine signaling (SOCS) family protein, a negative regulator of the Janus kinase/STAT signaling pathway, contributes to helper T cell differentiation during immune responses, the role of SOCS proteins within the structural cells of a target organ has not been clarified in allergy. OBJECTIVES: To study the local function of SOCS in the development of asthma. METHODS: We used mouse models of IL-13- and ovalbumin (OVA)-induced allergic airway disease. Airway smooth muscle cells were cultured from patients with asthma. MEASUREMENTS AND MAIN RESULTS: The administration of IL-13 induced not only airway responses but also SOCS1 expression at the local inflammatory site. The up-regulated SOCS1 markedly suppressed IL-13-dependent STAT6 activation and eotaxin expression and subsequently down-regulated IL-13-induced airway inflammatory responses. The inactivation of SOCS1 induced airway hyperresponsiveness after IL-13 treatment even in hyporesponsive C57BL/6 background mice. In an OVA-induced model of allergic airway disease, allergen exposure up-regulated local SOCS1 expression, and the induction of SOCS1 in the airways attenuated allergen-induced airway responses. Inactivation of IL-13 inhibited SOCS1 induction in a model of allergic airway disease. Interestingly, airway smooth muscle cells from individuals with asthma had impaired up-regulation of SOCS1 after IL-13 stimulation. CONCLUSIONS: SOCS1 induction by IL-13 in airway structural cells is critical to negatively control allergic airway disease.","corpus_id":21458938,"score":1},{"doc_id":"19494515","title":"Role of IL-23-Th17 cell axis in allergic airway inflammation.","abstract":"Asthma is characterized by chronic airway inflammation with intense eosinophil and lymphocyte infiltration, mucus hyperproduction, and airway hyperresponsiveness to a variety of stimuli. It is now generally accepted that antigen-specific Th2 cells and their cytokines orchestrate these pathognomonic features of asthma. On the other hand, Th17 cells and IL-23, a cytokine that preferentially expands Th17 cells, play a significant role in the development of chronic inflammatory diseases, including autoimmune diseases. Recently, we have shown that IL-23 and Th17 cells enhance not only neutrophilic airway inflammation but also Th2 cell-mediated eosinophilic airway inflammation in a murine asthma model. In this review, we will discuss the roles of IL-23 and Th17 cells in airway inflammation in asthma.","corpus_id":44691759,"score":1},{"doc_id":"19689377","title":"IRAK-4 inhibitors for inflammation.","abstract":"Interleukin-1 receptor-associated kinases (IRAKs) are key components in the signal transduction pathways utilized by interleukin-1 receptor (IL-1R), interleukin-18 receptor (IL-18R), and Toll-like receptors (TLRs). Out of four members in the mammalian IRAK family, IRAK-4 is considered to be the \"master IRAK\", the only family member indispensable for IL-1R/TLR signaling. In humans, mutations resulting in IRAK-4 deficiency have been linked to susceptibility to bacterial infections, especially recurrent pyogenic bacterial infections. Furthermore, knock-in experiments by several groups have clearly demonstrated that IRAK-4 requires its kinase activity for its function. Given the critical role of IRAK-4 in inflammatory processes, modulation of IRAK-4 kinase activity presents an attractive therapeutic approach for the treatment of immune and inflammatory diseases. The recent success in the determination of the 3-dimensional structure of the IRAK-4 kinase domain in complex with inhibitors has facilitated the understanding of the mechanistic role of IRAK-4 in immunity and inflammation as well as the development of specific IRAK-4 kinase inhibitors. In this article, we review the biological function of IRAK-4, the structural characteristics of the kinase domain, and the development of small molecule inhibitors targeting the kinase activity. We also review the key pharmacophores required for several classes of inhibitors as well as important features for optimal protein/inhibitor interactions. Lastly, we summarize how these insights can be translated into strategies to develop potent IRAK-4 inhibitors with desired properties as new anti-inflammatory therapeutic agents.","corpus_id":8392671,"score":1},{"doc_id":"19935773","title":"IL-23 signaling enhances Th2 polarization and regulates allergic airway inflammation.","abstract":"IL-23/IL-17 axis is an important regulator in various inflammatory diseases. However, the role of IL-23 in allergic airway inflammation is not well understood. In this study, we show that in an allergen-induced asthma model, mice with transgenic overexpression of IL-23R exhibited increased airway infiltration of eosinophils and Th2 cytokine production, whereas those deficient in IL-23 displayed reduced airway inflammation. In vitro, IL-23-IL-23R signaling promoted GATA-3 expression and enhanced Th2 cytokine expression. Conversely, in the absence of this signal, Th2 cell differentiation was partially inhibited. Therefore, IL-23 signaling may regulate allergic asthma through modulation of Th2 cell differentiation.","corpus_id":7043435,"score":1},{"doc_id":"19965981","title":"Intelectin is required for IL-13-induced monocyte chemotactic protein-1 and -3 expression in lung epithelial cells and promotes allergic airway inflammation.","abstract":"Asthma is characterized by airway inflammation, mucus overproduction, airway hyperreactivity, and peribronchial fibrosis. Intelectin has been shown to be increased in airway epithelium of asthmatics. However, the role of intelectin in the pathogenesis of asthma is unknown. Airway epithelial cells can secrete chemokines such as monocyte chemotactic protein (MCP)-1 and -3 that play crucial roles in asthmatic airway inflammation. We hypothesized that intelectin plays a role in allergic airway inflammation by regulating chemokine expression. In a mouse allergic asthma model, we found that mRNA expression of intelectin-2 as well as MCP-1 and -3 in mouse lung was increased very early (within 2 h) after allergen challenge. Expression of intelectin protein was localized to mucous cells in airway epithelium. Treatment of MLE12 mouse lung epithelial cells with interleukin IL-13, a critical mediator of allergic airway disease, induced expression of intelectin-1 and -2 as well as MCP-1 and -3. When IL-13-induced intelectin-1 and -2 expression was inhibited by RNA interference, IL-13-induced extracellular signal-regulated kinase 1/2 phosphorylation and MCP-1 and -3 production by MLE12 cells was inhibited. Furthermore, inhibition of intelectin expression by airway transfection with shRNA targeting intelectin-1 and -2 attenuated allergen-induced airway inflammation. We conclude that intelectin, a molecule expressed by airway epithelial cells and upregulated in asthma, is required for IL-13-induced MCP-1 and -3 production in mouse lung epithelial cells and contributes to allergic airway inflammation.","corpus_id":174859,"score":1},{"doc_id":"20709826","title":"A novel phycobiliprotein alleviates allergic airway inflammation by modulating immune responses.","abstract":"RATIONALE: it has been claimed that phycocyanin exhibits pharmaceutical functions in inhibiting histamine release and leukotriene biosynthesis. In allergic asthma, these inflammatory mediators are crucial for disease progression. OBJECTIVES: the aim of this study was to evaluate the therapeutic potential of R-phycocyanin (R-PC) against allergic airway inflammation. METHODS: mouse bone marrow-derived dendritic cells (BMDCs) were used to evaluate the immunomodulatory functions of R-PC. In addition, an airway inflammatory model was used to evaluate the therapeutic potential of R-PC. MEASUREMENTS AND MAIN RESULTS: R-PC treatment resulted in a decrease of endocytosis, increase of costimulatory molecule expression, and enhancement of interleukin-12 production in mouse BMDCs. Moreover, R-PC-treated cultured dendritic cells were able to promote CD4(+) T-cell stimulatory capacity and increase interferon-γ expression in CD4(+) T cells. Intraperitoneal administration of R-PC suppressed ovalbumin (OVA)-induced airway hyperresponsiveness, serum levels of OVA-specific IgE and IgG1, eosinophil infiltration, Th2 cytokine levels, and eotaxin in bronchoalveolar lavage fluid of mice. Antibody against Toll-like receptor-4 was able to inhibit R-PC-induced IL-12 p70 production. Moreover, inhibition of nuclear factor-κB (NF-κB) by helenalin and inhibition of the JNK pathway by JNK inhibitor II inhibited R-PC-induced IL-12 p70 production. Western blotting and electrophoretic mobility shift assays showed that R-PC augmented phosphorylation of the inhibitors of NF-κB and inhibitors of NF-κB kinase and facilitated NF-κB activity. CONCLUSIONS: our data demonstrated that R-PC promoted activation and maturation of cultured dendritic cells and skewed the immunological function toward Th1 activity. Therefore, R-PC may have potential in regulating immune responses and application in reducing allergic asthma.","corpus_id":5594072,"score":1},{"doc_id":"20726961","title":"CD14+ cell-derived IL-29 modulates proinflammatory cytokine production in patients with allergic airway inflammation.","abstract":"BACKGROUND: Interleukin (IL)-29 is a newly described cytokine that has anti-viral activity, induces tumor cell death and regulates immune function. Whether it plays a role in immune disorders is unclear. This study aims to examine the role of IL-29 in the modulation of immune response under allergic environment. METHODS: A group of patients with allergic asthma or/and allergic rhinitis was recruited to this study. Serum samples were collected from the patients in both in-season and out-season; the serum levels of IL-29 were determined by enzyme-linked immunoassay. Cell types of IL-29-producing cells in upper airway mucosa were identified with immune staining and examined by immunohistochemistry and flow cytometry. RESULTS: High serum levels of IL-29 were detected in patients with allergic asthma in in-season, but not in out-season. The majority of IL-29(+) cells in upper airway tissue were CD14(+) cells. Exposure to specific antigens triggered the release of IL-4 from antigen-specific CD4(+) T cells; the released IL-4 activated CD14(+) cells to release IL-29; the released IL-29 further triggered the release of IL-6 and tumor necrosis factor from CD4(+) T cells. CONCLUSIONS: Interleukin-29 is involved in the pathogenesis of allergic inflammation via modulating immune cells' function to release proinflammatory cytokines.","corpus_id":19739993,"score":1},{"doc_id":"21297073","title":"Dual Role of IL-22 in allergic airway inflammation and its cross-talk with IL-17A.","abstract":"RATIONALE: IL-22 has both proinflammatory and antiinflammatory properties. Its role in allergic lung inflammation has not been explored. OBJECTIVES: To investigate the expression and roles of IL-22 in the onset and resolution of experimental allergic asthma and its cross-talk with IL-17A. METHODS: IL-22 expression was assessed in patient samples and in the lung of mice immunized and challenged with ovalbumin. IL-22 functions in allergic airway inflammation were evaluated using mice deficient in IL-22 or anti-IL-22 neutralizing antibodies. Moreover, the effects of recombinant IL-22 and IL-17A neutralizing antibodies were investigated. MEASUREMENTS AND MAIN RESULTS: Increased pulmonary IL-22 expression is found in the serum of patients with asthma and mice immunized and challenged with ovalbumin. Allergic lung inflammation is IL-22 dependent because eosinophil recruitment, Th2 cytokine including IL-13 and IL-33, chemokine production, airway hyperreactivity, and mucus production are drastically reduced in mice deficient in IL-22 or by IL-22 antibody neutralization during immunization of wild-type mice. By contrast, IL-22 neutralization during antigen challenge enhanced allergic lung inflammation with increased Th2 cytokines. Consistent with this, recombinant IL-22 given with allergen challenge protects mice from lung inflammation. Finally, IL-22 may regulate the expression and proinflammatory properties of IL-17A in allergic lung inflammation. CONCLUSIONS: IL-22 is required for the onset of allergic asthma, but functions as a negative regulator of established allergic inflammation. Our study reveals that IL-22 contributes to the proinflammatory properties of IL-17A in experimental allergic asthma.","corpus_id":28209854,"score":1},{"doc_id":"21660049","title":"A critical step for JNK activation: isomerization by the prolyl isomerase Pin1.","abstract":"c-Jun N-terminal kinase (JNK) is activated by dual phosphorylation of both threonine and tyrosine residues in the phosphorylation loop of the protein in response to several stress factors. However, the precise molecular mechanisms for activation after phosphorylation remain elusive. Here we show that Pin1, a peptidyl-prolyl isomerase, has a key role in the JNK1 activation process by modulating a phospho-Thr-Pro motif in the phosphorylation loop. Pin1 overexpression in human breast cancer cell lines correlates with increased JNK activity. In addition, small interfering RNA (siRNA) analyses showed that knockdown of Pin1 in a human breast cancer cell line decreased JNK1 activity. Pin1 associates with JNK1, and then catalyzes prolyl isomerization of the phospho-Thr-Pro motif in JNK1 from trans- to cis-conformation. Furthermore, Pin1 enhances the association of JNK1 with its substrates. As a result, Pin1(-/-) cells are defective in JNK activation and resistant to oxidative stress. These results provide novel insights that, following stress-induced phosphorylation of Thr in the Thr-Pro motif of JNK1, JNK1 associates with Pin1 and undergoes conformational changes to promote the binding of JNK1 to its substrates, resulting in cellular responses from extracellular signals.","corpus_id":9606829,"score":1},{"doc_id":"21746900","title":"Stereospecific gating of functional motions in Pin1.","abstract":"Pin1 is a modular enzyme that accelerates the cis-trans isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival. We have used NMR to investigate the interaction of Pin1 with three related ligands that include a pS-P substrate peptide, and two pS-P substrate analogue inhibitors locked in the cis and trans conformations. Specifically, we compared the ligand binding modes and binding-induced changes in Pin1 side-chain flexibility. The cis and trans binding modes differ, and produce different mobility in Pin1. The cis-locked inhibitor and substrate produced a loss of side-chain flexibility along an internal conduit of conserved hydrophobic residues, connecting the domain interface with the isomerase active site. The trans-locked inhibitor produces a weaker conduit response. Thus, the conduit response is stereoselective. We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication. Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins.","corpus_id":19692660,"score":1},{"doc_id":"21998459","title":"High expression of IL-22 suppresses antigen-induced immune responses and eosinophilic airway inflammation via an IL-10-associated mechanism.","abstract":"Allergic inflammation in the airway is generally considered a Th2-type immune response. However, Th17-type immune responses also play important roles in this process, especially in the pathogenesis of severe asthma. IL-22 is a Th17-type cytokine and thus might play roles in the development of allergic airway inflammation. There is increasing evidence that IL-22 can act as a proinflammatory or anti-inflammatory cytokine depending on the inflammatory context. However, its role in Ag-induced immune responses is not well understood. This study examined whether IL-22 could suppress allergic airway inflammation and its mechanism of action. BALB/c mice were sensitized and challenged with OVA-Ag to induce airway inflammation. An IL-22-producing plasmid vector was delivered before the systemic sensitization or immediately before the airway challenge. Delivery of the IL-22 gene before sensitization, but not immediately before challenge, suppressed eosinophilic airway inflammation. IL-22 gene delivery suppressed Ag-induced proliferation and overall cytokine production in CD4(+) T cells, indicating that it could suppress Ag-induced T cell priming. Antagonism of IL-22 by IL-22-binding protein abolished IL-22-induced immune suppression, suggesting that IL-22 protein itself played an essential role. IL-22 gene delivery neither increased regulatory T cells nor suppressed dendritic cell functions. The suppression by IL-22 was abolished by deletion of the IL-10 gene or neutralization of the IL-10 protein. Finally, IL-22 gene delivery increased IL-10 production in draining lymph nodes. These findings suggested that IL-22 could have an immunosuppressive effect during the early stage of an immune response. Furthermore, IL-10 plays an important role in the immune suppression by IL-22.","corpus_id":32345877,"score":1},{"doc_id":"22154382","title":"IL-13 dampens human airway epithelial innate immunity through induction of IL-1 receptor-associated kinase M.","abstract":"BACKGROUND: Impaired airway mucosal immunity can contribute to increased respiratory tract infections in asthmatic patients, but the involved molecular mechanisms have not been fully clarified. Airway epithelial cells serve as the first line of respiratory mucosal defense to eliminate inhaled pathogens through various mechanisms, including Toll-like receptor (TLR) pathways. Our previous studies suggest that impaired TLR2 function in T(H)2 cytokine-exposed airways might decrease immune responses to pathogens and subsequently exacerbate allergic inflammation. IL-1 receptor-associated kinase M (IRAK-M) negatively regulates TLR signaling. However, IRAK-M expression in airway epithelium from asthmatic patients and its functions under a T(H)2 cytokine milieu remain unclear. OBJECTIVES: We sought to evaluate the role of IRAK-M in IL-13-inhibited TLR2 signaling in human airway epithelial cells. METHODS: We examined IRAK-M protein expression in epithelia from asthmatic patients versus that in normal airway epithelia. Moreover, IRAK-M regulation and function in modulating innate immunity (eg, TLR2 signaling) were investigated in cultured human airway epithelial cells with or without IL-13 stimulation. RESULTS: IRAK-M protein levels were increased in asthmatic airway epithelium. Furthermore, in primary human airway epithelial cells, IL-13 consistently upregulated IRAK-M expression, largely through activation of phosphoinositide 3-kinase pathway. Specifically, phosphoinositide 3-kinase activation led to c-Jun binding to human IRAK-M gene promoter and IRAK-M upregulation. Functionally, IL-13-induced IRAK-M suppressed airway epithelial TLR2 signaling activation (eg, TLR2 and human β-defensin 2), partly through inhibiting activation of nuclear factor κB. CONCLUSIONS: Our data indicate that epithelial IRAK-M overexpression in T(H)2 cytokine-exposed airways inhibits TLR2 signaling, providing a novel mechanism for the increased susceptibility of infections in asthmatic patients.","corpus_id":21249199,"score":1},{"doc_id":"22886503","title":"Pulmonary surfactant protein A and surfactant lipids upregulate IRAK-M, a negative regulator of TLR-mediated inflammation in human macrophages.","abstract":"Alveolar macrophages (AMs) are exposed to frequent challenges from inhaled particulates and microbes and function as a first line of defense with a highly regulated immune response because of their unique biology as prototypic alternatively activated macrophages. Lung collectins, particularly surfactant protein A (SP-A), contribute to this activation state by fine-tuning the macrophage inflammatory response. During short-term (10 min-2 h) exposure, SP-A's regulation of human macrophage responses occurs through decreased activity of kinases required for proinflammatory cytokine production. However, AMs are continuously exposed to surfactant, and the biochemical pathways underlying long-term reduction of proinflammatory cytokine activity are not known. We investigated the molecular mechanism(s) underlying SP-A- and surfactant lipid-mediated suppression of proinflammatory cytokine production in response to Toll-like receptor (TLR) 4 (TLR4) activation over longer time periods. We found that exposure of human macrophages to SP-A for 6-24 h upregulates expression of IL-1 receptor-associated kinase M (IRAK-M), a negative regulator of TLR-mediated NF-κB activation. Exposure to Survanta, a natural bovine lung extract lacking SP-A, also enhances IRAK-M expression, but at lower magnitude and for a shorter duration than SP-A. Surfactant-mediated upregulation of IRAK-M in macrophages suppresses TLR4-mediated TNF-α and IL-6 production in response to LPS, and IRAK-M knockdown by small interfering RNA reverses this suppression. In contrast to TNF-α and IL-6, the surfactant components upregulate LPS-mediated immunoregulatory IL-10 production, an effect reversed by IRAK-M knockdown. In conclusion, these data identify an important signaling regulator in human macrophages that is used by surfactant to control the long-term alveolar inflammatory response, i.e., enhanced IRAK-M activity.","corpus_id":378691,"score":1},{"doc_id":"23577040","title":"Roles of IL-22 in Allergic Airway Inflammation.","abstract":"IL-23- and IL-17A-producing CD4(+) T cell (Th17 cell) axis plays a crucial role in the development of chronic inflammatory diseases. In addition, it has been demonstrated that Th17 cells and their cytokines such as IL-17A and IL-17F are involved in the pathogenesis of severe asthma. Recently, IL-22, an IL-10 family cytokine that is produced by Th17 cells, has been shown to be expressed at the site of allergic airway inflammation and to inhibit allergic inflammation in mice. In addition to Th17 cells, innate lymphoid cells also produce IL-22 in response to allergen challenge. Functional IL-22 receptor complex is expressed on lung epithelial cells, and IL-22 inhibits cytokine and chemokine production from lung epithelial cells. In this paper, we summarize the recent progress on the roles of IL-22 in the regulation of allergic airway inflammation and discuss its therapeutic potential in asthma.","corpus_id":18863973,"score":1},{"doc_id":"23776703","title":"IRAK-M expression limits dendritic cell activation and proinflammatory cytokine production in response to Helicobacter pylori.","abstract":"Helicobacter pylori (H. pylori) infects the gastric mucosa and persists for the life of the host. Bacterial persistence may be due to the induction of regulatory T cells (Tregs) whichmay have protective effects against other diseases such as asthma. It has been shown that H. pylori modulates the T cell response through dendritic cell reprogramming but the molecular pathways involved are relatively unknown. The goal of this study was to identify critical elements of dendritic cell (DC) activation and evaluate potential influence on immune activation. Microarray analysis was used to demonstrate limited gene expression changes in H. pylori stimulated bone marrow derived DCs (BMDCs) compared to the BMDCs stimulated with E. coli. IRAK-M, a negative regulator of TLR signaling, was upregulated and we selectedit for investigation of its role in modulating the DC and T cell responses. IRAK-M(-/-) and wild type BMDC were compared for their response to H. pylori. Cells lacking IRAK-M produced significantly greater amounts of proinflammatory MIP-2 and reduced amounts of immunomodulatory IL-10 than wild type BMDC. IRAK-M(-/-) cells also demonstrated increased MHC II expression upon activation. However, IRAK-M(-/-) BMDCs were comparable to wild type BMDCs in inducing T-helper 17 (TH17) and Treg responses as demonstrated in vitro using BMDC CD4+ T cells co-culture assays,and in vivo though the adoptive transfer of CD4(+) FoxP3-GFP T cells into H. pylori infected IRAK-M(-/-) mice. These results suggest that H. pylori infection leads to the upregulation of anti-inflammatory molecules like IRAK-M and that IRAK-M has a direct impact on innate functions in DCs such as cytokine and costimulation molecule upregulation but may not affect T cell skewing.","corpus_id":2352022,"score":1},{"doc_id":"23872113","title":"Procyanidin dimer B2-mediated IRAK-M induction negatively regulates TLR4 signaling in macrophages.","abstract":"Polyphenolic compounds have been found to possess a wide range of physiological activities that may contribute to their beneficial effects against inflammation-related diseases; however, the molecular mechanisms underlying this anti-inflammatory activity are not completely characterized, and many features remain to be elucidated. In this study, we investigated the molecular basis for the down-regulation of toll-like receptor 4 (TLR4) signal transduction by procyanidin dimer B2 (Pro B2) in macrophages. Pro B2 markedly elevated the expression of the interleukin (IL)-1 receptor-associated kinase (IRAK)-M protein, a negative regulator of TLR signaling. Lipopolysaccharide (LPS)-induced expression of cell surface molecules (CD80, CD86, and MHC class I/II) and production of pro-inflammatory cytokines (tumor necrosis factor-α, IL-1β, IL-6, and IL-12p70) were inhibited by Pro B2, and this action was prevented by IRAK-M silencing. In addition, Pro B2-treated macrophages inhibited LPS-induced activation of mitogen-activated protein kinases such as extracellular signal-regulated kinase 1/2, p38, and c-Jun N-terminal kinase and the translocation of nuclear factor κB and p65 through IRAK-M. We also found that Pro B2-treated macrophages inactivated naïve T cells by inhibiting LPS-induced interferon-γ and IL-2 secretion through IRAK-M. These novel findings provide new insights into the understanding of negative regulatory mechanisms of the TLR4 signaling pathway and the immune-pharmacological role of Pro B2 in the immune response against the development and progression of many chronic diseases.","corpus_id":25678755,"score":1},{"doc_id":"24506934","title":"Receptor for advanced glycation end products and its ligand high-mobility group box-1 mediate allergic airway sensitization and airway inflammation.","abstract":"BACKGROUND: The receptor for advanced glycation end products (RAGE) shares common ligands and signaling pathways with TLR4, a key mediator of house dust mite (Dermatophagoides pteronyssinus) (HDM) sensitization. We hypothesized that RAGE and its ligand high-mobility group box-1 (HMGB1) cooperate with TLR4 to mediate HDM sensitization. OBJECTIVES: To determine the requirement for HMGB1 and RAGE, and their relationship with TLR4, in airway sensitization. METHODS: TLR4(-/-), RAGE(-/-), and RAGE-TLR4(-/-) mice were intranasally exposed to HDM or cockroach (Blatella germanica) extracts, and features of allergic inflammation were measured during the sensitization or challenge phase. Anti-HMGB1 antibody and the IL-1 receptor antagonist Anakinra were used to inhibit HMGB1 and the IL-1 receptor, respectively. RESULTS: The magnitude of allergic airway inflammation in response to either HDM or cockroach sensitization and/or challenge was significantly reduced in the absence of RAGE but not further diminished in the absence of both RAGE and TLR4. HDM sensitization induced the release of HMGB1 from the airway epithelium in a biphasic manner, which corresponded to the sequential activation of TLR4 then RAGE. Release of HMGB1 in response to cockroach sensitization also was RAGE dependent. Significantly, HMGB1 release occurred downstream of TLR4-induced IL-1α, and upstream of IL-25 and IL-33 production. Adoptive transfer of HDM-pulsed RAGE(+/+)dendritic cells to RAGE(-/-) mice recapitulated the allergic responses after HDM challenge. Immunoneutralization of HMGB1 attenuated HDM-induced allergic airway inflammation. CONCLUSION: The HMGB1-RAGE axis mediates allergic airway sensitization and airway inflammation. Activation of this axis in response to different allergens acts to amplify the allergic inflammatory response, which exposes it as an attractive target for therapeutic intervention.","corpus_id":34906766,"score":1},{"doc_id":"24517997","title":"Interleukin-22 promotes epithelial cell transformation and breast tumorigenesis via MAP3K8 activation.","abstract":"Interleukin-22 (IL-22), one of the cytokines secreted by T-helper 17 (Th17) cells, binds to a class II cytokine receptor containing an IL-22 receptor 1 (IL-22R1) and IL-10R2 and influences a variety of immune reactions. IL-22 has also been shown to modulate cell cycle and proliferation mediators such as extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK), but little is known about the underlying molecular mechanisms of IL-22 in tumorigenesis. In this paper, we propose that IL-22 has a crucial role to play in controlling epithelial cell proliferation and tumorigenesis in the breast. IL-22 increased MAP3K8 phosphorylation through IL-22R1, followed by the induction of MEK-ERK, JNK-c-Jun, and STAT3 signaling pathways. Furthermore, IL-22-IL-22R1 signaling pathway activated activator protein-1 and HER2 promoter activity. In addition, Pin1 was identified as a key positive regulator for the phosphorylation-dependent MEK, c-Jun and STAT3 activity induced by IL-22. Pin1(-/-) mouse embryonic fibroblasts (MEF) exhibited significantly a decrease in IL-22-induced MEK1/2, c-Jun, and STAT3 phosphorylation compared with Pin1(+/+) MEF. In addition, a knockdown of Pin1 prevented phosphorylation induced by IL-22. The in vivo chorioallantoic membrane assay also showed that IL-22 increased tumor formation of JB6 Cl41 cells. Moreover, the knockdown of MAP3K8 and Pin1 attenuated tumorigenicity of MCF7 cells. Consistent with these observations, IL-22 levels positively correlate with MAP3K8 and Pin1 expression in human breast cancer. Overall, our findings point to a critical role for the IL-22-induced MAP3K8 signaling pathway in promoting cancer-associated inflammation in the tumor microenvironment.","corpus_id":24807729,"score":1},{"doc_id":"24588637","title":"Dectin-2 promotes house dust mite-induced T helper type 2 and type 17 cell differentiation and allergic airway inflammation in mice.","abstract":"The fact that sensitization against fungi is closely related to the severity of asthma suggests that immune systems recognizing fungi are involved in the pathogenesis of severe asthma. Recently, Dectin-2 (gene symbol, Clec4n), a C-type lectin receptor, has been shown to function as not only a major pattern-recognition receptor for fungi, but also a receptor for some components of house dust mite (HDM) extract, a major allergen for asthma. However, the roles of Dectin-2 in the induction of HDM-induced allergic airway inflammation remain largely unknown. Our objective was to determine the roles of Dectin-2 in HDM-induced allergic airway inflammation. We examined the roles of Dectin-2 in the induction of HDM-induced T helper (Th) 2 and Th17 cell differentiation and subsequent allergic airway inflammation by using Clec4n-deficient (Clec4n(-/-)) mice. We also investigated Dectin-2-expressing cells in the lung and their roles in HDM-induced allergic airway inflammation. Clec4n(-/-) mice showed significantly attenuated HDM-induced allergic airway inflammation and decreased Th2 and Th17 cell differentiation. Dectin-2 mRNA, together with Dectin-3 and Fc receptor-γ mRNAs, was expressed in CD11b(+) dendritic cells (DCs), but not in CD4(+) T cells or epithelial cells in the lung. CD11b(+) DCs isolated from Clec4n(-/-) mice expressed lower amounts of proinflammatory cytokines and costimulatory molecules, which could lead to Th2 and Th17 cell differentiation than those from wild-type mice. HDM-pulsed Clec4n(-/-) DCs were less efficient for the induction of allergic airway inflammation than HDM-pulsed wild-type DCs. In conclusion, Dectin-2 expressed on CD11b(+) DCs promotes HDM-induced Th2 and Th17 cell differentiation and allergic airway inflammation.","corpus_id":20485428,"score":1},{"doc_id":"26041536","title":"CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.","abstract":"Innate immune responses to allergens by airway epithelial cells (AECs) help initiate and propagate the adaptive immune response associated with allergic airway inflammation in asthma. Activation of the transcription factor NF-κB in AECs by allergens or secondary mediators via G protein-coupled receptors (GPCRs) is an important component of this multifaceted inflammatory cascade. Members of the caspase recruitment domain family of proteins display tissue-specific expression and help mediate NF-κB activity in response to numerous stimuli. We have previously shown that caspase recruitment domain-containing membrane-associated guanylate kinase protein (CARMA)3 is specifically expressed in AECs and mediates NF-κB activation in these cells in response to stimulation with the GPCR agonist lysophosphatidic acid. In this study, we demonstrate that reduced levels of CARMA3 in normal human bronchial epithelial cells decreases the production of proasthmatic mediators in response to a panel of asthma-relevant GPCR ligands such as lysophosphatidic acid, adenosine triphosphate, and allergens that activate GPCRs such as Alternaria alternata and house dust mite. We then show that genetically modified mice with CARMA3-deficient AECs have reduced airway eosinophilia and proinflammatory cytokine production in a murine model of allergic airway inflammation. Additionally, we demonstrate that these mice have impaired dendritic cell maturation in the lung and that dendritic cells from mice with CARMA3-deficient AECs have impaired Ag processing. In conclusion, we show that AEC CARMA3 helps mediate allergic airway inflammation, and that CARMA3 is a critical signaling molecule bridging the innate and adaptive immune responses in the lung.","corpus_id":24524720,"score":1},{"doc_id":"26542797","title":"The role of Interleukin Receptor Associated Kinase (IRAK)-M in regulation of myofibroblast phenotype in vitro, and in an experimental model of non-reperfused myocardial infarction.","abstract":"In the infarcted myocardium, necrotic cardiomyocytes activate innate immune pathways, stimulating pro-inflammatory signaling cascades. Although inflammation plays an important role in clearance of the infarct from dead cells and matrix debris, repair of the infarcted heart requires timely activation of signals that negatively regulate the innate immune response, limiting inflammatory injury. We have previously demonstrated that Interleukin receptor-associated kinase (IRAK)-M, a member of the IRAK family that suppresses toll-like receptor/interleukin-1 signaling, is upregulated in the infarcted heart in both macrophages and fibroblasts, and restrains pro-inflammatory activation attenuating adverse remodeling. Although IRAK-M is known to suppress inflammatory activation of macrophages, its role in fibroblasts remains unknown. Our current investigation examines the effects of IRAK-M on fibroblast phenotype and function. In vitro, IRAK-M null cardiac fibroblasts have impaired capacity to contract free-floating collagen pads. IRAK-M loss reduces transforming growth factor (TGF)-β-mediated α-smooth muscle actin (α-SMA) expression. IRAK-M deficient cardiac fibroblasts exhibit a modest reduction in TGF-β-stimulated Smad activation and increased expression of the α-SMA repressor, Y-box binding protein (YB)-1. In a model of non-reperfused myocardial infarction, IRAK-M absence does not affect collagen content and myofibroblast density in the infarcted and remodeling myocardium, but increases YB-1 levels and is associated with attenuated α-SMA expression in isolated infarct myofibroblasts. Our findings suggest that, in addition to its role in restraining inflammation following reperfused infarction, IRAK-M may also contribute to myofibroblast conversion.","corpus_id":24873915,"score":1},{"doc_id":"26561030","title":"Allergic airway inflammation: unravelling the relationship between IL-37, IL-18Rα and Tir8/SIGIRR.","abstract":"The hallmarks of allergic bronchial asthma arise from chronic airway inflammation. Thus, elucidating the mechanisms regulating the maintenance of this chronic inflammatory response is key to understanding asthma pathogenesis. To date, it is not clear whether a predominance of proinflammatory factors or a reduced capacity of counterbalancing anti-inflammatory mediators is the pivotal factor predisposing individuals towards asthma development. The IL-1 cytokine family and its receptor systems comprise a variety of proinflammatory cytokines like IL-1β and IL-18 and anti-inflammatory molecules such as the Toll/interleukin-1 receptor 8/single Ig IL-1 receptor (IL-R)-related molecule (Tir8/SIGIRR) and the recently established cytokine IL-37. This article reviews the functions of these IL-1 cytokine family members in the regulation of allergic airway inflammation and asthma as they have been assessed clinically, in vitro and in mouse models.","corpus_id":207207017,"score":1},{"doc_id":"27027963","title":"Effect of IL-37 on Allergic Airway Inflammation.","abstract":"RATIONALE: The new cytokine IL-37 has been described as a negative regulator of innate immunity. It reduces activation of dendritic cells and the production of proinflammatory mediators in murine and human immune cells. Although recent results from the CLARA childhood asthma cohort suggested an impact of IL-37 on human asthma pathogenesis, the receptor for IL-37 and its implication in adaptive immune responses have not been determined. OBJECTIVES: This study aimed to clarify whether IL-37 also provides antiinflammatory effects on adaptive immune responses and through which receptor it exerts its effects. METHODS: IL-37 levels in supernatants of restimulated peripheral blood mononuclear cells isolated from children with asthma and healthy children were determined. Mice (wild-type, IL-18Rα(-/-), and SIGIRR/IL-1R8(-/-)) were sensitized to ovalbumin (OVA) and challenged with OVA aerosol to induce acute allergic experimental asthma, and IL-37 was applied intranasally during OVA challenge. Airway hyperresponsiveness was determined. A cytometric bead array was used to assess cytokine levels in bronchoalveolar lavage fluid. Epithelial mucus was quantified on the basis of lung sections stained with periodic acid-Schiff reagent, using the newCAST microscope system. MEASUREMENTS AND MAIN RESULTS: Human peripheral blood mononuclear cells of subjects with allergic asthma produce less IL-37 compared with healthy control subjects. In mice, intranasal administration of IL-37 dampened allergic airway inflammation as well as proinflammatory cytokine production, mucus hyperproduction, and airway hyperresponsiveness. However, the antiinflammatory effects of IL-37 were completely abolished in mice deficient for IL-18Rα or SIGIRR/IL-1R8. CONCLUSIONS: This study demonstrates that IL-37 reduces allergic airway inflammation directed by type 2 helper T cells and the hallmarks of experimental asthma in mice, suggesting that IL-37 may be critical for asthma pathogenesis in particular and may have an impact on adaptive immunity in general. Furthermore, these data suggest a mode of action of IL-37 that involves binding to IL-18Rα and subsequent heterodimerization with or activation of SIGIRR/IL-1R8. Therefore, IL-37 or its receptors could be potential targets for asthma intervention.","corpus_id":38483958,"score":1},{"doc_id":"27159270","title":"Pin1-Targeted Therapy for Systemic Lupus Erythematosus.","abstract":"OBJECTIVE: Systemic lupus erythematosus (SLE) is a debilitating autoimmune disease affecting multiple organs in the body, but therapeutic options are still very limited and often come with adverse effects. Increasing evidence has underlined an important role of the Toll-like receptor 7 (TLR-7)/TLR-9/interleukin-1 receptor-associated kinase 1 (IRAK-1)/interferon regulatory factor 7 (IRF-7) pathway in the development and progression of SLE. Notably, the prolyl isomerase Pin1 is an essential regulator of IRAK-1 in TLR-7/TLR-9 signaling, but its role in SLE is unknown. We undertook this study to determine whether Pin1 is activated and plays any role in the development and treatment of SLE. METHODS: Activation of Pin1 and TLR-7/TLR-9/IRAK-1/IRF-7 signaling was determined in various cell types among peripheral blood mononuclear cells from healthy controls and SLE patients. The effects of Pin1 and TLR signaling on SLE development were determined using validated Pin1 short hairpin RNA (shRNA), Pin1 genetic knockout, and the small-molecule Pin1 inhibitor all-trans-retinoic acid (ATRA) in immune cells and in several strains of lupus-prone mice. RESULTS: We found abnormal activation of Pin1 and its downstream targets IRAK-1 and IRF-7 in SLE patients. Furthermore, inhibition of Pin1 using either validated Pin1 shRNA or ATRA blocked TLR-7-induced activation of IRAK-1 and IRF-7 in SLE patient-derived immune cells. Moreover, in multiple lupus-prone animals, both Pin1 knockout and ATRA strikingly attenuated the expression of autoimmunity, including skin lesions, lymphadenopathy, splenomegaly, glomerulonephritis, proteinuria, and production of anti-double-stranded DNA antibodies and CD4-CD8- T cells, and also prolonged overall survival in MRL/lpr and B6.lpr mice. CONCLUSION: Pin1 plays a critical role in the development of SLE, and Pin1-targeted therapy offers a promising new strategy for treating SLE.","corpus_id":205432715,"score":1},{"doc_id":"27194325","title":"Pin1 Modulates the Synaptic Content of NMDA Receptors via Prolyl-Isomerization of PSD-95.","abstract":"UNLABELLED: Phosphorylation of serine/threonine residues preceding a proline regulates the fate of its targets through postphosphorylation conformational changes catalyzed by the peptidyl-prolyl cis-/trans isomerase Pin1. By flipping the substrate between two different functional conformations, this enzyme exerts a fine-tuning of phosphorylation signals. Pin1 has been detected in dendritic spines and shafts where it regulates protein synthesis required to sustain the late phase of long-term potentiation (LTP). Here, we demonstrate that Pin1 residing in postsynaptic structures can interact with postsynaptic density protein-95 (PSD-95), a key scaffold protein that anchors NMDA receptors (NMDARs) in PSD via GluN2-type receptor subunits. Pin1 recruitment by PSD-95 occurs at specific serine-threonine/proline consensus motifs localized in the linker region connecting PDZ2 to PDZ3 domains. Upon binding, Pin1 triggers structural changes in PSD-95, thus negatively affecting its ability to interact with NMDARs. In electrophysiological experiments, larger NMDA-mediated synaptic currents, evoked in CA1 principal cells by Schaffer collateral stimulation, were detected in hippocampal slices obtained from Pin1(-/-) mice compared with controls. Similar results were obtained in cultured hippocampal cells expressing a PSD-95 mutant unable to undergo prolyl-isomerization, thus indicating that the action of Pin1 on PSD-95 is critical for this effect. In addition, an enhancement in spine density and size was detected in CA1 principal cells of Pin1(-/-) or in Thy-1GFP mice treated with the pharmacological inhibitor of Pin1 catalytic activity PiB.Our data indicate that Pin1 controls synaptic content of NMDARs via PSD-95 prolyl-isomerization and the expression of dendritic spines, both required for LTP maintenance. SIGNIFICANCE STATEMENT: PSD-95, a membrane-associated guanylate kinase, is the major scaffolding protein at excitatory postsynaptic densities and a potent regulator of synaptic strength and plasticity. The activity of PSD-95 is tightly controlled by several post-translational mechanisms including proline-directed phosphorylation. This signaling cascade regulates the fate of its targets through postphosphorylation conformational modifications catalyzed by the peptidyl-prolyl cis-/trans isomerase Pin1. Here, we uncover a new role of Pin1 in glutamatergic signaling. By interacting with PSD-95, Pin1 dampens PSD-95 ability to complex with NMDARs, thus negatively affecting NMDAR signaling and spine morphology. Our findings further emphasize the emerging role of Pin1 as a key modulator of synaptic transmission.","corpus_id":37475356,"score":1},{"doc_id":"27439514","title":"Lack of IL-1 Receptor-Associated Kinase-4 Leads to Defective Th1 Cell Responses and Renders Mice Susceptible to Mycobacterial Infection.","abstract":"The Toll-like and IL-1 family receptors play critical roles in innate and adaptive immunity against intracellular pathogens. Although previous data demonstrated the importance of TLRs and IL-1R signaling events for the establishment of an effective immune response to mycobacteria, the possible function of the adaptor molecule IL-1R-associated kinase (IRAK)-4 against this pathogen has not been addressed. In this study, we determined the role of IRAK-4 in signaling pathways responsible for controlling mycobacterial infections. This kinase is important for the production of IL-12 and TNF-α by macrophages and dendritic cells exposed to mycobacteria. Moreover, Mycobacterium bovis-infected IRAK-4-knockout macrophages displayed impaired MAPK and NF-κB activation. IL-1β secretion and caspase-1 activation were also dependent on IRAK-4 signaling. Mice lacking IRAK-4 showed increased M. bovis burden in spleen, liver, and lungs and smaller liver granulomas during 60 d of infection compared with wild-type mice. Furthermore, 80% of IRAK-4(-/-) mice succumbed to virulent M. tuberculosis within 100 d following low-dose infection. This increased susceptibility to mycobacteria correlated with reduced IFN-γ/TNF-α recall responses by splenocytes, as well as fewer IL-12p70-producing APCs. Additionally, we observed that IRAK-4 is also important for the production of IFN-γ by CD4(+) T cells from infected mice. Finally, THP-1 cells treated with an IRAK-4 inhibitor and exposed to M. bovis showed reduced TNF-α and IL-12, suggesting that the results found in mice can be extended to humans. In summary, these data demonstrate that IRAK-4 is essential for innate and adaptive immunity and necessary for efficient control of mycobacterial infections.","corpus_id":207433100,"score":1},{"doc_id":"27492144","title":"MicroRNA-155 is a critical regulator of type 2 innate lymphoid cells and IL-33 signaling in experimental models of allergic airway inflammation.","abstract":"BACKGROUND: Allergic airway inflammation is triggered by allergen exposure through several steps including release of IL-33, which promotes cytokine (IL-5, IL-13) production by type 2 innate lymphoid cells (ILC2s). MicroRNA (miR)-155 has recently been described to regulate adaptive responses in allergic inflammation. However, the role of miR-155 in the regulation of ILC2s remains unexplored. OBJECTIVE: We sought to elucidate the contribution of miR-155 in ILC2 expansion using experimental murine models of allergic airway inflammation. METHODS: To determine the role of miR-155 in the regulation of ILC2s in allergic airway inflammation, miR-155 deficient (miR-155(-/-)) and wild-type (WT) mice were subjected to acute or chronic allergen-induced inflammation or treated with recombinant IL-33. RESULTS: miR-155 was 10-fold upregulated in WT-derived ILC2s in response to IL-33. Furthermore, miR-155(-/-) mice demonstrated impaired lung IL-33 levels in response to allergen challenge and the number of ILC2s was significantly reduced in allergen-challenged miR-155(-/-) mice compared with WT mice. Exogenous IL-33 treatment revealed that miR-155 is needed for IL-33-induced ILC2 expansion and eosinophilic airway inflammation. Indeed, ILC2s from IL-33-challenged miR-155(-/-) lungs exhibited impaired proliferation, GATA-3 expression, and IL-13 production as compared with IL-33-challenged WT ILC2s. CONCLUSIONS: Our findings for the first time demonstrate that ILC2s and IL-33 signaling are regulated by miR-155 in allergic airway inflammation.","corpus_id":27996843,"score":1},{"doc_id":"27503209","title":"TLR2 Activation Limits Rhinovirus-Stimulated CXCL-10 by Attenuating IRAK-1-Dependent IL-33 Receptor Signaling in Human Bronchial Epithelial Cells.","abstract":"Airway epithelial cells are the major target for rhinovirus (RV) infection and express proinflammatory chemokines and antiviral cytokines that play a role in innate immunity. Previously, we demonstrated that RV interaction with TLR2 causes ILR-associated kinase-1 (IRAK-1) depletion in both airway epithelial cells and macrophages. Further, IRAK-1 degradation caused by TLR2 activation was shown to inhibit ssRNA-induced IFN expression in dendritic cells. Therefore, in this study, we examined the role of TLR2 and IRAK-1 in RV-induced IFN-β, IFN-λ1, and CXCL-10, which require signaling by viral RNA. In airway epithelial cells, blocking TLR2 enhanced RV-induced expression of IFNs and CXCL-10. By contrast, IRAK-1 inhibition abrogated RV-induced expression of CXCL-10, but not IFNs in these cells. Neutralization of IL-33 or its receptor, ST2, which requires IRAK-1 for signaling, inhibited RV-stimulated CXCL-10 expression. In addition, RV induced expression of both ST2 and IL-33 in airway epithelial cells. In macrophages, however, RV-stimulated CXCL-10 expression was primarily dependent on TLR2/IL-1R. Interestingly, in a mouse model of RV infection, blocking ST2 not only attenuated RV-induced CXCL-10, but also lung inflammation. Finally, influenza- and respiratory syncytial virus-induced CXCL-10 was also found to be partially dependent on IL-33/ST2/IRAK-1 signaling in airway epithelial cells. Together, our results indicate that RV stimulates CXCL-10 expression via the IL-33/ST2 signaling axis, and that TLR2 signaling limits RV-induced CXCL-10 via IRAK-1 depletion at least in airway epithelial cells. To our knowledge, this is the first report to demonstrate the role of respiratory virus-induced IL-33 in the induction of CXCL-10 in airway epithelial cells.","corpus_id":207433477,"score":1},{"doc_id":"27545879","title":"The RNA Binding Protein Mex-3B Is Required for IL-33 Induction in the Development of Allergic Airway Inflammation.","abstract":"Allergic airway inflammation is one of the primary features of allergic asthma. Interleukin-33 (IL-33) is recognized as a key pro-inflammatory cytokine that mediates allergic airway inflammation, and its expression is elevated in this condition, but little is known about the regulatory mechanisms underlying IL-33 induction. Here, we show that the RNA binding protein Mex-3B plays a critical role in the induction of IL-33 in the development of allergic airway inflammation. We generated Mex3b(-/-) mice and found that they develop significantly less airway inflammation than wild-type mice due to reduced induction of IL-33. Furthermore, we show that Mex-3B directly upregulates IL-33 expression by inhibiting miR-487b-3p-mediated repression of IL-33. Moreover, we show that inhalation of an antisense oligonucleotide targeting Mex-3B suppresses allergic airway inflammation. Our data identify a signaling pathway that post-transcriptionally regulates IL-33 expression and suggest that Mex-3B could be a promising molecular target for the treatment of allergic asthma.","corpus_id":20294754,"score":1},{"doc_id":"27984001","title":"Psoriatic inflammation enhances allergic airway inflammation through IL-23/STAT3 signaling in a murine model.","abstract":"Psoriasis is an autoimmune inflammatory skin disease characterized by activated IL-23/STAT3/Th17 axis. Recently psoriatic inflammation has been shown to be associated with asthma. However, no study has previously explored how psoriatic inflammation affects airway inflammation. Therefore, this study investigated the effect of imiquimod (IMQ)-induced psoriatic inflammation on cockroach extract (CE)-induced airway inflammation in murine models. Mice were subjected to topical and intranasal administration of IMQ and CE to develop psoriatic and airway inflammation respectively. Various analyses in lung/spleen related to inflammation, Th17/Th2/Th1 cell immune responses, and their signature cytokines/transcription factors were carried out. Psoriatic inflammation in allergic mice was associated with increased airway inflammation with concurrent increase in Th2/Th17 cells/signature cytokines/transcription factors. Splenic CD4+ T and CD11c+ dendritic cells in psoriatic mice had increased STAT3/RORC and IL-23 mRNA expression respectively. This led us to explore the effect of systemic IL-23/STAT3 signaling on airway inflammation. Topical application of STA-21, a small molecule STAT3 inhibitor significantly reduced airway inflammation in allergic mice having psoriatic inflammation. On the other hand, adoptive transfer of IL-23-treated splenic CD4+ T cells from allergic mice into naive recipient mice produced mixed neutrophilic/eosinophilic airway inflammation similar to allergic mice with psoriatic inflammation. Our data suggest that systemic IL-23/STAT3 axis is responsible for enhanced airway inflammation during psoriasis. The current study also suggests that only anti-asthma therapy may not be sufficient to alleviate airway inflammatory burden in asthmatics with psoriasis.","corpus_id":22699967,"score":1},{"doc_id":"28125291","title":"Epstein-Barr Virus-induced Gene 2 Mediates Allergen-induced Leukocyte Migration into Airways.","abstract":"RATIONALE: Leukocyte recruitment to sites of allergic inflammation depends on the local production of priming cytokines, chemokines, and potentially other mediators. Previously, we showed that eosinophils (Eos) express numerous orphan G-protein-coupled receptors, including Epstein-Barr virus-induced gene 2 (EBI2). Despite its contribution to inflammatory diseases, the role of EBI2 in pulmonary eosinophilia is unknown. OBJECTIVES: To determine whether oxysterol ligands for EBI2 are increased in asthma exacerbation, and if or how they promote Eos pulmonary migration. METHODS: EBI2 ligands and pulmonary eosinophilia were measured in the bronchoalveolar lavage fluid from patients with mild asthma 48 hours after acute allergen challenge. In vitro, the ability of EBI2 ligands alone or in combination with IL-5 priming to induce the migration of human blood Eos was assessed. MEASUREMENTS AND MAIN RESULTS: EBI2 was constitutively and stably expressed in peripheral blood Eos. Eos treated with the EBI2 ligands showed significantly increased transwell migration that was enhanced by priming with physiologic doses of IL-5. Migration was suppressed by inhibitors of the prolyl isomerase Pin1 or extracellular signal-regulated kinases (ERK) 1/2 or by pertussis toxin. EBI2 signaling activated Pin1 isomerase activity through a cascade that was sensitive to ERK inhibitors and pertussis toxin. The concentration of EBI2 ligands was significantly increased in the bronchoalveolar lavage fluid 48 hours after segmental allergen challenge and strongly correlated with the increased numbers of Eos, lymphocytes, and neutrophils in the airways. CONCLUSIONS: Oxysterols are increased in inflamed airways after allergen challenge and, through G-protein subunit α, ERK, and Pin1 signaling, likely participate in the regulation of Eos migration into the lung in people with asthma.","corpus_id":21076766,"score":1},{"doc_id":"28490737","title":"Intradermal administration of IL-33 induces allergic airway inflammation.","abstract":"Approximately half of all atopic dermatitis (AD) patients subsequently develop asthma, particularly those with severe AD. This association, suggesting a role for AD as an entry point for subsequent allergic disease, is a phenomenon known as the \"atopic march\". While the underlying cause of the atopic march remains unknown, recent evidence suggests that epithelial cell (EC)-derived cytokines play a major role. We showed that mice exposed to antigen through the skin, in the presence of IL-33, developed antigen-specific airway inflammation when later challenged in the lung. IL-33 signaling was dispensable during effector/challenge phase. These data reveal critical roles for IL-33 in the \"atopic march\" and will offer a new therapeutic target in the treatment and prevention of allergic asthma.","corpus_id":19546450,"score":1},{"doc_id":"28658555","title":"IL-25 in allergic inflammation.","abstract":"IL-25, also known as IL-17E, is a member of the IL-17 cytokine family mostly produced by epithelial cells and innate immune cells. After binding to the IL-17RB/IL-17RA complex, IL-25 induces downstream signaling responses in epithelial cells and type 2 lymphocytes, which initiates, propagates, and sustains type 2 immunity. The function of IL-25 in allergic diseases such as asthma has been well established, and now also is extended to diseases such as inflammatory bowel disease and cancer. This review summarizes the literature on IL-25 and discusses the unsolved questions. Our knowledge on IL-25 will pave the pathway for targeting this cytokine in inflammatory diseases.","corpus_id":4415550,"score":1},{"doc_id":"28701510","title":"Immunomodulatory Molecule IRAK-M Balances Macrophage Polarization and Determines Macrophage Responses during Renal Fibrosis.","abstract":"Activation of various innate immune receptors results in IL-1 receptor-associated kinase (IRAK)-1/IRAK-4-mediated signaling and secretion of proinflammatory cytokines such as IL-12, IL-6, or TNF-α, all of which are implicated in tissue injury and elevated during tissue remodeling processes. IRAK-M, also known as IRAK-3, is an inhibitor of proinflammatory cytokine and chemokine expression in intrarenal macrophages. Innate immune activation contributes to both acute kidney injury and tissue remodeling that is associated with chronic kidney disease (CKD). Our study assessed the contribution of macrophages in CKD and the role of IRAK-M in modulating disease progression. To evaluate the effect of IRAK-M in chronic renal injury in vivo, a mouse model of unilateral ureteral obstruction (UUO) was employed. The expression of IRAK-M increased within 2 d after UUO in obstructed compared with unobstructed kidneys. Mice deficient in IRAK-M were protected from fibrosis and displayed a diminished number of alternatively activated macrophages. Compared to wild-type mice, IRAK-M-deficient mice showed reduced tubular injury, leukocyte infiltration, and inflammation following renal injury as determined by light microscopy, immunohistochemistry, and intrarenal mRNA expression of proinflammatory and profibrotic mediators. Taken together, these results strongly support a role for IRAK-M in renal injury and identify IRAK-M as a possible modulator in driving an alternatively activated profibrotic macrophage phenotype in UUO-induced CKD.","corpus_id":12178565,"score":1},{"doc_id":"29394345","title":"Roles of IL-22 in allergic airway inflammation in mice and humans.","abstract":"Asthma is a chronic inflammatory disease of the airways that is characterized by eosinophilic inflammation, mucus hypersecretion and airway remodeling that leads to airway obstruction. Although these pathognomonic features of asthma are primarily mediated by allergen-specific T helper type 2 cells (Th2 cells) and their cytokines, recent studies have revealed critical roles of lung epithelial cells in the pathogenesis of asthma. Lung epithelial cells not only form physical barriers by covering the surfaces of the airways but also sense inhaled allergens and initiate communication between the environment and the immune system. The causative involvement of lung epithelium in the pathogenesis of asthma suggests that some molecules that modulate epithelial function have a regulatory role in asthma. IL-22, an IL-10-family cytokine produced by IL-17A-producing T helper cells (Th17 cells), γδ T cells and group 3 innate lymphoid cells (ILC3s), primarily targets epithelial cells and promotes their proliferation. In addition, IL-22 has been shown to induce epithelial production of various molecules that regulate local immune responses. These findings indicate that IL-22 plays crucial roles in the pathogenesis of asthma by regulating epithelial function. Here, we review the current understanding of the molecular and cellular mechanisms underlying IL-22-mediated regulation of airway inflammation in asthma.","corpus_id":23040450,"score":1},{"doc_id":"23606538","title":"Pin1-FADD interactions regulate Fas-mediated apoptosis in activated eosinophils.","abstract":"Abnormally long-lived eosinophils (Eos) are the major inflammatory component of allergic responses in the lungs of active asthmatics. Eos recruited to the airways after allergen exposure produce and respond to IL-5 and GM-CSF, enhancing their survival. Prosurvival signaling activates Pin1, a peptidyl-prolyl cis-trans isomerase that binds to Bax and prevents its activation. How long-lived Eos, despite the continued presence of GM-CSF or IL-5, eventually undergo apoptosis to end allergic inflammation remains unclear. In this study, we show that Pin1 location, activity, and protein interactions are jointly influenced by Fas and the prosurvival cytokine IL-5. Fas signaling strongly induced the phosphorylation of FADD at Ser(194) and Pin1 at Ser(16), as well as their nuclear accumulation. Phospho-mimic Ser(194)Glu FADD mutants accelerated Eos apoptosis compared with wild-type or Ser(194)Ala mutants. Downstream of FADD phosphorylation, caspase 8, 9, and 3 cleavage, as well as Eos apoptosis induced by Fas, were reduced by constitutively active Pin1 and enhanced by Pin1 inhibition. Pin1 was activated by IL-5, whereas simultaneous IL-5 and anti-Fas treatment modestly reduced peptidyl isomerase activity but induced Pin1 to associate with FADD after its phosphorylation at Ser(194). Mechanistically, Pin1-mediated isomerization facilitated the subsequent dephosphorylation of Ser(194) FADD and maintenance of cytoplasmic location. In vivo-activated bronchoalveolar Eos obtained after allergen challenge showed elevated survival and Pin1 activity that could be reversed by anti-Fas. Therefore, our data suggest that Pin1 is a critical link between FADD-mediated cell death and IL-5-mediated prosurvival signaling.","corpus_id":30783341,"score":0},{"doc_id":"24309188","title":"Macrophage phenotype controls long-term AKI outcomes--kidney regeneration versus atrophy.","abstract":"The mechanisms that determine full recovery versus subsequent progressive CKD after AKI are largely unknown. Because macrophages regulate inflammation as well as epithelial recovery, we investigated whether macrophage activation influences AKI outcomes. IL-1 receptor-associated kinase-M (IRAK-M) is a macrophage-specific inhibitor of Toll-like receptor (TLR) and IL-1 receptor signaling that prevents polarization toward a proinflammatory phenotype. In postischemic kidneys of wild-type mice, IRAK-M expression increased for 3 weeks after AKI and declined thereafter. However, genetic depletion of IRAK-M did not affect immunopathology and renal dysfunction during early postischemic AKI. Regarding long-term outcomes, wild-type kidneys regenerated completely within 5 weeks after AKI. In contrast, IRAK-M(-/-) kidneys progressively lost up to two-thirds of their original mass due to tubule loss, leaving atubular glomeruli and interstitial scarring. Moreover, M1 macrophages accumulated in the renal interstitial compartment, coincident with increased expression of proinflammatory cytokines and chemokines. Injection of bacterial CpG DNA induced the same effects in wild-type mice, and TNF-α blockade with etanercept partially prevented renal atrophy in IRAK-M(-/-) mice. These results suggest that IRAK-M induction during the healing phase of AKI supports the resolution of M1 macrophage- and TNF-α-dependent renal inflammation, allowing structural regeneration and functional recovery of the injured kidney. Conversely, IRAK-M loss-of-function mutations or transient exposure to bacterial DNA may drive persistent inflammatory mononuclear phagocyte infiltrates, which impair kidney regeneration and promote CKD. Overall, these results support a novel role for IRAK-M in the regulation of wound healing and tissue regeneration.","corpus_id":31475732,"score":0},{"doc_id":"27001469","title":"Human eosinophil activin A synthesis and mRNA stabilization are induced by the combination of IL-3 plus TNF.","abstract":"Eosinophils contribute to immune regulation and wound healing/fibrosis in various diseases, including asthma. Growing appreciation for the role of activin A in such processes led us to hypothesize that eosinophils are a source of this transforming growth factor-ß superfamily member. Tumor necrosis factor-α (TNF) induces activin A by other cell types and is often present at the site of allergic inflammation along with the eosinophil-activating common ß (ßc) chain-signaling cytokines (interleukin (IL)-5, IL-3, granulocyte-macrophages colony-stimulating factor (GM-CSF)). Previously, we established that the combination of TNF plus a ßc chain-signaling cytokine synergistically induces eosinophil synthesis of the remodeling enzyme matrix metalloproteinase-9. Therefore, eosinophils were stimulated ex vivo by these cytokines and in vivo through an allergen-induced airway inflammatory response. In contrast to IL-5+TNF or GM-CSF+TNF, the combination of IL-3+TNF synergistically induced activin A synthesis and release by human blood eosinophils. IL-3+TNF enhanced activin A mRNA stability, which required sustained signaling of pathways downstream of p38 and extracellular signal-regulated kinase mitogen-activated protein kinases. In vivo, following segmental airway allergen challenge of subjects with mild allergic asthma, activin A mRNA was upregulated in airway eosinophils compared with circulating eosinophils, and ex vivo, circulating eosinophils tended to release more activin A in response to IL-3+TNF. These data provide evidence that eosinophils release activin A and that this function is enhanced when eosinophils are present in an allergen-induced inflammatory environment. Moreover, these data provide the first evidence for posttranscriptional control of activin A mRNA. We propose that an environment rich in IL-3+TNF will lead to eosinophil-derived activin A, which has an important role in regulating inflammation and/or fibrosis.","corpus_id":19553664,"score":0},{"doc_id":"28432060","title":"Toll-like receptor 2 dominance over Toll-like receptor 4 in stressful conditions for its detrimental role in the heart.","abstract":"It has been suggested that Toll-like receptor (TLR)4 promotes IL-10-mediated cardiac cell survival, whereas another receptor, TLR2, from the same family, is detrimental. Here, we examined the interactive role of these two innate signaling molecules under stressful conditions, including IL-10 knockout (IL-10(-/-)) mice, global ischemia-reperfusion (I/R) injury in rat hearts, and in vitro short hairpin RNA experimental models in the presence or absence of IL-10 (10 ng/ml). Circulating and myocardial levels of TNF-α as well as apoptosis and fibrosis were higher in IL-10(-/-) mice. The increase in TLR2 in IL-10(-/-) hearts indicated its negative regulation by IL-10. Ex vivo I/R also caused a marked upregulation of TLR2 and TNF-α as well as apoptotic and fibrotic signals. However, a 40-min reperfusion with IL-10 triggered an increase in TLR4 expression and improved recovery of cardiac function. The increase in IL-1 receptor-associated kinase (IRAK)-M and IRAK-2 activity during I/R injury suggested their role in TLR2 signaling. In vitro inhibition of TLR4 activity as a consequence of RNA inhibition-mediated suppression of myeloid differentiation gene (MyD)88 suggested MyD88-dependent activation of TLR4. The inclusion of IL-10 during reperfusion also downregulated the expression of IRAK-2, TNF-α receptor-associated factor 1-interacting protein (TRAIP) and apoptotic signals, caspase-3, and the Bax-to-Bcl-xL ratio. IL-10 reduced the TNF-α receptor-associated increase in TRAIP-induced apoptosis during I/R injury, which led to an increase in IL-1β to mitigate transforming growth factor-β receptor type I-mediated fibrosis. The IL-10 mitigation of these changes suggests that the stimulation through TLR4 signaling promotes IRAK-4 and phosphorylates IRAK-1 instead of IRAK-2 and may be an important therapeutic approach in restoring heart health in stress. NEW & NOTEWORTHY Under stress conditions such as downregulation of the IL-10 gene or ischemia-reperfusion injury, Toll-like receptor (TLR)4 and IL-1 receptor-associated kinase (IRAK)-1 activation is suppressed, along with the upregulation of TLR-2 and IRAK-2, resulting in fibrosis and apoptosis. It is suggested that IL-10 helps to maintain heart function during stress via myeloid differentiation gene 88/IRAK-4/IRAK-1-dependent TLR4 signaling.","corpus_id":19061954,"score":0}],"string":"[\n {\n \"doc_id\": \"18188456\",\n \"title\": \"Pin1 regulates TGF-beta1 production by activated human and murine eosinophils and contributes to allergic lung fibrosis.\",\n \"abstract\": \"Eosinophilic inflammation is a cornerstone of chronic asthma that often culminates in subepithelial fibrosis with variable airway obstruction. Pulmonary eosinophils (Eos) are a predominant source of TGF-beta1, which drives fibroblast proliferation and extracellular matrix deposition. We investigated the regulation of TGF-beta1 and show here that the peptidyl-prolyl isomerase (PPIase) Pin1 promoted the stability of TGF-beta1 mRNA in human Eos. In addition, Pin1 regulated cytokine production by both in vitro and in vivo activated human Eos. We found that Pin1 interacted with both PKC-alpha and protein phosphatase 2A, which together control Pin1 isomerase activity. Pharmacologic blockade of Pin1 in a rat asthma model selectively reduced eosinophilic pulmonary inflammation, TGF-beta1 and collagen expression, and airway remodeling. Furthermore, chronically challenged Pin1(-/-) mice showed reduced peribronchiolar collagen deposition compared with wild-type controls. These data suggest that pharmacologic suppression of Pin1 may be a novel therapeutic option to prevent airway fibrosis in individuals with chronic asthma.\",\n \"corpus_id\": 207693447,\n \"score\": 2\n },\n {\n \"doc_id\": \"18802081\",\n \"title\": \"IL-33 induces antigen-specific IL-5+ T cells and promotes allergic-induced airway inflammation independent of IL-4.\",\n \"abstract\": \"Type 2 cytokines (IL-4, IL-5, and IL-13) play a pivotal role in helminthic infection and allergic disorders. CD4(+) T cells which produce type 2 cytokines can be generated via IL-4-dependent and -independent pathways. Although the IL-4-dependent pathway is well documented, factors that drive IL-4-independent Th2 cell differentiation remain obscure. We report here that the new cytokine IL-33, in the presence of Ag, polarizes murine and human naive CD4(+) T cells into a population of T cells which produce mainly IL-5 but not IL-4. This polarization requires IL-1R-related molecule and MyD88 but not IL-4 or STAT6. The IL-33-induced T cell differentiation is also dependent on the phosphorylation of MAPKs and NF-kappaB but not the induction of GATA3 or T-bet. In vivo, ST2(-/-) mice developed attenuated airway inflammation and IL-5 production in a murine model of asthma. Conversely, IL-33 administration induced the IL-5-producing T cells and exacerbated allergen-induced airway inflammation in wild-type as well as IL-4(-/-) mice. Finally, adoptive transfer of IL-33-polarized IL-5(+)IL-4(-)T cells triggered airway inflammation in naive IL-4(-/-) mice. Thus, we demonstrate here that, in the presence of Ag, IL-33 induces IL-5-producing T cells and promotes airway inflammation independent of IL-4.\",\n \"corpus_id\": 33713359,\n \"score\": 2\n },\n {\n \"doc_id\": \"19996739\",\n \"title\": \"Signaling pathways critical for allergic airway inflammation.\",\n \"abstract\": \"PURPOSE OF REVIEW: Activated mast cells, basophils, and CD4 helper T cells have critical roles in allergic inflammation. Therefore, devising ways to specifically inhibit these cells will likely be useful for controlling allergic inflammation. We summarize recent findings regarding the role of mast cells and basophils in allergic responses and the regulation of signaling pathways downstream of the IgE receptor, the chief inducer of mast cell and basophil activation. We also highlight studies addressing the roles of the protein tyrosine kinases Zap-70 and Itk in immune system development and in the regulation of CD4 helper T cell responses. RECENT FINDINGS: Recent work has demonstrated that mast cell function is unexpectedly diverse and that basophils have a more prominent role in Th2-type immune responses than previously appreciated. Biochemical analysis of the IgE receptor signaling pathway has led to insights regarding the roles of phosphatases and other enzymes in this process. Studies of Zap-70 and Itk have helped to define the potential outcomes and complications of inhibiting these enzymes in order to suppress allergic inflammation. SUMMARY: Analysis of genetically engineered mice and biochemical studies continue to help unravel the molecular pathways that drive allergic inflammatory reactions. The knowledge acquired may lead to novel approaches for suppressing allergic inflammation.\",\n \"corpus_id\": 31147422,\n \"score\": 2\n },\n {\n \"doc_id\": \"20029461\",\n \"title\": \"Intracellular signaling mechanisms regulating the activation of human eosinophils by the novel Th2 cytokine IL-33: implications for allergic inflammation.\",\n \"abstract\": \"The novel interleukin (IL)-1 family cytokine IL-33 has been shown to activate T helper 2 (Th2) lymphocytes, mast cells and basophils to produce an array of proinflammatory cytokines, as well as to mediate blood eosinophilia, IgE secretion and hypertrophy of airway epithelium in mice. In the present study, we characterized the activation of human eosinophils by IL-33, and investigated the underlying intracellular signaling mechanisms. IL-33 markedly enhanced eosinophil survival and upregulated cell surface expression of the adhesion molecule intercellular adhesion molecule (ICAM)-1 on eosinophils, but it suppressed that of ICAM-3 and L-selectin. In addition, IL-33 mediates significant release of the proinflammatory cytokine IL-6 and the chemokines CXCL8 and CCL2. We found that IL-33-mediated enhancement of survival, induction of adhesion molecules, and release of cytokines and chemokines were differentially regulated by activation of the nuclear factor (NF)-kappaB, p38 mitogen-activated protein kinase (MAPK) and extracellular signal-regulated kinase (ERK) pathways. Furthermore, we compared the above IL-33 activities with two structurally and functionally related cytokines, IL-1beta and IL-18. IL-1beta, but not IL-18, markedly upregulated cell surface expression of ICAM-1. IL-1beta and IL-18 also significantly enhanced eosinophil survival, and induced the release of IL-6 and chemokines CXCL8 and CCL2 via the activation of the NF-kappaB, p38 MAPK and ERK pathways. Synergistic effects on the release of IL-6 were also observed in combined treatment with IL-1beta, IL-18 and IL-33. Taken together, our findings provide insight into IL-33-mediated activation of eosinophils via differential intracellular signaling cascades in the immunopathogenesis of allergic inflammation.\",\n \"corpus_id\": 25497766,\n \"score\": 2\n },\n {\n \"doc_id\": \"20357831\",\n \"title\": \"Cytokine gene-modulated dendritic cells protect against allergic airway inflammation by inducing IL-10(+)IFN-gamma(+)CD4(+) T cells.\",\n \"abstract\": \"Asthma is characterized by allergen-induced airway inflammation orchestrated by Th2 cells. Dendritic cells (DCs) were found to efficiently prime naive T-helper cells. Thus, modification of DC function may be used as an ideal tool to treat allergic asthma by changing CD4(+) T-cell differentiation or suppressing Th2 development. In this study, we examined whether a DC-based vaccine can be applied to DCs modified with interleukin (IL)-10- and IL-12-expressing adenoviruses to prevent ovalbumin (OVA)-induced asthma in mice. Herein, we show that these modified DCs efficiently moderated the characteristics of asthma, including expressions of OVA-specific antibodies, airway hyperresponsiveness, eosinophilic airway inflammation, and Th2 cytokines production. Additionally, IL-10 and IL-12 gene-modified DCs enhanced the development of both T-helper type 1 (Th1) and IL-10(+)IFN-gamma(+) (interferon-gamma) double-positive T cells in vivo. In vitro-generated OVA-specific IL-10(+)IFN-gamma(+)CD4(+) T cells inhibited the proliferation of naive CD4(+) T cells, and this suppressive effect was a cell contact-dependent mechanism. Furthermore, we showed that combined cytokine-modulated DCs could alleviate established allergic airway inflammation. Taken together, these results suggest that IL-10 and IL-12 gene-modulated DCs are effective in suppressing asthmatic airway inflammation through both immune deviation and immune suppression and are a potential therapeutic approach for asthma.\",\n \"corpus_id\": 20661600,\n \"score\": 2\n },\n {\n \"doc_id\": \"20425513\",\n \"title\": \"Pathogenesis of allergic airway inflammation.\",\n \"abstract\": \"Advances have been made in defining the mechanisms for the control of allergic airway inflammation in response to inhaled antigens. Several genes, including ADAM33, DPP10, PHF11, GPRA, TIM-1, PDE4D, OPN3, and ORMDL3, have been implicated in the pathogenesis and susceptibility to atopy and asthma. Growing evidence associates asthma with a systemic propensity for allergic T-helper type 2 cytokines. Disordered coagulation and fibrinolysis also exacerbate asthma symptoms. Balance among functionally distinct dendritic cell subsets contributes to the outcome of T-cell-mediated immunity. Allergen-specific T-regulatory cells play a pivotal role in the development of tolerance to allergens and immune suppression. The major emphasis on immunotherapy for asthma during the past decade has been to direct the immune response to a type 1 response, or immune tolerance. In this review, we discuss the current information on the pathogenesis of allergic airway inflammation and potential immunotherapy, which could be beneficial in the treatment of airway inflammation, allergy, and asthma.\",\n \"corpus_id\": 7754748,\n \"score\": 2\n },\n {\n \"doc_id\": \"20599782\",\n \"title\": \"The interleukin-1 receptor-associated kinases: critical regulators of innate immune signalling.\",\n \"abstract\": \"The interleukin receptor-associated kinase (IRAK) family are involved in regulating Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways. TLRs are pattern recognition receptors of the innate immune response that are responsible for sensing pathogens and initiating immunity, while IL-1 is one of the key cytokines that mediates inflammation. As such, IL-1/TLR signalling pathways and the IRAK family are critical in anti-pathogen responses, inflammation and autoimmunity. The family comprises of four members, IRAK-1, IRAK-2, IRAK-M (IRAK-3) and IRAK-4, and has a role in both positive and negative regulation of signal transduction. While it was once thought that the family displayed some redundancy, each member of the family is emerging as a distinct and vital contributor to IL-1/TLR signalling mechanisms. Knockout mouse studies have explored the relative contribution of each of the IRAKs in IL-1/TLR signalling, while the recent generation of kinase-inactive knock-in IRAK-4 mice have revealed which of IRAK-4 functions require its kinase activity. IRAK-2, previously thought of as a pseudokinase, has recently been proposed to have kinase activity that is essential for TLR signalling. Not surprisingly given their critical role in IL-1/TLR signalling, the IRAK family members have been implicated in certain disease models including human immunodeficiencies. Thus the potential targeting of these essential protein kinases therapeutically is also discussed.\",\n \"corpus_id\": 22566434,\n \"score\": 2\n },\n {\n \"doc_id\": \"21461246\",\n \"title\": \"IL-33 and Airway Inflammation.\",\n \"abstract\": \"Interleukin-33 (IL-33) is the 11th member of IL-1 cytokine family which includes IL-1 and IL-18. Unlike IL-1β and IL-18, IL-33 is suggested to function as an alarmin that is released upon endothelial or epithelial cell damage and may not enhance acquired immune responses through activation of inflammasome. ST2, a IL-33 receptor component, is preferentially expressed by T-helper type (Th) 2 cells, mast cells, eosinophils and basophils, compared to Th1 cells, Th17 cells and neutrophils. Thus, IL-33 profoundly enhances allergic inflammation through increased expression of proallergic cytokines and chemokines. Indeed, IL-33 and its receptor genes are recognized as the most susceptible genes for asthma by several recent genomewide association studies. It has also recently been shown that IL-33 plays a crucial role in innate eosinophilic airway inflammation rather than acquired immune responses such as IgE production. As such, IL-33 provides a unique therapeutic way for asthma, i.e., ameliorating innate airway inflammation.\",\n \"corpus_id\": 9260626,\n \"score\": 2\n },\n {\n \"doc_id\": \"21469105\",\n \"title\": \"IL-33-activated dendritic cells are critical for allergic airway inflammation.\",\n \"abstract\": \"IL-33, a new member of the IL-1 family cytokine, is involved in Th2-type responses in a wide range of diseases and signals through the ST2 receptor expressed on many immune cells. Since the effects of IL-33 on DCs remain controversial, we investigated the ability of IL-33 to modulate DC functions in vitro and in vivo. Here, we report that IL-33 activates myeloid DCs to produce IL-6, IL-1b, TNF, CCL17 and to express high levels of CD40, CD80 OX40L and CCR7. Importantly, IL-33-activated DCs prime naive lymphocytes to produce the Th2 cytokines IL-5 and IL-13, but not IL-4. In vivo, IL-33 exposure induces DC recruitment and activation in the lung. Using an OVA-induced allergic lung inflammation model, we demonstrate that the reduced airway inflammation in ST2-deficient mice correlates with the failure in DC activation and migration to the draining LN. Finally, we show that adoptive transfer of IL-33-activated DCs exacerbates lung inflammation in a DC-driven model of allergic airway inflammation. These data demonstrate for the first time that IL-33 activates DCs during antigen presentation and thereby drives a Th2-type response in allergic lung inflammation.\",\n \"corpus_id\": 1822987,\n \"score\": 2\n },\n {\n \"doc_id\": \"21624504\",\n \"title\": \"The active contribution of Toll-like receptors to allergic airway inflammation.\",\n \"abstract\": \"Epithelia lining the respiratory tract represent a major portal of entry for microorganisms and allergens and are equipped with innate and adaptive immune signaling receptors for host protection. These include Toll-like receptors (TLRs) that recognize microbial components and evoke diverse responses in cells of the respiratory system. TLR stimulation by microorganism-derived molecules activates antigen presenting cells, control T helper (Th) 1, Th2, and Th17 immune cell differentiation, cytokine production by mast cells, and activation of eosinophils. It is clear that TLR are involved in the pathophysiology of allergic airway diseases such as asthma. Dendritic cells (DCs), a kind of antigen presenting cells, which play a key role in the induction of allergic airway inflammation, are privileged targets for pathogen associated molecular patterns (PAMPs). During the allergic responses, engagement of TLRs on DCs determines the Th2 polarization of the T cells. TLR signaling in mast cells increases the release of IL-5, and TLR activation of airway epithelial cells forces the generation of proallergic Th2 type of cytokines. Although these responses aim to protect the host, they may also result in inflammatory tissue damage in the airway. Under certain conditions, stimulation of TLRs, in particular, TLR9, may reduce Th2-dependent allergic inflammation by induction of Th1 responses. Therefore, understanding the complex regulatory roles of TLRs in the pathogenesis of allergic airway inflammation should facilitate the development of preventive and therapeutic measures for asthmatic patients.\",\n \"corpus_id\": 30335225,\n \"score\": 2\n },\n {\n \"doc_id\": \"24446582\",\n \"title\": \"Blockade of IL-33/ST2 ameliorates airway inflammation in a murine model of allergic asthma.\",\n \"abstract\": \"OBJECTIVE: Interleukin (IL)-33 is involved in the development of lung inflammation by inducing or amplifying Th2 type-mediated responses in various animal models of allergic asthma. The ST2 gene is a member of the IL-1 receptor family, producing a transmembrane form (ST2L) and a soluble secreted form (sST2). sST2 has been shown to block this IL-33/ST2 signaling pathway. This study aimed to investigate whether anti-IL-33 and sST2 reduced airway inflammation in a murine model of asthma. METHODS: BALB/c mice were sensitized and challenged with ovalbumin (OVA), and the effect of sST2 and anti-IL-33 antibody on airway inflammation and airway hyperresponsiveness (AHR) was evaluated. Furthermore, we measured changes in various cytokines in the bronchoalveolar lavage (BAL) fluid when treated with sST2 or anti-IL-33. RESULTS: We observed that anti-IL-33 antibody and sST2 exert a negative regulation on OVA-mediated allergic airway inflammation. Both treatments reduced total cell counts and eosinophil counts in BAL fluid and AHR to methacholine. The Th2 cytokines, such as IL-4, IL-5, and IL-13 in BAL fluid were also significantly decreased after both treatments. However, there were no changes in the level of TGF- ß1 and IL-10 after each treatment. CONCLUSIONS: These results suggest that anti-IL-33 as well as sST2 have therapeutic potential for allergic asthma through inhibition of Th2 cytokine production.\",\n \"corpus_id\": 22974724,\n \"score\": 2\n },\n {\n \"doc_id\": \"24487979\",\n \"title\": \"IL-25 promotes Th2 immunity responses in airway inflammation of asthmatic mice via activation of dendritic cells.\",\n \"abstract\": \"Allergic asthma occurs as a consequence of inappropriate immunologic inflammation to allergens and characterized by Th2 adaptive immune response. Recent studies indicated that interleukin (IL)-25, a member of the IL-17 cytokine family, had been implicated in inducing Th2 cell-dependent inflammation in airway epithelium and IL-25-deficient mice exhibit impaired Th2 immunity responses; however, how these cytokines influence innate immune responses remains poorly understood. In this study, we used ovalbumin (OVA) sensitization and challenge to induce the murine asthmatic model and confirmed by histological analysis of lung tissues and serum levels of total and OVA-specific immunoglobulin (Ig)-E. The expression of IL-25 was detected by quantitative real-time PCR and immunohistochemistry, respectively, and the dendritic cells (DCs) activation was detected by levels of CD80 and CD86 in bronchoalveolar lavage fluid (BALF) by flow cytometry. The mice sensitized and challenged with OVA showed high expression of IL-25 in both mRNA and protein levels in lungs. We detected the expression of CD80 and CD86 in BALF was also increased. A tight correlation between IL-25 mRNA and other Th2 cells producing cytokines such as IL-4, IL-5, and IL-13 in BALF was identified. Furthermore, when the asthmatic mice were treated with inhaled corticosteroids, the inflammatory cells infiltration and the inflammatory cytokines secretion were significantly decreased. In this study, we show that IL-25 promoted the accumulation of co-stimulatory molecules of CD80 and CD86 on DCs and then induced the differentiation of prime naive CD4(+) T cells to become proinflammatory Th2 cells and promoted Th2 cytokine responses in OVA-induced airway inflammation. The ability of IL-25 to promote the activation and differentiation of DCs population was identified as a link between the IL-17 cytokine family and the innate immune response and suggested a previously unrecognized innate immune pathway that promotes Th2 cytokine responses in asthmatic airway inflammation. Inhaled corticosteroids might be capable of inhibiting the promotion of IL-25 and present a promising strategy for the treatment of asthma.\",\n \"corpus_id\": 21571675,\n \"score\": 2\n },\n {\n \"doc_id\": \"25479317\",\n \"title\": \"The paradigm of cytokine networks in allergic airway inflammation.\",\n \"abstract\": \"PURPOSE OF REVIEW: Cytokines are immunomodulatory proteins important in cell signaling. Complex interactions of innate and adaptive immune cells, as well as structural cells and their cytokines, play crucial roles in regulating allergic airway inflammation. Here, we summarize current knowledge about the potential roles of known and newly identified helper T cells and epithelial cell-derived cytokines [interleukin (IL)-9, IL-17, IL-22, IL-25, and IL-33] in allergic rhinitis and asthma. RECENT FINDINGS: Although T-helper (Th)2 cells were considered to be the main orchestrators of allergic airway inflammation, recent studies have revealed the potential interaction of other helper T cells and their cytokines in this process. Th17 cells may have a role in allergic rhinitis and asthma, and chronic rhinosinusitis with nasal polyps. An IL-9-producing subset called Th9 cells, Th22 cells which primarily secrete IL-22, IL-13, tumor necrosis factor-α, Th25 cells via producing IL-25 and epithelial cell-derived thymic stromal lymphopoietin, IL-33, IL-31, and IL-25 are believed to be important for the initiation of allergic reactions and inducing airway inflammation. SUMMARY: A new paradigm of an interplay of cytokines is important in allergic rhinitis and asthma in orchestrating the allergic inflammatory response. Potential therapeutic applications emerging from the roles of these cytokines are promising, but need further research.\",\n \"corpus_id\": 3281721,\n \"score\": 2\n },\n {\n \"doc_id\": \"25878673\",\n \"title\": \"Therapeutic potential of anti-IL-6 therapies for granulocytic airway inflammation in asthma.\",\n \"abstract\": \"BACKGROUND: Determining the cellular and molecular phenotypes of inflammation in asthma can identify patient populations that may best benefit from targeted therapies. Although elevated IL-6 and polymorphisms in IL-6 signalling are associated with lung dysfunction in asthma, it remains unknown if elevated IL-6 levels are associated with a specific cellular inflammatory phenotype, and how IL-6 blockade might impact such inflammatory responses. METHODS: Patients undergoing exacerbations of asthma were phenotyped according to their airway inflammatory characteristics (normal cell count, eosinophilic, neutrophilic, mixed granulocytic), sputum cytokine profiles, and lung function. Mice were exposed to the common allergen, house dust-mite (HDM), in the presence or absence of endogenous IL-6. The intensity and nature of lung inflammation, and levels of pro-granulocytic cytokines and chemokines under these conditions were analyzed. RESULTS: Elevated IL-6 was associated with a lower FEV1 in patients with mixed eosinophilic-neutrophilic bronchitis. In mice, allergen exposure increased lung IL-6 and IL-6 was produced by dendritic cells and alveolar macrophages. Loss-of-function of IL-6 signalling (knockout or antibody-mediated neutralization) abrogated elevations of eosinophil and neutrophil recruiting cytokines/chemokines and allergen-induced airway inflammation in mice. CONCLUSIONS: We demonstrate the association of pleiotropic cellular airway inflammation with IL-6 using human and animal data. These data suggest that exacerbations of asthma, particularly those with a combined eosinophilic and neutrophilic bronchitis, may respond to therapies targeting the IL-6 pathway and therefore, provide a rational basis for initiation of clinical trials to evaluate this.\",\n \"corpus_id\": 8376496,\n \"score\": 2\n },\n {\n \"doc_id\": \"26232935\",\n \"title\": \"Critical role of IL-6 in dendritic cell-induced allergic inflammation of asthma.\",\n \"abstract\": \"UNLABELLED: Interleukin (IL)-6 plays important roles in autoimmunity and inflammation and is essential for T helper (Th) 2 and Th17 differentiation. However, whether it is involved in the development and function of dendritic cells (DCs) during allergen-induced airway inflammation and airway hyper-reactivity (AHR) remains undefined. In this study, Dermatophagoides pteronyssinus (Der p)-induced airway inflammation and AHR were studied in IL-6 knockout (KO) mice. Der p-loaded bone marrow-derived DCs (BMDCs) from IL-6 KO mice were used to assaying their ability to induce airway inflammation in naïve wild-type mice. Our results showed that IL-6 KO mice showed reduced AHR, significant decreases in inflammatory cell recruitment and Th2 and Th17 cytokine production in the airways, and lowered Der p-specific immunoglobulin G1 after Der p exposure. Further exploration of BMDCs from IL-6 KO mice revealed decreased activity of phagocytosis and reduced expression of MHC class II and CD86 after Der p stimulation. Adoptive transfer of Der p-loaded BMDCs from IL-6 KO mice also showed a functional defect in their inability to induce Th2 and Th17 immune responses and trigger airway inflammation and AHR in recipient mice. Finally, in allergic asthmatics, DCs that differentiated from monocytes treated with anti-IL-6 receptor antibody (tocilizumab) had poor capacity for eliciting Th2 polarization as compared to DCs generated from monocytes without antibody treatment. In conclusion, IL-6 signaling in DCs is essential for their uptake of allergens, maturation, and initiation of Th2/Th17-mediated airway inflammation and AHR in asthma, thus providing a new potential target for treating allergic asthma. KEY MESSAGES: IL-6 signaling is important for DCs to take up allergens and to initiate Th2/Th17-mediated airway inflammation. DCs from allergic asthmatics treated with anti-IL-6 receptor antibody had poor capacity for eliciting Th2 polarization. Anti-IL-6 treatment may provide a new potential target for treating allergic asthma.\",\n \"corpus_id\": 17019620,\n \"score\": 2\n },\n {\n \"doc_id\": \"28665693\",\n \"title\": \"Critical Role of IRAK-M in Regulating Antigen-induced Airway Inflammation.\",\n \"abstract\": \"Asthma is an airway epithelium disorder involving allergic lung inflammation. IRAK-M is a negative regulator of Toll-like receptor (TLR) signaling on airway epithelial cells and macrophages and known to limit overproduction of cytokines during the inflammatory process. However, the direct role of IRAK-M on asthma pathogenesis is unclear. In the present study, we found significant elevation of IRAK-M expression in mouse lungs following ovalbumin (OVA) exposure. Compared to wild type (WT) mice, IRAK-M knockout (KO) mice responded to OVA challenge with significantly worse infiltration of airway inflammatory cells, greater airway responsiveness, higher proinflammatory cytokine levels in lung homogenates, and more prominent Th2 and Th17 deviation. OVA exposure also induced higher activities of dendritic cells (DCs) and macrophages from IRAK-M KO mouse lungs. Furthermore, adoptive transfer of either IRAK-M KO bone marrow derived-DCs or -macrophages into WT mice aggravated OVA-induced airway inflammation. In vitro experiments showed that IRAK-M KO naïve CD4+ T cells were more prone to differentiate to Th17, but not Tregs. Consistently, activation of IκBζ was significantly increased in absence of IRAK-M to facilitate Th17 polarization. These findings suggest that IRAK-M plays a crucial role in the regulation of allergic airway inflammation through modifying the function of airway epithelia, DCs, macrophages and differentiation of naïve CD4+ T cell. Modulation of IRAK-M may provide a novel target to control asthma.\",\n \"corpus_id\": 207718594,\n \"score\": 2\n },\n {\n \"doc_id\": \"28951634\",\n \"title\": \"Effect of IRAK-M on Airway Inflammation Induced by Cigarette Smoking.\",\n \"abstract\": \"BACKGROUND: IRAK-M, negatively regulating Toll-like receptor, is shown the dual properties in the varied disease contexts. We studied the effect of IRAK-M deficiency on cigarette smoking- (CS-) induced airway inflammation under acute or subacute conditions in a mouse model. METHODS: A number of cellular and molecular techniques were used to detect the differences between IRAK-M knockout (KO) and wild type (WT) mice exposed to 3-day or 7-week CS. RESULTS: Airway inflammation was comparable between IRAK-M KO and WT mice under 3-day CS exposure. Upon short-term CS exposure and lipopolysaccharide (LPS) inhalation, IRAK-M KO mice demonstrated worse airway inflammation, significantly higher percentage of Th17 cells and concentrations of proinflammatory cytokines in the lungs, and significantly elevated expression of costimulatory molecules CD40 and CD86 by lung dendritic cells (DCs) or macrophages. Conversely, 7-week CS exposed IRAK-M KO mice demonstrated significantly attenuated airway inflammation, significantly lower concentrations of proinflammatory cytokines in the lungs, significantly increased percentage of Tregs, and lower expression of CD11b and CD86 by lung DCs or macrophages. CONCLUSIONS: IRAK-M plays distinctive effect on CS-induced airway inflammation, and influences Treg/Th17 balance and expression of costimulatory molecules by DCs and macrophages, depending on duration and intensity of stimulus.\",\n \"corpus_id\": 21161981,\n \"score\": 2\n },\n {\n \"doc_id\": \"29556000\",\n \"title\": \"Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33.\",\n \"abstract\": \"Allergic inflammation has crucial roles in allergic diseases such as asthma. It is therefore important to understand why and how the immune system responds to allergens. Here we found that full-length interleukin 33 (IL-33FL), an alarmin cytokine with critical roles in type 2 immunity and asthma, functioned as a protease sensor that detected proteolytic activities associated with various environmental allergens across four kingdoms, including fungi, house dust mites, bacteria and pollens. When exposed to allergen proteases, IL-33FL was rapidly cleaved in its central 'sensor' domain, which led to activation of the production of type 2 cytokines in group 2 innate lymphoid cells. Preventing cleavage of IL-33FL reduced allergic airway inflammation. Our findings reveal a molecular mechanism for the rapid induction of allergic type 2 inflammation following allergen exposure, with important implications for allergic diseases.\",\n \"corpus_id\": 4015423,\n \"score\": 2\n },\n {\n \"doc_id\": \"18178860\",\n \"title\": \"The IL-3/IL-5/GM-CSF common receptor plays a pivotal role in the regulation of Th2 immunity and allergic airway inflammation.\",\n \"abstract\": \"The eosinophil is a central effector cell in allergic asthma. Differentiation and function of eosinophils are regulated by the CD4 Th2 cytokines IL-3, IL-5, and GM-CSF, which all signal through a common beta receptor subunit (betac). Recent therapeutic approaches targeting IL-5 alone have not ablated tissue accumulation of eosinophils and have had limited effects on disease progression, suggesting important roles for IL-3 and GM-CSF. By using a mouse model of allergic airways inflammation, we show that allergen-induced expansion and accumulation of eosinophils in the lung are abolished in betac-deficient (betac-/-) mice. Moreover, betac deficiency resulted in inhibition of hallmark features of asthma, including airways hypersensitivity, mucus hypersecretion, and production of Ag-specific IgE. Surprisingly, we also identified a critical role for this receptor in regulating type 2 immunity. Th2 cells in the lung of allergen-challenged betac-/- mice were limited in their ability to proliferate, produce cytokines, and migrate to effector sites, which was attributed to reduced numbers of myeloid dendritic cells in the lung compartment. Thus, the betac plays a critical role in allergen-induced eosinophil expansion and infiltration and is pivotal in regulating molecules that promote both early and late phases of allergic inflammation, representing a novel target for therapy.\",\n \"corpus_id\": 11571451,\n \"score\": 1\n },\n {\n \"doc_id\": \"19155487\",\n \"title\": \"Potential contribution of IL-7 to allergen-induced eosinophilic airway inflammation in asthma.\",\n \"abstract\": \"The primary function of IL-7 is to promote maturation and survival of T cells. Through microarray expression analysis, we previously observed that human blood eosinophils express mRNA for IL-7R alpha (CD127) and its common gamma chain (CD132). The purpose of this study was to determine whether eosinophils have functional IL-7 receptors and to assess the potential contribution of IL-7 to eosinophilic airway inflammation by evaluating its presence in bronchoalveolar lavage (BAL) fluid of subjects with atopic asthma before and after segmental bronchoprovocation with allergen. Immunoblot analysis revealed that CD127 is present in highly purified human blood eosinophils. Furthermore, eosinophils responded to IL-7 with phosphorylation of STAT5, up-regulation of the activation marker CD69, and prolonged survival. Neutralization of GM-CSF but not IL-5 significantly blunted these functional responses, suggesting that IL-7 mediates its effects by promoting eosinophil release of autologous GM-CSF. Notably, the suppressive effect of anti-GM-CSF on STAT5 phosphorylation occurred within 10 min of eosinophil exposure to IL-7. Thus, IL-7 likely activates eosinophil release of preformed rather than newly synthesized GM-CSF. The biological relevance of IL-7 to eosinophilia in vivo was implicated in a study of airway allergen challenge in patients with allergic asthma. IL-7 concentrations in BAL fluid increased significantly 48 h after segmental allergen challenge and were highly correlated with BAL eosinophils (r = 0.7, p < 0.001). In conclusion, the airway response to allergen is associated with the generation of IL-7, which may contribute to airway inflammation by promoting enhanced eosinophil activation and survival. Activation of eosinophils is a novel function for IL-7.\",\n \"corpus_id\": 17422887,\n \"score\": 1\n },\n {\n \"doc_id\": \"19181383\",\n \"title\": \"The kinase activities of interleukin-1 receptor associated kinase (IRAK)-1 and 4 are redundant in the control of inflammatory cytokine expression in human cells.\",\n \"abstract\": \"IRAK-1 and IRAK-4 are protein kinases that mediate signaling by Toll/IL1/Plant R (TIR) domain-containing receptors including the IL-1, IL-18, and Toll-like receptors (TLRs). Although well studied in mouse systems, the mechanism by which they function in human systems is less clear. To extend our knowledge of how these proteins regulate inflammatory signaling in human cells, we genetically and pharmacologically manipulated IRAK-1 and IRAK-4 kinase activities in vitro. Ablation of IRAK-4 expression in human umbilical vein endothelial cells (HUVEC) with siRNA suppressed IL-1beta induced IL-6 and IL-8 production whereas IRAK-1 siRNA suppressed TNFalpha induced but not IL-1beta induced cytokine production. Complementation of IRAK-4-depleted cells with a kinase-inactive allele restored IL-1beta induced cytokine gene expression suggesting that the IRAK-4 kinase activity is dispensable relative to its scaffolding function. Consistent with this finding, an IRAK-4 selective kinase inhibitor (RO6245) that inhibited IRAK-1 degradation failed to block IL-1beta induced cytokine production. In contrast, an inhibitor of both IRAK-1 and IRAK-4 (RO0884) reduced IL-1beta induced p38 MAP kinase, c-Jun N-terminal kinase activation, and IL-6 production in HUVEC. RO0884 also antagonized IL-1beta, TNFalpha, and TLR-mediated cytokine production in human fibroblast-like synoviocytes and peripheral blood mononuclear cells. Therefore in human cells the non-kinase functions of IRAK-4 are essential, whereas the kinase activity of IRAK-4 appears redundant with that of IRAK-1. Pharmacologic inhibition of both kinases appears necessary to block pro-inflammatory cytokine production.\",\n \"corpus_id\": 23928452,\n \"score\": 1\n },\n {\n \"doc_id\": \"19299500\",\n \"title\": \"Pulmonary suppressor of cytokine signaling-1 induced by IL-13 regulates allergic asthma phenotype.\",\n \"abstract\": \"RATIONALE: Th2 cytokines play an important role in allergic diseases. These cytokines activate signal transduction pathways, including Janus kinase/signal transducer and activator of transcription (STAT) signaling. Although the suppressor of cytokine signaling (SOCS) family protein, a negative regulator of the Janus kinase/STAT signaling pathway, contributes to helper T cell differentiation during immune responses, the role of SOCS proteins within the structural cells of a target organ has not been clarified in allergy. OBJECTIVES: To study the local function of SOCS in the development of asthma. METHODS: We used mouse models of IL-13- and ovalbumin (OVA)-induced allergic airway disease. Airway smooth muscle cells were cultured from patients with asthma. MEASUREMENTS AND MAIN RESULTS: The administration of IL-13 induced not only airway responses but also SOCS1 expression at the local inflammatory site. The up-regulated SOCS1 markedly suppressed IL-13-dependent STAT6 activation and eotaxin expression and subsequently down-regulated IL-13-induced airway inflammatory responses. The inactivation of SOCS1 induced airway hyperresponsiveness after IL-13 treatment even in hyporesponsive C57BL/6 background mice. In an OVA-induced model of allergic airway disease, allergen exposure up-regulated local SOCS1 expression, and the induction of SOCS1 in the airways attenuated allergen-induced airway responses. Inactivation of IL-13 inhibited SOCS1 induction in a model of allergic airway disease. Interestingly, airway smooth muscle cells from individuals with asthma had impaired up-regulation of SOCS1 after IL-13 stimulation. CONCLUSIONS: SOCS1 induction by IL-13 in airway structural cells is critical to negatively control allergic airway disease.\",\n \"corpus_id\": 21458938,\n \"score\": 1\n },\n {\n \"doc_id\": \"19494515\",\n \"title\": \"Role of IL-23-Th17 cell axis in allergic airway inflammation.\",\n \"abstract\": \"Asthma is characterized by chronic airway inflammation with intense eosinophil and lymphocyte infiltration, mucus hyperproduction, and airway hyperresponsiveness to a variety of stimuli. It is now generally accepted that antigen-specific Th2 cells and their cytokines orchestrate these pathognomonic features of asthma. On the other hand, Th17 cells and IL-23, a cytokine that preferentially expands Th17 cells, play a significant role in the development of chronic inflammatory diseases, including autoimmune diseases. Recently, we have shown that IL-23 and Th17 cells enhance not only neutrophilic airway inflammation but also Th2 cell-mediated eosinophilic airway inflammation in a murine asthma model. In this review, we will discuss the roles of IL-23 and Th17 cells in airway inflammation in asthma.\",\n \"corpus_id\": 44691759,\n \"score\": 1\n },\n {\n \"doc_id\": \"19689377\",\n \"title\": \"IRAK-4 inhibitors for inflammation.\",\n \"abstract\": \"Interleukin-1 receptor-associated kinases (IRAKs) are key components in the signal transduction pathways utilized by interleukin-1 receptor (IL-1R), interleukin-18 receptor (IL-18R), and Toll-like receptors (TLRs). Out of four members in the mammalian IRAK family, IRAK-4 is considered to be the \\\"master IRAK\\\", the only family member indispensable for IL-1R/TLR signaling. In humans, mutations resulting in IRAK-4 deficiency have been linked to susceptibility to bacterial infections, especially recurrent pyogenic bacterial infections. Furthermore, knock-in experiments by several groups have clearly demonstrated that IRAK-4 requires its kinase activity for its function. Given the critical role of IRAK-4 in inflammatory processes, modulation of IRAK-4 kinase activity presents an attractive therapeutic approach for the treatment of immune and inflammatory diseases. The recent success in the determination of the 3-dimensional structure of the IRAK-4 kinase domain in complex with inhibitors has facilitated the understanding of the mechanistic role of IRAK-4 in immunity and inflammation as well as the development of specific IRAK-4 kinase inhibitors. In this article, we review the biological function of IRAK-4, the structural characteristics of the kinase domain, and the development of small molecule inhibitors targeting the kinase activity. We also review the key pharmacophores required for several classes of inhibitors as well as important features for optimal protein/inhibitor interactions. Lastly, we summarize how these insights can be translated into strategies to develop potent IRAK-4 inhibitors with desired properties as new anti-inflammatory therapeutic agents.\",\n \"corpus_id\": 8392671,\n \"score\": 1\n },\n {\n \"doc_id\": \"19935773\",\n \"title\": \"IL-23 signaling enhances Th2 polarization and regulates allergic airway inflammation.\",\n \"abstract\": \"IL-23/IL-17 axis is an important regulator in various inflammatory diseases. However, the role of IL-23 in allergic airway inflammation is not well understood. In this study, we show that in an allergen-induced asthma model, mice with transgenic overexpression of IL-23R exhibited increased airway infiltration of eosinophils and Th2 cytokine production, whereas those deficient in IL-23 displayed reduced airway inflammation. In vitro, IL-23-IL-23R signaling promoted GATA-3 expression and enhanced Th2 cytokine expression. Conversely, in the absence of this signal, Th2 cell differentiation was partially inhibited. Therefore, IL-23 signaling may regulate allergic asthma through modulation of Th2 cell differentiation.\",\n \"corpus_id\": 7043435,\n \"score\": 1\n },\n {\n \"doc_id\": \"19965981\",\n \"title\": \"Intelectin is required for IL-13-induced monocyte chemotactic protein-1 and -3 expression in lung epithelial cells and promotes allergic airway inflammation.\",\n \"abstract\": \"Asthma is characterized by airway inflammation, mucus overproduction, airway hyperreactivity, and peribronchial fibrosis. Intelectin has been shown to be increased in airway epithelium of asthmatics. However, the role of intelectin in the pathogenesis of asthma is unknown. Airway epithelial cells can secrete chemokines such as monocyte chemotactic protein (MCP)-1 and -3 that play crucial roles in asthmatic airway inflammation. We hypothesized that intelectin plays a role in allergic airway inflammation by regulating chemokine expression. In a mouse allergic asthma model, we found that mRNA expression of intelectin-2 as well as MCP-1 and -3 in mouse lung was increased very early (within 2 h) after allergen challenge. Expression of intelectin protein was localized to mucous cells in airway epithelium. Treatment of MLE12 mouse lung epithelial cells with interleukin IL-13, a critical mediator of allergic airway disease, induced expression of intelectin-1 and -2 as well as MCP-1 and -3. When IL-13-induced intelectin-1 and -2 expression was inhibited by RNA interference, IL-13-induced extracellular signal-regulated kinase 1/2 phosphorylation and MCP-1 and -3 production by MLE12 cells was inhibited. Furthermore, inhibition of intelectin expression by airway transfection with shRNA targeting intelectin-1 and -2 attenuated allergen-induced airway inflammation. We conclude that intelectin, a molecule expressed by airway epithelial cells and upregulated in asthma, is required for IL-13-induced MCP-1 and -3 production in mouse lung epithelial cells and contributes to allergic airway inflammation.\",\n \"corpus_id\": 174859,\n \"score\": 1\n },\n {\n \"doc_id\": \"20709826\",\n \"title\": \"A novel phycobiliprotein alleviates allergic airway inflammation by modulating immune responses.\",\n \"abstract\": \"RATIONALE: it has been claimed that phycocyanin exhibits pharmaceutical functions in inhibiting histamine release and leukotriene biosynthesis. In allergic asthma, these inflammatory mediators are crucial for disease progression. OBJECTIVES: the aim of this study was to evaluate the therapeutic potential of R-phycocyanin (R-PC) against allergic airway inflammation. METHODS: mouse bone marrow-derived dendritic cells (BMDCs) were used to evaluate the immunomodulatory functions of R-PC. In addition, an airway inflammatory model was used to evaluate the therapeutic potential of R-PC. MEASUREMENTS AND MAIN RESULTS: R-PC treatment resulted in a decrease of endocytosis, increase of costimulatory molecule expression, and enhancement of interleukin-12 production in mouse BMDCs. Moreover, R-PC-treated cultured dendritic cells were able to promote CD4(+) T-cell stimulatory capacity and increase interferon-γ expression in CD4(+) T cells. Intraperitoneal administration of R-PC suppressed ovalbumin (OVA)-induced airway hyperresponsiveness, serum levels of OVA-specific IgE and IgG1, eosinophil infiltration, Th2 cytokine levels, and eotaxin in bronchoalveolar lavage fluid of mice. Antibody against Toll-like receptor-4 was able to inhibit R-PC-induced IL-12 p70 production. Moreover, inhibition of nuclear factor-κB (NF-κB) by helenalin and inhibition of the JNK pathway by JNK inhibitor II inhibited R-PC-induced IL-12 p70 production. Western blotting and electrophoretic mobility shift assays showed that R-PC augmented phosphorylation of the inhibitors of NF-κB and inhibitors of NF-κB kinase and facilitated NF-κB activity. CONCLUSIONS: our data demonstrated that R-PC promoted activation and maturation of cultured dendritic cells and skewed the immunological function toward Th1 activity. Therefore, R-PC may have potential in regulating immune responses and application in reducing allergic asthma.\",\n \"corpus_id\": 5594072,\n \"score\": 1\n },\n {\n \"doc_id\": \"20726961\",\n \"title\": \"CD14+ cell-derived IL-29 modulates proinflammatory cytokine production in patients with allergic airway inflammation.\",\n \"abstract\": \"BACKGROUND: Interleukin (IL)-29 is a newly described cytokine that has anti-viral activity, induces tumor cell death and regulates immune function. Whether it plays a role in immune disorders is unclear. This study aims to examine the role of IL-29 in the modulation of immune response under allergic environment. METHODS: A group of patients with allergic asthma or/and allergic rhinitis was recruited to this study. Serum samples were collected from the patients in both in-season and out-season; the serum levels of IL-29 were determined by enzyme-linked immunoassay. Cell types of IL-29-producing cells in upper airway mucosa were identified with immune staining and examined by immunohistochemistry and flow cytometry. RESULTS: High serum levels of IL-29 were detected in patients with allergic asthma in in-season, but not in out-season. The majority of IL-29(+) cells in upper airway tissue were CD14(+) cells. Exposure to specific antigens triggered the release of IL-4 from antigen-specific CD4(+) T cells; the released IL-4 activated CD14(+) cells to release IL-29; the released IL-29 further triggered the release of IL-6 and tumor necrosis factor from CD4(+) T cells. CONCLUSIONS: Interleukin-29 is involved in the pathogenesis of allergic inflammation via modulating immune cells' function to release proinflammatory cytokines.\",\n \"corpus_id\": 19739993,\n \"score\": 1\n },\n {\n \"doc_id\": \"21297073\",\n \"title\": \"Dual Role of IL-22 in allergic airway inflammation and its cross-talk with IL-17A.\",\n \"abstract\": \"RATIONALE: IL-22 has both proinflammatory and antiinflammatory properties. Its role in allergic lung inflammation has not been explored. OBJECTIVES: To investigate the expression and roles of IL-22 in the onset and resolution of experimental allergic asthma and its cross-talk with IL-17A. METHODS: IL-22 expression was assessed in patient samples and in the lung of mice immunized and challenged with ovalbumin. IL-22 functions in allergic airway inflammation were evaluated using mice deficient in IL-22 or anti-IL-22 neutralizing antibodies. Moreover, the effects of recombinant IL-22 and IL-17A neutralizing antibodies were investigated. MEASUREMENTS AND MAIN RESULTS: Increased pulmonary IL-22 expression is found in the serum of patients with asthma and mice immunized and challenged with ovalbumin. Allergic lung inflammation is IL-22 dependent because eosinophil recruitment, Th2 cytokine including IL-13 and IL-33, chemokine production, airway hyperreactivity, and mucus production are drastically reduced in mice deficient in IL-22 or by IL-22 antibody neutralization during immunization of wild-type mice. By contrast, IL-22 neutralization during antigen challenge enhanced allergic lung inflammation with increased Th2 cytokines. Consistent with this, recombinant IL-22 given with allergen challenge protects mice from lung inflammation. Finally, IL-22 may regulate the expression and proinflammatory properties of IL-17A in allergic lung inflammation. CONCLUSIONS: IL-22 is required for the onset of allergic asthma, but functions as a negative regulator of established allergic inflammation. Our study reveals that IL-22 contributes to the proinflammatory properties of IL-17A in experimental allergic asthma.\",\n \"corpus_id\": 28209854,\n \"score\": 1\n },\n {\n \"doc_id\": \"21660049\",\n \"title\": \"A critical step for JNK activation: isomerization by the prolyl isomerase Pin1.\",\n \"abstract\": \"c-Jun N-terminal kinase (JNK) is activated by dual phosphorylation of both threonine and tyrosine residues in the phosphorylation loop of the protein in response to several stress factors. However, the precise molecular mechanisms for activation after phosphorylation remain elusive. Here we show that Pin1, a peptidyl-prolyl isomerase, has a key role in the JNK1 activation process by modulating a phospho-Thr-Pro motif in the phosphorylation loop. Pin1 overexpression in human breast cancer cell lines correlates with increased JNK activity. In addition, small interfering RNA (siRNA) analyses showed that knockdown of Pin1 in a human breast cancer cell line decreased JNK1 activity. Pin1 associates with JNK1, and then catalyzes prolyl isomerization of the phospho-Thr-Pro motif in JNK1 from trans- to cis-conformation. Furthermore, Pin1 enhances the association of JNK1 with its substrates. As a result, Pin1(-/-) cells are defective in JNK activation and resistant to oxidative stress. These results provide novel insights that, following stress-induced phosphorylation of Thr in the Thr-Pro motif of JNK1, JNK1 associates with Pin1 and undergoes conformational changes to promote the binding of JNK1 to its substrates, resulting in cellular responses from extracellular signals.\",\n \"corpus_id\": 9606829,\n \"score\": 1\n },\n {\n \"doc_id\": \"21746900\",\n \"title\": \"Stereospecific gating of functional motions in Pin1.\",\n \"abstract\": \"Pin1 is a modular enzyme that accelerates the cis-trans isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival. We have used NMR to investigate the interaction of Pin1 with three related ligands that include a pS-P substrate peptide, and two pS-P substrate analogue inhibitors locked in the cis and trans conformations. Specifically, we compared the ligand binding modes and binding-induced changes in Pin1 side-chain flexibility. The cis and trans binding modes differ, and produce different mobility in Pin1. The cis-locked inhibitor and substrate produced a loss of side-chain flexibility along an internal conduit of conserved hydrophobic residues, connecting the domain interface with the isomerase active site. The trans-locked inhibitor produces a weaker conduit response. Thus, the conduit response is stereoselective. We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication. Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins.\",\n \"corpus_id\": 19692660,\n \"score\": 1\n },\n {\n \"doc_id\": \"21998459\",\n \"title\": \"High expression of IL-22 suppresses antigen-induced immune responses and eosinophilic airway inflammation via an IL-10-associated mechanism.\",\n \"abstract\": \"Allergic inflammation in the airway is generally considered a Th2-type immune response. However, Th17-type immune responses also play important roles in this process, especially in the pathogenesis of severe asthma. IL-22 is a Th17-type cytokine and thus might play roles in the development of allergic airway inflammation. There is increasing evidence that IL-22 can act as a proinflammatory or anti-inflammatory cytokine depending on the inflammatory context. However, its role in Ag-induced immune responses is not well understood. This study examined whether IL-22 could suppress allergic airway inflammation and its mechanism of action. BALB/c mice were sensitized and challenged with OVA-Ag to induce airway inflammation. An IL-22-producing plasmid vector was delivered before the systemic sensitization or immediately before the airway challenge. Delivery of the IL-22 gene before sensitization, but not immediately before challenge, suppressed eosinophilic airway inflammation. IL-22 gene delivery suppressed Ag-induced proliferation and overall cytokine production in CD4(+) T cells, indicating that it could suppress Ag-induced T cell priming. Antagonism of IL-22 by IL-22-binding protein abolished IL-22-induced immune suppression, suggesting that IL-22 protein itself played an essential role. IL-22 gene delivery neither increased regulatory T cells nor suppressed dendritic cell functions. The suppression by IL-22 was abolished by deletion of the IL-10 gene or neutralization of the IL-10 protein. Finally, IL-22 gene delivery increased IL-10 production in draining lymph nodes. These findings suggested that IL-22 could have an immunosuppressive effect during the early stage of an immune response. Furthermore, IL-10 plays an important role in the immune suppression by IL-22.\",\n \"corpus_id\": 32345877,\n \"score\": 1\n },\n {\n \"doc_id\": \"22154382\",\n \"title\": \"IL-13 dampens human airway epithelial innate immunity through induction of IL-1 receptor-associated kinase M.\",\n \"abstract\": \"BACKGROUND: Impaired airway mucosal immunity can contribute to increased respiratory tract infections in asthmatic patients, but the involved molecular mechanisms have not been fully clarified. Airway epithelial cells serve as the first line of respiratory mucosal defense to eliminate inhaled pathogens through various mechanisms, including Toll-like receptor (TLR) pathways. Our previous studies suggest that impaired TLR2 function in T(H)2 cytokine-exposed airways might decrease immune responses to pathogens and subsequently exacerbate allergic inflammation. IL-1 receptor-associated kinase M (IRAK-M) negatively regulates TLR signaling. However, IRAK-M expression in airway epithelium from asthmatic patients and its functions under a T(H)2 cytokine milieu remain unclear. OBJECTIVES: We sought to evaluate the role of IRAK-M in IL-13-inhibited TLR2 signaling in human airway epithelial cells. METHODS: We examined IRAK-M protein expression in epithelia from asthmatic patients versus that in normal airway epithelia. Moreover, IRAK-M regulation and function in modulating innate immunity (eg, TLR2 signaling) were investigated in cultured human airway epithelial cells with or without IL-13 stimulation. RESULTS: IRAK-M protein levels were increased in asthmatic airway epithelium. Furthermore, in primary human airway epithelial cells, IL-13 consistently upregulated IRAK-M expression, largely through activation of phosphoinositide 3-kinase pathway. Specifically, phosphoinositide 3-kinase activation led to c-Jun binding to human IRAK-M gene promoter and IRAK-M upregulation. Functionally, IL-13-induced IRAK-M suppressed airway epithelial TLR2 signaling activation (eg, TLR2 and human β-defensin 2), partly through inhibiting activation of nuclear factor κB. CONCLUSIONS: Our data indicate that epithelial IRAK-M overexpression in T(H)2 cytokine-exposed airways inhibits TLR2 signaling, providing a novel mechanism for the increased susceptibility of infections in asthmatic patients.\",\n \"corpus_id\": 21249199,\n \"score\": 1\n },\n {\n \"doc_id\": \"22886503\",\n \"title\": \"Pulmonary surfactant protein A and surfactant lipids upregulate IRAK-M, a negative regulator of TLR-mediated inflammation in human macrophages.\",\n \"abstract\": \"Alveolar macrophages (AMs) are exposed to frequent challenges from inhaled particulates and microbes and function as a first line of defense with a highly regulated immune response because of their unique biology as prototypic alternatively activated macrophages. Lung collectins, particularly surfactant protein A (SP-A), contribute to this activation state by fine-tuning the macrophage inflammatory response. During short-term (10 min-2 h) exposure, SP-A's regulation of human macrophage responses occurs through decreased activity of kinases required for proinflammatory cytokine production. However, AMs are continuously exposed to surfactant, and the biochemical pathways underlying long-term reduction of proinflammatory cytokine activity are not known. We investigated the molecular mechanism(s) underlying SP-A- and surfactant lipid-mediated suppression of proinflammatory cytokine production in response to Toll-like receptor (TLR) 4 (TLR4) activation over longer time periods. We found that exposure of human macrophages to SP-A for 6-24 h upregulates expression of IL-1 receptor-associated kinase M (IRAK-M), a negative regulator of TLR-mediated NF-κB activation. Exposure to Survanta, a natural bovine lung extract lacking SP-A, also enhances IRAK-M expression, but at lower magnitude and for a shorter duration than SP-A. Surfactant-mediated upregulation of IRAK-M in macrophages suppresses TLR4-mediated TNF-α and IL-6 production in response to LPS, and IRAK-M knockdown by small interfering RNA reverses this suppression. In contrast to TNF-α and IL-6, the surfactant components upregulate LPS-mediated immunoregulatory IL-10 production, an effect reversed by IRAK-M knockdown. In conclusion, these data identify an important signaling regulator in human macrophages that is used by surfactant to control the long-term alveolar inflammatory response, i.e., enhanced IRAK-M activity.\",\n \"corpus_id\": 378691,\n \"score\": 1\n },\n {\n \"doc_id\": \"23577040\",\n \"title\": \"Roles of IL-22 in Allergic Airway Inflammation.\",\n \"abstract\": \"IL-23- and IL-17A-producing CD4(+) T cell (Th17 cell) axis plays a crucial role in the development of chronic inflammatory diseases. In addition, it has been demonstrated that Th17 cells and their cytokines such as IL-17A and IL-17F are involved in the pathogenesis of severe asthma. Recently, IL-22, an IL-10 family cytokine that is produced by Th17 cells, has been shown to be expressed at the site of allergic airway inflammation and to inhibit allergic inflammation in mice. In addition to Th17 cells, innate lymphoid cells also produce IL-22 in response to allergen challenge. Functional IL-22 receptor complex is expressed on lung epithelial cells, and IL-22 inhibits cytokine and chemokine production from lung epithelial cells. In this paper, we summarize the recent progress on the roles of IL-22 in the regulation of allergic airway inflammation and discuss its therapeutic potential in asthma.\",\n \"corpus_id\": 18863973,\n \"score\": 1\n },\n {\n \"doc_id\": \"23776703\",\n \"title\": \"IRAK-M expression limits dendritic cell activation and proinflammatory cytokine production in response to Helicobacter pylori.\",\n \"abstract\": \"Helicobacter pylori (H. pylori) infects the gastric mucosa and persists for the life of the host. Bacterial persistence may be due to the induction of regulatory T cells (Tregs) whichmay have protective effects against other diseases such as asthma. It has been shown that H. pylori modulates the T cell response through dendritic cell reprogramming but the molecular pathways involved are relatively unknown. The goal of this study was to identify critical elements of dendritic cell (DC) activation and evaluate potential influence on immune activation. Microarray analysis was used to demonstrate limited gene expression changes in H. pylori stimulated bone marrow derived DCs (BMDCs) compared to the BMDCs stimulated with E. coli. IRAK-M, a negative regulator of TLR signaling, was upregulated and we selectedit for investigation of its role in modulating the DC and T cell responses. IRAK-M(-/-) and wild type BMDC were compared for their response to H. pylori. Cells lacking IRAK-M produced significantly greater amounts of proinflammatory MIP-2 and reduced amounts of immunomodulatory IL-10 than wild type BMDC. IRAK-M(-/-) cells also demonstrated increased MHC II expression upon activation. However, IRAK-M(-/-) BMDCs were comparable to wild type BMDCs in inducing T-helper 17 (TH17) and Treg responses as demonstrated in vitro using BMDC CD4+ T cells co-culture assays,and in vivo though the adoptive transfer of CD4(+) FoxP3-GFP T cells into H. pylori infected IRAK-M(-/-) mice. These results suggest that H. pylori infection leads to the upregulation of anti-inflammatory molecules like IRAK-M and that IRAK-M has a direct impact on innate functions in DCs such as cytokine and costimulation molecule upregulation but may not affect T cell skewing.\",\n \"corpus_id\": 2352022,\n \"score\": 1\n },\n {\n \"doc_id\": \"23872113\",\n \"title\": \"Procyanidin dimer B2-mediated IRAK-M induction negatively regulates TLR4 signaling in macrophages.\",\n \"abstract\": \"Polyphenolic compounds have been found to possess a wide range of physiological activities that may contribute to their beneficial effects against inflammation-related diseases; however, the molecular mechanisms underlying this anti-inflammatory activity are not completely characterized, and many features remain to be elucidated. In this study, we investigated the molecular basis for the down-regulation of toll-like receptor 4 (TLR4) signal transduction by procyanidin dimer B2 (Pro B2) in macrophages. Pro B2 markedly elevated the expression of the interleukin (IL)-1 receptor-associated kinase (IRAK)-M protein, a negative regulator of TLR signaling. Lipopolysaccharide (LPS)-induced expression of cell surface molecules (CD80, CD86, and MHC class I/II) and production of pro-inflammatory cytokines (tumor necrosis factor-α, IL-1β, IL-6, and IL-12p70) were inhibited by Pro B2, and this action was prevented by IRAK-M silencing. In addition, Pro B2-treated macrophages inhibited LPS-induced activation of mitogen-activated protein kinases such as extracellular signal-regulated kinase 1/2, p38, and c-Jun N-terminal kinase and the translocation of nuclear factor κB and p65 through IRAK-M. We also found that Pro B2-treated macrophages inactivated naïve T cells by inhibiting LPS-induced interferon-γ and IL-2 secretion through IRAK-M. These novel findings provide new insights into the understanding of negative regulatory mechanisms of the TLR4 signaling pathway and the immune-pharmacological role of Pro B2 in the immune response against the development and progression of many chronic diseases.\",\n \"corpus_id\": 25678755,\n \"score\": 1\n },\n {\n \"doc_id\": \"24506934\",\n \"title\": \"Receptor for advanced glycation end products and its ligand high-mobility group box-1 mediate allergic airway sensitization and airway inflammation.\",\n \"abstract\": \"BACKGROUND: The receptor for advanced glycation end products (RAGE) shares common ligands and signaling pathways with TLR4, a key mediator of house dust mite (Dermatophagoides pteronyssinus) (HDM) sensitization. We hypothesized that RAGE and its ligand high-mobility group box-1 (HMGB1) cooperate with TLR4 to mediate HDM sensitization. OBJECTIVES: To determine the requirement for HMGB1 and RAGE, and their relationship with TLR4, in airway sensitization. METHODS: TLR4(-/-), RAGE(-/-), and RAGE-TLR4(-/-) mice were intranasally exposed to HDM or cockroach (Blatella germanica) extracts, and features of allergic inflammation were measured during the sensitization or challenge phase. Anti-HMGB1 antibody and the IL-1 receptor antagonist Anakinra were used to inhibit HMGB1 and the IL-1 receptor, respectively. RESULTS: The magnitude of allergic airway inflammation in response to either HDM or cockroach sensitization and/or challenge was significantly reduced in the absence of RAGE but not further diminished in the absence of both RAGE and TLR4. HDM sensitization induced the release of HMGB1 from the airway epithelium in a biphasic manner, which corresponded to the sequential activation of TLR4 then RAGE. Release of HMGB1 in response to cockroach sensitization also was RAGE dependent. Significantly, HMGB1 release occurred downstream of TLR4-induced IL-1α, and upstream of IL-25 and IL-33 production. Adoptive transfer of HDM-pulsed RAGE(+/+)dendritic cells to RAGE(-/-) mice recapitulated the allergic responses after HDM challenge. Immunoneutralization of HMGB1 attenuated HDM-induced allergic airway inflammation. CONCLUSION: The HMGB1-RAGE axis mediates allergic airway sensitization and airway inflammation. Activation of this axis in response to different allergens acts to amplify the allergic inflammatory response, which exposes it as an attractive target for therapeutic intervention.\",\n \"corpus_id\": 34906766,\n \"score\": 1\n },\n {\n \"doc_id\": \"24517997\",\n \"title\": \"Interleukin-22 promotes epithelial cell transformation and breast tumorigenesis via MAP3K8 activation.\",\n \"abstract\": \"Interleukin-22 (IL-22), one of the cytokines secreted by T-helper 17 (Th17) cells, binds to a class II cytokine receptor containing an IL-22 receptor 1 (IL-22R1) and IL-10R2 and influences a variety of immune reactions. IL-22 has also been shown to modulate cell cycle and proliferation mediators such as extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK), but little is known about the underlying molecular mechanisms of IL-22 in tumorigenesis. In this paper, we propose that IL-22 has a crucial role to play in controlling epithelial cell proliferation and tumorigenesis in the breast. IL-22 increased MAP3K8 phosphorylation through IL-22R1, followed by the induction of MEK-ERK, JNK-c-Jun, and STAT3 signaling pathways. Furthermore, IL-22-IL-22R1 signaling pathway activated activator protein-1 and HER2 promoter activity. In addition, Pin1 was identified as a key positive regulator for the phosphorylation-dependent MEK, c-Jun and STAT3 activity induced by IL-22. Pin1(-/-) mouse embryonic fibroblasts (MEF) exhibited significantly a decrease in IL-22-induced MEK1/2, c-Jun, and STAT3 phosphorylation compared with Pin1(+/+) MEF. In addition, a knockdown of Pin1 prevented phosphorylation induced by IL-22. The in vivo chorioallantoic membrane assay also showed that IL-22 increased tumor formation of JB6 Cl41 cells. Moreover, the knockdown of MAP3K8 and Pin1 attenuated tumorigenicity of MCF7 cells. Consistent with these observations, IL-22 levels positively correlate with MAP3K8 and Pin1 expression in human breast cancer. Overall, our findings point to a critical role for the IL-22-induced MAP3K8 signaling pathway in promoting cancer-associated inflammation in the tumor microenvironment.\",\n \"corpus_id\": 24807729,\n \"score\": 1\n },\n {\n \"doc_id\": \"24588637\",\n \"title\": \"Dectin-2 promotes house dust mite-induced T helper type 2 and type 17 cell differentiation and allergic airway inflammation in mice.\",\n \"abstract\": \"The fact that sensitization against fungi is closely related to the severity of asthma suggests that immune systems recognizing fungi are involved in the pathogenesis of severe asthma. Recently, Dectin-2 (gene symbol, Clec4n), a C-type lectin receptor, has been shown to function as not only a major pattern-recognition receptor for fungi, but also a receptor for some components of house dust mite (HDM) extract, a major allergen for asthma. However, the roles of Dectin-2 in the induction of HDM-induced allergic airway inflammation remain largely unknown. Our objective was to determine the roles of Dectin-2 in HDM-induced allergic airway inflammation. We examined the roles of Dectin-2 in the induction of HDM-induced T helper (Th) 2 and Th17 cell differentiation and subsequent allergic airway inflammation by using Clec4n-deficient (Clec4n(-/-)) mice. We also investigated Dectin-2-expressing cells in the lung and their roles in HDM-induced allergic airway inflammation. Clec4n(-/-) mice showed significantly attenuated HDM-induced allergic airway inflammation and decreased Th2 and Th17 cell differentiation. Dectin-2 mRNA, together with Dectin-3 and Fc receptor-γ mRNAs, was expressed in CD11b(+) dendritic cells (DCs), but not in CD4(+) T cells or epithelial cells in the lung. CD11b(+) DCs isolated from Clec4n(-/-) mice expressed lower amounts of proinflammatory cytokines and costimulatory molecules, which could lead to Th2 and Th17 cell differentiation than those from wild-type mice. HDM-pulsed Clec4n(-/-) DCs were less efficient for the induction of allergic airway inflammation than HDM-pulsed wild-type DCs. In conclusion, Dectin-2 expressed on CD11b(+) DCs promotes HDM-induced Th2 and Th17 cell differentiation and allergic airway inflammation.\",\n \"corpus_id\": 20485428,\n \"score\": 1\n },\n {\n \"doc_id\": \"26041536\",\n \"title\": \"CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.\",\n \"abstract\": \"Innate immune responses to allergens by airway epithelial cells (AECs) help initiate and propagate the adaptive immune response associated with allergic airway inflammation in asthma. Activation of the transcription factor NF-κB in AECs by allergens or secondary mediators via G protein-coupled receptors (GPCRs) is an important component of this multifaceted inflammatory cascade. Members of the caspase recruitment domain family of proteins display tissue-specific expression and help mediate NF-κB activity in response to numerous stimuli. We have previously shown that caspase recruitment domain-containing membrane-associated guanylate kinase protein (CARMA)3 is specifically expressed in AECs and mediates NF-κB activation in these cells in response to stimulation with the GPCR agonist lysophosphatidic acid. In this study, we demonstrate that reduced levels of CARMA3 in normal human bronchial epithelial cells decreases the production of proasthmatic mediators in response to a panel of asthma-relevant GPCR ligands such as lysophosphatidic acid, adenosine triphosphate, and allergens that activate GPCRs such as Alternaria alternata and house dust mite. We then show that genetically modified mice with CARMA3-deficient AECs have reduced airway eosinophilia and proinflammatory cytokine production in a murine model of allergic airway inflammation. Additionally, we demonstrate that these mice have impaired dendritic cell maturation in the lung and that dendritic cells from mice with CARMA3-deficient AECs have impaired Ag processing. In conclusion, we show that AEC CARMA3 helps mediate allergic airway inflammation, and that CARMA3 is a critical signaling molecule bridging the innate and adaptive immune responses in the lung.\",\n \"corpus_id\": 24524720,\n \"score\": 1\n },\n {\n \"doc_id\": \"26542797\",\n \"title\": \"The role of Interleukin Receptor Associated Kinase (IRAK)-M in regulation of myofibroblast phenotype in vitro, and in an experimental model of non-reperfused myocardial infarction.\",\n \"abstract\": \"In the infarcted myocardium, necrotic cardiomyocytes activate innate immune pathways, stimulating pro-inflammatory signaling cascades. Although inflammation plays an important role in clearance of the infarct from dead cells and matrix debris, repair of the infarcted heart requires timely activation of signals that negatively regulate the innate immune response, limiting inflammatory injury. We have previously demonstrated that Interleukin receptor-associated kinase (IRAK)-M, a member of the IRAK family that suppresses toll-like receptor/interleukin-1 signaling, is upregulated in the infarcted heart in both macrophages and fibroblasts, and restrains pro-inflammatory activation attenuating adverse remodeling. Although IRAK-M is known to suppress inflammatory activation of macrophages, its role in fibroblasts remains unknown. Our current investigation examines the effects of IRAK-M on fibroblast phenotype and function. In vitro, IRAK-M null cardiac fibroblasts have impaired capacity to contract free-floating collagen pads. IRAK-M loss reduces transforming growth factor (TGF)-β-mediated α-smooth muscle actin (α-SMA) expression. IRAK-M deficient cardiac fibroblasts exhibit a modest reduction in TGF-β-stimulated Smad activation and increased expression of the α-SMA repressor, Y-box binding protein (YB)-1. In a model of non-reperfused myocardial infarction, IRAK-M absence does not affect collagen content and myofibroblast density in the infarcted and remodeling myocardium, but increases YB-1 levels and is associated with attenuated α-SMA expression in isolated infarct myofibroblasts. Our findings suggest that, in addition to its role in restraining inflammation following reperfused infarction, IRAK-M may also contribute to myofibroblast conversion.\",\n \"corpus_id\": 24873915,\n \"score\": 1\n },\n {\n \"doc_id\": \"26561030\",\n \"title\": \"Allergic airway inflammation: unravelling the relationship between IL-37, IL-18Rα and Tir8/SIGIRR.\",\n \"abstract\": \"The hallmarks of allergic bronchial asthma arise from chronic airway inflammation. Thus, elucidating the mechanisms regulating the maintenance of this chronic inflammatory response is key to understanding asthma pathogenesis. To date, it is not clear whether a predominance of proinflammatory factors or a reduced capacity of counterbalancing anti-inflammatory mediators is the pivotal factor predisposing individuals towards asthma development. The IL-1 cytokine family and its receptor systems comprise a variety of proinflammatory cytokines like IL-1β and IL-18 and anti-inflammatory molecules such as the Toll/interleukin-1 receptor 8/single Ig IL-1 receptor (IL-R)-related molecule (Tir8/SIGIRR) and the recently established cytokine IL-37. This article reviews the functions of these IL-1 cytokine family members in the regulation of allergic airway inflammation and asthma as they have been assessed clinically, in vitro and in mouse models.\",\n \"corpus_id\": 207207017,\n \"score\": 1\n },\n {\n \"doc_id\": \"27027963\",\n \"title\": \"Effect of IL-37 on Allergic Airway Inflammation.\",\n \"abstract\": \"RATIONALE: The new cytokine IL-37 has been described as a negative regulator of innate immunity. It reduces activation of dendritic cells and the production of proinflammatory mediators in murine and human immune cells. Although recent results from the CLARA childhood asthma cohort suggested an impact of IL-37 on human asthma pathogenesis, the receptor for IL-37 and its implication in adaptive immune responses have not been determined. OBJECTIVES: This study aimed to clarify whether IL-37 also provides antiinflammatory effects on adaptive immune responses and through which receptor it exerts its effects. METHODS: IL-37 levels in supernatants of restimulated peripheral blood mononuclear cells isolated from children with asthma and healthy children were determined. Mice (wild-type, IL-18Rα(-/-), and SIGIRR/IL-1R8(-/-)) were sensitized to ovalbumin (OVA) and challenged with OVA aerosol to induce acute allergic experimental asthma, and IL-37 was applied intranasally during OVA challenge. Airway hyperresponsiveness was determined. A cytometric bead array was used to assess cytokine levels in bronchoalveolar lavage fluid. Epithelial mucus was quantified on the basis of lung sections stained with periodic acid-Schiff reagent, using the newCAST microscope system. MEASUREMENTS AND MAIN RESULTS: Human peripheral blood mononuclear cells of subjects with allergic asthma produce less IL-37 compared with healthy control subjects. In mice, intranasal administration of IL-37 dampened allergic airway inflammation as well as proinflammatory cytokine production, mucus hyperproduction, and airway hyperresponsiveness. However, the antiinflammatory effects of IL-37 were completely abolished in mice deficient for IL-18Rα or SIGIRR/IL-1R8. CONCLUSIONS: This study demonstrates that IL-37 reduces allergic airway inflammation directed by type 2 helper T cells and the hallmarks of experimental asthma in mice, suggesting that IL-37 may be critical for asthma pathogenesis in particular and may have an impact on adaptive immunity in general. Furthermore, these data suggest a mode of action of IL-37 that involves binding to IL-18Rα and subsequent heterodimerization with or activation of SIGIRR/IL-1R8. Therefore, IL-37 or its receptors could be potential targets for asthma intervention.\",\n \"corpus_id\": 38483958,\n \"score\": 1\n },\n {\n \"doc_id\": \"27159270\",\n \"title\": \"Pin1-Targeted Therapy for Systemic Lupus Erythematosus.\",\n \"abstract\": \"OBJECTIVE: Systemic lupus erythematosus (SLE) is a debilitating autoimmune disease affecting multiple organs in the body, but therapeutic options are still very limited and often come with adverse effects. Increasing evidence has underlined an important role of the Toll-like receptor 7 (TLR-7)/TLR-9/interleukin-1 receptor-associated kinase 1 (IRAK-1)/interferon regulatory factor 7 (IRF-7) pathway in the development and progression of SLE. Notably, the prolyl isomerase Pin1 is an essential regulator of IRAK-1 in TLR-7/TLR-9 signaling, but its role in SLE is unknown. We undertook this study to determine whether Pin1 is activated and plays any role in the development and treatment of SLE. METHODS: Activation of Pin1 and TLR-7/TLR-9/IRAK-1/IRF-7 signaling was determined in various cell types among peripheral blood mononuclear cells from healthy controls and SLE patients. The effects of Pin1 and TLR signaling on SLE development were determined using validated Pin1 short hairpin RNA (shRNA), Pin1 genetic knockout, and the small-molecule Pin1 inhibitor all-trans-retinoic acid (ATRA) in immune cells and in several strains of lupus-prone mice. RESULTS: We found abnormal activation of Pin1 and its downstream targets IRAK-1 and IRF-7 in SLE patients. Furthermore, inhibition of Pin1 using either validated Pin1 shRNA or ATRA blocked TLR-7-induced activation of IRAK-1 and IRF-7 in SLE patient-derived immune cells. Moreover, in multiple lupus-prone animals, both Pin1 knockout and ATRA strikingly attenuated the expression of autoimmunity, including skin lesions, lymphadenopathy, splenomegaly, glomerulonephritis, proteinuria, and production of anti-double-stranded DNA antibodies and CD4-CD8- T cells, and also prolonged overall survival in MRL/lpr and B6.lpr mice. CONCLUSION: Pin1 plays a critical role in the development of SLE, and Pin1-targeted therapy offers a promising new strategy for treating SLE.\",\n \"corpus_id\": 205432715,\n \"score\": 1\n },\n {\n \"doc_id\": \"27194325\",\n \"title\": \"Pin1 Modulates the Synaptic Content of NMDA Receptors via Prolyl-Isomerization of PSD-95.\",\n \"abstract\": \"UNLABELLED: Phosphorylation of serine/threonine residues preceding a proline regulates the fate of its targets through postphosphorylation conformational changes catalyzed by the peptidyl-prolyl cis-/trans isomerase Pin1. By flipping the substrate between two different functional conformations, this enzyme exerts a fine-tuning of phosphorylation signals. Pin1 has been detected in dendritic spines and shafts where it regulates protein synthesis required to sustain the late phase of long-term potentiation (LTP). Here, we demonstrate that Pin1 residing in postsynaptic structures can interact with postsynaptic density protein-95 (PSD-95), a key scaffold protein that anchors NMDA receptors (NMDARs) in PSD via GluN2-type receptor subunits. Pin1 recruitment by PSD-95 occurs at specific serine-threonine/proline consensus motifs localized in the linker region connecting PDZ2 to PDZ3 domains. Upon binding, Pin1 triggers structural changes in PSD-95, thus negatively affecting its ability to interact with NMDARs. In electrophysiological experiments, larger NMDA-mediated synaptic currents, evoked in CA1 principal cells by Schaffer collateral stimulation, were detected in hippocampal slices obtained from Pin1(-/-) mice compared with controls. Similar results were obtained in cultured hippocampal cells expressing a PSD-95 mutant unable to undergo prolyl-isomerization, thus indicating that the action of Pin1 on PSD-95 is critical for this effect. In addition, an enhancement in spine density and size was detected in CA1 principal cells of Pin1(-/-) or in Thy-1GFP mice treated with the pharmacological inhibitor of Pin1 catalytic activity PiB.Our data indicate that Pin1 controls synaptic content of NMDARs via PSD-95 prolyl-isomerization and the expression of dendritic spines, both required for LTP maintenance. SIGNIFICANCE STATEMENT: PSD-95, a membrane-associated guanylate kinase, is the major scaffolding protein at excitatory postsynaptic densities and a potent regulator of synaptic strength and plasticity. The activity of PSD-95 is tightly controlled by several post-translational mechanisms including proline-directed phosphorylation. This signaling cascade regulates the fate of its targets through postphosphorylation conformational modifications catalyzed by the peptidyl-prolyl cis-/trans isomerase Pin1. Here, we uncover a new role of Pin1 in glutamatergic signaling. By interacting with PSD-95, Pin1 dampens PSD-95 ability to complex with NMDARs, thus negatively affecting NMDAR signaling and spine morphology. Our findings further emphasize the emerging role of Pin1 as a key modulator of synaptic transmission.\",\n \"corpus_id\": 37475356,\n \"score\": 1\n },\n {\n \"doc_id\": \"27439514\",\n \"title\": \"Lack of IL-1 Receptor-Associated Kinase-4 Leads to Defective Th1 Cell Responses and Renders Mice Susceptible to Mycobacterial Infection.\",\n \"abstract\": \"The Toll-like and IL-1 family receptors play critical roles in innate and adaptive immunity against intracellular pathogens. Although previous data demonstrated the importance of TLRs and IL-1R signaling events for the establishment of an effective immune response to mycobacteria, the possible function of the adaptor molecule IL-1R-associated kinase (IRAK)-4 against this pathogen has not been addressed. In this study, we determined the role of IRAK-4 in signaling pathways responsible for controlling mycobacterial infections. This kinase is important for the production of IL-12 and TNF-α by macrophages and dendritic cells exposed to mycobacteria. Moreover, Mycobacterium bovis-infected IRAK-4-knockout macrophages displayed impaired MAPK and NF-κB activation. IL-1β secretion and caspase-1 activation were also dependent on IRAK-4 signaling. Mice lacking IRAK-4 showed increased M. bovis burden in spleen, liver, and lungs and smaller liver granulomas during 60 d of infection compared with wild-type mice. Furthermore, 80% of IRAK-4(-/-) mice succumbed to virulent M. tuberculosis within 100 d following low-dose infection. This increased susceptibility to mycobacteria correlated with reduced IFN-γ/TNF-α recall responses by splenocytes, as well as fewer IL-12p70-producing APCs. Additionally, we observed that IRAK-4 is also important for the production of IFN-γ by CD4(+) T cells from infected mice. Finally, THP-1 cells treated with an IRAK-4 inhibitor and exposed to M. bovis showed reduced TNF-α and IL-12, suggesting that the results found in mice can be extended to humans. In summary, these data demonstrate that IRAK-4 is essential for innate and adaptive immunity and necessary for efficient control of mycobacterial infections.\",\n \"corpus_id\": 207433100,\n \"score\": 1\n },\n {\n \"doc_id\": \"27492144\",\n \"title\": \"MicroRNA-155 is a critical regulator of type 2 innate lymphoid cells and IL-33 signaling in experimental models of allergic airway inflammation.\",\n \"abstract\": \"BACKGROUND: Allergic airway inflammation is triggered by allergen exposure through several steps including release of IL-33, which promotes cytokine (IL-5, IL-13) production by type 2 innate lymphoid cells (ILC2s). MicroRNA (miR)-155 has recently been described to regulate adaptive responses in allergic inflammation. However, the role of miR-155 in the regulation of ILC2s remains unexplored. OBJECTIVE: We sought to elucidate the contribution of miR-155 in ILC2 expansion using experimental murine models of allergic airway inflammation. METHODS: To determine the role of miR-155 in the regulation of ILC2s in allergic airway inflammation, miR-155 deficient (miR-155(-/-)) and wild-type (WT) mice were subjected to acute or chronic allergen-induced inflammation or treated with recombinant IL-33. RESULTS: miR-155 was 10-fold upregulated in WT-derived ILC2s in response to IL-33. Furthermore, miR-155(-/-) mice demonstrated impaired lung IL-33 levels in response to allergen challenge and the number of ILC2s was significantly reduced in allergen-challenged miR-155(-/-) mice compared with WT mice. Exogenous IL-33 treatment revealed that miR-155 is needed for IL-33-induced ILC2 expansion and eosinophilic airway inflammation. Indeed, ILC2s from IL-33-challenged miR-155(-/-) lungs exhibited impaired proliferation, GATA-3 expression, and IL-13 production as compared with IL-33-challenged WT ILC2s. CONCLUSIONS: Our findings for the first time demonstrate that ILC2s and IL-33 signaling are regulated by miR-155 in allergic airway inflammation.\",\n \"corpus_id\": 27996843,\n \"score\": 1\n },\n {\n \"doc_id\": \"27503209\",\n \"title\": \"TLR2 Activation Limits Rhinovirus-Stimulated CXCL-10 by Attenuating IRAK-1-Dependent IL-33 Receptor Signaling in Human Bronchial Epithelial Cells.\",\n \"abstract\": \"Airway epithelial cells are the major target for rhinovirus (RV) infection and express proinflammatory chemokines and antiviral cytokines that play a role in innate immunity. Previously, we demonstrated that RV interaction with TLR2 causes ILR-associated kinase-1 (IRAK-1) depletion in both airway epithelial cells and macrophages. Further, IRAK-1 degradation caused by TLR2 activation was shown to inhibit ssRNA-induced IFN expression in dendritic cells. Therefore, in this study, we examined the role of TLR2 and IRAK-1 in RV-induced IFN-β, IFN-λ1, and CXCL-10, which require signaling by viral RNA. In airway epithelial cells, blocking TLR2 enhanced RV-induced expression of IFNs and CXCL-10. By contrast, IRAK-1 inhibition abrogated RV-induced expression of CXCL-10, but not IFNs in these cells. Neutralization of IL-33 or its receptor, ST2, which requires IRAK-1 for signaling, inhibited RV-stimulated CXCL-10 expression. In addition, RV induced expression of both ST2 and IL-33 in airway epithelial cells. In macrophages, however, RV-stimulated CXCL-10 expression was primarily dependent on TLR2/IL-1R. Interestingly, in a mouse model of RV infection, blocking ST2 not only attenuated RV-induced CXCL-10, but also lung inflammation. Finally, influenza- and respiratory syncytial virus-induced CXCL-10 was also found to be partially dependent on IL-33/ST2/IRAK-1 signaling in airway epithelial cells. Together, our results indicate that RV stimulates CXCL-10 expression via the IL-33/ST2 signaling axis, and that TLR2 signaling limits RV-induced CXCL-10 via IRAK-1 depletion at least in airway epithelial cells. To our knowledge, this is the first report to demonstrate the role of respiratory virus-induced IL-33 in the induction of CXCL-10 in airway epithelial cells.\",\n \"corpus_id\": 207433477,\n \"score\": 1\n },\n {\n \"doc_id\": \"27545879\",\n \"title\": \"The RNA Binding Protein Mex-3B Is Required for IL-33 Induction in the Development of Allergic Airway Inflammation.\",\n \"abstract\": \"Allergic airway inflammation is one of the primary features of allergic asthma. Interleukin-33 (IL-33) is recognized as a key pro-inflammatory cytokine that mediates allergic airway inflammation, and its expression is elevated in this condition, but little is known about the regulatory mechanisms underlying IL-33 induction. Here, we show that the RNA binding protein Mex-3B plays a critical role in the induction of IL-33 in the development of allergic airway inflammation. We generated Mex3b(-/-) mice and found that they develop significantly less airway inflammation than wild-type mice due to reduced induction of IL-33. Furthermore, we show that Mex-3B directly upregulates IL-33 expression by inhibiting miR-487b-3p-mediated repression of IL-33. Moreover, we show that inhalation of an antisense oligonucleotide targeting Mex-3B suppresses allergic airway inflammation. Our data identify a signaling pathway that post-transcriptionally regulates IL-33 expression and suggest that Mex-3B could be a promising molecular target for the treatment of allergic asthma.\",\n \"corpus_id\": 20294754,\n \"score\": 1\n },\n {\n \"doc_id\": \"27984001\",\n \"title\": \"Psoriatic inflammation enhances allergic airway inflammation through IL-23/STAT3 signaling in a murine model.\",\n \"abstract\": \"Psoriasis is an autoimmune inflammatory skin disease characterized by activated IL-23/STAT3/Th17 axis. Recently psoriatic inflammation has been shown to be associated with asthma. However, no study has previously explored how psoriatic inflammation affects airway inflammation. Therefore, this study investigated the effect of imiquimod (IMQ)-induced psoriatic inflammation on cockroach extract (CE)-induced airway inflammation in murine models. Mice were subjected to topical and intranasal administration of IMQ and CE to develop psoriatic and airway inflammation respectively. Various analyses in lung/spleen related to inflammation, Th17/Th2/Th1 cell immune responses, and their signature cytokines/transcription factors were carried out. Psoriatic inflammation in allergic mice was associated with increased airway inflammation with concurrent increase in Th2/Th17 cells/signature cytokines/transcription factors. Splenic CD4+ T and CD11c+ dendritic cells in psoriatic mice had increased STAT3/RORC and IL-23 mRNA expression respectively. This led us to explore the effect of systemic IL-23/STAT3 signaling on airway inflammation. Topical application of STA-21, a small molecule STAT3 inhibitor significantly reduced airway inflammation in allergic mice having psoriatic inflammation. On the other hand, adoptive transfer of IL-23-treated splenic CD4+ T cells from allergic mice into naive recipient mice produced mixed neutrophilic/eosinophilic airway inflammation similar to allergic mice with psoriatic inflammation. Our data suggest that systemic IL-23/STAT3 axis is responsible for enhanced airway inflammation during psoriasis. The current study also suggests that only anti-asthma therapy may not be sufficient to alleviate airway inflammatory burden in asthmatics with psoriasis.\",\n \"corpus_id\": 22699967,\n \"score\": 1\n },\n {\n \"doc_id\": \"28125291\",\n \"title\": \"Epstein-Barr Virus-induced Gene 2 Mediates Allergen-induced Leukocyte Migration into Airways.\",\n \"abstract\": \"RATIONALE: Leukocyte recruitment to sites of allergic inflammation depends on the local production of priming cytokines, chemokines, and potentially other mediators. Previously, we showed that eosinophils (Eos) express numerous orphan G-protein-coupled receptors, including Epstein-Barr virus-induced gene 2 (EBI2). Despite its contribution to inflammatory diseases, the role of EBI2 in pulmonary eosinophilia is unknown. OBJECTIVES: To determine whether oxysterol ligands for EBI2 are increased in asthma exacerbation, and if or how they promote Eos pulmonary migration. METHODS: EBI2 ligands and pulmonary eosinophilia were measured in the bronchoalveolar lavage fluid from patients with mild asthma 48 hours after acute allergen challenge. In vitro, the ability of EBI2 ligands alone or in combination with IL-5 priming to induce the migration of human blood Eos was assessed. MEASUREMENTS AND MAIN RESULTS: EBI2 was constitutively and stably expressed in peripheral blood Eos. Eos treated with the EBI2 ligands showed significantly increased transwell migration that was enhanced by priming with physiologic doses of IL-5. Migration was suppressed by inhibitors of the prolyl isomerase Pin1 or extracellular signal-regulated kinases (ERK) 1/2 or by pertussis toxin. EBI2 signaling activated Pin1 isomerase activity through a cascade that was sensitive to ERK inhibitors and pertussis toxin. The concentration of EBI2 ligands was significantly increased in the bronchoalveolar lavage fluid 48 hours after segmental allergen challenge and strongly correlated with the increased numbers of Eos, lymphocytes, and neutrophils in the airways. CONCLUSIONS: Oxysterols are increased in inflamed airways after allergen challenge and, through G-protein subunit α, ERK, and Pin1 signaling, likely participate in the regulation of Eos migration into the lung in people with asthma.\",\n \"corpus_id\": 21076766,\n \"score\": 1\n },\n {\n \"doc_id\": \"28490737\",\n \"title\": \"Intradermal administration of IL-33 induces allergic airway inflammation.\",\n \"abstract\": \"Approximately half of all atopic dermatitis (AD) patients subsequently develop asthma, particularly those with severe AD. This association, suggesting a role for AD as an entry point for subsequent allergic disease, is a phenomenon known as the \\\"atopic march\\\". While the underlying cause of the atopic march remains unknown, recent evidence suggests that epithelial cell (EC)-derived cytokines play a major role. We showed that mice exposed to antigen through the skin, in the presence of IL-33, developed antigen-specific airway inflammation when later challenged in the lung. IL-33 signaling was dispensable during effector/challenge phase. These data reveal critical roles for IL-33 in the \\\"atopic march\\\" and will offer a new therapeutic target in the treatment and prevention of allergic asthma.\",\n \"corpus_id\": 19546450,\n \"score\": 1\n },\n {\n \"doc_id\": \"28658555\",\n \"title\": \"IL-25 in allergic inflammation.\",\n \"abstract\": \"IL-25, also known as IL-17E, is a member of the IL-17 cytokine family mostly produced by epithelial cells and innate immune cells. After binding to the IL-17RB/IL-17RA complex, IL-25 induces downstream signaling responses in epithelial cells and type 2 lymphocytes, which initiates, propagates, and sustains type 2 immunity. The function of IL-25 in allergic diseases such as asthma has been well established, and now also is extended to diseases such as inflammatory bowel disease and cancer. This review summarizes the literature on IL-25 and discusses the unsolved questions. Our knowledge on IL-25 will pave the pathway for targeting this cytokine in inflammatory diseases.\",\n \"corpus_id\": 4415550,\n \"score\": 1\n },\n {\n \"doc_id\": \"28701510\",\n \"title\": \"Immunomodulatory Molecule IRAK-M Balances Macrophage Polarization and Determines Macrophage Responses during Renal Fibrosis.\",\n \"abstract\": \"Activation of various innate immune receptors results in IL-1 receptor-associated kinase (IRAK)-1/IRAK-4-mediated signaling and secretion of proinflammatory cytokines such as IL-12, IL-6, or TNF-α, all of which are implicated in tissue injury and elevated during tissue remodeling processes. IRAK-M, also known as IRAK-3, is an inhibitor of proinflammatory cytokine and chemokine expression in intrarenal macrophages. Innate immune activation contributes to both acute kidney injury and tissue remodeling that is associated with chronic kidney disease (CKD). Our study assessed the contribution of macrophages in CKD and the role of IRAK-M in modulating disease progression. To evaluate the effect of IRAK-M in chronic renal injury in vivo, a mouse model of unilateral ureteral obstruction (UUO) was employed. The expression of IRAK-M increased within 2 d after UUO in obstructed compared with unobstructed kidneys. Mice deficient in IRAK-M were protected from fibrosis and displayed a diminished number of alternatively activated macrophages. Compared to wild-type mice, IRAK-M-deficient mice showed reduced tubular injury, leukocyte infiltration, and inflammation following renal injury as determined by light microscopy, immunohistochemistry, and intrarenal mRNA expression of proinflammatory and profibrotic mediators. Taken together, these results strongly support a role for IRAK-M in renal injury and identify IRAK-M as a possible modulator in driving an alternatively activated profibrotic macrophage phenotype in UUO-induced CKD.\",\n \"corpus_id\": 12178565,\n \"score\": 1\n },\n {\n \"doc_id\": \"29394345\",\n \"title\": \"Roles of IL-22 in allergic airway inflammation in mice and humans.\",\n \"abstract\": \"Asthma is a chronic inflammatory disease of the airways that is characterized by eosinophilic inflammation, mucus hypersecretion and airway remodeling that leads to airway obstruction. Although these pathognomonic features of asthma are primarily mediated by allergen-specific T helper type 2 cells (Th2 cells) and their cytokines, recent studies have revealed critical roles of lung epithelial cells in the pathogenesis of asthma. Lung epithelial cells not only form physical barriers by covering the surfaces of the airways but also sense inhaled allergens and initiate communication between the environment and the immune system. The causative involvement of lung epithelium in the pathogenesis of asthma suggests that some molecules that modulate epithelial function have a regulatory role in asthma. IL-22, an IL-10-family cytokine produced by IL-17A-producing T helper cells (Th17 cells), γδ T cells and group 3 innate lymphoid cells (ILC3s), primarily targets epithelial cells and promotes their proliferation. In addition, IL-22 has been shown to induce epithelial production of various molecules that regulate local immune responses. These findings indicate that IL-22 plays crucial roles in the pathogenesis of asthma by regulating epithelial function. Here, we review the current understanding of the molecular and cellular mechanisms underlying IL-22-mediated regulation of airway inflammation in asthma.\",\n \"corpus_id\": 23040450,\n \"score\": 1\n },\n {\n \"doc_id\": \"23606538\",\n \"title\": \"Pin1-FADD interactions regulate Fas-mediated apoptosis in activated eosinophils.\",\n \"abstract\": \"Abnormally long-lived eosinophils (Eos) are the major inflammatory component of allergic responses in the lungs of active asthmatics. Eos recruited to the airways after allergen exposure produce and respond to IL-5 and GM-CSF, enhancing their survival. Prosurvival signaling activates Pin1, a peptidyl-prolyl cis-trans isomerase that binds to Bax and prevents its activation. How long-lived Eos, despite the continued presence of GM-CSF or IL-5, eventually undergo apoptosis to end allergic inflammation remains unclear. In this study, we show that Pin1 location, activity, and protein interactions are jointly influenced by Fas and the prosurvival cytokine IL-5. Fas signaling strongly induced the phosphorylation of FADD at Ser(194) and Pin1 at Ser(16), as well as their nuclear accumulation. Phospho-mimic Ser(194)Glu FADD mutants accelerated Eos apoptosis compared with wild-type or Ser(194)Ala mutants. Downstream of FADD phosphorylation, caspase 8, 9, and 3 cleavage, as well as Eos apoptosis induced by Fas, were reduced by constitutively active Pin1 and enhanced by Pin1 inhibition. Pin1 was activated by IL-5, whereas simultaneous IL-5 and anti-Fas treatment modestly reduced peptidyl isomerase activity but induced Pin1 to associate with FADD after its phosphorylation at Ser(194). Mechanistically, Pin1-mediated isomerization facilitated the subsequent dephosphorylation of Ser(194) FADD and maintenance of cytoplasmic location. In vivo-activated bronchoalveolar Eos obtained after allergen challenge showed elevated survival and Pin1 activity that could be reversed by anti-Fas. Therefore, our data suggest that Pin1 is a critical link between FADD-mediated cell death and IL-5-mediated prosurvival signaling.\",\n \"corpus_id\": 30783341,\n \"score\": 0\n },\n {\n \"doc_id\": \"24309188\",\n \"title\": \"Macrophage phenotype controls long-term AKI outcomes--kidney regeneration versus atrophy.\",\n \"abstract\": \"The mechanisms that determine full recovery versus subsequent progressive CKD after AKI are largely unknown. Because macrophages regulate inflammation as well as epithelial recovery, we investigated whether macrophage activation influences AKI outcomes. IL-1 receptor-associated kinase-M (IRAK-M) is a macrophage-specific inhibitor of Toll-like receptor (TLR) and IL-1 receptor signaling that prevents polarization toward a proinflammatory phenotype. In postischemic kidneys of wild-type mice, IRAK-M expression increased for 3 weeks after AKI and declined thereafter. However, genetic depletion of IRAK-M did not affect immunopathology and renal dysfunction during early postischemic AKI. Regarding long-term outcomes, wild-type kidneys regenerated completely within 5 weeks after AKI. In contrast, IRAK-M(-/-) kidneys progressively lost up to two-thirds of their original mass due to tubule loss, leaving atubular glomeruli and interstitial scarring. Moreover, M1 macrophages accumulated in the renal interstitial compartment, coincident with increased expression of proinflammatory cytokines and chemokines. Injection of bacterial CpG DNA induced the same effects in wild-type mice, and TNF-α blockade with etanercept partially prevented renal atrophy in IRAK-M(-/-) mice. These results suggest that IRAK-M induction during the healing phase of AKI supports the resolution of M1 macrophage- and TNF-α-dependent renal inflammation, allowing structural regeneration and functional recovery of the injured kidney. Conversely, IRAK-M loss-of-function mutations or transient exposure to bacterial DNA may drive persistent inflammatory mononuclear phagocyte infiltrates, which impair kidney regeneration and promote CKD. Overall, these results support a novel role for IRAK-M in the regulation of wound healing and tissue regeneration.\",\n \"corpus_id\": 31475732,\n \"score\": 0\n },\n {\n \"doc_id\": \"27001469\",\n \"title\": \"Human eosinophil activin A synthesis and mRNA stabilization are induced by the combination of IL-3 plus TNF.\",\n \"abstract\": \"Eosinophils contribute to immune regulation and wound healing/fibrosis in various diseases, including asthma. Growing appreciation for the role of activin A in such processes led us to hypothesize that eosinophils are a source of this transforming growth factor-ß superfamily member. Tumor necrosis factor-α (TNF) induces activin A by other cell types and is often present at the site of allergic inflammation along with the eosinophil-activating common ß (ßc) chain-signaling cytokines (interleukin (IL)-5, IL-3, granulocyte-macrophages colony-stimulating factor (GM-CSF)). Previously, we established that the combination of TNF plus a ßc chain-signaling cytokine synergistically induces eosinophil synthesis of the remodeling enzyme matrix metalloproteinase-9. Therefore, eosinophils were stimulated ex vivo by these cytokines and in vivo through an allergen-induced airway inflammatory response. In contrast to IL-5+TNF or GM-CSF+TNF, the combination of IL-3+TNF synergistically induced activin A synthesis and release by human blood eosinophils. IL-3+TNF enhanced activin A mRNA stability, which required sustained signaling of pathways downstream of p38 and extracellular signal-regulated kinase mitogen-activated protein kinases. In vivo, following segmental airway allergen challenge of subjects with mild allergic asthma, activin A mRNA was upregulated in airway eosinophils compared with circulating eosinophils, and ex vivo, circulating eosinophils tended to release more activin A in response to IL-3+TNF. These data provide evidence that eosinophils release activin A and that this function is enhanced when eosinophils are present in an allergen-induced inflammatory environment. Moreover, these data provide the first evidence for posttranscriptional control of activin A mRNA. We propose that an environment rich in IL-3+TNF will lead to eosinophil-derived activin A, which has an important role in regulating inflammation and/or fibrosis.\",\n \"corpus_id\": 19553664,\n \"score\": 0\n },\n {\n \"doc_id\": \"28432060\",\n \"title\": \"Toll-like receptor 2 dominance over Toll-like receptor 4 in stressful conditions for its detrimental role in the heart.\",\n \"abstract\": \"It has been suggested that Toll-like receptor (TLR)4 promotes IL-10-mediated cardiac cell survival, whereas another receptor, TLR2, from the same family, is detrimental. Here, we examined the interactive role of these two innate signaling molecules under stressful conditions, including IL-10 knockout (IL-10(-/-)) mice, global ischemia-reperfusion (I/R) injury in rat hearts, and in vitro short hairpin RNA experimental models in the presence or absence of IL-10 (10 ng/ml). Circulating and myocardial levels of TNF-α as well as apoptosis and fibrosis were higher in IL-10(-/-) mice. The increase in TLR2 in IL-10(-/-) hearts indicated its negative regulation by IL-10. Ex vivo I/R also caused a marked upregulation of TLR2 and TNF-α as well as apoptotic and fibrotic signals. However, a 40-min reperfusion with IL-10 triggered an increase in TLR4 expression and improved recovery of cardiac function. The increase in IL-1 receptor-associated kinase (IRAK)-M and IRAK-2 activity during I/R injury suggested their role in TLR2 signaling. In vitro inhibition of TLR4 activity as a consequence of RNA inhibition-mediated suppression of myeloid differentiation gene (MyD)88 suggested MyD88-dependent activation of TLR4. The inclusion of IL-10 during reperfusion also downregulated the expression of IRAK-2, TNF-α receptor-associated factor 1-interacting protein (TRAIP) and apoptotic signals, caspase-3, and the Bax-to-Bcl-xL ratio. IL-10 reduced the TNF-α receptor-associated increase in TRAIP-induced apoptosis during I/R injury, which led to an increase in IL-1β to mitigate transforming growth factor-β receptor type I-mediated fibrosis. The IL-10 mitigation of these changes suggests that the stimulation through TLR4 signaling promotes IRAK-4 and phosphorylates IRAK-1 instead of IRAK-2 and may be an important therapeutic approach in restoring heart health in stress. NEW & NOTEWORTHY Under stress conditions such as downregulation of the IL-10 gene or ischemia-reperfusion injury, Toll-like receptor (TLR)4 and IL-1 receptor-associated kinase (IRAK)-1 activation is suppressed, along with the upregulation of TLR-2 and IRAK-2, resulting in fibrosis and apoptosis. It is suggested that IL-10 helps to maintain heart function during stress via myeloid differentiation gene 88/IRAK-4/IRAK-1-dependent TLR4 signaling.\",\n \"corpus_id\": 19061954,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":52,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29481401\",\n \"title\": \"A Systematic Review and Meta-Analysis on the Strength and Consistency of the Associations between Dupuytren Disease and Diabetes Mellitus, Liver Disease, and Epilepsy.\",\n \"abstract\": \"BACKGROUND: The role of diabetes mellitus, liver disease, and epilepsy as risk factors for Dupuytren disease remains unclear. In this systematic review and meta-analysis, the strength and consistency of these associations were examined. METHODS: The MEDLINE, EMBASE, and Web of Science databases were searched for articles reporting an association between Dupuytren disease and diabetes mellitus, liver disease, and epilepsy published before September 26, 2016. The frequencies of Dupuytren disease and diabetes mellitus, liver disease, and epilepsy were extracted, as was information on potential confounders. Generalized linear mixed models were applied to estimate pooled odds ratios, adjusted for confounders. Heterogeneity between studies was quantified using an intraclass correlation coefficient and was accounted for by a random effect for study. RESULTS: One thousand two hundred sixty unique studies were identified, of which 32 were used in the meta-analyses. An association between Dupuytren disease and diabetes mellitus was observed (OR, 3.06; 95 percent CI, 2.69 to 3.48, adjusted for age), which was stronger for type 1 diabetes mellitus than for type 2 diabetes mellitus but was not statistically significant (p = 0.24). An association between Dupuytren disease and liver disease was observed (OR, 2.92; 95 percent CI, 2.08 to 4.12, adjusted for sex). Dupuytren disease and epilepsy were associated, yielding an OR of 2.80 (95 percent CI, 2.49 to 3.15). Heterogeneity between studies was moderate to low. CONCLUSIONS: These findings demonstrate an association between Dupuytren disease and diabetes mellitus, liver disease, and epilepsy. Prospective, longitudinal studies are needed to elucidate the pathways causing these associations.\",\n \"corpus_id\": -1\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19109117","title":"Birth weight and risk of type 2 diabetes: a systematic review.","abstract":"CONTEXT: Low birth weight is implicated as a risk factor for type 2 diabetes. However, the strength, consistency, independence, and shape of the association have not been systematically examined. OBJECTIVE: To conduct a quantitative systematic review examining published evidence on the association of birth weight and type 2 diabetes in adults. DATA SOURCES AND STUDY SELECTION: Relevant studies published by June 2008 were identified through literature searches using EMBASE (from 1980), MEDLINE (from 1950), and Web of Science (from 1980), with a combination of text words and Medical Subject Headings. Studies with either quantitative or qualitative estimates of the association between birth weight and type 2 diabetes were included. DATA EXTRACTION: Estimates of association (odds ratio [OR] per kilogram of increase in birth weight) were obtained from authors or from published reports in models that allowed the effects of adjustment (for body mass index and socioeconomic status) and the effects of exclusion (for macrosomia and maternal diabetes) to be examined. Estimates were pooled using random-effects models, allowing for the possibility that true associations differed between populations. DATA SYNTHESIS: Of 327 reports identified, 31 were found to be relevant. Data were obtained from 30 of these reports (31 populations; 6090 diabetes cases; 152 084 individuals). Inverse birth weight-type 2 diabetes associations were observed in 23 populations (9 of which were statistically significant) and positive associations were found in 8 (2 of which were statistically significant). Appreciable heterogeneity between populations (I(2) = 66%; 95% confidence interval [CI], 51%-77%) was largely explained by positive associations in 2 native North American populations with high prevalences of maternal diabetes and in 1 other population of young adults. In the remaining 28 populations, the pooled OR of type 2 diabetes, adjusted for age and sex, was 0.75 (95% CI, 0.70-0.81) per kilogram. The shape of the birth weight-type 2 diabetes association was strongly graded, particularly at birth weights of 3 kg or less. Adjustment for current body mass index slightly strengthened the association (OR, 0.76 [95% CI, 0.70-0.82] before adjustment and 0.70 [95% CI, 0.65-0.76] after adjustment). Adjustment for socioeconomic status did not materially affect the association (OR, 0.77 [95% CI, 0.70-0.84] before adjustment and 0.78 [95% CI, 0.72-0.84] after adjustment). There was no strong evidence of publication or small study bias. CONCLUSION: In most populations studied, birth weight was inversely related to type 2 diabetes risk.","corpus_id":-1,"score":1},{"doc_id":"19465232","title":"Type 2 diabetes mellitus after gestational diabetes: a systematic review and meta-analysis.","abstract":"BACKGROUND: Women with gestational diabetes are at increased risk of developing type 2 diabetes, but the risk and time of onset have not been fully quantified. We therefore did a comprehensive systematic review and meta-analysis to assess the strength of association between these conditions and the effect of factors that might modify the risk. METHODS: We identified cohort studies in which women who had developed type 2 diabetes after gestational diabetes were followed up between Jan 1, 1960, and Jan 31, 2009, from Embase and Medline. 205 relevant reports were hand searched. We selected 20 studies that included 675 455 women and 10 859 type 2 diabetic events. We calculated and pooled unadjusted relative risks (RRs) with 95% CIs for each study using a random-effects model. Subgroups analysed were the number of cases of type 2 diabetes, ethnic origin, duration of follow-up, maternal age, body-mass index, and diagnostic criteria. FINDINGS: Women with gestational diabetes had an increased risk of developing type 2 diabetes compared with those who had a normoglycaemic pregnancy (RR 7.43, 95% CI 4.79-11.51). Although the largest study (659 164 women; 9502 cases of type 2 diabetes) had the largest RR (12.6, 95% CI 12.15-13.19), RRs were generally consistent among the subgroups assessed. INTERPRETATION: Increased awareness of the magnitude and timing of the risk of type 2 diabetes after gestational diabetes among patients and clinicians could provide an opportunity to test and use dietary, lifestyle, and pharmacological interventions that might prevent or delay the onset of type 2 diabetes in affected women. FUNDING: None.","corpus_id":-1,"score":1},{"doc_id":"21711420","title":"Systematic review with meta-analyses of studies on the association between cirrhosis and liver metastases.","abstract":"The hemodynamic, cellular and metabolic changes seen in patients with cirrhosis may reduce the risk of liver metastases. The aim of this case-control is to compare the risk of liver metastases from extrahepatic malignant diseases among patients with or without cirrhosis. Electronic searches (Medline, Embase, and Web of Science) and manual searches were combined (October 2010) to identify observational studies on patients with malignant disease reporting the risk of liver metastases among cases (with cirrhosis) and controls (without liver disease). Meta-analysis was performed using random effects models due to an expected clinical heterogeneity. Sixteen studies were included. Evidence of liver metastases was diagnosed in 22% of cases and 38% of controls based on autopsies (n = 14 studies) or laparoscopy (n = 2 studies). Random effects meta-analysis suggested that patients with cirrhosis had a lower risk of liver metastases (relative risk = 0.53; 95% confidence interval = 0.42-0.66). The conclusions were confirmed in sensitivity and subgroup analyses accounting for the year of publication, matching for age, sex and location of tumors (within the portal vein). No statistical evidence of bias was identified and the analyses were confirmed when adjusting for multiple testing. The present review suggests that cirrhosis reduces the risk of liver metastases. However, additional evidence from prospective studies adjusting for confounding factors is still needed.","corpus_id":-1,"score":1},{"doc_id":"21889332","title":"Type 2 diabetes mellitus and colorectal cancer: meta-analysis on sex-specific differences.","abstract":"Although there is consent concerning a higher risk for colorectal cancer (CRC) amongst patients with type 2 diabetes mellitus (T2DM), there remains uncertainty regarding potential sex differences in the strength of this association. We reviewed and summarised epidemiological studies assessing the sex-specific association of T2DM with the risk for CRC. All relevant studies published until 14th February 2011 were identified by a systematic search of MEDLINE, EMBASE, BIOSIS Previews and ISI Web of Knowledge databases and cross-referencing. We included observational studies that reported relative risk (RR) or odds ratio (OR) estimates with 95% confidence intervals (CIs) for the association between T2DM and CRC. Two authors independently extracted data and assessed study quality of each study in a standardised manner. Study-specific estimates were pooled for both sexes separately using random-effects models. A total of 29 eligible studies were used for meta-analysis. Overall estimates of relative risk (RR) were very similar amongst men (RR=1.29; 95%-confidence interval (CI): 1.19-1.140) and women (RR=1.34; 95%-CI: 1.22-1.47). In both men and women, risk estimates from case-control studies were slightly higher than those from cohort studies. Overall, T2DM is associated with a moderate increase in CRC risk in both men and women.","corpus_id":-1,"score":1},{"doc_id":"21898753","title":"Diabetes mellitus and risk of hepatocellular carcinoma: a systematic review and meta-analysis.","abstract":"Studies of diabetes and hepatocellular carcinoma (HCC) yielded inconsistent findings. This meta-analysis was conducted to examine the association between diabetes and risk of HCC. Studies were identified by searching PUBMED and MEDLINE database up to February 2011. Pooled risk estimates were calculated using the random-effects model. Potential sources of heterogeneity were explored by subgroup analyses. A total of 17 case-control studies and 32 cohort studies were included in the meta-analysis. The combined risk estimate of all studies showed a statistically significant increased risk of HCC prevalence among diabetic individuals (RR = 2.31, 95% CI: 1.87-2.84). The pooled risk estimate of 17 case-control studies (OR = 2.40, 95% CI: 1.85-3.11) was slightly higher than that from 25 cohort studies (RR = 2.23, 95% CI: 1.68-2.96). Metformin treatment was potentially protective. On the contrary, long duration of diabetes and sulfonylureas or insulin treatment possibly increase HCC risk. Also meta-analysis of 7 cohort studies found a statistically significant increased risk of HCC mortality (RR = 2.43, 95% CI: 1.66-3.55) for individuals with (versus without) diabetes. This meta-analysis shows that diabetes is associated with moderately increased risk of HCC prevalence, as well as HCC mortality. Considering the rapidly increasing prevalence of diabetes mellitus, the study underlines the need for cancer prevention in diabetic individuals. Further investigation is needed to focus on the potential mechanism for the pathogenesis of HCC and the link between HCC and different types, severity, treatment and duration of diabetes.","corpus_id":-1,"score":1},{"doc_id":"23074528","title":"Community-based care for the management of type 2 diabetes: an evidence-based analysis.","abstract":"UNLABELLED: In June 2008, the Medical Advisory Secretariat began work on the Diabetes Strategy Evidence Project, an evidence-based review of the literature surrounding strategies for successful management and treatment of diabetes. This project came about when the Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the Ministry's newly released Diabetes Strategy. After an initial review of the strategy and consultation with experts, the secretariat identified five key areas in which evidence was needed. Evidence-based analyses have been prepared for each of these five areas: insulin pumps, behavioural interventions, bariatric surgery, home telemonitoring, and community based care. For each area, an economic analysis was completed where appropriate and is described in a separate report. To review these titles within the Diabetes Strategy Evidence series, please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/mas_about.html,DIABETES STRATEGY EVIDENCE PLATFORM: Summary of Evidence-Based AnalysesContinuous Subcutaneous Insulin Infusion Pumps for Type 1 and Type 2 Adult Diabetics: An Evidence-Based AnalysisBehavioural Interventions for Type 2 Diabetes: An Evidence-Based AnalysisBARIATRIC SURGERY FOR PEOPLE WITH DIABETES AND MORBID OBESITY: An Evidence-Based SummaryCommunity-Based Care for the Management of Type 2 Diabetes: An Evidence-Based AnalysisHome Telemonitoring for Type 2 Diabetes: An Evidence-Based AnalysisApplication of the Ontario Diabetes Economic Model (ODEM) to Determine the Cost-effectiveness and Budget Impact of Selected Type 2 Diabetes Interventions in Ontario OBJECTIVE: The objective of this report is to determine the efficacy of specialized multidisciplinary community care for the management of type 2 diabetes compared to usual care. CLINICAL NEED: TARGET POPULATION AND CONDITION Diabetes (i.e. diabetes mellitus) is a highly prevalent chronic metabolic disorder that interferes with the body's ability to produce or effectively use insulin. The majority (90%) of diabetes patients have type 2 diabetes. ( 1) Based on the United Kingdom Prospective Diabetes Study (UKPDS), intensive blood glucose and blood pressure control significantly reduce the risk of microvascular and macrovascular complications in type 2 diabetics. While many studies have documented that patients often do not meet the glycemic control targets specified by national and international guidelines, factors associated with glycemic control are less well studied, one of which is the provider(s) of care. Multidisciplinary approaches to care may be particularly important for diabetes management. According guidelines from the Canadian Diabetes Association (CDA), the diabetes health care team should be multi-and interdisciplinary. Presently in Ontario, the core diabetes health care team consists of at least a family physician and/or diabetes specialist, and diabetes educators (registered nurse and registered dietician). Increasing the role played by allied health care professionals in diabetes care and their collaboration with physicians may represent a more cost-effective option for diabetes management. Several systematic reviews and meta-analyses have examined multidisciplinary care programs, but these have either been limited to a specific component of multidisciplinary care (e.g. intensified education programs), or were conducted as part of a broader disease management program, of which not all were multidisciplinary in nature. Most reviews also do not clearly define the intervention(s) of interest, making the evaluation of such multidisciplinary community programs challenging. EVIDENCE-BASED ANALYSIS METHODS: RESEARCH QUESTIONS: What is the evidence of efficacy of specialized multidisciplinary community care provided by at least a registered nurse, registered dietician and physician (primary care and/or specialist) for the management of type 2 diabetes compared to usual care? [ Henceforth referred to as Model 1]What is the evidence of efficacy of specialized multidisciplinary community care provided by at least a pharmacist and a primary care physician for the management of type 2 diabetes compared to usual care? [ Henceforth referred to as Model 2] INCLUSION CRITERIA: English language full-reportsPublished between January 1, 2000 and September 28, 2008Randomized controlled trials (RCTs), systematic reviews and meta-analysesType 2 diabetic adult population (≥18 years of age)Total sample size ≥30Describe specialized multidisciplinary community care defined as ambulatory-based care provided by at least two health care disciplines (of which at least one must be a specialist in diabetes) with integrated communication between the care providers. Compared to usual care (defined as health care provision by non-specialist(s) in diabetes, such as primary care providers; may include referral to other health care professionals/services as necessary)≥6 months follow-up EXCLUSION CRITERIA: Studies where discrete results on diabetes cannot be abstractedPredominantly home-based interventionsInpatient-based interventions OUTCOMES OF INTEREST: The primary outcomes for this review were glycosylated hemoglobin (rHbA1c) levels and systolic blood pressure (SBP). SEARCH STRATEGY: A literature search was performed on September 28, 2008 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published between January 1, 2000 and September 28, 2008. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any additional relevant studies not identified through the search. Articles with unknown eligibility were reviewed with a second clinical epidemiologist, then a group of epidemiologists until consensus was established. The quality of evidence was assessed as high, moderate, low or very low according to GRADE methodology. Given the high clinical heterogeneity of the articles that met the inclusion criteria, specific models of specialized multidisciplinary community care were examined based on models of care that are currently being supported in Ontario, models of care that were commonly reported in the literature, as well as suggestions from an Expert Advisory Panel Meeting held on January 21, 2009. SUMMARY OF FINDINGS: The initial search yielded 2,116 unique citations, from which 22 RCTs trials and nine systematic reviews published were identified as meeting the eligibility criteria. Of these, five studies focused on care provided by at least a nurse, dietician, and physician (primary care and/or specialist) model of care (Model 1; see Table ES 1), while three studies focused on care provided by at least a pharmacist and primary care physician (Model 2; see Table ES 2). Based on moderate quality evidence, specialized multidisciplinary community care Model 2 has demonstrated a statistically and clinically significant reduction in HbA1c of 1.0% compared with usual care. The effects of this model on SBP, however, are uncertain compared with usual care, based on very-low quality evidence. Specialized multidisciplinary community care Model 2 has demonstrated a statistically and clinically significant reduction in both HbA1c of 1.05% (based on high quality evidence) and SBP of 7.13 mm Hg (based on moderate quality evidence) compared to usual care. For both models, the evidence does not suggest a preferred setting of care delivery (i.e., primary care vs. hospital outpatient clinic vs. community clinic). Table ES1:Summary of Results of Meta-Analyses of the Effects of Multidisciplinary Care Model 1OutcomeEstimate of effect(95% CI)Heterogeneity I(2)(p-value)GRADEGlycosylated Hemoglobin (HbA1c [%])-1.00 [-1.27, -0.73]4% (p=0.37)Moderate-quality Subgroup: Moderate-to-High Quality-0.91 [-1.19, -0.62]0% (p=0.74)Systolic Blood Pressure (mm Hg)-2.04 [-13.80, 9.72]89% (p=0.002)Very-low quality*Mean change from baseline to follow-up between intervention and control groupsTable ES2:Summary of Results of Meta-Analyses of the Effects of Multidisciplinary Care Model 2OutcomeEstimate of effect(95% CI)Heterogeneity I(2)(p-value)GRADEGlycosylated Hemoglobin (HbA1c [%])-1.05 [-1.57, -0.52]0% (p=0.75)High-qualitySystolic Blood Pressure (mm Hg)-7.13 [-11.78, -2.48]46% (p=0.17)Moderate quality*Mean change from baseline to follow-up between intervention and control groups.","corpus_id":40547459,"score":1},{"doc_id":"23772556","title":"Psoriasis, psoriatic arthritis and type 2 diabetes mellitus: a systematic review and meta-analysis.","abstract":"Several observational studies have assessed the association between psoriasis, psoriatic arthritis (PsA) and type 2 diabetes mellitus, with inconclusive results. We set out to investigate the association between psoriasis, PsA and type 2 diabetes mellitus. Observational studies assessing the relationship between psoriasis or PsA and type 2 diabetes mellitus up to December 2012 were identified by electronic and hand searches in Medline, Embase, PubMed, the Cochrane Database of Systematic Reviews and Google Scholar. For each study we collected the first author's last name, publication year, country of origin, study design, characteristics of participants (sample size, age and sex), the variables incorporated into the multivariable analyses, and the odds ratios (ORs) of psoriasis associated with diabetes along with the corresponding 95% confidence intervals (CIs). From the data provided in each article, the crude OR was also calculated. Forty-four observational studies (in 37 articles) were identified for the final analysis. The pooled OR from random-effects analysis was determined to be 1·76 (95% CI 1·59-1·96). The highest risk was for patients suffering from PsA (OR 2·18, 95% CI 1·36-3·50). We also observed a dose effect in the risk of suffering from type 2 diabetes mellitus, as patients considered as having severe psoriasis had higher risk (OR 2·10, 95% CI 1·73-2·55) than the pooled OR. We perform meta-regression and sensitivity analyses to explore sources of heterogeneity among the studies and to determine how they would influence the estimates, and found no significant influence in the results of the meta-analyses. The findings support the association between psoriasis, PsA and type 2 diabetes mellitus. Some caution must be taken in the interpretation of these results because there may be heterogeneity between studies.","corpus_id":-1,"score":1},{"doc_id":"24098798","title":"The association between diabetes mellitus and nonarteritic anterior ischemic optic neuropathy: a systematic review and meta-analysis.","abstract":"BACKGROUND: The association of diabetes mellitus (DM) with nonarteritic anterior ischemic optic neuropathy (NAION) has been inconclusive. PURPOSE: To determine whether DM is associated with an increased risk of NAION. METHODS: A comprehensive literature search was performed for published studies reporting both DM and NAION based on PubMed and EMBASE. After reviewing characteristics of all the included studies systematically, meta-analytical method was employed to calculate the pooled odds ratio (OR) and associated 95% confidence interval (CI) from random-effects models. Heterogeneity was assessed by Q-statistic test. Funnel Plot, Begg's and Egger's linear regression test were applied to evaluate publication bias. A sensitivity analysis and meta-regression analysis were also performed to assess the robustness of results. RESULTS: 2,096 participants from 12 case-control studies were pooled for a meta-analysis. The result of meta-analysis of these studies indicated that DM is associated with increased risk of NAION (pooled OR = 1.64, 95% CI = 1.17-2.30; P = 0.004). Sensitivity analysis indicated our findings are robust, and meta-regression analysis revealed no significant effect in terms of geographical area, gender, age of patients with NAION, the year of the publication, source of the controls, and sample size (all p>0.05). Evidence of publication bias was not observed in our study. CONCLUSION: Meta-analysis suggests that DM might be associated with increased risk of NAION.","corpus_id":-1,"score":1},{"doc_id":"24263394","title":"A systematic review and meta-analysis on the prevalence of Dupuytren disease in the general population of Western countries.","abstract":"BACKGROUND: Dupuytren disease is a fibroproliferative disease of palmar fascia of the hand. Its prevalence has been the subject of several reviews; however, an accurate description of the prevalence range in the general population--and of the relation between age and disease--is lacking. METHODS: Embase and PubMed were searched using database-specific Medical Subject Headings; titles and abstracts were searched for the words \"Dupuytren,\" \"incidence,\" and \"prevalence.\" Two reviewers independently assessed the articles using inclusion and exclusion criteria, and rated the included studies with a quality assessment instrument. In a meta-analysis, the median prevalence, as a function of age by sex, was estimated, accompanied by 95 percent prediction intervals. The observed heterogeneity in prevalence was investigated with respect to study quality and geographic location. RESULTS: Twenty-three of 199 unique identified articles were included. The number of participants ranged from 37 to 97,537, and age ranged from 18 to 100 years. Prevalence varied from 0.6 to 31.6 percent. The quality of studies differed but could not explain the heterogeneity among studies. Mean prevalence was estimated as 12, 21, and 29 percent at ages 55, 65, and 75 years, respectively, based on the relation between age and prevalence determined from 10 studies. CONCLUSIONS: The authors describe a prevalence range of Dupuytren disease in the general population of Western countries. The relation between age and prevalence of Dupuytren disease is given according to sex, including 95 percent prediction intervals. It is possible to determine disease prevalence at a certain age for the total population, and for men and women separately.","corpus_id":-1,"score":1},{"doc_id":"24278229","title":"Association between telomere length and type 2 diabetes mellitus: a meta-analysis.","abstract":"BACKGROUND: Several epidemiological studies have examined the association between shortened telomere length and type 2 diabetes mellitus (T2DM), while the results remained conflicting. We conducted a meta-analysis to derive a more precise estimation of the relationship between them. METHODS: We systematically reviewed the databases of PubMed, EMBASE, and Web of Science for all studies on the association between telomere length and T2DM. We conducted this study assessed by STATA 11.0. Data were summarized using random-effects or fixed-effects meta-analysis. The heterogeneity and publication bias among studies were examined by using χ(2)-based Q statistic test and Egger's test, respectively. RESULTS: Nine cohorts consisting of 5759 cases and 6518 controls were selected into the meta-analysis. The results indicated that shortened telomere length was significantly associated with T2DM risk (OR: 1.291; 95% CI: 1.112, 1.498; P<0.001) with heterogeneity (I(2) = 71.6%). When three cohorts responsible for the heterogeneity were excluded, the pooled OR for the remaining cohorts indicated a significant association between shortened telomere length and T2DM (OR: 1.117; 95% CI: 1.002, 1.246; P = 0.045) without heterogeneity. CONCLUSION: We found a statistically significant association between shortened telomere length and T2DM.","corpus_id":-1,"score":1},{"doc_id":"24830459","title":"Diabetes mellitus and poorer prognosis in hepatocellular carcinoma: a systematic review and meta-analysis.","abstract":"BACKGROUND: Previous studies suggested that diabetes mellitus was associated with cancer risk and prognosis, but studies investigating the relationship between diabetes mellitus and survival in patients with hepatocellular carcinoma (HCC) reported inconsistent findings. To derive a more precise estimate of the prognostic role of diabetes mellitus in HCC, we systematically reviewed published studies and carried out a meta-analysis. METHODS: Eligible articles were identified in electronic databases from their inception through September 16, 2013. To evaluate the correlation between diabetes mellitus and prognosis in HCC, the pooled hazard ratios (HR) and their 95% confidence intervals (95% CI) for poorer overall and disease-free survivals were calculated by standard meta-analysis techniques with fixed-effects or random-effects models. RESULTS: 21 studies with a total of 9,767 HCC patients stratifying overall survival and/or disease-free survival in HCC patients by diabetes mellitus status were eligible for meta-analysis. 20 studies with a total of 9,727 HCC cases investigated the overall survival, and 10 studies with a total of 2,412 HCC patients investigated the disease-free survival. The pooled HRs for overall survival and disease-free survival were 1.46 (95% CI, 1.29 to 1.66; P<0.001) and 1.57 (95% CI, 1.21 to 2.05; P = 0.001), respectively. The adjusted HRs for overall survival and disease-free survival were 1.55 (95% CI, 1.27 to 1.91; P<0.001) and 2.15 (95% CI, 1.75 to 2.63; P<0.001), respectively. In addition, for patients receiving hepatic resection, diabetes mellitus was associated with both poorer overall survival and poorer disease-free survival, and for patients receiving non-surgical treatment or patients receiving radiofrequency ablation, diabetes mellitus was associated with poorer overall survival. There was no evidence for publication bias. CONCLUSION: Diabetes mellitus is independently associated with both poorer overall survival and poorer disease-free survival in HCC patients.","corpus_id":-1,"score":1},{"doc_id":"25228184","title":"The association of gallstone disease and diabetes mellitus. A meta-analysis.","abstract":"OBJECTIVES: To assess the association between diabetes mellitus and gallstone disease (GSD) by meta-analysis. METHODS: This study was carried out at Xiangya Hospital, Changsha, Hunan, China in September 2013. First, eligible studies were searched in PubMed and Cochrane Central databases from their inception to September 2013. Then, a random effect model was used to calculate the overall combined risk estimates. The meta-analysis included 403,001 cases and 411,877 controls from 6 case-control studies, 3 cohort studies, and 13 cross-sectional studies. Finally, statistical analyses were conducted according to the classification of study. RESULTS: Risk ratios for diabetes mellitus and GSD were 1.75 (95% confidence interval [CI]: 1.44-2.13, p<0.00001], 1.76 (95% CI: 1.24-2.5, p<0.00001), and 2.02 (95% CI: 1.59-2.58, p<0.00001). Sensitivity analysis based on the exclusion of any study did not change the heterogeneity I-square test, and risk ratios. Little evidence of publication bias was observed. CONCLUSION: This meta-analysis suggested that there was a very strong positive association between diabetes mellitus and risk of GSD in the patients.","corpus_id":-1,"score":1},{"doc_id":"25238063","title":"Diabetes mellitus and risk of age-related macular degeneration: a systematic review and meta-analysis.","abstract":"Age-related macular degeneration (AMD) is a major cause of severe vision loss in elderly people. Diabetes mellitus is a common endocrine disorder with serious consequences, and diabetic retinopathy (DR) is the main ophthalmic complication. DR and AMD are different diseases and we seek to explore the relationship between diabetes and AMD. MEDLINE, EMBASE, and the Cochrane Library were searched for potentially eligible studies. Studies based on longitudinal cohort, cross-sectional, and case-control associations, reporting evaluation data of diabetes as an independent factor for AMD were included. Reports of relative risks (RRs), hazard ratios (HRs), odds ratio (ORs), or evaluation data of diabetes as an independent factor for AMD were included. Review Manager and STATA were used for the meta-analysis. Twenty four articles involving 27 study populations were included for meta-analysis. In 7 cohort studies, diabetes was shown to be a risk factor for AMD (OR, 1.05; 95% CI, 1.00-1.14). Results of 9 cross-sectional studies revealed consistent association of diabetes with AMD (OR, 1.21; 95% CI, 1.00-1.45), especially for late AMD (OR, 1.48; 95% CI, 1.44-1.51). Similar association was also detected for AMD (OR, 1.29; 95% CI, 1.13-1.49) and late AMD (OR, 1.16; 95% CI, 1.11-1.21) in 11 case-control studies. The pooled ORs for risk of neovascular AMD (nAMD) were 1.10 (95% CI, 0.96-1.26), 1.48 (95% CI, 1.44-1.51), and 1.15 (95% CI, 1.11-1.21) from cohort, cross-sectional and case-control studies, respectively. No obvious divergence existed among different ethnic groups. Therefore, we find diabetes a risk factor for AMD, stronger for late AMD than earlier stages. However, most of the included studies only adjusted for age and sex; we thus cannot rule out confounding as a potential explanation for the association. More well-designed prospective cohort studies are still warranted to further examine the association.","corpus_id":-1,"score":1},{"doc_id":"25262110","title":"Air pollution and risk of type 2 diabetes mellitus: a systematic review and meta-analysis.","abstract":"AIM: Whether exposure to relatively high levels of air pollution is associated with diabetes occurrence remains unclear. We sought to assess and quantify the association between exposure to major air pollutants and risk of type 2 diabetes. METHODS: PubMed and EMBASE databases (through September 2013) were searched using a combination of terms related to exposure to gaseous (NO2 and NOx) or particulate matter pollutants (PM2.5, PM10 and PM10-2.5) and type 2 diabetes. Descriptive and quantitative information were extracted from selected studies. We used random-effects models meta-analysis to derive overall risk estimates per type of pollutant. RESULTS: We included ten studies (five cross-sectional and five prospective), assessing the effects of air pollutants on the occurrence of diabetes. In prospective investigations, the overall effect on diabetes occurrence was significant for both NO2 (adjusted hazard ratio [HR], 1.13; 95% confidence interval [95%CI], 1.01-1.22; p < 0.001; I(2) = 36.4%, pheterogeneity = 0.208) and PM2.5 (HR, 1.11; 95%CI, 1.03-1.20; p < 0.001; I(2) = 0.0%, pheterogeneity = 0.827). Odds ratios were reported by two cross-sectional studies which revealed similar associations between both NO2 and PM2.5 with type 2 diabetes. Across studies, risk estimates were generally adjusted for age, gender, body mass index and cigarette smoking. CONCLUSIONS: Available evidence supports a prospective association of main air pollutants with an increased risk for type 2 diabetes. This finding may have implications for population-based strategies to reduce diabetes risk.","corpus_id":-1,"score":1},{"doc_id":"25329153","title":"Exposure to organochlorine pollutants and type 2 diabetes: a systematic review and meta-analysis.","abstract":"OBJECTIVE: Though exposure to organochlorine pollutants (OCPs) is considered a risk factor for type 2 diabetes (T2DM), epidemiological evidence for the association remains controversial. A systematic review and meta-analysis was applied to quantitatively evaluate the association between exposure to OCPs and incidence of T2DM and pool the inconsistent evidence. DESIGN AND METHODS: Publications in English were searched in MEDLINE and WEB OF SCIENCE databases and related reference lists up to August 2013. Quantitative estimates and information regarding study characteristics were extracted from 23 original studies. Quality assessments of external validity, bias, exposure measurement and confounding were performed, and subgroup analyses were conducted to examine the heterogeneity sources. RESULTS: We retrieved 23 eligible articles to conduct this meta-analysis. OR (odds ratio) or RR (risk ratio) estimates in each subgroup were discussed, and the strong associations were observed in PCB-153 (OR, 1.52; 95% CI, 1.19-1.94), PCBs (OR, 2.14; 95% CI, 1.53-2.99), and p,p'-DDE (OR, 1.33; 95% CI, 1.15-1.54) based on a random-effects model. CONCLUSIONS: This meta-analysis provides quantitative evidence supporting the conclusion that exposure to organochlorine pollutants is associated with an increased risk of incidence of T2DM.","corpus_id":-1,"score":1},{"doc_id":"25657765","title":"Prevalence of epilepsy in iran: a meta-analysis and systematic review.","abstract":"OBJECTIVE: Epilepsy is one of the most common diseases in Iran contributing to an array of health problems. In light of this, the aim of the present study is to examine the prevalence of epilepsy in Iran through a systematic review and meta-analysis. MATERIALS & METHODS: A systematic search of several databases including PubMed, scientific information databases, Google, Google scholar, Elsevier and Scopus was conducted in June 2013. Observational studies were considered for inclusion if they were published in Iranian and examined epilepsy prevalence and/or related risk factors. Meta-analysis was conducted using a random effect model with the DerSimonian/Laird method. Heterogeneity was examined using the Breslow- Day test and inconsistency using the I2 statistic. RESULTS: A total of 45 studies were identified from the search strategy. Of these, nine published manuscripts with a total of 7,723 participants were included within the review. The pooled prevalence of epilepsy in Iran was estimated to be around 5% (95% confident interval (CI) 2 to 8). For each region the prevalence of epilepsy in central, northern and eastern Iran were 5% (95%CI 2 to 8), 1% (95%CI -1 to 3) and 4% (95%CI 3 to 11) respectively. The most common risk factors in order of prevalence were somatic diseases 39% (95%CI 15 to 62), convulsion 38% (95%CI 11 to 65), mental diseases 36% (95%CI 15 to 95) and hereditary development 26% (95%CI 9 to 42). A meta-regression model identified a declining trend in the prevalence of epilepsy within Iran for the last decade. CONCLUSION: Pooled analyses from the nine included publications in this review estimate the prevalence of epilepsy in Iran to be around 5%. Although this result is much higher than rates in other countries, a declining trend in prevalence over the past decade was also identified.","corpus_id":-1,"score":1},{"doc_id":"25780309","title":"Association between diabetes mellitus and gastroesophageal reflux disease: A meta-analysis.","abstract":"AIM: To investigate whether there is a link between diabetes mellitus (DM) and gastroesophageal reflux disease (GERD). METHODS: We conducted a systematic search of PubMed and Web of Science databases, from their respective inceptions until December 31, 2013, for articles evaluating the relationship between DM and GERD. Studies were selected for analysis based on certain inclusion and exclusion criteria. Data were extracted from each study on the basis of predefined items. A meta-analysis was performed to compare the odds ratio (OR) in DM between individuals with and without GERD using a fixed effect or random effect model, depending on the absence or presence of significant heterogeneity. Subgroup analyses were used to identify sources of heterogeneity. Publication bias was assessed by Begg's test. To evaluate the results, we also performed a sensitivity analysis. RESULTS: When the electronic database and hand searches were combined, a total of nine eligible articles involving 9067 cases and 81 968 controls were included in our meta-analysis. Based on the random-effects model, these studies identified a significant association between DM and the risk of GERD (overall OR = 1.61; 95%CI: 1.36-1.91; P = 0.003). Subgroup analyses indicated that this result persisted in studies on populations from Eastern countries (OR = 1.71; 95%CI: 1.38-2.12; P = 0.003) and in younger patients (mean age < 50 years) (OR = 1.70; 95%CI: 1.22-2.37; P = 0.001). No significant publication bias was observed in this meta-analysis using Begg(')s test (P = 0.175). The sensitivity analysis also confirmed the stability of our results. CONCLUSION: This meta-analysis suggests that patients with DM are at greater risk of GERD than those who do not have DM.","corpus_id":-1,"score":1},{"doc_id":"25909054","title":"Type 2 diabetes mellitus and risk of malignant melanoma: a systematic review and meta-analysis of cohort studies.","abstract":"BACKGROUND: Epidemiology studies have demonstrated inconsistent associations between type 2 diabetes mellitus and the risk of malignant melanoma. To this end, the aim was to perform a meta-analysis of cohort studies. METHOD: Medline, PubMed, Embase and the Cochrane Library were searched up to February 2014. Cohort studies addressing the relative risk of type 2 diabetes mellitus on malignant melanoma were included in this meta-analysis. The Newcastle-Ottawa Scale was applied for quality evaluation. The pooled relative risks with the corresponding 95% confidence intervals (95% CIs) were calculated by using random-effects or random-effects model. Heterogeneity and publication bias were evaluated by I (2) and funnel plot analysis, respectively. Data was analyzed using STATA 11.0. RESULTS: A total of 9 independent cohorts from 8 manuscripts were entered this meta-analysis. Type 2 diabetes mellitus was slightly associated with an increased risk of malignant melanoma, and the pooled relative risk was 1.15 (95% CI, 1.00-1.32) in diabetes compared with non-diabetes with significant evidence of heterogeneity among these studies (P=0.016, I (2) =57.6%). For the studies adjusted for age, gender and obesity, the relative risks were 1.21 (95% CI, 1.03-1.42), 1.17 (95% CI, 1.01-1.35) and 1.11 (95% CI, 1.00-1.24), respectively. For the population-based studies in which case cohort established, the relative risk was 1.85 (95% CI, 1.31-2.62). CONCLUSION: Type 2 diabetes might be an independent risk factor for malignant melanoma. Further studies are needed to specifically test the effect, and fully elucidate the underlying pathophysiologic mechanisms.","corpus_id":-1,"score":1},{"doc_id":"26019469","title":"Association of type 2 diabetes mellitus and the risk of colorectal cancer: A meta-analysis and systematic review.","abstract":"AIM: To provide a quantitative assessment of the association between type 2 diabetes mellitus (T2DM) and the risk of colorectal cancer (CRC). METHODS: Systematic review was conducted thorough MEDLINE, EMBASE, Cochrane Library, and ISI Web of knowledge databases till 31(st) January 2014. This meta-analysis included the cohort studies that illustrated relative risk (RR) or odds ratio estimates with 95%CI for the predictive risk of CRC by T2DM. Summary relative risks with 95%CI were analyzed by using an effects summary ratio model. Heterogeneity among studies was assessed by the Cochran's Q and I (2) statistics. RESULTS: The meta analysis of 8 finally selected studies showed a positive correlation of T2DM with the risk of CRC as depicted by effects summary RR of 1.21 (95%CI: 1.02-1.42). Diabetic women showed greater risk of developing CRC as their effect summary RR of 1.22 (95%CI: 1.01-49) with significant overall Z test at 5% level of significance was higher than the effect summary RR of 1.17 (95%CI: 1.00-1.37) of men showing insignificant Z test. The effect summary RR of 1.19 with 95%CI of 1.07-1.33 indicate a positive relationship between DM and increased risk of CRC with significant heterogeneity (I (2) = 92% and P-value < 0.05). CONCLUSION: Results from this systematic review and meta-analysis report that diabetic people have an increased risk of CRC as compared to non-diabetics.","corpus_id":-1,"score":1},{"doc_id":"26173490","title":"Diabetes as a risk factor for carpal tunnel syndrome: a systematic review and meta-analysis.","abstract":"AIMS: To assess whether diabetes increases the risk of carpal tunnel syndrome and to estimate the magnitude of the association with Type 1 and Type 2 diabetes. METHODS: We conducted a systematic search of PubMed, Embase, Web of Science, Scopus, Google Scholar and ResearchGate for articles published between 1950 and January 2015. A total of 36 studies (eight cross-sectional, 21 case-control and seven cohort studies) qualified for meta-analysis. We used a random-effects meta-analysis and assessed heterogeneity and publication bias. RESULTS: The pooled odds ratio of 25 studies (including a total of 92 564 individuals) that reported unadjusted estimates for the association between diabetes and carpal tunnel syndrome or carpal tunnel release was 1.97 (95% CI 1.56-2.49). The pooled odds ratio of 18 case-control or cohort studies consisting of >37 million individuals that reported estimates after controlling for potential confounders was 1.69 (95% CI 1.45-1.96). The association did not differ for Type 1 and Type 2 diabetes. Furthermore, there was no publication bias. CONCLUSION: This meta-analysis suggests that both Type 1 and Type 2 diabetes are risk factors for carpal tunnel syndrome.","corpus_id":-1,"score":1},{"doc_id":"26234220","title":"Diabetes mellitus is associated with increased risk of surgical site infections: A meta-analysis of prospective cohort studies.","abstract":"BACKGROUND AND OBJECTIVE: Observational studies have suggested an association between diabetes mellitus and the risk of surgical site infections (SSIs), but the results remain inconclusive. We conducted a meta-analysis of prospective cohort studies to elucidate the relationship between diabetes mellitus and SSIs. METHODS: We searched PubMed, Embase, and Web of Science databases and reviewed the reference lists of the retrieved articles to identify relevant studies. Associations were tested in subgroups representing different patient characteristics and study quality criteria. The random-effect model was used to calculate the overall relative risk (RR). RESULTS: Fourteen prospective cohort studies (N = 91,094 participants) were included in this meta-analysis, and the pooled crude RR was 2.02 (95% confidence interval, 1.68-2.43) with significant between-study heterogeneity observed (I(2) = 56.50%). Significant association was also detected after we derived adjusted RRs for studies not reporting the adjusted RRs and calculated the combined adjusted RR of the 14 studies (RR, 1.69; 95% confidence interval, 1.33-2.13). Results were consistent and statistically significant in all subgroups. Stratified analyses found the number of confounders adjusted for, sample size, and method of diabetes case ascertainment might be the potential sources of heterogeneity. Sensitivity analysis further demonstrated the robustness of the result. CONCLUSIONS: This meta-analysis suggests diabetes mellitus is significantly associated with increased risk of SSIs. Future studies are encouraged to reveal the mechanisms underlying this association.","corpus_id":-1,"score":1},{"doc_id":"26417844","title":"Prevalence of hypertriglyceridemic waist and association with risk of type 2 diabetes mellitus: a meta-analysis.","abstract":"INTRODUCTION: A meta-analysis of studies assessing the prevalence of hypertriglyceridemic waist and an association with risk of type 2 diabetes mellitus (T2DM). MATERIALS AND METHODS: PubMed, EMBASE, Web of Science, CNKI, CQVIP and Wanfang databases were searched for studies of the prevalence of hypertriglyceridemic waist or association with risk of T2DM. Reference lists of each original article were also searched. A random-effects model was used to synthesize the combined prevalence and odds ratios. Publication bias and substantial heterogeneity were examined. RESULTS: Twenty-five eligible studies involving 93 194 participants (93 194 for prevalence and 34 199 for odds ratios): 17 articles of prevalence, and 8 of both prevalence and risk of T2DM. Prevalence of hypertriglyceridemic waist ranged from 4% to 47%, with pooled prevalence of 18% (95% CI 13-23%), overall: 18% (95% CI 13-23%) for men and 19% (95% CI 13-24%) for women. Odds ratios ranged from 2.8 to 9.6 for T2MD in overall, with pooled odds ratios of 4.18 (95% CI 3.55-4.92), overall: 3.55 (95% CI 2.93-4.31) for men and 4.18 (95% CI 3.43-5.09) for women. DISCUSSION/CONCLUSION: The prevalence of hypertriglyceridemic waist has reached an alarming level and is closely associated with increased risk of T2DM in the general population, particularly among women and among brown-skinned men and women. Copyright © 2015 John Wiley & Sons, Ltd.","corpus_id":-1,"score":1},{"doc_id":"26507303","title":"Is diabetes mellitus a risk factor for venous thromboembolism? A systematic review and meta-analysis of case-control and cohort studies.","abstract":"OBJECTIVE: Diabetes mellitus is a well-established risk factor for atherosclerotic disease, but its role in the occurrence of venous thromboembolism (VTE) has not been elucidated. We conducted a meta-analysis of published cohort and case-control studies to assess whether diabetes mellitus is a risk factor for VTE. RESEARCH DESIGN AND METHODS: We systematically searched MEDLINE and EMBASE for case-control and prospective cohort studies assessing association between the risk of venous thromboembolism and diabetes. Odds ratios (OR) from case-control studies were combined while for prospective studies hazard ratios (HR) were combined. Models with random effects were used. Meta-analyses were conducted separately for raw and adjusted measures of association. RESULTS: 24 studies were identified including 10 cohort studies (274,501 patients) and 14 case-control studies (1,157,086 patients). Meta-analysis of the prospective cohort studies demonstrated a significant association between diabetes and VTE (HR 1.60; 95% CI 1.35 to 1.89). This association was no longer present after analysis of multi-adjusted HRs (HR 1.10; 95% CI 0.77 to 1.56). Meta-analysis of case-control studies showed a significant association between diabetes and VTE (OR 1.57; 95%CI 1.17 to 2.12), but this association was no longer present when adjusted ORs were used (OR 1.18; 95%CI 0.89 to 1.56). CONCLUSIONS: The increased risk of VTE associated with diabetes mainly results from confounders rather than an intrinsic effect of diabetes on venous thrombotic risk. Therefore, no specific recommendations should apply for the management of diabetic patients at risk for VTE.","corpus_id":-1,"score":1},{"doc_id":"26598716","title":"Is there an association between tendinopathy and diabetes mellitus? A systematic review with meta-analysis.","abstract":"BACKGROUND: Musculoskeletal symptoms limit adherence to exercise interventions for individuals with type 2 diabetes. People with diabetes may be susceptible to tendinopathy due to chronically elevated blood glucose levels. Therefore, we aimed to investigate this potential association by systematically reviewing and meta-analysing case-control, cross-sectional, and studies that considered both of these conditions. METHODS: Nine medical databases and hand searching methods were used without year limits to identify all relevant English language articles that considered diabetes and tendinopathy. Two authors applied exclusion criteria and one author extracted data with verification by a second author. Meta-analysis was conducted using a random effects model. Results were expressed as odds ratio (OR), mean difference or standardised mean difference with a confidence intervals (95% CI). Heterogeneity was assessed by I(2). FINDINGS: 31 studies were included in the final analysis of which 26 recruited people with diabetes and five recruited people with tendinopathy. Tendinopathy was more prevalent in people with diabetes (17 studies, OR 3·67, 95% CI 2·71 to 4·97), diabetes was more prevalent in people with tendinopathy (5 studies, OR 1·28, 95% CI 1·10 to 1·49), people with diabetes and tendinopathy had a longer duration of diabetes than people with diabetes only (6 studies, mean difference 5·26 years, 95% CI 4·15 to 6·36) and people with diabetes had thicker tendons than controls (9 studies, standardised mean difference 0·79 95% CI 0·47 to 1·12). INTERPRETATION: These findings provide strong evidence that diabetes is associated with higher risk of tendinopathy. This is clinically relevant as tendinopathy may affect adherence to exercise interventions for diabetes.","corpus_id":-1,"score":1},{"doc_id":"26612139","title":"Diabetes mellitus and venous thromboembolism: A systematic review and meta-analysis.","abstract":"Diabetes mellitus (DM) may be a risk factor for venous thromboembolism (VTE) but results are inconsistent. AIM: We conducted a systematic review and meta-analysis of epidemiologic studies to quantify the association between DM and VTE. METHODS AND RESULTS: We included studies identified in PubMed, Web of Science, and CINAHL through 07/31/2014. We identified 19 studies that met our selection criteria. We pooled RRs using a random-effects model: the pooled RR for the association of DM with VTE was 1.10 (95% CI: 0.94-1.29). Between-study heterogeneity was explored with a forest plot, funnel plot, meta-regression, and a stratified analysis. Between-study heterogeneity was observed and not explained by study design, method of DM assessment, or degree of adjustment for confounding. Sensitivity analyses omitted one study at a time to assess the influence of any single study on the pooled estimate. These analyses indicated that one large study was highly influential; when this study was excluded, the pooled estimate increased and just reached statistical significance: 1.16 (95% CI: 1.01-1.34). CONCLUSIONS: This meta-analysis suggests either no association or a modest positive one between DM and VTE in the general population. DM is unlikely to play a major role in VTE development.","corpus_id":-1,"score":1},{"doc_id":"26993825","title":"Significant Association Between Gallstone Disease and Nonalcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis.","abstract":"BACKGROUND: Gallstone disease (GD) and nonalcoholic fatty liver disease (NAFLD) are common digestive disorders worldwide. Both conditions share certain risk factors including obesity, insulin resistance and diabetes. Several epidemiologic studies have reported the relationship between these two conditions. AIM: We conducted a systematic review and meta-analysis to characterize the association between GD and NAFLD. METHODS: A comprehensive search of the databases MEDLINE and EMBASE was performed from inception through November 2015. The inclusion criterion was the observational studies' assessment of the association between GD and NAFLD in adult participants. Pooled odds ratio (OR) and 95 % confidence interval (CI) were calculated using a random-effects model. RESULTS: Data were extracted from 12 observational studies (9 cross-sectional studies, 1 case-control study and 2 cohort studies). The pooled OR of NAFLD in patients who had GD was 1.55 (95 % CI 1.31-1.82). The statistical between-studies heterogeneity (I (2)) was 64 %. The association remained significant when limited to cohort studies with pooled OR 1.33 (95 % CI 1.14-1.55, I (2) = 0 %). CONCLUSION: Our meta-analysis demonstrated that GD is significantly associated with NAFLD. Further prospective studies exploring the underlying mechanism of this association should be pursued.","corpus_id":-1,"score":1},{"doc_id":"27396752","title":"Association of circulating total bilirubin with the metabolic syndrome and type 2 diabetes: A systematic review and meta-analysis of observational evidence.","abstract":"OBJECTIVE: Emerging evidence suggests that bilirubin levels might be associated with the metabolic syndrome (MetS) and type 2 diabetes (T2D), although the nature of the association remains unclear. DESIGN: This systematic review and meta-analysis investigated the relationship between total plasma bilirubin and the risk of MetS and T2D. DATA SOURCES: Relevant studies were identified using five databases (Embase, Medline [Ovid], Web of Science, PubMed, Cochrane Central and Google Scholar), with the last search done on 21 October 2015. Study references were checked and authors contacted to identify additional studies. STUDY SELECTION: Randomized controlled trials, and cohort, case-control and cross-sectional studies of adults examining the association between blood bilirubin levels and MetS and T2D were included, irrespective of language and date of publication. Abstract and full-text selection was done by two independent reviewers, with a third reviewer available in case of disagreement. DATA EXTRACTION: Data were extracted by two independent reviewers using a predesigned data collection form. MAIN OUTCOMES AND MEASURES: MetS and T2D. METHODS: Summary estimates were obtained by random-effects meta-analysis. RESULTS: Of the 2313 searched references, 16 observational studies (11 cross-sectional, two prospective, one that was both cross-sectional and prospective, two retrospective and one national survey) met our inclusion criteria. Overall, data were available for 175,911 non-overlapping participants, including 7414 MetS cases and 9406 T2D cases. In the meta-analysis of seven cross-sectional studies, the pooled odds ratio (95% confidence interval) for MetS in a comparison of extreme tertiles of serum bilirubin levels was 0.70 (95% CI: 0.62, 0.78), whereas no significant association was found for the pooled estimated relative risk between two prospective studies (0.57, 95% CI: 0.11, 2.94). The corresponding estimate was 0.77 (95% CI: 0.67, 0.87) for T2D from four cross-sectional studies. CONCLUSION: The available evidence, mainly from cross-sectional studies, supports an inverse association of bilirubin levels with adverse metabolic outcomes. Large-scale prospective studies are now needed to establish whether bilirubin levels may be useful in the prevention of MetS and T2D.","corpus_id":-1,"score":1},{"doc_id":"27477292","title":"Diabetes mellitus as a risk factor for incident chronic kidney disease and end-stage renal disease in women compared with men: a systematic review and meta-analysis.","abstract":"Diabetes mellitus is a strong risk factor for chronic kidney disease and end-stage renal disease. Whether sex differences in chronic kidney disease and end-stage renal disease incidence exist among diabetic patients remains unclear. This systematic review and meta-analysis was conducted to evaluate the relative effect of diabetes on chronic kidney disease and end-stage renal disease risk in women compared with men. We systematically searched Embase, PubMed, and the Cochrane Library for both cohort and case-control studies until October 2015. Studies were selected if they reported a sex-specific relationship between diabetes mellitus and chronic kidney disease or end-stage renal disease. We generated pooled estimates across studies using random-effects meta-analysis after log transformation with inverse variance weighting. Ten studies with data from more than 5 million participants were included. The pooled adjusted risk ratio of chronic kidney disease associated with diabetes mellitus was 3.34 (95 % CI 2.27, 4.93) in women and 2.84 (95 % CI 1.73, 4.68) in men. The data showed no difference in diabetes-related chronic kidney disease risk between the sexes (pooled adjusted women-to-men relative risk ratio was 1.14 [95 % CI 0.97, 1.34]) except for end-stage renal disease-the pooled adjusted women-to men relative risk ratio was 1.38 (95 % CI 1.22, 1.55; p = 0.114, I² = 38.1 %). The study found no evidence of a sex difference in the association between diabetes mellitus and chronic kidney disease. However, the excess risk for end-stage renal disease was higher in women with diabetes than in men with the same condition, from which we assume that the female gender could accelerate the disease progression. Further studies are needed to support this notion and elucidate the underlying mechanisms.","corpus_id":-1,"score":1},{"doc_id":"27515679","title":"Diabetes mellitus and risk of falls in older adults: a systematic review and meta-analysis.","abstract":"BACKGROUND: intensive or very loose glycemic control may contribute to the risk of falls in diabetic patients. However, studies on diabetes mellitus and the risk of falls have yielded conflicting results. Our objective was to investigate the effect of diabetes mellitus on the risk of falls in older adults by conducting a systematic review and meta-analysis. METHODS: the PubMed and Embase databases were searched for relevant studies published until November 2015. Only prospective cohort studies reporting at least age-adjusted risk estimate of falls compared diabetic to non-diabetic individuals were selected. Diabetes mellitus was ascertained by a combination of medical history and laboratory tests or use of anti-diabetic drugs. RESULTS: a total of six studies involving 14,685 participants were identified. The number of falls in diabetic and non-diabetic individuals was 423 of 1,692 (25.0%) and 2,368 of 13,011 (18.2%), respectively. Diabetes mellitus was associated with an increased risk of falls (risk ratio [RR] = 1.64; 95% confidence intervals [CI] 1.27-2.11) in a random-effects model. Subgroup analyses showed that the risk of falls seemed more pronounced among both gender groups (RR = 1.81; 95% CI 1.19-2.76) than among women (RR = 1.52; 95% CI 1.04-2.21). Diabetes increased 94% (RR = 1.94; 95% CI 1.42-2.63) and 27% (RR = 1.27; 95% CI 1.06-1.52) risk of falls in insulin-treated and no-insulin-treated patients, respectively. CONCLUSIONS: this meta-analysis reveals that older adults with diabetes mellitus are associated with greater risk of falls, and this association is more pronounced in insulin-treated patients.","corpus_id":-1,"score":1},{"doc_id":"27658134","title":"Systematic review and meta-analysis of the association between mumps during childhood and risk of type 1 diabetes mellitus.","abstract":"We conducted a systematic review and meta-analysis of the association between mumps and risk of type 1 diabetes mellitus (T1DM). Literature searches were conducted using Medline, EMBASE and Web of Science including studies published before February 2014. Crude and, where available, adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were extracted from the published reports of each included study. Combined OR estimates and tests of heterogeneity were obtained using meta-analysis techniques. The analysis was repeated in subgroups of studies on the basis of quality defined by the score on the Newcastle-Ottawa scale (NOS). In total, 18 articles met the eligibility criteria, and overall there was some evidence of a weak association between clinically diagnosed mumps and T1DM (OR=1.23, 95% CI 1.00-1.51; p=0.05) but marked heterogeneity between studies (I2=49%; p for heterogeneity=0.01). Restricting analyses to 13 high quality studies, there was little evidence of association between clinically diagnosed mumps and T1DM (OR=1.11, 95% CI 0.91-1.35; p=0.29) and there was much less heterogeneity (I2=26%; p for heterogeneity=0.18). Overall there was little evidence of any strong association between mumps infection and T1DM.","corpus_id":-1,"score":1},{"doc_id":"28397967","title":"The association between dementia and epilepsy: A systematic review and meta-analysis.","abstract":"OBJECTIVE: Dementia is among the top 15 conditions with the most substantial increase in burden of disease in the past decade, and along with epilepsy, among the top 25 causes of years lived with disability worldwide. The epidemiology of dementia in persons with epilepsy, and vice versa, is not well characterized. The purpose of this systematic review was to examine the prevalence, incidence, and reported risk factors for dementia in epilepsy and epilepsy in dementia. METHODS: Embase, PsycINFO, MEDLINE, and the Cochrane databases were searched from inception. Papers were included if they reported the incidence and/or prevalence of dementia and epilepsy. Two individuals independently performed duplicate abstract and full-text review, data extraction, and quality assessment. Random-effects models were used to generate pooled estimates when feasible. RESULTS: Of the 3,043 citations identified, 64 were reviewed in full text and 19 articles were included. The period prevalence of dementia ranged from 8.1 to 17.5 per 100 persons among persons with epilepsy (insufficient data to pool). The pooled period prevalence of epilepsy among persons with dementia was 5 per 100 persons (95% confidence interval [CI] 1-9) in population-based settings and 4 per 100 persons (95% CI 1-6) in clinic settings. There were insufficient data to report a pooled overall incidence rate and only limited data on risk factors. SIGNIFICANCE: There are significant gaps in knowledge regarding the epidemiology of epilepsy in dementia and vice versa. Accurate estimates are needed to inform public health policy and prevention, and to understand health resource needs for these populations.","corpus_id":22832684,"score":1},{"doc_id":"28643299","title":"The association between circulating fetuin-A levels and type 2 diabetes mellitus risk: systematic review and meta-analysis of observational studies.","abstract":"BACKGROUND AND OBJECTIVE: Fetuin-A is a liver-derived circulating protein that is associated with insulin resistance and diabetes. The objective of this systematic review and meta-analysis of published observational studies was to investigate mean levels of fetuin-A in T2D patients and the relationship between blood fetuin-A levels and T2D risk. MATERIALS AND METHODS: PubMed, Embase, Google Scholar, Web of Science, and The Cochrane Library were systematically searched for potential relevant studies up to 1 December 2016. Natural logarithm-transformed estimate risks, standard mean differences on the basis of Hedges's adjusted g, and 95% confidence intervals (CIs) were calculated for all eligible studies and were combined to measure the pooled data using random-effects model. RESULTS: A total of 32 studies including 27 case-control and 5 cohort studies were included in the current study. Fetuin-A levels in T2D patients were significantly higher than control groups [Hedges' g = 1.73, 95% CI (1.25-2.22), P < 0.001], with significant heterogeneity across studies (P < 0.001, I (2) = 98.46%). Findings from meta-analyses of cohort studies showed a statistically significant association between fetuin-A levels and T2D risk [rate ratio = 1.62, 95% CI (1.26-2.08), P < 0.001], with no significant heterogeneity (P = 0.10, I (2) = 46.06%). CONCLUSION: We found a significant relationship between the fetuin-A levels with T2D risk. Although fetuin-A may be as a potential screening and prediction biomarker or a therapeutic target in T2D patients, further studies are required in this regard.","corpus_id":-1,"score":1},{"doc_id":"28757515","title":"Association between type 1 diabetes mellitus and risk of epilepsy: A meta-analysis of observational studies.","abstract":"A potential association between type 1 diabetes mellitus and subsequent epilepsy emerged in recent studies. This study aimed to evaluate the possible relationship between type 1 diabetes mellitus and epilepsy using meta-analysis. Pubmed, ISI Web of Knowledge, Embase and Cochrane Library were searched for potential studies of the association between type 1 diabetes mellitus and epilepsy from inception to February 1, 2017. Two investigators independently screened studies for inclusion and extracted related data; discrepancies were solved by consensus. Random effects model of Hazard Ratio (HR) was used to estimate the strength of association. We identified 13 papers from potentially relevant articles of which 3 cohort studies met the inclusion criteria. Random effects meta-analysis showed that type 1 diabetes mellitus was associated with an increased risk of epilepsy with HR = 3.29 (95% CI: 2.61-4.14; I(2) = 0, p = 0.689). Similar results were observed in type 1 diabetes mellitus patents younger than 18-years-old with HR = 2.96 (95% CI: 2.28-3.84; I(2) = 0, p = 0.571). Meta-analysis of 2 studies that adjusted for potential confounders yielded an increased risk of epilepsy with HR = 2.89 (95% CI: 2.26-3.70; I(2) = 0, p = 0.831). The meta-analysis indicates that type 1 diabetes mellitus is associated with a statistically significant increased risk for epilepsy compared to those without type 1 diabetes mellitus.","corpus_id":-1,"score":1},{"doc_id":"28858123","title":"Diabetes mellitus carries a risk of esophageal cancer: A meta-analysis.","abstract":"BACKGROUND: Many studies have showed that diabetes mellitus (DM) might be a risk factor for certain types of cancers. However, there are still inconsistent results on the effects of DM on the risk of esophageal cancer (EC). The objective of this study is to investigate the association and to quantify the correlation between DM and EC by a meta-analysis. METHODS: The initial search identified 339 articles. Those publications that did not report the exact number of EC cases were removed. Finally, 13 meaningful studies were extracted from the databases of PubMed, MEDLINE, and Web of Science. All pooled analyses of risk ratios (RRs) and 95% confidence intervals (CIs) were assessed by a random-effect or fixed-effect model. Subgroup analysis was implemented on the basis of the sex or ethnicity. I value was used to assess heterogeneity, and funnel plot analysis was for publication bias. RESULTS: The result showed that there was a positive correlation between type 2 diabetes mellitus (T2DM) and EC risk (RR = 1.28, 95% CI: 1.12-1.47, P < .001). Subgroup analysis based on gender showed that male was an important risk factor for EC (RR = 1.53, 95% CI: 1.44-1.62, P < .001), but female was not (RR = 1.23, 95% CI: 0.41-3.69, P = .71). In addition, subgroup analysis based on ethnicity showed that DM was significantly correlated to EC in North America subjects (RR = 1.39, 95% CI: 1.31-1.47, P < .001), and in Europe subjects (RR = 1.37, 95% CI: 1.02-1.83, P = .04), whereas no correlation was found in Asian subjects (RR = 0.98, 95% CI: 0.50-1.95, P = .96). Furthermore, DM had a correlation to an increased risk of esophageal adenocarcinoma (EAC) (RR = 1.43, 95% CI: 1.35-1.51, P < .001). CONCLUSION: This meta-analysis indicates that DM is positively correlated to EC. However, the results should be interpreted with caution because of the limitations on potential clinical confounding factors in each study included in this meta-analysis.","corpus_id":-1,"score":1},{"doc_id":"28862239","title":"Insomnia and risk of nonalcoholic fatty liver disease: A systematic review and meta-analysis.","abstract":"AIM: This sudy aims to investigate the association between insomnia or excessive daytime sleepiness (EDS) and risk of nonalcoholic fatty liver disease (NAFLD). METHODS: We searched published studies indexed in MEDLINE and EMBASE database from inception to December 2015. Studies that reported odds ratios (ORs), risk ratios, hazard ratios or standardized incidence ratio with 95% confidence intervals (CI) comparing the risk of NAFLD among participants who had insomnia or EDS versus those without insomnia or EDS were included. Pooled ORs and 95% CI were calculated using a random-effect, generic inverse variance method of DerSimonian and Laird. Cochran's Q test and I2 statistic were used to determine the between-study heterogeneity. RESULTS: Our search strategy yielded 2117 potentially relevant articles (781 articles from MEDLINE and 1336 articles from EMBASE). After comprehensive review, seven studies (three cross-sectional studies and four case-control studies) were found to be eligible and were included in the meta-analysis. The risk of NAFLD in participants who had insomnia was significantly higher with the pooled OR of 1.13 (95% CI, 1.00-1.27). The statistical heterogeneity was moderate with an I2 of 62%. Elevated risk of NAFLD was also observed among participants with EDS even though the 95% CI was wider and did not reach statistical significance (pooled OR 2.21; 95% CI, 0.84-5.82). The statistical heterogeneity was moderate with an I2 of 62%. CONCLUSIONS: Our study demonstrated an increased risk of NAFLD among participants who had insomnia or EDS. Whether this association is causal needs further investigations.","corpus_id":-1,"score":1},{"doc_id":"28899519","title":"The association between daytime napping and risk of diabetes: a systematic review and meta-analysis of observational studies.","abstract":"OBJECTIVE: To investigate the association between daytime napping and prevalent/incident diabetes mellitus (DM) based on systematic review and meta-analytic data. METHODS: The electronic databases of Embase, Medline, Pubmed and Web of Science were searched. Relevant studies were extracted by two reviewers independently. The associations between daytime napping (irrespective of duration), long nap (≥1 h/day) and short nap (<1 h/day), and risk of DM were assessed according to study types. Overall estimates were pooled using either fixed- or random-effect with inverse variance meta-analysis. Heterogeneity of included studies was assessed using the I2 test and possible cause of the heterogeneity was examined by meta-regression analyses. RESULTS: Ten studies (four cross-sectional and six longitudinal cohort) comprising a total of 304,885 individuals and 20,857 cases of DM were included in the systematic review, with an average napping prevalence of 47%. Nappers were found to have increased risk of DM in both cross-sectional and cohort studies. However, significant heterogeneity was present. Long nap (≥1 h/day) was associated with both prevalent and incident DM; in particular, those with a daily nap over 1 h had a 31% increased risk of developing DM during follow-up (95% confidence interval: 2-67%). Conversely, no such association was found in individuals with short naps (<1 h/day) in cohort studies. CONCLUSIONS: Long daytime napping over 1 h per day was associated with increased risk of both prevalent and incident DM. Further studies are needed to confirm the findings.","corpus_id":-1,"score":1},{"doc_id":"29063028","title":"Elevation of serum uric acid and incidence of type 2 diabetes: A systematic review and meta-analysis.","abstract":"OBJECTIVE: Recently, several cohort studies suggested a positive relationship between serum uric acid (SUA) and type 2 diabetes mellitus (T2DM), which is inconsistent with the results of functional research. Our aim was to further evaluate this correlation by conducting a systematic review. METHODS: Computerized literature searches of the Medline database, EMBASE database, and PubMed were used to evaluate the relationship between SUA and T2DM in cohort studies. Cochran's Q and I2 statistics were used to evaluate heterogeneity among studies, and pooled relative risk (RR) and odds ratio (OR) with 95% confidence intervals (CIs) were calculated using random-effects and fixed-effects models. The summary RR and OR of per 1 mg/ml-SUA increase were calculated separately because of their different epidemiological implications and calculation methods. Additionally, sensitivity analysis, stratified analysis, meta-regression, and multiple meta-regression were applied to investigate the heterogeneity among studies. RESULTS: A total of 970 articles were retrieved from the searches. Sixteen publications of cohort studies containing 61,714 participants were included. The pooled RR was 1.131 (95% CI: 1.084-1.179) with significant heterogeneity among studies (I 2 = 51.9%, P = 0.018). Adjusted RR to evaluate the stability of the relationship between SUA and T2DM in the sensitivity analysis was similar (RR = 1.140, 95% CI: 1.087-1.197), with statistically significant heterogeneity (I 2 = 54.5%, P = 0.015). Stratified analysis and meta-regression showed that the positive relationship remained irrespective of age, sex, region, and adjustment for confounding factors including body mass index, fasting blood glucose, systolic blood pressure, diastolic blood pressure, alcohol consumption, smoking, blood cholesterol, waist circumference, fatty liver, and drugs affecting SUA. CONCLUSION: Although SUA is independently associated with development of T2DM, insulin resistance increased as the baseline SUA concentration increased; thus, the correlation between SUA and T2DM requires further evaluation and the baseline insulin resistance status should also be considered.","corpus_id":24181712,"score":1},{"doc_id":"29113364","title":"Alpha-glucosidase inhibitors and risk of cancer in patients with diabetes mellitus: a systematic review and meta-analysis.","abstract":"Several studies have shown that anti-diabetic medications may modify the risk of cancer. We performed a systematic review and meta-analysis to evaluate the effect of alpha-glucosidase inhibitors (AGIs) on the risk of cancer in patients with diabetes mellitus. We conducted a systematic search of Medline, EMBASE, and Web of Science databases, up to September 30, 2016. Random-effects model was used to estimate the summary odds ratios (ORs) with 95% CI. Twenty-five studies (14 cohort, 7 case-control, and 4 randomized controlled trials) involving 1,285,433 patients with diabetes were included. Meta-analysis of observational studies showed that the use of AGIs was associated with a lower risk of developing cancer (OR = 0.86, 95% CI 0.78-0.96), especially gastrointestinal cancer (OR = 0.83, 95% CI 0.71-0.97). There was considerable heterogeneity across the studies introduced partly by the quality of included studies and adjustment for potential confounders. Meta-analysis of randomized controlled trials did not reveal any significant association between AGIs and cancer risk. Meta-analysis of observational studies indicated that AGIs may decrease the risk of cancer in individuals with diabetes.","corpus_id":-1,"score":1},{"doc_id":"29161276","title":"Association between diabetes mellitus and active tuberculosis: A systematic review and meta-analysis.","abstract":"The burgeoning epidemic of diabetes mellitus (DM) is one of the major global health challenges. We systematically reviewed the published literature to provide a summary estimate of the association between DM and active tuberculosis (TB). We searched Medline and EMBASE databases for studies reporting adjusted estimates on the TB-DM association published before December 22, 2015, with no restrictions on region and language. In the meta-analysis, adjusted estimates were pooled using a DerSimonian-Laird random-effects model, according to study design. Risk of bias assessment and sensitivity analyses were conducted. 44 eligible studies were included, which consisted of 58,468,404 subjects from 16 countries. Compared with non-DM patients, DM patients had 3.59-fold (95% confidence interval (CI) 2.25-5.73), 1.55-fold (95% CI 1.39-1.72), and 2.09-fold (95% CI 1.71-2.55) increased risk of active TB in four prospective, 16 retrospective, and 17 case-control studies, respectively. Country income level (3.16-fold in low/middle-vs. 1.73-fold in high-income countries), background TB incidence (2.05-fold in countries with >50 vs. 1.89-fold in countries with ≤50 TB cases per 100,000 person-year), and geographical region (2.44-fold in Asia vs. 1.71-fold in Europe and 1.73-fold in USA/Canada) affected appreciably the estimated association, but potential risk of bias, type of population (general versus clinical), and potential for duplicate data, did not. Microbiological ascertainment for TB (3.03-fold) and/or blood testing for DM (3.10-fold), as well as uncontrolled DM (3.30-fold), resulted in stronger estimated association. DM is associated with a two- to four-fold increased risk of active TB. The association was stronger when ascertainment was based on biological testing rather than medical records or self-report. The burgeoning DM epidemic could impact upon the achievements of the WHO \"End TB Strategy\" for reducing TB incidence.","corpus_id":-1,"score":1},{"doc_id":"29399359","title":"Association between smoking and non-alcoholic fatty liver disease: A systematic review and meta-analysis.","abstract":"Background/aims: Non-alcoholic fatty liver disease is one of the most common chronic liver diseases. Some risk factors are known to influence the development of non-alcoholic fatty liver disease, but the effect of tobacco smoking on the progression of non-alcoholic fatty liver disease is controversial. The main goal of this systematic review and meta-analysis is to investigate the association between smoking and non-alcoholic fatty liver disease. Method: Electronic databases (PubMed, Scopus, and ISI Web of Science) were searched to find published articles on non-alcoholic fatty liver disease and smoking until December 2016. All relevant studies were screened by inclusion and exclusion criteria and compatible studies were chosen. The Newcastle-Ottawa Scale was used to assess the methodological quality of eligible articles. Subsequently, information was gathered based on the following: author, publication year, keywords, country, inclusion and exclusion criteria, main results, study design, conclusion, and confounder variables (age, body mass index, gender, ethnicity, and diabetes). Finally, analyses were performed using Comprehensive Meta-Analysis Software. Results: Data were extracted from 20 observational studies (9 cross-sectional, 6 case-control, 4 cohort studies, and 1 retrospective cohort study). A significant association was observed between smoking and non-alcoholic fatty liver disease with a pooled odds ratio of 1.110 (95% confidence interval, 1.028-1.199), p-value = 0.008. The statistical heterogeneity was medium with an I2 of 40.012%, p-heterogeneity = 0.074. Also there was a significant relation between non-alcoholic fatty liver disease and passive smoking with a pooled odds ratio of 1.380 (95% confidence interval, 1.199-1.588; p-value = 0.001; I2 = 59.41; p-heterogeneity = 0.117). Conclusion: Our meta-analysis demonstrated that smoking is significantly associated with non-alcoholic fatty liver disease. Further prospective studies exploring the underlying mechanisms of this association should be pursued. Also passive smoking increases the risk of non-alcoholic fatty liver disease about 1.38-fold. The effects of smoking cigarettes on active smokers (current smoker, former smoker, and total smoker) are less than passive smokers. Further studies are needed to compare the of effects of passive and active smoking on non-alcoholic fatty liver disease.","corpus_id":-1,"score":1},{"doc_id":"29511464","title":"Type 2 diabetes mellitus and non-alcoholic fatty liver disease: a systematic review and meta-analysis.","abstract":"Aim: The aim of this study was the evaluation of the prevalence of NAFLD in patients with type 2 diabetes mellitus. Background: Non-alcoholic fatty liver disease (NAFLD) is an emerging disease with high prevalence in patients with type 2 diabetes mellitus (T2DM). Many studies have reported the prevalence of NAFLD in type 2 diabetes mellitus patients. However, these results are inconsistent. Methods: A Literature search was conducted in PubMed, Scopus, web of science and Science Direct from 2005 to August 2017. The necessary information was extracted. Heterogeneity was evaluated using I2 statistic. Meta-regression analyses were performed to the estimation of the relationship between the year of study and sample size with the prevalence of NAFLD. Publication bias was assessed by both Begg rank correlation and Egger tests. Subgroup analysis was performed for identification of sources heterogeneity. Results: Seventeen studies involving 10897 type 2 diabetes mellitus patients with NAFLD were included in this meta-analysis. The overall prevalence of NAFLD in type 2 diabetes mellitus patients by random effects models was 54% (95% CI, 45%- 64%). There is a significant heterogeneity across studies with (I2= 99%, p> 0.01). The funnel plot as graphically and Begg and Egger as statistically showed no publication bias among studies. Subgroup analysis indicated that the prevalence of NAFLD in type 2 diabetes mellitus patients differed in predictive factors such as lipid profile, BMI, HbA1c, AST, and ALT. This finding in spite of heterogeneity of documents is corresponding to the positive correlation between NAFLD and type 2 diabetes mellitus. Conclusion: The findings indicated that the overall prevalence of NAFLD among type 2 diabetes mellitus patients is significantly higher. It can be concluded that type 2 diabetes mellitus patients should be managed to prevent NAFLD.","corpus_id":-1,"score":1},{"doc_id":"29721679","title":"The association of household food insecurity with the risk of type 2 diabetes mellitus in adults: a systematic review and meta-analysis.","abstract":"BACKGROUND: The link between household food insecurity and risk of type 2 diabetes mellitus still remains controversial. Therefore, we performed a systematic review and meta-analysis to clarify the association between household food insecurity and type 2 diabetes mellitus. METHODS: EMBASE, PubMed, ISI Web of Science and Scopus databases were searched up to March 2017. The selection of studies, data extraction and assessing the risk of bias in the included studies were carried out by two reviewers independently. Study-specific odds ratios (ORs) were pooled using a random effects model. RESULTS: A total of 18 articles including a total of 55,353,915 adult participants were included in the meta-analysis. The pooled ORs of the cross-sectional studies revealed that household food insecurity was significantly associated with the odds of T2DM (OR 1.27, 95% CI 1.11-1.42) with no evidence of publication bias (p = 0.63) but heterogeneity between studies (I2 = 61.1%). Similarly, subgroup analyses showed that the country where the study conducted and household food insecurity assessment tool used to influence the effect of household food insecurity on the odds of T2DM. However, the pooled ORs for two case-control and one cohort studies were not significantly associated between household food insecurity and T2DM in adults. CONCLUSION: This study strengthens the hypothesis of the household food insecurity effect on the odds of T2DM among adults. Further longitudinal studies based on larger, and more representative samples are needed to identify the underlying relationships between food insecurity and type 2 diabetes mellitus.","corpus_id":-1,"score":1},{"doc_id":"23074521","title":"Community-based care for the specialized management of heart failure: an evidence-based analysis.","abstract":"UNLABELLED: In August 2008, the Medical Advisory Secretariat (MAS) presented a vignette to the Ontario Health Technology Advisory Committee (OHTAC) on a proposed targeted health care delivery model for chronic care. The proposed model was defined as multidisciplinary, ambulatory, community-based care that bridged the gap between primary and tertiary care, and was intended for individuals with a chronic disease who were at risk of a hospital admission or emergency department visit. The goals of this care model were thought to include: the prevention of emergency department visits, a reduction in hospital admissions and re-admissions, facilitation of earlier hospital discharge, a reduction or delay in long-term care admissions, and an improvement in mortality and other disease-specific patient outcomes. OHTAC approved the development of an evidence-based assessment to determine the effectiveness of specialized community based care for the management of heart failure, Type 2 diabetes and chronic wounds. PLEASE VISIT THE MEDICAL ADVISORY SECRETARIAT WEB SITE AT: www.health.gov.on.ca/ohtas to review the following reports associated with the Specialized Multidisciplinary Community-Based care series. Specialized multidisciplinary community-based care series: a summary of evidence-based analysesCommunity-based care for the specialized management of heart failure: an evidence-based analysisCommunity-based care for chronic wound management: an evidence-based analysisPlease note that the evidence-based analysis of specialized community-based care for the management of diabetes titled: \"Community-based care for the management of type 2 diabetes: an evidence-based analysis\" has been published as part of the Diabetes Strategy Evidence Platform at this URL: http://www.health.gov.on.ca/english/providers/program/mas/tech/ohtas/tech_diabetes_20091020.htmlPLEASE VISIT THE TORONTO HEALTH ECONOMICS AND TECHNOLOGY ASSESSMENT COLLABORATIVE WEB SITE AT: http://theta.utoronto.ca/papers/MAS_CHF_Clinics_Report.pdf to review the following economic project associated with this series:Community-based Care for the specialized management of heart failure: a cost-effectiveness and budget impact analysis. OBJECTIVE: The objective of this evidence-based analysis was to determine the effectiveness of specialized multidisciplinary care in the management of heart failure (HF). CLINICAL NEED: TARGET POPULATION AND CONDITION HF is a progressive, chronic condition in which the heart becomes unable to sufficiently pump blood throughout the body. There are several risk factors for developing the condition including hypertension, diabetes, obesity, previous myocardial infarction, and valvular heart disease.(1) Based on data from a 2005 study of the Canadian Community Health Survey (CCHS), the prevalence of congestive heart failure in Canada is approximately 1% of the population over the age of 12.(2) This figure rises sharply after the age of 45, with prevalence reports ranging from 2.2% to 12%.(3) Extrapolating this to the Ontario population, an estimated 98,000 residents in Ontario are believed to have HF. Disease management programs are multidisciplinary approaches to care for chronic disease that coordinate comprehensive care strategies along the disease continuum and across healthcare delivery systems.(4) Evidence for the effectiveness of disease management programs for HF has been provided by seven systematic reviews completed between 2004 and 2007 (Table 1) with consistency of effect demonstrated across four main outcomes measures: all cause mortality and hospitalization, and heart-failure specific mortality and hospitalization. ( 4-10) However, while disease management programs are multidisciplinary by definition, the published evidence lacks consistency and clarity as to the exact nature of each program and usual care comparators are generally ill defined. Consequently, the effectiveness of multidisciplinary care for the management of persons with HF is still uncertain. Therefore, MAS has completed a systematic review of specialized, multidisciplinary, community-based care disease management programs compared to a well-defined usual care group for persons with HF. EVIDENCE-BASED ANALYSIS METHODS: RESEARCH QUESTIONS: What is the effectiveness of specialized, multidisciplinary, community-based care (SMCCC) compared with usual care for persons with HF? LITERATURE SEARCH STRATEGY: A comprehensive literature search was completed of electronic databases including MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, Cochrane Library and Cumulative Index to Nursing & Allied Health Literature. Bibliographic references of selected studies were also searched. After a review of the title and abstracts, relevant studies were obtained and the full reports evaluated. All studies meeting explicit inclusion and exclusion criteria were retained. Where appropriate, a meta-analysis was undertaken to determine the pooled estimate of effect of specialized multidisciplinary community-based care for explicit outcomes. The quality of the body of evidence, defined as one or more relevant studies was determined using GRADE Working Group criteria. ( 11) INCLUSION CRITERIA: Randomized controlled trialSystematic review with meta analysisPopulation includes persons with New York Heart Association (NYHA) classification 1-IV HFThe intervention includes a team consisting of a nurse and physician one of which is a specialist in HF management. The control group receives care by a single practitioner (e.g. primary care physician (PCP) or cardiologist)The intervention begins after discharge from the hospitalThe study reports 1-year outcomes EXCLUSION CRITERIA: The intervention is delivered predominately through home-visitsStudies with mixed populations where discrete data for HF is not reported OUTCOMES OF INTEREST: All cause mortalityAll cause hospitalizationHF specific mortalityHF specific hospitalizationAll cause duration of hospital stayHF specific duration of hospital stayEmergency room visitsQuality of Life SUMMARY OF FINDINGS: One large and seven small randomized controlled trials were obtained from the literature search. A meta-analysis was completed for four of the seven outcomes including: All cause mortalityHF-specific mortalityAll cause hospitalizationHF-specific hospitalization. Where the pooled analysis was associated with significant heterogeneity, subgroup analyses were completed using two primary categories: direct and indirect model of care; andtype of control group (PCP or cardiologist).The direct model of care was a clinic-based multidisciplinary HF program and the indirect model of care was a physician supervised, nurse-led telephonic HF program. All studies, except one, were completed in jurisdictions outside North America. ( 12-19) Similarly, all but one study had a sample size of less than 250. The mean age in the studies ranged from 65 to 77 years. Six of the studies(12;14-18) included populations with a NYHA classification of II-III. In two studies, the control treatment was a cardiologist (12;15) and two studies reported the inclusion of a dietitian, physiotherapist and psychologist as members of the multidisciplinary team (12;19). ALL CAUSE MORTALITY: Eight studies reported all cause mortality (number of persons) at 1 year follow-up. ( 12-19) When the results of all eight studies were pooled, there was a statistically significant RRR of 29% with moderate heterogeneity (I(2) of 38%). The results of the subgroup analyses indicated a significant RRR of 40% in all cause mortality when SMCCC is delivered through a direct team model (clinic) and a 35% RRR when SMCCC was compared with a primary care practitioner. HF-SPECIFIC MORTALITY: Three studies reported HF-specific mortality (number of persons) at 1 year follow-up. ( 15;18;19) When the results of these were pooled, there was an insignificant RRR of 42% with high statistical heterogeneity (I(2) of 60%). The GRADE quality of evidence is moderate for the pooled analysis of all studies. ALL CAUSE HOSPITALIZATION: Seven studies reported all cause hospitalization at 1-year follow-up (13-15;17-19). When pooled, their results showed a statistically insignificant 12% increase in hospitalizations in the SMCCC group with high statistical heterogeneity (I(2) of 81%). A significant RRR of 12% in all cause hospitalization in favour of the SMCCC care group was achieved when SMCCC was delivered using an indirect model (telephonic) with an associated (I(2) of 0%). The Grade quality of evidence was found to be low for the pooled analysis of all studies and moderate for the subgroup analysis of the indirect team care model. HF-SPECIFIC HOSPITALIZATION: Six studies reported HF-specific hospitalization at 1-year follow-up. ( 13-15;17;19) When pooled, the results of these studies showed an insignificant RRR of 14% with high statistical heterogeneity (I(2) of 60%); however, the quality of evidence for the pooled analysis of was low. DURATION OF HOSPITAL STAY: Seven studies reported duration of hospital stay, four in terms of mean duration of stay in days (14;16;17;19) and three in terms of total hospital bed days (12;13;18). Most studies reported all cause duration of hospital stay while two also reported HF-specific duration of hospital stay. These data were not amenable to meta-analyses as standard deviations were not provided in the reports. However, in general (and in all but one study) it appears that persons receiving SMCCC had shorter hospital stays, whether measured as mean days in hospital or total hospital bed days. EMERGENCY ROOM VISITS: Only one study reported emergency room visits. ( 14) This was presented as a composite of readmissions and ER visits, where the authors reported that 77% (59/76) of the SMCCC group and 84% (63/75) of the usual care group were either readmitted or had an ER visit within the 1 year of follow-up (P=0.029). ( ABSTRACT TRUNCATED)","corpus_id":32798964,"score":0},{"doc_id":"23349152","title":"A systematic review and meta-analysis of the association between depression and insulin resistance.","abstract":"OBJECTIVE: Depression is associated with the onset of type 2 diabetes. A systematic review and meta-analysis of observational studies, controlled trials, and unpublished data was conducted to examine the association between depression and insulin resistance (IR). RESEARCH DESIGN AND METHODS: Medline, EMBASE, and PsycINFO were searched for studies published up to September 2011. Two independent reviewers assessed the eligibility of each report based on predefined inclusion criteria (study design and measure of depression and IR, excluding prevalent cases of diabetes). Individual effect sizes were standardized, and a meta-analysis was performed to calculate a pooled effect size using random effects. Subgroup analyses and meta-regression were conducted to explore any potential source of heterogeneity between studies. RESULTS: Of 967 abstracts reviewed, 21 studies met the inclusion criteria of which 18 studies had appropriate data for the meta-analysis (n = 25,847). The pooled effect size (95% CI) was 0.19 (0.11-0.27) with marked heterogeneity (I(2) = 82.2%) using the random-effects model. Heterogeneity between studies was not explained by age or sex, but could be partly explained by the methods of depression and IR assessments. CONCLUSIONS: A small but significant cross-sectional association was observed between depression and IR, despite heterogeneity between studies. The pathophysiology mechanisms and direction of this association need further study using a purposively designed prospective or intervention study in samples at high risk for diabetes.","corpus_id":14745073,"score":0},{"doc_id":"23399556","title":"Anti-diabetic medications and risk of pancreatic cancer in patients with diabetes mellitus: a systematic review and meta-analysis.","abstract":"OBJECTIVES: Several preclinical and observational studies have shown that anti-diabetic medications (ADMs) may modify the risk of pancreatic cancer (PaC). We performed a systematic review and meta-analysis evaluating the effect of metformin, sulfonylureas (SUs), thiazolidinediones (TZDs), and insulin on the risk of PaC in patients with diabetes mellitus (DM). METHODS: We conducted a systematic search of Medline, EMBASE, and Web of Science, up to June 2012, and published abstracts from major gastroenterology and oncology meetings from 2003 to 2012. Studies were included if they (1) evaluated and clearly defined exposure to metformin, SU, TZDs, and/or insulin, (2) reported PaC outcomes in patients with DM and (3) reported relative risks or odds ratio (OR) or provided data for their estimation. Summary OR estimates with 95% confidence intervals (CIs) were estimated using the random-effects model. RESULTS: Eleven studies (6 cohort, 3 case-control, and 2 randomized controlled trials (RCTs)) reported 1770 cases of PaC in 730,664 patients with DM. Meta-analysis of observational studies showed no significant association between metformin (n=9 studies; adjusted OR 0.76, 95% CI 0.57-1.03, P=0.073), insulin (n=7 studies; adjusted OR 1.59, 95% CI 0.85-2.96, P=0.144), or TZD (n=4 studies; adjusted OR 1.02, 95% CI 0.81-1.30, P=0.844) use and risk of developing PaC. Use of SU was associated with a 70% increase in the odds of PaC (n=8 studies; adjusted OR 1.70, 95% CI 1.27-2.28, P<0.001). There was considerable inherent heterogeneity between studies not explained by study design, setting, or comparator drug and is likely related to confounding by indication and reverse causality. The pooled analyses of the two RCTs were underpowered and provided non-significant results with wide, non-informative 95% CIs. CONCLUSIONS: Although SU seems to be associated with increased risk of PaC, meta-analysis of existing studies does not support a protective or harmful association between ADM use and risk of PaC in patients with DM. There was considerable heterogeneity across studies, and future, well-designed, prospective studies would be required to understand this association better.","corpus_id":-1,"score":0},{"doc_id":"23415577","title":"Depression and risk of mortality in individuals with diabetes: a meta-analysis and systematic review.","abstract":"OBJECTIVES: To estimate risk of comorbid depression on all-cause mortality over time among individuals with diabetes. METHODS: The Medline, Cumulative Index to Nursing and Allied Health Literature, Cochrane Library, Embase and Science Direct databases were searched through September 30, 2012. We limited our search to longitudinal or prospective studies reporting all-cause mortality among those having depression and diabetes, compared with those having diabetes alone that used hazard ratios (HRs) as the main outcome. Two reviewers independently extracted primary data and evaluated the quality of studies using predetermined criteria. The pooled random effects adjusted HRs were estimated using meta-analysis. The impact of moderator variables on study effect size was examined with meta-regression. RESULTS: A total of 42,363 respondents from 10 studies were included in the analysis. Depression was significantly associated with risk of mortality (pooled HR=1.50, 95% confidence interval=1.35-1.66). Little evidence for heterogeneity was found across the studies (Cochran Q=13.52, P=.20, I(2)=26.03). No significant possibility of publication bias was detected (Egger's regression intercept=0.98, P=.23). CONCLUSION: Depression significantly increases the risk of mortality among individuals with diabetes. Early detection and treatment of depression may improve health outcomes in this population.","corpus_id":45294239,"score":0},{"doc_id":"24439841","title":"Breastfeeding and the maternal risk of type 2 diabetes: a systematic review and dose-response meta-analysis of cohort studies.","abstract":"BACKGROUND AND AIMS: Breastfeeding has been associated with reduced risk of maternal type 2 diabetes in some cohort studies, but the evidence from published studies have differed with regard to the strength of the association. To clarify this association we conducted a systematic review and dose-response meta-analysis of breastfeeding and maternal risk of type 2 diabetes. METHODS AND RESULTS: We conducted a systematic review and dose-response meta-analysis of prospective studies of breastfeeding and maternal risk of type 2 diabetes. We searched the PubMed, Embase and Ovid databases up to September 19th 2013. Summary relative risks were estimated using a random effects model. Six cohort studies including 10,842 cases among 273,961 participants were included in the meta-analysis. The summary RR for the highest duration of breastfeeding vs. the lowest was 0.68 (95% CI: 0.57-0.82, I(2) = 75%, p heterogeneity = 0.001, n = 6). The summary RR for a three month increase in the duration of breastfeeding per child was 0.89 (95% CI: 0.77-1.04, I(2) = 93%, p heterogeneity < 0.0001, n = 3) and the summary RR for a one year increase in the total duration of breastfeeding was 0.91 (95% CI: 0.86-0.96, I(2) = 81%, p heterogeneity = 0.001, n = 4). There was little difference in the summary estimates whether or not BMI had been adjusted for. The inverse associations appeared to be nonlinear, p nonlinearity < 0.0001 for both analyses, and in both analyses the reduction in risk was steeper when increasing breastfeeding from low levels. CONCLUSION: This meta-analysis suggests that there is a statistically significant inverse association between breastfeeding and maternal risk of type 2 diabetes.","corpus_id":-1,"score":0},{"doc_id":"25257241","title":"Relationship between homocysteine level and diabetic retinopathy: a systematic review and meta-analysis.","abstract":"BACKGROUND: The relationship between homocysteine (Hcy) and diabetic retinopathy (DR) remains unclear to date. Therefore, a systematic review and meta-analysis was performed on the relationship between Hcy level and DR. METHODS: Studies were identified by searching PubMed, Embase, and Web of Science databases until 5 May, 2014. RESULTS: A total of 31 studies involving 6,394 participants were included in the meta-analysis. After pooling the data from each included study, the blood Hcy concentration in the DR group was observed to be higher than that in the control group [WMD=2.55; 95% confidence interval (CI), 1.70-3.40], and diabetes mellitus (DM) patients with hyperhomocysteinemia were at a risk for DR [odds ratio (OR)=1.93; 95% CI, 1.46-2.53]. Considering the different DM types, hyperhomocysteinemia in T1DM (OR=1.83, 95% CI, 1.28-2.62) was associated with DR rather than in T2DM (OR=1.59, 95% CI, 0.72-3.51). Considerable statistical heterogeneity in the overall summary estimates was partly explained by the geographical differences. CONCLUSIONS: Results from this current meta-analysis indicate that hyperhomocysteinemia is a risk factor for DR, especially proliferative DR. Differences between geographical regions were observed in the relationship between hyperhomocysteinemia with T1DM risk. Given the heterogeneous results, the relationship between high Hcy and DR needs further investigation. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_167.","corpus_id":-1,"score":0},{"doc_id":"25271098","title":"Bias due to selective inclusion and reporting of outcomes and analyses in systematic reviews of randomised trials of healthcare interventions.","abstract":"BACKGROUND: Systematic reviews may be compromised by selective inclusion and reporting of outcomes and analyses. Selective inclusion occurs when there are multiple effect estimates in a trial report that could be included in a particular meta-analysis (e.g. from multiple measurement scales and time points) and the choice of effect estimate to include in the meta-analysis is based on the results (e.g. statistical significance, magnitude or direction of effect). Selective reporting occurs when the reporting of a subset of outcomes and analyses in the systematic review is based on the results (e.g. a protocol-defined outcome is omitted from the published systematic review). OBJECTIVES: To summarise the characteristics and synthesise the results of empirical studies that have investigated the prevalence of selective inclusion or reporting in systematic reviews of randomised controlled trials (RCTs), investigated the factors (e.g. statistical significance or direction of effect) associated with the prevalence and quantified the bias. SEARCH METHODS: We searched the Cochrane Methodology Register (to July 2012), Ovid MEDLINE, Ovid EMBASE, Ovid PsycINFO and ISI Web of Science (each up to May 2013), and the US Agency for Healthcare Research and Quality (AHRQ) Effective Healthcare Program's Scientific Resource Center (SRC) Methods Library (to June 2013). We also searched the abstract books of the 2011 and 2012 Cochrane Colloquia and the article alerts for methodological work in research synthesis published from 2009 to 2011 and compiled in Research Synthesis Methods. SELECTION CRITERIA: We included both published and unpublished empirical studies that investigated the prevalence and factors associated with selective inclusion or reporting, or both, in systematic reviews of RCTs of healthcare interventions. We included empirical studies assessing any type of selective inclusion or reporting, such as investigations of how frequently RCT outcome data is selectively included in systematic reviews based on the results, outcomes and analyses are discrepant between protocol and published review or non-significant outcomes are partially reported in the full text or summary within systematic reviews. DATA COLLECTION AND ANALYSIS: Two review authors independently selected empirical studies for inclusion, extracted the data and performed a risk of bias assessment. A third review author resolved any disagreements about inclusion or exclusion of empirical studies, data extraction and risk of bias. We contacted authors of included studies for additional unpublished data. Primary outcomes included overall prevalence of selective inclusion or reporting, association between selective inclusion or reporting and the statistical significance of the effect estimate, and association between selective inclusion or reporting and the direction of the effect estimate. We combined prevalence estimates and risk ratios (RRs) using a random-effects meta-analysis model. MAIN RESULTS: Seven studies met the inclusion criteria. No studies had investigated selective inclusion of results in systematic reviews, or discrepancies in outcomes and analyses between systematic review registry entries and published systematic reviews. Based on a meta-analysis of four studies (including 485 Cochrane Reviews), 38% (95% confidence interval (CI) 23% to 54%) of systematic reviews added, omitted, upgraded or downgraded at least one outcome between the protocol and published systematic review. The association between statistical significance and discrepant outcome reporting between protocol and published systematic review was uncertain. The meta-analytic estimate suggested an increased risk of adding or upgrading (i.e. changing a secondary outcome to primary) when the outcome was statistically significant, although the 95% CI included no association and a decreased risk as plausible estimates (RR 1.43, 95% CI 0.71 to 2.85; two studies, n = 552 meta-analyses). Also, the meta-analytic estimate suggested an increased risk of downgrading (i.e. changing a primary outcome to secondary) when the outcome was statistically significant, although the 95% CI included no association and a decreased risk as plausible estimates (RR 1.26, 95% CI 0.60 to 2.62; two studies, n = 484 meta-analyses). None of the included studies had investigated whether the association between statistical significance and adding, upgrading or downgrading of outcomes was modified by the type of comparison, direction of effect or type of outcome; or whether there is an association between direction of the effect estimate and discrepant outcome reporting. Several secondary outcomes were reported in the included studies. Two studies found that reasons for discrepant outcome reporting were infrequently reported in published systematic reviews (6% in one study and 22% in the other). One study (including 62 Cochrane Reviews) found that 32% (95% CI 21% to 45%) of systematic reviews did not report all primary outcomes in the abstract. Another study (including 64 Cochrane and 118 non-Cochrane reviews) found that statistically significant primary outcomes were more likely to be completely reported in the systematic review abstract than non-significant primary outcomes (RR 2.66, 95% CI 1.81 to 3.90). None of the studies included systematic reviews published after 2009 when reporting standards for systematic reviews (Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) Statement, and Methodological Expectations of Cochrane Intervention Reviews (MECIR)) were disseminated, so the results might not be generalisable to more recent systematic reviews. AUTHORS' CONCLUSIONS: Discrepant outcome reporting between the protocol and published systematic review is fairly common, although the association between statistical significance and discrepant outcome reporting is uncertain. Complete reporting of outcomes in systematic review abstracts is associated with statistical significance of the results for those outcomes. Systematic review outcomes and analysis plans should be specified prior to seeing the results of included studies to minimise post-hoc decisions that may be based on the observed results. Modifications that occur once the review has commenced, along with their justification, should be clearly reported. Effect estimates and CIs should be reported for all systematic review outcomes regardless of the results. The lack of research on selective inclusion of results in systematic reviews needs to be addressed and studies that avoid the methodological weaknesses of existing research are also needed.","corpus_id":21550830,"score":0},{"doc_id":"26034369","title":"Risk factors for new onset diabetes mellitus after liver transplantation: A meta-analysis.","abstract":"AIM: To determine the risk factors for new-onset diabetes mellitus (NODM) after liver transplantation by conducting a systematic review and meta-analysis. METHODS: We electronically searched the databases of MEDLINE, EMBASE and the Cochrane Library from January 1980 to December 2013 to identify relevant studies reporting risk factors for NODM after liver transplantation. Two authors independently assessed the trials for inclusion and extracted the data. Discrepancies were resolved in consultation with a third reviewer. All statistical analyses were performed with the RevMan5.0 software (The Cochrane Collaboration, Oxford, United Kingdom). Pooled odds ratios (OR) or weighted mean differences (WMD) with 95% confidence intervals (CIs) were calculated using either a fixed effects or a random effects model, based on the presence (I (2) < 50%) or absence (I (2) > 50%) of significant heterogeneity. RESULTS: Twenty studies with 4580 patients were included in the meta-analysis, all of which were retrospective. The meta-analysis identified the following significant risk factors: hepatitis C virus (HCV) infection (OR = 2.68; 95%CI: 1.92-3.72); a family history of diabetes (OR = 1.69, 95%CI: 1.09-2.63, P < 0.00001); male gender (OR = 1.53; 95%CI: 1.24-1.90; P < 0.0001); impaired fasting glucose (IFG; OR = 3.27; 95%CI: 1.84-5.81; P < 0.0001); a family history of diabetes (OR = 1.69; 95%CI: 1.09-2.63; P = 0.02); use of tacrolimus (OR = 1.34; 95%CI: 1.03-1.76; P = 0.03) and body mass index (BMI)(WMD = 1.19, 95%CI: 0.69-1.68, P < 0.00001). Other factors, such as hepatitis B virus infection and alcoholism, were not found to be associated with the incidence of NODM. CONCLUSION: The study showed that HCV infection, IFG, a family history of diabetes, male gender, tacrolimus and BMI are risk factors for NODM after liver transplantation.","corpus_id":-1,"score":0},{"doc_id":"26111459","title":"Associations of coeliac disease with coronary heart disease and cerebrovascular disease: A systematic review and meta-analysis.","abstract":"AIMS: Clinical experience suggests that atherosclerotic disease is common in individuals with coeliac disease, but epidemiological studies have had contradicting findings. To summarise the currently available evidence, we systematically reviewed and analysed observational studies of the association of coeliac disease or dermatitis herpetiformis with coronary heart disease (CHD) or stroke. DATA SYNTHESIS: We searched for studies comparing CHD or stroke outcomes with individuals with and without coeliac disease or dermatitis herpetiformis. Three investigators independently searched electronic databases, identified relevant studies and extracted data. Study-specific results were combined in random-effects meta-analyses, and heterogeneity was quantified using the I(2) statistic and meta-regression. Twenty-one studies were included in our systematic review and 18 in the meta-analyses. For CHD, the pooled hazard ratio for incident disease was 1.05 (95% confidence interval (CI): 0.93, 1.19) and the overall standardised mortality ratio was 1.21 (0.99, 1.49). For stroke and brain haemorrhage, the corresponding estimates were 1.10 (95% CI: 1.00, 1.21) and 1.43 (0.97, 2.10), respectively. There was moderate to considerable heterogeneity among the study-specific estimates. In addition, many estimates were based on small numbers of outcomes and they had limitations in terms of adjustment for potential confounders. CONCLUSION: Our meta-analyses lend some support to an association between coeliac disease and CHD or cerebrovascular disease, but the evidence base was heterogeneous and had limitations. Our systematic review highlighted a need in this area for adequately powered prospective studies with appropriate adjustment for potentially confounding factors.","corpus_id":24423111,"score":0},{"doc_id":"26334246","title":"Association Between Periodontitis and Gestational Diabetes Mellitus: Systematic Review and Meta-Analysis.","abstract":"BACKGROUND: To the best of the authors' knowledge, there is no systematic review of the potential association between periodontitis and gestational diabetes mellitus (GDM) in the current literature. The aim of the present systematic review and meta-analysis is to search for scientific evidence regarding the association between periodontitis and GDM. METHODS: The present study was conducted in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and registered (CRD2014010728) with PROSPERO (International prospective register for systematic reviews, University of York, York, UK). A search was conducted in three electronic databases without restrictions regarding language or date of publication. From 190 studies selected, 15 underwent full-text analysis. Eight studies were eligible (five cross-sectional and three case-control studies), and seven were entered in the meta-analysis. Meta-analysis was performed with tests for sensitivity and statistical heterogeneity. Summary effect measures were calculated by odds ratio (OR) and 95% confidence interval (CI). RESULTS: There was a significant association between periodontitis and GDM in the meta-analyses of four cross-sectional studies (OR 1.67, 95% CI 1.20 to 2.32) and two case-control studies (OR 2.66, 95% CI 1.52 to 4.65). However, sensitivity tests for case-control studies showed a lack of consistency in data; when including one case-control study, the significance was null (meta-analysis of three case-control studies: OR 1.69, 95% CI 0.68 to 4.21). CONCLUSIONS: There was substantial clinical, methodologic, and statistical heterogeneity among the studies. The scientific evidence cannot affirm a positive association between periodontitis and GDM. Future studies with different designs in distinct populations should be conducted to investigate this association.","corpus_id":-1,"score":0},{"doc_id":"26959738","title":"Cholesterol consumption and risk of endometrial cancer: a systematic review and dose-response meta-analysis of observational studies.","abstract":"In vivo and in vitro studies have indicated the link of cholesterol consumption and endometrial cancer risk, however, previous observational studies have yielded inconsistent results. Additionally, a previous meta-analysis published in 2007 found limited evidence of aforementioned association. Therefore, we performed the dose-response meta-analysis to address this concern. Studies were identified using the PubMed, EMBASE and Web of Science databases from the database inception to the end of June 2015 as well as by examining the references of retrieved articles. Two authors independently performed the eligibility evaluation and data extraction. The summary risk estimates and 95% confidence intervals (CIs) were summarized by the random-effects models. One cohort and nine case-control studies were included in the dose-response analyses. Risk of endometrial cancer increased by 6% for 100 mg/day increment in the dietary consumption of cholesterol (Odds ratio (OR) = 1.06; 95% CI = 1.00-1.12), with significant heterogeneity (I2 = 64.2, P = 0.003). When stratified by study design, the result was significant in case-control studies (OR = 1.07; 95% CI = 1.01-1.13). Additionally, although the direction of the associations were consistent in the subgroup analyses stratified by study characteristics and adjustment for potential confounders, not all of them showed statistical significance. In summary, findings of the present dose-response meta-analysis partly support the positive association between dietary cholesterol consumption and risk of endometrial cancer. Since only one cohort study was included, more prospective studies and pooled analysis of observational studies are warranted to confirm our findings in the future.","corpus_id":-1,"score":0},{"doc_id":"27058589","title":"Transcription Factor 7-Like 2 (TCF7L2) rs7903146 Polymorphism as a Risk Factor for Gestational Diabetes Mellitus: A Meta-Analysis.","abstract":"BACKGROUND: There are racial and ethnic differences in the prevalence of gestational diabetes mellitus (GDM). Prior meta-analyses included small samples and very limited non-Caucasian populations. Studies to determine the relationship between transcription factor 7 like-2 (TCF7L2) rs7903146 polymorphism and risk of GDM in Hispanics/Latinos are recently available. The present meta-analysis was to estimate the impact of allele variants of TCF7L2 rs7903146 polymorphism on GDM susceptibility in overall population and racial/ethnic subgroups. METHODS: Literature was searched in multiple databases including PubMed, Web of Science, EMBASE (Ovid SP), Airiti Library, Medline Complete, and ProQuest up to July 2015. Allelic frequency for TCF7L2 rs7903146 polymorphism in GDM and control subjects was extracted and statistical analysis was performed using Comprehensive Meta-Analysis (CMA) 2.0 statistical software. The association between TCF7L2 rs7903146 polymorphism and GDM risk was assessed by pooled odd ratios (ORs) using five gene models (dominant, recessive, homozygote, heterozygote, and allele). Stratified analysis based on race/ethnicity was also conducted. The between-study heterogeneity and contribution of each single study to the final result was tested by Cochran Q test and sensitivity analyses, respectively. Publication bias was evaluated using Egger's linear regression test. RESULTS: A total of 16 studies involving 4,853 cases and 10,631 controls were included in this meta-analysis. Significant association between the T-allele of rs7903146 and GDM risk was observed under all genetic models, dominant model (OR = 1.44, 95% CI = 1.19-1.74), recessive model (OR = 1.35, 95% CI = 1.08-1.70), heterozygous model (OR = 1.31, 95% CI = 1.12-1.53), homozygous model (OR = 1.67, 95% CI = 1.31-2.12), and allele model (OR = 1.31, 95% CI = 1.12-1.53). Stratified analysis by race/ethnicity showed a statistically significant association between rs7903146 polymorphism and susceptibility to GDM under homozygous genetic model (TT versus CC) among whites, Hispanics/Latinos and Asians. Sensitivity analysis showed that the overall findings were robust to potentially influential decisions of the 16 studies included. No significant evidence for publication bias was observed in this meta-analysis for overall studies and subgroup studies. CONCLUSIONS: This meta-analysis showed that the T allele of TCF7L2 rs7903146 polymorphism was associated with susceptibility of GDM in overall population in white, Hispanic/Latino and Asian sub-groups. Asians with homozygous TT allele of rs7903146 polymorphism have highest risk of GDM (OR = 2.08) followed by Hispanics/Latinos (OR = 1.80) and whites (OR = 1.51). The highest and lowest frequency of T allele of rs7903146 was found in Malaysia and South Korea, respectively. Future studies are needed to profile genetic risk for GDM among high risk Asian and Pacific Islander subgroups.","corpus_id":-1,"score":0},{"doc_id":"27355649","title":"Is Butter Back? A Systematic Review and Meta-Analysis of Butter Consumption and Risk of Cardiovascular Disease, Diabetes, and Total Mortality.","abstract":"BACKGROUND: Dietary guidelines recommend avoiding foods high in saturated fat. Yet, emerging evidence suggests cardiometabolic benefits of dairy products and dairy fat. Evidence on the role of butter, with high saturated dairy fat content, for total mortality, cardiovascular disease, and type 2 diabetes remains unclear. We aimed to systematically review and meta-analyze the association of butter consumption with all-cause mortality, cardiovascular disease, and diabetes in general populations. METHODS AND FINDINGS: We searched 9 databases from inception to May 2015 without restriction on setting, or language, using keywords related to butter consumption and cardiometabolic outcomes. Prospective cohorts or randomized clinical trials providing estimates of effects of butter intake on mortality, cardiovascular disease including coronary heart disease and stroke, or diabetes in adult populations were included. One investigator screened titles and abstracts; and two reviewed full-text articles independently in duplicate, and extracted study and participant characteristics, exposure and outcome definitions and assessment methods, analysis methods, and adjusted effects and associated uncertainty, all independently in duplicate. Study quality was evaluated by a modified Newcastle-Ottawa score. Random and fixed effects meta-analysis pooled findings, with heterogeneity assessed using the I2 statistic and publication bias by Egger's test and visual inspection of funnel plots. We identified 9 publications including 15 country-specific cohorts, together reporting on 636,151 unique participants with 6.5 million person-years of follow-up and including 28,271 total deaths, 9,783 cases of incident cardiovascular disease, and 23,954 cases of incident diabetes. No RCTs were identified. Butter consumption was weakly associated with all-cause mortality (N = 9 country-specific cohorts; per 14g(1 tablespoon)/day: RR = 1.01, 95%CI = 1.00, 1.03, P = 0.045); was not significantly associated with any cardiovascular disease (N = 4; RR = 1.00, 95%CI = 0.98, 1.02; P = 0.704), coronary heart disease (N = 3; RR = 0.99, 95%CI = 0.96, 1.03; P = 0.537), or stroke (N = 3; RR = 1.01, 95%CI = 0.98, 1.03; P = 0.737), and was inversely associated with incidence of diabetes (N = 11; RR = 0.96, 95%CI = 0.93, 0.99; P = 0.021). We did not identify evidence for heterogeneity nor publication bias. CONCLUSIONS: This systematic review and meta-analysis suggests relatively small or neutral overall associations of butter with mortality, CVD, and diabetes. These findings do not support a need for major emphasis in dietary guidelines on either increasing or decreasing butter consumption, in comparison to other better established dietary priorities; while also highlighting the need for additional investigation of health and metabolic effects of butter and dairy fat.","corpus_id":-1,"score":0},{"doc_id":"27749986","title":"Insulin secretagogues for prevention or delay of type 2 diabetes mellitus and its associated complications in persons at increased risk for the development of type 2 diabetes mellitus.","abstract":"BACKGROUND: The projected rise in the incidence of type 2 diabetes mellitus (T2DM) could develop into a substantial health problem worldwide. Whether insulin secretagogues (sulphonylureas and meglitinide analogues) are able to prevent or delay T2DM and its associated complications in people at risk for the development of T2DM is unknown. OBJECTIVES: To assess the effects of insulin secretagogues on the prevention or delay of T2DM and its associated complications in people with impaired glucose tolerance, impaired fasting blood glucose, moderately elevated glycosylated haemoglobin A1c (HbA1c) or any combination of these. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials, MEDLINE, PubMed, Embase, ClinicalTrials.gov, the World Health Organization International Clinical Trials Registry Platform, and the reference lists of systematic reviews, articles and health technology assessment reports. We asked investigators of the included trials for information about additional trials. The date of the last search of all databases was April 2016. SELECTION CRITERIA: We included randomised controlled trials (RCTs) with a duration of 12 weeks or more comparing insulin secretagogues with any pharmacological glucose-lowering intervention, behaviour-changing intervention, placebo or no intervention in people with impaired fasting glucose, impaired glucose tolerance, moderately elevated HbA1c or combinations of these. DATA COLLECTION AND ANALYSIS: Two review authors read all abstracts and full-text articles/records, assessed quality and extracted outcome data independently. One review author extracted data which were checked by a second review author. We resolved discrepancies by consensus or the involvement of a third review author. For meta-analyses we used a random-effects model with investigation of risk ratios (RRs) for dichotomous outcomes and mean differences (MDs) for continuous outcomes, using 95% confidence intervals (CIs) for effect estimates. We carried out trial sequential analyses (TSAs) for all outcomes that could be meta-analysed. We assessed the overall quality of the evidence by using the GRADE instrument. MAIN RESULTS: We included six RCTs with 10,018 participants; 4791 participants with data on allocation to intervention groups were randomised to a second- or third-generation sulphonylurea or a meglitinide analogue as monotherapy and 29 participants were randomised to a second-generation sulphonylurea plus metformin. Three trials investigated a second-generation sulphonylurea, two trials investigated a third-generation sulphonylurea and one trial a meglitinide analogue. A total of 4873 participants with data on allocation to control groups were randomised to a comparator group; 4820 participants were randomised to placebo, 23 to diet and exercise, and 30 participants to metformin monotherapy. One RCT of nateglinide contributed 95% of all participants. The duration of the intervention varied from six months to five years. We judged none of the included trials as at low risk of bias for all 'Risk of bias' domains. All-cause and cardiovascular mortality following sulphonylurea (glimepiride) treatment were rarely observed (very low-quality evidence). The RR for incidence of T2DM comparing glimepiride monotherapy with placebo was 0.75; 95% CI 0.54 to 1.04; P = 0.08; 2 trials; 307 participants; very low-quality evidence. One of the trials reporting on the incidence of T2DM did not define the diagnostic criteria used. The other trial diagnosed T2DM as two consecutive fasting blood glucose values ≥ 6.1 mmol/L. TSA showed that only 4.5% of the diversity-adjusted required information size was accrued so far. No trial reported data on serious adverse events, non-fatal myocardial infarction (MI), non-fatal stroke, congestive heart failure (HF), health-related quality of life or socioeconomic effects. One trial with a follow-up of five years compared a meglitinide analogue (nateglinide) with placebo. A total of 310/4645 (6.7%) participants allocated to nateglinide died compared with 312/4661 (6.7%) participants allocated to placebo (hazard ratio (HR) 1.00; 95% CI 0.85 to 1.17; P = 0.98; moderate-quality evidence). The two main criteria for diagnosing T2DM were a fasting plasma glucose level ≥ 7.0 mmol/L or a 2-hour post challenge glucose ≥ 11.1 mmol/L. T2DM developed in 1674/4645 (36.0%) participants in the nateglinide group and in 1580/4661 (33.9%) in the placebo group (HR 1.07; 95% CI 1.00 to 1.15; P = 0.05; moderate-quality evidence). One or more serious adverse event was reported in 2066/4602 (44.9%) participants allocated to nateglinide compared with 2089/4599 (45.6%) participants allocated to placebo. A total of 126/4645 (2.7%) participants allocated to nateglinide died because of cardiovascular disease compared with 118/4661 (2.5%) participants allocated to placebo (HR 1.07; 95% CI 0.83 to 1.38; P = 0.60; moderate-quality evidence). Comparing participants receiving nateglinide with those receiving placebo for the outcomes MI, non-fatal stroke and HF gave the following event rates: MI 116/4645 (2.5%) versus 122/4661 (2.6%), stroke 100/4645 (2.2%) versus 110/4661 (2.4%) and numbers hospitalised for HF 85/4645 (1.8%) versus 100/4661 (2.1%) - (HR 0.85; 95% CI 0.64 to 1.14; P = 0.27). The quality of the evidence was moderate for all these outcomes. Health-related quality of life or socioeconomic effects were not reported. AUTHORS' CONCLUSIONS: There is insufficient evidence to demonstrate whether insulin secretagogues compared mainly with placebo reduce the risk of developing T2DM and its associated complications in people at increased risk for the development of T2DM. Most trials did not investigate patient-important outcomes.","corpus_id":29269326,"score":0},{"doc_id":"27825315","title":"Periodontitis and gestational diabetes mellitus: a systematic review and meta-analysis of observational studies.","abstract":"BACKGROUND: Gestational diabetes mellitus (GDM) is glucose intolerance with first onset during pregnancy and is associated with serious maternal and fetal complications. The etiology of GDM is not well understood, but systemic inflammation effects on insulin signaling and glucose metabolism is suspected. Periodontal disease is a chronic inflammatory condition that induces local and host immune responses and has been evaluated for a potential role in development of GDM. Results from studies evaluating the association between periodontitis and GDM are mixed. We performed a systematic review and meta-analysis to summarize available data regarding the association between periodontitis and GDM. METHODS: Twelve electronic databases were searched for observational studies of the association between periodontitis and GDM through March 2016. Eligible studies were assessed for quality and heterogeneity. Random effects models were used to estimate summary measures of association. RESULTS: We identified 44 articles from 115 potentially relevant reports of which 10 studies met our eligibility criteria. Clinical diagnostic criteria for periodontitis and GDM varied widely among studies, and moderate heterogeneity was observed. Random effects meta-analysis of all included studies with a total of 5724 participants including 624 cases, showed that periodontitis is associated with an increased risk of GDM by 66 %, (OR = 1.66, 95 % CI: 1.17 to 2.36; p < 0.05), I(2) = 50.5 %. Similar results were seen in sub-analysis restricted to data from methodologically high quality case-control studies including 1176 participants including 380 cases, (OR = 1.85, 95 % CI: 1.03 to 3.32); p < 0.05), I(2) = 68.4 %. Meta-analysis of studies that adjusted for potential confounders estimated more than 2-fold increased odds of GDM among women with periodontitis (aOR = 2.08, 95 % CI: 1.21 to 3.58, p = 0.009, I(2) = 36.9 %). CONCLUSION: Meta-analysis suggests that periodontitis is associated with a statistically significant increased risk for GDM compared to women without periodontitis. Robust prospective study designs and uniform definition for periodontitis and GDM definitions are urgently needed to substantiate these findings.","corpus_id":-1,"score":0},{"doc_id":"29210061","title":"The association with cardiovascular disease and type 2 diabetes in adults with atopic dermatitis: a systematic review and meta-analysis.","abstract":"BACKGROUND: Recent studies examining the association between atopic dermatitis (AD) and cardiovascular disease (CVD) and type 2 diabetes have shown inconsistent results. OBJECTIVES: To carry out a systematic review and meta-analysis that examines the association with cardiovascular disease and type 2 diabetes in adults with AD. METHODS: We compared the risk of CVD and diabetes for adult patients with and without AD by searching the PubMed, Embase and Web of Science databases. Data extraction was carried out by two independent reviewers. We found a total of 2855 citations, of which 53 were considered relevant based on title and abstract. Overall, 16 publications were included in the qualitative analysis, of which 13 were also included in a quantitative meta-analysis of crude data. RESULTS: No association was observed between AD and unspecified but suspected type 2 diabetes [pooled odds ratio (OR) 1·11; 95% confidence interval (CI) 0·87-1·42], hypertension (pooled OR 1·16; 95% CI 0·98-1·37), stroke (pooled OR 1·15; 95% CI 0·95-1·39) or myocardial infarction (pooled OR 1·14; 95% CI 0·83-1·56), but a positive association was observed with angina pectoris (OR 1·73; 95% CI 1·27-2·37). Meta-analysis of adjusted data gave similar results. CONCLUSIONS: While adults with AD in some populations have an increased prevalence of cardiovascular risk factors, such as obesity and smoking, it is unlikely that AD represents an independent and clinically relevant risk factor for cardiometabolic disease.","corpus_id":-1,"score":0},{"doc_id":"29415723","title":"Characterizing undiagnosed chronic obstructive pulmonary disease: a systematic review and meta-analysis.","abstract":"BACKGROUND: A significant proportion of patients with chronic obstructive pulmonary disease (COPD) remain undiagnosed. Characterizing these patients can increase our understanding of the 'hidden' burden of COPD and the effectiveness of case detection interventions. METHODS: We conducted a systematic review and meta-analysis to compare patient and disease factors between patients with undiagnosed persistent airflow limitation and those with diagnosed COPD. We searched MEDLINE and EMBASE for observational studies of adult patients meeting accepted spirometric definitions of COPD. We extracted and pooled summary data on the proportion or mean of each risk factor among diagnosed and undiagnosed patients (unadjusted analysis), and coefficients for the adjusted association between risk factors and diagnosis status (adjusted analysis). RESULTS: Two thousand eighty-three records were identified through database searching and 16 articles were used in the meta-analyses. Diagnosed patients were less likely to have mild (v. moderate to very severe) COPD (odds ratio [OR] 0.30, 95%CI 0.24-0.37, 6 studies) in unadjusted analysis. This association remained significant but its strength was attenuated in the adjusted analysis (OR 0.72, 95%CI 0.58-0.89, 2 studies). Diagnosed patients were more likely to report respiratory symptoms such as wheezing (OR 3.51, 95%CI 2.19-5.63, 3 studies) and phlegm (OR 2.16, 95% CI 1.38-3.38, 3 studies), had more severe dyspnea (mean difference in modified Medical Research Council scale 0.52, 95%CI 0.40-0.64, 3 studies), and slightly greater smoking history than undiagnosed patients. Patient age, sex, current smoking status, and the presence of coughing were not associated with a previous diagnosis. CONCLUSIONS: Undiagnosed patients had less severe airflow obstruction and fewer respiratory symptoms than diagnosed patients. The lower disease burden in undiagnosed patients may significantly delay the diagnosis of COPD.","corpus_id":-1,"score":0},{"doc_id":"29802639","title":"Associations of health literacy with diabetic foot outcomes: a systematic review and meta-analysis.","abstract":"BACKGROUND: People with diabetes have low health literacy, but the role of the latter in diabetic foot disease is unclear. AIM: To determine, through a systematic review and meta-analysis, if health literacy is associated with diabetic foot disease, its risk factors, or foot care. METHODS: We searched PubMed, EMBASE, CINAHL, Web of Science, Scopus and Science Direct. All studies were screened and data extracted by two independent reviewers. Studies in English with valid and reliable measures of health literacy and published tests of association were included. Data were extracted on the associations between the outcomes and health literacy. Meta-analyses were performed using random effects models. RESULTS: Sixteen articles were included in the systematic review, with 11 in the meta-analysis. In people with inadequate health literacy, the odds of having diabetic foot disease were twice those in people with adequate health literacy, but this was not statistically significant [odds ratio 1.99 (95% CI 0.83, 4.78); two studies in 1278 participants]. There was no statistically significant difference in health literacy levels between people with and without peripheral neuropathy [standardized mean difference -0.14 (95% CI -0.47, 0.18); two studies in 399 participants]. There was no association between health literacy and foot care [correlation coefficient 0.01 (95% CI -0.07, 0.10); seven studies in 1033 participants]. CONCLUSIONS: There were insufficient data to exclude associations between health literacy and diabetic foot disease and its risk factors, but health literacy appears unlikely to have a role in foot care. The contribution of low health literacy to diabetic foot disease requires definitive assessment through robust longitudinal studies.","corpus_id":-1,"score":0}],"string":"[\n {\n \"doc_id\": \"19109117\",\n \"title\": \"Birth weight and risk of type 2 diabetes: a systematic review.\",\n \"abstract\": \"CONTEXT: Low birth weight is implicated as a risk factor for type 2 diabetes. However, the strength, consistency, independence, and shape of the association have not been systematically examined. OBJECTIVE: To conduct a quantitative systematic review examining published evidence on the association of birth weight and type 2 diabetes in adults. DATA SOURCES AND STUDY SELECTION: Relevant studies published by June 2008 were identified through literature searches using EMBASE (from 1980), MEDLINE (from 1950), and Web of Science (from 1980), with a combination of text words and Medical Subject Headings. Studies with either quantitative or qualitative estimates of the association between birth weight and type 2 diabetes were included. DATA EXTRACTION: Estimates of association (odds ratio [OR] per kilogram of increase in birth weight) were obtained from authors or from published reports in models that allowed the effects of adjustment (for body mass index and socioeconomic status) and the effects of exclusion (for macrosomia and maternal diabetes) to be examined. Estimates were pooled using random-effects models, allowing for the possibility that true associations differed between populations. DATA SYNTHESIS: Of 327 reports identified, 31 were found to be relevant. Data were obtained from 30 of these reports (31 populations; 6090 diabetes cases; 152 084 individuals). Inverse birth weight-type 2 diabetes associations were observed in 23 populations (9 of which were statistically significant) and positive associations were found in 8 (2 of which were statistically significant). Appreciable heterogeneity between populations (I(2) = 66%; 95% confidence interval [CI], 51%-77%) was largely explained by positive associations in 2 native North American populations with high prevalences of maternal diabetes and in 1 other population of young adults. In the remaining 28 populations, the pooled OR of type 2 diabetes, adjusted for age and sex, was 0.75 (95% CI, 0.70-0.81) per kilogram. The shape of the birth weight-type 2 diabetes association was strongly graded, particularly at birth weights of 3 kg or less. Adjustment for current body mass index slightly strengthened the association (OR, 0.76 [95% CI, 0.70-0.82] before adjustment and 0.70 [95% CI, 0.65-0.76] after adjustment). Adjustment for socioeconomic status did not materially affect the association (OR, 0.77 [95% CI, 0.70-0.84] before adjustment and 0.78 [95% CI, 0.72-0.84] after adjustment). There was no strong evidence of publication or small study bias. CONCLUSION: In most populations studied, birth weight was inversely related to type 2 diabetes risk.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"19465232\",\n \"title\": \"Type 2 diabetes mellitus after gestational diabetes: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: Women with gestational diabetes are at increased risk of developing type 2 diabetes, but the risk and time of onset have not been fully quantified. We therefore did a comprehensive systematic review and meta-analysis to assess the strength of association between these conditions and the effect of factors that might modify the risk. METHODS: We identified cohort studies in which women who had developed type 2 diabetes after gestational diabetes were followed up between Jan 1, 1960, and Jan 31, 2009, from Embase and Medline. 205 relevant reports were hand searched. We selected 20 studies that included 675 455 women and 10 859 type 2 diabetic events. We calculated and pooled unadjusted relative risks (RRs) with 95% CIs for each study using a random-effects model. Subgroups analysed were the number of cases of type 2 diabetes, ethnic origin, duration of follow-up, maternal age, body-mass index, and diagnostic criteria. FINDINGS: Women with gestational diabetes had an increased risk of developing type 2 diabetes compared with those who had a normoglycaemic pregnancy (RR 7.43, 95% CI 4.79-11.51). Although the largest study (659 164 women; 9502 cases of type 2 diabetes) had the largest RR (12.6, 95% CI 12.15-13.19), RRs were generally consistent among the subgroups assessed. INTERPRETATION: Increased awareness of the magnitude and timing of the risk of type 2 diabetes after gestational diabetes among patients and clinicians could provide an opportunity to test and use dietary, lifestyle, and pharmacological interventions that might prevent or delay the onset of type 2 diabetes in affected women. FUNDING: None.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"21711420\",\n \"title\": \"Systematic review with meta-analyses of studies on the association between cirrhosis and liver metastases.\",\n \"abstract\": \"The hemodynamic, cellular and metabolic changes seen in patients with cirrhosis may reduce the risk of liver metastases. The aim of this case-control is to compare the risk of liver metastases from extrahepatic malignant diseases among patients with or without cirrhosis. Electronic searches (Medline, Embase, and Web of Science) and manual searches were combined (October 2010) to identify observational studies on patients with malignant disease reporting the risk of liver metastases among cases (with cirrhosis) and controls (without liver disease). Meta-analysis was performed using random effects models due to an expected clinical heterogeneity. Sixteen studies were included. Evidence of liver metastases was diagnosed in 22% of cases and 38% of controls based on autopsies (n = 14 studies) or laparoscopy (n = 2 studies). Random effects meta-analysis suggested that patients with cirrhosis had a lower risk of liver metastases (relative risk = 0.53; 95% confidence interval = 0.42-0.66). The conclusions were confirmed in sensitivity and subgroup analyses accounting for the year of publication, matching for age, sex and location of tumors (within the portal vein). No statistical evidence of bias was identified and the analyses were confirmed when adjusting for multiple testing. The present review suggests that cirrhosis reduces the risk of liver metastases. However, additional evidence from prospective studies adjusting for confounding factors is still needed.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"21889332\",\n \"title\": \"Type 2 diabetes mellitus and colorectal cancer: meta-analysis on sex-specific differences.\",\n \"abstract\": \"Although there is consent concerning a higher risk for colorectal cancer (CRC) amongst patients with type 2 diabetes mellitus (T2DM), there remains uncertainty regarding potential sex differences in the strength of this association. We reviewed and summarised epidemiological studies assessing the sex-specific association of T2DM with the risk for CRC. All relevant studies published until 14th February 2011 were identified by a systematic search of MEDLINE, EMBASE, BIOSIS Previews and ISI Web of Knowledge databases and cross-referencing. We included observational studies that reported relative risk (RR) or odds ratio (OR) estimates with 95% confidence intervals (CIs) for the association between T2DM and CRC. Two authors independently extracted data and assessed study quality of each study in a standardised manner. Study-specific estimates were pooled for both sexes separately using random-effects models. A total of 29 eligible studies were used for meta-analysis. Overall estimates of relative risk (RR) were very similar amongst men (RR=1.29; 95%-confidence interval (CI): 1.19-1.140) and women (RR=1.34; 95%-CI: 1.22-1.47). In both men and women, risk estimates from case-control studies were slightly higher than those from cohort studies. Overall, T2DM is associated with a moderate increase in CRC risk in both men and women.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"21898753\",\n \"title\": \"Diabetes mellitus and risk of hepatocellular carcinoma: a systematic review and meta-analysis.\",\n \"abstract\": \"Studies of diabetes and hepatocellular carcinoma (HCC) yielded inconsistent findings. This meta-analysis was conducted to examine the association between diabetes and risk of HCC. Studies were identified by searching PUBMED and MEDLINE database up to February 2011. Pooled risk estimates were calculated using the random-effects model. Potential sources of heterogeneity were explored by subgroup analyses. A total of 17 case-control studies and 32 cohort studies were included in the meta-analysis. The combined risk estimate of all studies showed a statistically significant increased risk of HCC prevalence among diabetic individuals (RR = 2.31, 95% CI: 1.87-2.84). The pooled risk estimate of 17 case-control studies (OR = 2.40, 95% CI: 1.85-3.11) was slightly higher than that from 25 cohort studies (RR = 2.23, 95% CI: 1.68-2.96). Metformin treatment was potentially protective. On the contrary, long duration of diabetes and sulfonylureas or insulin treatment possibly increase HCC risk. Also meta-analysis of 7 cohort studies found a statistically significant increased risk of HCC mortality (RR = 2.43, 95% CI: 1.66-3.55) for individuals with (versus without) diabetes. This meta-analysis shows that diabetes is associated with moderately increased risk of HCC prevalence, as well as HCC mortality. Considering the rapidly increasing prevalence of diabetes mellitus, the study underlines the need for cancer prevention in diabetic individuals. Further investigation is needed to focus on the potential mechanism for the pathogenesis of HCC and the link between HCC and different types, severity, treatment and duration of diabetes.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23074528\",\n \"title\": \"Community-based care for the management of type 2 diabetes: an evidence-based analysis.\",\n \"abstract\": \"UNLABELLED: In June 2008, the Medical Advisory Secretariat began work on the Diabetes Strategy Evidence Project, an evidence-based review of the literature surrounding strategies for successful management and treatment of diabetes. This project came about when the Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the Ministry's newly released Diabetes Strategy. After an initial review of the strategy and consultation with experts, the secretariat identified five key areas in which evidence was needed. Evidence-based analyses have been prepared for each of these five areas: insulin pumps, behavioural interventions, bariatric surgery, home telemonitoring, and community based care. For each area, an economic analysis was completed where appropriate and is described in a separate report. To review these titles within the Diabetes Strategy Evidence series, please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/mas_about.html,DIABETES STRATEGY EVIDENCE PLATFORM: Summary of Evidence-Based AnalysesContinuous Subcutaneous Insulin Infusion Pumps for Type 1 and Type 2 Adult Diabetics: An Evidence-Based AnalysisBehavioural Interventions for Type 2 Diabetes: An Evidence-Based AnalysisBARIATRIC SURGERY FOR PEOPLE WITH DIABETES AND MORBID OBESITY: An Evidence-Based SummaryCommunity-Based Care for the Management of Type 2 Diabetes: An Evidence-Based AnalysisHome Telemonitoring for Type 2 Diabetes: An Evidence-Based AnalysisApplication of the Ontario Diabetes Economic Model (ODEM) to Determine the Cost-effectiveness and Budget Impact of Selected Type 2 Diabetes Interventions in Ontario OBJECTIVE: The objective of this report is to determine the efficacy of specialized multidisciplinary community care for the management of type 2 diabetes compared to usual care. CLINICAL NEED: TARGET POPULATION AND CONDITION Diabetes (i.e. diabetes mellitus) is a highly prevalent chronic metabolic disorder that interferes with the body's ability to produce or effectively use insulin. The majority (90%) of diabetes patients have type 2 diabetes. ( 1) Based on the United Kingdom Prospective Diabetes Study (UKPDS), intensive blood glucose and blood pressure control significantly reduce the risk of microvascular and macrovascular complications in type 2 diabetics. While many studies have documented that patients often do not meet the glycemic control targets specified by national and international guidelines, factors associated with glycemic control are less well studied, one of which is the provider(s) of care. Multidisciplinary approaches to care may be particularly important for diabetes management. According guidelines from the Canadian Diabetes Association (CDA), the diabetes health care team should be multi-and interdisciplinary. Presently in Ontario, the core diabetes health care team consists of at least a family physician and/or diabetes specialist, and diabetes educators (registered nurse and registered dietician). Increasing the role played by allied health care professionals in diabetes care and their collaboration with physicians may represent a more cost-effective option for diabetes management. Several systematic reviews and meta-analyses have examined multidisciplinary care programs, but these have either been limited to a specific component of multidisciplinary care (e.g. intensified education programs), or were conducted as part of a broader disease management program, of which not all were multidisciplinary in nature. Most reviews also do not clearly define the intervention(s) of interest, making the evaluation of such multidisciplinary community programs challenging. EVIDENCE-BASED ANALYSIS METHODS: RESEARCH QUESTIONS: What is the evidence of efficacy of specialized multidisciplinary community care provided by at least a registered nurse, registered dietician and physician (primary care and/or specialist) for the management of type 2 diabetes compared to usual care? [ Henceforth referred to as Model 1]What is the evidence of efficacy of specialized multidisciplinary community care provided by at least a pharmacist and a primary care physician for the management of type 2 diabetes compared to usual care? [ Henceforth referred to as Model 2] INCLUSION CRITERIA: English language full-reportsPublished between January 1, 2000 and September 28, 2008Randomized controlled trials (RCTs), systematic reviews and meta-analysesType 2 diabetic adult population (≥18 years of age)Total sample size ≥30Describe specialized multidisciplinary community care defined as ambulatory-based care provided by at least two health care disciplines (of which at least one must be a specialist in diabetes) with integrated communication between the care providers. Compared to usual care (defined as health care provision by non-specialist(s) in diabetes, such as primary care providers; may include referral to other health care professionals/services as necessary)≥6 months follow-up EXCLUSION CRITERIA: Studies where discrete results on diabetes cannot be abstractedPredominantly home-based interventionsInpatient-based interventions OUTCOMES OF INTEREST: The primary outcomes for this review were glycosylated hemoglobin (rHbA1c) levels and systolic blood pressure (SBP). SEARCH STRATEGY: A literature search was performed on September 28, 2008 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published between January 1, 2000 and September 28, 2008. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any additional relevant studies not identified through the search. Articles with unknown eligibility were reviewed with a second clinical epidemiologist, then a group of epidemiologists until consensus was established. The quality of evidence was assessed as high, moderate, low or very low according to GRADE methodology. Given the high clinical heterogeneity of the articles that met the inclusion criteria, specific models of specialized multidisciplinary community care were examined based on models of care that are currently being supported in Ontario, models of care that were commonly reported in the literature, as well as suggestions from an Expert Advisory Panel Meeting held on January 21, 2009. SUMMARY OF FINDINGS: The initial search yielded 2,116 unique citations, from which 22 RCTs trials and nine systematic reviews published were identified as meeting the eligibility criteria. Of these, five studies focused on care provided by at least a nurse, dietician, and physician (primary care and/or specialist) model of care (Model 1; see Table ES 1), while three studies focused on care provided by at least a pharmacist and primary care physician (Model 2; see Table ES 2). Based on moderate quality evidence, specialized multidisciplinary community care Model 2 has demonstrated a statistically and clinically significant reduction in HbA1c of 1.0% compared with usual care. The effects of this model on SBP, however, are uncertain compared with usual care, based on very-low quality evidence. Specialized multidisciplinary community care Model 2 has demonstrated a statistically and clinically significant reduction in both HbA1c of 1.05% (based on high quality evidence) and SBP of 7.13 mm Hg (based on moderate quality evidence) compared to usual care. For both models, the evidence does not suggest a preferred setting of care delivery (i.e., primary care vs. hospital outpatient clinic vs. community clinic). Table ES1:Summary of Results of Meta-Analyses of the Effects of Multidisciplinary Care Model 1OutcomeEstimate of effect(95% CI)Heterogeneity I(2)(p-value)GRADEGlycosylated Hemoglobin (HbA1c [%])-1.00 [-1.27, -0.73]4% (p=0.37)Moderate-quality Subgroup: Moderate-to-High Quality-0.91 [-1.19, -0.62]0% (p=0.74)Systolic Blood Pressure (mm Hg)-2.04 [-13.80, 9.72]89% (p=0.002)Very-low quality*Mean change from baseline to follow-up between intervention and control groupsTable ES2:Summary of Results of Meta-Analyses of the Effects of Multidisciplinary Care Model 2OutcomeEstimate of effect(95% CI)Heterogeneity I(2)(p-value)GRADEGlycosylated Hemoglobin (HbA1c [%])-1.05 [-1.57, -0.52]0% (p=0.75)High-qualitySystolic Blood Pressure (mm Hg)-7.13 [-11.78, -2.48]46% (p=0.17)Moderate quality*Mean change from baseline to follow-up between intervention and control groups.\",\n \"corpus_id\": 40547459,\n \"score\": 1\n },\n {\n \"doc_id\": \"23772556\",\n \"title\": \"Psoriasis, psoriatic arthritis and type 2 diabetes mellitus: a systematic review and meta-analysis.\",\n \"abstract\": \"Several observational studies have assessed the association between psoriasis, psoriatic arthritis (PsA) and type 2 diabetes mellitus, with inconclusive results. We set out to investigate the association between psoriasis, PsA and type 2 diabetes mellitus. Observational studies assessing the relationship between psoriasis or PsA and type 2 diabetes mellitus up to December 2012 were identified by electronic and hand searches in Medline, Embase, PubMed, the Cochrane Database of Systematic Reviews and Google Scholar. For each study we collected the first author's last name, publication year, country of origin, study design, characteristics of participants (sample size, age and sex), the variables incorporated into the multivariable analyses, and the odds ratios (ORs) of psoriasis associated with diabetes along with the corresponding 95% confidence intervals (CIs). From the data provided in each article, the crude OR was also calculated. Forty-four observational studies (in 37 articles) were identified for the final analysis. The pooled OR from random-effects analysis was determined to be 1·76 (95% CI 1·59-1·96). The highest risk was for patients suffering from PsA (OR 2·18, 95% CI 1·36-3·50). We also observed a dose effect in the risk of suffering from type 2 diabetes mellitus, as patients considered as having severe psoriasis had higher risk (OR 2·10, 95% CI 1·73-2·55) than the pooled OR. We perform meta-regression and sensitivity analyses to explore sources of heterogeneity among the studies and to determine how they would influence the estimates, and found no significant influence in the results of the meta-analyses. The findings support the association between psoriasis, PsA and type 2 diabetes mellitus. Some caution must be taken in the interpretation of these results because there may be heterogeneity between studies.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24098798\",\n \"title\": \"The association between diabetes mellitus and nonarteritic anterior ischemic optic neuropathy: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: The association of diabetes mellitus (DM) with nonarteritic anterior ischemic optic neuropathy (NAION) has been inconclusive. PURPOSE: To determine whether DM is associated with an increased risk of NAION. METHODS: A comprehensive literature search was performed for published studies reporting both DM and NAION based on PubMed and EMBASE. After reviewing characteristics of all the included studies systematically, meta-analytical method was employed to calculate the pooled odds ratio (OR) and associated 95% confidence interval (CI) from random-effects models. Heterogeneity was assessed by Q-statistic test. Funnel Plot, Begg's and Egger's linear regression test were applied to evaluate publication bias. A sensitivity analysis and meta-regression analysis were also performed to assess the robustness of results. RESULTS: 2,096 participants from 12 case-control studies were pooled for a meta-analysis. The result of meta-analysis of these studies indicated that DM is associated with increased risk of NAION (pooled OR = 1.64, 95% CI = 1.17-2.30; P = 0.004). Sensitivity analysis indicated our findings are robust, and meta-regression analysis revealed no significant effect in terms of geographical area, gender, age of patients with NAION, the year of the publication, source of the controls, and sample size (all p>0.05). Evidence of publication bias was not observed in our study. CONCLUSION: Meta-analysis suggests that DM might be associated with increased risk of NAION.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24263394\",\n \"title\": \"A systematic review and meta-analysis on the prevalence of Dupuytren disease in the general population of Western countries.\",\n \"abstract\": \"BACKGROUND: Dupuytren disease is a fibroproliferative disease of palmar fascia of the hand. Its prevalence has been the subject of several reviews; however, an accurate description of the prevalence range in the general population--and of the relation between age and disease--is lacking. METHODS: Embase and PubMed were searched using database-specific Medical Subject Headings; titles and abstracts were searched for the words \\\"Dupuytren,\\\" \\\"incidence,\\\" and \\\"prevalence.\\\" Two reviewers independently assessed the articles using inclusion and exclusion criteria, and rated the included studies with a quality assessment instrument. In a meta-analysis, the median prevalence, as a function of age by sex, was estimated, accompanied by 95 percent prediction intervals. The observed heterogeneity in prevalence was investigated with respect to study quality and geographic location. RESULTS: Twenty-three of 199 unique identified articles were included. The number of participants ranged from 37 to 97,537, and age ranged from 18 to 100 years. Prevalence varied from 0.6 to 31.6 percent. The quality of studies differed but could not explain the heterogeneity among studies. Mean prevalence was estimated as 12, 21, and 29 percent at ages 55, 65, and 75 years, respectively, based on the relation between age and prevalence determined from 10 studies. CONCLUSIONS: The authors describe a prevalence range of Dupuytren disease in the general population of Western countries. The relation between age and prevalence of Dupuytren disease is given according to sex, including 95 percent prediction intervals. It is possible to determine disease prevalence at a certain age for the total population, and for men and women separately.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24278229\",\n \"title\": \"Association between telomere length and type 2 diabetes mellitus: a meta-analysis.\",\n \"abstract\": \"BACKGROUND: Several epidemiological studies have examined the association between shortened telomere length and type 2 diabetes mellitus (T2DM), while the results remained conflicting. We conducted a meta-analysis to derive a more precise estimation of the relationship between them. METHODS: We systematically reviewed the databases of PubMed, EMBASE, and Web of Science for all studies on the association between telomere length and T2DM. We conducted this study assessed by STATA 11.0. Data were summarized using random-effects or fixed-effects meta-analysis. The heterogeneity and publication bias among studies were examined by using χ(2)-based Q statistic test and Egger's test, respectively. RESULTS: Nine cohorts consisting of 5759 cases and 6518 controls were selected into the meta-analysis. The results indicated that shortened telomere length was significantly associated with T2DM risk (OR: 1.291; 95% CI: 1.112, 1.498; P<0.001) with heterogeneity (I(2) = 71.6%). When three cohorts responsible for the heterogeneity were excluded, the pooled OR for the remaining cohorts indicated a significant association between shortened telomere length and T2DM (OR: 1.117; 95% CI: 1.002, 1.246; P = 0.045) without heterogeneity. CONCLUSION: We found a statistically significant association between shortened telomere length and T2DM.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24830459\",\n \"title\": \"Diabetes mellitus and poorer prognosis in hepatocellular carcinoma: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: Previous studies suggested that diabetes mellitus was associated with cancer risk and prognosis, but studies investigating the relationship between diabetes mellitus and survival in patients with hepatocellular carcinoma (HCC) reported inconsistent findings. To derive a more precise estimate of the prognostic role of diabetes mellitus in HCC, we systematically reviewed published studies and carried out a meta-analysis. METHODS: Eligible articles were identified in electronic databases from their inception through September 16, 2013. To evaluate the correlation between diabetes mellitus and prognosis in HCC, the pooled hazard ratios (HR) and their 95% confidence intervals (95% CI) for poorer overall and disease-free survivals were calculated by standard meta-analysis techniques with fixed-effects or random-effects models. RESULTS: 21 studies with a total of 9,767 HCC patients stratifying overall survival and/or disease-free survival in HCC patients by diabetes mellitus status were eligible for meta-analysis. 20 studies with a total of 9,727 HCC cases investigated the overall survival, and 10 studies with a total of 2,412 HCC patients investigated the disease-free survival. The pooled HRs for overall survival and disease-free survival were 1.46 (95% CI, 1.29 to 1.66; P<0.001) and 1.57 (95% CI, 1.21 to 2.05; P = 0.001), respectively. The adjusted HRs for overall survival and disease-free survival were 1.55 (95% CI, 1.27 to 1.91; P<0.001) and 2.15 (95% CI, 1.75 to 2.63; P<0.001), respectively. In addition, for patients receiving hepatic resection, diabetes mellitus was associated with both poorer overall survival and poorer disease-free survival, and for patients receiving non-surgical treatment or patients receiving radiofrequency ablation, diabetes mellitus was associated with poorer overall survival. There was no evidence for publication bias. CONCLUSION: Diabetes mellitus is independently associated with both poorer overall survival and poorer disease-free survival in HCC patients.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25228184\",\n \"title\": \"The association of gallstone disease and diabetes mellitus. A meta-analysis.\",\n \"abstract\": \"OBJECTIVES: To assess the association between diabetes mellitus and gallstone disease (GSD) by meta-analysis. METHODS: This study was carried out at Xiangya Hospital, Changsha, Hunan, China in September 2013. First, eligible studies were searched in PubMed and Cochrane Central databases from their inception to September 2013. Then, a random effect model was used to calculate the overall combined risk estimates. The meta-analysis included 403,001 cases and 411,877 controls from 6 case-control studies, 3 cohort studies, and 13 cross-sectional studies. Finally, statistical analyses were conducted according to the classification of study. RESULTS: Risk ratios for diabetes mellitus and GSD were 1.75 (95% confidence interval [CI]: 1.44-2.13, p<0.00001], 1.76 (95% CI: 1.24-2.5, p<0.00001), and 2.02 (95% CI: 1.59-2.58, p<0.00001). Sensitivity analysis based on the exclusion of any study did not change the heterogeneity I-square test, and risk ratios. Little evidence of publication bias was observed. CONCLUSION: This meta-analysis suggested that there was a very strong positive association between diabetes mellitus and risk of GSD in the patients.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25238063\",\n \"title\": \"Diabetes mellitus and risk of age-related macular degeneration: a systematic review and meta-analysis.\",\n \"abstract\": \"Age-related macular degeneration (AMD) is a major cause of severe vision loss in elderly people. Diabetes mellitus is a common endocrine disorder with serious consequences, and diabetic retinopathy (DR) is the main ophthalmic complication. DR and AMD are different diseases and we seek to explore the relationship between diabetes and AMD. MEDLINE, EMBASE, and the Cochrane Library were searched for potentially eligible studies. Studies based on longitudinal cohort, cross-sectional, and case-control associations, reporting evaluation data of diabetes as an independent factor for AMD were included. Reports of relative risks (RRs), hazard ratios (HRs), odds ratio (ORs), or evaluation data of diabetes as an independent factor for AMD were included. Review Manager and STATA were used for the meta-analysis. Twenty four articles involving 27 study populations were included for meta-analysis. In 7 cohort studies, diabetes was shown to be a risk factor for AMD (OR, 1.05; 95% CI, 1.00-1.14). Results of 9 cross-sectional studies revealed consistent association of diabetes with AMD (OR, 1.21; 95% CI, 1.00-1.45), especially for late AMD (OR, 1.48; 95% CI, 1.44-1.51). Similar association was also detected for AMD (OR, 1.29; 95% CI, 1.13-1.49) and late AMD (OR, 1.16; 95% CI, 1.11-1.21) in 11 case-control studies. The pooled ORs for risk of neovascular AMD (nAMD) were 1.10 (95% CI, 0.96-1.26), 1.48 (95% CI, 1.44-1.51), and 1.15 (95% CI, 1.11-1.21) from cohort, cross-sectional and case-control studies, respectively. No obvious divergence existed among different ethnic groups. Therefore, we find diabetes a risk factor for AMD, stronger for late AMD than earlier stages. However, most of the included studies only adjusted for age and sex; we thus cannot rule out confounding as a potential explanation for the association. More well-designed prospective cohort studies are still warranted to further examine the association.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25262110\",\n \"title\": \"Air pollution and risk of type 2 diabetes mellitus: a systematic review and meta-analysis.\",\n \"abstract\": \"AIM: Whether exposure to relatively high levels of air pollution is associated with diabetes occurrence remains unclear. We sought to assess and quantify the association between exposure to major air pollutants and risk of type 2 diabetes. METHODS: PubMed and EMBASE databases (through September 2013) were searched using a combination of terms related to exposure to gaseous (NO2 and NOx) or particulate matter pollutants (PM2.5, PM10 and PM10-2.5) and type 2 diabetes. Descriptive and quantitative information were extracted from selected studies. We used random-effects models meta-analysis to derive overall risk estimates per type of pollutant. RESULTS: We included ten studies (five cross-sectional and five prospective), assessing the effects of air pollutants on the occurrence of diabetes. In prospective investigations, the overall effect on diabetes occurrence was significant for both NO2 (adjusted hazard ratio [HR], 1.13; 95% confidence interval [95%CI], 1.01-1.22; p < 0.001; I(2) = 36.4%, pheterogeneity = 0.208) and PM2.5 (HR, 1.11; 95%CI, 1.03-1.20; p < 0.001; I(2) = 0.0%, pheterogeneity = 0.827). Odds ratios were reported by two cross-sectional studies which revealed similar associations between both NO2 and PM2.5 with type 2 diabetes. Across studies, risk estimates were generally adjusted for age, gender, body mass index and cigarette smoking. CONCLUSIONS: Available evidence supports a prospective association of main air pollutants with an increased risk for type 2 diabetes. This finding may have implications for population-based strategies to reduce diabetes risk.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25329153\",\n \"title\": \"Exposure to organochlorine pollutants and type 2 diabetes: a systematic review and meta-analysis.\",\n \"abstract\": \"OBJECTIVE: Though exposure to organochlorine pollutants (OCPs) is considered a risk factor for type 2 diabetes (T2DM), epidemiological evidence for the association remains controversial. A systematic review and meta-analysis was applied to quantitatively evaluate the association between exposure to OCPs and incidence of T2DM and pool the inconsistent evidence. DESIGN AND METHODS: Publications in English were searched in MEDLINE and WEB OF SCIENCE databases and related reference lists up to August 2013. Quantitative estimates and information regarding study characteristics were extracted from 23 original studies. Quality assessments of external validity, bias, exposure measurement and confounding were performed, and subgroup analyses were conducted to examine the heterogeneity sources. RESULTS: We retrieved 23 eligible articles to conduct this meta-analysis. OR (odds ratio) or RR (risk ratio) estimates in each subgroup were discussed, and the strong associations were observed in PCB-153 (OR, 1.52; 95% CI, 1.19-1.94), PCBs (OR, 2.14; 95% CI, 1.53-2.99), and p,p'-DDE (OR, 1.33; 95% CI, 1.15-1.54) based on a random-effects model. CONCLUSIONS: This meta-analysis provides quantitative evidence supporting the conclusion that exposure to organochlorine pollutants is associated with an increased risk of incidence of T2DM.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25657765\",\n \"title\": \"Prevalence of epilepsy in iran: a meta-analysis and systematic review.\",\n \"abstract\": \"OBJECTIVE: Epilepsy is one of the most common diseases in Iran contributing to an array of health problems. In light of this, the aim of the present study is to examine the prevalence of epilepsy in Iran through a systematic review and meta-analysis. MATERIALS & METHODS: A systematic search of several databases including PubMed, scientific information databases, Google, Google scholar, Elsevier and Scopus was conducted in June 2013. Observational studies were considered for inclusion if they were published in Iranian and examined epilepsy prevalence and/or related risk factors. Meta-analysis was conducted using a random effect model with the DerSimonian/Laird method. Heterogeneity was examined using the Breslow- Day test and inconsistency using the I2 statistic. RESULTS: A total of 45 studies were identified from the search strategy. Of these, nine published manuscripts with a total of 7,723 participants were included within the review. The pooled prevalence of epilepsy in Iran was estimated to be around 5% (95% confident interval (CI) 2 to 8). For each region the prevalence of epilepsy in central, northern and eastern Iran were 5% (95%CI 2 to 8), 1% (95%CI -1 to 3) and 4% (95%CI 3 to 11) respectively. The most common risk factors in order of prevalence were somatic diseases 39% (95%CI 15 to 62), convulsion 38% (95%CI 11 to 65), mental diseases 36% (95%CI 15 to 95) and hereditary development 26% (95%CI 9 to 42). A meta-regression model identified a declining trend in the prevalence of epilepsy within Iran for the last decade. CONCLUSION: Pooled analyses from the nine included publications in this review estimate the prevalence of epilepsy in Iran to be around 5%. Although this result is much higher than rates in other countries, a declining trend in prevalence over the past decade was also identified.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25780309\",\n \"title\": \"Association between diabetes mellitus and gastroesophageal reflux disease: A meta-analysis.\",\n \"abstract\": \"AIM: To investigate whether there is a link between diabetes mellitus (DM) and gastroesophageal reflux disease (GERD). METHODS: We conducted a systematic search of PubMed and Web of Science databases, from their respective inceptions until December 31, 2013, for articles evaluating the relationship between DM and GERD. Studies were selected for analysis based on certain inclusion and exclusion criteria. Data were extracted from each study on the basis of predefined items. A meta-analysis was performed to compare the odds ratio (OR) in DM between individuals with and without GERD using a fixed effect or random effect model, depending on the absence or presence of significant heterogeneity. Subgroup analyses were used to identify sources of heterogeneity. Publication bias was assessed by Begg's test. To evaluate the results, we also performed a sensitivity analysis. RESULTS: When the electronic database and hand searches were combined, a total of nine eligible articles involving 9067 cases and 81 968 controls were included in our meta-analysis. Based on the random-effects model, these studies identified a significant association between DM and the risk of GERD (overall OR = 1.61; 95%CI: 1.36-1.91; P = 0.003). Subgroup analyses indicated that this result persisted in studies on populations from Eastern countries (OR = 1.71; 95%CI: 1.38-2.12; P = 0.003) and in younger patients (mean age < 50 years) (OR = 1.70; 95%CI: 1.22-2.37; P = 0.001). No significant publication bias was observed in this meta-analysis using Begg(')s test (P = 0.175). The sensitivity analysis also confirmed the stability of our results. CONCLUSION: This meta-analysis suggests that patients with DM are at greater risk of GERD than those who do not have DM.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25909054\",\n \"title\": \"Type 2 diabetes mellitus and risk of malignant melanoma: a systematic review and meta-analysis of cohort studies.\",\n \"abstract\": \"BACKGROUND: Epidemiology studies have demonstrated inconsistent associations between type 2 diabetes mellitus and the risk of malignant melanoma. To this end, the aim was to perform a meta-analysis of cohort studies. METHOD: Medline, PubMed, Embase and the Cochrane Library were searched up to February 2014. Cohort studies addressing the relative risk of type 2 diabetes mellitus on malignant melanoma were included in this meta-analysis. The Newcastle-Ottawa Scale was applied for quality evaluation. The pooled relative risks with the corresponding 95% confidence intervals (95% CIs) were calculated by using random-effects or random-effects model. Heterogeneity and publication bias were evaluated by I (2) and funnel plot analysis, respectively. Data was analyzed using STATA 11.0. RESULTS: A total of 9 independent cohorts from 8 manuscripts were entered this meta-analysis. Type 2 diabetes mellitus was slightly associated with an increased risk of malignant melanoma, and the pooled relative risk was 1.15 (95% CI, 1.00-1.32) in diabetes compared with non-diabetes with significant evidence of heterogeneity among these studies (P=0.016, I (2) =57.6%). For the studies adjusted for age, gender and obesity, the relative risks were 1.21 (95% CI, 1.03-1.42), 1.17 (95% CI, 1.01-1.35) and 1.11 (95% CI, 1.00-1.24), respectively. For the population-based studies in which case cohort established, the relative risk was 1.85 (95% CI, 1.31-2.62). CONCLUSION: Type 2 diabetes might be an independent risk factor for malignant melanoma. Further studies are needed to specifically test the effect, and fully elucidate the underlying pathophysiologic mechanisms.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26019469\",\n \"title\": \"Association of type 2 diabetes mellitus and the risk of colorectal cancer: A meta-analysis and systematic review.\",\n \"abstract\": \"AIM: To provide a quantitative assessment of the association between type 2 diabetes mellitus (T2DM) and the risk of colorectal cancer (CRC). METHODS: Systematic review was conducted thorough MEDLINE, EMBASE, Cochrane Library, and ISI Web of knowledge databases till 31(st) January 2014. This meta-analysis included the cohort studies that illustrated relative risk (RR) or odds ratio estimates with 95%CI for the predictive risk of CRC by T2DM. Summary relative risks with 95%CI were analyzed by using an effects summary ratio model. Heterogeneity among studies was assessed by the Cochran's Q and I (2) statistics. RESULTS: The meta analysis of 8 finally selected studies showed a positive correlation of T2DM with the risk of CRC as depicted by effects summary RR of 1.21 (95%CI: 1.02-1.42). Diabetic women showed greater risk of developing CRC as their effect summary RR of 1.22 (95%CI: 1.01-49) with significant overall Z test at 5% level of significance was higher than the effect summary RR of 1.17 (95%CI: 1.00-1.37) of men showing insignificant Z test. The effect summary RR of 1.19 with 95%CI of 1.07-1.33 indicate a positive relationship between DM and increased risk of CRC with significant heterogeneity (I (2) = 92% and P-value < 0.05). CONCLUSION: Results from this systematic review and meta-analysis report that diabetic people have an increased risk of CRC as compared to non-diabetics.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26173490\",\n \"title\": \"Diabetes as a risk factor for carpal tunnel syndrome: a systematic review and meta-analysis.\",\n \"abstract\": \"AIMS: To assess whether diabetes increases the risk of carpal tunnel syndrome and to estimate the magnitude of the association with Type 1 and Type 2 diabetes. METHODS: We conducted a systematic search of PubMed, Embase, Web of Science, Scopus, Google Scholar and ResearchGate for articles published between 1950 and January 2015. A total of 36 studies (eight cross-sectional, 21 case-control and seven cohort studies) qualified for meta-analysis. We used a random-effects meta-analysis and assessed heterogeneity and publication bias. RESULTS: The pooled odds ratio of 25 studies (including a total of 92 564 individuals) that reported unadjusted estimates for the association between diabetes and carpal tunnel syndrome or carpal tunnel release was 1.97 (95% CI 1.56-2.49). The pooled odds ratio of 18 case-control or cohort studies consisting of >37 million individuals that reported estimates after controlling for potential confounders was 1.69 (95% CI 1.45-1.96). The association did not differ for Type 1 and Type 2 diabetes. Furthermore, there was no publication bias. CONCLUSION: This meta-analysis suggests that both Type 1 and Type 2 diabetes are risk factors for carpal tunnel syndrome.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26234220\",\n \"title\": \"Diabetes mellitus is associated with increased risk of surgical site infections: A meta-analysis of prospective cohort studies.\",\n \"abstract\": \"BACKGROUND AND OBJECTIVE: Observational studies have suggested an association between diabetes mellitus and the risk of surgical site infections (SSIs), but the results remain inconclusive. We conducted a meta-analysis of prospective cohort studies to elucidate the relationship between diabetes mellitus and SSIs. METHODS: We searched PubMed, Embase, and Web of Science databases and reviewed the reference lists of the retrieved articles to identify relevant studies. Associations were tested in subgroups representing different patient characteristics and study quality criteria. The random-effect model was used to calculate the overall relative risk (RR). RESULTS: Fourteen prospective cohort studies (N = 91,094 participants) were included in this meta-analysis, and the pooled crude RR was 2.02 (95% confidence interval, 1.68-2.43) with significant between-study heterogeneity observed (I(2) = 56.50%). Significant association was also detected after we derived adjusted RRs for studies not reporting the adjusted RRs and calculated the combined adjusted RR of the 14 studies (RR, 1.69; 95% confidence interval, 1.33-2.13). Results were consistent and statistically significant in all subgroups. Stratified analyses found the number of confounders adjusted for, sample size, and method of diabetes case ascertainment might be the potential sources of heterogeneity. Sensitivity analysis further demonstrated the robustness of the result. CONCLUSIONS: This meta-analysis suggests diabetes mellitus is significantly associated with increased risk of SSIs. Future studies are encouraged to reveal the mechanisms underlying this association.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26417844\",\n \"title\": \"Prevalence of hypertriglyceridemic waist and association with risk of type 2 diabetes mellitus: a meta-analysis.\",\n \"abstract\": \"INTRODUCTION: A meta-analysis of studies assessing the prevalence of hypertriglyceridemic waist and an association with risk of type 2 diabetes mellitus (T2DM). MATERIALS AND METHODS: PubMed, EMBASE, Web of Science, CNKI, CQVIP and Wanfang databases were searched for studies of the prevalence of hypertriglyceridemic waist or association with risk of T2DM. Reference lists of each original article were also searched. A random-effects model was used to synthesize the combined prevalence and odds ratios. Publication bias and substantial heterogeneity were examined. RESULTS: Twenty-five eligible studies involving 93 194 participants (93 194 for prevalence and 34 199 for odds ratios): 17 articles of prevalence, and 8 of both prevalence and risk of T2DM. Prevalence of hypertriglyceridemic waist ranged from 4% to 47%, with pooled prevalence of 18% (95% CI 13-23%), overall: 18% (95% CI 13-23%) for men and 19% (95% CI 13-24%) for women. Odds ratios ranged from 2.8 to 9.6 for T2MD in overall, with pooled odds ratios of 4.18 (95% CI 3.55-4.92), overall: 3.55 (95% CI 2.93-4.31) for men and 4.18 (95% CI 3.43-5.09) for women. DISCUSSION/CONCLUSION: The prevalence of hypertriglyceridemic waist has reached an alarming level and is closely associated with increased risk of T2DM in the general population, particularly among women and among brown-skinned men and women. Copyright © 2015 John Wiley & Sons, Ltd.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26507303\",\n \"title\": \"Is diabetes mellitus a risk factor for venous thromboembolism? A systematic review and meta-analysis of case-control and cohort studies.\",\n \"abstract\": \"OBJECTIVE: Diabetes mellitus is a well-established risk factor for atherosclerotic disease, but its role in the occurrence of venous thromboembolism (VTE) has not been elucidated. We conducted a meta-analysis of published cohort and case-control studies to assess whether diabetes mellitus is a risk factor for VTE. RESEARCH DESIGN AND METHODS: We systematically searched MEDLINE and EMBASE for case-control and prospective cohort studies assessing association between the risk of venous thromboembolism and diabetes. Odds ratios (OR) from case-control studies were combined while for prospective studies hazard ratios (HR) were combined. Models with random effects were used. Meta-analyses were conducted separately for raw and adjusted measures of association. RESULTS: 24 studies were identified including 10 cohort studies (274,501 patients) and 14 case-control studies (1,157,086 patients). Meta-analysis of the prospective cohort studies demonstrated a significant association between diabetes and VTE (HR 1.60; 95% CI 1.35 to 1.89). This association was no longer present after analysis of multi-adjusted HRs (HR 1.10; 95% CI 0.77 to 1.56). Meta-analysis of case-control studies showed a significant association between diabetes and VTE (OR 1.57; 95%CI 1.17 to 2.12), but this association was no longer present when adjusted ORs were used (OR 1.18; 95%CI 0.89 to 1.56). CONCLUSIONS: The increased risk of VTE associated with diabetes mainly results from confounders rather than an intrinsic effect of diabetes on venous thrombotic risk. Therefore, no specific recommendations should apply for the management of diabetic patients at risk for VTE.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26598716\",\n \"title\": \"Is there an association between tendinopathy and diabetes mellitus? A systematic review with meta-analysis.\",\n \"abstract\": \"BACKGROUND: Musculoskeletal symptoms limit adherence to exercise interventions for individuals with type 2 diabetes. People with diabetes may be susceptible to tendinopathy due to chronically elevated blood glucose levels. Therefore, we aimed to investigate this potential association by systematically reviewing and meta-analysing case-control, cross-sectional, and studies that considered both of these conditions. METHODS: Nine medical databases and hand searching methods were used without year limits to identify all relevant English language articles that considered diabetes and tendinopathy. Two authors applied exclusion criteria and one author extracted data with verification by a second author. Meta-analysis was conducted using a random effects model. Results were expressed as odds ratio (OR), mean difference or standardised mean difference with a confidence intervals (95% CI). Heterogeneity was assessed by I(2). FINDINGS: 31 studies were included in the final analysis of which 26 recruited people with diabetes and five recruited people with tendinopathy. Tendinopathy was more prevalent in people with diabetes (17 studies, OR 3·67, 95% CI 2·71 to 4·97), diabetes was more prevalent in people with tendinopathy (5 studies, OR 1·28, 95% CI 1·10 to 1·49), people with diabetes and tendinopathy had a longer duration of diabetes than people with diabetes only (6 studies, mean difference 5·26 years, 95% CI 4·15 to 6·36) and people with diabetes had thicker tendons than controls (9 studies, standardised mean difference 0·79 95% CI 0·47 to 1·12). INTERPRETATION: These findings provide strong evidence that diabetes is associated with higher risk of tendinopathy. This is clinically relevant as tendinopathy may affect adherence to exercise interventions for diabetes.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26612139\",\n \"title\": \"Diabetes mellitus and venous thromboembolism: A systematic review and meta-analysis.\",\n \"abstract\": \"Diabetes mellitus (DM) may be a risk factor for venous thromboembolism (VTE) but results are inconsistent. AIM: We conducted a systematic review and meta-analysis of epidemiologic studies to quantify the association between DM and VTE. METHODS AND RESULTS: We included studies identified in PubMed, Web of Science, and CINAHL through 07/31/2014. We identified 19 studies that met our selection criteria. We pooled RRs using a random-effects model: the pooled RR for the association of DM with VTE was 1.10 (95% CI: 0.94-1.29). Between-study heterogeneity was explored with a forest plot, funnel plot, meta-regression, and a stratified analysis. Between-study heterogeneity was observed and not explained by study design, method of DM assessment, or degree of adjustment for confounding. Sensitivity analyses omitted one study at a time to assess the influence of any single study on the pooled estimate. These analyses indicated that one large study was highly influential; when this study was excluded, the pooled estimate increased and just reached statistical significance: 1.16 (95% CI: 1.01-1.34). CONCLUSIONS: This meta-analysis suggests either no association or a modest positive one between DM and VTE in the general population. DM is unlikely to play a major role in VTE development.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26993825\",\n \"title\": \"Significant Association Between Gallstone Disease and Nonalcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis.\",\n \"abstract\": \"BACKGROUND: Gallstone disease (GD) and nonalcoholic fatty liver disease (NAFLD) are common digestive disorders worldwide. Both conditions share certain risk factors including obesity, insulin resistance and diabetes. Several epidemiologic studies have reported the relationship between these two conditions. AIM: We conducted a systematic review and meta-analysis to characterize the association between GD and NAFLD. METHODS: A comprehensive search of the databases MEDLINE and EMBASE was performed from inception through November 2015. The inclusion criterion was the observational studies' assessment of the association between GD and NAFLD in adult participants. Pooled odds ratio (OR) and 95 % confidence interval (CI) were calculated using a random-effects model. RESULTS: Data were extracted from 12 observational studies (9 cross-sectional studies, 1 case-control study and 2 cohort studies). The pooled OR of NAFLD in patients who had GD was 1.55 (95 % CI 1.31-1.82). The statistical between-studies heterogeneity (I (2)) was 64 %. The association remained significant when limited to cohort studies with pooled OR 1.33 (95 % CI 1.14-1.55, I (2) = 0 %). CONCLUSION: Our meta-analysis demonstrated that GD is significantly associated with NAFLD. Further prospective studies exploring the underlying mechanism of this association should be pursued.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"27396752\",\n \"title\": \"Association of circulating total bilirubin with the metabolic syndrome and type 2 diabetes: A systematic review and meta-analysis of observational evidence.\",\n \"abstract\": \"OBJECTIVE: Emerging evidence suggests that bilirubin levels might be associated with the metabolic syndrome (MetS) and type 2 diabetes (T2D), although the nature of the association remains unclear. DESIGN: This systematic review and meta-analysis investigated the relationship between total plasma bilirubin and the risk of MetS and T2D. DATA SOURCES: Relevant studies were identified using five databases (Embase, Medline [Ovid], Web of Science, PubMed, Cochrane Central and Google Scholar), with the last search done on 21 October 2015. Study references were checked and authors contacted to identify additional studies. STUDY SELECTION: Randomized controlled trials, and cohort, case-control and cross-sectional studies of adults examining the association between blood bilirubin levels and MetS and T2D were included, irrespective of language and date of publication. Abstract and full-text selection was done by two independent reviewers, with a third reviewer available in case of disagreement. DATA EXTRACTION: Data were extracted by two independent reviewers using a predesigned data collection form. MAIN OUTCOMES AND MEASURES: MetS and T2D. METHODS: Summary estimates were obtained by random-effects meta-analysis. RESULTS: Of the 2313 searched references, 16 observational studies (11 cross-sectional, two prospective, one that was both cross-sectional and prospective, two retrospective and one national survey) met our inclusion criteria. Overall, data were available for 175,911 non-overlapping participants, including 7414 MetS cases and 9406 T2D cases. In the meta-analysis of seven cross-sectional studies, the pooled odds ratio (95% confidence interval) for MetS in a comparison of extreme tertiles of serum bilirubin levels was 0.70 (95% CI: 0.62, 0.78), whereas no significant association was found for the pooled estimated relative risk between two prospective studies (0.57, 95% CI: 0.11, 2.94). The corresponding estimate was 0.77 (95% CI: 0.67, 0.87) for T2D from four cross-sectional studies. CONCLUSION: The available evidence, mainly from cross-sectional studies, supports an inverse association of bilirubin levels with adverse metabolic outcomes. Large-scale prospective studies are now needed to establish whether bilirubin levels may be useful in the prevention of MetS and T2D.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"27477292\",\n \"title\": \"Diabetes mellitus as a risk factor for incident chronic kidney disease and end-stage renal disease in women compared with men: a systematic review and meta-analysis.\",\n \"abstract\": \"Diabetes mellitus is a strong risk factor for chronic kidney disease and end-stage renal disease. Whether sex differences in chronic kidney disease and end-stage renal disease incidence exist among diabetic patients remains unclear. This systematic review and meta-analysis was conducted to evaluate the relative effect of diabetes on chronic kidney disease and end-stage renal disease risk in women compared with men. We systematically searched Embase, PubMed, and the Cochrane Library for both cohort and case-control studies until October 2015. Studies were selected if they reported a sex-specific relationship between diabetes mellitus and chronic kidney disease or end-stage renal disease. We generated pooled estimates across studies using random-effects meta-analysis after log transformation with inverse variance weighting. Ten studies with data from more than 5 million participants were included. The pooled adjusted risk ratio of chronic kidney disease associated with diabetes mellitus was 3.34 (95 % CI 2.27, 4.93) in women and 2.84 (95 % CI 1.73, 4.68) in men. The data showed no difference in diabetes-related chronic kidney disease risk between the sexes (pooled adjusted women-to-men relative risk ratio was 1.14 [95 % CI 0.97, 1.34]) except for end-stage renal disease-the pooled adjusted women-to men relative risk ratio was 1.38 (95 % CI 1.22, 1.55; p = 0.114, I² = 38.1 %). The study found no evidence of a sex difference in the association between diabetes mellitus and chronic kidney disease. However, the excess risk for end-stage renal disease was higher in women with diabetes than in men with the same condition, from which we assume that the female gender could accelerate the disease progression. Further studies are needed to support this notion and elucidate the underlying mechanisms.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"27515679\",\n \"title\": \"Diabetes mellitus and risk of falls in older adults: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: intensive or very loose glycemic control may contribute to the risk of falls in diabetic patients. However, studies on diabetes mellitus and the risk of falls have yielded conflicting results. Our objective was to investigate the effect of diabetes mellitus on the risk of falls in older adults by conducting a systematic review and meta-analysis. METHODS: the PubMed and Embase databases were searched for relevant studies published until November 2015. Only prospective cohort studies reporting at least age-adjusted risk estimate of falls compared diabetic to non-diabetic individuals were selected. Diabetes mellitus was ascertained by a combination of medical history and laboratory tests or use of anti-diabetic drugs. RESULTS: a total of six studies involving 14,685 participants were identified. The number of falls in diabetic and non-diabetic individuals was 423 of 1,692 (25.0%) and 2,368 of 13,011 (18.2%), respectively. Diabetes mellitus was associated with an increased risk of falls (risk ratio [RR] = 1.64; 95% confidence intervals [CI] 1.27-2.11) in a random-effects model. Subgroup analyses showed that the risk of falls seemed more pronounced among both gender groups (RR = 1.81; 95% CI 1.19-2.76) than among women (RR = 1.52; 95% CI 1.04-2.21). Diabetes increased 94% (RR = 1.94; 95% CI 1.42-2.63) and 27% (RR = 1.27; 95% CI 1.06-1.52) risk of falls in insulin-treated and no-insulin-treated patients, respectively. CONCLUSIONS: this meta-analysis reveals that older adults with diabetes mellitus are associated with greater risk of falls, and this association is more pronounced in insulin-treated patients.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"27658134\",\n \"title\": \"Systematic review and meta-analysis of the association between mumps during childhood and risk of type 1 diabetes mellitus.\",\n \"abstract\": \"We conducted a systematic review and meta-analysis of the association between mumps and risk of type 1 diabetes mellitus (T1DM). Literature searches were conducted using Medline, EMBASE and Web of Science including studies published before February 2014. Crude and, where available, adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were extracted from the published reports of each included study. Combined OR estimates and tests of heterogeneity were obtained using meta-analysis techniques. The analysis was repeated in subgroups of studies on the basis of quality defined by the score on the Newcastle-Ottawa scale (NOS). In total, 18 articles met the eligibility criteria, and overall there was some evidence of a weak association between clinically diagnosed mumps and T1DM (OR=1.23, 95% CI 1.00-1.51; p=0.05) but marked heterogeneity between studies (I2=49%; p for heterogeneity=0.01). Restricting analyses to 13 high quality studies, there was little evidence of association between clinically diagnosed mumps and T1DM (OR=1.11, 95% CI 0.91-1.35; p=0.29) and there was much less heterogeneity (I2=26%; p for heterogeneity=0.18). Overall there was little evidence of any strong association between mumps infection and T1DM.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28397967\",\n \"title\": \"The association between dementia and epilepsy: A systematic review and meta-analysis.\",\n \"abstract\": \"OBJECTIVE: Dementia is among the top 15 conditions with the most substantial increase in burden of disease in the past decade, and along with epilepsy, among the top 25 causes of years lived with disability worldwide. The epidemiology of dementia in persons with epilepsy, and vice versa, is not well characterized. The purpose of this systematic review was to examine the prevalence, incidence, and reported risk factors for dementia in epilepsy and epilepsy in dementia. METHODS: Embase, PsycINFO, MEDLINE, and the Cochrane databases were searched from inception. Papers were included if they reported the incidence and/or prevalence of dementia and epilepsy. Two individuals independently performed duplicate abstract and full-text review, data extraction, and quality assessment. Random-effects models were used to generate pooled estimates when feasible. RESULTS: Of the 3,043 citations identified, 64 were reviewed in full text and 19 articles were included. The period prevalence of dementia ranged from 8.1 to 17.5 per 100 persons among persons with epilepsy (insufficient data to pool). The pooled period prevalence of epilepsy among persons with dementia was 5 per 100 persons (95% confidence interval [CI] 1-9) in population-based settings and 4 per 100 persons (95% CI 1-6) in clinic settings. There were insufficient data to report a pooled overall incidence rate and only limited data on risk factors. SIGNIFICANCE: There are significant gaps in knowledge regarding the epidemiology of epilepsy in dementia and vice versa. Accurate estimates are needed to inform public health policy and prevention, and to understand health resource needs for these populations.\",\n \"corpus_id\": 22832684,\n \"score\": 1\n },\n {\n \"doc_id\": \"28643299\",\n \"title\": \"The association between circulating fetuin-A levels and type 2 diabetes mellitus risk: systematic review and meta-analysis of observational studies.\",\n \"abstract\": \"BACKGROUND AND OBJECTIVE: Fetuin-A is a liver-derived circulating protein that is associated with insulin resistance and diabetes. The objective of this systematic review and meta-analysis of published observational studies was to investigate mean levels of fetuin-A in T2D patients and the relationship between blood fetuin-A levels and T2D risk. MATERIALS AND METHODS: PubMed, Embase, Google Scholar, Web of Science, and The Cochrane Library were systematically searched for potential relevant studies up to 1 December 2016. Natural logarithm-transformed estimate risks, standard mean differences on the basis of Hedges's adjusted g, and 95% confidence intervals (CIs) were calculated for all eligible studies and were combined to measure the pooled data using random-effects model. RESULTS: A total of 32 studies including 27 case-control and 5 cohort studies were included in the current study. Fetuin-A levels in T2D patients were significantly higher than control groups [Hedges' g = 1.73, 95% CI (1.25-2.22), P < 0.001], with significant heterogeneity across studies (P < 0.001, I (2) = 98.46%). Findings from meta-analyses of cohort studies showed a statistically significant association between fetuin-A levels and T2D risk [rate ratio = 1.62, 95% CI (1.26-2.08), P < 0.001], with no significant heterogeneity (P = 0.10, I (2) = 46.06%). CONCLUSION: We found a significant relationship between the fetuin-A levels with T2D risk. Although fetuin-A may be as a potential screening and prediction biomarker or a therapeutic target in T2D patients, further studies are required in this regard.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28757515\",\n \"title\": \"Association between type 1 diabetes mellitus and risk of epilepsy: A meta-analysis of observational studies.\",\n \"abstract\": \"A potential association between type 1 diabetes mellitus and subsequent epilepsy emerged in recent studies. This study aimed to evaluate the possible relationship between type 1 diabetes mellitus and epilepsy using meta-analysis. Pubmed, ISI Web of Knowledge, Embase and Cochrane Library were searched for potential studies of the association between type 1 diabetes mellitus and epilepsy from inception to February 1, 2017. Two investigators independently screened studies for inclusion and extracted related data; discrepancies were solved by consensus. Random effects model of Hazard Ratio (HR) was used to estimate the strength of association. We identified 13 papers from potentially relevant articles of which 3 cohort studies met the inclusion criteria. Random effects meta-analysis showed that type 1 diabetes mellitus was associated with an increased risk of epilepsy with HR = 3.29 (95% CI: 2.61-4.14; I(2) = 0, p = 0.689). Similar results were observed in type 1 diabetes mellitus patents younger than 18-years-old with HR = 2.96 (95% CI: 2.28-3.84; I(2) = 0, p = 0.571). Meta-analysis of 2 studies that adjusted for potential confounders yielded an increased risk of epilepsy with HR = 2.89 (95% CI: 2.26-3.70; I(2) = 0, p = 0.831). The meta-analysis indicates that type 1 diabetes mellitus is associated with a statistically significant increased risk for epilepsy compared to those without type 1 diabetes mellitus.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28858123\",\n \"title\": \"Diabetes mellitus carries a risk of esophageal cancer: A meta-analysis.\",\n \"abstract\": \"BACKGROUND: Many studies have showed that diabetes mellitus (DM) might be a risk factor for certain types of cancers. However, there are still inconsistent results on the effects of DM on the risk of esophageal cancer (EC). The objective of this study is to investigate the association and to quantify the correlation between DM and EC by a meta-analysis. METHODS: The initial search identified 339 articles. Those publications that did not report the exact number of EC cases were removed. Finally, 13 meaningful studies were extracted from the databases of PubMed, MEDLINE, and Web of Science. All pooled analyses of risk ratios (RRs) and 95% confidence intervals (CIs) were assessed by a random-effect or fixed-effect model. Subgroup analysis was implemented on the basis of the sex or ethnicity. I value was used to assess heterogeneity, and funnel plot analysis was for publication bias. RESULTS: The result showed that there was a positive correlation between type 2 diabetes mellitus (T2DM) and EC risk (RR = 1.28, 95% CI: 1.12-1.47, P < .001). Subgroup analysis based on gender showed that male was an important risk factor for EC (RR = 1.53, 95% CI: 1.44-1.62, P < .001), but female was not (RR = 1.23, 95% CI: 0.41-3.69, P = .71). In addition, subgroup analysis based on ethnicity showed that DM was significantly correlated to EC in North America subjects (RR = 1.39, 95% CI: 1.31-1.47, P < .001), and in Europe subjects (RR = 1.37, 95% CI: 1.02-1.83, P = .04), whereas no correlation was found in Asian subjects (RR = 0.98, 95% CI: 0.50-1.95, P = .96). Furthermore, DM had a correlation to an increased risk of esophageal adenocarcinoma (EAC) (RR = 1.43, 95% CI: 1.35-1.51, P < .001). CONCLUSION: This meta-analysis indicates that DM is positively correlated to EC. However, the results should be interpreted with caution because of the limitations on potential clinical confounding factors in each study included in this meta-analysis.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28862239\",\n \"title\": \"Insomnia and risk of nonalcoholic fatty liver disease: A systematic review and meta-analysis.\",\n \"abstract\": \"AIM: This sudy aims to investigate the association between insomnia or excessive daytime sleepiness (EDS) and risk of nonalcoholic fatty liver disease (NAFLD). METHODS: We searched published studies indexed in MEDLINE and EMBASE database from inception to December 2015. Studies that reported odds ratios (ORs), risk ratios, hazard ratios or standardized incidence ratio with 95% confidence intervals (CI) comparing the risk of NAFLD among participants who had insomnia or EDS versus those without insomnia or EDS were included. Pooled ORs and 95% CI were calculated using a random-effect, generic inverse variance method of DerSimonian and Laird. Cochran's Q test and I2 statistic were used to determine the between-study heterogeneity. RESULTS: Our search strategy yielded 2117 potentially relevant articles (781 articles from MEDLINE and 1336 articles from EMBASE). After comprehensive review, seven studies (three cross-sectional studies and four case-control studies) were found to be eligible and were included in the meta-analysis. The risk of NAFLD in participants who had insomnia was significantly higher with the pooled OR of 1.13 (95% CI, 1.00-1.27). The statistical heterogeneity was moderate with an I2 of 62%. Elevated risk of NAFLD was also observed among participants with EDS even though the 95% CI was wider and did not reach statistical significance (pooled OR 2.21; 95% CI, 0.84-5.82). The statistical heterogeneity was moderate with an I2 of 62%. CONCLUSIONS: Our study demonstrated an increased risk of NAFLD among participants who had insomnia or EDS. Whether this association is causal needs further investigations.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28899519\",\n \"title\": \"The association between daytime napping and risk of diabetes: a systematic review and meta-analysis of observational studies.\",\n \"abstract\": \"OBJECTIVE: To investigate the association between daytime napping and prevalent/incident diabetes mellitus (DM) based on systematic review and meta-analytic data. METHODS: The electronic databases of Embase, Medline, Pubmed and Web of Science were searched. Relevant studies were extracted by two reviewers independently. The associations between daytime napping (irrespective of duration), long nap (≥1 h/day) and short nap (<1 h/day), and risk of DM were assessed according to study types. Overall estimates were pooled using either fixed- or random-effect with inverse variance meta-analysis. Heterogeneity of included studies was assessed using the I2 test and possible cause of the heterogeneity was examined by meta-regression analyses. RESULTS: Ten studies (four cross-sectional and six longitudinal cohort) comprising a total of 304,885 individuals and 20,857 cases of DM were included in the systematic review, with an average napping prevalence of 47%. Nappers were found to have increased risk of DM in both cross-sectional and cohort studies. However, significant heterogeneity was present. Long nap (≥1 h/day) was associated with both prevalent and incident DM; in particular, those with a daily nap over 1 h had a 31% increased risk of developing DM during follow-up (95% confidence interval: 2-67%). Conversely, no such association was found in individuals with short naps (<1 h/day) in cohort studies. CONCLUSIONS: Long daytime napping over 1 h per day was associated with increased risk of both prevalent and incident DM. Further studies are needed to confirm the findings.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29063028\",\n \"title\": \"Elevation of serum uric acid and incidence of type 2 diabetes: A systematic review and meta-analysis.\",\n \"abstract\": \"OBJECTIVE: Recently, several cohort studies suggested a positive relationship between serum uric acid (SUA) and type 2 diabetes mellitus (T2DM), which is inconsistent with the results of functional research. Our aim was to further evaluate this correlation by conducting a systematic review. METHODS: Computerized literature searches of the Medline database, EMBASE database, and PubMed were used to evaluate the relationship between SUA and T2DM in cohort studies. Cochran's Q and I2 statistics were used to evaluate heterogeneity among studies, and pooled relative risk (RR) and odds ratio (OR) with 95% confidence intervals (CIs) were calculated using random-effects and fixed-effects models. The summary RR and OR of per 1 mg/ml-SUA increase were calculated separately because of their different epidemiological implications and calculation methods. Additionally, sensitivity analysis, stratified analysis, meta-regression, and multiple meta-regression were applied to investigate the heterogeneity among studies. RESULTS: A total of 970 articles were retrieved from the searches. Sixteen publications of cohort studies containing 61,714 participants were included. The pooled RR was 1.131 (95% CI: 1.084-1.179) with significant heterogeneity among studies (I 2 = 51.9%, P = 0.018). Adjusted RR to evaluate the stability of the relationship between SUA and T2DM in the sensitivity analysis was similar (RR = 1.140, 95% CI: 1.087-1.197), with statistically significant heterogeneity (I 2 = 54.5%, P = 0.015). Stratified analysis and meta-regression showed that the positive relationship remained irrespective of age, sex, region, and adjustment for confounding factors including body mass index, fasting blood glucose, systolic blood pressure, diastolic blood pressure, alcohol consumption, smoking, blood cholesterol, waist circumference, fatty liver, and drugs affecting SUA. CONCLUSION: Although SUA is independently associated with development of T2DM, insulin resistance increased as the baseline SUA concentration increased; thus, the correlation between SUA and T2DM requires further evaluation and the baseline insulin resistance status should also be considered.\",\n \"corpus_id\": 24181712,\n \"score\": 1\n },\n {\n \"doc_id\": \"29113364\",\n \"title\": \"Alpha-glucosidase inhibitors and risk of cancer in patients with diabetes mellitus: a systematic review and meta-analysis.\",\n \"abstract\": \"Several studies have shown that anti-diabetic medications may modify the risk of cancer. We performed a systematic review and meta-analysis to evaluate the effect of alpha-glucosidase inhibitors (AGIs) on the risk of cancer in patients with diabetes mellitus. We conducted a systematic search of Medline, EMBASE, and Web of Science databases, up to September 30, 2016. Random-effects model was used to estimate the summary odds ratios (ORs) with 95% CI. Twenty-five studies (14 cohort, 7 case-control, and 4 randomized controlled trials) involving 1,285,433 patients with diabetes were included. Meta-analysis of observational studies showed that the use of AGIs was associated with a lower risk of developing cancer (OR = 0.86, 95% CI 0.78-0.96), especially gastrointestinal cancer (OR = 0.83, 95% CI 0.71-0.97). There was considerable heterogeneity across the studies introduced partly by the quality of included studies and adjustment for potential confounders. Meta-analysis of randomized controlled trials did not reveal any significant association between AGIs and cancer risk. Meta-analysis of observational studies indicated that AGIs may decrease the risk of cancer in individuals with diabetes.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29161276\",\n \"title\": \"Association between diabetes mellitus and active tuberculosis: A systematic review and meta-analysis.\",\n \"abstract\": \"The burgeoning epidemic of diabetes mellitus (DM) is one of the major global health challenges. We systematically reviewed the published literature to provide a summary estimate of the association between DM and active tuberculosis (TB). We searched Medline and EMBASE databases for studies reporting adjusted estimates on the TB-DM association published before December 22, 2015, with no restrictions on region and language. In the meta-analysis, adjusted estimates were pooled using a DerSimonian-Laird random-effects model, according to study design. Risk of bias assessment and sensitivity analyses were conducted. 44 eligible studies were included, which consisted of 58,468,404 subjects from 16 countries. Compared with non-DM patients, DM patients had 3.59-fold (95% confidence interval (CI) 2.25-5.73), 1.55-fold (95% CI 1.39-1.72), and 2.09-fold (95% CI 1.71-2.55) increased risk of active TB in four prospective, 16 retrospective, and 17 case-control studies, respectively. Country income level (3.16-fold in low/middle-vs. 1.73-fold in high-income countries), background TB incidence (2.05-fold in countries with >50 vs. 1.89-fold in countries with ≤50 TB cases per 100,000 person-year), and geographical region (2.44-fold in Asia vs. 1.71-fold in Europe and 1.73-fold in USA/Canada) affected appreciably the estimated association, but potential risk of bias, type of population (general versus clinical), and potential for duplicate data, did not. Microbiological ascertainment for TB (3.03-fold) and/or blood testing for DM (3.10-fold), as well as uncontrolled DM (3.30-fold), resulted in stronger estimated association. DM is associated with a two- to four-fold increased risk of active TB. The association was stronger when ascertainment was based on biological testing rather than medical records or self-report. The burgeoning DM epidemic could impact upon the achievements of the WHO \\\"End TB Strategy\\\" for reducing TB incidence.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29399359\",\n \"title\": \"Association between smoking and non-alcoholic fatty liver disease: A systematic review and meta-analysis.\",\n \"abstract\": \"Background/aims: Non-alcoholic fatty liver disease is one of the most common chronic liver diseases. Some risk factors are known to influence the development of non-alcoholic fatty liver disease, but the effect of tobacco smoking on the progression of non-alcoholic fatty liver disease is controversial. The main goal of this systematic review and meta-analysis is to investigate the association between smoking and non-alcoholic fatty liver disease. Method: Electronic databases (PubMed, Scopus, and ISI Web of Science) were searched to find published articles on non-alcoholic fatty liver disease and smoking until December 2016. All relevant studies were screened by inclusion and exclusion criteria and compatible studies were chosen. The Newcastle-Ottawa Scale was used to assess the methodological quality of eligible articles. Subsequently, information was gathered based on the following: author, publication year, keywords, country, inclusion and exclusion criteria, main results, study design, conclusion, and confounder variables (age, body mass index, gender, ethnicity, and diabetes). Finally, analyses were performed using Comprehensive Meta-Analysis Software. Results: Data were extracted from 20 observational studies (9 cross-sectional, 6 case-control, 4 cohort studies, and 1 retrospective cohort study). A significant association was observed between smoking and non-alcoholic fatty liver disease with a pooled odds ratio of 1.110 (95% confidence interval, 1.028-1.199), p-value = 0.008. The statistical heterogeneity was medium with an I2 of 40.012%, p-heterogeneity = 0.074. Also there was a significant relation between non-alcoholic fatty liver disease and passive smoking with a pooled odds ratio of 1.380 (95% confidence interval, 1.199-1.588; p-value = 0.001; I2 = 59.41; p-heterogeneity = 0.117). Conclusion: Our meta-analysis demonstrated that smoking is significantly associated with non-alcoholic fatty liver disease. Further prospective studies exploring the underlying mechanisms of this association should be pursued. Also passive smoking increases the risk of non-alcoholic fatty liver disease about 1.38-fold. The effects of smoking cigarettes on active smokers (current smoker, former smoker, and total smoker) are less than passive smokers. Further studies are needed to compare the of effects of passive and active smoking on non-alcoholic fatty liver disease.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29511464\",\n \"title\": \"Type 2 diabetes mellitus and non-alcoholic fatty liver disease: a systematic review and meta-analysis.\",\n \"abstract\": \"Aim: The aim of this study was the evaluation of the prevalence of NAFLD in patients with type 2 diabetes mellitus. Background: Non-alcoholic fatty liver disease (NAFLD) is an emerging disease with high prevalence in patients with type 2 diabetes mellitus (T2DM). Many studies have reported the prevalence of NAFLD in type 2 diabetes mellitus patients. However, these results are inconsistent. Methods: A Literature search was conducted in PubMed, Scopus, web of science and Science Direct from 2005 to August 2017. The necessary information was extracted. Heterogeneity was evaluated using I2 statistic. Meta-regression analyses were performed to the estimation of the relationship between the year of study and sample size with the prevalence of NAFLD. Publication bias was assessed by both Begg rank correlation and Egger tests. Subgroup analysis was performed for identification of sources heterogeneity. Results: Seventeen studies involving 10897 type 2 diabetes mellitus patients with NAFLD were included in this meta-analysis. The overall prevalence of NAFLD in type 2 diabetes mellitus patients by random effects models was 54% (95% CI, 45%- 64%). There is a significant heterogeneity across studies with (I2= 99%, p> 0.01). The funnel plot as graphically and Begg and Egger as statistically showed no publication bias among studies. Subgroup analysis indicated that the prevalence of NAFLD in type 2 diabetes mellitus patients differed in predictive factors such as lipid profile, BMI, HbA1c, AST, and ALT. This finding in spite of heterogeneity of documents is corresponding to the positive correlation between NAFLD and type 2 diabetes mellitus. Conclusion: The findings indicated that the overall prevalence of NAFLD among type 2 diabetes mellitus patients is significantly higher. It can be concluded that type 2 diabetes mellitus patients should be managed to prevent NAFLD.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29721679\",\n \"title\": \"The association of household food insecurity with the risk of type 2 diabetes mellitus in adults: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: The link between household food insecurity and risk of type 2 diabetes mellitus still remains controversial. Therefore, we performed a systematic review and meta-analysis to clarify the association between household food insecurity and type 2 diabetes mellitus. METHODS: EMBASE, PubMed, ISI Web of Science and Scopus databases were searched up to March 2017. The selection of studies, data extraction and assessing the risk of bias in the included studies were carried out by two reviewers independently. Study-specific odds ratios (ORs) were pooled using a random effects model. RESULTS: A total of 18 articles including a total of 55,353,915 adult participants were included in the meta-analysis. The pooled ORs of the cross-sectional studies revealed that household food insecurity was significantly associated with the odds of T2DM (OR 1.27, 95% CI 1.11-1.42) with no evidence of publication bias (p = 0.63) but heterogeneity between studies (I2 = 61.1%). Similarly, subgroup analyses showed that the country where the study conducted and household food insecurity assessment tool used to influence the effect of household food insecurity on the odds of T2DM. However, the pooled ORs for two case-control and one cohort studies were not significantly associated between household food insecurity and T2DM in adults. CONCLUSION: This study strengthens the hypothesis of the household food insecurity effect on the odds of T2DM among adults. Further longitudinal studies based on larger, and more representative samples are needed to identify the underlying relationships between food insecurity and type 2 diabetes mellitus.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23074521\",\n \"title\": \"Community-based care for the specialized management of heart failure: an evidence-based analysis.\",\n \"abstract\": \"UNLABELLED: In August 2008, the Medical Advisory Secretariat (MAS) presented a vignette to the Ontario Health Technology Advisory Committee (OHTAC) on a proposed targeted health care delivery model for chronic care. The proposed model was defined as multidisciplinary, ambulatory, community-based care that bridged the gap between primary and tertiary care, and was intended for individuals with a chronic disease who were at risk of a hospital admission or emergency department visit. The goals of this care model were thought to include: the prevention of emergency department visits, a reduction in hospital admissions and re-admissions, facilitation of earlier hospital discharge, a reduction or delay in long-term care admissions, and an improvement in mortality and other disease-specific patient outcomes. OHTAC approved the development of an evidence-based assessment to determine the effectiveness of specialized community based care for the management of heart failure, Type 2 diabetes and chronic wounds. PLEASE VISIT THE MEDICAL ADVISORY SECRETARIAT WEB SITE AT: www.health.gov.on.ca/ohtas to review the following reports associated with the Specialized Multidisciplinary Community-Based care series. Specialized multidisciplinary community-based care series: a summary of evidence-based analysesCommunity-based care for the specialized management of heart failure: an evidence-based analysisCommunity-based care for chronic wound management: an evidence-based analysisPlease note that the evidence-based analysis of specialized community-based care for the management of diabetes titled: \\\"Community-based care for the management of type 2 diabetes: an evidence-based analysis\\\" has been published as part of the Diabetes Strategy Evidence Platform at this URL: http://www.health.gov.on.ca/english/providers/program/mas/tech/ohtas/tech_diabetes_20091020.htmlPLEASE VISIT THE TORONTO HEALTH ECONOMICS AND TECHNOLOGY ASSESSMENT COLLABORATIVE WEB SITE AT: http://theta.utoronto.ca/papers/MAS_CHF_Clinics_Report.pdf to review the following economic project associated with this series:Community-based Care for the specialized management of heart failure: a cost-effectiveness and budget impact analysis. OBJECTIVE: The objective of this evidence-based analysis was to determine the effectiveness of specialized multidisciplinary care in the management of heart failure (HF). CLINICAL NEED: TARGET POPULATION AND CONDITION HF is a progressive, chronic condition in which the heart becomes unable to sufficiently pump blood throughout the body. There are several risk factors for developing the condition including hypertension, diabetes, obesity, previous myocardial infarction, and valvular heart disease.(1) Based on data from a 2005 study of the Canadian Community Health Survey (CCHS), the prevalence of congestive heart failure in Canada is approximately 1% of the population over the age of 12.(2) This figure rises sharply after the age of 45, with prevalence reports ranging from 2.2% to 12%.(3) Extrapolating this to the Ontario population, an estimated 98,000 residents in Ontario are believed to have HF. Disease management programs are multidisciplinary approaches to care for chronic disease that coordinate comprehensive care strategies along the disease continuum and across healthcare delivery systems.(4) Evidence for the effectiveness of disease management programs for HF has been provided by seven systematic reviews completed between 2004 and 2007 (Table 1) with consistency of effect demonstrated across four main outcomes measures: all cause mortality and hospitalization, and heart-failure specific mortality and hospitalization. ( 4-10) However, while disease management programs are multidisciplinary by definition, the published evidence lacks consistency and clarity as to the exact nature of each program and usual care comparators are generally ill defined. Consequently, the effectiveness of multidisciplinary care for the management of persons with HF is still uncertain. Therefore, MAS has completed a systematic review of specialized, multidisciplinary, community-based care disease management programs compared to a well-defined usual care group for persons with HF. EVIDENCE-BASED ANALYSIS METHODS: RESEARCH QUESTIONS: What is the effectiveness of specialized, multidisciplinary, community-based care (SMCCC) compared with usual care for persons with HF? LITERATURE SEARCH STRATEGY: A comprehensive literature search was completed of electronic databases including MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, Cochrane Library and Cumulative Index to Nursing & Allied Health Literature. Bibliographic references of selected studies were also searched. After a review of the title and abstracts, relevant studies were obtained and the full reports evaluated. All studies meeting explicit inclusion and exclusion criteria were retained. Where appropriate, a meta-analysis was undertaken to determine the pooled estimate of effect of specialized multidisciplinary community-based care for explicit outcomes. The quality of the body of evidence, defined as one or more relevant studies was determined using GRADE Working Group criteria. ( 11) INCLUSION CRITERIA: Randomized controlled trialSystematic review with meta analysisPopulation includes persons with New York Heart Association (NYHA) classification 1-IV HFThe intervention includes a team consisting of a nurse and physician one of which is a specialist in HF management. The control group receives care by a single practitioner (e.g. primary care physician (PCP) or cardiologist)The intervention begins after discharge from the hospitalThe study reports 1-year outcomes EXCLUSION CRITERIA: The intervention is delivered predominately through home-visitsStudies with mixed populations where discrete data for HF is not reported OUTCOMES OF INTEREST: All cause mortalityAll cause hospitalizationHF specific mortalityHF specific hospitalizationAll cause duration of hospital stayHF specific duration of hospital stayEmergency room visitsQuality of Life SUMMARY OF FINDINGS: One large and seven small randomized controlled trials were obtained from the literature search. A meta-analysis was completed for four of the seven outcomes including: All cause mortalityHF-specific mortalityAll cause hospitalizationHF-specific hospitalization. Where the pooled analysis was associated with significant heterogeneity, subgroup analyses were completed using two primary categories: direct and indirect model of care; andtype of control group (PCP or cardiologist).The direct model of care was a clinic-based multidisciplinary HF program and the indirect model of care was a physician supervised, nurse-led telephonic HF program. All studies, except one, were completed in jurisdictions outside North America. ( 12-19) Similarly, all but one study had a sample size of less than 250. The mean age in the studies ranged from 65 to 77 years. Six of the studies(12;14-18) included populations with a NYHA classification of II-III. In two studies, the control treatment was a cardiologist (12;15) and two studies reported the inclusion of a dietitian, physiotherapist and psychologist as members of the multidisciplinary team (12;19). ALL CAUSE MORTALITY: Eight studies reported all cause mortality (number of persons) at 1 year follow-up. ( 12-19) When the results of all eight studies were pooled, there was a statistically significant RRR of 29% with moderate heterogeneity (I(2) of 38%). The results of the subgroup analyses indicated a significant RRR of 40% in all cause mortality when SMCCC is delivered through a direct team model (clinic) and a 35% RRR when SMCCC was compared with a primary care practitioner. HF-SPECIFIC MORTALITY: Three studies reported HF-specific mortality (number of persons) at 1 year follow-up. ( 15;18;19) When the results of these were pooled, there was an insignificant RRR of 42% with high statistical heterogeneity (I(2) of 60%). The GRADE quality of evidence is moderate for the pooled analysis of all studies. ALL CAUSE HOSPITALIZATION: Seven studies reported all cause hospitalization at 1-year follow-up (13-15;17-19). When pooled, their results showed a statistically insignificant 12% increase in hospitalizations in the SMCCC group with high statistical heterogeneity (I(2) of 81%). A significant RRR of 12% in all cause hospitalization in favour of the SMCCC care group was achieved when SMCCC was delivered using an indirect model (telephonic) with an associated (I(2) of 0%). The Grade quality of evidence was found to be low for the pooled analysis of all studies and moderate for the subgroup analysis of the indirect team care model. HF-SPECIFIC HOSPITALIZATION: Six studies reported HF-specific hospitalization at 1-year follow-up. ( 13-15;17;19) When pooled, the results of these studies showed an insignificant RRR of 14% with high statistical heterogeneity (I(2) of 60%); however, the quality of evidence for the pooled analysis of was low. DURATION OF HOSPITAL STAY: Seven studies reported duration of hospital stay, four in terms of mean duration of stay in days (14;16;17;19) and three in terms of total hospital bed days (12;13;18). Most studies reported all cause duration of hospital stay while two also reported HF-specific duration of hospital stay. These data were not amenable to meta-analyses as standard deviations were not provided in the reports. However, in general (and in all but one study) it appears that persons receiving SMCCC had shorter hospital stays, whether measured as mean days in hospital or total hospital bed days. EMERGENCY ROOM VISITS: Only one study reported emergency room visits. ( 14) This was presented as a composite of readmissions and ER visits, where the authors reported that 77% (59/76) of the SMCCC group and 84% (63/75) of the usual care group were either readmitted or had an ER visit within the 1 year of follow-up (P=0.029). ( ABSTRACT TRUNCATED)\",\n \"corpus_id\": 32798964,\n \"score\": 0\n },\n {\n \"doc_id\": \"23349152\",\n \"title\": \"A systematic review and meta-analysis of the association between depression and insulin resistance.\",\n \"abstract\": \"OBJECTIVE: Depression is associated with the onset of type 2 diabetes. A systematic review and meta-analysis of observational studies, controlled trials, and unpublished data was conducted to examine the association between depression and insulin resistance (IR). RESEARCH DESIGN AND METHODS: Medline, EMBASE, and PsycINFO were searched for studies published up to September 2011. Two independent reviewers assessed the eligibility of each report based on predefined inclusion criteria (study design and measure of depression and IR, excluding prevalent cases of diabetes). Individual effect sizes were standardized, and a meta-analysis was performed to calculate a pooled effect size using random effects. Subgroup analyses and meta-regression were conducted to explore any potential source of heterogeneity between studies. RESULTS: Of 967 abstracts reviewed, 21 studies met the inclusion criteria of which 18 studies had appropriate data for the meta-analysis (n = 25,847). The pooled effect size (95% CI) was 0.19 (0.11-0.27) with marked heterogeneity (I(2) = 82.2%) using the random-effects model. Heterogeneity between studies was not explained by age or sex, but could be partly explained by the methods of depression and IR assessments. CONCLUSIONS: A small but significant cross-sectional association was observed between depression and IR, despite heterogeneity between studies. The pathophysiology mechanisms and direction of this association need further study using a purposively designed prospective or intervention study in samples at high risk for diabetes.\",\n \"corpus_id\": 14745073,\n \"score\": 0\n },\n {\n \"doc_id\": \"23399556\",\n \"title\": \"Anti-diabetic medications and risk of pancreatic cancer in patients with diabetes mellitus: a systematic review and meta-analysis.\",\n \"abstract\": \"OBJECTIVES: Several preclinical and observational studies have shown that anti-diabetic medications (ADMs) may modify the risk of pancreatic cancer (PaC). We performed a systematic review and meta-analysis evaluating the effect of metformin, sulfonylureas (SUs), thiazolidinediones (TZDs), and insulin on the risk of PaC in patients with diabetes mellitus (DM). METHODS: We conducted a systematic search of Medline, EMBASE, and Web of Science, up to June 2012, and published abstracts from major gastroenterology and oncology meetings from 2003 to 2012. Studies were included if they (1) evaluated and clearly defined exposure to metformin, SU, TZDs, and/or insulin, (2) reported PaC outcomes in patients with DM and (3) reported relative risks or odds ratio (OR) or provided data for their estimation. Summary OR estimates with 95% confidence intervals (CIs) were estimated using the random-effects model. RESULTS: Eleven studies (6 cohort, 3 case-control, and 2 randomized controlled trials (RCTs)) reported 1770 cases of PaC in 730,664 patients with DM. Meta-analysis of observational studies showed no significant association between metformin (n=9 studies; adjusted OR 0.76, 95% CI 0.57-1.03, P=0.073), insulin (n=7 studies; adjusted OR 1.59, 95% CI 0.85-2.96, P=0.144), or TZD (n=4 studies; adjusted OR 1.02, 95% CI 0.81-1.30, P=0.844) use and risk of developing PaC. Use of SU was associated with a 70% increase in the odds of PaC (n=8 studies; adjusted OR 1.70, 95% CI 1.27-2.28, P<0.001). There was considerable inherent heterogeneity between studies not explained by study design, setting, or comparator drug and is likely related to confounding by indication and reverse causality. The pooled analyses of the two RCTs were underpowered and provided non-significant results with wide, non-informative 95% CIs. CONCLUSIONS: Although SU seems to be associated with increased risk of PaC, meta-analysis of existing studies does not support a protective or harmful association between ADM use and risk of PaC in patients with DM. There was considerable heterogeneity across studies, and future, well-designed, prospective studies would be required to understand this association better.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"23415577\",\n \"title\": \"Depression and risk of mortality in individuals with diabetes: a meta-analysis and systematic review.\",\n \"abstract\": \"OBJECTIVES: To estimate risk of comorbid depression on all-cause mortality over time among individuals with diabetes. METHODS: The Medline, Cumulative Index to Nursing and Allied Health Literature, Cochrane Library, Embase and Science Direct databases were searched through September 30, 2012. We limited our search to longitudinal or prospective studies reporting all-cause mortality among those having depression and diabetes, compared with those having diabetes alone that used hazard ratios (HRs) as the main outcome. Two reviewers independently extracted primary data and evaluated the quality of studies using predetermined criteria. The pooled random effects adjusted HRs were estimated using meta-analysis. The impact of moderator variables on study effect size was examined with meta-regression. RESULTS: A total of 42,363 respondents from 10 studies were included in the analysis. Depression was significantly associated with risk of mortality (pooled HR=1.50, 95% confidence interval=1.35-1.66). Little evidence for heterogeneity was found across the studies (Cochran Q=13.52, P=.20, I(2)=26.03). No significant possibility of publication bias was detected (Egger's regression intercept=0.98, P=.23). CONCLUSION: Depression significantly increases the risk of mortality among individuals with diabetes. Early detection and treatment of depression may improve health outcomes in this population.\",\n \"corpus_id\": 45294239,\n \"score\": 0\n },\n {\n \"doc_id\": \"24439841\",\n \"title\": \"Breastfeeding and the maternal risk of type 2 diabetes: a systematic review and dose-response meta-analysis of cohort studies.\",\n \"abstract\": \"BACKGROUND AND AIMS: Breastfeeding has been associated with reduced risk of maternal type 2 diabetes in some cohort studies, but the evidence from published studies have differed with regard to the strength of the association. To clarify this association we conducted a systematic review and dose-response meta-analysis of breastfeeding and maternal risk of type 2 diabetes. METHODS AND RESULTS: We conducted a systematic review and dose-response meta-analysis of prospective studies of breastfeeding and maternal risk of type 2 diabetes. We searched the PubMed, Embase and Ovid databases up to September 19th 2013. Summary relative risks were estimated using a random effects model. Six cohort studies including 10,842 cases among 273,961 participants were included in the meta-analysis. The summary RR for the highest duration of breastfeeding vs. the lowest was 0.68 (95% CI: 0.57-0.82, I(2) = 75%, p heterogeneity = 0.001, n = 6). The summary RR for a three month increase in the duration of breastfeeding per child was 0.89 (95% CI: 0.77-1.04, I(2) = 93%, p heterogeneity < 0.0001, n = 3) and the summary RR for a one year increase in the total duration of breastfeeding was 0.91 (95% CI: 0.86-0.96, I(2) = 81%, p heterogeneity = 0.001, n = 4). There was little difference in the summary estimates whether or not BMI had been adjusted for. The inverse associations appeared to be nonlinear, p nonlinearity < 0.0001 for both analyses, and in both analyses the reduction in risk was steeper when increasing breastfeeding from low levels. CONCLUSION: This meta-analysis suggests that there is a statistically significant inverse association between breastfeeding and maternal risk of type 2 diabetes.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"25257241\",\n \"title\": \"Relationship between homocysteine level and diabetic retinopathy: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: The relationship between homocysteine (Hcy) and diabetic retinopathy (DR) remains unclear to date. Therefore, a systematic review and meta-analysis was performed on the relationship between Hcy level and DR. METHODS: Studies were identified by searching PubMed, Embase, and Web of Science databases until 5 May, 2014. RESULTS: A total of 31 studies involving 6,394 participants were included in the meta-analysis. After pooling the data from each included study, the blood Hcy concentration in the DR group was observed to be higher than that in the control group [WMD=2.55; 95% confidence interval (CI), 1.70-3.40], and diabetes mellitus (DM) patients with hyperhomocysteinemia were at a risk for DR [odds ratio (OR)=1.93; 95% CI, 1.46-2.53]. Considering the different DM types, hyperhomocysteinemia in T1DM (OR=1.83, 95% CI, 1.28-2.62) was associated with DR rather than in T2DM (OR=1.59, 95% CI, 0.72-3.51). Considerable statistical heterogeneity in the overall summary estimates was partly explained by the geographical differences. CONCLUSIONS: Results from this current meta-analysis indicate that hyperhomocysteinemia is a risk factor for DR, especially proliferative DR. Differences between geographical regions were observed in the relationship between hyperhomocysteinemia with T1DM risk. Given the heterogeneous results, the relationship between high Hcy and DR needs further investigation. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_167.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"25271098\",\n \"title\": \"Bias due to selective inclusion and reporting of outcomes and analyses in systematic reviews of randomised trials of healthcare interventions.\",\n \"abstract\": \"BACKGROUND: Systematic reviews may be compromised by selective inclusion and reporting of outcomes and analyses. Selective inclusion occurs when there are multiple effect estimates in a trial report that could be included in a particular meta-analysis (e.g. from multiple measurement scales and time points) and the choice of effect estimate to include in the meta-analysis is based on the results (e.g. statistical significance, magnitude or direction of effect). Selective reporting occurs when the reporting of a subset of outcomes and analyses in the systematic review is based on the results (e.g. a protocol-defined outcome is omitted from the published systematic review). OBJECTIVES: To summarise the characteristics and synthesise the results of empirical studies that have investigated the prevalence of selective inclusion or reporting in systematic reviews of randomised controlled trials (RCTs), investigated the factors (e.g. statistical significance or direction of effect) associated with the prevalence and quantified the bias. SEARCH METHODS: We searched the Cochrane Methodology Register (to July 2012), Ovid MEDLINE, Ovid EMBASE, Ovid PsycINFO and ISI Web of Science (each up to May 2013), and the US Agency for Healthcare Research and Quality (AHRQ) Effective Healthcare Program's Scientific Resource Center (SRC) Methods Library (to June 2013). We also searched the abstract books of the 2011 and 2012 Cochrane Colloquia and the article alerts for methodological work in research synthesis published from 2009 to 2011 and compiled in Research Synthesis Methods. SELECTION CRITERIA: We included both published and unpublished empirical studies that investigated the prevalence and factors associated with selective inclusion or reporting, or both, in systematic reviews of RCTs of healthcare interventions. We included empirical studies assessing any type of selective inclusion or reporting, such as investigations of how frequently RCT outcome data is selectively included in systematic reviews based on the results, outcomes and analyses are discrepant between protocol and published review or non-significant outcomes are partially reported in the full text or summary within systematic reviews. DATA COLLECTION AND ANALYSIS: Two review authors independently selected empirical studies for inclusion, extracted the data and performed a risk of bias assessment. A third review author resolved any disagreements about inclusion or exclusion of empirical studies, data extraction and risk of bias. We contacted authors of included studies for additional unpublished data. Primary outcomes included overall prevalence of selective inclusion or reporting, association between selective inclusion or reporting and the statistical significance of the effect estimate, and association between selective inclusion or reporting and the direction of the effect estimate. We combined prevalence estimates and risk ratios (RRs) using a random-effects meta-analysis model. MAIN RESULTS: Seven studies met the inclusion criteria. No studies had investigated selective inclusion of results in systematic reviews, or discrepancies in outcomes and analyses between systematic review registry entries and published systematic reviews. Based on a meta-analysis of four studies (including 485 Cochrane Reviews), 38% (95% confidence interval (CI) 23% to 54%) of systematic reviews added, omitted, upgraded or downgraded at least one outcome between the protocol and published systematic review. The association between statistical significance and discrepant outcome reporting between protocol and published systematic review was uncertain. The meta-analytic estimate suggested an increased risk of adding or upgrading (i.e. changing a secondary outcome to primary) when the outcome was statistically significant, although the 95% CI included no association and a decreased risk as plausible estimates (RR 1.43, 95% CI 0.71 to 2.85; two studies, n = 552 meta-analyses). Also, the meta-analytic estimate suggested an increased risk of downgrading (i.e. changing a primary outcome to secondary) when the outcome was statistically significant, although the 95% CI included no association and a decreased risk as plausible estimates (RR 1.26, 95% CI 0.60 to 2.62; two studies, n = 484 meta-analyses). None of the included studies had investigated whether the association between statistical significance and adding, upgrading or downgrading of outcomes was modified by the type of comparison, direction of effect or type of outcome; or whether there is an association between direction of the effect estimate and discrepant outcome reporting. Several secondary outcomes were reported in the included studies. Two studies found that reasons for discrepant outcome reporting were infrequently reported in published systematic reviews (6% in one study and 22% in the other). One study (including 62 Cochrane Reviews) found that 32% (95% CI 21% to 45%) of systematic reviews did not report all primary outcomes in the abstract. Another study (including 64 Cochrane and 118 non-Cochrane reviews) found that statistically significant primary outcomes were more likely to be completely reported in the systematic review abstract than non-significant primary outcomes (RR 2.66, 95% CI 1.81 to 3.90). None of the studies included systematic reviews published after 2009 when reporting standards for systematic reviews (Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) Statement, and Methodological Expectations of Cochrane Intervention Reviews (MECIR)) were disseminated, so the results might not be generalisable to more recent systematic reviews. AUTHORS' CONCLUSIONS: Discrepant outcome reporting between the protocol and published systematic review is fairly common, although the association between statistical significance and discrepant outcome reporting is uncertain. Complete reporting of outcomes in systematic review abstracts is associated with statistical significance of the results for those outcomes. Systematic review outcomes and analysis plans should be specified prior to seeing the results of included studies to minimise post-hoc decisions that may be based on the observed results. Modifications that occur once the review has commenced, along with their justification, should be clearly reported. Effect estimates and CIs should be reported for all systematic review outcomes regardless of the results. The lack of research on selective inclusion of results in systematic reviews needs to be addressed and studies that avoid the methodological weaknesses of existing research are also needed.\",\n \"corpus_id\": 21550830,\n \"score\": 0\n },\n {\n \"doc_id\": \"26034369\",\n \"title\": \"Risk factors for new onset diabetes mellitus after liver transplantation: A meta-analysis.\",\n \"abstract\": \"AIM: To determine the risk factors for new-onset diabetes mellitus (NODM) after liver transplantation by conducting a systematic review and meta-analysis. METHODS: We electronically searched the databases of MEDLINE, EMBASE and the Cochrane Library from January 1980 to December 2013 to identify relevant studies reporting risk factors for NODM after liver transplantation. Two authors independently assessed the trials for inclusion and extracted the data. Discrepancies were resolved in consultation with a third reviewer. All statistical analyses were performed with the RevMan5.0 software (The Cochrane Collaboration, Oxford, United Kingdom). Pooled odds ratios (OR) or weighted mean differences (WMD) with 95% confidence intervals (CIs) were calculated using either a fixed effects or a random effects model, based on the presence (I (2) < 50%) or absence (I (2) > 50%) of significant heterogeneity. RESULTS: Twenty studies with 4580 patients were included in the meta-analysis, all of which were retrospective. The meta-analysis identified the following significant risk factors: hepatitis C virus (HCV) infection (OR = 2.68; 95%CI: 1.92-3.72); a family history of diabetes (OR = 1.69, 95%CI: 1.09-2.63, P < 0.00001); male gender (OR = 1.53; 95%CI: 1.24-1.90; P < 0.0001); impaired fasting glucose (IFG; OR = 3.27; 95%CI: 1.84-5.81; P < 0.0001); a family history of diabetes (OR = 1.69; 95%CI: 1.09-2.63; P = 0.02); use of tacrolimus (OR = 1.34; 95%CI: 1.03-1.76; P = 0.03) and body mass index (BMI)(WMD = 1.19, 95%CI: 0.69-1.68, P < 0.00001). Other factors, such as hepatitis B virus infection and alcoholism, were not found to be associated with the incidence of NODM. CONCLUSION: The study showed that HCV infection, IFG, a family history of diabetes, male gender, tacrolimus and BMI are risk factors for NODM after liver transplantation.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"26111459\",\n \"title\": \"Associations of coeliac disease with coronary heart disease and cerebrovascular disease: A systematic review and meta-analysis.\",\n \"abstract\": \"AIMS: Clinical experience suggests that atherosclerotic disease is common in individuals with coeliac disease, but epidemiological studies have had contradicting findings. To summarise the currently available evidence, we systematically reviewed and analysed observational studies of the association of coeliac disease or dermatitis herpetiformis with coronary heart disease (CHD) or stroke. DATA SYNTHESIS: We searched for studies comparing CHD or stroke outcomes with individuals with and without coeliac disease or dermatitis herpetiformis. Three investigators independently searched electronic databases, identified relevant studies and extracted data. Study-specific results were combined in random-effects meta-analyses, and heterogeneity was quantified using the I(2) statistic and meta-regression. Twenty-one studies were included in our systematic review and 18 in the meta-analyses. For CHD, the pooled hazard ratio for incident disease was 1.05 (95% confidence interval (CI): 0.93, 1.19) and the overall standardised mortality ratio was 1.21 (0.99, 1.49). For stroke and brain haemorrhage, the corresponding estimates were 1.10 (95% CI: 1.00, 1.21) and 1.43 (0.97, 2.10), respectively. There was moderate to considerable heterogeneity among the study-specific estimates. In addition, many estimates were based on small numbers of outcomes and they had limitations in terms of adjustment for potential confounders. CONCLUSION: Our meta-analyses lend some support to an association between coeliac disease and CHD or cerebrovascular disease, but the evidence base was heterogeneous and had limitations. Our systematic review highlighted a need in this area for adequately powered prospective studies with appropriate adjustment for potentially confounding factors.\",\n \"corpus_id\": 24423111,\n \"score\": 0\n },\n {\n \"doc_id\": \"26334246\",\n \"title\": \"Association Between Periodontitis and Gestational Diabetes Mellitus: Systematic Review and Meta-Analysis.\",\n \"abstract\": \"BACKGROUND: To the best of the authors' knowledge, there is no systematic review of the potential association between periodontitis and gestational diabetes mellitus (GDM) in the current literature. The aim of the present systematic review and meta-analysis is to search for scientific evidence regarding the association between periodontitis and GDM. METHODS: The present study was conducted in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and registered (CRD2014010728) with PROSPERO (International prospective register for systematic reviews, University of York, York, UK). A search was conducted in three electronic databases without restrictions regarding language or date of publication. From 190 studies selected, 15 underwent full-text analysis. Eight studies were eligible (five cross-sectional and three case-control studies), and seven were entered in the meta-analysis. Meta-analysis was performed with tests for sensitivity and statistical heterogeneity. Summary effect measures were calculated by odds ratio (OR) and 95% confidence interval (CI). RESULTS: There was a significant association between periodontitis and GDM in the meta-analyses of four cross-sectional studies (OR 1.67, 95% CI 1.20 to 2.32) and two case-control studies (OR 2.66, 95% CI 1.52 to 4.65). However, sensitivity tests for case-control studies showed a lack of consistency in data; when including one case-control study, the significance was null (meta-analysis of three case-control studies: OR 1.69, 95% CI 0.68 to 4.21). CONCLUSIONS: There was substantial clinical, methodologic, and statistical heterogeneity among the studies. The scientific evidence cannot affirm a positive association between periodontitis and GDM. Future studies with different designs in distinct populations should be conducted to investigate this association.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"26959738\",\n \"title\": \"Cholesterol consumption and risk of endometrial cancer: a systematic review and dose-response meta-analysis of observational studies.\",\n \"abstract\": \"In vivo and in vitro studies have indicated the link of cholesterol consumption and endometrial cancer risk, however, previous observational studies have yielded inconsistent results. Additionally, a previous meta-analysis published in 2007 found limited evidence of aforementioned association. Therefore, we performed the dose-response meta-analysis to address this concern. Studies were identified using the PubMed, EMBASE and Web of Science databases from the database inception to the end of June 2015 as well as by examining the references of retrieved articles. Two authors independently performed the eligibility evaluation and data extraction. The summary risk estimates and 95% confidence intervals (CIs) were summarized by the random-effects models. One cohort and nine case-control studies were included in the dose-response analyses. Risk of endometrial cancer increased by 6% for 100 mg/day increment in the dietary consumption of cholesterol (Odds ratio (OR) = 1.06; 95% CI = 1.00-1.12), with significant heterogeneity (I2 = 64.2, P = 0.003). When stratified by study design, the result was significant in case-control studies (OR = 1.07; 95% CI = 1.01-1.13). Additionally, although the direction of the associations were consistent in the subgroup analyses stratified by study characteristics and adjustment for potential confounders, not all of them showed statistical significance. In summary, findings of the present dose-response meta-analysis partly support the positive association between dietary cholesterol consumption and risk of endometrial cancer. Since only one cohort study was included, more prospective studies and pooled analysis of observational studies are warranted to confirm our findings in the future.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"27058589\",\n \"title\": \"Transcription Factor 7-Like 2 (TCF7L2) rs7903146 Polymorphism as a Risk Factor for Gestational Diabetes Mellitus: A Meta-Analysis.\",\n \"abstract\": \"BACKGROUND: There are racial and ethnic differences in the prevalence of gestational diabetes mellitus (GDM). Prior meta-analyses included small samples and very limited non-Caucasian populations. Studies to determine the relationship between transcription factor 7 like-2 (TCF7L2) rs7903146 polymorphism and risk of GDM in Hispanics/Latinos are recently available. The present meta-analysis was to estimate the impact of allele variants of TCF7L2 rs7903146 polymorphism on GDM susceptibility in overall population and racial/ethnic subgroups. METHODS: Literature was searched in multiple databases including PubMed, Web of Science, EMBASE (Ovid SP), Airiti Library, Medline Complete, and ProQuest up to July 2015. Allelic frequency for TCF7L2 rs7903146 polymorphism in GDM and control subjects was extracted and statistical analysis was performed using Comprehensive Meta-Analysis (CMA) 2.0 statistical software. The association between TCF7L2 rs7903146 polymorphism and GDM risk was assessed by pooled odd ratios (ORs) using five gene models (dominant, recessive, homozygote, heterozygote, and allele). Stratified analysis based on race/ethnicity was also conducted. The between-study heterogeneity and contribution of each single study to the final result was tested by Cochran Q test and sensitivity analyses, respectively. Publication bias was evaluated using Egger's linear regression test. RESULTS: A total of 16 studies involving 4,853 cases and 10,631 controls were included in this meta-analysis. Significant association between the T-allele of rs7903146 and GDM risk was observed under all genetic models, dominant model (OR = 1.44, 95% CI = 1.19-1.74), recessive model (OR = 1.35, 95% CI = 1.08-1.70), heterozygous model (OR = 1.31, 95% CI = 1.12-1.53), homozygous model (OR = 1.67, 95% CI = 1.31-2.12), and allele model (OR = 1.31, 95% CI = 1.12-1.53). Stratified analysis by race/ethnicity showed a statistically significant association between rs7903146 polymorphism and susceptibility to GDM under homozygous genetic model (TT versus CC) among whites, Hispanics/Latinos and Asians. Sensitivity analysis showed that the overall findings were robust to potentially influential decisions of the 16 studies included. No significant evidence for publication bias was observed in this meta-analysis for overall studies and subgroup studies. CONCLUSIONS: This meta-analysis showed that the T allele of TCF7L2 rs7903146 polymorphism was associated with susceptibility of GDM in overall population in white, Hispanic/Latino and Asian sub-groups. Asians with homozygous TT allele of rs7903146 polymorphism have highest risk of GDM (OR = 2.08) followed by Hispanics/Latinos (OR = 1.80) and whites (OR = 1.51). The highest and lowest frequency of T allele of rs7903146 was found in Malaysia and South Korea, respectively. Future studies are needed to profile genetic risk for GDM among high risk Asian and Pacific Islander subgroups.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"27355649\",\n \"title\": \"Is Butter Back? A Systematic Review and Meta-Analysis of Butter Consumption and Risk of Cardiovascular Disease, Diabetes, and Total Mortality.\",\n \"abstract\": \"BACKGROUND: Dietary guidelines recommend avoiding foods high in saturated fat. Yet, emerging evidence suggests cardiometabolic benefits of dairy products and dairy fat. Evidence on the role of butter, with high saturated dairy fat content, for total mortality, cardiovascular disease, and type 2 diabetes remains unclear. We aimed to systematically review and meta-analyze the association of butter consumption with all-cause mortality, cardiovascular disease, and diabetes in general populations. METHODS AND FINDINGS: We searched 9 databases from inception to May 2015 without restriction on setting, or language, using keywords related to butter consumption and cardiometabolic outcomes. Prospective cohorts or randomized clinical trials providing estimates of effects of butter intake on mortality, cardiovascular disease including coronary heart disease and stroke, or diabetes in adult populations were included. One investigator screened titles and abstracts; and two reviewed full-text articles independently in duplicate, and extracted study and participant characteristics, exposure and outcome definitions and assessment methods, analysis methods, and adjusted effects and associated uncertainty, all independently in duplicate. Study quality was evaluated by a modified Newcastle-Ottawa score. Random and fixed effects meta-analysis pooled findings, with heterogeneity assessed using the I2 statistic and publication bias by Egger's test and visual inspection of funnel plots. We identified 9 publications including 15 country-specific cohorts, together reporting on 636,151 unique participants with 6.5 million person-years of follow-up and including 28,271 total deaths, 9,783 cases of incident cardiovascular disease, and 23,954 cases of incident diabetes. No RCTs were identified. Butter consumption was weakly associated with all-cause mortality (N = 9 country-specific cohorts; per 14g(1 tablespoon)/day: RR = 1.01, 95%CI = 1.00, 1.03, P = 0.045); was not significantly associated with any cardiovascular disease (N = 4; RR = 1.00, 95%CI = 0.98, 1.02; P = 0.704), coronary heart disease (N = 3; RR = 0.99, 95%CI = 0.96, 1.03; P = 0.537), or stroke (N = 3; RR = 1.01, 95%CI = 0.98, 1.03; P = 0.737), and was inversely associated with incidence of diabetes (N = 11; RR = 0.96, 95%CI = 0.93, 0.99; P = 0.021). We did not identify evidence for heterogeneity nor publication bias. CONCLUSIONS: This systematic review and meta-analysis suggests relatively small or neutral overall associations of butter with mortality, CVD, and diabetes. These findings do not support a need for major emphasis in dietary guidelines on either increasing or decreasing butter consumption, in comparison to other better established dietary priorities; while also highlighting the need for additional investigation of health and metabolic effects of butter and dairy fat.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"27749986\",\n \"title\": \"Insulin secretagogues for prevention or delay of type 2 diabetes mellitus and its associated complications in persons at increased risk for the development of type 2 diabetes mellitus.\",\n \"abstract\": \"BACKGROUND: The projected rise in the incidence of type 2 diabetes mellitus (T2DM) could develop into a substantial health problem worldwide. Whether insulin secretagogues (sulphonylureas and meglitinide analogues) are able to prevent or delay T2DM and its associated complications in people at risk for the development of T2DM is unknown. OBJECTIVES: To assess the effects of insulin secretagogues on the prevention or delay of T2DM and its associated complications in people with impaired glucose tolerance, impaired fasting blood glucose, moderately elevated glycosylated haemoglobin A1c (HbA1c) or any combination of these. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials, MEDLINE, PubMed, Embase, ClinicalTrials.gov, the World Health Organization International Clinical Trials Registry Platform, and the reference lists of systematic reviews, articles and health technology assessment reports. We asked investigators of the included trials for information about additional trials. The date of the last search of all databases was April 2016. SELECTION CRITERIA: We included randomised controlled trials (RCTs) with a duration of 12 weeks or more comparing insulin secretagogues with any pharmacological glucose-lowering intervention, behaviour-changing intervention, placebo or no intervention in people with impaired fasting glucose, impaired glucose tolerance, moderately elevated HbA1c or combinations of these. DATA COLLECTION AND ANALYSIS: Two review authors read all abstracts and full-text articles/records, assessed quality and extracted outcome data independently. One review author extracted data which were checked by a second review author. We resolved discrepancies by consensus or the involvement of a third review author. For meta-analyses we used a random-effects model with investigation of risk ratios (RRs) for dichotomous outcomes and mean differences (MDs) for continuous outcomes, using 95% confidence intervals (CIs) for effect estimates. We carried out trial sequential analyses (TSAs) for all outcomes that could be meta-analysed. We assessed the overall quality of the evidence by using the GRADE instrument. MAIN RESULTS: We included six RCTs with 10,018 participants; 4791 participants with data on allocation to intervention groups were randomised to a second- or third-generation sulphonylurea or a meglitinide analogue as monotherapy and 29 participants were randomised to a second-generation sulphonylurea plus metformin. Three trials investigated a second-generation sulphonylurea, two trials investigated a third-generation sulphonylurea and one trial a meglitinide analogue. A total of 4873 participants with data on allocation to control groups were randomised to a comparator group; 4820 participants were randomised to placebo, 23 to diet and exercise, and 30 participants to metformin monotherapy. One RCT of nateglinide contributed 95% of all participants. The duration of the intervention varied from six months to five years. We judged none of the included trials as at low risk of bias for all 'Risk of bias' domains. All-cause and cardiovascular mortality following sulphonylurea (glimepiride) treatment were rarely observed (very low-quality evidence). The RR for incidence of T2DM comparing glimepiride monotherapy with placebo was 0.75; 95% CI 0.54 to 1.04; P = 0.08; 2 trials; 307 participants; very low-quality evidence. One of the trials reporting on the incidence of T2DM did not define the diagnostic criteria used. The other trial diagnosed T2DM as two consecutive fasting blood glucose values ≥ 6.1 mmol/L. TSA showed that only 4.5% of the diversity-adjusted required information size was accrued so far. No trial reported data on serious adverse events, non-fatal myocardial infarction (MI), non-fatal stroke, congestive heart failure (HF), health-related quality of life or socioeconomic effects. One trial with a follow-up of five years compared a meglitinide analogue (nateglinide) with placebo. A total of 310/4645 (6.7%) participants allocated to nateglinide died compared with 312/4661 (6.7%) participants allocated to placebo (hazard ratio (HR) 1.00; 95% CI 0.85 to 1.17; P = 0.98; moderate-quality evidence). The two main criteria for diagnosing T2DM were a fasting plasma glucose level ≥ 7.0 mmol/L or a 2-hour post challenge glucose ≥ 11.1 mmol/L. T2DM developed in 1674/4645 (36.0%) participants in the nateglinide group and in 1580/4661 (33.9%) in the placebo group (HR 1.07; 95% CI 1.00 to 1.15; P = 0.05; moderate-quality evidence). One or more serious adverse event was reported in 2066/4602 (44.9%) participants allocated to nateglinide compared with 2089/4599 (45.6%) participants allocated to placebo. A total of 126/4645 (2.7%) participants allocated to nateglinide died because of cardiovascular disease compared with 118/4661 (2.5%) participants allocated to placebo (HR 1.07; 95% CI 0.83 to 1.38; P = 0.60; moderate-quality evidence). Comparing participants receiving nateglinide with those receiving placebo for the outcomes MI, non-fatal stroke and HF gave the following event rates: MI 116/4645 (2.5%) versus 122/4661 (2.6%), stroke 100/4645 (2.2%) versus 110/4661 (2.4%) and numbers hospitalised for HF 85/4645 (1.8%) versus 100/4661 (2.1%) - (HR 0.85; 95% CI 0.64 to 1.14; P = 0.27). The quality of the evidence was moderate for all these outcomes. Health-related quality of life or socioeconomic effects were not reported. AUTHORS' CONCLUSIONS: There is insufficient evidence to demonstrate whether insulin secretagogues compared mainly with placebo reduce the risk of developing T2DM and its associated complications in people at increased risk for the development of T2DM. Most trials did not investigate patient-important outcomes.\",\n \"corpus_id\": 29269326,\n \"score\": 0\n },\n {\n \"doc_id\": \"27825315\",\n \"title\": \"Periodontitis and gestational diabetes mellitus: a systematic review and meta-analysis of observational studies.\",\n \"abstract\": \"BACKGROUND: Gestational diabetes mellitus (GDM) is glucose intolerance with first onset during pregnancy and is associated with serious maternal and fetal complications. The etiology of GDM is not well understood, but systemic inflammation effects on insulin signaling and glucose metabolism is suspected. Periodontal disease is a chronic inflammatory condition that induces local and host immune responses and has been evaluated for a potential role in development of GDM. Results from studies evaluating the association between periodontitis and GDM are mixed. We performed a systematic review and meta-analysis to summarize available data regarding the association between periodontitis and GDM. METHODS: Twelve electronic databases were searched for observational studies of the association between periodontitis and GDM through March 2016. Eligible studies were assessed for quality and heterogeneity. Random effects models were used to estimate summary measures of association. RESULTS: We identified 44 articles from 115 potentially relevant reports of which 10 studies met our eligibility criteria. Clinical diagnostic criteria for periodontitis and GDM varied widely among studies, and moderate heterogeneity was observed. Random effects meta-analysis of all included studies with a total of 5724 participants including 624 cases, showed that periodontitis is associated with an increased risk of GDM by 66 %, (OR = 1.66, 95 % CI: 1.17 to 2.36; p < 0.05), I(2) = 50.5 %. Similar results were seen in sub-analysis restricted to data from methodologically high quality case-control studies including 1176 participants including 380 cases, (OR = 1.85, 95 % CI: 1.03 to 3.32); p < 0.05), I(2) = 68.4 %. Meta-analysis of studies that adjusted for potential confounders estimated more than 2-fold increased odds of GDM among women with periodontitis (aOR = 2.08, 95 % CI: 1.21 to 3.58, p = 0.009, I(2) = 36.9 %). CONCLUSION: Meta-analysis suggests that periodontitis is associated with a statistically significant increased risk for GDM compared to women without periodontitis. Robust prospective study designs and uniform definition for periodontitis and GDM definitions are urgently needed to substantiate these findings.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"29210061\",\n \"title\": \"The association with cardiovascular disease and type 2 diabetes in adults with atopic dermatitis: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: Recent studies examining the association between atopic dermatitis (AD) and cardiovascular disease (CVD) and type 2 diabetes have shown inconsistent results. OBJECTIVES: To carry out a systematic review and meta-analysis that examines the association with cardiovascular disease and type 2 diabetes in adults with AD. METHODS: We compared the risk of CVD and diabetes for adult patients with and without AD by searching the PubMed, Embase and Web of Science databases. Data extraction was carried out by two independent reviewers. We found a total of 2855 citations, of which 53 were considered relevant based on title and abstract. Overall, 16 publications were included in the qualitative analysis, of which 13 were also included in a quantitative meta-analysis of crude data. RESULTS: No association was observed between AD and unspecified but suspected type 2 diabetes [pooled odds ratio (OR) 1·11; 95% confidence interval (CI) 0·87-1·42], hypertension (pooled OR 1·16; 95% CI 0·98-1·37), stroke (pooled OR 1·15; 95% CI 0·95-1·39) or myocardial infarction (pooled OR 1·14; 95% CI 0·83-1·56), but a positive association was observed with angina pectoris (OR 1·73; 95% CI 1·27-2·37). Meta-analysis of adjusted data gave similar results. CONCLUSIONS: While adults with AD in some populations have an increased prevalence of cardiovascular risk factors, such as obesity and smoking, it is unlikely that AD represents an independent and clinically relevant risk factor for cardiometabolic disease.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"29415723\",\n \"title\": \"Characterizing undiagnosed chronic obstructive pulmonary disease: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: A significant proportion of patients with chronic obstructive pulmonary disease (COPD) remain undiagnosed. Characterizing these patients can increase our understanding of the 'hidden' burden of COPD and the effectiveness of case detection interventions. METHODS: We conducted a systematic review and meta-analysis to compare patient and disease factors between patients with undiagnosed persistent airflow limitation and those with diagnosed COPD. We searched MEDLINE and EMBASE for observational studies of adult patients meeting accepted spirometric definitions of COPD. We extracted and pooled summary data on the proportion or mean of each risk factor among diagnosed and undiagnosed patients (unadjusted analysis), and coefficients for the adjusted association between risk factors and diagnosis status (adjusted analysis). RESULTS: Two thousand eighty-three records were identified through database searching and 16 articles were used in the meta-analyses. Diagnosed patients were less likely to have mild (v. moderate to very severe) COPD (odds ratio [OR] 0.30, 95%CI 0.24-0.37, 6 studies) in unadjusted analysis. This association remained significant but its strength was attenuated in the adjusted analysis (OR 0.72, 95%CI 0.58-0.89, 2 studies). Diagnosed patients were more likely to report respiratory symptoms such as wheezing (OR 3.51, 95%CI 2.19-5.63, 3 studies) and phlegm (OR 2.16, 95% CI 1.38-3.38, 3 studies), had more severe dyspnea (mean difference in modified Medical Research Council scale 0.52, 95%CI 0.40-0.64, 3 studies), and slightly greater smoking history than undiagnosed patients. Patient age, sex, current smoking status, and the presence of coughing were not associated with a previous diagnosis. CONCLUSIONS: Undiagnosed patients had less severe airflow obstruction and fewer respiratory symptoms than diagnosed patients. The lower disease burden in undiagnosed patients may significantly delay the diagnosis of COPD.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"29802639\",\n \"title\": \"Associations of health literacy with diabetic foot outcomes: a systematic review and meta-analysis.\",\n \"abstract\": \"BACKGROUND: People with diabetes have low health literacy, but the role of the latter in diabetic foot disease is unclear. AIM: To determine, through a systematic review and meta-analysis, if health literacy is associated with diabetic foot disease, its risk factors, or foot care. METHODS: We searched PubMed, EMBASE, CINAHL, Web of Science, Scopus and Science Direct. All studies were screened and data extracted by two independent reviewers. Studies in English with valid and reliable measures of health literacy and published tests of association were included. Data were extracted on the associations between the outcomes and health literacy. Meta-analyses were performed using random effects models. RESULTS: Sixteen articles were included in the systematic review, with 11 in the meta-analysis. In people with inadequate health literacy, the odds of having diabetic foot disease were twice those in people with adequate health literacy, but this was not statistically significant [odds ratio 1.99 (95% CI 0.83, 4.78); two studies in 1278 participants]. There was no statistically significant difference in health literacy levels between people with and without peripheral neuropathy [standardized mean difference -0.14 (95% CI -0.47, 0.18); two studies in 399 participants]. There was no association between health literacy and foot care [correlation coefficient 0.01 (95% CI -0.07, 0.10); seven studies in 1033 participants]. CONCLUSIONS: There were insufficient data to exclude associations between health literacy and diabetic foot disease and its risk factors, but health literacy appears unlikely to have a role in foot care. The contribution of low health literacy to diabetic foot disease requires definitive assessment through robust longitudinal studies.\",\n \"corpus_id\": -1,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":53,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29704067\",\n \"title\": \"Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR.\",\n \"abstract\": \"The Sichuan takin (Budorcas taxicolor tibetana) is a rare and endangered ruminant distributed in the eastern Himalayas. However, little information is available regarding the intestinal microbiota of the takin. In this study, Illumina Miseq platform targeting the V4 region of the 16S rRNA was employed to characterize microbial community and diversity in the feces of wild (n = 6) and captive takins (n = 6). The takin exhibited an intestinal microbiota dominated by three phyla: Firmicutes (57.4%), Bacteroidetes (24.2%) and Proteobacteria (12.3%). At family/genus level, Ruminococcaceae, Bacteroidaceae, Acinetobacter, Clostridium, Lachnospiraceae, Rikenellaceae, Bacillus, Comamonas and Spirochaetaceae were dominant. Distinctive microbiotas between wild and captive takins were observed based on microbial community structure, captive takins having significantly higher community diversity. Quantitative real-time PCR were also utilized to monitor predominant bacteria in three Sichuan takin individuals housed in Chengdu Zoo over a half-year period, which showed that microbial communities of the three takins were relatively similar to each other and stable during our study period. Our results suggested that diet was a major driver for shaping microbial community composition.\",\n \"corpus_id\": 13699093\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"23922920","title":"The microbial community in the feces of the white rhinoceros (Ceratotherium simum) as determined by barcoded pyrosequencing analysis.","abstract":"As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.","corpus_id":17958222,"score":2},{"doc_id":"24352967","title":"Investigation of bacterial diversity in the feces of cattle fed different diets.","abstract":"The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.","corpus_id":14782674,"score":2},{"doc_id":"25604266","title":"First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing.","abstract":"The digestive systems of mammals harbor a complex gut microbiome, comprising bacteria and other microorganisms that confer metabolic and immunological benefits to the host. Ruminants that digest plant-based foods have a four-compartment stomach consisting of the rumen, reticulum, omasum, and abomasum. The microorganisms in the stomach are essential for providing the host with critical nutrients. However, the majority of these microorganisms are unknown species. The microbiome of the stomach is diverse, and the majority of these organisms cannot be cultured. Next-generation sequencing (NGS) combined with bioinformatic analysis tools have allowed the dissection of the composition of the microbiome in samples collected from a specific environment. In this study, for the first time, the bacterial composition in two compartments, the reticulum and the omasum, of bovine were analyzed using a metagenomic approach and compared to the bacterial composition of the rumen. These data will assist in understanding the biology of ruminants and benefit the agricultural industry. The diversity and composition of the bacterial community in samples collected from the rumen, reticulum, and omasum of bovines in the Changchun Region of Northeast China were analyzed by sequencing the V3 region of the 16S rRNA gene using a barcoded Illumina paired-end sequencing technique, and the primary composition of the microbiome in the rumen, reticulum, and omasum of the bovines was determined. These microbiomes contained 17 phyla and 107 genera in all three samples. Five phyla, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Lentisphaerae, were the most abundant taxonomic groups. Additionally, the different stomach compartments harbored different compositions of the microorganisms.","corpus_id":8848102,"score":2},{"doc_id":"25931374","title":"Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis.","abstract":"A balanced gastrointestinal microbial ecosystem is crucial for the health and growth of animals. In the gastrointestinal tract (GIT) of ruminants, cellulolytic bacteria aid in the digestion and absorption of nutrients. Rumen contents and feces in ruminants are often used to assess gastrointestinal microbial communities; however, these sites do not guarantee to represent the diversity of microbes found in the entire GIT. In this study, we investigated the microbiota along the GIT of five Chinese Mongolian sheep using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbiota were more abundant in the stomach and large intestine than in the small intestine. DGGE and real-time PCR revealed the predominance of Firmicutes and Bacteroidetes in the GIT. Meanwhile, Ruminococcus flavefaciens and Clostridium cluster IV showed significant difference in their abundance along the GIT (P < 0.05). Fibrobacter succinogenes was the most dominant species, followed by Ruminococcus albus and R. flavefaciens. The ileum harbored a larger number of cellulolytic bacteria, particularly-Clostridium cluster IV, than reported previously. In addition, comparisons between microbiota in the rumen and rectum indicated similar number of total bacteria, Firmicutes, Bacteroidetes, F. succinogenes, Butyrivibrio fibrisolvens, Clostridium cluster IV, and Clostridium cluster XIVa, whereas the number of R. albus and R. flavefaciens was higher in the rumen. This study investigated the composition and quantification of GIT microbial community in Chinese Mongolian sheep, and revealed for the first time the cellulolytic bacterial community in these sheep.","corpus_id":13118691,"score":2},{"doc_id":"27037116","title":"Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea).","abstract":"UNLABELLED: Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE: The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.","corpus_id":4778535,"score":2},{"doc_id":"27135948","title":"Exploring the Goat Rumen Microbiome from Seven Days to Two Years.","abstract":"Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.","corpus_id":2684889,"score":2},{"doc_id":"27258373","title":"Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.","abstract":"This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers.","corpus_id":15328491,"score":2},{"doc_id":"27383798","title":"Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis.","abstract":"OBJECTIVE: The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep's health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. METHODS: This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. RESULTS: The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). CONCLUSION: This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.","corpus_id":18866742,"score":2},{"doc_id":"28378284","title":"Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity.","abstract":"Chinese Mongolian sheep are an important ruminant raised for wool and meat production. However, little is known about the microbiota of the gastrointestinal tract (GIT) of Chinese Mongolian sheep. To increase our understanding of the microbial community composition in the GIT of Chinese Mongolian sheep, microbiota of five sheep is investigate for the first time using the Illumina MiSeq platform. High microbial diversity was obtained from the GIT, and the microbiota exhibited a higher biodiversity in the stomach and large intestine than in the small intestine. Firmicutes (44.62%), Bacteroidetes (38.49%), and Proteobacteria (4.11%) were the three most abundant phyla present in the GIT of the sheep. The present study also revealed the core genera of Prevotella, Bacteroides, Ruminococcus, Oscillospira, Treponema, and Desulfovibrio in the GIT. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States indicated that the metabolic pathway related to carbohydrate metabolism was the richest in the sheep GIT. In addition, a series of metabolic pathways related to plant secondary metabolism was most abundant in the stomach and large intestine than in the small intestine. Overall, the present study provides insight into the microbial community composition in GIT of the Chinese Mongolian sheep which is highly diverse and needs to be studied further to exploit the complex interactions with the host.","corpus_id":17233711,"score":2},{"doc_id":"28413853","title":"Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi).","abstract":"The gut microbiota of mammals is a complex ecosystem, which is essential for maintaining gut homeostasis and the host's health. The high throughput sequencing allowed us to gain a deeper insight into the bacterial structure and diversity. In order to improve the health status of the endangered golden takins, we first characterized the fecal microbiota of healthy golden takins using high throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions. Our results showed that, Firstly, the gut microbiota community comprised 21 phyla, 40 classes, 62 orders, 96 families, and 216 genera. Firmicutes (67.59%) was the most abundant phylum, followed by Bacteroidetes (23.57%) and Proteobacteria (2.37%). Secondly, the golden takin maintained higher richness in spring than in the winter while community diversity and evenness was not significantly different. Thirdly, four female golden takins demonstrated highly similar microbiota and the five golden takin males had relatively highly similar microbiota. All of our results might indicate that the fecal microbiota of golden takins were influenced by the season and the animal's sex. The findings provided theoretical basis regarding the gut microbiota of golden takins and may offer new insights to protect this endangered species.","corpus_id":23685543,"score":2},{"doc_id":"28431497","title":"Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers.","abstract":"BACKGROUND: Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community. RESULTS: Most of the sequences were assigned to Firmicutes (56.67%) and Bacteroidetes (35.90%), followed by Proteobacteria (1.87%), Verrucomicrobia (1.80%) and Tenericutes (1.37%). The predominant genera were 5-7 N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia (1.11%). No significant differences were observed in the numbers of Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17), and Tenericutes (p = 0.75) populations between the treatment groups. At the genus level, genera classified with high abundance (more than 0.1%) belonged primarily to Bacteroidetes and Firmicutes. Furthermore, no differences were observed at the genus level: 5-7 N15, CF231, Oscillospira, Paludibacter, and Akkermansia (p > 0.05 in all cases), except that rc4-4 was lower in the CON and SMFP groups than in the EML group (p = 0.02). There were no significant differences in the richness estimate and diversity indices between the groups (p > 0.16), and the different diets did not significantly influence most selected fecal bacterial species (p > 0.06), except for Ruminococcus albus, which was higher in the EML group (p < 0.01) and Streptococcus bovis, which was lower in the CON group (p < 0.01) relative to the other groups. CONCLUSIONS: In conclusion, diets supplemented with EML and SMFP have little influence on the fecal bacterial community composition in finishing steers.","corpus_id":2870031,"score":2},{"doc_id":"28601892","title":"Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage.","abstract":"The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected from six farms in Japan and China, and high-throughput Illumina sequencing of the V4 hypervariable region of 16S rRNA genes was performed. Lactobacillaceae were dominant in all silages, followed by Acetobacteraceae, Bacillaceae, and Enterobacteriaceae. In feces, the predominant families were Ruminococcaceae, Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Rikenellaceae, and Paraprevotellaceae. Therefore, Lactobacillaceae of corn silage appeared to be eliminated in the gastrointestinal tract. Although fecal microbiota composition was similar in most samples, relative abundances of several families, such as Ruminococcaceae, Christensenellaceae, Turicibacteraceae, and Succinivibrionaceae, varied between farms and countries. In addition to the geographical location, differences in feeding management between total mixed ration feeding and separate feeding appeared to be involved in the variations. Moreover, a cow-to-cow variation for concentrate-associated families was demonstrated at the same farm; two cows showed high abundance of Succinivibrionaceae and Prevotellaceae, whereas another had a high abundance of Porphyromonadaceae. There was a negative correlation between forage-associated Ruminococcaceae and concentrate-associated Succinivibrionaceae and Prevotellaceae in 18 feces samples. Succinivibrionaceae, Prevotellaceae, p-2534-18B5, and Spirochaetaceae were regarded as highly variable taxa in this study. These findings help to improve our understanding of variation and similarity of the fecal microbiota of dairy cows with regard to individuals, farms, and countries. Microbiota of naturally fermented corn silage had no influence on the fecal microbiota of dairy cows.","corpus_id":3852013,"score":2},{"doc_id":"28955315","title":"Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing.","abstract":"Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student's t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student's t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.","corpus_id":10335006,"score":2},{"doc_id":"29170893","title":"Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing.","abstract":"The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.","corpus_id":5977224,"score":2},{"doc_id":"22248568","title":"Does a temperate ungulate that breeds in summer exhibit rut-induced hypophagia? Analysis of time budgets of male takin (Budorcas taxicolor) in Sichuan, China.","abstract":"Mammals maximize fitness by optimizing time and energy allocation between reproduction and survival. Describing time budgets is a way to understand a species' constraints in energy allocation. We describe a time budget for male takin (Budorcas taxicolor) in Tangjiahe Nature Reserve, China, to better understand rut-induced hypophagia, which is frequently observed in temperate ungulates that breed in autumn or in winter. Observations generally occurred at two elevations (1200-1600m and 2600-3200m), using 20-min focal animal scan sampling from 2007 to 2009. Feeding behaviors accounted for the majority in takin's time budget (61.1%) during daylight hours, relative to the other observed behaviors, such as rest (14.1%), alert behavior (10.2%) and locomotion (6.8%). We found a negative correlation between feeding behavior and rutting behavior during the rutting season. A ratio of feeding time to resting time increased from pre-rut to rut, while resting behavior did not change significantly across seasons. These results suggest the \"energy saving\" hypothesis could explain reduced foraging in male takin during the rut, but aspects of the species biology suggest that hypotheses for rut-induced hypophagia developed for other temperate ungulates do not apply to takin. We suggest that the unusual summer rutting season of takin releases males from the energy constraints encountered by temperate ungulates that breed in the autumn and has other benefits for offspring survival. Further research should be conducted on ungulates that exhibit rut during the summer and tropical ungulates that might not experience limited food availability following the mating season to improve our understanding on rut-induced hypophagia.","corpus_id":35442875,"score":1},{"doc_id":"22626770","title":"Characterizing the behavior and reproductive biology of zoo-housed Sichuan takin (Budorcas taxicolor tibetana) using non-invasive techniques.","abstract":"The Sichuan takin (takin; Budorcas taxicolor tibetana) is distributed in the Gansu and Sichuan providences of southern China and along eastern Tibet. Because of their ecology, few data on takin reproductive biology exist, with the exception of its mating season in the Sichuan province, which occurs from July through August. Therefore, the objectives were to: 1) characterize reproductive hormones in zoo-housed male and female takin, including pregnancy in the female, using non-invasive fecal steroid hormonal monitoring; 2) characterize behaviors of zoo-housed takin, emphasizing reproductive behaviors and activity budget; and 3) assess the influence of season on births in North America and reproductive hormonal and behavioral activity. Fecal samples were collected 3 to 5 times per week from two adult males and three adult females. Extracted hormones were analyzed using an enzyme immunoassay for progestagen and androgen concentrations. Behavioral observations were collected for 2 yrs using an ethogram. In this study, season affected reproduction, specifically birth occurrences, reproductive cyclicity in females and androgen production in males. The duration of the estrous cycle was approximately 35 d and cycles occurred June through December. Androgen concentrations peaked in May through August. Season did not influence behavior; however, age and sex may affect some behaviors, including activity level, foraging and drinking, social affiliative behavior, and visibility from the visitor's viewpoint. In conclusion, fecal hormonal and behavioral analyses can provide information for management and conservation of this herd species.","corpus_id":2343413,"score":1},{"doc_id":"23217205","title":"The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows.","abstract":"BACKGROUND: Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with fatty acids during SARA. Four cannulated primiparous (60 to 90 day in milk) Holstein dairy cows were assigned to two diets in a 2 × 2 crossover experimental design. The diets contained (on a dry matter basis): 40% (control diet, COD) and 70% (SARA induction diet, SAID) concentrate feeds. Samples of ruminal fluid and feces were collected on day 12, 15, 17 and 21 of the treatment period, and the pH was measured in the ruminal and fecal samples; the fecal microbiota was determined by pyrosequencing analysis of the V1-V3 region of amplified 16S ribosomal RNA (16S rRNA). RESULTS: SAID decreased ruminal and fecal pH and increased the propionate, butyrate and total volatile fatty acid (TVFA) concentration in feces when compared with the COD. A barcoded DNA pyrosequencing method was used to generate 2116 16S operational taxonomic units (OTUs). A total of 11 phyla were observed, distributed amongst all cattle on both diets; however, only 5 phyla were observed in all animals regardless of dietary treatment, and considerable animal to animal variation was revealed. The average abundance and its range of the 5 phyla were as follows: Firmicutes (63.7%, 29.1-84.1%), Proteobacteria (18.3%, 3.4-46.9%), Actinobacteria (6.8%, 0.4-39.9%), Bacteroidetes (7.6%, 2.2-17.7%) and Tenericutes (1.6%, 0.3-3%). Feeding the SAID resulted in significant shifts in the structure of the fecal microbial community when compared with the traditional COD. Among the 2116 OTUs detected in the present study, 88 OTUs were affected significantly by diet; and the proportion of these OTUs was 20.6% and 17.4% among the total number of sequences, respectively. Among the OTUs affected, the predominant species, including OTU2140 (G: Turicibacter), OTU1695 (G: Stenotrophomonas) and OTU8143 (F: Lachnospiraceae), were increased, while the abundance of OTU1266 (S: Solibacillus silvestris) and OTU2022 (G: Lysinibacillus) was reduced in the SAID group compared with the COD. Further, our results indicated that the fecal volatile fatty acid (VFA) concentrations were significantly related to presence of some certain species of Bacteroidetes and Firmicutes in the feces. CONCLUSIONS: This is, to our knowledge, the first study that has used barcoded DNA pyrosequencing to survey the fecal microbiome of dairy cattle during SARA. Our results suggest that particular bacteria and their metabolites in the feces appear to contribute to differences in host health between those given SAID and traditional COD feeding. A better understanding of these microbial populations will allow for improved nutrient management and increased animal growth performance.","corpus_id":10734966,"score":1},{"doc_id":"23333862","title":"High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria.","abstract":"Fecal microbiota transplantation (FMT) is becoming a more widely used technology for treatment of recurrent Clostridum difficile infection (CDI). While previous treatments used fresh fecal slurries as a source of microbiota for FMT, we recently reported the successful use of standardized, partially purified and frozen fecal microbiota to treat CDI. Here we report that high-throughput 16S rRNA gene sequencing showed stable engraftment of gut microbiota following FMT using frozen fecal bacteria from a healthy donor. Similar bacterial taxa were found in post-transplantation samples obtained from the recipients and donor samples, but the relative abundance varied considerably between patients and time points. Post FMT samples from patients showed an increase in the abundance of Firmicutes and Bacteroidetes, representing 75-80% of the total sequence reads. Proteobacteria and Actinobacteria were less abundant (< 5%) than that found in patients prior to FMT. Post FMT samples from two patients were very similar to donor samples, with the Bacteroidetes phylum represented by a great abundance of members of the families Bacteroidaceae, Rikenellaceae and Porphyromonadaceae, and were largely comprised of Bacteroides, Alistipes and Parabacteroides genera. Members of the phylum Firmicutes were represented by Ruminococcaceae, Lachnospiraceae, Verrucomicrobiaceae and unclassified Clostridiales and members of the Firmicutes. One patient subsequently received antibiotics for an unrelated infection, resulting in an increase in the number of intestinal Proteobacteria, primarily Enterobacteriaceae. Our results demonstrate that frozen fecal microbiota from a healthy donor can be used to effectively treat recurrent CDI resulting in restoration of the structure of gut microbiota and clearing of Clostridum difficile.","corpus_id":13519972,"score":1},{"doc_id":"23354293","title":"Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides.","abstract":"One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.","corpus_id":17678112,"score":1},{"doc_id":"24173964","title":"Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia.","abstract":"PURPOSE: The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined. METHODS: This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire. RESULTS: Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p < 0.05 and p < 0.01) and decrease in Bifidobacterium with age (p < 0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4 % of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet. CONCLUSIONS: Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.","corpus_id":22998385,"score":1},{"doc_id":"24212576","title":"Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides.","abstract":"One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented: Firmicutes (51.9%), Bacteroidetes (30.9%), Proteobacteria (11.1%), Actinobacteria (3.5%), Synergistetes (1.5%), and Fusobacteria (1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, B. ovatus, and B. xylanisolvens and members of the Porphyromonadaceae family. Many of the Firmicutes and Bacteroidetes isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.","corpus_id":206732566,"score":1},{"doc_id":"24558975","title":"An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.","abstract":"BACKGROUND: To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing platforms. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality. RESULTS: Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We introduced a 0 to 7 bp \"heterogeneity spacer\" to the index sequence that allows an equal proportion of samples to be sequenced out of phase. CONCLUSIONS: Our approach yields high quality sequence data from 16S rRNA gene amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a flexible and cost-effective sequencing option.","corpus_id":11231363,"score":1},{"doc_id":"24730432","title":"Severe laminitis in multiple zoo species.","abstract":"A 10-year record review from a zoological institution in the western USA identified four cases of severe laminitis resulting in rotation and protrusion of the third phalanx through the sole. Laminitis is reported in a Masai giraffe (Giraffa camelopardalis tippelskirchi), a Sichuan takin (Budorcas taxicolor tibetana), a greater Malayan chevrotain (Tragulus napu) and a giant eland (Taurotragus derbianus). This is the first report of severe laminitis with pedal bone rotation and protrusion in multiple species of non-domestic hoofstock, and the first report of this disease in three of these species (takin, chevrotain, and giant eland).","corpus_id":205499321,"score":1},{"doc_id":"25928424","title":"Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole.","abstract":"Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.","corpus_id":2369097,"score":1},{"doc_id":"26024129","title":"Phylogenetic analysis of the endangered takin in the confluent zone of the Qinling and Minshan Mountains using mtDNA control region.","abstract":"The takin (Budorcas taxicolor) is an Endangered ungulate. We analyzed the variation within mtDNA control region sequences of takin populations in the Qinling Mountains, the Minshan Mountains and the confluence of these two mountain ranges. We did not find any shared haplotypes among the populations. We observed apparent variation in the control region length among the three populations, and independent population expansions in the late of Pleistocene, which suggests these populations may have independent evolutionary histories. We found only one haplotype, and the lowest measures of genetic diversity (h = 0; π = 0) in the population from the confluent zone, which suggests populations in the confluent zone may have grown from small founder populations and gene flow with other populations has ceased. Based on their phylogenetic relationships, we concluded that the takin population in the confluent zone was in the same clade as the Tangjiahe population, which suggests that these takin populations are Sichuan takin (Budorcas taxicolor tibetana).","corpus_id":6896537,"score":1},{"doc_id":"26084274","title":"Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis.","abstract":"BACKGROUND: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon sequencing for environmental microbial community analysis is challenging due to the problem of low base diversity. RESULTS: A new phasing amplicon sequencing approach (PAS) was developed by shifting sequencing phases among different community samples from both directions via adding various numbers of bases (0-7) as spacers to both forward and reverse primers. Our results first indicated that the PAS method substantially ameliorated the problem of unbalanced base composition. Second, the PAS method substantially improved the sequence read base quality (an average of 10 % higher of bases above Q30). Third, the PAS method effectively increased raw sequence throughput (~15 % more raw reads). In addition, the PAS method significantly increased effective reads (9-47 %) and the effective read sequence length (16-96 more bases) after quality trim at Q30 with window 5. In addition, the PAS method reduced half of the sequencing errors (0.54-1.1 % less). Finally, two-step PCR amplification of the PAS method effectively ameliorated the amplification biases introduced by the long barcoded PCR primers. CONCLUSION: The developed strategy is robust for 16S rRNA gene amplicon sequencing. In addition, a similar strategy could also be used for sequencing other genes important to ecosystem functional processes.","corpus_id":516467,"score":1},{"doc_id":"26426811","title":"An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms.","abstract":"The primary 16S rRNA sequencing protocol for microbial community analysis using Illumina platforms includes a single-indexing approach that allows pooling of hundreds of samples in each sequencing run. The protocol targets the V4 hypervariable region (HVR) of 16S rRNA using 150 bp paired-end (PE) sequencing. However, the latest improvement in Illumina chemistry has increased the read length up to 600 bp using 300 bp PE sequencing. To take advantage of the longer read length, a dual-indexing approach was previously developed for targeting different HVRs. However, due to simple working protocols, the single-index 150 bp PE approach still continues to be attractive to many researchers. Here, we described an extended single-indexing protocol for 300 bp PE illumina sequencing that targets the V3-V4 HVRs of 16S rRNA. The new primer set led to increased read length and alignment resolution, as well as increased richness and diversity of resulting microbial profile compared to that obtained from150 bp PE protocol for V4 sequencing. The β-diversity profile also differed qualitatively and quantitatively between the two approaches. Both primer sets had high coverage rates and specificity to detect dominant phyla; however, their coverage rate with regards to the rare biosphere varied. Our data further confirms that the choice of primer is the most deterministic factor in sequencing coverage and specificity.","corpus_id":7965706,"score":1},{"doc_id":"26728019","title":"Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene.","abstract":"Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host's health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63-38.97 %), Firmicutes (20.97-44.01 %), Proteobacteria (9.33-17.60 %), Fusobacteria (9.11-17.90 %), and Actinobacteria (1.22-2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.","corpus_id":18524507,"score":1},{"doc_id":"27299740","title":"Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity.","abstract":"Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities.","corpus_id":1891149,"score":1},{"doc_id":"27305787","title":"[Biases on community structure during DNA extraction of shrimp intestinal microbiota revealed by high-throughput sequencing].","abstract":"OBJECTIVES: High-throughput sequencing technology is increasingly applied in intestinal microbiota of aquatic animals including shrimp. However, there is a lack of standard method or kit for DNA isolation from shrimp intestinal microbiota, and little is known about the effectiveness and biases regarding DNA extraction based on high-throughput sequencing. The aim of this study was to study the biases of different DNA extraction kits on community structure of shrimp intestinal microbiota through high-throughput sequencing, and to better understand the structure and composition of bacterial flora associated with healthy Litopenaeus vannamei. METHODS: We extracted the total DNA of intestinal microbiota from L. vannamei with three commercial kits designed for DNA extraction from bacteria, stool and tissue (Omega, USA). DNA quality was evaluated based on the absorbance ratios of 260/280 nm by NanoDrop, while DNA concentration was quantified using PicoGreen. Then Illumina MiSeq high-throughput sequencing was used to examine the intestinal bacterial communities following PCR amplification of 16S rDNA V4 region. RESULTS: The yield and purity of the DNA from the Bacterial Kit (SIB) were superior to those from the Stool Kit (SIS), whereas the DNA from Tissue Kit (SIT) presented too small amount to be amplified efficiently. The average sequence reads obtained from SIB and SIS samples were 52151 ± 5085 and 55296 ± 5147 respectively. After resampling at the same depth of 46800 reads, the operational taxonomic unit (OTU) number and Shannon diversity index of SIS samples were significantly higher than those of SIB samples. By contrast, the reproducibility of OTU among SIB replicates was higher than that among SIS replicates. The dominant phyla of SIS and SIB samples were identical, including Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, and Cyanobacteria. However, the relative abundances of almost all the dominant groups at various taxonomic levels differed greatly between these two samples. CONCLUSION: Significant biases on community structure of shrimp intestinal microbiota were detected which originated from DNA extraction. And the core microbiota of the healthy L. vannamei in this study was mainly composed of genera Photobacterium, Lactococcus, Aliivibrio, Vibrio, as well as three other unclassified groups.","corpus_id":23740199,"score":1},{"doc_id":"27365218","title":"Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides).","abstract":"Swan goose (Anser cygnoides) is currently one of the most popular economic wildfowl for rare birds breeding industries in several provinces of China. However, the farmed Swan geese, reared in artificial environment and fed on both natural and artificial diets, display a reduced reproductive rate compared to wild species. Little is known about the gut microbiota of this species, which could play a role in nutrient and energy metabolism, immune homeostasis and reproduction. The present comparative study was designed to provide a first characterization of gut microbial communities related to both wild and farmed Swan geese by 16 S rRNA sequences using the Illumina HiSeq platform. The results showed that dominant microbial components in both groups consisted of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The abundances of these four phyla were not statistically different between the groups. At the genus level, significantly decreased abundance of Clostridium and increased abundance of SMB53, Enterococcus and Paenibacillus were observed in farmed group compared to wild group. The marked differences of genus level group-specific microbes create a baseline for future Swan goose microbiology research and make a valuable contribution to forming relationships between gut microbiota and domestic bird reproduction.","corpus_id":206136201,"score":1},{"doc_id":"27400733","title":"High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite.","abstract":"BACKGROUND: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform. RESULTS: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples. CONCLUSIONS: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.","corpus_id":10285369,"score":1},{"doc_id":"27514729","title":"Environment shapes the fecal microbiome of invasive carp species.","abstract":"BACKGROUND: Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. RESULTS: We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. CONCLUSIONS: The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.","corpus_id":17903306,"score":1},{"doc_id":"27568186","title":"Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing.","abstract":"Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.","corpus_id":32166092,"score":1},{"doc_id":"27603009","title":"Characterization of Intestinal Microbiomes of Hirschsprung's Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing.","abstract":"Hirschsprung-associated enterocolitis (HAEC) is a life-threatening complication of Hirschsprung's disease (HD). Although the pathological mechanisms are still unclear, studies have shown that HAEC has a close relationship with the disturbance of intestinal microbiota. This study aimed to investigate the characteristics of the intestinal microbiome of HD patients with or without enterocolitis. During routine or emergency surgery, we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis who were in a HAEC remission (HAEC-R) phase. Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs) were defined by 97% sequence similarity. Principal coordinate analysis (PCoA) of weighted UniFrac distances was performed to evaluate the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by the prevalence of Bacteroidetes) and HAEC patients (characterized by the prevalence of Proteobacteria), while the microbiota of the HAEC-R patients was more similar to that of the HAEC patients. We also observed that the specimens from different intestinal sites of each HD patient differed significantly, while the specimens from different intestinal sites of each HAEC and HAEC-R patient were more similar. In conclusion, the microbiome pattern of the HAEC-R patients was more similar to that of the HAEC patients than to that of the HD patients. The HD patients had a relatively distinct, more stable community than the HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patient's uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following symptom resolution and can be implicated in the symptom recurrence.","corpus_id":14626589,"score":1},{"doc_id":"27692708","title":"Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants.","abstract":"Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.","corpus_id":21410465,"score":1},{"doc_id":"27734418","title":"Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene.","abstract":"The composition of mammalian intestinal microflora is related to many environmental and geographical factors, and it plays an important role in many aspects such as growth and development. Sequencing data of the bacterial 16S rRNA gene from sable (Martes zibellina) samples using next-generation sequencing technology are limited. In our research, 84,116 reads obtained by high-throughput sequencing were analyzed to characterize and compare the intestinal microflora of wild sables and housed sables. Firmicutes (31.1 %), Bacteroidetes (26.0 %) and Proteobacteria (21.5 %) were the three most abundant phyla present in wild sables, whereas Firmicutes (55.6 %), Proteobacteria (29.1 %) and Actinobacteria (6.0 %) were the three predominant phyla present in housed sables. At the phylum level, wild sables exhibited a significant difference in the relative abundances of Bacteroidetes and Actinobacteria, whereas housed sables only exhibited significant changes in TM7 at the phylum level, and Clostridia, at the class level. The predominance of Bacteroidetes in wild sables warrants further research. These results indicate that a sudden change in diet may be a key factor that influences fecal bacterial diversity in mammals.","corpus_id":10259387,"score":1},{"doc_id":"27744590","title":"Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.","abstract":"Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH4(+)-N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.","corpus_id":207280588,"score":1},{"doc_id":"27770389","title":"Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics.","abstract":"Antibiotics have been widely used for the prevention and the treatment of diseases to humans and animals, and they have fed additives for agricultural animals to promote growth. However, there is a growing concern over the practice due to its side effects on intestinal microbial communities which plays a vital role in animals' health. To investigate the effect of antibiotics on the bacterial population of the caecum in rex rabbits, 80 rex rabbits were randomly divided into four groups: control group (B, basal diet), chlortetracycline group (C, 50 mg/kg), colistin sulfate group (S, 20 mg/kg) and zinc bacitracin group (Z, 40 mg/kg). Caecum microbial communities of rex rabbits from the four groups were analyzed through Illumina Miseq platform after being fed 28 days. The results showed that most obtained sequences belongs to Firmicutes followed by Bacteroidetes, and the ratio of Bacteroidetes/Firmicutes in C group (42.31 %) was higher than that in Z group (21.84 %). Zinc bacitracin supplementation caused a significant decreased of the Proteobacteria phylum and Lactobacillus spp. ( P < 0.05), while the Lactobacillus spp. significantly increased in S group (P < 0.05). In addition, Ruminococcus spp., especially Ruminococcus albus were the predominant bacterial species found in both S and Z groups. The proportion of Coprococcus spp. significantly increased in Z group (P < 0.05). These findings suggested that the antibiotics used may cause significant changes in the caecum microbiota of rex rabbits, and we also found C group had a similarity caecum bacteria structure with B group which was probably due to the high levels of chlortetracycline resistance.","corpus_id":14565233,"score":1},{"doc_id":"27837973","title":"Effects of the dose and viability of Saccharomyces cerevisiae. 1. Diversity of ruminal microbes as analyzed by Illumina MiSeq sequencing and quantitative PCR.","abstract":"This study was conducted to examine effects of the dose and viability of supplemental Saccharomyces cerevisiae on the ruminal fermentation and bacteria population and the performance of lactating dairy cows. Four ruminally cannulated lactating cows averaging 284±18d in milk were assigned to 4 treatments arranged in a 4×4 Latin square design with four 21-d periods. Cows were fed a total mixed ration containing 41.7% corn silage, 12.1% brewer's grains, and 46.2% concentrate on a dry matter basis. The diet was supplemented with no yeast (control) or with a low dose of live yeast (5.7×10(7) cfu/cow per day; LLY), a high dose of live yeast (6.0×10(8) cfu/cow per day; HLY), or a high dose of killed yeast (6.0×10(8) cfu/cow per day; HDY). Microbial diversity was examined by high-throughput Illumina MiSeq sequencing (Illumina Inc., San Diego, CA) of the V4 region of the 16S rRNA gene. The relative abundance of select ruminal bacteria was also quantified by quantitative PCR (qPCR). Adding LLY to the diet increased the relative abundance of some ruminal cellulolytic bacteria (Ruminococcus and Fibrobacter succinogenes) and amylolytic bacteria (Ruminobacter, Bifidobacterium, and Selenomonas ruminantium). Adding live instead of killed yeast increased the relative abundance of Ruminococcus and F. succinogenes; adding HDY increased the relative abundance of Ruminobacter, Bifidobacterium, Streptococcus bovis, and Selenomonas ruminantium. The most dominant (≥1% of total sequences) bacteria that responded to LLY addition whose functions are among the least understood in relation to the mode of action of yeast include Paraprevotellaceae, CF231, Treponema, and Lachnospiraceae. Future studies should aim to speciate, culture, and examine the function of these bacteria to better understand their roles in the mode of action of yeast. A relatively precise relationship was detected between the relative abundance of F. succinogenes (R(2)=0.67) from qPCR and MiSeq sequencing, but weak relationships were detected for Megasphaera elsdenii, Ruminococcus flavefaciens, and S. ruminantium (R(2)≤0.19).","corpus_id":21547300,"score":1},{"doc_id":"27992473","title":"High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation.","abstract":"Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.","corpus_id":15005009,"score":1},{"doc_id":"28028611","title":"Comparative analysis of the gut microbiota of black bears in China using high-throughput sequencing.","abstract":"The Asiatic black bear (Ursus thibetanus) is a protected species from eastern Asia. In China, the Asiatic black bear occurs in 17 provinces from northeast to southwest regions. To date, information on microbial diversity in the gut of the Asiatic black bears from different populations remains limited. To determine the species composition and community structure of the gut microbiota in the Asiatic black bear, we characterized 36 fecal samples from Sichuan, Yunnan, and Heilongjiang provinces, China, by pyrosequencing the 16S V3-V4 hypervariable regions using the Illumina Miseq platform. Results showed that Firmicutes and Proteobacteria were the predominant phyla in the samples, which were largely comprised Escherichia-Shigella, Peptostreptococcaceae_incertae_sedis, Turicibacter, Streptococcus, and Clostridium. By analyzing the community structure from these 36 samples, we found that there were significant differences in the species diversity and richness between Sichuan, Yunnan, and Heilongjiang populations. In conclusion, our results reveal the species composition and structure of the gut microbiota in captive black bears in China, and suggest that biogeography could affect the black bear' gut microbiota.","corpus_id":26334752,"score":1},{"doc_id":"28175972","title":"Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge.","abstract":"The effects of a grain-based subacute ruminal acidosis (SARA) challenge on bacteria in the rumen and feces of lactating dairy cows were determined. Six lactating, rumen-cannulated Danish Holstein cows were used in a cross-over study with two periods. Periods included two cows on a control diet and two cows on a SARA challenge. The control diet was a total mixed ration containing 45.5% dry matter (DM), 43.8% DM neutral detergent fiber, and 19.6% DM starch. The SARA challenge was conducted by gradually substituting the control diet with pellets containing 50% wheat and 50% barley over 3 days to reach a diet containing 55.6% DM, 31.3% DM neutral detergent fiber, and 31.8% DM starch, which was fed for four more days. Rumen fluid samples were collected at day 7 and 10 of experimental periods. Feces samples were collected on days 8 and 10 of these periods. Extracted DNA from the rumen and feces samples was analyzed to assess their bacterial communities using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. The induction of SARA reduced the richness, diversity, and stability of bacterial communities and resulted in distinctly different microbiota in the rumen and feces. Bacteroidetes and Firmicutes were the most abundant phyla and, combined, they represented 76.9 and 94.4% of the bacterial community in the rumen fluid and the feces, respectively. Only the relative abundance of Firmicutes in the rumen was increased by the SARA challenge. In rumen fluid and feces, the abundances of nine out of the 90 and 25 out of the 89 taxa, respectively, were affected by the challenge. Hence, SARA challenge altered the composition of the bacterial community at the lower taxonomical level in the feces and therefore also likely in the hindgut, as well as in the rumen. However, only reductions in the bacterial richness and diversity in the rumen fluid and feces were in agreement with those of other studies and had a biological basis. Although the composition of the bacterial community of the feces was affected by the SARA challenge, bacterial taxa in the feces that can be used for accurate and non-invasive diagnosis of SARA could not be identified.","corpus_id":7201001,"score":1},{"doc_id":"28339527","title":"Microbial community mapping in intestinal tract of broiler chicken.","abstract":"Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.","corpus_id":42174787,"score":1},{"doc_id":"28379996","title":"The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China.","abstract":"Soil bacteria are important drivers of biogeochemical cycles and participate in many nutrient transformations in the soil. Meanwhile, bacterial diversity and community composition are related to soil physic-chemical properties and vegetation factors. However, how the soil and vegetation factors affect the diversity and community composition of bacteria is poorly understood, especially for bacteria associated with evergreen and deciduous trees in subtropical forest ecosystems. In the present paper, the microbial communities of rhizospheric soils associated with different types of trees were analyzed by Illumina MiSeq sequencing the V3-V4 region of the 16S rRNA gene. A total of 121,219 effective 16S rRNA gene sequences were obtained, which were classified into 29 bacterial phyla and 2 archaeal phyla. The dominant phyla across all samples (>5% of good-quality sequences in each sample) were Proteobacteria, Acidobacteria, Firmicutes and Bacteroidetes. The bacterial community composition and diversity were largely affected by both soil pH and tree species. The soil pH was the key factor influencing bacterial diversity, with lower pH associated with less diverse communities. Meanwhile, the contents of NO3- were higher in evergreen tree soils than those associated with deciduous trees, while less NH4+ than those associated with deciduous trees, leading to a lower pH and indirectly influencing the diversity and composition of the bacteria. The co-occurrence patterns were assessed by network analysis. A total of 415 pairs of significant and robust correlations (co-occurrence and negative) were identified from 89 genera. Sixteen hubs of co-occurrence patterns, mainly under the phyla Acidobacteria, Proteobacteria, Firmicutes and Bacteroidetes, may play important roles in sustaining the stability of the rhizospheric microbial communities. In general, our results suggested that local environmental conditions and soil pH were important in shaping the bacterial community of the Taihu Lake zone in east China.","corpus_id":18412432,"score":1},{"doc_id":"28453559","title":"Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.","abstract":"Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.","corpus_id":32030973,"score":1},{"doc_id":"28505482","title":"Conservation efforts of captive golden takin (Budorcas taxicolor bedfordi) are potentially compromised by the elevated chemical elements exposure.","abstract":"Chemical elements exposure of endangered golden takins (Budorcas taxicolor bedfordi) living in the Qinling Mountains and in a captive breeding center was assessed by analyzing fecal samples. Concentrations of As, Co, Cr, Cu, Ni and Se were significantly higher in the feces of captive golden takins than the wild. There was no significant difference in the fecal concentrations of Cd, Mn, Hg, Pb or Zn for wild and captive animals. The element concentration of fecal samples collected from captive animals varied seasonally, with concentrations being lowest in spring and highest in winter and/or autumn. The food provided to captive animals varied both in the composition and the concentration of element present. Consumptions of feedstuff and additional foods such as D. sanguinalis and A. mangostanus for the captive golden takins were identified as the possible sources of chemical element exposure. The estimations of dietary intake of most elements by captive takins were below the oral reference dose, except for As and Pb, indicating that As and Pb were the key components which contributed to the potential non-carcinogenic risk for captive golden takins. In conclusion, captive golden takins were exposed to higher concentrations of chemical elements compared with the wild, which were likely due to their dietary difference. Conservation efforts of captive golden takin are potentially compromised by the elevated chemical element exposure and effort should focus on providing uncontaminated food for captive animals.","corpus_id":1918079,"score":1},{"doc_id":"28642971","title":"High Diversity of Bacterial Communities in Developmental Stages of Bactrocera carambolae (Insecta: Tephritidae) Revealed by Illumina MiSeq Sequencing of 16S rRNA Gene.","abstract":"Bactrocera carambolae is a highly polyphagous fruit pest of agricultural importance. This study reports the bacterial communities associated with the developmental stages of B. carambolae. The microbiota of the developmental stages were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. At 97% similarity, there were 19 bacterial phyla and unassigned bacteria, comprising 39 classes, 86 orders, 159 families and 311 genera. The bacterial composition varied among the specimens of developmental stage and across developmental stages as well as exuviae. Four phyla of bacteria (with relative abundance of ≥1% in at least one specimen)-Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria-were recovered from the larva, pupa, adult stages and exuviae. Proteobacteria was the predominant phylum in all the developmental stages as well as the exuviae. Enterobacteriaceae (Proteobacteria) was the predominant family in the adult flies while the family [Weeksellaceae] (Bacteroidetes) was predominant in the larval and pupal stages. Among the genera occurring in more than one developmental stage of B. carambolae, Erwinia was more abundant in the larval stage, Halomonas more abundant in adult female, Stenotrophomonas more abundant in adult male, and Chryseobacterium more abundant in the larval and pupal stages. The results indicate transmission of bacteria OTUs from immatures to the newly emerged adults, and from exuviae to the environment.","corpus_id":4526500,"score":1},{"doc_id":"28697583","title":"The gut microbiota in larvae of the housefly Musca domestica and their horizontal transfer through feeding.","abstract":"House fly larvae provide a prolific and sustainable source of proteins used in poultry and fish feed. Wheat bran is a superior diet for house fly larvae and has been widely investigated to exploit its potential in the food and feed area. Using Illumina MiSeq 16S rDNA sequencing, this study investigated the gut microbiota of house fly larvae feeding on wheat bran and the bacterial community in the wheat bran. The bacterial communities in the house fly larvae were dominated by the phyla Proteobacteria and Firmicutes. Enterobacteriaceae and Providencia were the predominant bacteria at the family and genus levels, respectively. Some bacteria in the phyla Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes may be transferred from the gut of house flies to the wheat bran during feeding and may be involved in degrading and utilizing polysaccharides in the cell wall of wheat bran. The significance of the gut microbiota of house fly larvae, their transferring and roles in degradation of wheat bran is discussed. These findings regarding the gut microbiota of house fly larvae will provide opportunities for research on the impact of microbial communities on poultry and fish.","corpus_id":23768787,"score":1},{"doc_id":"28972993","title":"Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets.","abstract":"BACKGROUND: Gut microbial composition is dependent on diet. Geese are herbivores and can digest crude fibre, but the relationship between composition of the microbiota and a fibre-rich diet in geese is not well understood. RESULTS: Here, caecal and faecal samples were collected simultaneously from all-grass-fed geese and high-grain-fed geese and the hypervariable V3-V4 regions of the bacterial 16S rRNA gene were sequenced. The results was identified that high-grass-fed geese possessed significantly higher alpha diversity both in caecum and faeces compared with that in all-grain-fed geese. In addition, the composition of dominant bacterium occurred remarkable shifting due to different diet patterns, Firmicutes were more abundant in all-grass-fed geese, whereas Bacteroidetes were abundant in high-grain-fed geese. Fusobacteria and Deferribacteres were obviously present in high-grain-fed geese and few in all-grass-fed geese. Most importantly, some specific microorgnisms such as Ruminococcaceae, Lachnospiraceae and Bacteroidaceae which may associated with cellulose-degrading that were characterized to show distinctly diverse between the two diet patterns. PICRUSt analysis revealed the metabolic pathways such as carbohydrate and amino acid metabolism were overrepresented in all-grass-fed geese. CONCLUSIONS: In conclusion, Firmicutes and Bacteroidetes were identified abundantly when the geese was fed with all-grass feed and high-grain feed, respectively. And Ruminococcaceae, Lachnospiraceae and Bacteroidaceae were recognized as main cellulose-degrading bacteria in the geese. The functional profiles of gut microbiota revealed the dominant microbiota communities were involved mainly in the carbohydrate metabolism in all-grass-fed geese.","corpus_id":23790194,"score":1},{"doc_id":"29057500","title":"The impact of rumen cannulation on the microbial community of goat rumens as measured using 16S rRNA high-throughput sequencing.","abstract":"The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high-throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene. High-throughput sequencing was performed using an Illumina MiSeq platform, and the sequences were analyzed primarily using the Quantitative Insights into Microbial Ecology pipeline software. The results showed that the Chao 1 index, the observed species index and the Shannon-Wiener index were not significantly different (p > 0.05) between the two groups. Bacteroidetes, Firmicutes, Tenericutes were the predominant phylum in both groups, and their relative abundance was 60.63%, 29.48%, 2.24% (n = 6, CT group) and 61.17%, 26.92%, 1.66% (n = 6, RC group) respectively. At the phylum level, the relative abundance of Proteobacteria was significantly higher (p < 0.001) in the microbial communities of RC goats, and Planctomycetes and Chloroflexi were significantly lower (p = 0.02). The abundances of other phyla were not significantly different between treatments. A total of 19 lower-level taxa also exhibited significant differences (p < 0.05) in relative abundance between the groups. In addition, there were 18 genera shared within the control group, 26 shared within the rumen-cannulated group, and 16 shared by both groups. Prevotella was the most abundant shared genus, although its abundance was not significantly different (p > 0.05) between the groups. In conclusion, although the most abundant microbes kept stable, rumen cannulation had the potential to significantly change rumen microbial communities in goats.","corpus_id":38957918,"score":1},{"doc_id":"29172724","title":"Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects.","abstract":"PURPOSE: The aim of this study was to identify differences in the major (core vs. variable) microbial genera of human subjects with and without diabetes. METHODS: Bacterial 16S rRNA genes obtained from conjunctival swabs of 19 healthy subjects and 30 diabetic patients were sequenced using the Illumina MiSeq platform, and the sequencing data were analyzed using QIIME 1.9.1. To elucidate the microbial diversity in the ocular surface (OS), test programs from various bioinformatics domains were used. RESULTS: Diversity index and rarefaction analysis showed that the microbial community of the diabetic patients was more diverse than that of the healthy subjects. Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria and Bacteroidetes were the dominant taxa present in the OS, and there was a significant difference in the relative abundance of the bacterial phyla between the diabetic patients and control subjects. Proteobacteria were more abundant in the diabetic group, whereas Firmicutes was more abundant in the control group. Analysis of bacterial taxa at the genus level showed that the core microbiome of diabetic patients comprised Acinetobacter, Burkholderia, Sphingomonas, and Ralstonia, whereas that of the controls comprised Bradyrhizobiaceae, Staphylococcus, Corynebacterium, Pseudomonas, Novosphingobium, Neisseriaceae, and Acinetobacter. CONCLUSIONS: There was a significant difference in the microbial community composition between diabetic patients and healthy subjects. A high abundance of Acinetobacter in the OS of diabetic patients may arise from the unique characteristics of the OS compared with those of other organ surfaces.","corpus_id":5344827,"score":1},{"doc_id":"29487373","title":"Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese.","abstract":"Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.","corpus_id":54629456,"score":1},{"doc_id":"29579944","title":"Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing.","abstract":"Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.","corpus_id":4430578,"score":1},{"doc_id":"29849646","title":"Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt.","abstract":"The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level, Prevotella, Bacillus, Porphyromonas, Streptococcus, and Bacteroides were the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.","corpus_id":44061314,"score":1},{"doc_id":"26496917","title":"Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing.","abstract":"This study was carried out to understand microbial diversity and function in the microbial enhanced oil recovery (MEOR) process and to assess the impact of MEOR treatment on the microbial community in an oil reservoir. The Illumina MiSeq-based method was used to investigate the structure and dynamics of the microbial community in a MEOR-treated block of the Baolige oilfield, China. The results showed that microbial diversity was high and that 23 phyla occurred in the analyzed samples. Proteobacteria, Firmicutes, Bacteroidetes, Thermotogae, and Euryarchaeota were present in relatively high abundance in all analyzed samples. Injection of bacteria and nutrients resulted in interesting changes in the composition of the microbial community. During MEOR treatment, the community was dominated by the known hydrocarbon-utilizing genera Pseudomonas and Acinetobacter. After the treatment, the two genera decreased in abundance over time while Methanobacteriaceae, as well as known syntrophic genera such as Syntrophomonas, Pelotomaculum, Desulfotomaculum, and Thermacetogenium gradually increased. The change in dominant microbial populations indicated the presence of a succession of microbial communities over time, and the hydrocarbon degradation and syntrophic oxidation of acetate and propionate to methane in the MEOR-treated oilfield. This work contributes to a better understanding of microbial processes in oil reservoirs and helps to optimize MEOR technology.","corpus_id":8870452,"score":0},{"doc_id":"26929931","title":"Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine.","abstract":"The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.","corpus_id":9074739,"score":0},{"doc_id":"28109256","title":"Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform.","abstract":"BACKGROUND: The composition of the skin microbiome is predicted to play a role in the development of conditions such as atopic eczema and psoriasis. 16S rRNA gene sequencing allows the investigation of bacterial microbiota. A significant challenge in this field is development of cost effective high throughput methodologies for the robust interrogation of the skin microbiota, where biomass is low. Here we describe validation of methodologies for 16S rRNA (ribosomal ribonucleic acid) gene sequencing from the skin microbiome, using the Illumina MiSeq platform, the selection of primer to amplify regions for sequencing and we compare results with the current standard protocols.. METHODS: DNA was obtained from two low density mock communities of 11 diverse bacterial strains (with and without human DNA supplementation) and from swabs taken from the skin of healthy volunteers. This was amplified using primer pairs covering hypervariable regions of the 16S rRNA gene: primers 63F and 519R (V1-V3); and 347F and 803R (V3-V4). The resultant libraries were indexed for the MiSeq and Roche454 and sequenced. Both data sets were denoised, cleaned of chimeras and analysed using QIIME. RESULTS: There was no significant difference in the diversity indices at the phylum and the genus level observed between the platforms. The capture of diversity using the low density mock community samples demonstrated that the primer pair spanning the V3-V4 hypervariable region had better capture when compared to the primer pair for the V1-V3 region and was robust to spiking with human DNA. The pilot data generated using the V3-V4 region from the skin of healthy volunteers was consistent with these results, even at the genus level (Staphylococcus, Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, Enhydrobacter and Deinococcus identified at similar abundances on both platforms). CONCLUSIONS: The results suggest that the bacterial community diversity captured using the V3-V4 16S rRNA hypervariable region from sequencing using the MiSeq platform is comparable to the Roche454 GS Junior platform. These findings provide evidence that the optimised method can be used in human clinical samples of low bacterial biomass such as the investigation of the skin microbiota.","corpus_id":8417168,"score":0},{"doc_id":"29131360","title":"Bacterial diversity and community structure during fermentation of Chinese sauerkraut with Lactobacillus casei 11MZ-5-1 by Illumina Miseq sequencing.","abstract":"The bacterial diversity and community structure involved in Chinese sauerkraut is one of the most important factors shaping the final characteristics of traditional foods. In this research, Lactobacillus casei 11MZ-5-1 was applied in Chinese sauerkraut fermentation as a starter culture. Illumina Miseq sequencing analysis was used to reveal the bacterial diversity and community structure during Chinese sauerkraut fermentation. A total of 177 283 high-quality reads of 16S rRNA V4 regions were obtained. The inoculation of L. casei 11MZ-5-1 decreased considerably the bacterial richness and bacterial diversity. This inoculum led to the replacement of Lactococcus by Lactobacillus. The levels of Pseudomonas and Enterobacter bacteria decreased. These findings reveal the evolution of important bacterial groups that are involved in fermentation and will facilitate improvements in the Chinese sauerkraut fermentation process. SIGNIFICANCE AND IMPACT OF THE STUDY: This research thoroughly revealed the effects of Lactobacillus casei 11MZ-5-1 starter cultures on bacterial communities during Chinese sauerkraut fermentation. Illumina Miseq sequencing was effective technique to monitor the bacterial diversity and community structure. The inoculation of L. casei 11MZ-5-1 led to the decline of bacterial richness and diversity together with a consistent predominance of Lactobacillus during spontaneous fermentation. The result collectively suggested L. casei 11MZ-5-1 is a promising starter in Chinese sauerkraut manufacturing.","corpus_id":3913194,"score":0},{"doc_id":"29478633","title":"Revealing the anaerobic acclimation of microbial community in a membrane bioreactor for coking wastewater treatment by Illumina Miseq sequencing.","abstract":"The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase-decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority (less than 1%) to the dominant bacterial group (54.0%) along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in \"rare biosphere\" might eventually become dominant in response to environmental change.","corpus_id":3538618,"score":0}],"string":"[\n {\n \"doc_id\": \"23922920\",\n \"title\": \"The microbial community in the feces of the white rhinoceros (Ceratotherium simum) as determined by barcoded pyrosequencing analysis.\",\n \"abstract\": \"As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.\",\n \"corpus_id\": 17958222,\n \"score\": 2\n },\n {\n \"doc_id\": \"24352967\",\n \"title\": \"Investigation of bacterial diversity in the feces of cattle fed different diets.\",\n \"abstract\": \"The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.\",\n \"corpus_id\": 14782674,\n \"score\": 2\n },\n {\n \"doc_id\": \"25604266\",\n \"title\": \"First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing.\",\n \"abstract\": \"The digestive systems of mammals harbor a complex gut microbiome, comprising bacteria and other microorganisms that confer metabolic and immunological benefits to the host. Ruminants that digest plant-based foods have a four-compartment stomach consisting of the rumen, reticulum, omasum, and abomasum. The microorganisms in the stomach are essential for providing the host with critical nutrients. However, the majority of these microorganisms are unknown species. The microbiome of the stomach is diverse, and the majority of these organisms cannot be cultured. Next-generation sequencing (NGS) combined with bioinformatic analysis tools have allowed the dissection of the composition of the microbiome in samples collected from a specific environment. In this study, for the first time, the bacterial composition in two compartments, the reticulum and the omasum, of bovine were analyzed using a metagenomic approach and compared to the bacterial composition of the rumen. These data will assist in understanding the biology of ruminants and benefit the agricultural industry. The diversity and composition of the bacterial community in samples collected from the rumen, reticulum, and omasum of bovines in the Changchun Region of Northeast China were analyzed by sequencing the V3 region of the 16S rRNA gene using a barcoded Illumina paired-end sequencing technique, and the primary composition of the microbiome in the rumen, reticulum, and omasum of the bovines was determined. These microbiomes contained 17 phyla and 107 genera in all three samples. Five phyla, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Lentisphaerae, were the most abundant taxonomic groups. Additionally, the different stomach compartments harbored different compositions of the microorganisms.\",\n \"corpus_id\": 8848102,\n \"score\": 2\n },\n {\n \"doc_id\": \"25931374\",\n \"title\": \"Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis.\",\n \"abstract\": \"A balanced gastrointestinal microbial ecosystem is crucial for the health and growth of animals. In the gastrointestinal tract (GIT) of ruminants, cellulolytic bacteria aid in the digestion and absorption of nutrients. Rumen contents and feces in ruminants are often used to assess gastrointestinal microbial communities; however, these sites do not guarantee to represent the diversity of microbes found in the entire GIT. In this study, we investigated the microbiota along the GIT of five Chinese Mongolian sheep using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbiota were more abundant in the stomach and large intestine than in the small intestine. DGGE and real-time PCR revealed the predominance of Firmicutes and Bacteroidetes in the GIT. Meanwhile, Ruminococcus flavefaciens and Clostridium cluster IV showed significant difference in their abundance along the GIT (P < 0.05). Fibrobacter succinogenes was the most dominant species, followed by Ruminococcus albus and R. flavefaciens. The ileum harbored a larger number of cellulolytic bacteria, particularly-Clostridium cluster IV, than reported previously. In addition, comparisons between microbiota in the rumen and rectum indicated similar number of total bacteria, Firmicutes, Bacteroidetes, F. succinogenes, Butyrivibrio fibrisolvens, Clostridium cluster IV, and Clostridium cluster XIVa, whereas the number of R. albus and R. flavefaciens was higher in the rumen. This study investigated the composition and quantification of GIT microbial community in Chinese Mongolian sheep, and revealed for the first time the cellulolytic bacterial community in these sheep.\",\n \"corpus_id\": 13118691,\n \"score\": 2\n },\n {\n \"doc_id\": \"27037116\",\n \"title\": \"Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea).\",\n \"abstract\": \"UNLABELLED: Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE: The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.\",\n \"corpus_id\": 4778535,\n \"score\": 2\n },\n {\n \"doc_id\": \"27135948\",\n \"title\": \"Exploring the Goat Rumen Microbiome from Seven Days to Two Years.\",\n \"abstract\": \"Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.\",\n \"corpus_id\": 2684889,\n \"score\": 2\n },\n {\n \"doc_id\": \"27258373\",\n \"title\": \"Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.\",\n \"abstract\": \"This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers.\",\n \"corpus_id\": 15328491,\n \"score\": 2\n },\n {\n \"doc_id\": \"27383798\",\n \"title\": \"Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis.\",\n \"abstract\": \"OBJECTIVE: The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep's health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. METHODS: This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. RESULTS: The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). CONCLUSION: This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.\",\n \"corpus_id\": 18866742,\n \"score\": 2\n },\n {\n \"doc_id\": \"28378284\",\n \"title\": \"Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity.\",\n \"abstract\": \"Chinese Mongolian sheep are an important ruminant raised for wool and meat production. However, little is known about the microbiota of the gastrointestinal tract (GIT) of Chinese Mongolian sheep. To increase our understanding of the microbial community composition in the GIT of Chinese Mongolian sheep, microbiota of five sheep is investigate for the first time using the Illumina MiSeq platform. High microbial diversity was obtained from the GIT, and the microbiota exhibited a higher biodiversity in the stomach and large intestine than in the small intestine. Firmicutes (44.62%), Bacteroidetes (38.49%), and Proteobacteria (4.11%) were the three most abundant phyla present in the GIT of the sheep. The present study also revealed the core genera of Prevotella, Bacteroides, Ruminococcus, Oscillospira, Treponema, and Desulfovibrio in the GIT. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States indicated that the metabolic pathway related to carbohydrate metabolism was the richest in the sheep GIT. In addition, a series of metabolic pathways related to plant secondary metabolism was most abundant in the stomach and large intestine than in the small intestine. Overall, the present study provides insight into the microbial community composition in GIT of the Chinese Mongolian sheep which is highly diverse and needs to be studied further to exploit the complex interactions with the host.\",\n \"corpus_id\": 17233711,\n \"score\": 2\n },\n {\n \"doc_id\": \"28413853\",\n \"title\": \"Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi).\",\n \"abstract\": \"The gut microbiota of mammals is a complex ecosystem, which is essential for maintaining gut homeostasis and the host's health. The high throughput sequencing allowed us to gain a deeper insight into the bacterial structure and diversity. In order to improve the health status of the endangered golden takins, we first characterized the fecal microbiota of healthy golden takins using high throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions. Our results showed that, Firstly, the gut microbiota community comprised 21 phyla, 40 classes, 62 orders, 96 families, and 216 genera. Firmicutes (67.59%) was the most abundant phylum, followed by Bacteroidetes (23.57%) and Proteobacteria (2.37%). Secondly, the golden takin maintained higher richness in spring than in the winter while community diversity and evenness was not significantly different. Thirdly, four female golden takins demonstrated highly similar microbiota and the five golden takin males had relatively highly similar microbiota. All of our results might indicate that the fecal microbiota of golden takins were influenced by the season and the animal's sex. The findings provided theoretical basis regarding the gut microbiota of golden takins and may offer new insights to protect this endangered species.\",\n \"corpus_id\": 23685543,\n \"score\": 2\n },\n {\n \"doc_id\": \"28431497\",\n \"title\": \"Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers.\",\n \"abstract\": \"BACKGROUND: Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community. RESULTS: Most of the sequences were assigned to Firmicutes (56.67%) and Bacteroidetes (35.90%), followed by Proteobacteria (1.87%), Verrucomicrobia (1.80%) and Tenericutes (1.37%). The predominant genera were 5-7 N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia (1.11%). No significant differences were observed in the numbers of Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17), and Tenericutes (p = 0.75) populations between the treatment groups. At the genus level, genera classified with high abundance (more than 0.1%) belonged primarily to Bacteroidetes and Firmicutes. Furthermore, no differences were observed at the genus level: 5-7 N15, CF231, Oscillospira, Paludibacter, and Akkermansia (p > 0.05 in all cases), except that rc4-4 was lower in the CON and SMFP groups than in the EML group (p = 0.02). There were no significant differences in the richness estimate and diversity indices between the groups (p > 0.16), and the different diets did not significantly influence most selected fecal bacterial species (p > 0.06), except for Ruminococcus albus, which was higher in the EML group (p < 0.01) and Streptococcus bovis, which was lower in the CON group (p < 0.01) relative to the other groups. CONCLUSIONS: In conclusion, diets supplemented with EML and SMFP have little influence on the fecal bacterial community composition in finishing steers.\",\n \"corpus_id\": 2870031,\n \"score\": 2\n },\n {\n \"doc_id\": \"28601892\",\n \"title\": \"Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage.\",\n \"abstract\": \"The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected from six farms in Japan and China, and high-throughput Illumina sequencing of the V4 hypervariable region of 16S rRNA genes was performed. Lactobacillaceae were dominant in all silages, followed by Acetobacteraceae, Bacillaceae, and Enterobacteriaceae. In feces, the predominant families were Ruminococcaceae, Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Rikenellaceae, and Paraprevotellaceae. Therefore, Lactobacillaceae of corn silage appeared to be eliminated in the gastrointestinal tract. Although fecal microbiota composition was similar in most samples, relative abundances of several families, such as Ruminococcaceae, Christensenellaceae, Turicibacteraceae, and Succinivibrionaceae, varied between farms and countries. In addition to the geographical location, differences in feeding management between total mixed ration feeding and separate feeding appeared to be involved in the variations. Moreover, a cow-to-cow variation for concentrate-associated families was demonstrated at the same farm; two cows showed high abundance of Succinivibrionaceae and Prevotellaceae, whereas another had a high abundance of Porphyromonadaceae. There was a negative correlation between forage-associated Ruminococcaceae and concentrate-associated Succinivibrionaceae and Prevotellaceae in 18 feces samples. Succinivibrionaceae, Prevotellaceae, p-2534-18B5, and Spirochaetaceae were regarded as highly variable taxa in this study. These findings help to improve our understanding of variation and similarity of the fecal microbiota of dairy cows with regard to individuals, farms, and countries. Microbiota of naturally fermented corn silage had no influence on the fecal microbiota of dairy cows.\",\n \"corpus_id\": 3852013,\n \"score\": 2\n },\n {\n \"doc_id\": \"28955315\",\n \"title\": \"Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing.\",\n \"abstract\": \"Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student's t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student's t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.\",\n \"corpus_id\": 10335006,\n \"score\": 2\n },\n {\n \"doc_id\": \"29170893\",\n \"title\": \"Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing.\",\n \"abstract\": \"The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.\",\n \"corpus_id\": 5977224,\n \"score\": 2\n },\n {\n \"doc_id\": \"22248568\",\n \"title\": \"Does a temperate ungulate that breeds in summer exhibit rut-induced hypophagia? Analysis of time budgets of male takin (Budorcas taxicolor) in Sichuan, China.\",\n \"abstract\": \"Mammals maximize fitness by optimizing time and energy allocation between reproduction and survival. Describing time budgets is a way to understand a species' constraints in energy allocation. We describe a time budget for male takin (Budorcas taxicolor) in Tangjiahe Nature Reserve, China, to better understand rut-induced hypophagia, which is frequently observed in temperate ungulates that breed in autumn or in winter. Observations generally occurred at two elevations (1200-1600m and 2600-3200m), using 20-min focal animal scan sampling from 2007 to 2009. Feeding behaviors accounted for the majority in takin's time budget (61.1%) during daylight hours, relative to the other observed behaviors, such as rest (14.1%), alert behavior (10.2%) and locomotion (6.8%). We found a negative correlation between feeding behavior and rutting behavior during the rutting season. A ratio of feeding time to resting time increased from pre-rut to rut, while resting behavior did not change significantly across seasons. These results suggest the \\\"energy saving\\\" hypothesis could explain reduced foraging in male takin during the rut, but aspects of the species biology suggest that hypotheses for rut-induced hypophagia developed for other temperate ungulates do not apply to takin. We suggest that the unusual summer rutting season of takin releases males from the energy constraints encountered by temperate ungulates that breed in the autumn and has other benefits for offspring survival. Further research should be conducted on ungulates that exhibit rut during the summer and tropical ungulates that might not experience limited food availability following the mating season to improve our understanding on rut-induced hypophagia.\",\n \"corpus_id\": 35442875,\n \"score\": 1\n },\n {\n \"doc_id\": \"22626770\",\n \"title\": \"Characterizing the behavior and reproductive biology of zoo-housed Sichuan takin (Budorcas taxicolor tibetana) using non-invasive techniques.\",\n \"abstract\": \"The Sichuan takin (takin; Budorcas taxicolor tibetana) is distributed in the Gansu and Sichuan providences of southern China and along eastern Tibet. Because of their ecology, few data on takin reproductive biology exist, with the exception of its mating season in the Sichuan province, which occurs from July through August. Therefore, the objectives were to: 1) characterize reproductive hormones in zoo-housed male and female takin, including pregnancy in the female, using non-invasive fecal steroid hormonal monitoring; 2) characterize behaviors of zoo-housed takin, emphasizing reproductive behaviors and activity budget; and 3) assess the influence of season on births in North America and reproductive hormonal and behavioral activity. Fecal samples were collected 3 to 5 times per week from two adult males and three adult females. Extracted hormones were analyzed using an enzyme immunoassay for progestagen and androgen concentrations. Behavioral observations were collected for 2 yrs using an ethogram. In this study, season affected reproduction, specifically birth occurrences, reproductive cyclicity in females and androgen production in males. The duration of the estrous cycle was approximately 35 d and cycles occurred June through December. Androgen concentrations peaked in May through August. Season did not influence behavior; however, age and sex may affect some behaviors, including activity level, foraging and drinking, social affiliative behavior, and visibility from the visitor's viewpoint. In conclusion, fecal hormonal and behavioral analyses can provide information for management and conservation of this herd species.\",\n \"corpus_id\": 2343413,\n \"score\": 1\n },\n {\n \"doc_id\": \"23217205\",\n \"title\": \"The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows.\",\n \"abstract\": \"BACKGROUND: Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with fatty acids during SARA. Four cannulated primiparous (60 to 90 day in milk) Holstein dairy cows were assigned to two diets in a 2 × 2 crossover experimental design. The diets contained (on a dry matter basis): 40% (control diet, COD) and 70% (SARA induction diet, SAID) concentrate feeds. Samples of ruminal fluid and feces were collected on day 12, 15, 17 and 21 of the treatment period, and the pH was measured in the ruminal and fecal samples; the fecal microbiota was determined by pyrosequencing analysis of the V1-V3 region of amplified 16S ribosomal RNA (16S rRNA). RESULTS: SAID decreased ruminal and fecal pH and increased the propionate, butyrate and total volatile fatty acid (TVFA) concentration in feces when compared with the COD. A barcoded DNA pyrosequencing method was used to generate 2116 16S operational taxonomic units (OTUs). A total of 11 phyla were observed, distributed amongst all cattle on both diets; however, only 5 phyla were observed in all animals regardless of dietary treatment, and considerable animal to animal variation was revealed. The average abundance and its range of the 5 phyla were as follows: Firmicutes (63.7%, 29.1-84.1%), Proteobacteria (18.3%, 3.4-46.9%), Actinobacteria (6.8%, 0.4-39.9%), Bacteroidetes (7.6%, 2.2-17.7%) and Tenericutes (1.6%, 0.3-3%). Feeding the SAID resulted in significant shifts in the structure of the fecal microbial community when compared with the traditional COD. Among the 2116 OTUs detected in the present study, 88 OTUs were affected significantly by diet; and the proportion of these OTUs was 20.6% and 17.4% among the total number of sequences, respectively. Among the OTUs affected, the predominant species, including OTU2140 (G: Turicibacter), OTU1695 (G: Stenotrophomonas) and OTU8143 (F: Lachnospiraceae), were increased, while the abundance of OTU1266 (S: Solibacillus silvestris) and OTU2022 (G: Lysinibacillus) was reduced in the SAID group compared with the COD. Further, our results indicated that the fecal volatile fatty acid (VFA) concentrations were significantly related to presence of some certain species of Bacteroidetes and Firmicutes in the feces. CONCLUSIONS: This is, to our knowledge, the first study that has used barcoded DNA pyrosequencing to survey the fecal microbiome of dairy cattle during SARA. Our results suggest that particular bacteria and their metabolites in the feces appear to contribute to differences in host health between those given SAID and traditional COD feeding. A better understanding of these microbial populations will allow for improved nutrient management and increased animal growth performance.\",\n \"corpus_id\": 10734966,\n \"score\": 1\n },\n {\n \"doc_id\": \"23333862\",\n \"title\": \"High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria.\",\n \"abstract\": \"Fecal microbiota transplantation (FMT) is becoming a more widely used technology for treatment of recurrent Clostridum difficile infection (CDI). While previous treatments used fresh fecal slurries as a source of microbiota for FMT, we recently reported the successful use of standardized, partially purified and frozen fecal microbiota to treat CDI. Here we report that high-throughput 16S rRNA gene sequencing showed stable engraftment of gut microbiota following FMT using frozen fecal bacteria from a healthy donor. Similar bacterial taxa were found in post-transplantation samples obtained from the recipients and donor samples, but the relative abundance varied considerably between patients and time points. Post FMT samples from patients showed an increase in the abundance of Firmicutes and Bacteroidetes, representing 75-80% of the total sequence reads. Proteobacteria and Actinobacteria were less abundant (< 5%) than that found in patients prior to FMT. Post FMT samples from two patients were very similar to donor samples, with the Bacteroidetes phylum represented by a great abundance of members of the families Bacteroidaceae, Rikenellaceae and Porphyromonadaceae, and were largely comprised of Bacteroides, Alistipes and Parabacteroides genera. Members of the phylum Firmicutes were represented by Ruminococcaceae, Lachnospiraceae, Verrucomicrobiaceae and unclassified Clostridiales and members of the Firmicutes. One patient subsequently received antibiotics for an unrelated infection, resulting in an increase in the number of intestinal Proteobacteria, primarily Enterobacteriaceae. Our results demonstrate that frozen fecal microbiota from a healthy donor can be used to effectively treat recurrent CDI resulting in restoration of the structure of gut microbiota and clearing of Clostridum difficile.\",\n \"corpus_id\": 13519972,\n \"score\": 1\n },\n {\n \"doc_id\": \"23354293\",\n \"title\": \"Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides.\",\n \"abstract\": \"One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.\",\n \"corpus_id\": 17678112,\n \"score\": 1\n },\n {\n \"doc_id\": \"24173964\",\n \"title\": \"Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia.\",\n \"abstract\": \"PURPOSE: The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined. METHODS: This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire. RESULTS: Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p < 0.05 and p < 0.01) and decrease in Bifidobacterium with age (p < 0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4 % of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet. CONCLUSIONS: Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.\",\n \"corpus_id\": 22998385,\n \"score\": 1\n },\n {\n \"doc_id\": \"24212576\",\n \"title\": \"Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides.\",\n \"abstract\": \"One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented: Firmicutes (51.9%), Bacteroidetes (30.9%), Proteobacteria (11.1%), Actinobacteria (3.5%), Synergistetes (1.5%), and Fusobacteria (1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, B. ovatus, and B. xylanisolvens and members of the Porphyromonadaceae family. Many of the Firmicutes and Bacteroidetes isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.\",\n \"corpus_id\": 206732566,\n \"score\": 1\n },\n {\n \"doc_id\": \"24558975\",\n \"title\": \"An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.\",\n \"abstract\": \"BACKGROUND: To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing platforms. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality. RESULTS: Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We introduced a 0 to 7 bp \\\"heterogeneity spacer\\\" to the index sequence that allows an equal proportion of samples to be sequenced out of phase. CONCLUSIONS: Our approach yields high quality sequence data from 16S rRNA gene amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a flexible and cost-effective sequencing option.\",\n \"corpus_id\": 11231363,\n \"score\": 1\n },\n {\n \"doc_id\": \"24730432\",\n \"title\": \"Severe laminitis in multiple zoo species.\",\n \"abstract\": \"A 10-year record review from a zoological institution in the western USA identified four cases of severe laminitis resulting in rotation and protrusion of the third phalanx through the sole. Laminitis is reported in a Masai giraffe (Giraffa camelopardalis tippelskirchi), a Sichuan takin (Budorcas taxicolor tibetana), a greater Malayan chevrotain (Tragulus napu) and a giant eland (Taurotragus derbianus). This is the first report of severe laminitis with pedal bone rotation and protrusion in multiple species of non-domestic hoofstock, and the first report of this disease in three of these species (takin, chevrotain, and giant eland).\",\n \"corpus_id\": 205499321,\n \"score\": 1\n },\n {\n \"doc_id\": \"25928424\",\n \"title\": \"Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole.\",\n \"abstract\": \"Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.\",\n \"corpus_id\": 2369097,\n \"score\": 1\n },\n {\n \"doc_id\": \"26024129\",\n \"title\": \"Phylogenetic analysis of the endangered takin in the confluent zone of the Qinling and Minshan Mountains using mtDNA control region.\",\n \"abstract\": \"The takin (Budorcas taxicolor) is an Endangered ungulate. We analyzed the variation within mtDNA control region sequences of takin populations in the Qinling Mountains, the Minshan Mountains and the confluence of these two mountain ranges. We did not find any shared haplotypes among the populations. We observed apparent variation in the control region length among the three populations, and independent population expansions in the late of Pleistocene, which suggests these populations may have independent evolutionary histories. We found only one haplotype, and the lowest measures of genetic diversity (h = 0; π = 0) in the population from the confluent zone, which suggests populations in the confluent zone may have grown from small founder populations and gene flow with other populations has ceased. Based on their phylogenetic relationships, we concluded that the takin population in the confluent zone was in the same clade as the Tangjiahe population, which suggests that these takin populations are Sichuan takin (Budorcas taxicolor tibetana).\",\n \"corpus_id\": 6896537,\n \"score\": 1\n },\n {\n \"doc_id\": \"26084274\",\n \"title\": \"Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis.\",\n \"abstract\": \"BACKGROUND: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon sequencing for environmental microbial community analysis is challenging due to the problem of low base diversity. RESULTS: A new phasing amplicon sequencing approach (PAS) was developed by shifting sequencing phases among different community samples from both directions via adding various numbers of bases (0-7) as spacers to both forward and reverse primers. Our results first indicated that the PAS method substantially ameliorated the problem of unbalanced base composition. Second, the PAS method substantially improved the sequence read base quality (an average of 10 % higher of bases above Q30). Third, the PAS method effectively increased raw sequence throughput (~15 % more raw reads). In addition, the PAS method significantly increased effective reads (9-47 %) and the effective read sequence length (16-96 more bases) after quality trim at Q30 with window 5. In addition, the PAS method reduced half of the sequencing errors (0.54-1.1 % less). Finally, two-step PCR amplification of the PAS method effectively ameliorated the amplification biases introduced by the long barcoded PCR primers. CONCLUSION: The developed strategy is robust for 16S rRNA gene amplicon sequencing. In addition, a similar strategy could also be used for sequencing other genes important to ecosystem functional processes.\",\n \"corpus_id\": 516467,\n \"score\": 1\n },\n {\n \"doc_id\": \"26426811\",\n \"title\": \"An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms.\",\n \"abstract\": \"The primary 16S rRNA sequencing protocol for microbial community analysis using Illumina platforms includes a single-indexing approach that allows pooling of hundreds of samples in each sequencing run. The protocol targets the V4 hypervariable region (HVR) of 16S rRNA using 150 bp paired-end (PE) sequencing. However, the latest improvement in Illumina chemistry has increased the read length up to 600 bp using 300 bp PE sequencing. To take advantage of the longer read length, a dual-indexing approach was previously developed for targeting different HVRs. However, due to simple working protocols, the single-index 150 bp PE approach still continues to be attractive to many researchers. Here, we described an extended single-indexing protocol for 300 bp PE illumina sequencing that targets the V3-V4 HVRs of 16S rRNA. The new primer set led to increased read length and alignment resolution, as well as increased richness and diversity of resulting microbial profile compared to that obtained from150 bp PE protocol for V4 sequencing. The β-diversity profile also differed qualitatively and quantitatively between the two approaches. Both primer sets had high coverage rates and specificity to detect dominant phyla; however, their coverage rate with regards to the rare biosphere varied. Our data further confirms that the choice of primer is the most deterministic factor in sequencing coverage and specificity.\",\n \"corpus_id\": 7965706,\n \"score\": 1\n },\n {\n \"doc_id\": \"26728019\",\n \"title\": \"Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene.\",\n \"abstract\": \"Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host's health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63-38.97 %), Firmicutes (20.97-44.01 %), Proteobacteria (9.33-17.60 %), Fusobacteria (9.11-17.90 %), and Actinobacteria (1.22-2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.\",\n \"corpus_id\": 18524507,\n \"score\": 1\n },\n {\n \"doc_id\": \"27299740\",\n \"title\": \"Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity.\",\n \"abstract\": \"Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities.\",\n \"corpus_id\": 1891149,\n \"score\": 1\n },\n {\n \"doc_id\": \"27305787\",\n \"title\": \"[Biases on community structure during DNA extraction of shrimp intestinal microbiota revealed by high-throughput sequencing].\",\n \"abstract\": \"OBJECTIVES: High-throughput sequencing technology is increasingly applied in intestinal microbiota of aquatic animals including shrimp. However, there is a lack of standard method or kit for DNA isolation from shrimp intestinal microbiota, and little is known about the effectiveness and biases regarding DNA extraction based on high-throughput sequencing. The aim of this study was to study the biases of different DNA extraction kits on community structure of shrimp intestinal microbiota through high-throughput sequencing, and to better understand the structure and composition of bacterial flora associated with healthy Litopenaeus vannamei. METHODS: We extracted the total DNA of intestinal microbiota from L. vannamei with three commercial kits designed for DNA extraction from bacteria, stool and tissue (Omega, USA). DNA quality was evaluated based on the absorbance ratios of 260/280 nm by NanoDrop, while DNA concentration was quantified using PicoGreen. Then Illumina MiSeq high-throughput sequencing was used to examine the intestinal bacterial communities following PCR amplification of 16S rDNA V4 region. RESULTS: The yield and purity of the DNA from the Bacterial Kit (SIB) were superior to those from the Stool Kit (SIS), whereas the DNA from Tissue Kit (SIT) presented too small amount to be amplified efficiently. The average sequence reads obtained from SIB and SIS samples were 52151 ± 5085 and 55296 ± 5147 respectively. After resampling at the same depth of 46800 reads, the operational taxonomic unit (OTU) number and Shannon diversity index of SIS samples were significantly higher than those of SIB samples. By contrast, the reproducibility of OTU among SIB replicates was higher than that among SIS replicates. The dominant phyla of SIS and SIB samples were identical, including Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, and Cyanobacteria. However, the relative abundances of almost all the dominant groups at various taxonomic levels differed greatly between these two samples. CONCLUSION: Significant biases on community structure of shrimp intestinal microbiota were detected which originated from DNA extraction. And the core microbiota of the healthy L. vannamei in this study was mainly composed of genera Photobacterium, Lactococcus, Aliivibrio, Vibrio, as well as three other unclassified groups.\",\n \"corpus_id\": 23740199,\n \"score\": 1\n },\n {\n \"doc_id\": \"27365218\",\n \"title\": \"Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides).\",\n \"abstract\": \"Swan goose (Anser cygnoides) is currently one of the most popular economic wildfowl for rare birds breeding industries in several provinces of China. However, the farmed Swan geese, reared in artificial environment and fed on both natural and artificial diets, display a reduced reproductive rate compared to wild species. Little is known about the gut microbiota of this species, which could play a role in nutrient and energy metabolism, immune homeostasis and reproduction. The present comparative study was designed to provide a first characterization of gut microbial communities related to both wild and farmed Swan geese by 16 S rRNA sequences using the Illumina HiSeq platform. The results showed that dominant microbial components in both groups consisted of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The abundances of these four phyla were not statistically different between the groups. At the genus level, significantly decreased abundance of Clostridium and increased abundance of SMB53, Enterococcus and Paenibacillus were observed in farmed group compared to wild group. The marked differences of genus level group-specific microbes create a baseline for future Swan goose microbiology research and make a valuable contribution to forming relationships between gut microbiota and domestic bird reproduction.\",\n \"corpus_id\": 206136201,\n \"score\": 1\n },\n {\n \"doc_id\": \"27400733\",\n \"title\": \"High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite.\",\n \"abstract\": \"BACKGROUND: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform. RESULTS: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples. CONCLUSIONS: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.\",\n \"corpus_id\": 10285369,\n \"score\": 1\n },\n {\n \"doc_id\": \"27514729\",\n \"title\": \"Environment shapes the fecal microbiome of invasive carp species.\",\n \"abstract\": \"BACKGROUND: Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. RESULTS: We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. CONCLUSIONS: The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.\",\n \"corpus_id\": 17903306,\n \"score\": 1\n },\n {\n \"doc_id\": \"27568186\",\n \"title\": \"Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing.\",\n \"abstract\": \"Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.\",\n \"corpus_id\": 32166092,\n \"score\": 1\n },\n {\n \"doc_id\": \"27603009\",\n \"title\": \"Characterization of Intestinal Microbiomes of Hirschsprung's Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing.\",\n \"abstract\": \"Hirschsprung-associated enterocolitis (HAEC) is a life-threatening complication of Hirschsprung's disease (HD). Although the pathological mechanisms are still unclear, studies have shown that HAEC has a close relationship with the disturbance of intestinal microbiota. This study aimed to investigate the characteristics of the intestinal microbiome of HD patients with or without enterocolitis. During routine or emergency surgery, we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis who were in a HAEC remission (HAEC-R) phase. Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs) were defined by 97% sequence similarity. Principal coordinate analysis (PCoA) of weighted UniFrac distances was performed to evaluate the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by the prevalence of Bacteroidetes) and HAEC patients (characterized by the prevalence of Proteobacteria), while the microbiota of the HAEC-R patients was more similar to that of the HAEC patients. We also observed that the specimens from different intestinal sites of each HD patient differed significantly, while the specimens from different intestinal sites of each HAEC and HAEC-R patient were more similar. In conclusion, the microbiome pattern of the HAEC-R patients was more similar to that of the HAEC patients than to that of the HD patients. The HD patients had a relatively distinct, more stable community than the HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patient's uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following symptom resolution and can be implicated in the symptom recurrence.\",\n \"corpus_id\": 14626589,\n \"score\": 1\n },\n {\n \"doc_id\": \"27692708\",\n \"title\": \"Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants.\",\n \"abstract\": \"Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.\",\n \"corpus_id\": 21410465,\n \"score\": 1\n },\n {\n \"doc_id\": \"27734418\",\n \"title\": \"Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene.\",\n \"abstract\": \"The composition of mammalian intestinal microflora is related to many environmental and geographical factors, and it plays an important role in many aspects such as growth and development. Sequencing data of the bacterial 16S rRNA gene from sable (Martes zibellina) samples using next-generation sequencing technology are limited. In our research, 84,116 reads obtained by high-throughput sequencing were analyzed to characterize and compare the intestinal microflora of wild sables and housed sables. Firmicutes (31.1 %), Bacteroidetes (26.0 %) and Proteobacteria (21.5 %) were the three most abundant phyla present in wild sables, whereas Firmicutes (55.6 %), Proteobacteria (29.1 %) and Actinobacteria (6.0 %) were the three predominant phyla present in housed sables. At the phylum level, wild sables exhibited a significant difference in the relative abundances of Bacteroidetes and Actinobacteria, whereas housed sables only exhibited significant changes in TM7 at the phylum level, and Clostridia, at the class level. The predominance of Bacteroidetes in wild sables warrants further research. These results indicate that a sudden change in diet may be a key factor that influences fecal bacterial diversity in mammals.\",\n \"corpus_id\": 10259387,\n \"score\": 1\n },\n {\n \"doc_id\": \"27744590\",\n \"title\": \"Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.\",\n \"abstract\": \"Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH4(+)-N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.\",\n \"corpus_id\": 207280588,\n \"score\": 1\n },\n {\n \"doc_id\": \"27770389\",\n \"title\": \"Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics.\",\n \"abstract\": \"Antibiotics have been widely used for the prevention and the treatment of diseases to humans and animals, and they have fed additives for agricultural animals to promote growth. However, there is a growing concern over the practice due to its side effects on intestinal microbial communities which plays a vital role in animals' health. To investigate the effect of antibiotics on the bacterial population of the caecum in rex rabbits, 80 rex rabbits were randomly divided into four groups: control group (B, basal diet), chlortetracycline group (C, 50 mg/kg), colistin sulfate group (S, 20 mg/kg) and zinc bacitracin group (Z, 40 mg/kg). Caecum microbial communities of rex rabbits from the four groups were analyzed through Illumina Miseq platform after being fed 28 days. The results showed that most obtained sequences belongs to Firmicutes followed by Bacteroidetes, and the ratio of Bacteroidetes/Firmicutes in C group (42.31 %) was higher than that in Z group (21.84 %). Zinc bacitracin supplementation caused a significant decreased of the Proteobacteria phylum and Lactobacillus spp. ( P < 0.05), while the Lactobacillus spp. significantly increased in S group (P < 0.05). In addition, Ruminococcus spp., especially Ruminococcus albus were the predominant bacterial species found in both S and Z groups. The proportion of Coprococcus spp. significantly increased in Z group (P < 0.05). These findings suggested that the antibiotics used may cause significant changes in the caecum microbiota of rex rabbits, and we also found C group had a similarity caecum bacteria structure with B group which was probably due to the high levels of chlortetracycline resistance.\",\n \"corpus_id\": 14565233,\n \"score\": 1\n },\n {\n \"doc_id\": \"27837973\",\n \"title\": \"Effects of the dose and viability of Saccharomyces cerevisiae. 1. Diversity of ruminal microbes as analyzed by Illumina MiSeq sequencing and quantitative PCR.\",\n \"abstract\": \"This study was conducted to examine effects of the dose and viability of supplemental Saccharomyces cerevisiae on the ruminal fermentation and bacteria population and the performance of lactating dairy cows. Four ruminally cannulated lactating cows averaging 284±18d in milk were assigned to 4 treatments arranged in a 4×4 Latin square design with four 21-d periods. Cows were fed a total mixed ration containing 41.7% corn silage, 12.1% brewer's grains, and 46.2% concentrate on a dry matter basis. The diet was supplemented with no yeast (control) or with a low dose of live yeast (5.7×10(7) cfu/cow per day; LLY), a high dose of live yeast (6.0×10(8) cfu/cow per day; HLY), or a high dose of killed yeast (6.0×10(8) cfu/cow per day; HDY). Microbial diversity was examined by high-throughput Illumina MiSeq sequencing (Illumina Inc., San Diego, CA) of the V4 region of the 16S rRNA gene. The relative abundance of select ruminal bacteria was also quantified by quantitative PCR (qPCR). Adding LLY to the diet increased the relative abundance of some ruminal cellulolytic bacteria (Ruminococcus and Fibrobacter succinogenes) and amylolytic bacteria (Ruminobacter, Bifidobacterium, and Selenomonas ruminantium). Adding live instead of killed yeast increased the relative abundance of Ruminococcus and F. succinogenes; adding HDY increased the relative abundance of Ruminobacter, Bifidobacterium, Streptococcus bovis, and Selenomonas ruminantium. The most dominant (≥1% of total sequences) bacteria that responded to LLY addition whose functions are among the least understood in relation to the mode of action of yeast include Paraprevotellaceae, CF231, Treponema, and Lachnospiraceae. Future studies should aim to speciate, culture, and examine the function of these bacteria to better understand their roles in the mode of action of yeast. A relatively precise relationship was detected between the relative abundance of F. succinogenes (R(2)=0.67) from qPCR and MiSeq sequencing, but weak relationships were detected for Megasphaera elsdenii, Ruminococcus flavefaciens, and S. ruminantium (R(2)≤0.19).\",\n \"corpus_id\": 21547300,\n \"score\": 1\n },\n {\n \"doc_id\": \"27992473\",\n \"title\": \"High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation.\",\n \"abstract\": \"Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.\",\n \"corpus_id\": 15005009,\n \"score\": 1\n },\n {\n \"doc_id\": \"28028611\",\n \"title\": \"Comparative analysis of the gut microbiota of black bears in China using high-throughput sequencing.\",\n \"abstract\": \"The Asiatic black bear (Ursus thibetanus) is a protected species from eastern Asia. In China, the Asiatic black bear occurs in 17 provinces from northeast to southwest regions. To date, information on microbial diversity in the gut of the Asiatic black bears from different populations remains limited. To determine the species composition and community structure of the gut microbiota in the Asiatic black bear, we characterized 36 fecal samples from Sichuan, Yunnan, and Heilongjiang provinces, China, by pyrosequencing the 16S V3-V4 hypervariable regions using the Illumina Miseq platform. Results showed that Firmicutes and Proteobacteria were the predominant phyla in the samples, which were largely comprised Escherichia-Shigella, Peptostreptococcaceae_incertae_sedis, Turicibacter, Streptococcus, and Clostridium. By analyzing the community structure from these 36 samples, we found that there were significant differences in the species diversity and richness between Sichuan, Yunnan, and Heilongjiang populations. In conclusion, our results reveal the species composition and structure of the gut microbiota in captive black bears in China, and suggest that biogeography could affect the black bear' gut microbiota.\",\n \"corpus_id\": 26334752,\n \"score\": 1\n },\n {\n \"doc_id\": \"28175972\",\n \"title\": \"Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge.\",\n \"abstract\": \"The effects of a grain-based subacute ruminal acidosis (SARA) challenge on bacteria in the rumen and feces of lactating dairy cows were determined. Six lactating, rumen-cannulated Danish Holstein cows were used in a cross-over study with two periods. Periods included two cows on a control diet and two cows on a SARA challenge. The control diet was a total mixed ration containing 45.5% dry matter (DM), 43.8% DM neutral detergent fiber, and 19.6% DM starch. The SARA challenge was conducted by gradually substituting the control diet with pellets containing 50% wheat and 50% barley over 3 days to reach a diet containing 55.6% DM, 31.3% DM neutral detergent fiber, and 31.8% DM starch, which was fed for four more days. Rumen fluid samples were collected at day 7 and 10 of experimental periods. Feces samples were collected on days 8 and 10 of these periods. Extracted DNA from the rumen and feces samples was analyzed to assess their bacterial communities using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. The induction of SARA reduced the richness, diversity, and stability of bacterial communities and resulted in distinctly different microbiota in the rumen and feces. Bacteroidetes and Firmicutes were the most abundant phyla and, combined, they represented 76.9 and 94.4% of the bacterial community in the rumen fluid and the feces, respectively. Only the relative abundance of Firmicutes in the rumen was increased by the SARA challenge. In rumen fluid and feces, the abundances of nine out of the 90 and 25 out of the 89 taxa, respectively, were affected by the challenge. Hence, SARA challenge altered the composition of the bacterial community at the lower taxonomical level in the feces and therefore also likely in the hindgut, as well as in the rumen. However, only reductions in the bacterial richness and diversity in the rumen fluid and feces were in agreement with those of other studies and had a biological basis. Although the composition of the bacterial community of the feces was affected by the SARA challenge, bacterial taxa in the feces that can be used for accurate and non-invasive diagnosis of SARA could not be identified.\",\n \"corpus_id\": 7201001,\n \"score\": 1\n },\n {\n \"doc_id\": \"28339527\",\n \"title\": \"Microbial community mapping in intestinal tract of broiler chicken.\",\n \"abstract\": \"Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.\",\n \"corpus_id\": 42174787,\n \"score\": 1\n },\n {\n \"doc_id\": \"28379996\",\n \"title\": \"The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China.\",\n \"abstract\": \"Soil bacteria are important drivers of biogeochemical cycles and participate in many nutrient transformations in the soil. Meanwhile, bacterial diversity and community composition are related to soil physic-chemical properties and vegetation factors. However, how the soil and vegetation factors affect the diversity and community composition of bacteria is poorly understood, especially for bacteria associated with evergreen and deciduous trees in subtropical forest ecosystems. In the present paper, the microbial communities of rhizospheric soils associated with different types of trees were analyzed by Illumina MiSeq sequencing the V3-V4 region of the 16S rRNA gene. A total of 121,219 effective 16S rRNA gene sequences were obtained, which were classified into 29 bacterial phyla and 2 archaeal phyla. The dominant phyla across all samples (>5% of good-quality sequences in each sample) were Proteobacteria, Acidobacteria, Firmicutes and Bacteroidetes. The bacterial community composition and diversity were largely affected by both soil pH and tree species. The soil pH was the key factor influencing bacterial diversity, with lower pH associated with less diverse communities. Meanwhile, the contents of NO3- were higher in evergreen tree soils than those associated with deciduous trees, while less NH4+ than those associated with deciduous trees, leading to a lower pH and indirectly influencing the diversity and composition of the bacteria. The co-occurrence patterns were assessed by network analysis. A total of 415 pairs of significant and robust correlations (co-occurrence and negative) were identified from 89 genera. Sixteen hubs of co-occurrence patterns, mainly under the phyla Acidobacteria, Proteobacteria, Firmicutes and Bacteroidetes, may play important roles in sustaining the stability of the rhizospheric microbial communities. In general, our results suggested that local environmental conditions and soil pH were important in shaping the bacterial community of the Taihu Lake zone in east China.\",\n \"corpus_id\": 18412432,\n \"score\": 1\n },\n {\n \"doc_id\": \"28453559\",\n \"title\": \"Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.\",\n \"abstract\": \"Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.\",\n \"corpus_id\": 32030973,\n \"score\": 1\n },\n {\n \"doc_id\": \"28505482\",\n \"title\": \"Conservation efforts of captive golden takin (Budorcas taxicolor bedfordi) are potentially compromised by the elevated chemical elements exposure.\",\n \"abstract\": \"Chemical elements exposure of endangered golden takins (Budorcas taxicolor bedfordi) living in the Qinling Mountains and in a captive breeding center was assessed by analyzing fecal samples. Concentrations of As, Co, Cr, Cu, Ni and Se were significantly higher in the feces of captive golden takins than the wild. There was no significant difference in the fecal concentrations of Cd, Mn, Hg, Pb or Zn for wild and captive animals. The element concentration of fecal samples collected from captive animals varied seasonally, with concentrations being lowest in spring and highest in winter and/or autumn. The food provided to captive animals varied both in the composition and the concentration of element present. Consumptions of feedstuff and additional foods such as D. sanguinalis and A. mangostanus for the captive golden takins were identified as the possible sources of chemical element exposure. The estimations of dietary intake of most elements by captive takins were below the oral reference dose, except for As and Pb, indicating that As and Pb were the key components which contributed to the potential non-carcinogenic risk for captive golden takins. In conclusion, captive golden takins were exposed to higher concentrations of chemical elements compared with the wild, which were likely due to their dietary difference. Conservation efforts of captive golden takin are potentially compromised by the elevated chemical element exposure and effort should focus on providing uncontaminated food for captive animals.\",\n \"corpus_id\": 1918079,\n \"score\": 1\n },\n {\n \"doc_id\": \"28642971\",\n \"title\": \"High Diversity of Bacterial Communities in Developmental Stages of Bactrocera carambolae (Insecta: Tephritidae) Revealed by Illumina MiSeq Sequencing of 16S rRNA Gene.\",\n \"abstract\": \"Bactrocera carambolae is a highly polyphagous fruit pest of agricultural importance. This study reports the bacterial communities associated with the developmental stages of B. carambolae. The microbiota of the developmental stages were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. At 97% similarity, there were 19 bacterial phyla and unassigned bacteria, comprising 39 classes, 86 orders, 159 families and 311 genera. The bacterial composition varied among the specimens of developmental stage and across developmental stages as well as exuviae. Four phyla of bacteria (with relative abundance of ≥1% in at least one specimen)-Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria-were recovered from the larva, pupa, adult stages and exuviae. Proteobacteria was the predominant phylum in all the developmental stages as well as the exuviae. Enterobacteriaceae (Proteobacteria) was the predominant family in the adult flies while the family [Weeksellaceae] (Bacteroidetes) was predominant in the larval and pupal stages. Among the genera occurring in more than one developmental stage of B. carambolae, Erwinia was more abundant in the larval stage, Halomonas more abundant in adult female, Stenotrophomonas more abundant in adult male, and Chryseobacterium more abundant in the larval and pupal stages. The results indicate transmission of bacteria OTUs from immatures to the newly emerged adults, and from exuviae to the environment.\",\n \"corpus_id\": 4526500,\n \"score\": 1\n },\n {\n \"doc_id\": \"28697583\",\n \"title\": \"The gut microbiota in larvae of the housefly Musca domestica and their horizontal transfer through feeding.\",\n \"abstract\": \"House fly larvae provide a prolific and sustainable source of proteins used in poultry and fish feed. Wheat bran is a superior diet for house fly larvae and has been widely investigated to exploit its potential in the food and feed area. Using Illumina MiSeq 16S rDNA sequencing, this study investigated the gut microbiota of house fly larvae feeding on wheat bran and the bacterial community in the wheat bran. The bacterial communities in the house fly larvae were dominated by the phyla Proteobacteria and Firmicutes. Enterobacteriaceae and Providencia were the predominant bacteria at the family and genus levels, respectively. Some bacteria in the phyla Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes may be transferred from the gut of house flies to the wheat bran during feeding and may be involved in degrading and utilizing polysaccharides in the cell wall of wheat bran. The significance of the gut microbiota of house fly larvae, their transferring and roles in degradation of wheat bran is discussed. These findings regarding the gut microbiota of house fly larvae will provide opportunities for research on the impact of microbial communities on poultry and fish.\",\n \"corpus_id\": 23768787,\n \"score\": 1\n },\n {\n \"doc_id\": \"28972993\",\n \"title\": \"Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets.\",\n \"abstract\": \"BACKGROUND: Gut microbial composition is dependent on diet. Geese are herbivores and can digest crude fibre, but the relationship between composition of the microbiota and a fibre-rich diet in geese is not well understood. RESULTS: Here, caecal and faecal samples were collected simultaneously from all-grass-fed geese and high-grain-fed geese and the hypervariable V3-V4 regions of the bacterial 16S rRNA gene were sequenced. The results was identified that high-grass-fed geese possessed significantly higher alpha diversity both in caecum and faeces compared with that in all-grain-fed geese. In addition, the composition of dominant bacterium occurred remarkable shifting due to different diet patterns, Firmicutes were more abundant in all-grass-fed geese, whereas Bacteroidetes were abundant in high-grain-fed geese. Fusobacteria and Deferribacteres were obviously present in high-grain-fed geese and few in all-grass-fed geese. Most importantly, some specific microorgnisms such as Ruminococcaceae, Lachnospiraceae and Bacteroidaceae which may associated with cellulose-degrading that were characterized to show distinctly diverse between the two diet patterns. PICRUSt analysis revealed the metabolic pathways such as carbohydrate and amino acid metabolism were overrepresented in all-grass-fed geese. CONCLUSIONS: In conclusion, Firmicutes and Bacteroidetes were identified abundantly when the geese was fed with all-grass feed and high-grain feed, respectively. And Ruminococcaceae, Lachnospiraceae and Bacteroidaceae were recognized as main cellulose-degrading bacteria in the geese. The functional profiles of gut microbiota revealed the dominant microbiota communities were involved mainly in the carbohydrate metabolism in all-grass-fed geese.\",\n \"corpus_id\": 23790194,\n \"score\": 1\n },\n {\n \"doc_id\": \"29057500\",\n \"title\": \"The impact of rumen cannulation on the microbial community of goat rumens as measured using 16S rRNA high-throughput sequencing.\",\n \"abstract\": \"The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high-throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene. High-throughput sequencing was performed using an Illumina MiSeq platform, and the sequences were analyzed primarily using the Quantitative Insights into Microbial Ecology pipeline software. The results showed that the Chao 1 index, the observed species index and the Shannon-Wiener index were not significantly different (p > 0.05) between the two groups. Bacteroidetes, Firmicutes, Tenericutes were the predominant phylum in both groups, and their relative abundance was 60.63%, 29.48%, 2.24% (n = 6, CT group) and 61.17%, 26.92%, 1.66% (n = 6, RC group) respectively. At the phylum level, the relative abundance of Proteobacteria was significantly higher (p < 0.001) in the microbial communities of RC goats, and Planctomycetes and Chloroflexi were significantly lower (p = 0.02). The abundances of other phyla were not significantly different between treatments. A total of 19 lower-level taxa also exhibited significant differences (p < 0.05) in relative abundance between the groups. In addition, there were 18 genera shared within the control group, 26 shared within the rumen-cannulated group, and 16 shared by both groups. Prevotella was the most abundant shared genus, although its abundance was not significantly different (p > 0.05) between the groups. In conclusion, although the most abundant microbes kept stable, rumen cannulation had the potential to significantly change rumen microbial communities in goats.\",\n \"corpus_id\": 38957918,\n \"score\": 1\n },\n {\n \"doc_id\": \"29172724\",\n \"title\": \"Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects.\",\n \"abstract\": \"PURPOSE: The aim of this study was to identify differences in the major (core vs. variable) microbial genera of human subjects with and without diabetes. METHODS: Bacterial 16S rRNA genes obtained from conjunctival swabs of 19 healthy subjects and 30 diabetic patients were sequenced using the Illumina MiSeq platform, and the sequencing data were analyzed using QIIME 1.9.1. To elucidate the microbial diversity in the ocular surface (OS), test programs from various bioinformatics domains were used. RESULTS: Diversity index and rarefaction analysis showed that the microbial community of the diabetic patients was more diverse than that of the healthy subjects. Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria and Bacteroidetes were the dominant taxa present in the OS, and there was a significant difference in the relative abundance of the bacterial phyla between the diabetic patients and control subjects. Proteobacteria were more abundant in the diabetic group, whereas Firmicutes was more abundant in the control group. Analysis of bacterial taxa at the genus level showed that the core microbiome of diabetic patients comprised Acinetobacter, Burkholderia, Sphingomonas, and Ralstonia, whereas that of the controls comprised Bradyrhizobiaceae, Staphylococcus, Corynebacterium, Pseudomonas, Novosphingobium, Neisseriaceae, and Acinetobacter. CONCLUSIONS: There was a significant difference in the microbial community composition between diabetic patients and healthy subjects. A high abundance of Acinetobacter in the OS of diabetic patients may arise from the unique characteristics of the OS compared with those of other organ surfaces.\",\n \"corpus_id\": 5344827,\n \"score\": 1\n },\n {\n \"doc_id\": \"29487373\",\n \"title\": \"Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese.\",\n \"abstract\": \"Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.\",\n \"corpus_id\": 54629456,\n \"score\": 1\n },\n {\n \"doc_id\": \"29579944\",\n \"title\": \"Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing.\",\n \"abstract\": \"Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.\",\n \"corpus_id\": 4430578,\n \"score\": 1\n },\n {\n \"doc_id\": \"29849646\",\n \"title\": \"Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt.\",\n \"abstract\": \"The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level, Prevotella, Bacillus, Porphyromonas, Streptococcus, and Bacteroides were the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.\",\n \"corpus_id\": 44061314,\n \"score\": 1\n },\n {\n \"doc_id\": \"26496917\",\n \"title\": \"Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing.\",\n \"abstract\": \"This study was carried out to understand microbial diversity and function in the microbial enhanced oil recovery (MEOR) process and to assess the impact of MEOR treatment on the microbial community in an oil reservoir. The Illumina MiSeq-based method was used to investigate the structure and dynamics of the microbial community in a MEOR-treated block of the Baolige oilfield, China. The results showed that microbial diversity was high and that 23 phyla occurred in the analyzed samples. Proteobacteria, Firmicutes, Bacteroidetes, Thermotogae, and Euryarchaeota were present in relatively high abundance in all analyzed samples. Injection of bacteria and nutrients resulted in interesting changes in the composition of the microbial community. During MEOR treatment, the community was dominated by the known hydrocarbon-utilizing genera Pseudomonas and Acinetobacter. After the treatment, the two genera decreased in abundance over time while Methanobacteriaceae, as well as known syntrophic genera such as Syntrophomonas, Pelotomaculum, Desulfotomaculum, and Thermacetogenium gradually increased. The change in dominant microbial populations indicated the presence of a succession of microbial communities over time, and the hydrocarbon degradation and syntrophic oxidation of acetate and propionate to methane in the MEOR-treated oilfield. This work contributes to a better understanding of microbial processes in oil reservoirs and helps to optimize MEOR technology.\",\n \"corpus_id\": 8870452,\n \"score\": 0\n },\n {\n \"doc_id\": \"26929931\",\n \"title\": \"Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine.\",\n \"abstract\": \"The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.\",\n \"corpus_id\": 9074739,\n \"score\": 0\n },\n {\n \"doc_id\": \"28109256\",\n \"title\": \"Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform.\",\n \"abstract\": \"BACKGROUND: The composition of the skin microbiome is predicted to play a role in the development of conditions such as atopic eczema and psoriasis. 16S rRNA gene sequencing allows the investigation of bacterial microbiota. A significant challenge in this field is development of cost effective high throughput methodologies for the robust interrogation of the skin microbiota, where biomass is low. Here we describe validation of methodologies for 16S rRNA (ribosomal ribonucleic acid) gene sequencing from the skin microbiome, using the Illumina MiSeq platform, the selection of primer to amplify regions for sequencing and we compare results with the current standard protocols.. METHODS: DNA was obtained from two low density mock communities of 11 diverse bacterial strains (with and without human DNA supplementation) and from swabs taken from the skin of healthy volunteers. This was amplified using primer pairs covering hypervariable regions of the 16S rRNA gene: primers 63F and 519R (V1-V3); and 347F and 803R (V3-V4). The resultant libraries were indexed for the MiSeq and Roche454 and sequenced. Both data sets were denoised, cleaned of chimeras and analysed using QIIME. RESULTS: There was no significant difference in the diversity indices at the phylum and the genus level observed between the platforms. The capture of diversity using the low density mock community samples demonstrated that the primer pair spanning the V3-V4 hypervariable region had better capture when compared to the primer pair for the V1-V3 region and was robust to spiking with human DNA. The pilot data generated using the V3-V4 region from the skin of healthy volunteers was consistent with these results, even at the genus level (Staphylococcus, Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, Enhydrobacter and Deinococcus identified at similar abundances on both platforms). CONCLUSIONS: The results suggest that the bacterial community diversity captured using the V3-V4 16S rRNA hypervariable region from sequencing using the MiSeq platform is comparable to the Roche454 GS Junior platform. These findings provide evidence that the optimised method can be used in human clinical samples of low bacterial biomass such as the investigation of the skin microbiota.\",\n \"corpus_id\": 8417168,\n \"score\": 0\n },\n {\n \"doc_id\": \"29131360\",\n \"title\": \"Bacterial diversity and community structure during fermentation of Chinese sauerkraut with Lactobacillus casei 11MZ-5-1 by Illumina Miseq sequencing.\",\n \"abstract\": \"The bacterial diversity and community structure involved in Chinese sauerkraut is one of the most important factors shaping the final characteristics of traditional foods. In this research, Lactobacillus casei 11MZ-5-1 was applied in Chinese sauerkraut fermentation as a starter culture. Illumina Miseq sequencing analysis was used to reveal the bacterial diversity and community structure during Chinese sauerkraut fermentation. A total of 177 283 high-quality reads of 16S rRNA V4 regions were obtained. The inoculation of L. casei 11MZ-5-1 decreased considerably the bacterial richness and bacterial diversity. This inoculum led to the replacement of Lactococcus by Lactobacillus. The levels of Pseudomonas and Enterobacter bacteria decreased. These findings reveal the evolution of important bacterial groups that are involved in fermentation and will facilitate improvements in the Chinese sauerkraut fermentation process. SIGNIFICANCE AND IMPACT OF THE STUDY: This research thoroughly revealed the effects of Lactobacillus casei 11MZ-5-1 starter cultures on bacterial communities during Chinese sauerkraut fermentation. Illumina Miseq sequencing was effective technique to monitor the bacterial diversity and community structure. The inoculation of L. casei 11MZ-5-1 led to the decline of bacterial richness and diversity together with a consistent predominance of Lactobacillus during spontaneous fermentation. The result collectively suggested L. casei 11MZ-5-1 is a promising starter in Chinese sauerkraut manufacturing.\",\n \"corpus_id\": 3913194,\n \"score\": 0\n },\n {\n \"doc_id\": \"29478633\",\n \"title\": \"Revealing the anaerobic acclimation of microbial community in a membrane bioreactor for coking wastewater treatment by Illumina Miseq sequencing.\",\n \"abstract\": \"The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase-decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority (less than 1%) to the dominant bacterial group (54.0%) along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in \\\"rare biosphere\\\" might eventually become dominant in response to environmental change.\",\n \"corpus_id\": 3538618,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":54,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29544493\",\n \"title\": \"Why people use herbal medicine: insights from a focus-group study in Germany.\",\n \"abstract\": \"BACKGROUND: The use of herbal medicine, as one element of complementary and alternative medicine, is increasing worldwide. Little is known about the reasons for and factors associated with its use. This study derives insights for the use of herbal medicine in Germany regarding the usage aims, role played by the type of illness, reasons for preferred usage and sources of information. METHODS: Using a qualitative methodological approach, six focus groups (n = 46) were conducted. Two groups with young, middle-aged and elderly participants, respectively. After audiotaping and verbatim transcription, the data were analysed with a qualitative content analysis. RESULTS: We found that treating illnesses was the most frequently discussed aim for using herbal medicine over all age groups. Preventing illnesses and promoting health were less frequently mentioned overall, but were important for elderly people. Discussions on herbal medicine were associated with either mild/moderate diseases or using herbal medicine as a starting treatment before applying conventional medicine. In this context, participants emphasized the limits of herbal medicine for severe illnesses. Dissatisfaction with conventional treatment, past good experiences, positive aspects associated with herbal medicine, as well as family traditions were the most commonly-mentioned reasons why herbal medicine was preferred as treatment. Concerning information sources, independent reading and family traditions were found to be equally or even more important than consulting medicinal experts. CONCLUSIONS: Although herbal medicine is used mostly for treating mild to moderate illnesses and participants were aware of its limits, the combination of self-medication, non-expert consultation and missing risk awareness of herbal medicine is potentially harmful. This is particularly relevant for elderly users as, even though they appeared to be more aware of health-related issues, they generally use more medicine compared to younger ones. In light of our finding that dissatisfaction with conventional medicine was the most important reason for a preferred use of herbal medicine, government bodies, doctors, and pharmaceutical companies need to be aware of this problem and should aim to establish a certain level of awareness among users concerning this issue.\",\n \"corpus_id\": 4056522\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18549476","title":"The role of complementary and alternative medicine (CAM) in Germany - a focus group study of GPs.","abstract":"BACKGROUND: There has been a marked increase in the use of complementary and alternative medicine (CAM) in recent years worldwide. In Germany, apart from 'Heilpraktiker' (= state-licensed, non-medical CAM practitioners), some general practitioners (GPs) provide CAM in their practices. This paper aims to explore the attitudes of GPs about the role of CAM in Germany, in relation to the healthcare system, quality of care, medical education and research. Furthermore, experiences of GPs integrating CAM in their daily practice were explored. METHODS: Using a qualitative methodological approach 3 focus groups with a convenience sample of 17 GPs were conducted. The discussions were transcribed verbatim and analysed using qualitative content analysis. RESULTS: The majority of the participating GPs had integrated one or more CAM therapies into their every-day practice. Four key themes were identified based on the topics covered in the focus groups: the role of CAM within the German healthcare system, quality of care, education and research. Within the theme 'role of CAM within the healthcare system' there were five categories: integration of CAM, CAM in the Statutory Health Insurance, modernisation of the Statutory Health Insurance Act, individual healthcare services and 'Heilpraktiker'. Regarding quality of care there were two broad groups of GPs: those who thought patients would benefit from standardizing CAM and those who feared that quality control would interfere with the individual approach of CAM. The main issues identified relating to research and education were the need for the development of alternative research strategies and the low quality of existing CAM education respectively. CONCLUSION: The majority of the participating GPs considered CAM as a reasonable complementary approach within primary care. The study increased our understanding of GPs attitudes about the role of CAM within the German healthcare system and the use of 'Heilpraktiker' as a competing CAM-provider. It seems to be a need for increased funding for research, better education and remuneration by the Statutory Health Insurance in order to improve access to 'Integrative medicine' in Germany.","corpus_id":1890860,"score":2},{"doc_id":"18845412","title":"\"I don't know how many of these [medicines] are necessary..\" - a focus group study among elderly users of multiple medicines.","abstract":"OBJECTIVE: The growing prevalence of multiple medicine use among elderly challenges health care. The aim was to conduct an exploratory study describing multiple medicine use from the elderly patient's perspective. METHODS: Twelve focus groups of 29 men and 30 women 65 years of age or older, using five or more medicines were analysed qualitatively. RESULTS: Initially the participants reported no problems with using multiple medicines; they felt fortunate that medicines existed and kept them alive. However, negative attitudes were also revealed, both similar to those presented in studies on lay experience of medicine-taking and some that appear more specific to users of multiple medicines. The foremost of these was that acceptance of medicines depends on not experiencing adverse effects and worrying whether multiple medicine use is 'good' for the body. Furthermore, participants' perception of their medicines depended on interaction with doctors, i.e. trusting 'good' doctors. CONCLUSION: The participants revealed co-existing accounts of both immediate gratitude and problems with using multiple medicines. Furthermore, the patient-doctor relationship coloured their attitudes towards their medicines. PRACTICE IMPLICATIONS: Importance of the patient-doctor relationship for treatment success is highlighted. Moreover, to be able to capture both accounts of the elderly in this study an appropriate consultation length is needed.","corpus_id":942688,"score":2},{"doc_id":"19442268","title":"The use of herbal medicines by people with cancer: a qualitative study.","abstract":"BACKGROUND: Between 7% and 48% of cancer patients report taking herbal medicines after diagnosis. Because of the possibility of unwanted side effects or interactions with conventional treatments, people with cancer are generally advised to tell the professionals treating them if they are taking any form of medication, including herbal medicines and supplements. Studies suggest that only about half do so and that the professionals themselves have at best very limited knowledge and feel unable to give informed advice. This study is intended to inform the future development of information resources for cancer patients, survivors and healthcare professionals including tools for use before or during consultation to make it easier for patients to mention, and for healthcare professionals to ask about, use of herbal medications. METHODS/DESIGN: This is a three-phase study. In phase 1, a systematic review of the literature on self-medication with herbal medicines among UK populations living with cancer will establish the current evidence base on use of herbal medicine, sources of information, characteristics and motivations. This will allow us to better understand what aspects need further investigation and inform the topic guide for a qualitative study (phase 2). Six focus groups of six to eight cancer patients who have used at least one herbal preparation since diagnosis will explore behaviour, beliefs, knowledge, information sources and needs in an informal conversational setting. Informed by the findings of the systematic review and qualitative study, in phase 3 we will construct and pilot a questionnaire for a future large-scale survey to quantify and prioritise people's beliefs, needs and information preferences. DISCUSSION: Despite known interactions with conventional cancer treatments and contraindications for some herbal remedies with specific cancers, reliable information resources for patients are very limited. Identifying cancer patients' information needs and preferences is the first step in creating a suitable resource for both the public and the professionals advising them.","corpus_id":10351583,"score":2},{"doc_id":"19797394","title":"The use of herbal medicines by people with cancer in the UK: a systematic review of the literature.","abstract":"BACKGROUND AND AIM: Little is known about the use of herbal medicines by people living with cancer in the UK. This systematic review aimed to estimate the prevalence of herbal medicine use by this group, the characteristics of users, factors motivating use, and attitudes towards herbal remedies. DESIGN AND METHODS: Fifteen electronic databases were searched. People who were research-active in the field were contacted and asked about further published or unpublished work. All studies identified as relevant to the purpose of the review were assessed. Searches were not restricted by publication type or date. RESULTS: Of 1288 unique references identified, 11 met the eligibility criteria. Studies were excluded where research had been conducted outside the UK; where information on herbal medicine use was not differentiated from that relating to complementary and alternative therapies more broadly, and where neither prevalence of use nor information on user characteristics was included. Prevalence estimates ranged from 3.1 to 24.9%. Most studies did not obtain information specifically on herbal medicines and only one examined the characteristics and motivations of users of herbal medicines as distinct from complementary and alternative therapies in general. CONCLUSION: The high degree of heterogeneity of methodology, sample selection and characteristics, and research design resulted in a wide range of estimates of prevalence. Well-designed research is needed to define the evidence base about the herbal medicines taken by people with cancer in the UK, the reasons for use, knowledge about possible effects and potential risks, and where people seek information.","corpus_id":24839125,"score":2},{"doc_id":"19942110","title":"Simply because it works better: exploring motives for the use of medical herbalism in contemporary U.K. health care.","abstract":"AIM: To clarify the reasons underlying people's use of medical herbalism in the context of contemporary U.K. health care. DESIGN: This qualitative, interpretative study recruited 19 adults who were consulting with registered medical herbalists in a region of southern England. Participants were interviewed about their experiences and the data were analysed thematically. Study methodology was informed by Gadamerian hermeneutic phenomenology. RESULTS: Few of the participants had initially set out to try herbalism, most looking for 'an alternative' to conventional health care. The main reason for exploring non-conventional options was to seek out health care that would more effectively meet their self-perceived needs in the treatment of a chronic condition. As a result of favourable outcomes from their initial treatment, participants subsequently continued to use herbalism for the management of more general, everyday health problems. CONCLUSIONS: Lay and professional ideas about what constitutes health care 'effectiveness' do not necessarily correspond. Participants reported that, in comparison to conventional medicine, medical herbalism satisfied their expectations of health care because it more readily met their own criteria for effectiveness and because it had greater consistency with their own understanding about health, illness and health care. Central to achieving this was the collaborative nature of the herbalist's approach, as well as the therapeutic effect and enduring history of the herbal therapy itself. Participants were in favour of a future integrative health care system provided this did not interfere with the unique attributes of herbalism that make it distinct from conventional medicine.","corpus_id":22691989,"score":2},{"doc_id":"22894888","title":"A pilot study to assess students' perceptions, familiarity, and knowledge in the use of complementary and alternative herbal supplements in health promotion.","abstract":"CONTEXT: According to the National Center for Complementary and Alternative Medicine (NCCAM), use of herbal supplements is increasing and will continue to rise. With parents administering medicinal herbs to children as a preventive alternative to traditional drugs, the research team thought it would be interesting to assess the use of these products during the transition into adulthood through college life. OBJECTIVE: This study examined participants' perceptions of, familiarity with, and knowledge of herbal supplements for health promotion. DESIGN: The research team invited participants to complete a 13-item Perception, Familiarity, and Knowledge Survey (PFKS). This online survey included questions regarding demographics, perceptions of complementary and alternative medicine, and familiarity with and knowledge of gingko, ginseng, St. John's wort, garlic, echinacea, and cinnamon. SETTING: The study occurred at a Midwestern university. PARTICIPANTS: Two-hundred and eighty-six college students participated. OUTCOME MEASURES: The research team used the Chi-square test of association to examine the class rank (freshmen/sophomores, juniors/seniors, and graduate students) of students (frequency) and their gender in relation to their perceptions of, familiarity with, and knowledge of herbal supplements. RESULTS: Chi-square analysis showed that 80.8% of participants were familiar with complementary and alternative medicine (CAM) (P = .000). Of participants who were aware of the six herbs, a majority was familiar with ginkgo (82.4%), ginseng (96.1%), St. John's wort (78.4%), garlic (98.4%), echinacea (65.6%), and cinnamon (96.8%). Despite students' familiarity with the herbs, 45.1% to 74.1% of the participants were unsure of their effectiveness in preventing disease or promoting good health. Participants perceived the barriers to their CAM awareness as (1) insufficient education (26.0%), (2) a lack of scientific evidence (25.9%), and (3) a lack of trained professionals (17.5%). Many students (85.8%) desired educational courses on CAM therapies, with nutrition professors being ranked highest as the providers of this education by 88.0%. Over 60.0% of participants thought that conventional medicine could benefit from integration with CAM and that medical professionals should integrate CAM into health-care practices. CONCLUSION: College students appear to be highly familiar with CAM and herbal supplements but currently have little experience with and knowledge of herbal supplements.","corpus_id":23942666,"score":2},{"doc_id":"22940254","title":"A prospective study on the safety of herbal medicines, used alone or with conventional medicines.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: Along with increase of herbal medicine use worldwide, the safety of traditional herbal medicines frequently becomes a medical issue. AIM OF THE STUDY: This study aimed to investigate the incidence of herbal medicine-induced adverse effects on liver functions. SUBJECTS AND METHODS: A prospective study was performed with 313 inpatients (87 male and 226 female) receiving herbal prescriptions during hospitalization. The patients were classified into two groups based on their treatments: one group received herbal medicines only (57 patients), and another received herbal and conventional medicines concurrently (256 patients). All patients were given liver and renal function tests at the start of hospitalization (baseline) and at approximately 2-week intervals thereafter, until discharge. RESULTS: Six of the 313 patients showed abnormal liver function without related clinical symptoms (1.9%, 95% CI 0.38-3.41); none of the patients in the herbal group had abnormal result in liver function tests (0% of 57 patients) while all six had received a combination of herbal and conventional medicines (2.3% of 256 patients, 95% CI 0.46-4.14). CONCLUSION: Our findings indicate that herbal drugs used alone are relatively safe, but the risk for adverse reactions may increase when herbal and conventional drugs are taken concurrently.","corpus_id":5133756,"score":2},{"doc_id":"23346197","title":"Herbal Medicine in Primary Healthcare in Germany: The Patient's Perspective.","abstract":"Herbal medicine (HM) is one of the most widely used Complementary and Alternative Medicine (CAM) therapies throughout the world. The WHO has recognized HM as an essential component of primary healthcare. The aim of this study was to explore patients' attitudes towards using HM, their sources of information and the role of costs. Within a qualitative research approach, semi-standardized interviews with 18 patients using HM were conducted and analyzed according to Mayring's content analysis. Patients highlighted their active role and perceived autonomy choosing HM. Most interviewees experienced HM as better, with more sustainable effects and fewer side effects compared to conventional medicine. All media, family, friends, and healthcare professionals were reported as sources of information. Some patients complained that doctors and pharmacists have insufficient knowledge of HM. Most patients expressed their regret that HM is not reimbursed by statutory health insurances but also their general willingness to pay extra for HM. The main challenge for German primary care, besides the reintroduction of reimbursement, is the promotion of knowledge and skill development in HM. This is to ensure patient safety and work in partnership with patients. Appropriate strategies for education must be tailored to the specific needs of health professional groups.","corpus_id":-1,"score":2},{"doc_id":"23820895","title":"Consumers' attitude towards the use and safety of herbal medicines and herbal dietary supplements in Serbia.","abstract":"BACKGROUND: The use of herbal medicines and herbal dietary supplements in Serbia is very common and many patients consume herbal preparations with conventional drug therapy. OBJECTIVE: The aim of this survey was to evaluate the consumers' awareness of herbal remedies and the safety of herbal dietary supplements, their attitude towards combining herbals and drugs, and the source of recommendations for their use. SETTING: The study included all consumers who bought herbal remedies and herbal dietary supplements in 15 pharmacies on the territory of Novi Sad during 2011 and who accepted to be interviewed. METHODS: Structured interviews using questionnaire, conducted by pharmacists. The questionnaire included 4 parts: socio-demographic characteristics of consumers, source of recommendations for the use of herbal products, attitude towards safety of herbal remedies and herbal dietary supplements use and their combination with regular drugs, as well as the question of purchased herbal products. MAIN OUTCOME MEASURE: Consumers' attitude towards the safety and use of herbal medicines and herbal dietary supplements measured by 9 items. RESULTS: The majority of interviewed participants were highly educated, aged 41-60 and they consumed herbal remedies on their own initiative or on recommendation of nonmedically educated person, without previous consultation with medical doctor or pharmacist. Out of all participants: 88.9 % did not consider it important to inform their physician or pharmacist about use of herbal remedies and herbal dietary supplements; 73.3 % found the use of herbal remedies harmless (where 9.4 % did not have any attitude towards that issue), while 40.3 % of participants regarded the combining of herbal and regular drugs unsafe. CONCLUSION: There is a need for consumers' education on reliable use of herbal medicines and herbal dietary supplements, in order to improve their awareness of the limits of herbal remedies safety and potential risks of their combination with drugs.","corpus_id":22226440,"score":2},{"doc_id":"24988878","title":"Use of herbal medicinal products among children and adolescents in Germany.","abstract":"BACKGROUND: Germany is a country with a high use of herbal medicinal products. Population-based data on the use of herbal medicinal products among children are lacking. The aim of this study is to investigate the prevalence, patterns and determinants of herbal medicine use among children and adolescents in Germany. METHODS: As data base served the German Health Interview and Examination Survey for Children and Adolescents (KiGGS), a representative population based survey conducted 2003-2006 by the Robert Koch Institute. 17,450 boys and girls aged 0-17 years provided information on drug use in the preceding seven days. Herbal medicinal products were defined according to the European and German drug laws. SPSS Complex Sample method was used to estimate prevalence rates and factors associated with herbal medicine use. RESULTS: The prevalence rate of herbal medicinal product use amounts to 5.8% (95% confidence interval 5.3-6.3%). Use of herbal medicine declines along with increasing age and shows no difference between boys and girls in younger age groups. Teenage girls are more likely to use herbal medicines than teenage boys. Two thirds of herbal medicines are used for the treatment of coughs and colds; nearly half of herbal medicines are prescribed by medical doctors. Determinants of herbal medicinal product use are younger age, residing in South Germany, having a poor health status, having no immigration background and coming from a higher social class family. Children's and parents-related health behavior is not found to be associated with herbal medicine use after adjusting for social class. CONCLUSIONS: Use of herbal medicinal products among children and adolescents between the ages of 0 and 17 years in Germany is widely spread and shows relatively higher rates compared to international data. This study provides a reference on the use of herbal medicinal products for policy-makers, health professionals and parents. Further studies are needed to investigate the effectiveness and safety of specific herbal medicinal products, potential effects of long term use as well as possible interactions of herbal medicinal products with concomitantly used conventional medicines.","corpus_id":5534312,"score":2},{"doc_id":"25885673","title":"Utilization of complementary and alternative medicine (CAM) among children from a German birth cohort (GINIplus): patterns, costs, and trends of use.","abstract":"BACKGROUND: The use of complementary and alternative medicine (CAM) is widespread among children in Germany and other European countries. Only a few studies are available on trends in pediatric CAM use over time. The study's objective was to present updated results for prevalence, predictors, and costs of CAM use among German children and a comparison with findings from a previous follow-up of the same birth cohort. METHODS: Data were collected for 3013 children on their utilization of medicinal products (during the last 4 weeks) and consultation with CAM providers (in the preceding year) from a German birth cohort study (GINIplus, 15-year follow-up) using a self-administered questionnaire. The reported medicinal CAMs were classified into six categories (homeopathy, herbal drugs, nutritionals, minerals and trace elements, microorganisms, further CAM). Drug prices were traced using pharmaceutical identification numbers (PZNs), or otherwise conservatively estimated. Finally, the results were compared with data obtained from the 10-year follow-up of the same birth cohort study by adopting the identical methodology. RESULTS: In all, 26% of the reported 2489 drugs were medicinal CAM. The 4-week prevalence for homeopathy and herbal drug use was 7.5% and 5.6%, respectively. Some 13.9% of the children used at least one type of medicinal CAM in the preceding 4 weeks. The 1-year prevalence for consultation with CAM providers was 10.8%. From the drugs identified as CAM, 53.7% were homeopathic remedies, and 30.8% were herbal drugs. Factors associated with higher medicinal CAM use were female gender, residing in Munich, and higher maternal education. A homeopathy user utilized on average homeopathic remedies worth EUR 15.28. The corresponding figure for herbal drug users was EUR 16.02, and EUR 18.72 for overall medicinal CAM users. Compared with the 10-year follow-up, the prevalence of homeopathy use was more than halved (-52%) and dropped substantially for herbal drug use (-36%) and overall CAM use (-38%) as well. CONCLUSION: CAM use among 15-year-old children in the GINIplus cohort is popular, but decreased noticeably compared with children from the same cohort at the age of 10 years. This is possibly mainly because German health legislation normally covers CAM for children younger than 12 years only.","corpus_id":16179819,"score":2},{"doc_id":"26385752","title":"Exploration of Why Alaskans Use Complementary Medicine: A Focus Group Study.","abstract":"PURPOSE: To explore why Alaskans choose to pursue complementary medicine as a health care option. DESIGN: Qualitative descriptive. METHOD: A purposive convenient recruitment methodology was used to recruit project participants. Focus groups were conducted to collect the research data. FINDINGS: Five themes were identified that highlighted why participants use complementary medicine: dissatisfaction, effective, holistic, relationship focused, and a personal journey.","corpus_id":253405,"score":2},{"doc_id":"26425496","title":"From Disappointment to Holistic Ideals: A Qualitative Study on Motives and Experiences of Using Complementary and Alternative Medicine in Sweden.","abstract":"BACKGROUND: Recent studies indicate increased use of complementary and alternative medicine (CAM) in western societies, to ameliorate health problems. Even if there is substantial research on general patterns of use, there is limited knowledge on individual motives. This study contributes to a qualitative understanding of experiences of choosing and using CAM. DESIGN AND METHODS: This study consists of in-depth interviews with 10 CAM users in Sweden. The participants represent different backgrounds and experiences of using CAM. The interviews have been analysed in accordance with content analysis. RESULTS: In analysing experiences of choosing and using CAM four main themes were identified: frustration and critique, values and ideology, individual responsibility, and combining treatments. In general, the participants were highly reflexive on issues concerning their health. They highlighted their own role and responsibility, combined a variety of treatments, and continuously dealt with questions on risks, even if they had relatively different approaches to if and when to use CAM. The results also show that motives may change over time. Even if initial choices were closely related to frustration and critique of conventional treatments (for example, by perceiving conventional health care as limited, not receiving proper diagnoses, or being critical to conventional drugs) was long-term use motivated by ideological characteristics of CAM (such as holistic and individualized treatments, and extensive interaction with practitioners). CONCLUSIONS: Four main themes, concerning experiences of choosing and using CAM were identified. This study also supports the idea that initial motives for choosing CAM may differ from those explaining long-term use. Significance for public healthRecent studies indicate increased use of complementary and alternative medicine (CAM), both in general western populations and specific patient groups. Well-documented motives for choosing CAM are related to disappointment and failure of conventional health care. In addition, there are findings that demonstrate that certain basic values (such as individualism and holistic orientations) are related to the use of CAM. A better understanding of individual motives behind people's choice of CAM, and how this is related to their perception of the health care system, is important for policy makers and health care professionals alike. This study contributes to a qualitative understanding of experiences of choosing and using CAM and how motives may change over time. It also contributes with knowledge on how users combine CAM with conventional health care and deal with risks.","corpus_id":5774801,"score":2},{"doc_id":"18365495","title":"[Use of complementary and alternative medicine among the patients in primary health care].","abstract":"Upotreba komplementarne i alternativne medicine kod pacijenata u primarnoj zdravstvenoj zastiti. OBJECTIVE: Use of complementary and alternative medicine (CAM) is widespread in western countries despite its unconfirmed effectiveness. The aim of the study was to show the use of CAM by patients in primary health care. PATIENTS AND METHODS: Cross-sectional method was used in a sample of 941 patients attending fourteen primary care practices from six Croatian cities who visited their family physician for whatever reason and filled in an anonymous questionnaire. On data analysis, distribution of frequencies and chi2-test were used. A probability value of p (two-tailed) indicated a statistically significant difference. RESULTS: The response rate was 70%. At least once in their lifetime CAM was utilized by 46% and in previous year by 32% of patients. Most frequent users were persons in the 46-55 age group years and those with higher education. A statistically significant difference was established between CAM utilization and age, education, employment and relaxation/stress reducing techniques. The most frequently used methods were herbalism (38%), homeopathy (15.6%) and acupuncture (13.1%). In 53.5% of subjects CAM was used together with conventional medicine. CAM was most often used for musculoskeletal diseases, gastrointestinal diseases, and for prevention. Chiropractic was most commonly used for musculoskeletal disorders, and herbalism and homeopathy for respiratory disorders. Supplements, natural healing products and homeopathic medicines were used by 80.1% of study subjects. Patients decide on the use of CAM because they believe it will help them (27%), conventional medicine failed to alleviate their complaints (19.7%) and they were afraid of side effects of drugs (13.3%). Satisfaction with CAM treatment was reported by 45.5% of study subjects. More than half of the patients notified their physician on the use of CAM (59.6%) and the majority (81.7%) of all subjects would like to discuss the use of CAM in their treatment with their family physician. DISCUSSION: In this study, the use of CAM was consistent with literature data. Frequent use of herbal method may lead to potential risks due to possible herb-drug interactions. The reason for the use of CAM is rarely dissatisfaction with their physician but often dissatisfaction with the results and side effects of conventional treatment. Doctors will require additional education on CAM methods, their effectiveness, safety, indications and contraindications in order to be well informed and able to discuss CAM use with their patients. CONCLUSION: The use of CAM is common among patients attending primary health care. Sociodemographic factors are important predictors of its use. Doctors should openly ask their patients about the use of CAM and receive proper education to be able to discuss the potential benefits versus possible risks of its use in individual cases.","corpus_id":10670206,"score":1},{"doc_id":"19942109","title":"Use of traditional and complementary medicine in Malaysia: a baseline study.","abstract":"BACKGROUND: The increasing popularity and use of traditional and complementary medicine (TCAM) in both developed and developing countries, including Malaysia, have raised significant public health policy issues. However, currently, there is a paucity of baseline data on such usage by the Malaysian community. OBJECTIVE: This study was conducted to identify and describe the prevalence and frequency of various TCAM modalities that are being used by the Malaysian population by age, gender, marital and working status, educational level and ethnic group for health issues and maintenance. DESIGN: A nationwide interviewer-administered questionnaire survey was conducted in August 2004. An open-ended questionnaire pertaining to TCAM modalities was used to increase the probability of capturing maximum data. This survey implemented a multistage design, stratified by state and urban/rural random sampling, proportionate to the size of the state population and was representative of the Malaysian population. Post-survey classification of modalities was done accordingly. Complex data analysis was carried out using SPSS 13.0. RESULTS: Various TCAM modalities that were used by the Malaysian population were identified and categorised. Biological-based therapies, which included herbal therapy, were most commonly used for health problems (88.9%) and for health maintenance (87.3%). Under this category, herb-based application/herb-based beauty product/herb-based hygiene product group was most commonly used for health issues (23.6%) while pure herbs were the ones most commonly used for health maintenance (29.6%). There was no significant difference across all groups in the usage of biological-based therapies for health issues. CONCLUSION: The study showed that there is a high prevalence of TCAM use by the Malaysian population, particularly in the use of herb-based therapies for both health issues and health maintenance. Thus, a strict guideline for herbal commercialisation as well as public education is important.","corpus_id":23066608,"score":1},{"doc_id":"20043858","title":"Attitude and use of herbal medicines among pregnant women in Nigeria.","abstract":"BACKGROUND: The use of herbal medicines among pregnant women in Nigeria has not been widely studied. METHODS: Opinion of 595 pregnant women in three geopolitical zones in Nigeria on the use of herbal medicines, safety on usage, knowledge of potential effects of herbal remedies on the fetus and potential benefits or harms that may be derived from combining herbal remedies with conventional therapies were obtained using a structured questionnaire between September 2007 and March 2008. Descriptive statistics and Fisher's exact tests were used at 95% confidence level to evaluate the data obtained. Level of significance was set at p<0.05. RESULTS: More than two-third of respondents [67.5%] had used herbal medicines in crude forms or as pharmaceutical prepackaged dosage forms, with 74.3% preferring self-prepared formulations. Almost 30% who were using herbal medicine at the time of the study believed that the use of herbal medicines during pregnancy is safe. Respondents' reasons for taking herbal medications were varied and included reasons such as herbs having better efficacy than conventional medicines [22.4%], herbs being natural, are safer to use during pregnancy than conventional medicines [21.1%], low efficacy of conventional medicines [19.7%], easier access to herbal medicines [11.2%], traditional and cultural belief in herbal medicines to cure many illnesses [12.5%], and comparatively low cost of herbal medicines [5.9%]. Over half the respondents, 56.6% did not support combining herbal medicines with conventional drugs to forestall drug-herb interaction. About 33.4% respondents believed herbal medicines possess no adverse effects while 181 [30.4%] were of the opinion that adverse/side effects of some herbal medicines could be dangerous. Marital status, geopolitical zones, and educational qualification of respondents had statistically significant effects on respondents views on side effects of herbal medicines [p<0.05)] while only geopolitical zones and educational qualifications seemed to have influence on respondents' opinion on the harmful effects of herbal medicines to the fetus [p<0.05]. CONCLUSION: The study emphasized the wide spread use of herbal medicines by pregnant women in Nigeria highlighting an urgent need for health care practitioners and other health care givers to be aware of this practice and make efforts in obtaining information about herb use during ante-natal care. This will help forestall possible interaction between herbal and conventional medicines.","corpus_id":6748392,"score":1},{"doc_id":"20367764","title":"Increasing health-care options: the perspectives of parents who use complementary and alternative medicines.","abstract":"AIM: To explore the relationship between conventional medicine and complementary and alternative medicine (CAM) with parents who use CAM, and to consider factors that may contribute to parent non-disclosure of CAM usage to their doctor. METHODS: Thirty-three parents participated in one of seven focus groups. Transcripts were analysed using an iterative process of theme identification and testing against transcript data. RESULTS: The participants believed they should trust their instincts as parents in caring for their child. It was important also to the participants that they understood why their child was ill, and a range of theories of health and illness were discussed. The use of CAM was attractive as it offered more options in health care than just relying on conventional medicine alone. The use of additional therapies was seen as a means to increase the likelihood that something would work. Many of the participants described bad experiences with doctors when they discussed CAM use previously so they had become more circumspect in mentioning it. The participants were most satisfied with medical care for their child when they felt the doctor respected their point of view and listened to them. CONCLUSIONS: Doctors caring for children and their families should expect that many parents are using CAM to increase health-care options. Inquiries about CAM usage should be made in a non-judgmental and encouraging manner so parents feel comfortable in providing an honest answer. Advice to parents about CAM may need to be backed up with evidence to address differing parent understanding of illness.","corpus_id":205469905,"score":1},{"doc_id":"21364591","title":"The use of herbal medicines by people with cancer: a cross-sectional survey.","abstract":"BACKGROUND: A large proportion of cancer patients are estimated to use herbal medicines, but data to substantiate this are lacking. This study aimed to investigate the prevalence of herbal medicine use among cancer patients in the West Midlands, and determine the characteristics predicting herbal medicine use. METHODS: A cross-sectional survey of oncology patients (n=1498) being followed up at a hospital in Coventry was undertaken. Recipients were asked about herbal medicine use since their cancer diagnosis, and the association between sociodemographic and cancer-related characteristics and herbal medicine use was evaluated. RESULTS: A total of 1134 responses were received (75.7%). The prevalence of herbal medicine use was 19.7% (95% CI: 17.4-22.1; n=223). Users were more likely to be affluent, female, and aged under 50 years. Usage increased with time since cancer diagnosis (X(2) for trend=4.63; P=0.031). A validation data set, derived from a survey of oncology patients in Birmingham (n=541) with differing socioeconomic characteristics showed no significant difference in estimated prevalence (16.6%; 95% CI: 11.9-22.2). CONCLUSION: A substantial number of people with cancer are likely to be taking herbal medicines. Understanding the self-medication behaviours of these individuals is essential if health-care professionals are to support treatment adherence and avoid unwanted pharmacological interactions.","corpus_id":405066,"score":1},{"doc_id":"21645607","title":"The prevalence of herbal medicine home use and concomitant use with pharmaceutical medicines in Jamaica.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: The work described in this paper aimed to study the prevalence of herbal medicine use in treating illness and concomitant use with pharmaceutical medicines in Jamaica. MATERIALS AND METHODS: A survey using a structured questionnaire was administered by a trained interviewer to randomly selected adults in systematically selected households within randomly selected urban and rural clusters. Categorical data analysis was performed using Stata version 10 software. RESULTS: 91.4%(372/407) of selected people agreed to participate. 72.6%(270/372) self-medicated with herbs within the previous year. Commonly treated were illnesses of the respiratory system (RS, 77.8%(210/270)), gastro-intestinal tract (GIT, 53.3%(144/270)) and health maintenance using tonics (29.6%(80/270)). 26.7%(72/270) of respondents used pharmaceuticals concomitantly with medicinal plants. Commonly treated were illnesses of the RS (20.4%(55/270)), GIT (13.7%(37/270)) and hypertension (10.0%(27/270)). 19.4% (14/72) of physicians knew of such practices. There was significant association of herb use with/without drugs with age (p<0.001), employment status (p<0.001), religion (p=0.004), gender (p=0.02) and educational level (p=0.031). Thus prevalence of herb use alone was greatest amongst people aged 35-44 and 45-54 years; those employed; Rastafarians; those without health insurance; males and people who had completed secondary education. Whilst prevalence of concomitant herb-drug use was greater amongst people aged 65 years and older; those retired; those of religions other than Rastafarians and Christians, females and people who had attained primary education and below. CONCLUSIONS: Self-medication with herbs in Jamaica is highly prevalent and highest for self-limiting conditions of the RS, GIT and health maintenance with tonics. Concomitant herb and drug use is highest for self-limiting conditions of the RS, GIT and hypertension, and the use of combined therapy highlights the need for investigations on potential drug-herb interactions. Physicians have limited awareness and knowledge of such concomitant usage, further highlighting the need for increased dialogue with patients, knowledge of medicinal plants and their uses and a heightened pharmacovigilance to avoid adversities that may arise from potential drug-herb interactions.","corpus_id":8636465,"score":1},{"doc_id":"21848581","title":"Why people choose to not use complementary therapies during cancer treatment: a focus group study.","abstract":"While 50% of cancer patients use complementary therapies (CT) during treatment, few studies have examined why individuals choose not to use CT. This study aimed to address this gap in knowledge using a focus group methodology, where 36 participants took part in one of eight groups; participants were recruited until saturation of themes was achieved. Three categories of participants were investigated: patients/recent survivors (n= 14); volunteers/advocates (n= 16), the majority of whom were also long-term survivors; and health professionals (n= 6). Focus groups were digitally audio-recorded, transcribed, and coded thematically using NVivo software. Reasons for non-use fell into four broad themes: (1) Resource barriers, particularly the cost and lack of time; (2) fear and distrust, including the potential for drug interactions; (3) lack of evidence, including the unproven nature of many CT practices; and (4) satisfaction with conventional treatment. Two further themes related to the benefits of non-use and reasons for discontinuation. A sub-analysis indicated that reasons for non-use differed by CT category, with non-use being mentioned more frequently for biologically based and body-based therapies. Differences in understanding CT non-use emerged between patients, volunteers and health professionals. Findings have clinical implications regarding tailoring information for patients during and after cancer.","corpus_id":23193275,"score":1},{"doc_id":"24330413","title":"Herbal medicine use in pregnancy: results of a multinational study.","abstract":"BACKGROUND: The use of complementary and alternative medicines (CAM) is growing in the general population. Herbal medicines are used in all countries of the world and are included in the top CAM therapies used. METHODS: A multinational study on how women treat disease and pregnancy-related health ailments was conducted between October 2011 and February 2012 in Europe, North and South America and Australia. In this study, the primary aim was to determine the prevalence of herbal medicine use in pregnancy and factors related to such use across participating countries and regions. The secondary aim was to investigate who recommended the use of herbal medication in pregnancy. RESULTS: There were 9,459 women from 23 countries participating in the study. Of these, 28.9% reported the use of herbal medicines in pregnancy. Most herbal medicines were used for pregnancy-related health ailments such as cold and nausea. Ginger, cranberry, valerian and raspberry were the most commonly used herbs in pregnancy. The highest reported rate of herbal use medicines was in Russia (69%). Women from Eastern Europe (51.8%) and Australia (43.8%) were twice as likely to use an herbal medicine versus other regions. Women using herbal medicines were characteristically having their first child, non-smokers, using folic acid and consuming some alcohol in pregnancy. Also, women who were currently students and women with an education other than a high school degree were more likely to use herbal medicines than other women. Although 1 out of 5 women stated that a physician had recommended the herbal use, most women used herbal medicine in pregnancy on their own initiative. CONCLUSIONS: In this multinational study herbal medicine use in pregnancy was high although there were distinct differences in the herbs and users of herbal medicines across regions. Most commonly the women self-medicated with herbal medicine to treat pregnancy-related health ailments. More knowledge regarding the efficacy and safety of herbal medicines in pregnancy is warranted.","corpus_id":31224768,"score":1},{"doc_id":"24669824","title":"Use of complementary and alternative medicine by older adults--a cross-sectional survey.","abstract":"BACKGROUND: Very little is known about complementary and alternative medicine (CAM) use by older adults in Germany. The aim of this study was to investigate the use of CAM and other health promoting substances (e.g., herbal teas) by older adults of at least 70 years of age. METHODS: A cross-sectional questionnaire study was conducted among persons of ≥70 years from metropolitan Berlin and rural parts of Brandenburg, Germany. Recorded were: demographics, current use of CAM, medical diagnoses, users' opinions and preferences. RESULTS: A total of 400 older adults, living as 'self-reliant' (n = 154), 'home care service user' (n = 97), or 'in nursing home' (n = 149), and with the legal status 'without guardian' (n = 355) or 'with guardian' (n = 45) were included (mean age 81.8 ± 7.4 years, 78.5% female). Any type of CAM used 61.3% of respondents (dietary supplements 35.5%, herbal medicines 33.3%, and external preparations 26.8%); 3.0% used drug-interaction causing preparations. Usage was based on recommendations (total 30.3%; in 20.0% by friends or family and 10.4% by pharmacists), own initiative (27.3%), and doctors' prescription (25.8%). Participants with legal guardian took almost solely prescribed dietary supplements. Of the others, only half (58.7%) informed their general practitioner (GP) of their CAM use. Participants expected significant (44.9%) or moderate (37.1%) improvement; half of them perceived a good effect (58.7%) and two-thirds (64.9%) generally preferred a combination of CAM and conventional medicine. More than half (57.9%) stated that they could neither assess whether their CAM preparations have side effects, nor assess what the side effects might be. Strongest predictors for CAM use were two treatment preferences (vs. 'conventional only': 'CAM only', OR = 3.98, p = 0.0042 and 'CAM + conventional', 3.02, 0.0028) and the type of health insurance ('statutory' vs. 'private', 3.57, 0.0356); against CAM use two subjective assessments predicted (vs. 'CAM causes no harm': 'CAM causes harmful drug interactions', 0.25, 0.0536 and 'I cannot assess side effects', 0.28, 0.0010). CONCLUSION: Older German adults frequently use CAM. They perceived it as an effective complement to conventional medicine, but are not sufficiently informed about risks and benefits.","corpus_id":7919846,"score":1},{"doc_id":"24969647","title":"Young people's opinions about herbal medicines in a suburban district of Central Uganda.","abstract":"BACKGROUND: Herbal medication is the most commonly used form of healthcare in Africa. However, little is known about its use by young Africans in the urban context. METHODS: This qualitative study explored opinions about herbal medicine and its uses among young people in the Wakiso district, Uganda. RESULTS: About a third of interview participants reported using herbal products, a choice influenced by religious faith, family preference, low cost and unavailability of biomedicines. Two participants stated that herbs could be used to deter alcohol dependence. CONCLUSIONS: This study indicated divergent opinions about the value of herbal medicine among young urban Ugandans.","corpus_id":205141272,"score":1},{"doc_id":"25174734","title":"Internal health locus of control in users of complementary and alternative medicine: a cross-sectional survey.","abstract":"BACKGROUND: Complementary and alternative medicine (CAM) is widely used in Germany, with some treatments eligible for health insurance reimbursements. CAM encourages patients to play an active role in their healing process. The belief that a person's own behavior influences health is assessed as the internal health locus of control (IHLOC). Studies on the association between IHLOC and CAM use yield inconsistent results. Using various indicators of CAM use, we evaluated whether there were differences in IHLOC between different groups of CAM users. METHODS: A cross-sectional online survey was conducted. IHLOC was compared between participants with high and low appraisal of CAM, between participants who used different types of medications (none, CAM, conventional, both), and who consulted with different health care professionals (none, CAM, conventional, both). Independent samples t-tests and ANOVAs were conducted for the total group and for subgroups of chronically ill and healthy participants. Post-hoc, we conducted a multivariate linear regression evaluating which indicators of CAM use or other characteristics showed the strongest association with IHLOC. RESULTS: A total of 1,054 undergraduate students completed the survey. Participants with high CAM appraisal showed higher IHLOC than those with low CAM appraisal, regardless of whether they were chronically ill (p < .001). Participants without chronic conditions showed higher IHLOC when only using CAM medications than when using either conventional medications alone or both conventional and CAM medications (p < .05). All participants showed higher IHLOC when visiting only CAM practitioners than when visiting either only conventional or both conventional and CAM practitioners (p < .05). CAM appraisal was associated the strongest with IHLOC in the linear regression model. CONCLUSIONS: Generally, participants using CAM more or exclusively, and participants with higher appraisal of CAM showed higher IHLOC than those with less CAM use or lower CAM appraisal. Because of the cross-sectional design, it is not possible to determine whether differences in IHLOC are reasons for or consequences of CAM use. Research using a longitudinal design is needed. The sample, though more representative than most student samples, might not represent the general population. Studies evaluating clinical populations might add to the findings.","corpus_id":15509599,"score":1},{"doc_id":"25888160","title":"Complementary and alternative medicine usage among cardiac patients: a descriptive study.","abstract":"BACKGROUND: The use of complementary and alternative medicine (CAM) persists, despite the availability of conventional medicine (CM), modernisation, globalisation, technological advancement, and limited scientific evidence supporting CAM. People with cardiovascular diseases often use CAM, despite possible major adverse effects and lack of evidence supporting CAM claims. This study explored CAM use among cardiac patients, the types of CAM used, reasons and factors that influence its use, and the association between patient demographics and CAM use. METHODS: This cross-sectional quantitative study was conducted using quota sampling to survey 329 public clinic adult cardiac patients within the South-West Regional Health Authority (SWRHA) of Trinidad and Tobago. From 1 July 2012 to 31August 2012, each participant completed questionnaires, after consenting to participate. Data analysis included χ(2) tests and binary logistic regression. RESULTS: One hundred eighty-five (56.2%; standard error [SE] = 2.74%) patients used CAM. Herbal medicine was the most common CAM (85.9%; SE = 2.56%), followed by spiritual therapy/mind-body systems (61.6%; SE = 3.58%), physical therapy/body manipulation (13.5%; SE = 2.51%), alternative systems (8.1%; SE = 2.01%), and other methods (3.8%; SE = 1. 41%). The patients believed that CAM promotes health and wellness (79.5%; SE = 2.97%), assists in fighting illness (78.9%; SE = 3.00%), addresses the limitations of CM (69.2%; SE = 3.56%), alleviates symptoms (21.6%; SE = 6.51%), costs less than CM (21.6 %, SE = 3.03), and has fewer adverse/damaging effects than CM (29.7, SE =3.36), or they were disappointed with CM (12.4%, SE = 2.42). Ethnicity and religion were associated with CAM usage, but only ethnicity was a useful predictor of CAM use. CONCLUSIONS: Complementary and alternative medicine use was high among cardiac patients (56.2%, SE = 2.74%), and associated with ethnicity and religion. Friends, family, and perceived mode of action influenced a patient's use of CAM.","corpus_id":8111927,"score":1},{"doc_id":"26383209","title":"Evaluation of Trends in the Use of Complementary and Alternative Medicine in Health Centers in Khorramabad (West of Iran).","abstract":"AIM: To determine the use of most popular forms of complementary and alternative medicine(CAM), sociodemographic characteristics of CAM users, and communication between CAM users and their physicians by adult Iranian in Khorramabad city. METHODS: This cross-sectional study was carried out on clients who were at least 15 years in age referring to health centers and hospitals in Khorramabad town in 2014. A multi-part questionnaire was used to gather information. The demographic data and details regarding usage (number of times and underlying reasons) of different kinds of complementary and traditional medicine in the past were gathered using a questionnaire. RESULTS: In this study 790 subjects were surveyed using the questionnaire. The mean age of the participant was 38.9 years. 79.8% of the subjects had used at least one of the methods of complementary medicine. Among the participants, 58.2% had used at least one of the complementary medicines in the previous year. Herbal medicine and prayers treatment had the highest use with 69.2% and 37.2%, respectively. Concerns of the side effects of medical therapy, beliefs in less risky being and fewer side effects of complementary medicine, Dissatisfaction of General Practitioners, the increase of being-well feelings in physical conditions, and were among the most important reasons of inclination towards such treatment methods. CONCLUSION: The analysis of using complementary medicine among people is the first step for planning proper use of the beneficial methods of complementary medicine and the prevention of inefficient and harmful methods in this respect.","corpus_id":33724086,"score":1},{"doc_id":"26401410","title":"Herbal medicine use among patients with chronic diseases.","abstract":"AIM: Complementary and alternative medicine (CAM) is commonly used all over the world, and herbal medicines are the most preferred ways of CAM. The aim of this study was to determine the frequency of herbal medicine use among patients with chronic diseases. METHODOLOGY: A cross-sectional descriptive study was conducted from April 2014 to December 2014 among patients who had been diagnosed with diabetes mellitus (DM), hypertension (HT), and hyperlipidemia (HL) in Family Medicine Department of Dışkapı Yıldırım Beyazıt Training and Research Hospital, in Ankara. A questionnaire about herbal drug use was applied by face to face interview to the participants. RESULTS: A total of 217 patients were included in this study. The mean age of the participants was 56.6 ± 9.7 years (55 male and 162 female). The rate of herbal medicine use was 29%. Herbal medicine use among female gender was significantly higher (P = 0.040). Conventional medication use was found to be lower among herbal medicine consumers. There was no relationship between herbal medicine use and type of chronic disease, living area, and occupation or education level. Most frequently used herbs were lemon (39.6%) and garlic (11.1%) for HT, cinnamon (12.7%) for DM, and walnut (6.3%) for HL. CONCLUSIONS: In this study, herbal medicine use was found to be higher among patients who had been diagnosed with chronic diseases. Therefore, physicians should be aware of herbal medicine usage of their patients and inform them about the effectivity and side effects of herbal medicines.","corpus_id":1259912,"score":1},{"doc_id":"26865257","title":"Herbal medicine use behaviour in Australian adults who experience anxiety: a descriptive study.","abstract":"BACKGROUND: Anxiety disorders are the most prevalent mental health condition in Australia. In addition, there are many people who experience problematic anxiety symptoms who do not receive an anxiety disorder diagnosis but require treatment. As herbal medicine use is popular in Australia, and little is known about how adults experiencing anxiety are using these medicines, this study aimed to identify how Australian adults who experience anxiety are using herbal medicines. METHODS: An online cross-sectional descriptive study was conducted using purposive convenience sampling to recruit Australian adults who have experienced anxiety symptoms and have used herbal medicines (N = 400). Descriptive statistics, chi-square test of contingency, analysis of variance, and simple logistic regression was used to analyse the data. RESULTS: Eighty two percent of participants experienced anxiety symptoms in the previous 12 months, with 47% reporting having previously been diagnosed with an anxiety disorder. In addition, 72.8% had used herbal medicines specifically for anxiety symptoms in their lifetime, while 55.3% had used prescribed pharmaceuticals, with 27.5% having used herbal medicines concurrently with prescribed pharmaceuticals. The Internet and family and friends were the most frequently used sources of information about herbal medicines. Forty eight percent of participants did not disclose their herbal medicine use to their doctor. CONCLUSIONS: Herbal medicines are being used by adults with anxiety and are commonly self-prescribed for anxiety symptoms. Health practitioners who are experts in herbal medicine prescribing are consulted infrequently. In addition, herbal medicine use is often not disclosed to health practitioners. These behaviours are concerning as people may not be receiving the most suitable treatments, and their use of herbal medicines may even be dangerous. It is critical we develop a better understanding of why people are using these medicines, and how we can develop improved health literacy to help with treatment decision making to ensure people receive optimal care.","corpus_id":13709848,"score":1},{"doc_id":"27125594","title":"Complementary and alternative medicine use among cancer patients in Palestine with special reference to safety-related concerns.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: The use of CAM including herbal medicine as the most preferred CAM modality, among cancer patients who are taking prescription medications has shown to be highly prevalent worldwide as well as in several Middle Eastern countries, with a high percentage of the patients do not disclose their CAM use to treating physician. AIM OF THE STUDY: The current study aimed to evaluate the patterns of CAM use among two cohorts of cancer patients in Palestine over a three-year period, and to identify socio-demographic factors that are associated with CAM use. MATERIALS AND METHODS: Across-sectional survey of patients attending outpatient cancer clinics. The method was based on a semi-structured questionnaire. In order to identify safety-related concerns associated with the products listed, a literature search was conducted using different databases (PubMed, Micromedex, AltMedDex, and the Natural Medicine Comprehensive Database). RESULTS: In 472 cancer patients including 372 of the 2011 cohort; and 100 of the 2014 cohort, the overall prevalence of CAM use was 69.5%. CAM users were more likely to be ≤65 years old, village resident, being in the midst of chemotherapy, to have high interest spiritual quest, and to have no other chronic diseases. A significant number of CAM users reported using herbal preparations (98.3%, and 89.6% in the two study cohorts, respectively). In the current study, a total of 40 plant taxa belonging to 23 botanical families were reported by ≥3 cancer patients in the two cohort groups. The top most commonly used plant in the 2011 cohort group was Arum palaestinum (43.5%), while Ephedra foeminea emerged as the top most commonly utilized plant (from 0.0% in 2011 to 55.2% in the 2014 cohort), mainly due to a recent publicizing and portraying of the plant in the local media as an effective cancer herbal remedy. Safety-related concerns were associated with 33 (82.5%) herbs, including herb-drug interactions with altered pharmacokinetics (8, 20% herbs), direct toxic effects (16, 40% herbs), and increased in vitro response of cancer cells to chemotherapy (30, 75% herbs). CONCLUSIONS: CAM use, especially herbal medicine in cancer is highly prevalent in Palestine. This study has demonstrated the role of the media on the emergence of new CAM herbal therapies among cancer patients in Palestine, and discussed its potential implications on patients and for oncologists who are treating them. Some of the most widely used herbal medicines by cancer patients in the present work are known to interact with conventional anticancer drugs. Hence, the disclosure of the use of herbal remedies by patients to health professionals with sufficient training in CAM use is important for the later in order to assess whether there are any possible herbal drug interactions and/or harmful drug reactions.","corpus_id":20517317,"score":1},{"doc_id":"27229306","title":"Facilitators and barriers of herbal medicine use in Accra, Ghana: an inductive exploratory study.","abstract":"BACKGROUND: The use of complementary and alternative medicine including herbal medicine is increasing in many countries including Ghana. However, there is paucity of research on the perspectives of patrons of herbal medicine regarding the facilitators and barriers of herbal medicine use. This study sought to investigate the facilitators and barriers of herbal medicine among Ghanaian adults who use one form of herbal medicine or the other. METHODS: The study employed an inductive exploratory qualitative approach. It was conducted at a private herbal clinic in Accra. Purposive sampling was employed to recruit 16 participants. Data collection was through individual face-to-face interviews and these were transcribed and analysed using content analysis procedures. RESULTS: It was realized that the factors that enhanced the use of herbal medicine included use of convincing information to enhance the initiation of herbal medicine use, effectiveness of herbal medicine, personal preference for herbal medicine, perceived ineffectiveness of western medicine and integration of spirituality in herbal medicine. The factors that hindered herbal medicine use included negative perceptions and attitudes about herbal medicine, poor vending environment, poor knowledge of vendors, high cost of herbal products at credible herbal clinics and inconsistent effectiveness of some herbal products. Participants desired that the national health insurance scheme will cover the cost of herbal medicine to alleviate the financial burden associated with herbal medicine use. CONCLUSION: Although some Ghanaians patronize herbal medicine, the negative perceptions about herbal medicine resulting from deceitful producers and vendors call for enhanced education and monitoring to ensure that effective herbal products are used.","corpus_id":16423866,"score":1},{"doc_id":"18366698","title":"The use of biomedicine, complementary and alternative medicine, and ethnomedicine for the treatment of epilepsy among people of South Asian origin in the UK.","abstract":"BACKGROUND: Studies have shown that a significant proportion of people with epilepsy use complementary and alternative medicine (CAM). CAM use is known to vary between different ethnic groups and cultural contexts; however, little attention has been devoted to inter-ethnic differences within the UK population. We studied the use of biomedicine, complementary and alternative medicine, and ethnomedicine in a sample of people with epilepsy of South Asian origin living in the north of England. METHODS: Interviews were conducted with 30 people of South Asian origin and 16 carers drawn from a sampling frame of patients over 18 years old with epilepsy, compiled from epilepsy registers and hospital databases. All interviews were tape-recorded, translated if required and transcribed. A framework approach was adopted to analyse the data. RESULTS: All those interviewed were taking conventional anti-epileptic drugs. Most had also sought help from traditional South Asian practitioners, but only two people had tried conventional CAM. Decisions to consult a traditional healer were taken by families rather than by individuals with epilepsy. Those who made the decision to consult a traditional healer were usually older family members and their motivations and perceptions of safety and efficacy often differed from those of the recipients of the treatment. No-one had discussed the use of traditional therapies with their doctor. The patterns observed in the UK mirrored those reported among people with epilepsy in India and Pakistan. CONCLUSION: The health care-seeking behaviour of study participants, although mainly confined within the ethnomedicine sector, shared much in common with that of people who use global CAM. The appeal of traditional therapies lay in their religious and moral legitimacy within the South Asian community, especially to the older generation who were disproportionately influential in the determination of treatment choices. As a second generation made up of people of Pakistani origin born in the UK reach the age when they are the influential decision makers in their families, resort to traditional therapies may decline. People had long experience of navigating plural systems of health care and avoided potential conflict by maintaining strict separation between different sectors. Health care practitioners need to approach these issues with sensitivity and to regard traditional healers as potential allies, rather than competitors or quacks.","corpus_id":3564219,"score":0},{"doc_id":"18466292","title":"The experiences of adults with intellectual disabilities and their carers in general hospitals: a focus group study.","abstract":"BACKGROUND: People with intellectual disabilities (ID) have higher levels of health needs compared with the general population, many of which are unrecognised and unmet. While there has been interest and research into the primary health provision for this group, there has been a more limited focus on addressing their care received in general hospitals. Access to health care has predominated in the literature, with less attention being paid to the experiences of people with ID as users of general hospital care. METHOD: A qualitative focus group methodology was used. Eleven adults with ID, nine parents and five paid carers of adults with ID participated. The focus groups were audiotaped and transcriptions were analysed using principles of grounded theory. RESULTS: The analysed data highlighted key themes identified from the experiences of participants. These were the interrelated issues of feelings, particularly anxiety and fear, communication and behaviour problems; the practicalities of being in or attending hospitals, including the role played by carers; and issues around perceived discrimination and negative comments. CONCLUSIONS: The experiences of participants in this study concur with and add to concern expressed in recent reports and published research. Wide ranging implications are discussed for further research, wider policy development, clinical practice, local health service provision and education of health professionals.","corpus_id":43900495,"score":0},{"doc_id":"18791806","title":"The DARTS tool for assessing online medicines information.","abstract":"OBJECTIVE: The use of the Internet as a source of medicines information is increasing. However, the quality of online information is highly variable. Equipping Internet users to distinguish good quality information is the aim of a new five-item quality assessment tool (DARTS) that was developed by the Working Group on Information to Patients under the Pharmaceutical Forum established by the European Commission. The objective of this study was to investigate how people with depression assess the quality of online medicines information and to study their opinions about the DARTS tool in assisting in this process. SETTING: Focus group discussions with Internet users were conducted in metropolitan Helsinki, Finland. METHOD: Six focus group discussions (67-109 min duration) were conducted with people with depression (n = 29). The DARTS tool was used as a stimulus after open discussion in relation to the evaluation of the quality of Internet-based medicines information. The focus groups were digitally audiotaped and transcribed verbatim. The transcripts were thematically content analysed by two researchers. RESULTS: Focus group participants were generally critical of the information they retrieved. However, few participants systematically applied quality assessment criteria when retrieving online information. No participants had knowledge or experience of any quality assessment tools. The DARTS tool was perceived as being concise and easy to use and understand. Many participants indicated it would allay some of their concerns related to information quality and act as a reminder. While several participants felt the tool should not be any more extensive, some of them believed it should include a more in-depth explanation to accompany each of the quality criteria. CONCLUSIONS: The DARTS tool may act as a prompt for people with depression to assess the quality of online information they obtain. The five DARTS criteria may form the basis of a systematic approach to quality assessment and the tool may also act as a reminder of quality issues in general. Further studies are needed to assess the actual value of the DARTS tool as well as its value in relation to other quality assessment instruments.","corpus_id":34002800,"score":0},{"doc_id":"19005129","title":"Complementary and alternative medicine use among Chinese and white Canadians.","abstract":"ABSTRACTOBJECTIVEThis study aimed to describe the level of complementary and alternative medicine (CAM) use and the factors associated with CAM use among Chinese and white Canadians. DESIGNA cross-sectional telephone survey conducted in English, Cantonese, and Mandarin. SETTINGCalgary, Alta. PARTICIPANTSChinese and white residents of Calgary aged 18 or older. MAIN OUTCOME MEASURESRates of use of 11 CAM therapies, particularly herbal therapy, massage, chiropractic care, and acupuncture; reasons for use of CAM therapies. RESULTSSixty percent of 835 Chinese respondents (95% confidence interval [CI] 56.5% to 63.2%) and 59% of 802 white respondents (95% CI 55.1% to 62.0%) had used CAM in the past year. Chinese respondents were more likely to use herbal therapy than white respondents were (48.7% vs 33.7%, P < .001), less likely to use massage (17.1% vs 30.4%, P < .001) and chiropractic care (8.4% vs 21.2%, P < .001), but equally likely to use acupuncture (8.3% vs 7.9%, P = .173). The common factor associated with herbal therapy, acupuncture, or massage use among Chinese and white respondents was receiving a CAM recommendation from a family member or friend. Factors unique to either Chinese or white CAM users varied by therapy. For example, herbal therapy use for Chinese respondents was associated with the presence of chronic disease (adjusted odds ratio [AOR] 2.15, 95% CI 1.09 to 4.24 for having 3 diseases compared with those without chronic disease), beliefs about the effectiveness of herbal therapy (AOR 1.56, 95% CI 1.12 to 2.17), and trust in herbal therapy practitioners (AOR 1.72, 95% CI 1.24 to 2.37). Herbal therapy use for white respondents was associated with the beliefs that herbal treatment had fewer side effects than prescription drugs (AOR 1.81, 95% CI 1.31 to 2.50) and that herbalists took a holistic approach (AOR 2.07, 95% CI 1.49 to 2.87).CONCLUSIONWhile the percentage of CAM use was similar in both groups, Chinese Canadians mainly used herbal therapy and white Canadians used a range of CAM therapies. Factors associated with CAM use varied with ethnicity and type of CAM therapy. Presence of chronic disease, however, was an important factor for Chinese Canadians. That finding suggests that Chinese Canadians use CAM for the treatment of chronic disease, while white Canadians use such therapies for disease treatment and health maintenance.","corpus_id":22348904,"score":0},{"doc_id":"19838830","title":"Back pain amongst 8,910 young Australian women: a longitudinal analysis of the use of conventional providers, complementary and alternative medicine (CAM) practitioners and self-prescribed CAM.","abstract":"Back problems and back pain are amongst the most prevalent conditions afflicting Australians and carry high direct and indirect costs for the health care systems of all developed countries. A major gap in the research literature on this topic is the longitudinal analysis of health seeking behaviour for people with back pain. All studies to date have been cross-sectional and it is important that the use of different providers (both conventional and complementary and alternative medicine, CAM) is examined over time. This study analysed data from a longitudinal study conducted over a 3-year period on 8,910 young Australian women. Information on health service use, self-prescribed treatments, and health status was obtained from two questionnaires mailed to study participants in 2003 and 2006. We found that there is little difference in the consultation practises or use of self-prescribed CAM between women who recently sought help for back pain and women who had longer-term back pain; the only difference being that women with longer-term back pain consulted more with chiropractors. We conclude that women who seek help for their back pain are frequent visitors to a range of conventional and CAM practitioners and are also high users of self-prescribed CAM treatments. The frequent use of a range of conventional providers and practitioner-based and self-prescribed CAM amongst women with back pain warrants further investigation.","corpus_id":21519748,"score":0},{"doc_id":"19857249","title":"Use of complementary and alternative medicine: a survey in Turkish gastroenterology patients.","abstract":"BACKGROUND: The study examined complementary and alternative medicine (CAM) usage by patients attending a Turkish gastroenterology outpatient clinic. METHODS: The survey was conducted on 216 patients presenting with gastrointestinal problems during their first visit to the clinic using a 31 item, self-report questionnaire between May and October 2005. Data included information on patient demographics and their gastrointestinal symptoms, as well as items to identify CAM use and patient satisfaction with these therapies. RESULTS: Seventy-nine patients (36.6%) reported using one or more forms of CAM. The most commonly used therapy was herbal therapy, usually taken as a tea or infusion. These were used by 27 people (29%) in this subgroup. Common indicators for their use were epigastric pain, constipation, bloating and dyspepsia or indigestion. CAM use among upper GI patients was marginally higher than lower GI patients (41.8% versus 41.2%), but the highest usage was amongst patients with liver disease where 53.8% reported using one or more CAM therapy. About half of the patients learned about CAM from their relatives or friends, with more women than men using the therapies (p < 0.05). Clinical characteristics such as diagnosis, duration of symptoms and prior surgical intervention did not differ between users and non-users of CAM therapies. Multivariate analysis showed that being female and higher educational status were positively associated with CAM usage (p < 0.05). CONCLUSION: CAM usage in our sample of gastrointestinal patients was lower than that described in other countries and other chronic disease groups. This could be due to their low perceived efficacy, or the relatively transient duration of symptoms experienced by the sample. Healthcare professionals need however, to be aware of CAM usage in order to educate patients appropriately about possible adverse effects or drug-interactions.","corpus_id":8259197,"score":0},{"doc_id":"19894247","title":"Complementary and alternative medicine use among long-term lymphoma survivors: a pilot study.","abstract":"No published survey has specifically addressed the beliefs, knowledge, and usage of complementary and alternative medicine (CAM) in long-term (5-20 years) lymphoma survivors alone. In this pilot project, 95 subjects were randomly selected from a population of 2,475 long-term lymphoma survivors and mailed a questionnaire. The median time from lymphoma diagnosis to completion of the questionnaire was 11 years (range 6-20). Overall, 68% (95% CI: 54-80%) of the long-term lymphoma survivors reported that they have used CAM, a rate higher than the estimated usage rate reported for the general population The most commonly used modalities were chiropractic (39%, 95% CI: 27-53%) and massage therapy (21%, 95% CI: 12-34%). Less than 10% used meditation (5%, 95% CI: 1-15%) and relaxation (7%, 95% CI: 2-17%). In terms of common herbal usage, 5% (95% CI: 1-15%) had used St. John's Wort and 7% (95% CI: 2-17%) had used shark cartilage. Although none of the patients reported that CAM usage was directed specifically towards treating their lymphoma, 4% (95% CI: 0-12%) of patients reported that CAM could cure cancer, and 14% (95% CI: 6-26%) reported that CAM could increase their feeling of control over their health. This pilot study suggests that long-term lymphoma survivors appear to use CAM at a rate higher than the general population. The use of potential agents of risk by the survivors and the lack of access to potentially beneficial modalities highlights the need for further study of CAM in this population.","corpus_id":19698699,"score":0},{"doc_id":"20090352","title":"[Complementary and alternative medicine in practice - the diagnostic-therapeutic process from the perspective of general practitioners: a qualitative study].","abstract":"Komplementärmedizin in der Praxis - der diagnostischtherapeutische Prozess aus Sicht von Hausärzten: Eine qualitative Studie. BACKGROUND: Complementary and alternative medicine (CAM) is widely used in general practices in Germany. This study aimed to explore the diagnostic-therapeutic process and relevant factors regarding the use of CAM from the perspective of general practitioners (GPs). METHODS: Within a qualitative approach 3 focus groups with a convenience sample of 17 GPs were conducted. Group discussions were analysed by qualitative content analysis. RESULTS: GPs view the diagnostic-therapeutic process in CAM as complex and less dependent on the methods used than on approach-independent factors. On the basis of the focus group transcripts, 4 main categories were identified that play a major role when CAM is used in primary care: patient factors, physician factors, relationship factors and generic factors of CAM. ' Constitution', 'expectation', and 'personal (life) concepts' were mentioned as relevant patient factors, 'empathy', 'respect' and 'authenticity' as relevant physician factors. At the level of the doctor-patient-relationship, 'time', 'confidence', 'matching', 'balance of power' and 'rituals' seem to play a major role. DISCUSSION: From the perspective of the GPs the diagnostic-therapeutic process can be considered as a cyclic process in which patient, physician and relationship elements as well as generic CAM factors are closely interweaved. According to this conception, CAM can be used for a wide range of health problems in primary care. Sufficient time and a trustful doctor-patient-relationship are, however, essential for the use of CAM. Due to the increasing economical pressure there is a risk that CAM is processualised, i.e. split into single processes and uncoupled from the doctor-patient-relationship. This would jeopardise efficacy of CAM in everyday practice.","corpus_id":12211659,"score":0},{"doc_id":"20392781","title":"Herbal medicines--what do clinicians know?","abstract":"In 1986, DTB published an article called Herbal medicines - safe and effective?, which discussed some of the issues around the availability, safety and efficacy of such treatments.1 We highlighted how the failure of orthodox medicines to cure, and anxiety about their potentially serious unwanted effects, had led some people to turn to herbal medicines for treatment for chronic and disabling conditions often in the belief, that natural medicines must be intrinsically safe. The article concluded by discussing the potential problems associated with herbal medicines and the role that doctors should play in asking about patients' use of such products. Revisiting these themes, here we present an overview of the results of an online survey conducted among DTB readers to explore four key issues: What do healthcare professionals know about herbal medicines? What challenges (if any) does patients' use of herbal medicines raise for healthcare professionals? What awareness do healthcare professionals have about the regulatory arrangements for herbal medicines? What sources of information (if any) do healthcare professionals use to inform themselves about herbal medicines?","corpus_id":6964685,"score":0},{"doc_id":"21491340","title":"Coping styles and self-regulation predict complementary and alternative medicine and herbal supplement use among college students.","abstract":"Studies have suggested that complementary and alternative medicine (CAM) and herbal supplement use may be high on college campuses. This study investigated the relationship between CAM and herbal supplement utilization and coping, self-regulatory, cognitive styles, and healthcare satisfaction among college students (n=370). Indeed, overall CAM and herbal supplement use during the past year appeared high; however, users of these practices appeared somewhat heterogeneous. Dispositional factors were predictive of utilization with active coping style associated with both practices, whereas support-seeking and intrinsic self-regulation were only associated with CAM use and avoidant coping was only related to use of herbal supplements. Notably, dissatisfaction with healthcare services was not associated with either CAM or herbal supplement use among students. The findings from this study offer insight regarding motives for usage that may assist in more openly dialoguing with students regarding their health-enhancing and/or health-compromising behaviors. Moreover, future studies assessing utilization of CAM will benefit from examining the definitional issues of CAM practices that are addressed.","corpus_id":25714358,"score":0},{"doc_id":"21614944","title":"The use of complementary and alternative medicine among Malay breast cancer survivors.","abstract":"BACKGROUND: A cross-sectional studywas carried out to determine the prevalence of complementary and alternative medicine (CAM) use by breast cancer survivors. METHODS: A descriptivesurveydesignwasdeveloped. Information on sociodemographic characteristics, cancer clinical treatment history, and use of CAM were obtained through a modified self-administered questionnaire from 116 Malay breast cancer survivors aged 21 to 67 years who were 2 years postdiagnosis and currently undergoing follow-up treatment at breast cancer clinics at Hospital Kuala Lumpur and Universiti Kebangsaan Malaysia Medical Centre. RESULTS: Data suggest that 64% of the participants were identified as CAM users; dietary supplements were the most common form used, followed by prayer and Malay traditional medicine. Within the wide range of dietary supplements, multivitamins were most often taken followed by spirulina, vitamin C, evening primrose oil, and herbal products. Contrary to other findings, the CAM users were found to be older, had secondary education levels, and were from middle-income households. However, there was no significant difference between CAM users and nonusers in this study. Family members played an important role as the main source of information along with doctors/health care providers, friends, and printed materials/mass media. The reasons participants gave for using CAM were mainly to assist in healing the body's inner strength, to cure cancer, and to reduce stress. Only half of the participants consulted with their physicians regarding the safety of CAM use. The participants began to use CAM while undergoing clinical treatments. Most of the participants used CAM for more than a year. About RM100 to RM149 (31.88 USD to 47.50 USD at press time) were spent monthly on CAM by 32% of the participants. The CAM use was found to be effective and beneficial for patients' disease states, and they were contented with the usage of the CAM therapies. Multivariate analysis revealed that thedecision to use or not to use CAM was not dependent on sociodemographic background or cancer clinical treatment history. CONCLUSIONS: CAM was commonly used by breast cancer survivors as a coping mechanism to battle the disease.","corpus_id":15882508,"score":0},{"doc_id":"22187618","title":"Complementary medicine use among Moroccan patients with cancer: a descriptive study.","abstract":"BACKGROUND: Complementary and alternative medicine (CAM) is a group of diverse medical and health care systems, practices, and products that are not generally considered part of conventional medicine. As cancer incidence rates and survival time increase, use of CAM will likely increase. However, little is known about the use of CAM in cancer patients, specifically in emerging countries. METHODS: We conducted a study in the medical oncology department at the University Hospital of Fez on the use of complementary medicine among cancer patient. The aims of this study were to estimate and describe the reasons of use of complementary medicine (CM) in patients with a cancer treated in a Moroccan oncology department. A specially designed questionnaire was completed for patient during treatment or follow-up in the oncology department after formal consent was obtained. It was a descriptive study among 100 patients over a period of 6 months between September 2008 and February 2009. RESULTS: A total of 100 patients participated in the study, 46 of them were identified as users of complementary medicine. The most substances used were plants 24%, pure honey 13% and water of Zem Zem (holy water from Mecca) 11%. Concerning techniques, religious practices 37%, special diets 22% and recourse to traditional healers 11% were most commonly used. No specific user profile was observed depending of different sociodemograhics and clinical parameters. The majority of the users of complementary medicine were not revealing their habits to their oncologist because the question was not raised in consultation. CONCLUSION: It seems that medical doctors should ask patients about their use of complementary medicine when they obtain medical history and they need to know more about complementary medicine to offer better consultation. Complementary medicine must benefit, as well as conventional medicine, from scientific studies to evaluate potential benefits, toxicity and interactions with the conventional treatment to enable the oncologist better inform his patients.","corpus_id":13968838,"score":0},{"doc_id":"22873496","title":"Use of complementary medicine amongst patients on antiretroviral drugs in an HIV treatment centre in Lagos, Nigeria.","abstract":"Traditional herbal remedies have been used to treat many ailments in Nigeria but the safety of herbal remedies has been the major concerns to many people especially when the chemical constituents of the products are not known. This study is therefore designed to evaluate the prevalence of use of complementary drugs with antiretroviral (ARV) therapy and possible treatment outcome of the concurrent utilization of these therapeutic agents. A descriptive cross-sectional survey of 354 HIV patients attending APIN clinics in LUTH using a consecutive sampling technique was used. There was also correlation of the data obtained from the patients with their clinical case notes. Results showed that only 8.2 % of the respondents' used herbal medicine concurrently with ARV therapy. Ninety percent of the participants were on a two nucleoside and one non-nucleoside based ARV therapy. The most common regimen (55%) was Zidovudine/lamivudine/Nevirapine fixed dose combination while 10% use a protease inhibitor based regimen. The commonly herbal drugs used ranges from Jobelyn [Sorghum bicolor plant leaves (13.8%)], Garlic [Allicin, γ-glutamyl- (s)-ally-L-Cysteine] (10.3%), Ginger [Essential oil] (17.2%) and Aloe vera [Hydroxyanthracene derivatives expressed as Barbaloin] (10.3%). The major reason for the commencement of herbal medicine is the perception that the medicine will boost their immunity (65.5%). However, there was a marginal improvement though not significant (p ≥ 0.05) in the CD4 counts (489.8 ± 195.2; 419.1 ± 236.2) and viral load (5117.8 ± 26092.0; 31136.7 ± 197954.6) of HIV patients on herbal drugs compared to those who are not on herbal drugs. Herbal medicines have potentials to interact with ARVs and thus result in adverse reactions and possibly therapeutic failure. There is need for thorough investigation of the pharmacological action of these herbal medicines in HIV treatment taking into consideration their pharmacokinetic and toxicological profile.","corpus_id":34288408,"score":0},{"doc_id":"22906201","title":"Herbal medicine: a survey of use in Nigerian presurgical patients booked for ambulatory anaesthesia.","abstract":"BACKGROUND: Utilization of herbal medicines in the preoperative period by Nigerian patients booked for day case surgery has not been explored. METHODS: Cross-sectional survey of 60 patients presenting for day-case surgery at a tertiary healthcare institution over a 3-week period in August 2011 was conducted. Using a structured questionnaire, inquiries were made concerning use of herbal medicines in the immediate preoperative period. Socio-demographic characteristics, information on use of concurrent medical prescriptions, types of herbs used, reasons for use, perceived side effects and perceived efficacy were obtained. Data were evaluated using descriptive statistics and Chi-square. RESULTS: Fifty-two (86.7%) were American Society of Anesthesiologists (ASA) class 1 while 8 (13%) were ASA 2. Most patients (86.7%) had their procedures done under local infiltration with monitored anaesthesia care (MAC), while 5.0% and 8.3% had their procedures done under regional and general anaesthesia, respectively. About 48.3% of respondents were on concurrent medical prescriptions while 51.7% were not. Forty percent (40%) of patients admitted to use of herbal medicine, all by the oral route, in the immediate perioperative period; 87.5% did not inform their doctor of their herbal use. Types of herbs used included 'dogonyaro', 'agbo', 'nchanwu', and Tahitian noni. Treatment of malaria was commonest reason for use in 29.2% of patients, while cough and concurrent surgical condition were reasons given by 12.5% of patients, respectively. Seventy-nine percent (79.2%) of patients considered their herbal medications effective. Perceived side effects of herbal medication (16.6%) included fever, waist pain and intoxication. There were no variations in use between ASA 1 and ASA 2 patients and none between respondents on conventional medication against those that were not. Variables such as age less than 35 years, female gender, being married and being an urban dweller did not show any significant difference in use. CONCLUSION: This survey revealed many patients were on one or more herbal preparations in the immediate preoperative period. In consideration of possible untoward drug interactions between conventional medication, herbal preparations and anaesthesia, doctors (especially anaesthetists) should routinely assess all patients booked to be anaesthetized, especially those for day case surgery. The authors recommend surveys with larger respondent numbers to determine prevalence of use and possible interactions between indigenous Nigerian herbs and anaesthesia.","corpus_id":8719566,"score":0},{"doc_id":"24082321","title":"Complementary and alternative medicine usage in cancer patients in southeast of Turkey.","abstract":"The aim of this study was to investigate the frequency of complementary and alternative medicine (CAM) methods and clinical characteristics in cancer patients in southeast of Turkey. A total of 324 patients (173 female) were enrolled to this study. Questionnaire was applied to all patients individually for approximately 15 minutes by a doctor. At least one CAM method was used by 62% (n=201) of the patients. 82.5% (n=166) of patients treated with CAM were using at least one herbal species. Likewise, 40.9% (68/166) of these patients were using herbal mixtures and 39.8% (66/166) of them were using single herbal as nettle (Urtica dioica) or its seed, 19.3 % (32/166) of them were using other herbals. CAM methods were preferred more frequently by the patients with metastatic stage (p=0.005), receiving palliative treatment (p<0.001), chemotherapy (p=0.020), in between 40-60 ages patient groups (p=0.002), and when duration of disease was lengthened (p=0.002). CAM use among cancer patients is quite common. Presence of metastatic cancer at diagnosis, receiving chemotherapy and palliative treatment and long disease duration were found as main associated factors for CAM usage.","corpus_id":38485847,"score":0},{"doc_id":"24171723","title":"The co-use of conventional drugs and herbs among patients in Norwegian general practice: a cross-sectional study.","abstract":"BACKGROUND: Different patient groups are known to use herbal remedies and conventional drugs concomitantly (co-use). This poses a potential risk of herb-drug interaction through altering the drug's pharmacokinetics or pharmacodynamics. Little is known about co-use among patients in general practice. The primary aim of this study was to compare patients in general practice that co-use herbal remedies and conventional drugs with those who do not. The secondary aim was to register the herb-drug combinations with potential clinical relevant interactions among the co-users. METHOD: A questionnaire based cross-sectional study conducted in the autumn 2011 in a general practice office with four general practitioners (GPs) and one intern in Western Norway. Adults >18 years who came for an office visit were invited. The questionnaire asked about demographics, herbal use, conventional drug use and communication about herbal use. Multivariable logistic regression was used to compare co-users to the other patients. RESULTS: Of the 381 patients who completed the questionnaire, the prevalence of herbal use was 44%, with bilberry (41%), green tea (31%), garlic (27%), Aloe vera (26%) and echinacea (18%) as the most frequently used. Among those using conventional drugs regularly, 108 (45%) co-used herbs. Close to 40% of patients on anticoagulants co-used herbs, with garlic and bilberry as the most frequent herbs. Compared to all other patients, co-users had significantly (p < 0.05) increased odds to be female (adjOR 2.0), age above 70 years (adjOR 3.3), use herbs to treat an illness (adjOR 4.2), use two or more herbs (polyherbacy, adjOR 12.1) and having experienced adverse effects of herbal use (adjOR 37.5). Co-use was also associated with use of analgesics or dermatological drugs (adjOR 5.1 and 7.9 respectively). Three out of four patients did not discuss herbal use with any health care professional. CONCLUSION: A sizable proportion of the GP patients co-used herbs with conventional drugs, also combinations with reported interaction potential or additive effects like anticoagulants and garlic. The low disclosure of herbal use to their GP, polyherbacy and the risk of interactions in vulnerable groups like elderly and chronically ill patients, warrant increased awareness among GPs.","corpus_id":1089923,"score":0},{"doc_id":"24219150","title":"The use of herbal medicines during breastfeeding: a population-based survey in Western Australia.","abstract":"BACKGROUND: Main concerns for lactating women about medications include the safety of their breastfed infants and the potential effects of medication on quantity and quality of breast milk. While medicine treatments include conventional and complementary medicines, most studies to date have focused on evaluating the safety aspect of conventional medicines. Despite increasing popularity of herbal medicines, there are currently limited data available on the pattern of use and safety of these medicines during breastfeeding. This study aimed to identify the pattern of use of herbal medicines during breastfeeding in Perth, Western Australia, and to identify aspects which require further clinical research. METHODS: This study was conducted using a self-administered questionnaire validated through two pilot studies. Participants were 18 years or older, breastfeeding or had breastfed in the past 12 months. Participants were recruited from various community and health centres, and through advertising in newspapers. Simple descriptive statistics were used to summarise the demographic profile and attitudes of respondents, using the SPSS statistical software. RESULTS: A total of 304 questionnaires from eligible participants were returned (27.2% response rate) and analysed. Amongst the respondents, 59.9% took at least one herb for medicinal purposes during breastfeeding, whilst 24.3% reported the use of at least one herb to increase breast milk supply. Most commonly used herbs were fenugreek (18.4%), ginger (11.8%), dong quai (7.9%), chamomile (7.2%), garlic (6.6%) and blessed thistle (5.9%). The majority of participants (70.1%) believed that there was a lack of information resources, whilst 43.4% perceived herbal medicines to be safer than conventional medicines. Only 28.6% of users notified their doctor of their decision to use herbal medicine(s) during breastfeeding; 71.6% had previously refused or avoided conventional medicine treatments due to concerns regarding safety of their breastfed infants. CONCLUSIONS: The use of herbal medicines is common amongst breastfeeding women, while information supporting their safety and efficacy is lacking. This study has demonstrated the need for further research into commonly used herbal medicines. Evidence-based information should be available to breastfeeding women who wish to consider use of all medicines, including complementary medicines, to avoid unnecessary cessation of breastfeeding or compromising of pharmacotherapy.","corpus_id":11720103,"score":0},{"doc_id":"24533750","title":"Use of bodily sensations as a risk assessment tool: exploring people with Multiple Sclerosis' views on risks of negative interactions between herbal medicine and conventional drug therapies.","abstract":"BACKGROUND: Most users of complementary and alternative medicine (CAM) combine it with conventional medicine. Recent risk assessment studies have shown risks of negative interactions between CAM and conventional medicine, particularly when combining herbal medicine and conventional drug therapies (CDT). Little is known about the way users consider such risks. The present paper aims to gain knowledge about this issue by exploring views on risks of negative interactions when combining herbal medicine and CDT among people with multiple sclerosis (MS). METHODS: This paper draws on a qualitative follow-up study on a survey among members of the Danish MS Society. Semi-structured, in-depth qualitative interviews were conducted with a strategic selection from the survey respondents. The study was inspired by a phenomenological approach and emerging themes were extracted from the data through meaning condensation. RESULTS: Four themes characterized the informants' views on risks of negative interactions when combining herbal medicine and CDT: 1) 'naturalness' in herbal medicine; 2) 'bodily sensations' as guidelines; 3) trust in the CAM practitioner; 4) lack of dialogue with medical doctor. CONCLUSIONS: Generally, the combination of herbal medicine and CDT was considered by the informants to be safe. In particular, they emphasized the 'non-chemical' nature of herbal medicine and of their own bodily sensations as warrants of safety. A trustful relation to the CAM practitioner furthermore made some of them feel safe in their use of herbal medicine and CDT in combination. The informants' use of bodily sensations as a non-discursive risk assessment may be a relevant element in understanding these issues.","corpus_id":14682417,"score":0},{"doc_id":"24748849","title":"What young people want from health-related online resources: a focus group study.","abstract":"The growth of the Internet as an information source about health, particularly amongst young people, is well established. The aim of this study was to explore young people's perceptions and experiences of engaging with health-related online content, particularly through social media websites. Between February and July 2011 nine focus groups were facilitated across Scotland with young people aged between 14 and 18 years. Health-related user-generated content seems to be appreciated by young people as a useful, if not always trustworthy, source of accounts of other people's experiences. The reliability and quality of both user-generated content and official factual content about health appear to be concerns for young people, and they employ specialised strategies for negotiating both areas of the online environment. Young people's engagement with health online is a dynamic area for research. Their perceptions and experiences of health-related content seem based on their wider familiarity with the online environment and, as the online environment develops, so too do young people's strategies and conventions for accessing it.","corpus_id":977448,"score":0},{"doc_id":"25370478","title":"Use of herbal medicine during pregnancy among women with access to public healthcare in Nairobi, Kenya: a cross-sectional survey.","abstract":"BACKGROUND: Maternal health is a public health priority in many African countries, but little is known about herbal medicine use in pregnancy. This study aimed to determine the pattern of use of herbal medicine in an urban setting, where women have relatively high access to public healthcare. METHODS: This cross-sectional study included 333 women attending a childcare clinic in a district public health hospital in Nairobi, Kenya, during January and February, 2012, and who had delivered a baby within the past 9 months. Qualitative and quantitative data on herbal medicine use during their latest pregnancy were collected through an interviewer-administered questionnaire. Data was analysed descriptively and the Chi square test and Fishers' exact test used to analyse relationships among variables. RESULTS: About 12% of women used herbal medicine during their most recent pregnancy. The use of herbal medicine was associated with a lower level of education (p = 0.007) and use before the index pregnancy (p <0.001). Only 12.5% of users disclosed such use to healthcare professionals, and about 20% used herbal medicine concomitantly with Western medicine for the same illness/condition. Women used herbal medicine for back pain, toothache, indigestion and infectious diseases, such as respiratory tract infections and malaria. A proportion of users took herbal medicine only to boost or maintain health. There were high rates of self-prescribing, as well as sourcing from family and friends. Beliefs about safety and efficacy were consistent with patterns of use or non-use, although both users and non-users were unsure about the safety and contraindications of Western medicine during pregnancy compared with that of herbal medicine. CONCLUSION: Herbal medicine is used by 12% of pregnant women with access to healthcare in an urban context in Kenya, and often occurs without the knowledge of healthcare practitioners. Healthcare professionals should play a role in rational use of both herbal and Western medicine, by discussing contraindications and the potential for drug-herb interactions with patients. More studies are needed into the use of herbal medicines during pregnancy, labour and the postpartum period in different geographical areas, and into the health outcomes associated with their use.","corpus_id":8782199,"score":0},{"doc_id":"25550393","title":"The man-in-the-moon face: a qualitative study of body image, self-image and medication use in systemic lupus erythematosus.","abstract":"OBJECTIVE: Little is yet known about the interactions between body image, self-image, medication use and adherence to medication in people with SLE. Using a qualitative mode of enquiry, we sought to understand these experiences within a group of patients diagnosed with SLE. METHODS: Fifteen participants (14 female, 1 male) with SLE took part in semi-structured interviews. Their ages ranged from 22 to 57 years and disease duration ranged from 3 to 20 years. Interviews were audio recorded and transcribed verbatim. Data were analysed using interpretative phenomenological analysis. RESULTS: Analysis revealed four themes that are presented set within the overarching concept of body and self-image: the road to diagnosis, communication and treatment concordance, living with the medication and self-image-faking it. Narratives revealed significant dissatisfaction with body image, an externally located concept. Worries about appearance and weight were most commonly mentioned and were often related to steroid use. Creative non-compliance with medication was frequently described and greater concordant relationships with physicians desired. Overall, participants sought increased investment in self-image, an internally located concept. CONCLUSION: Body and self-image are important issues for individuals with SLE. Yet participants in our study generally felt that their health care providers did not give enough consideration to their concerns over the outward appearance effects of both the disease and its treatment.","corpus_id":19677433,"score":0},{"doc_id":"25586865","title":"Patient perspectives on online health information and communication with doctors: a qualitative study of patients 50 years old and over.","abstract":"BACKGROUND: As health care systems around the world shift toward models that emphasize self-care management, there is increasing pressure for patients to obtain health information online. It is critical that patients are able to identify potential problems with using the Internet to diagnose and treat a health issue and that they feel comfortable communicating with their doctor about the health information they acquire from the Internet. OBJECTIVE: Our aim was to examine patient-identified (1) problems with using the Internet to identify and treat a health issue, (2) barriers to communication with a doctor about online health information seeking, and (3) facilitators of communication with a doctor about patient searches for health information on the Internet. METHODS: For this qualitative exploratory study, semistructured interviews were conducted with a sample of 56 adults age 50 years old and over. General concerns regarding use of the Internet to diagnose and treat a health issue were examined separately for participants based on whether they had ever discussed health information obtained through the Internet with a doctor. Discussions about barriers to and facilitators of communication about patient searches for health information on the Internet with a doctor were analyzed using thematic analysis. RESULTS: Six higher-level general concerns emerged: (1) limitations in own ability, (2) credibility/limitations of online information, (3) anxiety, (4) time consumption, (5) conflict, and (6) non-physical harm. The most prevalent concern raised by participants who communicated with a doctor about their online health information seeking related to the credibility or limitations in online information. Participants who had never communicated with a doctor about their online health information seeking most commonly reported concerns about non-physical harm. Four barriers to communication emerged: (1) concerns about embarrassment, (2) concerns that the doctor doesn't want to hear about it, (3) belief that there is no need to bring it up, and (4) forgetting to bring it up. Facilitators of communication included: (1) having a family member present at doctor visits, (2) doctor-initiated inquiries, and (3) encountering an advertisement that suggested talking with a doctor. CONCLUSIONS: Overall, participants displayed awareness of potential problems related to online health information seeking. Findings from this study point to a set of barriers as well as facilitators of communication about online health information seeking between patients and doctors. This study highlights the need for enhanced patient communication skills, eHealth literacy assessments that are accompanied by targeted resources pointing individuals to high-quality credible online health information, and the need to remind patients of the importance of consulting a medical professional when they use online health resources to diagnose and treat a health issue.","corpus_id":20696176,"score":0},{"doc_id":"26133063","title":"\"The medicine from behind\": The frequent use of enemas in western African traditional medicine.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: Purgative enemas form an integral part of African traditional medicine. Besides possible benefits, serious health risks of rectal herbal therapy have been described in literature. To design appropriate health education programs, it is essential to understand traditional herbal practices and local perceptions of health and illness. Little is known about the herbal ingredients of enemas in Sub-Saharan Africa and consumers' personal reasons to use them. AIM OF THE STUDY: To analyze the importance of enema use with regard to plant species used and illnesses treated in West and Central Africa, to understand the local health beliefs that underlie frequent enema use and to evaluate which recipes and practices could be beneficial or harmful. MATERIALS AND METHODS: We extracted data from 266 ethnobotanical questionnaires on medicinal (in particular women's health and childcare) and ritual plant use in Ghana, Benin and Gabon. Plants mentioned during interviews were vouchered and identified in herbaria. Health issues treated by means of enemas were ranked according to the number of plant species used for a specific illness. We compared our results with findings of medical research on benefits and risks of enema use in Sub-Saharan Africa. RESULTS: We recorded ca. 213 different plant species used in hundreds of recipes for rectal insertions, mostly in Ghana and Gabon. Stomachache, abdominal pain, female infertility and birth facilitation were treated with the highest number of plants species. Cleansing the intestines of young children to promote their health by getting rid of 'dirt', instead of treating constipation, was an important cultural practice that required the rectal application of herbal medicine, as well as other cultural bound health issues like stimulating children to walk at an early age. Tradition, the bitter taste of herbal medicine and the rapid effect of enemas were frequently mentioned reasons for enema use. DISCUSSION AND CONCLUSIONS: Literature indicates that although enemas can help to improve the hygienic conditions of a household with young infants, frequent enema use can pose serious risks like direct toxicity caused by harmful ingredients, mechanical injury and infections. In Africa, enemas containing herbal medicine are common methods of administering herbal medicine for a variety of diseases, rather than just medicinal treatments for constipation as previously thought. Health professionals should be aware of the extent of, and motivation behind enema use to develop culturally appropriate education programs, especially targeted at vulnerable groups such as elderly people, parents of young infants and pregnant women.","corpus_id":40581988,"score":0},{"doc_id":"26726906","title":"Use and users of complementary and alternative medicine among people with multiple sclerosis in Denmark.","abstract":"BACKGROUND: It is known that complementary and alternative medicine (CAM) is popular among people with multiple Sclerosis (MS) and that use is widespread. However, very limited knowledge exists about use and users of CAM among people with MS in a Danish context. AIMS: The overall aim of the thesis is to investigate how and why people with MS in Denmark include CAM in managing their life with a chronic disease and to discuss their experiences and beliefs linked to CAM use. METHODS: A mixed methods research design was applied, combining an Internet-based survey with two qualitative in-depth interview studies. A total of 6,850 people with MS from the five Nordic countries, of these 3,500 from Denmark, were invited to participate in the survey. The average response rate was 56.1%. Based on analyses of the Danish survey data, two specific issues regarding the use of CAM were selected for further investigation and two qualitative interview studies were performed (n = 17, n = 11), using program theory and meaning categorization as analytical tools. RESULTS: The results of the study indicate that the use of CAM among people with MS is widespread in Denmark as well as in the other Nordic countries. The results furthermore suggest that this use is generally embedded in a preventative, autonomous approach to treatment and that the users' choices regarding CAM may be related to many personal factors and do not necessarily represent a distrust of the medical system. PERSPECTIVES: The results of the study point to the relevance of healthcare professionals engaging in understanding patients' different motives for - and experiences with - using different types of treatments. Thereby, the results of the study also point to the importance of enhancing and qualifying communication between patients and representatives of conventional healthcare systems regarding the patients' use of CAM, both with the aim of mutual learning and for reasons of safety.","corpus_id":6778329,"score":0},{"doc_id":"27382428","title":"A qualitative study exploring medicines use pattern and practice among general public in Malaysia.","abstract":"OBJECTIVE: The objective of this study is to explore the pattern and practice of medicine use among the general public; and to explore the key factors influencing medicine use among medicine users. METHODS: A qualitative approach using focus group discussions was conducted to get in-depth information about medicines use pattern and practice from the general public. Adult people who reported using medicines at the time of study or in the previous month were approached. Two focus group discussions were audio-recorded and transcribed verbatim. The obtained data were analysed using thematic content analysis. RESULTS: This study found that there are some misunderstanding about the appropriate use of medicines. The majority of the participants reported that they were complying with their medication regimen. However, forgetting to take medicines was stated by 4 participants while 2 participants stopped taking medicines when they felt better. In addition, 10 participants reporting using medicines according to their own knowledge and past experience. Whereas 4 participants took medicines according to other informal resources such as family, friends or the media. Seven participants have experienced side effects with using medicines, 4 of them informed their doctor while 3 participants stopped taking medicines without informing their doctor. CONCLUSION: There was a misunderstanding about medicines use in terms of medication compliance, self-management of the illness and the resources of information about using medicines. Many efforts are still needed from health care professionals to provide sufficient information about medicines use in order to decrease the risk of inappropriate use of medicines and to achieve better therapeutic outcome.","corpus_id":15109891,"score":0},{"doc_id":"27400742","title":"Use of complementary and alternative medicines in haemodialysis patients: a cross-sectional study from Palestine.","abstract":"BACKGROUND: Complementary and alternative medicine (CAM), and herbal therapies, are accepted worldwide, and have been important from medical, sociological and economic perspectives, among haemodialysis (HD) patients. The primary aim of this study was to evaluate the use of CAM among patients with end-stage renal disease (ESRD) who are undergoing HD. METHODS: Face-to-face interviews of patients with ESRD undergoing HD from ten outpatient renal departments at a national level in Palestine were conducted from June 2014 to January 2015. A survey questionnaire, which included questions on socio-demographic and clinical characteristics, and on the CAM therapies that were used, was administered. RESULTS: Out of 267 patients interviewed, 172 patients used at least one type of CAM in the last month prior to the interview, and thus the utilisation rate was 64.4 %. Forty one (15.4 %) patients reported using one type of CAMs, while 18.7 % used two different CAMs and 30.3 % used more than two types of CAMs for their health status. Of the patients who used CAM, herbal therapies were used most often (43.5 %), followed by honey (35.6 %), diet (22.8 %), and exorcism in Islam (16.9 %). The herbal therapies mentioned most often were Nigella sativa L. (18.7 %), followed by Salvia officinalis L. (16.9 %), and Pimpinella anisum L. (10.5 %). CONCLUSIONS: In conclusion, the prevalence of CAM is relatively high in the selected population. Most patients used biological therapies such as herbal remedies, thus highlighting a greater need for patient education regarding CAM therapies and possible herb-drug interactions. Health care providers must be aware of the potential benefits and risks related to CAM use. There is a need for more clinical research pertaining to CAM to reach stronger evidence regarding potential benefits and risks related to CAM use.","corpus_id":15492556,"score":0},{"doc_id":"28472987","title":"Use of complementary and alternative medicine by patients with end-stage renal disease on haemodialysis in Trinidad: A descriptive study.","abstract":"BACKGROUND: Despite the paucity of scientific evidence, complementary and alternative medicine (CAM) is widely used for the prevention and treatment of illness, holistic care, and counteracting the adverse effects of conventional medicine (CM). This study investigates the use of CAM by patients with end-stage renal disease (ESRD) on haemodialysis. METHODS: This quantitative study was conducted from November 1, 2014 to December 31, 2014 in the haemodialysis unit at San Fernando General Hospital (San Fernando, Trinidad). Face-to-face questionnaire-based interviews were held with101of 125 eligible patients (response rate, 80.5%) at the chairside during haemodialysis. The completed questionnaires were entered into a secure computer database. Data analysis included descriptive analysis, χ(2) tests, and binary logistic regression analysis. RESULTS: A minority of the patients were CAM users (n = 19; 18.8%). All 19 CAM users took medicinal herbs, 78.9% (n = 15) used spiritual therapy, and 10.5% (n = 2) used alternative systems. Medicinal tea (n = 15; 78.9%), garlic (Allium sativum) (n = 17; 73.7%), and ginger (Zingiber officinale roscoe) (n = 13; 68.4%) were the most commonly used medicinal herbs. Seven (36.8%) patients used Chinese herbal medicines and 3 (15.8%) patients used Aloe vera. All CAM users were willing to use CAM without supervision or monitoring by their doctors while receiving CM. The use of CAM could not be predicted by age, sex, ethnicity, education, religion, marital status, or employment. Nearly all (98%) patients were satisfied with CAM. More than one-third (36.8%) of patients did not disclose their use of CAM to their doctors, who were generally indifferent to such therapy. CONCLUSIONS: The use of CAM by patients with ESRD was relatively infrequent. All patients used medicinal herbs, most patients used spiritual therapy, and a minority of patients used alternative systems. Complementary and alternative medicine was primarily used for spiritual reasons and the likelihood of its use was influenced by family, friends, and other patients. Patients continued using CM with one or more CAM therapies without informing their healthcare providers, which is a major health risk.","corpus_id":5024638,"score":0},{"doc_id":"28724031","title":"Methodological challenges in the use of focus groups with people with severe mental illness.","abstract":"This study addresses the practical, methodological and ethical challenges that were found in three studies that used focus groups with people with severe mental illness, in the context of community mental health services in Brazil. Focus groups are a powerful tool in health research that need to be better discussed in research with people with severe mental illness, in the context of community mental health facilities. This study is based on the authors' experience of conducting and analyzing focus groups in three different cities - Campinas, Rio de Janeiro and Salvador - between 2006-2010. The implementation of focus groups with people with severe mental illness is discussed in the following categories; planning, group design, sampling, recruitment, group interview guides, and conduction. The importance of connecting mental healthcare providers as part of the research context is emphasized. Ethical issues and challenges are highlighted, as well as the establishment of a sensitive and empathic group atmosphere, wherein mutual respect can facilitate interpersonal relations and enable people diagnosed with severe mental illness to make sense of the experience. We emphasize the relevance of the interaction between clinical and research teams in order to create collaborative work, achieve inquiry aims, and elicit narratives of mental health users and professionals.","corpus_id":22658474,"score":0},{"doc_id":"29610108","title":"Preferences for Web-Based Information Material for Low Back Pain: Qualitative Interview Study on People Consulting a General Practitioner.","abstract":"BACKGROUND: Information on self-management, including addressing people's fears and concerns, are core aspects of managing patients with low back pain (LBP). Web apps with patient information may be used to extend patient-physician consultations and encourage self-management outside of the consultation room. It is, however, important to identify the end users' needs and preferences in order to maximize acceptance. OBJECTIVE: The aim of this study was to identify preferences for the content, design, and functionality of a Web app with evidence-based information and advice for people with LBP in Denmark. METHODS: This is a phenomenological qualitative study. Adults who had consulted their general practitioner because of LBP within the past 14 days were included. Each participated in a semistructured interview, which was audiotaped and transcribed for text condensation. Interviews were conducted at the participant's home by 2 interviewers. Participants also completed a questionnaire that requested information on age, gender, internet usage, interest in searching new knowledge, LBP-related function, and pain. RESULTS: Fifteen 45-min interviews were conducted. Participants had a median age of 40 years (range 22-68 years) and reported a median disability of 7 points (range 0-18) using the 23-item Roland Morris Disability Questionnaire. Participants reported that Web-based information should be easy to find and read, easily overviewed, and not be overloaded with information. Subjects found existing Web-based information confusing, often difficult to comprehend, and not relevant for them, and they questioned the motives driving most hosting companies or organizations. The Patient Handbook, a Danish government-funded website that provides information to Danes about health, was mentioned as a trustworthy and preferred site when searching for information and advice regarding LBP. CONCLUSIONS: This study identified important issues to consider when developing and supplementing existing general practice treatment with Web-based information and advice for patients with LBP. Development of a Web app should consider patient input, and developers should carefully address the following domains: readability, customization, design, credibility, and usability.","corpus_id":4626418,"score":0}],"string":"[\n {\n \"doc_id\": \"18549476\",\n \"title\": \"The role of complementary and alternative medicine (CAM) in Germany - a focus group study of GPs.\",\n \"abstract\": \"BACKGROUND: There has been a marked increase in the use of complementary and alternative medicine (CAM) in recent years worldwide. In Germany, apart from 'Heilpraktiker' (= state-licensed, non-medical CAM practitioners), some general practitioners (GPs) provide CAM in their practices. This paper aims to explore the attitudes of GPs about the role of CAM in Germany, in relation to the healthcare system, quality of care, medical education and research. Furthermore, experiences of GPs integrating CAM in their daily practice were explored. METHODS: Using a qualitative methodological approach 3 focus groups with a convenience sample of 17 GPs were conducted. The discussions were transcribed verbatim and analysed using qualitative content analysis. RESULTS: The majority of the participating GPs had integrated one or more CAM therapies into their every-day practice. Four key themes were identified based on the topics covered in the focus groups: the role of CAM within the German healthcare system, quality of care, education and research. Within the theme 'role of CAM within the healthcare system' there were five categories: integration of CAM, CAM in the Statutory Health Insurance, modernisation of the Statutory Health Insurance Act, individual healthcare services and 'Heilpraktiker'. Regarding quality of care there were two broad groups of GPs: those who thought patients would benefit from standardizing CAM and those who feared that quality control would interfere with the individual approach of CAM. The main issues identified relating to research and education were the need for the development of alternative research strategies and the low quality of existing CAM education respectively. CONCLUSION: The majority of the participating GPs considered CAM as a reasonable complementary approach within primary care. The study increased our understanding of GPs attitudes about the role of CAM within the German healthcare system and the use of 'Heilpraktiker' as a competing CAM-provider. It seems to be a need for increased funding for research, better education and remuneration by the Statutory Health Insurance in order to improve access to 'Integrative medicine' in Germany.\",\n \"corpus_id\": 1890860,\n \"score\": 2\n },\n {\n \"doc_id\": \"18845412\",\n \"title\": \"\\\"I don't know how many of these [medicines] are necessary..\\\" - a focus group study among elderly users of multiple medicines.\",\n \"abstract\": \"OBJECTIVE: The growing prevalence of multiple medicine use among elderly challenges health care. The aim was to conduct an exploratory study describing multiple medicine use from the elderly patient's perspective. METHODS: Twelve focus groups of 29 men and 30 women 65 years of age or older, using five or more medicines were analysed qualitatively. RESULTS: Initially the participants reported no problems with using multiple medicines; they felt fortunate that medicines existed and kept them alive. However, negative attitudes were also revealed, both similar to those presented in studies on lay experience of medicine-taking and some that appear more specific to users of multiple medicines. The foremost of these was that acceptance of medicines depends on not experiencing adverse effects and worrying whether multiple medicine use is 'good' for the body. Furthermore, participants' perception of their medicines depended on interaction with doctors, i.e. trusting 'good' doctors. CONCLUSION: The participants revealed co-existing accounts of both immediate gratitude and problems with using multiple medicines. Furthermore, the patient-doctor relationship coloured their attitudes towards their medicines. PRACTICE IMPLICATIONS: Importance of the patient-doctor relationship for treatment success is highlighted. Moreover, to be able to capture both accounts of the elderly in this study an appropriate consultation length is needed.\",\n \"corpus_id\": 942688,\n \"score\": 2\n },\n {\n \"doc_id\": \"19442268\",\n \"title\": \"The use of herbal medicines by people with cancer: a qualitative study.\",\n \"abstract\": \"BACKGROUND: Between 7% and 48% of cancer patients report taking herbal medicines after diagnosis. Because of the possibility of unwanted side effects or interactions with conventional treatments, people with cancer are generally advised to tell the professionals treating them if they are taking any form of medication, including herbal medicines and supplements. Studies suggest that only about half do so and that the professionals themselves have at best very limited knowledge and feel unable to give informed advice. This study is intended to inform the future development of information resources for cancer patients, survivors and healthcare professionals including tools for use before or during consultation to make it easier for patients to mention, and for healthcare professionals to ask about, use of herbal medications. METHODS/DESIGN: This is a three-phase study. In phase 1, a systematic review of the literature on self-medication with herbal medicines among UK populations living with cancer will establish the current evidence base on use of herbal medicine, sources of information, characteristics and motivations. This will allow us to better understand what aspects need further investigation and inform the topic guide for a qualitative study (phase 2). Six focus groups of six to eight cancer patients who have used at least one herbal preparation since diagnosis will explore behaviour, beliefs, knowledge, information sources and needs in an informal conversational setting. Informed by the findings of the systematic review and qualitative study, in phase 3 we will construct and pilot a questionnaire for a future large-scale survey to quantify and prioritise people's beliefs, needs and information preferences. DISCUSSION: Despite known interactions with conventional cancer treatments and contraindications for some herbal remedies with specific cancers, reliable information resources for patients are very limited. Identifying cancer patients' information needs and preferences is the first step in creating a suitable resource for both the public and the professionals advising them.\",\n \"corpus_id\": 10351583,\n \"score\": 2\n },\n {\n \"doc_id\": \"19797394\",\n \"title\": \"The use of herbal medicines by people with cancer in the UK: a systematic review of the literature.\",\n \"abstract\": \"BACKGROUND AND AIM: Little is known about the use of herbal medicines by people living with cancer in the UK. This systematic review aimed to estimate the prevalence of herbal medicine use by this group, the characteristics of users, factors motivating use, and attitudes towards herbal remedies. DESIGN AND METHODS: Fifteen electronic databases were searched. People who were research-active in the field were contacted and asked about further published or unpublished work. All studies identified as relevant to the purpose of the review were assessed. Searches were not restricted by publication type or date. RESULTS: Of 1288 unique references identified, 11 met the eligibility criteria. Studies were excluded where research had been conducted outside the UK; where information on herbal medicine use was not differentiated from that relating to complementary and alternative therapies more broadly, and where neither prevalence of use nor information on user characteristics was included. Prevalence estimates ranged from 3.1 to 24.9%. Most studies did not obtain information specifically on herbal medicines and only one examined the characteristics and motivations of users of herbal medicines as distinct from complementary and alternative therapies in general. CONCLUSION: The high degree of heterogeneity of methodology, sample selection and characteristics, and research design resulted in a wide range of estimates of prevalence. Well-designed research is needed to define the evidence base about the herbal medicines taken by people with cancer in the UK, the reasons for use, knowledge about possible effects and potential risks, and where people seek information.\",\n \"corpus_id\": 24839125,\n \"score\": 2\n },\n {\n \"doc_id\": \"19942110\",\n \"title\": \"Simply because it works better: exploring motives for the use of medical herbalism in contemporary U.K. health care.\",\n \"abstract\": \"AIM: To clarify the reasons underlying people's use of medical herbalism in the context of contemporary U.K. health care. DESIGN: This qualitative, interpretative study recruited 19 adults who were consulting with registered medical herbalists in a region of southern England. Participants were interviewed about their experiences and the data were analysed thematically. Study methodology was informed by Gadamerian hermeneutic phenomenology. RESULTS: Few of the participants had initially set out to try herbalism, most looking for 'an alternative' to conventional health care. The main reason for exploring non-conventional options was to seek out health care that would more effectively meet their self-perceived needs in the treatment of a chronic condition. As a result of favourable outcomes from their initial treatment, participants subsequently continued to use herbalism for the management of more general, everyday health problems. CONCLUSIONS: Lay and professional ideas about what constitutes health care 'effectiveness' do not necessarily correspond. Participants reported that, in comparison to conventional medicine, medical herbalism satisfied their expectations of health care because it more readily met their own criteria for effectiveness and because it had greater consistency with their own understanding about health, illness and health care. Central to achieving this was the collaborative nature of the herbalist's approach, as well as the therapeutic effect and enduring history of the herbal therapy itself. Participants were in favour of a future integrative health care system provided this did not interfere with the unique attributes of herbalism that make it distinct from conventional medicine.\",\n \"corpus_id\": 22691989,\n \"score\": 2\n },\n {\n \"doc_id\": \"22894888\",\n \"title\": \"A pilot study to assess students' perceptions, familiarity, and knowledge in the use of complementary and alternative herbal supplements in health promotion.\",\n \"abstract\": \"CONTEXT: According to the National Center for Complementary and Alternative Medicine (NCCAM), use of herbal supplements is increasing and will continue to rise. With parents administering medicinal herbs to children as a preventive alternative to traditional drugs, the research team thought it would be interesting to assess the use of these products during the transition into adulthood through college life. OBJECTIVE: This study examined participants' perceptions of, familiarity with, and knowledge of herbal supplements for health promotion. DESIGN: The research team invited participants to complete a 13-item Perception, Familiarity, and Knowledge Survey (PFKS). This online survey included questions regarding demographics, perceptions of complementary and alternative medicine, and familiarity with and knowledge of gingko, ginseng, St. John's wort, garlic, echinacea, and cinnamon. SETTING: The study occurred at a Midwestern university. PARTICIPANTS: Two-hundred and eighty-six college students participated. OUTCOME MEASURES: The research team used the Chi-square test of association to examine the class rank (freshmen/sophomores, juniors/seniors, and graduate students) of students (frequency) and their gender in relation to their perceptions of, familiarity with, and knowledge of herbal supplements. RESULTS: Chi-square analysis showed that 80.8% of participants were familiar with complementary and alternative medicine (CAM) (P = .000). Of participants who were aware of the six herbs, a majority was familiar with ginkgo (82.4%), ginseng (96.1%), St. John's wort (78.4%), garlic (98.4%), echinacea (65.6%), and cinnamon (96.8%). Despite students' familiarity with the herbs, 45.1% to 74.1% of the participants were unsure of their effectiveness in preventing disease or promoting good health. Participants perceived the barriers to their CAM awareness as (1) insufficient education (26.0%), (2) a lack of scientific evidence (25.9%), and (3) a lack of trained professionals (17.5%). Many students (85.8%) desired educational courses on CAM therapies, with nutrition professors being ranked highest as the providers of this education by 88.0%. Over 60.0% of participants thought that conventional medicine could benefit from integration with CAM and that medical professionals should integrate CAM into health-care practices. CONCLUSION: College students appear to be highly familiar with CAM and herbal supplements but currently have little experience with and knowledge of herbal supplements.\",\n \"corpus_id\": 23942666,\n \"score\": 2\n },\n {\n \"doc_id\": \"22940254\",\n \"title\": \"A prospective study on the safety of herbal medicines, used alone or with conventional medicines.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: Along with increase of herbal medicine use worldwide, the safety of traditional herbal medicines frequently becomes a medical issue. AIM OF THE STUDY: This study aimed to investigate the incidence of herbal medicine-induced adverse effects on liver functions. SUBJECTS AND METHODS: A prospective study was performed with 313 inpatients (87 male and 226 female) receiving herbal prescriptions during hospitalization. The patients were classified into two groups based on their treatments: one group received herbal medicines only (57 patients), and another received herbal and conventional medicines concurrently (256 patients). All patients were given liver and renal function tests at the start of hospitalization (baseline) and at approximately 2-week intervals thereafter, until discharge. RESULTS: Six of the 313 patients showed abnormal liver function without related clinical symptoms (1.9%, 95% CI 0.38-3.41); none of the patients in the herbal group had abnormal result in liver function tests (0% of 57 patients) while all six had received a combination of herbal and conventional medicines (2.3% of 256 patients, 95% CI 0.46-4.14). CONCLUSION: Our findings indicate that herbal drugs used alone are relatively safe, but the risk for adverse reactions may increase when herbal and conventional drugs are taken concurrently.\",\n \"corpus_id\": 5133756,\n \"score\": 2\n },\n {\n \"doc_id\": \"23346197\",\n \"title\": \"Herbal Medicine in Primary Healthcare in Germany: The Patient's Perspective.\",\n \"abstract\": \"Herbal medicine (HM) is one of the most widely used Complementary and Alternative Medicine (CAM) therapies throughout the world. The WHO has recognized HM as an essential component of primary healthcare. The aim of this study was to explore patients' attitudes towards using HM, their sources of information and the role of costs. Within a qualitative research approach, semi-standardized interviews with 18 patients using HM were conducted and analyzed according to Mayring's content analysis. Patients highlighted their active role and perceived autonomy choosing HM. Most interviewees experienced HM as better, with more sustainable effects and fewer side effects compared to conventional medicine. All media, family, friends, and healthcare professionals were reported as sources of information. Some patients complained that doctors and pharmacists have insufficient knowledge of HM. Most patients expressed their regret that HM is not reimbursed by statutory health insurances but also their general willingness to pay extra for HM. The main challenge for German primary care, besides the reintroduction of reimbursement, is the promotion of knowledge and skill development in HM. This is to ensure patient safety and work in partnership with patients. Appropriate strategies for education must be tailored to the specific needs of health professional groups.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23820895\",\n \"title\": \"Consumers' attitude towards the use and safety of herbal medicines and herbal dietary supplements in Serbia.\",\n \"abstract\": \"BACKGROUND: The use of herbal medicines and herbal dietary supplements in Serbia is very common and many patients consume herbal preparations with conventional drug therapy. OBJECTIVE: The aim of this survey was to evaluate the consumers' awareness of herbal remedies and the safety of herbal dietary supplements, their attitude towards combining herbals and drugs, and the source of recommendations for their use. SETTING: The study included all consumers who bought herbal remedies and herbal dietary supplements in 15 pharmacies on the territory of Novi Sad during 2011 and who accepted to be interviewed. METHODS: Structured interviews using questionnaire, conducted by pharmacists. The questionnaire included 4 parts: socio-demographic characteristics of consumers, source of recommendations for the use of herbal products, attitude towards safety of herbal remedies and herbal dietary supplements use and their combination with regular drugs, as well as the question of purchased herbal products. MAIN OUTCOME MEASURE: Consumers' attitude towards the safety and use of herbal medicines and herbal dietary supplements measured by 9 items. RESULTS: The majority of interviewed participants were highly educated, aged 41-60 and they consumed herbal remedies on their own initiative or on recommendation of nonmedically educated person, without previous consultation with medical doctor or pharmacist. Out of all participants: 88.9 % did not consider it important to inform their physician or pharmacist about use of herbal remedies and herbal dietary supplements; 73.3 % found the use of herbal remedies harmless (where 9.4 % did not have any attitude towards that issue), while 40.3 % of participants regarded the combining of herbal and regular drugs unsafe. CONCLUSION: There is a need for consumers' education on reliable use of herbal medicines and herbal dietary supplements, in order to improve their awareness of the limits of herbal remedies safety and potential risks of their combination with drugs.\",\n \"corpus_id\": 22226440,\n \"score\": 2\n },\n {\n \"doc_id\": \"24988878\",\n \"title\": \"Use of herbal medicinal products among children and adolescents in Germany.\",\n \"abstract\": \"BACKGROUND: Germany is a country with a high use of herbal medicinal products. Population-based data on the use of herbal medicinal products among children are lacking. The aim of this study is to investigate the prevalence, patterns and determinants of herbal medicine use among children and adolescents in Germany. METHODS: As data base served the German Health Interview and Examination Survey for Children and Adolescents (KiGGS), a representative population based survey conducted 2003-2006 by the Robert Koch Institute. 17,450 boys and girls aged 0-17 years provided information on drug use in the preceding seven days. Herbal medicinal products were defined according to the European and German drug laws. SPSS Complex Sample method was used to estimate prevalence rates and factors associated with herbal medicine use. RESULTS: The prevalence rate of herbal medicinal product use amounts to 5.8% (95% confidence interval 5.3-6.3%). Use of herbal medicine declines along with increasing age and shows no difference between boys and girls in younger age groups. Teenage girls are more likely to use herbal medicines than teenage boys. Two thirds of herbal medicines are used for the treatment of coughs and colds; nearly half of herbal medicines are prescribed by medical doctors. Determinants of herbal medicinal product use are younger age, residing in South Germany, having a poor health status, having no immigration background and coming from a higher social class family. Children's and parents-related health behavior is not found to be associated with herbal medicine use after adjusting for social class. CONCLUSIONS: Use of herbal medicinal products among children and adolescents between the ages of 0 and 17 years in Germany is widely spread and shows relatively higher rates compared to international data. This study provides a reference on the use of herbal medicinal products for policy-makers, health professionals and parents. Further studies are needed to investigate the effectiveness and safety of specific herbal medicinal products, potential effects of long term use as well as possible interactions of herbal medicinal products with concomitantly used conventional medicines.\",\n \"corpus_id\": 5534312,\n \"score\": 2\n },\n {\n \"doc_id\": \"25885673\",\n \"title\": \"Utilization of complementary and alternative medicine (CAM) among children from a German birth cohort (GINIplus): patterns, costs, and trends of use.\",\n \"abstract\": \"BACKGROUND: The use of complementary and alternative medicine (CAM) is widespread among children in Germany and other European countries. Only a few studies are available on trends in pediatric CAM use over time. The study's objective was to present updated results for prevalence, predictors, and costs of CAM use among German children and a comparison with findings from a previous follow-up of the same birth cohort. METHODS: Data were collected for 3013 children on their utilization of medicinal products (during the last 4 weeks) and consultation with CAM providers (in the preceding year) from a German birth cohort study (GINIplus, 15-year follow-up) using a self-administered questionnaire. The reported medicinal CAMs were classified into six categories (homeopathy, herbal drugs, nutritionals, minerals and trace elements, microorganisms, further CAM). Drug prices were traced using pharmaceutical identification numbers (PZNs), or otherwise conservatively estimated. Finally, the results were compared with data obtained from the 10-year follow-up of the same birth cohort study by adopting the identical methodology. RESULTS: In all, 26% of the reported 2489 drugs were medicinal CAM. The 4-week prevalence for homeopathy and herbal drug use was 7.5% and 5.6%, respectively. Some 13.9% of the children used at least one type of medicinal CAM in the preceding 4 weeks. The 1-year prevalence for consultation with CAM providers was 10.8%. From the drugs identified as CAM, 53.7% were homeopathic remedies, and 30.8% were herbal drugs. Factors associated with higher medicinal CAM use were female gender, residing in Munich, and higher maternal education. A homeopathy user utilized on average homeopathic remedies worth EUR 15.28. The corresponding figure for herbal drug users was EUR 16.02, and EUR 18.72 for overall medicinal CAM users. Compared with the 10-year follow-up, the prevalence of homeopathy use was more than halved (-52%) and dropped substantially for herbal drug use (-36%) and overall CAM use (-38%) as well. CONCLUSION: CAM use among 15-year-old children in the GINIplus cohort is popular, but decreased noticeably compared with children from the same cohort at the age of 10 years. This is possibly mainly because German health legislation normally covers CAM for children younger than 12 years only.\",\n \"corpus_id\": 16179819,\n \"score\": 2\n },\n {\n \"doc_id\": \"26385752\",\n \"title\": \"Exploration of Why Alaskans Use Complementary Medicine: A Focus Group Study.\",\n \"abstract\": \"PURPOSE: To explore why Alaskans choose to pursue complementary medicine as a health care option. DESIGN: Qualitative descriptive. METHOD: A purposive convenient recruitment methodology was used to recruit project participants. Focus groups were conducted to collect the research data. FINDINGS: Five themes were identified that highlighted why participants use complementary medicine: dissatisfaction, effective, holistic, relationship focused, and a personal journey.\",\n \"corpus_id\": 253405,\n \"score\": 2\n },\n {\n \"doc_id\": \"26425496\",\n \"title\": \"From Disappointment to Holistic Ideals: A Qualitative Study on Motives and Experiences of Using Complementary and Alternative Medicine in Sweden.\",\n \"abstract\": \"BACKGROUND: Recent studies indicate increased use of complementary and alternative medicine (CAM) in western societies, to ameliorate health problems. Even if there is substantial research on general patterns of use, there is limited knowledge on individual motives. This study contributes to a qualitative understanding of experiences of choosing and using CAM. DESIGN AND METHODS: This study consists of in-depth interviews with 10 CAM users in Sweden. The participants represent different backgrounds and experiences of using CAM. The interviews have been analysed in accordance with content analysis. RESULTS: In analysing experiences of choosing and using CAM four main themes were identified: frustration and critique, values and ideology, individual responsibility, and combining treatments. In general, the participants were highly reflexive on issues concerning their health. They highlighted their own role and responsibility, combined a variety of treatments, and continuously dealt with questions on risks, even if they had relatively different approaches to if and when to use CAM. The results also show that motives may change over time. Even if initial choices were closely related to frustration and critique of conventional treatments (for example, by perceiving conventional health care as limited, not receiving proper diagnoses, or being critical to conventional drugs) was long-term use motivated by ideological characteristics of CAM (such as holistic and individualized treatments, and extensive interaction with practitioners). CONCLUSIONS: Four main themes, concerning experiences of choosing and using CAM were identified. This study also supports the idea that initial motives for choosing CAM may differ from those explaining long-term use. Significance for public healthRecent studies indicate increased use of complementary and alternative medicine (CAM), both in general western populations and specific patient groups. Well-documented motives for choosing CAM are related to disappointment and failure of conventional health care. In addition, there are findings that demonstrate that certain basic values (such as individualism and holistic orientations) are related to the use of CAM. A better understanding of individual motives behind people's choice of CAM, and how this is related to their perception of the health care system, is important for policy makers and health care professionals alike. This study contributes to a qualitative understanding of experiences of choosing and using CAM and how motives may change over time. It also contributes with knowledge on how users combine CAM with conventional health care and deal with risks.\",\n \"corpus_id\": 5774801,\n \"score\": 2\n },\n {\n \"doc_id\": \"18365495\",\n \"title\": \"[Use of complementary and alternative medicine among the patients in primary health care].\",\n \"abstract\": \"Upotreba komplementarne i alternativne medicine kod pacijenata u primarnoj zdravstvenoj zastiti. OBJECTIVE: Use of complementary and alternative medicine (CAM) is widespread in western countries despite its unconfirmed effectiveness. The aim of the study was to show the use of CAM by patients in primary health care. PATIENTS AND METHODS: Cross-sectional method was used in a sample of 941 patients attending fourteen primary care practices from six Croatian cities who visited their family physician for whatever reason and filled in an anonymous questionnaire. On data analysis, distribution of frequencies and chi2-test were used. A probability value of p (two-tailed) indicated a statistically significant difference. RESULTS: The response rate was 70%. At least once in their lifetime CAM was utilized by 46% and in previous year by 32% of patients. Most frequent users were persons in the 46-55 age group years and those with higher education. A statistically significant difference was established between CAM utilization and age, education, employment and relaxation/stress reducing techniques. The most frequently used methods were herbalism (38%), homeopathy (15.6%) and acupuncture (13.1%). In 53.5% of subjects CAM was used together with conventional medicine. CAM was most often used for musculoskeletal diseases, gastrointestinal diseases, and for prevention. Chiropractic was most commonly used for musculoskeletal disorders, and herbalism and homeopathy for respiratory disorders. Supplements, natural healing products and homeopathic medicines were used by 80.1% of study subjects. Patients decide on the use of CAM because they believe it will help them (27%), conventional medicine failed to alleviate their complaints (19.7%) and they were afraid of side effects of drugs (13.3%). Satisfaction with CAM treatment was reported by 45.5% of study subjects. More than half of the patients notified their physician on the use of CAM (59.6%) and the majority (81.7%) of all subjects would like to discuss the use of CAM in their treatment with their family physician. DISCUSSION: In this study, the use of CAM was consistent with literature data. Frequent use of herbal method may lead to potential risks due to possible herb-drug interactions. The reason for the use of CAM is rarely dissatisfaction with their physician but often dissatisfaction with the results and side effects of conventional treatment. Doctors will require additional education on CAM methods, their effectiveness, safety, indications and contraindications in order to be well informed and able to discuss CAM use with their patients. CONCLUSION: The use of CAM is common among patients attending primary health care. Sociodemographic factors are important predictors of its use. Doctors should openly ask their patients about the use of CAM and receive proper education to be able to discuss the potential benefits versus possible risks of its use in individual cases.\",\n \"corpus_id\": 10670206,\n \"score\": 1\n },\n {\n \"doc_id\": \"19942109\",\n \"title\": \"Use of traditional and complementary medicine in Malaysia: a baseline study.\",\n \"abstract\": \"BACKGROUND: The increasing popularity and use of traditional and complementary medicine (TCAM) in both developed and developing countries, including Malaysia, have raised significant public health policy issues. However, currently, there is a paucity of baseline data on such usage by the Malaysian community. OBJECTIVE: This study was conducted to identify and describe the prevalence and frequency of various TCAM modalities that are being used by the Malaysian population by age, gender, marital and working status, educational level and ethnic group for health issues and maintenance. DESIGN: A nationwide interviewer-administered questionnaire survey was conducted in August 2004. An open-ended questionnaire pertaining to TCAM modalities was used to increase the probability of capturing maximum data. This survey implemented a multistage design, stratified by state and urban/rural random sampling, proportionate to the size of the state population and was representative of the Malaysian population. Post-survey classification of modalities was done accordingly. Complex data analysis was carried out using SPSS 13.0. RESULTS: Various TCAM modalities that were used by the Malaysian population were identified and categorised. Biological-based therapies, which included herbal therapy, were most commonly used for health problems (88.9%) and for health maintenance (87.3%). Under this category, herb-based application/herb-based beauty product/herb-based hygiene product group was most commonly used for health issues (23.6%) while pure herbs were the ones most commonly used for health maintenance (29.6%). There was no significant difference across all groups in the usage of biological-based therapies for health issues. CONCLUSION: The study showed that there is a high prevalence of TCAM use by the Malaysian population, particularly in the use of herb-based therapies for both health issues and health maintenance. Thus, a strict guideline for herbal commercialisation as well as public education is important.\",\n \"corpus_id\": 23066608,\n \"score\": 1\n },\n {\n \"doc_id\": \"20043858\",\n \"title\": \"Attitude and use of herbal medicines among pregnant women in Nigeria.\",\n \"abstract\": \"BACKGROUND: The use of herbal medicines among pregnant women in Nigeria has not been widely studied. METHODS: Opinion of 595 pregnant women in three geopolitical zones in Nigeria on the use of herbal medicines, safety on usage, knowledge of potential effects of herbal remedies on the fetus and potential benefits or harms that may be derived from combining herbal remedies with conventional therapies were obtained using a structured questionnaire between September 2007 and March 2008. Descriptive statistics and Fisher's exact tests were used at 95% confidence level to evaluate the data obtained. Level of significance was set at p<0.05. RESULTS: More than two-third of respondents [67.5%] had used herbal medicines in crude forms or as pharmaceutical prepackaged dosage forms, with 74.3% preferring self-prepared formulations. Almost 30% who were using herbal medicine at the time of the study believed that the use of herbal medicines during pregnancy is safe. Respondents' reasons for taking herbal medications were varied and included reasons such as herbs having better efficacy than conventional medicines [22.4%], herbs being natural, are safer to use during pregnancy than conventional medicines [21.1%], low efficacy of conventional medicines [19.7%], easier access to herbal medicines [11.2%], traditional and cultural belief in herbal medicines to cure many illnesses [12.5%], and comparatively low cost of herbal medicines [5.9%]. Over half the respondents, 56.6% did not support combining herbal medicines with conventional drugs to forestall drug-herb interaction. About 33.4% respondents believed herbal medicines possess no adverse effects while 181 [30.4%] were of the opinion that adverse/side effects of some herbal medicines could be dangerous. Marital status, geopolitical zones, and educational qualification of respondents had statistically significant effects on respondents views on side effects of herbal medicines [p<0.05)] while only geopolitical zones and educational qualifications seemed to have influence on respondents' opinion on the harmful effects of herbal medicines to the fetus [p<0.05]. CONCLUSION: The study emphasized the wide spread use of herbal medicines by pregnant women in Nigeria highlighting an urgent need for health care practitioners and other health care givers to be aware of this practice and make efforts in obtaining information about herb use during ante-natal care. This will help forestall possible interaction between herbal and conventional medicines.\",\n \"corpus_id\": 6748392,\n \"score\": 1\n },\n {\n \"doc_id\": \"20367764\",\n \"title\": \"Increasing health-care options: the perspectives of parents who use complementary and alternative medicines.\",\n \"abstract\": \"AIM: To explore the relationship between conventional medicine and complementary and alternative medicine (CAM) with parents who use CAM, and to consider factors that may contribute to parent non-disclosure of CAM usage to their doctor. METHODS: Thirty-three parents participated in one of seven focus groups. Transcripts were analysed using an iterative process of theme identification and testing against transcript data. RESULTS: The participants believed they should trust their instincts as parents in caring for their child. It was important also to the participants that they understood why their child was ill, and a range of theories of health and illness were discussed. The use of CAM was attractive as it offered more options in health care than just relying on conventional medicine alone. The use of additional therapies was seen as a means to increase the likelihood that something would work. Many of the participants described bad experiences with doctors when they discussed CAM use previously so they had become more circumspect in mentioning it. The participants were most satisfied with medical care for their child when they felt the doctor respected their point of view and listened to them. CONCLUSIONS: Doctors caring for children and their families should expect that many parents are using CAM to increase health-care options. Inquiries about CAM usage should be made in a non-judgmental and encouraging manner so parents feel comfortable in providing an honest answer. Advice to parents about CAM may need to be backed up with evidence to address differing parent understanding of illness.\",\n \"corpus_id\": 205469905,\n \"score\": 1\n },\n {\n \"doc_id\": \"21364591\",\n \"title\": \"The use of herbal medicines by people with cancer: a cross-sectional survey.\",\n \"abstract\": \"BACKGROUND: A large proportion of cancer patients are estimated to use herbal medicines, but data to substantiate this are lacking. This study aimed to investigate the prevalence of herbal medicine use among cancer patients in the West Midlands, and determine the characteristics predicting herbal medicine use. METHODS: A cross-sectional survey of oncology patients (n=1498) being followed up at a hospital in Coventry was undertaken. Recipients were asked about herbal medicine use since their cancer diagnosis, and the association between sociodemographic and cancer-related characteristics and herbal medicine use was evaluated. RESULTS: A total of 1134 responses were received (75.7%). The prevalence of herbal medicine use was 19.7% (95% CI: 17.4-22.1; n=223). Users were more likely to be affluent, female, and aged under 50 years. Usage increased with time since cancer diagnosis (X(2) for trend=4.63; P=0.031). A validation data set, derived from a survey of oncology patients in Birmingham (n=541) with differing socioeconomic characteristics showed no significant difference in estimated prevalence (16.6%; 95% CI: 11.9-22.2). CONCLUSION: A substantial number of people with cancer are likely to be taking herbal medicines. Understanding the self-medication behaviours of these individuals is essential if health-care professionals are to support treatment adherence and avoid unwanted pharmacological interactions.\",\n \"corpus_id\": 405066,\n \"score\": 1\n },\n {\n \"doc_id\": \"21645607\",\n \"title\": \"The prevalence of herbal medicine home use and concomitant use with pharmaceutical medicines in Jamaica.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: The work described in this paper aimed to study the prevalence of herbal medicine use in treating illness and concomitant use with pharmaceutical medicines in Jamaica. MATERIALS AND METHODS: A survey using a structured questionnaire was administered by a trained interviewer to randomly selected adults in systematically selected households within randomly selected urban and rural clusters. Categorical data analysis was performed using Stata version 10 software. RESULTS: 91.4%(372/407) of selected people agreed to participate. 72.6%(270/372) self-medicated with herbs within the previous year. Commonly treated were illnesses of the respiratory system (RS, 77.8%(210/270)), gastro-intestinal tract (GIT, 53.3%(144/270)) and health maintenance using tonics (29.6%(80/270)). 26.7%(72/270) of respondents used pharmaceuticals concomitantly with medicinal plants. Commonly treated were illnesses of the RS (20.4%(55/270)), GIT (13.7%(37/270)) and hypertension (10.0%(27/270)). 19.4% (14/72) of physicians knew of such practices. There was significant association of herb use with/without drugs with age (p<0.001), employment status (p<0.001), religion (p=0.004), gender (p=0.02) and educational level (p=0.031). Thus prevalence of herb use alone was greatest amongst people aged 35-44 and 45-54 years; those employed; Rastafarians; those without health insurance; males and people who had completed secondary education. Whilst prevalence of concomitant herb-drug use was greater amongst people aged 65 years and older; those retired; those of religions other than Rastafarians and Christians, females and people who had attained primary education and below. CONCLUSIONS: Self-medication with herbs in Jamaica is highly prevalent and highest for self-limiting conditions of the RS, GIT and health maintenance with tonics. Concomitant herb and drug use is highest for self-limiting conditions of the RS, GIT and hypertension, and the use of combined therapy highlights the need for investigations on potential drug-herb interactions. Physicians have limited awareness and knowledge of such concomitant usage, further highlighting the need for increased dialogue with patients, knowledge of medicinal plants and their uses and a heightened pharmacovigilance to avoid adversities that may arise from potential drug-herb interactions.\",\n \"corpus_id\": 8636465,\n \"score\": 1\n },\n {\n \"doc_id\": \"21848581\",\n \"title\": \"Why people choose to not use complementary therapies during cancer treatment: a focus group study.\",\n \"abstract\": \"While 50% of cancer patients use complementary therapies (CT) during treatment, few studies have examined why individuals choose not to use CT. This study aimed to address this gap in knowledge using a focus group methodology, where 36 participants took part in one of eight groups; participants were recruited until saturation of themes was achieved. Three categories of participants were investigated: patients/recent survivors (n= 14); volunteers/advocates (n= 16), the majority of whom were also long-term survivors; and health professionals (n= 6). Focus groups were digitally audio-recorded, transcribed, and coded thematically using NVivo software. Reasons for non-use fell into four broad themes: (1) Resource barriers, particularly the cost and lack of time; (2) fear and distrust, including the potential for drug interactions; (3) lack of evidence, including the unproven nature of many CT practices; and (4) satisfaction with conventional treatment. Two further themes related to the benefits of non-use and reasons for discontinuation. A sub-analysis indicated that reasons for non-use differed by CT category, with non-use being mentioned more frequently for biologically based and body-based therapies. Differences in understanding CT non-use emerged between patients, volunteers and health professionals. Findings have clinical implications regarding tailoring information for patients during and after cancer.\",\n \"corpus_id\": 23193275,\n \"score\": 1\n },\n {\n \"doc_id\": \"24330413\",\n \"title\": \"Herbal medicine use in pregnancy: results of a multinational study.\",\n \"abstract\": \"BACKGROUND: The use of complementary and alternative medicines (CAM) is growing in the general population. Herbal medicines are used in all countries of the world and are included in the top CAM therapies used. METHODS: A multinational study on how women treat disease and pregnancy-related health ailments was conducted between October 2011 and February 2012 in Europe, North and South America and Australia. In this study, the primary aim was to determine the prevalence of herbal medicine use in pregnancy and factors related to such use across participating countries and regions. The secondary aim was to investigate who recommended the use of herbal medication in pregnancy. RESULTS: There were 9,459 women from 23 countries participating in the study. Of these, 28.9% reported the use of herbal medicines in pregnancy. Most herbal medicines were used for pregnancy-related health ailments such as cold and nausea. Ginger, cranberry, valerian and raspberry were the most commonly used herbs in pregnancy. The highest reported rate of herbal use medicines was in Russia (69%). Women from Eastern Europe (51.8%) and Australia (43.8%) were twice as likely to use an herbal medicine versus other regions. Women using herbal medicines were characteristically having their first child, non-smokers, using folic acid and consuming some alcohol in pregnancy. Also, women who were currently students and women with an education other than a high school degree were more likely to use herbal medicines than other women. Although 1 out of 5 women stated that a physician had recommended the herbal use, most women used herbal medicine in pregnancy on their own initiative. CONCLUSIONS: In this multinational study herbal medicine use in pregnancy was high although there were distinct differences in the herbs and users of herbal medicines across regions. Most commonly the women self-medicated with herbal medicine to treat pregnancy-related health ailments. More knowledge regarding the efficacy and safety of herbal medicines in pregnancy is warranted.\",\n \"corpus_id\": 31224768,\n \"score\": 1\n },\n {\n \"doc_id\": \"24669824\",\n \"title\": \"Use of complementary and alternative medicine by older adults--a cross-sectional survey.\",\n \"abstract\": \"BACKGROUND: Very little is known about complementary and alternative medicine (CAM) use by older adults in Germany. The aim of this study was to investigate the use of CAM and other health promoting substances (e.g., herbal teas) by older adults of at least 70 years of age. METHODS: A cross-sectional questionnaire study was conducted among persons of ≥70 years from metropolitan Berlin and rural parts of Brandenburg, Germany. Recorded were: demographics, current use of CAM, medical diagnoses, users' opinions and preferences. RESULTS: A total of 400 older adults, living as 'self-reliant' (n = 154), 'home care service user' (n = 97), or 'in nursing home' (n = 149), and with the legal status 'without guardian' (n = 355) or 'with guardian' (n = 45) were included (mean age 81.8 ± 7.4 years, 78.5% female). Any type of CAM used 61.3% of respondents (dietary supplements 35.5%, herbal medicines 33.3%, and external preparations 26.8%); 3.0% used drug-interaction causing preparations. Usage was based on recommendations (total 30.3%; in 20.0% by friends or family and 10.4% by pharmacists), own initiative (27.3%), and doctors' prescription (25.8%). Participants with legal guardian took almost solely prescribed dietary supplements. Of the others, only half (58.7%) informed their general practitioner (GP) of their CAM use. Participants expected significant (44.9%) or moderate (37.1%) improvement; half of them perceived a good effect (58.7%) and two-thirds (64.9%) generally preferred a combination of CAM and conventional medicine. More than half (57.9%) stated that they could neither assess whether their CAM preparations have side effects, nor assess what the side effects might be. Strongest predictors for CAM use were two treatment preferences (vs. 'conventional only': 'CAM only', OR = 3.98, p = 0.0042 and 'CAM + conventional', 3.02, 0.0028) and the type of health insurance ('statutory' vs. 'private', 3.57, 0.0356); against CAM use two subjective assessments predicted (vs. 'CAM causes no harm': 'CAM causes harmful drug interactions', 0.25, 0.0536 and 'I cannot assess side effects', 0.28, 0.0010). CONCLUSION: Older German adults frequently use CAM. They perceived it as an effective complement to conventional medicine, but are not sufficiently informed about risks and benefits.\",\n \"corpus_id\": 7919846,\n \"score\": 1\n },\n {\n \"doc_id\": \"24969647\",\n \"title\": \"Young people's opinions about herbal medicines in a suburban district of Central Uganda.\",\n \"abstract\": \"BACKGROUND: Herbal medication is the most commonly used form of healthcare in Africa. However, little is known about its use by young Africans in the urban context. METHODS: This qualitative study explored opinions about herbal medicine and its uses among young people in the Wakiso district, Uganda. RESULTS: About a third of interview participants reported using herbal products, a choice influenced by religious faith, family preference, low cost and unavailability of biomedicines. Two participants stated that herbs could be used to deter alcohol dependence. CONCLUSIONS: This study indicated divergent opinions about the value of herbal medicine among young urban Ugandans.\",\n \"corpus_id\": 205141272,\n \"score\": 1\n },\n {\n \"doc_id\": \"25174734\",\n \"title\": \"Internal health locus of control in users of complementary and alternative medicine: a cross-sectional survey.\",\n \"abstract\": \"BACKGROUND: Complementary and alternative medicine (CAM) is widely used in Germany, with some treatments eligible for health insurance reimbursements. CAM encourages patients to play an active role in their healing process. The belief that a person's own behavior influences health is assessed as the internal health locus of control (IHLOC). Studies on the association between IHLOC and CAM use yield inconsistent results. Using various indicators of CAM use, we evaluated whether there were differences in IHLOC between different groups of CAM users. METHODS: A cross-sectional online survey was conducted. IHLOC was compared between participants with high and low appraisal of CAM, between participants who used different types of medications (none, CAM, conventional, both), and who consulted with different health care professionals (none, CAM, conventional, both). Independent samples t-tests and ANOVAs were conducted for the total group and for subgroups of chronically ill and healthy participants. Post-hoc, we conducted a multivariate linear regression evaluating which indicators of CAM use or other characteristics showed the strongest association with IHLOC. RESULTS: A total of 1,054 undergraduate students completed the survey. Participants with high CAM appraisal showed higher IHLOC than those with low CAM appraisal, regardless of whether they were chronically ill (p < .001). Participants without chronic conditions showed higher IHLOC when only using CAM medications than when using either conventional medications alone or both conventional and CAM medications (p < .05). All participants showed higher IHLOC when visiting only CAM practitioners than when visiting either only conventional or both conventional and CAM practitioners (p < .05). CAM appraisal was associated the strongest with IHLOC in the linear regression model. CONCLUSIONS: Generally, participants using CAM more or exclusively, and participants with higher appraisal of CAM showed higher IHLOC than those with less CAM use or lower CAM appraisal. Because of the cross-sectional design, it is not possible to determine whether differences in IHLOC are reasons for or consequences of CAM use. Research using a longitudinal design is needed. The sample, though more representative than most student samples, might not represent the general population. Studies evaluating clinical populations might add to the findings.\",\n \"corpus_id\": 15509599,\n \"score\": 1\n },\n {\n \"doc_id\": \"25888160\",\n \"title\": \"Complementary and alternative medicine usage among cardiac patients: a descriptive study.\",\n \"abstract\": \"BACKGROUND: The use of complementary and alternative medicine (CAM) persists, despite the availability of conventional medicine (CM), modernisation, globalisation, technological advancement, and limited scientific evidence supporting CAM. People with cardiovascular diseases often use CAM, despite possible major adverse effects and lack of evidence supporting CAM claims. This study explored CAM use among cardiac patients, the types of CAM used, reasons and factors that influence its use, and the association between patient demographics and CAM use. METHODS: This cross-sectional quantitative study was conducted using quota sampling to survey 329 public clinic adult cardiac patients within the South-West Regional Health Authority (SWRHA) of Trinidad and Tobago. From 1 July 2012 to 31August 2012, each participant completed questionnaires, after consenting to participate. Data analysis included χ(2) tests and binary logistic regression. RESULTS: One hundred eighty-five (56.2%; standard error [SE] = 2.74%) patients used CAM. Herbal medicine was the most common CAM (85.9%; SE = 2.56%), followed by spiritual therapy/mind-body systems (61.6%; SE = 3.58%), physical therapy/body manipulation (13.5%; SE = 2.51%), alternative systems (8.1%; SE = 2.01%), and other methods (3.8%; SE = 1. 41%). The patients believed that CAM promotes health and wellness (79.5%; SE = 2.97%), assists in fighting illness (78.9%; SE = 3.00%), addresses the limitations of CM (69.2%; SE = 3.56%), alleviates symptoms (21.6%; SE = 6.51%), costs less than CM (21.6 %, SE = 3.03), and has fewer adverse/damaging effects than CM (29.7, SE =3.36), or they were disappointed with CM (12.4%, SE = 2.42). Ethnicity and religion were associated with CAM usage, but only ethnicity was a useful predictor of CAM use. CONCLUSIONS: Complementary and alternative medicine use was high among cardiac patients (56.2%, SE = 2.74%), and associated with ethnicity and religion. Friends, family, and perceived mode of action influenced a patient's use of CAM.\",\n \"corpus_id\": 8111927,\n \"score\": 1\n },\n {\n \"doc_id\": \"26383209\",\n \"title\": \"Evaluation of Trends in the Use of Complementary and Alternative Medicine in Health Centers in Khorramabad (West of Iran).\",\n \"abstract\": \"AIM: To determine the use of most popular forms of complementary and alternative medicine(CAM), sociodemographic characteristics of CAM users, and communication between CAM users and their physicians by adult Iranian in Khorramabad city. METHODS: This cross-sectional study was carried out on clients who were at least 15 years in age referring to health centers and hospitals in Khorramabad town in 2014. A multi-part questionnaire was used to gather information. The demographic data and details regarding usage (number of times and underlying reasons) of different kinds of complementary and traditional medicine in the past were gathered using a questionnaire. RESULTS: In this study 790 subjects were surveyed using the questionnaire. The mean age of the participant was 38.9 years. 79.8% of the subjects had used at least one of the methods of complementary medicine. Among the participants, 58.2% had used at least one of the complementary medicines in the previous year. Herbal medicine and prayers treatment had the highest use with 69.2% and 37.2%, respectively. Concerns of the side effects of medical therapy, beliefs in less risky being and fewer side effects of complementary medicine, Dissatisfaction of General Practitioners, the increase of being-well feelings in physical conditions, and were among the most important reasons of inclination towards such treatment methods. CONCLUSION: The analysis of using complementary medicine among people is the first step for planning proper use of the beneficial methods of complementary medicine and the prevention of inefficient and harmful methods in this respect.\",\n \"corpus_id\": 33724086,\n \"score\": 1\n },\n {\n \"doc_id\": \"26401410\",\n \"title\": \"Herbal medicine use among patients with chronic diseases.\",\n \"abstract\": \"AIM: Complementary and alternative medicine (CAM) is commonly used all over the world, and herbal medicines are the most preferred ways of CAM. The aim of this study was to determine the frequency of herbal medicine use among patients with chronic diseases. METHODOLOGY: A cross-sectional descriptive study was conducted from April 2014 to December 2014 among patients who had been diagnosed with diabetes mellitus (DM), hypertension (HT), and hyperlipidemia (HL) in Family Medicine Department of Dışkapı Yıldırım Beyazıt Training and Research Hospital, in Ankara. A questionnaire about herbal drug use was applied by face to face interview to the participants. RESULTS: A total of 217 patients were included in this study. The mean age of the participants was 56.6 ± 9.7 years (55 male and 162 female). The rate of herbal medicine use was 29%. Herbal medicine use among female gender was significantly higher (P = 0.040). Conventional medication use was found to be lower among herbal medicine consumers. There was no relationship between herbal medicine use and type of chronic disease, living area, and occupation or education level. Most frequently used herbs were lemon (39.6%) and garlic (11.1%) for HT, cinnamon (12.7%) for DM, and walnut (6.3%) for HL. CONCLUSIONS: In this study, herbal medicine use was found to be higher among patients who had been diagnosed with chronic diseases. Therefore, physicians should be aware of herbal medicine usage of their patients and inform them about the effectivity and side effects of herbal medicines.\",\n \"corpus_id\": 1259912,\n \"score\": 1\n },\n {\n \"doc_id\": \"26865257\",\n \"title\": \"Herbal medicine use behaviour in Australian adults who experience anxiety: a descriptive study.\",\n \"abstract\": \"BACKGROUND: Anxiety disorders are the most prevalent mental health condition in Australia. In addition, there are many people who experience problematic anxiety symptoms who do not receive an anxiety disorder diagnosis but require treatment. As herbal medicine use is popular in Australia, and little is known about how adults experiencing anxiety are using these medicines, this study aimed to identify how Australian adults who experience anxiety are using herbal medicines. METHODS: An online cross-sectional descriptive study was conducted using purposive convenience sampling to recruit Australian adults who have experienced anxiety symptoms and have used herbal medicines (N = 400). Descriptive statistics, chi-square test of contingency, analysis of variance, and simple logistic regression was used to analyse the data. RESULTS: Eighty two percent of participants experienced anxiety symptoms in the previous 12 months, with 47% reporting having previously been diagnosed with an anxiety disorder. In addition, 72.8% had used herbal medicines specifically for anxiety symptoms in their lifetime, while 55.3% had used prescribed pharmaceuticals, with 27.5% having used herbal medicines concurrently with prescribed pharmaceuticals. The Internet and family and friends were the most frequently used sources of information about herbal medicines. Forty eight percent of participants did not disclose their herbal medicine use to their doctor. CONCLUSIONS: Herbal medicines are being used by adults with anxiety and are commonly self-prescribed for anxiety symptoms. Health practitioners who are experts in herbal medicine prescribing are consulted infrequently. In addition, herbal medicine use is often not disclosed to health practitioners. These behaviours are concerning as people may not be receiving the most suitable treatments, and their use of herbal medicines may even be dangerous. It is critical we develop a better understanding of why people are using these medicines, and how we can develop improved health literacy to help with treatment decision making to ensure people receive optimal care.\",\n \"corpus_id\": 13709848,\n \"score\": 1\n },\n {\n \"doc_id\": \"27125594\",\n \"title\": \"Complementary and alternative medicine use among cancer patients in Palestine with special reference to safety-related concerns.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: The use of CAM including herbal medicine as the most preferred CAM modality, among cancer patients who are taking prescription medications has shown to be highly prevalent worldwide as well as in several Middle Eastern countries, with a high percentage of the patients do not disclose their CAM use to treating physician. AIM OF THE STUDY: The current study aimed to evaluate the patterns of CAM use among two cohorts of cancer patients in Palestine over a three-year period, and to identify socio-demographic factors that are associated with CAM use. MATERIALS AND METHODS: Across-sectional survey of patients attending outpatient cancer clinics. The method was based on a semi-structured questionnaire. In order to identify safety-related concerns associated with the products listed, a literature search was conducted using different databases (PubMed, Micromedex, AltMedDex, and the Natural Medicine Comprehensive Database). RESULTS: In 472 cancer patients including 372 of the 2011 cohort; and 100 of the 2014 cohort, the overall prevalence of CAM use was 69.5%. CAM users were more likely to be ≤65 years old, village resident, being in the midst of chemotherapy, to have high interest spiritual quest, and to have no other chronic diseases. A significant number of CAM users reported using herbal preparations (98.3%, and 89.6% in the two study cohorts, respectively). In the current study, a total of 40 plant taxa belonging to 23 botanical families were reported by ≥3 cancer patients in the two cohort groups. The top most commonly used plant in the 2011 cohort group was Arum palaestinum (43.5%), while Ephedra foeminea emerged as the top most commonly utilized plant (from 0.0% in 2011 to 55.2% in the 2014 cohort), mainly due to a recent publicizing and portraying of the plant in the local media as an effective cancer herbal remedy. Safety-related concerns were associated with 33 (82.5%) herbs, including herb-drug interactions with altered pharmacokinetics (8, 20% herbs), direct toxic effects (16, 40% herbs), and increased in vitro response of cancer cells to chemotherapy (30, 75% herbs). CONCLUSIONS: CAM use, especially herbal medicine in cancer is highly prevalent in Palestine. This study has demonstrated the role of the media on the emergence of new CAM herbal therapies among cancer patients in Palestine, and discussed its potential implications on patients and for oncologists who are treating them. Some of the most widely used herbal medicines by cancer patients in the present work are known to interact with conventional anticancer drugs. Hence, the disclosure of the use of herbal remedies by patients to health professionals with sufficient training in CAM use is important for the later in order to assess whether there are any possible herbal drug interactions and/or harmful drug reactions.\",\n \"corpus_id\": 20517317,\n \"score\": 1\n },\n {\n \"doc_id\": \"27229306\",\n \"title\": \"Facilitators and barriers of herbal medicine use in Accra, Ghana: an inductive exploratory study.\",\n \"abstract\": \"BACKGROUND: The use of complementary and alternative medicine including herbal medicine is increasing in many countries including Ghana. However, there is paucity of research on the perspectives of patrons of herbal medicine regarding the facilitators and barriers of herbal medicine use. This study sought to investigate the facilitators and barriers of herbal medicine among Ghanaian adults who use one form of herbal medicine or the other. METHODS: The study employed an inductive exploratory qualitative approach. It was conducted at a private herbal clinic in Accra. Purposive sampling was employed to recruit 16 participants. Data collection was through individual face-to-face interviews and these were transcribed and analysed using content analysis procedures. RESULTS: It was realized that the factors that enhanced the use of herbal medicine included use of convincing information to enhance the initiation of herbal medicine use, effectiveness of herbal medicine, personal preference for herbal medicine, perceived ineffectiveness of western medicine and integration of spirituality in herbal medicine. The factors that hindered herbal medicine use included negative perceptions and attitudes about herbal medicine, poor vending environment, poor knowledge of vendors, high cost of herbal products at credible herbal clinics and inconsistent effectiveness of some herbal products. Participants desired that the national health insurance scheme will cover the cost of herbal medicine to alleviate the financial burden associated with herbal medicine use. CONCLUSION: Although some Ghanaians patronize herbal medicine, the negative perceptions about herbal medicine resulting from deceitful producers and vendors call for enhanced education and monitoring to ensure that effective herbal products are used.\",\n \"corpus_id\": 16423866,\n \"score\": 1\n },\n {\n \"doc_id\": \"18366698\",\n \"title\": \"The use of biomedicine, complementary and alternative medicine, and ethnomedicine for the treatment of epilepsy among people of South Asian origin in the UK.\",\n \"abstract\": \"BACKGROUND: Studies have shown that a significant proportion of people with epilepsy use complementary and alternative medicine (CAM). CAM use is known to vary between different ethnic groups and cultural contexts; however, little attention has been devoted to inter-ethnic differences within the UK population. We studied the use of biomedicine, complementary and alternative medicine, and ethnomedicine in a sample of people with epilepsy of South Asian origin living in the north of England. METHODS: Interviews were conducted with 30 people of South Asian origin and 16 carers drawn from a sampling frame of patients over 18 years old with epilepsy, compiled from epilepsy registers and hospital databases. All interviews were tape-recorded, translated if required and transcribed. A framework approach was adopted to analyse the data. RESULTS: All those interviewed were taking conventional anti-epileptic drugs. Most had also sought help from traditional South Asian practitioners, but only two people had tried conventional CAM. Decisions to consult a traditional healer were taken by families rather than by individuals with epilepsy. Those who made the decision to consult a traditional healer were usually older family members and their motivations and perceptions of safety and efficacy often differed from those of the recipients of the treatment. No-one had discussed the use of traditional therapies with their doctor. The patterns observed in the UK mirrored those reported among people with epilepsy in India and Pakistan. CONCLUSION: The health care-seeking behaviour of study participants, although mainly confined within the ethnomedicine sector, shared much in common with that of people who use global CAM. The appeal of traditional therapies lay in their religious and moral legitimacy within the South Asian community, especially to the older generation who were disproportionately influential in the determination of treatment choices. As a second generation made up of people of Pakistani origin born in the UK reach the age when they are the influential decision makers in their families, resort to traditional therapies may decline. People had long experience of navigating plural systems of health care and avoided potential conflict by maintaining strict separation between different sectors. Health care practitioners need to approach these issues with sensitivity and to regard traditional healers as potential allies, rather than competitors or quacks.\",\n \"corpus_id\": 3564219,\n \"score\": 0\n },\n {\n \"doc_id\": \"18466292\",\n \"title\": \"The experiences of adults with intellectual disabilities and their carers in general hospitals: a focus group study.\",\n \"abstract\": \"BACKGROUND: People with intellectual disabilities (ID) have higher levels of health needs compared with the general population, many of which are unrecognised and unmet. While there has been interest and research into the primary health provision for this group, there has been a more limited focus on addressing their care received in general hospitals. Access to health care has predominated in the literature, with less attention being paid to the experiences of people with ID as users of general hospital care. METHOD: A qualitative focus group methodology was used. Eleven adults with ID, nine parents and five paid carers of adults with ID participated. The focus groups were audiotaped and transcriptions were analysed using principles of grounded theory. RESULTS: The analysed data highlighted key themes identified from the experiences of participants. These were the interrelated issues of feelings, particularly anxiety and fear, communication and behaviour problems; the practicalities of being in or attending hospitals, including the role played by carers; and issues around perceived discrimination and negative comments. CONCLUSIONS: The experiences of participants in this study concur with and add to concern expressed in recent reports and published research. Wide ranging implications are discussed for further research, wider policy development, clinical practice, local health service provision and education of health professionals.\",\n \"corpus_id\": 43900495,\n \"score\": 0\n },\n {\n \"doc_id\": \"18791806\",\n \"title\": \"The DARTS tool for assessing online medicines information.\",\n \"abstract\": \"OBJECTIVE: The use of the Internet as a source of medicines information is increasing. However, the quality of online information is highly variable. Equipping Internet users to distinguish good quality information is the aim of a new five-item quality assessment tool (DARTS) that was developed by the Working Group on Information to Patients under the Pharmaceutical Forum established by the European Commission. The objective of this study was to investigate how people with depression assess the quality of online medicines information and to study their opinions about the DARTS tool in assisting in this process. SETTING: Focus group discussions with Internet users were conducted in metropolitan Helsinki, Finland. METHOD: Six focus group discussions (67-109 min duration) were conducted with people with depression (n = 29). The DARTS tool was used as a stimulus after open discussion in relation to the evaluation of the quality of Internet-based medicines information. The focus groups were digitally audiotaped and transcribed verbatim. The transcripts were thematically content analysed by two researchers. RESULTS: Focus group participants were generally critical of the information they retrieved. However, few participants systematically applied quality assessment criteria when retrieving online information. No participants had knowledge or experience of any quality assessment tools. The DARTS tool was perceived as being concise and easy to use and understand. Many participants indicated it would allay some of their concerns related to information quality and act as a reminder. While several participants felt the tool should not be any more extensive, some of them believed it should include a more in-depth explanation to accompany each of the quality criteria. CONCLUSIONS: The DARTS tool may act as a prompt for people with depression to assess the quality of online information they obtain. The five DARTS criteria may form the basis of a systematic approach to quality assessment and the tool may also act as a reminder of quality issues in general. Further studies are needed to assess the actual value of the DARTS tool as well as its value in relation to other quality assessment instruments.\",\n \"corpus_id\": 34002800,\n \"score\": 0\n },\n {\n \"doc_id\": \"19005129\",\n \"title\": \"Complementary and alternative medicine use among Chinese and white Canadians.\",\n \"abstract\": \"ABSTRACTOBJECTIVEThis study aimed to describe the level of complementary and alternative medicine (CAM) use and the factors associated with CAM use among Chinese and white Canadians. DESIGNA cross-sectional telephone survey conducted in English, Cantonese, and Mandarin. SETTINGCalgary, Alta. PARTICIPANTSChinese and white residents of Calgary aged 18 or older. MAIN OUTCOME MEASURESRates of use of 11 CAM therapies, particularly herbal therapy, massage, chiropractic care, and acupuncture; reasons for use of CAM therapies. RESULTSSixty percent of 835 Chinese respondents (95% confidence interval [CI] 56.5% to 63.2%) and 59% of 802 white respondents (95% CI 55.1% to 62.0%) had used CAM in the past year. Chinese respondents were more likely to use herbal therapy than white respondents were (48.7% vs 33.7%, P < .001), less likely to use massage (17.1% vs 30.4%, P < .001) and chiropractic care (8.4% vs 21.2%, P < .001), but equally likely to use acupuncture (8.3% vs 7.9%, P = .173). The common factor associated with herbal therapy, acupuncture, or massage use among Chinese and white respondents was receiving a CAM recommendation from a family member or friend. Factors unique to either Chinese or white CAM users varied by therapy. For example, herbal therapy use for Chinese respondents was associated with the presence of chronic disease (adjusted odds ratio [AOR] 2.15, 95% CI 1.09 to 4.24 for having 3 diseases compared with those without chronic disease), beliefs about the effectiveness of herbal therapy (AOR 1.56, 95% CI 1.12 to 2.17), and trust in herbal therapy practitioners (AOR 1.72, 95% CI 1.24 to 2.37). Herbal therapy use for white respondents was associated with the beliefs that herbal treatment had fewer side effects than prescription drugs (AOR 1.81, 95% CI 1.31 to 2.50) and that herbalists took a holistic approach (AOR 2.07, 95% CI 1.49 to 2.87).CONCLUSIONWhile the percentage of CAM use was similar in both groups, Chinese Canadians mainly used herbal therapy and white Canadians used a range of CAM therapies. Factors associated with CAM use varied with ethnicity and type of CAM therapy. Presence of chronic disease, however, was an important factor for Chinese Canadians. That finding suggests that Chinese Canadians use CAM for the treatment of chronic disease, while white Canadians use such therapies for disease treatment and health maintenance.\",\n \"corpus_id\": 22348904,\n \"score\": 0\n },\n {\n \"doc_id\": \"19838830\",\n \"title\": \"Back pain amongst 8,910 young Australian women: a longitudinal analysis of the use of conventional providers, complementary and alternative medicine (CAM) practitioners and self-prescribed CAM.\",\n \"abstract\": \"Back problems and back pain are amongst the most prevalent conditions afflicting Australians and carry high direct and indirect costs for the health care systems of all developed countries. A major gap in the research literature on this topic is the longitudinal analysis of health seeking behaviour for people with back pain. All studies to date have been cross-sectional and it is important that the use of different providers (both conventional and complementary and alternative medicine, CAM) is examined over time. This study analysed data from a longitudinal study conducted over a 3-year period on 8,910 young Australian women. Information on health service use, self-prescribed treatments, and health status was obtained from two questionnaires mailed to study participants in 2003 and 2006. We found that there is little difference in the consultation practises or use of self-prescribed CAM between women who recently sought help for back pain and women who had longer-term back pain; the only difference being that women with longer-term back pain consulted more with chiropractors. We conclude that women who seek help for their back pain are frequent visitors to a range of conventional and CAM practitioners and are also high users of self-prescribed CAM treatments. The frequent use of a range of conventional providers and practitioner-based and self-prescribed CAM amongst women with back pain warrants further investigation.\",\n \"corpus_id\": 21519748,\n \"score\": 0\n },\n {\n \"doc_id\": \"19857249\",\n \"title\": \"Use of complementary and alternative medicine: a survey in Turkish gastroenterology patients.\",\n \"abstract\": \"BACKGROUND: The study examined complementary and alternative medicine (CAM) usage by patients attending a Turkish gastroenterology outpatient clinic. METHODS: The survey was conducted on 216 patients presenting with gastrointestinal problems during their first visit to the clinic using a 31 item, self-report questionnaire between May and October 2005. Data included information on patient demographics and their gastrointestinal symptoms, as well as items to identify CAM use and patient satisfaction with these therapies. RESULTS: Seventy-nine patients (36.6%) reported using one or more forms of CAM. The most commonly used therapy was herbal therapy, usually taken as a tea or infusion. These were used by 27 people (29%) in this subgroup. Common indicators for their use were epigastric pain, constipation, bloating and dyspepsia or indigestion. CAM use among upper GI patients was marginally higher than lower GI patients (41.8% versus 41.2%), but the highest usage was amongst patients with liver disease where 53.8% reported using one or more CAM therapy. About half of the patients learned about CAM from their relatives or friends, with more women than men using the therapies (p < 0.05). Clinical characteristics such as diagnosis, duration of symptoms and prior surgical intervention did not differ between users and non-users of CAM therapies. Multivariate analysis showed that being female and higher educational status were positively associated with CAM usage (p < 0.05). CONCLUSION: CAM usage in our sample of gastrointestinal patients was lower than that described in other countries and other chronic disease groups. This could be due to their low perceived efficacy, or the relatively transient duration of symptoms experienced by the sample. Healthcare professionals need however, to be aware of CAM usage in order to educate patients appropriately about possible adverse effects or drug-interactions.\",\n \"corpus_id\": 8259197,\n \"score\": 0\n },\n {\n \"doc_id\": \"19894247\",\n \"title\": \"Complementary and alternative medicine use among long-term lymphoma survivors: a pilot study.\",\n \"abstract\": \"No published survey has specifically addressed the beliefs, knowledge, and usage of complementary and alternative medicine (CAM) in long-term (5-20 years) lymphoma survivors alone. In this pilot project, 95 subjects were randomly selected from a population of 2,475 long-term lymphoma survivors and mailed a questionnaire. The median time from lymphoma diagnosis to completion of the questionnaire was 11 years (range 6-20). Overall, 68% (95% CI: 54-80%) of the long-term lymphoma survivors reported that they have used CAM, a rate higher than the estimated usage rate reported for the general population The most commonly used modalities were chiropractic (39%, 95% CI: 27-53%) and massage therapy (21%, 95% CI: 12-34%). Less than 10% used meditation (5%, 95% CI: 1-15%) and relaxation (7%, 95% CI: 2-17%). In terms of common herbal usage, 5% (95% CI: 1-15%) had used St. John's Wort and 7% (95% CI: 2-17%) had used shark cartilage. Although none of the patients reported that CAM usage was directed specifically towards treating their lymphoma, 4% (95% CI: 0-12%) of patients reported that CAM could cure cancer, and 14% (95% CI: 6-26%) reported that CAM could increase their feeling of control over their health. This pilot study suggests that long-term lymphoma survivors appear to use CAM at a rate higher than the general population. The use of potential agents of risk by the survivors and the lack of access to potentially beneficial modalities highlights the need for further study of CAM in this population.\",\n \"corpus_id\": 19698699,\n \"score\": 0\n },\n {\n \"doc_id\": \"20090352\",\n \"title\": \"[Complementary and alternative medicine in practice - the diagnostic-therapeutic process from the perspective of general practitioners: a qualitative study].\",\n \"abstract\": \"Komplementärmedizin in der Praxis - der diagnostischtherapeutische Prozess aus Sicht von Hausärzten: Eine qualitative Studie. BACKGROUND: Complementary and alternative medicine (CAM) is widely used in general practices in Germany. This study aimed to explore the diagnostic-therapeutic process and relevant factors regarding the use of CAM from the perspective of general practitioners (GPs). METHODS: Within a qualitative approach 3 focus groups with a convenience sample of 17 GPs were conducted. Group discussions were analysed by qualitative content analysis. RESULTS: GPs view the diagnostic-therapeutic process in CAM as complex and less dependent on the methods used than on approach-independent factors. On the basis of the focus group transcripts, 4 main categories were identified that play a major role when CAM is used in primary care: patient factors, physician factors, relationship factors and generic factors of CAM. ' Constitution', 'expectation', and 'personal (life) concepts' were mentioned as relevant patient factors, 'empathy', 'respect' and 'authenticity' as relevant physician factors. At the level of the doctor-patient-relationship, 'time', 'confidence', 'matching', 'balance of power' and 'rituals' seem to play a major role. DISCUSSION: From the perspective of the GPs the diagnostic-therapeutic process can be considered as a cyclic process in which patient, physician and relationship elements as well as generic CAM factors are closely interweaved. According to this conception, CAM can be used for a wide range of health problems in primary care. Sufficient time and a trustful doctor-patient-relationship are, however, essential for the use of CAM. Due to the increasing economical pressure there is a risk that CAM is processualised, i.e. split into single processes and uncoupled from the doctor-patient-relationship. This would jeopardise efficacy of CAM in everyday practice.\",\n \"corpus_id\": 12211659,\n \"score\": 0\n },\n {\n \"doc_id\": \"20392781\",\n \"title\": \"Herbal medicines--what do clinicians know?\",\n \"abstract\": \"In 1986, DTB published an article called Herbal medicines - safe and effective?, which discussed some of the issues around the availability, safety and efficacy of such treatments.1 We highlighted how the failure of orthodox medicines to cure, and anxiety about their potentially serious unwanted effects, had led some people to turn to herbal medicines for treatment for chronic and disabling conditions often in the belief, that natural medicines must be intrinsically safe. The article concluded by discussing the potential problems associated with herbal medicines and the role that doctors should play in asking about patients' use of such products. Revisiting these themes, here we present an overview of the results of an online survey conducted among DTB readers to explore four key issues: What do healthcare professionals know about herbal medicines? What challenges (if any) does patients' use of herbal medicines raise for healthcare professionals? What awareness do healthcare professionals have about the regulatory arrangements for herbal medicines? What sources of information (if any) do healthcare professionals use to inform themselves about herbal medicines?\",\n \"corpus_id\": 6964685,\n \"score\": 0\n },\n {\n \"doc_id\": \"21491340\",\n \"title\": \"Coping styles and self-regulation predict complementary and alternative medicine and herbal supplement use among college students.\",\n \"abstract\": \"Studies have suggested that complementary and alternative medicine (CAM) and herbal supplement use may be high on college campuses. This study investigated the relationship between CAM and herbal supplement utilization and coping, self-regulatory, cognitive styles, and healthcare satisfaction among college students (n=370). Indeed, overall CAM and herbal supplement use during the past year appeared high; however, users of these practices appeared somewhat heterogeneous. Dispositional factors were predictive of utilization with active coping style associated with both practices, whereas support-seeking and intrinsic self-regulation were only associated with CAM use and avoidant coping was only related to use of herbal supplements. Notably, dissatisfaction with healthcare services was not associated with either CAM or herbal supplement use among students. The findings from this study offer insight regarding motives for usage that may assist in more openly dialoguing with students regarding their health-enhancing and/or health-compromising behaviors. Moreover, future studies assessing utilization of CAM will benefit from examining the definitional issues of CAM practices that are addressed.\",\n \"corpus_id\": 25714358,\n \"score\": 0\n },\n {\n \"doc_id\": \"21614944\",\n \"title\": \"The use of complementary and alternative medicine among Malay breast cancer survivors.\",\n \"abstract\": \"BACKGROUND: A cross-sectional studywas carried out to determine the prevalence of complementary and alternative medicine (CAM) use by breast cancer survivors. METHODS: A descriptivesurveydesignwasdeveloped. Information on sociodemographic characteristics, cancer clinical treatment history, and use of CAM were obtained through a modified self-administered questionnaire from 116 Malay breast cancer survivors aged 21 to 67 years who were 2 years postdiagnosis and currently undergoing follow-up treatment at breast cancer clinics at Hospital Kuala Lumpur and Universiti Kebangsaan Malaysia Medical Centre. RESULTS: Data suggest that 64% of the participants were identified as CAM users; dietary supplements were the most common form used, followed by prayer and Malay traditional medicine. Within the wide range of dietary supplements, multivitamins were most often taken followed by spirulina, vitamin C, evening primrose oil, and herbal products. Contrary to other findings, the CAM users were found to be older, had secondary education levels, and were from middle-income households. However, there was no significant difference between CAM users and nonusers in this study. Family members played an important role as the main source of information along with doctors/health care providers, friends, and printed materials/mass media. The reasons participants gave for using CAM were mainly to assist in healing the body's inner strength, to cure cancer, and to reduce stress. Only half of the participants consulted with their physicians regarding the safety of CAM use. The participants began to use CAM while undergoing clinical treatments. Most of the participants used CAM for more than a year. About RM100 to RM149 (31.88 USD to 47.50 USD at press time) were spent monthly on CAM by 32% of the participants. The CAM use was found to be effective and beneficial for patients' disease states, and they were contented with the usage of the CAM therapies. Multivariate analysis revealed that thedecision to use or not to use CAM was not dependent on sociodemographic background or cancer clinical treatment history. CONCLUSIONS: CAM was commonly used by breast cancer survivors as a coping mechanism to battle the disease.\",\n \"corpus_id\": 15882508,\n \"score\": 0\n },\n {\n \"doc_id\": \"22187618\",\n \"title\": \"Complementary medicine use among Moroccan patients with cancer: a descriptive study.\",\n \"abstract\": \"BACKGROUND: Complementary and alternative medicine (CAM) is a group of diverse medical and health care systems, practices, and products that are not generally considered part of conventional medicine. As cancer incidence rates and survival time increase, use of CAM will likely increase. However, little is known about the use of CAM in cancer patients, specifically in emerging countries. METHODS: We conducted a study in the medical oncology department at the University Hospital of Fez on the use of complementary medicine among cancer patient. The aims of this study were to estimate and describe the reasons of use of complementary medicine (CM) in patients with a cancer treated in a Moroccan oncology department. A specially designed questionnaire was completed for patient during treatment or follow-up in the oncology department after formal consent was obtained. It was a descriptive study among 100 patients over a period of 6 months between September 2008 and February 2009. RESULTS: A total of 100 patients participated in the study, 46 of them were identified as users of complementary medicine. The most substances used were plants 24%, pure honey 13% and water of Zem Zem (holy water from Mecca) 11%. Concerning techniques, religious practices 37%, special diets 22% and recourse to traditional healers 11% were most commonly used. No specific user profile was observed depending of different sociodemograhics and clinical parameters. The majority of the users of complementary medicine were not revealing their habits to their oncologist because the question was not raised in consultation. CONCLUSION: It seems that medical doctors should ask patients about their use of complementary medicine when they obtain medical history and they need to know more about complementary medicine to offer better consultation. Complementary medicine must benefit, as well as conventional medicine, from scientific studies to evaluate potential benefits, toxicity and interactions with the conventional treatment to enable the oncologist better inform his patients.\",\n \"corpus_id\": 13968838,\n \"score\": 0\n },\n {\n \"doc_id\": \"22873496\",\n \"title\": \"Use of complementary medicine amongst patients on antiretroviral drugs in an HIV treatment centre in Lagos, Nigeria.\",\n \"abstract\": \"Traditional herbal remedies have been used to treat many ailments in Nigeria but the safety of herbal remedies has been the major concerns to many people especially when the chemical constituents of the products are not known. This study is therefore designed to evaluate the prevalence of use of complementary drugs with antiretroviral (ARV) therapy and possible treatment outcome of the concurrent utilization of these therapeutic agents. A descriptive cross-sectional survey of 354 HIV patients attending APIN clinics in LUTH using a consecutive sampling technique was used. There was also correlation of the data obtained from the patients with their clinical case notes. Results showed that only 8.2 % of the respondents' used herbal medicine concurrently with ARV therapy. Ninety percent of the participants were on a two nucleoside and one non-nucleoside based ARV therapy. The most common regimen (55%) was Zidovudine/lamivudine/Nevirapine fixed dose combination while 10% use a protease inhibitor based regimen. The commonly herbal drugs used ranges from Jobelyn [Sorghum bicolor plant leaves (13.8%)], Garlic [Allicin, γ-glutamyl- (s)-ally-L-Cysteine] (10.3%), Ginger [Essential oil] (17.2%) and Aloe vera [Hydroxyanthracene derivatives expressed as Barbaloin] (10.3%). The major reason for the commencement of herbal medicine is the perception that the medicine will boost their immunity (65.5%). However, there was a marginal improvement though not significant (p ≥ 0.05) in the CD4 counts (489.8 ± 195.2; 419.1 ± 236.2) and viral load (5117.8 ± 26092.0; 31136.7 ± 197954.6) of HIV patients on herbal drugs compared to those who are not on herbal drugs. Herbal medicines have potentials to interact with ARVs and thus result in adverse reactions and possibly therapeutic failure. There is need for thorough investigation of the pharmacological action of these herbal medicines in HIV treatment taking into consideration their pharmacokinetic and toxicological profile.\",\n \"corpus_id\": 34288408,\n \"score\": 0\n },\n {\n \"doc_id\": \"22906201\",\n \"title\": \"Herbal medicine: a survey of use in Nigerian presurgical patients booked for ambulatory anaesthesia.\",\n \"abstract\": \"BACKGROUND: Utilization of herbal medicines in the preoperative period by Nigerian patients booked for day case surgery has not been explored. METHODS: Cross-sectional survey of 60 patients presenting for day-case surgery at a tertiary healthcare institution over a 3-week period in August 2011 was conducted. Using a structured questionnaire, inquiries were made concerning use of herbal medicines in the immediate preoperative period. Socio-demographic characteristics, information on use of concurrent medical prescriptions, types of herbs used, reasons for use, perceived side effects and perceived efficacy were obtained. Data were evaluated using descriptive statistics and Chi-square. RESULTS: Fifty-two (86.7%) were American Society of Anesthesiologists (ASA) class 1 while 8 (13%) were ASA 2. Most patients (86.7%) had their procedures done under local infiltration with monitored anaesthesia care (MAC), while 5.0% and 8.3% had their procedures done under regional and general anaesthesia, respectively. About 48.3% of respondents were on concurrent medical prescriptions while 51.7% were not. Forty percent (40%) of patients admitted to use of herbal medicine, all by the oral route, in the immediate perioperative period; 87.5% did not inform their doctor of their herbal use. Types of herbs used included 'dogonyaro', 'agbo', 'nchanwu', and Tahitian noni. Treatment of malaria was commonest reason for use in 29.2% of patients, while cough and concurrent surgical condition were reasons given by 12.5% of patients, respectively. Seventy-nine percent (79.2%) of patients considered their herbal medications effective. Perceived side effects of herbal medication (16.6%) included fever, waist pain and intoxication. There were no variations in use between ASA 1 and ASA 2 patients and none between respondents on conventional medication against those that were not. Variables such as age less than 35 years, female gender, being married and being an urban dweller did not show any significant difference in use. CONCLUSION: This survey revealed many patients were on one or more herbal preparations in the immediate preoperative period. In consideration of possible untoward drug interactions between conventional medication, herbal preparations and anaesthesia, doctors (especially anaesthetists) should routinely assess all patients booked to be anaesthetized, especially those for day case surgery. The authors recommend surveys with larger respondent numbers to determine prevalence of use and possible interactions between indigenous Nigerian herbs and anaesthesia.\",\n \"corpus_id\": 8719566,\n \"score\": 0\n },\n {\n \"doc_id\": \"24082321\",\n \"title\": \"Complementary and alternative medicine usage in cancer patients in southeast of Turkey.\",\n \"abstract\": \"The aim of this study was to investigate the frequency of complementary and alternative medicine (CAM) methods and clinical characteristics in cancer patients in southeast of Turkey. A total of 324 patients (173 female) were enrolled to this study. Questionnaire was applied to all patients individually for approximately 15 minutes by a doctor. At least one CAM method was used by 62% (n=201) of the patients. 82.5% (n=166) of patients treated with CAM were using at least one herbal species. Likewise, 40.9% (68/166) of these patients were using herbal mixtures and 39.8% (66/166) of them were using single herbal as nettle (Urtica dioica) or its seed, 19.3 % (32/166) of them were using other herbals. CAM methods were preferred more frequently by the patients with metastatic stage (p=0.005), receiving palliative treatment (p<0.001), chemotherapy (p=0.020), in between 40-60 ages patient groups (p=0.002), and when duration of disease was lengthened (p=0.002). CAM use among cancer patients is quite common. Presence of metastatic cancer at diagnosis, receiving chemotherapy and palliative treatment and long disease duration were found as main associated factors for CAM usage.\",\n \"corpus_id\": 38485847,\n \"score\": 0\n },\n {\n \"doc_id\": \"24171723\",\n \"title\": \"The co-use of conventional drugs and herbs among patients in Norwegian general practice: a cross-sectional study.\",\n \"abstract\": \"BACKGROUND: Different patient groups are known to use herbal remedies and conventional drugs concomitantly (co-use). This poses a potential risk of herb-drug interaction through altering the drug's pharmacokinetics or pharmacodynamics. Little is known about co-use among patients in general practice. The primary aim of this study was to compare patients in general practice that co-use herbal remedies and conventional drugs with those who do not. The secondary aim was to register the herb-drug combinations with potential clinical relevant interactions among the co-users. METHOD: A questionnaire based cross-sectional study conducted in the autumn 2011 in a general practice office with four general practitioners (GPs) and one intern in Western Norway. Adults >18 years who came for an office visit were invited. The questionnaire asked about demographics, herbal use, conventional drug use and communication about herbal use. Multivariable logistic regression was used to compare co-users to the other patients. RESULTS: Of the 381 patients who completed the questionnaire, the prevalence of herbal use was 44%, with bilberry (41%), green tea (31%), garlic (27%), Aloe vera (26%) and echinacea (18%) as the most frequently used. Among those using conventional drugs regularly, 108 (45%) co-used herbs. Close to 40% of patients on anticoagulants co-used herbs, with garlic and bilberry as the most frequent herbs. Compared to all other patients, co-users had significantly (p < 0.05) increased odds to be female (adjOR 2.0), age above 70 years (adjOR 3.3), use herbs to treat an illness (adjOR 4.2), use two or more herbs (polyherbacy, adjOR 12.1) and having experienced adverse effects of herbal use (adjOR 37.5). Co-use was also associated with use of analgesics or dermatological drugs (adjOR 5.1 and 7.9 respectively). Three out of four patients did not discuss herbal use with any health care professional. CONCLUSION: A sizable proportion of the GP patients co-used herbs with conventional drugs, also combinations with reported interaction potential or additive effects like anticoagulants and garlic. The low disclosure of herbal use to their GP, polyherbacy and the risk of interactions in vulnerable groups like elderly and chronically ill patients, warrant increased awareness among GPs.\",\n \"corpus_id\": 1089923,\n \"score\": 0\n },\n {\n \"doc_id\": \"24219150\",\n \"title\": \"The use of herbal medicines during breastfeeding: a population-based survey in Western Australia.\",\n \"abstract\": \"BACKGROUND: Main concerns for lactating women about medications include the safety of their breastfed infants and the potential effects of medication on quantity and quality of breast milk. While medicine treatments include conventional and complementary medicines, most studies to date have focused on evaluating the safety aspect of conventional medicines. Despite increasing popularity of herbal medicines, there are currently limited data available on the pattern of use and safety of these medicines during breastfeeding. This study aimed to identify the pattern of use of herbal medicines during breastfeeding in Perth, Western Australia, and to identify aspects which require further clinical research. METHODS: This study was conducted using a self-administered questionnaire validated through two pilot studies. Participants were 18 years or older, breastfeeding or had breastfed in the past 12 months. Participants were recruited from various community and health centres, and through advertising in newspapers. Simple descriptive statistics were used to summarise the demographic profile and attitudes of respondents, using the SPSS statistical software. RESULTS: A total of 304 questionnaires from eligible participants were returned (27.2% response rate) and analysed. Amongst the respondents, 59.9% took at least one herb for medicinal purposes during breastfeeding, whilst 24.3% reported the use of at least one herb to increase breast milk supply. Most commonly used herbs were fenugreek (18.4%), ginger (11.8%), dong quai (7.9%), chamomile (7.2%), garlic (6.6%) and blessed thistle (5.9%). The majority of participants (70.1%) believed that there was a lack of information resources, whilst 43.4% perceived herbal medicines to be safer than conventional medicines. Only 28.6% of users notified their doctor of their decision to use herbal medicine(s) during breastfeeding; 71.6% had previously refused or avoided conventional medicine treatments due to concerns regarding safety of their breastfed infants. CONCLUSIONS: The use of herbal medicines is common amongst breastfeeding women, while information supporting their safety and efficacy is lacking. This study has demonstrated the need for further research into commonly used herbal medicines. Evidence-based information should be available to breastfeeding women who wish to consider use of all medicines, including complementary medicines, to avoid unnecessary cessation of breastfeeding or compromising of pharmacotherapy.\",\n \"corpus_id\": 11720103,\n \"score\": 0\n },\n {\n \"doc_id\": \"24533750\",\n \"title\": \"Use of bodily sensations as a risk assessment tool: exploring people with Multiple Sclerosis' views on risks of negative interactions between herbal medicine and conventional drug therapies.\",\n \"abstract\": \"BACKGROUND: Most users of complementary and alternative medicine (CAM) combine it with conventional medicine. Recent risk assessment studies have shown risks of negative interactions between CAM and conventional medicine, particularly when combining herbal medicine and conventional drug therapies (CDT). Little is known about the way users consider such risks. The present paper aims to gain knowledge about this issue by exploring views on risks of negative interactions when combining herbal medicine and CDT among people with multiple sclerosis (MS). METHODS: This paper draws on a qualitative follow-up study on a survey among members of the Danish MS Society. Semi-structured, in-depth qualitative interviews were conducted with a strategic selection from the survey respondents. The study was inspired by a phenomenological approach and emerging themes were extracted from the data through meaning condensation. RESULTS: Four themes characterized the informants' views on risks of negative interactions when combining herbal medicine and CDT: 1) 'naturalness' in herbal medicine; 2) 'bodily sensations' as guidelines; 3) trust in the CAM practitioner; 4) lack of dialogue with medical doctor. CONCLUSIONS: Generally, the combination of herbal medicine and CDT was considered by the informants to be safe. In particular, they emphasized the 'non-chemical' nature of herbal medicine and of their own bodily sensations as warrants of safety. A trustful relation to the CAM practitioner furthermore made some of them feel safe in their use of herbal medicine and CDT in combination. The informants' use of bodily sensations as a non-discursive risk assessment may be a relevant element in understanding these issues.\",\n \"corpus_id\": 14682417,\n \"score\": 0\n },\n {\n \"doc_id\": \"24748849\",\n \"title\": \"What young people want from health-related online resources: a focus group study.\",\n \"abstract\": \"The growth of the Internet as an information source about health, particularly amongst young people, is well established. The aim of this study was to explore young people's perceptions and experiences of engaging with health-related online content, particularly through social media websites. Between February and July 2011 nine focus groups were facilitated across Scotland with young people aged between 14 and 18 years. Health-related user-generated content seems to be appreciated by young people as a useful, if not always trustworthy, source of accounts of other people's experiences. The reliability and quality of both user-generated content and official factual content about health appear to be concerns for young people, and they employ specialised strategies for negotiating both areas of the online environment. Young people's engagement with health online is a dynamic area for research. Their perceptions and experiences of health-related content seem based on their wider familiarity with the online environment and, as the online environment develops, so too do young people's strategies and conventions for accessing it.\",\n \"corpus_id\": 977448,\n \"score\": 0\n },\n {\n \"doc_id\": \"25370478\",\n \"title\": \"Use of herbal medicine during pregnancy among women with access to public healthcare in Nairobi, Kenya: a cross-sectional survey.\",\n \"abstract\": \"BACKGROUND: Maternal health is a public health priority in many African countries, but little is known about herbal medicine use in pregnancy. This study aimed to determine the pattern of use of herbal medicine in an urban setting, where women have relatively high access to public healthcare. METHODS: This cross-sectional study included 333 women attending a childcare clinic in a district public health hospital in Nairobi, Kenya, during January and February, 2012, and who had delivered a baby within the past 9 months. Qualitative and quantitative data on herbal medicine use during their latest pregnancy were collected through an interviewer-administered questionnaire. Data was analysed descriptively and the Chi square test and Fishers' exact test used to analyse relationships among variables. RESULTS: About 12% of women used herbal medicine during their most recent pregnancy. The use of herbal medicine was associated with a lower level of education (p = 0.007) and use before the index pregnancy (p <0.001). Only 12.5% of users disclosed such use to healthcare professionals, and about 20% used herbal medicine concomitantly with Western medicine for the same illness/condition. Women used herbal medicine for back pain, toothache, indigestion and infectious diseases, such as respiratory tract infections and malaria. A proportion of users took herbal medicine only to boost or maintain health. There were high rates of self-prescribing, as well as sourcing from family and friends. Beliefs about safety and efficacy were consistent with patterns of use or non-use, although both users and non-users were unsure about the safety and contraindications of Western medicine during pregnancy compared with that of herbal medicine. CONCLUSION: Herbal medicine is used by 12% of pregnant women with access to healthcare in an urban context in Kenya, and often occurs without the knowledge of healthcare practitioners. Healthcare professionals should play a role in rational use of both herbal and Western medicine, by discussing contraindications and the potential for drug-herb interactions with patients. More studies are needed into the use of herbal medicines during pregnancy, labour and the postpartum period in different geographical areas, and into the health outcomes associated with their use.\",\n \"corpus_id\": 8782199,\n \"score\": 0\n },\n {\n \"doc_id\": \"25550393\",\n \"title\": \"The man-in-the-moon face: a qualitative study of body image, self-image and medication use in systemic lupus erythematosus.\",\n \"abstract\": \"OBJECTIVE: Little is yet known about the interactions between body image, self-image, medication use and adherence to medication in people with SLE. Using a qualitative mode of enquiry, we sought to understand these experiences within a group of patients diagnosed with SLE. METHODS: Fifteen participants (14 female, 1 male) with SLE took part in semi-structured interviews. Their ages ranged from 22 to 57 years and disease duration ranged from 3 to 20 years. Interviews were audio recorded and transcribed verbatim. Data were analysed using interpretative phenomenological analysis. RESULTS: Analysis revealed four themes that are presented set within the overarching concept of body and self-image: the road to diagnosis, communication and treatment concordance, living with the medication and self-image-faking it. Narratives revealed significant dissatisfaction with body image, an externally located concept. Worries about appearance and weight were most commonly mentioned and were often related to steroid use. Creative non-compliance with medication was frequently described and greater concordant relationships with physicians desired. Overall, participants sought increased investment in self-image, an internally located concept. CONCLUSION: Body and self-image are important issues for individuals with SLE. Yet participants in our study generally felt that their health care providers did not give enough consideration to their concerns over the outward appearance effects of both the disease and its treatment.\",\n \"corpus_id\": 19677433,\n \"score\": 0\n },\n {\n \"doc_id\": \"25586865\",\n \"title\": \"Patient perspectives on online health information and communication with doctors: a qualitative study of patients 50 years old and over.\",\n \"abstract\": \"BACKGROUND: As health care systems around the world shift toward models that emphasize self-care management, there is increasing pressure for patients to obtain health information online. It is critical that patients are able to identify potential problems with using the Internet to diagnose and treat a health issue and that they feel comfortable communicating with their doctor about the health information they acquire from the Internet. OBJECTIVE: Our aim was to examine patient-identified (1) problems with using the Internet to identify and treat a health issue, (2) barriers to communication with a doctor about online health information seeking, and (3) facilitators of communication with a doctor about patient searches for health information on the Internet. METHODS: For this qualitative exploratory study, semistructured interviews were conducted with a sample of 56 adults age 50 years old and over. General concerns regarding use of the Internet to diagnose and treat a health issue were examined separately for participants based on whether they had ever discussed health information obtained through the Internet with a doctor. Discussions about barriers to and facilitators of communication about patient searches for health information on the Internet with a doctor were analyzed using thematic analysis. RESULTS: Six higher-level general concerns emerged: (1) limitations in own ability, (2) credibility/limitations of online information, (3) anxiety, (4) time consumption, (5) conflict, and (6) non-physical harm. The most prevalent concern raised by participants who communicated with a doctor about their online health information seeking related to the credibility or limitations in online information. Participants who had never communicated with a doctor about their online health information seeking most commonly reported concerns about non-physical harm. Four barriers to communication emerged: (1) concerns about embarrassment, (2) concerns that the doctor doesn't want to hear about it, (3) belief that there is no need to bring it up, and (4) forgetting to bring it up. Facilitators of communication included: (1) having a family member present at doctor visits, (2) doctor-initiated inquiries, and (3) encountering an advertisement that suggested talking with a doctor. CONCLUSIONS: Overall, participants displayed awareness of potential problems related to online health information seeking. Findings from this study point to a set of barriers as well as facilitators of communication about online health information seeking between patients and doctors. This study highlights the need for enhanced patient communication skills, eHealth literacy assessments that are accompanied by targeted resources pointing individuals to high-quality credible online health information, and the need to remind patients of the importance of consulting a medical professional when they use online health resources to diagnose and treat a health issue.\",\n \"corpus_id\": 20696176,\n \"score\": 0\n },\n {\n \"doc_id\": \"26133063\",\n \"title\": \"\\\"The medicine from behind\\\": The frequent use of enemas in western African traditional medicine.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: Purgative enemas form an integral part of African traditional medicine. Besides possible benefits, serious health risks of rectal herbal therapy have been described in literature. To design appropriate health education programs, it is essential to understand traditional herbal practices and local perceptions of health and illness. Little is known about the herbal ingredients of enemas in Sub-Saharan Africa and consumers' personal reasons to use them. AIM OF THE STUDY: To analyze the importance of enema use with regard to plant species used and illnesses treated in West and Central Africa, to understand the local health beliefs that underlie frequent enema use and to evaluate which recipes and practices could be beneficial or harmful. MATERIALS AND METHODS: We extracted data from 266 ethnobotanical questionnaires on medicinal (in particular women's health and childcare) and ritual plant use in Ghana, Benin and Gabon. Plants mentioned during interviews were vouchered and identified in herbaria. Health issues treated by means of enemas were ranked according to the number of plant species used for a specific illness. We compared our results with findings of medical research on benefits and risks of enema use in Sub-Saharan Africa. RESULTS: We recorded ca. 213 different plant species used in hundreds of recipes for rectal insertions, mostly in Ghana and Gabon. Stomachache, abdominal pain, female infertility and birth facilitation were treated with the highest number of plants species. Cleansing the intestines of young children to promote their health by getting rid of 'dirt', instead of treating constipation, was an important cultural practice that required the rectal application of herbal medicine, as well as other cultural bound health issues like stimulating children to walk at an early age. Tradition, the bitter taste of herbal medicine and the rapid effect of enemas were frequently mentioned reasons for enema use. DISCUSSION AND CONCLUSIONS: Literature indicates that although enemas can help to improve the hygienic conditions of a household with young infants, frequent enema use can pose serious risks like direct toxicity caused by harmful ingredients, mechanical injury and infections. In Africa, enemas containing herbal medicine are common methods of administering herbal medicine for a variety of diseases, rather than just medicinal treatments for constipation as previously thought. Health professionals should be aware of the extent of, and motivation behind enema use to develop culturally appropriate education programs, especially targeted at vulnerable groups such as elderly people, parents of young infants and pregnant women.\",\n \"corpus_id\": 40581988,\n \"score\": 0\n },\n {\n \"doc_id\": \"26726906\",\n \"title\": \"Use and users of complementary and alternative medicine among people with multiple sclerosis in Denmark.\",\n \"abstract\": \"BACKGROUND: It is known that complementary and alternative medicine (CAM) is popular among people with multiple Sclerosis (MS) and that use is widespread. However, very limited knowledge exists about use and users of CAM among people with MS in a Danish context. AIMS: The overall aim of the thesis is to investigate how and why people with MS in Denmark include CAM in managing their life with a chronic disease and to discuss their experiences and beliefs linked to CAM use. METHODS: A mixed methods research design was applied, combining an Internet-based survey with two qualitative in-depth interview studies. A total of 6,850 people with MS from the five Nordic countries, of these 3,500 from Denmark, were invited to participate in the survey. The average response rate was 56.1%. Based on analyses of the Danish survey data, two specific issues regarding the use of CAM were selected for further investigation and two qualitative interview studies were performed (n = 17, n = 11), using program theory and meaning categorization as analytical tools. RESULTS: The results of the study indicate that the use of CAM among people with MS is widespread in Denmark as well as in the other Nordic countries. The results furthermore suggest that this use is generally embedded in a preventative, autonomous approach to treatment and that the users' choices regarding CAM may be related to many personal factors and do not necessarily represent a distrust of the medical system. PERSPECTIVES: The results of the study point to the relevance of healthcare professionals engaging in understanding patients' different motives for - and experiences with - using different types of treatments. Thereby, the results of the study also point to the importance of enhancing and qualifying communication between patients and representatives of conventional healthcare systems regarding the patients' use of CAM, both with the aim of mutual learning and for reasons of safety.\",\n \"corpus_id\": 6778329,\n \"score\": 0\n },\n {\n \"doc_id\": \"27382428\",\n \"title\": \"A qualitative study exploring medicines use pattern and practice among general public in Malaysia.\",\n \"abstract\": \"OBJECTIVE: The objective of this study is to explore the pattern and practice of medicine use among the general public; and to explore the key factors influencing medicine use among medicine users. METHODS: A qualitative approach using focus group discussions was conducted to get in-depth information about medicines use pattern and practice from the general public. Adult people who reported using medicines at the time of study or in the previous month were approached. Two focus group discussions were audio-recorded and transcribed verbatim. The obtained data were analysed using thematic content analysis. RESULTS: This study found that there are some misunderstanding about the appropriate use of medicines. The majority of the participants reported that they were complying with their medication regimen. However, forgetting to take medicines was stated by 4 participants while 2 participants stopped taking medicines when they felt better. In addition, 10 participants reporting using medicines according to their own knowledge and past experience. Whereas 4 participants took medicines according to other informal resources such as family, friends or the media. Seven participants have experienced side effects with using medicines, 4 of them informed their doctor while 3 participants stopped taking medicines without informing their doctor. CONCLUSION: There was a misunderstanding about medicines use in terms of medication compliance, self-management of the illness and the resources of information about using medicines. Many efforts are still needed from health care professionals to provide sufficient information about medicines use in order to decrease the risk of inappropriate use of medicines and to achieve better therapeutic outcome.\",\n \"corpus_id\": 15109891,\n \"score\": 0\n },\n {\n \"doc_id\": \"27400742\",\n \"title\": \"Use of complementary and alternative medicines in haemodialysis patients: a cross-sectional study from Palestine.\",\n \"abstract\": \"BACKGROUND: Complementary and alternative medicine (CAM), and herbal therapies, are accepted worldwide, and have been important from medical, sociological and economic perspectives, among haemodialysis (HD) patients. The primary aim of this study was to evaluate the use of CAM among patients with end-stage renal disease (ESRD) who are undergoing HD. METHODS: Face-to-face interviews of patients with ESRD undergoing HD from ten outpatient renal departments at a national level in Palestine were conducted from June 2014 to January 2015. A survey questionnaire, which included questions on socio-demographic and clinical characteristics, and on the CAM therapies that were used, was administered. RESULTS: Out of 267 patients interviewed, 172 patients used at least one type of CAM in the last month prior to the interview, and thus the utilisation rate was 64.4 %. Forty one (15.4 %) patients reported using one type of CAMs, while 18.7 % used two different CAMs and 30.3 % used more than two types of CAMs for their health status. Of the patients who used CAM, herbal therapies were used most often (43.5 %), followed by honey (35.6 %), diet (22.8 %), and exorcism in Islam (16.9 %). The herbal therapies mentioned most often were Nigella sativa L. (18.7 %), followed by Salvia officinalis L. (16.9 %), and Pimpinella anisum L. (10.5 %). CONCLUSIONS: In conclusion, the prevalence of CAM is relatively high in the selected population. Most patients used biological therapies such as herbal remedies, thus highlighting a greater need for patient education regarding CAM therapies and possible herb-drug interactions. Health care providers must be aware of the potential benefits and risks related to CAM use. There is a need for more clinical research pertaining to CAM to reach stronger evidence regarding potential benefits and risks related to CAM use.\",\n \"corpus_id\": 15492556,\n \"score\": 0\n },\n {\n \"doc_id\": \"28472987\",\n \"title\": \"Use of complementary and alternative medicine by patients with end-stage renal disease on haemodialysis in Trinidad: A descriptive study.\",\n \"abstract\": \"BACKGROUND: Despite the paucity of scientific evidence, complementary and alternative medicine (CAM) is widely used for the prevention and treatment of illness, holistic care, and counteracting the adverse effects of conventional medicine (CM). This study investigates the use of CAM by patients with end-stage renal disease (ESRD) on haemodialysis. METHODS: This quantitative study was conducted from November 1, 2014 to December 31, 2014 in the haemodialysis unit at San Fernando General Hospital (San Fernando, Trinidad). Face-to-face questionnaire-based interviews were held with101of 125 eligible patients (response rate, 80.5%) at the chairside during haemodialysis. The completed questionnaires were entered into a secure computer database. Data analysis included descriptive analysis, χ(2) tests, and binary logistic regression analysis. RESULTS: A minority of the patients were CAM users (n = 19; 18.8%). All 19 CAM users took medicinal herbs, 78.9% (n = 15) used spiritual therapy, and 10.5% (n = 2) used alternative systems. Medicinal tea (n = 15; 78.9%), garlic (Allium sativum) (n = 17; 73.7%), and ginger (Zingiber officinale roscoe) (n = 13; 68.4%) were the most commonly used medicinal herbs. Seven (36.8%) patients used Chinese herbal medicines and 3 (15.8%) patients used Aloe vera. All CAM users were willing to use CAM without supervision or monitoring by their doctors while receiving CM. The use of CAM could not be predicted by age, sex, ethnicity, education, religion, marital status, or employment. Nearly all (98%) patients were satisfied with CAM. More than one-third (36.8%) of patients did not disclose their use of CAM to their doctors, who were generally indifferent to such therapy. CONCLUSIONS: The use of CAM by patients with ESRD was relatively infrequent. All patients used medicinal herbs, most patients used spiritual therapy, and a minority of patients used alternative systems. Complementary and alternative medicine was primarily used for spiritual reasons and the likelihood of its use was influenced by family, friends, and other patients. Patients continued using CM with one or more CAM therapies without informing their healthcare providers, which is a major health risk.\",\n \"corpus_id\": 5024638,\n \"score\": 0\n },\n {\n \"doc_id\": \"28724031\",\n \"title\": \"Methodological challenges in the use of focus groups with people with severe mental illness.\",\n \"abstract\": \"This study addresses the practical, methodological and ethical challenges that were found in three studies that used focus groups with people with severe mental illness, in the context of community mental health services in Brazil. Focus groups are a powerful tool in health research that need to be better discussed in research with people with severe mental illness, in the context of community mental health facilities. This study is based on the authors' experience of conducting and analyzing focus groups in three different cities - Campinas, Rio de Janeiro and Salvador - between 2006-2010. The implementation of focus groups with people with severe mental illness is discussed in the following categories; planning, group design, sampling, recruitment, group interview guides, and conduction. The importance of connecting mental healthcare providers as part of the research context is emphasized. Ethical issues and challenges are highlighted, as well as the establishment of a sensitive and empathic group atmosphere, wherein mutual respect can facilitate interpersonal relations and enable people diagnosed with severe mental illness to make sense of the experience. We emphasize the relevance of the interaction between clinical and research teams in order to create collaborative work, achieve inquiry aims, and elicit narratives of mental health users and professionals.\",\n \"corpus_id\": 22658474,\n \"score\": 0\n },\n {\n \"doc_id\": \"29610108\",\n \"title\": \"Preferences for Web-Based Information Material for Low Back Pain: Qualitative Interview Study on People Consulting a General Practitioner.\",\n \"abstract\": \"BACKGROUND: Information on self-management, including addressing people's fears and concerns, are core aspects of managing patients with low back pain (LBP). Web apps with patient information may be used to extend patient-physician consultations and encourage self-management outside of the consultation room. It is, however, important to identify the end users' needs and preferences in order to maximize acceptance. OBJECTIVE: The aim of this study was to identify preferences for the content, design, and functionality of a Web app with evidence-based information and advice for people with LBP in Denmark. METHODS: This is a phenomenological qualitative study. Adults who had consulted their general practitioner because of LBP within the past 14 days were included. Each participated in a semistructured interview, which was audiotaped and transcribed for text condensation. Interviews were conducted at the participant's home by 2 interviewers. Participants also completed a questionnaire that requested information on age, gender, internet usage, interest in searching new knowledge, LBP-related function, and pain. RESULTS: Fifteen 45-min interviews were conducted. Participants had a median age of 40 years (range 22-68 years) and reported a median disability of 7 points (range 0-18) using the 23-item Roland Morris Disability Questionnaire. Participants reported that Web-based information should be easy to find and read, easily overviewed, and not be overloaded with information. Subjects found existing Web-based information confusing, often difficult to comprehend, and not relevant for them, and they questioned the motives driving most hosting companies or organizations. The Patient Handbook, a Danish government-funded website that provides information to Danes about health, was mentioned as a trustworthy and preferred site when searching for information and advice regarding LBP. CONCLUSIONS: This study identified important issues to consider when developing and supplementing existing general practice treatment with Web-based information and advice for patients with LBP. Development of a Web app should consider patient input, and developers should carefully address the following domains: readability, customization, design, credibility, and usability.\",\n \"corpus_id\": 4626418,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":55,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29439589\",\n \"title\": \"Measurement properties of the Dutch Unité Rhumatologique des Affections de la Main and its ability to measure change due to Dupuytren's disease progression compared with the Michigan Hand outcomes Questionnaire.\",\n \"abstract\": \"Data of a prospective longitudinal cohort study including 233 Dupuytren's patients was used to determine: (1) whether the Unité Rhumatologique des Affections de la Main scale and Michigan Hand outcomes Questionnaire can detect change in hand function due to Dupuytren's disease progression and to compare their abilities; (2) the concurrent validity, reliability, responsiveness and interpretability of the Dutch Unité Rhumatologique des Affections de la Main. The Unité Rhumatologique des Affections de la Main and Michigan Hand outcomes Questionnaire had comparable measurement properties, and were both able to distinguish participants with disease progression from those without progression (resp. U = 1252.5, p = 0.008, and U = 1086.0, p < 0.001), but only at a group level. Individual cases of progression could not be detected using these outcome measures, as indicated by the fact that the smallest detectable change was larger than the minimal important change, and area under the receiver operating curve (AUC) values of 0.75 for Michigan Hand outcomes Questionnaire and 0.67 for Unité Rhumatologique des Affections de la Main. LEVEL OF EVIDENCE: II.\",\n \"corpus_id\": 3279401\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18332014","title":"Which questionnaire is best? The reliability, validity and ease of use of the Patient Evaluation Measure, the Disabilities of the Arm, Shoulder and Hand and the Michigan Hand Outcome Measure.","abstract":"The Patient Evaluation Measure (PEM), The Michigan Hand Outcome Questionnaire (MHQ) and the Disabilities of the Arm, Shoulder and Hand (DASH) score were assessed independent of their originators for reliability, construct and criterion validity and acceptability, using an ease of use questionnaire. These were administered in random order to 100 patients with different hand and wrist disorders and with different impairments of movement, pain, sensation and strength. The internal consistency of all three questionnaires was very high suggesting redundancy in the questions. All questionnaires were reproducible and valid for finger and wrist disorders, but less for nerve disorders. All had poor construct validity. The PEM was the easiest to understand and complete, taking the least time. Correlation between the scales is high and conversion equations were calculated. All three are reliable and reproducible patient completed questionnaires, but the PEM is the easiest to use. The validity of all is suspected for nerve disorders.","corpus_id":6949461,"score":2},{"doc_id":"19220604","title":"The lived experience of Dupuytren's disease of the hand.","abstract":"AIMS: To describe patients' experiences of living with Dupuytren's disease. BACKGROUND: Dupuytren's disease is a chronic, progressive deformity of the hand which limits active extension of the fingers due to advancing and irreversible flexion deformity. It is estimated that two million people are affected by the condition in the UK. Nurses may frequently encounter patients with this condition in a wide range of settings. However, the disease is neglected in the nursing literature and little is known about patients' experience of living with the condition. DESIGN: A phenomenological approach, using Coliazzi's method, was employed. METHOD: Semi-structured interviews were conducted with six men and one woman diagnosed with Dupuytren's disease. RESULTS: Four interlinking themes emerged. Theme 1: Awareness of Dupuytren's disease describes participants' experiences of recognising and acknowledging the disease, which often did not occur until functional ability was restricted. Theme 2: Living with Dupuytren's disease describes how patients coped with the disease and adapted their activities to maintain independence. Theme 3: Deciding on treatment illuminates how patients decided on treatment and highlights a lack of information and support from health professionals. Theme 4: Receiving treatment articulates participants' experience of surgical treatment and post surgical rehabilitation. CONCLUSIONS: The findings revealed that people living with Dupuytren's disease receive little information about their condition and possible treatment from health professionals yet high quality and accurate information is required for patients to understand their condition and the treatment options available. RELEVANCE TO CLINICAL PRACTICE: People with Dupuytren's disease do not always recognise their condition until it has significantly progressed. Following diagnosis they need accurate and up-to-date information about their condition and treatment options. Nurses have an important role to play in raising awareness of the disease, educating patients about its features and progression and enabling them to become active partners in decisions about treatment.","corpus_id":29994450,"score":2},{"doc_id":"21701336","title":"Development of a brief, 12-item version of the Michigan Hand Questionnaire.","abstract":"BACKGROUND: The Michigan Hand Questionnaire is one of the most widely used hand-specific surveys that measure health status relevant to patients with acute and chronic hand disorders. However, item redundancy exists in the original version, and an abbreviated survey could minimize responder burden and offer broader applicability. METHODS: Patients (n = 422) with four specific hand conditions--rheumatoid arthritis (n = 162), thumb carpometacarpal osteoarthritis (n = 31), carpal tunnel syndrome (n = 97), and distal radius fracture (n = 132)--completed the Michigan Hand Questionnaire at two time points. Correlation analysis identified two items from each of six domains (i.e., function, activities of daily living, work, pain, aesthetics, and satisfaction). The Brief Michigan Hand Questionnaire score was calculated as the sum of the responses to the 12 items. Psychometric analysis was performed to describe the reliability, validity, and responsiveness of the Brief Michigan Hand Questionnaire. RESULTS: The Brief Michigan Hand Questionnaire includes 12 items that were highly correlated with the summary Michigan Hand Questionnaire score (r = 0.99, p < 0.001). The Brief Michigan Hand Questionnaire scores were highly correlated between the two time periods (r = 0.78, p < 0.001) and by disease type. Responsiveness of the Brief Michigan Hand Questionnaire was high for all diseases and similar to that of the original Michigan Hand Questionnaire. CONCLUSIONS: The 12-item Brief Michigan Hand Questionnaire is an efficient and versatile outcomes instrument specific to hand disability that retains the psychometric properties of the original Michigan Hand Questionnaire. The Brief Michigan Hand Questionnaire is an important tool with which to measure patient outcomes and the quality of care in hand surgery. CLINICAL QUESTION/LEVEL OF EVIDENCE: Diagnostic, I.(Figure is included in full-text article.).","corpus_id":30061214,"score":2},{"doc_id":"21786431","title":"Unité Rhumatologique des Affections de la Main (URAM) scale: development and validation of a tool to assess Dupuytren's disease-specific disability.","abstract":"OBJECTIVE: To our knowledge, no functional outcome measure has been developed and validated for Dupuytren's disease. We aimed to develop and validate a patient-reported functional outcome measure for Dupuytren's disease. METHODS: Patients with Dupuytren's disease (n = 9) and medical experts (n = 7) provided input and opinions about limiting activities that were difficult to perform because of Dupuytren's disease for item generation. The provisional scale was studied in an independent sample of patients (n = 85) for item reduction according to response distribution, reliability, redundancy, and loading in a 1-factor solution. The final scale was evaluated as follows: reliability using Cronbach's alpha coefficient and test-retest intraclass correlation coefficient from the previous 85-patient population, and construct validity and responsiveness after needle aponeurotomy in another independent 53-patient sample. For construct validity, convergent validity and divergent validity were tested. The clinically important change was estimated relative to a 1-point categorical change on the Tubiana scale. RESULTS: A 52-item provisional scale was generated and reduced to the final 9-item scale called the Unité Rhumatologique des Affections de la Main (URAM) scale (total score 0-45). The scale showed good to excellent reliability and suitable construct validity. The URAM score improved after needle aponeurotomy: the standardized effect size was 0.56. The estimated clinically important change of the URAM scale was 2.9 points. CONCLUSION: We provide the first patient-reported functional measure for Dupuytren's disease. The URAM scale demonstrated suitable psychometric properties, and is short and convenient enough for easy use in daily practice and in clinical studies.","corpus_id":22095503,"score":2},{"doc_id":"23575442","title":"Optimal functional outcome measures for assessing treatment for Dupuytren's disease: a systematic review and recommendations for future practice.","abstract":"BACKGROUND: Dupuytren's disease of the hand is a common condition affecting the palmar fascia, resulting in progressive flexion deformities of the digits and hence limitation of hand function. The optimal treatment remains unclear as outcomes studies have used a variety of measures for assessment. METHODS: A literature search was performed for all publications describing surgical treatment, percutaneous needle aponeurotomy or collagenase injection for primary or recurrent Dupuytren's disease where outcomes had been monitored using functional measures. RESULTS: Ninety-one studies met the inclusion criteria. Twenty-two studies reported outcomes using patient reported outcome measures (PROMs) ranging from validated questionnaires to self-reported measures for return to work and self-rated disability. The Disability of Arm, Shoulder and Hand (DASH) score was the most utilised patient-reported function measure (n=11). Patient satisfaction was reported by eighteen studies but no single method was used consistently. Range of movement was the most frequent physical measure and was reported in all 91 studies. However, the methods of measurement and reporting varied, with seventeen different techniques being used. Other physical measures included grip and pinch strength and sensibility, again with variations in measurement protocols. The mean follow-up time ranged from 2 weeks to 17 years. CONCLUSIONS: There is little consistency in the reporting of outcomes for interventions in patients with Dupuytren's disease, making it impossible to compare the efficacy of different treatment modalities. Although there are limitations to the existing generic patient reported outcomes measures, a combination of these together with a disease-specific questionnaire, and physical measures of active and passive individual joint Range of movement (ROM), grip and sensibility using standardised protocols should be used for future outcomes studies. As Dupuytren's disease tends to recur following treatment as well as extend to involve other areas of the hand, follow-up times should be standardised and designed to capture both short and long term outcomes.","corpus_id":13313666,"score":2},{"doc_id":"23629117","title":"The Michigan hand outcomes questionnaire after 15 years of field trial.","abstract":"BACKGROUND: The Michigan Hand Outcomes Questionnaire has been used to assess a variety of hand and upper extremity injuries and conditions for nearly 15 years. It has been included in several overviews of upper extremity outcomes measures, but it has not been systematically examined regarding its clinometric properties during field trials. METHODS: The authors conducted a review of the Michigan Hand Outcomes Questionnaire in the English language literature from 1998 through March of 2012. Data from clinical studies were abstracted and compiled. RESULTS: The Michigan Hand Outcomes Questionnaire has been used in 58 clinical studies, and its clinometric properties have been analyzed in an additional 18 publications. The Michigan Hand Outcomes Questionnaire compares favorably with other hand outcomes instruments in the areas of test-retest reliability, validity, and responsiveness. High internal consistency may indicate redundancy within the items in the Michigan Hand Outcomes Questionnaire. The strength of the Michigan Hand Outcomes Questionnaire is its multidimensional construct in measuring patient-rated outcomes in symptom, function, aesthetics, and satisfaction. CONCLUSIONS: The Michigan Hand Outcomes Questionnaire has been applied across a variety of conditions affecting the hand and upper limb. Its psychometric properties have been tested through field trials in various clinical settings around the world.","corpus_id":36691926,"score":2},{"doc_id":"23728243","title":"Reliability and internal validity of the michigan hand questionnaire.","abstract":"BACKGROUND: The Michigan Hand Outcomes Questionnaire (MHQ) remains one of very few to be based on validated and systematic methods in its creation. However, test-retest reliability and internal validity have not been appropriately investigated in any other English-speaking population outside the original development sample. The objective of this study is to examine the reliability and internal validity of the MHQ in a Canadian population. METHODS: All patients with a clinical hand problem but no hand immobilization who attended our Plastic Surgery Clinic were invited to participate in this study. Patients were asked to complete the MHQ, and then contacted to arrange for completion of the MHQ a second time. Internal validity was estimated using Cronbach alpha. Reliability was estimated using the method of Bland and Altman, and intraclass correlation coefficients. Correlation analysis between score differences and time between tests was performed. RESULTS: Full versions of the MHQ were completed by 116 participants on their initial visit, while only 77 participants completed a second MHQ. Cronbach alpha ranged from 0.84 to 0.95 for the MHQ subscales. Intraclass-correlation coefficients ranged from 0.71 to 0.84 for the subscales. The magnitude of the limits of agreement for the subscales ranged from 13.8 to 26.2. The difference in scores between the first and second tests was not related to the time between tests. CONCLUSION: The high values of Cronbach alpha indicate high internal validity, but that there may be redundancy between items in the MHQ, which could be eliminated without losing information. Reliability of the MHQ is considered moderate. The limits of agreement are considered wide, indicating potential issues with respect to interpretation of a change in score between 2 administrations of the MHQ.","corpus_id":206038293,"score":2},{"doc_id":"24563499","title":"What patients want from the treatment of Dupuytren's disease--is the Unité Rhumatologique des Affections de la Main (URAM) scale relevant?","abstract":"Patients awaiting surgery for Dupuytren's contractures listed the problems from their Dupuytren's disease that had led them to request surgery and their relative priorities of the results of surgery. The listed problems were compared with the nine items comprising the Unité Rhumatologique des Affections de la Main (URAM) Dupuytren's disease-specific outcome measure. One hundred and ten patients reported 278 problems. Ninety-four different combinations of problems were provided by patients, and over half (55%) of the problems were not captured by items in the URAM scale. The long-term outcome from surgery was relatively more important to patients than speed of recovery. The URAM tool may not be relevant to patients in the UK, and further assessment of its face validity is required before it is used.","corpus_id":43412090,"score":2},{"doc_id":"24565887","title":"URAM scale for functional assessment in Dupuytren's disease: a comparative study of its properties.","abstract":"OBJECTIVE: To test the convergent validity and ease of use of the Unité Rhumatologique des Affections de la Main (URAM) scale for patients with Dupuytren's disease. METHODS: Patients were prospectively included. We compared the convergent validity of the URAM scale, the Cochin Hand Function Scale (CHFS) and the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, in terms of their correlation with the Tubiana score and self-assessed disability on a visual analog scale (VAS). Pearson's correlation was used for the convergent validity study. The response time for questionnaire completion was the outcome for ease of implementation. RESULTS: We included 53 patients with Dupuytren's disease in the convergent validity study and 30 other patients with the disease in the time-response assessment. The URAM scale showed strong convergence with the Tubiana scale (r=0.64) and self-assessed disability on a VAS (r=0.69). Convergence with the Tubiana and self-assessed disability was higher for the URAM scale than the CHFS or DASH questionnaire. The mean [SD] response time was shorter for the URAM scale than the CHFS or DASH questionnaire (42 [20] vs 71 [35] and 103 [59] s, respectively, P<0.0001). CONCLUSIONS: The results reinforce the psychometric merits of the URAM scale. Furthermore, the response time for assessing disability was shorter with the URAM scale than the CHFS or DASH questionnaire. This evidence supports the high recommendation for the use of the URAM scale in clinical practice and clinical studies to assess disability in Dupuytren's disease.","corpus_id":21987375,"score":2},{"doc_id":"26307142","title":"Validity of the Disability of the Arm, Shoulder and Hand patient-reported outcome measure (DASH) and the Quickdash when used in Dupuytren's disease.","abstract":"This study investigated aspects of the validity and reliability of the 30-item Disability of the Arm, Shoulder and Hand patient-reported outcome measure (DASH) and its relationship with the shorter 11-item QuickDASH in patients with Dupuytren's disease. Seven hundred and fifty-nine DASH questionnaires were studied, covering pre- and postoperative patients undergoing different treatments for Dupuytren's disease. Items related to pain rose early after treatment before returning to baseline, suggesting that studying pain is relevant during postoperative recovery. Across all 759 sets of responses, the QuickDASH agreed closely with the DASH. In exploratory factor analysis, the DASH was not unidimensional, questioning the validity of the DASH summary score in Dupuytren's disease. Further validation of existing PROMs for use in Dupuytren's disease is needed. These data suggest that pain is a relevant symptom to study during postoperative recovery following treatment for Dupuytren's disease. LEVEL OF EVIDENCE: III.","corpus_id":34214889,"score":2},{"doc_id":"27469936","title":"Measurement Properties of the Brief Michigan Hand Outcomes Questionnaire in Patients With Dupuytren Contracture.","abstract":"PURPOSE: The brief Michigan Hand Outcomes Questionnaire (briefMHQ) was developed as a shorter version of the Michigan Hand Outcomes Questionnaire (MHQ), but its measurement properties have not been investigated in patients with Dupuytren contracture. The objective of the study was to investigate the reliability, validity, responsiveness, and interpretability of the briefMHQ. METHODS: Fifty-seven patients diagnosed with Dupuytren contracture completed the briefMHQ as well as the full-length MHQ and Quick Disabilities of the Arm, Shoulder, and Hand (QuickDASH) questionnaire at baseline. Two to 14 days after baseline and 1 year after collagenase injection or surgery, patients again filled out the briefMHQ. Reliability was determined using the intraclass correlation coefficient and by calculating internal consistency (Cronbach alpha). Validity was tested by quantifying correlations with the full-length MHQ and QuickDASH. Responsiveness, based on the standardized response mean and the minimally clinically important change, was also determined. RESULTS: The briefMHQ had an intraclass correlation coefficient of 0.87, Cronbach alpha of 0.88, and correlations of r = 0.88 and -0.82 with the original MHQ and QuickDASH, respectively. The standardized response mean was 0.9 and the minimally clinically important change was 7 points. CONCLUSIONS: Overall, the briefMHQ demonstrates excellent reliability, good validity, and high responsiveness in patients with Dupuytren contracture. CLINICAL RELEVANCE: The briefMHQ is an accurate and time-saving tool to evaluate patients with Dupuytren contracture and the effect of a corresponding treatment.","corpus_id":5715093,"score":2},{"doc_id":"27872343","title":"Recovery, responsiveness and interpretability of patient-reported outcome measures after surgery for Dupuytren's disease.","abstract":"This prospective cohort study investigated the responsiveness and interpretability of the Disabilities of the Arm, Shoulder and Hand (DASH) and Unité Rhumatologique des Affections de la Main (URAM) outcome measures for assessing recovery after fasciectomy and dermofasciectomy for Dupuytren's disease. DASH outcome scores at 1 year were significantly better than at 6 weeks, suggesting that recovery is not complete by 6 weeks. Of the 101 patients recruited to the DASH cohort, 71 completed preoperative, 6 week and 1 year postoperative DASH scores; 68 of them completed preoperative and 1 year postoperative DASH scores and an external anchor question. In the URAM cohort, 30/44 completed the preoperative and the 1 year postoperative URAM scores and the anchor question. The DASH score exhibited moderate responsiveness but poor interpretability on receiver operating characteristic curve analysis, such that a minimal important change could not be estimated. The URAM score showed acceptable responsiveness, and an MIC of 10.5 on receiver operating characteristic analysis. LEVEL OF EVIDENCE: II.","corpus_id":28205488,"score":2},{"doc_id":"28841615","title":"Normative Values of the Michigan Hand Outcomes Questionnaire for Patients with and without Hand Conditions.","abstract":"BACKGROUND: The Michigan Hand Outcomes Questionnaire has been widely used for nearly 20 years to assess patients with a variety of hand and upper extremity conditions. However, normative data have not previously been collected, limiting interpretation. METHODS: The Michigan Hand Outcomes Questionnaire was administered to 579 participants recruited from the general population. In addition, participants were asked to identify any problem affecting their hand(s), including trauma, hand disease/condition, systemic illness, or nonspecific symptoms. Comorbidities and demographic data were also collected. RESULTS: Total Michigan Hand Outcomes Questionnaire score for healthy individuals was indicative of generally good hand function (95.2; 95 percent CI, 94.3 to 96.1). Individuals with unilateral trauma scored for their affected hand (90.3; 95 percent CI, 87.9 to 92.6) lower than their healthy hand (mean difference, 5.7; 95 percent CI, 3.2 to 8.3). For individuals with and without hand trauma, total Michigan Hand Outcomes Questionnaire score decreased with increasing number of comorbidities. Many of the differences in Michigan Hand Outcomes Questionnaire score between the problem hand and unaffected hand were smaller than the minimal clinically important difference of 3.0 to 23.0 for known abnormalities of the hand and upper extremity. CONCLUSIONS: These normative data provide appropriate baseline information for individuals with and without underlying hand conditions. Most notably, these findings suggest that individuals with a unilateral problem establish new subnormative values for both their affected and unaffected hands. These data will encourage an appropriate understanding of the results of future studies using the Michigan Hand Outcomes Questionnaire.","corpus_id":205962193,"score":2},{"doc_id":"18503809","title":"Responsiveness of the Michigan Hand Outcomes Questionnaire--Dutch language version in patients with rheumatoid arthritis.","abstract":"OBJECTIVE: To investigate the responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with rheumatoid arthritis (RA) who were treated in a multidisciplinary hand clinic. DESIGN: Observational study comparing the responsiveness of the MHQ with that of various other outcome measures for hand function. SETTING: Multidisciplinary hand clinic within a tertiary referral center for rheumatologic care. PARTICIPANTS: Twenty-eight patients with problems in hand function due to RA were assessed before and 3 months after conservative and/or surgical treatment. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Assessments included, apart from a previously validated Dutch language version of the MHQ, a visual analog scale for pain, grip strength, the Sequential Occupational Dexterity Assessment, the Arthritis Impact Measurement Scales (AIMS) hand and finger function scale, and each patient's rating of subjective change in hand function. Measurements of responsiveness included the standardized response mean (SRM), effect size, and responsiveness ratio. In addition, the Spearman rank correlations (rho) between the change scores of the MHQ and those of other measures of hand function were calculated. RESULTS: The mean MHQ total score improved significantly between baseline (mean +/- standard deviation, 48.3+/-12.2) and follow-up (mean, 54.7+/-16.9) (change score, -7.2; 95% confidence interval, -11.1 to -3.3). The SRM, effect size, and responsiveness ratio of the MHQ total score were -0.72, -0.52, and -1.99, respectively. Significant associations were found between the changes of the MHQ total score and each patient's rating of subjective change in hand function (rho=.64, P=.001) and the change score of the AIMS hand function scale (rho=-.24, P=.260). CONCLUSIONS: The MHQ proved to be a responsive measure of hand function in patients with RA who were treated in connection with a multidisciplinary hand clinic.","corpus_id":22699150,"score":1},{"doc_id":"18669144","title":"Dupuytren's palmar contracture in women.","abstract":"BACKGROUND: Dupuytren's disease is a fibroproliferative disorder of the palmar fascia that can cause disabling digital contractures. The pathogensis of the disease is still unclear, and it afflicts predominantly white males of northern European origin. Gender-related differences of Dupuytren's disease and the distinctive characteristics of the disease in females are not yet well defined. OBJECTIVES: To evaluate and illustrate the distinctive characteristics of Dupuytren's disease in females. METHODS: A retrospective study was performed of all female patients with Dupuytren's disease seen and followed at our Hand Surgery Unit over a 20 year period. The study group consisted of 48 women (56 hands). The collected data included clinical and epidemiological features on admission, and outcome of surgical intervention. RESULTS: Of the 48 women (56 hands) with Dupuytren's disease, 23 (26 hands) underwent limited fasciectomy. The average age at presentation was 60.1 years. A few of the patients originated from Asia and Africa. Manifestations and pattern of the disease were nearly comparable to those observed in the male group, except for a slightly higher incidence of proximal interphalangeal joint contracture in female patients. Generally, females expressed less severe contractures on presentation and a slower progression thereafter. A favorable functional postoperative outcome was observed. Seven patients had minor complications including local hematoma and painful scars. Two patients developed moderate signs of complex regional pain syndrome. CONCLUSIONS: Further investigations are needed to assess the potential role of androgens in the pathogenesis of Dupuytren's disease, and a possible protective role of estrogenic hormones, rendering Dupuytren's contracture a postmenopausal affliction.","corpus_id":46604907,"score":1},{"doc_id":"19181227","title":"Comparative responsiveness of the Michigan Hand Outcomes Questionnaire and the Carpal Tunnel Questionnaire after carpal tunnel release.","abstract":"PURPOSE: The literature supports self-administered questionnaire assessment tools for the measurement of outcome after surgical treatment of carpal tunnel syndrome (CTS). Traditional physical measures are less sensitive to clinical changes following carpal tunnel release (CTR) than fully validated designed outcome questionnaires. A number of validated outcome instruments have been compared to determine which is optimal with regard to sensitivity and responsiveness following surgery. To our knowledge, the Michigan Hand Outcomes Questionnaire (MHQ) and the Carpal Tunnel Questionnaire (CTQ) have not been compared in regard to their responsiveness and sensitivity to change following CTR. The aim of this prospective study was to compare the responsiveness of these 2 instruments when evaluating outcomes after CTR. METHODS: Seventy-eight patients diagnosed with CTS and scheduled for unilateral open CTR were recruited and informed consent was obtained after ethics approval. Inclusion criteria were primary procedure, history, clinical signs, and conduction studies consistent with CTS. The MHQ and CTQ were both completed by each patient preoperatively and 6 months postoperatively. RESULTS: Results for all domains of the MHQ and all domains of the CTQ showed significant postoperative improvement. The overall responsiveness of both MHQ and CTQ were large (standardized response mean >or=0.8), however the CTQ demonstrated increased sensitivity to change after CTR compared to the MHQ. Although the standardized response mean (SRM) of the MHQ was 0.8, the SRM of the CTQ was 1.22. Both domains of the CTQ had an SRM well above 0.8, whereas half of the MHQ domains had an SRM below 0.8. CONCLUSIONS: The CTQ has demonstrated a greater responsiveness to clinical change following CTR than the MHQ. Therefore, the CTQ is a more sensitive instrument and researchers in the field of CTS should bear these findings in mind when choosing an outcome instrument for future studies. TYPE OF STUDY/LEVEL OF EVIDENCE: Diagnostic I.","corpus_id":34764932,"score":1},{"doc_id":"19258150","title":"The minimal clinically important difference of the Michigan hand outcomes questionnaire.","abstract":"PURPOSE: To determine the change in score required in various domains of the Michigan Hand Outcomes Questionnaire (MHQ) to indicate meaningful patient improvement, or the minimal clinically important difference (MCID), for 3 common hand conditions: rheumatoid arthritis (RA), carpal tunnel syndrome (CTS) and distal radius fracture (DRF). METHODS: The MHQ was administered to patients at 2 time points. Patient satisfaction was defined as a satisfaction score > or =80% of the standard deviation of that patient sample. The minimal change in score in specific MHQ domains that corresponded with patient satisfaction was determined using receiver operating characteristic curves. RESULTS: For CTS patients, MCIDs of 23, 13, and 8 were identified for the pain, function, and work domains, respectively. For RA patients, pain and function were also identified as having discriminative ability, with MCIDs of 11 and 13, respectively. An MCID of 3 was identified for the activities of daily living domain. For DRF patients, no MHQ domains showed discriminative ability because of the ceiling effect at the 3-month assessment period. CONCLUSIONS: Individual domains of the MHQ can be used to discriminate between patients who are satisfied and those who are not after either carpal tunnel release or silicone arthroplasty of the metacarpophalangeal joints for RA. Pain and function are the domains of the MHQ that are best able to discriminate between patients who are satisfied and those who are not. The identical function MCID for both RA patients and CTS patients, despite markedly different preoperative values, indicates that a standard amount of functional change may indicate patient satisfaction. High postoperative satisfaction, even only 3 months after surgery, prevented any domains from showing discriminative ability for the DRF patients.","corpus_id":24402380,"score":1},{"doc_id":"19259747","title":"Which outcome measure is the best? Evaluating responsiveness of the Disabilities of the Arm, Shoulder, and Hand Questionnaire, the Michigan Hand Questionnaire and the Patient-Specific Functional Scale following hand and wrist surgery.","abstract":"The purpose of this study was to determine and compare the responsiveness of the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, the Michigan Hand Questionnaire (MHQ), and the Patient-Specific Functional Scale (PSFS) in patients with carpal tunnel syndrome, wrist pain, finger contracture, or tumor. Eighty-one subjects prospectively completed each questionnaire shortly before and 3 and 6 months after surgery. Data were analyzed using one-way analysis of variance and Newman-Keuls multiple comparison tests. Responsiveness to clinical change was calculated using standardized response means. The DASH was responsive for those with carpal tunnel syndrome (0.77), wrist pain (0.61), and tumor (0.55); the MHQ was responsive for those with carpal tunnel syndrome (1.04), wrist pain (0.87), and finger contracture (0.62); and the PSFS was responsive for those with carpal tunnel syndrome (0.65) and finger contracture (0.64). The interval during which the highest responsiveness occurred for the carpal tunnel, wrist pain, and finger contracture groups was the preoperative to 6-month period. The tumor group experienced the highest responsiveness during the preoperative to 3-month period. Our results indicate that one or more of the instruments evaluated are suitable for outcomes research related to surgery to treat carpal tunnel syndrome, wrist pain, finger contracture, and tumor.","corpus_id":3146177,"score":1},{"doc_id":"19999612","title":"[Use of questionnaires in outcome measurement in hand surgery].","abstract":"Zastosowanie kwestionariuszy w ocenie wyników leczenia w chirurgii reki. An assessment of outcomes of the treatment of the diseases and injuries to the hand should include both objective parameters, i.e. range of motion or grip strength, and subjective parameters i.e. intensity of complaints or dexterity of the hand in various tasks of daily activity. Questionnaires were developed to evaluate subjective parameters in objective and systematic manner. They indeed allow us to better apprehend what is important from our patients' perspective. Questionnaire (called also form or test) is a list of queries concerning the issue being a subject of the assessment. The queries are designed in the way allowing answers to imply an important and possible objective information on the problem of interest. The objective of this article was to attract notice on the problems associated with the use of questionnaires in a research, with particular attention on hand surgery. Authors referred to the parameters which characterise these instruments: responsiveness, validity and reliability. Brief descriptions of most commonly used forms were provided, including DASH, Levine, PEM, Michigan and CISS. Shortcomings and pitfalls associated with the use of questionnaires and possible sources of bias were emphasised, e.g. difficulties in precise assignation of scores, answering some particular questions and accuracy of the completion of the form. Attention was paid on the choice of the questionnaire to be well-matched for an aim of a given research project both in substantial and formal manner. An opinion was supported that modem research projects measuring outcomes in hand surgery must include questionnaires as an obligatory component of a complex assessment.","corpus_id":25296582,"score":1},{"doc_id":"20138712","title":"Responsiveness of the Michigan Hand Outcomes Questionnaire and the Disabilities of the Arm, Shoulder, and Hand questionnaire in patients with hand injury.","abstract":"PURPOSE: To compare responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) with that of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire in patients with hand injuries. We postulated that the MHQ may be more sensitive to functional changes in the hands, whereas the DASH questionnaire would have a closer association with days of disability. METHODS: Patients with hand injuries were consecutively recruited from 2 community hospitals. Each patient was asked to complete out the MHQ, the DASH questionnaire, the satisfaction with their health-related quality of life (Sat-HRQOL) measure, and Chinese Health Questionnaire (CHQ), which is a measure of psychological stressors. Disability days were defined as the duration of restricted activities of daily living during the previous 4 weeks. Patients repeated the same questionnaires between 2 and 9 months after enrollment (average: 4 mo). RESULTS: A total of 105 patients with hand injuries were recruited, and 50 of the 105 patients returned for the second evaluation. There were no statistical differences between responders and nonresponders for age, gender, disability days, the MHQ, the DASH questionnaire, the CHQ, or the Sat-HRQOL. Responsiveness was evaluated by effect sizes and standardized response means: Those for the MHQ were 0.84 and 1.05, and those for the DASH were 0.67 and 0.86, respectively. A mixed model analysis for repeated measurements of the 50 participants showed a significant influence of psychological factors (CHQ) for both the Sat-HRQOL and disability days. After adjustment for the effects of age, gender, and the CHQ, there was an increment of one Sat-HRQOL unit for an MHQ score increment of 3.2, whereas the score decrement for the DASH questionnaire was 3.3 units. CONCLUSIONS: The MHQ might be slightly more sensitive to functional changes, but the DASH questionnaire seemed more correlated with disability days. Psychological factors are the strongest determinants of the HRQOL and disability.","corpus_id":42776421,"score":1},{"doc_id":"22094744","title":"Dupuytren's disease in the Hispanic population: a 10-year retrospective review.","abstract":"BACKGROUND: Dupuytren's disease is a common benign fibroproliferative disorder of the hand. Epidemiologic studies have reported significant variation in disease prevalence among races, focusing primarily on those of northern European descent. In contrast, Dupuytren's disease in the Hispanic population has received little attention. Thus, in this study, the authors aimed to determine the prevalence and operative rate of Dupuytren's disease in the Hispanic, black, white, Asian, Native American, and other races and to characterize the disease presentation in Hispanics who required surgical treatment. METHODS: A retrospective review was conducted to identify the racial distribution of Dupuytren's disease patients seen at Bellevue Hospital between July of 2000 and August of 2010. In Hispanic patients requiring surgical treatment for their disease, data were collected on the following parameters: age, sex, ethnicity, hand dominance, hand affected, and digits operated on. Epidemiologic factors including smoking, alcoholism, diabetes mellitus, hypercholesterolemia, epilepsy, and hypertension were also evaluated. RESULTS: Dupuytren's disease prevalence was found to be 533 per 100,000 in Hispanics. Of these patients, 1.8 percent required surgical treatment, and this group was characterized by the following comorbidities: smoking (57.1 percent), hypertension (57.1 percent), alcoholism (52.4 percent), diabetes mellitus (47.6 percent), and hypercholesterolemia (19.0 percent). CONCLUSIONS: The authors' results indicate that Dupuytren's disease is more prevalent in the Hispanic population than previously reported. Although the epidemiologic factors identified in Hispanics with Dupuytren's disease are similar to those in other races investigated, there are important differences with respect to clinical presentation and surgical treatment.","corpus_id":36941149,"score":1},{"doc_id":"22333510","title":"The patient-specific functional scale: validity, reliability, and responsiveness in patients with upper extremity musculoskeletal problems.","abstract":"STUDY DESIGN: Clinical measurement, longitudinal; multicenter prospective cohort study. OBJECTIVES: To examine the validity, reliability, and responsiveness of the Patient-Specific Functional Scale (PSFS) in patients with musculoskeletal upper extremity problems being treated in physical therapy. BACKGROUND: The clinimetric properties of the PSFS have not been established nor compared with region-specific outcome measures in patients with upper extremity problems. METHODS: Patients completed the PSFS, Upper Extremity Functional Index (UEFI), and numeric pain rating scale (NPRS) at baseline and follow-up, and were categorized as improved, stable, or worsened, using the global rating of change. Construct validity was assessed by comparing the change scores of the stable and improved groups, using independent-samples t tests. Reliability was evaluated using intraclass correlation coefficient (ICC2,1) with 95% confidence intervals. Bland-Altman plots determined limits of agreement. Responsiveness and minimal important difference (MID) were determined with receiver operator characteristic (ROC) curves. RESULTS: One hundred eighty patients met the inclusion criteria. Construct validity was supported for the PSFS and the UEFI (P<.001). Reliability was moderate to good for the PSFS (ICC2,1 = 0.713) and UEFI (ICC2,1 = 0.848). Reported estimates of reliability may be lower than true values because the group of \"stable\" patients from this cohort had, on average, a small positive change. Bland-Altman plots indicated good agreement. The area under the ROC curve (AUC) was significantly different from the null value of 0.5 for the PSFS (0.887) and the UEFI (0.877), indicating good accuracy in distinguishing improved patients from stable patients. MID was 1.2 for the PSFS (scale, 0-10) and 8.5 for the UEFI (scale, 0-80). CONCLUSION: The PSFS is a valid, reliable, and responsive outcome measure for patients with upper extremity problems.","corpus_id":35426489,"score":1},{"doc_id":"22872850","title":"The Surgical Release of Dupuytren's Contracture Using Multiple Transverse Incisions.","abstract":"Dupuytren's contracture is a condition commonly encountered by hand surgeons, although it is rare in the Asian population. Various surgical procedures for Dupuytren's contracture have been reported, and the outcomes vary according to the treatment modalities. We report the treatment results of segmental fasciectomies with multiple transverse incisions for patients with Dupuytren's contracture. The cases of seven patients who underwent multiple segmental fasciectomies with multiple transverse incisions for Dupuytren's contracture from 2006 to 2011 were reviewed retrospectively. Multiple transverse incisions to the severe contracture sites were performed initially, and additional incisions to the metacarpophalangeal (MCP) joints, and the proximal interphalangeal (PIP) joints were performed if necessary. Segmental fasciectomies by removing the fibromatous nodules or cords between the incision lines were performed and the wound margins were approximated. The mean range of motion of the involved MCP joints and PIP joints was fully recovered. During the follow-up periods, there was no evidence of recurrence or progression of disease. Multiple transverse incisions for Dupuytren's contracture are technically challenging, and require a high skill level of hand surgeons. However, we achieved excellent correction of contractures with no associated complications. Therefore, segmental fasciectomies with multiple transverse incisions can be a good treatment option for Dupuytren's contracture.","corpus_id":2709612,"score":1},{"doc_id":"23982906","title":"Measurement properties of the German Michigan Hand Outcomes Questionnaire in patients with trapeziometacarpal osteoarthritis.","abstract":"OBJECTIVE: To investigate the reliability, validity, and responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with trapeziometacarpal (TMC) joint osteoarthritis (OA). METHODS: In this prospective observational study, patients diagnosed with TMC joint OA who received either conservative or surgical treatment were included. At baseline and at 1 year following the beginning of treatment, we measured key pinch strength and the patients filled out the MHQ, the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, and the Short Form 12 health survey. Patients also completed these questionnaires 2-11 days after the last study visit. In order to analyze the measurement properties of the MHQ, we calculated test-retest reliability (intraclass correlation coefficient [ICC]), internal consistency (Cronbach's alpha for the 6 subscales), construct validity (Pearson's correlation coefficient [r]), responsiveness (effect sizes), and the minimum important change (MIC). RESULTS: We included 177 patients, of whom 109 were scheduled for surgery. The mean ± SD MHQ total score for surgical patients increased from 48 ± 14 at baseline to 75 ± 18 at 1 year (P ≤ 0.001). In contrast, no treatment effect was observed in the conservative group (P = 0.74). The MHQ total score showed excellent test-retest reliability (ICC 0.95) and correlated strongly with the DASH (r = -0.77). Internal consistency of the MHQ subscales ranged between 0.77 and 0.89. A large effect size of 1.7 was found for the surgical patients, with an MIC of 17 points. CONCLUSION: The MHQ demonstrated good reliability, validity, and responsiveness in patients with TMC joint OA and can be recommended as a suitable assessment instrument in this population.","corpus_id":8788770,"score":1},{"doc_id":"24129389","title":"Epidemiological study for personal risk factors and quality of life related to Dupuytren's disease in a mountain village of Japan.","abstract":"BACKGROUND: This study investigated the etiology, personal risk factors, and quality of life related to Dupuytren's disease among residents of a mountain village in Japan. METHODS: Medical examinations were conducted of 401 adult residents (163 men, 238 women; average age of 66.7 years, range 40-92) of a mountain village in Japan. All had completed a self-administered questionnaire including items for gender, weight, height, dominant hand, occupation, history of diabetes mellitus, and frequency of smoking tobacco and drinking alcohol, in addition to EuroQol-5-Dimensions-3-level Japanese version. Blood samples were collected and assessed for biochemical markers related to Dupuytren's disease. The Dupuytren's disease diagnosis was based on clinical signs. Meyerding's classification was used to ascertain the disease severity. After examining background data and physical examination data related to Dupuytren's disease, we evaluated the association of Dupuytren's disease with those factors using univariate and logistic regression analysis. RESULTS: Dupuytren's disease was diagnosed in 28 subjects (7.0%). Univariate analysis revealed associations of age, male gender, occupation, history of diabetes mellitus, and alcohol intake with Dupuytren's disease. Logistic regression analysis after adjustment for age revealed a significant association between Dupuytren's disease and male gender, occupation, and history of alcohol intake. No significant difference was found between Dupuytren's disease patients and participants without this disease in the scoring and visual analog scale of EuroQol. No relation was found in scoring, the visual analog scale of EuroQol, or grading of Meyerding's classification in participants with Dupuytren's disease. CONCLUSION: This cross-sectional study revealed Dupuytren's disease in 7.0% of 401 subjects among the general population of a mountain village in Japan. The prevalence is higher with age and is apparently associated with male gender, occupation and alcohol intake. Risk factors associated with Dupuytren's disease were identified as age, male gender, occupation, and alcohol consumption habits.","corpus_id":4820236,"score":1},{"doc_id":"24470559","title":"Collagenase clostridium histolyticum in patients with Dupuytren's contracture: results from POINT X, an open-label study of clinical and patient-reported outcomes.","abstract":"In POINT X, a study designed to reflect clinical practice and patient treatment choices, 254 European patients received open-label collagenase for Dupuytren's contracture. The most severely affected joint was treated first in 74% of patients. In total, 52%, 41%, 7%, and 1% of patients selected the little, ring, middle, and index finger, respectively; 79% had one or two joints treated. Only 9% of patients (n = 24) received 4 or 5 injections. The mean improvement in total passive extension deficit (TPED) was 34° on day 1, improving further by day 7 to 42°. This secondary improvement was maintained by day 90 and month 6. The mean number of injections/joint was 1.2 for the metacarpophalangeal joint and 1.25 for the proximal interphalangeal joint. Median time to recovery was 4 days; the mean improvement in hand function was clinically relevant as measured by the Unité Rhumatologique des Affections de la Main (URAM) score. In total, 87% and 86% of patients and physicians, respectively, were very satisfied or satisfied with treatment at month 6, although correlation between TPED and patient satisfaction was weak (Spearman -0.18, 95% CI -0.32 to -0.06). Collagenase was well tolerated, with 10 (3.9%) patients experiencing severe adverse events. As a real-world study, the POINT X findings can be generalized to the at-large population.","corpus_id":10785955,"score":1},{"doc_id":"24477316","title":"Association among work exposure, alcohol intake, smoking and Dupuytren's disease in a large cohort study (GAZEL).","abstract":"OBJECTIVES: In view of the debate of factors in Dupuytren's disease, we aimed to describe its relationship with certain occupational factors, alcohol intake and smoking. SETTING: The French GAZEL cohort (employees of Electricité de France and Gaz de France). PARTICIPANTS: Participants of the cohort who answered a questionnaire in 2012, that is, 13 587 participants (73.7% of the questionnaire sent). In 2007, self-assessed lifetime occupational biomechanical exposure was recorded (carrying loads, manipulating a vibrating tool and climbing stairs), as well as alcohol intake, smoking and diabetes mellitus. Analyses were performed on high alcohol intake, smoking and duration of relevant work exposure, stratified by gender. PRIMARY AND SECONDARY OUTCOME MEASURES: From a specific question on Dupuytren's disease assessed in 2012, the outcome measures were self-reported Dupuytren's disease (yes/no) and disabling Dupuytren's disease (including surgery). RESULTS: A total of 10 017 men and 3570 women, aged 64-73 years, were included; the mean age for men was 68 years and for women was 65 years. Among men, the following were significantly associated with Dupuytren's disease: age (OR 1.03 (1.00; 1.06)), diabetes (OR 1.31 (1.07; 1.60)), heavy drinking (OR 1.36 (1.10; 1.69)) and over 15 years of manipulating a vibrating tool at work (OR 1.52 (1.15; 2.02)); except for diabetes, the association with these factors was stronger for disabling Dupuytren's disease (or surgery), with OR 1.07 (1.03; 1.11), 1.71 (1.25; 2.33) and 1.98(1.34; 2.91), respectively, for age, heavy drinking and over 15 years of manipulating a vibrating tool at work. Among the 3570 women included, 160 reported Dupuytren's disease (4.5%). The number of cases in the group of women was too low to reach conclusions, although the findings seemed similar for age, diabetes and vibration exposure. CONCLUSIONS: In this large French cohort study, Dupuytren's disease in men was associated with high levels of alcohol consumption and exposure to hand-transmitted vibration. It is likely that the same applied to women.","corpus_id":2350971,"score":1},{"doc_id":"24569424","title":"Health-related quality of life in patients undergoing palmar fasciectomy for Dupuytren's disease.","abstract":"BACKGROUND: The present study was undertaken to assess the health-related quality of life in patients with Dupuytren's disease who undergo palmar fasciectomy. METHODS: A prospective cohort of patients with Dupuytren's disease undergoing palmar and/or digital fasciectomy was recruited from the practice of three plastic surgeons in Hamilton, Ontario, Canada. After written informed consent was obtained, participants were asked to complete three health-related quality-of-life questionnaires (i.e., Short Form-36, Michigan Hand Outcomes Questionnaire, and Health Utility Index Mark 3) at five time points: at 1 week and 1 day preoperatively, and at 1, 3, 6, and 12 months postoperatively. Ranges of motion and grip strength measurement were also recorded. RESULTS: For the 26 patients in the study, the multiattribute scores of the Health Utility Index Mark 3 improved from 0.80 before surgery to 0.83 at 12 months postoperatively (p > 0.05). There was no difference in the Short Form-36 scores, but the Michigan Hand Outcomes Questionnaire scores improved from 74 at 1 week preoperatively to 90 at the 12-month postoperative visit (p < 0.001). CONCLUSIONS: Patients who undergo palmar fasciectomy for Dupuytren's disease experience a substantial improvement in their health-related quality of life 12 months after surgery. In the authors' study population, a benefit of 0.85 quality-adjusted life-year within 12 months was observed. This can be translated as follows: the average patient who undergoes palmar fasciectomy gains the equivalent of approximately 14.4 days (0.48 months) in perfect health by undergoing palmar fasciectomy. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.","corpus_id":22980363,"score":1},{"doc_id":"24572853","title":"Determining the Michigan Hand Outcomes Questionnaire minimal clinically important difference by means of three methods.","abstract":"BACKGROUND: To interpret patient-rated outcome measures, clinicians rely on the minimal clinically important difference. The authors studied the range of minimal clinically important difference scores for the overall Michigan Hand Outcomes Questionnaire score its and subscales in a population with various diagnoses and treatments. METHODS: Patients with a single, unilateral, atraumatic hand/forearm diagnosis completed the Michigan Hand Outcomes Questionnaire before treatment and at 4 ± 1 weeks and 12 ± 2 weeks after treatment. Three methods were used to calculate the minimal clinically important difference: two anchor question methods based on satisfaction (mean change and receiver operating characteristic) and a statistical distribution method. RESULTS: One hundred eighty-six patients were enrolled, with a baseline median overall questionnaire score of 60.7. Using the mean change method, a minimal clinically important difference of 13 was calculated for the overall questionnaire score. Using a receiver operating characteristic curve (0.8 effect size), the minimal clinically important difference was 9, with an area under the curve of 0.92. When receiver operating characteristic analysis was based on dichotomization of reported satisfaction, the minimal clinically important difference was 12, with an area under the curve of 0.85. Calculating the difference by statistical distribution gave a value of 8. For the subscales, by all methods, triangulated minimal clinically important difference estimates ranged from 10.9 to 14.4. CONCLUSIONS: The minimal clinically important difference for the overall Michigan Hand Outcomes Questionnaire score in atraumatic hand/forearm conditions falls between 8 and 13. Multiple analytic methods produce nonidentical but similar minimal clinically important differences. The authors recommend using difference estimates in these ranges when planning a clinical trial to investigate hand/forearm function across a range of diagnoses and treatments.","corpus_id":205955797,"score":1},{"doc_id":"24605402","title":"[Dupuytren's disease].","abstract":"Dupuytren's disease is a fibromatosis affecting the hand. The disease affects the hand and fingers and may present with a contracture causing increasing disability of the hand. We can treat the symptoms but not its cause. In this article we review the background, diagnosis and methods of treatment of the disease. Although the mainstay of treatment accepted by most is surgical, use of collagenase injections aimed at chemically disintegrating pathologic cords may emerge as an important addition to the armamentarium of treatments for Dupuytren's disease.","corpus_id":22187309,"score":1},{"doc_id":"24839417","title":"Psychometric properties of health-related quality of life instruments in patients undergoing palmar fasciectomy for dupuytren's disease: a prospective study.","abstract":"BACKGROUND: The traditional outcome measured following treatment of Dupuytren's Disease (DD) has been digital range of motion; specifically the gain in digital extension. The outcomes research movement in the last three decades however has been advocating the measurement of outcomes from the patient's perspective using Health-Related Quality of Life questionnaires (HRQOL). Although several generic and region-specific HRQOL questionnaires exist, there is no guidance as to which one is the most appropriate for this population. The objective of this study is to evaluate the psychometric properties of three self-reported HRQOL outcome measures in patients with DD. METHODS: Patients with DD were enrolled from the practices of three plastic surgeons. Test-retest reliability, concurrent validity and responsiveness of three HRQOL questionnaires were compared in a prospective study design. The HRQOL measures included Health Utilities Index Mark 3 (HUI3), Short Form-36 (SF-36), and the Michigan Hand Questionnaire (MHQ). RESULTS: All three measures demonstrated good test-retest reliability (ICC = 0.77-0.85). Concurrent validity was found between the HUI3 pain and dexterity attributes and SF-36 physical summary score. The sensitivity of the MHQ to detect changes in the status of the patient was found to be high (effect size = 1.14) whereas that of the SF-36 was trivial. CONCLUSIONS: The HUI3 and the MHQ seem to be reliable and valid tools to assess the HRQOL in patients with Dupuytren's Disease.","corpus_id":207294246,"score":1},{"doc_id":"24900903","title":"Responsiveness of the Korean version of the Michigan Hand Outcomes Questionnaire after carpal tunnel release.","abstract":"BACKGROUND: The Korean version of the Michigan Hand Outcomes Questionnaire (K-MHQ) was recently validated; however, the questionnaire's responsiveness as well as the degree to which the instrument is sensitive to change has not been thoroughly evaluated in a specific condition in Koreans. We evaluated the responsiveness of the K-MHQ in a homogenous cohort of patients with carpal tunnel syndrome (CTS) and we compared it with that of the Korean version of the Disability of the Arm, Shoulder, and Hand Questionnaire (K-DASH), which was found to have a large degree of responsiveness after carpal tunnel release for Korean patients with CTS. METHODS: Thirty-seven patients with CTS prospectively completed the K-MHQ and the K-DASH before and 6 months after surgery. The responsiveness statistics were assessed for both the K-MHQ and the K-DASH by using the standardized response mean (SRM), which was defined as the mean change of the original scores after surgery divided by the standard deviation of the change. RESULTS: All domains of the K-MHQ significantly improved after carpal tunnel release (p < 0.001). The SRM for all scales but one (the aesthetics scale) showed large responsiveness of ≥ 0.8. The aesthetics scale showed medium responsiveness of 0.6. The combined function/symptom scale of the K-DASH significantly improved after surgery (p < 0.001). The SRM of the K-DASH revealed large responsiveness of 0.9. CONCLUSIONS: The K-MHQ was found to have a large degree of responsiveness after carpal tunnel release for Korean patients with CTS, which is comparable not only to the K-DASH, but also to the original version of the MHQ. The region-specific K-MHQ can be useful for outcomes research related to carpal tunnel surgery, especially for research comparing CTS with various other hand and wrist health conditions.","corpus_id":10170030,"score":1},{"doc_id":"25358527","title":"Psychometric evaluation of the Disabilities of the Arm, Shoulder and Hand (DASH) with Dupuytren's contracture: validity evidence using Rasch modeling.","abstract":"BACKGROUND: Dupuytren's contracture is a progressive, fibroproliferative disorder that causes fixed finger contractures and can lead to disability. With the advances of new therapeutic interventions, the necessity to assess the functional repercussions of this condition using valid, reliable and sensitive outcome measures is of growing interest. The Disabilities of the Arm, Shoulder and Hand (DASH) is one frequently used patient-reported outcome measure but its reliability and validity have never been demonstrated specifically for a population affected with Dupuytren's contracture. The objective of this study was to evaluate the psychometric properties of the DASH, with focus on validity evidence using the Rasch measurement model. METHODS: Secondary analysis was performed on data collected as part of a randomised clinical trial. One hundred fifty-three participants diagnosed with Dupuytren's contracture completed the DASH at four time points (pre-op, 3, 6 and 12 months post-op). Baseline data were analysed using traditional analysis and to test whether they adhered to the expectations of the Rasch model. Post-intervention data were subsequently included and analyzed to determine the effect of the intervention on the items. RESULTS: DASH scores demonstrated large ceiling effects at all time points. Initial fit to the Rasch model revealed that the DASH did not adhere to the expectations of the Rasch partial credit model (χ2=119.92; p<0.05). Multiple items displayed inadequate response categories and two items displayed differential item functioning by gender. Items were transformed and one item deleted leading to an adequate fit. Remaining items fit the Rasch model but still do not target well the population under study. CONCLUSIONS: The original version of the 30-item DASH did not display adequate validity evidence for use in a population with Dupuytren's contracture. Further development is required to improve the DASH for this population.","corpus_id":8398666,"score":1},{"doc_id":"26456499","title":"Validity of the Michigan Hand Outcomes Questionnaire in Patients With Stroke.","abstract":"OBJECTIVE: To investigate the measurement properties of the Dutch version of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with stroke. DESIGN: Validation study. SETTING: Outpatient rehabilitation clinic. PARTICIPANTS: Consecutive patients with stroke (N=51; mean age, 60±11y; 16 women [31%]). INTERVENTIONS: Patients were asked to complete the MHQ (57 items) and Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36). Additional assessments included the Barthel Index and performance tests for hand function (Action Research Arm Test, Nine Hole Peg Test, Frenchay Arm Test, Motricity Index). MAIN OUTCOME MEASURES: Associations between the MHQ and other outcome measures were determined using Spearman correlation coefficients and the internal consistency of the MHQ using Cronbach α. Floor or ceiling effects were present if >15% of the patients scored minimal or maximal scores, respectively. Test-retest reliability was established by the intraclass correlation coefficient. RESULTS: The mean MHQ total score was 70.0±22.4, with Cronbach α being .97. The MHQ total score correlated significantly with the physical component summary of the SF-36, the Barthel Index, and all hand function performance tests (P<.01). The MHQ total score showed no floor or ceiling effects. The test-retest intraclass correlation coefficient was .97. CONCLUSIONS: This study provides preliminary evidence that the MHQ is an internally consistent, valid, and reliable hand function questionnaire in outpatients after stroke, although these results need to be further confirmed.","corpus_id":1217569,"score":1},{"doc_id":"27454507","title":"Reliability and Validity of the Japanese Version of the Michigan Hand Outcomes Questionnaire: A Comparison with the DASH and SF-36 Questionnaires.","abstract":"BACKGROUND: The Michigan Hand Outcomes Questionnaire (MHQ) has shown reliability, validity and responsiveness and has been used to assess surgical outcomes mainly in North America. We established a Japanese version of the MHQ and evaluated its reliability and validity compared with both the short-form 36 (SF-36) questionnaire and the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire in a Japanese-speaking population. METHODS: The MHQ was cross-culturally adapted to a Japanese version according to guidelines. Sixty-eight patients with hand conditions were enrolled in this study and answered the MHQ, DASH questionnaire and SF-36 questionnaire. The MHQ was completed again with an interval of one or two weeks. Reproducibility and internal consistency were statistically assessed by the test-retest method and calculating Cronbach's alpha. Spearman's rank correlation was calculated to assess associations between the MHQ and the SF-36 questionnaire as well as the DASH questionnaire. RESULTS: The intraclass correlation coefficients of MHQ subscales ranged from 0.68 to 0.93. Aesthetics subscale of the left hand showed the lowest intraclass correlation but still a good correlation. Cronbach's alpha values of the MHQ ranged from 0.81 to 0.96 for all subscales. The absolute values of Spearman's rank correlation coefficient between MHQ subscales and DASH function/symptoms scores ranged from 0.49 to 0.82. Spearman's correlation coefficients of the MHQ total score to subscales of the SF-36 questionnaire ranged from 0.42 to 0.68. The strongest correlations were found between work performance of the MHQ and rolephysical of the SF-36 questionnaire. CONCLUSIONS: The Japanese version of the MHQ has adequate instrument properties for assessing hand outcomes compared with the SF-36 questionnaire as well as the DASH questionnaire.","corpus_id":21441963,"score":1},{"doc_id":"27473921","title":"Comparison of Treatment Outcome After Collagenase and Needle Fasciotomy for Dupuytren Contracture: A Randomized, Single-Blinded, Clinical Trial With a 1-Year Follow-Up.","abstract":"PURPOSE: This study compared the efficacy of collagenase treatment and needle fasciotomy for contracture of the metacarpophalangeal (MCP) joint in Dupuytren disease. METHODS: This is a prospective, single-blinded, randomized study with follow-up 1 week and 1 year after treatment. One hundred and forty patients with an MCP contracture of 20° or more in a single finger were enrolled, of whom 69 patients were randomized to collagenase treatment and 71 patients to needle fasciotomy. The patients were followed at 1 week and were examined by a physiotherapist after 1 year. Measurements of joint movement and grip strength were recorded as well as patient-perceived outcomes measured by the Unité Rhumatologique des Affections de la Main (URAM) questionnaire and a visual analog scale (VAS) for the estimation of procedural pain and subjective treatment efficacy. RESULTS: Eighty-eight percent of the patients in the collagenase group and 90% of the patients in the needle fasciotomy group had a reduction in their MCP contracture to less than 5° 1 week after treatment, and the median gains in passive MCP movement were 48° and 46°, respectively. The median VAS score for procedural pain was 4.9 of 10 in the collagenase group and 2.7 of 10 in the needle fasciotomy group. After 1 year, 90% of the patients in both groups had full extension of the treated MCP joint. One patient in each group had a recurrence of the contracture. The median improvement in URAM score was 8 units in both groups and the VAS estimation of treatment efficacy by the patients was 8.7 of 10 in both groups. CONCLUSIONS: There was no significant difference between the treatment outcomes after collagenase and needle fasciotomy treatment after 1 year. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic I.","corpus_id":10592543,"score":1},{"doc_id":"27556605","title":"Predictors of Patient Satisfaction with Hand Function after Fasciectomy for Dupuytren's Contracture.","abstract":"BACKGROUND: This study examined patient satisfaction with hand function after fasciectomy for Dupuytren's contracture and determined which preoperative patient- and disease-specific factors predicted this satisfaction. METHODS: Demographics and disease-specific factors were assessed from a prospective cohort of 194 patients who completed the Michigan Hand Outcomes Questionnaire preoperatively and underwent limited fasciectomy between 2011 and 2014 at six hand surgery practice sites. To evaluate satisfaction with hand function, patients were asked to complete the Michigan Hand Outcomes Questionnaire during the first year after fasciectomy. After patients were classified into a satisfied and an unsatisfied category using the question that specifically pertains to satisfaction with hand function, the authors applied multivariate logistic regression modeling to identify independent predictors of patient satisfaction. RESULTS: At an average of 10 months (range, 6 to 12 months) after fasciectomy, 84 percent (n = 163) of the patients were satisfied with their hand function. In multivariate analyses adjusting for the degree of postoperative residual contracture (p < 0.001) and complications (p < 0.001), a higher preoperative Michigan Hand Outcomes Questionnaire hand appearance subscore and male gender predicted a higher likelihood of becoming satisfied after fasciectomy. Other patient- and disease-specific factors did not show evidence for an association with patient satisfaction. CONCLUSIONS: The findings of this study suggest that providers should consider assessing concerns about the appearance of the hand in patients with Dupuytren's contracture. They also highlight the importance of complication prevention and full contracture correction from the patient's perspective. CLINICAL QUESTION/LEVEL OF EVIDENCE: Risk, III.","corpus_id":205960525,"score":1},{"doc_id":"27682305","title":"Effectiveness and safety of collagenase Clostridium histolyticum in Dupuytren's disease : an observational study in Belgium.","abstract":"Dupuytren's disease is a connective tissue disorder leading to contractures. It can be treated surgically or through injections of collagenase Clostridium histolyticum (CCH). Patients with Dupuytren's contracture (> 20°) and a palpable cord were included in this observational study, aiming to characterise the Belgian patient population and to assess the effectiveness and safety of CCH. Overall, 108 patients (114 joints) received at least one injection of CCH, and 104 patients completed the study. The percentages of joints achieving a degree of contracture of 5° or less, or a relative contracture reduction of at least 50% after the extension procedure were 64.9% and 90.1%, respectively. The mean number of injections per cord was 1.0. The Unité Rhumatologique des Affections de la Main score decreased from 29.4 ± 11.0 to 12.9 ± 6.3 (mean ± SD ; p < 0.0001). CCH was demonstrated to be effective, safe and able to increase quality of life.","corpus_id":7415691,"score":1},{"doc_id":"28118833","title":"An empirical evaluation of the SF-12, SF-6D, EQ-5D and Michigan Hand Outcome Questionnaire in patients with rheumatoid arthritis of the hand.","abstract":"BACKGROUND: The aim of this study was to assess the psychometric properties, namely acceptability, validity, reliability, interpretability and responsiveness of the EuroQol EQ-5D (EQ-5D visual analogue (VAS) and EQ-5D (utility)), Short Form 12 Dimensions (SF-12), SF-6D and Michigan Hand Outcome Questionnaire (MHQ) in patients with rheumatoid arthritis (RA) of the hand. METHODS: The empirical investigation was based upon data from a randomised controlled trial of 488 adults with rheumatoid arthritis who had pain and dysfunction of the hands and/or wrists. Participants completed the EQ-5D, SF-12 and MHQ at baseline and at 4 and 12 months follow up. Acceptability was measured using completion rates over time; construct validity using the \"known groups\" approach, based on pain troublesomeness; convergent validity using spearman's rho correlation (ρ); reliability using internal consistency (Cronbach's alpha); interpretability using minimal important differences (MID); and responsiveness using effect sizes and standardised response means (SRM) stratified by level of self-rated improvement in hand and wrist function or level of self-rated benefit and satisfaction from trial treatments. RESULTS: At baseline, the study population had a mean age of 62.4 years, a mean MHQ score of 52.1 and included 76% women. The EQ-5D (utility) had the highest completion rates across time points. All instruments discriminated between pre-specified groups based on pain troublesomeness. Convergent validity analysis indicated that the MHQ score correlated strongly with the EQ-5D (ρ = 0.65) and SF-6D (ρ = 0.63) utility scores. The MHQ was most responsive at detecting change in indicators of RA pain severity between baseline and 4 months, whilst minimal important differences varied considerably across PROMs. CONCLUSIONS: The instruments evaluated in this study displayed varying psychometric properties in the context of RA of the hand. The selection of a preferred instrument in evaluative studies should ultimately depend on the relative importance placed on individual psychometric properties and the importance placed on generation of health utilities for economic evaluation purposes.","corpus_id":4463750,"score":1},{"doc_id":"28490266","title":"Radiotherapy in Dupuytren's disease: a systematic review of the evidence.","abstract":"Radiotherapy has been advocated as an alternative treatment in early Dupuytren's disease. We have systematically reviewed the evidence on the use of radiotherapy in Dupuytren's disease. Only six articles met a minimum set standard, five of which were retrospective cohort studies and one a randomized controlled study. A total of 770 Dupuytren's hands, nearly all with Tubiana stage 0-1 disease, were irradiated with an average 30 Gy. Disease regression ranged from 0%-56%, stability from 14%-98% and progression from 2%-86%. Salvage surgery was successful in all cases of disease progression post-radiotherapy. There were no reports of adverse wound healing problems associated with such surgery or radiotherapy-associated malignancy. On balance, radiotherapy should be considered an unproven treatment for early Dupuytren's disease due to a scarce evidence base and unknown long-term adverse effects. Well-designed randomized controlled studies are required to confirm the benefits of radiotherapy treatment. LEVEL OF EVIDENCE: II.","corpus_id":206785758,"score":1},{"doc_id":"28595612","title":"Responsiveness and minimal important change of the Norwegian version of the Disabilities of the Arm, Shoulder and Hand questionnaire (DASH) in patients with subacromial pain syndrome.","abstract":"BACKGROUND: The Disabilities of the Arm, Shoulder, and Hand questionnaire (DASH) is a valid and reliable patient-reported outcome measure (PROM). It was designed to measure physical disability and symptoms in patients with musculoskeletal disorders of the upper extremity, and is one of the most commonly used PROMs for patients with shoulder pain. The aim of this study was to examine responsiveness, the smallest detectable change (SDC) and the minimal important change (MIC) of the DASH, in line with international (COSMIN) recommendations. METHODS: The study sample consisted of 50 patients with subacromial pain syndrome, undergoing physical therapy for 3-4 months. Responsiveness to change was examined by calculating area under the receiver operating characteristic curves (AUC) and testing a priori-formulated hypothesis regarding correlations with changes in other instruments that measuring the same construct. The SDC was calculated using a test re-test protocol, and the MIC was calculated by the anchor-based MIC distribution. MIC values for patients with low and high baseline scores were also calculated. RESULTS: DASH appeared to be responsive, as it was able to distinguish patients who reported to be improved from those unchanged (AUC 0.77). All of the hypotheses were accepted. The SDC was 11.8, and the MIC was 4.4. CONCLUSION: This study shows that the Norwegian version of the DASH has good responsiveness to change and may thus be recommended to measure outcome in patients with shoulder pain in Norway.","corpus_id":4411658,"score":1},{"doc_id":"28774258","title":"The Hand of Sabazios: Evidence of Dupuytren's Disease in Antiquity and the Origin of the Hand of Benediction.","abstract":"Dupuytren's disease gained its eponym from the surgeon Baron Guillaume Dupuytren (1777-1835). However, the terms \"Cline's contracture\" and \"Cooper's contracture,\" named after the two surgeons who proposed the treatment for the palmar contractures prior to Dupuytren, have also been used to describe the disease. In addition to the eponyms attributed to these three surgeons, a number of other appellations with interesting provenance exist for Dupuytren's disease including the \"Curse of the MacCrimmons,\" \"Celtic hand,\" \"Viking's disease,\" and the \"Hand of Benediction.\" These terms all have interesting provenance; however, contention exists with regard to the appropriateness of their coinage. Of these terms, the \"Hand of Benediction\" is based upon the oldest history, supposedly thought to be a result of an early Pope afflicted with Dupuytren's disease. This report suggests that Dupuytren's disease was recorded in history prior Christianity, the Vikings, as well as Dupuytren, Cline, and Cooper. Nearly 100 votive \"Hand of Sabazios\" artifacts from Antiquity appear to document Dupuytren's disease via sculpture. The report posits that Dupuytren's disease may have been represented by the \"Hand of Sabazios,\" subsequently inspiring the \"Hand of Benediction\" and \"Hand of God\" that has permeated Christian art and culture for thousands of years.","corpus_id":5264100,"score":1},{"doc_id":"28893147","title":"The Polish version of the Michigan Hand Outcomes Questionnaire: Cross-cultural adaptation, reliability, construct validity, and measurement error.","abstract":"The aims of this study were to translate the Michigan Hand Outcomes Questionnaire into the Polish language and to test the measurement properties of its quality criteria. A total of 120 patients with hand complaints completed the Polish Michigan Hand Outcomes Questionnaire and the Disabilities of the Arm, Shoulder, and Hand questionnaire on the first assessment, along with the grip test, pinch test, and pain sore assessed using a visual analogue scale during activity. After 7 days, 76 patients completed the Michigan Hand Outcomes Questionnaire the second time. The Cronbach alpha of the Michigan Hand Outcomes Questionnaire subscales ranged from 0.79 to 0.96. The intraclass correlation coefficient varied from 0.82-0.97, and the Bland-Altman method indicated the Michigan Hand Outcomes Questionnaire total score limit of agreement was -13.2-12.3 and -9.18-9.62 for the right and left hand, respectively. The construct validity revealed a moderate to strong correlation between every subscale of the Polish Michigan Hand Outcomes Questionnaire and Disabilities of the Arm, Shoulder, and Hand, but they only correlated with the grip test and the visual analogue scale, and neither correlated with the pinch test. The study demonstrated properties similar to the original version, validating the belief that the use of this questionnaire in medical practice in Poland is justified.","corpus_id":1631239,"score":1},{"doc_id":"29062986","title":"Cultural adaptation of the Michigan Hand Outcomes Questionnaire in patients with Carpal Tunnel Syndrome: A Turkish version study.","abstract":"OBJECTIVE: Cultural adaptations of the questionnaires are important for easy use. We aimed to assess the reliability and validity of the Turkish Version of the Michigan Hand Outcomes Questionnaire in patients with Carpal Tunnel Syndrome. METHODS: To assess test-retest reliability, the Turkish \"Michigan Hand Outcomes Questionnaire\" and \"Disabilities of Arm, Shoulder and Hand\" questionnaires were answered by patients and controls and were repeated a week later. For testing internal consistency, the Cronbach's alpha test was used. For testing validity, correlations between the subscales of the \"Michigan Hand Outcomes Questionnaire\" and \"Disabilities of Arm, Shoulder and Hand\" questionnaire were measured in patient groups. One hundred patients with idiopathic Carpal Tunnel Syndrome and 50 healthy participants were included in the study. RESULTS: In test-retest reliability, intraclass correlations of the subscales of the \"Michigan Hand Outcomes Questionnaire\" were high. Cronbach's alphas were found to be high in all subscales. There was no significant correlation between asthetics and pain scales. We found significant differences between patients and controls regarding all subscales of the \"Michigan Hand Outcomes Questionnaire\". Correlations between subscales of the \"Michigan Hand Outcomes Questionnaire\" and \"Disabilities of Arm, Shoulder and Hand\" questionnaire were significant. We found no difference between one-hand effected and two-hand effected patients, in terms of the \"Michigan Hand Outcomes Questionnaire\", \"Disabilities of Arm, Shoulder and Hand\" questionnaire Function/Symptom and Work average scores. CONCLUSION: This study showed that the Turkish version of the \"Michigan Hand Outcomes Questionnaire\" is reliable and valid and can be used in Turkish patients with Carpal Tunnel Syndrome because it is comprehensible and practicable.","corpus_id":31731253,"score":1},{"doc_id":"29799370","title":"Michigan Hand Outcomes Questionnaire for the Evaluation of Patients with Mucopolysaccharidosis.","abstract":"This study evaluates hand functioning in patients with mucopolysaccharidosis (MPS) and validates the Michigan Hand Outcomes Questionnaire (MHQ) as a measure of hand functioning evaluation. Patients with diagnosis of MPS between the ages of 8 and 21 years were eligible for enrolment in the study irrespective of whether they were or were not receiving treatment (enzyme replacement therapy). Individuals with mental disorders and those who had already undergone hand surgery were excluded. Clinical and demographic data were collected as well as hand functioning evaluation based on the Brazilian-Portuguese version of the MHQ. The global score and domains score of the entire group is presented. With regard to the validation of the MHQ, internal consistency of the domains were evaluated using Cronbach's α correlation coefficient. Ten individuals were women and six were men; two were type II MPS and 14 were type VI. Mean age was 11.7 ± 4.4 years and five patients had signs and symptoms suggestive of carpal tunnel syndrome. The MHQ global and domains mean scores were: global, 56.68 ± 16.17; hand function, 64.17 ± 21.62; activities of daily living, 46.87 ± 27.78; school performance, 56.01 ± 32.69; pain, 79.33 ± 30.87; aesthetics, 77.81 ± 11.16; and satisfaction, 74.57 ± 27.16. Global and domain internal consistency were: global, 0.888 (good); hand function, 0.815 (good); activities of daily living, 0.873 (good); school performance, 0.815 (good); pain, 0.468 (poor); aesthetics, -0.044 (unacceptable); and satisfaction.","corpus_id":44160955,"score":1},{"doc_id":"20025754","title":"Measurement properties of the Dizziness Handicap Inventory by cross-sectional and longitudinal designs.","abstract":"BACKGROUND: The impact of dizziness on quality of life is often assessed by the Dizziness Handicap Inventory (DHI), which is used as a discriminate and evaluative measure. The aim of the present study was to examine reliability and validity of a translated Norwegian version (DHI-N), also examining responsiveness to important change in the construct being measured. METHODS: Two samples (n = 92 and n = 27) included participants with dizziness of mainly vestibular origin. A cross-sectional design was used to examine the factor structure (exploratory factor analysis), internal consistency (Cronbach's alpha), concurrent validity (Pearson's product moment correlation r), and discriminate ability (ROC curve analysis). Longitudinal designs were used to examine test-retest reliability (intraclass correlation coefficient (ICC) statistics, smallest detectable difference (SDD)), and responsiveness (Pearson's product moment correlation, ROC curve analysis; area under the ROC curve (AUC), and minimally important change (MIC)). The DHI scores range from 0 to 100. RESULTS: Factor analysis revealed a different factor structure than the original DHI, resulting in dismissal of subscale scores in the DHI-N. Acceptable internal consistency was found for the total scale (alpha = 0.95). Concurrent correlations between the DHI-N and other related measures were moderate to high, highest with Vertigo Symptom Scale-short form-Norwegian version (r = 0.69), and lowest with preferred gait (r = - 0.36). The DHI-N demonstrated excellent ability to discriminate between participants with and without 'disability', AUC being 0.89 and best cut-off point = 29 points. Satisfactory test-retest reliability was demonstrated, and the change for an individual should be >/= 20 DHI-N points to exceed measurement error (SDD). Correlations between change scores of DHI-N and other self-report measures of functional health and symptoms were high (r = 0.50 - 0.57). Responsiveness of the DHI-N was excellent, AUC = 0.83, discriminating between self-perceived 'improved' versus 'unchanged' participants. The MIC was identified as 11 DHI-N points. CONCLUSIONS: The DHI-N total scale demonstrated satisfactory measurement properties. This is the first study that has addressed and demonstrated responsiveness to important change of the DHI, and provided values of SDD and MIC to help interpret change scores.","corpus_id":17860663,"score":0},{"doc_id":"21277691","title":"Focused extracorporeal shockwave therapy in Dupuytren's disease--a hypothesis.","abstract":"Dupuytren's disease is a progressive disease due to unknown causal agents or genetics. An epidemiological analysis of 566 cases in North Germany estimated that around 1.9 million Germans are suffering from Dupuytren's disease. Beside Dupuytren's disease, there are a number of further less common forms of progressive fibromatosis, such as knuckle pads, plantar fibromatosis or Peyronie's disease. Surgery in plantar fasciectomy yields to a 60% recurrence rate depending on the extent of the plantar fasciectomy. Peyronie's disease of the penis affects middle-aged men between 40 and 60 years with penile pain, curvature during erection and potential erectile dysfunction. In a clinical randomized-controlled trial in Peyronie's disease 2000 focused extracorporeal shock waves reduced pain significantly and improved erectile function and quality of life. We hypothesize that focused extracorporeal shock wave therapy is able to reduce Dupuytren's contracture, a fibromatosis of the palm and improve function. Given the fact that recurrence rate in Dupuytren's disease is high und unpredictable extracorporeal shockwave therapy as a non-invasive tool might be applicable both, in primary and secondary prevention of the progression as well as for treatment. As such we have planned a randomized-controlled trial (ClinicialTrials.gov, NCT01184586) studying the effect of high-energy focused extracorporeal shockwave therapy on patients suffering Dupuytren's disease with patient-related outcome measures such as the DASH score and the Michigan Hand Outcome Questionnaire (MHQ) as primary outcome parameters.","corpus_id":25381674,"score":0},{"doc_id":"22288720","title":"Body awareness rating questionnaire: measurement properties.","abstract":"The purpose of present study was to investigate important measurement properties of the Body Awareness Rating Questionnaire (BARQ) subscales: Function; Mood; Feelings; and Awareness. Samples of 50 patients with prolonged musculoskeletal pain and psychosomatic disorders, and 50 gender and age-matched healthy persons participated in the study. Relative (ICC 2,1) and absolute reliability (S(w)) were calculated. Construct validity was examined by testing hypothesis using Pearson (r) or Spearman rank (r(s)) correlation. Discriminate ability was examined using a receiver operating characteristic (ROC) curve, the area under the curve (aROC) being the measure of discriminative validity. All patients reported more or less improvement after treatment, using the Patient Global Impression of Change (PGIC) as an external indicator of important change. Responsiveness to important change was therefore examined by one-way repeated measures analysis of variance (ANOVA), relating change scores of BARQ subscales to the PGIC categories. Relative and absolute reliability values were within recommended limits for all four subscales. Construct and discriminate validity was indicated for Function, Feelings and Awareness, but not for Mood. Responsiveness was indicated for the subscales Function and Awareness, but not for Feelings and Mood. Further research is needed to complement the subscales of BARQ, found with appropriate measurement properties.","corpus_id":37180124,"score":0},{"doc_id":"22748143","title":"The Dutch Lower Extremity Functional Scale was highly reliable, valid and responsive in individuals with hip/knee osteoarthritis: a validation study.","abstract":"BACKGROUND: The WOMAC is the most widely used self-report measure to evaluate physical functioning in hip or knee osteoarthritis, however its ability to discriminate pain and physical functioning (i.e. discriminate validity) has repeatedly been questioned. Little to no data is available on the discriminant validity of alternative questionnaires that measure the same construct, for instance the Hip and Knee Osteoarthritis Outcome Score (HOOS and KOOS, respectively) and the Lower Extremity Function Scale (LEFS). Therefore, we translated the LEFS to Dutch and studied its psychometric properties (i.e. validity, reliability and responsiveness). In addition, we assessed the discriminate validity of the LEFS, HOOS and KOOS. METHODS: After translation with a forward/backward protocol, 401 individuals with hip or knee osteoarthritis completed the LEFS, HOOS/KOOS, SF-36, Hospital Anxiety and Depression Scale and Checklist Individual Strength questionnaires. To assess reliability and responsiveness, a sample of 106 and 108 patients completed a comparable set of questionnaires within 3 weeks and 3 months, respectively. Feasibility, validity, reliability and responsiveness were evaluated. Discriminant validity of the LEFS, HOOS and KOOS was examined by contrasting the scales' correlations with the physical functioning subscale of the SF-36 with the scales' correlations with the bodily pain subscale of the SF-36. RESULTS: The Dutch version of the LEFS was feasible, had good internal consistency (0.96), good reliability (ICC = 0.86), good construct and discriminant validity, and showed no floor or ceiling effects. The minimal detectable change (MDC90) was ten points. Area under the receiver operating characteristic curve (AUC) analyses revealed good (AUC = 0.76) and fair (AUC = 0.63) responsiveness for the LEFS in improved and worsened patients, respectively. Discriminant validity for pain was apparent for the LEFS (p < 0.01), but not for the HOOS and KOOS (p = 0.21 and p = 0.20, respectively). CONCLUSIONS: Considering the LEFS' good psychometric qualities and ability to discriminate between pain and functioning, we recommend the LEFS as the outcome measure of choice to assess self-reported physical functioning in individuals with hip or knee osteoarthritis.","corpus_id":8941616,"score":0},{"doc_id":"23431165","title":"Unraveling the signaling pathways promoting fibrosis in Dupuytren's disease reveals TNF as a therapeutic target.","abstract":"Dupuytren's disease is a very common progressive fibrosis of the palm leading to flexion deformities of the digits that impair hand function. The cell responsible for development of the disease is the myofibroblast. There is currently no treatment for early disease or for preventing recurrence following surgical excision of affected tissue in advanced disease. Therefore, we sought to unravel the signaling pathways leading to the development of myofibroblasts in Dupuytren's disease. We characterized the cells present in Dupuytren's tissue and found significant numbers of immune cells, including classically activated macrophages. High levels of proinflammatory cytokines were also detected in tissue from Dupuytren's patients. We compared the effects of these cytokines on contraction and profibrotic signaling pathways in fibroblasts from the palmar and nonpalmar dermis of Dupuytren's patients and palmar fibroblasts from non-Dupuytren's patients. Exogenous addition of TNF, but not other cytokines, including IL-6 and IL-1β, promoted differentiation into specifically of palmar dermal fibroblasts from Dupuytren's patients in to myofibroblasts. We also demonstrated that TNF acts via the Wnt signaling pathway to drive contraction and profibrotic signaling in these cells. Finally, we examined the effects of targeted cytokine inhibition. Neutralizing antibodies to TNF inhibited the contractile activity of myofibroblasts derived from Dupuytren's patients, reduced their expression of α-smooth muscle actin, and mediated disassembly of the contractile apparatus. Therefore, we showed that localized inflammation in Dupuytren's disease contributes to the development and progression of this fibroproliferative disorder and identified TNF as a therapeutic target to down-regulate myofibroblast differentiation and activity.","corpus_id":9917433,"score":0},{"doc_id":"23750436","title":"[An attempt to objectify the assessment of extension or recurrence of Dupuytren's disease on the basis of ultrasound].","abstract":"Próba obiektywizacji oceny nawrotu lub wznowy choroby Dupuytrena w oparciu o badanie ultrasonograficzne. Dupuytren's contracture is a disease of unknown etiology, leading with time to decreased hand function caused by increasing contracture of fingers. Excision of contracted longitudinal palmar fascia constitutes the most important way of treatment. Due to fact that disease has progressive course in many patients recurrence (i.e. overgrowth of longitudinal palmar aponeurosis apart from the operated site) or extension (i.e. similar process affecting formerly operated site) occurs. An attempt to objectify the assessment of recurrence or extension of Dupuytren's disease on the basis of sonographic examination of palmar surface of the hand during distant (at least 24 months from surgery) followup constituted the aim of the study. 41 patients operated on from January 2000 to February 2009 in 2nd Department of General Surgery in Krakow due to Dupuytren's contracture constituted the study material. Mean age of the patients reached 62,78 years (SD +/- 9,32), and mean follow up time 5,74 years (SD +/- 2,90). Sonographic assessment was performed in 26 operated on left hands and 24 right hands. 9 patients had both hands operated on. In most of the patients during surgery the contralateral hand was also affected by the disease. Extension of Dupuytren's disease was found in 11 hands, recurrence--in 18 hands, while concurrent extension and recurrence was found in 17 hands. Extension usually was found on the radial side and affected mainly I interphalangeal space followed by disease affecting I and III ray of the hand. In one patient 2 independent foci of the disease were found within I interphalangeal space. Recurrences affected mainly ulnar side of the hand: V and IV rays of the hand. Concurrently found extension and recurrence affected 2 or 3 rays. In the cases of 3 rays affected extension dominated (2 rays vs. 1 ray of recurrence). On sonographic assessment mean diameters of lesions during distant follow- up were 12,69 x 4,62 x 3,95 [mm] with recurrent lesions being larger than mean values found in extensions. With partial fasciectomy being the most commonly performed operation in cases of Dupuytren's disease ultrasound can constitute very important technique of assessment of exacerbation of the lesions of palmar aponeurosis allowing for the choice of appropriate surgical technique for particular case, detection of postoperative extension and/or recurrence and for the cases clinically doubtful.","corpus_id":32313277,"score":0},{"doc_id":"23893345","title":"Measurement properties of the Work Limitations Questionnaire were sufficient among cancer survivors.","abstract":"PURPOSE: The purpose of this study was to determine reproducibility, validity, and responsiveness of the Work Limitations Questionnaire (WLQ) among cancer survivors. METHODS: A cohort of 53 cancer survivors completed the WLQ and other questionnaires at baseline, 4-week, and 6-month follow-up. We assessed internal consistency, intraclass correlation coefficient, standard error of measurement, floor- and ceiling effects and compared the WLQ with other constructs. For responsiveness, we assessed the following anchor-based measures: minimal important change (MIC) versus smallest detectable change (SDC) and area under the curve (AUC) of receiver operation characteristic (ROC). RESULTS: We found sufficient reproducibility at group level but not at individual level as the MIC (4.0) exceeded SDC at group level (3.1) but not at individual level (18.0). There was no indication of systematic bias or proportional bias. The internal consistency and construct validity for the WLQ and its subscales were sufficient or slightly less than sufficient. There was a floor effect for one subscale, but there were no ceiling effects. Responsiveness was sufficient with an AUC of a ROC of 0.65. CONCLUSIONS: The WLQ is reproducible, valid, and responsive for use at group level among cancer survivors but not sufficiently reproducible for use at individual level.","corpus_id":23084589,"score":0},{"doc_id":"23975101","title":"Social participation in older adults with joint pain and comorbidity; testing the measurement properties of the Dutch Keele Assessment of Participation.","abstract":"OBJECTIVE: The Keele Assessment of Participation (KAP) questionnaire measures person-perceived participation in 11 aspects of life. Participation allows fulfilment of valued life activities and social roles, which are important to older adults. Since we aimed to use the KAP in a larger Dutch cohort, we examined the measurement properties of KAP in a Dutch sample of older adults with joint pain and comorbidity. DESIGN: Cohort study. SETTING: A community-based sample in Amsterdam, the Netherlands and North Staffordshire, UK. PARTICIPANTS: Participants were aged 65 years and over, had at least two chronic diseases (identified through general practice consultation) and reported joint pain on most days (questionnaire). The Dutch cohort provided baseline data (n=407), follow-up data at 6 months (n=364) and test-retest data 2 weeks after 6 months (n=122). The UK cohort provided comparable data (n=404). OUTCOME MEASURES: The primary outcome was person-perceived participation, as measured with the KAP. The measurement properties examined were the following: structural validity (factor analysis), internal consistency (Cronbach's α), reliability (intraclass correlation coefficients; ICC), construct validity (hypothesis testing), responsiveness (hypothesis testing and area under the curve) and cross-cultural validity (differential item functioning; DIF). RESULTS: Factor analysis revealed two domains: KAPd1: 'participation in basic activities' and KAPd2: 'participation in complex activities', with Cronbach's α of 0.74 and 0.57 and moderate test-retest reliability: ICC of 0.63 and 0.57, respectively. Further analyses of KAPd1 showed poor construct validity and responsiveness. Despite the uniform DIF in item 'interpersonal relations', the total KAPd1 score seemed comparable between the Dutch and UK sample. CONCLUSIONS: Only KAP domain 'participation in basic activities' showed good internal consistency and sufficient reliability. KAPd2 lacks sufficient measurement properties for application in studies, although items may be used as single items. Further development of the concept 'participation' may help the development and validation of instruments to measure participation.","corpus_id":3126350,"score":0},{"doc_id":"24257471","title":"The Otitis Media-6 questionnaire: psychometric properties with emphasis on factor structure and interpretability.","abstract":"BACKGROUND: The Otitis Media-6 questionnaire (OM-6) is the most frequently used instrument to measure health related quality of life in children with otitis media. The main objectives of this study are 1) to translate and cross-culturally adapt the OM-6 into Danish, and 2) to assess important psychometric properties including structural validity and interpretability of the OM-6 in a Danish population of children suffering from otitis media. METHODS: The OM-6 was translated and cross-culturally adapted according to international guidelines. A longitudinal validation study enrolled 491 children and their families, and the measurement properties of the OM-6 were evaluated using the Cosmin taxonomy. The properties assessed were construct and structural validity (confirmatory factor analysis) including internal consistency, reproducibility (test-retest reliability and smallest detectable change), responsiveness and interpretability. RESULTS: A total of 435 children were eligible to participate in the study. Analyses of structural validity and internal consistency indicated that parent appraisal of hearing and speech problems may be problematic. Both scales showed similarly good test-retest reliability and construct validity, were able to discriminate between diagnostic subgroups and responsive to change. Cut-off values of 16.7 and 30.0 were found to represent minimal important change for the patients. CONCLUSIONS: The Danish version of the OM-6 is a reliable, valid, responsive and interpretable questionnaire to measure quality of life in children with otitis media. This study sheds light on possible weaknesses of the instrument that needs to be acknowledged in the utilization of the instrument. However, despite these issues our results support the continuing use of OM-6 as a 1-factor functional health scale with a separate global health rating. Furthermore, indications of values representing minimal important change as perceived by the respondent are presented.","corpus_id":14126783,"score":0},{"doc_id":"24445668","title":"Validation of the Pelvic Floor Distress Inventory (PFDI-20) and Pelvic Floor Impact Questionnaire (PFIQ-7) in a Dutch population.","abstract":"INTRODUCTION AND HYPOTHESIS: The objective of this study was to validate the Pelvic Floor Distress Inventory (PFDI-20) and Pelvic Floor Impact Questionnaire (PFIQ-7) in Dutch women. METHODS: Patients with pelvic floor dysfunction completed the Dutch questionnaires at (1) inclusion to evaluate internal consistency, (2) 1 week later to assess test-retest reliability, and (3) 6 months later to assess responsiveness and interpretability of change. To assess validity, floor and ceiling effects and construct validity were tested. A population-based sample (reference group) completed the questionnaires once. RESULTS: Data of 111 patients and 283 reference group participants were analyzed. Internal consistency of baseline scores in patient and reference groups was moderate (Cronbach's alpha 0.52-0.60) to adequate in the PFDI-20 (Cronbach's alpha 0.71-0.84) and adequate in the PFIQ-7 (Cronbach's alpha 0.88-0.94). Both measures presented adequate test-retest reliability (intraclass correlation coefficient 0.79-0.91) and adequate responsiveness (area under the receiver-operating characteristic curve both 0.77). Interpretability was adequate for PFDI-20 and acceptable for PFIQ-7 with a clinically relevant minimally important change of -23 and -29 points, respectively. At baseline, the scales of the PFIQ-7 showed floor effects (44-55 %) in patients, though the PFIQ-7 summary score did not. No ceiling effects were observed. Construct validity was adequate with all predefined hypotheses confirmed regarding subgroup discrimination using pooled patient and reference group baseline data. CONCLUSIONS: For assessing distress and health-related quality of life of pelvic floor dysfunction, the Dutch PFDI-20 and PFIQ-7 are reliable and valid in the general Dutch population, and also responsive and interpretable among tertiary care-seeking women.","corpus_id":33954586,"score":0},{"doc_id":"26704805","title":"Evaluation of the Dutch version of the Foot and Ankle Outcome Score (FAOS): responsiveness and Minimally Important Change.","abstract":"PURPOSE: The aim of this study was to evaluate the responsiveness of the Foot and Ankle Outcome Score (FAOS) and provide data on the Minimally Important Change (MIC) in patients 1 year after hindfoot and ankle surgery. METHODS: Prospective pre-operative and 1 year post-operative FAOS scores were collected from 145 patients. A patient's global assessment and a longitudinal derived Function Change Score were used as external anchors. To assess responsiveness, effect sizes (ES) and Standardized Response Means (SRM) were calculated and hypotheses on their magnitudes were formulated. Additional ROC curve analysis was performed, and the Area Under the Curve (AUC) was calculated as a measure of responsiveness. MIC values were estimated using two different methods: (1) the mean change method and (2) the optimal cut-off point of the ROC curve. RESULTS: Responsiveness was supported by confirmation of 84 % of the hypothesized ES and SRM and almost all AUCs exceeding 0.70. MIC values ranged from 7 (symptoms) to 38 (sport) points. They varied between calculation methods and were negatively associated with baseline values. A considerable amount of MIC values did not exceed the smallest detectable change limit, indicating that the FAOS is more suitable at group level than for longitudinally following individual patients. CONCLUSIONS: The FAOS demonstrated good responsiveness in patients 1 year after hindfoot and ankle surgery. Due to their wide variation, MIC estimates derived in this study should be interpreted with caution. However, these estimates can be of value to facilitate sample size calculation in future studies. LEVEL OF EVIDENCE: Diagnostic study, Level I.","corpus_id":19380692,"score":0},{"doc_id":"27506524","title":"Responsiveness and minimal important change for the ProFitMap-neck questionnaire and the Neck Disability Index in women with neck-shoulder pain.","abstract":"PURPOSE: The aim was to determine the responsiveness and minimal important change (MIC) of the questionnaire ProFitMap-neck that measures symptoms and functional limitations in women with neck pain. The same measurement properties were determined for Neck Disability Index (NDI) for comparison purposes. METHODS: Longitudinal data were derived from two randomized controlled trials, including 103 and 120 women with non-specific neck pain, with questionnaire measurements performed before and after interventions. Sensitivity and specificity to discriminate between improved and not or little changed participants, based on categorization of a global rating of change scale (GRCS), were determined for the ProFitMap-neck indices and NDI by using area under receiver operating characteristic curves (AUC). Correlations between the GRCS anchor and change scores of the questionnaires were also used to assess responsiveness. The change score that showed the highest combination of sensitivity and specificity was set for MIC. RESULTS: The ProFitMap-neck indices showed similar responsiveness as NDI with AUC exceeding 0.70 (Range: ProFitMap-neck, 0.74-0.83; NDI, 0.75-0.86). The MIC in the two samples ranged between 6.6 and 13.6 % for ProFitMap-neck indices and 5.2 and 6.3 % for NDI. Both questionnaires had significant correlations with GRCS (Spearman's rho 0.47-0.72). CONCLUSIONS: Validity of change scores was endorsed for the ProFitMap-neck indices and NDI with adequate ability to discriminate between improved and not or little changed participants. Values of minimal important change were presented.","corpus_id":12160392,"score":0},{"doc_id":"27780237","title":"Psychometric Properties of a Generic, Patient-Centred Palliative Care Outcome Measure of Symptom Burden for People with Progressive Long Term Neurological Conditions.","abstract":"BACKGROUND: There is no standard palliative care outcome measure for people with progressive long term neurological conditions (LTNC). This study aims to determine the psychometric properties of a new 8-item palliative care outcome scale of symptom burden (IPOS Neuro-S8) in this population. DATA AND METHODS: Data were merged from a Phase II palliative care intervention study in multiple sclerosis (MS) and a longitudinal observational study in idiopathic Parkinson's disease (IPD), multiple system atrophy (MSA) and progressive supranuclear palsy (PSP). The IPOS Neuro-S8 was assessed for its data quality, score distribution, ceiling and floor effects, reliability, factor structure, convergent and discriminant validity, concurrent validity with generic (Palliative care Outcome Scale) and condition specific measures (Multiple Sclerosis Impact Scale; Non-motor Symptoms Questionnaire; Parkinson's Disease Questionnaire), responsiveness and minimally clinically important difference. RESULTS: Of the 134 participants, MS patients had a mean Extended Disability Status Scale score 7.8 (SD = 1.0), patients with an IPD, MSA or PSP were in Hoehn & Yahr stage 3-5. The IPOS Neuro-S8 had high data quality (2% missing), mean score 8 (SD = 5; range 0-32), no ceiling effects, borderline floor effects, good internal consistency (Cronbach's α = 0.7) and moderate test-retest reliability (intraclass coefficient = 0.6). The results supported a moderately correlated two-factor structure (Pearson's r = 0.5). It was moderately correlated with generic and condition specific measures (Pearson's r: 0.5-0.6). There was some evidence for discriminant validity in IPD, MSA and PSP (p = 0.020), and for good responsiveness and longitudinal construct validity. CONCLUSIONS: IPOS Neuro-S8 shows acceptable to promising psychometric properties in common forms of progressive LTNCs. Future work needs to confirm these findings with larger samples and its usefulness in wider disease groups.","corpus_id":6751389,"score":0},{"doc_id":"28158958","title":"The Responsiveness and Interpretability of the Shoulder Pain and Disability Index.","abstract":"Study Design Clinical measurement study, prospective cohort design. Background Shoulder pain is a common disorder, and treatment is most often focused on a reduction of pain and functional disabilities. Several reviews have encouraged the use of the Shoulder Pain and Disability Index (SPADI) to objectify functional disability. It is important to assess the responsiveness and interpretability of the SPADI in patients seeking physical therapy treatment for their shoulder pain in a primary care setting. Objective To assess the responsiveness and interpretability of the SPADI in patients with shoulder pain visiting a physical therapist in primary care. Methods The target population consisted of patients who consulted a physical therapist for their shoulder pain. The patients received physical therapy treatment and completed the Dutch-language version of the SPADI at baseline and at 26-week follow-up. The interpretability floor and ceiling effects and the minimal important change (MIC) were assessed using the receiver operating characteristic method, and a visual anchor-based MIC distribution method was used to assess several Global Perceived Effect scale (GPE)-based anchors. The measurement error was calculated using the smallest detectable change. For the responsiveness, the area under the receiver operating characteristic curve was used, and correlations with the GPE and the change score of the Shoulder Disability Questionnaire (as this questionnaire measures the same construct) were assessed. Results A total of 356 patients participated at baseline and 237 (67%) returned the SPADI after 26 weeks. The mean score on the SPADI at baseline was 46.7 points (on a 0-100 scale). The SPADI showed no signs of floor and ceiling effects. The smallest detectable change was 19.7 points. The MIC was 20 (43% of baseline value), and therefore a change of 43% or more in an individual patient was considered to be clinically relevant. The area under the receiver operating characteristic curve (AUC) was 0.81, the Spearman correlation between the SPADI change score and the GPE was 0.53, and the Pearson correlation between the Shoulder Disability Questionnaire and the SPADI change score was 0.71. Conclusion The results of this study confirm the responsiveness of the SPADI, making it a useful instrument to assess functional disability in longitudinal studies; however, the measurement error should be taken into account when making decisions in individual patients. J Orthop Sports Phys Ther 2017;47(4):278-286. Epub 3 Feb 2017. doi:10.2519/jospt.2017.7079.","corpus_id":37439348,"score":0},{"doc_id":"28658044","title":"The Modified Low Back Pain Disability Questionnaire: Reliability, Validity and Responsiveness of a Dutch Language Version.","abstract":"STUDY DESIGN: Cross sectional study OBJECTIVE.: The goal of this study is to translate the English version of the Modified Low Back Pain Disability Questionnaire (MDQ) into a Dutch version and investigate its clinimetric properties for patients with nonspecific chronic low back pain (CLBP). SUMMARY OF BACKGROUND DATA: Fritz et al (2001) developed a modified version of the Oswestry Disability Questionnaire (ODI) to assess functional status and named it the MDQ. In this version, a question regarding employment and homemaking ability was substituted for the question related to sex life. Good clinimetric properties for the MDQ were identified but up until now it is not clear if the clinimetric properties of the MDQ would change if it was translated into a Dutch version. METHODS: translation of the MDQ into Dutch was done in four steps. Test-retest reliability was investigated using the intraclass correlation coefficient (ICC) model. Validity was calculated using Pearson correlations and a 2-way analysis of variance (ANOVA) for repeated measures. Finally, responsiveness was calculated with the area under the curve (AUC), minimal detectable change (MDC) and the standardized response mean (SRM). RESULTS: A total of 80 completed questionnaires were collected in three different hospitals and a total of 43 patients finished a 9 weeks intervention period, completing the retest. Test-retest reliability was excellent with an ICC of 0.89 (95% CI, 0.74-0.95). To confirm the convergent validity, the MDQ answered all predefined hypothesises (r = -0.65-0.69 / p = 0.01-0.00) and good results for construct validity were found (p = 0.02). The MDQ had an AUC of 0.64 (95% CI, 0.47-0.81), an MDC of 8.80 points and a SRM of 0.65. CONCLUSION: The Dutch version of the MDQ shows good clinimetric properties and is shown to be usable in the assessment of the functional status of Dutch speaking patients with nonspecific CLBP. LEVEL OF EVIDENCE: 3.","corpus_id":52229829,"score":0}],"string":"[\n {\n \"doc_id\": \"18332014\",\n \"title\": \"Which questionnaire is best? The reliability, validity and ease of use of the Patient Evaluation Measure, the Disabilities of the Arm, Shoulder and Hand and the Michigan Hand Outcome Measure.\",\n \"abstract\": \"The Patient Evaluation Measure (PEM), The Michigan Hand Outcome Questionnaire (MHQ) and the Disabilities of the Arm, Shoulder and Hand (DASH) score were assessed independent of their originators for reliability, construct and criterion validity and acceptability, using an ease of use questionnaire. These were administered in random order to 100 patients with different hand and wrist disorders and with different impairments of movement, pain, sensation and strength. The internal consistency of all three questionnaires was very high suggesting redundancy in the questions. All questionnaires were reproducible and valid for finger and wrist disorders, but less for nerve disorders. All had poor construct validity. The PEM was the easiest to understand and complete, taking the least time. Correlation between the scales is high and conversion equations were calculated. All three are reliable and reproducible patient completed questionnaires, but the PEM is the easiest to use. The validity of all is suspected for nerve disorders.\",\n \"corpus_id\": 6949461,\n \"score\": 2\n },\n {\n \"doc_id\": \"19220604\",\n \"title\": \"The lived experience of Dupuytren's disease of the hand.\",\n \"abstract\": \"AIMS: To describe patients' experiences of living with Dupuytren's disease. BACKGROUND: Dupuytren's disease is a chronic, progressive deformity of the hand which limits active extension of the fingers due to advancing and irreversible flexion deformity. It is estimated that two million people are affected by the condition in the UK. Nurses may frequently encounter patients with this condition in a wide range of settings. However, the disease is neglected in the nursing literature and little is known about patients' experience of living with the condition. DESIGN: A phenomenological approach, using Coliazzi's method, was employed. METHOD: Semi-structured interviews were conducted with six men and one woman diagnosed with Dupuytren's disease. RESULTS: Four interlinking themes emerged. Theme 1: Awareness of Dupuytren's disease describes participants' experiences of recognising and acknowledging the disease, which often did not occur until functional ability was restricted. Theme 2: Living with Dupuytren's disease describes how patients coped with the disease and adapted their activities to maintain independence. Theme 3: Deciding on treatment illuminates how patients decided on treatment and highlights a lack of information and support from health professionals. Theme 4: Receiving treatment articulates participants' experience of surgical treatment and post surgical rehabilitation. CONCLUSIONS: The findings revealed that people living with Dupuytren's disease receive little information about their condition and possible treatment from health professionals yet high quality and accurate information is required for patients to understand their condition and the treatment options available. RELEVANCE TO CLINICAL PRACTICE: People with Dupuytren's disease do not always recognise their condition until it has significantly progressed. Following diagnosis they need accurate and up-to-date information about their condition and treatment options. Nurses have an important role to play in raising awareness of the disease, educating patients about its features and progression and enabling them to become active partners in decisions about treatment.\",\n \"corpus_id\": 29994450,\n \"score\": 2\n },\n {\n \"doc_id\": \"21701336\",\n \"title\": \"Development of a brief, 12-item version of the Michigan Hand Questionnaire.\",\n \"abstract\": \"BACKGROUND: The Michigan Hand Questionnaire is one of the most widely used hand-specific surveys that measure health status relevant to patients with acute and chronic hand disorders. However, item redundancy exists in the original version, and an abbreviated survey could minimize responder burden and offer broader applicability. METHODS: Patients (n = 422) with four specific hand conditions--rheumatoid arthritis (n = 162), thumb carpometacarpal osteoarthritis (n = 31), carpal tunnel syndrome (n = 97), and distal radius fracture (n = 132)--completed the Michigan Hand Questionnaire at two time points. Correlation analysis identified two items from each of six domains (i.e., function, activities of daily living, work, pain, aesthetics, and satisfaction). The Brief Michigan Hand Questionnaire score was calculated as the sum of the responses to the 12 items. Psychometric analysis was performed to describe the reliability, validity, and responsiveness of the Brief Michigan Hand Questionnaire. RESULTS: The Brief Michigan Hand Questionnaire includes 12 items that were highly correlated with the summary Michigan Hand Questionnaire score (r = 0.99, p < 0.001). The Brief Michigan Hand Questionnaire scores were highly correlated between the two time periods (r = 0.78, p < 0.001) and by disease type. Responsiveness of the Brief Michigan Hand Questionnaire was high for all diseases and similar to that of the original Michigan Hand Questionnaire. CONCLUSIONS: The 12-item Brief Michigan Hand Questionnaire is an efficient and versatile outcomes instrument specific to hand disability that retains the psychometric properties of the original Michigan Hand Questionnaire. The Brief Michigan Hand Questionnaire is an important tool with which to measure patient outcomes and the quality of care in hand surgery. CLINICAL QUESTION/LEVEL OF EVIDENCE: Diagnostic, I.(Figure is included in full-text article.).\",\n \"corpus_id\": 30061214,\n \"score\": 2\n },\n {\n \"doc_id\": \"21786431\",\n \"title\": \"Unité Rhumatologique des Affections de la Main (URAM) scale: development and validation of a tool to assess Dupuytren's disease-specific disability.\",\n \"abstract\": \"OBJECTIVE: To our knowledge, no functional outcome measure has been developed and validated for Dupuytren's disease. We aimed to develop and validate a patient-reported functional outcome measure for Dupuytren's disease. METHODS: Patients with Dupuytren's disease (n = 9) and medical experts (n = 7) provided input and opinions about limiting activities that were difficult to perform because of Dupuytren's disease for item generation. The provisional scale was studied in an independent sample of patients (n = 85) for item reduction according to response distribution, reliability, redundancy, and loading in a 1-factor solution. The final scale was evaluated as follows: reliability using Cronbach's alpha coefficient and test-retest intraclass correlation coefficient from the previous 85-patient population, and construct validity and responsiveness after needle aponeurotomy in another independent 53-patient sample. For construct validity, convergent validity and divergent validity were tested. The clinically important change was estimated relative to a 1-point categorical change on the Tubiana scale. RESULTS: A 52-item provisional scale was generated and reduced to the final 9-item scale called the Unité Rhumatologique des Affections de la Main (URAM) scale (total score 0-45). The scale showed good to excellent reliability and suitable construct validity. The URAM score improved after needle aponeurotomy: the standardized effect size was 0.56. The estimated clinically important change of the URAM scale was 2.9 points. CONCLUSION: We provide the first patient-reported functional measure for Dupuytren's disease. The URAM scale demonstrated suitable psychometric properties, and is short and convenient enough for easy use in daily practice and in clinical studies.\",\n \"corpus_id\": 22095503,\n \"score\": 2\n },\n {\n \"doc_id\": \"23575442\",\n \"title\": \"Optimal functional outcome measures for assessing treatment for Dupuytren's disease: a systematic review and recommendations for future practice.\",\n \"abstract\": \"BACKGROUND: Dupuytren's disease of the hand is a common condition affecting the palmar fascia, resulting in progressive flexion deformities of the digits and hence limitation of hand function. The optimal treatment remains unclear as outcomes studies have used a variety of measures for assessment. METHODS: A literature search was performed for all publications describing surgical treatment, percutaneous needle aponeurotomy or collagenase injection for primary or recurrent Dupuytren's disease where outcomes had been monitored using functional measures. RESULTS: Ninety-one studies met the inclusion criteria. Twenty-two studies reported outcomes using patient reported outcome measures (PROMs) ranging from validated questionnaires to self-reported measures for return to work and self-rated disability. The Disability of Arm, Shoulder and Hand (DASH) score was the most utilised patient-reported function measure (n=11). Patient satisfaction was reported by eighteen studies but no single method was used consistently. Range of movement was the most frequent physical measure and was reported in all 91 studies. However, the methods of measurement and reporting varied, with seventeen different techniques being used. Other physical measures included grip and pinch strength and sensibility, again with variations in measurement protocols. The mean follow-up time ranged from 2 weeks to 17 years. CONCLUSIONS: There is little consistency in the reporting of outcomes for interventions in patients with Dupuytren's disease, making it impossible to compare the efficacy of different treatment modalities. Although there are limitations to the existing generic patient reported outcomes measures, a combination of these together with a disease-specific questionnaire, and physical measures of active and passive individual joint Range of movement (ROM), grip and sensibility using standardised protocols should be used for future outcomes studies. As Dupuytren's disease tends to recur following treatment as well as extend to involve other areas of the hand, follow-up times should be standardised and designed to capture both short and long term outcomes.\",\n \"corpus_id\": 13313666,\n \"score\": 2\n },\n {\n \"doc_id\": \"23629117\",\n \"title\": \"The Michigan hand outcomes questionnaire after 15 years of field trial.\",\n \"abstract\": \"BACKGROUND: The Michigan Hand Outcomes Questionnaire has been used to assess a variety of hand and upper extremity injuries and conditions for nearly 15 years. It has been included in several overviews of upper extremity outcomes measures, but it has not been systematically examined regarding its clinometric properties during field trials. METHODS: The authors conducted a review of the Michigan Hand Outcomes Questionnaire in the English language literature from 1998 through March of 2012. Data from clinical studies were abstracted and compiled. RESULTS: The Michigan Hand Outcomes Questionnaire has been used in 58 clinical studies, and its clinometric properties have been analyzed in an additional 18 publications. The Michigan Hand Outcomes Questionnaire compares favorably with other hand outcomes instruments in the areas of test-retest reliability, validity, and responsiveness. High internal consistency may indicate redundancy within the items in the Michigan Hand Outcomes Questionnaire. The strength of the Michigan Hand Outcomes Questionnaire is its multidimensional construct in measuring patient-rated outcomes in symptom, function, aesthetics, and satisfaction. CONCLUSIONS: The Michigan Hand Outcomes Questionnaire has been applied across a variety of conditions affecting the hand and upper limb. Its psychometric properties have been tested through field trials in various clinical settings around the world.\",\n \"corpus_id\": 36691926,\n \"score\": 2\n },\n {\n \"doc_id\": \"23728243\",\n \"title\": \"Reliability and internal validity of the michigan hand questionnaire.\",\n \"abstract\": \"BACKGROUND: The Michigan Hand Outcomes Questionnaire (MHQ) remains one of very few to be based on validated and systematic methods in its creation. However, test-retest reliability and internal validity have not been appropriately investigated in any other English-speaking population outside the original development sample. The objective of this study is to examine the reliability and internal validity of the MHQ in a Canadian population. METHODS: All patients with a clinical hand problem but no hand immobilization who attended our Plastic Surgery Clinic were invited to participate in this study. Patients were asked to complete the MHQ, and then contacted to arrange for completion of the MHQ a second time. Internal validity was estimated using Cronbach alpha. Reliability was estimated using the method of Bland and Altman, and intraclass correlation coefficients. Correlation analysis between score differences and time between tests was performed. RESULTS: Full versions of the MHQ were completed by 116 participants on their initial visit, while only 77 participants completed a second MHQ. Cronbach alpha ranged from 0.84 to 0.95 for the MHQ subscales. Intraclass-correlation coefficients ranged from 0.71 to 0.84 for the subscales. The magnitude of the limits of agreement for the subscales ranged from 13.8 to 26.2. The difference in scores between the first and second tests was not related to the time between tests. CONCLUSION: The high values of Cronbach alpha indicate high internal validity, but that there may be redundancy between items in the MHQ, which could be eliminated without losing information. Reliability of the MHQ is considered moderate. The limits of agreement are considered wide, indicating potential issues with respect to interpretation of a change in score between 2 administrations of the MHQ.\",\n \"corpus_id\": 206038293,\n \"score\": 2\n },\n {\n \"doc_id\": \"24563499\",\n \"title\": \"What patients want from the treatment of Dupuytren's disease--is the Unité Rhumatologique des Affections de la Main (URAM) scale relevant?\",\n \"abstract\": \"Patients awaiting surgery for Dupuytren's contractures listed the problems from their Dupuytren's disease that had led them to request surgery and their relative priorities of the results of surgery. The listed problems were compared with the nine items comprising the Unité Rhumatologique des Affections de la Main (URAM) Dupuytren's disease-specific outcome measure. One hundred and ten patients reported 278 problems. Ninety-four different combinations of problems were provided by patients, and over half (55%) of the problems were not captured by items in the URAM scale. The long-term outcome from surgery was relatively more important to patients than speed of recovery. The URAM tool may not be relevant to patients in the UK, and further assessment of its face validity is required before it is used.\",\n \"corpus_id\": 43412090,\n \"score\": 2\n },\n {\n \"doc_id\": \"24565887\",\n \"title\": \"URAM scale for functional assessment in Dupuytren's disease: a comparative study of its properties.\",\n \"abstract\": \"OBJECTIVE: To test the convergent validity and ease of use of the Unité Rhumatologique des Affections de la Main (URAM) scale for patients with Dupuytren's disease. METHODS: Patients were prospectively included. We compared the convergent validity of the URAM scale, the Cochin Hand Function Scale (CHFS) and the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, in terms of their correlation with the Tubiana score and self-assessed disability on a visual analog scale (VAS). Pearson's correlation was used for the convergent validity study. The response time for questionnaire completion was the outcome for ease of implementation. RESULTS: We included 53 patients with Dupuytren's disease in the convergent validity study and 30 other patients with the disease in the time-response assessment. The URAM scale showed strong convergence with the Tubiana scale (r=0.64) and self-assessed disability on a VAS (r=0.69). Convergence with the Tubiana and self-assessed disability was higher for the URAM scale than the CHFS or DASH questionnaire. The mean [SD] response time was shorter for the URAM scale than the CHFS or DASH questionnaire (42 [20] vs 71 [35] and 103 [59] s, respectively, P<0.0001). CONCLUSIONS: The results reinforce the psychometric merits of the URAM scale. Furthermore, the response time for assessing disability was shorter with the URAM scale than the CHFS or DASH questionnaire. This evidence supports the high recommendation for the use of the URAM scale in clinical practice and clinical studies to assess disability in Dupuytren's disease.\",\n \"corpus_id\": 21987375,\n \"score\": 2\n },\n {\n \"doc_id\": \"26307142\",\n \"title\": \"Validity of the Disability of the Arm, Shoulder and Hand patient-reported outcome measure (DASH) and the Quickdash when used in Dupuytren's disease.\",\n \"abstract\": \"This study investigated aspects of the validity and reliability of the 30-item Disability of the Arm, Shoulder and Hand patient-reported outcome measure (DASH) and its relationship with the shorter 11-item QuickDASH in patients with Dupuytren's disease. Seven hundred and fifty-nine DASH questionnaires were studied, covering pre- and postoperative patients undergoing different treatments for Dupuytren's disease. Items related to pain rose early after treatment before returning to baseline, suggesting that studying pain is relevant during postoperative recovery. Across all 759 sets of responses, the QuickDASH agreed closely with the DASH. In exploratory factor analysis, the DASH was not unidimensional, questioning the validity of the DASH summary score in Dupuytren's disease. Further validation of existing PROMs for use in Dupuytren's disease is needed. These data suggest that pain is a relevant symptom to study during postoperative recovery following treatment for Dupuytren's disease. LEVEL OF EVIDENCE: III.\",\n \"corpus_id\": 34214889,\n \"score\": 2\n },\n {\n \"doc_id\": \"27469936\",\n \"title\": \"Measurement Properties of the Brief Michigan Hand Outcomes Questionnaire in Patients With Dupuytren Contracture.\",\n \"abstract\": \"PURPOSE: The brief Michigan Hand Outcomes Questionnaire (briefMHQ) was developed as a shorter version of the Michigan Hand Outcomes Questionnaire (MHQ), but its measurement properties have not been investigated in patients with Dupuytren contracture. The objective of the study was to investigate the reliability, validity, responsiveness, and interpretability of the briefMHQ. METHODS: Fifty-seven patients diagnosed with Dupuytren contracture completed the briefMHQ as well as the full-length MHQ and Quick Disabilities of the Arm, Shoulder, and Hand (QuickDASH) questionnaire at baseline. Two to 14 days after baseline and 1 year after collagenase injection or surgery, patients again filled out the briefMHQ. Reliability was determined using the intraclass correlation coefficient and by calculating internal consistency (Cronbach alpha). Validity was tested by quantifying correlations with the full-length MHQ and QuickDASH. Responsiveness, based on the standardized response mean and the minimally clinically important change, was also determined. RESULTS: The briefMHQ had an intraclass correlation coefficient of 0.87, Cronbach alpha of 0.88, and correlations of r = 0.88 and -0.82 with the original MHQ and QuickDASH, respectively. The standardized response mean was 0.9 and the minimally clinically important change was 7 points. CONCLUSIONS: Overall, the briefMHQ demonstrates excellent reliability, good validity, and high responsiveness in patients with Dupuytren contracture. CLINICAL RELEVANCE: The briefMHQ is an accurate and time-saving tool to evaluate patients with Dupuytren contracture and the effect of a corresponding treatment.\",\n \"corpus_id\": 5715093,\n \"score\": 2\n },\n {\n \"doc_id\": \"27872343\",\n \"title\": \"Recovery, responsiveness and interpretability of patient-reported outcome measures after surgery for Dupuytren's disease.\",\n \"abstract\": \"This prospective cohort study investigated the responsiveness and interpretability of the Disabilities of the Arm, Shoulder and Hand (DASH) and Unité Rhumatologique des Affections de la Main (URAM) outcome measures for assessing recovery after fasciectomy and dermofasciectomy for Dupuytren's disease. DASH outcome scores at 1 year were significantly better than at 6 weeks, suggesting that recovery is not complete by 6 weeks. Of the 101 patients recruited to the DASH cohort, 71 completed preoperative, 6 week and 1 year postoperative DASH scores; 68 of them completed preoperative and 1 year postoperative DASH scores and an external anchor question. In the URAM cohort, 30/44 completed the preoperative and the 1 year postoperative URAM scores and the anchor question. The DASH score exhibited moderate responsiveness but poor interpretability on receiver operating characteristic curve analysis, such that a minimal important change could not be estimated. The URAM score showed acceptable responsiveness, and an MIC of 10.5 on receiver operating characteristic analysis. LEVEL OF EVIDENCE: II.\",\n \"corpus_id\": 28205488,\n \"score\": 2\n },\n {\n \"doc_id\": \"28841615\",\n \"title\": \"Normative Values of the Michigan Hand Outcomes Questionnaire for Patients with and without Hand Conditions.\",\n \"abstract\": \"BACKGROUND: The Michigan Hand Outcomes Questionnaire has been widely used for nearly 20 years to assess patients with a variety of hand and upper extremity conditions. However, normative data have not previously been collected, limiting interpretation. METHODS: The Michigan Hand Outcomes Questionnaire was administered to 579 participants recruited from the general population. In addition, participants were asked to identify any problem affecting their hand(s), including trauma, hand disease/condition, systemic illness, or nonspecific symptoms. Comorbidities and demographic data were also collected. RESULTS: Total Michigan Hand Outcomes Questionnaire score for healthy individuals was indicative of generally good hand function (95.2; 95 percent CI, 94.3 to 96.1). Individuals with unilateral trauma scored for their affected hand (90.3; 95 percent CI, 87.9 to 92.6) lower than their healthy hand (mean difference, 5.7; 95 percent CI, 3.2 to 8.3). For individuals with and without hand trauma, total Michigan Hand Outcomes Questionnaire score decreased with increasing number of comorbidities. Many of the differences in Michigan Hand Outcomes Questionnaire score between the problem hand and unaffected hand were smaller than the minimal clinically important difference of 3.0 to 23.0 for known abnormalities of the hand and upper extremity. CONCLUSIONS: These normative data provide appropriate baseline information for individuals with and without underlying hand conditions. Most notably, these findings suggest that individuals with a unilateral problem establish new subnormative values for both their affected and unaffected hands. These data will encourage an appropriate understanding of the results of future studies using the Michigan Hand Outcomes Questionnaire.\",\n \"corpus_id\": 205962193,\n \"score\": 2\n },\n {\n \"doc_id\": \"18503809\",\n \"title\": \"Responsiveness of the Michigan Hand Outcomes Questionnaire--Dutch language version in patients with rheumatoid arthritis.\",\n \"abstract\": \"OBJECTIVE: To investigate the responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with rheumatoid arthritis (RA) who were treated in a multidisciplinary hand clinic. DESIGN: Observational study comparing the responsiveness of the MHQ with that of various other outcome measures for hand function. SETTING: Multidisciplinary hand clinic within a tertiary referral center for rheumatologic care. PARTICIPANTS: Twenty-eight patients with problems in hand function due to RA were assessed before and 3 months after conservative and/or surgical treatment. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Assessments included, apart from a previously validated Dutch language version of the MHQ, a visual analog scale for pain, grip strength, the Sequential Occupational Dexterity Assessment, the Arthritis Impact Measurement Scales (AIMS) hand and finger function scale, and each patient's rating of subjective change in hand function. Measurements of responsiveness included the standardized response mean (SRM), effect size, and responsiveness ratio. In addition, the Spearman rank correlations (rho) between the change scores of the MHQ and those of other measures of hand function were calculated. RESULTS: The mean MHQ total score improved significantly between baseline (mean +/- standard deviation, 48.3+/-12.2) and follow-up (mean, 54.7+/-16.9) (change score, -7.2; 95% confidence interval, -11.1 to -3.3). The SRM, effect size, and responsiveness ratio of the MHQ total score were -0.72, -0.52, and -1.99, respectively. Significant associations were found between the changes of the MHQ total score and each patient's rating of subjective change in hand function (rho=.64, P=.001) and the change score of the AIMS hand function scale (rho=-.24, P=.260). CONCLUSIONS: The MHQ proved to be a responsive measure of hand function in patients with RA who were treated in connection with a multidisciplinary hand clinic.\",\n \"corpus_id\": 22699150,\n \"score\": 1\n },\n {\n \"doc_id\": \"18669144\",\n \"title\": \"Dupuytren's palmar contracture in women.\",\n \"abstract\": \"BACKGROUND: Dupuytren's disease is a fibroproliferative disorder of the palmar fascia that can cause disabling digital contractures. The pathogensis of the disease is still unclear, and it afflicts predominantly white males of northern European origin. Gender-related differences of Dupuytren's disease and the distinctive characteristics of the disease in females are not yet well defined. OBJECTIVES: To evaluate and illustrate the distinctive characteristics of Dupuytren's disease in females. METHODS: A retrospective study was performed of all female patients with Dupuytren's disease seen and followed at our Hand Surgery Unit over a 20 year period. The study group consisted of 48 women (56 hands). The collected data included clinical and epidemiological features on admission, and outcome of surgical intervention. RESULTS: Of the 48 women (56 hands) with Dupuytren's disease, 23 (26 hands) underwent limited fasciectomy. The average age at presentation was 60.1 years. A few of the patients originated from Asia and Africa. Manifestations and pattern of the disease were nearly comparable to those observed in the male group, except for a slightly higher incidence of proximal interphalangeal joint contracture in female patients. Generally, females expressed less severe contractures on presentation and a slower progression thereafter. A favorable functional postoperative outcome was observed. Seven patients had minor complications including local hematoma and painful scars. Two patients developed moderate signs of complex regional pain syndrome. CONCLUSIONS: Further investigations are needed to assess the potential role of androgens in the pathogenesis of Dupuytren's disease, and a possible protective role of estrogenic hormones, rendering Dupuytren's contracture a postmenopausal affliction.\",\n \"corpus_id\": 46604907,\n \"score\": 1\n },\n {\n \"doc_id\": \"19181227\",\n \"title\": \"Comparative responsiveness of the Michigan Hand Outcomes Questionnaire and the Carpal Tunnel Questionnaire after carpal tunnel release.\",\n \"abstract\": \"PURPOSE: The literature supports self-administered questionnaire assessment tools for the measurement of outcome after surgical treatment of carpal tunnel syndrome (CTS). Traditional physical measures are less sensitive to clinical changes following carpal tunnel release (CTR) than fully validated designed outcome questionnaires. A number of validated outcome instruments have been compared to determine which is optimal with regard to sensitivity and responsiveness following surgery. To our knowledge, the Michigan Hand Outcomes Questionnaire (MHQ) and the Carpal Tunnel Questionnaire (CTQ) have not been compared in regard to their responsiveness and sensitivity to change following CTR. The aim of this prospective study was to compare the responsiveness of these 2 instruments when evaluating outcomes after CTR. METHODS: Seventy-eight patients diagnosed with CTS and scheduled for unilateral open CTR were recruited and informed consent was obtained after ethics approval. Inclusion criteria were primary procedure, history, clinical signs, and conduction studies consistent with CTS. The MHQ and CTQ were both completed by each patient preoperatively and 6 months postoperatively. RESULTS: Results for all domains of the MHQ and all domains of the CTQ showed significant postoperative improvement. The overall responsiveness of both MHQ and CTQ were large (standardized response mean >or=0.8), however the CTQ demonstrated increased sensitivity to change after CTR compared to the MHQ. Although the standardized response mean (SRM) of the MHQ was 0.8, the SRM of the CTQ was 1.22. Both domains of the CTQ had an SRM well above 0.8, whereas half of the MHQ domains had an SRM below 0.8. CONCLUSIONS: The CTQ has demonstrated a greater responsiveness to clinical change following CTR than the MHQ. Therefore, the CTQ is a more sensitive instrument and researchers in the field of CTS should bear these findings in mind when choosing an outcome instrument for future studies. TYPE OF STUDY/LEVEL OF EVIDENCE: Diagnostic I.\",\n \"corpus_id\": 34764932,\n \"score\": 1\n },\n {\n \"doc_id\": \"19258150\",\n \"title\": \"The minimal clinically important difference of the Michigan hand outcomes questionnaire.\",\n \"abstract\": \"PURPOSE: To determine the change in score required in various domains of the Michigan Hand Outcomes Questionnaire (MHQ) to indicate meaningful patient improvement, or the minimal clinically important difference (MCID), for 3 common hand conditions: rheumatoid arthritis (RA), carpal tunnel syndrome (CTS) and distal radius fracture (DRF). METHODS: The MHQ was administered to patients at 2 time points. Patient satisfaction was defined as a satisfaction score > or =80% of the standard deviation of that patient sample. The minimal change in score in specific MHQ domains that corresponded with patient satisfaction was determined using receiver operating characteristic curves. RESULTS: For CTS patients, MCIDs of 23, 13, and 8 were identified for the pain, function, and work domains, respectively. For RA patients, pain and function were also identified as having discriminative ability, with MCIDs of 11 and 13, respectively. An MCID of 3 was identified for the activities of daily living domain. For DRF patients, no MHQ domains showed discriminative ability because of the ceiling effect at the 3-month assessment period. CONCLUSIONS: Individual domains of the MHQ can be used to discriminate between patients who are satisfied and those who are not after either carpal tunnel release or silicone arthroplasty of the metacarpophalangeal joints for RA. Pain and function are the domains of the MHQ that are best able to discriminate between patients who are satisfied and those who are not. The identical function MCID for both RA patients and CTS patients, despite markedly different preoperative values, indicates that a standard amount of functional change may indicate patient satisfaction. High postoperative satisfaction, even only 3 months after surgery, prevented any domains from showing discriminative ability for the DRF patients.\",\n \"corpus_id\": 24402380,\n \"score\": 1\n },\n {\n \"doc_id\": \"19259747\",\n \"title\": \"Which outcome measure is the best? Evaluating responsiveness of the Disabilities of the Arm, Shoulder, and Hand Questionnaire, the Michigan Hand Questionnaire and the Patient-Specific Functional Scale following hand and wrist surgery.\",\n \"abstract\": \"The purpose of this study was to determine and compare the responsiveness of the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, the Michigan Hand Questionnaire (MHQ), and the Patient-Specific Functional Scale (PSFS) in patients with carpal tunnel syndrome, wrist pain, finger contracture, or tumor. Eighty-one subjects prospectively completed each questionnaire shortly before and 3 and 6 months after surgery. Data were analyzed using one-way analysis of variance and Newman-Keuls multiple comparison tests. Responsiveness to clinical change was calculated using standardized response means. The DASH was responsive for those with carpal tunnel syndrome (0.77), wrist pain (0.61), and tumor (0.55); the MHQ was responsive for those with carpal tunnel syndrome (1.04), wrist pain (0.87), and finger contracture (0.62); and the PSFS was responsive for those with carpal tunnel syndrome (0.65) and finger contracture (0.64). The interval during which the highest responsiveness occurred for the carpal tunnel, wrist pain, and finger contracture groups was the preoperative to 6-month period. The tumor group experienced the highest responsiveness during the preoperative to 3-month period. Our results indicate that one or more of the instruments evaluated are suitable for outcomes research related to surgery to treat carpal tunnel syndrome, wrist pain, finger contracture, and tumor.\",\n \"corpus_id\": 3146177,\n \"score\": 1\n },\n {\n \"doc_id\": \"19999612\",\n \"title\": \"[Use of questionnaires in outcome measurement in hand surgery].\",\n \"abstract\": \"Zastosowanie kwestionariuszy w ocenie wyników leczenia w chirurgii reki. An assessment of outcomes of the treatment of the diseases and injuries to the hand should include both objective parameters, i.e. range of motion or grip strength, and subjective parameters i.e. intensity of complaints or dexterity of the hand in various tasks of daily activity. Questionnaires were developed to evaluate subjective parameters in objective and systematic manner. They indeed allow us to better apprehend what is important from our patients' perspective. Questionnaire (called also form or test) is a list of queries concerning the issue being a subject of the assessment. The queries are designed in the way allowing answers to imply an important and possible objective information on the problem of interest. The objective of this article was to attract notice on the problems associated with the use of questionnaires in a research, with particular attention on hand surgery. Authors referred to the parameters which characterise these instruments: responsiveness, validity and reliability. Brief descriptions of most commonly used forms were provided, including DASH, Levine, PEM, Michigan and CISS. Shortcomings and pitfalls associated with the use of questionnaires and possible sources of bias were emphasised, e.g. difficulties in precise assignation of scores, answering some particular questions and accuracy of the completion of the form. Attention was paid on the choice of the questionnaire to be well-matched for an aim of a given research project both in substantial and formal manner. An opinion was supported that modem research projects measuring outcomes in hand surgery must include questionnaires as an obligatory component of a complex assessment.\",\n \"corpus_id\": 25296582,\n \"score\": 1\n },\n {\n \"doc_id\": \"20138712\",\n \"title\": \"Responsiveness of the Michigan Hand Outcomes Questionnaire and the Disabilities of the Arm, Shoulder, and Hand questionnaire in patients with hand injury.\",\n \"abstract\": \"PURPOSE: To compare responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) with that of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire in patients with hand injuries. We postulated that the MHQ may be more sensitive to functional changes in the hands, whereas the DASH questionnaire would have a closer association with days of disability. METHODS: Patients with hand injuries were consecutively recruited from 2 community hospitals. Each patient was asked to complete out the MHQ, the DASH questionnaire, the satisfaction with their health-related quality of life (Sat-HRQOL) measure, and Chinese Health Questionnaire (CHQ), which is a measure of psychological stressors. Disability days were defined as the duration of restricted activities of daily living during the previous 4 weeks. Patients repeated the same questionnaires between 2 and 9 months after enrollment (average: 4 mo). RESULTS: A total of 105 patients with hand injuries were recruited, and 50 of the 105 patients returned for the second evaluation. There were no statistical differences between responders and nonresponders for age, gender, disability days, the MHQ, the DASH questionnaire, the CHQ, or the Sat-HRQOL. Responsiveness was evaluated by effect sizes and standardized response means: Those for the MHQ were 0.84 and 1.05, and those for the DASH were 0.67 and 0.86, respectively. A mixed model analysis for repeated measurements of the 50 participants showed a significant influence of psychological factors (CHQ) for both the Sat-HRQOL and disability days. After adjustment for the effects of age, gender, and the CHQ, there was an increment of one Sat-HRQOL unit for an MHQ score increment of 3.2, whereas the score decrement for the DASH questionnaire was 3.3 units. CONCLUSIONS: The MHQ might be slightly more sensitive to functional changes, but the DASH questionnaire seemed more correlated with disability days. Psychological factors are the strongest determinants of the HRQOL and disability.\",\n \"corpus_id\": 42776421,\n \"score\": 1\n },\n {\n \"doc_id\": \"22094744\",\n \"title\": \"Dupuytren's disease in the Hispanic population: a 10-year retrospective review.\",\n \"abstract\": \"BACKGROUND: Dupuytren's disease is a common benign fibroproliferative disorder of the hand. Epidemiologic studies have reported significant variation in disease prevalence among races, focusing primarily on those of northern European descent. In contrast, Dupuytren's disease in the Hispanic population has received little attention. Thus, in this study, the authors aimed to determine the prevalence and operative rate of Dupuytren's disease in the Hispanic, black, white, Asian, Native American, and other races and to characterize the disease presentation in Hispanics who required surgical treatment. METHODS: A retrospective review was conducted to identify the racial distribution of Dupuytren's disease patients seen at Bellevue Hospital between July of 2000 and August of 2010. In Hispanic patients requiring surgical treatment for their disease, data were collected on the following parameters: age, sex, ethnicity, hand dominance, hand affected, and digits operated on. Epidemiologic factors including smoking, alcoholism, diabetes mellitus, hypercholesterolemia, epilepsy, and hypertension were also evaluated. RESULTS: Dupuytren's disease prevalence was found to be 533 per 100,000 in Hispanics. Of these patients, 1.8 percent required surgical treatment, and this group was characterized by the following comorbidities: smoking (57.1 percent), hypertension (57.1 percent), alcoholism (52.4 percent), diabetes mellitus (47.6 percent), and hypercholesterolemia (19.0 percent). CONCLUSIONS: The authors' results indicate that Dupuytren's disease is more prevalent in the Hispanic population than previously reported. Although the epidemiologic factors identified in Hispanics with Dupuytren's disease are similar to those in other races investigated, there are important differences with respect to clinical presentation and surgical treatment.\",\n \"corpus_id\": 36941149,\n \"score\": 1\n },\n {\n \"doc_id\": \"22333510\",\n \"title\": \"The patient-specific functional scale: validity, reliability, and responsiveness in patients with upper extremity musculoskeletal problems.\",\n \"abstract\": \"STUDY DESIGN: Clinical measurement, longitudinal; multicenter prospective cohort study. OBJECTIVES: To examine the validity, reliability, and responsiveness of the Patient-Specific Functional Scale (PSFS) in patients with musculoskeletal upper extremity problems being treated in physical therapy. BACKGROUND: The clinimetric properties of the PSFS have not been established nor compared with region-specific outcome measures in patients with upper extremity problems. METHODS: Patients completed the PSFS, Upper Extremity Functional Index (UEFI), and numeric pain rating scale (NPRS) at baseline and follow-up, and were categorized as improved, stable, or worsened, using the global rating of change. Construct validity was assessed by comparing the change scores of the stable and improved groups, using independent-samples t tests. Reliability was evaluated using intraclass correlation coefficient (ICC2,1) with 95% confidence intervals. Bland-Altman plots determined limits of agreement. Responsiveness and minimal important difference (MID) were determined with receiver operator characteristic (ROC) curves. RESULTS: One hundred eighty patients met the inclusion criteria. Construct validity was supported for the PSFS and the UEFI (P<.001). Reliability was moderate to good for the PSFS (ICC2,1 = 0.713) and UEFI (ICC2,1 = 0.848). Reported estimates of reliability may be lower than true values because the group of \\\"stable\\\" patients from this cohort had, on average, a small positive change. Bland-Altman plots indicated good agreement. The area under the ROC curve (AUC) was significantly different from the null value of 0.5 for the PSFS (0.887) and the UEFI (0.877), indicating good accuracy in distinguishing improved patients from stable patients. MID was 1.2 for the PSFS (scale, 0-10) and 8.5 for the UEFI (scale, 0-80). CONCLUSION: The PSFS is a valid, reliable, and responsive outcome measure for patients with upper extremity problems.\",\n \"corpus_id\": 35426489,\n \"score\": 1\n },\n {\n \"doc_id\": \"22872850\",\n \"title\": \"The Surgical Release of Dupuytren's Contracture Using Multiple Transverse Incisions.\",\n \"abstract\": \"Dupuytren's contracture is a condition commonly encountered by hand surgeons, although it is rare in the Asian population. Various surgical procedures for Dupuytren's contracture have been reported, and the outcomes vary according to the treatment modalities. We report the treatment results of segmental fasciectomies with multiple transverse incisions for patients with Dupuytren's contracture. The cases of seven patients who underwent multiple segmental fasciectomies with multiple transverse incisions for Dupuytren's contracture from 2006 to 2011 were reviewed retrospectively. Multiple transverse incisions to the severe contracture sites were performed initially, and additional incisions to the metacarpophalangeal (MCP) joints, and the proximal interphalangeal (PIP) joints were performed if necessary. Segmental fasciectomies by removing the fibromatous nodules or cords between the incision lines were performed and the wound margins were approximated. The mean range of motion of the involved MCP joints and PIP joints was fully recovered. During the follow-up periods, there was no evidence of recurrence or progression of disease. Multiple transverse incisions for Dupuytren's contracture are technically challenging, and require a high skill level of hand surgeons. However, we achieved excellent correction of contractures with no associated complications. Therefore, segmental fasciectomies with multiple transverse incisions can be a good treatment option for Dupuytren's contracture.\",\n \"corpus_id\": 2709612,\n \"score\": 1\n },\n {\n \"doc_id\": \"23982906\",\n \"title\": \"Measurement properties of the German Michigan Hand Outcomes Questionnaire in patients with trapeziometacarpal osteoarthritis.\",\n \"abstract\": \"OBJECTIVE: To investigate the reliability, validity, and responsiveness of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with trapeziometacarpal (TMC) joint osteoarthritis (OA). METHODS: In this prospective observational study, patients diagnosed with TMC joint OA who received either conservative or surgical treatment were included. At baseline and at 1 year following the beginning of treatment, we measured key pinch strength and the patients filled out the MHQ, the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, and the Short Form 12 health survey. Patients also completed these questionnaires 2-11 days after the last study visit. In order to analyze the measurement properties of the MHQ, we calculated test-retest reliability (intraclass correlation coefficient [ICC]), internal consistency (Cronbach's alpha for the 6 subscales), construct validity (Pearson's correlation coefficient [r]), responsiveness (effect sizes), and the minimum important change (MIC). RESULTS: We included 177 patients, of whom 109 were scheduled for surgery. The mean ± SD MHQ total score for surgical patients increased from 48 ± 14 at baseline to 75 ± 18 at 1 year (P ≤ 0.001). In contrast, no treatment effect was observed in the conservative group (P = 0.74). The MHQ total score showed excellent test-retest reliability (ICC 0.95) and correlated strongly with the DASH (r = -0.77). Internal consistency of the MHQ subscales ranged between 0.77 and 0.89. A large effect size of 1.7 was found for the surgical patients, with an MIC of 17 points. CONCLUSION: The MHQ demonstrated good reliability, validity, and responsiveness in patients with TMC joint OA and can be recommended as a suitable assessment instrument in this population.\",\n \"corpus_id\": 8788770,\n \"score\": 1\n },\n {\n \"doc_id\": \"24129389\",\n \"title\": \"Epidemiological study for personal risk factors and quality of life related to Dupuytren's disease in a mountain village of Japan.\",\n \"abstract\": \"BACKGROUND: This study investigated the etiology, personal risk factors, and quality of life related to Dupuytren's disease among residents of a mountain village in Japan. METHODS: Medical examinations were conducted of 401 adult residents (163 men, 238 women; average age of 66.7 years, range 40-92) of a mountain village in Japan. All had completed a self-administered questionnaire including items for gender, weight, height, dominant hand, occupation, history of diabetes mellitus, and frequency of smoking tobacco and drinking alcohol, in addition to EuroQol-5-Dimensions-3-level Japanese version. Blood samples were collected and assessed for biochemical markers related to Dupuytren's disease. The Dupuytren's disease diagnosis was based on clinical signs. Meyerding's classification was used to ascertain the disease severity. After examining background data and physical examination data related to Dupuytren's disease, we evaluated the association of Dupuytren's disease with those factors using univariate and logistic regression analysis. RESULTS: Dupuytren's disease was diagnosed in 28 subjects (7.0%). Univariate analysis revealed associations of age, male gender, occupation, history of diabetes mellitus, and alcohol intake with Dupuytren's disease. Logistic regression analysis after adjustment for age revealed a significant association between Dupuytren's disease and male gender, occupation, and history of alcohol intake. No significant difference was found between Dupuytren's disease patients and participants without this disease in the scoring and visual analog scale of EuroQol. No relation was found in scoring, the visual analog scale of EuroQol, or grading of Meyerding's classification in participants with Dupuytren's disease. CONCLUSION: This cross-sectional study revealed Dupuytren's disease in 7.0% of 401 subjects among the general population of a mountain village in Japan. The prevalence is higher with age and is apparently associated with male gender, occupation and alcohol intake. Risk factors associated with Dupuytren's disease were identified as age, male gender, occupation, and alcohol consumption habits.\",\n \"corpus_id\": 4820236,\n \"score\": 1\n },\n {\n \"doc_id\": \"24470559\",\n \"title\": \"Collagenase clostridium histolyticum in patients with Dupuytren's contracture: results from POINT X, an open-label study of clinical and patient-reported outcomes.\",\n \"abstract\": \"In POINT X, a study designed to reflect clinical practice and patient treatment choices, 254 European patients received open-label collagenase for Dupuytren's contracture. The most severely affected joint was treated first in 74% of patients. In total, 52%, 41%, 7%, and 1% of patients selected the little, ring, middle, and index finger, respectively; 79% had one or two joints treated. Only 9% of patients (n = 24) received 4 or 5 injections. The mean improvement in total passive extension deficit (TPED) was 34° on day 1, improving further by day 7 to 42°. This secondary improvement was maintained by day 90 and month 6. The mean number of injections/joint was 1.2 for the metacarpophalangeal joint and 1.25 for the proximal interphalangeal joint. Median time to recovery was 4 days; the mean improvement in hand function was clinically relevant as measured by the Unité Rhumatologique des Affections de la Main (URAM) score. In total, 87% and 86% of patients and physicians, respectively, were very satisfied or satisfied with treatment at month 6, although correlation between TPED and patient satisfaction was weak (Spearman -0.18, 95% CI -0.32 to -0.06). Collagenase was well tolerated, with 10 (3.9%) patients experiencing severe adverse events. As a real-world study, the POINT X findings can be generalized to the at-large population.\",\n \"corpus_id\": 10785955,\n \"score\": 1\n },\n {\n \"doc_id\": \"24477316\",\n \"title\": \"Association among work exposure, alcohol intake, smoking and Dupuytren's disease in a large cohort study (GAZEL).\",\n \"abstract\": \"OBJECTIVES: In view of the debate of factors in Dupuytren's disease, we aimed to describe its relationship with certain occupational factors, alcohol intake and smoking. SETTING: The French GAZEL cohort (employees of Electricité de France and Gaz de France). PARTICIPANTS: Participants of the cohort who answered a questionnaire in 2012, that is, 13 587 participants (73.7% of the questionnaire sent). In 2007, self-assessed lifetime occupational biomechanical exposure was recorded (carrying loads, manipulating a vibrating tool and climbing stairs), as well as alcohol intake, smoking and diabetes mellitus. Analyses were performed on high alcohol intake, smoking and duration of relevant work exposure, stratified by gender. PRIMARY AND SECONDARY OUTCOME MEASURES: From a specific question on Dupuytren's disease assessed in 2012, the outcome measures were self-reported Dupuytren's disease (yes/no) and disabling Dupuytren's disease (including surgery). RESULTS: A total of 10 017 men and 3570 women, aged 64-73 years, were included; the mean age for men was 68 years and for women was 65 years. Among men, the following were significantly associated with Dupuytren's disease: age (OR 1.03 (1.00; 1.06)), diabetes (OR 1.31 (1.07; 1.60)), heavy drinking (OR 1.36 (1.10; 1.69)) and over 15 years of manipulating a vibrating tool at work (OR 1.52 (1.15; 2.02)); except for diabetes, the association with these factors was stronger for disabling Dupuytren's disease (or surgery), with OR 1.07 (1.03; 1.11), 1.71 (1.25; 2.33) and 1.98(1.34; 2.91), respectively, for age, heavy drinking and over 15 years of manipulating a vibrating tool at work. Among the 3570 women included, 160 reported Dupuytren's disease (4.5%). The number of cases in the group of women was too low to reach conclusions, although the findings seemed similar for age, diabetes and vibration exposure. CONCLUSIONS: In this large French cohort study, Dupuytren's disease in men was associated with high levels of alcohol consumption and exposure to hand-transmitted vibration. It is likely that the same applied to women.\",\n \"corpus_id\": 2350971,\n \"score\": 1\n },\n {\n \"doc_id\": \"24569424\",\n \"title\": \"Health-related quality of life in patients undergoing palmar fasciectomy for Dupuytren's disease.\",\n \"abstract\": \"BACKGROUND: The present study was undertaken to assess the health-related quality of life in patients with Dupuytren's disease who undergo palmar fasciectomy. METHODS: A prospective cohort of patients with Dupuytren's disease undergoing palmar and/or digital fasciectomy was recruited from the practice of three plastic surgeons in Hamilton, Ontario, Canada. After written informed consent was obtained, participants were asked to complete three health-related quality-of-life questionnaires (i.e., Short Form-36, Michigan Hand Outcomes Questionnaire, and Health Utility Index Mark 3) at five time points: at 1 week and 1 day preoperatively, and at 1, 3, 6, and 12 months postoperatively. Ranges of motion and grip strength measurement were also recorded. RESULTS: For the 26 patients in the study, the multiattribute scores of the Health Utility Index Mark 3 improved from 0.80 before surgery to 0.83 at 12 months postoperatively (p > 0.05). There was no difference in the Short Form-36 scores, but the Michigan Hand Outcomes Questionnaire scores improved from 74 at 1 week preoperatively to 90 at the 12-month postoperative visit (p < 0.001). CONCLUSIONS: Patients who undergo palmar fasciectomy for Dupuytren's disease experience a substantial improvement in their health-related quality of life 12 months after surgery. In the authors' study population, a benefit of 0.85 quality-adjusted life-year within 12 months was observed. This can be translated as follows: the average patient who undergoes palmar fasciectomy gains the equivalent of approximately 14.4 days (0.48 months) in perfect health by undergoing palmar fasciectomy. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.\",\n \"corpus_id\": 22980363,\n \"score\": 1\n },\n {\n \"doc_id\": \"24572853\",\n \"title\": \"Determining the Michigan Hand Outcomes Questionnaire minimal clinically important difference by means of three methods.\",\n \"abstract\": \"BACKGROUND: To interpret patient-rated outcome measures, clinicians rely on the minimal clinically important difference. The authors studied the range of minimal clinically important difference scores for the overall Michigan Hand Outcomes Questionnaire score its and subscales in a population with various diagnoses and treatments. METHODS: Patients with a single, unilateral, atraumatic hand/forearm diagnosis completed the Michigan Hand Outcomes Questionnaire before treatment and at 4 ± 1 weeks and 12 ± 2 weeks after treatment. Three methods were used to calculate the minimal clinically important difference: two anchor question methods based on satisfaction (mean change and receiver operating characteristic) and a statistical distribution method. RESULTS: One hundred eighty-six patients were enrolled, with a baseline median overall questionnaire score of 60.7. Using the mean change method, a minimal clinically important difference of 13 was calculated for the overall questionnaire score. Using a receiver operating characteristic curve (0.8 effect size), the minimal clinically important difference was 9, with an area under the curve of 0.92. When receiver operating characteristic analysis was based on dichotomization of reported satisfaction, the minimal clinically important difference was 12, with an area under the curve of 0.85. Calculating the difference by statistical distribution gave a value of 8. For the subscales, by all methods, triangulated minimal clinically important difference estimates ranged from 10.9 to 14.4. CONCLUSIONS: The minimal clinically important difference for the overall Michigan Hand Outcomes Questionnaire score in atraumatic hand/forearm conditions falls between 8 and 13. Multiple analytic methods produce nonidentical but similar minimal clinically important differences. The authors recommend using difference estimates in these ranges when planning a clinical trial to investigate hand/forearm function across a range of diagnoses and treatments.\",\n \"corpus_id\": 205955797,\n \"score\": 1\n },\n {\n \"doc_id\": \"24605402\",\n \"title\": \"[Dupuytren's disease].\",\n \"abstract\": \"Dupuytren's disease is a fibromatosis affecting the hand. The disease affects the hand and fingers and may present with a contracture causing increasing disability of the hand. We can treat the symptoms but not its cause. In this article we review the background, diagnosis and methods of treatment of the disease. Although the mainstay of treatment accepted by most is surgical, use of collagenase injections aimed at chemically disintegrating pathologic cords may emerge as an important addition to the armamentarium of treatments for Dupuytren's disease.\",\n \"corpus_id\": 22187309,\n \"score\": 1\n },\n {\n \"doc_id\": \"24839417\",\n \"title\": \"Psychometric properties of health-related quality of life instruments in patients undergoing palmar fasciectomy for dupuytren's disease: a prospective study.\",\n \"abstract\": \"BACKGROUND: The traditional outcome measured following treatment of Dupuytren's Disease (DD) has been digital range of motion; specifically the gain in digital extension. The outcomes research movement in the last three decades however has been advocating the measurement of outcomes from the patient's perspective using Health-Related Quality of Life questionnaires (HRQOL). Although several generic and region-specific HRQOL questionnaires exist, there is no guidance as to which one is the most appropriate for this population. The objective of this study is to evaluate the psychometric properties of three self-reported HRQOL outcome measures in patients with DD. METHODS: Patients with DD were enrolled from the practices of three plastic surgeons. Test-retest reliability, concurrent validity and responsiveness of three HRQOL questionnaires were compared in a prospective study design. The HRQOL measures included Health Utilities Index Mark 3 (HUI3), Short Form-36 (SF-36), and the Michigan Hand Questionnaire (MHQ). RESULTS: All three measures demonstrated good test-retest reliability (ICC = 0.77-0.85). Concurrent validity was found between the HUI3 pain and dexterity attributes and SF-36 physical summary score. The sensitivity of the MHQ to detect changes in the status of the patient was found to be high (effect size = 1.14) whereas that of the SF-36 was trivial. CONCLUSIONS: The HUI3 and the MHQ seem to be reliable and valid tools to assess the HRQOL in patients with Dupuytren's Disease.\",\n \"corpus_id\": 207294246,\n \"score\": 1\n },\n {\n \"doc_id\": \"24900903\",\n \"title\": \"Responsiveness of the Korean version of the Michigan Hand Outcomes Questionnaire after carpal tunnel release.\",\n \"abstract\": \"BACKGROUND: The Korean version of the Michigan Hand Outcomes Questionnaire (K-MHQ) was recently validated; however, the questionnaire's responsiveness as well as the degree to which the instrument is sensitive to change has not been thoroughly evaluated in a specific condition in Koreans. We evaluated the responsiveness of the K-MHQ in a homogenous cohort of patients with carpal tunnel syndrome (CTS) and we compared it with that of the Korean version of the Disability of the Arm, Shoulder, and Hand Questionnaire (K-DASH), which was found to have a large degree of responsiveness after carpal tunnel release for Korean patients with CTS. METHODS: Thirty-seven patients with CTS prospectively completed the K-MHQ and the K-DASH before and 6 months after surgery. The responsiveness statistics were assessed for both the K-MHQ and the K-DASH by using the standardized response mean (SRM), which was defined as the mean change of the original scores after surgery divided by the standard deviation of the change. RESULTS: All domains of the K-MHQ significantly improved after carpal tunnel release (p < 0.001). The SRM for all scales but one (the aesthetics scale) showed large responsiveness of ≥ 0.8. The aesthetics scale showed medium responsiveness of 0.6. The combined function/symptom scale of the K-DASH significantly improved after surgery (p < 0.001). The SRM of the K-DASH revealed large responsiveness of 0.9. CONCLUSIONS: The K-MHQ was found to have a large degree of responsiveness after carpal tunnel release for Korean patients with CTS, which is comparable not only to the K-DASH, but also to the original version of the MHQ. The region-specific K-MHQ can be useful for outcomes research related to carpal tunnel surgery, especially for research comparing CTS with various other hand and wrist health conditions.\",\n \"corpus_id\": 10170030,\n \"score\": 1\n },\n {\n \"doc_id\": \"25358527\",\n \"title\": \"Psychometric evaluation of the Disabilities of the Arm, Shoulder and Hand (DASH) with Dupuytren's contracture: validity evidence using Rasch modeling.\",\n \"abstract\": \"BACKGROUND: Dupuytren's contracture is a progressive, fibroproliferative disorder that causes fixed finger contractures and can lead to disability. With the advances of new therapeutic interventions, the necessity to assess the functional repercussions of this condition using valid, reliable and sensitive outcome measures is of growing interest. The Disabilities of the Arm, Shoulder and Hand (DASH) is one frequently used patient-reported outcome measure but its reliability and validity have never been demonstrated specifically for a population affected with Dupuytren's contracture. The objective of this study was to evaluate the psychometric properties of the DASH, with focus on validity evidence using the Rasch measurement model. METHODS: Secondary analysis was performed on data collected as part of a randomised clinical trial. One hundred fifty-three participants diagnosed with Dupuytren's contracture completed the DASH at four time points (pre-op, 3, 6 and 12 months post-op). Baseline data were analysed using traditional analysis and to test whether they adhered to the expectations of the Rasch model. Post-intervention data were subsequently included and analyzed to determine the effect of the intervention on the items. RESULTS: DASH scores demonstrated large ceiling effects at all time points. Initial fit to the Rasch model revealed that the DASH did not adhere to the expectations of the Rasch partial credit model (χ2=119.92; p<0.05). Multiple items displayed inadequate response categories and two items displayed differential item functioning by gender. Items were transformed and one item deleted leading to an adequate fit. Remaining items fit the Rasch model but still do not target well the population under study. CONCLUSIONS: The original version of the 30-item DASH did not display adequate validity evidence for use in a population with Dupuytren's contracture. Further development is required to improve the DASH for this population.\",\n \"corpus_id\": 8398666,\n \"score\": 1\n },\n {\n \"doc_id\": \"26456499\",\n \"title\": \"Validity of the Michigan Hand Outcomes Questionnaire in Patients With Stroke.\",\n \"abstract\": \"OBJECTIVE: To investigate the measurement properties of the Dutch version of the Michigan Hand Outcomes Questionnaire (MHQ) in patients with stroke. DESIGN: Validation study. SETTING: Outpatient rehabilitation clinic. PARTICIPANTS: Consecutive patients with stroke (N=51; mean age, 60±11y; 16 women [31%]). INTERVENTIONS: Patients were asked to complete the MHQ (57 items) and Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36). Additional assessments included the Barthel Index and performance tests for hand function (Action Research Arm Test, Nine Hole Peg Test, Frenchay Arm Test, Motricity Index). MAIN OUTCOME MEASURES: Associations between the MHQ and other outcome measures were determined using Spearman correlation coefficients and the internal consistency of the MHQ using Cronbach α. Floor or ceiling effects were present if >15% of the patients scored minimal or maximal scores, respectively. Test-retest reliability was established by the intraclass correlation coefficient. RESULTS: The mean MHQ total score was 70.0±22.4, with Cronbach α being .97. The MHQ total score correlated significantly with the physical component summary of the SF-36, the Barthel Index, and all hand function performance tests (P<.01). The MHQ total score showed no floor or ceiling effects. The test-retest intraclass correlation coefficient was .97. CONCLUSIONS: This study provides preliminary evidence that the MHQ is an internally consistent, valid, and reliable hand function questionnaire in outpatients after stroke, although these results need to be further confirmed.\",\n \"corpus_id\": 1217569,\n \"score\": 1\n },\n {\n \"doc_id\": \"27454507\",\n \"title\": \"Reliability and Validity of the Japanese Version of the Michigan Hand Outcomes Questionnaire: A Comparison with the DASH and SF-36 Questionnaires.\",\n \"abstract\": \"BACKGROUND: The Michigan Hand Outcomes Questionnaire (MHQ) has shown reliability, validity and responsiveness and has been used to assess surgical outcomes mainly in North America. We established a Japanese version of the MHQ and evaluated its reliability and validity compared with both the short-form 36 (SF-36) questionnaire and the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire in a Japanese-speaking population. METHODS: The MHQ was cross-culturally adapted to a Japanese version according to guidelines. Sixty-eight patients with hand conditions were enrolled in this study and answered the MHQ, DASH questionnaire and SF-36 questionnaire. The MHQ was completed again with an interval of one or two weeks. Reproducibility and internal consistency were statistically assessed by the test-retest method and calculating Cronbach's alpha. Spearman's rank correlation was calculated to assess associations between the MHQ and the SF-36 questionnaire as well as the DASH questionnaire. RESULTS: The intraclass correlation coefficients of MHQ subscales ranged from 0.68 to 0.93. Aesthetics subscale of the left hand showed the lowest intraclass correlation but still a good correlation. Cronbach's alpha values of the MHQ ranged from 0.81 to 0.96 for all subscales. The absolute values of Spearman's rank correlation coefficient between MHQ subscales and DASH function/symptoms scores ranged from 0.49 to 0.82. Spearman's correlation coefficients of the MHQ total score to subscales of the SF-36 questionnaire ranged from 0.42 to 0.68. The strongest correlations were found between work performance of the MHQ and rolephysical of the SF-36 questionnaire. CONCLUSIONS: The Japanese version of the MHQ has adequate instrument properties for assessing hand outcomes compared with the SF-36 questionnaire as well as the DASH questionnaire.\",\n \"corpus_id\": 21441963,\n \"score\": 1\n },\n {\n \"doc_id\": \"27473921\",\n \"title\": \"Comparison of Treatment Outcome After Collagenase and Needle Fasciotomy for Dupuytren Contracture: A Randomized, Single-Blinded, Clinical Trial With a 1-Year Follow-Up.\",\n \"abstract\": \"PURPOSE: This study compared the efficacy of collagenase treatment and needle fasciotomy for contracture of the metacarpophalangeal (MCP) joint in Dupuytren disease. METHODS: This is a prospective, single-blinded, randomized study with follow-up 1 week and 1 year after treatment. One hundred and forty patients with an MCP contracture of 20° or more in a single finger were enrolled, of whom 69 patients were randomized to collagenase treatment and 71 patients to needle fasciotomy. The patients were followed at 1 week and were examined by a physiotherapist after 1 year. Measurements of joint movement and grip strength were recorded as well as patient-perceived outcomes measured by the Unité Rhumatologique des Affections de la Main (URAM) questionnaire and a visual analog scale (VAS) for the estimation of procedural pain and subjective treatment efficacy. RESULTS: Eighty-eight percent of the patients in the collagenase group and 90% of the patients in the needle fasciotomy group had a reduction in their MCP contracture to less than 5° 1 week after treatment, and the median gains in passive MCP movement were 48° and 46°, respectively. The median VAS score for procedural pain was 4.9 of 10 in the collagenase group and 2.7 of 10 in the needle fasciotomy group. After 1 year, 90% of the patients in both groups had full extension of the treated MCP joint. One patient in each group had a recurrence of the contracture. The median improvement in URAM score was 8 units in both groups and the VAS estimation of treatment efficacy by the patients was 8.7 of 10 in both groups. CONCLUSIONS: There was no significant difference between the treatment outcomes after collagenase and needle fasciotomy treatment after 1 year. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic I.\",\n \"corpus_id\": 10592543,\n \"score\": 1\n },\n {\n \"doc_id\": \"27556605\",\n \"title\": \"Predictors of Patient Satisfaction with Hand Function after Fasciectomy for Dupuytren's Contracture.\",\n \"abstract\": \"BACKGROUND: This study examined patient satisfaction with hand function after fasciectomy for Dupuytren's contracture and determined which preoperative patient- and disease-specific factors predicted this satisfaction. METHODS: Demographics and disease-specific factors were assessed from a prospective cohort of 194 patients who completed the Michigan Hand Outcomes Questionnaire preoperatively and underwent limited fasciectomy between 2011 and 2014 at six hand surgery practice sites. To evaluate satisfaction with hand function, patients were asked to complete the Michigan Hand Outcomes Questionnaire during the first year after fasciectomy. After patients were classified into a satisfied and an unsatisfied category using the question that specifically pertains to satisfaction with hand function, the authors applied multivariate logistic regression modeling to identify independent predictors of patient satisfaction. RESULTS: At an average of 10 months (range, 6 to 12 months) after fasciectomy, 84 percent (n = 163) of the patients were satisfied with their hand function. In multivariate analyses adjusting for the degree of postoperative residual contracture (p < 0.001) and complications (p < 0.001), a higher preoperative Michigan Hand Outcomes Questionnaire hand appearance subscore and male gender predicted a higher likelihood of becoming satisfied after fasciectomy. Other patient- and disease-specific factors did not show evidence for an association with patient satisfaction. CONCLUSIONS: The findings of this study suggest that providers should consider assessing concerns about the appearance of the hand in patients with Dupuytren's contracture. They also highlight the importance of complication prevention and full contracture correction from the patient's perspective. CLINICAL QUESTION/LEVEL OF EVIDENCE: Risk, III.\",\n \"corpus_id\": 205960525,\n \"score\": 1\n },\n {\n \"doc_id\": \"27682305\",\n \"title\": \"Effectiveness and safety of collagenase Clostridium histolyticum in Dupuytren's disease : an observational study in Belgium.\",\n \"abstract\": \"Dupuytren's disease is a connective tissue disorder leading to contractures. It can be treated surgically or through injections of collagenase Clostridium histolyticum (CCH). Patients with Dupuytren's contracture (> 20°) and a palpable cord were included in this observational study, aiming to characterise the Belgian patient population and to assess the effectiveness and safety of CCH. Overall, 108 patients (114 joints) received at least one injection of CCH, and 104 patients completed the study. The percentages of joints achieving a degree of contracture of 5° or less, or a relative contracture reduction of at least 50% after the extension procedure were 64.9% and 90.1%, respectively. The mean number of injections per cord was 1.0. The Unité Rhumatologique des Affections de la Main score decreased from 29.4 ± 11.0 to 12.9 ± 6.3 (mean ± SD ; p < 0.0001). CCH was demonstrated to be effective, safe and able to increase quality of life.\",\n \"corpus_id\": 7415691,\n \"score\": 1\n },\n {\n \"doc_id\": \"28118833\",\n \"title\": \"An empirical evaluation of the SF-12, SF-6D, EQ-5D and Michigan Hand Outcome Questionnaire in patients with rheumatoid arthritis of the hand.\",\n \"abstract\": \"BACKGROUND: The aim of this study was to assess the psychometric properties, namely acceptability, validity, reliability, interpretability and responsiveness of the EuroQol EQ-5D (EQ-5D visual analogue (VAS) and EQ-5D (utility)), Short Form 12 Dimensions (SF-12), SF-6D and Michigan Hand Outcome Questionnaire (MHQ) in patients with rheumatoid arthritis (RA) of the hand. METHODS: The empirical investigation was based upon data from a randomised controlled trial of 488 adults with rheumatoid arthritis who had pain and dysfunction of the hands and/or wrists. Participants completed the EQ-5D, SF-12 and MHQ at baseline and at 4 and 12 months follow up. Acceptability was measured using completion rates over time; construct validity using the \\\"known groups\\\" approach, based on pain troublesomeness; convergent validity using spearman's rho correlation (ρ); reliability using internal consistency (Cronbach's alpha); interpretability using minimal important differences (MID); and responsiveness using effect sizes and standardised response means (SRM) stratified by level of self-rated improvement in hand and wrist function or level of self-rated benefit and satisfaction from trial treatments. RESULTS: At baseline, the study population had a mean age of 62.4 years, a mean MHQ score of 52.1 and included 76% women. The EQ-5D (utility) had the highest completion rates across time points. All instruments discriminated between pre-specified groups based on pain troublesomeness. Convergent validity analysis indicated that the MHQ score correlated strongly with the EQ-5D (ρ = 0.65) and SF-6D (ρ = 0.63) utility scores. The MHQ was most responsive at detecting change in indicators of RA pain severity between baseline and 4 months, whilst minimal important differences varied considerably across PROMs. CONCLUSIONS: The instruments evaluated in this study displayed varying psychometric properties in the context of RA of the hand. The selection of a preferred instrument in evaluative studies should ultimately depend on the relative importance placed on individual psychometric properties and the importance placed on generation of health utilities for economic evaluation purposes.\",\n \"corpus_id\": 4463750,\n \"score\": 1\n },\n {\n \"doc_id\": \"28490266\",\n \"title\": \"Radiotherapy in Dupuytren's disease: a systematic review of the evidence.\",\n \"abstract\": \"Radiotherapy has been advocated as an alternative treatment in early Dupuytren's disease. We have systematically reviewed the evidence on the use of radiotherapy in Dupuytren's disease. Only six articles met a minimum set standard, five of which were retrospective cohort studies and one a randomized controlled study. A total of 770 Dupuytren's hands, nearly all with Tubiana stage 0-1 disease, were irradiated with an average 30 Gy. Disease regression ranged from 0%-56%, stability from 14%-98% and progression from 2%-86%. Salvage surgery was successful in all cases of disease progression post-radiotherapy. There were no reports of adverse wound healing problems associated with such surgery or radiotherapy-associated malignancy. On balance, radiotherapy should be considered an unproven treatment for early Dupuytren's disease due to a scarce evidence base and unknown long-term adverse effects. Well-designed randomized controlled studies are required to confirm the benefits of radiotherapy treatment. LEVEL OF EVIDENCE: II.\",\n \"corpus_id\": 206785758,\n \"score\": 1\n },\n {\n \"doc_id\": \"28595612\",\n \"title\": \"Responsiveness and minimal important change of the Norwegian version of the Disabilities of the Arm, Shoulder and Hand questionnaire (DASH) in patients with subacromial pain syndrome.\",\n \"abstract\": \"BACKGROUND: The Disabilities of the Arm, Shoulder, and Hand questionnaire (DASH) is a valid and reliable patient-reported outcome measure (PROM). It was designed to measure physical disability and symptoms in patients with musculoskeletal disorders of the upper extremity, and is one of the most commonly used PROMs for patients with shoulder pain. The aim of this study was to examine responsiveness, the smallest detectable change (SDC) and the minimal important change (MIC) of the DASH, in line with international (COSMIN) recommendations. METHODS: The study sample consisted of 50 patients with subacromial pain syndrome, undergoing physical therapy for 3-4 months. Responsiveness to change was examined by calculating area under the receiver operating characteristic curves (AUC) and testing a priori-formulated hypothesis regarding correlations with changes in other instruments that measuring the same construct. The SDC was calculated using a test re-test protocol, and the MIC was calculated by the anchor-based MIC distribution. MIC values for patients with low and high baseline scores were also calculated. RESULTS: DASH appeared to be responsive, as it was able to distinguish patients who reported to be improved from those unchanged (AUC 0.77). All of the hypotheses were accepted. The SDC was 11.8, and the MIC was 4.4. CONCLUSION: This study shows that the Norwegian version of the DASH has good responsiveness to change and may thus be recommended to measure outcome in patients with shoulder pain in Norway.\",\n \"corpus_id\": 4411658,\n \"score\": 1\n },\n {\n \"doc_id\": \"28774258\",\n \"title\": \"The Hand of Sabazios: Evidence of Dupuytren's Disease in Antiquity and the Origin of the Hand of Benediction.\",\n \"abstract\": \"Dupuytren's disease gained its eponym from the surgeon Baron Guillaume Dupuytren (1777-1835). However, the terms \\\"Cline's contracture\\\" and \\\"Cooper's contracture,\\\" named after the two surgeons who proposed the treatment for the palmar contractures prior to Dupuytren, have also been used to describe the disease. In addition to the eponyms attributed to these three surgeons, a number of other appellations with interesting provenance exist for Dupuytren's disease including the \\\"Curse of the MacCrimmons,\\\" \\\"Celtic hand,\\\" \\\"Viking's disease,\\\" and the \\\"Hand of Benediction.\\\" These terms all have interesting provenance; however, contention exists with regard to the appropriateness of their coinage. Of these terms, the \\\"Hand of Benediction\\\" is based upon the oldest history, supposedly thought to be a result of an early Pope afflicted with Dupuytren's disease. This report suggests that Dupuytren's disease was recorded in history prior Christianity, the Vikings, as well as Dupuytren, Cline, and Cooper. Nearly 100 votive \\\"Hand of Sabazios\\\" artifacts from Antiquity appear to document Dupuytren's disease via sculpture. The report posits that Dupuytren's disease may have been represented by the \\\"Hand of Sabazios,\\\" subsequently inspiring the \\\"Hand of Benediction\\\" and \\\"Hand of God\\\" that has permeated Christian art and culture for thousands of years.\",\n \"corpus_id\": 5264100,\n \"score\": 1\n },\n {\n \"doc_id\": \"28893147\",\n \"title\": \"The Polish version of the Michigan Hand Outcomes Questionnaire: Cross-cultural adaptation, reliability, construct validity, and measurement error.\",\n \"abstract\": \"The aims of this study were to translate the Michigan Hand Outcomes Questionnaire into the Polish language and to test the measurement properties of its quality criteria. A total of 120 patients with hand complaints completed the Polish Michigan Hand Outcomes Questionnaire and the Disabilities of the Arm, Shoulder, and Hand questionnaire on the first assessment, along with the grip test, pinch test, and pain sore assessed using a visual analogue scale during activity. After 7 days, 76 patients completed the Michigan Hand Outcomes Questionnaire the second time. The Cronbach alpha of the Michigan Hand Outcomes Questionnaire subscales ranged from 0.79 to 0.96. The intraclass correlation coefficient varied from 0.82-0.97, and the Bland-Altman method indicated the Michigan Hand Outcomes Questionnaire total score limit of agreement was -13.2-12.3 and -9.18-9.62 for the right and left hand, respectively. The construct validity revealed a moderate to strong correlation between every subscale of the Polish Michigan Hand Outcomes Questionnaire and Disabilities of the Arm, Shoulder, and Hand, but they only correlated with the grip test and the visual analogue scale, and neither correlated with the pinch test. The study demonstrated properties similar to the original version, validating the belief that the use of this questionnaire in medical practice in Poland is justified.\",\n \"corpus_id\": 1631239,\n \"score\": 1\n },\n {\n \"doc_id\": \"29062986\",\n \"title\": \"Cultural adaptation of the Michigan Hand Outcomes Questionnaire in patients with Carpal Tunnel Syndrome: A Turkish version study.\",\n \"abstract\": \"OBJECTIVE: Cultural adaptations of the questionnaires are important for easy use. We aimed to assess the reliability and validity of the Turkish Version of the Michigan Hand Outcomes Questionnaire in patients with Carpal Tunnel Syndrome. METHODS: To assess test-retest reliability, the Turkish \\\"Michigan Hand Outcomes Questionnaire\\\" and \\\"Disabilities of Arm, Shoulder and Hand\\\" questionnaires were answered by patients and controls and were repeated a week later. For testing internal consistency, the Cronbach's alpha test was used. For testing validity, correlations between the subscales of the \\\"Michigan Hand Outcomes Questionnaire\\\" and \\\"Disabilities of Arm, Shoulder and Hand\\\" questionnaire were measured in patient groups. One hundred patients with idiopathic Carpal Tunnel Syndrome and 50 healthy participants were included in the study. RESULTS: In test-retest reliability, intraclass correlations of the subscales of the \\\"Michigan Hand Outcomes Questionnaire\\\" were high. Cronbach's alphas were found to be high in all subscales. There was no significant correlation between asthetics and pain scales. We found significant differences between patients and controls regarding all subscales of the \\\"Michigan Hand Outcomes Questionnaire\\\". Correlations between subscales of the \\\"Michigan Hand Outcomes Questionnaire\\\" and \\\"Disabilities of Arm, Shoulder and Hand\\\" questionnaire were significant. We found no difference between one-hand effected and two-hand effected patients, in terms of the \\\"Michigan Hand Outcomes Questionnaire\\\", \\\"Disabilities of Arm, Shoulder and Hand\\\" questionnaire Function/Symptom and Work average scores. CONCLUSION: This study showed that the Turkish version of the \\\"Michigan Hand Outcomes Questionnaire\\\" is reliable and valid and can be used in Turkish patients with Carpal Tunnel Syndrome because it is comprehensible and practicable.\",\n \"corpus_id\": 31731253,\n \"score\": 1\n },\n {\n \"doc_id\": \"29799370\",\n \"title\": \"Michigan Hand Outcomes Questionnaire for the Evaluation of Patients with Mucopolysaccharidosis.\",\n \"abstract\": \"This study evaluates hand functioning in patients with mucopolysaccharidosis (MPS) and validates the Michigan Hand Outcomes Questionnaire (MHQ) as a measure of hand functioning evaluation. Patients with diagnosis of MPS between the ages of 8 and 21 years were eligible for enrolment in the study irrespective of whether they were or were not receiving treatment (enzyme replacement therapy). Individuals with mental disorders and those who had already undergone hand surgery were excluded. Clinical and demographic data were collected as well as hand functioning evaluation based on the Brazilian-Portuguese version of the MHQ. The global score and domains score of the entire group is presented. With regard to the validation of the MHQ, internal consistency of the domains were evaluated using Cronbach's α correlation coefficient. Ten individuals were women and six were men; two were type II MPS and 14 were type VI. Mean age was 11.7 ± 4.4 years and five patients had signs and symptoms suggestive of carpal tunnel syndrome. The MHQ global and domains mean scores were: global, 56.68 ± 16.17; hand function, 64.17 ± 21.62; activities of daily living, 46.87 ± 27.78; school performance, 56.01 ± 32.69; pain, 79.33 ± 30.87; aesthetics, 77.81 ± 11.16; and satisfaction, 74.57 ± 27.16. Global and domain internal consistency were: global, 0.888 (good); hand function, 0.815 (good); activities of daily living, 0.873 (good); school performance, 0.815 (good); pain, 0.468 (poor); aesthetics, -0.044 (unacceptable); and satisfaction.\",\n \"corpus_id\": 44160955,\n \"score\": 1\n },\n {\n \"doc_id\": \"20025754\",\n \"title\": \"Measurement properties of the Dizziness Handicap Inventory by cross-sectional and longitudinal designs.\",\n \"abstract\": \"BACKGROUND: The impact of dizziness on quality of life is often assessed by the Dizziness Handicap Inventory (DHI), which is used as a discriminate and evaluative measure. The aim of the present study was to examine reliability and validity of a translated Norwegian version (DHI-N), also examining responsiveness to important change in the construct being measured. METHODS: Two samples (n = 92 and n = 27) included participants with dizziness of mainly vestibular origin. A cross-sectional design was used to examine the factor structure (exploratory factor analysis), internal consistency (Cronbach's alpha), concurrent validity (Pearson's product moment correlation r), and discriminate ability (ROC curve analysis). Longitudinal designs were used to examine test-retest reliability (intraclass correlation coefficient (ICC) statistics, smallest detectable difference (SDD)), and responsiveness (Pearson's product moment correlation, ROC curve analysis; area under the ROC curve (AUC), and minimally important change (MIC)). The DHI scores range from 0 to 100. RESULTS: Factor analysis revealed a different factor structure than the original DHI, resulting in dismissal of subscale scores in the DHI-N. Acceptable internal consistency was found for the total scale (alpha = 0.95). Concurrent correlations between the DHI-N and other related measures were moderate to high, highest with Vertigo Symptom Scale-short form-Norwegian version (r = 0.69), and lowest with preferred gait (r = - 0.36). The DHI-N demonstrated excellent ability to discriminate between participants with and without 'disability', AUC being 0.89 and best cut-off point = 29 points. Satisfactory test-retest reliability was demonstrated, and the change for an individual should be >/= 20 DHI-N points to exceed measurement error (SDD). Correlations between change scores of DHI-N and other self-report measures of functional health and symptoms were high (r = 0.50 - 0.57). Responsiveness of the DHI-N was excellent, AUC = 0.83, discriminating between self-perceived 'improved' versus 'unchanged' participants. The MIC was identified as 11 DHI-N points. CONCLUSIONS: The DHI-N total scale demonstrated satisfactory measurement properties. This is the first study that has addressed and demonstrated responsiveness to important change of the DHI, and provided values of SDD and MIC to help interpret change scores.\",\n \"corpus_id\": 17860663,\n \"score\": 0\n },\n {\n \"doc_id\": \"21277691\",\n \"title\": \"Focused extracorporeal shockwave therapy in Dupuytren's disease--a hypothesis.\",\n \"abstract\": \"Dupuytren's disease is a progressive disease due to unknown causal agents or genetics. An epidemiological analysis of 566 cases in North Germany estimated that around 1.9 million Germans are suffering from Dupuytren's disease. Beside Dupuytren's disease, there are a number of further less common forms of progressive fibromatosis, such as knuckle pads, plantar fibromatosis or Peyronie's disease. Surgery in plantar fasciectomy yields to a 60% recurrence rate depending on the extent of the plantar fasciectomy. Peyronie's disease of the penis affects middle-aged men between 40 and 60 years with penile pain, curvature during erection and potential erectile dysfunction. In a clinical randomized-controlled trial in Peyronie's disease 2000 focused extracorporeal shock waves reduced pain significantly and improved erectile function and quality of life. We hypothesize that focused extracorporeal shock wave therapy is able to reduce Dupuytren's contracture, a fibromatosis of the palm and improve function. Given the fact that recurrence rate in Dupuytren's disease is high und unpredictable extracorporeal shockwave therapy as a non-invasive tool might be applicable both, in primary and secondary prevention of the progression as well as for treatment. As such we have planned a randomized-controlled trial (ClinicialTrials.gov, NCT01184586) studying the effect of high-energy focused extracorporeal shockwave therapy on patients suffering Dupuytren's disease with patient-related outcome measures such as the DASH score and the Michigan Hand Outcome Questionnaire (MHQ) as primary outcome parameters.\",\n \"corpus_id\": 25381674,\n \"score\": 0\n },\n {\n \"doc_id\": \"22288720\",\n \"title\": \"Body awareness rating questionnaire: measurement properties.\",\n \"abstract\": \"The purpose of present study was to investigate important measurement properties of the Body Awareness Rating Questionnaire (BARQ) subscales: Function; Mood; Feelings; and Awareness. Samples of 50 patients with prolonged musculoskeletal pain and psychosomatic disorders, and 50 gender and age-matched healthy persons participated in the study. Relative (ICC 2,1) and absolute reliability (S(w)) were calculated. Construct validity was examined by testing hypothesis using Pearson (r) or Spearman rank (r(s)) correlation. Discriminate ability was examined using a receiver operating characteristic (ROC) curve, the area under the curve (aROC) being the measure of discriminative validity. All patients reported more or less improvement after treatment, using the Patient Global Impression of Change (PGIC) as an external indicator of important change. Responsiveness to important change was therefore examined by one-way repeated measures analysis of variance (ANOVA), relating change scores of BARQ subscales to the PGIC categories. Relative and absolute reliability values were within recommended limits for all four subscales. Construct and discriminate validity was indicated for Function, Feelings and Awareness, but not for Mood. Responsiveness was indicated for the subscales Function and Awareness, but not for Feelings and Mood. Further research is needed to complement the subscales of BARQ, found with appropriate measurement properties.\",\n \"corpus_id\": 37180124,\n \"score\": 0\n },\n {\n \"doc_id\": \"22748143\",\n \"title\": \"The Dutch Lower Extremity Functional Scale was highly reliable, valid and responsive in individuals with hip/knee osteoarthritis: a validation study.\",\n \"abstract\": \"BACKGROUND: The WOMAC is the most widely used self-report measure to evaluate physical functioning in hip or knee osteoarthritis, however its ability to discriminate pain and physical functioning (i.e. discriminate validity) has repeatedly been questioned. Little to no data is available on the discriminant validity of alternative questionnaires that measure the same construct, for instance the Hip and Knee Osteoarthritis Outcome Score (HOOS and KOOS, respectively) and the Lower Extremity Function Scale (LEFS). Therefore, we translated the LEFS to Dutch and studied its psychometric properties (i.e. validity, reliability and responsiveness). In addition, we assessed the discriminate validity of the LEFS, HOOS and KOOS. METHODS: After translation with a forward/backward protocol, 401 individuals with hip or knee osteoarthritis completed the LEFS, HOOS/KOOS, SF-36, Hospital Anxiety and Depression Scale and Checklist Individual Strength questionnaires. To assess reliability and responsiveness, a sample of 106 and 108 patients completed a comparable set of questionnaires within 3 weeks and 3 months, respectively. Feasibility, validity, reliability and responsiveness were evaluated. Discriminant validity of the LEFS, HOOS and KOOS was examined by contrasting the scales' correlations with the physical functioning subscale of the SF-36 with the scales' correlations with the bodily pain subscale of the SF-36. RESULTS: The Dutch version of the LEFS was feasible, had good internal consistency (0.96), good reliability (ICC = 0.86), good construct and discriminant validity, and showed no floor or ceiling effects. The minimal detectable change (MDC90) was ten points. Area under the receiver operating characteristic curve (AUC) analyses revealed good (AUC = 0.76) and fair (AUC = 0.63) responsiveness for the LEFS in improved and worsened patients, respectively. Discriminant validity for pain was apparent for the LEFS (p < 0.01), but not for the HOOS and KOOS (p = 0.21 and p = 0.20, respectively). CONCLUSIONS: Considering the LEFS' good psychometric qualities and ability to discriminate between pain and functioning, we recommend the LEFS as the outcome measure of choice to assess self-reported physical functioning in individuals with hip or knee osteoarthritis.\",\n \"corpus_id\": 8941616,\n \"score\": 0\n },\n {\n \"doc_id\": \"23431165\",\n \"title\": \"Unraveling the signaling pathways promoting fibrosis in Dupuytren's disease reveals TNF as a therapeutic target.\",\n \"abstract\": \"Dupuytren's disease is a very common progressive fibrosis of the palm leading to flexion deformities of the digits that impair hand function. The cell responsible for development of the disease is the myofibroblast. There is currently no treatment for early disease or for preventing recurrence following surgical excision of affected tissue in advanced disease. Therefore, we sought to unravel the signaling pathways leading to the development of myofibroblasts in Dupuytren's disease. We characterized the cells present in Dupuytren's tissue and found significant numbers of immune cells, including classically activated macrophages. High levels of proinflammatory cytokines were also detected in tissue from Dupuytren's patients. We compared the effects of these cytokines on contraction and profibrotic signaling pathways in fibroblasts from the palmar and nonpalmar dermis of Dupuytren's patients and palmar fibroblasts from non-Dupuytren's patients. Exogenous addition of TNF, but not other cytokines, including IL-6 and IL-1β, promoted differentiation into specifically of palmar dermal fibroblasts from Dupuytren's patients in to myofibroblasts. We also demonstrated that TNF acts via the Wnt signaling pathway to drive contraction and profibrotic signaling in these cells. Finally, we examined the effects of targeted cytokine inhibition. Neutralizing antibodies to TNF inhibited the contractile activity of myofibroblasts derived from Dupuytren's patients, reduced their expression of α-smooth muscle actin, and mediated disassembly of the contractile apparatus. Therefore, we showed that localized inflammation in Dupuytren's disease contributes to the development and progression of this fibroproliferative disorder and identified TNF as a therapeutic target to down-regulate myofibroblast differentiation and activity.\",\n \"corpus_id\": 9917433,\n \"score\": 0\n },\n {\n \"doc_id\": \"23750436\",\n \"title\": \"[An attempt to objectify the assessment of extension or recurrence of Dupuytren's disease on the basis of ultrasound].\",\n \"abstract\": \"Próba obiektywizacji oceny nawrotu lub wznowy choroby Dupuytrena w oparciu o badanie ultrasonograficzne. Dupuytren's contracture is a disease of unknown etiology, leading with time to decreased hand function caused by increasing contracture of fingers. Excision of contracted longitudinal palmar fascia constitutes the most important way of treatment. Due to fact that disease has progressive course in many patients recurrence (i.e. overgrowth of longitudinal palmar aponeurosis apart from the operated site) or extension (i.e. similar process affecting formerly operated site) occurs. An attempt to objectify the assessment of recurrence or extension of Dupuytren's disease on the basis of sonographic examination of palmar surface of the hand during distant (at least 24 months from surgery) followup constituted the aim of the study. 41 patients operated on from January 2000 to February 2009 in 2nd Department of General Surgery in Krakow due to Dupuytren's contracture constituted the study material. Mean age of the patients reached 62,78 years (SD +/- 9,32), and mean follow up time 5,74 years (SD +/- 2,90). Sonographic assessment was performed in 26 operated on left hands and 24 right hands. 9 patients had both hands operated on. In most of the patients during surgery the contralateral hand was also affected by the disease. Extension of Dupuytren's disease was found in 11 hands, recurrence--in 18 hands, while concurrent extension and recurrence was found in 17 hands. Extension usually was found on the radial side and affected mainly I interphalangeal space followed by disease affecting I and III ray of the hand. In one patient 2 independent foci of the disease were found within I interphalangeal space. Recurrences affected mainly ulnar side of the hand: V and IV rays of the hand. Concurrently found extension and recurrence affected 2 or 3 rays. In the cases of 3 rays affected extension dominated (2 rays vs. 1 ray of recurrence). On sonographic assessment mean diameters of lesions during distant follow- up were 12,69 x 4,62 x 3,95 [mm] with recurrent lesions being larger than mean values found in extensions. With partial fasciectomy being the most commonly performed operation in cases of Dupuytren's disease ultrasound can constitute very important technique of assessment of exacerbation of the lesions of palmar aponeurosis allowing for the choice of appropriate surgical technique for particular case, detection of postoperative extension and/or recurrence and for the cases clinically doubtful.\",\n \"corpus_id\": 32313277,\n \"score\": 0\n },\n {\n \"doc_id\": \"23893345\",\n \"title\": \"Measurement properties of the Work Limitations Questionnaire were sufficient among cancer survivors.\",\n \"abstract\": \"PURPOSE: The purpose of this study was to determine reproducibility, validity, and responsiveness of the Work Limitations Questionnaire (WLQ) among cancer survivors. METHODS: A cohort of 53 cancer survivors completed the WLQ and other questionnaires at baseline, 4-week, and 6-month follow-up. We assessed internal consistency, intraclass correlation coefficient, standard error of measurement, floor- and ceiling effects and compared the WLQ with other constructs. For responsiveness, we assessed the following anchor-based measures: minimal important change (MIC) versus smallest detectable change (SDC) and area under the curve (AUC) of receiver operation characteristic (ROC). RESULTS: We found sufficient reproducibility at group level but not at individual level as the MIC (4.0) exceeded SDC at group level (3.1) but not at individual level (18.0). There was no indication of systematic bias or proportional bias. The internal consistency and construct validity for the WLQ and its subscales were sufficient or slightly less than sufficient. There was a floor effect for one subscale, but there were no ceiling effects. Responsiveness was sufficient with an AUC of a ROC of 0.65. CONCLUSIONS: The WLQ is reproducible, valid, and responsive for use at group level among cancer survivors but not sufficiently reproducible for use at individual level.\",\n \"corpus_id\": 23084589,\n \"score\": 0\n },\n {\n \"doc_id\": \"23975101\",\n \"title\": \"Social participation in older adults with joint pain and comorbidity; testing the measurement properties of the Dutch Keele Assessment of Participation.\",\n \"abstract\": \"OBJECTIVE: The Keele Assessment of Participation (KAP) questionnaire measures person-perceived participation in 11 aspects of life. Participation allows fulfilment of valued life activities and social roles, which are important to older adults. Since we aimed to use the KAP in a larger Dutch cohort, we examined the measurement properties of KAP in a Dutch sample of older adults with joint pain and comorbidity. DESIGN: Cohort study. SETTING: A community-based sample in Amsterdam, the Netherlands and North Staffordshire, UK. PARTICIPANTS: Participants were aged 65 years and over, had at least two chronic diseases (identified through general practice consultation) and reported joint pain on most days (questionnaire). The Dutch cohort provided baseline data (n=407), follow-up data at 6 months (n=364) and test-retest data 2 weeks after 6 months (n=122). The UK cohort provided comparable data (n=404). OUTCOME MEASURES: The primary outcome was person-perceived participation, as measured with the KAP. The measurement properties examined were the following: structural validity (factor analysis), internal consistency (Cronbach's α), reliability (intraclass correlation coefficients; ICC), construct validity (hypothesis testing), responsiveness (hypothesis testing and area under the curve) and cross-cultural validity (differential item functioning; DIF). RESULTS: Factor analysis revealed two domains: KAPd1: 'participation in basic activities' and KAPd2: 'participation in complex activities', with Cronbach's α of 0.74 and 0.57 and moderate test-retest reliability: ICC of 0.63 and 0.57, respectively. Further analyses of KAPd1 showed poor construct validity and responsiveness. Despite the uniform DIF in item 'interpersonal relations', the total KAPd1 score seemed comparable between the Dutch and UK sample. CONCLUSIONS: Only KAP domain 'participation in basic activities' showed good internal consistency and sufficient reliability. KAPd2 lacks sufficient measurement properties for application in studies, although items may be used as single items. Further development of the concept 'participation' may help the development and validation of instruments to measure participation.\",\n \"corpus_id\": 3126350,\n \"score\": 0\n },\n {\n \"doc_id\": \"24257471\",\n \"title\": \"The Otitis Media-6 questionnaire: psychometric properties with emphasis on factor structure and interpretability.\",\n \"abstract\": \"BACKGROUND: The Otitis Media-6 questionnaire (OM-6) is the most frequently used instrument to measure health related quality of life in children with otitis media. The main objectives of this study are 1) to translate and cross-culturally adapt the OM-6 into Danish, and 2) to assess important psychometric properties including structural validity and interpretability of the OM-6 in a Danish population of children suffering from otitis media. METHODS: The OM-6 was translated and cross-culturally adapted according to international guidelines. A longitudinal validation study enrolled 491 children and their families, and the measurement properties of the OM-6 were evaluated using the Cosmin taxonomy. The properties assessed were construct and structural validity (confirmatory factor analysis) including internal consistency, reproducibility (test-retest reliability and smallest detectable change), responsiveness and interpretability. RESULTS: A total of 435 children were eligible to participate in the study. Analyses of structural validity and internal consistency indicated that parent appraisal of hearing and speech problems may be problematic. Both scales showed similarly good test-retest reliability and construct validity, were able to discriminate between diagnostic subgroups and responsive to change. Cut-off values of 16.7 and 30.0 were found to represent minimal important change for the patients. CONCLUSIONS: The Danish version of the OM-6 is a reliable, valid, responsive and interpretable questionnaire to measure quality of life in children with otitis media. This study sheds light on possible weaknesses of the instrument that needs to be acknowledged in the utilization of the instrument. However, despite these issues our results support the continuing use of OM-6 as a 1-factor functional health scale with a separate global health rating. Furthermore, indications of values representing minimal important change as perceived by the respondent are presented.\",\n \"corpus_id\": 14126783,\n \"score\": 0\n },\n {\n \"doc_id\": \"24445668\",\n \"title\": \"Validation of the Pelvic Floor Distress Inventory (PFDI-20) and Pelvic Floor Impact Questionnaire (PFIQ-7) in a Dutch population.\",\n \"abstract\": \"INTRODUCTION AND HYPOTHESIS: The objective of this study was to validate the Pelvic Floor Distress Inventory (PFDI-20) and Pelvic Floor Impact Questionnaire (PFIQ-7) in Dutch women. METHODS: Patients with pelvic floor dysfunction completed the Dutch questionnaires at (1) inclusion to evaluate internal consistency, (2) 1 week later to assess test-retest reliability, and (3) 6 months later to assess responsiveness and interpretability of change. To assess validity, floor and ceiling effects and construct validity were tested. A population-based sample (reference group) completed the questionnaires once. RESULTS: Data of 111 patients and 283 reference group participants were analyzed. Internal consistency of baseline scores in patient and reference groups was moderate (Cronbach's alpha 0.52-0.60) to adequate in the PFDI-20 (Cronbach's alpha 0.71-0.84) and adequate in the PFIQ-7 (Cronbach's alpha 0.88-0.94). Both measures presented adequate test-retest reliability (intraclass correlation coefficient 0.79-0.91) and adequate responsiveness (area under the receiver-operating characteristic curve both 0.77). Interpretability was adequate for PFDI-20 and acceptable for PFIQ-7 with a clinically relevant minimally important change of -23 and -29 points, respectively. At baseline, the scales of the PFIQ-7 showed floor effects (44-55 %) in patients, though the PFIQ-7 summary score did not. No ceiling effects were observed. Construct validity was adequate with all predefined hypotheses confirmed regarding subgroup discrimination using pooled patient and reference group baseline data. CONCLUSIONS: For assessing distress and health-related quality of life of pelvic floor dysfunction, the Dutch PFDI-20 and PFIQ-7 are reliable and valid in the general Dutch population, and also responsive and interpretable among tertiary care-seeking women.\",\n \"corpus_id\": 33954586,\n \"score\": 0\n },\n {\n \"doc_id\": \"26704805\",\n \"title\": \"Evaluation of the Dutch version of the Foot and Ankle Outcome Score (FAOS): responsiveness and Minimally Important Change.\",\n \"abstract\": \"PURPOSE: The aim of this study was to evaluate the responsiveness of the Foot and Ankle Outcome Score (FAOS) and provide data on the Minimally Important Change (MIC) in patients 1 year after hindfoot and ankle surgery. METHODS: Prospective pre-operative and 1 year post-operative FAOS scores were collected from 145 patients. A patient's global assessment and a longitudinal derived Function Change Score were used as external anchors. To assess responsiveness, effect sizes (ES) and Standardized Response Means (SRM) were calculated and hypotheses on their magnitudes were formulated. Additional ROC curve analysis was performed, and the Area Under the Curve (AUC) was calculated as a measure of responsiveness. MIC values were estimated using two different methods: (1) the mean change method and (2) the optimal cut-off point of the ROC curve. RESULTS: Responsiveness was supported by confirmation of 84 % of the hypothesized ES and SRM and almost all AUCs exceeding 0.70. MIC values ranged from 7 (symptoms) to 38 (sport) points. They varied between calculation methods and were negatively associated with baseline values. A considerable amount of MIC values did not exceed the smallest detectable change limit, indicating that the FAOS is more suitable at group level than for longitudinally following individual patients. CONCLUSIONS: The FAOS demonstrated good responsiveness in patients 1 year after hindfoot and ankle surgery. Due to their wide variation, MIC estimates derived in this study should be interpreted with caution. However, these estimates can be of value to facilitate sample size calculation in future studies. LEVEL OF EVIDENCE: Diagnostic study, Level I.\",\n \"corpus_id\": 19380692,\n \"score\": 0\n },\n {\n \"doc_id\": \"27506524\",\n \"title\": \"Responsiveness and minimal important change for the ProFitMap-neck questionnaire and the Neck Disability Index in women with neck-shoulder pain.\",\n \"abstract\": \"PURPOSE: The aim was to determine the responsiveness and minimal important change (MIC) of the questionnaire ProFitMap-neck that measures symptoms and functional limitations in women with neck pain. The same measurement properties were determined for Neck Disability Index (NDI) for comparison purposes. METHODS: Longitudinal data were derived from two randomized controlled trials, including 103 and 120 women with non-specific neck pain, with questionnaire measurements performed before and after interventions. Sensitivity and specificity to discriminate between improved and not or little changed participants, based on categorization of a global rating of change scale (GRCS), were determined for the ProFitMap-neck indices and NDI by using area under receiver operating characteristic curves (AUC). Correlations between the GRCS anchor and change scores of the questionnaires were also used to assess responsiveness. The change score that showed the highest combination of sensitivity and specificity was set for MIC. RESULTS: The ProFitMap-neck indices showed similar responsiveness as NDI with AUC exceeding 0.70 (Range: ProFitMap-neck, 0.74-0.83; NDI, 0.75-0.86). The MIC in the two samples ranged between 6.6 and 13.6 % for ProFitMap-neck indices and 5.2 and 6.3 % for NDI. Both questionnaires had significant correlations with GRCS (Spearman's rho 0.47-0.72). CONCLUSIONS: Validity of change scores was endorsed for the ProFitMap-neck indices and NDI with adequate ability to discriminate between improved and not or little changed participants. Values of minimal important change were presented.\",\n \"corpus_id\": 12160392,\n \"score\": 0\n },\n {\n \"doc_id\": \"27780237\",\n \"title\": \"Psychometric Properties of a Generic, Patient-Centred Palliative Care Outcome Measure of Symptom Burden for People with Progressive Long Term Neurological Conditions.\",\n \"abstract\": \"BACKGROUND: There is no standard palliative care outcome measure for people with progressive long term neurological conditions (LTNC). This study aims to determine the psychometric properties of a new 8-item palliative care outcome scale of symptom burden (IPOS Neuro-S8) in this population. DATA AND METHODS: Data were merged from a Phase II palliative care intervention study in multiple sclerosis (MS) and a longitudinal observational study in idiopathic Parkinson's disease (IPD), multiple system atrophy (MSA) and progressive supranuclear palsy (PSP). The IPOS Neuro-S8 was assessed for its data quality, score distribution, ceiling and floor effects, reliability, factor structure, convergent and discriminant validity, concurrent validity with generic (Palliative care Outcome Scale) and condition specific measures (Multiple Sclerosis Impact Scale; Non-motor Symptoms Questionnaire; Parkinson's Disease Questionnaire), responsiveness and minimally clinically important difference. RESULTS: Of the 134 participants, MS patients had a mean Extended Disability Status Scale score 7.8 (SD = 1.0), patients with an IPD, MSA or PSP were in Hoehn & Yahr stage 3-5. The IPOS Neuro-S8 had high data quality (2% missing), mean score 8 (SD = 5; range 0-32), no ceiling effects, borderline floor effects, good internal consistency (Cronbach's α = 0.7) and moderate test-retest reliability (intraclass coefficient = 0.6). The results supported a moderately correlated two-factor structure (Pearson's r = 0.5). It was moderately correlated with generic and condition specific measures (Pearson's r: 0.5-0.6). There was some evidence for discriminant validity in IPD, MSA and PSP (p = 0.020), and for good responsiveness and longitudinal construct validity. CONCLUSIONS: IPOS Neuro-S8 shows acceptable to promising psychometric properties in common forms of progressive LTNCs. Future work needs to confirm these findings with larger samples and its usefulness in wider disease groups.\",\n \"corpus_id\": 6751389,\n \"score\": 0\n },\n {\n \"doc_id\": \"28158958\",\n \"title\": \"The Responsiveness and Interpretability of the Shoulder Pain and Disability Index.\",\n \"abstract\": \"Study Design Clinical measurement study, prospective cohort design. Background Shoulder pain is a common disorder, and treatment is most often focused on a reduction of pain and functional disabilities. Several reviews have encouraged the use of the Shoulder Pain and Disability Index (SPADI) to objectify functional disability. It is important to assess the responsiveness and interpretability of the SPADI in patients seeking physical therapy treatment for their shoulder pain in a primary care setting. Objective To assess the responsiveness and interpretability of the SPADI in patients with shoulder pain visiting a physical therapist in primary care. Methods The target population consisted of patients who consulted a physical therapist for their shoulder pain. The patients received physical therapy treatment and completed the Dutch-language version of the SPADI at baseline and at 26-week follow-up. The interpretability floor and ceiling effects and the minimal important change (MIC) were assessed using the receiver operating characteristic method, and a visual anchor-based MIC distribution method was used to assess several Global Perceived Effect scale (GPE)-based anchors. The measurement error was calculated using the smallest detectable change. For the responsiveness, the area under the receiver operating characteristic curve was used, and correlations with the GPE and the change score of the Shoulder Disability Questionnaire (as this questionnaire measures the same construct) were assessed. Results A total of 356 patients participated at baseline and 237 (67%) returned the SPADI after 26 weeks. The mean score on the SPADI at baseline was 46.7 points (on a 0-100 scale). The SPADI showed no signs of floor and ceiling effects. The smallest detectable change was 19.7 points. The MIC was 20 (43% of baseline value), and therefore a change of 43% or more in an individual patient was considered to be clinically relevant. The area under the receiver operating characteristic curve (AUC) was 0.81, the Spearman correlation between the SPADI change score and the GPE was 0.53, and the Pearson correlation between the Shoulder Disability Questionnaire and the SPADI change score was 0.71. Conclusion The results of this study confirm the responsiveness of the SPADI, making it a useful instrument to assess functional disability in longitudinal studies; however, the measurement error should be taken into account when making decisions in individual patients. J Orthop Sports Phys Ther 2017;47(4):278-286. Epub 3 Feb 2017. doi:10.2519/jospt.2017.7079.\",\n \"corpus_id\": 37439348,\n \"score\": 0\n },\n {\n \"doc_id\": \"28658044\",\n \"title\": \"The Modified Low Back Pain Disability Questionnaire: Reliability, Validity and Responsiveness of a Dutch Language Version.\",\n \"abstract\": \"STUDY DESIGN: Cross sectional study OBJECTIVE.: The goal of this study is to translate the English version of the Modified Low Back Pain Disability Questionnaire (MDQ) into a Dutch version and investigate its clinimetric properties for patients with nonspecific chronic low back pain (CLBP). SUMMARY OF BACKGROUND DATA: Fritz et al (2001) developed a modified version of the Oswestry Disability Questionnaire (ODI) to assess functional status and named it the MDQ. In this version, a question regarding employment and homemaking ability was substituted for the question related to sex life. Good clinimetric properties for the MDQ were identified but up until now it is not clear if the clinimetric properties of the MDQ would change if it was translated into a Dutch version. METHODS: translation of the MDQ into Dutch was done in four steps. Test-retest reliability was investigated using the intraclass correlation coefficient (ICC) model. Validity was calculated using Pearson correlations and a 2-way analysis of variance (ANOVA) for repeated measures. Finally, responsiveness was calculated with the area under the curve (AUC), minimal detectable change (MDC) and the standardized response mean (SRM). RESULTS: A total of 80 completed questionnaires were collected in three different hospitals and a total of 43 patients finished a 9 weeks intervention period, completing the retest. Test-retest reliability was excellent with an ICC of 0.89 (95% CI, 0.74-0.95). To confirm the convergent validity, the MDQ answered all predefined hypothesises (r = -0.65-0.69 / p = 0.01-0.00) and good results for construct validity were found (p = 0.02). The MDQ had an AUC of 0.64 (95% CI, 0.47-0.81), an MDC of 8.80 points and a SRM of 0.65. CONCLUSION: The Dutch version of the MDQ shows good clinimetric properties and is shown to be usable in the assessment of the functional status of Dutch speaking patients with nonspecific CLBP. LEVEL OF EVIDENCE: 3.\",\n \"corpus_id\": 52229829,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":56,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29346586\",\n \"title\": \"PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.\",\n \"abstract\": \"Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions.\",\n \"corpus_id\": 52819554\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20538725","title":"cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.","abstract":"SUMMARY: Huge amount of metagenomic sequence data have been produced as a result of the rapidly increasing efforts worldwide in studying microbial communities as a whole. Most, if not all, sequenced metagenomes are complex mixtures of chromosomal and plasmid sequence fragments from multiple organisms, possibly from different kingdoms. Computational methods for prediction of genomic elements such as genes are significantly different for chromosomes and plasmids, hence raising the need for separation of chromosomal from plasmid sequences in a metagenome. We present a program for classification of a metagenome set into chromosomal and plasmid sequences, based on their distinguishing pentamer frequencies. On a large training set consisting of all the sequenced prokaryotic chromosomes and plasmids, the program achieves approximately 92% in classification accuracy. On a large set of simulated metagenomes with sequence lengths ranging from 300 bp to 100 kbp, the program has classification accuracy from 64.45% to 88.75%. On a large independent test set, the program achieves 88.29% classification accuracy. AVAILABILITY: The program has been implemented as a standalone prediction program, cBar, which is available at http://csbl.bmb.uga.edu/~ffzhou/cBar.","corpus_id":6418530,"score":2},{"doc_id":"20851899","title":"Predicting plasmid promiscuity based on genomic signature.","abstract":"Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.","corpus_id":206763372,"score":2},{"doc_id":"22647039","title":"Metamobilomics--expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing.","abstract":"A metamobilome is defined as a metagenome of circular genetic elements within a certain community. Metagenomic analyses of plasmids provide insights into the composition and structure of environmental plasmid communities. It is a promising method that will provide information about the types of plasmids that are present within environmental samples, and will give overviews about occurrences of plasmids as well as accessory genetic elements carried on these plasmids. A metamobilome library was constructed by combining multiple displacement amplification with pyrosequencing. This method provided a fast, efficient and unbiased strategy to investigate the communal gene pool of circular genetic elements (the metamobilome). We compared our wastewater metamobilome library with a wastewater metagenome library, against chromosomes, plasmids, phages and IS element databases, respectively. This showed that very few strictly chromosomal reads were present in our metamobilome library. Furthermore, data analysis showed that our library was strongly enriched for genes encoding plasmid-selfish traits, such as stability and conjugation, and most strikingly several hundred new putative plasmid replicases have been recovered.","corpus_id":23141585,"score":2},{"doc_id":"23268604","title":"Comparison of metagenomic samples using sequence signatures.","abstract":"BACKGROUND: Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. RESULTS: We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao's group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. CONCLUSIONS: Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d2S dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths.","corpus_id":5331942,"score":2},{"doc_id":"24503942","title":"Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.","abstract":"Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, complete circular sequences are rarely identified, and have required manual curation. We propose a robust in silico procedure for identifying complete small plasmids in metagenomic datasets from whole genome shotgun sequencing. From one very pure and exhaustively sequenced metamobilome from rat cecum, we identified a total of 616 circular sequences, 160 of which were carrying a gene with plasmid replication domain. Further homology analyses indicated that the majority of these plasmid sequences are novel. We confirmed the circularity of the complete plasmid candidates using an inverse-type PCR approach on a subset of sequences with 95% success, confirming the existence and length of discrete sequences. The implication of these findings is a broadened understanding of the traits of circular elements in nature and the possibility of massive data mining in existing metagenomic datasets to discover novel pools of complete plasmids thus vastly expanding the current plasmid database.","corpus_id":13478671,"score":2},{"doc_id":"27466620","title":"plasmidSPAdes: assembling plasmids from whole genome sequencing data.","abstract":"MOTIVATION: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. RESULTS: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. AVAILABILITY AND IMPLEMENTATION: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":13636652,"score":2},{"doc_id":"28003256","title":"Recycler: an algorithm for detecting plasmids from de novo assembly graphs.","abstract":"Motivation: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements. Results: We introduce Recycler, the first tool that can extract complete circular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data. We show that Recycler greatly increases the number of true plasmids recovered relative to other approaches while remaining highly accurate. We demonstrate this trend via simulations of plasmidomes, comparisons of predictions with reference data for isolate samples, and assessments of annotation accuracy on metagenome data. In addition, we provide validation by DNA amplification of 77 plasmids predicted by Recycler from the different sequenced samples in which Recycler showed mean accuracy of 89% across all data types-isolate, microbiome and plasmidome. Availability and Implementation: Recycler is available at http://github.com/Shamir-Lab/Recycler. Contact: imizrahi@bgu.ac.il. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":2473719,"score":2},{"doc_id":"29036588","title":"A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.","abstract":"Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets. Availability and implementation: MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941. Contact: liuj@cs.uky.edu. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4630014,"score":2},{"doc_id":"19302541","title":"Metagenomic signatures of 86 microbial and viral metagenomes.","abstract":"Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa.","corpus_id":205525232,"score":1},{"doc_id":"20085629","title":"Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.","abstract":"BACKGROUND: Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. RESULTS: Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90%) to two plasmids (pTRACA10 and pTRACA22) were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA) addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. CONCLUSIONS: The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota.","corpus_id":10352331,"score":1},{"doc_id":"20181243","title":"Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome.","abstract":"BACKGROUND: Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online. RESULTS: By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed. CONCLUSIONS: We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.","corpus_id":15248785,"score":1},{"doc_id":"20545752","title":"Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles.","abstract":"Two novel viral genomes and four plasmids were assembled from an environmental sample collected from a hot spring at Yellowstone National Park, USA, and maintained anaerobically in a bioreactor at 85°C and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and HAV2. Genomic DNA was obtained from samples enriched in filamentous and tadpole-shaped virus-like particles respectively. They yielded few significant matches in public sequence databases reinforcing, further, the wide diversity of archaeal viruses. Several variants of HAV1 exhibit major genomic alterations, presumed to arise from viral adaptation to different hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and genes with extensively altered sequences. Some result from recombination events occurring at low complexity direct repeats distributed along the genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized, encoding a possible conjugative apparatus, as well as three cryptic plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively. Strategies are considered for assembling genomes of smaller genetic elements from complex environmental samples, and for establishing possible host identities on the basis of sequence similarity to host CRISPR immune systems.","corpus_id":46446764,"score":1},{"doc_id":"21989143","title":"Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.","abstract":"BACKGROUND: A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. RESULTS: We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic classifier MetaPhyler (http://metaphyler.cbcb.umd.edu), which uses phylogenetic marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results by analyzing a real metagenomic dataset. CONCLUSIONS: We have introduced a novel taxonomic classification method for analyzing the microbial diversity from whole-metagenome shotgun sequences. Compared with previous approaches, MetaPhyler is much more accurate in estimating the phylogenetic composition. In addition, we have shown that MetaPhyler can be used to guide the discovery of novel organisms from metagenomic samples.","corpus_id":15815732,"score":1},{"doc_id":"22059529","title":"Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments.","abstract":"Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.","corpus_id":205527536,"score":1},{"doc_id":"22126801","title":"Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome.","abstract":"Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.","corpus_id":8679910,"score":1},{"doc_id":"23026555","title":"MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.","abstract":"Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.","corpus_id":28540316,"score":1},{"doc_id":"23407308","title":"Community-wide plasmid gene mobilization and selection.","abstract":"Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.","corpus_id":52848683,"score":1},{"doc_id":"24589583","title":"MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.","abstract":"Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100-2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.","corpus_id":8898863,"score":1},{"doc_id":"24631045","title":"Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.","abstract":"Because a vast majority (99%) of microbes in a given community is likely to be non-cultivable, metagenomics has gradually entered the mainstream of microbial research methods. With the development of high-throughput sequencing techniques, an increasing number of sequencing read data sets of metagenomes from various microbial communities have become available. For these data sets, metagenomic analysis based on mapping reads to microbial genomes has been hampered by the limited number of microbial genomes that are available. Further, this type of analysis is computationally intensive. Thus alignment-free methods, which characterize the sequencing reads with a genomic signature instead of with genomic alignments, can be applied. However, the main requirement of these alignment-free methods is a stable genomic signature that performs reliably. Here, we propose a novel genomic signature of microbial genomes called the intrinsic correlation of oligonucleotides (ICOs). This signature represents the quantification of an intrinsic relationship between any two oligonucleotides. We analyzed microbial genomes at different taxonomic levels using ICO profiles and confirmed the wide availability of useful ICOs. We used intra-genomic and inter-genomic distances and relational grades to evaluate the performance of ICOs as a genomic signature. The results of these experiments showed that ICOs can characterize microbial genomes well, and ICOs were better at distinguishing species than tetranucleotide composition, not only in terms of whole genomes but also in terms of sequence fragments. In addition, we evaluated the performance of a hybrid feature that combined ICOs and tetranucleotide composition. The experimental results showed that the hybrid feature performed better than ICOs or tetranucleotide composition alone. ICOs can characterize microbial genomes successfully and are capable of distinguishing organisms at different taxonomic levels. ICOs perform better than tetranucleotide composition in characterizing microbial genomes. The hybrid feature that used a combination of the two kinds of sequence features had advantages over a single sequence feature.","corpus_id":39407410,"score":1},{"doc_id":"25136443","title":"MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.","abstract":"BACKGROUND: Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. RESULTS: We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity. CONCLUSIONS: The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.","corpus_id":18851295,"score":1},{"doc_id":"25522143","title":"Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.","abstract":"Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.","corpus_id":15840910,"score":1},{"doc_id":"25657641","title":"Current strategies for mobilome research.","abstract":"Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.","corpus_id":5231126,"score":1},{"doc_id":"25765641","title":"Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.","abstract":"A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.","corpus_id":6107235,"score":1},{"doc_id":"26441947","title":"Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants.","abstract":"Plasmids operate as independent genetic elements in microorganism communities. Through horizontal gene transfer (HGT), they can provide their host microorganisms with important functions such as antibiotic resistance and heavy metal resistance. In this study, six metagenomic libraries were constructed with plasmid DNA extracted from influent, activated sludge (AS) and digested sludge (DS) of two wastewater treatment plants (WWTPs). Compared with the metagenomes of the total DNA extracted from the same sectors of the wastewater treatment plant, the plasmid metagenomes had significantly higher annotation rates, indicating that the functional genes on plasmids are commonly shared by those studied microorganisms. Meanwhile, the plasmid metagenomes also encoded many more genes related to defense mechanisms, including ARGs. Searching against an antibiotic resistance genes (ARGs) database and a metal resistance genes (MRGs) database revealed a broad-spectrum of antibiotic (323 out of a total 618 subtypes) and MRGs (23 out of a total 23 types) on these plasmid metagenomes. The influent plasmid metagenomes contained many more resistance genes (both ARGs and MRGs) than the AS and the DS metagenomes. Sixteen novel plasmids with a complete circular structure that carried these resistance genes were assembled from the plasmid metagenomes. The results of this study demonstrated that the plasmids in WWTPs could be important reservoirs for resistance genes, and may play a significant role in the horizontal transfer of these genes.","corpus_id":16569806,"score":1},{"doc_id":"26515820","title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.","abstract":"The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning a single sample as well as comparing the microbial community composition between different sampling environments. AVAILABILITY AND IMPLEMENTATION: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license. CONTACT: ywwei@lbl.govSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":21179931,"score":1},{"doc_id":"27067514","title":"Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.","abstract":"Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.","corpus_id":5691985,"score":1},{"doc_id":"27587676","title":"MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.","abstract":"MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial communities, a process referred to as binning, is one of the most challenging tasks when analyzing metagenomic reads data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species and the limitations due to short read lengths and sequencing errors. RESULTS: MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning. The novelty of MetaProb derives from solving a few important problems: how to divide reads into groups of independent reads, so that k-mer frequencies are not overestimated; how to convert k-mer counts into probabilistic sequence signatures, that will correct for variable distribution of k-mers, and for unbalanced groups of reads, in order to produce better estimates of the underlying genome statistic; how to estimate the number of species in a dataset. We show that MetaProb is more accurate and efficient than other state-of-the-art tools in binning both short reads datasets (F-measure 0.87) and long reads datasets (F-measure 0.97) for various abundance ratios. Also, the estimation of the number of species is more accurate than MetaCluster. On a real human stool dataset MetaProb identifies the most predominant species, in line with previous human gut studies. AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/samu661/metaprob CONTACTS: cinzia.pizzi@dei.unipd.it or comin@dei.unipd.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":26478112,"score":1},{"doc_id":"28321234","title":"A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data.","abstract":"The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such \"bioprospecting\" requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.","corpus_id":10368694,"score":1},{"doc_id":"28586714","title":"Towards a taxonomy of conjugative plasmids.","abstract":"Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.","corpus_id":29200035,"score":1},{"doc_id":"28611742","title":"Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism.","abstract":"Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.","corpus_id":23707565,"score":1},{"doc_id":"29227468","title":"Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.","abstract":"Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.","corpus_id":205285622,"score":1},{"doc_id":"18442389","title":"Gene prediction in metagenomic fragments: a large scale machine learning approach.","abstract":"BACKGROUND: Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. RESULTS: We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. CONCLUSION: Large scale machine learning methods are well-suited for gene prediction in metagenomic DNA fragments. In particular, the combination of linear discriminants and neural networks is promising and should be considered for integration into metagenomic analysis pipelines. The data sets can be downloaded from the URL provided (see Availability and requirements section).","corpus_id":2811583,"score":0},{"doc_id":"18642606","title":"Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples.","abstract":"Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria. Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities. Through a series of hybridizations and pblymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.","corpus_id":20756160,"score":0},{"doc_id":"18798991","title":"Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.","abstract":"BACKGROUND: Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. RESULTS: From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes. CONCLUSION: That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.","corpus_id":8949984,"score":0},{"doc_id":"18841204","title":"MetaSim: a sequencing simulator for genomics and metagenomics.","abstract":"BACKGROUND: The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. METHODOLOGY/PRINCIPAL FINDINGS: To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. CONCLUSIONS/SIGNIFICANCE: MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.","corpus_id":2471276,"score":0},{"doc_id":"19146522","title":"Metagenomics.","abstract":"The total number of prokaryotic cells on earth has been estimated to be approximately 4-6 x 10(30), with the majority of these being uncharacterized. This diversity represents a vast genetic bounty that may be exploited for the discovery of novel genes, entire metabolic pathways and potentially valuable end-products thereof. Metagenomics constitutes the functional and sequence-based analysis of the collective microbial genomes (microbiome) in a particular environment or environmental niche. Herein, we review the most recent sequence-based metagenomic analyses of some of the most microbiologically diverse locations on earth; including soil, marine water and the insect and human gut. Such studies have helped to uncover several previously unknown facts; from the true microbial diversity of extreme environments to the actual extent of symbiosis that exists in the insect and human gut. In this respect, metagenomics has and will continue to play an essential part in the new and evolving area of microbial systems biology.","corpus_id":221921639,"score":0},{"doc_id":"19288513","title":"Metagenomics: Concept, methodology, ecological inference and recent advances.","abstract":"Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.","corpus_id":3665077,"score":0},{"doc_id":"21431770","title":"Metagenomics.","abstract":"Metagenomics has evolved over the last 3 decades from the analysis of single genes and their apparent diversity in an ecosystem to the provision of complex genetic information relating to whole ecosystems. Metagenomics is a vast subject area in terms of methodology, which encompasses a suite of molecular technologies employed to investigate genomic information from all members of a microbial community. However, the relatively recent developments in high-throughput sequencing platforms have meant that metagenomic can be performed simply by extracting DNA and sequencing it. Here, we outline explicit methodologies for the extraction of metagenomic DNA from marine and sediments/soil environmental samples, the subsequent production and sequencing of large-insert metagenomic libraries, and also shotgun pyrosequencing considerations. We also provide relevant advice on bioinformatic analyses of the complex metagenomic datasets. We hope that the information provided here will be useful to establish the techniques in most reasonably equipped molecular biology laboratories.","corpus_id":-1,"score":0},{"doc_id":"22227326","title":"From genomics to metagenomics.","abstract":"Next-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational cost is the obvious issue, as is tool limitations, considering most of the tools we routinely use have been built for clonal genomics or are being adapted to microbial communities. The current trend in metagenomics analysis is toward reducing computational costs through improved algorithms and through analysis strategies. Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high.","corpus_id":45797180,"score":0},{"doc_id":"22384016","title":"Assessment of metagenomic assembly using simulated next generation sequencing data.","abstract":"Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.","corpus_id":9917423,"score":0},{"doc_id":"23418187","title":"Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.","abstract":"MOTIVATION: Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases. RESULTS: We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure. AVAILABILITY: http://gobics.de/TaxyPro. SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.","corpus_id":6311256,"score":0},{"doc_id":"23828782","title":"Scalable metagenomic taxonomy classification using a reference genome database.","abstract":"MOTIVATION: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. RESULTS: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. AVAILABILITY: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat CONTACT: allen99@llnl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":6819045,"score":0},{"doc_id":"24055388","title":"A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.","abstract":"Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.","corpus_id":8036405,"score":0},{"doc_id":"24146609","title":"Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.","abstract":"Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic data, this deconvolution framework provides an essential tool for characterizing microbial taxa never before seen, laying the foundation for addressing fundamental questions concerning the taxa comprising diverse microbial communities.","corpus_id":15656396,"score":0},{"doc_id":"24289541","title":"Identification of novel antimicrobial resistance genes from microbiota on retail spinach.","abstract":"BACKGROUND: Drug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. Here, we chose to study the microbial communities on retail spinach because it is commonly eaten raw and has previously been associated with outbreaks of bacterial infections. RESULTS: We created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. We identified five unique plasmids that increased resistance to antimicrobial drugs in the E. coli host. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all 5 plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items. CONCLUSIONS: Here we show that microbiota of retail spinach contains DNA sequences previously unidentified as conferring antibiotic resistance. Many of these novel sequences show similarity to genes found in species of bacteria, which have previously been identified as commensal or saprophytic bacteria found on plants. We showed that these resistance genes are capable of conferring clinically relevant levels of resistance to antimicrobial agents. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens.","corpus_id":844713,"score":0},{"doc_id":"24361423","title":"The future of skin metagenomics.","abstract":"Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin (\"skin microbiome\"). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications.","corpus_id":23500784,"score":0},{"doc_id":"24515370","title":"Metagenomics using next-generation sequencing.","abstract":"Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as \"metagenomics\" or \"community genomics\". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun (\"random\") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.","corpus_id":23553499,"score":0},{"doc_id":"24615381","title":"Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis.","abstract":"In the present study, a newly developed metagenomic analysis approach was applied to investigate the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aquaculture farm sediments, activated sludge, biofilm, anaerobic digestion sludge, and river water. BLASTX analysis against the Comprehensive Antibiotic Resistance Database was conducted for the metagenomic sequence data of each sample and then the ARG-like sequences were sorted based on structured sub-database using customized scripts. The results showed that freshwater fishpond sediment had the highest abundance (196 ppm), and anaerobic digestion sludge possessed the highest diversity (133 subtypes) of ARGs among the samples in this study. Significantly, rifampin resistance genes were universal in all the diverse samples and consistently accounted for 26.9~38.6 % of the total annotated ARG sequences. Furthermore, a significant linear correlation (R (2) = 0.924) was found between diversities (number of subtypes) of ARGs and diversities of plasmids in diverse samples. This work provided a wide spectrum scan of ARGs and MGEs in different environments and revealed the prevalence of rifampin resistance genes and the strong correlation between ARG diversity and plasmid diversity for the first time.","corpus_id":18712868,"score":0},{"doc_id":"24736651","title":"MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.","abstract":"The identification of virulent proteins in any de-novo sequenced genome is useful in estimating its pathogenic ability and understanding the mechanism of pathogenesis. Similarly, the identification of such proteins could be valuable in comparing the metagenome of healthy and diseased individuals and estimating the proportion of pathogenic species. However, the common challenge in both the above tasks is the identification of virulent proteins since a significant proportion of genomic and metagenomic proteins are novel and yet unannotated. The currently available tools which carry out the identification of virulent proteins provide limited accuracy and cannot be used on large datasets. Therefore, we have developed an MP3 standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets. MP3 is developed using an integrated Support Vector Machine (SVM) and Hidden Markov Model (HMM) approach to carry out highly fast, sensitive and accurate prediction of pathogenic proteins. It displayed Sensitivity, Specificity, MCC and accuracy values of 92%, 100%, 0.92 and 96%, respectively, on blind dataset constructed using complete proteins. On the two metagenomic blind datasets (Blind A: 51-100 amino acids and Blind B: 30-50 amino acids), it displayed Sensitivity, Specificity, MCC and accuracy values of 82.39%, 97.86%, 0.80 and 89.32% for Blind A and 71.60%, 94.48%, 0.67 and 81.86% for Blind B, respectively. In addition, the performance of MP3 was validated on selected bacterial genomic and real metagenomic datasets. To our knowledge, MP3 is the only program that specializes in fast and accurate identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs exceptionally well on complete protein sequences. MP3 is publicly available at http://metagenomics.iiserb.ac.in/mp3/index.php.","corpus_id":8320296,"score":0},{"doc_id":"25027647","title":"Accurate genome relative abundance estimation for closely related species in a metagenomic sample.","abstract":"BACKGROUND: Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree. RESULTS: We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease. CONCLUSIONS: By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.","corpus_id":16363612,"score":0},{"doc_id":"25957349","title":"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.","abstract":"MOTIVATION: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. RESULTS: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. AVAILABILITY AND IMPLEMENTATION: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/. CONTACT: kasshau@gwdg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":791719,"score":0},{"doc_id":"25983555","title":"Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.","abstract":"Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of \"metagenomics\", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.","corpus_id":16030777,"score":0},{"doc_id":"26130132","title":"BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.","abstract":"BACKGROUND: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. RESULTS: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). CONCLUSION: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.","corpus_id":3174192,"score":0},{"doc_id":"26254872","title":"From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.","abstract":"Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.","corpus_id":18304975,"score":0},{"doc_id":"26442255","title":"Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.","abstract":"Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus, calculations using contigs as different OTUs ultimately overestimate diversity when compared to diversity calculated from species coverage. In order to compare the effect of coverage and fragmentation, we generated three sets of simulated Illumina paired-end reads with different sequencing depths. We compared different assemblies performed with RayMeta, CLC Assembly Cell, MEGAHIT, SPAdes, Meta-IDBA, SOAPdenovo, Velvet, Metavelvet, and MIRA with the best attainable assemblies for each dataset (formed by arranging data using known genome coordinates) by calculating different assembly statistics. A new fragmentation score was included to estimate the degree of genome fragmentation of each taxon and adjust the coverage accordingly. The abundance in the metagenome was compared by bootstrapping the assembly data and hierarchically clustering them with the best possible assembly. Additionally, richness and diversity indexes were calculated for all the resulting assemblies and were assessed under two distributions: contigs as independent OTUs and sequences classified by species. Finally, we search for the strongest correlations between the diversity indexes and the different assembly statistics. Although fragmentation was dependent of genome coverage, it was not as heavily influenced by the assembler. The sequencing depth was the predominant attractor that influenced the success of the assemblies. The coverage increased notoriously in larger datasets, whereas fragmentation values remained lower and unsaturated. While still far from obtaining the ideal assemblies, the RayMeta, SPAdes, and the CLC assemblers managed to build the most accurate contigs with larger datasets while Meta-IDBA showed a good performance with the medium-sized dataset, even after the adjusted coverage was calculated. Their resulting assemblies showed the highest coverage scores and the lowest fragmentation values. Alpha diversity calculated from contigs as OTUs resulted in significantly higher values for all assemblies when compared with actual species distribution, showing an overestimation due to the increased predicted abundance. Conversely, using PHACCS resulted in lower values for all assemblers. Different association methods (random-forest, generalized linear models, and the Spearman correlation index) support the number of contigs, the coverage, and fragmentation as the assembly parameters that most affect the estimation of the alpha diversity. Coverage calculations may provide an insight into relative completeness of a genome but they overlook missing fragments or overly separated sequences in a genome. The assembly of a highly fragmented genomes with high coverage may still lead to the clustering of different OTUs that are actually different fragments of a genome. Thus, it proves useful to penalize coverage with a fragmentation score. Using contigs for calculating alpha diversity result in overestimation but it is usually the only approach available. Still, it is enough for sample comparison. The best approach may be determined by choosing the assembler that better fits the sequencing depth and adjusting the parameters for longer accurate contigs whenever possible whereas diversity may be calculated considering taxonomical and genomic information if available.","corpus_id":16881464,"score":0},{"doc_id":"26498126","title":"Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola.","abstract":"BACKGROUND: Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. METHODS: The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. RESULTS: The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. CONCLUSIONS: pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.","corpus_id":1718201,"score":0},{"doc_id":"27587670","title":"Assemble CRISPRs from metagenomic sequencing data.","abstract":"MOTIVATION: Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) allows more specific and efficient gene editing than all previous genetic engineering systems. These exciting discoveries stem from the finding of the CRISPR system being an adaptive immune system that protects the prokaryotes against exogenous genetic elements such as phages. Despite the exciting discoveries, almost all knowledge about CRISPRs is based only on microorganisms that can be isolated, cultured and sequenced in labs. However, about 95% of bacterial species cannot be cultured in labs. The fast accumulation of metagenomic data, which contains DNA sequences of microbial species from natural samples, provides a unique opportunity for CRISPR annotation in uncultivable microbial species. However, the large amount of data, heterogeneous coverage and shared leader sequences of some CRISPRs pose challenges for identifying CRISPRs efficiently in metagenomic data. RESULTS: In this study, we developed a CRISPR finding tool for metagenomic data without relying on generic assembly, which is error-prone and computationally expensive for complex data. Our tool can run on commonly available machines in small labs. It employs properties of CRISPRs to decompose generic assembly into local assembly. We tested it on both mock and real metagenomic data and benchmarked the performance with state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION: The source code and the documentation of metaCRISPR is available at https://github.com/hangelwen/metaCRISPR CONTACT: yannisun@msu.edu.","corpus_id":12369504,"score":0},{"doc_id":"27694768","title":"A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM).","abstract":"With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.","corpus_id":6693815,"score":0},{"doc_id":"29329522","title":"A-GAME: improving the assembly of pooled functional metagenomics sequence data.","abstract":"BACKGROUND: Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such \"functional metagenomics\" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications. RESULTS: Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation. CONCLUSION: In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame.","corpus_id":10026256,"score":0},{"doc_id":"29515540","title":"Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.","abstract":"Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.","corpus_id":3351926,"score":0}],"string":"[\n {\n \"doc_id\": \"20538725\",\n \"title\": \"cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.\",\n \"abstract\": \"SUMMARY: Huge amount of metagenomic sequence data have been produced as a result of the rapidly increasing efforts worldwide in studying microbial communities as a whole. Most, if not all, sequenced metagenomes are complex mixtures of chromosomal and plasmid sequence fragments from multiple organisms, possibly from different kingdoms. Computational methods for prediction of genomic elements such as genes are significantly different for chromosomes and plasmids, hence raising the need for separation of chromosomal from plasmid sequences in a metagenome. We present a program for classification of a metagenome set into chromosomal and plasmid sequences, based on their distinguishing pentamer frequencies. On a large training set consisting of all the sequenced prokaryotic chromosomes and plasmids, the program achieves approximately 92% in classification accuracy. On a large set of simulated metagenomes with sequence lengths ranging from 300 bp to 100 kbp, the program has classification accuracy from 64.45% to 88.75%. On a large independent test set, the program achieves 88.29% classification accuracy. AVAILABILITY: The program has been implemented as a standalone prediction program, cBar, which is available at http://csbl.bmb.uga.edu/~ffzhou/cBar.\",\n \"corpus_id\": 6418530,\n \"score\": 2\n },\n {\n \"doc_id\": \"20851899\",\n \"title\": \"Predicting plasmid promiscuity based on genomic signature.\",\n \"abstract\": \"Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.\",\n \"corpus_id\": 206763372,\n \"score\": 2\n },\n {\n \"doc_id\": \"22647039\",\n \"title\": \"Metamobilomics--expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing.\",\n \"abstract\": \"A metamobilome is defined as a metagenome of circular genetic elements within a certain community. Metagenomic analyses of plasmids provide insights into the composition and structure of environmental plasmid communities. It is a promising method that will provide information about the types of plasmids that are present within environmental samples, and will give overviews about occurrences of plasmids as well as accessory genetic elements carried on these plasmids. A metamobilome library was constructed by combining multiple displacement amplification with pyrosequencing. This method provided a fast, efficient and unbiased strategy to investigate the communal gene pool of circular genetic elements (the metamobilome). We compared our wastewater metamobilome library with a wastewater metagenome library, against chromosomes, plasmids, phages and IS element databases, respectively. This showed that very few strictly chromosomal reads were present in our metamobilome library. Furthermore, data analysis showed that our library was strongly enriched for genes encoding plasmid-selfish traits, such as stability and conjugation, and most strikingly several hundred new putative plasmid replicases have been recovered.\",\n \"corpus_id\": 23141585,\n \"score\": 2\n },\n {\n \"doc_id\": \"23268604\",\n \"title\": \"Comparison of metagenomic samples using sequence signatures.\",\n \"abstract\": \"BACKGROUND: Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. RESULTS: We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao's group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. CONCLUSIONS: Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d2S dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths.\",\n \"corpus_id\": 5331942,\n \"score\": 2\n },\n {\n \"doc_id\": \"24503942\",\n \"title\": \"Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.\",\n \"abstract\": \"Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, complete circular sequences are rarely identified, and have required manual curation. We propose a robust in silico procedure for identifying complete small plasmids in metagenomic datasets from whole genome shotgun sequencing. From one very pure and exhaustively sequenced metamobilome from rat cecum, we identified a total of 616 circular sequences, 160 of which were carrying a gene with plasmid replication domain. Further homology analyses indicated that the majority of these plasmid sequences are novel. We confirmed the circularity of the complete plasmid candidates using an inverse-type PCR approach on a subset of sequences with 95% success, confirming the existence and length of discrete sequences. The implication of these findings is a broadened understanding of the traits of circular elements in nature and the possibility of massive data mining in existing metagenomic datasets to discover novel pools of complete plasmids thus vastly expanding the current plasmid database.\",\n \"corpus_id\": 13478671,\n \"score\": 2\n },\n {\n \"doc_id\": \"27466620\",\n \"title\": \"plasmidSPAdes: assembling plasmids from whole genome sequencing data.\",\n \"abstract\": \"MOTIVATION: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. RESULTS: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. AVAILABILITY AND IMPLEMENTATION: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 13636652,\n \"score\": 2\n },\n {\n \"doc_id\": \"28003256\",\n \"title\": \"Recycler: an algorithm for detecting plasmids from de novo assembly graphs.\",\n \"abstract\": \"Motivation: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements. Results: We introduce Recycler, the first tool that can extract complete circular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data. We show that Recycler greatly increases the number of true plasmids recovered relative to other approaches while remaining highly accurate. We demonstrate this trend via simulations of plasmidomes, comparisons of predictions with reference data for isolate samples, and assessments of annotation accuracy on metagenome data. In addition, we provide validation by DNA amplification of 77 plasmids predicted by Recycler from the different sequenced samples in which Recycler showed mean accuracy of 89% across all data types-isolate, microbiome and plasmidome. Availability and Implementation: Recycler is available at http://github.com/Shamir-Lab/Recycler. Contact: imizrahi@bgu.ac.il. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 2473719,\n \"score\": 2\n },\n {\n \"doc_id\": \"29036588\",\n \"title\": \"A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.\",\n \"abstract\": \"Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets. Availability and implementation: MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941. Contact: liuj@cs.uky.edu. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4630014,\n \"score\": 2\n },\n {\n \"doc_id\": \"19302541\",\n \"title\": \"Metagenomic signatures of 86 microbial and viral metagenomes.\",\n \"abstract\": \"Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa.\",\n \"corpus_id\": 205525232,\n \"score\": 1\n },\n {\n \"doc_id\": \"20085629\",\n \"title\": \"Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.\",\n \"abstract\": \"BACKGROUND: Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. RESULTS: Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90%) to two plasmids (pTRACA10 and pTRACA22) were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA) addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. CONCLUSIONS: The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota.\",\n \"corpus_id\": 10352331,\n \"score\": 1\n },\n {\n \"doc_id\": \"20181243\",\n \"title\": \"Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome.\",\n \"abstract\": \"BACKGROUND: Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online. RESULTS: By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed. CONCLUSIONS: We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.\",\n \"corpus_id\": 15248785,\n \"score\": 1\n },\n {\n \"doc_id\": \"20545752\",\n \"title\": \"Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles.\",\n \"abstract\": \"Two novel viral genomes and four plasmids were assembled from an environmental sample collected from a hot spring at Yellowstone National Park, USA, and maintained anaerobically in a bioreactor at 85°C and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and HAV2. Genomic DNA was obtained from samples enriched in filamentous and tadpole-shaped virus-like particles respectively. They yielded few significant matches in public sequence databases reinforcing, further, the wide diversity of archaeal viruses. Several variants of HAV1 exhibit major genomic alterations, presumed to arise from viral adaptation to different hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and genes with extensively altered sequences. Some result from recombination events occurring at low complexity direct repeats distributed along the genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized, encoding a possible conjugative apparatus, as well as three cryptic plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively. Strategies are considered for assembling genomes of smaller genetic elements from complex environmental samples, and for establishing possible host identities on the basis of sequence similarity to host CRISPR immune systems.\",\n \"corpus_id\": 46446764,\n \"score\": 1\n },\n {\n \"doc_id\": \"21989143\",\n \"title\": \"Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.\",\n \"abstract\": \"BACKGROUND: A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. RESULTS: We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic classifier MetaPhyler (http://metaphyler.cbcb.umd.edu), which uses phylogenetic marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results by analyzing a real metagenomic dataset. CONCLUSIONS: We have introduced a novel taxonomic classification method for analyzing the microbial diversity from whole-metagenome shotgun sequences. Compared with previous approaches, MetaPhyler is much more accurate in estimating the phylogenetic composition. In addition, we have shown that MetaPhyler can be used to guide the discovery of novel organisms from metagenomic samples.\",\n \"corpus_id\": 15815732,\n \"score\": 1\n },\n {\n \"doc_id\": \"22059529\",\n \"title\": \"Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments.\",\n \"abstract\": \"Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.\",\n \"corpus_id\": 205527536,\n \"score\": 1\n },\n {\n \"doc_id\": \"22126801\",\n \"title\": \"Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome.\",\n \"abstract\": \"Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.\",\n \"corpus_id\": 8679910,\n \"score\": 1\n },\n {\n \"doc_id\": \"23026555\",\n \"title\": \"MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.\",\n \"abstract\": \"Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.\",\n \"corpus_id\": 28540316,\n \"score\": 1\n },\n {\n \"doc_id\": \"23407308\",\n \"title\": \"Community-wide plasmid gene mobilization and selection.\",\n \"abstract\": \"Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.\",\n \"corpus_id\": 52848683,\n \"score\": 1\n },\n {\n \"doc_id\": \"24589583\",\n \"title\": \"MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.\",\n \"abstract\": \"Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100-2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.\",\n \"corpus_id\": 8898863,\n \"score\": 1\n },\n {\n \"doc_id\": \"24631045\",\n \"title\": \"Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.\",\n \"abstract\": \"Because a vast majority (99%) of microbes in a given community is likely to be non-cultivable, metagenomics has gradually entered the mainstream of microbial research methods. With the development of high-throughput sequencing techniques, an increasing number of sequencing read data sets of metagenomes from various microbial communities have become available. For these data sets, metagenomic analysis based on mapping reads to microbial genomes has been hampered by the limited number of microbial genomes that are available. Further, this type of analysis is computationally intensive. Thus alignment-free methods, which characterize the sequencing reads with a genomic signature instead of with genomic alignments, can be applied. However, the main requirement of these alignment-free methods is a stable genomic signature that performs reliably. Here, we propose a novel genomic signature of microbial genomes called the intrinsic correlation of oligonucleotides (ICOs). This signature represents the quantification of an intrinsic relationship between any two oligonucleotides. We analyzed microbial genomes at different taxonomic levels using ICO profiles and confirmed the wide availability of useful ICOs. We used intra-genomic and inter-genomic distances and relational grades to evaluate the performance of ICOs as a genomic signature. The results of these experiments showed that ICOs can characterize microbial genomes well, and ICOs were better at distinguishing species than tetranucleotide composition, not only in terms of whole genomes but also in terms of sequence fragments. In addition, we evaluated the performance of a hybrid feature that combined ICOs and tetranucleotide composition. The experimental results showed that the hybrid feature performed better than ICOs or tetranucleotide composition alone. ICOs can characterize microbial genomes successfully and are capable of distinguishing organisms at different taxonomic levels. ICOs perform better than tetranucleotide composition in characterizing microbial genomes. The hybrid feature that used a combination of the two kinds of sequence features had advantages over a single sequence feature.\",\n \"corpus_id\": 39407410,\n \"score\": 1\n },\n {\n \"doc_id\": \"25136443\",\n \"title\": \"MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.\",\n \"abstract\": \"BACKGROUND: Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. RESULTS: We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity. CONCLUSIONS: The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.\",\n \"corpus_id\": 18851295,\n \"score\": 1\n },\n {\n \"doc_id\": \"25522143\",\n \"title\": \"Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.\",\n \"abstract\": \"Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.\",\n \"corpus_id\": 15840910,\n \"score\": 1\n },\n {\n \"doc_id\": \"25657641\",\n \"title\": \"Current strategies for mobilome research.\",\n \"abstract\": \"Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.\",\n \"corpus_id\": 5231126,\n \"score\": 1\n },\n {\n \"doc_id\": \"25765641\",\n \"title\": \"Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.\",\n \"abstract\": \"A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.\",\n \"corpus_id\": 6107235,\n \"score\": 1\n },\n {\n \"doc_id\": \"26441947\",\n \"title\": \"Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants.\",\n \"abstract\": \"Plasmids operate as independent genetic elements in microorganism communities. Through horizontal gene transfer (HGT), they can provide their host microorganisms with important functions such as antibiotic resistance and heavy metal resistance. In this study, six metagenomic libraries were constructed with plasmid DNA extracted from influent, activated sludge (AS) and digested sludge (DS) of two wastewater treatment plants (WWTPs). Compared with the metagenomes of the total DNA extracted from the same sectors of the wastewater treatment plant, the plasmid metagenomes had significantly higher annotation rates, indicating that the functional genes on plasmids are commonly shared by those studied microorganisms. Meanwhile, the plasmid metagenomes also encoded many more genes related to defense mechanisms, including ARGs. Searching against an antibiotic resistance genes (ARGs) database and a metal resistance genes (MRGs) database revealed a broad-spectrum of antibiotic (323 out of a total 618 subtypes) and MRGs (23 out of a total 23 types) on these plasmid metagenomes. The influent plasmid metagenomes contained many more resistance genes (both ARGs and MRGs) than the AS and the DS metagenomes. Sixteen novel plasmids with a complete circular structure that carried these resistance genes were assembled from the plasmid metagenomes. The results of this study demonstrated that the plasmids in WWTPs could be important reservoirs for resistance genes, and may play a significant role in the horizontal transfer of these genes.\",\n \"corpus_id\": 16569806,\n \"score\": 1\n },\n {\n \"doc_id\": \"26515820\",\n \"title\": \"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.\",\n \"abstract\": \"The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning a single sample as well as comparing the microbial community composition between different sampling environments. AVAILABILITY AND IMPLEMENTATION: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license. CONTACT: ywwei@lbl.govSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 21179931,\n \"score\": 1\n },\n {\n \"doc_id\": \"27067514\",\n \"title\": \"Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.\",\n \"abstract\": \"Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.\",\n \"corpus_id\": 5691985,\n \"score\": 1\n },\n {\n \"doc_id\": \"27587676\",\n \"title\": \"MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.\",\n \"abstract\": \"MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial communities, a process referred to as binning, is one of the most challenging tasks when analyzing metagenomic reads data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species and the limitations due to short read lengths and sequencing errors. RESULTS: MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning. The novelty of MetaProb derives from solving a few important problems: how to divide reads into groups of independent reads, so that k-mer frequencies are not overestimated; how to convert k-mer counts into probabilistic sequence signatures, that will correct for variable distribution of k-mers, and for unbalanced groups of reads, in order to produce better estimates of the underlying genome statistic; how to estimate the number of species in a dataset. We show that MetaProb is more accurate and efficient than other state-of-the-art tools in binning both short reads datasets (F-measure 0.87) and long reads datasets (F-measure 0.97) for various abundance ratios. Also, the estimation of the number of species is more accurate than MetaCluster. On a real human stool dataset MetaProb identifies the most predominant species, in line with previous human gut studies. AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/samu661/metaprob CONTACTS: cinzia.pizzi@dei.unipd.it or comin@dei.unipd.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 26478112,\n \"score\": 1\n },\n {\n \"doc_id\": \"28321234\",\n \"title\": \"A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data.\",\n \"abstract\": \"The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such \\\"bioprospecting\\\" requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.\",\n \"corpus_id\": 10368694,\n \"score\": 1\n },\n {\n \"doc_id\": \"28586714\",\n \"title\": \"Towards a taxonomy of conjugative plasmids.\",\n \"abstract\": \"Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.\",\n \"corpus_id\": 29200035,\n \"score\": 1\n },\n {\n \"doc_id\": \"28611742\",\n \"title\": \"Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism.\",\n \"abstract\": \"Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.\",\n \"corpus_id\": 23707565,\n \"score\": 1\n },\n {\n \"doc_id\": \"29227468\",\n \"title\": \"Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.\",\n \"abstract\": \"Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.\",\n \"corpus_id\": 205285622,\n \"score\": 1\n },\n {\n \"doc_id\": \"18442389\",\n \"title\": \"Gene prediction in metagenomic fragments: a large scale machine learning approach.\",\n \"abstract\": \"BACKGROUND: Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. RESULTS: We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. CONCLUSION: Large scale machine learning methods are well-suited for gene prediction in metagenomic DNA fragments. In particular, the combination of linear discriminants and neural networks is promising and should be considered for integration into metagenomic analysis pipelines. The data sets can be downloaded from the URL provided (see Availability and requirements section).\",\n \"corpus_id\": 2811583,\n \"score\": 0\n },\n {\n \"doc_id\": \"18642606\",\n \"title\": \"Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples.\",\n \"abstract\": \"Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria. Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities. Through a series of hybridizations and pblymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.\",\n \"corpus_id\": 20756160,\n \"score\": 0\n },\n {\n \"doc_id\": \"18798991\",\n \"title\": \"Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.\",\n \"abstract\": \"BACKGROUND: Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. RESULTS: From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes. CONCLUSION: That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.\",\n \"corpus_id\": 8949984,\n \"score\": 0\n },\n {\n \"doc_id\": \"18841204\",\n \"title\": \"MetaSim: a sequencing simulator for genomics and metagenomics.\",\n \"abstract\": \"BACKGROUND: The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. METHODOLOGY/PRINCIPAL FINDINGS: To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. CONCLUSIONS/SIGNIFICANCE: MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.\",\n \"corpus_id\": 2471276,\n \"score\": 0\n },\n {\n \"doc_id\": \"19146522\",\n \"title\": \"Metagenomics.\",\n \"abstract\": \"The total number of prokaryotic cells on earth has been estimated to be approximately 4-6 x 10(30), with the majority of these being uncharacterized. This diversity represents a vast genetic bounty that may be exploited for the discovery of novel genes, entire metabolic pathways and potentially valuable end-products thereof. Metagenomics constitutes the functional and sequence-based analysis of the collective microbial genomes (microbiome) in a particular environment or environmental niche. Herein, we review the most recent sequence-based metagenomic analyses of some of the most microbiologically diverse locations on earth; including soil, marine water and the insect and human gut. Such studies have helped to uncover several previously unknown facts; from the true microbial diversity of extreme environments to the actual extent of symbiosis that exists in the insect and human gut. In this respect, metagenomics has and will continue to play an essential part in the new and evolving area of microbial systems biology.\",\n \"corpus_id\": 221921639,\n \"score\": 0\n },\n {\n \"doc_id\": \"19288513\",\n \"title\": \"Metagenomics: Concept, methodology, ecological inference and recent advances.\",\n \"abstract\": \"Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.\",\n \"corpus_id\": 3665077,\n \"score\": 0\n },\n {\n \"doc_id\": \"21431770\",\n \"title\": \"Metagenomics.\",\n \"abstract\": \"Metagenomics has evolved over the last 3 decades from the analysis of single genes and their apparent diversity in an ecosystem to the provision of complex genetic information relating to whole ecosystems. Metagenomics is a vast subject area in terms of methodology, which encompasses a suite of molecular technologies employed to investigate genomic information from all members of a microbial community. However, the relatively recent developments in high-throughput sequencing platforms have meant that metagenomic can be performed simply by extracting DNA and sequencing it. Here, we outline explicit methodologies for the extraction of metagenomic DNA from marine and sediments/soil environmental samples, the subsequent production and sequencing of large-insert metagenomic libraries, and also shotgun pyrosequencing considerations. We also provide relevant advice on bioinformatic analyses of the complex metagenomic datasets. We hope that the information provided here will be useful to establish the techniques in most reasonably equipped molecular biology laboratories.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"22227326\",\n \"title\": \"From genomics to metagenomics.\",\n \"abstract\": \"Next-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational cost is the obvious issue, as is tool limitations, considering most of the tools we routinely use have been built for clonal genomics or are being adapted to microbial communities. The current trend in metagenomics analysis is toward reducing computational costs through improved algorithms and through analysis strategies. Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high.\",\n \"corpus_id\": 45797180,\n \"score\": 0\n },\n {\n \"doc_id\": \"22384016\",\n \"title\": \"Assessment of metagenomic assembly using simulated next generation sequencing data.\",\n \"abstract\": \"Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.\",\n \"corpus_id\": 9917423,\n \"score\": 0\n },\n {\n \"doc_id\": \"23418187\",\n \"title\": \"Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.\",\n \"abstract\": \"MOTIVATION: Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases. RESULTS: We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure. AVAILABILITY: http://gobics.de/TaxyPro. SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.\",\n \"corpus_id\": 6311256,\n \"score\": 0\n },\n {\n \"doc_id\": \"23828782\",\n \"title\": \"Scalable metagenomic taxonomy classification using a reference genome database.\",\n \"abstract\": \"MOTIVATION: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. RESULTS: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. AVAILABILITY: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat CONTACT: allen99@llnl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 6819045,\n \"score\": 0\n },\n {\n \"doc_id\": \"24055388\",\n \"title\": \"A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.\",\n \"abstract\": \"Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.\",\n \"corpus_id\": 8036405,\n \"score\": 0\n },\n {\n \"doc_id\": \"24146609\",\n \"title\": \"Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.\",\n \"abstract\": \"Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic data, this deconvolution framework provides an essential tool for characterizing microbial taxa never before seen, laying the foundation for addressing fundamental questions concerning the taxa comprising diverse microbial communities.\",\n \"corpus_id\": 15656396,\n \"score\": 0\n },\n {\n \"doc_id\": \"24289541\",\n \"title\": \"Identification of novel antimicrobial resistance genes from microbiota on retail spinach.\",\n \"abstract\": \"BACKGROUND: Drug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. Here, we chose to study the microbial communities on retail spinach because it is commonly eaten raw and has previously been associated with outbreaks of bacterial infections. RESULTS: We created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. We identified five unique plasmids that increased resistance to antimicrobial drugs in the E. coli host. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all 5 plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items. CONCLUSIONS: Here we show that microbiota of retail spinach contains DNA sequences previously unidentified as conferring antibiotic resistance. Many of these novel sequences show similarity to genes found in species of bacteria, which have previously been identified as commensal or saprophytic bacteria found on plants. We showed that these resistance genes are capable of conferring clinically relevant levels of resistance to antimicrobial agents. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens.\",\n \"corpus_id\": 844713,\n \"score\": 0\n },\n {\n \"doc_id\": \"24361423\",\n \"title\": \"The future of skin metagenomics.\",\n \"abstract\": \"Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin (\\\"skin microbiome\\\"). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications.\",\n \"corpus_id\": 23500784,\n \"score\": 0\n },\n {\n \"doc_id\": \"24515370\",\n \"title\": \"Metagenomics using next-generation sequencing.\",\n \"abstract\": \"Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as \\\"metagenomics\\\" or \\\"community genomics\\\". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun (\\\"random\\\") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.\",\n \"corpus_id\": 23553499,\n \"score\": 0\n },\n {\n \"doc_id\": \"24615381\",\n \"title\": \"Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis.\",\n \"abstract\": \"In the present study, a newly developed metagenomic analysis approach was applied to investigate the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aquaculture farm sediments, activated sludge, biofilm, anaerobic digestion sludge, and river water. BLASTX analysis against the Comprehensive Antibiotic Resistance Database was conducted for the metagenomic sequence data of each sample and then the ARG-like sequences were sorted based on structured sub-database using customized scripts. The results showed that freshwater fishpond sediment had the highest abundance (196 ppm), and anaerobic digestion sludge possessed the highest diversity (133 subtypes) of ARGs among the samples in this study. Significantly, rifampin resistance genes were universal in all the diverse samples and consistently accounted for 26.9~38.6 % of the total annotated ARG sequences. Furthermore, a significant linear correlation (R (2) = 0.924) was found between diversities (number of subtypes) of ARGs and diversities of plasmids in diverse samples. This work provided a wide spectrum scan of ARGs and MGEs in different environments and revealed the prevalence of rifampin resistance genes and the strong correlation between ARG diversity and plasmid diversity for the first time.\",\n \"corpus_id\": 18712868,\n \"score\": 0\n },\n {\n \"doc_id\": \"24736651\",\n \"title\": \"MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.\",\n \"abstract\": \"The identification of virulent proteins in any de-novo sequenced genome is useful in estimating its pathogenic ability and understanding the mechanism of pathogenesis. Similarly, the identification of such proteins could be valuable in comparing the metagenome of healthy and diseased individuals and estimating the proportion of pathogenic species. However, the common challenge in both the above tasks is the identification of virulent proteins since a significant proportion of genomic and metagenomic proteins are novel and yet unannotated. The currently available tools which carry out the identification of virulent proteins provide limited accuracy and cannot be used on large datasets. Therefore, we have developed an MP3 standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets. MP3 is developed using an integrated Support Vector Machine (SVM) and Hidden Markov Model (HMM) approach to carry out highly fast, sensitive and accurate prediction of pathogenic proteins. It displayed Sensitivity, Specificity, MCC and accuracy values of 92%, 100%, 0.92 and 96%, respectively, on blind dataset constructed using complete proteins. On the two metagenomic blind datasets (Blind A: 51-100 amino acids and Blind B: 30-50 amino acids), it displayed Sensitivity, Specificity, MCC and accuracy values of 82.39%, 97.86%, 0.80 and 89.32% for Blind A and 71.60%, 94.48%, 0.67 and 81.86% for Blind B, respectively. In addition, the performance of MP3 was validated on selected bacterial genomic and real metagenomic datasets. To our knowledge, MP3 is the only program that specializes in fast and accurate identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs exceptionally well on complete protein sequences. MP3 is publicly available at http://metagenomics.iiserb.ac.in/mp3/index.php.\",\n \"corpus_id\": 8320296,\n \"score\": 0\n },\n {\n \"doc_id\": \"25027647\",\n \"title\": \"Accurate genome relative abundance estimation for closely related species in a metagenomic sample.\",\n \"abstract\": \"BACKGROUND: Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree. RESULTS: We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease. CONCLUSIONS: By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.\",\n \"corpus_id\": 16363612,\n \"score\": 0\n },\n {\n \"doc_id\": \"25957349\",\n \"title\": \"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.\",\n \"abstract\": \"MOTIVATION: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. RESULTS: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. AVAILABILITY AND IMPLEMENTATION: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/. CONTACT: kasshau@gwdg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 791719,\n \"score\": 0\n },\n {\n \"doc_id\": \"25983555\",\n \"title\": \"Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.\",\n \"abstract\": \"Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of \\\"metagenomics\\\", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.\",\n \"corpus_id\": 16030777,\n \"score\": 0\n },\n {\n \"doc_id\": \"26130132\",\n \"title\": \"BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.\",\n \"abstract\": \"BACKGROUND: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. RESULTS: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). CONCLUSION: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.\",\n \"corpus_id\": 3174192,\n \"score\": 0\n },\n {\n \"doc_id\": \"26254872\",\n \"title\": \"From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.\",\n \"abstract\": \"Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.\",\n \"corpus_id\": 18304975,\n \"score\": 0\n },\n {\n \"doc_id\": \"26442255\",\n \"title\": \"Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.\",\n \"abstract\": \"Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus, calculations using contigs as different OTUs ultimately overestimate diversity when compared to diversity calculated from species coverage. In order to compare the effect of coverage and fragmentation, we generated three sets of simulated Illumina paired-end reads with different sequencing depths. We compared different assemblies performed with RayMeta, CLC Assembly Cell, MEGAHIT, SPAdes, Meta-IDBA, SOAPdenovo, Velvet, Metavelvet, and MIRA with the best attainable assemblies for each dataset (formed by arranging data using known genome coordinates) by calculating different assembly statistics. A new fragmentation score was included to estimate the degree of genome fragmentation of each taxon and adjust the coverage accordingly. The abundance in the metagenome was compared by bootstrapping the assembly data and hierarchically clustering them with the best possible assembly. Additionally, richness and diversity indexes were calculated for all the resulting assemblies and were assessed under two distributions: contigs as independent OTUs and sequences classified by species. Finally, we search for the strongest correlations between the diversity indexes and the different assembly statistics. Although fragmentation was dependent of genome coverage, it was not as heavily influenced by the assembler. The sequencing depth was the predominant attractor that influenced the success of the assemblies. The coverage increased notoriously in larger datasets, whereas fragmentation values remained lower and unsaturated. While still far from obtaining the ideal assemblies, the RayMeta, SPAdes, and the CLC assemblers managed to build the most accurate contigs with larger datasets while Meta-IDBA showed a good performance with the medium-sized dataset, even after the adjusted coverage was calculated. Their resulting assemblies showed the highest coverage scores and the lowest fragmentation values. Alpha diversity calculated from contigs as OTUs resulted in significantly higher values for all assemblies when compared with actual species distribution, showing an overestimation due to the increased predicted abundance. Conversely, using PHACCS resulted in lower values for all assemblers. Different association methods (random-forest, generalized linear models, and the Spearman correlation index) support the number of contigs, the coverage, and fragmentation as the assembly parameters that most affect the estimation of the alpha diversity. Coverage calculations may provide an insight into relative completeness of a genome but they overlook missing fragments or overly separated sequences in a genome. The assembly of a highly fragmented genomes with high coverage may still lead to the clustering of different OTUs that are actually different fragments of a genome. Thus, it proves useful to penalize coverage with a fragmentation score. Using contigs for calculating alpha diversity result in overestimation but it is usually the only approach available. Still, it is enough for sample comparison. The best approach may be determined by choosing the assembler that better fits the sequencing depth and adjusting the parameters for longer accurate contigs whenever possible whereas diversity may be calculated considering taxonomical and genomic information if available.\",\n \"corpus_id\": 16881464,\n \"score\": 0\n },\n {\n \"doc_id\": \"26498126\",\n \"title\": \"Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola.\",\n \"abstract\": \"BACKGROUND: Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. METHODS: The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. RESULTS: The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. CONCLUSIONS: pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.\",\n \"corpus_id\": 1718201,\n \"score\": 0\n },\n {\n \"doc_id\": \"27587670\",\n \"title\": \"Assemble CRISPRs from metagenomic sequencing data.\",\n \"abstract\": \"MOTIVATION: Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) allows more specific and efficient gene editing than all previous genetic engineering systems. These exciting discoveries stem from the finding of the CRISPR system being an adaptive immune system that protects the prokaryotes against exogenous genetic elements such as phages. Despite the exciting discoveries, almost all knowledge about CRISPRs is based only on microorganisms that can be isolated, cultured and sequenced in labs. However, about 95% of bacterial species cannot be cultured in labs. The fast accumulation of metagenomic data, which contains DNA sequences of microbial species from natural samples, provides a unique opportunity for CRISPR annotation in uncultivable microbial species. However, the large amount of data, heterogeneous coverage and shared leader sequences of some CRISPRs pose challenges for identifying CRISPRs efficiently in metagenomic data. RESULTS: In this study, we developed a CRISPR finding tool for metagenomic data without relying on generic assembly, which is error-prone and computationally expensive for complex data. Our tool can run on commonly available machines in small labs. It employs properties of CRISPRs to decompose generic assembly into local assembly. We tested it on both mock and real metagenomic data and benchmarked the performance with state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION: The source code and the documentation of metaCRISPR is available at https://github.com/hangelwen/metaCRISPR CONTACT: yannisun@msu.edu.\",\n \"corpus_id\": 12369504,\n \"score\": 0\n },\n {\n \"doc_id\": \"27694768\",\n \"title\": \"A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM).\",\n \"abstract\": \"With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.\",\n \"corpus_id\": 6693815,\n \"score\": 0\n },\n {\n \"doc_id\": \"29329522\",\n \"title\": \"A-GAME: improving the assembly of pooled functional metagenomics sequence data.\",\n \"abstract\": \"BACKGROUND: Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such \\\"functional metagenomics\\\" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications. RESULTS: Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation. CONCLUSION: In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame.\",\n \"corpus_id\": 10026256,\n \"score\": 0\n },\n {\n \"doc_id\": \"29515540\",\n \"title\": \"Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.\",\n \"abstract\": \"Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.\",\n \"corpus_id\": 3351926,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":57,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29700149\",\n \"title\": \"Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.\",\n \"abstract\": \"Here, we report the complete closed genome sequence and methylome analysis of Beggiatoa leptomitoformis strain D-401 (DSM 14945, UNIQEMU 779), which is quite different from the previously described Beggiatoa leptomitoformis neotype strain D-402T (DSM 14946, UNIQEM U 779) with regard to morphology and lithotrophic growth in the presence of thiosulfate.\",\n \"corpus_id\": 13805766\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18621874","title":"Methylotrophy in freshwater Beggiatoa alba strains.","abstract":"Two freshwater strains of the gammaproteobacterium Beggiatoa alba, B18LD and OH75-2a, are able to use methanol as a sole carbon and energy source under microoxic conditions. Genes encoding a methanol dehydrogenase large-subunit homolog and four enzymes of the tetrahydromethanopterin-dependent C(1) oxidation pathway were identified in B18LD. No evidence of methanotrophy was detected.","corpus_id":46417230,"score":2},{"doc_id":"20207153","title":"Comparative analysis of Beggiatoa from hypersaline and marine environments.","abstract":"The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34 microm, and their lengths ranged from 10 microm to over 30 mm. Narrow trichomes moved by gliding at 3.0 microm/s; large filaments moved at 1.5 microm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers.","corpus_id":37094386,"score":2},{"doc_id":"20827290","title":"Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain.","abstract":"Sulfur bacteria such as Beggiatoa or Thiomargarita have a particularly high capacity for storage because of their large size. In addition to sulfur and nitrate, these bacteria also store phosphorus in the form of polyphosphate. Thiomargarita namibiensis has been shown to release phosphate from internally stored polyphosphate in pulses creating steep peaks of phosphate in the sediment and thereby inducing the precipitation of phosphorus-rich minerals. Large sulfur bacteria populate sediments at the sites of recent phosphorite formation and are found as fossils in ancient phosphorite deposits. Therefore, it can be assumed that this physiology contributes to the removal of bioavailable phosphorus from the marine system and thus is important for the global phosphorus cycle. We investigated under defined laboratory conditions which parameters stimulate the decomposition of polyphosphate and the release of phosphate in a marine Beggiatoa strain. Initially, we tested phosphate release in response to anoxia and high concentrations of acetate, because acetate is described as the relevant stimulus for phosphate release in activated sludge. To our surprise, the Beggiatoa strain did not release phosphate in response to this treatment. Instead, we could clearly show that increasing sulfide concentrations and anoxia resulted in a decomposition of polyphosphate. This physiological reaction is a yet unknown mode of bacterial polyphosphate usage and provides a new explanation for high phosphate concentrations in sulfidic marine sediments.","corpus_id":22900900,"score":2},{"doc_id":"21909788","title":"Unusual polyphosphate inclusions observed in a marine Beggiatoa strain.","abstract":"Sulfide-oxidizing bacteria of the genus Beggiatoa are known to accumulate phosphate intracellularly as polyphosphate but little is known about the structure and properties of these inclusions. Application of different staining techniques revealed the presence of unusually large polyphosphate inclusions in the marine Beggiatoa strain 35Flor. The inclusions showed a co-occurrence of polyphosphate, calcium and magnesium when analyzed by scanning electron microscopy and energy dispersive X-ray analysis. Similar to polyphosphate-enriched acidocalcisomes of prokaryotes and eukaryotes, the polyphosphate inclusions in Beggiatoa strain 35Flor are enclosed by a lipid layer and store cations. However, they are not notably acidic. 16S rRNA gene sequence-based phylogenetic reconstruction showed an affiliation of Beggiatoa strain 35Flor to a monophyletic branch, comprising other narrow vacuolated and non-vacuolated Beggiatoa species. The polyphosphate inclusions represent a new type of membrane surrounded storage compartment within the genus Beggiatoa, distinct from the mostly nitrate-storing vacuoles known from other marine sulfide-oxidizing bacteria of the family Beggiatoaceae.","corpus_id":14947543,"score":2},{"doc_id":"22123768","title":"Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain AM4, capable of organotrophic growth and growth at the expense of hydrogenogenic or sulfidogenic oxidation of carbon monoxide.","abstract":"Analysis of the complete genome of Thermococcus sp. strain AM4, which was the first lithotrophic Thermococcales isolate described and the first archaeal isolate to exhibit a capacity for hydrogenogenic carboxydotrophy, reveals a proximity with Thermococcus gammatolerans, corresponding to close but distinct species that differ significantly in their lithotrophic capacities.","corpus_id":43133826,"score":2},{"doc_id":"22841519","title":"Enrichment and identification of large filamentous sulfur bacteria related to Beggiatoa species from brackishwater ecosystems of Tamil Nadu along the southeast coast of India.","abstract":"Beggiatoa species are filamentous sulfide-oxidizing bacteria belonging to the family Beggiatoaceae that contains several largest bacteria known today. These large sulfur bacteria occur in diverse ecosystems and play an important role in the global sulfur, nitrogen and phosphorus cycle. In this study, sediment samples from brackishwater shrimp culture ponds and other brackishwater ecosystems from Tamil Nadu, southeast coast of India, were enriched for Beggiatoa species. Extracted hay medium supplemented with catalase was used and were incubated for two weeks at 28°C. Out of seven set-ups, four yielded positive growth of filamentous sulfide-oxidizing bacteria. The filaments were several millimeters long, ranged in width between 2 and 15 μm and exhibited typical gliding motility. The 16S rRNA gene of four single filaments representing the four positive enrichments was subjected to PCR-DGGE followed by sequencing. All four filaments were affiliated to the Beggiatoaceae, but showed less than 89% identity with the Beggiatoa type strain Beggiatoa alba and less than 93% identity with any other sequence of the family. One of the four filaments revealed a nearly full-length 16S rDNA sequence (1411bp) and it formed a monophyletic cluster with two of the partial DGGE-16S rRNA gene sequences (99-100% identity) within the Beggiatoa species cluster. These organisms could possibly represent a novel genus within the family Beggiatoaceae. The fourth partial sequence affiliated with less than 93% sequence identity to the genera Parabeggiatoa, Thioploca and Thiopilula, and was likewise strongly delineated from any sequence published in the family.","corpus_id":28291326,"score":2},{"doc_id":"24012537","title":"Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.","abstract":"A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability.","corpus_id":33723170,"score":2},{"doc_id":"26603120","title":"Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.","abstract":"Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.","corpus_id":6782854,"score":2},{"doc_id":"26659680","title":"Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T.","abstract":"In this report, we announce the availability of a complete closed genome sequence and methylome analysis of Beggiatoa leptomitiformis neotype strain D-402(T) (DSM 14946, UNIQEM U 779).","corpus_id":4964304,"score":2},{"doc_id":"26744373","title":"Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.","abstract":"We report the complete, closed genome sequence and complete methylome of Azospirillum thiophilum strain BV-S(T).","corpus_id":9932982,"score":2},{"doc_id":"26896131","title":"Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain.","abstract":"UNLABELLED: A chemolithoautotrophic strain of the family Beggiatoaceae, Beggiatoa sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration. Beggiatoa sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide Beggiatoa sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of Beggiatoa ceae to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow. IMPORTANCE: Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic Beggiatoa ceae, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of Beggiatoa ceaein several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies.","corpus_id":18362101,"score":2},{"doc_id":"27516520","title":"Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.","abstract":"The genus Comamonas contains species isolated from various environments, such as termite guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we report the draft genome sequence of Comamonas thiooxydans strain S23(T) capable of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas thiooxydans whole-genome sequence will help understand the metabolic diversity in sulfur oxidation pathways.","corpus_id":19049101,"score":2},{"doc_id":"27832308","title":"Mechanism of electron transport during thiosulfate oxidation in an obligately mixotrophic bacterium Thiomonas bhubaneswarensis strain S10 (DSM 18181(T)).","abstract":"This study describes the thiosulfate-supported respiratory electron transport activity of Thiomonas bhubaneswarensis strain S10 (DSM 18181(T)). Whole-genome sequence analysis revealed the presence of complete sox (sulfur oxidation) gene cluster (soxCDYZAXB) including the sulfur oxygenase reductase (SOR), sulfide quinone reductase (SQR), sulfide dehydrogenase (flavocytochrome c (fcc)), thiosulfate dehydrogenase (Tsd), sulfite dehydrogenase (SorAB), and intracellular sulfur oxidation protein (DsrE/DsrF). In addition, genes encoding respiratory electron transport chain components viz. complex I (NADH dehydrogenase), complex II (succinate dehydrogenase), complex III (ubiquinone-cytochrome c reductase), and various types of terminal oxidases (cytochrome c and quinol oxidase) were identified in the genome. Using site-specific electron donors and inhibitors and by analyzing the cytochrome spectra, we identified the shortest thiosulfate-dependent electron transport chain in T. bhubaneswarensis DSM 18181(T). Our results showed that thiosulfate supports the electron transport activity in a bifurcated manner, donating electrons to quinol (bd) and cytochrome c (Caa 3 ) oxidase; these two sites (quinol oxidase and cytochrome c oxidase) also showed differences in their phosphate esterification potential (oxidative phosphorylation efficiency (P/O)). Further, it was evidenced that the substrate-level phosphorylation is the major contributor to the total energy budget in this bacterium.","corpus_id":-1,"score":2},{"doc_id":"27902215","title":"Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth.","abstract":"A strain of filamentous sulfur bacteria was isolated from freshwater spring contaminated with residential and agricultural wastewater in Moscow region, Russia. According to the results of phylogenetic analysis, strain D-402T belonged to the genus Beggiatoa within the family Beggiatoaceae of the class Gammaproteobacteria. Within the genus Beggiatoa, strain D-402T was most closely related to Beggiatoa alba strains. Strain D-402T had a DNA G+C content 42.1 mol%. The DNA-DNA hybridization value between strain D-402T and Beggiatoa alba strain B15LD was 33 %. Predominant fatty acids were C18 : 1 (46.1 and 53.3 %), C16 : 0 (15.5 and 16.2 %) and C16 : 1 (32.9 and 25.4 %) for strains D-402T and B15LD, respectively. In contrast to known representatives of Beggiatoa, strain D-402T was capable of chemolithoautotrophic growth with sulfide and thiosulfate as electron donors. Oxidation of sulfide and thiosulfate was accompanied by deposition of sulfur globules within the cells. Strain D-402T was capable of heterotrophic growth. The strain was capable of using different organic compounds, sulfur compounds and hydrogen as electron donors. Based on these observations, strain D-402T is considered as a representative of a species Beggiatoa leptomitoformis sp. nov. of the genus Beggiatoa. The type strain is D-402T (=DSM 14946T=UNIQEM U 779T).","corpus_id":21211138,"score":2},{"doc_id":"28860255","title":"Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.","abstract":"In this report, we announce the availability of a whole-genome sequence and methylome analysis of Thioflexothrix psekupsii strain D3.","corpus_id":34737196,"score":2},{"doc_id":"20023012","title":"Completed genome sequence of the anaerobic iron-oxidizing bacterium Acidovorax ebreus strain TPSY.","abstract":"Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.","corpus_id":24077466,"score":1},{"doc_id":"20495027","title":"Taxonomic investigation of representatives of the genus Sphaerotilus: descriptions of Sphaerotilus montanus sp. nov., Sphaerotilus hippei sp. nov., Sphaerotilus natans subsp. natans subsp. nov. and Sphaerotilus natans subsp. sulfidivorans subsp. nov., and an emended description of the genus Sphaerotilus.","abstract":"Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501(T), D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HS(T)) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strains of Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575(T), DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C(16 : 1)ω7, C(16 : 0) and C(18 : 1)ω7 as the major fatty acids. The DNA-DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501(T), D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575(T). However, strains D-501(T), D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575(T) by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501(T), D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501(T) = DSM 22545(T) = VKM B-2573(T)) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575(T). Strains D-380 and S. natans DSM 6575(T) were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575(T) = ATCC 13338(T)). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HS(T) and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575(T). Strain HS(T) shared 99 % DNA-DNA relatedness with strain.","corpus_id":26662232,"score":1},{"doc_id":"20817842","title":"Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons.","abstract":"The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the species Bacillus amyloliquefaciens or Bacillus subtilis are used commercially to promote the growth and improve the health of crop plants. Previous investigations revealed that a group of strains represented a distinct ecotype related to B. amyloliquefaciens; however, the exact taxonomic position of this group remains elusive (Reva et al., 2004). In the present study, we demonstrated the ability of a group of Bacillus strains closely related to strain FZB42(T) to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7(T) but differed considerably from this type strain in the DNA sequences of genes encoding 16S rRNA, gyrase subunit A (gyrA) and histidine kinase (cheA). Phylogenetic analysis performed with partial 16S rRNA, gyrA and cheA gene sequences revealed that the plant-associated strains of the genus Bacillus, including strain FZB42(T), formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7(T). DNA-DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7(T) and FZB42(T) yielded relatedness values of 63.7-71.2 %. Several methods of genomic analysis, such as direct whole-genome comparison, digital DDH and microarray-based comparative genomichybridization (M-CGH) were used as complementary tests. The group of plant-associated strains could be distinguished from strain DSM 7(T) and the type strain of B. subtilis by differences in the potential to synthesize non-ribosomal lipopeptides and polyketides. Based on the differences found in the marker gene sequences and the whole genomes of these strains, we propose two novel subspecies, designated B. amyloliquefaciens subsp. plantarum subsp. nov., with the type strain FZB42(T) ( = DSM 23117(T) = BGSC 10A6(T)), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7(T)( = ATCC 23350(T) = Fukumoto Strain F(T)), for plant-associated and non-plant-associated representatives, respecitvely. This is in agreement with results of DDH and M-CGH tests and the MALDI-TOF MS of cellular components, all of which suggested that the ecovars represent two different subspecies.","corpus_id":206171386,"score":1},{"doc_id":"21148737","title":"Complete genome sequence of Mycoplasma hyopneumoniae strain 168.","abstract":"Mycoplasma hyopneumoniae strain 168, a pathogenic strain prevalent in China, was isolated in 1974. Although this strain has been widespread for a long time, the genome sequence had not been determined. Here, we announce the complete genome sequence of M. hyopneumoniae strain 168.","corpus_id":206769421,"score":1},{"doc_id":"21304667","title":"Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).","abstract":"Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and with nitrate as electron acceptor. The strain, whose genome is described in this report, is a free-living, motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S rRNA that differ from each other by up to 9%. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence from the poorly populated genus Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.","corpus_id":30708047,"score":1},{"doc_id":"21304736","title":"Complete genome sequence of Methanothermus fervidus type strain (V24S).","abstract":"Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H(2) + CO(2). This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.","corpus_id":14198044,"score":1},{"doc_id":"22180807","title":"Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).","abstract":"Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.","corpus_id":17477068,"score":1},{"doc_id":"22328745","title":"Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1.","abstract":"Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.","corpus_id":43438027,"score":1},{"doc_id":"22488572","title":"Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate-reducing bacterium from hypersaline chloride-sulfate lakes in Central Asia.","abstract":"Four strains of lithotrophic sulfate-reducing bacteria (SRB) have been enriched and isolated from anoxic sediments of hypersaline chloride-sulfate lakes in the Kulunda Steppe (Altai, Russia) at 2 M NaCl and pH 7.5. According to the 16S rRNA gene sequence analysis, the isolates were closely related to each other and belonged to the genus Desulfonatronovibrio, which, so far, included only obligately alkaliphilic members found exclusively in soda lakes. The isolates utilized formate, H(2) and pyruvate as electron donors and sulfate, sulfite and thiosulfate as electron acceptors. In contrast to the described species of the genus Desulfonatronovibrio, the salt lake isolates could only tolerate high pH (up to pH 9.4), while they grow optimally at a neutral pH. They belonged to the moderate halophiles growing between 0.2 and 2 M NaCl with an optimum at 0.5 M. On the basis of their distinct phenotype and phylogeny, the described halophilic SRB are proposed to form a novel species within the genus Desulfonatronovibrio, D. halophilus (type strain HTR1(T) = DSM24312(T) = UNIQEM U802(T)).","corpus_id":-1,"score":1},{"doc_id":"22984137","title":"Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh.","abstract":"A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) ( = ATCC BAA-1436(T) = DSM 18854(T)).","corpus_id":38462245,"score":1},{"doc_id":"23209244","title":"Complete genome sequence of the copiotrophic marine bacterium Alteromonas macleodii strain ATCC 27126T.","abstract":"The genome of Alteromonas macleodii strain ATCC 27126(T) has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium.","corpus_id":38561732,"score":1},{"doc_id":"23950115","title":"Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592.","abstract":"We report the complete genome sequence of Serratia liquefaciens strain ATCC 27592, which was previously identified as capable of growth under low-pressure conditions. To the best of our knowledge, this is the first announcement of the complete genome sequence of an S. liquefaciens strain.","corpus_id":26977798,"score":1},{"doc_id":"24051316","title":"Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.","abstract":"Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus.","corpus_id":7021027,"score":1},{"doc_id":"24187023","title":"Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum.","abstract":"Ten species of the order Myxococcales with validly published names are devoid of living type strains. Four species of the genus Chondromyces are represented by dead herbarium samples as the type material. For a species of the genus Melittangium and two species of the genus Polyangium, no physical type material was assigned at the time of validation of the names or later on. In accordance with rule 18f of the International Code of Nomenclature of Bacteria the following type strains are designated for these species: strain Cm a14(T) ( = DSM 14605(T) = JCM 12615(T)) as the type strain of Chondromyces apiculatus, strain Cm c5(T) ( = DSM 14714(T) = JCM 12616(T)) as the type strain of Chondromyces crocatus, strain Sy t2(T) ( = DSM 14631(T) = JCM 12617(T)) as the type strain of Chondromyces lanuginosus, strain Cm p51(T) ( = DSM 14607(T) = JCM 12618(T)) as the type strain of Chondromyces pediculatus, strain Me b8(T) ( = DSM 14713(T) = JCM 12633(T)) as the type strain of Melittangium boletus, strain Pl s12(T) ( = DSM 14670(T) = JCM 12637(T)) as the type strain of Polyangium sorediatum and strain Pl sm5(T) ( = DSM 14734(T) = JCM 12638(T)) as the type strain of Polyangium spumosum. Furthermore, the type strains given for three species of the genera Cystobacter and Polyangium had been kept at one university institute and have been lost according to our investigations. In accordance with Rule 18c of the Bacteriological Code, we propose the following neotype strains: strain Cb fe18 ( = DSM 14716 = JCM 12624) as the neotype strain of Cystobacter ferrugineus, strain Cb m2 ( = DSM 14751 = JCM 12627) as the neotype strain of Cystobacter minus and strain Pl fu5 ( = DSM 14668 = JCM 12636) as the neotype strain of Polyangium fumosum. The proposals of the strains are based on the descriptions and strain proposals given in the respective chapters of Bergey's Manual of Systematic Bacteriology (2005).","corpus_id":7299532,"score":1},{"doc_id":"24976890","title":"Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.","abstract":"Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.","corpus_id":7536703,"score":1},{"doc_id":"24984700","title":"Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.","abstract":"A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).","corpus_id":2339052,"score":1},{"doc_id":"25197473","title":"Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).","abstract":"Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.","corpus_id":17686998,"score":1},{"doc_id":"25270020","title":"Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).","abstract":"The neotype strain Methanobacterium formicicum MF(T) (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074bp in size, featuring a GC content of 41.23%. M. formicicum MF(T) encodes several genes predicted to be involved in adaptation to abiotic stress such as high osmolarity. The strain MF(T) is of biotechnological importance since M. formicicum strains are often found in production-scale biogas plants and it is suggested as a starter culture for the anaerobic biomethanation process.","corpus_id":31035473,"score":1},{"doc_id":"25477405","title":"Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.","abstract":"Originally isolated from a pediatric patient with otitis media, Haemophilus influenzae strain 375 (Hi375) has been extensively studied as a model system for intracellular invasion of airway epithelial cells and other pathogenesis traits. Here, we report its complete genome sequence and methylome.","corpus_id":30151188,"score":1},{"doc_id":"25523782","title":"Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi.","abstract":"We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.","corpus_id":29938881,"score":1},{"doc_id":"25700417","title":"Complete genome sequence and methylome analysis of bacillus strain x1.","abstract":"Bacillus strain X1 is the source strain for the restriction enzyme BstXI. Its complete sequence and full methylome was determined using single-molecule real-time (SMRT) sequencing.","corpus_id":26361179,"score":1},{"doc_id":"25975625","title":"Complete genome sequence of Serratia multitudinisentens RB-25(T), a novel chitinolytic bacterium.","abstract":"Serratia multitudinisentens RB-25(T) (=DSM 28811(T) =LMG 28304(T)) is a newly proposed type strain in the genus of Serratia isolated from a municipal landfill site. Here, we present the complete genome of S. multitudinisentens RB-25(T) which contains a complete chitinase operon and other chitin and N-acetylglucosamine utilisation enzymes. To our knowledge, this is the first report of the complete genome sequence of this novel isolate and its chitinase gene discovery.","corpus_id":34691120,"score":1},{"doc_id":"26044413","title":"Complete Genome Sequence of Rat Cytomegalovirus Strain ALL-03 (Malaysian Strain).","abstract":"The complete genome sequence of the ALL-03 strain of rat cytomegalovirus (RCMV) has been determined. The RCMV genome has a length of 197,958 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. This strain is closely related to the English strain of RCMV in terms of genetic arrangement but differs slightly in size.","corpus_id":16792934,"score":1},{"doc_id":"26203330","title":"Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.","abstract":"Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.","corpus_id":15811385,"score":1},{"doc_id":"26209507","title":"Complete genome sequence of a keratin-degrading bacterium Chryseobacterium gallinarum strain DSM 27622(T) isolated from chicken.","abstract":"Chryseobacterium gallinarum strain DSM 27622(T) is a keratin-degrading bacterium belonging to the class Flavobacteriia, which was isolated from chicken. Here, we report the 4633,632bp complete genome sequence of the strain DSM 27622(T) with 4161 genes.","corpus_id":7844966,"score":1},{"doc_id":"26450731","title":"Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella thermoacetica DSM 521T.","abstract":"Here we report the closed genome sequence of the type strain Moorella thermoacetica DSM 521(T), an acetogenic bacterium, which is able to grow autotrophically on H2 + CO2 and/or CO, using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb).","corpus_id":5589486,"score":1},{"doc_id":"26689480","title":"The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484(T).","abstract":"Leuconostoc species are widespread in the natural environment and play an important role in several types of industrial and food fermentation processes. Here, we report the 1,854,727-bp complete genome sequence of the Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484(T).","corpus_id":29277588,"score":1},{"doc_id":"26744606","title":"Complete genome sequence of Methanospirillum hungatei type strain JF1.","abstract":"Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae within the order Methanomicrobiales. Its genome was selected for sequencing due to its ability to utilize hydrogen and carbon dioxide and/or formate as a sole source of energy. Ecologically, M. hungatei functions as the hydrogen- and/or formate-using partner with many species of syntrophic bacteria. Its morphology is distinct from other methanogens with the ability to form long chains of cells (up to 100 μm in length), which are enclosed within a sheath-like structure, and terminal cells with polar flagella. The genome of M. hungatei strain JF1 is the first completely sequenced genome of the family Methanospirillaceae, and it has a circular genome of 3,544,738 bp containing 3,239 protein coding and 68 RNA genes. The large genome of M. hungatei JF1 suggests the presence of unrecognized biochemical/physiological properties that likely extend to the other Methanospirillaceae and include the ability to form the unusual sheath-like structure and to successfully interact with syntrophic bacteria.","corpus_id":6305702,"score":1},{"doc_id":"26779304","title":"Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.","abstract":"Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism. We identified 60 effector genes, and observed that this effector repertoire is distinct when compared to those from other phylotype IIB strains. Eleven of the effectors appear to be nonfunctional due to disruptive mutations. We also report a methylome analysis of this genome, the first for a R. solanacearum strain. This analysis helped us note the presence of a toxin gene within a region of probable phage origin, raising the hypothesis that this gene may play a role in this strain's virulence.","corpus_id":3921099,"score":1},{"doc_id":"26924237","title":"Complete genome sequence of thiosulfate-oxidizing Bosea sp. strain PAMC26642 isolated from an Arctic lichen.","abstract":"Thiosulfate-oxidizing Bosea sp. strain PAMC26642 was isolated from the Arctic lichen Stereocaulon sp. Complete genome sequencing of Bosea sp. PAMC26642 revealed several genes involved in thiosulfate oxidation. An analysis of the Bosea sp. PAMC26642 genome will provide novel insight into the genetic basis of its physiology and enable further analysis of key genes in the thiosulfate oxidation pathway.","corpus_id":39365774,"score":1},{"doc_id":"27056230","title":"Complete Genome Sequence of a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205.","abstract":"Here, we report the complete genome sequence of a γ-hexachlorocyclohexane (γ-HCH)-degrading bacterium,Sphingobiumsp. strain MI1205. The genome of MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb. All thelingenes for γ-HCH metabolism are dispersed on the four plasmids.","corpus_id":26924038,"score":1},{"doc_id":"27107724","title":"Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect.","abstract":"Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.","corpus_id":43583837,"score":1},{"doc_id":"27231356","title":"Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.","abstract":"Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains.","corpus_id":3069391,"score":1},{"doc_id":"27834722","title":"Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781.","abstract":"We report here the complete genomic sequence and methylome of Aggregatibacter actinomycetemcomitans strain IDH781. This rough strain is used extensively as a model organism to characterize localized aggressive periodontitis pathogenesis, the basic biology and oral cavity colonization of A. actinomycetemcomitans, and its interactions with other members of the oral microbiome.","corpus_id":24265201,"score":1},{"doc_id":"27881545","title":"Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01.","abstract":"Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve health status in immunocompromised people. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insights into its functional activity and safety assessment.","corpus_id":12373184,"score":1},{"doc_id":"28153900","title":"Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab.","abstract":"Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species collected from the East Sea of Korea. Here, we report the complete genome sequence of strain UJ101 for the study of major metabolic pathways related to microbial species from marine invertebrate species.","corpus_id":20641755,"score":1},{"doc_id":"28495770","title":"Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352.","abstract":"Here, we report the complete genome sequence for the Bacillus circulans Jordan strain 32352. This species is a soil dwelling bacterium that expresses glycosyl hydrolase enzymes degrading pneumococcal capsular polysaccharides.","corpus_id":4787511,"score":1},{"doc_id":"28496940","title":"Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434.","abstract":"The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl a synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.","corpus_id":11760815,"score":1},{"doc_id":"28785416","title":"Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.","abstract":"Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.","corpus_id":1564074,"score":1},{"doc_id":"29276571","title":"Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.","abstract":"A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.","corpus_id":256419642,"score":1},{"doc_id":"29348347","title":"Completed Genome Sequences of Strains from 36 Serotypes of Salmonella.","abstract":"We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comparative genomics of Salmonella.","corpus_id":30082453,"score":1},{"doc_id":"29348359","title":"Complete Genome Sequence of the Type Strain of Macrococcus canis.","abstract":"The first complete genome sequence of the recently described Macrococcus canis species has been determined for the strain KM45013T (=DSM 101690T = CCOS 969T = CCUG 68920T = CCM 8748T). The strain was isolated from a dog with rhinitis and contains a putative γ-hemolysin and a mecB-carrying staphylococcal cassette chromosome mec element (SCCmecKM45013).","corpus_id":2404667,"score":1},{"doc_id":"29775788","title":"Complete genome sequence of Achromobacter spanius type strain DSM 23806T, a pathogen isolated from human blood.","abstract":"OBJECTIVES: Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level. METHODS: The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: The complete genome of DSM 23806T consists of one circular DNA chromosome of 6425783bp with a G+C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes. CONCLUSIONS: These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius.","corpus_id":21733633,"score":1},{"doc_id":"21268899","title":"[Isolation and identification of a thermophilic anaerobic bacterium].","abstract":"OBJECTIVE: To find new microbial resources from a high-temperature oil reservoir. METHODS: Strain HL-3 was isolated by Hungate Anaerobic Technique from oil reservoir water sampled from Dagang oilfield, China. Through physiological, biochemical and phylogenetic analysis, the strain HL-3 was classified. RESULTS: Cells were Gram-positive. The temperature range for growth was 40 degrees C-75 degrees C (optimum at 60 degrees C) and the pH range was 5.0-8.0 (optimum at 6.5). The isolate could grow in the presence of 0%-3.2% NaCl (optimum at 0.25%). Glucose, ribose, mannose, xylose and cellobiose could be metabolized. Metabolites of glucose were ethanol, acetate, CO2 and trace amount of propionate and butanol. The G + C content of DNA was 33.9 mol%. Based on 16S rRNA studies,strain HL-3 was most close to T. uzonensis DSM 18761T (EF530067) with 98.8% similarity and to T. sulfurigignens DSM 17917T (AF234164) with the 98.1% similarity. Strain HL-3 tolerated to high sulfite (0. 1mol/L) ions and extremely high concentration of thiosulfate (0.8 mol/L). When the concentration of thiosulfate was higher than 0.075 mol/L, the cell would generate S element granular. The presence of H2S gas was detected inside of space at the top of serum bottle. Strain HL-3 together with T. uzonensis DSM 18761T differed greatly in toleration of thiosulfate and sulfite. The toleration of strain HL-3 to thiosulfate and sulfite was most close to T. sulfurigignens DSM 17917T (AF234164). In addition, strain HL-3 to metabolite thiosulfate and sulfite was also similar with T. sulfurigignens DSM 17917T (AF234164). However, it differs largely from both of them to metabolize glucose. CONCLUSION: Therefore, strain HL-3 may be a new spieces of the Thermoanaerobacter, and the definitive classification positioning is still awaiting for further verified with the method of determination of whole-genome DNA-DNA similarity","corpus_id":11071646,"score":0},{"doc_id":"23868136","title":"Complete genome sequence of a human enterovirus 71 strain isolated in brunei in 2006.","abstract":"The complete genome sequence of a human enterovirus 71 strain isolated in Brunei in 2006 was determined. Phylogenetic analysis based on the complete genome sequence classified this strain into subgenogroup B5.","corpus_id":20744082,"score":0}],"string":"[\n {\n \"doc_id\": \"18621874\",\n \"title\": \"Methylotrophy in freshwater Beggiatoa alba strains.\",\n \"abstract\": \"Two freshwater strains of the gammaproteobacterium Beggiatoa alba, B18LD and OH75-2a, are able to use methanol as a sole carbon and energy source under microoxic conditions. Genes encoding a methanol dehydrogenase large-subunit homolog and four enzymes of the tetrahydromethanopterin-dependent C(1) oxidation pathway were identified in B18LD. No evidence of methanotrophy was detected.\",\n \"corpus_id\": 46417230,\n \"score\": 2\n },\n {\n \"doc_id\": \"20207153\",\n \"title\": \"Comparative analysis of Beggiatoa from hypersaline and marine environments.\",\n \"abstract\": \"The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34 microm, and their lengths ranged from 10 microm to over 30 mm. Narrow trichomes moved by gliding at 3.0 microm/s; large filaments moved at 1.5 microm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers.\",\n \"corpus_id\": 37094386,\n \"score\": 2\n },\n {\n \"doc_id\": \"20827290\",\n \"title\": \"Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain.\",\n \"abstract\": \"Sulfur bacteria such as Beggiatoa or Thiomargarita have a particularly high capacity for storage because of their large size. In addition to sulfur and nitrate, these bacteria also store phosphorus in the form of polyphosphate. Thiomargarita namibiensis has been shown to release phosphate from internally stored polyphosphate in pulses creating steep peaks of phosphate in the sediment and thereby inducing the precipitation of phosphorus-rich minerals. Large sulfur bacteria populate sediments at the sites of recent phosphorite formation and are found as fossils in ancient phosphorite deposits. Therefore, it can be assumed that this physiology contributes to the removal of bioavailable phosphorus from the marine system and thus is important for the global phosphorus cycle. We investigated under defined laboratory conditions which parameters stimulate the decomposition of polyphosphate and the release of phosphate in a marine Beggiatoa strain. Initially, we tested phosphate release in response to anoxia and high concentrations of acetate, because acetate is described as the relevant stimulus for phosphate release in activated sludge. To our surprise, the Beggiatoa strain did not release phosphate in response to this treatment. Instead, we could clearly show that increasing sulfide concentrations and anoxia resulted in a decomposition of polyphosphate. This physiological reaction is a yet unknown mode of bacterial polyphosphate usage and provides a new explanation for high phosphate concentrations in sulfidic marine sediments.\",\n \"corpus_id\": 22900900,\n \"score\": 2\n },\n {\n \"doc_id\": \"21909788\",\n \"title\": \"Unusual polyphosphate inclusions observed in a marine Beggiatoa strain.\",\n \"abstract\": \"Sulfide-oxidizing bacteria of the genus Beggiatoa are known to accumulate phosphate intracellularly as polyphosphate but little is known about the structure and properties of these inclusions. Application of different staining techniques revealed the presence of unusually large polyphosphate inclusions in the marine Beggiatoa strain 35Flor. The inclusions showed a co-occurrence of polyphosphate, calcium and magnesium when analyzed by scanning electron microscopy and energy dispersive X-ray analysis. Similar to polyphosphate-enriched acidocalcisomes of prokaryotes and eukaryotes, the polyphosphate inclusions in Beggiatoa strain 35Flor are enclosed by a lipid layer and store cations. However, they are not notably acidic. 16S rRNA gene sequence-based phylogenetic reconstruction showed an affiliation of Beggiatoa strain 35Flor to a monophyletic branch, comprising other narrow vacuolated and non-vacuolated Beggiatoa species. The polyphosphate inclusions represent a new type of membrane surrounded storage compartment within the genus Beggiatoa, distinct from the mostly nitrate-storing vacuoles known from other marine sulfide-oxidizing bacteria of the family Beggiatoaceae.\",\n \"corpus_id\": 14947543,\n \"score\": 2\n },\n {\n \"doc_id\": \"22123768\",\n \"title\": \"Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain AM4, capable of organotrophic growth and growth at the expense of hydrogenogenic or sulfidogenic oxidation of carbon monoxide.\",\n \"abstract\": \"Analysis of the complete genome of Thermococcus sp. strain AM4, which was the first lithotrophic Thermococcales isolate described and the first archaeal isolate to exhibit a capacity for hydrogenogenic carboxydotrophy, reveals a proximity with Thermococcus gammatolerans, corresponding to close but distinct species that differ significantly in their lithotrophic capacities.\",\n \"corpus_id\": 43133826,\n \"score\": 2\n },\n {\n \"doc_id\": \"22841519\",\n \"title\": \"Enrichment and identification of large filamentous sulfur bacteria related to Beggiatoa species from brackishwater ecosystems of Tamil Nadu along the southeast coast of India.\",\n \"abstract\": \"Beggiatoa species are filamentous sulfide-oxidizing bacteria belonging to the family Beggiatoaceae that contains several largest bacteria known today. These large sulfur bacteria occur in diverse ecosystems and play an important role in the global sulfur, nitrogen and phosphorus cycle. In this study, sediment samples from brackishwater shrimp culture ponds and other brackishwater ecosystems from Tamil Nadu, southeast coast of India, were enriched for Beggiatoa species. Extracted hay medium supplemented with catalase was used and were incubated for two weeks at 28°C. Out of seven set-ups, four yielded positive growth of filamentous sulfide-oxidizing bacteria. The filaments were several millimeters long, ranged in width between 2 and 15 μm and exhibited typical gliding motility. The 16S rRNA gene of four single filaments representing the four positive enrichments was subjected to PCR-DGGE followed by sequencing. All four filaments were affiliated to the Beggiatoaceae, but showed less than 89% identity with the Beggiatoa type strain Beggiatoa alba and less than 93% identity with any other sequence of the family. One of the four filaments revealed a nearly full-length 16S rDNA sequence (1411bp) and it formed a monophyletic cluster with two of the partial DGGE-16S rRNA gene sequences (99-100% identity) within the Beggiatoa species cluster. These organisms could possibly represent a novel genus within the family Beggiatoaceae. The fourth partial sequence affiliated with less than 93% sequence identity to the genera Parabeggiatoa, Thioploca and Thiopilula, and was likewise strongly delineated from any sequence published in the family.\",\n \"corpus_id\": 28291326,\n \"score\": 2\n },\n {\n \"doc_id\": \"24012537\",\n \"title\": \"Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.\",\n \"abstract\": \"A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability.\",\n \"corpus_id\": 33723170,\n \"score\": 2\n },\n {\n \"doc_id\": \"26603120\",\n \"title\": \"Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.\",\n \"abstract\": \"Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.\",\n \"corpus_id\": 6782854,\n \"score\": 2\n },\n {\n \"doc_id\": \"26659680\",\n \"title\": \"Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T.\",\n \"abstract\": \"In this report, we announce the availability of a complete closed genome sequence and methylome analysis of Beggiatoa leptomitiformis neotype strain D-402(T) (DSM 14946, UNIQEM U 779).\",\n \"corpus_id\": 4964304,\n \"score\": 2\n },\n {\n \"doc_id\": \"26744373\",\n \"title\": \"Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.\",\n \"abstract\": \"We report the complete, closed genome sequence and complete methylome of Azospirillum thiophilum strain BV-S(T).\",\n \"corpus_id\": 9932982,\n \"score\": 2\n },\n {\n \"doc_id\": \"26896131\",\n \"title\": \"Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain.\",\n \"abstract\": \"UNLABELLED: A chemolithoautotrophic strain of the family Beggiatoaceae, Beggiatoa sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration. Beggiatoa sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide Beggiatoa sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of Beggiatoa ceae to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow. IMPORTANCE: Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic Beggiatoa ceae, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of Beggiatoa ceaein several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies.\",\n \"corpus_id\": 18362101,\n \"score\": 2\n },\n {\n \"doc_id\": \"27516520\",\n \"title\": \"Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.\",\n \"abstract\": \"The genus Comamonas contains species isolated from various environments, such as termite guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we report the draft genome sequence of Comamonas thiooxydans strain S23(T) capable of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas thiooxydans whole-genome sequence will help understand the metabolic diversity in sulfur oxidation pathways.\",\n \"corpus_id\": 19049101,\n \"score\": 2\n },\n {\n \"doc_id\": \"27832308\",\n \"title\": \"Mechanism of electron transport during thiosulfate oxidation in an obligately mixotrophic bacterium Thiomonas bhubaneswarensis strain S10 (DSM 18181(T)).\",\n \"abstract\": \"This study describes the thiosulfate-supported respiratory electron transport activity of Thiomonas bhubaneswarensis strain S10 (DSM 18181(T)). Whole-genome sequence analysis revealed the presence of complete sox (sulfur oxidation) gene cluster (soxCDYZAXB) including the sulfur oxygenase reductase (SOR), sulfide quinone reductase (SQR), sulfide dehydrogenase (flavocytochrome c (fcc)), thiosulfate dehydrogenase (Tsd), sulfite dehydrogenase (SorAB), and intracellular sulfur oxidation protein (DsrE/DsrF). In addition, genes encoding respiratory electron transport chain components viz. complex I (NADH dehydrogenase), complex II (succinate dehydrogenase), complex III (ubiquinone-cytochrome c reductase), and various types of terminal oxidases (cytochrome c and quinol oxidase) were identified in the genome. Using site-specific electron donors and inhibitors and by analyzing the cytochrome spectra, we identified the shortest thiosulfate-dependent electron transport chain in T. bhubaneswarensis DSM 18181(T). Our results showed that thiosulfate supports the electron transport activity in a bifurcated manner, donating electrons to quinol (bd) and cytochrome c (Caa 3 ) oxidase; these two sites (quinol oxidase and cytochrome c oxidase) also showed differences in their phosphate esterification potential (oxidative phosphorylation efficiency (P/O)). Further, it was evidenced that the substrate-level phosphorylation is the major contributor to the total energy budget in this bacterium.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"27902215\",\n \"title\": \"Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth.\",\n \"abstract\": \"A strain of filamentous sulfur bacteria was isolated from freshwater spring contaminated with residential and agricultural wastewater in Moscow region, Russia. According to the results of phylogenetic analysis, strain D-402T belonged to the genus Beggiatoa within the family Beggiatoaceae of the class Gammaproteobacteria. Within the genus Beggiatoa, strain D-402T was most closely related to Beggiatoa alba strains. Strain D-402T had a DNA G+C content 42.1 mol%. The DNA-DNA hybridization value between strain D-402T and Beggiatoa alba strain B15LD was 33 %. Predominant fatty acids were C18 : 1 (46.1 and 53.3 %), C16 : 0 (15.5 and 16.2 %) and C16 : 1 (32.9 and 25.4 %) for strains D-402T and B15LD, respectively. In contrast to known representatives of Beggiatoa, strain D-402T was capable of chemolithoautotrophic growth with sulfide and thiosulfate as electron donors. Oxidation of sulfide and thiosulfate was accompanied by deposition of sulfur globules within the cells. Strain D-402T was capable of heterotrophic growth. The strain was capable of using different organic compounds, sulfur compounds and hydrogen as electron donors. Based on these observations, strain D-402T is considered as a representative of a species Beggiatoa leptomitoformis sp. nov. of the genus Beggiatoa. The type strain is D-402T (=DSM 14946T=UNIQEM U 779T).\",\n \"corpus_id\": 21211138,\n \"score\": 2\n },\n {\n \"doc_id\": \"28860255\",\n \"title\": \"Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.\",\n \"abstract\": \"In this report, we announce the availability of a whole-genome sequence and methylome analysis of Thioflexothrix psekupsii strain D3.\",\n \"corpus_id\": 34737196,\n \"score\": 2\n },\n {\n \"doc_id\": \"20023012\",\n \"title\": \"Completed genome sequence of the anaerobic iron-oxidizing bacterium Acidovorax ebreus strain TPSY.\",\n \"abstract\": \"Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.\",\n \"corpus_id\": 24077466,\n \"score\": 1\n },\n {\n \"doc_id\": \"20495027\",\n \"title\": \"Taxonomic investigation of representatives of the genus Sphaerotilus: descriptions of Sphaerotilus montanus sp. nov., Sphaerotilus hippei sp. nov., Sphaerotilus natans subsp. natans subsp. nov. and Sphaerotilus natans subsp. sulfidivorans subsp. nov., and an emended description of the genus Sphaerotilus.\",\n \"abstract\": \"Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501(T), D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HS(T)) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strains of Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575(T), DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C(16 : 1)ω7, C(16 : 0) and C(18 : 1)ω7 as the major fatty acids. The DNA-DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501(T), D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575(T). However, strains D-501(T), D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575(T) by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501(T), D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501(T) = DSM 22545(T) = VKM B-2573(T)) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575(T). Strains D-380 and S. natans DSM 6575(T) were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575(T) = ATCC 13338(T)). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HS(T) and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575(T). Strain HS(T) shared 99 % DNA-DNA relatedness with strain.\",\n \"corpus_id\": 26662232,\n \"score\": 1\n },\n {\n \"doc_id\": \"20817842\",\n \"title\": \"Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons.\",\n \"abstract\": \"The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the species Bacillus amyloliquefaciens or Bacillus subtilis are used commercially to promote the growth and improve the health of crop plants. Previous investigations revealed that a group of strains represented a distinct ecotype related to B. amyloliquefaciens; however, the exact taxonomic position of this group remains elusive (Reva et al., 2004). In the present study, we demonstrated the ability of a group of Bacillus strains closely related to strain FZB42(T) to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7(T) but differed considerably from this type strain in the DNA sequences of genes encoding 16S rRNA, gyrase subunit A (gyrA) and histidine kinase (cheA). Phylogenetic analysis performed with partial 16S rRNA, gyrA and cheA gene sequences revealed that the plant-associated strains of the genus Bacillus, including strain FZB42(T), formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7(T). DNA-DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7(T) and FZB42(T) yielded relatedness values of 63.7-71.2 %. Several methods of genomic analysis, such as direct whole-genome comparison, digital DDH and microarray-based comparative genomichybridization (M-CGH) were used as complementary tests. The group of plant-associated strains could be distinguished from strain DSM 7(T) and the type strain of B. subtilis by differences in the potential to synthesize non-ribosomal lipopeptides and polyketides. Based on the differences found in the marker gene sequences and the whole genomes of these strains, we propose two novel subspecies, designated B. amyloliquefaciens subsp. plantarum subsp. nov., with the type strain FZB42(T) ( = DSM 23117(T) = BGSC 10A6(T)), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7(T)( = ATCC 23350(T) = Fukumoto Strain F(T)), for plant-associated and non-plant-associated representatives, respecitvely. This is in agreement with results of DDH and M-CGH tests and the MALDI-TOF MS of cellular components, all of which suggested that the ecovars represent two different subspecies.\",\n \"corpus_id\": 206171386,\n \"score\": 1\n },\n {\n \"doc_id\": \"21148737\",\n \"title\": \"Complete genome sequence of Mycoplasma hyopneumoniae strain 168.\",\n \"abstract\": \"Mycoplasma hyopneumoniae strain 168, a pathogenic strain prevalent in China, was isolated in 1974. Although this strain has been widespread for a long time, the genome sequence had not been determined. Here, we announce the complete genome sequence of M. hyopneumoniae strain 168.\",\n \"corpus_id\": 206769421,\n \"score\": 1\n },\n {\n \"doc_id\": \"21304667\",\n \"title\": \"Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).\",\n \"abstract\": \"Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and with nitrate as electron acceptor. The strain, whose genome is described in this report, is a free-living, motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S rRNA that differ from each other by up to 9%. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence from the poorly populated genus Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.\",\n \"corpus_id\": 30708047,\n \"score\": 1\n },\n {\n \"doc_id\": \"21304736\",\n \"title\": \"Complete genome sequence of Methanothermus fervidus type strain (V24S).\",\n \"abstract\": \"Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H(2) + CO(2). This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.\",\n \"corpus_id\": 14198044,\n \"score\": 1\n },\n {\n \"doc_id\": \"22180807\",\n \"title\": \"Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).\",\n \"abstract\": \"Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.\",\n \"corpus_id\": 17477068,\n \"score\": 1\n },\n {\n \"doc_id\": \"22328745\",\n \"title\": \"Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1.\",\n \"abstract\": \"Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.\",\n \"corpus_id\": 43438027,\n \"score\": 1\n },\n {\n \"doc_id\": \"22488572\",\n \"title\": \"Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate-reducing bacterium from hypersaline chloride-sulfate lakes in Central Asia.\",\n \"abstract\": \"Four strains of lithotrophic sulfate-reducing bacteria (SRB) have been enriched and isolated from anoxic sediments of hypersaline chloride-sulfate lakes in the Kulunda Steppe (Altai, Russia) at 2 M NaCl and pH 7.5. According to the 16S rRNA gene sequence analysis, the isolates were closely related to each other and belonged to the genus Desulfonatronovibrio, which, so far, included only obligately alkaliphilic members found exclusively in soda lakes. The isolates utilized formate, H(2) and pyruvate as electron donors and sulfate, sulfite and thiosulfate as electron acceptors. In contrast to the described species of the genus Desulfonatronovibrio, the salt lake isolates could only tolerate high pH (up to pH 9.4), while they grow optimally at a neutral pH. They belonged to the moderate halophiles growing between 0.2 and 2 M NaCl with an optimum at 0.5 M. On the basis of their distinct phenotype and phylogeny, the described halophilic SRB are proposed to form a novel species within the genus Desulfonatronovibrio, D. halophilus (type strain HTR1(T) = DSM24312(T) = UNIQEM U802(T)).\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"22984137\",\n \"title\": \"Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh.\",\n \"abstract\": \"A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) ( = ATCC BAA-1436(T) = DSM 18854(T)).\",\n \"corpus_id\": 38462245,\n \"score\": 1\n },\n {\n \"doc_id\": \"23209244\",\n \"title\": \"Complete genome sequence of the copiotrophic marine bacterium Alteromonas macleodii strain ATCC 27126T.\",\n \"abstract\": \"The genome of Alteromonas macleodii strain ATCC 27126(T) has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium.\",\n \"corpus_id\": 38561732,\n \"score\": 1\n },\n {\n \"doc_id\": \"23950115\",\n \"title\": \"Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592.\",\n \"abstract\": \"We report the complete genome sequence of Serratia liquefaciens strain ATCC 27592, which was previously identified as capable of growth under low-pressure conditions. To the best of our knowledge, this is the first announcement of the complete genome sequence of an S. liquefaciens strain.\",\n \"corpus_id\": 26977798,\n \"score\": 1\n },\n {\n \"doc_id\": \"24051316\",\n \"title\": \"Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.\",\n \"abstract\": \"Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus.\",\n \"corpus_id\": 7021027,\n \"score\": 1\n },\n {\n \"doc_id\": \"24187023\",\n \"title\": \"Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum.\",\n \"abstract\": \"Ten species of the order Myxococcales with validly published names are devoid of living type strains. Four species of the genus Chondromyces are represented by dead herbarium samples as the type material. For a species of the genus Melittangium and two species of the genus Polyangium, no physical type material was assigned at the time of validation of the names or later on. In accordance with rule 18f of the International Code of Nomenclature of Bacteria the following type strains are designated for these species: strain Cm a14(T) ( = DSM 14605(T) = JCM 12615(T)) as the type strain of Chondromyces apiculatus, strain Cm c5(T) ( = DSM 14714(T) = JCM 12616(T)) as the type strain of Chondromyces crocatus, strain Sy t2(T) ( = DSM 14631(T) = JCM 12617(T)) as the type strain of Chondromyces lanuginosus, strain Cm p51(T) ( = DSM 14607(T) = JCM 12618(T)) as the type strain of Chondromyces pediculatus, strain Me b8(T) ( = DSM 14713(T) = JCM 12633(T)) as the type strain of Melittangium boletus, strain Pl s12(T) ( = DSM 14670(T) = JCM 12637(T)) as the type strain of Polyangium sorediatum and strain Pl sm5(T) ( = DSM 14734(T) = JCM 12638(T)) as the type strain of Polyangium spumosum. Furthermore, the type strains given for three species of the genera Cystobacter and Polyangium had been kept at one university institute and have been lost according to our investigations. In accordance with Rule 18c of the Bacteriological Code, we propose the following neotype strains: strain Cb fe18 ( = DSM 14716 = JCM 12624) as the neotype strain of Cystobacter ferrugineus, strain Cb m2 ( = DSM 14751 = JCM 12627) as the neotype strain of Cystobacter minus and strain Pl fu5 ( = DSM 14668 = JCM 12636) as the neotype strain of Polyangium fumosum. The proposals of the strains are based on the descriptions and strain proposals given in the respective chapters of Bergey's Manual of Systematic Bacteriology (2005).\",\n \"corpus_id\": 7299532,\n \"score\": 1\n },\n {\n \"doc_id\": \"24976890\",\n \"title\": \"Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.\",\n \"abstract\": \"Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.\",\n \"corpus_id\": 7536703,\n \"score\": 1\n },\n {\n \"doc_id\": \"24984700\",\n \"title\": \"Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.\",\n \"abstract\": \"A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).\",\n \"corpus_id\": 2339052,\n \"score\": 1\n },\n {\n \"doc_id\": \"25197473\",\n \"title\": \"Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).\",\n \"abstract\": \"Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.\",\n \"corpus_id\": 17686998,\n \"score\": 1\n },\n {\n \"doc_id\": \"25270020\",\n \"title\": \"Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).\",\n \"abstract\": \"The neotype strain Methanobacterium formicicum MF(T) (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074bp in size, featuring a GC content of 41.23%. M. formicicum MF(T) encodes several genes predicted to be involved in adaptation to abiotic stress such as high osmolarity. The strain MF(T) is of biotechnological importance since M. formicicum strains are often found in production-scale biogas plants and it is suggested as a starter culture for the anaerobic biomethanation process.\",\n \"corpus_id\": 31035473,\n \"score\": 1\n },\n {\n \"doc_id\": \"25477405\",\n \"title\": \"Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.\",\n \"abstract\": \"Originally isolated from a pediatric patient with otitis media, Haemophilus influenzae strain 375 (Hi375) has been extensively studied as a model system for intracellular invasion of airway epithelial cells and other pathogenesis traits. Here, we report its complete genome sequence and methylome.\",\n \"corpus_id\": 30151188,\n \"score\": 1\n },\n {\n \"doc_id\": \"25523782\",\n \"title\": \"Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi.\",\n \"abstract\": \"We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.\",\n \"corpus_id\": 29938881,\n \"score\": 1\n },\n {\n \"doc_id\": \"25700417\",\n \"title\": \"Complete genome sequence and methylome analysis of bacillus strain x1.\",\n \"abstract\": \"Bacillus strain X1 is the source strain for the restriction enzyme BstXI. Its complete sequence and full methylome was determined using single-molecule real-time (SMRT) sequencing.\",\n \"corpus_id\": 26361179,\n \"score\": 1\n },\n {\n \"doc_id\": \"25975625\",\n \"title\": \"Complete genome sequence of Serratia multitudinisentens RB-25(T), a novel chitinolytic bacterium.\",\n \"abstract\": \"Serratia multitudinisentens RB-25(T) (=DSM 28811(T) =LMG 28304(T)) is a newly proposed type strain in the genus of Serratia isolated from a municipal landfill site. Here, we present the complete genome of S. multitudinisentens RB-25(T) which contains a complete chitinase operon and other chitin and N-acetylglucosamine utilisation enzymes. To our knowledge, this is the first report of the complete genome sequence of this novel isolate and its chitinase gene discovery.\",\n \"corpus_id\": 34691120,\n \"score\": 1\n },\n {\n \"doc_id\": \"26044413\",\n \"title\": \"Complete Genome Sequence of Rat Cytomegalovirus Strain ALL-03 (Malaysian Strain).\",\n \"abstract\": \"The complete genome sequence of the ALL-03 strain of rat cytomegalovirus (RCMV) has been determined. The RCMV genome has a length of 197,958 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. This strain is closely related to the English strain of RCMV in terms of genetic arrangement but differs slightly in size.\",\n \"corpus_id\": 16792934,\n \"score\": 1\n },\n {\n \"doc_id\": \"26203330\",\n \"title\": \"Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.\",\n \"abstract\": \"Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.\",\n \"corpus_id\": 15811385,\n \"score\": 1\n },\n {\n \"doc_id\": \"26209507\",\n \"title\": \"Complete genome sequence of a keratin-degrading bacterium Chryseobacterium gallinarum strain DSM 27622(T) isolated from chicken.\",\n \"abstract\": \"Chryseobacterium gallinarum strain DSM 27622(T) is a keratin-degrading bacterium belonging to the class Flavobacteriia, which was isolated from chicken. Here, we report the 4633,632bp complete genome sequence of the strain DSM 27622(T) with 4161 genes.\",\n \"corpus_id\": 7844966,\n \"score\": 1\n },\n {\n \"doc_id\": \"26450731\",\n \"title\": \"Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella thermoacetica DSM 521T.\",\n \"abstract\": \"Here we report the closed genome sequence of the type strain Moorella thermoacetica DSM 521(T), an acetogenic bacterium, which is able to grow autotrophically on H2 + CO2 and/or CO, using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb).\",\n \"corpus_id\": 5589486,\n \"score\": 1\n },\n {\n \"doc_id\": \"26689480\",\n \"title\": \"The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484(T).\",\n \"abstract\": \"Leuconostoc species are widespread in the natural environment and play an important role in several types of industrial and food fermentation processes. Here, we report the 1,854,727-bp complete genome sequence of the Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484(T).\",\n \"corpus_id\": 29277588,\n \"score\": 1\n },\n {\n \"doc_id\": \"26744606\",\n \"title\": \"Complete genome sequence of Methanospirillum hungatei type strain JF1.\",\n \"abstract\": \"Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae within the order Methanomicrobiales. Its genome was selected for sequencing due to its ability to utilize hydrogen and carbon dioxide and/or formate as a sole source of energy. Ecologically, M. hungatei functions as the hydrogen- and/or formate-using partner with many species of syntrophic bacteria. Its morphology is distinct from other methanogens with the ability to form long chains of cells (up to 100 μm in length), which are enclosed within a sheath-like structure, and terminal cells with polar flagella. The genome of M. hungatei strain JF1 is the first completely sequenced genome of the family Methanospirillaceae, and it has a circular genome of 3,544,738 bp containing 3,239 protein coding and 68 RNA genes. The large genome of M. hungatei JF1 suggests the presence of unrecognized biochemical/physiological properties that likely extend to the other Methanospirillaceae and include the ability to form the unusual sheath-like structure and to successfully interact with syntrophic bacteria.\",\n \"corpus_id\": 6305702,\n \"score\": 1\n },\n {\n \"doc_id\": \"26779304\",\n \"title\": \"Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.\",\n \"abstract\": \"Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism. We identified 60 effector genes, and observed that this effector repertoire is distinct when compared to those from other phylotype IIB strains. Eleven of the effectors appear to be nonfunctional due to disruptive mutations. We also report a methylome analysis of this genome, the first for a R. solanacearum strain. This analysis helped us note the presence of a toxin gene within a region of probable phage origin, raising the hypothesis that this gene may play a role in this strain's virulence.\",\n \"corpus_id\": 3921099,\n \"score\": 1\n },\n {\n \"doc_id\": \"26924237\",\n \"title\": \"Complete genome sequence of thiosulfate-oxidizing Bosea sp. strain PAMC26642 isolated from an Arctic lichen.\",\n \"abstract\": \"Thiosulfate-oxidizing Bosea sp. strain PAMC26642 was isolated from the Arctic lichen Stereocaulon sp. Complete genome sequencing of Bosea sp. PAMC26642 revealed several genes involved in thiosulfate oxidation. An analysis of the Bosea sp. PAMC26642 genome will provide novel insight into the genetic basis of its physiology and enable further analysis of key genes in the thiosulfate oxidation pathway.\",\n \"corpus_id\": 39365774,\n \"score\": 1\n },\n {\n \"doc_id\": \"27056230\",\n \"title\": \"Complete Genome Sequence of a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205.\",\n \"abstract\": \"Here, we report the complete genome sequence of a γ-hexachlorocyclohexane (γ-HCH)-degrading bacterium,Sphingobiumsp. strain MI1205. The genome of MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb. All thelingenes for γ-HCH metabolism are dispersed on the four plasmids.\",\n \"corpus_id\": 26924038,\n \"score\": 1\n },\n {\n \"doc_id\": \"27107724\",\n \"title\": \"Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect.\",\n \"abstract\": \"Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.\",\n \"corpus_id\": 43583837,\n \"score\": 1\n },\n {\n \"doc_id\": \"27231356\",\n \"title\": \"Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.\",\n \"abstract\": \"Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains.\",\n \"corpus_id\": 3069391,\n \"score\": 1\n },\n {\n \"doc_id\": \"27834722\",\n \"title\": \"Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781.\",\n \"abstract\": \"We report here the complete genomic sequence and methylome of Aggregatibacter actinomycetemcomitans strain IDH781. This rough strain is used extensively as a model organism to characterize localized aggressive periodontitis pathogenesis, the basic biology and oral cavity colonization of A. actinomycetemcomitans, and its interactions with other members of the oral microbiome.\",\n \"corpus_id\": 24265201,\n \"score\": 1\n },\n {\n \"doc_id\": \"27881545\",\n \"title\": \"Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01.\",\n \"abstract\": \"Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve health status in immunocompromised people. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insights into its functional activity and safety assessment.\",\n \"corpus_id\": 12373184,\n \"score\": 1\n },\n {\n \"doc_id\": \"28153900\",\n \"title\": \"Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab.\",\n \"abstract\": \"Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species collected from the East Sea of Korea. Here, we report the complete genome sequence of strain UJ101 for the study of major metabolic pathways related to microbial species from marine invertebrate species.\",\n \"corpus_id\": 20641755,\n \"score\": 1\n },\n {\n \"doc_id\": \"28495770\",\n \"title\": \"Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352.\",\n \"abstract\": \"Here, we report the complete genome sequence for the Bacillus circulans Jordan strain 32352. This species is a soil dwelling bacterium that expresses glycosyl hydrolase enzymes degrading pneumococcal capsular polysaccharides.\",\n \"corpus_id\": 4787511,\n \"score\": 1\n },\n {\n \"doc_id\": \"28496940\",\n \"title\": \"Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434.\",\n \"abstract\": \"The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl a synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.\",\n \"corpus_id\": 11760815,\n \"score\": 1\n },\n {\n \"doc_id\": \"28785416\",\n \"title\": \"Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.\",\n \"abstract\": \"Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.\",\n \"corpus_id\": 1564074,\n \"score\": 1\n },\n {\n \"doc_id\": \"29276571\",\n \"title\": \"Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.\",\n \"abstract\": \"A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.\",\n \"corpus_id\": 256419642,\n \"score\": 1\n },\n {\n \"doc_id\": \"29348347\",\n \"title\": \"Completed Genome Sequences of Strains from 36 Serotypes of Salmonella.\",\n \"abstract\": \"We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comparative genomics of Salmonella.\",\n \"corpus_id\": 30082453,\n \"score\": 1\n },\n {\n \"doc_id\": \"29348359\",\n \"title\": \"Complete Genome Sequence of the Type Strain of Macrococcus canis.\",\n \"abstract\": \"The first complete genome sequence of the recently described Macrococcus canis species has been determined for the strain KM45013T (=DSM 101690T = CCOS 969T = CCUG 68920T = CCM 8748T). The strain was isolated from a dog with rhinitis and contains a putative γ-hemolysin and a mecB-carrying staphylococcal cassette chromosome mec element (SCCmecKM45013).\",\n \"corpus_id\": 2404667,\n \"score\": 1\n },\n {\n \"doc_id\": \"29775788\",\n \"title\": \"Complete genome sequence of Achromobacter spanius type strain DSM 23806T, a pathogen isolated from human blood.\",\n \"abstract\": \"OBJECTIVES: Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level. METHODS: The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: The complete genome of DSM 23806T consists of one circular DNA chromosome of 6425783bp with a G+C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes. CONCLUSIONS: These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius.\",\n \"corpus_id\": 21733633,\n \"score\": 1\n },\n {\n \"doc_id\": \"21268899\",\n \"title\": \"[Isolation and identification of a thermophilic anaerobic bacterium].\",\n \"abstract\": \"OBJECTIVE: To find new microbial resources from a high-temperature oil reservoir. METHODS: Strain HL-3 was isolated by Hungate Anaerobic Technique from oil reservoir water sampled from Dagang oilfield, China. Through physiological, biochemical and phylogenetic analysis, the strain HL-3 was classified. RESULTS: Cells were Gram-positive. The temperature range for growth was 40 degrees C-75 degrees C (optimum at 60 degrees C) and the pH range was 5.0-8.0 (optimum at 6.5). The isolate could grow in the presence of 0%-3.2% NaCl (optimum at 0.25%). Glucose, ribose, mannose, xylose and cellobiose could be metabolized. Metabolites of glucose were ethanol, acetate, CO2 and trace amount of propionate and butanol. The G + C content of DNA was 33.9 mol%. Based on 16S rRNA studies,strain HL-3 was most close to T. uzonensis DSM 18761T (EF530067) with 98.8% similarity and to T. sulfurigignens DSM 17917T (AF234164) with the 98.1% similarity. Strain HL-3 tolerated to high sulfite (0. 1mol/L) ions and extremely high concentration of thiosulfate (0.8 mol/L). When the concentration of thiosulfate was higher than 0.075 mol/L, the cell would generate S element granular. The presence of H2S gas was detected inside of space at the top of serum bottle. Strain HL-3 together with T. uzonensis DSM 18761T differed greatly in toleration of thiosulfate and sulfite. The toleration of strain HL-3 to thiosulfate and sulfite was most close to T. sulfurigignens DSM 17917T (AF234164). In addition, strain HL-3 to metabolite thiosulfate and sulfite was also similar with T. sulfurigignens DSM 17917T (AF234164). However, it differs largely from both of them to metabolize glucose. CONCLUSION: Therefore, strain HL-3 may be a new spieces of the Thermoanaerobacter, and the definitive classification positioning is still awaiting for further verified with the method of determination of whole-genome DNA-DNA similarity\",\n \"corpus_id\": 11071646,\n \"score\": 0\n },\n {\n \"doc_id\": \"23868136\",\n \"title\": \"Complete genome sequence of a human enterovirus 71 strain isolated in brunei in 2006.\",\n \"abstract\": \"The complete genome sequence of a human enterovirus 71 strain isolated in Brunei in 2006 was determined. Phylogenetic analysis based on the complete genome sequence classified this strain into subgenogroup B5.\",\n \"corpus_id\": 20744082,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":58,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29670091\",\n \"title\": \"Inhibition of the mevalonate pathway enhances cancer cell oncolysis mediated by M1 virus.\",\n \"abstract\": \"Oncolytic virus is an attractive anticancer agent that selectively lyses cancer through targeting cancer cells rather than normal cells. Although M1 virus is effective against several cancer types, certain cancer cells present low sensitivity to it. Here we identified that most of the components in the cholesterol biosynthesis pathway are downregulated after M1 virus infection. Further functional studies illustrate that mevalonate/protein farnesylation/ras homolog family member Q (RHOQ) axis inhibits M1 virus replication. Further transcriptome analysis shows that RHOQ knockdown obviously suppresses Rab GTPase and ATP-mediated membrane transporter system, which may mediate the antiviral effect of RHOQ. Based on this, inhibition of the above pathway significantly enhances the anticancer potency of M1 virus in vitro, in vivo, and ex vivo. Our research provides an intriguing strategy for the rational combination of M1 virus with farnesyl transferase inhibitors to enhance therapeutic efficacy.\",\n \"corpus_id\": 4940164\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"25288727","title":"Identification and characterization of alphavirus M1 as a selective oncolytic virus targeting ZAP-defective human cancers.","abstract":"Oncolytic virotherapy is a growing treatment modality that uses replicating viruses as selective antineoplastic agents. Safety and efficacy considerations dictate that an ideal oncolytic agent would discriminate between normal and cancer cells on the basis of common genetic abnormalities in human cancers. Here, we identify a naturally occurring alphavirus (M1) as a novel selective killer targeting zinc-finger antiviral protein (ZAP)-deficient cancer cells. In vitro, in vivo, and ex vivo studies showed potent oncolytic efficacy and high tumor tropism of M1. We showed that the selectivity depends on ZAP deficiency by systematic identification. A large-scale multicenter pathology study using tissue microarrays reveals that ZAP is commonly deficient in human cancers, suggesting extensive application prospects for M1. Additionally, M1 killed cancer cells by inducing endoplasmic reticulum stress-mediated apoptosis. Our report provides novel insights into potentially personalized cancer therapy using oncolytic viruses.","corpus_id":19342751,"score":2},{"doc_id":"26373347","title":"Activation of Cyclic Adenosine Monophosphate Pathway Increases the Sensitivity of Cancer Cells to the Oncolytic Virus M1.","abstract":"Oncolytic virotherapy is a novel and emerging treatment modality that uses replication-competent viruses to destroy cancer cells. Although diverse cancer cell types are sensitive to oncolytic viruses, one of the major challenges of oncolytic virotherapy is that the sensitivity to oncolysis ranges among different cancer cell types. Furthermore, the underlying mechanism of action is not fully understood. Here, we report that activation of cyclic adenosine monophosphate (cAMP) signaling significantly sensitizes refractory cancer cells to alphavirus M1 in vitro, in vivo, and ex vivo. We find that activation of the cAMP signaling pathway inhibits M1-induced expression of antiviral factors in refractory cancer cells, leading to prolonged and severe endoplasmic reticulum (ER) stress, and cell apoptosis. We also demonstrate that M1-mediated oncolysis, which is enhanced by cAMP signaling, involves the factor, exchange protein directly activated by cAMP 1 (Epac1), but not the classical cAMP-dependent protein kinase A (PKA). Taken together, cAMP/Epac1 signaling pathway activation inhibits antiviral factors and improves responsiveness of refractory cancer cells to M1-mediated virotherapy. Molecular Therapy (2015); doi:10.1038/mt.2015.172.","corpus_id":491391,"score":2},{"doc_id":"27296553","title":"Naturally Existing Oncolytic Virus M1 Is Nonpathogenic for the Nonhuman Primates After Multiple Rounds of Repeated Intravenous Injections.","abstract":"Cancers figure among the leading causes of morbidity and mortality worldwide. The number of new cases is expected to rise by about 70% over the next 2 decades. Development of novel therapeutic agents is urgently needed for clinical cancer therapy. Alphavirus M1 is a Getah-like virus isolated from China with a genome of positive single-strand RNA. We have previously identified that alphavirus M1 is a naturally existing oncolytic virus with significant anticancer activity against different kinds of cancer (e.g., liver cancer, bladder cancer, and colon cancer). To support the incoming clinical trial of intravenous administration of alphavirus M1 to cancer patients, we assessed the safety of M1 in adult nonhuman primates. We previously presented the genome sequencing data of the cynomolgus macaques (Macaca fascicularis), which was demonstrated as an ideal animal species for virus infection study. Therefore, we chose cynomolgus macaques of either sex for the present safety study of oncolytic virus M1. In the first round of administration, five experimental macaques were intravenously injected with six times of oncolytic virus M1 (1 × 10(9) pfu/dose) in 1 week, compared with five vehicle-injected control animals. The last two rounds of injections were further completed in the following months in the same way as the first round. Body weight, temperature, complete blood count, clinical biochemistries, cytokine profiles, lymphocytes subsets, neutralizing antibody, and clinical symptoms were closely monitored at different time points. Magnetic resonance imaging was also performed to assess the possibility of encephalitis or arthritis. As a result, no clinical, biochemical, immunological, or medical imaging or other pathological evidence of toxicity was found during the whole process of the study. Our results in cynomolgus macaques suggested the safety of intravenous administration of oncolytic virus M1 in cancer patients in the future.","corpus_id":206189492,"score":2},{"doc_id":"28445966","title":"Interferon alpha antagonizes the anti-hepatoma activity of the oncolytic virus M1 by stimulating anti-viral immunity.","abstract":"Alpha virus M1 is an oncolytic virus that targets zinc-finger antiviral protein (ZAP)-defective cancer cells, and may be useful for treatment of hepatocellular carcinoma (HCC). Most of HCC patients have hepatitis and need long-term antiviral medication. Thus, it is necessary to clarify whether anti-virus medicines influence oncolytic effect of M1. We examined the effect of drugs used to treat hepatitis B/C on M1-mediated oncolysis in vitro and in vivo. Interferon (IFN)-α induces expression of antiviral IFN-stimulated genes (ISGs) in HCC cells with moderate sensitivity to M1 virus. This leads to reduced replication of M1, and blocking of M1-mediated apoptosis. The antagonistic effect of IFN-α is positively related with the expressive level of ISGs. We also examined a population of 147 HCC patients. A total of 107 patients (73%) had low ZAP expression in liver tissues relative to adjacent tissues. Among these 107 patients, 77% were positive for hepatitis B and 2% were positive for hepatitis C. A combination of M1 virus and IFN should be avoided in those patients with HBV or HCV infection, of who ZAP expression is low but ISGs expression is moderate. In conclusion, this study provides a basis for anti-viral regimens for HCC patients with hepatitis B or C who are given oncolytic virus M1.","corpus_id":27580022,"score":2},{"doc_id":"28607091","title":"Selective replication of oncolytic virus M1 results in a bystander killing effect that is potentiated by Smac mimetics.","abstract":"Oncolytic virotherapy is a treatment modality that uses native or genetically modified viruses that selectively replicate in and kill tumor cells. Viruses represent a type of pathogen-associated molecular pattern and thereby induce the up-regulation of dozens of cytokines via activating the host innate immune system. Second mitochondria-derived activator of caspases (Smac) mimetic compounds (SMCs), which antagonize the function of inhibitor of apoptosis proteins (IAPs) and induce apoptosis, sensitize tumor cells to multiple cytokines. Therefore, we sought to determine whether SMCs sensitize tumor cells to cytokines induced by the oncolytic M1 virus, thus enhancing a bystander killing effect. Here, we report that SMCs potentiate the oncolytic effect of M1 in vitro, in vivo, and ex vivo. This strengthened oncolytic efficacy resulted from the enhanced bystander killing effect caused by the M1 virus via cytokine induction. Through a microarray analysis and subsequent validation using recombinant cytokines, we identified IL-8, IL-1A, and TRAIL as the key cytokines in the bystander killing effect. Furthermore, SMCs increased the replication of M1, and the accumulation of virus protein induced irreversible endoplasmic reticulum stress- and c-Jun N-terminal kinase-mediated apoptosis. Nevertheless, the combined treatment with M1 and SMCs had little effect on normal and human primary cells. Because SMCs selectively and significantly enhance the bystander killing effect and the replication of oncolytic virus M1 specifically in cancer cells, this combined treatment may represent a promising therapeutic strategy.","corpus_id":13914978,"score":2},{"doc_id":"28750564","title":"Selective antagonism of Bcl-xL potentiates M1 oncolysis by enhancing mitochondrial apoptosis.","abstract":"Oncolytic virotherapy is a novel and intriguing treatment strategy for cancer therapy. However, the clinical potential of oncolytic virus as single agent is limited. M1 virus is a promising oncolytic virus that has been tested in preclinical studies. In this study, we investigated the effect of the combination use of M1 virus and Bcl-2 family inhibitors. A chemical compounds screening including ten Bcl-2 family inhibitors demonstrated that pan-Bcl-2 inhibitors selectively augmented M1 virus oncolysis in cancer cells at very low doses. The mechanism of the enhanced antitumor effect of pan-Bcl-2 inhibitors with M1 virus is mainly due to the inhibition of Bcl-xL, which synergizes with M1-induced up-regulation of Bak to trigger apoptosis. In xenograft mouse models and patient-derived tumor tissues, combination of M1 and pan-Bcl-2 inhibitors significantly inhibited tumor growth and prolonged survival, suggesting the potential therapeutic value of this strategy. These findings offer insights into the synergy between Bcl-xL inhibition and oncolytic virus M1 as a combination anti-cancer treatment modality.","corpus_id":4774013,"score":2},{"doc_id":"28835517","title":"Targeting VCP enhances anticancer activity of oncolytic virus M1 in hepatocellular carcinoma.","abstract":"Oncolytic virotherapy is rapidly progressing through clinical evaluation. However, the therapeutic efficacy of oncolytic viruses in humans has been less than expected from preclinical studies. We describe an anticancer drug screen for compounds that enhance M1 oncolytic virus activity in hepatocellular carcinoma (HCC). An inhibitor of the valosin-containing protein (VCP) was identified as the top sensitizer, selectively increasing potency of the oncolytic virus up to 3600-fold. Further investigation revealed that VCP inhibitors cooperated with M1 virus-suppressed inositol-requiring enzyme 1α (IRE1α)-X-box binding protein 1 (XBP1) pathway and triggered irresolvable endoplasmic reticulum (ER) stress, subsequently promoting robust apoptosis in HCC. We show that VCP inhibitor improved the oncolytic efficacy of M1 virus in several mouse models of HCC and primary HCC tissues. Finally, this combinatorial therapeutic strategy was well tolerated in nonhuman primates. Our study identifies combined VCP inhibition and oncolytic virus as a potential treatment for HCC and demonstrates promising therapeutic potential.","corpus_id":28236078,"score":2},{"doc_id":"29263275","title":"Deficiency of the IRE1α-Autophagy Axis Enhances the Antitumor Effects of the Oncolytic Virus M1.","abstract":"Oncolytic virotherapy is an emerging treatment modality that uses replication-competent viruses to destroy cancer cells. M1 is a naturally occurring alphavirus (Togaviridae) which shows potent oncolytic activities against many cancers. Accumulation of unfolded proteins during virus replication leads to a transcriptional/translational response known as the unfolded protein response (UPR), which might counteract the antitumor effect of the oncolytic virus. In this report, we show that either pharmacological or biological inhibition of IRE1α or PERK, but not ATF6, substantially increases the oncolytic effects of the M1 virus. Moreover, inhibition of IRE1α blocks M1 virus-induced autophagy, which restricts the antitumor effects of the M1 virus through degradation of viral protein, in glioma cells. In addition, IRE1α suppression significantly increases the oncolytic effect of M1 virus in an orthotopic glioma model. From a molecular pathology study, we found that IRE1α is expressed at lower levels in higher-grade gliomas, suggesting greater antitumor efficacy of the oncolytic virus M1. Taken together, these findings illustrate a defensive mechanism of glioma cells against the oncolytic virus M1 and identify possible approaches to enhance the oncolytic viral protein accumulation and the subsequent lysis of tumor cells. IMPORTANCE Although oncolytic virotherapy is showing great promise in clinical applications, not all patients are benefiting. Identifying inhibitory signals in refractory cancer cells for each oncolytic virus would provide a good chance to increase the therapeutic effect. Here we describe that infection with the oncolytic virus M1 triggers the unfolded protein response (UPR) and subsequent autophagy, while blocking the UPR-autophagy axis significantly potentiates the antitumor efficacy of M1 in vitro and in vivo A survey of cancer tissue banks revealed that IRE1α, a key element in the UPR pathway, is commonly downregulated in higher-grade human gliomas, suggesting favorable prospects for the application of M1. Our work provides a potential predictor and target for enhancement of the therapeutic effectiveness of the M1 virus. We predict that the mechanism-based combination therapy will promote cancer virotherapy in the future.","corpus_id":4770393,"score":2},{"doc_id":"29449555","title":"Intravenous injections of the oncolytic virus M1 as a novel therapy for muscle-invasive bladder cancer.","abstract":"Muscle-invasive bladder cancer (MIBC) is associated with low survival and high recurrence rates even in cases in which patients receive systemic treatments, such as surgery and chemotherapy. Here, we found that a naturally existing alphavirus, namely, M1, selectively kills bladder cancer cells but not normal cells, findings supported by our observations of changes in viral replication and MIBC and patient-derived MIBC cell apoptosis. Transcriptome analysis revealed that interferon-stimulated genes (ISGs) are expressed at low levels in sensitive bladder cancer cells and high levels in resistant cells. Knocking down ZC3HAV1 (ZAP), an antiviral factor in ISGs, restores M1 virus reactivity in resistant cells, and overexpressing ZAP partially reverses M1 virus-induced decreases in cell viability in sensitive cells. In orthotopic MIBC mice, tail vein injections of M1 significant inhibit tumor growth and prolong survival period, antitumor effects of M1 are stronger than those of the first-line chemotherapy agent cisplatin (CDDP). Treated tumors display enhanced cleaved-caspase-3 signals, which are representative of cell apoptosis, and decreased Ki-67 signals, which are representative of cell proliferation. Moreover, tissue microarray (TMA) analyses of clinical tumor specimens revealed that up to 45.6% of cases of MIBC presented with low ZAP expression, a finding that is prevalent in advanced MIBC. Our results indicate that the oncolytic virus M1 is a novel agent capable of functioning as a precise and effective therapy for MIBC.","corpus_id":3319018,"score":2},{"doc_id":"18239605","title":"Oncolytic adenovirus-mediated shRNA against Apollon inhibits tumor cell growth and enhances antitumor effect of 5-fluorouracil.","abstract":"Apollon, a membrane-associated inhibitor of apoptosis protein, protects cells against apoptosis and is upregulated in certain tumor cells. In this study, the effects of Apollon protein knockdown by RNA interference on the growth of human HeLa, HT-1080 and MCF-7 cells in vitro and in vivo were investigated. An oncolytic adenovirus (ZD55) containing the RNA polymerase III-dependent U6 promoter to express short hairpin RNA (shRNA) directed against Apollon (ZD55-siApollon) was constructed. Our data show that ZD55-siApollon successfully exerts a gene knockdown effect and causes the inhibition of tumor cell growth both in culture and in athymic mice in vivo. Cell cycle analysis, 4',6-diamidino-2-phenylindole staining and western blot analysis reveal that ZD55-siApollon-mediated suppression of Apollon induces apoptosis. Intratumoral injection of ZD55-siApollon significantly inhibits tumor growth in HT-1080 xenograft mice. Furthermore, ZD55-siApollon enhances the antitumor effect of 5-fluorouracil, a chemotherapeutic agent. In conclusion, these results suggest that the depletion of Apollon by oncolytic adenovirus-shRNA delivery system provides a promising method for cancer therapy.","corpus_id":40196237,"score":1},{"doc_id":"18846115","title":"Enhanced oncolytic potency of vesicular stomatitis virus through vector-mediated inhibition of NK and NKT cells.","abstract":"Recombinant oncolytic viruses represent a promising alternative option for the treatment of malignant cancers. We have reported earlier the safety and efficacy of recombinant vesicular stomatitis virus (VSV) vectors in a rat model of hepatocellular carcinoma (HCC). However, the full potential of VSV therapy is limited by a sudden decline in intratumoral virus replication observed early after viral administration, a phenomenon that coincides with an accumulation of inflammatory cells within infected lesions. To overcome the antiviral function of these cells, we present a recombinant virus, rVSV-UL141, which expresses a protein from human cytomegalovirus known to downregulate the natural killer (NK) cell-activating ligand CD155. The modified vector resulted in an inhibition of NK cell recruitment in vitro, as well as decreased intratumoral accumulations of NK and NKT cells in vivo. Administration of rVSV-UL141 through hepatic artery infusion in immune-competent Buffalo rats harboring orthotopic, multi-focal HCC lesions resulted in a one-log elevation of intratumoral virus replication over a control rVSV vector, which translated to enhance tumor necrosis and substantial prolongation of survival. Moreover, these results were achieved in the absence of apparent toxicities. The present study suggests the applicability of this strategy for the development of effective and safe oncolytic agents to treat multi-focal HCC, and potentially a multitude of other cancers, in the future.","corpus_id":22382666,"score":1},{"doc_id":"19508172","title":"Targeting the mevalonate pathway for improved anticancer therapy.","abstract":"The mevalonate pathway is important for the generation of isoprene moieties thereby providing the basis for the biosynthesis of molecules required for maintaining membrane integrity, steroid production and cell respiration. Additionally, isoprene precursors are indispensable for the prenylation of regulatory proteins such as Ras and Ras-homologous (Rho) GTPases. These low molecular GTP-binding proteins play key roles in numerous signal transduction pathways stimulated upon activation of cell surface receptors by ligand binding. Thus, Ras/Rho proteins eventually regulate cell proliferation, tumor progression and cell death induced by anticancer therapeutics. Lipid modification of Ras/Rho proteins at their C-terminal CAAX-box is essential for their correct intracellular localization and function. Therefore, pharmacological inhibition of the isoprene metabolism is anticipated to impact the manifold biological functions attributed to Ras/Rho proteins. Here, the pros and cons of compounds that interfere with the mevalonate pathway for cancer treatment are summarized and discussed.","corpus_id":10396680,"score":1},{"doc_id":"20338582","title":"Lovastatin inhibits thrombospondin-1-induced smooth muscle cell chemotaxis.","abstract":"BACKGROUND: Thrombospondin-1 (TSP-1) induces vascular smooth muscle cell (VSMC) migration and is important in the development of intimal hyperplasia. HMG-CoA reductase inhibitors, such as lovastatin, reduce the incidence of vascular restenosis after angioplasty by both cholesterol lowering and pleiotropic effects. Inhibition of the mevalonate pathway is largely responsible for these pleiotropic properties. This inhibition prevents isoprenylation of the small G proteins, Rho and Ras, by geranylgeranyl and farnesyl pyrophosphate, respectively. Isoprenylation is required for Ras and Rho activation, which is relevant for cell migration. HYPOTHESIS: Lovastatin inhibits TSP-1-induced VSMC chemotaxis by inhibiting small G proteins via the mevalonate pathway. METHODS: Chemotaxis was assessed using a modified Boyden chamber. Quiescent VSMCs were pretreated with serum free media (SFM), lovastatin with or without mevalonate farnesyl (FTI), geranylgeranyl transferase inhibitors (GGTI), farnesyl transferase inhibitor (FPT), or the Rho kinase inhibitor (Y-27632). Chemoattractants were SFM or TSP-1. Comparisons were made by ANOVA followed by post-hoc testing (P<0.05). The effect of lovastatin on Ras activation was evaluated using cells pretreated with SFM or lovastatin, with or without mevalonate prior to TSP-1 exposure. Western blot for Ras activation was performed. RESULTS: Lovastatin dose-dependently inhibited TSP-1-induced chemotaxis, which was reversed by mevalonate. Mevalonate did not induce chemotaxis independently. FTI and FPT, but not GGTI or Y-27632, inhibited TSP-1-induced Ras activation and TSP-1-induced chemotaxis. Lovastatin inhibition of Ras activation was reversed with mevalonate. CONCLUSION: Ras, not Rho, is relevant for TSP-1-induced VSMC chemotaxis. These data suggest that lovastatin suppresses TSP-1-induced chemotaxis by inhibition of Ras.","corpus_id":32246639,"score":1},{"doc_id":"20519142","title":"Pamidronate inhibits antiapoptotic bcl-2 expression through inhibition of the mevalonate pathway in prostate cancer PC-3 cells.","abstract":"Bisphosphonates are expected to be efficacious to prevent the growth of metastatic cancer in bone tissue. Bone metastases often occur in patients with various cancers, such as breast, lung and prostate cancer. Bcl-2 is a potent antiapoptotic protein and its expression is known to be closely related to its function. In this study, to investigate the effect of bisphosphonates on cancer cells, we focused on bcl-2 expression in bisphosphonate-treated prostate cancer cells. First, we observed that bcl-2 mRNA expression in PC-3 was significantly inhibited to 12% of the control level by treatment with 100 microM pamidronate for 12h. Inhibition was seen in cells treated with nitrogen-containing bisphosphonates, which have the ability to inhibit isoprenoid biosynthesis via the mevalonate pathway, but not in non-nitrogen-containing etidronate. Simultaneous treatment with geranylgeraniol, an intermediate of the mevalonate pathway, significantly blocked inhibition by pamidronate, and treatment with geranylgeranyl transferase inhibitor GGTI-286 also suppressed bcl-2 mRNA expression. Furthermore, pamidronate inhibited the translocation of Rap1 protein to the membrane fraction, suggesting that a change in posttranslational modification of Rap1 occurred in treated cells. Finally, knockdown of Rap1 by siRNA resulted in the inhibition of bcl-2 expression. These results strongly indicate that bcl-2 reduction in bisphosphonate-treated PC-3 cells is dependent on inhibition of the mevalonate pathway. The inhibitory effect of bisphosphonates on bcl-2 expression shown in prostate cancer cell line should be tested in animal experiments and clinical studies.","corpus_id":12693267,"score":1},{"doc_id":"20647775","title":"Endogenous expression of proteases in colon cancer cells facilitate influenza A viruses mediated oncolysis.","abstract":"Previously we have developed a prototype for conditionally replicating oncolytic influenza A virus which is based on deletions in the non-structural (NS1) protein. Multi-cycle replication of influenza A virus in malignant tissue is critically dependent on a protease which cleaves the viral entry protein. Here we demonstrate that the malignant colon cancer cell lines Caco-2, HT-29 and SW-620 can endogenously provide a virus-activating protease, which allows lytic multi-cycle replication of NS1 deletion viruses in those cancer cells in vitro. The oncolytic potency of an influenza NS1 deletion virus (NS1-80) was further tested in SCID mice bearing HT-29 derived tumors. The intra-tumoral injection of live, but not of heat inactivated NS1-80 virus significantly inhibited progression of established tumors. We conclude that a selected set of human cancer expressing virus activating- proteases will be a preferred target for oncolytic tumor therapy using influenza A virus mutants.","corpus_id":1517720,"score":1},{"doc_id":"21276246","title":"Oncolytic targeting of androgen-sensitive prostate tumor by the respiratory syncytial virus (RSV): consequences of deficient interferon-dependent antiviral defense.","abstract":"BACKGROUND: Oncolytic virotherapy for cancer treatment utilizes viruses for selective infection and death of cancer cells without any adverse effect on normal cells. We previously reported that the human respiratory syncytial virus (RSV) is a novel oncolytic virus against androgen-independent PC-3 human prostate cancer cells. The present study extends the result to androgen-dependent prostate cancer, and explores the underlying mechanism that triggers RSV-induced oncolysis of prostate cancer cells. METHODS: The oncolytic effect of RSV on androgen-sensitive LNCaP human prostate cancer cells and on androgen-independent RM1 murine prostate cancer cells was studied in vitro in culture and in vivo in a xenograft or allograft tumor model. In vitro, cell viability, infectivity and apoptosis were monitored by MTT assay, viral plaque assay and annexin V staining, respectively. In vivo studies involved virus administration to prostate tumors grown in immune compromised nude mice and in syngeneic immune competent C57BL/6J mice. Anti-tumorogenic oncolytic activity was monitored by measuring tumor volume, imaging bioluminescent tumors in live animals and performing histopathological analysis and TUNEL assay with tumors RESULTS: We show that RSV imposes a potent oncolytic effect on LNCaP prostate cancer cells. RSV infectivity was markedly higher in LNCaP cells compared to the non-tumorigenic RWPE-1 human prostate cells. The enhanced viral burden led to LNCaP cell apoptosis and growth inhibition of LNCaP xenograft tumors in nude mice. A functional host immune response did not interfere with RSV-induced oncolysis, since growth of xenograft tumors in syngeneic C57BL/6J mice from murine RM1 cells was inhibited upon RSV administration. LNCaP cells failed to activate the type-I interferon (IFNα/β)-induced transcription factor STAT-1, which is required for antiviral gene expression, although these cells could produce IFN in response to RSV infection. The essential role of IFN in restricting infection was further borne out by our finding that neutralizing IFN activity resulted in enhanced RSV infection in non-tumorigenic RWPE-1 prostate cells. CONCLUSIONS: We demonstrated that RSV is potentially a useful therapeutic tool in the treatment of androgen-sensitive and androgen-independent prostate cancer. Moreover, impaired IFN-mediated antiviral response is the likely cause of higher viral burden and resulting oncolysis of androgen-sensitive prostate cancer cells.","corpus_id":8188053,"score":1},{"doc_id":"21283510","title":"Enhancement of vaccinia virus based oncolysis with histone deacetylase inhibitors.","abstract":"Histone deacetylase inhibitors (HDI) dampen cellular innate immune response by decreasing interferon production and have been shown to increase the growth of vesicular stomatitis virus and HSV. As attenuated tumour-selective oncolytic vaccinia viruses (VV) are already undergoing clinical evaluation, the goal of this study is to determine whether HDI can also enhance the potency of these poxviruses in infection-resistant cancer cell lines. Multiple HDIs were tested and Trichostatin A (TSA) was found to potently enhance the spread and replication of a tumour selective vaccinia virus in several infection-resistant cancer cell lines. TSA significantly decreased the number of lung metastases in a syngeneic B16F10LacZ lung metastasis model yet did not increase the replication of vaccinia in normal tissues. The combination of TSA and VV increased survival of mice harbouring human HCT116 colon tumour xenografts as compared to mice treated with either agent alone. We conclude that TSA can selectively and effectively enhance the replication and spread of oncolytic vaccinia virus in cancer cells.","corpus_id":5911989,"score":1},{"doc_id":"21324313","title":"Inhibition of geranylgeranylation mediates sensitivity to CHOP-induced cell death of DLBCL cell lines.","abstract":"Prenylation is a post-translational hydrophobic modification of proteins, important for their membrane localization and biological function. The use of inhibitors of prenylation has proven to be a useful tool in the activation of apoptotic pathways in tumor cell lines. Rab geranylgeranyl transferase (Rab GGT) is responsible for the prenylation of the Rab family. Overexpression of Rab GGTbeta has been identified in CHOP refractory diffuse large B cell lymphoma (DLBCL). Using a cell line-based model for CHOP resistant DLBCL, we show that treatment with simvastatin, which inhibits protein farnesylation and geranylgeranylation, sensitizes DLBCL cells to cytotoxic treatment. Treatment with the farnesyl transferase inhibitor FTI-277 or the geranylgeranyl transferase I inhibitor GGTI-298 indicates that the reduction in cell viability was restricted to inhibition of geranylgeranylation. In addition, treatment with BMS1, a combined inhibitor of farnesyl transferase and Rab GGT, resulted in a high cytostatic effect in WSU-NHL cells, demonstrated by reduced cell viability and decreased proliferation. Co-treatment of BMS1 or GGTI-298 with CHOP showed synergistic effects with regard to markers of apoptosis. We propose that inhibition of protein geranylgeranylation together with conventional cytostatic therapy is a potential novel strategy for treating patients with CHOP refractory DLBCL.","corpus_id":7417278,"score":1},{"doc_id":"21608020","title":"Arctigenin enhances chemosensitivity of cancer cells to cisplatin through inhibition of the STAT3 signaling pathway.","abstract":"Arctigenin is a dibenzylbutyrolactone lignan isolated from Bardanae fructus, Arctium lappa L, Saussureamedusa, Torreya nucifera, and Ipomea cairica. It has been reported to exhibit anti-inflammatory activities, which is mainly mediated through its inhibitory effect on nuclear transcription factor-kappaB (NF-κB). But the role of arctigenin in JAK-STAT3 signaling pathways is still unclear. In present study, we investigated the effect of arctigenin on signal transducer and activator of transcription 3 (STAT3) pathway and evaluated whether suppression of STAT3 activity by arctigenin could sensitize cancer cells to a chemotherapeutic drug cisplatin. Our results show that arctigenin significantly suppressed both constitutively activated and IL-6-induced STAT3 phosphorylation and subsequent nuclear translocation in cancer cells. Inhibition of STAT3 tyrosine phosphorylation was found to be achieved through suppression of Src, JAK1, and JAK2, while suppression of STAT3 serine phosphorylation was mediated by inhibition of ERK activation. Pervanadate reversed the arctigenin-induced downregulation of STAT3 activation, suggesting the involvement of a protein tyrosine phosphatase. Indeed, arctigenin can obviously induce the expression of the PTP SHP-2. Furthermore, the constitutive activation level of STAT3 was found to be correlated to the resistance of cancer cells to cisplatin-induced apoptosis. Arctigenin dramatically promoted cisplatin-induced cell death in cancer cells, indicating that arctigenin enhanced the sensitivity of cancer cells to cisplatin mainly via STAT3 suppression. These observations suggest a novel anticancer function of arctigenin and a potential therapeutic strategy of using arctigenin in combination with chemotherapeutic agents for cancer treatment.","corpus_id":32983855,"score":1},{"doc_id":"22076990","title":"Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway.","abstract":"OBJECTIVES: Hepatitis C virus (HCV) infection causes chronic liver disease and is a major public health problem worldwide. The aim of this study was to evaluate the potential of Monascus pigment derivatives, which were derived from a microbial secondary metabolite synthesized from polyketides by Monascus spp., as HCV antiviral agents. METHODS: We performed an in vitro RNA-dependent RNA polymerase (RdRp) assay to screen for HCV RdRp inhibitors. The anti-HCV activity of RdRp inhibitors in HCV-replicating cells was evaluated by quantification of the RNA viral genome. Molecular docking analysis was performed to predict the binding sites of the selected RdRp inhibitors. RESULTS: We have identified a Monascus pigment and its derivatives as inhibitors of the HCV NS5B RdRp. A group of Monascus orange pigment (MOP) amino acid derivatives, in which the reactive oxygen moiety was changed to amino acids, significantly inhibited HCV replication. Further, combination of the MOP derivatives (Phe, Val or Leu conjugates) with interferon (IFN)-α inhibited HCV replication more than IFN-α treatment alone. Lastly, molecular docking studies indicate the inhibitors may bind to a thumb subdomain allosteric site of NS5B. The antiviral activity of the MOP derivatives was related to a modulation of the mevalonate pathway, since the mevalonate-induced increase in HCV replication was suppressed by the MOP compounds. CONCLUSIONS: Our results identify amino acid derivatives of MOP as potential anti-HCV agents and suggest that their combination with IFN-α might offer an alternative strategy for the control of HCV replication.","corpus_id":11559087,"score":1},{"doc_id":"22322451","title":"Involvement of the mevalonate pathway in the antiproliferative effect of zoledronate on ACHN renal cell carcinoma cells.","abstract":"Renal cell carcinoma (RCC) has been shown to be resistant to chemotherapy and radiotherapy. In order to examine the potential of zoledronate (ZOL), a bisphosphonate, as an anticancer agent, we investigated the effects of ZOL on RCC cells and the involvement of the mevalonate pathway in antiproliferative effects, as well as the effects of ZOL administration on mice inoculated with RCC. ACHN cells were used and cell viability was measured via intra-cellular reductase activity. Chromatin condensation was detected by Hoechst 33342 staining. Proteins were detected by western blot analysis. Tumor volume was measured bidimensionally in mice inoculated with ACHN cells after vehicle or ZOL subcutaneous administration. ZOL exhibited antiproliferative effects with an IC50 value of 2.29±0.53 µM in ACHN cells and chromatin condensation was observed when treated with ZOL. Farnesol (FOH) and geranylgeraniol (GGOH), precursors of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, exhibited potency to rescue cells treated with ZOL. Additionally, Ras and RhoA proteins located in the membrane fraction decreased when treated with ZOL and recovered by FOH or GGOH treatment, suggesting that ZOL inhibited the mevalonate pathway, thereby suppressing the translocation of prenylated Ras and RhoA proteins to membrane fractions. An in vivo study showed the inhibitory potential of ZOL on tumor growth in mice without changes in body weight. Our study showed that ZOL could be useful as an anticancer agent for the treatment of RCC, and the mevalonate pathway could be an efficient target for novel therapeutic agents against RCC.","corpus_id":39894469,"score":1},{"doc_id":"22414636","title":"In vivo evaluation of a cancer therapy strategy combining HSV1716-mediated oncolysis with gene transfer and targeted radiotherapy.","abstract":"UNLABELLED: Oncolytic herpes viruses show promise for cancer treatment. However, it is unlikely that they will fulfill their therapeutic potential when used as monotherapies. An alternative strategy is to use these viruses not only as oncolytic agents but also as a delivery mechanism of therapeutic transgenes to enhance tumor cell killing. The herpes simplex virus 1 deletion mutant HSV1716 is a conditionally replicating oncolytic virus that selectively replicates in and lyses dividing tumor cells. It has a proven safety profile in clinical trials and has demonstrated efficacy as a gene-delivery vehicle. To enhance its therapeutic potential, we have engineered HSV1716 to convey the noradrenaline transporter (NAT) gene (HSV1716/NAT), whose expression endows infected cells with the capacity to accumulate the noradrenaline analog metaiodobenzylguanidine (MIBG). Thus, the NAT gene-infected cells are susceptible to targeted radiotherapy using radiolabeled (131)I-MIBG, a strategy that has already shown promise for combined targeted radiotherapy-gene therapy in cancer cells after plasmid-mediated transfection. METHODS: We used HSV1716/NAT as a dual cell lysis-gene delivery vehicle for targeting the NAT transgene to human tumor xenografts in vivo. RESULTS: In tumor xenografts that did not express NAT, intratumoral or intravenous injection of HSV1716/NAT induced the capacity for active uptake of (131)I-MIBG. Administration of HSV1716/NAT and (131)I-MIBG resulted in decreased tumor growth and enhanced survival relative to injection of either agent alone. Efficacy was dependent on the scheduling of delivery of the 2 agents. CONCLUSION: These findings support a role for combination radiotherapy-gene therapy for cancer using HSV1716 expressing the NAT transgene and targeted radionuclide therapy.","corpus_id":20517209,"score":1},{"doc_id":"22605458","title":"Mevalonate metabolism regulates Basal breast cancer stem cells and is a potential therapeutic target.","abstract":"There is increasing evidence that breast tumors are organized in a hierarchy, with a subpopulation of tumorigenic cancer cells, the cancer stem cells (CSCs), which sustain tumor growth. The characterization of protein networks that govern CSC behavior is paramount to design new therapeutic strategies targeting this subpopulation of cells. We have sought to identify specific molecular pathways of CSCs isolated from 13 different breast cancer cell lines of luminal or basal/mesenchymal subtypes. We compared the gene expression profiling of cancer cells grown in adherent conditions to those of matched tumorsphere cultures. No specific pathway was identified to be commonly regulated in luminal tumorspheres, resulting from a minor CSC enrichment in tumorsphere passages from luminal cell lines. However, in basal/mesenchymal tumorspheres, the enzymes of the mevalonate metabolic pathway were overexpressed compared to those in cognate adherent cells. Inhibition of this pathway with hydroxy-3-methylglutaryl CoA reductase blockers resulted in a reduction of breast CSC independent of inhibition of cholesterol biosynthesis and of protein farnesylation. Further modulation of this metabolic pathway demonstrated that protein geranylgeranylation (GG) is critical to breast CSC maintenance. A small molecule inhibitor of the geranylgeranyl transferase I (GGTI) enzyme reduced the breast CSC subpopulation both in vitro and in primary breast cancer xenografts. We found that the GGTI effect on the CSC subpopulation is mediated by inactivation of Ras homolog family member A (RHOA) and increased accumulation of P27(kip1) in the nucleus. The identification of protein GG as a major contributor to CSC maintenance opens promising perspectives for CSC targeted therapy in basal breast cancer.","corpus_id":5930968,"score":1},{"doc_id":"22729516","title":"An armed oncolytic herpes simplex virus expressing thrombospondin-1 has an enhanced in vivo antitumor effect against human gastric cancer.","abstract":"Advanced gastric cancer is a common disease, but the conventional treatments are unsatisfactory because of the high recurrence rate. One of the promising new therapies is oncolytic virotherapy, using oncolytic herpes simplex viruses (HSVs). Thrombospondin-1 (TSP-1) suppresses tumor progression via multiple mechanisms including antiangiogenesis. Our approach to enhance the effects of oncolytic HSVs is to generate an armed oncolytic HSV that combines the direct viral oncolysis with TSP-1-mediated function for gastric cancer treatment. Using the bacterial artificial chromosome (BAC) system, a 3rd generation oncolytic HSV (T-TSP-1) expressing human TSP-1 was constructed for human gastric cancer treatment. The enhanced efficacy of T-TSP-1 was determined in both human gastric cancer cell lines in vitro and subcutaneous tumor xenografts of human gastric cancer cells in vivo. In addition, we examined the apoptotic effect of T-TSP-1 in vitro, and the antiangiogenic effect of T-TSP-1 in vivo compared with a non-armed 3rd generation oncolytic HSV, T-01. No apparent apoptotic induction by T-TSP-1 was observed for human gastric cancer cell lines TMK-1 cells but for MKN1 cells in vitro. Arming the viruses with TSP-1 slightly inhibited their replication in some gastric cancer cell lines, but the viral cytotoxicity was not attenuated. In addition, T-TSP-1 exhibited enhanced therapeutic efficacy and inhibition of angiogenesis compared with T-01 in vivo. In this study, we established a novel armed oncolytic HSV, T-TSP-1, which enhanced the antitumor efficacy by providing a combination of direct viral oncolysis with antiangiogenesis. Arming oncolytic HSVs may be a useful therapeutic strategy for gastric cancer therapy.","corpus_id":26315198,"score":1},{"doc_id":"22920673","title":"Reovirus exerts potent oncolytic effects in head and neck cancer cell lines that are independent of signalling in the EGFR pathway.","abstract":"BACKGROUND: Reovirus exploits aberrant signalling downstream of Ras to mediate tumor-specific oncolysis. Since ~90% squamous cell carcinomas of the head and neck (SCCHN) over-express EGFR and SCCHN cell lines are sensitive to oncolytic reovirus, we conducted a detailed analysis of the effects of reovirus in 15 head and neck cancer cell lines. Both pre- and post-entry events were studied in an attempt to define biomarkers predictive of sensitivity/resistance to reovirus. In particular, we analysed the role of EGFR/Ras signalling in determining virus-mediated cytotoxicity in SCCHN. METHODS: To test whether EGFR pathway activity was predictive of increased sensitivity to reovirus, correlative analyses between reoviral IC50 by MTT assay and EGFR levels by western blot and FACS were conducted. Inhibition or stimulation of EGFR signalling were analysed for their effect on reoviral oncolysis by MTT assay, and viral growth by TCID50 assay. We next analysed the effects of inhibiting signalling downstream of Ras, by specific inhibitors of p38MAPK, PI3-K or MEK, on reoviral killing examined by MTT assay. The role of PKR in reoviral killing was also determined by blockade of PKR using 2-aminopurine and assaying for cell survival by MTT assay. The apoptotic response of SCCHN to reovirus was examined by western blot analysis of caspase 3 cleavage. RESULTS: Correlative analyses between reoviral sensitivity and EGFR levels revealed no association. Intermediate sub-viral and core particles showed the same infectivity/cytotoxicity as intact reovirus. Therefore, sensitivity was not determined by cell entry. In 4 cell lines, oncolysis and viral growth were both unaffected by inhibition or stimulation of EGFR signalling. Inhibition of signalling downstream of Ras did not abrogate reoviral oncolysis and, in addition, modulation of PKR using 2-aminopurine did not alter reovirus sensitivity in resistant cell lines. Caspase 3 cleavage was not detected in infected cells and oncolysis was observed in pan-caspase inhibited cells. CONCLUSIONS: In summary, reovirus is potently oncolytic in a broad panel of SCCHN cell lines. Attempts to define sensitivity/resistance by analysis of the EGFR/Ras/MAPK pathway have failed to provide a clear predictive biomarker of response. Further analysis of material from in vitro and clinical studies is ongoing in an attempt to shed further light on this issue.","corpus_id":15141840,"score":1},{"doc_id":"23447049","title":"Growth inhibition effect of peptide P110 plus cisplatin on various cancer cells and xenotransplanted tumors in mice.","abstract":"The combined use of currently used anticancer genotoxins with other drugs is a therapeutic tool for potentially increasing the efficacy of the genotoxins. In the present study, the effects of a RasGAP-derived peptide, P110 (RasGAP301-316), designed to target Ras-GTPase activating protein SH3 domain-binding proteins (G3BPs), on the chemotherapeutic agent, cisplatin (DDP), were examined. P110 was demonstrated to enhance the effect of DPP in vitro and in vivo. The results indicate that P110 significantly increased the DDP-induced apoptosis in SGC-7901, HCT-116, HeLa and A-549 cells. Furthermore, P110 combined with DDP significantly suppressed the growth of C26 xenograft tumors in a dose-dependent manner. This synergistic effect may be associated with DDP-induced apoptosis, involving the downregulation of Bcl-2 and the upregulation of Bax, cytochrome c and caspase-3. The results of the present study indicate that P110, in combination with chemotherapeutics, is likely to represent a potential therapeutic strategy for cancer.","corpus_id":27885309,"score":1},{"doc_id":"23524243","title":"Regulation of mevalonate metabolism in cancer and immune cells.","abstract":"The mevalonate pathway is a highly conserved metabolic cascade and provides isoprenoid building blocks for the biosynthesis of vital cellular products such as cholesterol or prenyl pyrophosphates that serve as substrates for the posttranslational prenylation of numerous proteins. The pathway, which is frequently hyperactive in cancer cells, is considered an important target in cancer therapy, since prenylated members of the Ras superfamily are crucially involved in the control of proliferation, survival, invasion and metastasis of tumour cells. Upstream accumulation and downstream depletion of mevalonate pathway intermediates as induced for instance by aminobisphosphonates translate into different effects in cancer and immune cells. Thus, mevalonate pathway regulation can affect tumour biology either directly or exhibit indirect antitumour effects through stimulating cancer immune surveillance. The present review summarizes major effects of pharmacologic mevalonate pathway regulation in cancer and immune cells that may collaboratively contribute to the efficacy of cancer therapy.","corpus_id":21782823,"score":1},{"doc_id":"23985699","title":"Triptolide-mediated inhibition of interferon signaling enhances vesicular stomatitis virus-based oncolysis.","abstract":"Preclinical and clinical trials demonstrated that use of oncolytic viruses (OVs) is a promising new therapeutic approach to treat multiple types of cancer. To further improve their viral oncolysis, experimental strategies are now combining OVs with different cytotoxic compounds. In this study, we investigated the capacity of triptolide - a natural anticancer molecule - to enhance vesicular stomatitis virus (VSV) oncolysis in OV-resistant cancer cells. Triptolide treatment increased VSV replication in the human prostate cancer cell line PC3 and in other VSV-resistant cells in a dose- and time-dependent manner in vitro and in vivo. Mechanistically, triptolide (TPL) inhibited the innate antiviral response by blocking type I interferon (IFN) signaling, downstream of IRF3 activation. Furthermore, triptolide-enhanced VSV-induced apoptosis in a dose-dependent fashion in VSV-resistant cells, as measured by annexin-V, cleaved caspase-3, and B-cell lymphoma 2 staining. In vivo, using the TSA mammary adenocarcinoma and PC3 mouse xenograft models, combination treatment with VSV and triptolide delayed tumor growth and prolonged survival of tumor-bearing animals by enhancing viral replication. Together, these results demonstrate that triptolide inhibition of IFN production sensitizes prostate cancer cells to VSV replication and virus-mediated apoptosis.","corpus_id":385028,"score":1},{"doc_id":"24258243","title":"Both the mevalonate and the non-mevalonate pathways are involved in ginsenoside biosynthesis.","abstract":"KEY MESSAGE: When one of them was inhibited, the two pathways could compensate with each other to guarantee normal growth. Moreover, the sterol biosynthesis inhibitor miconazole could enhance ginsenoside level. ABSTRACT: Ginsenosides, a kind of triterpenoid saponins derived from isopentenyl pyrophosphate (IPP), represent the main pharmacologically active constituents of ginseng. In plants, two pathways contribute to IPP biosynthesis, namely, the mevalonate pathway in cytosol and the non-mevalonate pathway in plastids. This motivates biologists to clarify the roles of the two pathways in biosynthesis of IPP-derived compounds. Here, we demonstrated that both pathways are involved in ginsenoside biosynthesis, based on the analysis of the effects from suppressing either or both of the pathways on ginsenoside accumulation in Panax ginseng hairy roots with mevinolin and fosmidomycin as specific inhibitors for the mevalonate and the non-mevalonate pathways, respectively. Furthermore, the sterol biosynthesis inhibitor miconazole could enhance ginsenoside levels in the hairy roots. These results shed some light on the way toward better understanding of ginsenoside biosynthesis.","corpus_id":17896989,"score":1},{"doc_id":"24327936","title":"Inhibition of the mevalonate pathway to override chemoresistance and promote the immunogenic demise of cancer cells: Killing two birds with one stone.","abstract":"The mevalonate pathway is an attractive target for cancer therapy not only to override multidrug resistance but also to promote the immunogenic demise of malignant cells. Recent data indicate that aminobisphosphonates are superior to statins for the pharmacological manipulation of the mevalonate pathway, since they exert therapeutically relevant effects on both cancer cells and the immune system.","corpus_id":35382663,"score":1},{"doc_id":"24371063","title":"Histone deacetylase inhibitors potentiate vesicular stomatitis virus oncolysis in prostate cancer cells by modulating NF-κB-dependent autophagy.","abstract":"Vesicular stomatitis virus (VSV) is an oncolytic virus that induces cancer cell death through activation of the apoptotic pathway. Intrinsic resistance to oncolysis is found in some cell lines and many primary tumors as a consequence of residual innate immunity to VSV. In resistant-tumor models, VSV oncolytic potential can be reversibly stimulated by combination with epigenetic modulators, such as the histone deacetylase inhibitor vorinostat. Based on this reversible effect of vorinostat, we reasoned that critical host genes involved in oncolysis may likewise be reversibly regulated by vorinostat. A transcriptome analysis in prostate cancer PC3 cells identified a subset of NF-κB target genes reversibly regulated by vorinostat, as well as a group of interferon (IFN)-stimulated genes (ISGs). Consistent with the induction of NF-κB target genes, vorinostat-mediated enhancement of VSV oncolysis increased hyperacetylation of NF-κB RELA/p65. Additional bioinformatics analysis revealed that NF-κB signaling also increased the expression of several autophagy-related genes. Kinetically, autophagy preceded apoptosis, and apoptosis was observed only when cells were treated with both VSV and vorinostat. VSV replication and cell killing were suppressed when NF-κB signaling was inhibited using pharmacological or genetic approaches. Inhibition of autophagy by 3-methyladenine (3-MA) enhanced expression of ISGs, and either 3-MA treatment or genetic ablation of the autophagic marker Atg5 decreased VSV replication and oncolysis. Together, these data demonstrate that vorinostat stimulates NF-κB activity in a reversible manner via modulation of RELA/p65 signaling, leading to induction of autophagy, suppression of the IFN-mediated response, and subsequent enhancement of VSV replication and apoptosis.","corpus_id":206816741,"score":1},{"doc_id":"24574393","title":"Mitophagy enhances oncolytic measles virus replication by mitigating DDX58/RIG-I-like receptor signaling.","abstract":"UNLABELLED: The success of future clinical trials with oncolytic viruses depends on the identification and the control of mechanisms that modulate their therapeutic efficacy. In particular, little is known about the role of autophagy in infection by attenuated measles virus of the Edmonston strain (MV-Edm). We investigated the interaction between autophagy, innate immune response, and oncolytic activity of MV-Edm, since the antiviral immune response is a known factor limiting virotherapies. We report that MV-Edm exploits selective autophagy to mitigate the innate immune response mediated by DDX58/RIG-I like receptors (RLRs) in non-small cell lung cancer (NSCLC) cells. Both RNA interference (RNAi) and overexpression approaches demonstrate that autophagy enhances viral replication and inhibits the production of type I interferons regulated by RLRs. We show that MV-Edm unexpectedly triggers SQSTM1/p62-mediated mitophagy, resulting in decreased mitochondrion-tethered mitochondrial antiviral signaling protein (MAVS) and subsequently weakening the innate immune response. These results unveil a novel infectious strategy based on the usurpation of mitophagy leading to mitigation of the innate immune response. This finding provides a rationale to modulate autophagy in oncolytic virotherapy. IMPORTANCE: In vitro studies, preclinical experiments in vivo, and clinical trials with humans all indicate that oncolytic viruses hold promise for cancer therapy. Measles virus of the Edmonston strain (MV-Edm), which is an attenuated virus derived from the common wild-type measles virus, is paradigmatic for therapeutic oncolytic viruses. MV-Edm replicates preferentially in and kills cancer cells. The efficiency of MV-Edm is limited by the immune response of the host against viruses. In our study, we revealed that MV-Edm usurps a homeostatic mechanism of intracellular degradation of mitochondria, coined mitophagy, to attenuate the innate immune response in cancer cells. This strategy might provide a replicative advantage for the virus against the development of antiviral immune responses by the host. These findings are important since they may not only indicate that inducers of autophagy could enhance the efficacy of oncolytic therapies but also provide clues for antiviral therapy by targeting SQSTM1/p62-mediated mitophagy.","corpus_id":206817600,"score":1},{"doc_id":"24696490","title":"Permissiveness of human cancer cells to oncolytic bovine herpesvirus 1 is mediated in part by KRAS activity.","abstract":"UNLABELLED: Oncolytic viruses (OVs) are attractive avenues of cancer therapy due to the absence of toxic side effects often seen with current treatment modalities. Bovine herpesvirus 1 (BHV-1) is a species-specific virus that does not induce cytotoxicity in normal primary human cells but can infect and kill various human immortalized and transformed cell lines. To gain a better understanding of the oncolytic breadth of BHV-1, the NCI panel of established human tumor cell lines was screened for sensitivity to the virus. Overall, 72% of the panel is permissive to BHV-1 infection, with corresponding decreases in cellular viability. This sensitivity is in comparison to a sensitivity of only 32% for a herpes simplex virus 1 (HSV-1)-based oncolytic vector. Strikingly, while 35% of the panel supports minimal or no BHV-1 replication, significant decreases in cellular viability still occur. These data suggest that BHV-1 is an OV with tropism for multiple tumor types and is able to induce cytotoxicity independent of significant virus replication. In contrast to other species-specific OVs, cellular sensitivity to BHV-1 does not correlate with type I interferon (IFN) signaling; however, mutations in KRAS were found to correlate with high levels of virus replication. The knockdown or overexpression of KRAS in human tumor cell lines yields modest changes in viral titers; however, overexpression of KRAS in normal primary cells elicits permissivity to BHV-1 infection. Together, these data suggest that BHV-1 is a broad-spectrum OV with a distinct mechanism of tumor targeting. IMPORTANCE: Cancer remains a significant health issue, and novel treatments are required, particularly for tumors that are refractory to conventional therapies. Oncolytic viruses are a novel platform given their ability to specifically target tumor cells while leaving healthy cells intact. For this strategy to be successful, a fundamental understanding of virus-host interactions is required. We previously identified bovine herpesvirus 1 as a novel oncolytic virus with many unique and clinically relevant features. Here, we show that BHV-1 can target a wide range of human cancer types, most potently lung cancer. In addition, we show that enhanced KRAS activity, a hallmark of many cancers, is one of the factors that increases BHV-1 oncolytic capacity. These findings hold potential for future treatments, particularly in the context of lung cancer, where KRAS mutations are a negative predictor of treatment efficacy.","corpus_id":25765959,"score":1},{"doc_id":"24928535","title":"The inhibition of constitutive androstane receptor-mediated pathway enhances the effects of anticancer agents in ovarian cancer cells.","abstract":"BACKGROUND: Ovarian cancer is commonly treated with anticancer agents; however, many tumors become resistant. Resistance is regulated, in part, by P-glycoprotein, which is encoded by the gene multiple drug resistance 1 (MDR1) and functions as a transmembrane efflux pump for the elimination of anticancer agents. Constitutive androstane receptor (CAR) is a nuclear receptor that regulates drug metabolism through control of MDR1 and other genes. PURPOSE: We examined whether the inhibition of CAR-mediated pathway could influence the cytotoxicity of three anticancer drugs, cisplatin, paclitaxel, and arsenic trioxide, in ovarian cancer cells. RESULTS: We observed that the cell proliferation of several ovarian cell lines expressing CAR significantly increased when CITCO was combined with anticancer agents compared with any anticancer agent alone. The up-regulation of MDR1 and UGT1A1 by anticancer agents was further enhanced in the presence of CITCO. We confirmed that combining CITCO with anticancer agents induced significantly lower levels of apoptosis than those achieved with any single anticancer drug. CAR down-regulation by RNA interference caused a significant increase in cell growth inhibition and enhancement of apoptosis in the presence of anticancer agents. Combination of CITCO with any anticancer agents significantly enhanced CAR-mediated transcription compared with any anticancer agents alone and CAR down-regulation completely inhibited the transcription in the presence of CITCO and/or anticancer agents. CONCLUSION: Inhibition of CAR pathway could be a novel therapeutic approach for the augmentation of sensitivity to anticancer agents, or to overcome resistance, in the treatment of ovarian cancer.","corpus_id":205968815,"score":1},{"doc_id":"25078870","title":"Pharmacological modulation of autophagy enhances Newcastle disease virus-mediated oncolysis in drug-resistant lung cancer cells.","abstract":"BACKGROUND: Oncolytic viruses represent a promising therapy against cancers with acquired drug resistance. However, low efficacy limits its clinical application. The objective of this study is to investigate whether pharmacologically modulating autophagy could enhance oncolytic Newcastle disease virus (NDV) strain NDV/FMW virotherapy of drug-resistant lung cancer cells. METHODS: The effect of NDV/FMW infection on autophagy machinery in A549 lung cancer cell lines resistant to cisplatin (A549/DDP) or paclitaxel (A549/PTX) was investigated by detection of GFP-microtubule-associated protein 1 light chain 3 (GFP-LC3) puncta, formation of double-membrane vesicles and conversion of the nonlipidated form of LC3 (LC3-I) to the phosphatidylethanolamine-conjugated form (LC3-II). The effects of autophagy inhibitor chloroquine (CQ) and autophagy inducer rapamycin on NDV/FMW-mediated antitumor activity were evaluated both in culture cells and in mice bearing drug-resistant lung cancer cells. RESULTS: We show that NDV/FMW triggers autophagy in A549/PTX cells via dampening the class I PI3K/Akt/mTOR/p70S6K pathway, which inhibits autophagy. On the contrary, NDV/FMW infection attenuates the autophagic process in A549/DDP cells through the activation of the negative regulatory pathway. Furthermore, combination with CQ or knockdown of ATG5 significantly enhances NDV/FMW-mediated antitumor effects on A549/DDP cells, while the oncolytic efficacy of NDV/FMW in A549/PTX cells is significantly improved by rapamycin. Interestingly, autophagy modulation does not increase virus progeny in these drug resistant cells. Importantly, CQ or rapamycin significantly potentiates NDV/FMW oncolytic activity in mice bearing A549/DDP or A549/PTX cells respectively. CONCLUSIONS: These results demonstrate that combination treatment with autophagy modulators is an effective strategy to augment the therapeutic activity of NDV/FMW against drug-resistant lung cancers.","corpus_id":7430046,"score":1},{"doc_id":"25347735","title":"Oncogenic Ras inhibits IRF1 to promote viral oncolysis.","abstract":"Oncolytic viruses exploit common molecular changes in cancer cells, which are not present in normal cells, to target and kill cancer cells. Ras transformation and defects in type I interferon (IFN)-mediated antiviral responses are known to be the major mechanisms underlying viral oncolysis. Previously, we demonstrated that oncogenic RAS/Mitogen-activated protein kinase kinase (Ras/MEK) activation suppresses the transcription of many IFN-inducible genes in human cancer cells, suggesting that Ras transformation underlies type I IFN defects in cancer cells. Here, we investigated how Ras/MEK downregulates IFN-induced transcription. By conducting promoter deletion analysis of IFN-inducible genes, namely guanylate-binding protein 2 and IFN gamma inducible protein 47 (Ifi47), we identified the IFN regulatory factor 1 (IRF1) binding site as the promoter region responsible for the regulation of transcription by MEK. MEK inhibition promoted transcription of the IFN-inducible genes in wild type mouse embryonic fibroblasts (MEFs), but not in IRF1(-/-) MEFs, showing that IRF1 is involved in MEK-mediated downregulation of IFN-inducible genes. Furthermore, IRF1 protein expression was lower in RasV12 cells compared with vector control NIH3T3 cells, but was restored to equivalent levels by inhibition of MEK. Similarly, the restoration of IRF1 expression by MEK inhibition was observed in human cancer cells. IRF1 re-expression in human cancer cells caused cells to become resistant to infection by the oncolytic vesicular stomatitis virus strain. Together, this work demonstrates that Ras/MEK activation in cancer cells downregulates transcription of IFN-inducible genes by targeting IRF1 expression, resulting in increased susceptibility to viral oncolysis.","corpus_id":25459095,"score":1},{"doc_id":"25575816","title":"Dichloroacetate blocks aerobic glycolytic adaptation to attenuated measles virus and promotes viral replication leading to enhanced oncolysis in glioblastoma.","abstract":"Targeting reprogrammed energy metabolism such as aerobic glycolysis is a potential strategy for cancer treatment. However, tumors exhibiting low-rate glycolysis or metabolic heterogeneity might be resistant to such treatment. We hypothesized that a therapeutic modality that drove cancer cells to high-rate glycolysis might sensitize cancer cells to interference directed against metabolic flux. In this study, we found that attenuated oncolytic measles virus Edmonston strain (MV-Edm) caused glioblastoma cells to shift to high-rate aerobic glycolysis; this adaptation was blocked by dichloroacetate (DCA), an inhibitor of glycolysis, leading to profound cell death of cancer cells but not of normal cells. DCA enhanced viral replication by mitigating mitochondrial antiviral signaling protein (MAVS)-mediated innate immune responses. In a subcutaneous glioblastoma (GBM) xenograft mouse model, low-dose MV-Edm and DCA significantly inhibited tumor growth in vivo. We found that DCA impaired glycolysis (blocking bioenergetic generation) and enhanced viral replication (increasing bioenergetic consumption), which, in combination, accelerated bioenergetic exhaustion leading to necrotic cell death. Taken together, oncolytic MV-Edm sensitized cancer cells to DCA, and in parallel, DCA promoted viral replication, thus, improving oncolysis. This novel therapeutic approach should be readily incorporated into clinical trials.","corpus_id":18633229,"score":1},{"doc_id":"25978957","title":"Inhibition of the mevalonate pathway affects epigenetic regulation in cancer cells.","abstract":"The mevalonate pathway provides metabolites for post-translational modifications such as farnesylation, which are critical for the activity of RAS downstream signaling. Subsequently occurring regulatory processes can induce an aberrant stimulation of DNA methyltransferase (DNMT1) as well as changes in histone deacetylases (HDACs) and microRNAs in many cancer cell lines. Inhibitors of the mevalonate pathway are increasingly recognized as anticancer drugs. Extensive evidence indicates an intense cross-talk between signaling pathways, which affect growth, differentiation, and apoptosis either directly or indirectly via epigenetic mechanisms. Herein, we show data obtained by novel transcriptomic and corresponding methylomic or proteomic analyses from cell lines treated with pharmacologic doses of respective inhibitors (i.e., simvastatin, ibandronate). Metabolic pathways and their epigenetic consequences appear to be affected by a changed concentration of NADPH. Moreover, since the mevalonate metabolism is part of a signaling network, including vitamin D metabolism or fatty acid synthesis, the epigenetic activity of associated pathways is also presented. This emphasizes the far-reaching epigenetic impact of metabolic therapies on cancer cells and provides some explanation for clinical observations, which indicate the anticancer activity of statins and bisphosphonates.","corpus_id":29701210,"score":1},{"doc_id":"25995245","title":"Interferon Beta and Interferon Alpha 2a Differentially Protect Head and Neck Cancer Cells from Vesicular Stomatitis Virus-Induced Oncolysis.","abstract":"UNLABELLED: Oncolytic viruses (OV) preferentially kill cancer cells due in part to defects in their antiviral responses upon exposure to type I interferons (IFNs). However, IFN responsiveness of some tumor cells confers resistance to OV treatment. The human type I IFNs include one IFN-β and multiple IFN-α subtypes that share the same receptor but are capable of differentially inducing biological responses. The role of individual IFN subtypes in promoting tumor cell resistance to OV is addressed here. Two human IFNs which have been produced for clinical use, IFN-α2a and IFN-β, were compared for activity in protecting human head and neck squamous cell carcinoma (HNSCC) lines from oncolysis by vesicular stomatitis virus (VSV). Susceptibility of HNSCC lines to killing by VSV varied. VSV infection induced increased production of IFN-β in resistant HNSCC cells. When added exogenously, IFN-β was significantly more effective at protecting HNSCC cells from VSV oncolysis than was IFN-α2a. In contrast, normal keratinocytes and endothelial cells were protected equivalently by both IFN subtypes. Differential responsiveness of tumor cells to IFN-α and -β was further supported by the finding that autocrine IFN-β but not IFN-α promoted survival of HNSCC cells during persistent VSV infection. Therefore, IFN-α and -β differentially affect VSV oncolysis, justifying the evaluation and comparison of IFN subtypes for use in combination with VSV therapy. Pairing VSV with IFN-α2a may enhance selectivity of oncolytic VSV therapy for HNSCC by inhibiting VSV replication in normal cells without a corresponding inhibition in cancer cells. IMPORTANCE: There has been a great deal of progress in the development of oncolytic viruses. However, a major problem is that individual cancers vary in their sensitivity to oncolytic viruses. In many cases this is due to differences in their production and response to interferons (IFNs). The experiments described here compared the responses of head and neck squamous cell carcinoma cell lines to two IFN subtypes, IFN-α2a and IFN-β, in protection from oncolytic vesicular stomatitis virus. We found that IFN-α2a was significantly less protective for cancer cells than was IFN-β, whereas normal cells were equivalently protected by both IFNs. These results suggest that from a therapeutic standpoint, selectivity for cancer versus normal cells may be enhanced by pairing VSV with IFN-α2a.","corpus_id":7057361,"score":1},{"doc_id":"26257065","title":"Genome-wide lentiviral shRNA screen identifies serine/arginine-rich splicing factor 2 as a determinant of oncolytic virus activity in breast cancer cells.","abstract":"Oncolytic human herpes simplex virus type 1 (HSV-1) shows promising treatment efficacy in late-stage clinical trials. The anticancer activity of oncolytic viruses relies on deregulated pathways in cancer cells, which make them permissive to oncolysis. To identify pathways that restrict HSV-1 KM100-mediated oncolysis, this study used a pooled genome-wide short hairpin RNA library and found that depletion of the splicing factor arginine-rich splicing factor 2 (SRSF2) leads to enhanced cytotoxicity of breast cancer cells by KM100. Serine/arginine-rich (SR) proteins are a family of RNA-binding phosphoproteins that control both constitutive and alternative pre-mRNA splicing. Further characterization showed that KM100 infection of HS578T cells under conditions of low SRSF2 leads to pronounced apoptosis without a corresponding increase in virus replication. As DNA topoisomerase I inhibitors can limit the phosphorylation of SRSF2, we combined a topoisomerase I inhibitor chemotherapeutic with KM100 and observed synergistic anticancer effect in vitro and prolonged survival of tumor-bearing mice in vivo. Oncogene advance online publication, 10 August 2015; doi:10.1038/onc.2015.303.","corpus_id":34609483,"score":1},{"doc_id":"26278331","title":"The Role of Neutrophils in Measles Virus-mediated Oncolysis Differs Between B-cell Malignancies and Is Not Always Enhanced by GCSF.","abstract":"The mechanism by which oncolytic measles virus (MV) kills cancer cells remains obscure. We previously showed that neutrophils are involved in MV-mediated tumor regressions and become activated, upon MV infection. In the present study, we attempted to enhance the neutrophil response toward MV-infected tumor targets by generating an oncolytic MV-expressing human granulocyte colony-stimulating factor (MVhGCSF). Evaluating the effects in two different models of B-cell malignancy, we showed that depletion of neutrophils abrogated the MV therapeutic effect in an in vivo Raji-but not Nalm-6 tumor model. Next, we compared MVhGCSF with the unmodified backbone virus MVNSe. MVhGCSF enhanced the oncolytic capacity of MV in the Raji model in vivo, whereas in the Nalm-6 model, the opposite was unexpectedly the case. This finding was recapitulated by exogenously administered hGCSF. MVhGCSF replicated within an MV-infectable CD46 transgenic mouse model with detectable serum levels of hGCSF but no toxicity. Our data suggest that a \"one-size-fits-all\" model of immune response to viral oncolysis is not appropriate, and each tumor target will need full characterization for the potential of both direct and indirect, innate immune responses to generate benefit. Molecular Therapy (2015); doi:10.1038/mt.2015.149.","corpus_id":25655712,"score":1},{"doc_id":"26358205","title":"Statin-mediated inhibition of cholesterol synthesis induces cytoprotective autophagy in human leukemic cells.","abstract":"Statins exhibit anti-leukemic properties due to suppression of the mevalonate pathway by the inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase, and subsequent depletion of cholesterol, farnesylpyrophosphate, and geranylgeranylpyrophosphate. We investigated the role of autophagy, a controlled intracellular self-digestion, in the anti-leukemic action of statins. Treatment with low concentrations (≤6 µM) of statins, cholesterol depletion, and specific inhibition of cholesterol synthesis and protein farnesylation or geranylgeranylation, all inhibited proliferation of leukemic cell lines and primary leukemic cells without inducing overt cell death. Statins and agents that selectively reduce intracellular cholesterol levels, but not the inhibition of protein farnesylation or geranylgeranylation, induced autophagy in leukemic cells. The observed autophagic response was associated with the reduction of phosphorylated Akt levels in the lipid rafts, accompanied by a decrease in the activation of the main autophagy suppressor mammalian target of rapamycin (mTOR) and its substrate ribosomal p70S6 kinase (p70S6K). No significant autophagy induction and downregulation of mTOR/p70S6K activation were observed in normal leukocytes. Autophagy suppression by bafilomycin A1 or RNA interference-mediated knockdown of beclin-1 and microtubule-associated protein 1 light chain 3B induced apoptotic death in statin-treated leukemic cells, an effect attenuated by the addition of mevalonate or squalene, but not farnesylpyrophosphate or geranylgeranylpyrophosphate. Therefore, while the inhibition of cholesterol synthesis, protein farnesylation, and geranylgeranylation all contributed to anti-leukemic effects of statins, the inhibition of cholesterol synthesis was solely responsible for the induction of cytoprotective autophagy. These data indicate that combined treatment with statins and autophagy inhibitors might be potentially useful in anti-leukemic therapy.","corpus_id":32452346,"score":1},{"doc_id":"26758953","title":"Mevalonate Pathway and Human Cancers.","abstract":"Mevalonate (MVA) is synthesized from 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) by HMG-CoA reductase (HMG-CoAR). MVA is further metabolized to farnesyl pyrophosphate (FPP), a precursor of cholesterol and sterols. FPP is also converted to geranylgeranyl pyrophosphate, and these lipids are used for post-translational modification of proteins that are involved in various aspects of tumor development and progression. Many studies showed that the MVA pathway is up-regulated in several cancers such as leukemia, lymphoma, multiple myeloma; as well as breast, hepatic, pancreatic, esophageal and prostate cancers. Several mechanisms may be involved in dysregulation of this pathway. They include p53 mutation, a mutation in HMG-CoAR and sterol-regulatory element binding protein (SREBP) cleavage-activating protein SCAP as its regulator, PKB/Akt activation, decreased AMPK activation, and activation of transcription factors such as: SREBP and HIF-1. Statins as inhibitors of MVA pathway might be useful for cancer prevention and/or treatment through their interactions with essential cellular functions, such as cell proliferation and differentiation. Other inhibitors are also designed for inhibition of this key pathway and their mechanism of action was investigated. In the present review, we will first describe about some inhibitors of MVA, including statins that have been suggested for cancer treatment. We will then discuss about the mechanisms involved in MVA dysregulation, especially in cancer.","corpus_id":26035255,"score":1},{"doc_id":"26909280","title":"Regulation of VEGF by mevalonate pathway inhibition in breast cancer.","abstract":"Aminobisphosphonates are used for the treatment of benign and malignant bone disorders. As inhibitors of the mevalonate pathway they exert direct anti-tumor effects in vitro and in preclinical models of bone metastases. Bisphosphonates are thought to have an anti-angiogenic activity as decreased levels of VEGF have been reported in some, although not all patients, following treatment with bisphosphonates. Direct effects of bisphosphonates on tumor derived VEGF have not been examined in detail. We therefore investigated VEGF expression in breast cancer cell lines following mevalonate pathway inhibition. Treatment of cell lines with increasing doses of zoledronic acid and atorvastatin resulted in increased levels of VEGF production. Similar results were seen with the geranylgeranyltransferase I inhibitor GGTI-298. The induction of VEGF was reversed by the supplementation of geranylgeranyl pyrophosphate but not by farnesyl pyrophosphate indicating that this effect is mediated by inhibited geranylgeranylation. Previous reports have reported decreased VEGF levels in patients following BP treatment in vivo. We assessed VEGF levels in patients with non-metastatic breast cancer following repeated treatment with zoledronic acid. In contrast to our in vitro findings, VEGF serum levels decreased in all patients after 6-9 months of treatment (by an average of 41%) as assessed in a small pilot trial. These results indicate that tissues other than breast tumors contribute to the serum pool of circulating VEGF and may be responsible for the observed VEGF decreases. The increases of VEGF in the cancer cells may provide a rationale for the combined treatment with VEGF inhibitors.","corpus_id":3157661,"score":1},{"doc_id":"26976483","title":"A mathematical model verifying potent oncolytic efficacy of M1 virus.","abstract":"Motivated by the latest findings in a recent medical experiment [19] which identify a naturally occurring alphavirus (M1) as a novel selective killer targeting zinc-finger antiviral protein (ZAP)-deficient cancer cells, we propose a mathematical model to illustrate the growth of normal cells, tumor cells and the M1 virus with limited nutrient. In order to better understand biological mechanisms, we discuss two cases of the model: without competition and with competition. In the first part, the explicit threshold conditions for the persistence of normal cells (or tumor cells) is obtained accompanying with the biological explanations. The second part indicates that when competing with tumor cells, the normal cells will extinct if M1 virus is ignored; Whereas, when M1 virus is considered, the growth trend of normal cells is similar to the one without competition. And by using uniformly strong repeller theorem, the minimum effective dosage of medication is explicitly found which is not reported in [19]. Furthermore, numerical simulations and corresponding biological interpretations are given to support our results.","corpus_id":13089023,"score":1},{"doc_id":"27019795","title":"Clinical development of reovirus for cancer therapy: An oncolytic virus with immune-mediated antitumor activity.","abstract":"Reovirus is a double-stranded RNA virus with demonstrated oncolysis or preferential replication in cancer cells. The oncolytic properties of reovirus appear to be dependent, in part, on activated Ras signaling. In addition, Ras-transformation promotes reovirus oncolysis by affecting several steps of the viral life cycle. Reovirus-mediated immune responses can present barriers to tumor targeting, serve protective functions against reovirus systemic toxicity, and contribute to therapeutic efficacy through antitumor immune-mediated effects via innate and adaptive responses. Preclinical studies have demonstrated the broad anticancer activity of wild-type, unmodified type 3 Dearing strain reovirus (Reolysin(®)) across a spectrum of malignancies. The development of reovirus as an anticancer agent and available clinical data reported from 22 clinical trials will be reviewed.","corpus_id":26763495,"score":1},{"doc_id":"27155373","title":"Could drugs inhibiting the mevalonate pathway also target cancer stem cells?","abstract":"Understanding the connection between metabolic pathways and cancer is very important for the development of new therapeutic approaches based on regulatory enzymes in pathways associated with tumorigenesis. The mevalonate cascade and its rate-liming enzyme HMG CoA-reductase has recently drawn the attention of cancer researchers because strong evidences arising mostly from epidemiologic studies, show that it could promote transformation. Hence, these studies pinpoint HMG CoA-reductase as a candidate proto-oncogene. Several recent epidemiological studies, in different populations, have proven that statins are beneficial for the treatment-outcome of various cancers, and may improve common cancer therapy strategies involving alkylating agents, and antimetabolites. Cancer stem cells/cancer initiating cells (CSC) are key to cancer progression and metastasis. Therefore, in the current review we address the different effects of statins on cancer stem cells. The mevalonate cascade is among the most pleiotropic, and highly interconnected signaling pathways. Through G-protein-coupled receptors (GRCP), it integrates extra-, and intracellular signals. The mevalonate pathway is implicated in cell stemness, cell proliferation, and organ size regulation through the Hippo pathway (e.g. Yap/Taz signaling axis). This pathway is a prime preventive target through the administration of statins for the prophylaxis of obesity-related cardiovascular diseases. Its prominent role in regulation of cell growth and stemness also invokes its role in cancer development and progression. The mevalonate pathway affects cancer metastasis in several ways by: (i) affecting epithelial-to-mesenchymal transition (EMT), (ii) affecting remodeling of the cytoskeleton as well as cell motility, (iii) affecting cell polarity (non-canonical Wnt/planar pathway), and (iv) modulation of mesenchymal-to-epithelial transition (MET). Herein we provide an overview of the mevalonate signaling network. We then briefly highlight diverse functions of various elements of this mevalonate pathway. We further discuss in detail the role of elements of the mevalonate cascade in stemness, carcinogenesis, cancer progression, metastasis and maintenance of cancer stem cells.","corpus_id":46868209,"score":1},{"doc_id":"27384486","title":"Enhanced cytotoxicity of reovirus and radiotherapy in melanoma cells is mediated through increased viral replication and mitochondrial apoptotic signalling.","abstract":"Oncolytic viruses selectively target and replicate in cancer cells, providing us with a unique tool with which to target and kill tumour cells. These viruses come from a diverse range of viral families including reovirus type 3 Dearing (RT3D), a non-pathogenic human double-stranded RNA oncolytic virus, which has been shown to be an effective therapeutic agent, both as a mono-therapy and in combination with traditional chemotherapeutic drugs. This study investigated the interaction between RT3D and radiotherapy in melanoma cell lines with a BRAF mutant, Ras mutant or BRAF/Ras wild type genotype. The data indicates that RT3D combined with radiotherapy significantly increased cytotoxicity relative to either single agent, independent of genotype, both in vitro and in vivo. The mechanism of enhanced cytotoxicity was dependent on an increase in viral replication, mediated by CUG2 up-regulation and subsequent down-regulation of pPKR and p-eIF2α, leading to the activation of mitochondrial apoptotic signalling resulting in increased cell death.","corpus_id":14979729,"score":1},{"doc_id":"27775703","title":"DNAJA1 controls the fate of misfolded mutant p53 through the mevalonate pathway.","abstract":"Stabilization of mutant p53 (mutp53) in tumours greatly contributes to malignant progression. However, little is known about the underlying mechanisms and therapeutic approaches to destabilize mutp53. Here, through high-throughput screening we identify statins, cholesterol-lowering drugs, as degradation inducers for conformational or misfolded p53 mutants with minimal effects on wild-type p53 (wtp53) and DNA contact mutants. Statins preferentially suppress mutp53-expressing cancer cell growth. Specific reduction of mevalonate-5-phosphate by statins or mevalonate kinase knockdown induces CHIP ubiquitin ligase-mediated nuclear export, ubiquitylation, and degradation of mutp53 by impairing interaction of mutp53 with DNAJA1, a Hsp40 family member. Knockdown of DNAJA1 also induces CHIP-mediated mutp53 degradation, while its overexpression antagonizes statin-induced mutp53 degradation. Our study reveals that DNAJA1 controls the fate of misfolded mutp53, provides insights into potential strategies to deplete mutp53 through the mevalonate pathway-DNAJA1 axis, and highlights the significance of p53 status in impacting statins' efficacy on cancer therapy.","corpus_id":20080529,"score":1},{"doc_id":"28566376","title":"Ruxolitinib and Polycation Combination Treatment Overcomes Multiple Mechanisms of Resistance of Pancreatic Cancer Cells to Oncolytic Vesicular Stomatitis Virus.","abstract":"Vesicular stomatitis virus (VSV) is a promising oncolytic virus (OV). Although VSV is effective against a majority of pancreatic ductal adenocarcinoma cell (PDAC) cell lines, some PDAC cell lines are highly resistant to VSV, and the mechanisms of resistance are still unclear. JAK1/2 inhibitors (such as ruxolitinib and JAK inhibitor I) strongly stimulate VSV replication and oncolysis in all resistant cell lines but only partially improve the susceptibility of resistant PDACs to VSV. VSV tumor tropism is generally dependent on the permissiveness of malignant cells to viral replication rather than on receptor specificity, with several ubiquitously expressed cell surface molecules playing a role in VSV attachment to host cells. However, as VSV attachment to PDAC cells has never been tested before, here we examined if it was possibly inhibited in resistant PDAC cells. Our data show a dramatically weaker attachment of VSV to HPAF-II cells, the most resistant human PDAC cell line. Although sequence analysis of low-density lipoprotein (LDL) receptor (LDLR) mRNA did not reveal any amino acid substitutions in this cell line, HPAF-II cells displayed the lowest level of LDLR expression and dramatically lower LDL uptake. Treatment of cells with various statins strongly increased LDLR expression levels but did not improve VSV attachment or LDL uptake in HPAF-II cells. However, LDLR-independent attachment of VSV to HPAF-II cells was dramatically improved by treating cells with Polybrene or DEAE-dextran. Moreover, combining VSV with ruxolitinib and Polybrene or DEAE-dextran successfully broke the resistance of HPAF-II cells to VSV by simultaneously improving VSV attachment and replication. IMPORTANCE Oncolytic virus (OV) therapy is an anticancer approach that uses viruses that selectively infect and kill cancer cells. This study focuses on oncolytic vesicular stomatitis virus (VSV) against pancreatic ductal adenocarcinoma (PDAC) cells. Although VSV is effective against most PDAC cells, some are highly resistant to VSV, and the mechanisms are still unclear. Here we examined if VSV attachment to cells was inhibited in resistant PDAC cells. Our data show very inefficient attachment of VSV to the most resistant human PDAC cell line, HPAF-II. However, VSV attachment to HPAF-II cells was dramatically improved by treating cells with polycations. Moreover, combining VSV with polycations and ruxolitinib (which inhibits antiviral signaling) successfully broke the resistance of HPAF-II cells to VSV by simultaneously improving VSV attachment and replication. We envision that this novel triple-combination approach could be used in the future to treat PDAC tumors that are highly resistant to OV therapy.","corpus_id":4534436,"score":1},{"doc_id":"28668359","title":"The balance between induction and inhibition of mevalonate pathway regulates cancer suppression by statins: A review of molecular mechanisms.","abstract":"Statins are widely used drugs for their role in decreasing cholesterol in hypercholesterolemic patients. Statins through inhibition of Hydroxy Methyl Glutaryl-CoA Reductase (HMGCR), the main enzyme of the cholesterol biosynthesis pathway, inhibit mevalonate pathway that provides isoprenoids for prenylation of different proteins such as Ras superfamily which has an essential role in cancer developing. Inhibition of the mevalonate/isoprenoid pathway is the cause of the cholesterol independent effects of statins or pleotropic effects. Depending on their penetrance into the extra-hepatic cells, statins have different effects on mevalonate/isoprenoid pathway. Lipophilic statins diffuse into all cells and hydrophilic ones use a variety of membrane transporters to gain access to cells other than hepatocytes. It has been suggested that the lower accessibility of statins for extra-hepatic tissues may result in the compensatory induction of mevalonate/isoprenoid pathway and so cancer developing. However, most of the population-based studies have demonstrated that statins have no effect on cancer developing, even decrease the risk of different types of cancer. In this review we focus on the cancer developing \"potentials\" and the anti-cancer \"activities\" of statins regarding the effects of statins on mevalonate/isoprenoid pathway in the liver and extra-hepatic tissues.","corpus_id":2604039,"score":1},{"doc_id":"28808351","title":"Inhibition of the mevalonate pathway augments the activity of pitavastatin against ovarian cancer cells.","abstract":"Only 40% of patients with advanced ovarian cancer survive more than 5 years. We have previously shown that pitavastatin induces regression of ovarian cancer xenografts in mice. To evaluate whether the response of ovarian cancer cells to pitavastatin is potentiated by farnesyl diphosphate synthase inhibitors or geranylgeraniol transferase I inhibitors, we evaluated combinations of pitavastatin with zoledronic acid, risedronate and GGTI-2133 in a panel of ovarian cancer cells. Pitavastatin (IC50 = 0.6-14 μM), zoledronic acid (IC50 = 21-57 μM), risedronate (IC50 > 100 μM) or GGTI-2133 (IC50 > 25 μM) inhibited the growth of ovarian cancer cell cultures. Combinations of pitavastatin with zoledronic acid displayed additive or synergistic effects in cell growth assays in 10 of 11 cell lines evaluated as well as in trypan blue exclusion, cellular ATP or caspase 3/7, 8 and 9 assays. Pitavastatin reduced levels of GGT-IIβ and the membrane localization of several small GTPases and this was potentiated by zoledronic acid. siRNA to GGT-Iβ and GGT-IIβ used in combination, but not when used individually, significantly increased the sensitivity of cells to pitavastatin. These data suggest that zoledronic acid, a drug already in clinical use, may be usefully combined with pitavastatin in the treatment of ovarian cancer.","corpus_id":205589699,"score":1},{"doc_id":"29069775","title":"Drug repositioning of mevalonate pathway inhibitors as antitumor agents for ovarian cancer.","abstract":"Drug repositioning is an alternative strategy redirecting existing drugs for new disease. We have previously reported an antitumor effect of statins, antidyslipidemic drugs, on ovarian cancer in vitro and in vivo. In this study, we investigated the antitumor effects of other mevalonate pathway inhibitors and the mechanism of the antitumor effect from a metabolic perspective. The effects of inhibitors of the mevalonate pathway on tumor cell growth were evaluated in vitro. Bisphosphonates that inhibit this pathway are commonly used as antiosteoporotic drugs, and antitumor effects of the bisphosphonate were examined in vitro and in vivo. Metabolites in SKOV3 ovarian cancer cells were analyzed before and after lovastatin treatment, using capillary electrophoresis-mass spectrometry. All mevalonate pathway inhibitors showed concentration-dependent inhibitory effects on tumor cell growth. Particularly marked effects were obtained with inhibitors of farnesyltransferase and geranylgeranyltransferase. The bisphosphonate was also shown to have an antitumor effect in vivo. The expression of autophagy marker LC3A/3B was increased in cells after treatment. In metabolomics analysis, lovastatin treatment increased the metabolites involved in the tricarboxylic acid cycle while reducing the metabolites associated with glycolysis. Also it decreased glutathione and resulted to work with chemotherapeutic agents synergistically. Inhibition at any point in the mevalonate pathway, and especially of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, suppresses growth of ovarian cancer cells. Inhibition of this pathway may induce autophagy, cause a shift to activation of the tricarboxylic acid cycle and enhance susceptibility to chemotherapy. Drug repositioning targeting mevalonate pathway for ovarian cancer deserves consideration for clinical application.","corpus_id":8080021,"score":1},{"doc_id":"29238070","title":"The interplay between mutant p53 and the mevalonate pathway.","abstract":"Missense mutations in the TP53 gene lead to accumulation of dysfunctional TP53 proteins in tumors, showing oncogenic gain-of-function (GOF) activities. Stabilization of mutant TP53 (mutp53) is required for the GOF; however, the mechanisms by which mutp53 promotes cancer progression and how mutp53 stability is regulated are not completely understood. Recent work from our laboratory has identified statins, inhibitors of the mevalonate pathway, as degraders of conformational mutp53. Specific reduction of mevalonate-5-phosphate (MVP), a metabolic intermediate in the mevalonate pathway, by statins or mevalonate kinase (MVK) knockdown triggers CHIP ubiquitin ligase-mediated degradation of conformational mutp53 by inhibiting interaction between mutp53 and DNAJA1, a Hsp40 family member. Thus, the mevalonate pathway contributes to mutp53 stabilization. Given that mutp53 is shown to promote cancer progression by upregulating mRNA expression of mevalonate pathway enzymes by binding to the sterol regulatory element-binding protein 2 (SREBP2) and subsequently increasing activities of mevalonate pathway-associated oncogenic proteins (e.g., Ras, Rho, YAP/TAZ), there is a positive-feedback loop between mutp53 and the mevalonate pathway. Here, we summarize recent evidence linking the mevalonate pathway-mutp53 axis with cancer progression and further discuss the clinical relevance of this axis.","corpus_id":3640094,"score":1},{"doc_id":"29252087","title":"Temozolomide renders murine cancer cells susceptible to oncolytic adenovirus replication and oncolysis.","abstract":"The preclinical evaluation of oncolytic adenoviruses (OAds) has been limited to cancer xenograft mouse models because OAds replicate poorly in murine cancer cells. The alkylating agent temozolomide (TMZ) has been shown to enhance oncolytic virotherapy in human cancer cells; therefore, we investigated whether TMZ could increase OAd replication and oncolysis in murine cancer cells. To test our hypothesis, three murine cancer cells were infected with OAd (E1b-deleted) alone or in combination with TMZ. TMZ increased OAd-mediated oncolysis in all three murine cancer cells tested. This increased oncolysis was, at least in part, due to productive virus replication, apoptosis, and autophagy induction. Most importantly, murine lung non-cancerous cells were not affected by OAd+TMZ. Moreover, TMZ increased Ad transduction efficiency. However, TMZ did not increase coxsackievirus and adenovirus receptor; therefore, other mechanism could be implicated on the transduction efficiency. These results showed, for the first time, that TMZ could render murine tumor cells more susceptible to oncolytic virotherapy. The proposed combination of OAds with TMZ presents an attractive approach towards the evaluation of OAd potency and safety in syngeneic mouse models using these murine cancer cell-lines in vivo.","corpus_id":3809781,"score":1},{"doc_id":"18579592","title":"Targeting the apoptotic pathway with BCL-2 inhibitors sensitizes primary chronic lymphocytic leukemia cells to vesicular stomatitis virus-induced oncolysis.","abstract":"Chronic lymphocytic leukemia (CLL) is characterized by clonal accumulation of CD5(+) CD19(+) B lymphocytes that are arrested in the G(0)/G(1) phase of the cell cycle and fail to undergo apoptosis because of overexpression of the antiapoptotic B-cell CLL/lymphoma 2 (BCL-2) protein. Oncolytic viruses, such as vesicular stomatitis virus (VSV), have emerged as potential anticancer agents that selectively target and kill malignant cells via the intrinsic mitochondrial pathway. Although primary CLL cells are largely resistant to VSV oncolysis, we postulated that targeting the apoptotic pathway via inhibition of BCL-2 may sensitize CLL cells to VSV oncolysis. In the present study, we examined the capacity of EM20-25--a small-molecule antagonist of the BCL-2 protein--to overcome CLL resistance to VSV oncolysis. We demonstrate a synergistic effect of the two agents in primary ex vivo CLL cells (combination index of 0.5; P < 0.0001). In a direct comparison of peripheral blood mononuclear cells from healthy volunteers with primary CLL, the two agents combined showed a therapeutic index of 19-fold; furthermore, the combination of VSV and EM20-25 increased apoptotic cell death in Karpas-422 and Granta-519 B-lymphoma cell lines (P < 0.005) via the intrinsic mitochondrial pathway. Mechanistically, EM20-25 blocked the ability of the BCL-2 protein to dimerize with proapoptotic BAX protein, thus sensitizing CLL to VSV oncolytic stress. Together, these data indicate that the use of BCL-2 inhibitors may improve VSV oncolysis in treatment-resistant hematological malignancies, such as CLL, with characterized defects in the apoptotic response.","corpus_id":22796262,"score":0},{"doc_id":"22204706","title":"The mevalonate pathway in C. elegans.","abstract":"The mevalonate pathway in human is responsible for the synthesis of cholesterol and other important biomolecules such as coenzyme Q, dolichols and isoprenoids. These molecules are required in the cell for functions ranging from signaling to membrane integrity, protein prenylation and glycosylation, and energy homeostasis. The pathway consists of a main trunk followed by sub-branches that synthesize the different biomolecules. The majority of our knowledge about the mevalonate pathway is currently focused on the cholesterol synthesis branch, which is the target of the cholesterol-lowering statins; less is known about the function and regulation of the non-cholesterol-related branches. To study them, we need a biological system where it is possible to specifically modulate these metabolic branches individually or in groups. The nematode Caenorhabditis elegans (C. elegans) is a promising model to study these non-cholesterol branches since its mevalonate pathway seems very well conserved with that in human except that it has no cholesterol synthesis branch. The simple genetic makeup and tractability of C. elegans makes it relatively easy to identify and manipulate key genetic components of the mevalonate pathway, and to evaluate the consequences of tampering with their activity. This general experimental approach should lead to new insights into the physiological roles of the non-cholesterol part of the mevalonate pathway. This review will focus on the current knowledge related to the mevalonate pathway in C. elegans and its possible applications as a model organism to study the non-cholesterol functions of this pathway.","corpus_id":977178,"score":0},{"doc_id":"22361350","title":"Propiconazole-enhanced hepatic cell proliferation is associated with dysregulation of the cholesterol biosynthesis pathway leading to activation of Erk1/2 through Ras farnesylation.","abstract":"Propiconazole is a mouse hepatotumorigenic fungicide designed to inhibit CYP51, a key enzyme in the biosynthesis of ergosterol in fungi and is widely used in agriculture to prevent fungal growth. Metabolomic studies in mice revealed that propiconazole increased levels of hepatic cholesterol metabolites and bile acids, and transcriptomic studies revealed that genes within the cholesterol biosynthesis, cholesterol metabolism and bile acid biosyntheses pathways were up-regulated. Hepatic cell proliferation was also increased by propiconazole. AML12 immortalized hepatocytes were used to study propiconazole's effects on cell proliferation focusing on the dysregulation of cholesterol biosynthesis and resulting effects on Ras farnesylation and Erk1/2 activation as a primary pathway. Mevalonate, a key intermediate in the cholesterol biosynthesis pathway, increases cell proliferation in several cancer cell lines and tumors in vivo and serves as the precursor for isoprenoids (e.g. farnesyl pyrophosphate) which are crucial in the farnesylation of the Ras protein by farnesyl transferase. Farnesylation targets Ras to the cell membrane where it is involved in signal transduction, including the mitogen-activated protein kinase (MAPK) pathway. In our studies, mevalonic acid lactone (MVAL), a source of mevalonic acid, increased cell proliferation in AML12 cells which was reduced by farnesyl transferase inhibitors (L-744,832 or manumycin) or simvastatin, an HMG-CoA reductase inhibitor, indicating that this cell system responded to alterations in the cholesterol biosynthesis pathway. Cell proliferation in AML12 cells was increased by propiconazole which was reversed by co-incubation with L-744,832 or simvastatin. Increasing concentrations of exogenous cholesterol muted the proliferative effects of propiconazole and the inhibitory effects of L-733,832, results ascribed to reduced stimulation of the endogenous cholesterol biosynthesis pathway. Western blot analysis of subcellular fractions from control, MVAL or propiconazole-treated cells revealed increased Ras protein in the cytoplasmic fraction of L-744,832-treated cells, while propiconazole or MVAL reversed these effects. Western blot analysis indicated that phosphorylation of Erk1/2, a protein downstream of Ras, was increased by propiconazole. These data indicate that propiconazole increases cell proliferation by increasing the levels of cholesterol biosynthesis intermediates presumably through a negative feedback mechanism within the pathway, a result of CYP51 inhibition. This feedback mechanism increases Erk1/2 signaling through mevalonate-mediated Ras activation. These results provide an explanation for the observed effects of propiconazole on hepatic cholesterol pathways and on the increased hepatic cell proliferation induced by propiconazole in mice.","corpus_id":38589320,"score":0},{"doc_id":"23586025","title":"Viability reduction and Rac1 gene downregulation of heterogeneous ex-vivo glioma acute slice infected by the oncolytic Newcastle disease virus strain V4UPM.","abstract":"Oncolytic viruses have been extensively evaluated for anticancer therapy because this virus preferentially infects cancer cells without interfering with normal cells. Newcastle Disease Virus (NDV) is an avian virus and one of the intensively studied oncolytic viruses affecting many types of cancer including glioma. Nevertheless, the capability of NDV infection on heterogeneous glioma tissue in a cerebrospinal fluid atmosphere has never been reported. Recently, Rac1 is reported to be required for efficient NDV replication in human cancer cells and established a link between tumourigenesis and sensitivity to NDV. Rac1 is a member of the Rho GTPases involved in the regulation of the cell migration and cell-cycle progression. Rac1 knockdown leads to significant inhibition of viral replication. In this work, we demonstrated that NDV treatment led to significant reduction of tumour tissue viability of freshly isolated heterogeneous human brain tumour slice, known as an ex vivo glioma acute slice (EGAS). Analysis of gene expression indicated that reduced tissue viability was associated with downregulation of Rac1. However, the viability reduction was not persistent. We conclude that NDV treatment induced EGAS viability suppression, but subsequent downregulation of Rac1 gene may reduce the NDV replication and lead to regrowth of EGAS tissue.","corpus_id":16428961,"score":0},{"doc_id":"26758947","title":"Interconnection of Estrogen/Testosterone Metabolism and Mevalonate Pathway in Breast and Prostate Cancers.","abstract":"The metabolic steroid hormones, 17β stradiol (E2) and testosterone play key roles in several functions including carbohydrate, lipid and protein metabolism, cellular signaling, cell proliferation, and cancer promotion. Steroid hormones have long been characterized as cell proliferation and differentiation regulators and are closely related to the development of breast and prostate cancers. Moreover, cholesterol metabolism, mainly in adipose tissue, leads to the production of steroids and cytokines, thus increasing the risk of metabolic syndrome, obesity, and ER+ breast cancer in postmenopausal women. Recent studies also shown that testosterone and E2 increase the levels of key enzymes of the mevalonate pathway, leading to post-translational prenylation and farnesylation of numerous proteins in RAS signaling in several cancers, including breast and prostate cancers. There is accumulating evidence both clinically and experimentally suggesting that changes in the metabolism of cholesterol may also have an important role in carcinogenesis. In this regard, the cells treated with mevalonate in culture showed elevated proliferation. Therefore, investigation on cholesterol as a precursor of steroid hormones has confirmed the effects cholesterol metabolite on breast and prostate cancers. Indeed, recent evidence strongly suggests that the MVA pathway and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCOA) have a crucial regulatory role in cellular proliferation and transformation. Therefore, the use of mevalonate inhibitors decreases the production of several biologically active downstream products of the mevalonate pathway, including cholesterol. Although for approximately 20 years statins have been identified as anticancer agents, recent studies have sparked some controversy. Therefore, further investigation to evaluate mevalonate- dependent therapeutic agents per se and in combination with other agents is merited. The current review is an attempt to elucidate the role of cholesterol and E2/testosterone, as well as the mevalonate pathway and its inhibitors in breast and prostate tissues in normal and pathological states.","corpus_id":27887498,"score":0}],"string":"[\n {\n \"doc_id\": \"25288727\",\n \"title\": \"Identification and characterization of alphavirus M1 as a selective oncolytic virus targeting ZAP-defective human cancers.\",\n \"abstract\": \"Oncolytic virotherapy is a growing treatment modality that uses replicating viruses as selective antineoplastic agents. Safety and efficacy considerations dictate that an ideal oncolytic agent would discriminate between normal and cancer cells on the basis of common genetic abnormalities in human cancers. Here, we identify a naturally occurring alphavirus (M1) as a novel selective killer targeting zinc-finger antiviral protein (ZAP)-deficient cancer cells. In vitro, in vivo, and ex vivo studies showed potent oncolytic efficacy and high tumor tropism of M1. We showed that the selectivity depends on ZAP deficiency by systematic identification. A large-scale multicenter pathology study using tissue microarrays reveals that ZAP is commonly deficient in human cancers, suggesting extensive application prospects for M1. Additionally, M1 killed cancer cells by inducing endoplasmic reticulum stress-mediated apoptosis. Our report provides novel insights into potentially personalized cancer therapy using oncolytic viruses.\",\n \"corpus_id\": 19342751,\n \"score\": 2\n },\n {\n \"doc_id\": \"26373347\",\n \"title\": \"Activation of Cyclic Adenosine Monophosphate Pathway Increases the Sensitivity of Cancer Cells to the Oncolytic Virus M1.\",\n \"abstract\": \"Oncolytic virotherapy is a novel and emerging treatment modality that uses replication-competent viruses to destroy cancer cells. Although diverse cancer cell types are sensitive to oncolytic viruses, one of the major challenges of oncolytic virotherapy is that the sensitivity to oncolysis ranges among different cancer cell types. Furthermore, the underlying mechanism of action is not fully understood. Here, we report that activation of cyclic adenosine monophosphate (cAMP) signaling significantly sensitizes refractory cancer cells to alphavirus M1 in vitro, in vivo, and ex vivo. We find that activation of the cAMP signaling pathway inhibits M1-induced expression of antiviral factors in refractory cancer cells, leading to prolonged and severe endoplasmic reticulum (ER) stress, and cell apoptosis. We also demonstrate that M1-mediated oncolysis, which is enhanced by cAMP signaling, involves the factor, exchange protein directly activated by cAMP 1 (Epac1), but not the classical cAMP-dependent protein kinase A (PKA). Taken together, cAMP/Epac1 signaling pathway activation inhibits antiviral factors and improves responsiveness of refractory cancer cells to M1-mediated virotherapy. Molecular Therapy (2015); doi:10.1038/mt.2015.172.\",\n \"corpus_id\": 491391,\n \"score\": 2\n },\n {\n \"doc_id\": \"27296553\",\n \"title\": \"Naturally Existing Oncolytic Virus M1 Is Nonpathogenic for the Nonhuman Primates After Multiple Rounds of Repeated Intravenous Injections.\",\n \"abstract\": \"Cancers figure among the leading causes of morbidity and mortality worldwide. The number of new cases is expected to rise by about 70% over the next 2 decades. Development of novel therapeutic agents is urgently needed for clinical cancer therapy. Alphavirus M1 is a Getah-like virus isolated from China with a genome of positive single-strand RNA. We have previously identified that alphavirus M1 is a naturally existing oncolytic virus with significant anticancer activity against different kinds of cancer (e.g., liver cancer, bladder cancer, and colon cancer). To support the incoming clinical trial of intravenous administration of alphavirus M1 to cancer patients, we assessed the safety of M1 in adult nonhuman primates. We previously presented the genome sequencing data of the cynomolgus macaques (Macaca fascicularis), which was demonstrated as an ideal animal species for virus infection study. Therefore, we chose cynomolgus macaques of either sex for the present safety study of oncolytic virus M1. In the first round of administration, five experimental macaques were intravenously injected with six times of oncolytic virus M1 (1 × 10(9) pfu/dose) in 1 week, compared with five vehicle-injected control animals. The last two rounds of injections were further completed in the following months in the same way as the first round. Body weight, temperature, complete blood count, clinical biochemistries, cytokine profiles, lymphocytes subsets, neutralizing antibody, and clinical symptoms were closely monitored at different time points. Magnetic resonance imaging was also performed to assess the possibility of encephalitis or arthritis. As a result, no clinical, biochemical, immunological, or medical imaging or other pathological evidence of toxicity was found during the whole process of the study. Our results in cynomolgus macaques suggested the safety of intravenous administration of oncolytic virus M1 in cancer patients in the future.\",\n \"corpus_id\": 206189492,\n \"score\": 2\n },\n {\n \"doc_id\": \"28445966\",\n \"title\": \"Interferon alpha antagonizes the anti-hepatoma activity of the oncolytic virus M1 by stimulating anti-viral immunity.\",\n \"abstract\": \"Alpha virus M1 is an oncolytic virus that targets zinc-finger antiviral protein (ZAP)-defective cancer cells, and may be useful for treatment of hepatocellular carcinoma (HCC). Most of HCC patients have hepatitis and need long-term antiviral medication. Thus, it is necessary to clarify whether anti-virus medicines influence oncolytic effect of M1. We examined the effect of drugs used to treat hepatitis B/C on M1-mediated oncolysis in vitro and in vivo. Interferon (IFN)-α induces expression of antiviral IFN-stimulated genes (ISGs) in HCC cells with moderate sensitivity to M1 virus. This leads to reduced replication of M1, and blocking of M1-mediated apoptosis. The antagonistic effect of IFN-α is positively related with the expressive level of ISGs. We also examined a population of 147 HCC patients. A total of 107 patients (73%) had low ZAP expression in liver tissues relative to adjacent tissues. Among these 107 patients, 77% were positive for hepatitis B and 2% were positive for hepatitis C. A combination of M1 virus and IFN should be avoided in those patients with HBV or HCV infection, of who ZAP expression is low but ISGs expression is moderate. In conclusion, this study provides a basis for anti-viral regimens for HCC patients with hepatitis B or C who are given oncolytic virus M1.\",\n \"corpus_id\": 27580022,\n \"score\": 2\n },\n {\n \"doc_id\": \"28607091\",\n \"title\": \"Selective replication of oncolytic virus M1 results in a bystander killing effect that is potentiated by Smac mimetics.\",\n \"abstract\": \"Oncolytic virotherapy is a treatment modality that uses native or genetically modified viruses that selectively replicate in and kill tumor cells. Viruses represent a type of pathogen-associated molecular pattern and thereby induce the up-regulation of dozens of cytokines via activating the host innate immune system. Second mitochondria-derived activator of caspases (Smac) mimetic compounds (SMCs), which antagonize the function of inhibitor of apoptosis proteins (IAPs) and induce apoptosis, sensitize tumor cells to multiple cytokines. Therefore, we sought to determine whether SMCs sensitize tumor cells to cytokines induced by the oncolytic M1 virus, thus enhancing a bystander killing effect. Here, we report that SMCs potentiate the oncolytic effect of M1 in vitro, in vivo, and ex vivo. This strengthened oncolytic efficacy resulted from the enhanced bystander killing effect caused by the M1 virus via cytokine induction. Through a microarray analysis and subsequent validation using recombinant cytokines, we identified IL-8, IL-1A, and TRAIL as the key cytokines in the bystander killing effect. Furthermore, SMCs increased the replication of M1, and the accumulation of virus protein induced irreversible endoplasmic reticulum stress- and c-Jun N-terminal kinase-mediated apoptosis. Nevertheless, the combined treatment with M1 and SMCs had little effect on normal and human primary cells. Because SMCs selectively and significantly enhance the bystander killing effect and the replication of oncolytic virus M1 specifically in cancer cells, this combined treatment may represent a promising therapeutic strategy.\",\n \"corpus_id\": 13914978,\n \"score\": 2\n },\n {\n \"doc_id\": \"28750564\",\n \"title\": \"Selective antagonism of Bcl-xL potentiates M1 oncolysis by enhancing mitochondrial apoptosis.\",\n \"abstract\": \"Oncolytic virotherapy is a novel and intriguing treatment strategy for cancer therapy. However, the clinical potential of oncolytic virus as single agent is limited. M1 virus is a promising oncolytic virus that has been tested in preclinical studies. In this study, we investigated the effect of the combination use of M1 virus and Bcl-2 family inhibitors. A chemical compounds screening including ten Bcl-2 family inhibitors demonstrated that pan-Bcl-2 inhibitors selectively augmented M1 virus oncolysis in cancer cells at very low doses. The mechanism of the enhanced antitumor effect of pan-Bcl-2 inhibitors with M1 virus is mainly due to the inhibition of Bcl-xL, which synergizes with M1-induced up-regulation of Bak to trigger apoptosis. In xenograft mouse models and patient-derived tumor tissues, combination of M1 and pan-Bcl-2 inhibitors significantly inhibited tumor growth and prolonged survival, suggesting the potential therapeutic value of this strategy. These findings offer insights into the synergy between Bcl-xL inhibition and oncolytic virus M1 as a combination anti-cancer treatment modality.\",\n \"corpus_id\": 4774013,\n \"score\": 2\n },\n {\n \"doc_id\": \"28835517\",\n \"title\": \"Targeting VCP enhances anticancer activity of oncolytic virus M1 in hepatocellular carcinoma.\",\n \"abstract\": \"Oncolytic virotherapy is rapidly progressing through clinical evaluation. However, the therapeutic efficacy of oncolytic viruses in humans has been less than expected from preclinical studies. We describe an anticancer drug screen for compounds that enhance M1 oncolytic virus activity in hepatocellular carcinoma (HCC). An inhibitor of the valosin-containing protein (VCP) was identified as the top sensitizer, selectively increasing potency of the oncolytic virus up to 3600-fold. Further investigation revealed that VCP inhibitors cooperated with M1 virus-suppressed inositol-requiring enzyme 1α (IRE1α)-X-box binding protein 1 (XBP1) pathway and triggered irresolvable endoplasmic reticulum (ER) stress, subsequently promoting robust apoptosis in HCC. We show that VCP inhibitor improved the oncolytic efficacy of M1 virus in several mouse models of HCC and primary HCC tissues. Finally, this combinatorial therapeutic strategy was well tolerated in nonhuman primates. Our study identifies combined VCP inhibition and oncolytic virus as a potential treatment for HCC and demonstrates promising therapeutic potential.\",\n \"corpus_id\": 28236078,\n \"score\": 2\n },\n {\n \"doc_id\": \"29263275\",\n \"title\": \"Deficiency of the IRE1α-Autophagy Axis Enhances the Antitumor Effects of the Oncolytic Virus M1.\",\n \"abstract\": \"Oncolytic virotherapy is an emerging treatment modality that uses replication-competent viruses to destroy cancer cells. M1 is a naturally occurring alphavirus (Togaviridae) which shows potent oncolytic activities against many cancers. Accumulation of unfolded proteins during virus replication leads to a transcriptional/translational response known as the unfolded protein response (UPR), which might counteract the antitumor effect of the oncolytic virus. In this report, we show that either pharmacological or biological inhibition of IRE1α or PERK, but not ATF6, substantially increases the oncolytic effects of the M1 virus. Moreover, inhibition of IRE1α blocks M1 virus-induced autophagy, which restricts the antitumor effects of the M1 virus through degradation of viral protein, in glioma cells. In addition, IRE1α suppression significantly increases the oncolytic effect of M1 virus in an orthotopic glioma model. From a molecular pathology study, we found that IRE1α is expressed at lower levels in higher-grade gliomas, suggesting greater antitumor efficacy of the oncolytic virus M1. Taken together, these findings illustrate a defensive mechanism of glioma cells against the oncolytic virus M1 and identify possible approaches to enhance the oncolytic viral protein accumulation and the subsequent lysis of tumor cells. IMPORTANCE Although oncolytic virotherapy is showing great promise in clinical applications, not all patients are benefiting. Identifying inhibitory signals in refractory cancer cells for each oncolytic virus would provide a good chance to increase the therapeutic effect. Here we describe that infection with the oncolytic virus M1 triggers the unfolded protein response (UPR) and subsequent autophagy, while blocking the UPR-autophagy axis significantly potentiates the antitumor efficacy of M1 in vitro and in vivo A survey of cancer tissue banks revealed that IRE1α, a key element in the UPR pathway, is commonly downregulated in higher-grade human gliomas, suggesting favorable prospects for the application of M1. Our work provides a potential predictor and target for enhancement of the therapeutic effectiveness of the M1 virus. We predict that the mechanism-based combination therapy will promote cancer virotherapy in the future.\",\n \"corpus_id\": 4770393,\n \"score\": 2\n },\n {\n \"doc_id\": \"29449555\",\n \"title\": \"Intravenous injections of the oncolytic virus M1 as a novel therapy for muscle-invasive bladder cancer.\",\n \"abstract\": \"Muscle-invasive bladder cancer (MIBC) is associated with low survival and high recurrence rates even in cases in which patients receive systemic treatments, such as surgery and chemotherapy. Here, we found that a naturally existing alphavirus, namely, M1, selectively kills bladder cancer cells but not normal cells, findings supported by our observations of changes in viral replication and MIBC and patient-derived MIBC cell apoptosis. Transcriptome analysis revealed that interferon-stimulated genes (ISGs) are expressed at low levels in sensitive bladder cancer cells and high levels in resistant cells. Knocking down ZC3HAV1 (ZAP), an antiviral factor in ISGs, restores M1 virus reactivity in resistant cells, and overexpressing ZAP partially reverses M1 virus-induced decreases in cell viability in sensitive cells. In orthotopic MIBC mice, tail vein injections of M1 significant inhibit tumor growth and prolong survival period, antitumor effects of M1 are stronger than those of the first-line chemotherapy agent cisplatin (CDDP). Treated tumors display enhanced cleaved-caspase-3 signals, which are representative of cell apoptosis, and decreased Ki-67 signals, which are representative of cell proliferation. Moreover, tissue microarray (TMA) analyses of clinical tumor specimens revealed that up to 45.6% of cases of MIBC presented with low ZAP expression, a finding that is prevalent in advanced MIBC. Our results indicate that the oncolytic virus M1 is a novel agent capable of functioning as a precise and effective therapy for MIBC.\",\n \"corpus_id\": 3319018,\n \"score\": 2\n },\n {\n \"doc_id\": \"18239605\",\n \"title\": \"Oncolytic adenovirus-mediated shRNA against Apollon inhibits tumor cell growth and enhances antitumor effect of 5-fluorouracil.\",\n \"abstract\": \"Apollon, a membrane-associated inhibitor of apoptosis protein, protects cells against apoptosis and is upregulated in certain tumor cells. In this study, the effects of Apollon protein knockdown by RNA interference on the growth of human HeLa, HT-1080 and MCF-7 cells in vitro and in vivo were investigated. An oncolytic adenovirus (ZD55) containing the RNA polymerase III-dependent U6 promoter to express short hairpin RNA (shRNA) directed against Apollon (ZD55-siApollon) was constructed. Our data show that ZD55-siApollon successfully exerts a gene knockdown effect and causes the inhibition of tumor cell growth both in culture and in athymic mice in vivo. Cell cycle analysis, 4',6-diamidino-2-phenylindole staining and western blot analysis reveal that ZD55-siApollon-mediated suppression of Apollon induces apoptosis. Intratumoral injection of ZD55-siApollon significantly inhibits tumor growth in HT-1080 xenograft mice. Furthermore, ZD55-siApollon enhances the antitumor effect of 5-fluorouracil, a chemotherapeutic agent. In conclusion, these results suggest that the depletion of Apollon by oncolytic adenovirus-shRNA delivery system provides a promising method for cancer therapy.\",\n \"corpus_id\": 40196237,\n \"score\": 1\n },\n {\n \"doc_id\": \"18846115\",\n \"title\": \"Enhanced oncolytic potency of vesicular stomatitis virus through vector-mediated inhibition of NK and NKT cells.\",\n \"abstract\": \"Recombinant oncolytic viruses represent a promising alternative option for the treatment of malignant cancers. We have reported earlier the safety and efficacy of recombinant vesicular stomatitis virus (VSV) vectors in a rat model of hepatocellular carcinoma (HCC). However, the full potential of VSV therapy is limited by a sudden decline in intratumoral virus replication observed early after viral administration, a phenomenon that coincides with an accumulation of inflammatory cells within infected lesions. To overcome the antiviral function of these cells, we present a recombinant virus, rVSV-UL141, which expresses a protein from human cytomegalovirus known to downregulate the natural killer (NK) cell-activating ligand CD155. The modified vector resulted in an inhibition of NK cell recruitment in vitro, as well as decreased intratumoral accumulations of NK and NKT cells in vivo. Administration of rVSV-UL141 through hepatic artery infusion in immune-competent Buffalo rats harboring orthotopic, multi-focal HCC lesions resulted in a one-log elevation of intratumoral virus replication over a control rVSV vector, which translated to enhance tumor necrosis and substantial prolongation of survival. Moreover, these results were achieved in the absence of apparent toxicities. The present study suggests the applicability of this strategy for the development of effective and safe oncolytic agents to treat multi-focal HCC, and potentially a multitude of other cancers, in the future.\",\n \"corpus_id\": 22382666,\n \"score\": 1\n },\n {\n \"doc_id\": \"19508172\",\n \"title\": \"Targeting the mevalonate pathway for improved anticancer therapy.\",\n \"abstract\": \"The mevalonate pathway is important for the generation of isoprene moieties thereby providing the basis for the biosynthesis of molecules required for maintaining membrane integrity, steroid production and cell respiration. Additionally, isoprene precursors are indispensable for the prenylation of regulatory proteins such as Ras and Ras-homologous (Rho) GTPases. These low molecular GTP-binding proteins play key roles in numerous signal transduction pathways stimulated upon activation of cell surface receptors by ligand binding. Thus, Ras/Rho proteins eventually regulate cell proliferation, tumor progression and cell death induced by anticancer therapeutics. Lipid modification of Ras/Rho proteins at their C-terminal CAAX-box is essential for their correct intracellular localization and function. Therefore, pharmacological inhibition of the isoprene metabolism is anticipated to impact the manifold biological functions attributed to Ras/Rho proteins. Here, the pros and cons of compounds that interfere with the mevalonate pathway for cancer treatment are summarized and discussed.\",\n \"corpus_id\": 10396680,\n \"score\": 1\n },\n {\n \"doc_id\": \"20338582\",\n \"title\": \"Lovastatin inhibits thrombospondin-1-induced smooth muscle cell chemotaxis.\",\n \"abstract\": \"BACKGROUND: Thrombospondin-1 (TSP-1) induces vascular smooth muscle cell (VSMC) migration and is important in the development of intimal hyperplasia. HMG-CoA reductase inhibitors, such as lovastatin, reduce the incidence of vascular restenosis after angioplasty by both cholesterol lowering and pleiotropic effects. Inhibition of the mevalonate pathway is largely responsible for these pleiotropic properties. This inhibition prevents isoprenylation of the small G proteins, Rho and Ras, by geranylgeranyl and farnesyl pyrophosphate, respectively. Isoprenylation is required for Ras and Rho activation, which is relevant for cell migration. HYPOTHESIS: Lovastatin inhibits TSP-1-induced VSMC chemotaxis by inhibiting small G proteins via the mevalonate pathway. METHODS: Chemotaxis was assessed using a modified Boyden chamber. Quiescent VSMCs were pretreated with serum free media (SFM), lovastatin with or without mevalonate farnesyl (FTI), geranylgeranyl transferase inhibitors (GGTI), farnesyl transferase inhibitor (FPT), or the Rho kinase inhibitor (Y-27632). Chemoattractants were SFM or TSP-1. Comparisons were made by ANOVA followed by post-hoc testing (P<0.05). The effect of lovastatin on Ras activation was evaluated using cells pretreated with SFM or lovastatin, with or without mevalonate prior to TSP-1 exposure. Western blot for Ras activation was performed. RESULTS: Lovastatin dose-dependently inhibited TSP-1-induced chemotaxis, which was reversed by mevalonate. Mevalonate did not induce chemotaxis independently. FTI and FPT, but not GGTI or Y-27632, inhibited TSP-1-induced Ras activation and TSP-1-induced chemotaxis. Lovastatin inhibition of Ras activation was reversed with mevalonate. CONCLUSION: Ras, not Rho, is relevant for TSP-1-induced VSMC chemotaxis. These data suggest that lovastatin suppresses TSP-1-induced chemotaxis by inhibition of Ras.\",\n \"corpus_id\": 32246639,\n \"score\": 1\n },\n {\n \"doc_id\": \"20519142\",\n \"title\": \"Pamidronate inhibits antiapoptotic bcl-2 expression through inhibition of the mevalonate pathway in prostate cancer PC-3 cells.\",\n \"abstract\": \"Bisphosphonates are expected to be efficacious to prevent the growth of metastatic cancer in bone tissue. Bone metastases often occur in patients with various cancers, such as breast, lung and prostate cancer. Bcl-2 is a potent antiapoptotic protein and its expression is known to be closely related to its function. In this study, to investigate the effect of bisphosphonates on cancer cells, we focused on bcl-2 expression in bisphosphonate-treated prostate cancer cells. First, we observed that bcl-2 mRNA expression in PC-3 was significantly inhibited to 12% of the control level by treatment with 100 microM pamidronate for 12h. Inhibition was seen in cells treated with nitrogen-containing bisphosphonates, which have the ability to inhibit isoprenoid biosynthesis via the mevalonate pathway, but not in non-nitrogen-containing etidronate. Simultaneous treatment with geranylgeraniol, an intermediate of the mevalonate pathway, significantly blocked inhibition by pamidronate, and treatment with geranylgeranyl transferase inhibitor GGTI-286 also suppressed bcl-2 mRNA expression. Furthermore, pamidronate inhibited the translocation of Rap1 protein to the membrane fraction, suggesting that a change in posttranslational modification of Rap1 occurred in treated cells. Finally, knockdown of Rap1 by siRNA resulted in the inhibition of bcl-2 expression. These results strongly indicate that bcl-2 reduction in bisphosphonate-treated PC-3 cells is dependent on inhibition of the mevalonate pathway. The inhibitory effect of bisphosphonates on bcl-2 expression shown in prostate cancer cell line should be tested in animal experiments and clinical studies.\",\n \"corpus_id\": 12693267,\n \"score\": 1\n },\n {\n \"doc_id\": \"20647775\",\n \"title\": \"Endogenous expression of proteases in colon cancer cells facilitate influenza A viruses mediated oncolysis.\",\n \"abstract\": \"Previously we have developed a prototype for conditionally replicating oncolytic influenza A virus which is based on deletions in the non-structural (NS1) protein. Multi-cycle replication of influenza A virus in malignant tissue is critically dependent on a protease which cleaves the viral entry protein. Here we demonstrate that the malignant colon cancer cell lines Caco-2, HT-29 and SW-620 can endogenously provide a virus-activating protease, which allows lytic multi-cycle replication of NS1 deletion viruses in those cancer cells in vitro. The oncolytic potency of an influenza NS1 deletion virus (NS1-80) was further tested in SCID mice bearing HT-29 derived tumors. The intra-tumoral injection of live, but not of heat inactivated NS1-80 virus significantly inhibited progression of established tumors. We conclude that a selected set of human cancer expressing virus activating- proteases will be a preferred target for oncolytic tumor therapy using influenza A virus mutants.\",\n \"corpus_id\": 1517720,\n \"score\": 1\n },\n {\n \"doc_id\": \"21276246\",\n \"title\": \"Oncolytic targeting of androgen-sensitive prostate tumor by the respiratory syncytial virus (RSV): consequences of deficient interferon-dependent antiviral defense.\",\n \"abstract\": \"BACKGROUND: Oncolytic virotherapy for cancer treatment utilizes viruses for selective infection and death of cancer cells without any adverse effect on normal cells. We previously reported that the human respiratory syncytial virus (RSV) is a novel oncolytic virus against androgen-independent PC-3 human prostate cancer cells. The present study extends the result to androgen-dependent prostate cancer, and explores the underlying mechanism that triggers RSV-induced oncolysis of prostate cancer cells. METHODS: The oncolytic effect of RSV on androgen-sensitive LNCaP human prostate cancer cells and on androgen-independent RM1 murine prostate cancer cells was studied in vitro in culture and in vivo in a xenograft or allograft tumor model. In vitro, cell viability, infectivity and apoptosis were monitored by MTT assay, viral plaque assay and annexin V staining, respectively. In vivo studies involved virus administration to prostate tumors grown in immune compromised nude mice and in syngeneic immune competent C57BL/6J mice. Anti-tumorogenic oncolytic activity was monitored by measuring tumor volume, imaging bioluminescent tumors in live animals and performing histopathological analysis and TUNEL assay with tumors RESULTS: We show that RSV imposes a potent oncolytic effect on LNCaP prostate cancer cells. RSV infectivity was markedly higher in LNCaP cells compared to the non-tumorigenic RWPE-1 human prostate cells. The enhanced viral burden led to LNCaP cell apoptosis and growth inhibition of LNCaP xenograft tumors in nude mice. A functional host immune response did not interfere with RSV-induced oncolysis, since growth of xenograft tumors in syngeneic C57BL/6J mice from murine RM1 cells was inhibited upon RSV administration. LNCaP cells failed to activate the type-I interferon (IFNα/β)-induced transcription factor STAT-1, which is required for antiviral gene expression, although these cells could produce IFN in response to RSV infection. The essential role of IFN in restricting infection was further borne out by our finding that neutralizing IFN activity resulted in enhanced RSV infection in non-tumorigenic RWPE-1 prostate cells. CONCLUSIONS: We demonstrated that RSV is potentially a useful therapeutic tool in the treatment of androgen-sensitive and androgen-independent prostate cancer. Moreover, impaired IFN-mediated antiviral response is the likely cause of higher viral burden and resulting oncolysis of androgen-sensitive prostate cancer cells.\",\n \"corpus_id\": 8188053,\n \"score\": 1\n },\n {\n \"doc_id\": \"21283510\",\n \"title\": \"Enhancement of vaccinia virus based oncolysis with histone deacetylase inhibitors.\",\n \"abstract\": \"Histone deacetylase inhibitors (HDI) dampen cellular innate immune response by decreasing interferon production and have been shown to increase the growth of vesicular stomatitis virus and HSV. As attenuated tumour-selective oncolytic vaccinia viruses (VV) are already undergoing clinical evaluation, the goal of this study is to determine whether HDI can also enhance the potency of these poxviruses in infection-resistant cancer cell lines. Multiple HDIs were tested and Trichostatin A (TSA) was found to potently enhance the spread and replication of a tumour selective vaccinia virus in several infection-resistant cancer cell lines. TSA significantly decreased the number of lung metastases in a syngeneic B16F10LacZ lung metastasis model yet did not increase the replication of vaccinia in normal tissues. The combination of TSA and VV increased survival of mice harbouring human HCT116 colon tumour xenografts as compared to mice treated with either agent alone. We conclude that TSA can selectively and effectively enhance the replication and spread of oncolytic vaccinia virus in cancer cells.\",\n \"corpus_id\": 5911989,\n \"score\": 1\n },\n {\n \"doc_id\": \"21324313\",\n \"title\": \"Inhibition of geranylgeranylation mediates sensitivity to CHOP-induced cell death of DLBCL cell lines.\",\n \"abstract\": \"Prenylation is a post-translational hydrophobic modification of proteins, important for their membrane localization and biological function. The use of inhibitors of prenylation has proven to be a useful tool in the activation of apoptotic pathways in tumor cell lines. Rab geranylgeranyl transferase (Rab GGT) is responsible for the prenylation of the Rab family. Overexpression of Rab GGTbeta has been identified in CHOP refractory diffuse large B cell lymphoma (DLBCL). Using a cell line-based model for CHOP resistant DLBCL, we show that treatment with simvastatin, which inhibits protein farnesylation and geranylgeranylation, sensitizes DLBCL cells to cytotoxic treatment. Treatment with the farnesyl transferase inhibitor FTI-277 or the geranylgeranyl transferase I inhibitor GGTI-298 indicates that the reduction in cell viability was restricted to inhibition of geranylgeranylation. In addition, treatment with BMS1, a combined inhibitor of farnesyl transferase and Rab GGT, resulted in a high cytostatic effect in WSU-NHL cells, demonstrated by reduced cell viability and decreased proliferation. Co-treatment of BMS1 or GGTI-298 with CHOP showed synergistic effects with regard to markers of apoptosis. We propose that inhibition of protein geranylgeranylation together with conventional cytostatic therapy is a potential novel strategy for treating patients with CHOP refractory DLBCL.\",\n \"corpus_id\": 7417278,\n \"score\": 1\n },\n {\n \"doc_id\": \"21608020\",\n \"title\": \"Arctigenin enhances chemosensitivity of cancer cells to cisplatin through inhibition of the STAT3 signaling pathway.\",\n \"abstract\": \"Arctigenin is a dibenzylbutyrolactone lignan isolated from Bardanae fructus, Arctium lappa L, Saussureamedusa, Torreya nucifera, and Ipomea cairica. It has been reported to exhibit anti-inflammatory activities, which is mainly mediated through its inhibitory effect on nuclear transcription factor-kappaB (NF-κB). But the role of arctigenin in JAK-STAT3 signaling pathways is still unclear. In present study, we investigated the effect of arctigenin on signal transducer and activator of transcription 3 (STAT3) pathway and evaluated whether suppression of STAT3 activity by arctigenin could sensitize cancer cells to a chemotherapeutic drug cisplatin. Our results show that arctigenin significantly suppressed both constitutively activated and IL-6-induced STAT3 phosphorylation and subsequent nuclear translocation in cancer cells. Inhibition of STAT3 tyrosine phosphorylation was found to be achieved through suppression of Src, JAK1, and JAK2, while suppression of STAT3 serine phosphorylation was mediated by inhibition of ERK activation. Pervanadate reversed the arctigenin-induced downregulation of STAT3 activation, suggesting the involvement of a protein tyrosine phosphatase. Indeed, arctigenin can obviously induce the expression of the PTP SHP-2. Furthermore, the constitutive activation level of STAT3 was found to be correlated to the resistance of cancer cells to cisplatin-induced apoptosis. Arctigenin dramatically promoted cisplatin-induced cell death in cancer cells, indicating that arctigenin enhanced the sensitivity of cancer cells to cisplatin mainly via STAT3 suppression. These observations suggest a novel anticancer function of arctigenin and a potential therapeutic strategy of using arctigenin in combination with chemotherapeutic agents for cancer treatment.\",\n \"corpus_id\": 32983855,\n \"score\": 1\n },\n {\n \"doc_id\": \"22076990\",\n \"title\": \"Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway.\",\n \"abstract\": \"OBJECTIVES: Hepatitis C virus (HCV) infection causes chronic liver disease and is a major public health problem worldwide. The aim of this study was to evaluate the potential of Monascus pigment derivatives, which were derived from a microbial secondary metabolite synthesized from polyketides by Monascus spp., as HCV antiviral agents. METHODS: We performed an in vitro RNA-dependent RNA polymerase (RdRp) assay to screen for HCV RdRp inhibitors. The anti-HCV activity of RdRp inhibitors in HCV-replicating cells was evaluated by quantification of the RNA viral genome. Molecular docking analysis was performed to predict the binding sites of the selected RdRp inhibitors. RESULTS: We have identified a Monascus pigment and its derivatives as inhibitors of the HCV NS5B RdRp. A group of Monascus orange pigment (MOP) amino acid derivatives, in which the reactive oxygen moiety was changed to amino acids, significantly inhibited HCV replication. Further, combination of the MOP derivatives (Phe, Val or Leu conjugates) with interferon (IFN)-α inhibited HCV replication more than IFN-α treatment alone. Lastly, molecular docking studies indicate the inhibitors may bind to a thumb subdomain allosteric site of NS5B. The antiviral activity of the MOP derivatives was related to a modulation of the mevalonate pathway, since the mevalonate-induced increase in HCV replication was suppressed by the MOP compounds. CONCLUSIONS: Our results identify amino acid derivatives of MOP as potential anti-HCV agents and suggest that their combination with IFN-α might offer an alternative strategy for the control of HCV replication.\",\n \"corpus_id\": 11559087,\n \"score\": 1\n },\n {\n \"doc_id\": \"22322451\",\n \"title\": \"Involvement of the mevalonate pathway in the antiproliferative effect of zoledronate on ACHN renal cell carcinoma cells.\",\n \"abstract\": \"Renal cell carcinoma (RCC) has been shown to be resistant to chemotherapy and radiotherapy. In order to examine the potential of zoledronate (ZOL), a bisphosphonate, as an anticancer agent, we investigated the effects of ZOL on RCC cells and the involvement of the mevalonate pathway in antiproliferative effects, as well as the effects of ZOL administration on mice inoculated with RCC. ACHN cells were used and cell viability was measured via intra-cellular reductase activity. Chromatin condensation was detected by Hoechst 33342 staining. Proteins were detected by western blot analysis. Tumor volume was measured bidimensionally in mice inoculated with ACHN cells after vehicle or ZOL subcutaneous administration. ZOL exhibited antiproliferative effects with an IC50 value of 2.29±0.53 µM in ACHN cells and chromatin condensation was observed when treated with ZOL. Farnesol (FOH) and geranylgeraniol (GGOH), precursors of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, exhibited potency to rescue cells treated with ZOL. Additionally, Ras and RhoA proteins located in the membrane fraction decreased when treated with ZOL and recovered by FOH or GGOH treatment, suggesting that ZOL inhibited the mevalonate pathway, thereby suppressing the translocation of prenylated Ras and RhoA proteins to membrane fractions. An in vivo study showed the inhibitory potential of ZOL on tumor growth in mice without changes in body weight. Our study showed that ZOL could be useful as an anticancer agent for the treatment of RCC, and the mevalonate pathway could be an efficient target for novel therapeutic agents against RCC.\",\n \"corpus_id\": 39894469,\n \"score\": 1\n },\n {\n \"doc_id\": \"22414636\",\n \"title\": \"In vivo evaluation of a cancer therapy strategy combining HSV1716-mediated oncolysis with gene transfer and targeted radiotherapy.\",\n \"abstract\": \"UNLABELLED: Oncolytic herpes viruses show promise for cancer treatment. However, it is unlikely that they will fulfill their therapeutic potential when used as monotherapies. An alternative strategy is to use these viruses not only as oncolytic agents but also as a delivery mechanism of therapeutic transgenes to enhance tumor cell killing. The herpes simplex virus 1 deletion mutant HSV1716 is a conditionally replicating oncolytic virus that selectively replicates in and lyses dividing tumor cells. It has a proven safety profile in clinical trials and has demonstrated efficacy as a gene-delivery vehicle. To enhance its therapeutic potential, we have engineered HSV1716 to convey the noradrenaline transporter (NAT) gene (HSV1716/NAT), whose expression endows infected cells with the capacity to accumulate the noradrenaline analog metaiodobenzylguanidine (MIBG). Thus, the NAT gene-infected cells are susceptible to targeted radiotherapy using radiolabeled (131)I-MIBG, a strategy that has already shown promise for combined targeted radiotherapy-gene therapy in cancer cells after plasmid-mediated transfection. METHODS: We used HSV1716/NAT as a dual cell lysis-gene delivery vehicle for targeting the NAT transgene to human tumor xenografts in vivo. RESULTS: In tumor xenografts that did not express NAT, intratumoral or intravenous injection of HSV1716/NAT induced the capacity for active uptake of (131)I-MIBG. Administration of HSV1716/NAT and (131)I-MIBG resulted in decreased tumor growth and enhanced survival relative to injection of either agent alone. Efficacy was dependent on the scheduling of delivery of the 2 agents. CONCLUSION: These findings support a role for combination radiotherapy-gene therapy for cancer using HSV1716 expressing the NAT transgene and targeted radionuclide therapy.\",\n \"corpus_id\": 20517209,\n \"score\": 1\n },\n {\n \"doc_id\": \"22605458\",\n \"title\": \"Mevalonate metabolism regulates Basal breast cancer stem cells and is a potential therapeutic target.\",\n \"abstract\": \"There is increasing evidence that breast tumors are organized in a hierarchy, with a subpopulation of tumorigenic cancer cells, the cancer stem cells (CSCs), which sustain tumor growth. The characterization of protein networks that govern CSC behavior is paramount to design new therapeutic strategies targeting this subpopulation of cells. We have sought to identify specific molecular pathways of CSCs isolated from 13 different breast cancer cell lines of luminal or basal/mesenchymal subtypes. We compared the gene expression profiling of cancer cells grown in adherent conditions to those of matched tumorsphere cultures. No specific pathway was identified to be commonly regulated in luminal tumorspheres, resulting from a minor CSC enrichment in tumorsphere passages from luminal cell lines. However, in basal/mesenchymal tumorspheres, the enzymes of the mevalonate metabolic pathway were overexpressed compared to those in cognate adherent cells. Inhibition of this pathway with hydroxy-3-methylglutaryl CoA reductase blockers resulted in a reduction of breast CSC independent of inhibition of cholesterol biosynthesis and of protein farnesylation. Further modulation of this metabolic pathway demonstrated that protein geranylgeranylation (GG) is critical to breast CSC maintenance. A small molecule inhibitor of the geranylgeranyl transferase I (GGTI) enzyme reduced the breast CSC subpopulation both in vitro and in primary breast cancer xenografts. We found that the GGTI effect on the CSC subpopulation is mediated by inactivation of Ras homolog family member A (RHOA) and increased accumulation of P27(kip1) in the nucleus. The identification of protein GG as a major contributor to CSC maintenance opens promising perspectives for CSC targeted therapy in basal breast cancer.\",\n \"corpus_id\": 5930968,\n \"score\": 1\n },\n {\n \"doc_id\": \"22729516\",\n \"title\": \"An armed oncolytic herpes simplex virus expressing thrombospondin-1 has an enhanced in vivo antitumor effect against human gastric cancer.\",\n \"abstract\": \"Advanced gastric cancer is a common disease, but the conventional treatments are unsatisfactory because of the high recurrence rate. One of the promising new therapies is oncolytic virotherapy, using oncolytic herpes simplex viruses (HSVs). Thrombospondin-1 (TSP-1) suppresses tumor progression via multiple mechanisms including antiangiogenesis. Our approach to enhance the effects of oncolytic HSVs is to generate an armed oncolytic HSV that combines the direct viral oncolysis with TSP-1-mediated function for gastric cancer treatment. Using the bacterial artificial chromosome (BAC) system, a 3rd generation oncolytic HSV (T-TSP-1) expressing human TSP-1 was constructed for human gastric cancer treatment. The enhanced efficacy of T-TSP-1 was determined in both human gastric cancer cell lines in vitro and subcutaneous tumor xenografts of human gastric cancer cells in vivo. In addition, we examined the apoptotic effect of T-TSP-1 in vitro, and the antiangiogenic effect of T-TSP-1 in vivo compared with a non-armed 3rd generation oncolytic HSV, T-01. No apparent apoptotic induction by T-TSP-1 was observed for human gastric cancer cell lines TMK-1 cells but for MKN1 cells in vitro. Arming the viruses with TSP-1 slightly inhibited their replication in some gastric cancer cell lines, but the viral cytotoxicity was not attenuated. In addition, T-TSP-1 exhibited enhanced therapeutic efficacy and inhibition of angiogenesis compared with T-01 in vivo. In this study, we established a novel armed oncolytic HSV, T-TSP-1, which enhanced the antitumor efficacy by providing a combination of direct viral oncolysis with antiangiogenesis. Arming oncolytic HSVs may be a useful therapeutic strategy for gastric cancer therapy.\",\n \"corpus_id\": 26315198,\n \"score\": 1\n },\n {\n \"doc_id\": \"22920673\",\n \"title\": \"Reovirus exerts potent oncolytic effects in head and neck cancer cell lines that are independent of signalling in the EGFR pathway.\",\n \"abstract\": \"BACKGROUND: Reovirus exploits aberrant signalling downstream of Ras to mediate tumor-specific oncolysis. Since ~90% squamous cell carcinomas of the head and neck (SCCHN) over-express EGFR and SCCHN cell lines are sensitive to oncolytic reovirus, we conducted a detailed analysis of the effects of reovirus in 15 head and neck cancer cell lines. Both pre- and post-entry events were studied in an attempt to define biomarkers predictive of sensitivity/resistance to reovirus. In particular, we analysed the role of EGFR/Ras signalling in determining virus-mediated cytotoxicity in SCCHN. METHODS: To test whether EGFR pathway activity was predictive of increased sensitivity to reovirus, correlative analyses between reoviral IC50 by MTT assay and EGFR levels by western blot and FACS were conducted. Inhibition or stimulation of EGFR signalling were analysed for their effect on reoviral oncolysis by MTT assay, and viral growth by TCID50 assay. We next analysed the effects of inhibiting signalling downstream of Ras, by specific inhibitors of p38MAPK, PI3-K or MEK, on reoviral killing examined by MTT assay. The role of PKR in reoviral killing was also determined by blockade of PKR using 2-aminopurine and assaying for cell survival by MTT assay. The apoptotic response of SCCHN to reovirus was examined by western blot analysis of caspase 3 cleavage. RESULTS: Correlative analyses between reoviral sensitivity and EGFR levels revealed no association. Intermediate sub-viral and core particles showed the same infectivity/cytotoxicity as intact reovirus. Therefore, sensitivity was not determined by cell entry. In 4 cell lines, oncolysis and viral growth were both unaffected by inhibition or stimulation of EGFR signalling. Inhibition of signalling downstream of Ras did not abrogate reoviral oncolysis and, in addition, modulation of PKR using 2-aminopurine did not alter reovirus sensitivity in resistant cell lines. Caspase 3 cleavage was not detected in infected cells and oncolysis was observed in pan-caspase inhibited cells. CONCLUSIONS: In summary, reovirus is potently oncolytic in a broad panel of SCCHN cell lines. Attempts to define sensitivity/resistance by analysis of the EGFR/Ras/MAPK pathway have failed to provide a clear predictive biomarker of response. Further analysis of material from in vitro and clinical studies is ongoing in an attempt to shed further light on this issue.\",\n \"corpus_id\": 15141840,\n \"score\": 1\n },\n {\n \"doc_id\": \"23447049\",\n \"title\": \"Growth inhibition effect of peptide P110 plus cisplatin on various cancer cells and xenotransplanted tumors in mice.\",\n \"abstract\": \"The combined use of currently used anticancer genotoxins with other drugs is a therapeutic tool for potentially increasing the efficacy of the genotoxins. In the present study, the effects of a RasGAP-derived peptide, P110 (RasGAP301-316), designed to target Ras-GTPase activating protein SH3 domain-binding proteins (G3BPs), on the chemotherapeutic agent, cisplatin (DDP), were examined. P110 was demonstrated to enhance the effect of DPP in vitro and in vivo. The results indicate that P110 significantly increased the DDP-induced apoptosis in SGC-7901, HCT-116, HeLa and A-549 cells. Furthermore, P110 combined with DDP significantly suppressed the growth of C26 xenograft tumors in a dose-dependent manner. This synergistic effect may be associated with DDP-induced apoptosis, involving the downregulation of Bcl-2 and the upregulation of Bax, cytochrome c and caspase-3. The results of the present study indicate that P110, in combination with chemotherapeutics, is likely to represent a potential therapeutic strategy for cancer.\",\n \"corpus_id\": 27885309,\n \"score\": 1\n },\n {\n \"doc_id\": \"23524243\",\n \"title\": \"Regulation of mevalonate metabolism in cancer and immune cells.\",\n \"abstract\": \"The mevalonate pathway is a highly conserved metabolic cascade and provides isoprenoid building blocks for the biosynthesis of vital cellular products such as cholesterol or prenyl pyrophosphates that serve as substrates for the posttranslational prenylation of numerous proteins. The pathway, which is frequently hyperactive in cancer cells, is considered an important target in cancer therapy, since prenylated members of the Ras superfamily are crucially involved in the control of proliferation, survival, invasion and metastasis of tumour cells. Upstream accumulation and downstream depletion of mevalonate pathway intermediates as induced for instance by aminobisphosphonates translate into different effects in cancer and immune cells. Thus, mevalonate pathway regulation can affect tumour biology either directly or exhibit indirect antitumour effects through stimulating cancer immune surveillance. The present review summarizes major effects of pharmacologic mevalonate pathway regulation in cancer and immune cells that may collaboratively contribute to the efficacy of cancer therapy.\",\n \"corpus_id\": 21782823,\n \"score\": 1\n },\n {\n \"doc_id\": \"23985699\",\n \"title\": \"Triptolide-mediated inhibition of interferon signaling enhances vesicular stomatitis virus-based oncolysis.\",\n \"abstract\": \"Preclinical and clinical trials demonstrated that use of oncolytic viruses (OVs) is a promising new therapeutic approach to treat multiple types of cancer. To further improve their viral oncolysis, experimental strategies are now combining OVs with different cytotoxic compounds. In this study, we investigated the capacity of triptolide - a natural anticancer molecule - to enhance vesicular stomatitis virus (VSV) oncolysis in OV-resistant cancer cells. Triptolide treatment increased VSV replication in the human prostate cancer cell line PC3 and in other VSV-resistant cells in a dose- and time-dependent manner in vitro and in vivo. Mechanistically, triptolide (TPL) inhibited the innate antiviral response by blocking type I interferon (IFN) signaling, downstream of IRF3 activation. Furthermore, triptolide-enhanced VSV-induced apoptosis in a dose-dependent fashion in VSV-resistant cells, as measured by annexin-V, cleaved caspase-3, and B-cell lymphoma 2 staining. In vivo, using the TSA mammary adenocarcinoma and PC3 mouse xenograft models, combination treatment with VSV and triptolide delayed tumor growth and prolonged survival of tumor-bearing animals by enhancing viral replication. Together, these results demonstrate that triptolide inhibition of IFN production sensitizes prostate cancer cells to VSV replication and virus-mediated apoptosis.\",\n \"corpus_id\": 385028,\n \"score\": 1\n },\n {\n \"doc_id\": \"24258243\",\n \"title\": \"Both the mevalonate and the non-mevalonate pathways are involved in ginsenoside biosynthesis.\",\n \"abstract\": \"KEY MESSAGE: When one of them was inhibited, the two pathways could compensate with each other to guarantee normal growth. Moreover, the sterol biosynthesis inhibitor miconazole could enhance ginsenoside level. ABSTRACT: Ginsenosides, a kind of triterpenoid saponins derived from isopentenyl pyrophosphate (IPP), represent the main pharmacologically active constituents of ginseng. In plants, two pathways contribute to IPP biosynthesis, namely, the mevalonate pathway in cytosol and the non-mevalonate pathway in plastids. This motivates biologists to clarify the roles of the two pathways in biosynthesis of IPP-derived compounds. Here, we demonstrated that both pathways are involved in ginsenoside biosynthesis, based on the analysis of the effects from suppressing either or both of the pathways on ginsenoside accumulation in Panax ginseng hairy roots with mevinolin and fosmidomycin as specific inhibitors for the mevalonate and the non-mevalonate pathways, respectively. Furthermore, the sterol biosynthesis inhibitor miconazole could enhance ginsenoside levels in the hairy roots. These results shed some light on the way toward better understanding of ginsenoside biosynthesis.\",\n \"corpus_id\": 17896989,\n \"score\": 1\n },\n {\n \"doc_id\": \"24327936\",\n \"title\": \"Inhibition of the mevalonate pathway to override chemoresistance and promote the immunogenic demise of cancer cells: Killing two birds with one stone.\",\n \"abstract\": \"The mevalonate pathway is an attractive target for cancer therapy not only to override multidrug resistance but also to promote the immunogenic demise of malignant cells. Recent data indicate that aminobisphosphonates are superior to statins for the pharmacological manipulation of the mevalonate pathway, since they exert therapeutically relevant effects on both cancer cells and the immune system.\",\n \"corpus_id\": 35382663,\n \"score\": 1\n },\n {\n \"doc_id\": \"24371063\",\n \"title\": \"Histone deacetylase inhibitors potentiate vesicular stomatitis virus oncolysis in prostate cancer cells by modulating NF-κB-dependent autophagy.\",\n \"abstract\": \"Vesicular stomatitis virus (VSV) is an oncolytic virus that induces cancer cell death through activation of the apoptotic pathway. Intrinsic resistance to oncolysis is found in some cell lines and many primary tumors as a consequence of residual innate immunity to VSV. In resistant-tumor models, VSV oncolytic potential can be reversibly stimulated by combination with epigenetic modulators, such as the histone deacetylase inhibitor vorinostat. Based on this reversible effect of vorinostat, we reasoned that critical host genes involved in oncolysis may likewise be reversibly regulated by vorinostat. A transcriptome analysis in prostate cancer PC3 cells identified a subset of NF-κB target genes reversibly regulated by vorinostat, as well as a group of interferon (IFN)-stimulated genes (ISGs). Consistent with the induction of NF-κB target genes, vorinostat-mediated enhancement of VSV oncolysis increased hyperacetylation of NF-κB RELA/p65. Additional bioinformatics analysis revealed that NF-κB signaling also increased the expression of several autophagy-related genes. Kinetically, autophagy preceded apoptosis, and apoptosis was observed only when cells were treated with both VSV and vorinostat. VSV replication and cell killing were suppressed when NF-κB signaling was inhibited using pharmacological or genetic approaches. Inhibition of autophagy by 3-methyladenine (3-MA) enhanced expression of ISGs, and either 3-MA treatment or genetic ablation of the autophagic marker Atg5 decreased VSV replication and oncolysis. Together, these data demonstrate that vorinostat stimulates NF-κB activity in a reversible manner via modulation of RELA/p65 signaling, leading to induction of autophagy, suppression of the IFN-mediated response, and subsequent enhancement of VSV replication and apoptosis.\",\n \"corpus_id\": 206816741,\n \"score\": 1\n },\n {\n \"doc_id\": \"24574393\",\n \"title\": \"Mitophagy enhances oncolytic measles virus replication by mitigating DDX58/RIG-I-like receptor signaling.\",\n \"abstract\": \"UNLABELLED: The success of future clinical trials with oncolytic viruses depends on the identification and the control of mechanisms that modulate their therapeutic efficacy. In particular, little is known about the role of autophagy in infection by attenuated measles virus of the Edmonston strain (MV-Edm). We investigated the interaction between autophagy, innate immune response, and oncolytic activity of MV-Edm, since the antiviral immune response is a known factor limiting virotherapies. We report that MV-Edm exploits selective autophagy to mitigate the innate immune response mediated by DDX58/RIG-I like receptors (RLRs) in non-small cell lung cancer (NSCLC) cells. Both RNA interference (RNAi) and overexpression approaches demonstrate that autophagy enhances viral replication and inhibits the production of type I interferons regulated by RLRs. We show that MV-Edm unexpectedly triggers SQSTM1/p62-mediated mitophagy, resulting in decreased mitochondrion-tethered mitochondrial antiviral signaling protein (MAVS) and subsequently weakening the innate immune response. These results unveil a novel infectious strategy based on the usurpation of mitophagy leading to mitigation of the innate immune response. This finding provides a rationale to modulate autophagy in oncolytic virotherapy. IMPORTANCE: In vitro studies, preclinical experiments in vivo, and clinical trials with humans all indicate that oncolytic viruses hold promise for cancer therapy. Measles virus of the Edmonston strain (MV-Edm), which is an attenuated virus derived from the common wild-type measles virus, is paradigmatic for therapeutic oncolytic viruses. MV-Edm replicates preferentially in and kills cancer cells. The efficiency of MV-Edm is limited by the immune response of the host against viruses. In our study, we revealed that MV-Edm usurps a homeostatic mechanism of intracellular degradation of mitochondria, coined mitophagy, to attenuate the innate immune response in cancer cells. This strategy might provide a replicative advantage for the virus against the development of antiviral immune responses by the host. These findings are important since they may not only indicate that inducers of autophagy could enhance the efficacy of oncolytic therapies but also provide clues for antiviral therapy by targeting SQSTM1/p62-mediated mitophagy.\",\n \"corpus_id\": 206817600,\n \"score\": 1\n },\n {\n \"doc_id\": \"24696490\",\n \"title\": \"Permissiveness of human cancer cells to oncolytic bovine herpesvirus 1 is mediated in part by KRAS activity.\",\n \"abstract\": \"UNLABELLED: Oncolytic viruses (OVs) are attractive avenues of cancer therapy due to the absence of toxic side effects often seen with current treatment modalities. Bovine herpesvirus 1 (BHV-1) is a species-specific virus that does not induce cytotoxicity in normal primary human cells but can infect and kill various human immortalized and transformed cell lines. To gain a better understanding of the oncolytic breadth of BHV-1, the NCI panel of established human tumor cell lines was screened for sensitivity to the virus. Overall, 72% of the panel is permissive to BHV-1 infection, with corresponding decreases in cellular viability. This sensitivity is in comparison to a sensitivity of only 32% for a herpes simplex virus 1 (HSV-1)-based oncolytic vector. Strikingly, while 35% of the panel supports minimal or no BHV-1 replication, significant decreases in cellular viability still occur. These data suggest that BHV-1 is an OV with tropism for multiple tumor types and is able to induce cytotoxicity independent of significant virus replication. In contrast to other species-specific OVs, cellular sensitivity to BHV-1 does not correlate with type I interferon (IFN) signaling; however, mutations in KRAS were found to correlate with high levels of virus replication. The knockdown or overexpression of KRAS in human tumor cell lines yields modest changes in viral titers; however, overexpression of KRAS in normal primary cells elicits permissivity to BHV-1 infection. Together, these data suggest that BHV-1 is a broad-spectrum OV with a distinct mechanism of tumor targeting. IMPORTANCE: Cancer remains a significant health issue, and novel treatments are required, particularly for tumors that are refractory to conventional therapies. Oncolytic viruses are a novel platform given their ability to specifically target tumor cells while leaving healthy cells intact. For this strategy to be successful, a fundamental understanding of virus-host interactions is required. We previously identified bovine herpesvirus 1 as a novel oncolytic virus with many unique and clinically relevant features. Here, we show that BHV-1 can target a wide range of human cancer types, most potently lung cancer. In addition, we show that enhanced KRAS activity, a hallmark of many cancers, is one of the factors that increases BHV-1 oncolytic capacity. These findings hold potential for future treatments, particularly in the context of lung cancer, where KRAS mutations are a negative predictor of treatment efficacy.\",\n \"corpus_id\": 25765959,\n \"score\": 1\n },\n {\n \"doc_id\": \"24928535\",\n \"title\": \"The inhibition of constitutive androstane receptor-mediated pathway enhances the effects of anticancer agents in ovarian cancer cells.\",\n \"abstract\": \"BACKGROUND: Ovarian cancer is commonly treated with anticancer agents; however, many tumors become resistant. Resistance is regulated, in part, by P-glycoprotein, which is encoded by the gene multiple drug resistance 1 (MDR1) and functions as a transmembrane efflux pump for the elimination of anticancer agents. Constitutive androstane receptor (CAR) is a nuclear receptor that regulates drug metabolism through control of MDR1 and other genes. PURPOSE: We examined whether the inhibition of CAR-mediated pathway could influence the cytotoxicity of three anticancer drugs, cisplatin, paclitaxel, and arsenic trioxide, in ovarian cancer cells. RESULTS: We observed that the cell proliferation of several ovarian cell lines expressing CAR significantly increased when CITCO was combined with anticancer agents compared with any anticancer agent alone. The up-regulation of MDR1 and UGT1A1 by anticancer agents was further enhanced in the presence of CITCO. We confirmed that combining CITCO with anticancer agents induced significantly lower levels of apoptosis than those achieved with any single anticancer drug. CAR down-regulation by RNA interference caused a significant increase in cell growth inhibition and enhancement of apoptosis in the presence of anticancer agents. Combination of CITCO with any anticancer agents significantly enhanced CAR-mediated transcription compared with any anticancer agents alone and CAR down-regulation completely inhibited the transcription in the presence of CITCO and/or anticancer agents. CONCLUSION: Inhibition of CAR pathway could be a novel therapeutic approach for the augmentation of sensitivity to anticancer agents, or to overcome resistance, in the treatment of ovarian cancer.\",\n \"corpus_id\": 205968815,\n \"score\": 1\n },\n {\n \"doc_id\": \"25078870\",\n \"title\": \"Pharmacological modulation of autophagy enhances Newcastle disease virus-mediated oncolysis in drug-resistant lung cancer cells.\",\n \"abstract\": \"BACKGROUND: Oncolytic viruses represent a promising therapy against cancers with acquired drug resistance. However, low efficacy limits its clinical application. The objective of this study is to investigate whether pharmacologically modulating autophagy could enhance oncolytic Newcastle disease virus (NDV) strain NDV/FMW virotherapy of drug-resistant lung cancer cells. METHODS: The effect of NDV/FMW infection on autophagy machinery in A549 lung cancer cell lines resistant to cisplatin (A549/DDP) or paclitaxel (A549/PTX) was investigated by detection of GFP-microtubule-associated protein 1 light chain 3 (GFP-LC3) puncta, formation of double-membrane vesicles and conversion of the nonlipidated form of LC3 (LC3-I) to the phosphatidylethanolamine-conjugated form (LC3-II). The effects of autophagy inhibitor chloroquine (CQ) and autophagy inducer rapamycin on NDV/FMW-mediated antitumor activity were evaluated both in culture cells and in mice bearing drug-resistant lung cancer cells. RESULTS: We show that NDV/FMW triggers autophagy in A549/PTX cells via dampening the class I PI3K/Akt/mTOR/p70S6K pathway, which inhibits autophagy. On the contrary, NDV/FMW infection attenuates the autophagic process in A549/DDP cells through the activation of the negative regulatory pathway. Furthermore, combination with CQ or knockdown of ATG5 significantly enhances NDV/FMW-mediated antitumor effects on A549/DDP cells, while the oncolytic efficacy of NDV/FMW in A549/PTX cells is significantly improved by rapamycin. Interestingly, autophagy modulation does not increase virus progeny in these drug resistant cells. Importantly, CQ or rapamycin significantly potentiates NDV/FMW oncolytic activity in mice bearing A549/DDP or A549/PTX cells respectively. CONCLUSIONS: These results demonstrate that combination treatment with autophagy modulators is an effective strategy to augment the therapeutic activity of NDV/FMW against drug-resistant lung cancers.\",\n \"corpus_id\": 7430046,\n \"score\": 1\n },\n {\n \"doc_id\": \"25347735\",\n \"title\": \"Oncogenic Ras inhibits IRF1 to promote viral oncolysis.\",\n \"abstract\": \"Oncolytic viruses exploit common molecular changes in cancer cells, which are not present in normal cells, to target and kill cancer cells. Ras transformation and defects in type I interferon (IFN)-mediated antiviral responses are known to be the major mechanisms underlying viral oncolysis. Previously, we demonstrated that oncogenic RAS/Mitogen-activated protein kinase kinase (Ras/MEK) activation suppresses the transcription of many IFN-inducible genes in human cancer cells, suggesting that Ras transformation underlies type I IFN defects in cancer cells. Here, we investigated how Ras/MEK downregulates IFN-induced transcription. By conducting promoter deletion analysis of IFN-inducible genes, namely guanylate-binding protein 2 and IFN gamma inducible protein 47 (Ifi47), we identified the IFN regulatory factor 1 (IRF1) binding site as the promoter region responsible for the regulation of transcription by MEK. MEK inhibition promoted transcription of the IFN-inducible genes in wild type mouse embryonic fibroblasts (MEFs), but not in IRF1(-/-) MEFs, showing that IRF1 is involved in MEK-mediated downregulation of IFN-inducible genes. Furthermore, IRF1 protein expression was lower in RasV12 cells compared with vector control NIH3T3 cells, but was restored to equivalent levels by inhibition of MEK. Similarly, the restoration of IRF1 expression by MEK inhibition was observed in human cancer cells. IRF1 re-expression in human cancer cells caused cells to become resistant to infection by the oncolytic vesicular stomatitis virus strain. Together, this work demonstrates that Ras/MEK activation in cancer cells downregulates transcription of IFN-inducible genes by targeting IRF1 expression, resulting in increased susceptibility to viral oncolysis.\",\n \"corpus_id\": 25459095,\n \"score\": 1\n },\n {\n \"doc_id\": \"25575816\",\n \"title\": \"Dichloroacetate blocks aerobic glycolytic adaptation to attenuated measles virus and promotes viral replication leading to enhanced oncolysis in glioblastoma.\",\n \"abstract\": \"Targeting reprogrammed energy metabolism such as aerobic glycolysis is a potential strategy for cancer treatment. However, tumors exhibiting low-rate glycolysis or metabolic heterogeneity might be resistant to such treatment. We hypothesized that a therapeutic modality that drove cancer cells to high-rate glycolysis might sensitize cancer cells to interference directed against metabolic flux. In this study, we found that attenuated oncolytic measles virus Edmonston strain (MV-Edm) caused glioblastoma cells to shift to high-rate aerobic glycolysis; this adaptation was blocked by dichloroacetate (DCA), an inhibitor of glycolysis, leading to profound cell death of cancer cells but not of normal cells. DCA enhanced viral replication by mitigating mitochondrial antiviral signaling protein (MAVS)-mediated innate immune responses. In a subcutaneous glioblastoma (GBM) xenograft mouse model, low-dose MV-Edm and DCA significantly inhibited tumor growth in vivo. We found that DCA impaired glycolysis (blocking bioenergetic generation) and enhanced viral replication (increasing bioenergetic consumption), which, in combination, accelerated bioenergetic exhaustion leading to necrotic cell death. Taken together, oncolytic MV-Edm sensitized cancer cells to DCA, and in parallel, DCA promoted viral replication, thus, improving oncolysis. This novel therapeutic approach should be readily incorporated into clinical trials.\",\n \"corpus_id\": 18633229,\n \"score\": 1\n },\n {\n \"doc_id\": \"25978957\",\n \"title\": \"Inhibition of the mevalonate pathway affects epigenetic regulation in cancer cells.\",\n \"abstract\": \"The mevalonate pathway provides metabolites for post-translational modifications such as farnesylation, which are critical for the activity of RAS downstream signaling. Subsequently occurring regulatory processes can induce an aberrant stimulation of DNA methyltransferase (DNMT1) as well as changes in histone deacetylases (HDACs) and microRNAs in many cancer cell lines. Inhibitors of the mevalonate pathway are increasingly recognized as anticancer drugs. Extensive evidence indicates an intense cross-talk between signaling pathways, which affect growth, differentiation, and apoptosis either directly or indirectly via epigenetic mechanisms. Herein, we show data obtained by novel transcriptomic and corresponding methylomic or proteomic analyses from cell lines treated with pharmacologic doses of respective inhibitors (i.e., simvastatin, ibandronate). Metabolic pathways and their epigenetic consequences appear to be affected by a changed concentration of NADPH. Moreover, since the mevalonate metabolism is part of a signaling network, including vitamin D metabolism or fatty acid synthesis, the epigenetic activity of associated pathways is also presented. This emphasizes the far-reaching epigenetic impact of metabolic therapies on cancer cells and provides some explanation for clinical observations, which indicate the anticancer activity of statins and bisphosphonates.\",\n \"corpus_id\": 29701210,\n \"score\": 1\n },\n {\n \"doc_id\": \"25995245\",\n \"title\": \"Interferon Beta and Interferon Alpha 2a Differentially Protect Head and Neck Cancer Cells from Vesicular Stomatitis Virus-Induced Oncolysis.\",\n \"abstract\": \"UNLABELLED: Oncolytic viruses (OV) preferentially kill cancer cells due in part to defects in their antiviral responses upon exposure to type I interferons (IFNs). However, IFN responsiveness of some tumor cells confers resistance to OV treatment. The human type I IFNs include one IFN-β and multiple IFN-α subtypes that share the same receptor but are capable of differentially inducing biological responses. The role of individual IFN subtypes in promoting tumor cell resistance to OV is addressed here. Two human IFNs which have been produced for clinical use, IFN-α2a and IFN-β, were compared for activity in protecting human head and neck squamous cell carcinoma (HNSCC) lines from oncolysis by vesicular stomatitis virus (VSV). Susceptibility of HNSCC lines to killing by VSV varied. VSV infection induced increased production of IFN-β in resistant HNSCC cells. When added exogenously, IFN-β was significantly more effective at protecting HNSCC cells from VSV oncolysis than was IFN-α2a. In contrast, normal keratinocytes and endothelial cells were protected equivalently by both IFN subtypes. Differential responsiveness of tumor cells to IFN-α and -β was further supported by the finding that autocrine IFN-β but not IFN-α promoted survival of HNSCC cells during persistent VSV infection. Therefore, IFN-α and -β differentially affect VSV oncolysis, justifying the evaluation and comparison of IFN subtypes for use in combination with VSV therapy. Pairing VSV with IFN-α2a may enhance selectivity of oncolytic VSV therapy for HNSCC by inhibiting VSV replication in normal cells without a corresponding inhibition in cancer cells. IMPORTANCE: There has been a great deal of progress in the development of oncolytic viruses. However, a major problem is that individual cancers vary in their sensitivity to oncolytic viruses. In many cases this is due to differences in their production and response to interferons (IFNs). The experiments described here compared the responses of head and neck squamous cell carcinoma cell lines to two IFN subtypes, IFN-α2a and IFN-β, in protection from oncolytic vesicular stomatitis virus. We found that IFN-α2a was significantly less protective for cancer cells than was IFN-β, whereas normal cells were equivalently protected by both IFNs. These results suggest that from a therapeutic standpoint, selectivity for cancer versus normal cells may be enhanced by pairing VSV with IFN-α2a.\",\n \"corpus_id\": 7057361,\n \"score\": 1\n },\n {\n \"doc_id\": \"26257065\",\n \"title\": \"Genome-wide lentiviral shRNA screen identifies serine/arginine-rich splicing factor 2 as a determinant of oncolytic virus activity in breast cancer cells.\",\n \"abstract\": \"Oncolytic human herpes simplex virus type 1 (HSV-1) shows promising treatment efficacy in late-stage clinical trials. The anticancer activity of oncolytic viruses relies on deregulated pathways in cancer cells, which make them permissive to oncolysis. To identify pathways that restrict HSV-1 KM100-mediated oncolysis, this study used a pooled genome-wide short hairpin RNA library and found that depletion of the splicing factor arginine-rich splicing factor 2 (SRSF2) leads to enhanced cytotoxicity of breast cancer cells by KM100. Serine/arginine-rich (SR) proteins are a family of RNA-binding phosphoproteins that control both constitutive and alternative pre-mRNA splicing. Further characterization showed that KM100 infection of HS578T cells under conditions of low SRSF2 leads to pronounced apoptosis without a corresponding increase in virus replication. As DNA topoisomerase I inhibitors can limit the phosphorylation of SRSF2, we combined a topoisomerase I inhibitor chemotherapeutic with KM100 and observed synergistic anticancer effect in vitro and prolonged survival of tumor-bearing mice in vivo. Oncogene advance online publication, 10 August 2015; doi:10.1038/onc.2015.303.\",\n \"corpus_id\": 34609483,\n \"score\": 1\n },\n {\n \"doc_id\": \"26278331\",\n \"title\": \"The Role of Neutrophils in Measles Virus-mediated Oncolysis Differs Between B-cell Malignancies and Is Not Always Enhanced by GCSF.\",\n \"abstract\": \"The mechanism by which oncolytic measles virus (MV) kills cancer cells remains obscure. We previously showed that neutrophils are involved in MV-mediated tumor regressions and become activated, upon MV infection. In the present study, we attempted to enhance the neutrophil response toward MV-infected tumor targets by generating an oncolytic MV-expressing human granulocyte colony-stimulating factor (MVhGCSF). Evaluating the effects in two different models of B-cell malignancy, we showed that depletion of neutrophils abrogated the MV therapeutic effect in an in vivo Raji-but not Nalm-6 tumor model. Next, we compared MVhGCSF with the unmodified backbone virus MVNSe. MVhGCSF enhanced the oncolytic capacity of MV in the Raji model in vivo, whereas in the Nalm-6 model, the opposite was unexpectedly the case. This finding was recapitulated by exogenously administered hGCSF. MVhGCSF replicated within an MV-infectable CD46 transgenic mouse model with detectable serum levels of hGCSF but no toxicity. Our data suggest that a \\\"one-size-fits-all\\\" model of immune response to viral oncolysis is not appropriate, and each tumor target will need full characterization for the potential of both direct and indirect, innate immune responses to generate benefit. Molecular Therapy (2015); doi:10.1038/mt.2015.149.\",\n \"corpus_id\": 25655712,\n \"score\": 1\n },\n {\n \"doc_id\": \"26358205\",\n \"title\": \"Statin-mediated inhibition of cholesterol synthesis induces cytoprotective autophagy in human leukemic cells.\",\n \"abstract\": \"Statins exhibit anti-leukemic properties due to suppression of the mevalonate pathway by the inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase, and subsequent depletion of cholesterol, farnesylpyrophosphate, and geranylgeranylpyrophosphate. We investigated the role of autophagy, a controlled intracellular self-digestion, in the anti-leukemic action of statins. Treatment with low concentrations (≤6 µM) of statins, cholesterol depletion, and specific inhibition of cholesterol synthesis and protein farnesylation or geranylgeranylation, all inhibited proliferation of leukemic cell lines and primary leukemic cells without inducing overt cell death. Statins and agents that selectively reduce intracellular cholesterol levels, but not the inhibition of protein farnesylation or geranylgeranylation, induced autophagy in leukemic cells. The observed autophagic response was associated with the reduction of phosphorylated Akt levels in the lipid rafts, accompanied by a decrease in the activation of the main autophagy suppressor mammalian target of rapamycin (mTOR) and its substrate ribosomal p70S6 kinase (p70S6K). No significant autophagy induction and downregulation of mTOR/p70S6K activation were observed in normal leukocytes. Autophagy suppression by bafilomycin A1 or RNA interference-mediated knockdown of beclin-1 and microtubule-associated protein 1 light chain 3B induced apoptotic death in statin-treated leukemic cells, an effect attenuated by the addition of mevalonate or squalene, but not farnesylpyrophosphate or geranylgeranylpyrophosphate. Therefore, while the inhibition of cholesterol synthesis, protein farnesylation, and geranylgeranylation all contributed to anti-leukemic effects of statins, the inhibition of cholesterol synthesis was solely responsible for the induction of cytoprotective autophagy. These data indicate that combined treatment with statins and autophagy inhibitors might be potentially useful in anti-leukemic therapy.\",\n \"corpus_id\": 32452346,\n \"score\": 1\n },\n {\n \"doc_id\": \"26758953\",\n \"title\": \"Mevalonate Pathway and Human Cancers.\",\n \"abstract\": \"Mevalonate (MVA) is synthesized from 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) by HMG-CoA reductase (HMG-CoAR). MVA is further metabolized to farnesyl pyrophosphate (FPP), a precursor of cholesterol and sterols. FPP is also converted to geranylgeranyl pyrophosphate, and these lipids are used for post-translational modification of proteins that are involved in various aspects of tumor development and progression. Many studies showed that the MVA pathway is up-regulated in several cancers such as leukemia, lymphoma, multiple myeloma; as well as breast, hepatic, pancreatic, esophageal and prostate cancers. Several mechanisms may be involved in dysregulation of this pathway. They include p53 mutation, a mutation in HMG-CoAR and sterol-regulatory element binding protein (SREBP) cleavage-activating protein SCAP as its regulator, PKB/Akt activation, decreased AMPK activation, and activation of transcription factors such as: SREBP and HIF-1. Statins as inhibitors of MVA pathway might be useful for cancer prevention and/or treatment through their interactions with essential cellular functions, such as cell proliferation and differentiation. Other inhibitors are also designed for inhibition of this key pathway and their mechanism of action was investigated. In the present review, we will first describe about some inhibitors of MVA, including statins that have been suggested for cancer treatment. We will then discuss about the mechanisms involved in MVA dysregulation, especially in cancer.\",\n \"corpus_id\": 26035255,\n \"score\": 1\n },\n {\n \"doc_id\": \"26909280\",\n \"title\": \"Regulation of VEGF by mevalonate pathway inhibition in breast cancer.\",\n \"abstract\": \"Aminobisphosphonates are used for the treatment of benign and malignant bone disorders. As inhibitors of the mevalonate pathway they exert direct anti-tumor effects in vitro and in preclinical models of bone metastases. Bisphosphonates are thought to have an anti-angiogenic activity as decreased levels of VEGF have been reported in some, although not all patients, following treatment with bisphosphonates. Direct effects of bisphosphonates on tumor derived VEGF have not been examined in detail. We therefore investigated VEGF expression in breast cancer cell lines following mevalonate pathway inhibition. Treatment of cell lines with increasing doses of zoledronic acid and atorvastatin resulted in increased levels of VEGF production. Similar results were seen with the geranylgeranyltransferase I inhibitor GGTI-298. The induction of VEGF was reversed by the supplementation of geranylgeranyl pyrophosphate but not by farnesyl pyrophosphate indicating that this effect is mediated by inhibited geranylgeranylation. Previous reports have reported decreased VEGF levels in patients following BP treatment in vivo. We assessed VEGF levels in patients with non-metastatic breast cancer following repeated treatment with zoledronic acid. In contrast to our in vitro findings, VEGF serum levels decreased in all patients after 6-9 months of treatment (by an average of 41%) as assessed in a small pilot trial. These results indicate that tissues other than breast tumors contribute to the serum pool of circulating VEGF and may be responsible for the observed VEGF decreases. The increases of VEGF in the cancer cells may provide a rationale for the combined treatment with VEGF inhibitors.\",\n \"corpus_id\": 3157661,\n \"score\": 1\n },\n {\n \"doc_id\": \"26976483\",\n \"title\": \"A mathematical model verifying potent oncolytic efficacy of M1 virus.\",\n \"abstract\": \"Motivated by the latest findings in a recent medical experiment [19] which identify a naturally occurring alphavirus (M1) as a novel selective killer targeting zinc-finger antiviral protein (ZAP)-deficient cancer cells, we propose a mathematical model to illustrate the growth of normal cells, tumor cells and the M1 virus with limited nutrient. In order to better understand biological mechanisms, we discuss two cases of the model: without competition and with competition. In the first part, the explicit threshold conditions for the persistence of normal cells (or tumor cells) is obtained accompanying with the biological explanations. The second part indicates that when competing with tumor cells, the normal cells will extinct if M1 virus is ignored; Whereas, when M1 virus is considered, the growth trend of normal cells is similar to the one without competition. And by using uniformly strong repeller theorem, the minimum effective dosage of medication is explicitly found which is not reported in [19]. Furthermore, numerical simulations and corresponding biological interpretations are given to support our results.\",\n \"corpus_id\": 13089023,\n \"score\": 1\n },\n {\n \"doc_id\": \"27019795\",\n \"title\": \"Clinical development of reovirus for cancer therapy: An oncolytic virus with immune-mediated antitumor activity.\",\n \"abstract\": \"Reovirus is a double-stranded RNA virus with demonstrated oncolysis or preferential replication in cancer cells. The oncolytic properties of reovirus appear to be dependent, in part, on activated Ras signaling. In addition, Ras-transformation promotes reovirus oncolysis by affecting several steps of the viral life cycle. Reovirus-mediated immune responses can present barriers to tumor targeting, serve protective functions against reovirus systemic toxicity, and contribute to therapeutic efficacy through antitumor immune-mediated effects via innate and adaptive responses. Preclinical studies have demonstrated the broad anticancer activity of wild-type, unmodified type 3 Dearing strain reovirus (Reolysin(®)) across a spectrum of malignancies. The development of reovirus as an anticancer agent and available clinical data reported from 22 clinical trials will be reviewed.\",\n \"corpus_id\": 26763495,\n \"score\": 1\n },\n {\n \"doc_id\": \"27155373\",\n \"title\": \"Could drugs inhibiting the mevalonate pathway also target cancer stem cells?\",\n \"abstract\": \"Understanding the connection between metabolic pathways and cancer is very important for the development of new therapeutic approaches based on regulatory enzymes in pathways associated with tumorigenesis. The mevalonate cascade and its rate-liming enzyme HMG CoA-reductase has recently drawn the attention of cancer researchers because strong evidences arising mostly from epidemiologic studies, show that it could promote transformation. Hence, these studies pinpoint HMG CoA-reductase as a candidate proto-oncogene. Several recent epidemiological studies, in different populations, have proven that statins are beneficial for the treatment-outcome of various cancers, and may improve common cancer therapy strategies involving alkylating agents, and antimetabolites. Cancer stem cells/cancer initiating cells (CSC) are key to cancer progression and metastasis. Therefore, in the current review we address the different effects of statins on cancer stem cells. The mevalonate cascade is among the most pleiotropic, and highly interconnected signaling pathways. Through G-protein-coupled receptors (GRCP), it integrates extra-, and intracellular signals. The mevalonate pathway is implicated in cell stemness, cell proliferation, and organ size regulation through the Hippo pathway (e.g. Yap/Taz signaling axis). This pathway is a prime preventive target through the administration of statins for the prophylaxis of obesity-related cardiovascular diseases. Its prominent role in regulation of cell growth and stemness also invokes its role in cancer development and progression. The mevalonate pathway affects cancer metastasis in several ways by: (i) affecting epithelial-to-mesenchymal transition (EMT), (ii) affecting remodeling of the cytoskeleton as well as cell motility, (iii) affecting cell polarity (non-canonical Wnt/planar pathway), and (iv) modulation of mesenchymal-to-epithelial transition (MET). Herein we provide an overview of the mevalonate signaling network. We then briefly highlight diverse functions of various elements of this mevalonate pathway. We further discuss in detail the role of elements of the mevalonate cascade in stemness, carcinogenesis, cancer progression, metastasis and maintenance of cancer stem cells.\",\n \"corpus_id\": 46868209,\n \"score\": 1\n },\n {\n \"doc_id\": \"27384486\",\n \"title\": \"Enhanced cytotoxicity of reovirus and radiotherapy in melanoma cells is mediated through increased viral replication and mitochondrial apoptotic signalling.\",\n \"abstract\": \"Oncolytic viruses selectively target and replicate in cancer cells, providing us with a unique tool with which to target and kill tumour cells. These viruses come from a diverse range of viral families including reovirus type 3 Dearing (RT3D), a non-pathogenic human double-stranded RNA oncolytic virus, which has been shown to be an effective therapeutic agent, both as a mono-therapy and in combination with traditional chemotherapeutic drugs. This study investigated the interaction between RT3D and radiotherapy in melanoma cell lines with a BRAF mutant, Ras mutant or BRAF/Ras wild type genotype. The data indicates that RT3D combined with radiotherapy significantly increased cytotoxicity relative to either single agent, independent of genotype, both in vitro and in vivo. The mechanism of enhanced cytotoxicity was dependent on an increase in viral replication, mediated by CUG2 up-regulation and subsequent down-regulation of pPKR and p-eIF2α, leading to the activation of mitochondrial apoptotic signalling resulting in increased cell death.\",\n \"corpus_id\": 14979729,\n \"score\": 1\n },\n {\n \"doc_id\": \"27775703\",\n \"title\": \"DNAJA1 controls the fate of misfolded mutant p53 through the mevalonate pathway.\",\n \"abstract\": \"Stabilization of mutant p53 (mutp53) in tumours greatly contributes to malignant progression. However, little is known about the underlying mechanisms and therapeutic approaches to destabilize mutp53. Here, through high-throughput screening we identify statins, cholesterol-lowering drugs, as degradation inducers for conformational or misfolded p53 mutants with minimal effects on wild-type p53 (wtp53) and DNA contact mutants. Statins preferentially suppress mutp53-expressing cancer cell growth. Specific reduction of mevalonate-5-phosphate by statins or mevalonate kinase knockdown induces CHIP ubiquitin ligase-mediated nuclear export, ubiquitylation, and degradation of mutp53 by impairing interaction of mutp53 with DNAJA1, a Hsp40 family member. Knockdown of DNAJA1 also induces CHIP-mediated mutp53 degradation, while its overexpression antagonizes statin-induced mutp53 degradation. Our study reveals that DNAJA1 controls the fate of misfolded mutp53, provides insights into potential strategies to deplete mutp53 through the mevalonate pathway-DNAJA1 axis, and highlights the significance of p53 status in impacting statins' efficacy on cancer therapy.\",\n \"corpus_id\": 20080529,\n \"score\": 1\n },\n {\n \"doc_id\": \"28566376\",\n \"title\": \"Ruxolitinib and Polycation Combination Treatment Overcomes Multiple Mechanisms of Resistance of Pancreatic Cancer Cells to Oncolytic Vesicular Stomatitis Virus.\",\n \"abstract\": \"Vesicular stomatitis virus (VSV) is a promising oncolytic virus (OV). Although VSV is effective against a majority of pancreatic ductal adenocarcinoma cell (PDAC) cell lines, some PDAC cell lines are highly resistant to VSV, and the mechanisms of resistance are still unclear. JAK1/2 inhibitors (such as ruxolitinib and JAK inhibitor I) strongly stimulate VSV replication and oncolysis in all resistant cell lines but only partially improve the susceptibility of resistant PDACs to VSV. VSV tumor tropism is generally dependent on the permissiveness of malignant cells to viral replication rather than on receptor specificity, with several ubiquitously expressed cell surface molecules playing a role in VSV attachment to host cells. However, as VSV attachment to PDAC cells has never been tested before, here we examined if it was possibly inhibited in resistant PDAC cells. Our data show a dramatically weaker attachment of VSV to HPAF-II cells, the most resistant human PDAC cell line. Although sequence analysis of low-density lipoprotein (LDL) receptor (LDLR) mRNA did not reveal any amino acid substitutions in this cell line, HPAF-II cells displayed the lowest level of LDLR expression and dramatically lower LDL uptake. Treatment of cells with various statins strongly increased LDLR expression levels but did not improve VSV attachment or LDL uptake in HPAF-II cells. However, LDLR-independent attachment of VSV to HPAF-II cells was dramatically improved by treating cells with Polybrene or DEAE-dextran. Moreover, combining VSV with ruxolitinib and Polybrene or DEAE-dextran successfully broke the resistance of HPAF-II cells to VSV by simultaneously improving VSV attachment and replication. IMPORTANCE Oncolytic virus (OV) therapy is an anticancer approach that uses viruses that selectively infect and kill cancer cells. This study focuses on oncolytic vesicular stomatitis virus (VSV) against pancreatic ductal adenocarcinoma (PDAC) cells. Although VSV is effective against most PDAC cells, some are highly resistant to VSV, and the mechanisms are still unclear. Here we examined if VSV attachment to cells was inhibited in resistant PDAC cells. Our data show very inefficient attachment of VSV to the most resistant human PDAC cell line, HPAF-II. However, VSV attachment to HPAF-II cells was dramatically improved by treating cells with polycations. Moreover, combining VSV with polycations and ruxolitinib (which inhibits antiviral signaling) successfully broke the resistance of HPAF-II cells to VSV by simultaneously improving VSV attachment and replication. We envision that this novel triple-combination approach could be used in the future to treat PDAC tumors that are highly resistant to OV therapy.\",\n \"corpus_id\": 4534436,\n \"score\": 1\n },\n {\n \"doc_id\": \"28668359\",\n \"title\": \"The balance between induction and inhibition of mevalonate pathway regulates cancer suppression by statins: A review of molecular mechanisms.\",\n \"abstract\": \"Statins are widely used drugs for their role in decreasing cholesterol in hypercholesterolemic patients. Statins through inhibition of Hydroxy Methyl Glutaryl-CoA Reductase (HMGCR), the main enzyme of the cholesterol biosynthesis pathway, inhibit mevalonate pathway that provides isoprenoids for prenylation of different proteins such as Ras superfamily which has an essential role in cancer developing. Inhibition of the mevalonate/isoprenoid pathway is the cause of the cholesterol independent effects of statins or pleotropic effects. Depending on their penetrance into the extra-hepatic cells, statins have different effects on mevalonate/isoprenoid pathway. Lipophilic statins diffuse into all cells and hydrophilic ones use a variety of membrane transporters to gain access to cells other than hepatocytes. It has been suggested that the lower accessibility of statins for extra-hepatic tissues may result in the compensatory induction of mevalonate/isoprenoid pathway and so cancer developing. However, most of the population-based studies have demonstrated that statins have no effect on cancer developing, even decrease the risk of different types of cancer. In this review we focus on the cancer developing \\\"potentials\\\" and the anti-cancer \\\"activities\\\" of statins regarding the effects of statins on mevalonate/isoprenoid pathway in the liver and extra-hepatic tissues.\",\n \"corpus_id\": 2604039,\n \"score\": 1\n },\n {\n \"doc_id\": \"28808351\",\n \"title\": \"Inhibition of the mevalonate pathway augments the activity of pitavastatin against ovarian cancer cells.\",\n \"abstract\": \"Only 40% of patients with advanced ovarian cancer survive more than 5 years. We have previously shown that pitavastatin induces regression of ovarian cancer xenografts in mice. To evaluate whether the response of ovarian cancer cells to pitavastatin is potentiated by farnesyl diphosphate synthase inhibitors or geranylgeraniol transferase I inhibitors, we evaluated combinations of pitavastatin with zoledronic acid, risedronate and GGTI-2133 in a panel of ovarian cancer cells. Pitavastatin (IC50 = 0.6-14 μM), zoledronic acid (IC50 = 21-57 μM), risedronate (IC50 > 100 μM) or GGTI-2133 (IC50 > 25 μM) inhibited the growth of ovarian cancer cell cultures. Combinations of pitavastatin with zoledronic acid displayed additive or synergistic effects in cell growth assays in 10 of 11 cell lines evaluated as well as in trypan blue exclusion, cellular ATP or caspase 3/7, 8 and 9 assays. Pitavastatin reduced levels of GGT-IIβ and the membrane localization of several small GTPases and this was potentiated by zoledronic acid. siRNA to GGT-Iβ and GGT-IIβ used in combination, but not when used individually, significantly increased the sensitivity of cells to pitavastatin. These data suggest that zoledronic acid, a drug already in clinical use, may be usefully combined with pitavastatin in the treatment of ovarian cancer.\",\n \"corpus_id\": 205589699,\n \"score\": 1\n },\n {\n \"doc_id\": \"29069775\",\n \"title\": \"Drug repositioning of mevalonate pathway inhibitors as antitumor agents for ovarian cancer.\",\n \"abstract\": \"Drug repositioning is an alternative strategy redirecting existing drugs for new disease. We have previously reported an antitumor effect of statins, antidyslipidemic drugs, on ovarian cancer in vitro and in vivo. In this study, we investigated the antitumor effects of other mevalonate pathway inhibitors and the mechanism of the antitumor effect from a metabolic perspective. The effects of inhibitors of the mevalonate pathway on tumor cell growth were evaluated in vitro. Bisphosphonates that inhibit this pathway are commonly used as antiosteoporotic drugs, and antitumor effects of the bisphosphonate were examined in vitro and in vivo. Metabolites in SKOV3 ovarian cancer cells were analyzed before and after lovastatin treatment, using capillary electrophoresis-mass spectrometry. All mevalonate pathway inhibitors showed concentration-dependent inhibitory effects on tumor cell growth. Particularly marked effects were obtained with inhibitors of farnesyltransferase and geranylgeranyltransferase. The bisphosphonate was also shown to have an antitumor effect in vivo. The expression of autophagy marker LC3A/3B was increased in cells after treatment. In metabolomics analysis, lovastatin treatment increased the metabolites involved in the tricarboxylic acid cycle while reducing the metabolites associated with glycolysis. Also it decreased glutathione and resulted to work with chemotherapeutic agents synergistically. Inhibition at any point in the mevalonate pathway, and especially of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, suppresses growth of ovarian cancer cells. Inhibition of this pathway may induce autophagy, cause a shift to activation of the tricarboxylic acid cycle and enhance susceptibility to chemotherapy. Drug repositioning targeting mevalonate pathway for ovarian cancer deserves consideration for clinical application.\",\n \"corpus_id\": 8080021,\n \"score\": 1\n },\n {\n \"doc_id\": \"29238070\",\n \"title\": \"The interplay between mutant p53 and the mevalonate pathway.\",\n \"abstract\": \"Missense mutations in the TP53 gene lead to accumulation of dysfunctional TP53 proteins in tumors, showing oncogenic gain-of-function (GOF) activities. Stabilization of mutant TP53 (mutp53) is required for the GOF; however, the mechanisms by which mutp53 promotes cancer progression and how mutp53 stability is regulated are not completely understood. Recent work from our laboratory has identified statins, inhibitors of the mevalonate pathway, as degraders of conformational mutp53. Specific reduction of mevalonate-5-phosphate (MVP), a metabolic intermediate in the mevalonate pathway, by statins or mevalonate kinase (MVK) knockdown triggers CHIP ubiquitin ligase-mediated degradation of conformational mutp53 by inhibiting interaction between mutp53 and DNAJA1, a Hsp40 family member. Thus, the mevalonate pathway contributes to mutp53 stabilization. Given that mutp53 is shown to promote cancer progression by upregulating mRNA expression of mevalonate pathway enzymes by binding to the sterol regulatory element-binding protein 2 (SREBP2) and subsequently increasing activities of mevalonate pathway-associated oncogenic proteins (e.g., Ras, Rho, YAP/TAZ), there is a positive-feedback loop between mutp53 and the mevalonate pathway. Here, we summarize recent evidence linking the mevalonate pathway-mutp53 axis with cancer progression and further discuss the clinical relevance of this axis.\",\n \"corpus_id\": 3640094,\n \"score\": 1\n },\n {\n \"doc_id\": \"29252087\",\n \"title\": \"Temozolomide renders murine cancer cells susceptible to oncolytic adenovirus replication and oncolysis.\",\n \"abstract\": \"The preclinical evaluation of oncolytic adenoviruses (OAds) has been limited to cancer xenograft mouse models because OAds replicate poorly in murine cancer cells. The alkylating agent temozolomide (TMZ) has been shown to enhance oncolytic virotherapy in human cancer cells; therefore, we investigated whether TMZ could increase OAd replication and oncolysis in murine cancer cells. To test our hypothesis, three murine cancer cells were infected with OAd (E1b-deleted) alone or in combination with TMZ. TMZ increased OAd-mediated oncolysis in all three murine cancer cells tested. This increased oncolysis was, at least in part, due to productive virus replication, apoptosis, and autophagy induction. Most importantly, murine lung non-cancerous cells were not affected by OAd+TMZ. Moreover, TMZ increased Ad transduction efficiency. However, TMZ did not increase coxsackievirus and adenovirus receptor; therefore, other mechanism could be implicated on the transduction efficiency. These results showed, for the first time, that TMZ could render murine tumor cells more susceptible to oncolytic virotherapy. The proposed combination of OAds with TMZ presents an attractive approach towards the evaluation of OAd potency and safety in syngeneic mouse models using these murine cancer cell-lines in vivo.\",\n \"corpus_id\": 3809781,\n \"score\": 1\n },\n {\n \"doc_id\": \"18579592\",\n \"title\": \"Targeting the apoptotic pathway with BCL-2 inhibitors sensitizes primary chronic lymphocytic leukemia cells to vesicular stomatitis virus-induced oncolysis.\",\n \"abstract\": \"Chronic lymphocytic leukemia (CLL) is characterized by clonal accumulation of CD5(+) CD19(+) B lymphocytes that are arrested in the G(0)/G(1) phase of the cell cycle and fail to undergo apoptosis because of overexpression of the antiapoptotic B-cell CLL/lymphoma 2 (BCL-2) protein. Oncolytic viruses, such as vesicular stomatitis virus (VSV), have emerged as potential anticancer agents that selectively target and kill malignant cells via the intrinsic mitochondrial pathway. Although primary CLL cells are largely resistant to VSV oncolysis, we postulated that targeting the apoptotic pathway via inhibition of BCL-2 may sensitize CLL cells to VSV oncolysis. In the present study, we examined the capacity of EM20-25--a small-molecule antagonist of the BCL-2 protein--to overcome CLL resistance to VSV oncolysis. We demonstrate a synergistic effect of the two agents in primary ex vivo CLL cells (combination index of 0.5; P < 0.0001). In a direct comparison of peripheral blood mononuclear cells from healthy volunteers with primary CLL, the two agents combined showed a therapeutic index of 19-fold; furthermore, the combination of VSV and EM20-25 increased apoptotic cell death in Karpas-422 and Granta-519 B-lymphoma cell lines (P < 0.005) via the intrinsic mitochondrial pathway. Mechanistically, EM20-25 blocked the ability of the BCL-2 protein to dimerize with proapoptotic BAX protein, thus sensitizing CLL to VSV oncolytic stress. Together, these data indicate that the use of BCL-2 inhibitors may improve VSV oncolysis in treatment-resistant hematological malignancies, such as CLL, with characterized defects in the apoptotic response.\",\n \"corpus_id\": 22796262,\n \"score\": 0\n },\n {\n \"doc_id\": \"22204706\",\n \"title\": \"The mevalonate pathway in C. elegans.\",\n \"abstract\": \"The mevalonate pathway in human is responsible for the synthesis of cholesterol and other important biomolecules such as coenzyme Q, dolichols and isoprenoids. These molecules are required in the cell for functions ranging from signaling to membrane integrity, protein prenylation and glycosylation, and energy homeostasis. The pathway consists of a main trunk followed by sub-branches that synthesize the different biomolecules. The majority of our knowledge about the mevalonate pathway is currently focused on the cholesterol synthesis branch, which is the target of the cholesterol-lowering statins; less is known about the function and regulation of the non-cholesterol-related branches. To study them, we need a biological system where it is possible to specifically modulate these metabolic branches individually or in groups. The nematode Caenorhabditis elegans (C. elegans) is a promising model to study these non-cholesterol branches since its mevalonate pathway seems very well conserved with that in human except that it has no cholesterol synthesis branch. The simple genetic makeup and tractability of C. elegans makes it relatively easy to identify and manipulate key genetic components of the mevalonate pathway, and to evaluate the consequences of tampering with their activity. This general experimental approach should lead to new insights into the physiological roles of the non-cholesterol part of the mevalonate pathway. This review will focus on the current knowledge related to the mevalonate pathway in C. elegans and its possible applications as a model organism to study the non-cholesterol functions of this pathway.\",\n \"corpus_id\": 977178,\n \"score\": 0\n },\n {\n \"doc_id\": \"22361350\",\n \"title\": \"Propiconazole-enhanced hepatic cell proliferation is associated with dysregulation of the cholesterol biosynthesis pathway leading to activation of Erk1/2 through Ras farnesylation.\",\n \"abstract\": \"Propiconazole is a mouse hepatotumorigenic fungicide designed to inhibit CYP51, a key enzyme in the biosynthesis of ergosterol in fungi and is widely used in agriculture to prevent fungal growth. Metabolomic studies in mice revealed that propiconazole increased levels of hepatic cholesterol metabolites and bile acids, and transcriptomic studies revealed that genes within the cholesterol biosynthesis, cholesterol metabolism and bile acid biosyntheses pathways were up-regulated. Hepatic cell proliferation was also increased by propiconazole. AML12 immortalized hepatocytes were used to study propiconazole's effects on cell proliferation focusing on the dysregulation of cholesterol biosynthesis and resulting effects on Ras farnesylation and Erk1/2 activation as a primary pathway. Mevalonate, a key intermediate in the cholesterol biosynthesis pathway, increases cell proliferation in several cancer cell lines and tumors in vivo and serves as the precursor for isoprenoids (e.g. farnesyl pyrophosphate) which are crucial in the farnesylation of the Ras protein by farnesyl transferase. Farnesylation targets Ras to the cell membrane where it is involved in signal transduction, including the mitogen-activated protein kinase (MAPK) pathway. In our studies, mevalonic acid lactone (MVAL), a source of mevalonic acid, increased cell proliferation in AML12 cells which was reduced by farnesyl transferase inhibitors (L-744,832 or manumycin) or simvastatin, an HMG-CoA reductase inhibitor, indicating that this cell system responded to alterations in the cholesterol biosynthesis pathway. Cell proliferation in AML12 cells was increased by propiconazole which was reversed by co-incubation with L-744,832 or simvastatin. Increasing concentrations of exogenous cholesterol muted the proliferative effects of propiconazole and the inhibitory effects of L-733,832, results ascribed to reduced stimulation of the endogenous cholesterol biosynthesis pathway. Western blot analysis of subcellular fractions from control, MVAL or propiconazole-treated cells revealed increased Ras protein in the cytoplasmic fraction of L-744,832-treated cells, while propiconazole or MVAL reversed these effects. Western blot analysis indicated that phosphorylation of Erk1/2, a protein downstream of Ras, was increased by propiconazole. These data indicate that propiconazole increases cell proliferation by increasing the levels of cholesterol biosynthesis intermediates presumably through a negative feedback mechanism within the pathway, a result of CYP51 inhibition. This feedback mechanism increases Erk1/2 signaling through mevalonate-mediated Ras activation. These results provide an explanation for the observed effects of propiconazole on hepatic cholesterol pathways and on the increased hepatic cell proliferation induced by propiconazole in mice.\",\n \"corpus_id\": 38589320,\n \"score\": 0\n },\n {\n \"doc_id\": \"23586025\",\n \"title\": \"Viability reduction and Rac1 gene downregulation of heterogeneous ex-vivo glioma acute slice infected by the oncolytic Newcastle disease virus strain V4UPM.\",\n \"abstract\": \"Oncolytic viruses have been extensively evaluated for anticancer therapy because this virus preferentially infects cancer cells without interfering with normal cells. Newcastle Disease Virus (NDV) is an avian virus and one of the intensively studied oncolytic viruses affecting many types of cancer including glioma. Nevertheless, the capability of NDV infection on heterogeneous glioma tissue in a cerebrospinal fluid atmosphere has never been reported. Recently, Rac1 is reported to be required for efficient NDV replication in human cancer cells and established a link between tumourigenesis and sensitivity to NDV. Rac1 is a member of the Rho GTPases involved in the regulation of the cell migration and cell-cycle progression. Rac1 knockdown leads to significant inhibition of viral replication. In this work, we demonstrated that NDV treatment led to significant reduction of tumour tissue viability of freshly isolated heterogeneous human brain tumour slice, known as an ex vivo glioma acute slice (EGAS). Analysis of gene expression indicated that reduced tissue viability was associated with downregulation of Rac1. However, the viability reduction was not persistent. We conclude that NDV treatment induced EGAS viability suppression, but subsequent downregulation of Rac1 gene may reduce the NDV replication and lead to regrowth of EGAS tissue.\",\n \"corpus_id\": 16428961,\n \"score\": 0\n },\n {\n \"doc_id\": \"26758947\",\n \"title\": \"Interconnection of Estrogen/Testosterone Metabolism and Mevalonate Pathway in Breast and Prostate Cancers.\",\n \"abstract\": \"The metabolic steroid hormones, 17β stradiol (E2) and testosterone play key roles in several functions including carbohydrate, lipid and protein metabolism, cellular signaling, cell proliferation, and cancer promotion. Steroid hormones have long been characterized as cell proliferation and differentiation regulators and are closely related to the development of breast and prostate cancers. Moreover, cholesterol metabolism, mainly in adipose tissue, leads to the production of steroids and cytokines, thus increasing the risk of metabolic syndrome, obesity, and ER+ breast cancer in postmenopausal women. Recent studies also shown that testosterone and E2 increase the levels of key enzymes of the mevalonate pathway, leading to post-translational prenylation and farnesylation of numerous proteins in RAS signaling in several cancers, including breast and prostate cancers. There is accumulating evidence both clinically and experimentally suggesting that changes in the metabolism of cholesterol may also have an important role in carcinogenesis. In this regard, the cells treated with mevalonate in culture showed elevated proliferation. Therefore, investigation on cholesterol as a precursor of steroid hormones has confirmed the effects cholesterol metabolite on breast and prostate cancers. Indeed, recent evidence strongly suggests that the MVA pathway and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCOA) have a crucial regulatory role in cellular proliferation and transformation. Therefore, the use of mevalonate inhibitors decreases the production of several biologically active downstream products of the mevalonate pathway, including cholesterol. Although for approximately 20 years statins have been identified as anticancer agents, recent studies have sparked some controversy. Therefore, further investigation to evaluate mevalonate- dependent therapeutic agents per se and in combination with other agents is merited. The current review is an attempt to elucidate the role of cholesterol and E2/testosterone, as well as the mevalonate pathway and its inhibitors in breast and prostate tissues in normal and pathological states.\",\n \"corpus_id\": 27887498,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":59,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29437099\",\n \"title\": \"Complete Genome Sequence of a Type Strain of Mycobacterium abscessus subsp. bolletii, a Member of the Mycobacterium abscessus Complex.\",\n \"abstract\": \"Mycobacterium abscessus subsp. bolletii is a rapidly growing mycobacterial organism for which the taxonomy is unclear. Here, we report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii type strain. This sequence will provide essential information for future taxonomic and comparative genome studies of these mycobacteria.\",\n \"corpus_id\": 3339271\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"22207751","title":"Whole-genome sequence of the emerging pathogen Mycobacterium abscessus strain 47J26.","abstract":"Mycobacterium abscessus is a rapidly growing environmental mycobacterium commonly found in soil and water which is often also associated with infections in humans, particularly of the lung. We report herein the draft genome sequence of M. abscessus strain 47J26.","corpus_id":37879192,"score":2},{"doc_id":"22535937","title":"Draft genome sequence of Mycobacterium abscessus subsp. bolletii BD(T).","abstract":"Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T).","corpus_id":36817549,"score":2},{"doc_id":"22628511","title":"Complete genome sequence of Mycobacterium phlei type strain RIVM601174.","abstract":"Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is typically nonpathogenic, with few reported cases of human disease. Here we report the whole genome sequence of M. phlei type strain RIVM601174.","corpus_id":13197937,"score":2},{"doc_id":"23105073","title":"Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621.","abstract":"Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM). It is ubiquitous in water and soil habitats, including hospital environments. M. fortuitum is increasingly recognized as an opportunistic nosocomial pathogen causing disseminated infection. Here we report the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.","corpus_id":12676089,"score":2},{"doc_id":"23105074","title":"Complete genome sequence of Mycobacterium vaccae type strain ATCC 25954.","abstract":"Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is generally not considered a human pathogen and is of major pharmaceutical interest as an immunotherapeutic agent. We report here the annotated genome sequence of the M. vaccae type strain, ATCC 25954.","corpus_id":23380235,"score":2},{"doc_id":"23658631","title":"MabsBase: a Mycobacterium abscessus genome and annotation database.","abstract":"SUMMARY: Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.","corpus_id":5873227,"score":2},{"doc_id":"23678183","title":"The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria.","abstract":"The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ∼3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram(-)) or Gram(+) bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.","corpus_id":13227878,"score":2},{"doc_id":"24197885","title":"Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in clinical isolates by multiplex PCR.","abstract":"The rapidly growing mycobacterium M. abscessus sensu lato is the causative agent of emerging pulmonary and skin diseases and of infections following cosmetic surgery and postsurgical procedures. M. abscessus sensu lato can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Clinical isolates of rapidly growing mycobacteria were previously identified as M. abscessus by DNA-DNA hybridization. More than 30% of these 117 clinical isolates were differentiated as M. abscessus subsp. massiliense using combinations of multilocus genotyping analyses. A much more cost-effective technique to distinguish M. abscessus subsp. massiliense from M. abscessus subsp. abscessus, a multiplex PCR assay, was developed using the whole-genome sequence of M. abscessus subsp. massiliense JCM15300 as a reference. Several primer sets were designed for single PCR to discriminate between the strains based on amplicons of different sizes. Two of these single-PCR target sites were chosen for development of the multiplex PCR assay. Multiplex PCR was successful in distinguishing clinical isolates of M. abscessus subsp. massiliense from samples previously identified as M. abscessus. This approach, which spans whole-genome sequencing and clinical diagnosis, will facilitate the acquisition of more-precise information about bacterial genomes, aid in the choice of more relevant therapies, and promote the advancement of novel discrimination and differential diagnostic assays.","corpus_id":206781514,"score":2},{"doc_id":"25503461","title":"Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.","abstract":"Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.","corpus_id":13403401,"score":2},{"doc_id":"26448181","title":"Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Complex.","abstract":"PURPOSE: Clarithromycin was considered the cornerstone for the treatment of Mycobacterium abscessus complex infections. Genetic resistance mechanisms have been described and many experts propose amikacin as an alternative. Nevertheless, clarithromycin has several advantages; therefore, it is necessary to identify the non-functional erm(41) allele to determine the most suitable treatment. The aims of this study were to characterize the molecular mechanisms of clarithromycin resistance in a collection of Mycobacterium abscessus complex isolates and to verify the relationship between these mechanisms and the antibiogram. MATERIALS AND METHODS: Clinical isolates of M. abscessus complex (n = 22) from 16 patients were identified using four housekeeping genes (rpoB, secA1, sodA and hsp65), and their genetic resistance was characterized by studying erm(41) and rrl genes. Nine strains were recovered from the clinical isolates and subjected to E-test and microdilution clarithromycin susceptibility tests, with readings at 3, 7 and 14 days. RESULTS: We classified 11/16 (68.8%) M. abscessus subsp. abscessus, 4/16 (25.0%) M. abscessus subsp. bolletii, and 1/16 (6.3%) M. abscessus subsp. massiliense. T28 erm(41) allele was observed in 8 Mycobacterium abscessus subps. abscessus and 3 Mycobacterium abscessus subsp. bolletii. One strain of M. abscessus subsp. bolletii had an erm(41) gene truncated and was susceptible to clarithromycin. No mutations were observed in rrl gene first isolates. In three patients, follow-up of initial rrl wild-type strains showed acquired resistance. CONCLUSIONS: Most clinical isolates of M. abscessus complex had inducible resistance to clarithromycin and total absence of constitutive resistance. Our findings showed that the acquisition of resistance mutations in rrl gene was associated with functional and non-functional erm(41) gene. Caution is needed when using erm(41) sequencing alone to identify M. abscessus subspecies. This study reports an acquired mutation at position 2057 of rrl gene, conferring medium-low clarithromycin constitutive resistance.","corpus_id":4639575,"score":2},{"doc_id":"26744369","title":"Complete Genome Sequence of a Novel Clinical Isolate, Mycobacterium abscessus Strain NOV0213.","abstract":"Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. We determined the complete genome sequence of the M. abscessus strain NOV0213, which was isolated from a patient with tuberculosis-like disease and with various antibiotic resistances.","corpus_id":6291417,"score":2},{"doc_id":"27284156","title":"Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii.","abstract":"We report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii isolate recovered from a sputum culture from an individual with cystic fibrosis. This sequence is the first completed whole-genome sequence of M. abscessus subsp. bolletii and adds value to studies of M. abscessus complex genomics.","corpus_id":32488496,"score":2},{"doc_id":"27660787","title":"Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains.","abstract":"We report the complete genome sequences of 17 rapidly growing nontuberculous mycobacterial (NTM) strains, including 16 Mycobacterium abscessus complex strains and one M. immunogenum strain. These sequences add value to studies of the genetic diversity of rapidly growing NTM strains recovered from human specimens.","corpus_id":29466791,"score":2},{"doc_id":"27688344","title":"Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.","abstract":"Mycobacterium ulcerans subsp. shinshuense produces mycolactone and causes Buruli ulcer. Here, we report the complete sequence of its genome, which comprises a 5.9-Mb chromosome and a 166-kb plasmid (pShT-P). The sequence will represent the essential data for future phylogenetic and comparative genome studies of mycolactone-producing mycobacteria.","corpus_id":31657969,"score":2},{"doc_id":"28818905","title":"Complete Genome Sequence of Mycobacterium stephanolepidis.","abstract":"Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine teleost fish (Stephanolepis cirrhifer) and is closely related to Mycobacterium chelonae Here, we report the complete sequence of its genome, comprising a 4.9-Mb chromosome. The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen.","corpus_id":10415640,"score":2},{"doc_id":"29449406","title":"Complete Genome Sequence of Mycobacterium sp. Strain 4858.","abstract":"Mycobacterium sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a Cambodian patient with a pulmonary infection. We report the first complete 5.6-Mbp-long genome sequence of Mycobacterium strain 4858, with 68.24% GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.","corpus_id":3283202,"score":2},{"doc_id":"29773624","title":"Complete Genome Sequence of Mycobacterium marinum ATCC 927T, Obtained Using Nanopore and Illumina Sequencing Technologies.","abstract":"Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.","corpus_id":21712933,"score":2},{"doc_id":"18753344","title":"Proportions of Mycobacterium massiliense and Mycobacterium bolletii strains among Korean Mycobacterium chelonae-Mycobacterium abscessus group isolates.","abstract":"Korean isolates of the Mycobacterium chelonae-Mycobacterium abscessus group, which had been isolated from two different hospitals in South Korea, were identified by PCR restriction analysis (PRA) and comparative sequence analysis of 16S rRNA genes, rpoB, and hsp65 to evaluate the proportion of four closely related species (M. chelonae, M. abscessus, M. massiliense, and M. bolletii). Of the 144 rapidly growing mycobacterial strains tested, 127 strains (88.2%) belonged to the M. chelonae-M. abscessus group. In this group, M. chelonae, M. abscessus, M. massiliense, and M. bolletii accounted for 0.8% (n = 1), 51.2% (n = 65), 46.5% (n = 59), and 1.6% (n = 2), respectively. Two isolates which showed discordant results, M. massiliense by rpoB sequence analysis and M. abscessus by hsp65 sequence analysis, were finally identified as M. massiliense based on the additional analysis of sodA and the 16S-23S internal transcribed spacer. M. abscessus group I isolates previously identified by hsp65 PRA were all found to be M. abscessus, whereas group II isolates were further identified as M. massiliense or M. bolletii by sequencing of rpoB and hsp65. Smooth, rough, or mixed colonies of both M. abscessus and M. massiliense isolates were observed. M. massiliense strains that were highly resistant to clarithromycin had a point mutation at the adenine at position 2058 (A(2058)) or 2059 (A(2059)) in the peptidyltransferase region of the 23S rRNA gene.","corpus_id":7521619,"score":1},{"doc_id":"19420162","title":"Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii.","abstract":"Mycobacterium abscessus is the most common cause of rapidly growing mycobacterial chronic lung disease. Recently, two new M. abscessus-related species, M. massiliense and M. bolletii, have been described. Health care-associated outbreaks have recently been investigated by the use of molecular identification and typing tools; however, very little is known about the natural epidemiology and pathogenicity of M. massiliense or M. bolletii outside of outbreak situations. The differentiation of these two species from M. abscessus is difficult and relies on the sequencing of one or more housekeeping genes. We performed extensive molecular identification and typing of 42 clinical isolates of M. abscessus, M. massiliense, and M. bolletii from patients monitored at the NIH between 1999 and 2007. The corresponding clinical data were also examined. Partial sequencing of rpoB, hsp65, and secA led to the unambiguous identification of 26 M. abscessus isolates, 7 M. massiliense isolates, and 2 M. bolletii isolates. The identification results for seven other isolates were ambiguous and warranted further sequencing and an integrated phylogenetic analysis. Strain relatedness was assessed by repetitive-sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE), which showed the characteristic clonal groups for each species. Five isolates with ambiguous species identities as M. abscessus-M. massiliense by rpoB, hsp65, and secA sequencing clustered as a distinct group by rep-PCR and PFGE together with the M. massiliense type strain. Overall, the clinical manifestations of disease caused by each species were similar. In summary, a multilocus sequencing approach (not just rpoB partial sequencing) is required for division of M. abscessus and closely related species. Molecular typing complements sequence-based identification and provides information on prevalent clones with possible relevant clinical aspects.","corpus_id":30935694,"score":1},{"doc_id":"19571015","title":"Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae-M. abscessus group is needed.","abstract":"An outbreak of postsurgical infections caused by rapidly growing mycobacteria has been ongoing in Brazil since 2004. The degrees of similarity of the rpoB and hsp65 sequences from the clinical isolates and the corresponding sequences from both the Mycobacterium massiliense and the M. bolletii type strains were above the accepted limit for interspecies variability, leading to conflicting identification results. Therefore, an extensive characterization of members of the M. chelonae-M. abscessus group was carried out. The M. abscessus, M. chelonae, M. immunogenum, M. massiliense, and M. bolletii type strains and a subset of clinical isolates were analyzed by biochemical tests, high-performance liquid chromatography, drug susceptibility testing, PCR-restriction enzyme analysis of hsp65 (PRA-hsp65), rpoB, and hsp65 gene sequencing and analysis of phylogenetic trees, DNA-DNA hybridization (DDH), and restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene (RFLP-16S rRNA). The clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains could not be separated by phenotypic tests and were grouped in the phylogenetic trees obtained. The results of DDH also confirmed the >70% relatedness of the clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains; and indistinguishable RFLP-16S rRNA patterns were obtained. On the contrary, the separation of clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains from M. chelonae and M. immunogenum was supported by the results of PRA-hsp65, DDH, and RFLP-16S rRNA and by the rpoB and hsp65 phylogenetic trees. Taken together, these results led to the proposition that M. abscessus, M. massiliense, and M. bolletii represent a single species, that of M. abscessus. Two subspecies are also proposed, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, and these two subspecies can be distinguished by two different PRA-hsp65 patterns, which differ by a single HaeIII band, and by differences in their rpoB (3.4%) and hsp65 (1.3%) sequences.","corpus_id":33583558,"score":1},{"doc_id":"21106786","title":"Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.","abstract":"Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.","corpus_id":11343426,"score":1},{"doc_id":"22628507","title":"Genome sequence of the Mycobacterium abscessus strain M93.","abstract":"Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. We report herein the draft genome sequence of M. abscessus strain M93.","corpus_id":44946809,"score":1},{"doc_id":"22843600","title":"Draft genome sequence of Mycobacterium bolletii strain M24, a rapidly growing mycobacterium of contentious taxonomic status.","abstract":"The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar lavage fluid of a Malaysian patient, is reported here. The circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of this organism within the M. abscessus complex and revealed the presence of proteins potentially important for pathogenicity in a human host.","corpus_id":39270814,"score":1},{"doc_id":"23012295","title":"Analysis of the genome of Mycobacterium abscessus strain M94 reveals an uncommon cluster of tRNAs.","abstract":"Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. Here, we report the annotated genome sequence of M. abscessus strain M94, which showed an unusual cluster of tRNAs.","corpus_id":20704821,"score":1},{"doc_id":"23045507","title":"Genomic analysis of Mycobacterium abscessus strain M139, which has an ambiguous subspecies taxonomic position.","abstract":"Mycobacterium abscessus is a ubiquitous, rapidly growing species of nontuberculous mycobacteria that colonizes organic surfaces and is frequently associated with opportunistic infections in humans. We report here the draft genome sequence of Mycobacterium abscessus strain M139, which shows genomic features reported to be characteristic of both Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. massiliense.","corpus_id":20597949,"score":1},{"doc_id":"23144407","title":"Genome sequence of Mycobacterium abscessus strain M152.","abstract":"Mycobacterium abscessus is an environmental bacterium with increasing clinical relevance. Here, we report the annotated whole-genome sequence of M. abscessus strain M152.","corpus_id":27949875,"score":1},{"doc_id":"23294800","title":"Mycobacterium abscessus multispacer sequence typing.","abstract":"BACKGROUND: Mycobacterium abscessus group includes antibiotic-resistant, opportunistic mycobacteria that are responsible for sporadic cases and outbreaks of cutaneous, pulmonary and disseminated infections. However, because of their close genetic relationships, accurate discrimination between the various strains of these mycobacteria remains difficult. In this report, we describe the development of a multispacer sequence typing (MST) analysis for the simultaneous identification and typing of M. abscessus mycobacteria. We also compared MST with the reference multilocus sequence analysis (MLSA) typing method. RESULTS: Based on the M. abscessus CIP104536T genome, eight intergenic spacers were selected, PCR amplified and sequenced in 21 M. abscessus isolates and analysed in 48 available M. abscessus genomes. MST and MLSA grouped 37 M. abscessus organisms into 12 and nine types, respectively; four formerly \"M. bolletii\" organisms and M. abscessus M139 into three and four types, respectively; and 27 formerly \"M. massiliense\" organisms grouped into nine and five types, respectively. The Hunter-Gaston index was off 0.912 for MST and of 0.903 for MLSA. The MST-derived tree was similar to that based on MLSA and rpoB gene sequencing and yielded three main clusters comprising each the type strain of the respective M. abscessus sub-species. Two isolates exhibited discordant MLSA- and rpoB gene sequence-derived position, one isolate exhibited discordant MST- and rpoB gene sequence-derived position and one isolate exhibited discordant MST- and MLSA-derived position. MST spacer n°2 sequencing alone allowed for the accurate identification of the different isolates at the sub-species level. CONCLUSIONS: MST is a new sequencing-based approach for both identifying and genotyping M. abscessus mycobacteria that clearly differentiates formerly \"M. massiliense\" organisms from other M. abscessus subsp. bolletii organisms.","corpus_id":14428949,"score":1},{"doc_id":"23295745","title":"Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil.","abstract":"A single strain of Mycobacterium abscessus subsp. bolletii, characterised by a particular rpoB sequevar and two highly related pulsed field gel electrophoresis patterns has been responsible for a nationwide outbreak of surgical infections in Brazil since 2004. In this study, we developed molecular tests based on polymerase chain reaction restriction-enzyme analysis (PRA) and sequencing for the rapid identification of this strain. Sequences of 15 DNA regions conserved in mycobacteria were retrieved from GenBank or sequenced and analysed in silico. Single nucleotide polymorphisms specific to the epidemic strain and located in enzyme recognition sites were detected in rpoB, the 3' region of the 16S rDNA and gyrB. The three tests that were developed, i.e., PRA-rpoB, PRA-16S and gyrB sequence analysis, showed 100%, 100% and 92.31% sensitivity and 93.06%, 90.28% and 100% specificity, respectively, for the discrimination of the surgical strain from other M. abscessus subsp. bolletii isolates, including 116 isolates from 95 patients, one environmental isolate and two type strains. The results of the three tests were stable, as shown by results obtained for different isolates from the same patient. In conclusion, due to the clinical and epidemiological importance of this strain, these tests could be implemented in reference laboratories for the rapid preliminary diagnosis and epidemiological surveillance of this epidemic strain.","corpus_id":12304829,"score":1},{"doc_id":"23565273","title":"The detection and sequencing of a broad-host-range conjugative IncP-1β plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii.","abstract":"BACKGROUND: An extended outbreak of mycobacterial surgical infections occurred in Brazil during 2004-2008. Most infections were caused by a single strain of Mycobacterium abscessus subsp. bolletii, which was characterized by a specific rpoB sequevar and two highly similar pulsed-field gel electrophoresis (PFGE) patterns differentiated by the presence of a ∼50 kb band. The nature of this band was investigated. METHODOLOGY/PRINCIPAL FINDINGS: Genomic sequencing of the prototype outbreak isolate INCQS 00594 using the SOLiD platform demonstrated the presence of a 56,267-bp [corrected] circular plasmid, designated pMAB01. Identity matrices, genetic distances and phylogeny analyses indicated that pMAB01 belongs to the broad-host-range plasmid subgroup IncP-1β and is highly related to BRA100, pJP4, pAKD33 and pB10. The presence of pMAB01-derived sequences in 41 M. abscessus subsp. bolletii isolates was evaluated using PCR, PFGE and Southern blot hybridization. Sixteen of the 41 isolates showed the presence of the plasmid. The plasmid was visualized as a ∼50-kb band using PFGE and Southern blot hybridization in 12 isolates. The remaining 25 isolates did not exhibit any evidence of this plasmid. The plasmid was successfully transferred to Escherichia coli by conjugation and transformation. Lateral transfer of pMAB01 to the high efficient plasmid transformation strain Mycobacterium smegmatis mc(2)155 could not be demonstrated. CONCLUSIONS/SIGNIFICANCE: The occurrence of a broad-host-range IncP-1β plasmid in mycobacteria is reported for the first time. Thus, genetic exchange could result in the emergence of specific strains that might be better adapted to cause human disease.","corpus_id":1360653,"score":1},{"doc_id":"23804391","title":"New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance.","abstract":"Mycobacterium abscessus (M. abscessus sensu lato, or the M. abscessus group) comprises three closely related taxa whose taxonomic statuses are under revision, i.e., M. abscessus sensu stricto, Mycobacterium bolletii, and Mycobacterium massiliense. We describe here a simple, robust, and cost-effective PCR-based method for distinguishing among M. abscessus, M. massiliense, and M. bolletii. Based on the M. abscessus ATCC 19977(T) genome, regions that discriminated between M. abscessus and M. massiliense were identified through array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense, and 2 M. bolletii isolates previously identified by multitarget sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full-length erm(41) gene instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for straightforward identification of M. abscessus, M. massiliense, and M. bolletii and the assessment of inducible clarithromycin resistance. This method can be easily integrated into a routine workflow to provide subspecies-level identification within 24 h after isolation of the M. abscessus group.","corpus_id":9701331,"score":1},{"doc_id":"23850022","title":"Further isolation of Mycobacterium abscessus subsp. abscessus and subsp. bolletii in different regions of Japan and susceptibility of these isolates to antimicrobial agents.","abstract":"The aim of this study was to genetically analyse Mycobacterium abscessus subsp. abscessus (hereafter M. abscessus) and M. abscessus subsp. bolletii (hereafter M. bolletii) isolates from six different regions of Japan and to determine the antimicrobial susceptibility of these isolates. Subspeciation of 143 clinical isolates of M. abscessus group was done by comparative sequence analysis of the rpoB and hsp65 genes and the internal transcribed spacer (ITS) region. Genetic analysis led to the identification of 90 M. abscessus (62.9%) and 53 M. bolletii (37.1%; comprising 50 'M. massiliense' and 3 'M. bolletii' in the old nomenclature). No significant differences were found between the M. abscessus and M. bolletii isolates in any characteristics. Susceptibility to clarithromycin and linezolid for M. bolletii isolates was significantly higher than that for M. abscessus (P<0.05). Moreover, the results demonstrated that 82 M. abscessus isolates with T28 sequevar were resistant to clarithromycin owing to the expression of erm(41), which was induced by clarithromycin, whilst 8 isolates with C28 sequevar were susceptible. Acquired clarithromycin resistance in 'M. bolletii' isolates was significantly associated with previous Mycobacterium avium complex (MAC) treatment compared with that of M. abscessus isolates; however, intrinsic inducible susceptibility of M. abscessus isolates was not associated with MAC treatment. However, acquired resistance to clarithromycin by mutation in the rrl gene encoding 23S rRNA did not occur in 14 of 18 resistant isolates. Strains with acquired resistance to clarithromycin and mutation in rrl consisted of two M. bolletii (one 'M. massiliense' and one 'M. bolletii') and two M. abscessus T28 sequevar.","corpus_id":5770482,"score":1},{"doc_id":"24009121","title":"Whole-Genome Sequence of Mycobacterium abscessus Clinical Strain V06705.","abstract":"Infection caused by Mycobacterium abscessus strains is a growing cause of concern in both community-acquired and health care-associated diseases, as these organisms naturally display multiple drug resistances. We report an annotated draft genome sequence of M. abscessus strain V06705 obtained from a patient in France.","corpus_id":11847130,"score":1},{"doc_id":"24055961","title":"Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains.","abstract":"Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents.","corpus_id":25962366,"score":1},{"doc_id":"24312320","title":"The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.","abstract":"Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.","corpus_id":4057249,"score":1},{"doc_id":"24523815","title":"The First Korean Case of Nontuberculous Mycobacterial Lung Disease Caused by Mycobacterium abscessus Subspecies bolletii in a Patient with Bronchiectasis.","abstract":"We report the first Korean case of lung diseases caused by Mycobacterium abscessus subsp. bolletii in a previously healthy male, except for a previous history of pulmonary tuberculosis and bronchiectasis. All serial isolates are identified as M. abscessus subsp. bolletii by multi-locus sequence analysis based on the hsp65, rpoB, and 16S rRNA fragments. At the genetic level, the isolate has the erm(41) gene with a T28 sequevar, associated with clarithromycin resistance, and no rrl mutation. The isolate is resistant to clarithromycin. Although the symptoms and radiographic findings have improved after combination of antibiotics, the follow-up sputum cultures are persistently positive.","corpus_id":5792327,"score":1},{"doc_id":"24671795","title":"Clonal relationship and differentiation among Mycobacterium abscessus isolates as determined using the semiautomated repetitive extragenic palindromic sequence PCR-based DiversiLab system.","abstract":"Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for M. abscessus genotyping. Since M. abscessus was shown to be composed of subspecies (M. abscessus subsp. massiliense, M. abscessus subsp. bolletii, and M. abscessus subsp. abscessus), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83 M. abscessus original isolates (43 M. abscessus subsp. abscessus, 12 M. abscessus subsp. bolletii, and 28 M. abscessus subsp. massiliense) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the M. abscessus subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of M. abscessus infections.","corpus_id":9080162,"score":1},{"doc_id":"24886480","title":"Genome analysis reveals three genomospecies in Mycobacterium abscessus.","abstract":"BACKGROUND: Mycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described. RESULTS: In-depth analysis of 14 published M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors (including PE, PPE, LpqH, MCE, Yrbe and type VII secretion system ESX3 and ESX4) varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by β-lactam antibiotics and an Ambler class A β-lactamase for which inhibitors exist. CONCLUSIONS: Our comparative analysis indicates that M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus.","corpus_id":13524467,"score":1},{"doc_id":"24899019","title":"Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.","abstract":"Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus.","corpus_id":6896187,"score":1},{"doc_id":"24932856","title":"Species identification of Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii using rpoB and hsp65, and susceptibility testing to eight antibiotics.","abstract":"OBJECTIVES: To separate Mycobacterium abscessus subsp. bolletii from Mycobacterium abscessus subsp. abscessus using species identification, and to investigate the in vitro activity of amikacin, cefoxitin, imipenem, levofloxacin, moxifloxacin, clarithromycin, azithromycin, and linezolid against Mycobacterium abscessus. METHODS: Seventy M. abscessus isolates, previously identified by 16S rRNA sequencing, were further identified by comparative sequence analysis of rpoB and hsp65. Drug susceptibility testing was conducted using the microplate Alamar Blue assay in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines and interpreted using CLSI breakpoints. RESULTS: Of the 70 strains, 45 (64%) were M. abscessus subsp. abscessus and 25 (36%) were M. abscessus subsp. bolletii. The majority of M. abscessus isolates were susceptible to azithromycin, amikacin, linezolid, and imipenem (M. abscessus subsp. abscessus: 93%, 98%, 93%, and 73%, respectively; M. abscessus subsp. bolletii: 96%, 96%, 80%, and 68%, respectively). Approximately half of the M. abscessus isolates were moderately susceptible to cefoxitin and moxifloxacin (M. abscessus subsp. abscessus 53% and 49%; M. abscessus subsp. bolletii 72% and 68%). Nearly all the M. abscessus isolates were resistant to levofloxacin (M. abscessus subsp. abscessus 96%, M. abscessus subsp. bolletii 100%). Inducible clarithromycin resistance was found in M. abscessus. After 14 days of incubation, 83% M. abscessus subsp. abscessus and 36% M. abscessus subsp. bolletii were resistant to clarithromycin. CONCLUSIONS: Using rpoB and hsp65, M. abscessus subsp. bolletii could be distinguished from M. abscessus subsp. abscessus. Amikacin and azithromycin showed excellent activity against M. abscessus in vitro. Imipenem, linezolid, cefoxitin, and moxifloxacin also showed good activity. Levofloxacin was inactive against M. abscessus. Although clarithromycin showed excellent activity against M. abscessus on day 3, inducible resistance occurred, and after 14 days clarithromycin showed little activity against M. abscessus subsp. abscessus, but still had good activity against M. abscessus subsp. bolletii.","corpus_id":205275560,"score":1},{"doc_id":"25268925","title":"Mycobacterium abscessus: challenges in diagnosis and treatment.","abstract":"PURPOSE OF REVIEW: Mycobacterium abscessus is the most common rapidly growing mycobacterium that causes lung disease. This review describes recently published literature regarding M. abscessus taxonomy, environmental niche, diagnosis, management and outcome in pulmonary disease in adults and adolescents with cystic fibrosis. RECENT FINDINGS: The classification of M. abscessus subsp. abscessus, M. abscessus subsp. massiliense and M. abscessus subsp. bolletii is useful clinically because of the discovery of the erm(41) gene, which is responsible for macrolide resistance in M. abscessus. Macrolide susceptibility is key for successful treatment of M. abscessus subsp. massiliense. The poor outcome and eradication of M. abscessus subsp. abscessus remains both a diagnostic and treatment challenge in approximately 80% of isolates that are macrolide resistant. Molecular studies, such as genotyping, may allow prediction of disease progression. Overall, there is a dearth of new literature surrounding M. abscessus. SUMMARY: New studies differentiating M. abscessus subsp. abscessus and M. abscessus subsp. massiliense based on the erm(41) gene demonstrate the latter to have a better prognosis and improved treatment outcomes. M. abscessus subsp. abscessus remains a formidable pathogen in diagnosis and treatment.","corpus_id":20505570,"score":1},{"doc_id":"25580261","title":"Mycobacterium abscessus subsp abscessus lung disease: 'trouble ahead, trouble behind…'.","abstract":"Mycobacterium abscessus subsp abscessus is the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria (NTM) and is also the most feared due to its well-deserved reputation for being refractory to antibiotic therapy. M. abscessus subsp abscessus has multiple innate antibiotic resistance mechanisms, but the most important one described so far is an inducible erythromycin methylase (erm) gene. M. abscessus subsp abscessus isolates may appear macrolide susceptible on initial in vitro testing but become macrolide resistant after exposure to macrolide. It is therefore very important to test clinically significant M. abscessus subsp abscessus isolates for erm gene activity. Remarkably, controversy still exists about the taxonomy and nomenclature of M. abscessus subspecies including subsp abscessus, subsp massiliense and subsp bolletii. Identification of these subspecies is not moot as M. abscessus subsp massiliense does not have an active erm gene resulting in both in vitro and in vivo susceptibility to macrolide. It is imperative from the clinician's perspective that mycobacterial laboratories correctly and rapidly identify M. abscessus to the subspecies level. Unfortunately, there are no reliably or predictably effective treatment regimens for M. abscessus subsp abscessus and better, more effective antimicrobial agents are badly needed. Surgical resection of involved lung tissue as an adjunct to antibiotic therapy is beneficial in selected patients but cannot be broadly applied. Overall, M. abscessus subsp abscessus remains a formidable respiratory mycobacterial pathogen, one that we are only beginning to understand microbiologically and one that as yet consistently evades our best efforts at successful therapeutic outcomes. ' trouble ahead, trouble behind, and you know that notion just crossed my mind'.Casey Jones, Grateful Dead (1970).","corpus_id":14184044,"score":1},{"doc_id":"25643064","title":"Mycobacterium abscessus. \"Pleased to meet you, hope you guess my name...\".","abstract":"Mycobacterium abscessus is a formidable and difficult-to-treat mycobacterial pathogen with multiple drug-resistance mechanisms. The most important of these mechanisms is the presence of an inducible erythromycin methylase (erm) gene, because it confers macrolide resistance. It has recently been found that \"M. abscessus\" can be split into three species or subspecies based on gene sequence analysis other than the 16S rRNA gene and the presence or absence of a functional erm(41) gene. Several names have been applied to these three organisms, including M. abscessus or M. abscessus subsp. abscessus, Mycobacterium massiliense or M. abscessus subsp. massiliense, and Mycobacterium bolletii or M. abscessus subsp. bolletii. No universally accepted or recognized species or subspecies designations have emerged, and no names have been universally adopted for these organisms. This uncertainty has led to inconsistencies in the medical literature and understandable confusion by clinicians about the appropriate labels for \"M. abscessus\" isolates. We discuss the complexities involved in mycobacterial species/subspecies identification and taxonomy and suggest possible ways to improve the present state of uncertainty surrounding the labels for \"M. abscessus\" clinical isolates. We also suggest necessary changes in mycobacterial laboratory processing and reporting procedures for mycobacterial isolates.","corpus_id":262931951,"score":1},{"doc_id":"26067970","title":"Draft Genome Sequence of Mycobacterium arupense Strain GUC1.","abstract":"We report the draft genome sequence of Mycobacterium arupense strain GUC1 from a sputum sample of a patient with bronchiectasis. This is the first draft genome sequence of Mycobacterium arupense, a rapidly growing nonchromogenic mycobacteria.","corpus_id":4476148,"score":1},{"doc_id":"26072272","title":"Molecular epidemiology of Mycobacterium abscessus complex isolates in Ireland.","abstract":"BACKGROUND: The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. METHODS: We performed rpoB gene sequencing and multi-locus sequence typing (MLST) on M. abscessus complex strains isolated from thirty-six patients in 2006-2012 (eighteen known CF patients). RESULTS: Twenty-eight strains (78%) were M. abscessus subsp. abscessus, eight M. abscessus subsp. massiliense, none were M. abscessus subsp. bolletii. Sequence type 1 (ST1) and ST26 (M. abscessus subsp. abscessus) were commonest. Seven M. abscessus subsp. abscessus STs (25%) were novel (two with novel alleles). Seven M. abscessus subsp. massiliense STs were previously reported (88%), including two ST23, the globally successful clone. In 2012, of 552 CF patients screened, eleven were infected with M. abscessus complex strains (2%). CONCLUSIONS: The most prevalent M. abscessus subsp. abscessus and M. abscessus subsp. massiliense strains in Ireland belong to widely-distributed STs, but there is evidence of high M. abscessus subsp. abscessus diversity.","corpus_id":11122548,"score":1},{"doc_id":"26295364","title":"Mycobacterium abscessus Complex Infections in Humans.","abstract":"Mycobacterium abscessus complex comprises a group of rapidly growing, multidrug-resistant, nontuberculous mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, bacteremia, and ocular and other infections. M. abscessus complex is differentiated into 3 subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. The 2 major subspecies, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, have different erm(41) gene patterns. This gene provides intrinsic resistance to macrolides, so the different patterns lead to different treatment outcomes. M. abscessus complex outbreaks associated with cosmetic procedures and nosocomial transmissions are not uncommon. Clarithromycin, amikacin, and cefoxitin are the current antimicrobial drugs of choice for treatment. However, new treatment regimens are urgently needed, as are rapid and inexpensive identification methods and measures to contain nosocomial transmission and outbreaks.","corpus_id":10028163,"score":1},{"doc_id":"26884275","title":"Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications.","abstract":"BACKGROUND: In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). RESULTS: Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal 'patchwork' architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. CONCLUSION: Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections.","corpus_id":10181102,"score":1},{"doc_id":"27231356","title":"Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.","abstract":"Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains.","corpus_id":3069391,"score":1},{"doc_id":"27499141","title":"Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacteriumabscessus subsp. bolletii and designation of Mycobacteriumabscessus subsp. massiliense comb. nov.","abstract":"The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).","corpus_id":40586077,"score":1},{"doc_id":"28303132","title":"Mycobacterium abscessus subsp. abscessus Is Capable of Degrading Pseudomonas aeruginosa Quinolone Signals.","abstract":"Pseudomonas aeruginosa employs 2-heptyl-3-hydroxy-4(1H)-quinolone (the Pseudomonas quinolone signal, PQS) and 2-heptyl-4(1H)-quinolone (HHQ) as quorum sensing signal molecules, which contribute to a sophisticated regulatory network controlling the production of virulence factors and antimicrobials. We demonstrate that Mycobacterium abscessus(T) and clinical M. abscessus isolates are capable of degrading these alkylquinolone signals. Genome sequences of 50 clinical M. abscessus isolates indicated the presence of aqdRABC genes, contributing to fast degradation of HHQ and PQS, in M. abscessus subsp. abscessus strains, but not in M. abscessus subsp. bolletii and M. abscessus subsp. massiliense isolates. A subset of 18 M. a. subsp. abscessus isolates contained the same five single nucleotide polymorphisms (SNPs) compared to the aqd region of the type strain. Interestingly, representatives of these isolates showed faster PQS degradation kinetics than the M. abscessus type strain. One of the SNPs is located in the predicted promoter region of the aqdR gene encoding a putative transcriptional regulator, and two others lead to a variant of the AqdC protein termed AqdC(II), which differs in two amino acids from AqdC(I) of the type strain. AqdC, the key enzyme of the degradation pathway, is a PQS dioxygenase catalyzing quinolone ring cleavage. While transcription of aqdR and aqdC is induced by PQS, transcript levels in a representative of the subset of 18 isolates were not significantly altered despite the detected SNP in the promoter region. However, purified recombinant AqdC(II) and AqdC(I) exhibit different kinetic properties, with approximate apparent Km values for PQS of 14 μM and 37 μM, and kcat values of 61 s(-1) and 98 s(-1), respectively, which may (at least in part) account for the observed differences in PQS degradation rates of the strains. In co-culture experiments of P. aeruginosa PAO1 and M. abscessus, strains harboring the aqd genes reduced the PQS levels, whereas mycobacteria lacking the aqd gene cluster even boosted PQS production. The results suggest that the presence and expression of the aqd genes in M. abscessus lead to a competitive advantage against P. aeruginosa.","corpus_id":18134820,"score":1},{"doc_id":"28820087","title":"Reinstating Mycobacterium massiliense and Mycobacterium bolletii as species of the Mycobacterium abscessus complex.","abstract":"TheMycobacterium abscessus complex is a group of rapidly growing, multiresistant mycobacteria previously divided into three species. Proposal for the union of Mycobacterium bolletii and Mycobacterium massiliense into one subspecies, so-called M. abscessus subsp. massiliense, created much confusion about the routine identification and reporting of M. abscessus clinical isolates for clinicians. Results derived from multigene sequencing unambiguously supported the reinstatement of M. massiliense and M. bolletii as species, culminating in the presence of erm(41)-encoded macrolide resistance in M. bolletii. Present genome-based analysis unambiguously supports the reinstatement of M. massiliense and M. bolletii as species after the average nucleotide identity values of 96.7 % for M. abscessus versus M. bolletii, and 96.4 % for M. abscessus versus M. massiliense, and the 96.6 % identity between M. bolletii and M. massiliense was put into the perspective of a larger, 28-species analysis. Accordingly, DNA-DNA hybridization values predicted by the complete rpoB gene sequencing analysis were between 68.7 and 72.3 % in this complex. These genomic data as well as the phenotypic characteristics prompted us to propose to reinstate the previously known M. massiliense and M. bolletii into two distinct species among the M. abscessus complex.","corpus_id":43899885,"score":1},{"doc_id":"29061748","title":"In Vitro Evaluation of Povidone-Iodine and Chlorhexidine against Outbreak and Nonoutbreak Strains of Mycobacterium abscessus Using Standard Quantitative Suspension and Carrier Testing.","abstract":"Povidone-iodine (PI) and chlorhexidine (CHX) are widely used antiseptics active against conventional Staphylococcus aureus, Enterobacteriaceae, Candida species, and viruses, but their efficacy against Mycobacterium abscessus remains unproven. We determined the in vitro potency of alcoholic PI and CHX against M. abscessus subsp. abscessus (ATCC 19977), M. abscessus subsp. bolletii (BCRC 16915), and our outbreak strain of M. abscessus subsp. massiliense (TPE 101) in reference to Staphylococcus aureus (ATCC 29213) by standard quantitative suspension and carrier methods (EN 14563). By suspension, all mycobacterial strains compared to S. aureus were significantly more resistant to CHX, but not PI. By carrier, the mean logarithmic reductions (LR) achieved by PI under clean (dirty) conditions were 6.575 (2.482), 5.540 (2.298), 4.595 (1.967), and 1.173 (0.889), while those achieved by CHX under clean (dirty) conditions were 3.164 (5.445), 5.307 (2.564), 3.844 (2.232), and 0.863 (0.389) for S. aureus, M. abscessus subsp. bolletii, M. abscessus subsp. abscessus, and M. abscessus subsp. massiliense, respectively. M. abscessus subsp. massiliense (outbreak strain) was significantly more resistant than the other tested strains to PI and CHX. By both methods, the mean LR achieved by PI was higher than for CHX for all mycobacterial strains, but under dirty conditions, neither antiseptic was effectively mycobactericidal (LR < 5). These preliminary findings caution against the universal replacement of PI with CHX as the first-line skin antiseptic, since all M. abscessus isolates were resistant to CHX. More studies are needed to establish the best practice for skin antisepsis if mycobacterial infections are also to be prevented.","corpus_id":12240230,"score":1},{"doc_id":"21037035","title":"Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus.","abstract":"The names 'Mycobacterium abscessus subsp. abscessus' and 'Mycobacterium abscessus subsp. massiliense', proposed by Leao et al. (2009, J Clin Microbiol 47, 2691-2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name 'Mycobacterium abscessus subsp. massiliense' is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.","corpus_id":19364471,"score":0},{"doc_id":"21903825","title":"Phenotypic and molecular characterization of quinolone resistance in Mycobacterium abscessus subsp. bolletii recovered from postsurgical infections.","abstract":"Several outbreaks of infections caused by rapidly growing mycobacteria (RGM) were reported in many Brazilian states (2032 notified cases) from 2004 to 2010. Most of the confirmed cases were mainly associated with Mycobacterium massiliense (recently renamed as Mycobacterium abscessus subsp. bolletii) BRA100 clone, recovered from patients who had undergone invasive procedures in which medical instruments had not been properly sterilized and/or disinfected. Since quinolones have been an option for the treatment of general RGM infections and have been suggested for therapeutic schemes for these outbreaks, we evaluated the in vitro activities of all generations of quinolones for clinical and reference RGM by broth microdilution, and analysed the peptide sequences of the quinolone resistance determining regions (QRDRs) of GyrA and GyrB after DNA sequencing followed by amino acid translation. Fifty-four isolates of M. abscessus subsp. bolletii, including clone BRA100, recovered in different states of Brazil, and 19 reference strains of RGM species were characterized. All 54 M. abscessus subsp. bolletii isolates were resistant to all generations of quinolones and showed the same amino acids in the QRDRs, including the Ala-83 in GyrA, and Arg-447 and Asp-464 in GyrB, described as being responsible for an intrinsic low level of resistance to quinolones in mycobacteria. However, other RGM species showed distinct susceptibilities to this class of antimicrobials and patterns of mutations contrary to what has been traditionally defined, suggesting that other mechanisms of resistance, different from gyrA or gyrB mutations, may also be involved in resistance to high levels of quinolones.","corpus_id":6798570,"score":0},{"doc_id":"22887675","title":"Annotated genome sequence of Mycobacterium massiliense strain M154, belonging to the recently created taxon Mycobacterium abscessus subsp. bolletii comb. nov.","abstract":"Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus subsp. bolletii comb. nov. Strain M154, a clinical isolate from the bronchoalveolar lavage fluid of a Malaysian patient presenting with lower respiratory tract infection, was subjected to shotgun DNA sequencing with the Illumina sequencing technology to obtain whole-genome sequence data for comparison with other genetically related strains within the M. abscessus species complex.","corpus_id":21783694,"score":0},{"doc_id":"22947084","title":"Probable disseminated Mycobacterium abscessus subspecies bolletii infection in a patient with idiopathic CD4+ T lymphocytopenia: a case report.","abstract":"UNLABELLED: INTRODUCTION: Rapidly growing mycobacteria are opportunistic pathogens in patients with underlying risk factors. Mycobacterium abscessus subsp. bolletii is a newly recognized member of rapidly growing mycobacteria, isolated from respiratory tract and cutaneous infections. CASE PRESENTATION: We describe a case of chronic disseminated infection caused by M. abscessus subsp. bolletii in a 38-year-old Sri Lankan man with idiopathic CD4+ T lymphocytopenia. Idiopathic CD4+ T lymphocytopenia is a rare cause of immunodysfunction that, similar to human immunodeficiency virus infection, causes a depletion of CD4+ T lymphocytes. M. abscessus subsp. bolletii infection was diagnosed by culture isolation from two sputum samples. CONCLUSIONS: To the best of our knowledge this is the first report of M. abscessus subsp. bolletii disseminated infection in a patient affected by idiopathic CD4+ T lymphocytopenia. In contrast to previous reports, the isolate of M. abscessus subsp. bolletii presented intermediate resistance to clarithromycin and was susceptible to cefoxitin and imipenem.","corpus_id":17192945,"score":0},{"doc_id":"23950125","title":"Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.","abstract":"Multiple isolates of Mycobacterium abscessus subsp. bolletii, collectively called BRA100, were associated with outbreaks of postsurgical skin infections across various regions of Brazil from 2003 to 2009. We announce the draft genome sequence of a newly sequenced BRA100 strain, M. abscessus subsp. bolletii CRM-0020, isolated from a patient in Rio de Janeiro, Brazil.","corpus_id":28019337,"score":0},{"doc_id":"24201191","title":"Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594.","abstract":"An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp. bolletii affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.","corpus_id":6110792,"score":0},{"doc_id":"24718088","title":"Bacteraemia caused by Mycobacterium abscessus subsp. abscessus and M. abscessus subsp. bolletii: clinical features and susceptibilities of the isolates.","abstract":"Mycobacterium abscessus complex (M. abscessus subsp. abscessus and M. abscessus subsp. bolletii) is an emerging pathogen causing various human infections. However, few studies have focused on M. abscessus complex bacteraemia with detailed species differentiation. The clinical characteristics of patients with bacteraemia due to M. abscessus complex treated at National Taiwan University Hospital from 2005-2012 were evaluated. Species identification was performed by molecular methods, and minimum inhibitory concentrations (MICs) were determined using a Sensititre RAPMYCO Panel Test for preserved M. abscessus complex isolates. During the study period, 15 patients with M. abscessus complex bacteraemia were found but only 14 isolates from 13 patients were preserved for analysis. One patient had two episodes of bacteraemia (one caused by M. abscessus subsp. bolletii and one by M .abscessus subsp. abscessus with a 9-month interval). Of the remaining 12 patients, 9 patients had M. abscessus subsp. bolletii bacteraemia and 3 had M .abscessus subsp. abscessus bacteraemia. Patients were mainly middle-aged adults with various co-morbidities. Steroid usage and malignancy (5/15) were the most common immunocompromised statuses, followed by diabetes mellitus (4/15). Surgical wound infection was the most common infection foci in all patients (5/15), particularly in M. abscessus subsp. bolletii bacteraemia patients. Clarithromycin and tigecycline exhibited good in vitro activities. Overall, the 14-day mortality was 20% (3/15). M. abscessus complex bacteraemia should be considered an emerging opportunistic infection in immunocompromised hosts. Clarithromycin and tigecycline have potent in vitro activities and are promising agents for treating infections due to M. abscessus complex.","corpus_id":20553506,"score":0},{"doc_id":"25038135","title":"Outbreaks due to Mycobacterium abscessus subsp. bolletii in southern Brazil: persistence of a single clone from 2007 to 2011.","abstract":"Outbreaks associated with rapidly growing mycobacteria (RGM) have been increasingly reported worldwide, including in Brazil. Among the RGM, the Mycobacterium abscessus complex is the most pathogenic and related to multidrug resistance. The aim of this study was to evaluate the antimicrobial susceptibility and molecular profile of RGM isolates involved in new postsurgical infection outbreaks in Brazil since 2007. Of the 109 cases reported in the state of Rio Grande do Sul between 2007 and 2011, 43 (39 %) had confirmed mycobacterial growth in culture. Clinical isolates were obtained from biopsy specimens or abscess aspirates. PRA-hsp65 restriction pattern identified the isolates as M. abscessus type 2, and partial rpoB sequencing confirmed the identification as M. abscessus subsp. bolletii. All isolates were susceptible to amikacin and resistant to ciprofloxacin, doxycycline, sulfamethoxazole, moxifloxacin and tobramycin. Most isolates (72 %) were fully susceptible to cefoxitin but six isolates (14 %) were fully resistant to clarithromycin. The latter differed from the susceptibility profiles of the previously described BRA100 clone from other Brazilian regions. Nevertheless, pulsed-field gel electrophoresis analysis revealed that these isolates belonged to a single BRA100 clone. In conclusion, our study reports the persistence of an emergent single and highly resistant clone of M. abscessus subsp. bolletii for several years even after national implementation of infection control measures.","corpus_id":9488047,"score":0},{"doc_id":"27524260","title":"Pseudooutbreak of rapidly growing mycobacteria due to Mycobacterium abscessus subsp bolletii in a digestive and respiratory endoscopy unit caused by the same clone as that of a countrywide outbreak.","abstract":"BACKGROUND: The nontuberculous mycobacteria (NTM) are widely spread. In Brazil, 2,520 cases of rapidly growing mycobacteria (RGM) infections after medical procedures were reported, with 5.4% of cases related to nonsurgical invasive procedures and with an occurrence of 1 clone (BRA100) of Mycobacterium abscessus subsp bolletii. OBJECTIVE: To describe a pseudooutbreak of M abscessus subsp bolletii in an endoscopy and bronchoscopy unit. METHODS: The alert for a pseudooutbreak was given when 3 patients, in the same week, had a positive bronchoalveolar lavage culture for M abscessus subsp bolletii. The patients had no symptoms/signs of mycobacterial infection; thus, contamination of bronchoscopes was suspected. Samples for culturing were collected from bronchoscopes, digestive endoscopes, automated disinfection machines, and the water supply. Clinical samples were identified by polymerase chain reaction restriction-enzyme analysis (PRA) of the hsp65 gene and their pulsed-field gel electrophoresis pattern was compared with environmental samples. RESULTS: The investigation demonstrated a contamination of bronchoscopes, digestive endoscopes, and disinfection machines. Molecular typing demonstrated that all strains belonged to the same clone (MAB01), identical to clone BRA100. DISCUSSION: Cross-transmission due to poor disinfection as well as resistance to glutaraldehyde may play roles in the spread of MAB01 M abscessus subsp bolletii, which may have a unique resistance to the environment and adaption to human hosts. However the water supply may have played a role. Attention is needed to ensure the quality of water used to rinse disinfected equipment.","corpus_id":44453490,"score":0}],"string":"[\n {\n \"doc_id\": \"22207751\",\n \"title\": \"Whole-genome sequence of the emerging pathogen Mycobacterium abscessus strain 47J26.\",\n \"abstract\": \"Mycobacterium abscessus is a rapidly growing environmental mycobacterium commonly found in soil and water which is often also associated with infections in humans, particularly of the lung. We report herein the draft genome sequence of M. abscessus strain 47J26.\",\n \"corpus_id\": 37879192,\n \"score\": 2\n },\n {\n \"doc_id\": \"22535937\",\n \"title\": \"Draft genome sequence of Mycobacterium abscessus subsp. bolletii BD(T).\",\n \"abstract\": \"Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T).\",\n \"corpus_id\": 36817549,\n \"score\": 2\n },\n {\n \"doc_id\": \"22628511\",\n \"title\": \"Complete genome sequence of Mycobacterium phlei type strain RIVM601174.\",\n \"abstract\": \"Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is typically nonpathogenic, with few reported cases of human disease. Here we report the whole genome sequence of M. phlei type strain RIVM601174.\",\n \"corpus_id\": 13197937,\n \"score\": 2\n },\n {\n \"doc_id\": \"23105073\",\n \"title\": \"Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621.\",\n \"abstract\": \"Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM). It is ubiquitous in water and soil habitats, including hospital environments. M. fortuitum is increasingly recognized as an opportunistic nosocomial pathogen causing disseminated infection. Here we report the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.\",\n \"corpus_id\": 12676089,\n \"score\": 2\n },\n {\n \"doc_id\": \"23105074\",\n \"title\": \"Complete genome sequence of Mycobacterium vaccae type strain ATCC 25954.\",\n \"abstract\": \"Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is generally not considered a human pathogen and is of major pharmaceutical interest as an immunotherapeutic agent. We report here the annotated genome sequence of the M. vaccae type strain, ATCC 25954.\",\n \"corpus_id\": 23380235,\n \"score\": 2\n },\n {\n \"doc_id\": \"23658631\",\n \"title\": \"MabsBase: a Mycobacterium abscessus genome and annotation database.\",\n \"abstract\": \"SUMMARY: Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.\",\n \"corpus_id\": 5873227,\n \"score\": 2\n },\n {\n \"doc_id\": \"23678183\",\n \"title\": \"The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria.\",\n \"abstract\": \"The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ∼3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram(-)) or Gram(+) bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.\",\n \"corpus_id\": 13227878,\n \"score\": 2\n },\n {\n \"doc_id\": \"24197885\",\n \"title\": \"Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in clinical isolates by multiplex PCR.\",\n \"abstract\": \"The rapidly growing mycobacterium M. abscessus sensu lato is the causative agent of emerging pulmonary and skin diseases and of infections following cosmetic surgery and postsurgical procedures. M. abscessus sensu lato can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Clinical isolates of rapidly growing mycobacteria were previously identified as M. abscessus by DNA-DNA hybridization. More than 30% of these 117 clinical isolates were differentiated as M. abscessus subsp. massiliense using combinations of multilocus genotyping analyses. A much more cost-effective technique to distinguish M. abscessus subsp. massiliense from M. abscessus subsp. abscessus, a multiplex PCR assay, was developed using the whole-genome sequence of M. abscessus subsp. massiliense JCM15300 as a reference. Several primer sets were designed for single PCR to discriminate between the strains based on amplicons of different sizes. Two of these single-PCR target sites were chosen for development of the multiplex PCR assay. Multiplex PCR was successful in distinguishing clinical isolates of M. abscessus subsp. massiliense from samples previously identified as M. abscessus. This approach, which spans whole-genome sequencing and clinical diagnosis, will facilitate the acquisition of more-precise information about bacterial genomes, aid in the choice of more relevant therapies, and promote the advancement of novel discrimination and differential diagnostic assays.\",\n \"corpus_id\": 206781514,\n \"score\": 2\n },\n {\n \"doc_id\": \"25503461\",\n \"title\": \"Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.\",\n \"abstract\": \"Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.\",\n \"corpus_id\": 13403401,\n \"score\": 2\n },\n {\n \"doc_id\": \"26448181\",\n \"title\": \"Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Complex.\",\n \"abstract\": \"PURPOSE: Clarithromycin was considered the cornerstone for the treatment of Mycobacterium abscessus complex infections. Genetic resistance mechanisms have been described and many experts propose amikacin as an alternative. Nevertheless, clarithromycin has several advantages; therefore, it is necessary to identify the non-functional erm(41) allele to determine the most suitable treatment. The aims of this study were to characterize the molecular mechanisms of clarithromycin resistance in a collection of Mycobacterium abscessus complex isolates and to verify the relationship between these mechanisms and the antibiogram. MATERIALS AND METHODS: Clinical isolates of M. abscessus complex (n = 22) from 16 patients were identified using four housekeeping genes (rpoB, secA1, sodA and hsp65), and their genetic resistance was characterized by studying erm(41) and rrl genes. Nine strains were recovered from the clinical isolates and subjected to E-test and microdilution clarithromycin susceptibility tests, with readings at 3, 7 and 14 days. RESULTS: We classified 11/16 (68.8%) M. abscessus subsp. abscessus, 4/16 (25.0%) M. abscessus subsp. bolletii, and 1/16 (6.3%) M. abscessus subsp. massiliense. T28 erm(41) allele was observed in 8 Mycobacterium abscessus subps. abscessus and 3 Mycobacterium abscessus subsp. bolletii. One strain of M. abscessus subsp. bolletii had an erm(41) gene truncated and was susceptible to clarithromycin. No mutations were observed in rrl gene first isolates. In three patients, follow-up of initial rrl wild-type strains showed acquired resistance. CONCLUSIONS: Most clinical isolates of M. abscessus complex had inducible resistance to clarithromycin and total absence of constitutive resistance. Our findings showed that the acquisition of resistance mutations in rrl gene was associated with functional and non-functional erm(41) gene. Caution is needed when using erm(41) sequencing alone to identify M. abscessus subspecies. This study reports an acquired mutation at position 2057 of rrl gene, conferring medium-low clarithromycin constitutive resistance.\",\n \"corpus_id\": 4639575,\n \"score\": 2\n },\n {\n \"doc_id\": \"26744369\",\n \"title\": \"Complete Genome Sequence of a Novel Clinical Isolate, Mycobacterium abscessus Strain NOV0213.\",\n \"abstract\": \"Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. We determined the complete genome sequence of the M. abscessus strain NOV0213, which was isolated from a patient with tuberculosis-like disease and with various antibiotic resistances.\",\n \"corpus_id\": 6291417,\n \"score\": 2\n },\n {\n \"doc_id\": \"27284156\",\n \"title\": \"Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii.\",\n \"abstract\": \"We report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii isolate recovered from a sputum culture from an individual with cystic fibrosis. This sequence is the first completed whole-genome sequence of M. abscessus subsp. bolletii and adds value to studies of M. abscessus complex genomics.\",\n \"corpus_id\": 32488496,\n \"score\": 2\n },\n {\n \"doc_id\": \"27660787\",\n \"title\": \"Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains.\",\n \"abstract\": \"We report the complete genome sequences of 17 rapidly growing nontuberculous mycobacterial (NTM) strains, including 16 Mycobacterium abscessus complex strains and one M. immunogenum strain. These sequences add value to studies of the genetic diversity of rapidly growing NTM strains recovered from human specimens.\",\n \"corpus_id\": 29466791,\n \"score\": 2\n },\n {\n \"doc_id\": \"27688344\",\n \"title\": \"Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.\",\n \"abstract\": \"Mycobacterium ulcerans subsp. shinshuense produces mycolactone and causes Buruli ulcer. Here, we report the complete sequence of its genome, which comprises a 5.9-Mb chromosome and a 166-kb plasmid (pShT-P). The sequence will represent the essential data for future phylogenetic and comparative genome studies of mycolactone-producing mycobacteria.\",\n \"corpus_id\": 31657969,\n \"score\": 2\n },\n {\n \"doc_id\": \"28818905\",\n \"title\": \"Complete Genome Sequence of Mycobacterium stephanolepidis.\",\n \"abstract\": \"Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine teleost fish (Stephanolepis cirrhifer) and is closely related to Mycobacterium chelonae Here, we report the complete sequence of its genome, comprising a 4.9-Mb chromosome. The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen.\",\n \"corpus_id\": 10415640,\n \"score\": 2\n },\n {\n \"doc_id\": \"29449406\",\n \"title\": \"Complete Genome Sequence of Mycobacterium sp. Strain 4858.\",\n \"abstract\": \"Mycobacterium sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a Cambodian patient with a pulmonary infection. We report the first complete 5.6-Mbp-long genome sequence of Mycobacterium strain 4858, with 68.24% GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.\",\n \"corpus_id\": 3283202,\n \"score\": 2\n },\n {\n \"doc_id\": \"29773624\",\n \"title\": \"Complete Genome Sequence of Mycobacterium marinum ATCC 927T, Obtained Using Nanopore and Illumina Sequencing Technologies.\",\n \"abstract\": \"Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.\",\n \"corpus_id\": 21712933,\n \"score\": 2\n },\n {\n \"doc_id\": \"18753344\",\n \"title\": \"Proportions of Mycobacterium massiliense and Mycobacterium bolletii strains among Korean Mycobacterium chelonae-Mycobacterium abscessus group isolates.\",\n \"abstract\": \"Korean isolates of the Mycobacterium chelonae-Mycobacterium abscessus group, which had been isolated from two different hospitals in South Korea, were identified by PCR restriction analysis (PRA) and comparative sequence analysis of 16S rRNA genes, rpoB, and hsp65 to evaluate the proportion of four closely related species (M. chelonae, M. abscessus, M. massiliense, and M. bolletii). Of the 144 rapidly growing mycobacterial strains tested, 127 strains (88.2%) belonged to the M. chelonae-M. abscessus group. In this group, M. chelonae, M. abscessus, M. massiliense, and M. bolletii accounted for 0.8% (n = 1), 51.2% (n = 65), 46.5% (n = 59), and 1.6% (n = 2), respectively. Two isolates which showed discordant results, M. massiliense by rpoB sequence analysis and M. abscessus by hsp65 sequence analysis, were finally identified as M. massiliense based on the additional analysis of sodA and the 16S-23S internal transcribed spacer. M. abscessus group I isolates previously identified by hsp65 PRA were all found to be M. abscessus, whereas group II isolates were further identified as M. massiliense or M. bolletii by sequencing of rpoB and hsp65. Smooth, rough, or mixed colonies of both M. abscessus and M. massiliense isolates were observed. M. massiliense strains that were highly resistant to clarithromycin had a point mutation at the adenine at position 2058 (A(2058)) or 2059 (A(2059)) in the peptidyltransferase region of the 23S rRNA gene.\",\n \"corpus_id\": 7521619,\n \"score\": 1\n },\n {\n \"doc_id\": \"19420162\",\n \"title\": \"Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii.\",\n \"abstract\": \"Mycobacterium abscessus is the most common cause of rapidly growing mycobacterial chronic lung disease. Recently, two new M. abscessus-related species, M. massiliense and M. bolletii, have been described. Health care-associated outbreaks have recently been investigated by the use of molecular identification and typing tools; however, very little is known about the natural epidemiology and pathogenicity of M. massiliense or M. bolletii outside of outbreak situations. The differentiation of these two species from M. abscessus is difficult and relies on the sequencing of one or more housekeeping genes. We performed extensive molecular identification and typing of 42 clinical isolates of M. abscessus, M. massiliense, and M. bolletii from patients monitored at the NIH between 1999 and 2007. The corresponding clinical data were also examined. Partial sequencing of rpoB, hsp65, and secA led to the unambiguous identification of 26 M. abscessus isolates, 7 M. massiliense isolates, and 2 M. bolletii isolates. The identification results for seven other isolates were ambiguous and warranted further sequencing and an integrated phylogenetic analysis. Strain relatedness was assessed by repetitive-sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE), which showed the characteristic clonal groups for each species. Five isolates with ambiguous species identities as M. abscessus-M. massiliense by rpoB, hsp65, and secA sequencing clustered as a distinct group by rep-PCR and PFGE together with the M. massiliense type strain. Overall, the clinical manifestations of disease caused by each species were similar. In summary, a multilocus sequencing approach (not just rpoB partial sequencing) is required for division of M. abscessus and closely related species. Molecular typing complements sequence-based identification and provides information on prevalent clones with possible relevant clinical aspects.\",\n \"corpus_id\": 30935694,\n \"score\": 1\n },\n {\n \"doc_id\": \"19571015\",\n \"title\": \"Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae-M. abscessus group is needed.\",\n \"abstract\": \"An outbreak of postsurgical infections caused by rapidly growing mycobacteria has been ongoing in Brazil since 2004. The degrees of similarity of the rpoB and hsp65 sequences from the clinical isolates and the corresponding sequences from both the Mycobacterium massiliense and the M. bolletii type strains were above the accepted limit for interspecies variability, leading to conflicting identification results. Therefore, an extensive characterization of members of the M. chelonae-M. abscessus group was carried out. The M. abscessus, M. chelonae, M. immunogenum, M. massiliense, and M. bolletii type strains and a subset of clinical isolates were analyzed by biochemical tests, high-performance liquid chromatography, drug susceptibility testing, PCR-restriction enzyme analysis of hsp65 (PRA-hsp65), rpoB, and hsp65 gene sequencing and analysis of phylogenetic trees, DNA-DNA hybridization (DDH), and restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene (RFLP-16S rRNA). The clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains could not be separated by phenotypic tests and were grouped in the phylogenetic trees obtained. The results of DDH also confirmed the >70% relatedness of the clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains; and indistinguishable RFLP-16S rRNA patterns were obtained. On the contrary, the separation of clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains from M. chelonae and M. immunogenum was supported by the results of PRA-hsp65, DDH, and RFLP-16S rRNA and by the rpoB and hsp65 phylogenetic trees. Taken together, these results led to the proposition that M. abscessus, M. massiliense, and M. bolletii represent a single species, that of M. abscessus. Two subspecies are also proposed, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, and these two subspecies can be distinguished by two different PRA-hsp65 patterns, which differ by a single HaeIII band, and by differences in their rpoB (3.4%) and hsp65 (1.3%) sequences.\",\n \"corpus_id\": 33583558,\n \"score\": 1\n },\n {\n \"doc_id\": \"21106786\",\n \"title\": \"Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.\",\n \"abstract\": \"Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.\",\n \"corpus_id\": 11343426,\n \"score\": 1\n },\n {\n \"doc_id\": \"22628507\",\n \"title\": \"Genome sequence of the Mycobacterium abscessus strain M93.\",\n \"abstract\": \"Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. We report herein the draft genome sequence of M. abscessus strain M93.\",\n \"corpus_id\": 44946809,\n \"score\": 1\n },\n {\n \"doc_id\": \"22843600\",\n \"title\": \"Draft genome sequence of Mycobacterium bolletii strain M24, a rapidly growing mycobacterium of contentious taxonomic status.\",\n \"abstract\": \"The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar lavage fluid of a Malaysian patient, is reported here. The circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of this organism within the M. abscessus complex and revealed the presence of proteins potentially important for pathogenicity in a human host.\",\n \"corpus_id\": 39270814,\n \"score\": 1\n },\n {\n \"doc_id\": \"23012295\",\n \"title\": \"Analysis of the genome of Mycobacterium abscessus strain M94 reveals an uncommon cluster of tRNAs.\",\n \"abstract\": \"Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. Here, we report the annotated genome sequence of M. abscessus strain M94, which showed an unusual cluster of tRNAs.\",\n \"corpus_id\": 20704821,\n \"score\": 1\n },\n {\n \"doc_id\": \"23045507\",\n \"title\": \"Genomic analysis of Mycobacterium abscessus strain M139, which has an ambiguous subspecies taxonomic position.\",\n \"abstract\": \"Mycobacterium abscessus is a ubiquitous, rapidly growing species of nontuberculous mycobacteria that colonizes organic surfaces and is frequently associated with opportunistic infections in humans. We report here the draft genome sequence of Mycobacterium abscessus strain M139, which shows genomic features reported to be characteristic of both Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. massiliense.\",\n \"corpus_id\": 20597949,\n \"score\": 1\n },\n {\n \"doc_id\": \"23144407\",\n \"title\": \"Genome sequence of Mycobacterium abscessus strain M152.\",\n \"abstract\": \"Mycobacterium abscessus is an environmental bacterium with increasing clinical relevance. Here, we report the annotated whole-genome sequence of M. abscessus strain M152.\",\n \"corpus_id\": 27949875,\n \"score\": 1\n },\n {\n \"doc_id\": \"23294800\",\n \"title\": \"Mycobacterium abscessus multispacer sequence typing.\",\n \"abstract\": \"BACKGROUND: Mycobacterium abscessus group includes antibiotic-resistant, opportunistic mycobacteria that are responsible for sporadic cases and outbreaks of cutaneous, pulmonary and disseminated infections. However, because of their close genetic relationships, accurate discrimination between the various strains of these mycobacteria remains difficult. In this report, we describe the development of a multispacer sequence typing (MST) analysis for the simultaneous identification and typing of M. abscessus mycobacteria. We also compared MST with the reference multilocus sequence analysis (MLSA) typing method. RESULTS: Based on the M. abscessus CIP104536T genome, eight intergenic spacers were selected, PCR amplified and sequenced in 21 M. abscessus isolates and analysed in 48 available M. abscessus genomes. MST and MLSA grouped 37 M. abscessus organisms into 12 and nine types, respectively; four formerly \\\"M. bolletii\\\" organisms and M. abscessus M139 into three and four types, respectively; and 27 formerly \\\"M. massiliense\\\" organisms grouped into nine and five types, respectively. The Hunter-Gaston index was off 0.912 for MST and of 0.903 for MLSA. The MST-derived tree was similar to that based on MLSA and rpoB gene sequencing and yielded three main clusters comprising each the type strain of the respective M. abscessus sub-species. Two isolates exhibited discordant MLSA- and rpoB gene sequence-derived position, one isolate exhibited discordant MST- and rpoB gene sequence-derived position and one isolate exhibited discordant MST- and MLSA-derived position. MST spacer n°2 sequencing alone allowed for the accurate identification of the different isolates at the sub-species level. CONCLUSIONS: MST is a new sequencing-based approach for both identifying and genotyping M. abscessus mycobacteria that clearly differentiates formerly \\\"M. massiliense\\\" organisms from other M. abscessus subsp. bolletii organisms.\",\n \"corpus_id\": 14428949,\n \"score\": 1\n },\n {\n \"doc_id\": \"23295745\",\n \"title\": \"Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil.\",\n \"abstract\": \"A single strain of Mycobacterium abscessus subsp. bolletii, characterised by a particular rpoB sequevar and two highly related pulsed field gel electrophoresis patterns has been responsible for a nationwide outbreak of surgical infections in Brazil since 2004. In this study, we developed molecular tests based on polymerase chain reaction restriction-enzyme analysis (PRA) and sequencing for the rapid identification of this strain. Sequences of 15 DNA regions conserved in mycobacteria were retrieved from GenBank or sequenced and analysed in silico. Single nucleotide polymorphisms specific to the epidemic strain and located in enzyme recognition sites were detected in rpoB, the 3' region of the 16S rDNA and gyrB. The three tests that were developed, i.e., PRA-rpoB, PRA-16S and gyrB sequence analysis, showed 100%, 100% and 92.31% sensitivity and 93.06%, 90.28% and 100% specificity, respectively, for the discrimination of the surgical strain from other M. abscessus subsp. bolletii isolates, including 116 isolates from 95 patients, one environmental isolate and two type strains. The results of the three tests were stable, as shown by results obtained for different isolates from the same patient. In conclusion, due to the clinical and epidemiological importance of this strain, these tests could be implemented in reference laboratories for the rapid preliminary diagnosis and epidemiological surveillance of this epidemic strain.\",\n \"corpus_id\": 12304829,\n \"score\": 1\n },\n {\n \"doc_id\": \"23565273\",\n \"title\": \"The detection and sequencing of a broad-host-range conjugative IncP-1β plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii.\",\n \"abstract\": \"BACKGROUND: An extended outbreak of mycobacterial surgical infections occurred in Brazil during 2004-2008. Most infections were caused by a single strain of Mycobacterium abscessus subsp. bolletii, which was characterized by a specific rpoB sequevar and two highly similar pulsed-field gel electrophoresis (PFGE) patterns differentiated by the presence of a ∼50 kb band. The nature of this band was investigated. METHODOLOGY/PRINCIPAL FINDINGS: Genomic sequencing of the prototype outbreak isolate INCQS 00594 using the SOLiD platform demonstrated the presence of a 56,267-bp [corrected] circular plasmid, designated pMAB01. Identity matrices, genetic distances and phylogeny analyses indicated that pMAB01 belongs to the broad-host-range plasmid subgroup IncP-1β and is highly related to BRA100, pJP4, pAKD33 and pB10. The presence of pMAB01-derived sequences in 41 M. abscessus subsp. bolletii isolates was evaluated using PCR, PFGE and Southern blot hybridization. Sixteen of the 41 isolates showed the presence of the plasmid. The plasmid was visualized as a ∼50-kb band using PFGE and Southern blot hybridization in 12 isolates. The remaining 25 isolates did not exhibit any evidence of this plasmid. The plasmid was successfully transferred to Escherichia coli by conjugation and transformation. Lateral transfer of pMAB01 to the high efficient plasmid transformation strain Mycobacterium smegmatis mc(2)155 could not be demonstrated. CONCLUSIONS/SIGNIFICANCE: The occurrence of a broad-host-range IncP-1β plasmid in mycobacteria is reported for the first time. Thus, genetic exchange could result in the emergence of specific strains that might be better adapted to cause human disease.\",\n \"corpus_id\": 1360653,\n \"score\": 1\n },\n {\n \"doc_id\": \"23804391\",\n \"title\": \"New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance.\",\n \"abstract\": \"Mycobacterium abscessus (M. abscessus sensu lato, or the M. abscessus group) comprises three closely related taxa whose taxonomic statuses are under revision, i.e., M. abscessus sensu stricto, Mycobacterium bolletii, and Mycobacterium massiliense. We describe here a simple, robust, and cost-effective PCR-based method for distinguishing among M. abscessus, M. massiliense, and M. bolletii. Based on the M. abscessus ATCC 19977(T) genome, regions that discriminated between M. abscessus and M. massiliense were identified through array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense, and 2 M. bolletii isolates previously identified by multitarget sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full-length erm(41) gene instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for straightforward identification of M. abscessus, M. massiliense, and M. bolletii and the assessment of inducible clarithromycin resistance. This method can be easily integrated into a routine workflow to provide subspecies-level identification within 24 h after isolation of the M. abscessus group.\",\n \"corpus_id\": 9701331,\n \"score\": 1\n },\n {\n \"doc_id\": \"23850022\",\n \"title\": \"Further isolation of Mycobacterium abscessus subsp. abscessus and subsp. bolletii in different regions of Japan and susceptibility of these isolates to antimicrobial agents.\",\n \"abstract\": \"The aim of this study was to genetically analyse Mycobacterium abscessus subsp. abscessus (hereafter M. abscessus) and M. abscessus subsp. bolletii (hereafter M. bolletii) isolates from six different regions of Japan and to determine the antimicrobial susceptibility of these isolates. Subspeciation of 143 clinical isolates of M. abscessus group was done by comparative sequence analysis of the rpoB and hsp65 genes and the internal transcribed spacer (ITS) region. Genetic analysis led to the identification of 90 M. abscessus (62.9%) and 53 M. bolletii (37.1%; comprising 50 'M. massiliense' and 3 'M. bolletii' in the old nomenclature). No significant differences were found between the M. abscessus and M. bolletii isolates in any characteristics. Susceptibility to clarithromycin and linezolid for M. bolletii isolates was significantly higher than that for M. abscessus (P<0.05). Moreover, the results demonstrated that 82 M. abscessus isolates with T28 sequevar were resistant to clarithromycin owing to the expression of erm(41), which was induced by clarithromycin, whilst 8 isolates with C28 sequevar were susceptible. Acquired clarithromycin resistance in 'M. bolletii' isolates was significantly associated with previous Mycobacterium avium complex (MAC) treatment compared with that of M. abscessus isolates; however, intrinsic inducible susceptibility of M. abscessus isolates was not associated with MAC treatment. However, acquired resistance to clarithromycin by mutation in the rrl gene encoding 23S rRNA did not occur in 14 of 18 resistant isolates. Strains with acquired resistance to clarithromycin and mutation in rrl consisted of two M. bolletii (one 'M. massiliense' and one 'M. bolletii') and two M. abscessus T28 sequevar.\",\n \"corpus_id\": 5770482,\n \"score\": 1\n },\n {\n \"doc_id\": \"24009121\",\n \"title\": \"Whole-Genome Sequence of Mycobacterium abscessus Clinical Strain V06705.\",\n \"abstract\": \"Infection caused by Mycobacterium abscessus strains is a growing cause of concern in both community-acquired and health care-associated diseases, as these organisms naturally display multiple drug resistances. We report an annotated draft genome sequence of M. abscessus strain V06705 obtained from a patient in France.\",\n \"corpus_id\": 11847130,\n \"score\": 1\n },\n {\n \"doc_id\": \"24055961\",\n \"title\": \"Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains.\",\n \"abstract\": \"Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents.\",\n \"corpus_id\": 25962366,\n \"score\": 1\n },\n {\n \"doc_id\": \"24312320\",\n \"title\": \"The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.\",\n \"abstract\": \"Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.\",\n \"corpus_id\": 4057249,\n \"score\": 1\n },\n {\n \"doc_id\": \"24523815\",\n \"title\": \"The First Korean Case of Nontuberculous Mycobacterial Lung Disease Caused by Mycobacterium abscessus Subspecies bolletii in a Patient with Bronchiectasis.\",\n \"abstract\": \"We report the first Korean case of lung diseases caused by Mycobacterium abscessus subsp. bolletii in a previously healthy male, except for a previous history of pulmonary tuberculosis and bronchiectasis. All serial isolates are identified as M. abscessus subsp. bolletii by multi-locus sequence analysis based on the hsp65, rpoB, and 16S rRNA fragments. At the genetic level, the isolate has the erm(41) gene with a T28 sequevar, associated with clarithromycin resistance, and no rrl mutation. The isolate is resistant to clarithromycin. Although the symptoms and radiographic findings have improved after combination of antibiotics, the follow-up sputum cultures are persistently positive.\",\n \"corpus_id\": 5792327,\n \"score\": 1\n },\n {\n \"doc_id\": \"24671795\",\n \"title\": \"Clonal relationship and differentiation among Mycobacterium abscessus isolates as determined using the semiautomated repetitive extragenic palindromic sequence PCR-based DiversiLab system.\",\n \"abstract\": \"Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for M. abscessus genotyping. Since M. abscessus was shown to be composed of subspecies (M. abscessus subsp. massiliense, M. abscessus subsp. bolletii, and M. abscessus subsp. abscessus), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83 M. abscessus original isolates (43 M. abscessus subsp. abscessus, 12 M. abscessus subsp. bolletii, and 28 M. abscessus subsp. massiliense) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the M. abscessus subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of M. abscessus infections.\",\n \"corpus_id\": 9080162,\n \"score\": 1\n },\n {\n \"doc_id\": \"24886480\",\n \"title\": \"Genome analysis reveals three genomospecies in Mycobacterium abscessus.\",\n \"abstract\": \"BACKGROUND: Mycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described. RESULTS: In-depth analysis of 14 published M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors (including PE, PPE, LpqH, MCE, Yrbe and type VII secretion system ESX3 and ESX4) varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by β-lactam antibiotics and an Ambler class A β-lactamase for which inhibitors exist. CONCLUSIONS: Our comparative analysis indicates that M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus.\",\n \"corpus_id\": 13524467,\n \"score\": 1\n },\n {\n \"doc_id\": \"24899019\",\n \"title\": \"Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.\",\n \"abstract\": \"Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus.\",\n \"corpus_id\": 6896187,\n \"score\": 1\n },\n {\n \"doc_id\": \"24932856\",\n \"title\": \"Species identification of Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii using rpoB and hsp65, and susceptibility testing to eight antibiotics.\",\n \"abstract\": \"OBJECTIVES: To separate Mycobacterium abscessus subsp. bolletii from Mycobacterium abscessus subsp. abscessus using species identification, and to investigate the in vitro activity of amikacin, cefoxitin, imipenem, levofloxacin, moxifloxacin, clarithromycin, azithromycin, and linezolid against Mycobacterium abscessus. METHODS: Seventy M. abscessus isolates, previously identified by 16S rRNA sequencing, were further identified by comparative sequence analysis of rpoB and hsp65. Drug susceptibility testing was conducted using the microplate Alamar Blue assay in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines and interpreted using CLSI breakpoints. RESULTS: Of the 70 strains, 45 (64%) were M. abscessus subsp. abscessus and 25 (36%) were M. abscessus subsp. bolletii. The majority of M. abscessus isolates were susceptible to azithromycin, amikacin, linezolid, and imipenem (M. abscessus subsp. abscessus: 93%, 98%, 93%, and 73%, respectively; M. abscessus subsp. bolletii: 96%, 96%, 80%, and 68%, respectively). Approximately half of the M. abscessus isolates were moderately susceptible to cefoxitin and moxifloxacin (M. abscessus subsp. abscessus 53% and 49%; M. abscessus subsp. bolletii 72% and 68%). Nearly all the M. abscessus isolates were resistant to levofloxacin (M. abscessus subsp. abscessus 96%, M. abscessus subsp. bolletii 100%). Inducible clarithromycin resistance was found in M. abscessus. After 14 days of incubation, 83% M. abscessus subsp. abscessus and 36% M. abscessus subsp. bolletii were resistant to clarithromycin. CONCLUSIONS: Using rpoB and hsp65, M. abscessus subsp. bolletii could be distinguished from M. abscessus subsp. abscessus. Amikacin and azithromycin showed excellent activity against M. abscessus in vitro. Imipenem, linezolid, cefoxitin, and moxifloxacin also showed good activity. Levofloxacin was inactive against M. abscessus. Although clarithromycin showed excellent activity against M. abscessus on day 3, inducible resistance occurred, and after 14 days clarithromycin showed little activity against M. abscessus subsp. abscessus, but still had good activity against M. abscessus subsp. bolletii.\",\n \"corpus_id\": 205275560,\n \"score\": 1\n },\n {\n \"doc_id\": \"25268925\",\n \"title\": \"Mycobacterium abscessus: challenges in diagnosis and treatment.\",\n \"abstract\": \"PURPOSE OF REVIEW: Mycobacterium abscessus is the most common rapidly growing mycobacterium that causes lung disease. This review describes recently published literature regarding M. abscessus taxonomy, environmental niche, diagnosis, management and outcome in pulmonary disease in adults and adolescents with cystic fibrosis. RECENT FINDINGS: The classification of M. abscessus subsp. abscessus, M. abscessus subsp. massiliense and M. abscessus subsp. bolletii is useful clinically because of the discovery of the erm(41) gene, which is responsible for macrolide resistance in M. abscessus. Macrolide susceptibility is key for successful treatment of M. abscessus subsp. massiliense. The poor outcome and eradication of M. abscessus subsp. abscessus remains both a diagnostic and treatment challenge in approximately 80% of isolates that are macrolide resistant. Molecular studies, such as genotyping, may allow prediction of disease progression. Overall, there is a dearth of new literature surrounding M. abscessus. SUMMARY: New studies differentiating M. abscessus subsp. abscessus and M. abscessus subsp. massiliense based on the erm(41) gene demonstrate the latter to have a better prognosis and improved treatment outcomes. M. abscessus subsp. abscessus remains a formidable pathogen in diagnosis and treatment.\",\n \"corpus_id\": 20505570,\n \"score\": 1\n },\n {\n \"doc_id\": \"25580261\",\n \"title\": \"Mycobacterium abscessus subsp abscessus lung disease: 'trouble ahead, trouble behind…'.\",\n \"abstract\": \"Mycobacterium abscessus subsp abscessus is the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria (NTM) and is also the most feared due to its well-deserved reputation for being refractory to antibiotic therapy. M. abscessus subsp abscessus has multiple innate antibiotic resistance mechanisms, but the most important one described so far is an inducible erythromycin methylase (erm) gene. M. abscessus subsp abscessus isolates may appear macrolide susceptible on initial in vitro testing but become macrolide resistant after exposure to macrolide. It is therefore very important to test clinically significant M. abscessus subsp abscessus isolates for erm gene activity. Remarkably, controversy still exists about the taxonomy and nomenclature of M. abscessus subspecies including subsp abscessus, subsp massiliense and subsp bolletii. Identification of these subspecies is not moot as M. abscessus subsp massiliense does not have an active erm gene resulting in both in vitro and in vivo susceptibility to macrolide. It is imperative from the clinician's perspective that mycobacterial laboratories correctly and rapidly identify M. abscessus to the subspecies level. Unfortunately, there are no reliably or predictably effective treatment regimens for M. abscessus subsp abscessus and better, more effective antimicrobial agents are badly needed. Surgical resection of involved lung tissue as an adjunct to antibiotic therapy is beneficial in selected patients but cannot be broadly applied. Overall, M. abscessus subsp abscessus remains a formidable respiratory mycobacterial pathogen, one that we are only beginning to understand microbiologically and one that as yet consistently evades our best efforts at successful therapeutic outcomes. ' trouble ahead, trouble behind, and you know that notion just crossed my mind'.Casey Jones, Grateful Dead (1970).\",\n \"corpus_id\": 14184044,\n \"score\": 1\n },\n {\n \"doc_id\": \"25643064\",\n \"title\": \"Mycobacterium abscessus. \\\"Pleased to meet you, hope you guess my name...\\\".\",\n \"abstract\": \"Mycobacterium abscessus is a formidable and difficult-to-treat mycobacterial pathogen with multiple drug-resistance mechanisms. The most important of these mechanisms is the presence of an inducible erythromycin methylase (erm) gene, because it confers macrolide resistance. It has recently been found that \\\"M. abscessus\\\" can be split into three species or subspecies based on gene sequence analysis other than the 16S rRNA gene and the presence or absence of a functional erm(41) gene. Several names have been applied to these three organisms, including M. abscessus or M. abscessus subsp. abscessus, Mycobacterium massiliense or M. abscessus subsp. massiliense, and Mycobacterium bolletii or M. abscessus subsp. bolletii. No universally accepted or recognized species or subspecies designations have emerged, and no names have been universally adopted for these organisms. This uncertainty has led to inconsistencies in the medical literature and understandable confusion by clinicians about the appropriate labels for \\\"M. abscessus\\\" isolates. We discuss the complexities involved in mycobacterial species/subspecies identification and taxonomy and suggest possible ways to improve the present state of uncertainty surrounding the labels for \\\"M. abscessus\\\" clinical isolates. We also suggest necessary changes in mycobacterial laboratory processing and reporting procedures for mycobacterial isolates.\",\n \"corpus_id\": 262931951,\n \"score\": 1\n },\n {\n \"doc_id\": \"26067970\",\n \"title\": \"Draft Genome Sequence of Mycobacterium arupense Strain GUC1.\",\n \"abstract\": \"We report the draft genome sequence of Mycobacterium arupense strain GUC1 from a sputum sample of a patient with bronchiectasis. This is the first draft genome sequence of Mycobacterium arupense, a rapidly growing nonchromogenic mycobacteria.\",\n \"corpus_id\": 4476148,\n \"score\": 1\n },\n {\n \"doc_id\": \"26072272\",\n \"title\": \"Molecular epidemiology of Mycobacterium abscessus complex isolates in Ireland.\",\n \"abstract\": \"BACKGROUND: The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. METHODS: We performed rpoB gene sequencing and multi-locus sequence typing (MLST) on M. abscessus complex strains isolated from thirty-six patients in 2006-2012 (eighteen known CF patients). RESULTS: Twenty-eight strains (78%) were M. abscessus subsp. abscessus, eight M. abscessus subsp. massiliense, none were M. abscessus subsp. bolletii. Sequence type 1 (ST1) and ST26 (M. abscessus subsp. abscessus) were commonest. Seven M. abscessus subsp. abscessus STs (25%) were novel (two with novel alleles). Seven M. abscessus subsp. massiliense STs were previously reported (88%), including two ST23, the globally successful clone. In 2012, of 552 CF patients screened, eleven were infected with M. abscessus complex strains (2%). CONCLUSIONS: The most prevalent M. abscessus subsp. abscessus and M. abscessus subsp. massiliense strains in Ireland belong to widely-distributed STs, but there is evidence of high M. abscessus subsp. abscessus diversity.\",\n \"corpus_id\": 11122548,\n \"score\": 1\n },\n {\n \"doc_id\": \"26295364\",\n \"title\": \"Mycobacterium abscessus Complex Infections in Humans.\",\n \"abstract\": \"Mycobacterium abscessus complex comprises a group of rapidly growing, multidrug-resistant, nontuberculous mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, bacteremia, and ocular and other infections. M. abscessus complex is differentiated into 3 subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. The 2 major subspecies, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, have different erm(41) gene patterns. This gene provides intrinsic resistance to macrolides, so the different patterns lead to different treatment outcomes. M. abscessus complex outbreaks associated with cosmetic procedures and nosocomial transmissions are not uncommon. Clarithromycin, amikacin, and cefoxitin are the current antimicrobial drugs of choice for treatment. However, new treatment regimens are urgently needed, as are rapid and inexpensive identification methods and measures to contain nosocomial transmission and outbreaks.\",\n \"corpus_id\": 10028163,\n \"score\": 1\n },\n {\n \"doc_id\": \"26884275\",\n \"title\": \"Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications.\",\n \"abstract\": \"BACKGROUND: In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). RESULTS: Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal 'patchwork' architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. CONCLUSION: Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections.\",\n \"corpus_id\": 10181102,\n \"score\": 1\n },\n {\n \"doc_id\": \"27231356\",\n \"title\": \"Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.\",\n \"abstract\": \"Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains.\",\n \"corpus_id\": 3069391,\n \"score\": 1\n },\n {\n \"doc_id\": \"27499141\",\n \"title\": \"Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacteriumabscessus subsp. bolletii and designation of Mycobacteriumabscessus subsp. massiliense comb. nov.\",\n \"abstract\": \"The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).\",\n \"corpus_id\": 40586077,\n \"score\": 1\n },\n {\n \"doc_id\": \"28303132\",\n \"title\": \"Mycobacterium abscessus subsp. abscessus Is Capable of Degrading Pseudomonas aeruginosa Quinolone Signals.\",\n \"abstract\": \"Pseudomonas aeruginosa employs 2-heptyl-3-hydroxy-4(1H)-quinolone (the Pseudomonas quinolone signal, PQS) and 2-heptyl-4(1H)-quinolone (HHQ) as quorum sensing signal molecules, which contribute to a sophisticated regulatory network controlling the production of virulence factors and antimicrobials. We demonstrate that Mycobacterium abscessus(T) and clinical M. abscessus isolates are capable of degrading these alkylquinolone signals. Genome sequences of 50 clinical M. abscessus isolates indicated the presence of aqdRABC genes, contributing to fast degradation of HHQ and PQS, in M. abscessus subsp. abscessus strains, but not in M. abscessus subsp. bolletii and M. abscessus subsp. massiliense isolates. A subset of 18 M. a. subsp. abscessus isolates contained the same five single nucleotide polymorphisms (SNPs) compared to the aqd region of the type strain. Interestingly, representatives of these isolates showed faster PQS degradation kinetics than the M. abscessus type strain. One of the SNPs is located in the predicted promoter region of the aqdR gene encoding a putative transcriptional regulator, and two others lead to a variant of the AqdC protein termed AqdC(II), which differs in two amino acids from AqdC(I) of the type strain. AqdC, the key enzyme of the degradation pathway, is a PQS dioxygenase catalyzing quinolone ring cleavage. While transcription of aqdR and aqdC is induced by PQS, transcript levels in a representative of the subset of 18 isolates were not significantly altered despite the detected SNP in the promoter region. However, purified recombinant AqdC(II) and AqdC(I) exhibit different kinetic properties, with approximate apparent Km values for PQS of 14 μM and 37 μM, and kcat values of 61 s(-1) and 98 s(-1), respectively, which may (at least in part) account for the observed differences in PQS degradation rates of the strains. In co-culture experiments of P. aeruginosa PAO1 and M. abscessus, strains harboring the aqd genes reduced the PQS levels, whereas mycobacteria lacking the aqd gene cluster even boosted PQS production. The results suggest that the presence and expression of the aqd genes in M. abscessus lead to a competitive advantage against P. aeruginosa.\",\n \"corpus_id\": 18134820,\n \"score\": 1\n },\n {\n \"doc_id\": \"28820087\",\n \"title\": \"Reinstating Mycobacterium massiliense and Mycobacterium bolletii as species of the Mycobacterium abscessus complex.\",\n \"abstract\": \"TheMycobacterium abscessus complex is a group of rapidly growing, multiresistant mycobacteria previously divided into three species. Proposal for the union of Mycobacterium bolletii and Mycobacterium massiliense into one subspecies, so-called M. abscessus subsp. massiliense, created much confusion about the routine identification and reporting of M. abscessus clinical isolates for clinicians. Results derived from multigene sequencing unambiguously supported the reinstatement of M. massiliense and M. bolletii as species, culminating in the presence of erm(41)-encoded macrolide resistance in M. bolletii. Present genome-based analysis unambiguously supports the reinstatement of M. massiliense and M. bolletii as species after the average nucleotide identity values of 96.7 % for M. abscessus versus M. bolletii, and 96.4 % for M. abscessus versus M. massiliense, and the 96.6 % identity between M. bolletii and M. massiliense was put into the perspective of a larger, 28-species analysis. Accordingly, DNA-DNA hybridization values predicted by the complete rpoB gene sequencing analysis were between 68.7 and 72.3 % in this complex. These genomic data as well as the phenotypic characteristics prompted us to propose to reinstate the previously known M. massiliense and M. bolletii into two distinct species among the M. abscessus complex.\",\n \"corpus_id\": 43899885,\n \"score\": 1\n },\n {\n \"doc_id\": \"29061748\",\n \"title\": \"In Vitro Evaluation of Povidone-Iodine and Chlorhexidine against Outbreak and Nonoutbreak Strains of Mycobacterium abscessus Using Standard Quantitative Suspension and Carrier Testing.\",\n \"abstract\": \"Povidone-iodine (PI) and chlorhexidine (CHX) are widely used antiseptics active against conventional Staphylococcus aureus, Enterobacteriaceae, Candida species, and viruses, but their efficacy against Mycobacterium abscessus remains unproven. We determined the in vitro potency of alcoholic PI and CHX against M. abscessus subsp. abscessus (ATCC 19977), M. abscessus subsp. bolletii (BCRC 16915), and our outbreak strain of M. abscessus subsp. massiliense (TPE 101) in reference to Staphylococcus aureus (ATCC 29213) by standard quantitative suspension and carrier methods (EN 14563). By suspension, all mycobacterial strains compared to S. aureus were significantly more resistant to CHX, but not PI. By carrier, the mean logarithmic reductions (LR) achieved by PI under clean (dirty) conditions were 6.575 (2.482), 5.540 (2.298), 4.595 (1.967), and 1.173 (0.889), while those achieved by CHX under clean (dirty) conditions were 3.164 (5.445), 5.307 (2.564), 3.844 (2.232), and 0.863 (0.389) for S. aureus, M. abscessus subsp. bolletii, M. abscessus subsp. abscessus, and M. abscessus subsp. massiliense, respectively. M. abscessus subsp. massiliense (outbreak strain) was significantly more resistant than the other tested strains to PI and CHX. By both methods, the mean LR achieved by PI was higher than for CHX for all mycobacterial strains, but under dirty conditions, neither antiseptic was effectively mycobactericidal (LR < 5). These preliminary findings caution against the universal replacement of PI with CHX as the first-line skin antiseptic, since all M. abscessus isolates were resistant to CHX. More studies are needed to establish the best practice for skin antisepsis if mycobacterial infections are also to be prevented.\",\n \"corpus_id\": 12240230,\n \"score\": 1\n },\n {\n \"doc_id\": \"21037035\",\n \"title\": \"Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus.\",\n \"abstract\": \"The names 'Mycobacterium abscessus subsp. abscessus' and 'Mycobacterium abscessus subsp. massiliense', proposed by Leao et al. (2009, J Clin Microbiol 47, 2691-2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name 'Mycobacterium abscessus subsp. massiliense' is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.\",\n \"corpus_id\": 19364471,\n \"score\": 0\n },\n {\n \"doc_id\": \"21903825\",\n \"title\": \"Phenotypic and molecular characterization of quinolone resistance in Mycobacterium abscessus subsp. bolletii recovered from postsurgical infections.\",\n \"abstract\": \"Several outbreaks of infections caused by rapidly growing mycobacteria (RGM) were reported in many Brazilian states (2032 notified cases) from 2004 to 2010. Most of the confirmed cases were mainly associated with Mycobacterium massiliense (recently renamed as Mycobacterium abscessus subsp. bolletii) BRA100 clone, recovered from patients who had undergone invasive procedures in which medical instruments had not been properly sterilized and/or disinfected. Since quinolones have been an option for the treatment of general RGM infections and have been suggested for therapeutic schemes for these outbreaks, we evaluated the in vitro activities of all generations of quinolones for clinical and reference RGM by broth microdilution, and analysed the peptide sequences of the quinolone resistance determining regions (QRDRs) of GyrA and GyrB after DNA sequencing followed by amino acid translation. Fifty-four isolates of M. abscessus subsp. bolletii, including clone BRA100, recovered in different states of Brazil, and 19 reference strains of RGM species were characterized. All 54 M. abscessus subsp. bolletii isolates were resistant to all generations of quinolones and showed the same amino acids in the QRDRs, including the Ala-83 in GyrA, and Arg-447 and Asp-464 in GyrB, described as being responsible for an intrinsic low level of resistance to quinolones in mycobacteria. However, other RGM species showed distinct susceptibilities to this class of antimicrobials and patterns of mutations contrary to what has been traditionally defined, suggesting that other mechanisms of resistance, different from gyrA or gyrB mutations, may also be involved in resistance to high levels of quinolones.\",\n \"corpus_id\": 6798570,\n \"score\": 0\n },\n {\n \"doc_id\": \"22887675\",\n \"title\": \"Annotated genome sequence of Mycobacterium massiliense strain M154, belonging to the recently created taxon Mycobacterium abscessus subsp. bolletii comb. nov.\",\n \"abstract\": \"Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus subsp. bolletii comb. nov. Strain M154, a clinical isolate from the bronchoalveolar lavage fluid of a Malaysian patient presenting with lower respiratory tract infection, was subjected to shotgun DNA sequencing with the Illumina sequencing technology to obtain whole-genome sequence data for comparison with other genetically related strains within the M. abscessus species complex.\",\n \"corpus_id\": 21783694,\n \"score\": 0\n },\n {\n \"doc_id\": \"22947084\",\n \"title\": \"Probable disseminated Mycobacterium abscessus subspecies bolletii infection in a patient with idiopathic CD4+ T lymphocytopenia: a case report.\",\n \"abstract\": \"UNLABELLED: INTRODUCTION: Rapidly growing mycobacteria are opportunistic pathogens in patients with underlying risk factors. Mycobacterium abscessus subsp. bolletii is a newly recognized member of rapidly growing mycobacteria, isolated from respiratory tract and cutaneous infections. CASE PRESENTATION: We describe a case of chronic disseminated infection caused by M. abscessus subsp. bolletii in a 38-year-old Sri Lankan man with idiopathic CD4+ T lymphocytopenia. Idiopathic CD4+ T lymphocytopenia is a rare cause of immunodysfunction that, similar to human immunodeficiency virus infection, causes a depletion of CD4+ T lymphocytes. M. abscessus subsp. bolletii infection was diagnosed by culture isolation from two sputum samples. CONCLUSIONS: To the best of our knowledge this is the first report of M. abscessus subsp. bolletii disseminated infection in a patient affected by idiopathic CD4+ T lymphocytopenia. In contrast to previous reports, the isolate of M. abscessus subsp. bolletii presented intermediate resistance to clarithromycin and was susceptible to cefoxitin and imipenem.\",\n \"corpus_id\": 17192945,\n \"score\": 0\n },\n {\n \"doc_id\": \"23950125\",\n \"title\": \"Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.\",\n \"abstract\": \"Multiple isolates of Mycobacterium abscessus subsp. bolletii, collectively called BRA100, were associated with outbreaks of postsurgical skin infections across various regions of Brazil from 2003 to 2009. We announce the draft genome sequence of a newly sequenced BRA100 strain, M. abscessus subsp. bolletii CRM-0020, isolated from a patient in Rio de Janeiro, Brazil.\",\n \"corpus_id\": 28019337,\n \"score\": 0\n },\n {\n \"doc_id\": \"24201191\",\n \"title\": \"Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594.\",\n \"abstract\": \"An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp. bolletii affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.\",\n \"corpus_id\": 6110792,\n \"score\": 0\n },\n {\n \"doc_id\": \"24718088\",\n \"title\": \"Bacteraemia caused by Mycobacterium abscessus subsp. abscessus and M. abscessus subsp. bolletii: clinical features and susceptibilities of the isolates.\",\n \"abstract\": \"Mycobacterium abscessus complex (M. abscessus subsp. abscessus and M. abscessus subsp. bolletii) is an emerging pathogen causing various human infections. However, few studies have focused on M. abscessus complex bacteraemia with detailed species differentiation. The clinical characteristics of patients with bacteraemia due to M. abscessus complex treated at National Taiwan University Hospital from 2005-2012 were evaluated. Species identification was performed by molecular methods, and minimum inhibitory concentrations (MICs) were determined using a Sensititre RAPMYCO Panel Test for preserved M. abscessus complex isolates. During the study period, 15 patients with M. abscessus complex bacteraemia were found but only 14 isolates from 13 patients were preserved for analysis. One patient had two episodes of bacteraemia (one caused by M. abscessus subsp. bolletii and one by M .abscessus subsp. abscessus with a 9-month interval). Of the remaining 12 patients, 9 patients had M. abscessus subsp. bolletii bacteraemia and 3 had M .abscessus subsp. abscessus bacteraemia. Patients were mainly middle-aged adults with various co-morbidities. Steroid usage and malignancy (5/15) were the most common immunocompromised statuses, followed by diabetes mellitus (4/15). Surgical wound infection was the most common infection foci in all patients (5/15), particularly in M. abscessus subsp. bolletii bacteraemia patients. Clarithromycin and tigecycline exhibited good in vitro activities. Overall, the 14-day mortality was 20% (3/15). M. abscessus complex bacteraemia should be considered an emerging opportunistic infection in immunocompromised hosts. Clarithromycin and tigecycline have potent in vitro activities and are promising agents for treating infections due to M. abscessus complex.\",\n \"corpus_id\": 20553506,\n \"score\": 0\n },\n {\n \"doc_id\": \"25038135\",\n \"title\": \"Outbreaks due to Mycobacterium abscessus subsp. bolletii in southern Brazil: persistence of a single clone from 2007 to 2011.\",\n \"abstract\": \"Outbreaks associated with rapidly growing mycobacteria (RGM) have been increasingly reported worldwide, including in Brazil. Among the RGM, the Mycobacterium abscessus complex is the most pathogenic and related to multidrug resistance. The aim of this study was to evaluate the antimicrobial susceptibility and molecular profile of RGM isolates involved in new postsurgical infection outbreaks in Brazil since 2007. Of the 109 cases reported in the state of Rio Grande do Sul between 2007 and 2011, 43 (39 %) had confirmed mycobacterial growth in culture. Clinical isolates were obtained from biopsy specimens or abscess aspirates. PRA-hsp65 restriction pattern identified the isolates as M. abscessus type 2, and partial rpoB sequencing confirmed the identification as M. abscessus subsp. bolletii. All isolates were susceptible to amikacin and resistant to ciprofloxacin, doxycycline, sulfamethoxazole, moxifloxacin and tobramycin. Most isolates (72 %) were fully susceptible to cefoxitin but six isolates (14 %) were fully resistant to clarithromycin. The latter differed from the susceptibility profiles of the previously described BRA100 clone from other Brazilian regions. Nevertheless, pulsed-field gel electrophoresis analysis revealed that these isolates belonged to a single BRA100 clone. In conclusion, our study reports the persistence of an emergent single and highly resistant clone of M. abscessus subsp. bolletii for several years even after national implementation of infection control measures.\",\n \"corpus_id\": 9488047,\n \"score\": 0\n },\n {\n \"doc_id\": \"27524260\",\n \"title\": \"Pseudooutbreak of rapidly growing mycobacteria due to Mycobacterium abscessus subsp bolletii in a digestive and respiratory endoscopy unit caused by the same clone as that of a countrywide outbreak.\",\n \"abstract\": \"BACKGROUND: The nontuberculous mycobacteria (NTM) are widely spread. In Brazil, 2,520 cases of rapidly growing mycobacteria (RGM) infections after medical procedures were reported, with 5.4% of cases related to nonsurgical invasive procedures and with an occurrence of 1 clone (BRA100) of Mycobacterium abscessus subsp bolletii. OBJECTIVE: To describe a pseudooutbreak of M abscessus subsp bolletii in an endoscopy and bronchoscopy unit. METHODS: The alert for a pseudooutbreak was given when 3 patients, in the same week, had a positive bronchoalveolar lavage culture for M abscessus subsp bolletii. The patients had no symptoms/signs of mycobacterial infection; thus, contamination of bronchoscopes was suspected. Samples for culturing were collected from bronchoscopes, digestive endoscopes, automated disinfection machines, and the water supply. Clinical samples were identified by polymerase chain reaction restriction-enzyme analysis (PRA) of the hsp65 gene and their pulsed-field gel electrophoresis pattern was compared with environmental samples. RESULTS: The investigation demonstrated a contamination of bronchoscopes, digestive endoscopes, and disinfection machines. Molecular typing demonstrated that all strains belonged to the same clone (MAB01), identical to clone BRA100. DISCUSSION: Cross-transmission due to poor disinfection as well as resistance to glutaraldehyde may play roles in the spread of MAB01 M abscessus subsp bolletii, which may have a unique resistance to the environment and adaption to human hosts. However the water supply may have played a role. Attention is needed to ensure the quality of water used to rinse disinfected equipment.\",\n \"corpus_id\": 44453490,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":60,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29703142\",\n \"title\": \"Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice.\",\n \"abstract\": \"BACKGROUND: Salmonella is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal Salmonella (NTS) serovars infect humans and animals, causing important health burden in the world. Susceptibility to salmonellosis varies between individuals under the control of host genes, as demonstrated by the identification of over 20 genetic loci in various mouse crosses. We have investigated the host response to S. Typhimurium infection in 35 Collaborative Cross (CC) strains, a genetic population which involves wild-derived strains that had not been previously assessed. RESULTS: One hundred and forty-eight mice from 35 CC strains were challenged intravenously with 1000 colony-forming units (CFUs) of S. Typhimurium. Bacterial load was measured in spleen and liver at day 4 post-infection. CC strains differed significantly (P < 0.0001) in spleen and liver bacterial loads, while sex and age had no effect. Two significant quantitative trait loci (QTLs) on chromosomes 8 and 10 and one suggestive QTL on chromosome 1 were found for spleen bacterial load, while two suggestive QTLs on chromosomes 6 and 17 were found for liver bacterial load. These QTLs are caused by distinct allelic patterns, principally involving alleles originating from the wild-derived founders. Using sequence variations between the eight CC founder strains combined with database mining for expression in target organs and known immune phenotypes, we were able to refine the QTLs intervals and establish a list of the most promising candidate genes. Furthermore, we identified one strain, CC042/GeniUnc (CC042), as highly susceptible to S. Typhimurium infection. CONCLUSIONS: By exploring a broader genetic variation, the Collaborative Cross population has revealed novel loci of resistance to Salmonella Typhimurium. It also led to the identification of CC042 as an extremely susceptible strain.\",\n \"corpus_id\": 13840120\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20429884","title":"Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review.","abstract":"Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species Salmonella enterica and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of S. enterica serovar Enteritidis or S. enterica serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to Salmonella differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes TLR4 and SLC11A1, the Major Histocompatibility Complex (MHC) and the QTL SAL1 are interesting for more in-depth studies. This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.","corpus_id":2352316,"score":2},{"doc_id":"20643856","title":"Role for neutrophils in host immune responses and genetic factors that modulate resistance to Salmonella enterica serovar typhimurium in the inbred mouse strain SPRET/Ei.","abstract":"Infection with Salmonella enterica serovar Typhimurium is a complex disease in which the host-bacterium interactions are strongly influenced by genetic factors of the host. We demonstrate that SPRET/Ei, an inbred mouse strain derived from Mus spretus, is resistant to S. Typhimurium infections. The kinetics of bacterial proliferation, as well as histological examinations of tissue sections, suggest that SPRET/Ei mice can control bacterial multiplication and spreading despite significant attenuation of the cytokine response. The resistance of SPRET/Ei mice to S. Typhimurium infection is associated with increased leukocyte counts in the circulation and enhanced neutrophil influx into the peritoneum during the course of infection. A critical role of neutrophils was confirmed by neutrophil depletion: neutropenic SPRET/Ei mice were sensitive to infection with S. Typhimurium and showed much higher bacterial loads. To identify genes that modulate the natural resistance of SPRET/Ei mice to S. Typhimurium infection, we performed a genome-wide study using an interspecific backcross between C3H/HeN and SPRET/Ei mice. The results of this analysis demonstrate that at least two loci, located on chromosomes 6 and 11, affect survival following lethal infection with S. Typhimurium. These two loci contain several interesting candidate genes which may have important implications for the search for genetic factors controlling Salmonella infections in humans and for our understanding of complex host-pathogen interactions in general.","corpus_id":44380068,"score":2},{"doc_id":"21493779","title":"Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection.","abstract":"The Collaborative Cross (CC) is a genetic reference panel of recombinant inbred lines of mice, designed for the dissection of complex traits and gene networks. Each line is independently descended from eight genetically diverse founder strains such that the genomes of the CC lines, once fully inbred, are fine-grained homozygous mosaics of the founder haplotypes. We present an analysis of 120 CC lines, from a cohort of the CC bred at Tel Aviv University in collaboration with the University of Oxford, which at the time of this study were between the sixth and 12th generations of inbreeding and substantially homozygous at 170,000 SNPs. We show how CC genomes decompose into mosaics, and we identify loci that carry a deficiency or excess of a founder, many being deficient for the wild-derived strains WSB/EiJ and PWK/PhJ. We phenotyped 371 mice from 66 CC lines for a susceptibility to Aspergillus fumigatus infection. The survival time after infection varied significantly between CC lines. Quantitative trait locus (QTL) mapping identified genome-wide significant QTLs on chromosomes 2, 3, 8, 10 (two QTLs), 15, and 18. Simulations show that QTL mapping resolution (the median distance between the QTL peak and true location) varied between 0.47 and 1.18 Mb. Most of the QTLs involved contrasts between wild-derived founder strains and therefore would not segregate between classical inbred strains. Use of variation data from the genomes of the CC founder strains refined these QTLs further and suggested several candidate genes. These results support the use of the CC for dissecting complex traits.","corpus_id":12448545,"score":2},{"doc_id":"21956657","title":"Refinement of the genetics of the host response to Salmonella infection in MOLF/Ei: regulation of type 1 IFN and TRP3 pathways by Ity2.","abstract":"Typhoid fever, which is caused by Salmonella typhi and paratyphi, is a severe systemic disease that remains a major public health issue in several areas of the world. We can model the human disease using mice infected with a related bacterium, Salmonella typhimurium. This model recapitulates several clinical aspects of the human disease and allows for the study of the host response to Salmonella typhimurium infection in vivo. Previous work in our laboratory has identified three Immunity to typhimurium loci (Ity, Ity2 and Ity3) in the wild-derived MOLF/Ei mice, influencing survival after infection with Salmonella typhimurium. The MOLF/Ei alleles at Ity and Ity2 are protective, while the MOLF/Ei allele at Ity3 confers susceptibility. In this paper, we have generated a novel cross combination between the highly susceptible strain, MOLF/Ei, and the resistant strain, 129S6, to better define the genetic architecture of susceptibility to infection in MOLF/Ei. Using this cross, we have replicated the locus on chr 11 (Ity2) and identified a novel locus on chr 13 (Ity13). Using microarrays and transcriptional profiling, we examined the response of uninfected and infected Ity2 congenic mice. These analyses demonstrate a role for both type-1-interferon (IFN) and TRP53 signaling in the pathogenesis of Salmonella infection.","corpus_id":34369048,"score":2},{"doc_id":"22384400","title":"Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice.","abstract":"Outbreaks of influenza occur on a yearly basis, causing a wide range of symptoms across the human population. Although evidence exists that the host response to influenza infection is influenced by genetic differences in the host, this has not been studied in a system with genetic diversity mirroring that of the human population. Here we used mice from 44 influenza-infected pre-Collaborative Cross lines determined to have extreme phenotypes with regard to the host response to influenza A virus infection. Global transcriptome profiling identified 2671 transcripts that were significantly differentially expressed between mice that showed a severe (\"high\") and mild (\"low\") response to infection. Expression quantitative trait loci mapping was performed on those transcripts that were differentially expressed because of differences in host response phenotype to identify putative regulatory regions potentially controlling their expression. Twenty-one significant expression quantitative trait loci were identified, which allowed direct examination of genes associated with regulation of host response to infection. To perform initial validation of our findings, quantitative polymerase chain reaction was performed in the infected founder strains, and we were able to confirm or partially confirm more than 70% of those tested. In addition, we explored putative causal and reactive (downstream) relationships between the significantly regulated genes and others in the high or low response groups using structural equation modeling. By using systems approaches and a genetically diverse population, we were able to develop a novel framework for identifying the underlying biological subnetworks under host genetic control during influenza virus infection.","corpus_id":29006112,"score":2},{"doc_id":"23055923","title":"Host-pathogen interaction in invasive Salmonellosis.","abstract":"Salmonella enterica infections result in diverse clinical manifestations. Typhoid fever, caused by S. enterica serovar Typhi (S. Typhi) and S. Paratyphi A, is a bacteremic illness but whose clinical features differ from other Gram-negative bacteremias. Non-typhoidal Salmonella (NTS) serovars cause self-limiting diarrhea with occasional secondary bacteremia. Primary NTS bacteremia can occur in the immunocompromised host and infants in sub-Saharan Africa. Recent studies on host-pathogen interactions in Salmonellosis using genome sequencing, murine models, and patient studies have provided new insights. The full genome sequences of numerous S. enterica serovars have been determined. The S. Typhi genome, compared to that of S. Typhimurium, harbors many inactivated or disrupted genes. This can partly explain the different immune responses both serovars induce upon entering their host. Similar genome degradation is also observed in the ST313 S. Typhimurium strain implicated in invasive infection in sub-Saharan Africa. Virulence factors, most notably, type III secretion systems, Vi antigen, lipopolysaccharide and other surface polysaccharides, flagella, and various factors essential for the intracellular life cycle of S. enterica have been characterized. Genes for these factors are commonly carried on Salmonella Pathogenicity Islands (SPIs). Plasmids also carry putative virulence-associated genes as well as those responsible for antimicrobial resistance. The interaction of Salmonella pathogen-associated molecular patterns (PAMPs) with Toll-like receptors (TLRs) and NOD-like receptors (NLRs) leads to inflammasome formation, activation, and recruitment of neutrophils and macrophages and the production of pro-inflammatory cytokines, most notably interleukin (IL)-6, IL-1β, tumor necrosis factor (TNF)-α, and interferon-gamma (IFN)-γ. The gut microbiome may be an important modulator of this immune response. S. Typhimurium usually causes a local intestinal immune response, whereas S. Typhi, by preventing neutrophil attraction resulting from activation of TLRs, evades the local response and causes systemic infection. Potential new therapeutic strategies may lead from an increased understanding of infection pathogenesis.","corpus_id":17208185,"score":2},{"doc_id":"23468633","title":"Modeling host genetic regulation of influenza pathogenesis in the collaborative cross.","abstract":"Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms and confounding environmental factors have made it difficult to identify polymorphic genes that contribute to differential disease outcomes in human populations. Therefore, to control for these confounding environmental variables in a system that models the levels of genetic diversity found in outbred populations such as humans, we used incipient lines of the highly genetically diverse Collaborative Cross (CC) recombinant inbred (RI) panel (the pre-CC population) to study how genetic variation impacts influenza associated disease across a genetically diverse population. A wide range of variation in influenza disease related phenotypes including virus replication, virus-induced inflammation, and weight loss was observed. Many of the disease associated phenotypes were correlated, with viral replication and virus-induced inflammation being predictors of virus-induced weight loss. Despite these correlations, pre-CC mice with unique and novel disease phenotype combinations were observed. We also identified sets of transcripts (modules) that were correlated with aspects of disease. In order to identify how host genetic polymorphisms contribute to the observed variation in disease, we conducted quantitative trait loci (QTL) mapping. We identified several QTL contributing to specific aspects of the host response including virus-induced weight loss, titer, pulmonary edema, neutrophil recruitment to the airways, and transcriptional expression. Existing whole-genome sequence data was applied to identify high priority candidate genes within QTL regions. A key host response QTL was located at the site of the known anti-influenza Mx1 gene. We sequenced the coding regions of Mx1 in the eight CC founder strains, and identified a novel Mx1 allele that showed reduced ability to inhibit viral replication, while maintaining protection from weight loss.","corpus_id":14682844,"score":2},{"doc_id":"25283706","title":"Susceptibility to Klebsiella pneumonaie infection in collaborative cross mice is a complex trait controlled by at least three loci acting at different time points.","abstract":"BACKGROUND: Klebsiella pneumoniae (Kp) is a bacterium causing severe pneumonia in immunocompromised hosts and is often associated with sepsis. With the rise of antibiotic resistant bacteria, there is a need for new effective and affordable control methods; understanding the genetic architecture of susceptibility to Kp will help in their development. We performed the first quantitative trait locus (QTL) mapping study of host susceptibility to Kp infection in immunocompetent Collaborative Cross mice (CC). We challenged 328 mice from 73 CC lines intraperitoneally with 104 colony forming units of Kp strain K2. Survival and body weight were monitored for 15 days post challenge. 48 of the CC lines were genotyped with 170,000 SNPs, with which we mapped QTLs. RESULTS: CC lines differed significantly (P < 0.05) in mean survival time, between 1 to 15 days post infection, and broad sense heritability was 0.45. Distinct QTL were mapped at specific time points during the challenge. A QTL on chromosome 4 was found only on day 2 post infection, and QTL on chromosomes 8 and 18, only on day 8. By using the sequence variations of the eight inbred strain founders of the CC to refine QTL localization we identify several candidate genes. CONCLUSION: Host susceptibility to Kp is a complex trait, controlled by multiple genetic factors that act sequentially during the course of infection.","corpus_id":870133,"score":2},{"doc_id":"25339955","title":"Salmonella-host interactions - modulation of the host innate immune system.","abstract":"Salmonella enterica (S. enterica) are Gram-negative bacteria that can invade a broad range of hosts causing both acute and chronic infections. This phenotype is related to its ability to replicate and persist within non-phagocytic host epithelial cells as well as phagocytic dendritic cells and macrophages of the innate immune system. Infection with S. enterica manifests itself through a broad range of clinical symptoms and can result in asymptomatic carriage, gastroenteritis, systemic disease such as typhoid fever and in severe cases, death (1). Exposure to S. enterica serovars Typhi and Paratyphi exhibits clinical symptoms including diarrhea, fatigue, fever, and temperature fluctuations. Other serovars such as the non-typhoidal Salmonella (NTS), of which there are over 2,500, are commonly contracted as, but not limited to, food-borne sources causing gastrointestinal symptoms, which include diarrhea and vomiting. The availability of complete genome sequences for many S. enterica serovars has facilitated research into the genetic determinants of virulence for this pathogen. This work has led to the identification of important bacterial components, including flagella, type III secretion systems, lipopolysaccharides, and Salmonella pathogenicity islands, all of which support the intracellular life cycle of S. enterica. Studies focusing on the host-pathogen interaction have provided insights into receptor activation of the innate immune system. Therefore, characterizing the host-S. enterica interaction is critical to understand the pathogenicity of the bacteria in a clinically relevant context. This review outlines salmonellosis and the clinical manifestations between typhoidal and NTS infections as well as discussing the host immune response to infection and the models that are being used to elucidate the mechanisms involved in Salmonella pathogenicity.","corpus_id":15841599,"score":2},{"doc_id":"26310945","title":"Host genetic diversity influences the severity of Pseudomonas aeruginosa pneumonia in the Collaborative Cross mice.","abstract":"BACKGROUND: Pseudomonas aeruginosa is one of the top three causes of opportunistic infections in humans. Patients with a compromised immune system, due to immunosuppressive therapies or underlying diseases such as cancer, AIDS or the hereditary disease cystic fibrosis, are at risk of developing P. aeruginosa infection. However, clinical evidence indicates extremely variable outcomes of P. aeruginosa infections in individuals at risk, suggesting that host multi-complex genetic traits may influence the severity of this opportunistic infection. Here, we have used an innovative experimental model to dissect whether host genetic background, such as those found in the outbred population, could influence the risk of morbidity and mortality to P. aeruginosa pneumonia. RESULTS: A highly genetically-diverse mouse resource population, Collaborative Cross (CC) mice, was infected with a clinical strain of P. aeruginosa and subsequently monitored for mortality, mean survival time, and morbidity, change in body weight for seven days post infection. Disease phenotypes ranged from complete resistance and recovery of body weight to lethal disease. Initial variables, including body weight, age and gender, have limited influence on P. aeruginosa outcome, emphasizing the role of host genetic background in defining the risk of morbidity and mortality. When broad-sense heritability of phenotypic traits was evaluated, it confirmed the influence of genetic profile rather than environmental factors among the CC lines during P. aeruginosa infection. CONCLUSION: This innovative model system can potentially reproduce the variables responses of disease severity observed in humans during P. aeruginosa pneumonia. Our results demonstrated that a widely-marked differential response to P. aeruginosa airway infection in term of morbidity and mortality, is mainly affected by host genetic factors, as multiple genetic loci or polymorphic variations.","corpus_id":9928638,"score":2},{"doc_id":"26452100","title":"Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross.","abstract":"New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations.","corpus_id":9981176,"score":2},{"doc_id":"26955808","title":"Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice.","abstract":"BACKGROUND: Typhoid fever caused by Salmonella enterica serovar Typhi (S. Typhi) is a severe systemic human disease and endemic in regions of the world with poor drinking water quality and sewage treatment facilities. A significant number of patients become asymptomatic life-long carriers of S. Typhi and serve as the reservoir for the disease. The specific mechanisms and adaptive strategies enabling S. Typhi to survive inside the host for extended periods are incompletely understood. Yet, elucidation of these processes is of major importance for improvement of therapeutic strategies. In the current study genetic adaptation during experimental chronic S. Typhimurium infections of mice, an established model of chronic typhoid fever, was probed as an approach for studying the molecular mechanisms of host-adaptation during long-term host-association. RESULTS: Individually sequence-tagged wild type strains of S. Typhimurium 4/74 were used to establish chronic infections of 129X1/SvJ mice. Over the course of infections, S. Typhimurium bacteria were isolated from feces and from livers and spleens upon termination of the experiment. In all samples dominant clones were identified and select clones were subjected to whole genome sequencing. Dominant clones isolated from either systemic organs or fecal samples exhibited distinct single nucleotide polymorphisms (SNPs). One mouse appeared to have distinct adapted clones in the spleen and liver, respectively. Three mice were colonized in the intestines by the same clone containing the same non-synonymous SNP in a transcriptional regulator, kdgR, of metabolic genes. This likely indicates transmission of this clone between mice. The mutation was tracked to have occurred prior to 2 weeks post infection in one of the three mice and had subsequently been transmitted to the other two mice. Re-infection with this clone confirmed that it is superior to the wild type for intestinal colonization. CONCLUSIONS: During 4 to 6 weeks of chronic infections, S. Typhimurium acquired distinct SNPs in known regulators of metabolic and virulence genes. One SNP, the kdgR-SNP was confirmed to confer selective advantage during chronic infections and constitute a true patho-adaptive mutation. Together, the results provide evidence for rapid genetic adaptation to the host of S. Typhimurium and validate experimental evolution in the context of host infection as a strategy for elucidating pathogen host interactions at the molecular level.","corpus_id":215628348,"score":2},{"doc_id":"27933544","title":"Dissection of Host Susceptibility to Bacterial Infections and Its Toxins.","abstract":"Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies. Most of current animal models used in complex traits diseases genetic mapping have limited genetic diversity. This limitation impedes the ability to create incorporated network using genetic interactions, epigenetics, environmental factors, microbiota, and other phenotypes. A novel mouse genetic reference population for high-resolution mapping and subsequently identifying genes underlying the QTL, namely the Collaborative Cross (CC) mouse genetic reference population (GRP) was recently developed. In this chapter, we discuss a variety of approaches using CC mice for mapping genes underlying quantitative trait loci (QTL) to dissect the host response to polygenic traits, including infectious disease caused by bacterial agents and its toxins.","corpus_id":13761546,"score":2},{"doc_id":"28592495","title":"Genomes of the Mouse Collaborative Cross.","abstract":"The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources.","corpus_id":21350942,"score":2},{"doc_id":"19718951","title":"Towards the selection of chickens resistant to Salmonella and Campylobacter infections.","abstract":"Resistance to infection with enteric pathogens such as Salmonella and Campylobacter can be at many levels and include both non-immune and immune mechanisms. Immune resistance mechanisms can be specific, at the level of the adaptive immune response, or non-specific, at the level of the innate immune response. Whilst we can extrapolate to some degree in birds from what is known about immune responses to these pathogens in mammals, chickens are not \"feathered mice\", but have a different repertoire of genes, molecules, cells and organs involved in their immune response compared to mammals. Fundamental work on the chicken's immune response to enteric pathogens is therefore still required. Our studies focus particularly on the innate immune response, as responses of heterophils (the avian neutrophil equivalent) from commercial birds, and macrophages from inbred lines of chickens, correlate with resistance or susceptibility to Salmonella infection with a variety of Salmonella serovars and infection models. We work on two basic resistance mechanisms - resistance to colonization with Salmonella or Campylobacter, and resistance to systemic salmonellosis (or fowl typhoid). To map genes involved in resistance to colonization with Salmonella and Campylobacter, we are using a combination of expression quantitative trait loci (eQTLs) from microarray studies, allied with whole genome SNP arrays (WGA), a candidate gene approach and analysis of copy number variation across the genome. For resistance to systemic salmonellosis, we have refined the location ofa novel resistance locus on Chromosome 5, designated SAL1, using high density SNP panels, combined with advanced back-crossing of resistant and susceptible lines. Using a 6th generation backcross mapping population we have confirmed and refined the SAL1 locus to 8-00 kb of Chromosome 5. This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homologue, AKT1.","corpus_id":25576489,"score":1},{"doc_id":"19729455","title":"Effect of age on susceptibility to Salmonella Typhimurium infection in C57BL/6 mice.","abstract":"Ageing is associated with a decline in immune function, which predisposes the elderly to a higher incidence of infections. Information on the mechanism of the age-related increase in susceptibility to Salmonella enterica serovar Typhimurium (S. Typhimurium) is limited. In particular, little is known regarding the involvement of the immune response in this age-related change. We employed streptomycin (Sm)-pretreated C57BL/6 mice to develop a mouse model that would demonstrate age-related differences in susceptibility and immune response to S. Typhimurium. In this model, old mice inoculated orally with doses of 3 x 10(8) or 1 x 10(6) c.f.u. S. Typhimurium had significantly greater S. Typhimurium colonization in the ileum, colon, Peyer's patches, spleen and liver than young mice. Old mice had significantly higher weight loss than young mice on days 1 and 2 post-infection. In response to S. Typhimurium infection, old mice failed to increase ex vivo production of IFN-gamma and TNF-alpha in the spleen and mesenteric lymph node cells to the same degree as observed in young mice; this was associated with their inability to maintain the presence of neutrophils and macrophages at a 'youthful' level. These results indicate that Sm-pretreated C57BL/6 old mice are more susceptible to S. Typhimurium infection than young mice, which might be due to impaired IFN-gamma and TNF-alpha production as well as a corresponding change in the number of neutrophils and macrophages in response to S. Typhimurium infection compared to young mice.","corpus_id":206188249,"score":1},{"doc_id":"20597881","title":"Fine mapping of the chicken salmonellosis resistance locus (SAL1).","abstract":"Salmonella enterica serovar Typhimurium is a Gram-negative bacterium that has a significant impact on both human and animal health. It is one of the most common food-borne pathogens responsible for a self-limiting gastroenteritis in humans and a similar disease in pigs, cattle and chickens. In contrast, intravenous challenge with S. Typhimurium provides a valuable model for systemic infection, often causing a typhoid-like infection, with bacterial replication resulting in the destruction of the spleen and liver of infected animals. Resistance to systemic salmonellosis in chickens is partly genetically determined, with bacterial numbers at systemic sites in resistant lines being up to 1000-fold fewer than in susceptible lines. Identification of genes contributing to disease resistance will enable genetic selection of resistant lines that will reduce Salmonella levels in poultry flocks. We previously identified a novel resistance locus on Chromosome 5, designated SAL1. Through the availability of high-density SNP panels in the chicken, combined with advanced back-crossing of the resistant and susceptible lines, we sought to refine the SAL1 locus and identify potential positional candidate genes. Using a 6(th) generation backcross mapping population, we have confirmed and refined the SAL1 locus as lying between 54.0 and 54.8 Mb on the long arm of Chromosome 5 (F = 8.72, P = 0.00475). This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homolog, AKT1 (protein kinase B, PKB).","corpus_id":36860629,"score":1},{"doc_id":"20623355","title":"A novel strategy for genetic dissection of complex traits: the population of specific chromosome substitution strains from laboratory and wild mice.","abstract":"The mouse is an irreplaceable model for understanding the precise genetic mechanisms of mammalian physiological pathways. Thousands of quantitative trait loci (QTLs) have been mapped onto the mouse genome during the last two decades. However, only a few genes' underlying complex traits have been successfully identified, and rapid fine mapping of QTL genes still remains a challenge for mouse geneticists. Currently, the Collaborative Cross (CC) has proceeded to the goal of establishing more than 1,000 recombinant inbred strains for the sub-centimorgan mapping resolution of QTL loci. In this article, a novel complementary strategy, designated as population of specific chromosome substitution strains or PSCSS, is proposed for rapid fine mapping of QTLs on the substituted chromosome. One specific chromosome (Chr 1) of recipient mouse strain C57BL/6 J has been substituted by homologous counterparts from five different inbred strains (C3H/He, FVB/N, AKR, NOD/LtJ, NZW/LacJ), an outbred line Kunmin mouse in China, and 23 wild mice captured in different localities. The primary genetic studies on the structure of these wild donor chromosomes (Chr 1) show that these donor chromosomes harbor extensive genetic polymorphisms, with a high density of SNP distribution, abundant variations of STR alleles, and a high level of historical recombination accumulation. These specific chromosome substitution strains eventually form a special population that has the identical genetic background of the recipient strain and differs only in the donor chromosomes. With simple association studies, known QTLs on the donor chromosome can be rapidly mapped in high resolution without requirement of further crosses. This approach, taking advantage of the extensive genetic polymorphisms of wild resources and chromosome substitution strategy, brings a new outlook for genetic dissection of complex traits.","corpus_id":5788050,"score":1},{"doc_id":"21200387","title":"Humanized mice are susceptible to Salmonella typhi infection.","abstract":"Salmonella enterica serovar Typhi is a pathogen that only infects humans. Currently, there is no animal model for studying this pathogen. Recently, alymphoid RAG-2(-/-)/γ(c)(-/-) mice engrafted with human leukocytes, known as humanized mice, have been successfully utilized to develop experimental models for several human-specific viral infections, including HIV, human-like dengue fever and hepatitis C virus. Little is known about the usefulness and feasibility of the humanized mouse model for the study of human-specific bacterial pathogens, such as S. typhi. The aim of this study was to determine if Salmonella enterica serovar Typhi could establish productive infection in humanized mice. Here we report that intravenous inoculation of S. typhi into humanized mice, but not controls, established S. typhi infections. High bacterial loads were found in the liver, spleen, blood and bone marrow of mice reconstituted with human leukocytes, but not in the unreconstituted control mice. Importantly, S. typhi-infected humanized mice lost significant body weight, and some of the infected mice displayed neurological symptoms. Our data suggest, for the first time, that humanized mice are susceptible to S. typhi challenge and that this model can be utilized to study the pathogenesis of S. typhi to develop novel therapeutic strategies.","corpus_id":20060237,"score":1},{"doc_id":"21427413","title":"Architecture of energy balance traits in emerging lines of the Collaborative Cross.","abstract":"The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32-10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5-38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2-83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4-48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9-89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance.","corpus_id":10300310,"score":1},{"doc_id":"21616112","title":"Mouse models to assess the efficacy of non-typhoidal Salmonella vaccines: revisiting the role of host innate susceptibility and routes of challenge.","abstract":"Non-typhoidal Salmonella enterica (NTS) serovars Typhimurium and Enteritidis are important causes of bacterial gastroenteritis in the USA and worldwide. In sub-Saharan Africa these two serovars are emerging as agents associated with lethal invasive disease (e.g., bacteremia, meningitis). The development of NTS vaccines, based on mucosally administered live attenuated strains and parenteral non-living antigens, could diminish the NTS disease burden globally. Mouse models of S. Typhimurium and S. Enteritidis invasive disease can accelerate the development of NTS vaccines. Live attenuated NTS vaccines elicit both cellular and humoral immunity in mice and their efficacy is well established. In contrast, non-living vaccines that primarily elicit humoral immunity have demonstrated variable efficacy. An analysis of the reported studies with non-living vaccines against S. Typhimurium and S. Enteritidis reveals that efficacy is influenced by two important independent variables: (1) the innate susceptibility to NTS infection that differs dramatically between commonly used mouse strains and (2) the virulence of the NTS strain used for challenge. Protection by non-living vaccines has generally been seen only in host-pathogen interactions where a sub-lethal infection results, such as challenging resistant mice with either highly virulent or weakly virulent strains or susceptible mice with weakly virulent strains. The immunologic basis of this discrepancy and the implications for human NTS vaccine development are reviewed herein.","corpus_id":39231602,"score":1},{"doc_id":"21628518","title":"Multigenic control and sex bias in host susceptibility to spore-induced pulmonary anthrax in mice.","abstract":"Mechanisms underlying susceptibility to anthrax infection are unknown. Using a phylogenetically diverse panel of inbred mice and spores of Bacillus anthracis Ames, we investigated host susceptibility to pulmonary anthrax. Susceptibility profiles for survival time and organ pathogen load differed across strains, indicating distinct genetic controls. Tissue infection kinetics analysis showed greater systemic dissemination in susceptible DBA/2J (D) mice but a higher terminal bacterial load in resistant BALB/cJ (C) mice. Interestingly, the most resistant strains, C and C57BL/6J (B), demonstrated a sex bias for susceptibility. For example, BALB/cJ females had a significantly higher survival time and required 4-fold more spores for 100% mortality compared to BALB/cJ males. To identify genetic regions associated with differential susceptibility, survival time and extent of organ infection were assessed using mice derived from two susceptibility models: (i) BXD advanced recombinant inbred strains and (ii) F2 offspring generated from polar responding C and D strains. Genome-wide analysis of BXD strain survival identified linkage on chromosomes 5, 6, 9, 11, and 14. Quantitative trait locus (QTL) analysis of the C×DF2 population revealed a significant QTL (designated Rpai1 for resistance to pulmonary anthrax infection, locus 1) for survival time on chromosome 17 and also identified a chromosome 11 locus for lung pathogen burden. The striking difference between genome-wide linkage profiles for these two mouse models of anthrax susceptibility supports our hypothesis that these are multigenic traits. Our data provide the first evidence for a differential sex response to anthrax resistance and further highlight the unlikelihood of a single common genetic contribution for this response across strains.","corpus_id":31451980,"score":1},{"doc_id":"22427645","title":"Mapping of clinical and expression quantitative trait loci in a sex-dependent effect of host susceptibility to mouse-adapted influenza H3N2/HK/1/68.","abstract":"Seasonal influenza outbreaks and recurrent influenza pandemics present major challenges to public health. By studying immunological responses to influenza in different host species, it may be possible to discover common mechanisms of susceptibility in response to various influenza strains. This could lead to novel therapeutic targets with wide clinical application. Using a mouse-adapted strain of influenza (A/HK/1/68-MA20 [H3N2]), we produced a mouse model of severe influenza that reproduces the hallmark high viral load and overexpression of cytokines associated with susceptibility to severe influenza in humans. We mapped genetic determinants of the host response using a panel of 29 closely related mouse strains (AcB/BcA panel of recombinant congenic strains) created from influenza-susceptible A/J and influenza-resistant C57BL/6J (B6) mice. Combined clinical quantitative trait loci (QTL) and lung expression QTL mapping identified candidate genes for two sex-specific QTL on chromosomes 2 and 17. The former includes the previously described Hc gene, a deficit of which is associated with the susceptibility phenotype in females. The latter includes the phospholipase gene Pla2g7 and Tnfrsf21, a member of the TNFR superfamily. Confirmation of the gene underlying the chromosome 17 QTL may reveal new strategies for influenza treatment.","corpus_id":207426864,"score":1},{"doc_id":"22613937","title":"A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state.","abstract":"BACKGROUND: The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. RESULTS: In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. CONCLUSIONS: Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were identified in several independent studies, which is the case of the QTL regions on chromosomes 2 and 3, involved in resistance to both Salmonella colonization and carrier state. These observations provide evidence of common genes controlling S. Typhimurium colonization and S. Enteritidis carrier-state in chickens.","corpus_id":15202562,"score":1},{"doc_id":"22905720","title":"Distinct gene loci control the host response to influenza H1N1 virus infection in a time-dependent manner.","abstract":"BACKGROUND: There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. In particular, C57BL/6J, the most widely used mouse strain in biomedical research, is comparatively resistant. In contrast, DBA/2J is highly susceptible. RESULTS: To map regions of the genome responsible for differences in influenza susceptibility, we infected a family of 53 BXD-type lines derived from a cross between C57BL/6J and DBA/2J strains with influenza A virus (PR8, H1N1). We monitored body weight, survival, and mean time to death for 13 days after infection. Qivr5 (quantitative trait for influenza virus resistance on chromosome 5) was the largest and most significant QTL for weight loss. The effect of Qivr5 was detectable on day 2 post infection, but was most pronounced on days 5 and 6. Survival rate mapped to Qivr5, but additionally revealed a second significant locus on chromosome 19 (Qivr19). Analysis of mean time to death affirmed both Qivr5 and Qivr19. In addition, we observed several regions of the genome with suggestive linkage. There are potentially complex combinatorial interactions of the parental alleles among loci. Analysis of multiple gene expression data sets and sequence variants in these strains highlights about 30 strong candidate genes across all loci that may control influenza A susceptibility and resistance. CONCLUSIONS: We have mapped influenza susceptibility loci to chromosomes 2, 5, 16, 17, and 19. Body weight and survival loci have a time-dependent profile that presumably reflects the temporal dynamic of the response to infection. We highlight candidate genes in the respective intervals and review their possible biological function during infection.","corpus_id":2488492,"score":1},{"doc_id":"22937698","title":"[Model of chronic salmonellosis: parameters of infection and immune response in inbred mice genetically variable in susceptibility to salmonellosis].","abstract":"AIM: Study parameters of chronic infection and immune response in I/St and A/Sn line mice in the model of per oral infection of mice with Salmonella enterica serovar Typhimurium. MATERIALS AND METHODS: Studies were carried out in I/StSnEgYCit (I/St), A/JsnYCit (A/Sn) inbred line mice as well as their back crossing hybrids [I/StrxF1(I/StxA/Sn)]BC. Mice were infected per os by S. enterica serovar Typhimurium strain IE147 at a dose of 2 x 10(5) PFU per mice. The number of salmonellae was determined at days 3, 5 and 7, weeks 3 and 4 after the infection in various organs, the number of antibody producers--by cell EIA. Pathomorphologic changes in mice spleens were studied histologically by using hematoxylin and eosin staining. In offspring of back crossing [I/St x F1(I/St x A/Sn)]BCl segregation genetic analysis of sensitivity to salmonella infection trait and mapping of loci taking part in salmonella infection were carried out. RESULTS: The course of chronic salmonellosis in susceptible I/St line was characterized by the presence of more pronounced pathomorphologic changes in spleen and significantly higher microbial load in organs (approximately by 1000 times) when compared with A/Sn mice. Interlinear differences in susceptibility to infection correlated with differences in the type of early local and systemic immune response. In I/St mice a higher level of salmonella specific IgG2a-, IgG1- and IgA forming cells in spleen compared with A/Sn mice was detected which correlates with a pronounced splenomegaly and high concentration of salmonellae. On the contrary A/Sn mice demonstrated a higher level of salmonella specific IgA forming cells in Peyer patches that probably leads to protection of A/Sn line during per oral infection. Genetic analysis of susceptibility to salmonellosis trait inheritance showed the presence of its coupling with D9Mit89 locus of chromosome 9 on which previously Tbs2 locus was mapped that plays a role in the control of tuberculosis infection. CONCLUSION: There is a probability of the presence of general mechanisms of genetic control of tuberculosis and salmonella infections in A/Sn and I/St mice.","corpus_id":10839082,"score":1},{"doc_id":"23390527","title":"Suppression of hepcidin expression and iron overload mediate Salmonella susceptibility in ankyrin 1 ENU-induced mutant.","abstract":"Salmonella, a ubiquitous Gram-negative intracellular bacterium, is a food borne pathogen that infects a broad range of hosts. Infection with Salmonella Typhimurium in mice is a broadly recognized experimental model resembling typhoid fever in humans. Using a N-ethyl-N-nitrosurea (ENU) mutagenesis recessive screen, we report the identification of Ity16 (Immunity to Typhimurium locus 16), a locus responsible for increased susceptibility to infection. The position of Ity16 was refined on chromosome 8 and a nonsense mutation was identified in the ankyrin 1 (Ank1) gene. ANK1 plays an important role in the formation and stabilization of the red cell cytoskeleton. The Ank1(Ity16/Ity16) mutation causes severe hemolytic anemia in uninfected mice resulting in splenomegaly, hyperbilirubinemia, jaundice, extramedullary erythropoiesis and iron overload in liver and kidneys. Ank1(Ity16/Ity16) mutant mice demonstrated low levels of hepcidin (Hamp) expression and significant increases in the expression of the growth differentiation factor 15 (Gdf15), erythropoietin (Epo) and heme oxygenase 1 (Hmox1) exacerbating extramedullary erythropoiesis, tissue iron deposition and splenomegaly. As the infection progresses in Ank1(Ity16/Ity16), the anemia worsens and bacterial load were high in liver and kidneys compared to wild type mice. Heterozygous Ank1(+/Ity16) mice were also more susceptible to Salmonella infection although to a lesser extent than Ank1(Ity16/Ity16) and they did not inherently present anemia and splenomegaly. During infection, iron accumulated in the kidneys of Ank1(+/Ity16) mice where bacterial loads were high compared to littermate controls. The critical role of HAMP in the host response to Salmonella infection was validated by showing increased susceptibility to infection in Hamp-deficient mice and significant survival benefits in Ank1(+/Ity16) heterozygous mice treated with HAMP peptide. This study illustrates that the regulation of Hamp and iron balance are crucial in the host response to Salmonella infection in Ank1 mutants.","corpus_id":12339250,"score":1},{"doc_id":"23433259","title":"High-precision genetic mapping of behavioral traits in the diversity outbred mouse population.","abstract":"Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light-dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics.","corpus_id":3130834,"score":1},{"doc_id":"24195963","title":"Using the emerging Collaborative Cross to probe the immune system.","abstract":"The Collaborative Cross (CC) is an emerging panel of recombinant inbred (RI) mouse strains. Each strain is genetically distinct but all descended from the same eight inbred founders. In 66 strains from incipient lines of the CC (pre-CC), as well as the 8 CC founders and some of their F1 offspring, we examined subsets of lymphocytes and antigen-presenting cells. We found significant variation among the founders, with even greater diversity in the pre-CC. Genome-wide association using inferred haplotypes detected highly significant loci controlling B-to-T cell ratio, CD8 T-cell numbers, CD11c and CD23 expression. Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology. For CD23, we found a strong QTL whose confidence interval contained the CD23 structural gene Fcer2a. Our data on the pre-CC demonstrate the utility of the CC for studying immunophenotypes and the value of integrating founder, CC and F1 data. The extreme immunophenotypes observed could have pleiotropic effects in other CC experiments.","corpus_id":8791248,"score":1},{"doc_id":"25350459","title":"Temporal and anatomical host resistance to chronic Salmonella infection is quantitatively dictated by Nramp1 and influenced by host genetic background.","abstract":"The lysosomal membrane transporter, Nramp1, plays a key role in innate immunity and resistance to infection with intracellular pathogens such as non-typhoidal Salmonella (NTS). NTS-susceptible C57BL/6 (B6) mice, which express the mutant Nramp1D169 allele, are unable to control acute infection with Salmonella enterica serovar Typhimurium following intraperitoneal or oral inoculation. Introducing functional Nramp1G169 into the B6 host background, either by constructing a congenic strain carrying Nramp1G169 from resistant A/J mice (Nramp-Cg) or overexpressing Nramp1G169 from a transgene (Nramp-Tg), conferred equivalent protection against acute Salmonella infection. In contrast, the contributions of Nramp1 for controlling chronic infection are more complex, involving temporal and anatomical differences in Nramp1-dependent host responses. Nramp-Cg, Nramp-Tg and NTS-resistant 129×1/SvJ mice survived oral Salmonella infection equally well for the first 2-3 weeks, providing evidence that Nramp1 contributes to the initial control of NTS bacteremia preceding establishment of chronic Salmonella infection. By day 30, increased host Nramp1 expression (Tg>Cg) provided greater protection as indicated by decreased splenic bacterial colonization (Tg<Cg). However, despite controlling bacterial growth within MLN as effectively as 129×1/SvJ mice, Nramp-Cg and Nramp-Tg mice eventually succumbed to infection. These data indicate: 1) discrete, anatomically localized host resistance is conferred by Nramp1 expression in NTS-susceptible mice, 2) restriction of systemic bacterial growth in the spleens of NTS-susceptible mice is enhanced by Nramp1 expression and dose-dependent, and 3) host genes other than Nramp1 also contribute to the ability of NTS-resistant 129×1/SvJ mice to control bacterial replication during chronic infection.","corpus_id":2614552,"score":1},{"doc_id":"25944860","title":"Genetic diversity in the collaborative cross model recapitulates human West Nile virus disease outcomes.","abstract":"UNLABELLED: West Nile virus (WNV) is an emerging neuroinvasive flavivirus that now causes significant morbidity and mortality worldwide. The innate and adaptive immune responses to WNV infection have been well studied in C57BL/6J inbred mice, but this model lacks the variations in susceptibility, immunity, and outcome to WNV infection that are observed in humans, thus limiting its usefulness to understand the mechanisms of WNV infection and immunity dynamics. To build a model of WNV infection that captures human infection outcomes, we have used the Collaborative Cross (CC) mouse model. We show that this model, which recapitulates the genetic diversity of the human population, demonstrates diversity in susceptibility and outcomes of WNV infection observed in humans. Using multiple F1 crosses of CC mice, we identified a wide range of susceptibilities to infection, as demonstrated through differences in survival, clinical disease score, viral titer, and innate and adaptive immune responses in both peripheral tissues and the central nervous system. Additionally, we examined the Oas1b alleles in the CC mice and confirmed the previous finding that Oas1b plays a role in susceptibility to WNV; however, even within a given Oas1b allele status, we identified a wide range of strain-specific WNV-associated phenotypes. These results confirmed that the CC model is effective for identifying a repertoire of host genes involved in WNV resistance and susceptibility. The CC effectively models a wide range of WNV clinical, virologic, and immune phenotypes, thus overcoming the limitations of the traditional C57BL/6J model, allowing genetic and mechanistic studies of WNV infection and immunity in differently susceptible populations. IMPORTANCE: Mouse models of West Nile virus infection have revealed important details regarding the innate and adaptive immune responses to this emerging viral infection. However, traditional mouse models lack the genetic diversity present in human populations and therefore limit our ability to study various disease outcomes and immunologic mechanisms subsequent to West Nile virus infection. In this study, we used the Collaborative Cross mouse model to more effectively model the wide range of clinical, virologic, and immune phenotypes present upon West Nile virus infection in humans.","corpus_id":17940625,"score":1},{"doc_id":"26109132","title":"Genetic susceptibility to invasive Salmonella disease.","abstract":"Invasive Salmonella disease, in the form of enteric fever and invasive non-typhoidal Salmonella (iNTS) disease, causes substantial morbidity and mortality in children and adults in the developing world. The study of genetic variations in humans and mice that influence susceptibility of the host to Salmonella infection provides important insights into immunity to Salmonella. In this Review, we discuss data that have helped to elucidate the host genetic determinants of human enteric fever and iNTS disease, alongside data from the mouse model of Salmonella infection. Considered together, these studies provide a detailed picture of the immunobiology of human invasive Salmonella disease.","corpus_id":3215705,"score":1},{"doc_id":"26921172","title":"Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice.","abstract":"BACKGROUND: Influenza A virus is a zoonotic pathogen that poses a major threat to human and animal health. The severe course of influenza infection is not only influenced by viral virulence factors but also by individual differences in the host response. To determine the extent to which the genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mouse strains. RESULTS: We observed highly divergent host responses between the CC founder strains with respect to survival, body weight loss, hematological parameters in the blood, relative lung weight and viral load. Mouse strain was the main factor with highest effect size on body weight loss after infection, demonstrating that this phenotype was highly heritable. Sex represented another significant main effect, although it was less strong. Analysis of survival rates and mean time to death suggested three groups of susceptibility phenotypes: highly susceptible (A/J, CAST/EiJ, WSB/EiJ), intermediate susceptible (C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ) and highly resistant strains (NZO/HlLtJ, PWK/PhJ). These three susceptibility groups were significantly different with respect to death/survival counts. Viral load was significantly different between susceptible and resistant strains but not between intermediate and highly susceptible strains. CAST/EiJ mice showed a unique phenotype. Despite high viral loads in their lungs, CAST/EiJ mice exhibited low counts of infiltrating granulocytes and showed increased numbers of macrophages in the lung. Histological studies of infected lungs and transcriptome analyses of peripheral blood cells and lungs confirmed an abnormal response in the leukocyte recruitment in CAST/EiJ mice. CONCLUSIONS: The eight CC founder strains exhibited a large diversity in their response to influenza infections. Therefore, the CC will represent an ideal mouse genetic reference population to study the influence of genetic variation on the susceptibility and resistance to influenza infections which will be important to understand individual variations of disease severity in humans. The unique phenotype combination in the CAST/EiJ strain resembles human leukocyte adhesion deficiency and may thus represent a new mouse model to understand this and related abnormal immune responses to infections in humans.","corpus_id":13925613,"score":1},{"doc_id":"27169516","title":"Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice.","abstract":"BACKGROUND: P. aeruginosa is one of the top three causes of opportunistic human bacterial infections. The remarkable variability in the clinical outcomes of this infection is thought to be associated with genetic predisposition. However, the genes underlying host susceptibility to P. aeruginosa infection are still largely unknown. RESULTS: As a step towards mapping these genes, we applied a genome wide linkage analysis approach to a mouse model. A large F2 intercross population, obtained by mating P. aeruginosa-resistant C3H/HeOuJ, and susceptible A/J mice, was used for quantitative trait locus (QTL) mapping. The F2 progenies were challenged with a P. aeruginosa clinical strain and monitored for the survival time up to 7 days post-infection, as a disease phenotype associated trait. Selected phenotypic extremes of the F2 distribution were genotyped with high-density single nucleotide polymorphic (SNP) markers, and subsequently QTL analysis was performed. A significant locus was mapped on chromosome 6 and was named P . aeruginosa infection resistance locus 1 (Pairl1). The most promising candidate genes, including Dok1, Tacr1, Cd207, Clec4f, Gp9, Gata2, Foxp1, are related to pathogen sensing, neutrophils and macrophages recruitment and inflammatory processes. CONCLUSIONS: We propose a set of genes involved in the pathogenesis of P. aeruginosa infection that may be explored to complement human studies.","corpus_id":6086649,"score":1},{"doc_id":"27422773","title":"Mapping liver fat female-dependent quantitative trait loci in collaborative cross mice.","abstract":"Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in the western world, with spectrum from simple steatosis to non-alcoholic steatohepatitis, which can progress to cirrhosis. NAFLD developments are known to be affected by host genetic background. Herein we emphasize the power of collaborative cross (CC) mouse for dissecting this complex trait and revealing quantitative trait loci (QTL) controlling hepatic fat accumulation in mice. 168 female and 338 male mice from 24 and 37 CC lines, respectively, of 18-20 weeks old, maintained on standard rodent diet, since weaning. Hepatic fat content was assessed, using dual DEXA scan in the liver. Using the available high-density genotype markers of the CC line, QTL mapping associated with percentage liver fat accumulation was performed. Our results revealed significant fatty liver accumulation QTL that were specifically, mapped in females. Two significant QTLs on chromosomes 17 and 18, with genomic intervals 3 and 2 Mb, respectively, were mapped. A third QTL, with a less significant P value, was mapped to chromosome 4, with genomic interval of 2 Mb. These QTLs were named Flal1-Flal3, referring to Fatty Liver Accumulation Locus 1-3, for the QTLs on chromosomes 17, 18, and 4, respectively. Unfortunately, no QTL was mapped with males. Searching the mouse genome database suggested several candidate genes involved in hepatic fat accumulation. Our results show that susceptibility to hepatic fat accumulations is a complex trait, controlled by multiple genetic factors in female mice, but not in male.","corpus_id":28384340,"score":1},{"doc_id":"27807798","title":"Glucose tolerance female-specific QTL mapped in collaborative cross mice.","abstract":"Type-2 diabetes (T2D) is a complex metabolic disease characterized by impaired glucose tolerance. Despite environmental high risk factors, host genetic background is a strong component of T2D development. Herein, novel highly genetically diverse strains of collaborative cross (CC) lines from mice were assessed to map quantitative trait loci (QTL) associated with variations of glucose-tolerance response. In total, 501 mice of 58 CC lines were maintained on high-fat (42 % fat) diet for 12 weeks. Thereafter, an intraperitoneal glucose tolerance test (IPGTT) was performed for 180 min. Subsequently, the values of Area under curve for the glucose at zero and 180 min (AUC0-180), were measured, and used for QTL mapping. Heritability and coefficient of variations in glucose tolerance (CVg) were calculated. One-way analysis of variation was significant (P < 0.001) for AUC0-180 between the CC lines as well between both sexes. Despite Significant variations for both sexes, QTL analysis was significant, only for females, reporting a significant female-sex-dependent QTL (~2.5 Mbp) associated with IPGTT AUC0-180 trait, located on Chromosome 8 (32-34.5 Mbp, containing 51 genes). Gene browse revealed QTL for body weight/size, genes involved in immune system, and two main protein-coding genes involved in the Glucose homeostasis, Mboat4 and Leprotl1. Heritability and coefficient of genetic variance (CVg) were 0.49 and 0.31 for females, while for males, these values 0.34 and 0.22, respectively. Our findings demonstrate the roles of genetic factors controlling glucose tolerance, which significantly differ between sexes requiring independent studies for females and males toward T2D prevention and therapy.","corpus_id":3682544,"score":1},{"doc_id":"21813203","title":"Roles of Salmonella enterica serovar Typhimurium encoded Peptidase N during systemic infection of Ifnγ-/- mice.","abstract":"Pathogen encoded peptidases are known to be important during infection; however, their roles in modulating host responses in immunocompromised individuals are not well studied. The roles of S. typhimurium (WT) encoded Peptidase N (PepN), a major aminopeptidase and sole M1 family member, was studied in mice lacking Interferon-γ (IFNγ), a cytokine important for immunity. S. typhimurium lacking pepN (ΔpepN) displays enhanced colony forming units (CFU) compared to WT in peripheral organs during systemic infection in C57BL/6 mice. However, Ifnγ(-/-) mice show higher CFU compared to C57BL/6 mice, resulting in lower fold differences between WT and ΔpepN. Concomitantly, reintroduction of pepN in ΔpepN (ΔpepN/pepN) reduces CFU, demonstrating pepN-dependence. Interestingly, expression of a catalytically inactive PepN (ΔpepN/E298A) also lowers CFU, demonstrating that the decrease in CFU is independent of the catalytic activity of PepN. In addition, three distinct differences are observed between infection of C57BL/6 and Ifnγ(-/-) mice: First, serum amounts of TNFα and IL1β post infection are significantly lower in Ifnγ(-/-) mice. Second, histological analysis of C57BL/6 mice reveals that damage in spleen and liver upon infection with WT or ΔpepN is greater compared to ΔpepN/pepN or ΔpepN/E298A. On the other hand, Ifnγ(-/-) mice are highly susceptible to organ damage by all strains of S. typhimurium used in this study. Finally, greater survival of C57BL/6, but not Ifnγ(-/-) mice, is observed upon infection with ΔpepN/pepN or ΔpepN/E298A. Overall, the roles of the host encoded IFNγ during infection with S. typhimurium strains with varying degrees of virulence are highlighted.","corpus_id":40516328,"score":0},{"doc_id":"21835179","title":"Identification of genetic loci affecting the establishment and development of Echinococcus multilocularis larvae in mice.","abstract":"Alveolar echinococcosis (AE) is a severe hepatic disorder caused by larval infection by the fox tapeworm Echinococcus multilocularis. The course of parasitic development and host reactions are known to vary significantly among host species, and even among different inbred strains of mice. As reported previously, after oral administration of parasite eggs, DBA/2 (D2) mice showed a higher rate of cyst establishment and more advanced protoscolex development in the liver than C57BL/6 (B6) mice. These findings strongly suggest that the outcome of AE is affected by host genetic factor(s). In the present study, the genetic basis of such strain-specific differences in susceptibility/resistance to AE in murine models was studied by whole-genome scanning for quantitative trait loci (QTLs) using a backcross of (B6×D2)F(1) and D2 mice with varying susceptibility to E. multilocularis infection. For cyst establishment, genome linkage analysis identified one suggestive and one significant QTL on chromosomes (Chrs.) 9 and 6, respectively, whereas for protoscolex development, two suggestive and one highly significant QTLs were detected on Chrs. 6, 17 and 1, respectively. Our QTL analyses using murine AE models revealed that multiple genetic factors regulated host susceptibility/resistance to E. multilocularis infection. Moreover, our findings show that establishment of the parasite cysts in the liver is affected by QTLs that are distinct from those associated with the subsequent protoscolex development of the parasite, indicating that different host factors are involved in the host-parasite interplay at each developmental stage of the larval parasite. Further identification of responsible genes located on the identified QTLs could lead to the development of effective disease prevention and control strategies, including an intensive screening and clinical follow-up of genetically high-risk groups for AE infection.","corpus_id":20463074,"score":0},{"doc_id":"22126848","title":"Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses.","abstract":"Inbred mouse strains MRL and LG share the ability to fully heal ear hole punches with the full range of appropriate tissues without scarring. They also share a common ancestry, MRL being formed from a multi-strain cross with two final backcrosses to LG before being inbred by brother-sister mating. Many gene-mapping studies for healing ability have been performed using these two strains, resulting in the location of about 20 quantitative trait loci (QTLs). Here, we combine two of these crosses (N = 638), MRL/lpr × C57BL/6NTac and LG/J × SM/J, in a single combined cross analysis to increase the mapping power, decrease QTL support intervals, separate multiple QTLs and establish allelic states at individual QTL. The combined cross analysis located 11 QTLs, 6 affecting only one cross (5 LG × SM and 1 MRL × B6) and 5 affecting both crosses, approximately the number of common QTLs expected given strain SNP similarity. Amongst the five QTLs mapped in both crosses, three had significantly different genetic effects, additive in one cross and over or underdominant in the other. It is possible that allelic states at these three loci are different in SM and B6 because they lead to differences in dominance interactions with the LG and MRL alleles. QTL support intervals are 40% smaller in the combined cross analysis than in either of the single crosses. Combined cross analysis was successful in enhancing the interpretation of earlier QTL results for these strains.","corpus_id":12644526,"score":0},{"doc_id":"22684724","title":"IFNγ expression by an attenuated strain of Salmonella enterica serovar Typhimurium improves vaccine efficacy in susceptible TLR4-defective C3H/HeJ mice.","abstract":"C3H/HeJ mice carry a mutated allele of TLR4 gene (TLR4 ( d )) and thus are hyporesponsive to the lethal effects of lipopolysaccharide (LPS). Characteristically, however, the mice are also hypersusceptible to infections, particularly by Gram-negative bacteria such as Salmonella enterica serovar Typhimurium (S. typhimurium) and are known to be difficult to vaccinate against virulent exposure. This is observed despite the expression of wild-type allele of Nramp1 gene, another important determinant of Salmonella susceptibility. In contrast, C3H/HeN mice (TLR4 ( n ) Nramp1 ( n )) express a functional TLR4 protein and are resistant to infection, even by virulent strains of S. typhimurium. In the present study, we describe the immune system-enhancing properties of an attenuated strain of S. typhimurium engineered to express murine IFN-γ. This strain (designated GIDIFN) was able to modulate immune responses following systemic inoculation by upregulating the production of inflammatory mediators (IL-6 and IL-12) and anti-bacterial effector molecules (nitric oxide; NO). Consequently, this led to a more effective control of bacterial proliferation in systemic target organs in both C3H/HeJ and C3H/HeN mice. Although evidence for the enhancement in immune responses could be observed as early as few hours post-inoculation, sustained improvements required 2-3 days to manifest. Vaccination of C3H/HeJ mice with GIDIFN strain, even at low doses, conferred a significantly higher degree of protection against challenge with virulent Salmonella in susceptible C3H/HeJ mice. Our data demonstrate that IFNγ-expressing Salmonella are immunogenic and confer excellent protection against virulent challenge in susceptible C3H/HeJ mice; in addition they may be used as an effective mucosal delivery vectors against virulent infection and for boosting immune responses in immunodeficient hosts.","corpus_id":18904226,"score":0},{"doc_id":"22911454","title":"Identification of exercise capacity QTL using association mapping in inbred mice.","abstract":"There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.","corpus_id":1251908,"score":0},{"doc_id":"23041268","title":"Genetic manipulation of pathogenicity loci in non-Typhimurium Salmonella.","abstract":"The traditional genetic tools used in Salmonella enterica serovar Typhimurium rely heavily on a high-transducing mutant of bacteriophage P22. P22 recognizes its hosts by the structure of their O-antigens, which vary among serovars of Salmonella; therefore, it cannot be used in most non-Typhimurium Salmonella, including the majority of those causing food-borne illnesses in both humans and livestock. Bacteriophage P1 infects a variety of enteric bacteria, including galE mutants of serovar Typhimurium; however, the degree to which the presence of coimmune prophages, the lack of required attachment sites or the lack of host factors act as barriers to using phage P1 in natural isolates of Salmonella is unknown. Here, we show that recombineering can be used to make virtually any serovar of Salmonella susceptible to P1 infection; as a result, P1 can be utilized for facile genetic manipulation of non-Typhimurium Salmonella, including movement of very large pathogenicity islands. A toolkit for easy manipulation of non-Typhimurium serovars of Salmonella is described.","corpus_id":7480518,"score":0},{"doc_id":"23409175","title":"A parent-of-origin effect determines the susceptibility of a non-informative F1 population to Trypanosoma cruzi infection in vivo.","abstract":"The development of Chagas disease is determined by a complex interaction between the genetic traits of both the protozoan parasite, T. cruzi, and the infected host. This process is regulated by multiple genes that control different aspects of the host-parasite interaction. While determination of the relevant genes in humans is extremely difficult, it is feasible to use inbred mouse strains to determine the genes and loci responsible for host resistance to infection. In this study, we investigated the susceptibility of several inbred mouse strains to infection with the highly virulent Y strain of T. cruzi and found a considerable difference in susceptibility between A/J and C57BL/6 mice. We explored the differences between these two mouse strains and found that the A/J strain presented higher mortality, exacerbated and uncontrolled parasitemia and distinct histopathology in the target organs, which were associated with a higher parasite burden and more extensive tissue lesions. We then employed a genetic approach to assess the pattern of inheritance of the resistance phenotype in an F1 population and detected a strong parent-of-origin effect determining the susceptibility of the F1 male mice. This effect is unlikely to result from imprinted genes because the inheritance of this susceptibility was affected by the direction of the parental crossing. Collectively, our genetic approach of using the F1 population suggests that genes contained in the murine chromosome X contribute to the natural resistance against T. cruzi infection. Future linkage studies may reveal the locus and genes participating on the host resistance process reported herein.","corpus_id":6975963,"score":0},{"doc_id":"23505508","title":"Virulence gene profiling and pathogenicity characterization of non-typhoidal Salmonella accounted for invasive disease in humans.","abstract":"Human infection with non-typhoidal Salmonella serovars (NTS) infrequently causes invasive systemic disease and bacteremia. To understand better the nature of invasive NTS (iNTS), we studied the gene content and the pathogenicity of bacteremic strains from twelve serovars (Typhimurium, Enteritidis, Choleraesuis, Dublin, Virchow, Newport, Bredeney, Heidelberg, Montevideo, Schwarzengrund, 9,12:l,v:- and Hadar). Comparative genomic hybridization using a Salmonella enterica microarray revealed a core of 3233 genes present in all of the iNTS strains, which include the Salmonella pathogenicity islands 1-5, 9, 13, 14; five fimbrial operons (bcf, csg, stb, sth, sti); three colonization factors (misL, bapA, sinH); and the invasion gene, pagN. In the iNTS variable genome, we identified 16 novel genomic islets; various NTS virulence factors; and six typhoid-associated virulence genes (tcfA, cdtB, hlyE, taiA, STY1413, STY1360), displaying a wider distribution among NTS than was previously known. Characterization of the bacteremic strains in C3H/HeN mice showed clear differences in disease manifestation. Previously unreported characterization of serovars Schwarzengrund, 9,12:l,v:-, Bredeney and Virchow in the mouse model showed low ability to elicit systemic disease, but a profound and elongated shedding of serovars Schwarzengrund and 9,12:l,v:- (as well as Enteritidis and Heidelberg) due to chronic infection of the mouse. Phenotypic comparison in macrophages and epithelial cell lines demonstrated a remarkable intra-serovar variation, but also showed that S. Typhimurium bacteremic strains tend to present lower intracellular growth than gastroenteritis isolates. Collectively, our data demonstrated a common core of virulence genes, which might be required for invasive salmonellosis, but also an impressive degree of genetic and phenotypic heterogeneity, highlighting that bacteremia is a complex phenotype, which cannot be attributed merely to an enhanced invasion or intracellular growth of a particular strain.","corpus_id":12372131,"score":0},{"doc_id":"23525445","title":"Genetic-genomic replication to identify candidate mouse atherosclerosis modifier genes.","abstract":"OBJECTIVE: Genetics plays a large role in atherosclerosis susceptibility in humans and mice. We attempted to confirm previously determined mouse atherosclerosis-associated loci and use bioinformatics and transcriptomics to create a catalog of candidate atherosclerosis modifier genes at these loci. METHODS AND RESULTS: A strain intercross was performed between AKR and DBA/2 mice on the apoE(-/-) background generating 166 F2 progeny. Using the phenotype log10 of the aortic root lesion area, we identified 3 suggestive atherosclerosis quantitative trait loci (Ath QTLs). When combined with our prior strain intercross, we confirmed 3 significant Ath QTLs on chromosomes 2, 15, and 17, with combined logarithm of odds scores of 5.9, 5.3, and 5.6, respectively, which each met the genome-wide 5% false discovery rate threshold. We identified all of the protein coding differences between these 2 mouse strains within the Ath QTL intervals. Microarray gene expression profiling was performed on macrophages and endothelial cells from this intercross to identify expression QTLs (eQTLs), the loci that are associated with variation in the expression levels of specific transcripts. Cross tissue eQTLs and macrophage eQTLs that replicated from a prior strain intercross were identified. These bioinformatic and eQTL analyses produced a comprehensive list of candidate genes that may be responsible for the Ath QTLs. CONCLUSIONS: Replication studies for clinical traits as well as gene expression traits are worthwhile in identifying true versus false genetic associations. We have replicated 3 loci on mouse chromosomes 2, 15, and 17 that are associated with atherosclerosis. We have also identified protein coding differences and multiple replicated eQTLs, which may be useful in the identification of atherosclerosis modifier genes.","corpus_id":10876858,"score":0},{"doc_id":"23592259","title":"Identification of salmonella pathogenicity island-2 type III secretion system effectors involved in intramacrophage replication of S. enterica serovar typhimurium: implications for rational vaccine design.","abstract":"UNLABELLED: Salmonella enterica serovars cause severe diseases in humans, such as gastroenteritis and typhoid fever. The development of systemic disease is dependent on a type III secretion system (T3SS) encoded by Salmonella pathogenicity island-2 (SPI-2). Translocation of effector proteins across the Salmonella-containing vacuole, via the SPI-2 T3SS, enables bacterial replication within host cells, including macrophages. Here, we investigated the contribution of these effectors to intramacrophage replication of Salmonella enterica serovar Typhimurium using Fluorescence Dilution, a dual-fluorescence tool which allows direct measurement of bacterial replication. Of 32 strains, each carrying single mutations in genes encoding effectors, 10 (lacking sifA, sseJ, sopD2, sseG, sseF, srfH, sseL, spvD, cigR, or steD) were attenuated in replication in mouse bone marrow-derived macrophages. The replication profiles of strains combining deletions in effector genes were also investigated: a strain lacking the genes sseG, sopD2, and srfH showed an increased replication defect compared to single-mutation strains and was very similar to SPI-2 T3SS-deficient bacteria with respect to its replication defect. This strain was substantially attenuated in virulence in vivo and yet retained intracellular vacuole integrity and a functional SPI-2 T3SS. Moreover, this strain was capable of SPI-2 T3SS-mediated delivery of a model antigen for major histocompatibility complex (MHC) class I-dependent T-cell activation. This work establishes a basis for the use of a poly-effector mutant strain as an attenuated vaccine carrier for delivery of heterologous antigens directly into the cytoplasm of host cells. IMPORTANCE: Live attenuated strains of Salmonella enterica serotype Typhi have generated much interest in the search for improved vaccines against typhoid fever and as vaccine vectors for the delivery of heterologous antigens. A promising vaccine candidate is the ΔaroC ΔssaV S. Typhi strain, which owes its attenuation mainly to lack of a type III secretion system (SPI-2 T3SS). The SPI-2 T3SS is important for bacterial proliferation inside macrophages, but not all of the effectors involved in this process have been identified. Here, we show that 10 effectors of the related strain S. Typhimurium contribute to intracellular replication in macrophages. Moreover, we establish that a poly-effector mutant strain of S. Typhimurium can have a severe replication defect and maintain a functional SPI-2 T3SS, which can be exploited for delivery of heterologous antigens.","corpus_id":14912066,"score":0},{"doc_id":"23643894","title":"Identification and characterization of OmpL as a potential vaccine candidate for immune-protection against salmonellosis in mice.","abstract":"Salmonella is gram-negative flagellated bacteria that can cause food and waterborne gastroenteritis and typhoid fever in humans. Despite the importance of Salmonella infections in human and animal health, the target antigens of Salmonella-specific immunity remain poorly defined, the effectiveness of the currently available vaccines is also limited. Outer membrane proteins (OMPs) of Salmonella have been considered possible candidates for conferring protection against salmonellosis. OMPs interface the cell with the environment, thus representing important potential vaccine candidate for pathogen infection. We showed that the outer membrane porin L (OmpL) is a transmembrane β barrel (TMBB) protein, which forms 12 transmembrane β-strands. OmpL of S. Typhimurium is highly immunogenic, OmpL could evoke humoral and cell-mediated immune responses, and confer 100% protection to immunized mice against challenge with very high doses of S. Typhimurium. Besides, very efficient clearance of bacteria from the reticuloendothelial systems of immunized mice was seen. The homology search further revealed that OmpL is widely distributed and conserved, homologous proteins were identified in S. Typhi and Paratyphi by RT-PCR and western blot. We also found that anti-rOmpL serum harber a high bactericidal activity for Salmonella serovars tested in this study. Therefore, OmpL provide a promising target for the development of a candidate vaccine against Salmonella infection.","corpus_id":25738032,"score":0},{"doc_id":"23937452","title":"Genotype is an important determinant factor of host susceptibility to periodontitis in the Collaborative Cross and inbred mouse populations.","abstract":"BACKGROUND: Periodontal infection (Periodontitis) is a chronic inflammatory disease, which results in the breakdown of the supporting tissues of the teeth. Previous epidemiological studies have suggested that resistance to chronic periodontitis is controlled to some extent by genetic factors of the host. The aim of this study was to determine the phenotypic response of inbred and Collaborative Cross (CC) mouse populations to periodontal bacterial challenge, using an experimental periodontitis model. In this model, mice are co-infected with Porphyromonas gingivalis and Fusobacterium nucleatum, bacterial strains associated with human periodontal disease. Six weeks following the infection, the maxillary jaws were harvested and analyzed for alveolar bone loss relative to uninfected controls, using computerized microtomography (microCT). Initially, four commercial inbred mouse strains were examined to calibrate the procedure and test for gender effects. Subsequently, we applied the same protocol to 23 lines (at inbreeding generations 10-18) from the newly developed mouse genetic reference population, the Collaborative Cross (CC) to determine heritability and genetic variation of control bone volume prior to infection (CBV, naïve bone volume around the teeth of uninfected mice), and residual bone volume (RBV, bone volume after infection) and loss of bone volume (LBV, the difference between CBV and RBV) following infection. RESULTS: BALB/CJ mice were highly susceptible (P<0.05) whereas DBA/2J, C57BL/6J and A/J mice were resistant. Six lines of the tested CC population were susceptible, whereas the remaining lines were resistant to alveolar bone loss. Gender effects on bone volume were tested across the four inbred and 23 CC lines, and found not to be significant. Based on ANOVA analyses, broad-sense heritabilities were statistically significant and equal to 0.4 for CBV and 0.2 for LBV. CONCLUSIONS: The moderate heritability values indicate that the variation in host susceptibility to the disease is controlled to an appreciable extent by genetic factors. These results strongly support the possibility of using the Collaborative Cross, as well as developing dedicated F2 (resistant x susceptible inbred strains) resource populations, for future dissection of genetic factors in periodontitis.","corpus_id":2644393,"score":0},{"doc_id":"24980971","title":"Coinfection with an intestinal helminth impairs host innate immunity against Salmonella enterica serovar Typhimurium and exacerbates intestinal inflammation in mice.","abstract":"Salmonella enterica serovar Typhimurium is a Gram-negative food-borne pathogen that is a major cause of acute gastroenteritis in humans. The ability of the host to control such bacterial pathogens may be influenced by host immune status and by concurrent infections. Helminth parasites are of particular interest in this context because of their ability to modulate host immune responses and because their geographic distribution coincides with those parts of the world where infectious gastroenteritis is most problematic. To test the hypothesis that helminth infection may negatively regulate host mucosal innate immunity against bacterial enteropathogens, a murine coinfection model was established by using the intestinal nematode Heligmosomoides polygyrus and S. Typhimurium. We found that mice coinfected with S. Typhimurium and H. polygyrus developed more severe intestinal inflammation than animals infected with S. Typhimurium alone. The enhanced susceptibility to Salmonella-induced intestinal injury in coinfected mice was found to be associated with diminished neutrophil recruitment to the site of bacterial infection that correlated with decreased expression of the chemoattractants CXCL2/macrophage inflammatory protein 2 (MIP-2) and CXCL1/keratinocyte-derived chemokine (KC), poor control of bacterial replication, and exacerbated intestinal inflammation. The mechanism of helminth-induced inhibition of MIP-2 and KC expression involved interleukin-10 (IL-10) and, to a lesser extent, IL-4 and IL-13. Ly6G antibody-mediated depletion of neutrophils reproduced the adverse effects of H. polygyrus on Salmonella infection. Our results suggest that impaired neutrophil recruitment is an important contributor to the enhanced severity of Salmonella enterocolitis associated with helminth coinfection.","corpus_id":23068391,"score":0},{"doc_id":"25136336","title":"Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ.","abstract":"Human infections by the bacterial pathogen Salmonella enterica represent major disease burdens worldwide. This highly ubiquitous species consists of more than 2600 different serovars that can be divided into typhoidal and non-typhoidal Salmonella (NTS) serovars. Despite their genetic similarity, these two groups elicit very different diseases and distinct immune responses in humans. Comparative analyses of the genomes of multiple Salmonella serovars have begun to explain the basis of the variation in disease manifestations. Recent advances in modeling both enteric fever and intestinal gastroenteritis in mice will facilitate investigation into both the bacterial- and host-mediated mechanisms involved in salmonelloses. Understanding the genetic and molecular mechanisms responsible for differences in disease outcome will augment our understanding of Salmonella pathogenesis, host immunity, and the molecular basis of host specificity. This review outlines the differences in epidemiology, clinical manifestations, and the human immune response to typhoidal and NTS infections and summarizes the current thinking on why these differences might exist.","corpus_id":2345473,"score":0},{"doc_id":"26396246","title":"A Highly Effective Component Vaccine against Nontyphoidal Salmonella enterica Infections.","abstract":"UNLABELLED: Nontyphoidal Salmonella enterica (NTS) infections are a major burden to global public health, as they lead to diseases ranging from gastroenteritis to systemic infections and there is currently no vaccine available. Here, we describe a highly effective component vaccine against S. enterica serovar Typhimurium in both gastroenteritis and systemic murine infection models. We devised an approach to generate supernatants of S. enterica serovar Typhimurium, an organism that is highly abundant in virulence factors. Immunization of mice with this supernatant resulted in dramatic protection against a challenge with serovar Typhimurium, showing increased survival in the systemic model and decreased intestinal pathology in the gastrointestinal model. Protection correlated with specific IgA and IgG levels in the serum and specific secretory IgA levels in the feces of immunized mice. Initial characterization of the protective antigens in the bacterial culture supernatants revealed a subset of antigens that exhibited remarkable stability, a highly desirable characteristic of an effective vaccine to be used under suboptimal environmental conditions in developing countries. We were able to purify a subset of the peptides present in the supernatants and show their potential for immunization of mice against serovar Typhimurium resulting in a decreased level of colonization. This component vaccine shows promise with regard to protecting against NTS, and further work should significantly help to establish vaccines against these prevalent infections. IMPORTANCE: Salmonella enterica infections other than typhoid and paratyphoid fever are a major global health burden, as they cause high morbidity and mortality worldwide. Strategies that prevent Salmonella-related diseases are greatly needed, and there is a significant push for the development of vaccines against nontyphoidal Salmonella enterica serovars. In this work, we describe an S. Typhimurium supernatant-derived vaccine that is effective in reducing bacterial colonization in mouse models of gastroenteritis as well as invasive disease. This is a component vaccine that shows high stability to heat, a feature that is important for use under suboptimal conditions, such as those found in sub-Saharan Africa.","corpus_id":13938061,"score":0},{"doc_id":"26537951","title":"Non-typhoidal Salmonella serotypes, antimicrobial resistance and co-infection with parasites among patients with diarrhea and other gastrointestinal complaints in Addis Ababa, Ethiopia.","abstract":"BACKGROUND: Non-typhoidal Salmonella (NTS) is an important public health problem worldwide. Consumption of animal-derived food products and direct and/or indirect contact with animals are the major routes of acquiring infection with NTS. Published information, particularly on the serotype distribution of NTS among human patients with gastroenteritis and associated risk factors, is scarce in Ethiopia. This study investigated the prevalence, risk factors, serotype distribution and antimicrobial susceptibility of Salmonella species among diarrheic out-patients attending health centers in Addis Ababa and patients with various gastrointestinal complaints at Tikur Anbessa Specialized Hospital (TASH). METHODS: Stool samples were cultured for Salmonella species according to the WHO Global Foodborne Infections Network laboratory protocol. Salmonella serotyping was conducted using slide agglutination and microplate agglutination techniques. Antibiotic susceptibility testing was performed using the disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. RESULTS: A total of 59 (6.2 %) stool samples, out of 957 were culture positive for Salmonella species. Fifty-five (7.2 %) of 765 diarrheic patients from health centers and 4 (2.1 %) of 192 patients from TASH were culture positive for Salmonella species. Multivariable logistic regression analysis after adjusting for all other variables revealed statistically significant association of Salmonella infection with consumption of raw vegetables (OR = 1.91, 95 % CI = 1.29-2.83, χ(2) = 4.74, p = 0.025) and symptom of watery diarrhea (OR = 3.3, 95 % CI = 1.23-8.88, χ(2) = 10.54, p = 0.005). Eleven serotypes were detected, and the most prominent were S. Typhimurium (37.3 %), S. Virchow (34 %), and S. Kottbus (10.2 %). Other serotypes were S. Miami, S. Kentucky, S. Newport, S. Enteritidis, S. Braenderup, S. Saintpaul, S. Concord and S. V:ROUGH-O. Resistance to three or more antimicrobials was detected in 27 (40.3 %) of the isolates. Resistance to five or more antimicrobials was detected in 17 (25.4 %). Resistance to individual antimicrobials was found at varying proportions: streptomycin (50; 74.6 %), nitrofurantoin (27; 40.3 %), sulfisoxazole (26; 38.8 %), kanamycin (23; 34.3 %), cephalothin (12; 17.9 %), and ampicillin (11; 16.4 %) respectively. Two S. Kentucky, one S. Typhimurium and one S. Concord isolates were multi-drug resistant to more than 10 antimicrobials. CONCLUSIONS: The study demonstrated significant association of Salmonella infection with consumption of raw vegetables. There was no significant association of Salmonella infection with co-occurring parasites. The study also showed the dominance of S. Typhimurium and S. Virchow in primary health care units. Overall, prevalence of MDR was low compared to previous studies. Although their proportion was low, S. Kentucky and S. Concord demonstrated wider spectrum of MDR. Continuous monitoring of circulating serotypes, antimicrobial resistance profile and characterization on molecular resistance determinants is essential for proper treatment of patients and for identifying potential environmental origins of antimicrobial resistance.","corpus_id":4256866,"score":0},{"doc_id":"26787719","title":"Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91-/- phox Mice.","abstract":"Salmonella enterica causes systemic diseases (typhoid and paratyphoid fever), nontyphoidal septicemia (NTS), and gastroenteritis in humans and other animals worldwide. An important but underrecognized emerging infectious disease problem in sub-Saharan Africa is NTS in children and immunocompromised adults. A current goal is to identify Salmonella mutants that are not pathogenic in the absence of key components of the immune system such as might be found in immunocompromised hosts. Such attenuated strains have the potential to be used as live vaccines. We have used transposon-directed insertion site sequencing (TraDIS) to screen mutants of Salmonella enterica serovar Typhimurium for their ability to infect and grow in the tissues of wild-type and immunodeficient mice. This was to identify bacterial genes that might be deleted for the development of live attenuated vaccines that would be safer to use in situations and/or geographical areas where immunodeficiencies are prevalent. The relative fitness of each of 9,356 transposon mutants, representing mutations in 3,139 different genes, was determined in gp91(-/-) phox mice. Mutations in certain genes led to reduced fitness in both wild-type and mutant mice. To validate these results, these genes were mutated by allelic replacement, and resultant mutants were retested for fitness in the mice. A defined deletion mutant of cysE was attenuated in C57BL/6 wild-type mice and immunodeficient gp91(-/-) phox mice and was effective as a live vaccine in wild-type mice.","corpus_id":4782466,"score":0},{"doc_id":"26956590","title":"Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress.","abstract":"UNLABELLED: Salmonella enterica serovar Typhimurium is one of the most common S. enterica serovars associated with U.S. foodborne outbreaks. S. Typhimurium bacteria isolated from humans exhibit wide-ranging virulence phenotypes in inbred mice, leading to speculation that some strains are more virulent in nature. However, it is unclear whether increased virulence in humans is related to organism characteristics or initial treatment failure due to antibiotic resistance. Strain diversity and genetic factors contributing to differential human pathogenicity remain poorly understood. We reconstructed phylogeny, resolved genetic population structure, determined gene content and nucleotide variants, and conducted targeted phenotyping assays for S. Typhimurium strains collected between 1946 and 2012 from humans and animals in the United States and abroad. Strains from recent U.S. salmonellosis cases were associated with five S. Typhimurium lineages distributed within three phylogenetic clades, which are not restricted by geography, year of acquisition, or host. Notably, two U.S. strains and four Mexican strains are more closely related to strains associated with human immunodeficiency virus (HIV)-infected individuals in sub-Saharan Africa than to other North American strains. Phenotyping studies linked variants specific to these strains in hmpA and katE to loss of fitness under nitrosative and oxidative stress, respectively. These results suggest that U.S. salmonellosis is caused by diverse S. Typhimurium strains circulating worldwide. One lineage has mutations in genes affecting fitness related to innate immune system strategies for fighting pathogens and may be adapting to immunocompromised humans by a reduction in virulence capability, possibly due to a lack of selection for its maintenance as a result of the worldwide HIV epidemic. IMPORTANCE: Nontyphoidal Salmonella bacteria cause an estimated 1.2 million illnesses annually in the United States, 80 million globally, due to ingestion of contaminated food or water. Salmonella Typhimurium is one of the most common serovars associated with foodborne illness, causing self-limiting gastroenteritis and, in approximately 5% of infected patients, systemic infection. Although some S. Typhimurium strains are speculated to be more virulent than others, it is unknown how strain diversity and genetic factors contribute to differential human pathogenicity. Ours is the first study to examine the diversity of S. Typhimurium associated with recent cases of U.S. salmonellosis and to provide some initial correlation between observed genotypes and phenotypes. Definition of specific S. Typhimurium lineages based on such phenotype/genotype correlations may identify strains with greater capability of associating with specific food sources, allowing outbreaks to be more quickly identified. Additionally, defining simple correlates of pathogenesis may have predictive value for patient outcome.","corpus_id":6445763,"score":0},{"doc_id":"27380139","title":"Quantitative trait loci identification and meta-analysis for rice panicle-related traits.","abstract":"Rice yield is a complex trait controlled by quantitative trait loci (QTLs). In the past three decades, thousands of QTLs for rice yield traits have been detected, but only a very small percentage has been cloned to date, as identifying the QTL genes requires a substantial investment of time and money. Meta-analysis provides a simple, reliable, and economical method for integrating information from multiple QTL studies across various environmental and genetic backgrounds, detecting consistent QTLs powerfully and estimating their genetic positions precisely. In this study, we aimed to locate consistent QTL regions associated with rice panicle traits by applying a genome-wide QTL meta-analysis approach. We first conducted a QTL analysis of 5 rice panicle traits using 172 plants in 2011 and 138 plants in 2012 from an F2 population derived from a cross between Nipponbare and H71D rice cultivators. A total of 54 QTLs were detected, and these were combined with 1085 QTLs collected from 82 previous studies to perform a meta-analysis using BioMercator v4.2. The integration of 82 maps resulted in a consensus map with 6970 markers and a total map length of 1823.1 centimorgan (cM), on which 837 QTLs were projected. These QTLs were then integrated into 87 meta-quantitative trait loci (MQTLs) by meta-analysis, and the 95 % confidence intervals (CI) of them were smaller than the mean value of the original QTLs. Also, 30 MQTLs covered 47 of the 54 QTLs detected from the cross between Nipponbare and H71D in this study. Among them, the two major and stable QTLs, spp10.1 and sd10.1, were found to be included in MQTL10.4. The three other major QTLs, pl3.1, sb2.1, and sb10.1, were included in MQTL3.3, MQTL2.2, and MQTL10.3, respectively. A total of 21 of the 87 MQTLs' phenotypic variation were >20 %. In total, 24 candidate genes were found in 15 MQTLs that spanned physical intervals <0.2 Mb, including genes that have been cloned previously, e.g., EP3, LP, MIP1, HTD1, DSH1, and OsPNH1. However, it would be beneficial to identify a greater number of candidate genes from these MQTLs. Mining new genes that modulate yield and its related traits would assist researchers to better understand the relevant molecular mechanisms. The MQTLs found in this study that have small physical and genetic intervals are useful not only for marker-assisted selection and pyramiding, but they also provide important information of rice yield and related gene mining for future research.","corpus_id":9198099,"score":0},{"doc_id":"27515598","title":"The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits.","abstract":"BACKGROUND: Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. RESULTS: We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. CONCLUSIONS: Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs.","corpus_id":7803470,"score":0},{"doc_id":"27785189","title":"Effect of Salmonella enteric Serovar Typhimurium in Pregnant Mice: A Biochemical and Histopathological Study.","abstract":"BACKGROUND: Food borne infections caused by Salmonella enterica species are increasing globally and pregnancy poses a significant threat in developing countries, where sanitation facilities are inadequate. Thus, the present study was designed to delineate the effect of Salmonella infection during pregnancy. METHOD: Pregnant, BALB/c mice were challenged orally with Salmonella enterica serovar Typhimurium on gestational day 10 and were monitored for bacterial load, hepatic injury, histopathological alterations vis-a-vis oxidant and antioxidant levels. RESULTS: Pregnant-Salmonella-infected mice had higher bacterial translocation in the liver, spleen as well as liver enzymes mainly aspartate aminotransferase, alanine aminotransferase and alkaline phosphatase compared with Salmonella-infected mice. The levels of lipid peroxidation were significantly higher in all the organs of both pregnant-Salmonella-infected and Salmonella-infected mice compared with control mice. However, the activities of antioxidant enzymes (reduced glutathione, superoxide dismutase and catalase) were lower in the liver, spleen and placenta of pregnant, pregnant-Salmonella-infected and Salmonella-infected mice compared with control mice, but the decrease was more in pregnant-Salmonella-infected mice indicating depression of antioxidant defense system. Histopathologically, pregnant-Salmonella-infected mice had more architectural damage in the liver, spleen and placenta compared with other groups. CONCLUSION: Pregnancy makes the host more vulnerable to typhoid fever by affecting the physiology of pivotal organs and highlighting the importance of early and prompts diagnosis so as to avoid the further materno-fetal complications.","corpus_id":17102068,"score":0},{"doc_id":"29294296","title":"Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility.","abstract":"Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro-computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (-log P = 5.3; false discovery rate = 0.06) on chromosomes 1 ( Perio3) and 14 ( Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes ( CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.","corpus_id":4963494,"score":0},{"doc_id":"29784861","title":"Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants.","abstract":"Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.","corpus_id":29169360,"score":0}],"string":"[\n {\n \"doc_id\": \"20429884\",\n \"title\": \"Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review.\",\n \"abstract\": \"Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species Salmonella enterica and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of S. enterica serovar Enteritidis or S. enterica serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to Salmonella differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes TLR4 and SLC11A1, the Major Histocompatibility Complex (MHC) and the QTL SAL1 are interesting for more in-depth studies. This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.\",\n \"corpus_id\": 2352316,\n \"score\": 2\n },\n {\n \"doc_id\": \"20643856\",\n \"title\": \"Role for neutrophils in host immune responses and genetic factors that modulate resistance to Salmonella enterica serovar typhimurium in the inbred mouse strain SPRET/Ei.\",\n \"abstract\": \"Infection with Salmonella enterica serovar Typhimurium is a complex disease in which the host-bacterium interactions are strongly influenced by genetic factors of the host. We demonstrate that SPRET/Ei, an inbred mouse strain derived from Mus spretus, is resistant to S. Typhimurium infections. The kinetics of bacterial proliferation, as well as histological examinations of tissue sections, suggest that SPRET/Ei mice can control bacterial multiplication and spreading despite significant attenuation of the cytokine response. The resistance of SPRET/Ei mice to S. Typhimurium infection is associated with increased leukocyte counts in the circulation and enhanced neutrophil influx into the peritoneum during the course of infection. A critical role of neutrophils was confirmed by neutrophil depletion: neutropenic SPRET/Ei mice were sensitive to infection with S. Typhimurium and showed much higher bacterial loads. To identify genes that modulate the natural resistance of SPRET/Ei mice to S. Typhimurium infection, we performed a genome-wide study using an interspecific backcross between C3H/HeN and SPRET/Ei mice. The results of this analysis demonstrate that at least two loci, located on chromosomes 6 and 11, affect survival following lethal infection with S. Typhimurium. These two loci contain several interesting candidate genes which may have important implications for the search for genetic factors controlling Salmonella infections in humans and for our understanding of complex host-pathogen interactions in general.\",\n \"corpus_id\": 44380068,\n \"score\": 2\n },\n {\n \"doc_id\": \"21493779\",\n \"title\": \"Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection.\",\n \"abstract\": \"The Collaborative Cross (CC) is a genetic reference panel of recombinant inbred lines of mice, designed for the dissection of complex traits and gene networks. Each line is independently descended from eight genetically diverse founder strains such that the genomes of the CC lines, once fully inbred, are fine-grained homozygous mosaics of the founder haplotypes. We present an analysis of 120 CC lines, from a cohort of the CC bred at Tel Aviv University in collaboration with the University of Oxford, which at the time of this study were between the sixth and 12th generations of inbreeding and substantially homozygous at 170,000 SNPs. We show how CC genomes decompose into mosaics, and we identify loci that carry a deficiency or excess of a founder, many being deficient for the wild-derived strains WSB/EiJ and PWK/PhJ. We phenotyped 371 mice from 66 CC lines for a susceptibility to Aspergillus fumigatus infection. The survival time after infection varied significantly between CC lines. Quantitative trait locus (QTL) mapping identified genome-wide significant QTLs on chromosomes 2, 3, 8, 10 (two QTLs), 15, and 18. Simulations show that QTL mapping resolution (the median distance between the QTL peak and true location) varied between 0.47 and 1.18 Mb. Most of the QTLs involved contrasts between wild-derived founder strains and therefore would not segregate between classical inbred strains. Use of variation data from the genomes of the CC founder strains refined these QTLs further and suggested several candidate genes. These results support the use of the CC for dissecting complex traits.\",\n \"corpus_id\": 12448545,\n \"score\": 2\n },\n {\n \"doc_id\": \"21956657\",\n \"title\": \"Refinement of the genetics of the host response to Salmonella infection in MOLF/Ei: regulation of type 1 IFN and TRP3 pathways by Ity2.\",\n \"abstract\": \"Typhoid fever, which is caused by Salmonella typhi and paratyphi, is a severe systemic disease that remains a major public health issue in several areas of the world. We can model the human disease using mice infected with a related bacterium, Salmonella typhimurium. This model recapitulates several clinical aspects of the human disease and allows for the study of the host response to Salmonella typhimurium infection in vivo. Previous work in our laboratory has identified three Immunity to typhimurium loci (Ity, Ity2 and Ity3) in the wild-derived MOLF/Ei mice, influencing survival after infection with Salmonella typhimurium. The MOLF/Ei alleles at Ity and Ity2 are protective, while the MOLF/Ei allele at Ity3 confers susceptibility. In this paper, we have generated a novel cross combination between the highly susceptible strain, MOLF/Ei, and the resistant strain, 129S6, to better define the genetic architecture of susceptibility to infection in MOLF/Ei. Using this cross, we have replicated the locus on chr 11 (Ity2) and identified a novel locus on chr 13 (Ity13). Using microarrays and transcriptional profiling, we examined the response of uninfected and infected Ity2 congenic mice. These analyses demonstrate a role for both type-1-interferon (IFN) and TRP53 signaling in the pathogenesis of Salmonella infection.\",\n \"corpus_id\": 34369048,\n \"score\": 2\n },\n {\n \"doc_id\": \"22384400\",\n \"title\": \"Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice.\",\n \"abstract\": \"Outbreaks of influenza occur on a yearly basis, causing a wide range of symptoms across the human population. Although evidence exists that the host response to influenza infection is influenced by genetic differences in the host, this has not been studied in a system with genetic diversity mirroring that of the human population. Here we used mice from 44 influenza-infected pre-Collaborative Cross lines determined to have extreme phenotypes with regard to the host response to influenza A virus infection. Global transcriptome profiling identified 2671 transcripts that were significantly differentially expressed between mice that showed a severe (\\\"high\\\") and mild (\\\"low\\\") response to infection. Expression quantitative trait loci mapping was performed on those transcripts that were differentially expressed because of differences in host response phenotype to identify putative regulatory regions potentially controlling their expression. Twenty-one significant expression quantitative trait loci were identified, which allowed direct examination of genes associated with regulation of host response to infection. To perform initial validation of our findings, quantitative polymerase chain reaction was performed in the infected founder strains, and we were able to confirm or partially confirm more than 70% of those tested. In addition, we explored putative causal and reactive (downstream) relationships between the significantly regulated genes and others in the high or low response groups using structural equation modeling. By using systems approaches and a genetically diverse population, we were able to develop a novel framework for identifying the underlying biological subnetworks under host genetic control during influenza virus infection.\",\n \"corpus_id\": 29006112,\n \"score\": 2\n },\n {\n \"doc_id\": \"23055923\",\n \"title\": \"Host-pathogen interaction in invasive Salmonellosis.\",\n \"abstract\": \"Salmonella enterica infections result in diverse clinical manifestations. Typhoid fever, caused by S. enterica serovar Typhi (S. Typhi) and S. Paratyphi A, is a bacteremic illness but whose clinical features differ from other Gram-negative bacteremias. Non-typhoidal Salmonella (NTS) serovars cause self-limiting diarrhea with occasional secondary bacteremia. Primary NTS bacteremia can occur in the immunocompromised host and infants in sub-Saharan Africa. Recent studies on host-pathogen interactions in Salmonellosis using genome sequencing, murine models, and patient studies have provided new insights. The full genome sequences of numerous S. enterica serovars have been determined. The S. Typhi genome, compared to that of S. Typhimurium, harbors many inactivated or disrupted genes. This can partly explain the different immune responses both serovars induce upon entering their host. Similar genome degradation is also observed in the ST313 S. Typhimurium strain implicated in invasive infection in sub-Saharan Africa. Virulence factors, most notably, type III secretion systems, Vi antigen, lipopolysaccharide and other surface polysaccharides, flagella, and various factors essential for the intracellular life cycle of S. enterica have been characterized. Genes for these factors are commonly carried on Salmonella Pathogenicity Islands (SPIs). Plasmids also carry putative virulence-associated genes as well as those responsible for antimicrobial resistance. The interaction of Salmonella pathogen-associated molecular patterns (PAMPs) with Toll-like receptors (TLRs) and NOD-like receptors (NLRs) leads to inflammasome formation, activation, and recruitment of neutrophils and macrophages and the production of pro-inflammatory cytokines, most notably interleukin (IL)-6, IL-1β, tumor necrosis factor (TNF)-α, and interferon-gamma (IFN)-γ. The gut microbiome may be an important modulator of this immune response. S. Typhimurium usually causes a local intestinal immune response, whereas S. Typhi, by preventing neutrophil attraction resulting from activation of TLRs, evades the local response and causes systemic infection. Potential new therapeutic strategies may lead from an increased understanding of infection pathogenesis.\",\n \"corpus_id\": 17208185,\n \"score\": 2\n },\n {\n \"doc_id\": \"23468633\",\n \"title\": \"Modeling host genetic regulation of influenza pathogenesis in the collaborative cross.\",\n \"abstract\": \"Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms and confounding environmental factors have made it difficult to identify polymorphic genes that contribute to differential disease outcomes in human populations. Therefore, to control for these confounding environmental variables in a system that models the levels of genetic diversity found in outbred populations such as humans, we used incipient lines of the highly genetically diverse Collaborative Cross (CC) recombinant inbred (RI) panel (the pre-CC population) to study how genetic variation impacts influenza associated disease across a genetically diverse population. A wide range of variation in influenza disease related phenotypes including virus replication, virus-induced inflammation, and weight loss was observed. Many of the disease associated phenotypes were correlated, with viral replication and virus-induced inflammation being predictors of virus-induced weight loss. Despite these correlations, pre-CC mice with unique and novel disease phenotype combinations were observed. We also identified sets of transcripts (modules) that were correlated with aspects of disease. In order to identify how host genetic polymorphisms contribute to the observed variation in disease, we conducted quantitative trait loci (QTL) mapping. We identified several QTL contributing to specific aspects of the host response including virus-induced weight loss, titer, pulmonary edema, neutrophil recruitment to the airways, and transcriptional expression. Existing whole-genome sequence data was applied to identify high priority candidate genes within QTL regions. A key host response QTL was located at the site of the known anti-influenza Mx1 gene. We sequenced the coding regions of Mx1 in the eight CC founder strains, and identified a novel Mx1 allele that showed reduced ability to inhibit viral replication, while maintaining protection from weight loss.\",\n \"corpus_id\": 14682844,\n \"score\": 2\n },\n {\n \"doc_id\": \"25283706\",\n \"title\": \"Susceptibility to Klebsiella pneumonaie infection in collaborative cross mice is a complex trait controlled by at least three loci acting at different time points.\",\n \"abstract\": \"BACKGROUND: Klebsiella pneumoniae (Kp) is a bacterium causing severe pneumonia in immunocompromised hosts and is often associated with sepsis. With the rise of antibiotic resistant bacteria, there is a need for new effective and affordable control methods; understanding the genetic architecture of susceptibility to Kp will help in their development. We performed the first quantitative trait locus (QTL) mapping study of host susceptibility to Kp infection in immunocompetent Collaborative Cross mice (CC). We challenged 328 mice from 73 CC lines intraperitoneally with 104 colony forming units of Kp strain K2. Survival and body weight were monitored for 15 days post challenge. 48 of the CC lines were genotyped with 170,000 SNPs, with which we mapped QTLs. RESULTS: CC lines differed significantly (P < 0.05) in mean survival time, between 1 to 15 days post infection, and broad sense heritability was 0.45. Distinct QTL were mapped at specific time points during the challenge. A QTL on chromosome 4 was found only on day 2 post infection, and QTL on chromosomes 8 and 18, only on day 8. By using the sequence variations of the eight inbred strain founders of the CC to refine QTL localization we identify several candidate genes. CONCLUSION: Host susceptibility to Kp is a complex trait, controlled by multiple genetic factors that act sequentially during the course of infection.\",\n \"corpus_id\": 870133,\n \"score\": 2\n },\n {\n \"doc_id\": \"25339955\",\n \"title\": \"Salmonella-host interactions - modulation of the host innate immune system.\",\n \"abstract\": \"Salmonella enterica (S. enterica) are Gram-negative bacteria that can invade a broad range of hosts causing both acute and chronic infections. This phenotype is related to its ability to replicate and persist within non-phagocytic host epithelial cells as well as phagocytic dendritic cells and macrophages of the innate immune system. Infection with S. enterica manifests itself through a broad range of clinical symptoms and can result in asymptomatic carriage, gastroenteritis, systemic disease such as typhoid fever and in severe cases, death (1). Exposure to S. enterica serovars Typhi and Paratyphi exhibits clinical symptoms including diarrhea, fatigue, fever, and temperature fluctuations. Other serovars such as the non-typhoidal Salmonella (NTS), of which there are over 2,500, are commonly contracted as, but not limited to, food-borne sources causing gastrointestinal symptoms, which include diarrhea and vomiting. The availability of complete genome sequences for many S. enterica serovars has facilitated research into the genetic determinants of virulence for this pathogen. This work has led to the identification of important bacterial components, including flagella, type III secretion systems, lipopolysaccharides, and Salmonella pathogenicity islands, all of which support the intracellular life cycle of S. enterica. Studies focusing on the host-pathogen interaction have provided insights into receptor activation of the innate immune system. Therefore, characterizing the host-S. enterica interaction is critical to understand the pathogenicity of the bacteria in a clinically relevant context. This review outlines salmonellosis and the clinical manifestations between typhoidal and NTS infections as well as discussing the host immune response to infection and the models that are being used to elucidate the mechanisms involved in Salmonella pathogenicity.\",\n \"corpus_id\": 15841599,\n \"score\": 2\n },\n {\n \"doc_id\": \"26310945\",\n \"title\": \"Host genetic diversity influences the severity of Pseudomonas aeruginosa pneumonia in the Collaborative Cross mice.\",\n \"abstract\": \"BACKGROUND: Pseudomonas aeruginosa is one of the top three causes of opportunistic infections in humans. Patients with a compromised immune system, due to immunosuppressive therapies or underlying diseases such as cancer, AIDS or the hereditary disease cystic fibrosis, are at risk of developing P. aeruginosa infection. However, clinical evidence indicates extremely variable outcomes of P. aeruginosa infections in individuals at risk, suggesting that host multi-complex genetic traits may influence the severity of this opportunistic infection. Here, we have used an innovative experimental model to dissect whether host genetic background, such as those found in the outbred population, could influence the risk of morbidity and mortality to P. aeruginosa pneumonia. RESULTS: A highly genetically-diverse mouse resource population, Collaborative Cross (CC) mice, was infected with a clinical strain of P. aeruginosa and subsequently monitored for mortality, mean survival time, and morbidity, change in body weight for seven days post infection. Disease phenotypes ranged from complete resistance and recovery of body weight to lethal disease. Initial variables, including body weight, age and gender, have limited influence on P. aeruginosa outcome, emphasizing the role of host genetic background in defining the risk of morbidity and mortality. When broad-sense heritability of phenotypic traits was evaluated, it confirmed the influence of genetic profile rather than environmental factors among the CC lines during P. aeruginosa infection. CONCLUSION: This innovative model system can potentially reproduce the variables responses of disease severity observed in humans during P. aeruginosa pneumonia. Our results demonstrated that a widely-marked differential response to P. aeruginosa airway infection in term of morbidity and mortality, is mainly affected by host genetic factors, as multiple genetic loci or polymorphic variations.\",\n \"corpus_id\": 9928638,\n \"score\": 2\n },\n {\n \"doc_id\": \"26452100\",\n \"title\": \"Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross.\",\n \"abstract\": \"New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations.\",\n \"corpus_id\": 9981176,\n \"score\": 2\n },\n {\n \"doc_id\": \"26955808\",\n \"title\": \"Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice.\",\n \"abstract\": \"BACKGROUND: Typhoid fever caused by Salmonella enterica serovar Typhi (S. Typhi) is a severe systemic human disease and endemic in regions of the world with poor drinking water quality and sewage treatment facilities. A significant number of patients become asymptomatic life-long carriers of S. Typhi and serve as the reservoir for the disease. The specific mechanisms and adaptive strategies enabling S. Typhi to survive inside the host for extended periods are incompletely understood. Yet, elucidation of these processes is of major importance for improvement of therapeutic strategies. In the current study genetic adaptation during experimental chronic S. Typhimurium infections of mice, an established model of chronic typhoid fever, was probed as an approach for studying the molecular mechanisms of host-adaptation during long-term host-association. RESULTS: Individually sequence-tagged wild type strains of S. Typhimurium 4/74 were used to establish chronic infections of 129X1/SvJ mice. Over the course of infections, S. Typhimurium bacteria were isolated from feces and from livers and spleens upon termination of the experiment. In all samples dominant clones were identified and select clones were subjected to whole genome sequencing. Dominant clones isolated from either systemic organs or fecal samples exhibited distinct single nucleotide polymorphisms (SNPs). One mouse appeared to have distinct adapted clones in the spleen and liver, respectively. Three mice were colonized in the intestines by the same clone containing the same non-synonymous SNP in a transcriptional regulator, kdgR, of metabolic genes. This likely indicates transmission of this clone between mice. The mutation was tracked to have occurred prior to 2 weeks post infection in one of the three mice and had subsequently been transmitted to the other two mice. Re-infection with this clone confirmed that it is superior to the wild type for intestinal colonization. CONCLUSIONS: During 4 to 6 weeks of chronic infections, S. Typhimurium acquired distinct SNPs in known regulators of metabolic and virulence genes. One SNP, the kdgR-SNP was confirmed to confer selective advantage during chronic infections and constitute a true patho-adaptive mutation. Together, the results provide evidence for rapid genetic adaptation to the host of S. Typhimurium and validate experimental evolution in the context of host infection as a strategy for elucidating pathogen host interactions at the molecular level.\",\n \"corpus_id\": 215628348,\n \"score\": 2\n },\n {\n \"doc_id\": \"27933544\",\n \"title\": \"Dissection of Host Susceptibility to Bacterial Infections and Its Toxins.\",\n \"abstract\": \"Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies. Most of current animal models used in complex traits diseases genetic mapping have limited genetic diversity. This limitation impedes the ability to create incorporated network using genetic interactions, epigenetics, environmental factors, microbiota, and other phenotypes. A novel mouse genetic reference population for high-resolution mapping and subsequently identifying genes underlying the QTL, namely the Collaborative Cross (CC) mouse genetic reference population (GRP) was recently developed. In this chapter, we discuss a variety of approaches using CC mice for mapping genes underlying quantitative trait loci (QTL) to dissect the host response to polygenic traits, including infectious disease caused by bacterial agents and its toxins.\",\n \"corpus_id\": 13761546,\n \"score\": 2\n },\n {\n \"doc_id\": \"28592495\",\n \"title\": \"Genomes of the Mouse Collaborative Cross.\",\n \"abstract\": \"The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources.\",\n \"corpus_id\": 21350942,\n \"score\": 2\n },\n {\n \"doc_id\": \"19718951\",\n \"title\": \"Towards the selection of chickens resistant to Salmonella and Campylobacter infections.\",\n \"abstract\": \"Resistance to infection with enteric pathogens such as Salmonella and Campylobacter can be at many levels and include both non-immune and immune mechanisms. Immune resistance mechanisms can be specific, at the level of the adaptive immune response, or non-specific, at the level of the innate immune response. Whilst we can extrapolate to some degree in birds from what is known about immune responses to these pathogens in mammals, chickens are not \\\"feathered mice\\\", but have a different repertoire of genes, molecules, cells and organs involved in their immune response compared to mammals. Fundamental work on the chicken's immune response to enteric pathogens is therefore still required. Our studies focus particularly on the innate immune response, as responses of heterophils (the avian neutrophil equivalent) from commercial birds, and macrophages from inbred lines of chickens, correlate with resistance or susceptibility to Salmonella infection with a variety of Salmonella serovars and infection models. We work on two basic resistance mechanisms - resistance to colonization with Salmonella or Campylobacter, and resistance to systemic salmonellosis (or fowl typhoid). To map genes involved in resistance to colonization with Salmonella and Campylobacter, we are using a combination of expression quantitative trait loci (eQTLs) from microarray studies, allied with whole genome SNP arrays (WGA), a candidate gene approach and analysis of copy number variation across the genome. For resistance to systemic salmonellosis, we have refined the location ofa novel resistance locus on Chromosome 5, designated SAL1, using high density SNP panels, combined with advanced back-crossing of resistant and susceptible lines. Using a 6th generation backcross mapping population we have confirmed and refined the SAL1 locus to 8-00 kb of Chromosome 5. This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homologue, AKT1.\",\n \"corpus_id\": 25576489,\n \"score\": 1\n },\n {\n \"doc_id\": \"19729455\",\n \"title\": \"Effect of age on susceptibility to Salmonella Typhimurium infection in C57BL/6 mice.\",\n \"abstract\": \"Ageing is associated with a decline in immune function, which predisposes the elderly to a higher incidence of infections. Information on the mechanism of the age-related increase in susceptibility to Salmonella enterica serovar Typhimurium (S. Typhimurium) is limited. In particular, little is known regarding the involvement of the immune response in this age-related change. We employed streptomycin (Sm)-pretreated C57BL/6 mice to develop a mouse model that would demonstrate age-related differences in susceptibility and immune response to S. Typhimurium. In this model, old mice inoculated orally with doses of 3 x 10(8) or 1 x 10(6) c.f.u. S. Typhimurium had significantly greater S. Typhimurium colonization in the ileum, colon, Peyer's patches, spleen and liver than young mice. Old mice had significantly higher weight loss than young mice on days 1 and 2 post-infection. In response to S. Typhimurium infection, old mice failed to increase ex vivo production of IFN-gamma and TNF-alpha in the spleen and mesenteric lymph node cells to the same degree as observed in young mice; this was associated with their inability to maintain the presence of neutrophils and macrophages at a 'youthful' level. These results indicate that Sm-pretreated C57BL/6 old mice are more susceptible to S. Typhimurium infection than young mice, which might be due to impaired IFN-gamma and TNF-alpha production as well as a corresponding change in the number of neutrophils and macrophages in response to S. Typhimurium infection compared to young mice.\",\n \"corpus_id\": 206188249,\n \"score\": 1\n },\n {\n \"doc_id\": \"20597881\",\n \"title\": \"Fine mapping of the chicken salmonellosis resistance locus (SAL1).\",\n \"abstract\": \"Salmonella enterica serovar Typhimurium is a Gram-negative bacterium that has a significant impact on both human and animal health. It is one of the most common food-borne pathogens responsible for a self-limiting gastroenteritis in humans and a similar disease in pigs, cattle and chickens. In contrast, intravenous challenge with S. Typhimurium provides a valuable model for systemic infection, often causing a typhoid-like infection, with bacterial replication resulting in the destruction of the spleen and liver of infected animals. Resistance to systemic salmonellosis in chickens is partly genetically determined, with bacterial numbers at systemic sites in resistant lines being up to 1000-fold fewer than in susceptible lines. Identification of genes contributing to disease resistance will enable genetic selection of resistant lines that will reduce Salmonella levels in poultry flocks. We previously identified a novel resistance locus on Chromosome 5, designated SAL1. Through the availability of high-density SNP panels in the chicken, combined with advanced back-crossing of the resistant and susceptible lines, we sought to refine the SAL1 locus and identify potential positional candidate genes. Using a 6(th) generation backcross mapping population, we have confirmed and refined the SAL1 locus as lying between 54.0 and 54.8 Mb on the long arm of Chromosome 5 (F = 8.72, P = 0.00475). This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homolog, AKT1 (protein kinase B, PKB).\",\n \"corpus_id\": 36860629,\n \"score\": 1\n },\n {\n \"doc_id\": \"20623355\",\n \"title\": \"A novel strategy for genetic dissection of complex traits: the population of specific chromosome substitution strains from laboratory and wild mice.\",\n \"abstract\": \"The mouse is an irreplaceable model for understanding the precise genetic mechanisms of mammalian physiological pathways. Thousands of quantitative trait loci (QTLs) have been mapped onto the mouse genome during the last two decades. However, only a few genes' underlying complex traits have been successfully identified, and rapid fine mapping of QTL genes still remains a challenge for mouse geneticists. Currently, the Collaborative Cross (CC) has proceeded to the goal of establishing more than 1,000 recombinant inbred strains for the sub-centimorgan mapping resolution of QTL loci. In this article, a novel complementary strategy, designated as population of specific chromosome substitution strains or PSCSS, is proposed for rapid fine mapping of QTLs on the substituted chromosome. One specific chromosome (Chr 1) of recipient mouse strain C57BL/6 J has been substituted by homologous counterparts from five different inbred strains (C3H/He, FVB/N, AKR, NOD/LtJ, NZW/LacJ), an outbred line Kunmin mouse in China, and 23 wild mice captured in different localities. The primary genetic studies on the structure of these wild donor chromosomes (Chr 1) show that these donor chromosomes harbor extensive genetic polymorphisms, with a high density of SNP distribution, abundant variations of STR alleles, and a high level of historical recombination accumulation. These specific chromosome substitution strains eventually form a special population that has the identical genetic background of the recipient strain and differs only in the donor chromosomes. With simple association studies, known QTLs on the donor chromosome can be rapidly mapped in high resolution without requirement of further crosses. This approach, taking advantage of the extensive genetic polymorphisms of wild resources and chromosome substitution strategy, brings a new outlook for genetic dissection of complex traits.\",\n \"corpus_id\": 5788050,\n \"score\": 1\n },\n {\n \"doc_id\": \"21200387\",\n \"title\": \"Humanized mice are susceptible to Salmonella typhi infection.\",\n \"abstract\": \"Salmonella enterica serovar Typhi is a pathogen that only infects humans. Currently, there is no animal model for studying this pathogen. Recently, alymphoid RAG-2(-/-)/γ(c)(-/-) mice engrafted with human leukocytes, known as humanized mice, have been successfully utilized to develop experimental models for several human-specific viral infections, including HIV, human-like dengue fever and hepatitis C virus. Little is known about the usefulness and feasibility of the humanized mouse model for the study of human-specific bacterial pathogens, such as S. typhi. The aim of this study was to determine if Salmonella enterica serovar Typhi could establish productive infection in humanized mice. Here we report that intravenous inoculation of S. typhi into humanized mice, but not controls, established S. typhi infections. High bacterial loads were found in the liver, spleen, blood and bone marrow of mice reconstituted with human leukocytes, but not in the unreconstituted control mice. Importantly, S. typhi-infected humanized mice lost significant body weight, and some of the infected mice displayed neurological symptoms. Our data suggest, for the first time, that humanized mice are susceptible to S. typhi challenge and that this model can be utilized to study the pathogenesis of S. typhi to develop novel therapeutic strategies.\",\n \"corpus_id\": 20060237,\n \"score\": 1\n },\n {\n \"doc_id\": \"21427413\",\n \"title\": \"Architecture of energy balance traits in emerging lines of the Collaborative Cross.\",\n \"abstract\": \"The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32-10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5-38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2-83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4-48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9-89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance.\",\n \"corpus_id\": 10300310,\n \"score\": 1\n },\n {\n \"doc_id\": \"21616112\",\n \"title\": \"Mouse models to assess the efficacy of non-typhoidal Salmonella vaccines: revisiting the role of host innate susceptibility and routes of challenge.\",\n \"abstract\": \"Non-typhoidal Salmonella enterica (NTS) serovars Typhimurium and Enteritidis are important causes of bacterial gastroenteritis in the USA and worldwide. In sub-Saharan Africa these two serovars are emerging as agents associated with lethal invasive disease (e.g., bacteremia, meningitis). The development of NTS vaccines, based on mucosally administered live attenuated strains and parenteral non-living antigens, could diminish the NTS disease burden globally. Mouse models of S. Typhimurium and S. Enteritidis invasive disease can accelerate the development of NTS vaccines. Live attenuated NTS vaccines elicit both cellular and humoral immunity in mice and their efficacy is well established. In contrast, non-living vaccines that primarily elicit humoral immunity have demonstrated variable efficacy. An analysis of the reported studies with non-living vaccines against S. Typhimurium and S. Enteritidis reveals that efficacy is influenced by two important independent variables: (1) the innate susceptibility to NTS infection that differs dramatically between commonly used mouse strains and (2) the virulence of the NTS strain used for challenge. Protection by non-living vaccines has generally been seen only in host-pathogen interactions where a sub-lethal infection results, such as challenging resistant mice with either highly virulent or weakly virulent strains or susceptible mice with weakly virulent strains. The immunologic basis of this discrepancy and the implications for human NTS vaccine development are reviewed herein.\",\n \"corpus_id\": 39231602,\n \"score\": 1\n },\n {\n \"doc_id\": \"21628518\",\n \"title\": \"Multigenic control and sex bias in host susceptibility to spore-induced pulmonary anthrax in mice.\",\n \"abstract\": \"Mechanisms underlying susceptibility to anthrax infection are unknown. Using a phylogenetically diverse panel of inbred mice and spores of Bacillus anthracis Ames, we investigated host susceptibility to pulmonary anthrax. Susceptibility profiles for survival time and organ pathogen load differed across strains, indicating distinct genetic controls. Tissue infection kinetics analysis showed greater systemic dissemination in susceptible DBA/2J (D) mice but a higher terminal bacterial load in resistant BALB/cJ (C) mice. Interestingly, the most resistant strains, C and C57BL/6J (B), demonstrated a sex bias for susceptibility. For example, BALB/cJ females had a significantly higher survival time and required 4-fold more spores for 100% mortality compared to BALB/cJ males. To identify genetic regions associated with differential susceptibility, survival time and extent of organ infection were assessed using mice derived from two susceptibility models: (i) BXD advanced recombinant inbred strains and (ii) F2 offspring generated from polar responding C and D strains. Genome-wide analysis of BXD strain survival identified linkage on chromosomes 5, 6, 9, 11, and 14. Quantitative trait locus (QTL) analysis of the C×DF2 population revealed a significant QTL (designated Rpai1 for resistance to pulmonary anthrax infection, locus 1) for survival time on chromosome 17 and also identified a chromosome 11 locus for lung pathogen burden. The striking difference between genome-wide linkage profiles for these two mouse models of anthrax susceptibility supports our hypothesis that these are multigenic traits. Our data provide the first evidence for a differential sex response to anthrax resistance and further highlight the unlikelihood of a single common genetic contribution for this response across strains.\",\n \"corpus_id\": 31451980,\n \"score\": 1\n },\n {\n \"doc_id\": \"22427645\",\n \"title\": \"Mapping of clinical and expression quantitative trait loci in a sex-dependent effect of host susceptibility to mouse-adapted influenza H3N2/HK/1/68.\",\n \"abstract\": \"Seasonal influenza outbreaks and recurrent influenza pandemics present major challenges to public health. By studying immunological responses to influenza in different host species, it may be possible to discover common mechanisms of susceptibility in response to various influenza strains. This could lead to novel therapeutic targets with wide clinical application. Using a mouse-adapted strain of influenza (A/HK/1/68-MA20 [H3N2]), we produced a mouse model of severe influenza that reproduces the hallmark high viral load and overexpression of cytokines associated with susceptibility to severe influenza in humans. We mapped genetic determinants of the host response using a panel of 29 closely related mouse strains (AcB/BcA panel of recombinant congenic strains) created from influenza-susceptible A/J and influenza-resistant C57BL/6J (B6) mice. Combined clinical quantitative trait loci (QTL) and lung expression QTL mapping identified candidate genes for two sex-specific QTL on chromosomes 2 and 17. The former includes the previously described Hc gene, a deficit of which is associated with the susceptibility phenotype in females. The latter includes the phospholipase gene Pla2g7 and Tnfrsf21, a member of the TNFR superfamily. Confirmation of the gene underlying the chromosome 17 QTL may reveal new strategies for influenza treatment.\",\n \"corpus_id\": 207426864,\n \"score\": 1\n },\n {\n \"doc_id\": \"22613937\",\n \"title\": \"A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state.\",\n \"abstract\": \"BACKGROUND: The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. RESULTS: In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. CONCLUSIONS: Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were identified in several independent studies, which is the case of the QTL regions on chromosomes 2 and 3, involved in resistance to both Salmonella colonization and carrier state. These observations provide evidence of common genes controlling S. Typhimurium colonization and S. Enteritidis carrier-state in chickens.\",\n \"corpus_id\": 15202562,\n \"score\": 1\n },\n {\n \"doc_id\": \"22905720\",\n \"title\": \"Distinct gene loci control the host response to influenza H1N1 virus infection in a time-dependent manner.\",\n \"abstract\": \"BACKGROUND: There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. In particular, C57BL/6J, the most widely used mouse strain in biomedical research, is comparatively resistant. In contrast, DBA/2J is highly susceptible. RESULTS: To map regions of the genome responsible for differences in influenza susceptibility, we infected a family of 53 BXD-type lines derived from a cross between C57BL/6J and DBA/2J strains with influenza A virus (PR8, H1N1). We monitored body weight, survival, and mean time to death for 13 days after infection. Qivr5 (quantitative trait for influenza virus resistance on chromosome 5) was the largest and most significant QTL for weight loss. The effect of Qivr5 was detectable on day 2 post infection, but was most pronounced on days 5 and 6. Survival rate mapped to Qivr5, but additionally revealed a second significant locus on chromosome 19 (Qivr19). Analysis of mean time to death affirmed both Qivr5 and Qivr19. In addition, we observed several regions of the genome with suggestive linkage. There are potentially complex combinatorial interactions of the parental alleles among loci. Analysis of multiple gene expression data sets and sequence variants in these strains highlights about 30 strong candidate genes across all loci that may control influenza A susceptibility and resistance. CONCLUSIONS: We have mapped influenza susceptibility loci to chromosomes 2, 5, 16, 17, and 19. Body weight and survival loci have a time-dependent profile that presumably reflects the temporal dynamic of the response to infection. We highlight candidate genes in the respective intervals and review their possible biological function during infection.\",\n \"corpus_id\": 2488492,\n \"score\": 1\n },\n {\n \"doc_id\": \"22937698\",\n \"title\": \"[Model of chronic salmonellosis: parameters of infection and immune response in inbred mice genetically variable in susceptibility to salmonellosis].\",\n \"abstract\": \"AIM: Study parameters of chronic infection and immune response in I/St and A/Sn line mice in the model of per oral infection of mice with Salmonella enterica serovar Typhimurium. MATERIALS AND METHODS: Studies were carried out in I/StSnEgYCit (I/St), A/JsnYCit (A/Sn) inbred line mice as well as their back crossing hybrids [I/StrxF1(I/StxA/Sn)]BC. Mice were infected per os by S. enterica serovar Typhimurium strain IE147 at a dose of 2 x 10(5) PFU per mice. The number of salmonellae was determined at days 3, 5 and 7, weeks 3 and 4 after the infection in various organs, the number of antibody producers--by cell EIA. Pathomorphologic changes in mice spleens were studied histologically by using hematoxylin and eosin staining. In offspring of back crossing [I/St x F1(I/St x A/Sn)]BCl segregation genetic analysis of sensitivity to salmonella infection trait and mapping of loci taking part in salmonella infection were carried out. RESULTS: The course of chronic salmonellosis in susceptible I/St line was characterized by the presence of more pronounced pathomorphologic changes in spleen and significantly higher microbial load in organs (approximately by 1000 times) when compared with A/Sn mice. Interlinear differences in susceptibility to infection correlated with differences in the type of early local and systemic immune response. In I/St mice a higher level of salmonella specific IgG2a-, IgG1- and IgA forming cells in spleen compared with A/Sn mice was detected which correlates with a pronounced splenomegaly and high concentration of salmonellae. On the contrary A/Sn mice demonstrated a higher level of salmonella specific IgA forming cells in Peyer patches that probably leads to protection of A/Sn line during per oral infection. Genetic analysis of susceptibility to salmonellosis trait inheritance showed the presence of its coupling with D9Mit89 locus of chromosome 9 on which previously Tbs2 locus was mapped that plays a role in the control of tuberculosis infection. CONCLUSION: There is a probability of the presence of general mechanisms of genetic control of tuberculosis and salmonella infections in A/Sn and I/St mice.\",\n \"corpus_id\": 10839082,\n \"score\": 1\n },\n {\n \"doc_id\": \"23390527\",\n \"title\": \"Suppression of hepcidin expression and iron overload mediate Salmonella susceptibility in ankyrin 1 ENU-induced mutant.\",\n \"abstract\": \"Salmonella, a ubiquitous Gram-negative intracellular bacterium, is a food borne pathogen that infects a broad range of hosts. Infection with Salmonella Typhimurium in mice is a broadly recognized experimental model resembling typhoid fever in humans. Using a N-ethyl-N-nitrosurea (ENU) mutagenesis recessive screen, we report the identification of Ity16 (Immunity to Typhimurium locus 16), a locus responsible for increased susceptibility to infection. The position of Ity16 was refined on chromosome 8 and a nonsense mutation was identified in the ankyrin 1 (Ank1) gene. ANK1 plays an important role in the formation and stabilization of the red cell cytoskeleton. The Ank1(Ity16/Ity16) mutation causes severe hemolytic anemia in uninfected mice resulting in splenomegaly, hyperbilirubinemia, jaundice, extramedullary erythropoiesis and iron overload in liver and kidneys. Ank1(Ity16/Ity16) mutant mice demonstrated low levels of hepcidin (Hamp) expression and significant increases in the expression of the growth differentiation factor 15 (Gdf15), erythropoietin (Epo) and heme oxygenase 1 (Hmox1) exacerbating extramedullary erythropoiesis, tissue iron deposition and splenomegaly. As the infection progresses in Ank1(Ity16/Ity16), the anemia worsens and bacterial load were high in liver and kidneys compared to wild type mice. Heterozygous Ank1(+/Ity16) mice were also more susceptible to Salmonella infection although to a lesser extent than Ank1(Ity16/Ity16) and they did not inherently present anemia and splenomegaly. During infection, iron accumulated in the kidneys of Ank1(+/Ity16) mice where bacterial loads were high compared to littermate controls. The critical role of HAMP in the host response to Salmonella infection was validated by showing increased susceptibility to infection in Hamp-deficient mice and significant survival benefits in Ank1(+/Ity16) heterozygous mice treated with HAMP peptide. This study illustrates that the regulation of Hamp and iron balance are crucial in the host response to Salmonella infection in Ank1 mutants.\",\n \"corpus_id\": 12339250,\n \"score\": 1\n },\n {\n \"doc_id\": \"23433259\",\n \"title\": \"High-precision genetic mapping of behavioral traits in the diversity outbred mouse population.\",\n \"abstract\": \"Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light-dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics.\",\n \"corpus_id\": 3130834,\n \"score\": 1\n },\n {\n \"doc_id\": \"24195963\",\n \"title\": \"Using the emerging Collaborative Cross to probe the immune system.\",\n \"abstract\": \"The Collaborative Cross (CC) is an emerging panel of recombinant inbred (RI) mouse strains. Each strain is genetically distinct but all descended from the same eight inbred founders. In 66 strains from incipient lines of the CC (pre-CC), as well as the 8 CC founders and some of their F1 offspring, we examined subsets of lymphocytes and antigen-presenting cells. We found significant variation among the founders, with even greater diversity in the pre-CC. Genome-wide association using inferred haplotypes detected highly significant loci controlling B-to-T cell ratio, CD8 T-cell numbers, CD11c and CD23 expression. Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology. For CD23, we found a strong QTL whose confidence interval contained the CD23 structural gene Fcer2a. Our data on the pre-CC demonstrate the utility of the CC for studying immunophenotypes and the value of integrating founder, CC and F1 data. The extreme immunophenotypes observed could have pleiotropic effects in other CC experiments.\",\n \"corpus_id\": 8791248,\n \"score\": 1\n },\n {\n \"doc_id\": \"25350459\",\n \"title\": \"Temporal and anatomical host resistance to chronic Salmonella infection is quantitatively dictated by Nramp1 and influenced by host genetic background.\",\n \"abstract\": \"The lysosomal membrane transporter, Nramp1, plays a key role in innate immunity and resistance to infection with intracellular pathogens such as non-typhoidal Salmonella (NTS). NTS-susceptible C57BL/6 (B6) mice, which express the mutant Nramp1D169 allele, are unable to control acute infection with Salmonella enterica serovar Typhimurium following intraperitoneal or oral inoculation. Introducing functional Nramp1G169 into the B6 host background, either by constructing a congenic strain carrying Nramp1G169 from resistant A/J mice (Nramp-Cg) or overexpressing Nramp1G169 from a transgene (Nramp-Tg), conferred equivalent protection against acute Salmonella infection. In contrast, the contributions of Nramp1 for controlling chronic infection are more complex, involving temporal and anatomical differences in Nramp1-dependent host responses. Nramp-Cg, Nramp-Tg and NTS-resistant 129×1/SvJ mice survived oral Salmonella infection equally well for the first 2-3 weeks, providing evidence that Nramp1 contributes to the initial control of NTS bacteremia preceding establishment of chronic Salmonella infection. By day 30, increased host Nramp1 expression (Tg>Cg) provided greater protection as indicated by decreased splenic bacterial colonization (Tg<Cg). However, despite controlling bacterial growth within MLN as effectively as 129×1/SvJ mice, Nramp-Cg and Nramp-Tg mice eventually succumbed to infection. These data indicate: 1) discrete, anatomically localized host resistance is conferred by Nramp1 expression in NTS-susceptible mice, 2) restriction of systemic bacterial growth in the spleens of NTS-susceptible mice is enhanced by Nramp1 expression and dose-dependent, and 3) host genes other than Nramp1 also contribute to the ability of NTS-resistant 129×1/SvJ mice to control bacterial replication during chronic infection.\",\n \"corpus_id\": 2614552,\n \"score\": 1\n },\n {\n \"doc_id\": \"25944860\",\n \"title\": \"Genetic diversity in the collaborative cross model recapitulates human West Nile virus disease outcomes.\",\n \"abstract\": \"UNLABELLED: West Nile virus (WNV) is an emerging neuroinvasive flavivirus that now causes significant morbidity and mortality worldwide. The innate and adaptive immune responses to WNV infection have been well studied in C57BL/6J inbred mice, but this model lacks the variations in susceptibility, immunity, and outcome to WNV infection that are observed in humans, thus limiting its usefulness to understand the mechanisms of WNV infection and immunity dynamics. To build a model of WNV infection that captures human infection outcomes, we have used the Collaborative Cross (CC) mouse model. We show that this model, which recapitulates the genetic diversity of the human population, demonstrates diversity in susceptibility and outcomes of WNV infection observed in humans. Using multiple F1 crosses of CC mice, we identified a wide range of susceptibilities to infection, as demonstrated through differences in survival, clinical disease score, viral titer, and innate and adaptive immune responses in both peripheral tissues and the central nervous system. Additionally, we examined the Oas1b alleles in the CC mice and confirmed the previous finding that Oas1b plays a role in susceptibility to WNV; however, even within a given Oas1b allele status, we identified a wide range of strain-specific WNV-associated phenotypes. These results confirmed that the CC model is effective for identifying a repertoire of host genes involved in WNV resistance and susceptibility. The CC effectively models a wide range of WNV clinical, virologic, and immune phenotypes, thus overcoming the limitations of the traditional C57BL/6J model, allowing genetic and mechanistic studies of WNV infection and immunity in differently susceptible populations. IMPORTANCE: Mouse models of West Nile virus infection have revealed important details regarding the innate and adaptive immune responses to this emerging viral infection. However, traditional mouse models lack the genetic diversity present in human populations and therefore limit our ability to study various disease outcomes and immunologic mechanisms subsequent to West Nile virus infection. In this study, we used the Collaborative Cross mouse model to more effectively model the wide range of clinical, virologic, and immune phenotypes present upon West Nile virus infection in humans.\",\n \"corpus_id\": 17940625,\n \"score\": 1\n },\n {\n \"doc_id\": \"26109132\",\n \"title\": \"Genetic susceptibility to invasive Salmonella disease.\",\n \"abstract\": \"Invasive Salmonella disease, in the form of enteric fever and invasive non-typhoidal Salmonella (iNTS) disease, causes substantial morbidity and mortality in children and adults in the developing world. The study of genetic variations in humans and mice that influence susceptibility of the host to Salmonella infection provides important insights into immunity to Salmonella. In this Review, we discuss data that have helped to elucidate the host genetic determinants of human enteric fever and iNTS disease, alongside data from the mouse model of Salmonella infection. Considered together, these studies provide a detailed picture of the immunobiology of human invasive Salmonella disease.\",\n \"corpus_id\": 3215705,\n \"score\": 1\n },\n {\n \"doc_id\": \"26921172\",\n \"title\": \"Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice.\",\n \"abstract\": \"BACKGROUND: Influenza A virus is a zoonotic pathogen that poses a major threat to human and animal health. The severe course of influenza infection is not only influenced by viral virulence factors but also by individual differences in the host response. To determine the extent to which the genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mouse strains. RESULTS: We observed highly divergent host responses between the CC founder strains with respect to survival, body weight loss, hematological parameters in the blood, relative lung weight and viral load. Mouse strain was the main factor with highest effect size on body weight loss after infection, demonstrating that this phenotype was highly heritable. Sex represented another significant main effect, although it was less strong. Analysis of survival rates and mean time to death suggested three groups of susceptibility phenotypes: highly susceptible (A/J, CAST/EiJ, WSB/EiJ), intermediate susceptible (C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ) and highly resistant strains (NZO/HlLtJ, PWK/PhJ). These three susceptibility groups were significantly different with respect to death/survival counts. Viral load was significantly different between susceptible and resistant strains but not between intermediate and highly susceptible strains. CAST/EiJ mice showed a unique phenotype. Despite high viral loads in their lungs, CAST/EiJ mice exhibited low counts of infiltrating granulocytes and showed increased numbers of macrophages in the lung. Histological studies of infected lungs and transcriptome analyses of peripheral blood cells and lungs confirmed an abnormal response in the leukocyte recruitment in CAST/EiJ mice. CONCLUSIONS: The eight CC founder strains exhibited a large diversity in their response to influenza infections. Therefore, the CC will represent an ideal mouse genetic reference population to study the influence of genetic variation on the susceptibility and resistance to influenza infections which will be important to understand individual variations of disease severity in humans. The unique phenotype combination in the CAST/EiJ strain resembles human leukocyte adhesion deficiency and may thus represent a new mouse model to understand this and related abnormal immune responses to infections in humans.\",\n \"corpus_id\": 13925613,\n \"score\": 1\n },\n {\n \"doc_id\": \"27169516\",\n \"title\": \"Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice.\",\n \"abstract\": \"BACKGROUND: P. aeruginosa is one of the top three causes of opportunistic human bacterial infections. The remarkable variability in the clinical outcomes of this infection is thought to be associated with genetic predisposition. However, the genes underlying host susceptibility to P. aeruginosa infection are still largely unknown. RESULTS: As a step towards mapping these genes, we applied a genome wide linkage analysis approach to a mouse model. A large F2 intercross population, obtained by mating P. aeruginosa-resistant C3H/HeOuJ, and susceptible A/J mice, was used for quantitative trait locus (QTL) mapping. The F2 progenies were challenged with a P. aeruginosa clinical strain and monitored for the survival time up to 7 days post-infection, as a disease phenotype associated trait. Selected phenotypic extremes of the F2 distribution were genotyped with high-density single nucleotide polymorphic (SNP) markers, and subsequently QTL analysis was performed. A significant locus was mapped on chromosome 6 and was named P . aeruginosa infection resistance locus 1 (Pairl1). The most promising candidate genes, including Dok1, Tacr1, Cd207, Clec4f, Gp9, Gata2, Foxp1, are related to pathogen sensing, neutrophils and macrophages recruitment and inflammatory processes. CONCLUSIONS: We propose a set of genes involved in the pathogenesis of P. aeruginosa infection that may be explored to complement human studies.\",\n \"corpus_id\": 6086649,\n \"score\": 1\n },\n {\n \"doc_id\": \"27422773\",\n \"title\": \"Mapping liver fat female-dependent quantitative trait loci in collaborative cross mice.\",\n \"abstract\": \"Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in the western world, with spectrum from simple steatosis to non-alcoholic steatohepatitis, which can progress to cirrhosis. NAFLD developments are known to be affected by host genetic background. Herein we emphasize the power of collaborative cross (CC) mouse for dissecting this complex trait and revealing quantitative trait loci (QTL) controlling hepatic fat accumulation in mice. 168 female and 338 male mice from 24 and 37 CC lines, respectively, of 18-20 weeks old, maintained on standard rodent diet, since weaning. Hepatic fat content was assessed, using dual DEXA scan in the liver. Using the available high-density genotype markers of the CC line, QTL mapping associated with percentage liver fat accumulation was performed. Our results revealed significant fatty liver accumulation QTL that were specifically, mapped in females. Two significant QTLs on chromosomes 17 and 18, with genomic intervals 3 and 2 Mb, respectively, were mapped. A third QTL, with a less significant P value, was mapped to chromosome 4, with genomic interval of 2 Mb. These QTLs were named Flal1-Flal3, referring to Fatty Liver Accumulation Locus 1-3, for the QTLs on chromosomes 17, 18, and 4, respectively. Unfortunately, no QTL was mapped with males. Searching the mouse genome database suggested several candidate genes involved in hepatic fat accumulation. Our results show that susceptibility to hepatic fat accumulations is a complex trait, controlled by multiple genetic factors in female mice, but not in male.\",\n \"corpus_id\": 28384340,\n \"score\": 1\n },\n {\n \"doc_id\": \"27807798\",\n \"title\": \"Glucose tolerance female-specific QTL mapped in collaborative cross mice.\",\n \"abstract\": \"Type-2 diabetes (T2D) is a complex metabolic disease characterized by impaired glucose tolerance. Despite environmental high risk factors, host genetic background is a strong component of T2D development. Herein, novel highly genetically diverse strains of collaborative cross (CC) lines from mice were assessed to map quantitative trait loci (QTL) associated with variations of glucose-tolerance response. In total, 501 mice of 58 CC lines were maintained on high-fat (42 % fat) diet for 12 weeks. Thereafter, an intraperitoneal glucose tolerance test (IPGTT) was performed for 180 min. Subsequently, the values of Area under curve for the glucose at zero and 180 min (AUC0-180), were measured, and used for QTL mapping. Heritability and coefficient of variations in glucose tolerance (CVg) were calculated. One-way analysis of variation was significant (P < 0.001) for AUC0-180 between the CC lines as well between both sexes. Despite Significant variations for both sexes, QTL analysis was significant, only for females, reporting a significant female-sex-dependent QTL (~2.5 Mbp) associated with IPGTT AUC0-180 trait, located on Chromosome 8 (32-34.5 Mbp, containing 51 genes). Gene browse revealed QTL for body weight/size, genes involved in immune system, and two main protein-coding genes involved in the Glucose homeostasis, Mboat4 and Leprotl1. Heritability and coefficient of genetic variance (CVg) were 0.49 and 0.31 for females, while for males, these values 0.34 and 0.22, respectively. Our findings demonstrate the roles of genetic factors controlling glucose tolerance, which significantly differ between sexes requiring independent studies for females and males toward T2D prevention and therapy.\",\n \"corpus_id\": 3682544,\n \"score\": 1\n },\n {\n \"doc_id\": \"21813203\",\n \"title\": \"Roles of Salmonella enterica serovar Typhimurium encoded Peptidase N during systemic infection of Ifnγ-/- mice.\",\n \"abstract\": \"Pathogen encoded peptidases are known to be important during infection; however, their roles in modulating host responses in immunocompromised individuals are not well studied. The roles of S. typhimurium (WT) encoded Peptidase N (PepN), a major aminopeptidase and sole M1 family member, was studied in mice lacking Interferon-γ (IFNγ), a cytokine important for immunity. S. typhimurium lacking pepN (ΔpepN) displays enhanced colony forming units (CFU) compared to WT in peripheral organs during systemic infection in C57BL/6 mice. However, Ifnγ(-/-) mice show higher CFU compared to C57BL/6 mice, resulting in lower fold differences between WT and ΔpepN. Concomitantly, reintroduction of pepN in ΔpepN (ΔpepN/pepN) reduces CFU, demonstrating pepN-dependence. Interestingly, expression of a catalytically inactive PepN (ΔpepN/E298A) also lowers CFU, demonstrating that the decrease in CFU is independent of the catalytic activity of PepN. In addition, three distinct differences are observed between infection of C57BL/6 and Ifnγ(-/-) mice: First, serum amounts of TNFα and IL1β post infection are significantly lower in Ifnγ(-/-) mice. Second, histological analysis of C57BL/6 mice reveals that damage in spleen and liver upon infection with WT or ΔpepN is greater compared to ΔpepN/pepN or ΔpepN/E298A. On the other hand, Ifnγ(-/-) mice are highly susceptible to organ damage by all strains of S. typhimurium used in this study. Finally, greater survival of C57BL/6, but not Ifnγ(-/-) mice, is observed upon infection with ΔpepN/pepN or ΔpepN/E298A. Overall, the roles of the host encoded IFNγ during infection with S. typhimurium strains with varying degrees of virulence are highlighted.\",\n \"corpus_id\": 40516328,\n \"score\": 0\n },\n {\n \"doc_id\": \"21835179\",\n \"title\": \"Identification of genetic loci affecting the establishment and development of Echinococcus multilocularis larvae in mice.\",\n \"abstract\": \"Alveolar echinococcosis (AE) is a severe hepatic disorder caused by larval infection by the fox tapeworm Echinococcus multilocularis. The course of parasitic development and host reactions are known to vary significantly among host species, and even among different inbred strains of mice. As reported previously, after oral administration of parasite eggs, DBA/2 (D2) mice showed a higher rate of cyst establishment and more advanced protoscolex development in the liver than C57BL/6 (B6) mice. These findings strongly suggest that the outcome of AE is affected by host genetic factor(s). In the present study, the genetic basis of such strain-specific differences in susceptibility/resistance to AE in murine models was studied by whole-genome scanning for quantitative trait loci (QTLs) using a backcross of (B6×D2)F(1) and D2 mice with varying susceptibility to E. multilocularis infection. For cyst establishment, genome linkage analysis identified one suggestive and one significant QTL on chromosomes (Chrs.) 9 and 6, respectively, whereas for protoscolex development, two suggestive and one highly significant QTLs were detected on Chrs. 6, 17 and 1, respectively. Our QTL analyses using murine AE models revealed that multiple genetic factors regulated host susceptibility/resistance to E. multilocularis infection. Moreover, our findings show that establishment of the parasite cysts in the liver is affected by QTLs that are distinct from those associated with the subsequent protoscolex development of the parasite, indicating that different host factors are involved in the host-parasite interplay at each developmental stage of the larval parasite. Further identification of responsible genes located on the identified QTLs could lead to the development of effective disease prevention and control strategies, including an intensive screening and clinical follow-up of genetically high-risk groups for AE infection.\",\n \"corpus_id\": 20463074,\n \"score\": 0\n },\n {\n \"doc_id\": \"22126848\",\n \"title\": \"Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses.\",\n \"abstract\": \"Inbred mouse strains MRL and LG share the ability to fully heal ear hole punches with the full range of appropriate tissues without scarring. They also share a common ancestry, MRL being formed from a multi-strain cross with two final backcrosses to LG before being inbred by brother-sister mating. Many gene-mapping studies for healing ability have been performed using these two strains, resulting in the location of about 20 quantitative trait loci (QTLs). Here, we combine two of these crosses (N = 638), MRL/lpr × C57BL/6NTac and LG/J × SM/J, in a single combined cross analysis to increase the mapping power, decrease QTL support intervals, separate multiple QTLs and establish allelic states at individual QTL. The combined cross analysis located 11 QTLs, 6 affecting only one cross (5 LG × SM and 1 MRL × B6) and 5 affecting both crosses, approximately the number of common QTLs expected given strain SNP similarity. Amongst the five QTLs mapped in both crosses, three had significantly different genetic effects, additive in one cross and over or underdominant in the other. It is possible that allelic states at these three loci are different in SM and B6 because they lead to differences in dominance interactions with the LG and MRL alleles. QTL support intervals are 40% smaller in the combined cross analysis than in either of the single crosses. Combined cross analysis was successful in enhancing the interpretation of earlier QTL results for these strains.\",\n \"corpus_id\": 12644526,\n \"score\": 0\n },\n {\n \"doc_id\": \"22684724\",\n \"title\": \"IFNγ expression by an attenuated strain of Salmonella enterica serovar Typhimurium improves vaccine efficacy in susceptible TLR4-defective C3H/HeJ mice.\",\n \"abstract\": \"C3H/HeJ mice carry a mutated allele of TLR4 gene (TLR4 ( d )) and thus are hyporesponsive to the lethal effects of lipopolysaccharide (LPS). Characteristically, however, the mice are also hypersusceptible to infections, particularly by Gram-negative bacteria such as Salmonella enterica serovar Typhimurium (S. typhimurium) and are known to be difficult to vaccinate against virulent exposure. This is observed despite the expression of wild-type allele of Nramp1 gene, another important determinant of Salmonella susceptibility. In contrast, C3H/HeN mice (TLR4 ( n ) Nramp1 ( n )) express a functional TLR4 protein and are resistant to infection, even by virulent strains of S. typhimurium. In the present study, we describe the immune system-enhancing properties of an attenuated strain of S. typhimurium engineered to express murine IFN-γ. This strain (designated GIDIFN) was able to modulate immune responses following systemic inoculation by upregulating the production of inflammatory mediators (IL-6 and IL-12) and anti-bacterial effector molecules (nitric oxide; NO). Consequently, this led to a more effective control of bacterial proliferation in systemic target organs in both C3H/HeJ and C3H/HeN mice. Although evidence for the enhancement in immune responses could be observed as early as few hours post-inoculation, sustained improvements required 2-3 days to manifest. Vaccination of C3H/HeJ mice with GIDIFN strain, even at low doses, conferred a significantly higher degree of protection against challenge with virulent Salmonella in susceptible C3H/HeJ mice. Our data demonstrate that IFNγ-expressing Salmonella are immunogenic and confer excellent protection against virulent challenge in susceptible C3H/HeJ mice; in addition they may be used as an effective mucosal delivery vectors against virulent infection and for boosting immune responses in immunodeficient hosts.\",\n \"corpus_id\": 18904226,\n \"score\": 0\n },\n {\n \"doc_id\": \"22911454\",\n \"title\": \"Identification of exercise capacity QTL using association mapping in inbred mice.\",\n \"abstract\": \"There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.\",\n \"corpus_id\": 1251908,\n \"score\": 0\n },\n {\n \"doc_id\": \"23041268\",\n \"title\": \"Genetic manipulation of pathogenicity loci in non-Typhimurium Salmonella.\",\n \"abstract\": \"The traditional genetic tools used in Salmonella enterica serovar Typhimurium rely heavily on a high-transducing mutant of bacteriophage P22. P22 recognizes its hosts by the structure of their O-antigens, which vary among serovars of Salmonella; therefore, it cannot be used in most non-Typhimurium Salmonella, including the majority of those causing food-borne illnesses in both humans and livestock. Bacteriophage P1 infects a variety of enteric bacteria, including galE mutants of serovar Typhimurium; however, the degree to which the presence of coimmune prophages, the lack of required attachment sites or the lack of host factors act as barriers to using phage P1 in natural isolates of Salmonella is unknown. Here, we show that recombineering can be used to make virtually any serovar of Salmonella susceptible to P1 infection; as a result, P1 can be utilized for facile genetic manipulation of non-Typhimurium Salmonella, including movement of very large pathogenicity islands. A toolkit for easy manipulation of non-Typhimurium serovars of Salmonella is described.\",\n \"corpus_id\": 7480518,\n \"score\": 0\n },\n {\n \"doc_id\": \"23409175\",\n \"title\": \"A parent-of-origin effect determines the susceptibility of a non-informative F1 population to Trypanosoma cruzi infection in vivo.\",\n \"abstract\": \"The development of Chagas disease is determined by a complex interaction between the genetic traits of both the protozoan parasite, T. cruzi, and the infected host. This process is regulated by multiple genes that control different aspects of the host-parasite interaction. While determination of the relevant genes in humans is extremely difficult, it is feasible to use inbred mouse strains to determine the genes and loci responsible for host resistance to infection. In this study, we investigated the susceptibility of several inbred mouse strains to infection with the highly virulent Y strain of T. cruzi and found a considerable difference in susceptibility between A/J and C57BL/6 mice. We explored the differences between these two mouse strains and found that the A/J strain presented higher mortality, exacerbated and uncontrolled parasitemia and distinct histopathology in the target organs, which were associated with a higher parasite burden and more extensive tissue lesions. We then employed a genetic approach to assess the pattern of inheritance of the resistance phenotype in an F1 population and detected a strong parent-of-origin effect determining the susceptibility of the F1 male mice. This effect is unlikely to result from imprinted genes because the inheritance of this susceptibility was affected by the direction of the parental crossing. Collectively, our genetic approach of using the F1 population suggests that genes contained in the murine chromosome X contribute to the natural resistance against T. cruzi infection. Future linkage studies may reveal the locus and genes participating on the host resistance process reported herein.\",\n \"corpus_id\": 6975963,\n \"score\": 0\n },\n {\n \"doc_id\": \"23505508\",\n \"title\": \"Virulence gene profiling and pathogenicity characterization of non-typhoidal Salmonella accounted for invasive disease in humans.\",\n \"abstract\": \"Human infection with non-typhoidal Salmonella serovars (NTS) infrequently causes invasive systemic disease and bacteremia. To understand better the nature of invasive NTS (iNTS), we studied the gene content and the pathogenicity of bacteremic strains from twelve serovars (Typhimurium, Enteritidis, Choleraesuis, Dublin, Virchow, Newport, Bredeney, Heidelberg, Montevideo, Schwarzengrund, 9,12:l,v:- and Hadar). Comparative genomic hybridization using a Salmonella enterica microarray revealed a core of 3233 genes present in all of the iNTS strains, which include the Salmonella pathogenicity islands 1-5, 9, 13, 14; five fimbrial operons (bcf, csg, stb, sth, sti); three colonization factors (misL, bapA, sinH); and the invasion gene, pagN. In the iNTS variable genome, we identified 16 novel genomic islets; various NTS virulence factors; and six typhoid-associated virulence genes (tcfA, cdtB, hlyE, taiA, STY1413, STY1360), displaying a wider distribution among NTS than was previously known. Characterization of the bacteremic strains in C3H/HeN mice showed clear differences in disease manifestation. Previously unreported characterization of serovars Schwarzengrund, 9,12:l,v:-, Bredeney and Virchow in the mouse model showed low ability to elicit systemic disease, but a profound and elongated shedding of serovars Schwarzengrund and 9,12:l,v:- (as well as Enteritidis and Heidelberg) due to chronic infection of the mouse. Phenotypic comparison in macrophages and epithelial cell lines demonstrated a remarkable intra-serovar variation, but also showed that S. Typhimurium bacteremic strains tend to present lower intracellular growth than gastroenteritis isolates. Collectively, our data demonstrated a common core of virulence genes, which might be required for invasive salmonellosis, but also an impressive degree of genetic and phenotypic heterogeneity, highlighting that bacteremia is a complex phenotype, which cannot be attributed merely to an enhanced invasion or intracellular growth of a particular strain.\",\n \"corpus_id\": 12372131,\n \"score\": 0\n },\n {\n \"doc_id\": \"23525445\",\n \"title\": \"Genetic-genomic replication to identify candidate mouse atherosclerosis modifier genes.\",\n \"abstract\": \"OBJECTIVE: Genetics plays a large role in atherosclerosis susceptibility in humans and mice. We attempted to confirm previously determined mouse atherosclerosis-associated loci and use bioinformatics and transcriptomics to create a catalog of candidate atherosclerosis modifier genes at these loci. METHODS AND RESULTS: A strain intercross was performed between AKR and DBA/2 mice on the apoE(-/-) background generating 166 F2 progeny. Using the phenotype log10 of the aortic root lesion area, we identified 3 suggestive atherosclerosis quantitative trait loci (Ath QTLs). When combined with our prior strain intercross, we confirmed 3 significant Ath QTLs on chromosomes 2, 15, and 17, with combined logarithm of odds scores of 5.9, 5.3, and 5.6, respectively, which each met the genome-wide 5% false discovery rate threshold. We identified all of the protein coding differences between these 2 mouse strains within the Ath QTL intervals. Microarray gene expression profiling was performed on macrophages and endothelial cells from this intercross to identify expression QTLs (eQTLs), the loci that are associated with variation in the expression levels of specific transcripts. Cross tissue eQTLs and macrophage eQTLs that replicated from a prior strain intercross were identified. These bioinformatic and eQTL analyses produced a comprehensive list of candidate genes that may be responsible for the Ath QTLs. CONCLUSIONS: Replication studies for clinical traits as well as gene expression traits are worthwhile in identifying true versus false genetic associations. We have replicated 3 loci on mouse chromosomes 2, 15, and 17 that are associated with atherosclerosis. We have also identified protein coding differences and multiple replicated eQTLs, which may be useful in the identification of atherosclerosis modifier genes.\",\n \"corpus_id\": 10876858,\n \"score\": 0\n },\n {\n \"doc_id\": \"23592259\",\n \"title\": \"Identification of salmonella pathogenicity island-2 type III secretion system effectors involved in intramacrophage replication of S. enterica serovar typhimurium: implications for rational vaccine design.\",\n \"abstract\": \"UNLABELLED: Salmonella enterica serovars cause severe diseases in humans, such as gastroenteritis and typhoid fever. The development of systemic disease is dependent on a type III secretion system (T3SS) encoded by Salmonella pathogenicity island-2 (SPI-2). Translocation of effector proteins across the Salmonella-containing vacuole, via the SPI-2 T3SS, enables bacterial replication within host cells, including macrophages. Here, we investigated the contribution of these effectors to intramacrophage replication of Salmonella enterica serovar Typhimurium using Fluorescence Dilution, a dual-fluorescence tool which allows direct measurement of bacterial replication. Of 32 strains, each carrying single mutations in genes encoding effectors, 10 (lacking sifA, sseJ, sopD2, sseG, sseF, srfH, sseL, spvD, cigR, or steD) were attenuated in replication in mouse bone marrow-derived macrophages. The replication profiles of strains combining deletions in effector genes were also investigated: a strain lacking the genes sseG, sopD2, and srfH showed an increased replication defect compared to single-mutation strains and was very similar to SPI-2 T3SS-deficient bacteria with respect to its replication defect. This strain was substantially attenuated in virulence in vivo and yet retained intracellular vacuole integrity and a functional SPI-2 T3SS. Moreover, this strain was capable of SPI-2 T3SS-mediated delivery of a model antigen for major histocompatibility complex (MHC) class I-dependent T-cell activation. This work establishes a basis for the use of a poly-effector mutant strain as an attenuated vaccine carrier for delivery of heterologous antigens directly into the cytoplasm of host cells. IMPORTANCE: Live attenuated strains of Salmonella enterica serotype Typhi have generated much interest in the search for improved vaccines against typhoid fever and as vaccine vectors for the delivery of heterologous antigens. A promising vaccine candidate is the ΔaroC ΔssaV S. Typhi strain, which owes its attenuation mainly to lack of a type III secretion system (SPI-2 T3SS). The SPI-2 T3SS is important for bacterial proliferation inside macrophages, but not all of the effectors involved in this process have been identified. Here, we show that 10 effectors of the related strain S. Typhimurium contribute to intracellular replication in macrophages. Moreover, we establish that a poly-effector mutant strain of S. Typhimurium can have a severe replication defect and maintain a functional SPI-2 T3SS, which can be exploited for delivery of heterologous antigens.\",\n \"corpus_id\": 14912066,\n \"score\": 0\n },\n {\n \"doc_id\": \"23643894\",\n \"title\": \"Identification and characterization of OmpL as a potential vaccine candidate for immune-protection against salmonellosis in mice.\",\n \"abstract\": \"Salmonella is gram-negative flagellated bacteria that can cause food and waterborne gastroenteritis and typhoid fever in humans. Despite the importance of Salmonella infections in human and animal health, the target antigens of Salmonella-specific immunity remain poorly defined, the effectiveness of the currently available vaccines is also limited. Outer membrane proteins (OMPs) of Salmonella have been considered possible candidates for conferring protection against salmonellosis. OMPs interface the cell with the environment, thus representing important potential vaccine candidate for pathogen infection. We showed that the outer membrane porin L (OmpL) is a transmembrane β barrel (TMBB) protein, which forms 12 transmembrane β-strands. OmpL of S. Typhimurium is highly immunogenic, OmpL could evoke humoral and cell-mediated immune responses, and confer 100% protection to immunized mice against challenge with very high doses of S. Typhimurium. Besides, very efficient clearance of bacteria from the reticuloendothelial systems of immunized mice was seen. The homology search further revealed that OmpL is widely distributed and conserved, homologous proteins were identified in S. Typhi and Paratyphi by RT-PCR and western blot. We also found that anti-rOmpL serum harber a high bactericidal activity for Salmonella serovars tested in this study. Therefore, OmpL provide a promising target for the development of a candidate vaccine against Salmonella infection.\",\n \"corpus_id\": 25738032,\n \"score\": 0\n },\n {\n \"doc_id\": \"23937452\",\n \"title\": \"Genotype is an important determinant factor of host susceptibility to periodontitis in the Collaborative Cross and inbred mouse populations.\",\n \"abstract\": \"BACKGROUND: Periodontal infection (Periodontitis) is a chronic inflammatory disease, which results in the breakdown of the supporting tissues of the teeth. Previous epidemiological studies have suggested that resistance to chronic periodontitis is controlled to some extent by genetic factors of the host. The aim of this study was to determine the phenotypic response of inbred and Collaborative Cross (CC) mouse populations to periodontal bacterial challenge, using an experimental periodontitis model. In this model, mice are co-infected with Porphyromonas gingivalis and Fusobacterium nucleatum, bacterial strains associated with human periodontal disease. Six weeks following the infection, the maxillary jaws were harvested and analyzed for alveolar bone loss relative to uninfected controls, using computerized microtomography (microCT). Initially, four commercial inbred mouse strains were examined to calibrate the procedure and test for gender effects. Subsequently, we applied the same protocol to 23 lines (at inbreeding generations 10-18) from the newly developed mouse genetic reference population, the Collaborative Cross (CC) to determine heritability and genetic variation of control bone volume prior to infection (CBV, naïve bone volume around the teeth of uninfected mice), and residual bone volume (RBV, bone volume after infection) and loss of bone volume (LBV, the difference between CBV and RBV) following infection. RESULTS: BALB/CJ mice were highly susceptible (P<0.05) whereas DBA/2J, C57BL/6J and A/J mice were resistant. Six lines of the tested CC population were susceptible, whereas the remaining lines were resistant to alveolar bone loss. Gender effects on bone volume were tested across the four inbred and 23 CC lines, and found not to be significant. Based on ANOVA analyses, broad-sense heritabilities were statistically significant and equal to 0.4 for CBV and 0.2 for LBV. CONCLUSIONS: The moderate heritability values indicate that the variation in host susceptibility to the disease is controlled to an appreciable extent by genetic factors. These results strongly support the possibility of using the Collaborative Cross, as well as developing dedicated F2 (resistant x susceptible inbred strains) resource populations, for future dissection of genetic factors in periodontitis.\",\n \"corpus_id\": 2644393,\n \"score\": 0\n },\n {\n \"doc_id\": \"24980971\",\n \"title\": \"Coinfection with an intestinal helminth impairs host innate immunity against Salmonella enterica serovar Typhimurium and exacerbates intestinal inflammation in mice.\",\n \"abstract\": \"Salmonella enterica serovar Typhimurium is a Gram-negative food-borne pathogen that is a major cause of acute gastroenteritis in humans. The ability of the host to control such bacterial pathogens may be influenced by host immune status and by concurrent infections. Helminth parasites are of particular interest in this context because of their ability to modulate host immune responses and because their geographic distribution coincides with those parts of the world where infectious gastroenteritis is most problematic. To test the hypothesis that helminth infection may negatively regulate host mucosal innate immunity against bacterial enteropathogens, a murine coinfection model was established by using the intestinal nematode Heligmosomoides polygyrus and S. Typhimurium. We found that mice coinfected with S. Typhimurium and H. polygyrus developed more severe intestinal inflammation than animals infected with S. Typhimurium alone. The enhanced susceptibility to Salmonella-induced intestinal injury in coinfected mice was found to be associated with diminished neutrophil recruitment to the site of bacterial infection that correlated with decreased expression of the chemoattractants CXCL2/macrophage inflammatory protein 2 (MIP-2) and CXCL1/keratinocyte-derived chemokine (KC), poor control of bacterial replication, and exacerbated intestinal inflammation. The mechanism of helminth-induced inhibition of MIP-2 and KC expression involved interleukin-10 (IL-10) and, to a lesser extent, IL-4 and IL-13. Ly6G antibody-mediated depletion of neutrophils reproduced the adverse effects of H. polygyrus on Salmonella infection. Our results suggest that impaired neutrophil recruitment is an important contributor to the enhanced severity of Salmonella enterocolitis associated with helminth coinfection.\",\n \"corpus_id\": 23068391,\n \"score\": 0\n },\n {\n \"doc_id\": \"25136336\",\n \"title\": \"Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ.\",\n \"abstract\": \"Human infections by the bacterial pathogen Salmonella enterica represent major disease burdens worldwide. This highly ubiquitous species consists of more than 2600 different serovars that can be divided into typhoidal and non-typhoidal Salmonella (NTS) serovars. Despite their genetic similarity, these two groups elicit very different diseases and distinct immune responses in humans. Comparative analyses of the genomes of multiple Salmonella serovars have begun to explain the basis of the variation in disease manifestations. Recent advances in modeling both enteric fever and intestinal gastroenteritis in mice will facilitate investigation into both the bacterial- and host-mediated mechanisms involved in salmonelloses. Understanding the genetic and molecular mechanisms responsible for differences in disease outcome will augment our understanding of Salmonella pathogenesis, host immunity, and the molecular basis of host specificity. This review outlines the differences in epidemiology, clinical manifestations, and the human immune response to typhoidal and NTS infections and summarizes the current thinking on why these differences might exist.\",\n \"corpus_id\": 2345473,\n \"score\": 0\n },\n {\n \"doc_id\": \"26396246\",\n \"title\": \"A Highly Effective Component Vaccine against Nontyphoidal Salmonella enterica Infections.\",\n \"abstract\": \"UNLABELLED: Nontyphoidal Salmonella enterica (NTS) infections are a major burden to global public health, as they lead to diseases ranging from gastroenteritis to systemic infections and there is currently no vaccine available. Here, we describe a highly effective component vaccine against S. enterica serovar Typhimurium in both gastroenteritis and systemic murine infection models. We devised an approach to generate supernatants of S. enterica serovar Typhimurium, an organism that is highly abundant in virulence factors. Immunization of mice with this supernatant resulted in dramatic protection against a challenge with serovar Typhimurium, showing increased survival in the systemic model and decreased intestinal pathology in the gastrointestinal model. Protection correlated with specific IgA and IgG levels in the serum and specific secretory IgA levels in the feces of immunized mice. Initial characterization of the protective antigens in the bacterial culture supernatants revealed a subset of antigens that exhibited remarkable stability, a highly desirable characteristic of an effective vaccine to be used under suboptimal environmental conditions in developing countries. We were able to purify a subset of the peptides present in the supernatants and show their potential for immunization of mice against serovar Typhimurium resulting in a decreased level of colonization. This component vaccine shows promise with regard to protecting against NTS, and further work should significantly help to establish vaccines against these prevalent infections. IMPORTANCE: Salmonella enterica infections other than typhoid and paratyphoid fever are a major global health burden, as they cause high morbidity and mortality worldwide. Strategies that prevent Salmonella-related diseases are greatly needed, and there is a significant push for the development of vaccines against nontyphoidal Salmonella enterica serovars. In this work, we describe an S. Typhimurium supernatant-derived vaccine that is effective in reducing bacterial colonization in mouse models of gastroenteritis as well as invasive disease. This is a component vaccine that shows high stability to heat, a feature that is important for use under suboptimal conditions, such as those found in sub-Saharan Africa.\",\n \"corpus_id\": 13938061,\n \"score\": 0\n },\n {\n \"doc_id\": \"26537951\",\n \"title\": \"Non-typhoidal Salmonella serotypes, antimicrobial resistance and co-infection with parasites among patients with diarrhea and other gastrointestinal complaints in Addis Ababa, Ethiopia.\",\n \"abstract\": \"BACKGROUND: Non-typhoidal Salmonella (NTS) is an important public health problem worldwide. Consumption of animal-derived food products and direct and/or indirect contact with animals are the major routes of acquiring infection with NTS. Published information, particularly on the serotype distribution of NTS among human patients with gastroenteritis and associated risk factors, is scarce in Ethiopia. This study investigated the prevalence, risk factors, serotype distribution and antimicrobial susceptibility of Salmonella species among diarrheic out-patients attending health centers in Addis Ababa and patients with various gastrointestinal complaints at Tikur Anbessa Specialized Hospital (TASH). METHODS: Stool samples were cultured for Salmonella species according to the WHO Global Foodborne Infections Network laboratory protocol. Salmonella serotyping was conducted using slide agglutination and microplate agglutination techniques. Antibiotic susceptibility testing was performed using the disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. RESULTS: A total of 59 (6.2 %) stool samples, out of 957 were culture positive for Salmonella species. Fifty-five (7.2 %) of 765 diarrheic patients from health centers and 4 (2.1 %) of 192 patients from TASH were culture positive for Salmonella species. Multivariable logistic regression analysis after adjusting for all other variables revealed statistically significant association of Salmonella infection with consumption of raw vegetables (OR = 1.91, 95 % CI = 1.29-2.83, χ(2) = 4.74, p = 0.025) and symptom of watery diarrhea (OR = 3.3, 95 % CI = 1.23-8.88, χ(2) = 10.54, p = 0.005). Eleven serotypes were detected, and the most prominent were S. Typhimurium (37.3 %), S. Virchow (34 %), and S. Kottbus (10.2 %). Other serotypes were S. Miami, S. Kentucky, S. Newport, S. Enteritidis, S. Braenderup, S. Saintpaul, S. Concord and S. V:ROUGH-O. Resistance to three or more antimicrobials was detected in 27 (40.3 %) of the isolates. Resistance to five or more antimicrobials was detected in 17 (25.4 %). Resistance to individual antimicrobials was found at varying proportions: streptomycin (50; 74.6 %), nitrofurantoin (27; 40.3 %), sulfisoxazole (26; 38.8 %), kanamycin (23; 34.3 %), cephalothin (12; 17.9 %), and ampicillin (11; 16.4 %) respectively. Two S. Kentucky, one S. Typhimurium and one S. Concord isolates were multi-drug resistant to more than 10 antimicrobials. CONCLUSIONS: The study demonstrated significant association of Salmonella infection with consumption of raw vegetables. There was no significant association of Salmonella infection with co-occurring parasites. The study also showed the dominance of S. Typhimurium and S. Virchow in primary health care units. Overall, prevalence of MDR was low compared to previous studies. Although their proportion was low, S. Kentucky and S. Concord demonstrated wider spectrum of MDR. Continuous monitoring of circulating serotypes, antimicrobial resistance profile and characterization on molecular resistance determinants is essential for proper treatment of patients and for identifying potential environmental origins of antimicrobial resistance.\",\n \"corpus_id\": 4256866,\n \"score\": 0\n },\n {\n \"doc_id\": \"26787719\",\n \"title\": \"Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91-/- phox Mice.\",\n \"abstract\": \"Salmonella enterica causes systemic diseases (typhoid and paratyphoid fever), nontyphoidal septicemia (NTS), and gastroenteritis in humans and other animals worldwide. An important but underrecognized emerging infectious disease problem in sub-Saharan Africa is NTS in children and immunocompromised adults. A current goal is to identify Salmonella mutants that are not pathogenic in the absence of key components of the immune system such as might be found in immunocompromised hosts. Such attenuated strains have the potential to be used as live vaccines. We have used transposon-directed insertion site sequencing (TraDIS) to screen mutants of Salmonella enterica serovar Typhimurium for their ability to infect and grow in the tissues of wild-type and immunodeficient mice. This was to identify bacterial genes that might be deleted for the development of live attenuated vaccines that would be safer to use in situations and/or geographical areas where immunodeficiencies are prevalent. The relative fitness of each of 9,356 transposon mutants, representing mutations in 3,139 different genes, was determined in gp91(-/-) phox mice. Mutations in certain genes led to reduced fitness in both wild-type and mutant mice. To validate these results, these genes were mutated by allelic replacement, and resultant mutants were retested for fitness in the mice. A defined deletion mutant of cysE was attenuated in C57BL/6 wild-type mice and immunodeficient gp91(-/-) phox mice and was effective as a live vaccine in wild-type mice.\",\n \"corpus_id\": 4782466,\n \"score\": 0\n },\n {\n \"doc_id\": \"26956590\",\n \"title\": \"Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress.\",\n \"abstract\": \"UNLABELLED: Salmonella enterica serovar Typhimurium is one of the most common S. enterica serovars associated with U.S. foodborne outbreaks. S. Typhimurium bacteria isolated from humans exhibit wide-ranging virulence phenotypes in inbred mice, leading to speculation that some strains are more virulent in nature. However, it is unclear whether increased virulence in humans is related to organism characteristics or initial treatment failure due to antibiotic resistance. Strain diversity and genetic factors contributing to differential human pathogenicity remain poorly understood. We reconstructed phylogeny, resolved genetic population structure, determined gene content and nucleotide variants, and conducted targeted phenotyping assays for S. Typhimurium strains collected between 1946 and 2012 from humans and animals in the United States and abroad. Strains from recent U.S. salmonellosis cases were associated with five S. Typhimurium lineages distributed within three phylogenetic clades, which are not restricted by geography, year of acquisition, or host. Notably, two U.S. strains and four Mexican strains are more closely related to strains associated with human immunodeficiency virus (HIV)-infected individuals in sub-Saharan Africa than to other North American strains. Phenotyping studies linked variants specific to these strains in hmpA and katE to loss of fitness under nitrosative and oxidative stress, respectively. These results suggest that U.S. salmonellosis is caused by diverse S. Typhimurium strains circulating worldwide. One lineage has mutations in genes affecting fitness related to innate immune system strategies for fighting pathogens and may be adapting to immunocompromised humans by a reduction in virulence capability, possibly due to a lack of selection for its maintenance as a result of the worldwide HIV epidemic. IMPORTANCE: Nontyphoidal Salmonella bacteria cause an estimated 1.2 million illnesses annually in the United States, 80 million globally, due to ingestion of contaminated food or water. Salmonella Typhimurium is one of the most common serovars associated with foodborne illness, causing self-limiting gastroenteritis and, in approximately 5% of infected patients, systemic infection. Although some S. Typhimurium strains are speculated to be more virulent than others, it is unknown how strain diversity and genetic factors contribute to differential human pathogenicity. Ours is the first study to examine the diversity of S. Typhimurium associated with recent cases of U.S. salmonellosis and to provide some initial correlation between observed genotypes and phenotypes. Definition of specific S. Typhimurium lineages based on such phenotype/genotype correlations may identify strains with greater capability of associating with specific food sources, allowing outbreaks to be more quickly identified. Additionally, defining simple correlates of pathogenesis may have predictive value for patient outcome.\",\n \"corpus_id\": 6445763,\n \"score\": 0\n },\n {\n \"doc_id\": \"27380139\",\n \"title\": \"Quantitative trait loci identification and meta-analysis for rice panicle-related traits.\",\n \"abstract\": \"Rice yield is a complex trait controlled by quantitative trait loci (QTLs). In the past three decades, thousands of QTLs for rice yield traits have been detected, but only a very small percentage has been cloned to date, as identifying the QTL genes requires a substantial investment of time and money. Meta-analysis provides a simple, reliable, and economical method for integrating information from multiple QTL studies across various environmental and genetic backgrounds, detecting consistent QTLs powerfully and estimating their genetic positions precisely. In this study, we aimed to locate consistent QTL regions associated with rice panicle traits by applying a genome-wide QTL meta-analysis approach. We first conducted a QTL analysis of 5 rice panicle traits using 172 plants in 2011 and 138 plants in 2012 from an F2 population derived from a cross between Nipponbare and H71D rice cultivators. A total of 54 QTLs were detected, and these were combined with 1085 QTLs collected from 82 previous studies to perform a meta-analysis using BioMercator v4.2. The integration of 82 maps resulted in a consensus map with 6970 markers and a total map length of 1823.1 centimorgan (cM), on which 837 QTLs were projected. These QTLs were then integrated into 87 meta-quantitative trait loci (MQTLs) by meta-analysis, and the 95 % confidence intervals (CI) of them were smaller than the mean value of the original QTLs. Also, 30 MQTLs covered 47 of the 54 QTLs detected from the cross between Nipponbare and H71D in this study. Among them, the two major and stable QTLs, spp10.1 and sd10.1, were found to be included in MQTL10.4. The three other major QTLs, pl3.1, sb2.1, and sb10.1, were included in MQTL3.3, MQTL2.2, and MQTL10.3, respectively. A total of 21 of the 87 MQTLs' phenotypic variation were >20 %. In total, 24 candidate genes were found in 15 MQTLs that spanned physical intervals <0.2 Mb, including genes that have been cloned previously, e.g., EP3, LP, MIP1, HTD1, DSH1, and OsPNH1. However, it would be beneficial to identify a greater number of candidate genes from these MQTLs. Mining new genes that modulate yield and its related traits would assist researchers to better understand the relevant molecular mechanisms. The MQTLs found in this study that have small physical and genetic intervals are useful not only for marker-assisted selection and pyramiding, but they also provide important information of rice yield and related gene mining for future research.\",\n \"corpus_id\": 9198099,\n \"score\": 0\n },\n {\n \"doc_id\": \"27515598\",\n \"title\": \"The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits.\",\n \"abstract\": \"BACKGROUND: Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. RESULTS: We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. CONCLUSIONS: Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs.\",\n \"corpus_id\": 7803470,\n \"score\": 0\n },\n {\n \"doc_id\": \"27785189\",\n \"title\": \"Effect of Salmonella enteric Serovar Typhimurium in Pregnant Mice: A Biochemical and Histopathological Study.\",\n \"abstract\": \"BACKGROUND: Food borne infections caused by Salmonella enterica species are increasing globally and pregnancy poses a significant threat in developing countries, where sanitation facilities are inadequate. Thus, the present study was designed to delineate the effect of Salmonella infection during pregnancy. METHOD: Pregnant, BALB/c mice were challenged orally with Salmonella enterica serovar Typhimurium on gestational day 10 and were monitored for bacterial load, hepatic injury, histopathological alterations vis-a-vis oxidant and antioxidant levels. RESULTS: Pregnant-Salmonella-infected mice had higher bacterial translocation in the liver, spleen as well as liver enzymes mainly aspartate aminotransferase, alanine aminotransferase and alkaline phosphatase compared with Salmonella-infected mice. The levels of lipid peroxidation were significantly higher in all the organs of both pregnant-Salmonella-infected and Salmonella-infected mice compared with control mice. However, the activities of antioxidant enzymes (reduced glutathione, superoxide dismutase and catalase) were lower in the liver, spleen and placenta of pregnant, pregnant-Salmonella-infected and Salmonella-infected mice compared with control mice, but the decrease was more in pregnant-Salmonella-infected mice indicating depression of antioxidant defense system. Histopathologically, pregnant-Salmonella-infected mice had more architectural damage in the liver, spleen and placenta compared with other groups. CONCLUSION: Pregnancy makes the host more vulnerable to typhoid fever by affecting the physiology of pivotal organs and highlighting the importance of early and prompts diagnosis so as to avoid the further materno-fetal complications.\",\n \"corpus_id\": 17102068,\n \"score\": 0\n },\n {\n \"doc_id\": \"29294296\",\n \"title\": \"Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility.\",\n \"abstract\": \"Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro-computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (-log P = 5.3; false discovery rate = 0.06) on chromosomes 1 ( Perio3) and 14 ( Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes ( CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.\",\n \"corpus_id\": 4963494,\n \"score\": 0\n },\n {\n \"doc_id\": \"29784861\",\n \"title\": \"Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants.\",\n \"abstract\": \"Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.\",\n \"corpus_id\": 29169360,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":61,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29522477\",\n \"title\": \"Promising Detoxification Strategies to Mitigate Mycotoxins in Food and Feed.\",\n \"abstract\": \"Mycotoxins are secondary fungal metabolites associated with adverse human health and animal productivity consequences.[...].\",\n \"corpus_id\": 3765932\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19238622","title":"Reduction of feed-contaminating mycotoxins by ultraviolet irradiation: an in vitro study.","abstract":"Ultraviolet (UV) germicidal irradiation has been applied to the sterilization of agricultural products including stored grain for foodstuffs or animal feed. Although UV treatment is known to be effective for killing pathogenic moulds that contaminate the surface of grain, it remains unclear how and to what extent such irradiation is able to eliminate mycotoxins, the fungal metabolites that have adverse effects on human and animal health. We evaluated in vitro the effects of mild (intensity = 0.1 mW cm(-2) at 254 nm UV-C) and strong (24 mW cm(-2)) UV irradiation on two feed-contaminating mycotoxins, zearalenone (ZEN) and deoxynivalenol (DON). When exposed to mild irradiation, the levels of ZEN and DON (both 30 mg kg(-1) initially) were reduced as irradiation time increased, and became undetectable at 60 min. Strong UV irradiation also reduced the mycotoxin levels in the same time-dependent manner, but more rapidly. It was therefore confirmed in vitro that UV irradiation is effective at reducing the levels of ZEN and DON. The present study provides preliminary data for establishing a practical method of using UV irradiation to reduce mycotoxin contamination in grain intended for use in feed.","corpus_id":40957854,"score":2},{"doc_id":"19645364","title":"The biotransformation of chosen mycotoxins.","abstract":"Despite the unfavourable influence of mycotoxins on human and animal health and few toxicological aspects that have been documented, about these biologically active substances has not been explored. Aiming at more knowledge and a better understanding of the effects and mechanism of mycotoxin action in mammals would provide the basics for developing strategies to restrain different mycotoxicoses. One of the processes not fully understood is biotransformation, to which mycotoxins are subjected the animal organism. Biotransformation is the conversion of mycotoxins to non-toxic metabolites and occurs mostly in the intestinal mucosal membrane and liver, although other tissues and systems also take part in this process. Mycotoxin biotransformation reactions can be considered bioinactivation or detoxication, but mycotoxin biotransformation processes could also result in products more toxic than the mycotoxin. It can be concluded from research studies that our knowledge of mycotoxin biotransformation is scarce.","corpus_id":24047148,"score":2},{"doc_id":"19777908","title":"Biological strategies to counteract the effects of mycotoxins.","abstract":"Mycotoxins are fungal secondary metabolites that if ingested can cause a variety of adverse effects on both humans and animals, ranging from allergic responses to death. Therefore, exposure to mycotoxins should be minimized. A variety of physical, chemical, and biological methods have been developed for decontamination and/or detoxification of mycotoxins from contaminated foods and feeds. This overview details the latest developments in the biological control of both fungal infection and mycotoxin formation and describes the detoxification of many of the most important mycotoxins by microorganisms. This review also addresses the potential for use of microorganisms as mycotoxin binders in the gastrointestinal tract of both humans and animals, thereby reducing the potential deleterious effects of exposure to these toxins.","corpus_id":20234933,"score":2},{"doc_id":"20234966","title":"Decontamination and detoxification strategies for the Fusarium mycotoxin deoxynivalenol in animal feed and the effectiveness of microbial biodegradation.","abstract":"Trichothecenes are a group of mycotoxins mainly produced by fungi of the Fusarium genus. Deoxynivalenol (DON) is one of the most abundant and important trichothecenes in food and feed, and is a significant contaminants due to its frequent occurrence in toxicologically relevant concentrations worldwide. Since toxin production depends strongly on environmental conditions, such as temperature and humidity, Fusarium toxin contamination can not be avoided completely. Therefore, exposure to this toxin is a permanent health risk for both humans and farm animals. As cereal crops are commonly contaminated with DON and animal diets consist mainly of cereals, it can be assumed that animals are frequently exposed to DON-contaminated feeds. Many strategies can be undertaken to reduce the toxic effect of DON. In addition to the general necessity for minimizing all risk factors that might influence the contamination of cereals with DON, such as the so-called field toxins before harvest, several post-harvest strategies can be applied to counteract possible deleterious effects of this mycotoxin in farm animals. Another approach for decontamination in feedstuffs is the use of adsorbent materials. Adsorbent materials may bind mycotoxins in the gastrointestinal tract and reduce absorption and systemic toxicity. It has been shown that some adsorbents are suitable to alleviate the toxic effects of specific mycotoxins, but its efficacy against trichothecenes is practically zero. Therefore, alternative strategies to reduce animal and human health risk are needed. The use of microbial additives is a method which uses microorganisms having the capability to detoxify mycotoxins by metabolism or degradation prior to their resorption in the gastrointestinal tract. DON has been reported to be completely transformed to de-epoxy-DON by ruminal and intestinal microflora. Eubacterium BBSH 797 was capable of DON degradation and counteracted the toxic effects of DON in animals. This review focuses on the efficacy of microbial feed additives in ameliorating the toxic effects of DON. According to the results of experiments to date, it appears that microorganisms are the main living organisms suitable for this mycotoxin biodegradation. However, the use of this approach depends on its effectiveness from both a practical and economic perspective.","corpus_id":44640939,"score":2},{"doc_id":"20653554","title":"Patented techniques for detoxification of mycotoxins in feeds and food matrices.","abstract":"Mycotoxins are found worldwide in cereal grains, animal feed and human food that are produced from contaminated grains. This presents food safety risks. A variety of methods has been developed to reduce the safety risks by removing mycotoxins from contaminated grain products, eliminate the bioavailability of mycotoxins in the gastrointestinal system, degrade mycotoxins in food and feed, reduce mycotoxins pre- and post-harvest, and prevent (mycotoxin involved) plant disease. These techniques include physical methods such as flotation, extraction and adsorption, chemical reactions such as alkalization, oxidation, heat and irradiation, as well as biological detoxifications using microorganisms, enzymes and resistant plants. Most of the recent patented techniques for detoxification of mycotoxins in feeds and food matrices are discussed for an improved understanding of the patent techniques and insights into detoxification of mycotoxins.","corpus_id":42997046,"score":2},{"doc_id":"21770849","title":"Review of mycotoxin reduction in food and feed: from prevention in the field to detoxification by adsorption or transformation.","abstract":"Mycotoxins are secondary metabolites present worldwide in agricultural commodities and produced by filamentous fungi that cause a toxic response (mycotoxicosis) when ingested by animals. Prevention of mycotoxicoses includes pre- and post-harvest strategies. The best way to reduce the mycotoxin content in food and feed is the prevention of mycotoxin formation in the field, but this is often not sufficient, so other methods are needed. To decontaminate and/or detoxify mycotoxin-contaminated food and feed, the most prevalent approach in the feed industry is the inclusion of sorbent materials in the feed thus obtaining more or less selective removal of toxins by adsorption during passage through the gastrointestinal tract. Another reliable approach is to add enzymes or microorganisms capable of detoxifying some mycotoxins. Through a comprehensive review of published reports on the strategies for mycotoxin removal, this present work aims to update our understanding of mycotoxin removal. It provides an insight into the detoxification of mycotoxin present in food and feed. In the future, more emphasis needs to be placed on adsorption of mycotoxins in the gastrointestinal tract. Concerning the enzymatic transformation of mycotoxins, further efforts are required in understanding detoxification reactions, the toxicity of transformation products and in the characterization of enzymes responsible for transformations.","corpus_id":24542714,"score":2},{"doc_id":"23816820","title":"Application of plant derived compounds to control fungal spoilage and mycotoxin production in foods.","abstract":"Food decay by spoilage fungi causes considerable economic losses and constitutes a health risk for consumers due to the potential for fungi to produce mycotoxins. The indiscriminate use of synthetic antifungals has led to the development of resistant strains which has necessitated utilization of higher concentrations, with the consequent increase in toxic residues in food products. Numerous studies have demonstrated that plant extracts contain diverse bioactive components that can control mould growth. The metabolites produced by plants are a promising alternative because plants generate a wide variety of compounds, either as part of their development or in response to stress or pathogen attack. The aim of this article is to summarize the results from the literature on in vitro and in vivo experiments regarding the effects of plant-derived products for controlling fungal growth. Data from research work on the mode of action of these metabolites inside the fungal cell and the influence of abiotic external factors such as pH and temperature are also covered in the present review. Furthermore, an analysis on how the stress factor derived from the presence of plant extracts and essential oils affects secondary metabolism of the fungus, specifically mycotoxin synthesis, is developed. Finally, the effectiveness of using plant-derived compounds in combination with other natural antimicrobials and its application in food using novel technologies is discussed.","corpus_id":25246791,"score":2},{"doc_id":"23846184","title":"Microbial detoxification of mycotoxins.","abstract":"Mycotoxins are fungal natural products that are toxic to vertebrate animals including humans. Microbes have been identified that enzymatically convert aflatoxin, zearalenone, ochratoxin, patulin, fumonisin, deoxynivalenol, and T-2 toxin to less toxic products. Mycotoxin-degrading fungi and bacteria have been isolated from agricultural soil, infested plant material, and animal digestive tracts. Biotransformation reactions include acetylation, glucosylation, ring cleavage, hydrolysis, deamination, and decarboxylation. Microbial mycotoxin degrading enzymes can be used as feed additives or to decontaminate agricultural commodities. Some detoxification genes have been expressed in plants to limit the pre-harvest mycotoxin production and to protect crop plants from the phytotoxic effects of mycotoxins. Toxin-deficient mutants may be useful in assessing the role of mycotoxins in the ecology of the microorganisms.","corpus_id":16490444,"score":2},{"doc_id":"23891865","title":"Mycotoxin-degradation profile of Rhodococcus strains.","abstract":"Mycotoxins are secondary fungal metabolites that may have mutagenic, carcinogenic, cytotoxic and endocrine disrupting effects. These substances frequently contaminate agricultural commodities despite efforts to prevent them, so successful detoxification tools are needed. The application of microorganisms to biodegrade mycotoxins is a novel strategy that shows potential for application in food and feed processing. In this study we investigated the mycotoxin degradation ability of thirty-two Rhodococcus strains on economically important mycotoxins: aflatoxin B1, zearalenone, fumonisin B1, T2 toxin and ochratoxin A, and monitored the safety of aflatoxin B1 and zearalenone degradation processes and degradation products using previously developed toxicity profiling methods. Moreover, experiments were performed to analyse multi-mycotoxin-degrading ability of the best toxin degrader/detoxifier strains on aflatoxin B1, zearalenone and T2 toxin mixtures. This enabled the safest and the most effective Rhodococcus strains to be selected, even for multi-mycotoxin degradation. We concluded that several Rhodococcus species are effective in the degradation of aromatic mycotoxins and their application in mycotoxin biodetoxification processes is a promising field of biotechnology.","corpus_id":36233509,"score":2},{"doc_id":"23971211","title":"Toxin-producing fungi on feed grains and application of yeasts for their detoxification.","abstract":"The research deals with the contamination of feeding crops with fungi, producing mycotoxins and use of selected yeasts for detoxification. The thin-layer chromatography and ELISA methods were applied for the analysis of fungal secondary metabolites. The results showed a high rate of the grain contamination with fungi, mainly from genera Penicillium, Fusarium, Aspergillus and Alternaria. Some of the fungal strains produced 6-9 toxic compounds. The novelty of the study was the application of the yeast strains in detoxification of aflatoxins, zearalenon and deoxynivalenol in feed.","corpus_id":387972,"score":2},{"doc_id":"25255390","title":"Mycotoxin contamination of animal feedingstuff: detoxification by gamma-irradiation and reduction of aflatoxins and ochratoxin A concentrations.","abstract":"Mycotoxins are fungal secondary metabolites identified in many agricultural products screened for toxigenic moulds. They have been reported to be carcinogenic, teratogenic, tremorogenic, haemorrhagic and dermatitic to a wide range of organisms. With the increasing stringent regulations for mycotoxins imposed by importing countries such as those of the European Union, many cereals that are not safe for human consumption are used in formulations intended for animal feed. Gamma-rays are reported in the scientific literature to destroy ochratoxin A and aflatoxin in food crops and feed. The present study provides preliminary data for establishing the effect of dose of gamma-irradiation, ranging from 0 to 15 kGy, on aflatoxins and ochratoxin A reduction in commercial animal feed. The mycotoxin levels were determined by means of immunoaffinity clean-up (IAC) and HPLC with fluorescence detection (HPLC-FLD). The maximum reductions found at 15 kGy were 23.9%, 18.2%, 11.0%, 21.1% and 13.6% for ochratoxin A, aflatoxin B₁, aflatoxin B₂, aflatoxin G₁ and aflatoxin G₂, respectively. Results showed that the gamma-rays even at 15 kGy were not effective in the complete destruction of ochratoxin A and aflatoxins in the tested feed.","corpus_id":11407201,"score":2},{"doc_id":"25840963","title":"Prevalence and effects of mycotoxins on poultry health and performance, and recent development in mycotoxin counteracting strategies.","abstract":"Extensive research over the last couple of decades has made it obvious that mycotoxins are commonly prevalent in majority of feed ingredients. A worldwide mycotoxin survey in 2013 revealed 81% of around 3,000 grain and feed samples analyzed had at least 1 mycotoxin, which was higher than the 10-year average (from 2004 to 2013) of 76% in a total of 25,944 samples. The considerable increase in the number of positive samples in 2013 may be due to the improvements in detection methods and their sensitivity. The recently developed liquid chromatography coupled to (tandem) mass spectrometry allows the inclusion of a high number of analytes and is the most selective, sensitive, and accurate of all the mycotoxin analytical methods. Mycotoxins can affect the animals either individually or additively in the presence of more than 1 mycotoxin, and may affect various organs such as gastrointestinal tract, liver, and immune system, essentially resulting in reduced productivity of the birds and mortality in extreme cases. While the use of mycotoxin binding agents has been a commonly used counteracting strategy, considering the great diversity in the chemical structures of mycotoxins, it is very obvious that there is no single method that can be used to deactivate mycotoxins in feed. Therefore, different strategies have to be combined in order to specifically target individual mycotoxins without impacting the quality of feed. Enzymatic or microbial detoxification, referred to as \"biotransformation\" or \"biodetoxification,\" utilizes microorganisms or purified enzymes thereof to catabolize the entire mycotoxin or transform or cleave it to less or non-toxic compounds. However, the awareness on the prevalence of mycotoxins, available modern techniques to analyze them, the effects of mycotoxicoses, and the recent developments in the ways to safely eliminate the mycotoxins from the feed are very minimal among the producers. This symposium review paper comprehensively discusses the above mentioned aspects.","corpus_id":13958963,"score":2},{"doc_id":"26648039","title":"Occurrence, detection and detoxification of mycotoxins.","abstract":"Mycotoxins have been identified as important toxins affecting animal species and humans ever since the discovery of aflatoxin B1 in 1960. Mycotoxigenic fungi are ubiquitous in nature and are held responsible for economic loss as they decrease crop yield and quality of food. The presence of fungi and their mycotoxins are reported not only in food grains but also in medicinal herbs and processed foods. Since prevention is not always possible, detoxification of mycotoxins have been attempted using several means; however, only few have been accepted for practical use, e.g. ammonia in the corn industry. Organizations such as the World Health Organization, US Food and Drug Administration and European Union have set regulations and safety limits of important mycotoxins, viz. aflatoxins, fusarium toxins, ochratoxin, patulin zearalenone, etc., to ensure the safety of the consumers. This review article is a brief and up-to-date account of the occurrence, detection and detoxification of mycotoxins for those interested in and considering research in this area.","corpus_id":16871258,"score":2},{"doc_id":"26786025","title":"Environment contamination by mycotoxins and their occurrence in food and feed: Physiological aspects and economical approach.","abstract":"The contamination of food and feed by mycotoxins as toxic metabolites of fungi is a risk not only for consumers resulting in various embarrassment regarding health status and well-being, but also for producers, companies and export market on the ground of economic losses and ruined stability of economic trade. As it is given in historical evidence, the contamination of food by mycotoxins is a topic as old as a history of mankind, finding some evidence even in the ancient books and records. Nowadays, the mycotoxins are used in modern biotechnological laboratories and are considered an agent for targeting the specific cells (e.g., defected cells to eliminate them). However, this promising procedure is only the beginning. More concern is focused on mycotoxins as abiotic hazard agents. The dealing with them, systematic monitoring, and development of techniques for their elimination from agricultural commodities are worldwide issues concerning all countries. They can be found alone or in co-occurrence with other mycotoxins. Thus, this review aims to provide widened information regarding mycotoxins contamination in environment with the consequences on health of animals and humans. The inevitability for more data that correctly determine the risk points linked to mycotoxins occurrence and their specific reactions in the environment is demonstrated. This review includes various symptoms in animals and humans that result from mycotoxin exposure. For better understanding of mycotoxin's impact on animals, the sensitivities of various animal species to various mycotoxins are listed. Strategies for elimination and preventing the risks of mycotoxins contamination as well as economical approach are discussed. To complete the topic, some data from past as historical evidences are presented.","corpus_id":1251615,"score":2},{"doc_id":"27554261","title":"Impact of food processing and detoxification treatments on mycotoxin contamination.","abstract":"Mycotoxins are fungal metabolites commonly occurring in food, which pose a health risk to the consumer. Maximum levels for major mycotoxins allowed in food have been established worldwide. Good agricultural practices, plant disease management, and adequate storage conditions limit mycotoxin levels in the food chain yet do not eliminate mycotoxins completely. Food processing can further reduce mycotoxin levels by physical removal and decontamination by chemical or enzymatic transformation of mycotoxins into less toxic products. Physical removal of mycotoxins is very efficient: manual sorting of grains, nuts, and fruits by farmers as well as automatic sorting by the industry significantly lowers the mean mycotoxin content. Further processing such as milling, steeping, and extrusion can also reduce mycotoxin content. Mycotoxins can be detoxified chemically by reacting with food components and technical aids; these reactions are facilitated by high temperature and alkaline or acidic conditions. Detoxification of mycotoxins can also be achieved enzymatically. Some enzymes able to transform mycotoxins naturally occur in food commodities or are produced during fermentation but more efficient detoxification can be achieved by deliberate introduction of purified enzymes. We recommend integrating evaluation of processing technologies for their impact on mycotoxins into risk management. Processing steps proven to mitigate mycotoxin contamination should be used whenever necessary. Development of detoxification technologies for high-risk commodities should be a priority for research. While physical techniques currently offer the most efficient post-harvest reduction of mycotoxin content in food, biotechnology possesses the largest potential for future developments.","corpus_id":6887962,"score":2},{"doc_id":"27933870","title":"Tools for Defusing a Major Global Food and Feed Safety Risk: Nonbiological Postharvest Procedures To Decontaminate Mycotoxins in Foods and Feeds.","abstract":"Mycotoxin contamination of foods and animal feeds is a worldwide problem for human and animal health. Controlling mycotoxin contamination has drawn the attention of scientists and other food and feed stakeholders all over the world. Despite best efforts targeting field and storage preventive measures, environmental conditions can still lead to mycotoxin contamination. This raises a need for developing decontamination methods to inactivate or remove the toxins from contaminated products. At present, decontamination methods applied include an array of both biological and nonbiological methods. The targeted use of nonbiological methods spans from the latter half of last century, when ammoniation and ozonation were first used to inactivate mycotoxins in animal feeds, to the novel techniques being developed today such as photosensitization. Effectiveness and drawbacks of different nonbiological methods have been reported in the literature, and this review examines the utility of these methods in addressing food safety. Particular consideration is given to the application of such methods in the developing world, where mycotoxin contamination is a serious food safety issue in staple crops such as maize and rice.","corpus_id":21386600,"score":2},{"doc_id":"28298196","title":"Microbial detoxification of eleven food and feed contaminating trichothecene mycotoxins.","abstract":"BACKGROUND: Contamination of agricultural commodities with multiple trichothecene mycotoxins, produced by toxigenic Fusarium species, is a food safety issue, which greatly affects grain production and marketing worldwide. Importantly, exposure to multiple trichothecenes may increase toxicity in animals due to their synergistic and/or additive effects. To address the problem this study aimed to achieve a novel biological trait capable of detoxifying various food and feed contaminating trichothecenes under aerobic and anaerobic conditions and wide range of temperatures. RESULTS: A highly enriched microbial consortium (called DX100) capable of transforming eleven trichothecenes to significantly less toxic de-epoxy forms was achieved after prolonged incubation of soil microbial culture with 200 μg/mL deoxynivalenol (DON). DX100 demonstrated de-epoxidation activity under aerobic and anaerobic conditions, a greater range of temperatures and around neutral pH. The consortium contains 70% known and 30% unknown bacterial species, dominated by Stenotrophomonas species. Probably novel bacteria including strains of Stenotrophomonas and Alkaliphilus-Blautia species complex could be involved in aerobic and anaerobic de-epoxidation of trichothecenes, respectively. DX100 showed rapid and stable activity by de-epoxidizing 100% of 50 μg/mL deoxynivalenol at 48 h of incubation and retaining de-epoxidation ability after 100 subcultures in mineral salts broth (MSB). It was able to de-epoxidize high concentration of DON (500 μg/mL), and transformed ten more food contaminating trichothecenes into de-epoxy forms and/or other known/unknown compounds. Microbial de-epoxidation rate increased with increasing trichothecene concentrations in the broth media, suggesting that DX100 maintains a robust trichothecene detoxifying mechanism. Furthermore, the nature of microbial de-epoxidation reaction and inhibition of the reaction by sodium azide and the finding that bacterial cell culture lysate retained activity suggests that certain cytoplasmic reductases may be responsible for the de-epoxidation activity. CONCLUSIONS: This study reports the enrichment procedure for obtaining an effective and stable microbial consortium DX100 capable of de-epoxidizing several food contaminating trichothecene mycotoxins. DX100, which has de-epoxidation ability under wide range of conditions, represents a unique enzymatic source which has great industrial potential for reducing contamination of foods/feeds with multiple trichothecenes, and minimizing their synergistic/additive cytotoxic effects on consumer health.","corpus_id":18627367,"score":2},{"doc_id":"28387743","title":"Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins.","abstract":"Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.","corpus_id":1641676,"score":2},{"doc_id":"28720287","title":"Occurrence, toxicity, bioaccessibility and mitigation strategies of beauvericin, a minor Fusarium mycotoxin.","abstract":"Emerging Fusarium mycotoxins include the toxic secondary metabolites fusaproliferin, enniatins, beauvericin (BEA), and moniliform. BEA is produced by some entomo- and phytopathogenic Fusarium species and occurs naturally on corn and corn-based foods and feeds infected by Fusarium spp. BEA has shown various biological activities (antibacterial, antifungal, and insecticidal) and possesses toxic activity, including the induction of apoptosis, increase cytoplasmic calcium concentration and lead to DNA fragmentation in mammalian cell lines. Cereals food processing has an important effect on mycotoxin stability, leading to less-contaminated food compared to the raw materials. Different industrial processes have shown to be effective practices to reduce BEA contents due to thermal food processing applied, such as cooking, boiling, baking, frying, roasting and pasteurization. Some studies demonstrated the capacity of lactic acid bacteria to reduce the presence of the BEA in model solution and in food chain through fermentation processes, modifying this mycotoxin in a less toxic derivate. Prebiotic and probiotic ingredient can modulate the bioaccessibility of BEA reducing the risk of intake of this minor Fusarium mycotoxin. This review summarizes the existing data on occurrence, toxicity and especially on BEA reduction strategies in food and feed such as chemical reduction, biocontrol and food processing.","corpus_id":11637397,"score":2},{"doc_id":"18258326","title":"Mycotoxin problem in Africa: current status, implications to food safety and health and possible management strategies.","abstract":"Mycotoxins are toxic secondary metabolites of fungal origin and contaminate agricultural commodities before or under post-harvest conditions. They are mainly produced by fungi in the Aspergillus, Penicillium and Fusarium genera. When ingested, inhaled or absorbed through the skin, mycotoxins will cause lowered performance, sickness or death on humans and animals. Factors that contribute to mycotoxin contamination of food and feed in Africa include environmental, socio-economic and food production. Environmental conditions especially high humidity and temperatures favour fungal proliferation resulting in contamination of food and feed. The socio-economic status of majority of inhabitants of sub-Saharan Africa predisposes them to consumption of mycotoxin contaminated products either directly or at various points in the food chain. The resulting implications include immuno-suppression, impaired growth, various cancers and death depending on the type, period and amount of exposure. A synergistic effect between mycotoxin exposure and some important diseases in the continent such as malaria, kwashiorkor and HIV/AIDS have been suggested. Mycotoxin concerns have grown during the last few decades because of their implications to human and animal health, productivity, economics of their management and trade. This has led to development of maximum tolerated limits for mycotoxins in various countries. Even with the standards in place, the greatest recorded fatal mycotoxin-poisoning outbreak caused by contamination of maize with aflatoxins occurred in Africa in 2004. Pre-harvest practices; time of harvesting; handling of produce during harvesting; moisture levels at harvesting, transportation, marketing and processing; insect damage all contribute to mycotoxin contamination. Possible intervention strategies include good agricultural practices such as early harvesting, proper drying, sanitation, proper storage and insect management among others. Other possible interventions include biological control, chemical control, decontamination, breeding for resistance as well as surveillance and awareness creation. There is need for efficient, cost-effective sampling and analytical methods that can be used for detection analysis of mycotoxins in developing countries.","corpus_id":31564911,"score":1},{"doc_id":"18274964","title":"Emerging fusarium-mycotoxins fusaproliferin, beauvericin, enniatins, and moniliformin: a review.","abstract":"The contamination of foods and feed with mycotoxins is a commonly known problem. Intense investigations have been conducted to study the occurrence, toxicity, and recently also the prevention and detoxification strategies of mycotoxins in human and animal food chains. Most of the studies have emphasized on \"traditional\" mycotoxins, such as aflatoxins, ochratoxin A, and trichothecenes. However, one of the most common grain-contaminating genus of fungi, Fusarium spp., is also capable of producing other toxic secondary metabolites - the so-called emerging mycotoxins such as fusaproliferin, beauvericin, enniatins, and moniliformin. So far, only limited data is available on these metabolites. This is not only due to their late recognition but especially the late understanding of their role as mycotoxins. This paper summarizes the existing data on the chemistry, analytical techniques, biosynthesis, production, toxicity, and occurrence data on fusaproliferin, beauvericin, enniatins, and moniliformin. Based on the available studies, attention should be paid to the studies on the distinct significance of these compounds in the human and animal food chains.","corpus_id":21330571,"score":1},{"doc_id":"18936919","title":"Rapid test strips for analysis of mycotoxins in food and feed.","abstract":"An overview is given on recent trends and applications of rapid immunodiagnostic tests for screening of food and feed for mycotoxins. Different test formats are discussed, and challenges in the development of lateral-flow devices for on-site determination of mycotoxins, with requirements such as being robust, fast, and cost-effective, are briefly elucidated.","corpus_id":43915454,"score":1},{"doc_id":"18949120","title":"Determination of mycotoxins in human foods.","abstract":"This tutorial review deals with the analytical methods available for the determination of mycotoxins in food commodities. As the secondary metabolites of a range of fungal species, mycotoxins possess diverse chemical structures, presenting analytical chemists with a unique set of challenges in the microg kg(-1) (ppb) range. A number of analytical methods have been applied to mycotoxin analysis. These include widely applicable HPLC methods with UV or fluorimetric detection, which are extensively used both in research and for legal enforcement of food safety legislation and for regulations in international agricultural trade. Other chromatographic methods, such as TLC and GC, are also employed for the determination of mycotoxins, whereas recent advances in analytical instrumentation have highlighted the potential of LC-MS methods, especially for multi-toxin determination and for confirmation purposes. Conventional chromatographic methods are generally time consuming and capital intensive, and hence a range of methods, mostly based on immunological principles, have been developed and commercialised for rapid analysis. These methods include, among others, enzyme-linked immunosorbent analysis (ELISA), direct fluorimetry, fluorescence polarization, and various biosensors and strip methods.","corpus_id":36851512,"score":1},{"doc_id":"20339844","title":"Determination of mycotoxins in foods: current state of analytical methods and limitations.","abstract":"Mycotoxins are natural contaminants produced by a range of fungal species. Their common occurrence in food and feed poses a threat to the health of humans and animals. This threat is caused either by the direct contamination of agricultural commodities or by a \"carry-over\" of mycotoxins and their metabolites into animal tissues, milk, and eggs after feeding of contaminated hay or corn. As a consequence of their diverse chemical structures and varying physical properties, mycotoxins exhibit a wide range of biological effects. Individual mycotoxins can be genotoxic, mutagenic, carcinogenic, teratogenic, and oestrogenic. To protect consumer health and to reduce economic losses, surveillance and control of mycotoxins in food and feed has become a major objective for producers, regulatory authorities and researchers worldwide. However, the variety of chemical structures makes it impossible to use one single technique for mycotoxin analysis. Hence, a vast number of analytical methods has been developed and validated. The heterogeneity of food matrices combined with the demand for a fast, simultaneous and accurate determination of multiple mycotoxins creates enormous challenges for routine analysis. The most crucial issues will be discussed in this review. These are (1) the collection of representative samples, (2) the performance of classical and emerging analytical methods based on chromatographic or immunochemical techniques, (3) the validation of official methods for enforcement, and (4) the limitations and future prospects of the current methods.","corpus_id":24974696,"score":1},{"doc_id":"20358681","title":"Toxicology of mycotoxins.","abstract":"Humans are exposed to mycotoxins via ingestion, contact and inhalation. This must have occurred throughout human history and led to severe outbreaks. Potential diseases range from akakabio-byo to stachybotryotoxicosis and cancer. The known molecular bases of toxicology run the gamut of 23 compounds, from aflatoxins (AFs) to zearalenone, ochratoxin A and deoxynivalenol. Ergotism is one of the oldest recognized mycotoxicosis, although mycotoxin science only commenced in the 1960s with the discovery of AFs in turkey feed. AFs are carcinogenic. Some others are suspected carcinogens. The effects of mycotoxins are acute or chronic in nature. Mycotoxins are well known in the scientific community, although they have a low profile in the general population. An incongruous situation occurs in United States where mycotoxins from \"moldy homes\" are considered to be a significant problem, although there is a general debate about seriousness. This contrasts with the thousands of deaths from mycotoxins that occur, even now, in the technologically less developed countries (e.g., Indonesia, China, and Africa). Mycotoxins are more toxic than pesticides. Studies are moving from whole animal work to investigating the biochemical mechanisms in isolated cells, and the mechanisms of toxicity at the molecular level are being elucidated. The stereochemical nature of AFs has been shown to be important. In addition, the effect of multiple mycotoxins is being increasingly investigated, which will more accurately represent the situation in nature. It is anticipated that more fungal metabolites will be recognized as dangerous toxins and permitted statutory levels will decrease in the future.","corpus_id":22945774,"score":1},{"doc_id":"20376161","title":"[Mycotoxins in food: legislation and thresholds.].","abstract":"Micotossine negli alimenti: normative e limiti di legge. Mycotoxins are chemical substances produced by fungal species belonging mostly to Aspergillus, Penicillium and Fusarium , and having a toxic effect on humans and farm animals. In recent years health authorities have dedicated much attention to food contamination by mycotoxins, especially with regards to aflatoxins, fumonisin, ocratoxin A, patulin, trichothecenes e zearalenone. The current European legislation CE n. 1881/2006 and n. 1126/2007 establish the maximum levels of mycotoxins allowed in human food. Despite the existence of such legislation, regulations regarding certain products are not very clear (i.e. milk products). More interest should be paid to these food products in terms of regulations and testing.","corpus_id":34067960,"score":1},{"doc_id":"21641127","title":"Ochratoxin A in feed of food-producing animals: an undesirable mycotoxin with health and performance effects.","abstract":"Mycotoxins are secondary fungal metabolites, whose presence in feed- and foodstuffs is unavoidable. Ochratoxin A (OTA) is one of the known mycotoxins with greatest public health and agro-economic significance. Several toxic effects have been ascribed following exposure, namely nephrotoxicity, as well negative impacts in the performance of farm animals, resulting in major economic implications. Of no less importance for the route of human exposure that can also embody the carry-over of OTA from feed into animal-derived products is also a concern. For all these reasons the present article updates the worldwide occurrence of OTA in different raw ingredients and finished feed destined to food-producing animals. After that a brief characterization of specie susceptibility and the major rationales is made. An historical overview of field outbreaks linked to OTA exposure in farm animals, concerning the implicated feeds, contamination levels and major clinical and productivity effects is presented. Finally a review of the major animal health and performance potential impacts of animals being reared on contaminated feed is made allied to a perspective regarding its co-occurrence with other mycotoxins, and simultaneous parasitic and bacterial infections. Ultimately, this article aims to be instructive and draw attention to a mycotoxin so often neglected and elapsed from the list of differential diagnosis in farm practice. For the unpredictability and unavoidability of occurrence, OTA will definitely be an enduring problem in animal production.","corpus_id":43819175,"score":1},{"doc_id":"21643911","title":"Analysis of multiple mycotoxins in food.","abstract":"Mycotoxins are secondary metabolites of microscopic filamentous fungi. With regard to the widespread distribution of fungi in the environment, mycotoxins are considered to be one of the most important natural contaminants in foods and feeds. To protect consumers' health and reduce economic losses, surveillance and control of mycotoxins in food and feed has become a major objective for producers, regulatory authorities, and researchers worldwide. In this context, availability of reliable analytical methods applicable for this purpose is essential. Since the variety of chemical structures of mycotoxins makes impossible to use one single technique for their analysis, a vast number of analytical methods has been developed and validated. Both a large variability of food matrices and growing demands for a fast, cost-saving and accurate determination of multiple mycotoxins by a single method outline new challenges for analytical research. This strong effort is facilitated by technical developments in mass spectrometry allowing decreasing the influence of matrix effects in spite of omitting sample clean-up step. The current state-of-the-art together with future trends is presented in this chapter. Attention is focused mainly on instrumental method; advances in biosensors and other screening bioanalytical approaches enabling analysis of multiple mycotoxins are not discussed in detail.","corpus_id":21505019,"score":1},{"doc_id":"22069600","title":"Real and perceived risks for mycotoxin contamination in foods and feeds: challenges for food safety control.","abstract":"Mycotoxins are toxic compounds, produced by the secondary metabolism of toxigenic moulds in the Aspergillus, Alternaria, Claviceps, Fusarium, Penicillium and Stachybotrys genera occurring in food and feed commodities both pre- and post-harvest. Adverse human health effects from the consumption of mycotoxins have occurred for many centuries. When ingested, mycotoxins may cause a mycotoxicosis which can result in an acute or chronic disease episode. Chronic conditions have a much greater impact, numerically, on human health in general, and induce diverse and powerful toxic effects in test systems: some are carcinogenic, mutagenic, teratogenic, estrogenic, hemorrhagic, immunotoxic, nephrotoxic, hepatotoxic, dermotoxic and neurotoxic. Although mycotoxin contamination of agricultural products still occurs in the developed world, the application of modern agricultural practices and the presence of a legislatively regulated food processing and marketing system have greatly reduced mycotoxin exposure in these populations. However, in developing countries, where climatic and crop storage conditions are frequently conducive to fungal growth and mycotoxin production, much of the population relies on subsistence farming or on unregulated local markets. Therefore both producers and governmental control authorities are directing their efforts toward the implementation of a correct and reliable evaluation of the real status of contamination of a lot of food commodity and, consequently, of the impact of mycotoxins on human and animal health.","corpus_id":5878422,"score":1},{"doc_id":"22725671","title":"Fungal and bacterial metabolites in commercial poultry feed from Nigeria.","abstract":"Metabolites of toxigenic fungi and bacteria occur as natural contaminants (e.g. mycotoxins) in feedstuffs making them unsafe to animals. The multi-toxin profiles in 58 commercial poultry feed samples collected from 19 districts in 17 states of Nigeria were determined by LC/ESI-MS/MS with a single extraction step and no clean-up. Sixty-three (56 fungal and seven bacterial) metabolites were detected with concentrations ranging up to 10,200 µg kg⁻¹ in the case of aurofusarin. Fusarium toxins were the most prevalent group of fungal metabolites, whereas valinomycin occurred in more than 50% of the samples. Twelve non-regulatory fungal and seven bacterial metabolites detected and quantified in this study have never been reported previously in naturally contaminated stored grains or finished feed. Among the regulatory toxins in poultry feed, aflatoxin concentrations in 62% of samples were above 20 µg kg⁻¹, demonstrating high prevalence of unsafe levels of aflatoxins in Nigeria. Deoxynivalenol concentrations exceeded 1000 µg kg⁻¹ in 10.3% of samples. Actions are required to reduce the consequences from regulatory mycotoxins and understand the risks of the single or co-occurrence of non-regulatory metabolites for the benefit of the poultry industry.","corpus_id":35148398,"score":1},{"doc_id":"23047235","title":"Masked mycotoxins: a review.","abstract":"The aim of this review is to give a comprehensive overview of the current knowledge on plant metabolites of mycotoxins, also called masked mycotoxins. Mycotoxins are secondary fungal metabolites, toxic to human and animals. Toxigenic fungi often grow on edible plants, thus contaminating food and feed. Plants, as living organisms, can alter the chemical structure of mycotoxins as part of their defence against xenobiotics. The extractable conjugated or non-extractable bound mycotoxins formed remain present in the plant tissue but are currently neither routinely screened for in food nor regulated by legislation, thus they may be considered masked. Fusarium mycotoxins (deoxynivalenol, zearalenone, fumonisins, nivalenol, fusarenon-X, T-2 toxin, HT-2 toxin, fusaric acid) are prone to metabolisation or binding by plants, but transformation of other mycotoxins by plants (ochratoxin A, patulin, destruxins) has also been described. Toxicological data are scarce, but several studies highlight the potential threat to consumer safety from these substances. In particular, the possible hydrolysis of masked mycotoxins back to their toxic parents during mammalian digestion raises concerns. Dedicated chapters of this article address plant metabolism as well as the occurrence of masked mycotoxins in food, analytical aspects for their determination, toxicology and their impact on stakeholders.","corpus_id":15401052,"score":1},{"doc_id":"23162698","title":"Current situation of mycotoxin contamination and co-occurrence in animal feed--focus on Europe.","abstract":"Mycotoxins are secondary metabolites produced by fungi especially those belonging to the genus Aspergillus, Penicillum and Fusarium. Mycotoxin contamination can occur in all agricultural commodities in the field and/or during storage, if conditions are favourable to fungal growth. Regarding animal feed, five mycotoxins (aflatoxins, deoxynivalenol, zearalenone, fumonisins and ochratoxin A) are covered by EU legislation (regulation or recommendation). Transgressions of these limits are rarely observed in official monitoring programs. However, low level contamination by Fusarium toxins is very common (e.g., deoxynivalenol (DON) is typically found in more than 50% of the samples) and co-contamination is frequently observed. Multi-mycotoxin studies reported 75%-100% of the samples to contain more than one mycotoxin which could impact animal health at already low doses. Co-occurrence of mycotoxins is likely to arise for at least three different reasons (i) most fungi are able to simultaneously produce a number of mycotoxins, (ii) commodities can be contaminated by several fungi, and (iii) completed feed is made from various commodities. In the present paper, we reviewed the data published since 2004 concerning the contamination of animal feed with single or combinations of mycotoxins and highlighted the occurrence of these co-contaminations.","corpus_id":43725891,"score":1},{"doc_id":"23605238","title":"Mycotoxins in horse feed.","abstract":"A total of 62 samples of commercial horse feed preparations (complementary feeds) containing cereal mixtures (\"muesli\" or mash, n = 39; pelleted feeds, n = 12), and plain horse feed grains (maize, n = 5; oats, n = 4; barley, n = 2) were purchased from 21 different producers/distributors from the German market. All samples were analysed by competitive enzyme immunoassays (EIA) for six different mycotoxins (mycotoxin groups). Analytes (detection limit, mean recovery) were: deoxynivalenol (DON, 10 µg/kg, 84%), zearalenone (ZEA, 5 µg/kg, 93%), fumonisin B1 (FB1, 2 µg/kg, 113%), T-2 toxin (T-2, 0.1 µg/kg, 71%), sum of T-2 + HT-2 toxin (T-2/HT2, 0.2 µg/kg, 97%), ochratoxin A (OTA, 0.2 µg/kg, 67%), and total ergot alkaloids (Generic Ergot Alkaloids \"GEA\", 30 µg/kg, 132%). All samples contained DON (16-4,900 µg/kg, median 220 µg/kg), T-2/HT-2 (0.8-230 µg/kg, median 24 µg/kg), and T-2 (0.3-91 µg/kg, median 7 µg/kg). ZEA was detected in 98% of the samples (7-310 µg/kg, median 61 µg/kg). Most samples (94%) were positive for FB1 (2-2,200 µg/kg, median 27 µg/kg). Ergot alkaloids were detected in 61% of samples (28-1,200 µg/kg, median 97 µg/kg), OTA was found in 42% of samples (0.2-4 µg/kg, median 0.35 µg/kg). The results demonstrate that a co-contamination with several mycotoxins is very common in commercial horse feed from the German market. The toxin concentrations were in most cases well below the levels which are usually considered as critical or even toxic. The highest mycotoxin concentrations were mostly found in single-grain cereal feed: the maximum values for DON and FB1 were found in maize, the highest T-2/HT-2 toxin concentrations were found in oats, and the highest concentration of ergot alkaloids was found in barley. In composed feeds, no correlation between cereal composition and mycotoxin levels could be found.","corpus_id":11697229,"score":1},{"doc_id":"23606076","title":"Mycotoxins in feedstuffs in Portugal: an overview.","abstract":"Mycotoxins are secondary metabolites produced by many genera of fungi in many commodities, under certain conditions. Mycotoxicological control of feed is a procedure that aims to protect human and animal health, avoiding the adverse effects of these undesirable substances. This component of the sanitary control of feed and food is essential to prevent the presence of those substances which can seriously affect the health of the animals. In Portugal, there is relatively few information related to the natural occurrence of mycotoxins in feed. In this context, the authors present results and data compilation concerning the occurrence of mycotoxins in raw materials and also feed for dairy cattle, swine, poultry, horses, fish, laboratory rats and pet; making a generic qualitative appreciation of the risks associated to the presence of mycotoxins in these feedstuffs. The mycotoxins studied: aflatoxins (AFs), ochratoxin A (OTA), fumonisin B1 and B2 (FB1, FB2) were analysed by High Performance Liquid Chromatoghraphy (HPLC). Deoxynivalenol (DON) and zearalenone (ZEN) were determined by Thin-Layer Chromatography (TLC). The results suggest that contaminations with these mycotoxins in feed are quite common, revealing the need for surveillance and monitoring programs for the prevention of the sanitary impacts of these \"non desirable substances\".","corpus_id":1735613,"score":1},{"doc_id":"23612752","title":"From the gut to the brain: journey and pathophysiological effects of the food-associated trichothecene mycotoxin deoxynivalenol.","abstract":"Mycotoxins are fungal secondary metabolites contaminating food and causing toxicity to animals and humans. Among the various mycotoxins found in crops used for food and feed production, the trichothecene toxin deoxynivalenol (DON or vomitoxin) is one of the most prevalent and hazardous. In addition to native toxins, food also contains a large amount of plant and fungal derivatives of DON, including acetyl-DON (3 and 15ADON), glucoside-DON (D3G), and potentially animal derivatives such as glucuronide metabolites (D3 and D15GA) present in animal tissues (e.g., blood, muscle and liver tissue). The present review summarizes previous and very recent experimental data collected in vivo and in vitro regarding the transport, detoxification/metabolism and physiological impact of DON and its derivatives on intestinal, immune, endocrine and neurologic functions during their journey from the gut to the brain.","corpus_id":10276932,"score":1},{"doc_id":"23768181","title":"Food safety and increasing hazard of mycotoxin occurrence in foods and feeds.","abstract":"The possible hazard of mycotoxin occurrence in foods and feeds and some food-borne mycotoxicoses is reviewed. Management of the risk of mycotoxin contamination using some useful preventive measures against mycotoxin contamination of foods/feeds during pre- and post-harvesting periods is considered. The physical and chemical methods of mycotoxin decontamination of foods/feeds are briefly described. The use of various feed additives as a method for prevention of the adverse effects of mycotoxins is reviewed. The processing of various foods and feeds is considered in a view to possible mycotoxin decontamination. The necessary hygiene control and risk assessment in regard to mycotoxin contamination of foods and feeds in addition to some useful prophylactic measures are briefly described. A short reference is made concerning the most successful methods of veterinary hygiene control in order to prevent a possible entering of some mycotoxins in commercial channels with a view to human health.","corpus_id":2305869,"score":1},{"doc_id":"24162094","title":"Fusarial toxins: secondary metabolites of Fusarium fungi.","abstract":"Exposure to mycotoxins occurs worldwide, even though there are geographic and climatic differences in the amounts produced and occurrence of these substances. Mycotoxins are secondary chemical metabolites of different fungi. They are natural contaminants of cereals, so their presence is often inevitable. Among many genera that produce mycotoxins, Fusarium fungi are the most widespread in cereal-growing areas of the planet. Fusarium fungi produce a diversity of mycotoxin types, whose distributions are also diverse. What is produced and where it is produced is influenced primarily by environmental conditions, and crop production and storage methods. The amount of toxin produced depends on physical (viz., moisture, relative humidity, temperature, and mechanical damage), chemical (viz., carbon dioxide,oxygen, composition of substrate, insecticides and fungicides), and biological factors (viz., plant variety, stress, insects, spore load, etc.). Moisture and temperature have a major influence on mold growth rate and mycotoxin production. Among the most toxic and prevalent fusaria) toxins are the following: zearalenone,fumonisins, moniliformin and trichothecenes (T-2/HT-2 toxin, deoxynivalenol,diacetoxyscirpenol, nivalenol). Zearalenone (ZEA; ZON, F-2 toxin) isaphy to estrogenic compound, primarily a field contaminant, which exhibits estrogenic activity and has been implicated in numerous mycotoxicoses of farm animals,especially pigs. Recently, evidence suggests that ZEA has potential to stimulate the growth of human breast cancer cells. Fumonisins are also cancer-promoting metabolites,of which Fumonisin 8 I (FBI) is the most important. Moniliformin (MON) isalso highly toxic to both animals and humans. Trichothecenes are classified as gastrointestinal toxins, dermatotoxins, immunotoxins, hematotoxins, and gene toxins. T-2 and HT-2 toxin, and diacetoxyscirpenol (DAS, anguidine) are the most toxic mycotoxins among the trichothecene group. Deoxynivalenol (DON, vomitoxin) and nivalenol although less toxic are important because they frequently occur at levels high enough to cause adverse effects. The presence of mycotoxins in the animal diet can produce significant production losses. Any considerable presence of mycotoxins, in major dietary components,confirms the need to adopt a continuous prevention and control program. Such programs are usually based on several common approaches to minimize mycotoxin contamination in the food chain. Major strategies include preventing fungal growth and therefore mycotoxin formation, reducing or eliminating mycotoxins from contaminated feedstuffs, or diverting contaminated products to low risk uses. Because of the complexity of their chemical structures, mycotoxins also present a major analytical challenge. They are also found in a vast array of feed matrices. Analysis is essential for determining the extent of mycotoxin contamination, for risk analysis, confirming the diagnosis of a mycotoxicosis and for monitoring mycotoxin mitigation strategies. For the future, adequately controlling the mycotoxin problem in the livestock economy will depend on implementing appropriate agricultural management policies,as well as augmenting production and storage systems and analysis methods. Only such policies offer the opportunity to bring solid and long-lasting economical results to the livestock industry that is afflicted with the mycotoxin problem.","corpus_id":44438391,"score":1},{"doc_id":"24377857","title":"Upstream regulation of mycotoxin biosynthesis.","abstract":"Mycotoxins are natural contaminants of food and feed products, posing a substantial health risk to humans and animals throughout the world. A plethora of filamentous fungi has been identified as mycotoxin producers and most of these fungal species belong to the genera Aspergillus, Fusarium, and Penicillium. A number of studies have been conducted to better understand the molecular mechanisms of biosynthesis of key mycotoxins and the regulatory cascades controlling toxigenesis. In many cases, the mycotoxin biosynthetic genes are clustered and regulated by one or more pathway-specific transcription factor(s). In addition, as biosynthesis of many secondary metabolites is coordinated with fungal growth and development, there are a number of upstream regulators affecting biosynthesis of mycotoxins in fungi. This review presents a concise summary of the regulation of mycotoxin biosynthesis, focusing on the roles of the upstream regulatory elements governing biosynthesis of aflatoxin and sterigmatocystin in Aspergillus.","corpus_id":8249845,"score":1},{"doc_id":"24572628","title":"An overview on mycotoxin contamination of foods in Africa.","abstract":"Mycotoxins are fungal secondary metabolites that contaminate various feedstuffs and agricultural crops. The contamination of food by mycotoxins can occur before production, during storage, processing, transportation or marketing of the food products. High temperature, moisture content and water activity are among the predisposing factors that facilitate the production of mycotoxins in food. Aflatoxins, ochratoxins, fumonisins, deoxynivalenol and zearalenone are all considered the major mycotoxins produced in food and feedstuffs. In Africa, mycotoxin contamination is considered to be a major problem with implications that affect human and animal health and economy. Aflatoxin-related hepatic diseases are reported in many African countries. Ochratoxin and fumonisin toxicity in humans and animals is widespread in Africa. The available, updated information on the incidence of mycotoxin contamination, decontamination and its public health importance in Africa is lacking. The aim of this review is to highlight, update and discuss the available information on the incidence of mycotoxins in African countries. The public health implications and the recommended strategies for control of mycotoxins in food and agricultural crops are also discussed.","corpus_id":16654472,"score":1},{"doc_id":"24769018","title":"Mycotoxins in a changing global environment--a review.","abstract":"Mycotoxins are toxic metabolites produced by fungal species that commonly contaminate staple foods and feeds. They represent an unavoidable problem due to their presence in globally consumed cereals such as rice, maize and wheat. Most mycotoxins are immunosuppressive agents and some are carcinogens, hepatotoxins, nephrotoxins, and neurotoxins. Worldwide trends envision a stricter control of mycotoxins, however, the changing global environment may not be the ideal setting to control and reduce the exposure to these toxins. Although new technologies allow us to inspect the multi-mycotoxin presence in foods, new sources of exposure, gaps in knowledge of mycotoxins interactions, appearance of \"emergent\" mycotoxins and elucidation of consequent health effects can complicate their control even more. While humans are adapting to cope with environmental changes, such as food scarcity, decreased food quality, mycotoxin regulations, crop production and seasonality, and other climate related modifications, fungal species are also adapting and increased cases of mycotoxin adverse health effects are likely to occur in the future. To guarantee access to quality food for all, we need a way to balance global mycotoxin standards with the realistic feasibility of reaching them, considering limitations of producers and designing strategies to reduce mycotoxin exposure based on sound research.","corpus_id":22508699,"score":1},{"doc_id":"24987806","title":"A Review of Mycotoxins in Food and Feed Products in Portugal and Estimation of Probable Daily Intakes.","abstract":"Mycotoxins are toxic secondary metabolites produced by filamentous fungi that occur naturally in agricultural commodities worldwide. Aflatoxins, ochratoxin A, patulin, fumonisins, zearalenone, trichothecenes, and ergot alkaloids are presently the most important for food and feed safety. These compounds are produced by several species that belong to the Aspergillus, Penicillium, Fusarium, and Claviceps genera and can be carcinogenic, mutagenic, teratogenic, cytotoxic, neurotoxic, nephrotoxic, estrogenic, and immunosuppressant. Human and animal exposure to mycotoxins is generally assessed by taking into account data on the occurrence of mycotoxins in food and feed as well as data on the consumption patterns of the concerned population. This evaluation is crucial to support measures to reduce consumer exposure to mycotoxins. This work reviews the occurrence and levels of mycotoxins in Portuguese food and feed to provide a global overview of this issue in Portugal. With the information collected, the exposure of the Portuguese population to those mycotoxins is assessed, and the estimated dietary intakes are presented.","corpus_id":39180109,"score":1},{"doc_id":"25126610","title":"Mycotoxins and mycotoxigenic fungi in poultry feed for food-producing animals.","abstract":"Moulds are capable of reducing the nutritional value of feedstuff as well as elaborating several mycotoxins. Mycotoxin-contaminated feed has adverse effects on animal health and productivity. Also, mycotoxins may be carried over into meat and eggs when poultry are fed with contaminated feed. In a point prevalence study feedstuff used for poultry nutrition in Argentina was analyzed for fungal flora, natural incidence of selected mycotoxins, and nutritional quality. Ten mould genera were recovered, six of them known to be mycotoxigenic. More than 28 species were determined. Fumonisins were detected in all the samples (median 1,750 ppb). Forty-four out of 49 samples (90%) were contaminated with DON (median 222 ppb) and OTA (median 5 ppb). Also, 44 out of 49 samples were contaminated with aflatoxins (median 2.685 ppb), 42 samples (86%) with ZEA (median 50 ppb), and 38 samples (78%) with T2-toxin (median 50 ppb). Ninety percent of the samples had at least one type of nutritional deficiency. This study indicates the need for continuous assessment of the mycological status of animal feed production, in order to feed animals for optimal performance ensuring food safety.","corpus_id":18439326,"score":1},{"doc_id":"25898143","title":"Keeping Mycotoxins Away from the Food: Does the Existence of Regulations Have any Impact in Africa?","abstract":"Following the discovery of aflatoxins in the early 1960s, there have been many studies leading to the uncovering of many mycotoxins and the understanding of associated health effects in animals and humans. Consequently, there has been a global increase in the number of countries with mycotoxin regulations in foods. However, many African countries have only regulations for aflatoxins (or a few other mycotoxins) in specific foods or no regulations at all. This article critically reviews the challenges thwarting the establishment of mycotoxin regulations and their impacts on human dietary mycotoxin exposure in Africa. Mycotoxin regulatory limits for different countries are compared with mycotoxin tolerable daily intakes established by international food safety bodies taking into account consumption patterns. The agrarian setup, food insecurity and mycotoxin analytical challenges in African countries are discussed; and more feasible mycotoxin dietary exposure reduction strategies proposed.","corpus_id":205692168,"score":1},{"doc_id":"26001087","title":"Emerging nanotechnology for detection of mycotoxins in food and feed.","abstract":"The term mycotoxin was coined for toxic metabolites secreted by some fungi in food, food products and feed. The most prominent mycotoxins include aflatoxins (AFs), deoxynivalenol, zearalenone, ochratoxin, fumonisin and patulin. Among these some are proved to be strong carcinogenic agents such as AFs B1 while others are under suspicion to have carcinogenic effects. Ingestion of such mycotoxin-contaminated food and feed pose to a threat, mycotoxicoses. Various conventional techniques are available for the detection of mycotoxins, but unfortunately as a consequence of their constraint, the development of new and rapid techniques is the need of the hour. The use of nanotechnology for the development of nanobiosensors would be the alternative sensitive methods for the rapid detection of mycotoxins. Implementation of nanomaterials in the fabrication of nanobiosensors and their use for the detection of the mycotoxins in food and feed is the centre of interest of this review. We have inventoried nanomaterials applied for weaving nanobiosensors, which includes carbon nanotubes, nanowires, nanoparticles, quantum dots, nanorods and nanofibers. In addition, we have extensively reviewed available nanobiosensors specific for different mycotoxins, their advantages and challenges.","corpus_id":21214332,"score":1},{"doc_id":"26449927","title":"Determination of the Mycotoxin Content in Distiller's Dried Grain with Solubles Using a Multianalyte UHPLC-MS/MS Method.","abstract":"There are more than 300 potential mycotoxins that can contaminate food and feed and cause adverse effects in humans and animals. The data on the co-occurrence of mycotoxins in novel animal feed materials, such as distiller's dried grain with solubles (DDGS), are limited. Thus, a UHPLC-MS/MS method for the quantitation of 77 mycotoxins and other fungal metabolites was used to analyze 169 DDGS samples produced from wheat, maize, and barley and 61 grain samples. All DDGS samples analyzed were contaminated with 13-34 different mycotoxins. Fumonisins were present in all 52 maize DDGS samples (81.0-6890 μg/kg for fumonisin B1), and deoxynivalenol was present in all 99 wheat DDGS samples (39.3-1120 μg/kg). A number of co-occurring mycotoxins were also identified. Due to the high co-occurrence of mycotoxins, routine screening of the animal feed ingredients is highly recommended to allow the highlighted risks to be effectively managed.","corpus_id":22575964,"score":1},{"doc_id":"26529017","title":"Effects of Mycotoxins on Mucosal Microbial Infection and Related Pathogenesis.","abstract":"Mycotoxins are fungal secondary metabolites detected in many agricultural commodities and water-damaged indoor environments. Susceptibility to mucosal infectious diseases is closely associated with immune dysfunction caused by mycotoxin exposure in humans and other animals. Many mycotoxins suppress immune function by decreasing the proliferation of activated lymphocytes, impairing phagocytic function of macrophages, and suppressing cytokine production, but some induce hypersensitive responses in different dose regimes. The present review describes various mycotoxin responses to infectious pathogens that trigger mucosa-associated diseases in the gastrointestinal and respiratory tracts of humans and other animals. In particular, it focuses on the effects of mycotoxin exposure on invasion, pathogen clearance, the production of cytokines and immunoglobulins, and the prognostic implications of interactions between infectious pathogens and mycotoxin exposure.","corpus_id":2751434,"score":1},{"doc_id":"26725999","title":"Overall internal exposure to mycotoxins and their occurrence in occupational and residential settings - An overview.","abstract":"Mycotoxins are toxic secondary metabolites of various fungal species that can contaminate food and feed, as well as indoor environments. Numerous studies have summarized the adverse health effects of mycotoxins and described severe intoxications of humans and animals. The major health concerns are caused via the alimentary route which unambiguously is the main source for human internal exposure; however, the relevance of other pathways under environmental and occupational conditions should also be considered. Thus firstly, this review aims in summarizing literature data on potentially inhalable mycotoxins occurring in dusts or air in residences and in working environments. Secondly, it gives an overview of the overall internal body burden of mycotoxins in humans in an attempt to characterize total human exposure. These data are also discussed in relation to the current toxicologically based values used for risk assessment.","corpus_id":24068429,"score":1},{"doc_id":"26891326","title":"Mycotoxin Contamination in the EU Feed Supply Chain: A Focus on Cereal Byproducts.","abstract":"Mycotoxins represent a risk to the feed supply chain with an impact on economies and international trade. A high percentage of feed samples have been reported to be contaminated with more than one mycotoxin. In most cases, the concentrations were low enough to ensure compliance with the European Union (EU) guidance values or maximum admitted levels. However, mycotoxin co-contamination might still exert adverse effects on animals due to additive/synergistic interactions. Studies on the fate of mycotoxins during cereal processing, such as milling, production of ethanol fuels, and beer brewing, have shown that mycotoxins are concentrated into fractions that are commonly used as animal feed. Published data show a high variability in mycotoxin repartitioning, mainly due to the type of mycotoxins, the level and extent of fungal contamination, and a failure to understand the complexity of food processing technologies. Precise knowledge of mycotoxin repartitioning during technological processes is critical and may provide a sound technical basis for feed managers to conform to legislation requirements and reduce the risk of severe adverse market and trade repercussions. Regular, economical and straightforward feed testing is critical to reach a quick and accurate diagnosis of feed quality. The use of rapid methods represents a future challenge.","corpus_id":5093889,"score":1},{"doc_id":"27417439","title":"The intestinal barrier as an emerging target in the toxicological assessment of mycotoxins.","abstract":"Mycotoxins, the secondary metabolites of fungal species, are the most frequently occurring natural food contaminants in human and animal diets. Risk assessment of mycotoxins focused as yet on their mutagenic, genotoxic and potential carcinogenic effects. Recently, there is an increasing awareness of the adverse effects of various mycotoxins on vulnerable structures in the intestines. In particular, an impairment of the barrier function of the epithelial lining cells and the sealing tight junction proteins has been noted, as this could result in an increased translocation of luminal antigens and pathogens and an excessive activation of the immune system. The current review aims to provide a summary of the available evidence regarding direct effects of various mycotoxins on the intestinal epithelial barrier. Available data, based on different cellular and animal studies, show that food-associated exposure to certain mycotoxins, especially trichothecenes and patulin, affects the intestinal barrier integrity and can result in an increased translocation of harmful stressors. It is therefore hypothesized that human exposure to certain mycotoxins, particularly deoxynivalenol, as the major trichothecene, may play an important role in etiology of various chronic intestinal inflammatory diseases, such as inflammatory bowel disease, and in the prevalence of food allergies, particularly in children.","corpus_id":11253120,"score":1},{"doc_id":"27886128","title":"Worldwide Mycotoxins Exposure in Pig and Poultry Feed Formulations.","abstract":"The purpose of this review is to present information about raw materials that can be used in pig and poultry diets and the factors responsible for variations in their mycotoxin contents. The levels of mycotoxins in pig and poultry feeds are calculated based on mycotoxin contamination levels of the raw materials with different diet formulations, to highlight the important role the stage of production and the raw materials used can have on mycotoxins levels in diets. Our analysis focuses on mycotoxins for which maximum tolerated levels or regulatory guidelines exist, and for which sufficient contamination data are available. Raw materials used in feed formulation vary considerably depending on the species of animal, and the stage of production. Mycotoxins are secondary fungal metabolites whose frequency and levels also vary considerably depending on the raw materials used and on the geographic location where they were produced. Although several reviews of existing data and of the literature on worldwide mycotoxin contamination of food and feed are available, the impact of the different raw materials used on feed formulation has not been widely studied.","corpus_id":14369542,"score":1},{"doc_id":"27924528","title":"Mycotoxins: An Underhand Food Problem.","abstract":"Among the food safety issues, the occurrence of fungal species able to produce toxic metabolites on the agro-food products has acquired a general attention. These compounds, the mycotoxins, generally provided of low molecular weight, are the result of the secondary metabolism of the toxigenic fungi. They may have toxic activity toward the plants, but mostly represent a serious risk for human and animal health worldwide, since they can be accumulated on many final crop products and they have a broad range of toxic biological activities. In particular, mainly cereals are the most sensitive crops to the colonization of toxigenic fungal species which accumulate in the grains the related mycotoxins both in the field, until the harvest stage, and in the storage. According to a Food and Agriculture Organization study, approximately 25 % of the global food and feed output is contaminated by mycotoxins. Therefore, since a large proportion of the world's population consumes, as a staple food, the cereals, the consumption of mycotoxin-contaminated cereals is a main issue for health risk worldwide. Furthermore, mycotoxin contamination can have a huge economic and social impact, especially when mycotoxin occurrence on the food commodities is over the regulation limits established by different national and transnational institutions, implying that contaminated products must be discarded. Finally, the climate change due to the global warming can alter stages and rates of toxigenic fungi development and modify host-resistance and host-pathogen interactions, influencing deeply also the conditions for mycotoxin production that vary for each individual pathogen. New combinations of mycotoxins/host plants/geographical areas are arising to the attention of the scientific community and require new diagnostic tools and deeper knowledge of both biology and genetics of toxigenic fungi. Moreover, to spread awareness and knowledge at international level on both the hazard that mycotoxins represent for consumers and costs for stakeholders is of key importance for developing all possible measures aimed to control such dangerous contaminants worldwide.","corpus_id":8001329,"score":1},{"doc_id":"27929415","title":"Co-Occurrence of Regulated, Masked and Emerging Mycotoxins and Secondary Metabolites in Finished Feed and Maize-An Extensive Survey.","abstract":"Global trade of agricultural commodities (e.g., animal feed) requires monitoring for fungal toxins. Also, little is known about masked and emerging toxins and metabolites. 1926 samples from 52 countries were analysed for toxins and metabolites. Of 162 compounds detected, up to 68 metabolites were found in a single sample. A subset of 1113 finished feed, maize and maize silage samples containing 57 compounds from 2012 to 2015 from 44 countries was investigated using liquid chromatography and mass spectrometry. Deoxynivalenol (DON), zearalenone (ZEN) and fumonisins showed large increases of annual medians in Europe. Within a region, distinct trends were observed, suggesting importance of local meteorology and cultivars. In 2015, median DON concentrations increased to 1400 μ g·kg - 1 in Austria, but were stable in Germany at 350 μ g·kg - 1 . In 2014, enniatins occurred at median concentrations of 250 μ g·kg - 1 in Europe, at levels similar to DON and ZEN. The latter were frequently correlated with DON-3-glucoside and ZEN-14-sulfate. Co-occurrence of regulated toxins was frequent with e.g., enniatins, and moniliformin. Correlation was observed between DON and DON-3-glucoside and with beauvericin. Results indicate that considerably more than 25% of agricultural commodities could be contaminated with mycotoxins as suggested by FAO, although this is at least partly due to the lower limits of detection in the current survey. Observed contamination percentages ranged from 7.1 to 79% for B trichothecenes and 88% for ZEN.","corpus_id":790135,"score":1},{"doc_id":"28067768","title":"The Status of Fusarium Mycotoxins in Sub-Saharan Africa: A Review of Emerging Trends and Post-Harvest Mitigation Strategies towards Food Control.","abstract":"Fusarium fungi are common plant pathogens causing several plant diseases. The presence of these molds in plants exposes crops to toxic secondary metabolites called Fusarium mycotoxins. The most studied Fusarium mycotoxins include fumonisins, zearalenone, and trichothecenes. Studies have highlighted the economic impact of mycotoxins produced by Fusarium. These arrays of toxins have been implicated as the causal agents of wide varieties of toxic health effects in humans and animals ranging from acute to chronic. Global surveillance of Fusarium mycotoxins has recorded significant progress in its control; however, little attention has been paid to Fusarium mycotoxins in sub-Saharan Africa, thus translating to limited occurrence data. In addition, legislative regulation is virtually non-existent. The emergence of modified Fusarium mycotoxins, which may contribute to additional toxic effects, worsens an already precarious situation. This review highlights the status of Fusarium mycotoxins in sub-Saharan Africa, the possible food processing mitigation strategies, as well as future perspectives.","corpus_id":17214000,"score":1},{"doc_id":"28125272","title":"Mechanisms of cell death induction by food-borne mycotoxins.","abstract":"Mycotoxins are secondary metabolites of fungi that contaminate a wide range of foods and feeds. Mycotoxin contamination is considered to be an important risk factor for food safety which poses serious threat to human and animal health. Cell death induction is suggested to be the key cellular event contributed to the pleiotropically toxic effects of mycotoxins. During the past decades, substantial progress has been made in uncovering the mechanisms of cell death induction by mycotoxins. Understanding of the mechanisms underlying mycotoxin-induced cytotoxicity will benefit the development of effective strategies for the management of mycotoxin-associated health issues. The current review will discuss the types of cell death induced by mycotoxins and summarize the present understanding of signaling pathways involved in mycotoxin-mediated cytotoxicities.","corpus_id":13767530,"score":1},{"doc_id":"28244108","title":"Occurrence of multiple mycotoxins and other fungal metabolites in animal feed and maize samples from Egypt using LC-MS/MS.","abstract":"BACKGROUND: The present study aimed to investigate the occurrence of multiple toxic fungal and bacterial metabolites in 156 animal feed (n = 77) and maize (n = 79) samples collected from three regions in Upper Egypt. The target analytes were quantified using the 'dilute and shoot' approach, followed by a liquid chromatography tandem mass spectrometry analysis. RESULTS: In total, 115 fungal and bacterial metabolites were detected in both matrices, including the regulated mycotoxins in the European Union, in addition to the modified forms such as deoxynivalenol-3-glucosid. Furthermore, some Fusarium, Alternaria, Aspergillus and Penicillum metabolites beside other fungal and bacterial metabolites were detected for the first time in Egypt. All of the samples were contaminated with at least four toxins. On average, 26 different metabolites were detected per sample with a trend of more metabolites in feed than in maize. The maximum number of analytes observed per samples was 54 analytes at maximum concentrations ranging from 0.04 µg kg(-1) for tentoxin to 25 040 µg kg(-1) for kojic acid. CONCLUSION: According to the international standards, the contamination rates in the investigated regions were not alarming, except for AFB1 in maize. The necessity of further and continuous monitoring is highly recommended to establish a database for mycotoxin occurrence. © 2017 Society of Chemical Industry.","corpus_id":34085555,"score":1},{"doc_id":"28608841","title":"Occurrence, Toxicity, and Analysis of Major Mycotoxins in Food.","abstract":"Mycotoxins are toxic secondary metabolites produced by certain filamentous fungi (molds). These low molecular weight compounds (usually less than 1000 Daltons) are naturally occurring and practically unavoidable. They can enter our food chain either directly from plant-based food components contaminated with mycotoxins or by indirect contamination from the growth of toxigenic fungi on food. Mycotoxins can accumulate in maturing corn, cereals, soybeans, sorghum, peanuts, and other food and feed crops in the field and in grain during transportation. Consumption of mycotoxin-contaminated food or feed can cause acute or chronic toxicity in human and animals. In addition to concerns over adverse effects from direct consumption of mycotoxin-contaminated foods and feeds, there is also public health concern over the potential ingestion of animal-derived food products, such as meat, milk, or eggs, containing residues or metabolites of mycotoxins. Members of three fungal genera, Aspergillus, Fusarium, and Penicillium, are the major mycotoxin producers. While over 300 mycotoxins have been identified, six (aflatoxins, trichothecenes, zearalenone, fumonisins, ochratoxins, and patulin) are regularly found in food, posing unpredictable and ongoing food safety problems worldwide. This review summarizes the toxicity of the six mycotoxins, foods commonly contaminated by one or more of them, and the current methods for detection and analysis of these mycotoxins.","corpus_id":5398472,"score":1},{"doc_id":"29243648","title":"Recent developments and applications of surface plasmon resonance biosensors for the detection of mycotoxins in foodstuffs.","abstract":"Over the past 10years, great efforts on the development of methods for rapid mycotoxin detection in foodstuffs have been made. As one of the relatively new analytical techniques, surface plasmon resonance (SPR) has been proven particularly advantageous for rapid, label-free, sensitive analyte detection. Using SPR, qualitative and quantitative analysis can be performed in real-time. Mycotoxins are a group of small, toxic products formed as secondary metabolites by a few fungal species. They can contaminate foodstuffs on a large scale and consequently threaten human health through food chain. Thus, rapid, sensitive, and selective determination of mycotoxin is of great significance for the food safety. This contribution addresses the basic principle of SPR, the existing detection methods, and the progress on mycotoxin detection using SPR biosensor.","corpus_id":29689230,"score":1},{"doc_id":"29384153","title":"Advances, challenges and opportunities for point-of-need screening of mycotoxins in foods and feeds.","abstract":"The assurance of food and feed safety, including the identification and effective monitoring of multiple biological and chemical hazards, is a major societal challenge, given the increasing pace at which food commodities are demanded, produced and traded across the globe. Within this context, mycotoxins are globally widespread secondary fungal metabolites, which can contaminate crops either in the field or during storage and have serious human and animal health impacts such as carcinogenic, teratogenic and hepatotoxic effects. Therefore, their presence in a wide range of foods and feeds is strictly regulated, particularly in the European Union. In order to perform effective and routine monitoring of mycotoxin levels in the field prior to further processing, during transport or during processing, rapid, simple, portable and sensitive means of screening of regulated mycotoxins are in high demand. This review focuses on (1) discussing the relevance of mycotoxins and the standard approaches for their sampling and monitoring; and (2) compiling and discussing recent advances in miniaturized analytical tools for mycotoxin detection. This provides insights into current research efforts and opportunities to develop a truly integrated and fit-for-purpose analytical tool, suitable for use at critical points of the food, feed and raw material processing and distribution chains.","corpus_id":3542968,"score":1},{"doc_id":"29685276","title":"Silage review: Mycotoxins in silage: Occurrence, effects, prevention, and mitigation.","abstract":"Ensiled forage, particularly corn silage, is an important component of dairy cow diets worldwide. Forages can be contaminated with several mycotoxins in the field pre-harvest, during storage, or after ensiling during feed-out. Exposure to dietary mycotoxins adversely affects the performance and health of livestock and can compromise human health. Several studies and surveys indicate that ruminants are often exposed to mycotoxins such as aflatoxins, trichothecenes, ochratoxin A, fumonisins, zearalenone, and many other fungal secondary metabolites, via the silage they ingest. Problems associated with mycotoxins in silage can be minimized by preventing fungal growth before and after ensiling. Proper silage management is essential to reduce mycotoxin contamination of dairy cow feeds, and certain mold-inhibiting chemical additives or microbial inoculants can also reduce the contamination levels. Several sequestering agents also can be added to diets to reduce mycotoxin levels, but their efficacy varies with the type and level of mycotoxin contamination. This article gives an overview of the types, prevalence, and levels of mycotoxin contamination in ensiled forages in different countries, and describes their adverse effects on health of ruminants, and effective prevention and mitigation strategies for dairy cow diets. Future research priorities discussed include research efforts to develop silage additives or rumen microbial innocula that degrade mycotoxins.","corpus_id":13811861,"score":1},{"doc_id":"29766989","title":"Mycotoxins and the intestine.","abstract":"Fungal biochemical pathways can yield various compounds that are not considered to be necessary for their growth and are thus referred to as secondary metabolites. These compounds have been found to have wide ranging biological effects and include potent poisons (mycotoxins). Mycotoxins invariably contaminate crops and (thus) animal feeds. The intestine is the key link between ingested mycotoxins and their detrimental effects on the animal. Effects on the intestine, or intestinal environment, and immune system have been reported with various mycotoxins. These effects are almost certainly occurring across species. Most, if not all, of the reported effects of mycotoxins are negative in terms of intestinal health, for example, decreased intestinal cell viability, reductions in short chain fatty acid (SCFA) concentrations and elimination of beneficial bacteria, increased expression of genes involved in promoting inflammation and counteracting oxidative stress. This challenge to intestinal health will predispose the animal to intestinal (and systemic) infections and impair efficient digestion and absorption of nutrients, with the associated effect on animal productivity.","corpus_id":21706057,"score":1}],"string":"[\n {\n \"doc_id\": \"19238622\",\n \"title\": \"Reduction of feed-contaminating mycotoxins by ultraviolet irradiation: an in vitro study.\",\n \"abstract\": \"Ultraviolet (UV) germicidal irradiation has been applied to the sterilization of agricultural products including stored grain for foodstuffs or animal feed. Although UV treatment is known to be effective for killing pathogenic moulds that contaminate the surface of grain, it remains unclear how and to what extent such irradiation is able to eliminate mycotoxins, the fungal metabolites that have adverse effects on human and animal health. We evaluated in vitro the effects of mild (intensity = 0.1 mW cm(-2) at 254 nm UV-C) and strong (24 mW cm(-2)) UV irradiation on two feed-contaminating mycotoxins, zearalenone (ZEN) and deoxynivalenol (DON). When exposed to mild irradiation, the levels of ZEN and DON (both 30 mg kg(-1) initially) were reduced as irradiation time increased, and became undetectable at 60 min. Strong UV irradiation also reduced the mycotoxin levels in the same time-dependent manner, but more rapidly. It was therefore confirmed in vitro that UV irradiation is effective at reducing the levels of ZEN and DON. The present study provides preliminary data for establishing a practical method of using UV irradiation to reduce mycotoxin contamination in grain intended for use in feed.\",\n \"corpus_id\": 40957854,\n \"score\": 2\n },\n {\n \"doc_id\": \"19645364\",\n \"title\": \"The biotransformation of chosen mycotoxins.\",\n \"abstract\": \"Despite the unfavourable influence of mycotoxins on human and animal health and few toxicological aspects that have been documented, about these biologically active substances has not been explored. Aiming at more knowledge and a better understanding of the effects and mechanism of mycotoxin action in mammals would provide the basics for developing strategies to restrain different mycotoxicoses. One of the processes not fully understood is biotransformation, to which mycotoxins are subjected the animal organism. Biotransformation is the conversion of mycotoxins to non-toxic metabolites and occurs mostly in the intestinal mucosal membrane and liver, although other tissues and systems also take part in this process. Mycotoxin biotransformation reactions can be considered bioinactivation or detoxication, but mycotoxin biotransformation processes could also result in products more toxic than the mycotoxin. It can be concluded from research studies that our knowledge of mycotoxin biotransformation is scarce.\",\n \"corpus_id\": 24047148,\n \"score\": 2\n },\n {\n \"doc_id\": \"19777908\",\n \"title\": \"Biological strategies to counteract the effects of mycotoxins.\",\n \"abstract\": \"Mycotoxins are fungal secondary metabolites that if ingested can cause a variety of adverse effects on both humans and animals, ranging from allergic responses to death. Therefore, exposure to mycotoxins should be minimized. A variety of physical, chemical, and biological methods have been developed for decontamination and/or detoxification of mycotoxins from contaminated foods and feeds. This overview details the latest developments in the biological control of both fungal infection and mycotoxin formation and describes the detoxification of many of the most important mycotoxins by microorganisms. This review also addresses the potential for use of microorganisms as mycotoxin binders in the gastrointestinal tract of both humans and animals, thereby reducing the potential deleterious effects of exposure to these toxins.\",\n \"corpus_id\": 20234933,\n \"score\": 2\n },\n {\n \"doc_id\": \"20234966\",\n \"title\": \"Decontamination and detoxification strategies for the Fusarium mycotoxin deoxynivalenol in animal feed and the effectiveness of microbial biodegradation.\",\n \"abstract\": \"Trichothecenes are a group of mycotoxins mainly produced by fungi of the Fusarium genus. Deoxynivalenol (DON) is one of the most abundant and important trichothecenes in food and feed, and is a significant contaminants due to its frequent occurrence in toxicologically relevant concentrations worldwide. Since toxin production depends strongly on environmental conditions, such as temperature and humidity, Fusarium toxin contamination can not be avoided completely. Therefore, exposure to this toxin is a permanent health risk for both humans and farm animals. As cereal crops are commonly contaminated with DON and animal diets consist mainly of cereals, it can be assumed that animals are frequently exposed to DON-contaminated feeds. Many strategies can be undertaken to reduce the toxic effect of DON. In addition to the general necessity for minimizing all risk factors that might influence the contamination of cereals with DON, such as the so-called field toxins before harvest, several post-harvest strategies can be applied to counteract possible deleterious effects of this mycotoxin in farm animals. Another approach for decontamination in feedstuffs is the use of adsorbent materials. Adsorbent materials may bind mycotoxins in the gastrointestinal tract and reduce absorption and systemic toxicity. It has been shown that some adsorbents are suitable to alleviate the toxic effects of specific mycotoxins, but its efficacy against trichothecenes is practically zero. Therefore, alternative strategies to reduce animal and human health risk are needed. The use of microbial additives is a method which uses microorganisms having the capability to detoxify mycotoxins by metabolism or degradation prior to their resorption in the gastrointestinal tract. DON has been reported to be completely transformed to de-epoxy-DON by ruminal and intestinal microflora. Eubacterium BBSH 797 was capable of DON degradation and counteracted the toxic effects of DON in animals. This review focuses on the efficacy of microbial feed additives in ameliorating the toxic effects of DON. According to the results of experiments to date, it appears that microorganisms are the main living organisms suitable for this mycotoxin biodegradation. However, the use of this approach depends on its effectiveness from both a practical and economic perspective.\",\n \"corpus_id\": 44640939,\n \"score\": 2\n },\n {\n \"doc_id\": \"20653554\",\n \"title\": \"Patented techniques for detoxification of mycotoxins in feeds and food matrices.\",\n \"abstract\": \"Mycotoxins are found worldwide in cereal grains, animal feed and human food that are produced from contaminated grains. This presents food safety risks. A variety of methods has been developed to reduce the safety risks by removing mycotoxins from contaminated grain products, eliminate the bioavailability of mycotoxins in the gastrointestinal system, degrade mycotoxins in food and feed, reduce mycotoxins pre- and post-harvest, and prevent (mycotoxin involved) plant disease. These techniques include physical methods such as flotation, extraction and adsorption, chemical reactions such as alkalization, oxidation, heat and irradiation, as well as biological detoxifications using microorganisms, enzymes and resistant plants. Most of the recent patented techniques for detoxification of mycotoxins in feeds and food matrices are discussed for an improved understanding of the patent techniques and insights into detoxification of mycotoxins.\",\n \"corpus_id\": 42997046,\n \"score\": 2\n },\n {\n \"doc_id\": \"21770849\",\n \"title\": \"Review of mycotoxin reduction in food and feed: from prevention in the field to detoxification by adsorption or transformation.\",\n \"abstract\": \"Mycotoxins are secondary metabolites present worldwide in agricultural commodities and produced by filamentous fungi that cause a toxic response (mycotoxicosis) when ingested by animals. Prevention of mycotoxicoses includes pre- and post-harvest strategies. The best way to reduce the mycotoxin content in food and feed is the prevention of mycotoxin formation in the field, but this is often not sufficient, so other methods are needed. To decontaminate and/or detoxify mycotoxin-contaminated food and feed, the most prevalent approach in the feed industry is the inclusion of sorbent materials in the feed thus obtaining more or less selective removal of toxins by adsorption during passage through the gastrointestinal tract. Another reliable approach is to add enzymes or microorganisms capable of detoxifying some mycotoxins. Through a comprehensive review of published reports on the strategies for mycotoxin removal, this present work aims to update our understanding of mycotoxin removal. It provides an insight into the detoxification of mycotoxin present in food and feed. In the future, more emphasis needs to be placed on adsorption of mycotoxins in the gastrointestinal tract. Concerning the enzymatic transformation of mycotoxins, further efforts are required in understanding detoxification reactions, the toxicity of transformation products and in the characterization of enzymes responsible for transformations.\",\n \"corpus_id\": 24542714,\n \"score\": 2\n },\n {\n \"doc_id\": \"23816820\",\n \"title\": \"Application of plant derived compounds to control fungal spoilage and mycotoxin production in foods.\",\n \"abstract\": \"Food decay by spoilage fungi causes considerable economic losses and constitutes a health risk for consumers due to the potential for fungi to produce mycotoxins. The indiscriminate use of synthetic antifungals has led to the development of resistant strains which has necessitated utilization of higher concentrations, with the consequent increase in toxic residues in food products. Numerous studies have demonstrated that plant extracts contain diverse bioactive components that can control mould growth. The metabolites produced by plants are a promising alternative because plants generate a wide variety of compounds, either as part of their development or in response to stress or pathogen attack. The aim of this article is to summarize the results from the literature on in vitro and in vivo experiments regarding the effects of plant-derived products for controlling fungal growth. Data from research work on the mode of action of these metabolites inside the fungal cell and the influence of abiotic external factors such as pH and temperature are also covered in the present review. Furthermore, an analysis on how the stress factor derived from the presence of plant extracts and essential oils affects secondary metabolism of the fungus, specifically mycotoxin synthesis, is developed. Finally, the effectiveness of using plant-derived compounds in combination with other natural antimicrobials and its application in food using novel technologies is discussed.\",\n \"corpus_id\": 25246791,\n \"score\": 2\n },\n {\n \"doc_id\": \"23846184\",\n \"title\": \"Microbial detoxification of mycotoxins.\",\n \"abstract\": \"Mycotoxins are fungal natural products that are toxic to vertebrate animals including humans. Microbes have been identified that enzymatically convert aflatoxin, zearalenone, ochratoxin, patulin, fumonisin, deoxynivalenol, and T-2 toxin to less toxic products. Mycotoxin-degrading fungi and bacteria have been isolated from agricultural soil, infested plant material, and animal digestive tracts. Biotransformation reactions include acetylation, glucosylation, ring cleavage, hydrolysis, deamination, and decarboxylation. Microbial mycotoxin degrading enzymes can be used as feed additives or to decontaminate agricultural commodities. Some detoxification genes have been expressed in plants to limit the pre-harvest mycotoxin production and to protect crop plants from the phytotoxic effects of mycotoxins. Toxin-deficient mutants may be useful in assessing the role of mycotoxins in the ecology of the microorganisms.\",\n \"corpus_id\": 16490444,\n \"score\": 2\n },\n {\n \"doc_id\": \"23891865\",\n \"title\": \"Mycotoxin-degradation profile of Rhodococcus strains.\",\n \"abstract\": \"Mycotoxins are secondary fungal metabolites that may have mutagenic, carcinogenic, cytotoxic and endocrine disrupting effects. These substances frequently contaminate agricultural commodities despite efforts to prevent them, so successful detoxification tools are needed. The application of microorganisms to biodegrade mycotoxins is a novel strategy that shows potential for application in food and feed processing. In this study we investigated the mycotoxin degradation ability of thirty-two Rhodococcus strains on economically important mycotoxins: aflatoxin B1, zearalenone, fumonisin B1, T2 toxin and ochratoxin A, and monitored the safety of aflatoxin B1 and zearalenone degradation processes and degradation products using previously developed toxicity profiling methods. Moreover, experiments were performed to analyse multi-mycotoxin-degrading ability of the best toxin degrader/detoxifier strains on aflatoxin B1, zearalenone and T2 toxin mixtures. This enabled the safest and the most effective Rhodococcus strains to be selected, even for multi-mycotoxin degradation. We concluded that several Rhodococcus species are effective in the degradation of aromatic mycotoxins and their application in mycotoxin biodetoxification processes is a promising field of biotechnology.\",\n \"corpus_id\": 36233509,\n \"score\": 2\n },\n {\n \"doc_id\": \"23971211\",\n \"title\": \"Toxin-producing fungi on feed grains and application of yeasts for their detoxification.\",\n \"abstract\": \"The research deals with the contamination of feeding crops with fungi, producing mycotoxins and use of selected yeasts for detoxification. The thin-layer chromatography and ELISA methods were applied for the analysis of fungal secondary metabolites. The results showed a high rate of the grain contamination with fungi, mainly from genera Penicillium, Fusarium, Aspergillus and Alternaria. Some of the fungal strains produced 6-9 toxic compounds. The novelty of the study was the application of the yeast strains in detoxification of aflatoxins, zearalenon and deoxynivalenol in feed.\",\n \"corpus_id\": 387972,\n \"score\": 2\n },\n {\n \"doc_id\": \"25255390\",\n \"title\": \"Mycotoxin contamination of animal feedingstuff: detoxification by gamma-irradiation and reduction of aflatoxins and ochratoxin A concentrations.\",\n \"abstract\": \"Mycotoxins are fungal secondary metabolites identified in many agricultural products screened for toxigenic moulds. They have been reported to be carcinogenic, teratogenic, tremorogenic, haemorrhagic and dermatitic to a wide range of organisms. With the increasing stringent regulations for mycotoxins imposed by importing countries such as those of the European Union, many cereals that are not safe for human consumption are used in formulations intended for animal feed. Gamma-rays are reported in the scientific literature to destroy ochratoxin A and aflatoxin in food crops and feed. The present study provides preliminary data for establishing the effect of dose of gamma-irradiation, ranging from 0 to 15 kGy, on aflatoxins and ochratoxin A reduction in commercial animal feed. The mycotoxin levels were determined by means of immunoaffinity clean-up (IAC) and HPLC with fluorescence detection (HPLC-FLD). The maximum reductions found at 15 kGy were 23.9%, 18.2%, 11.0%, 21.1% and 13.6% for ochratoxin A, aflatoxin B₁, aflatoxin B₂, aflatoxin G₁ and aflatoxin G₂, respectively. Results showed that the gamma-rays even at 15 kGy were not effective in the complete destruction of ochratoxin A and aflatoxins in the tested feed.\",\n \"corpus_id\": 11407201,\n \"score\": 2\n },\n {\n \"doc_id\": \"25840963\",\n \"title\": \"Prevalence and effects of mycotoxins on poultry health and performance, and recent development in mycotoxin counteracting strategies.\",\n \"abstract\": \"Extensive research over the last couple of decades has made it obvious that mycotoxins are commonly prevalent in majority of feed ingredients. A worldwide mycotoxin survey in 2013 revealed 81% of around 3,000 grain and feed samples analyzed had at least 1 mycotoxin, which was higher than the 10-year average (from 2004 to 2013) of 76% in a total of 25,944 samples. The considerable increase in the number of positive samples in 2013 may be due to the improvements in detection methods and their sensitivity. The recently developed liquid chromatography coupled to (tandem) mass spectrometry allows the inclusion of a high number of analytes and is the most selective, sensitive, and accurate of all the mycotoxin analytical methods. Mycotoxins can affect the animals either individually or additively in the presence of more than 1 mycotoxin, and may affect various organs such as gastrointestinal tract, liver, and immune system, essentially resulting in reduced productivity of the birds and mortality in extreme cases. While the use of mycotoxin binding agents has been a commonly used counteracting strategy, considering the great diversity in the chemical structures of mycotoxins, it is very obvious that there is no single method that can be used to deactivate mycotoxins in feed. Therefore, different strategies have to be combined in order to specifically target individual mycotoxins without impacting the quality of feed. Enzymatic or microbial detoxification, referred to as \\\"biotransformation\\\" or \\\"biodetoxification,\\\" utilizes microorganisms or purified enzymes thereof to catabolize the entire mycotoxin or transform or cleave it to less or non-toxic compounds. However, the awareness on the prevalence of mycotoxins, available modern techniques to analyze them, the effects of mycotoxicoses, and the recent developments in the ways to safely eliminate the mycotoxins from the feed are very minimal among the producers. This symposium review paper comprehensively discusses the above mentioned aspects.\",\n \"corpus_id\": 13958963,\n \"score\": 2\n },\n {\n \"doc_id\": \"26648039\",\n \"title\": \"Occurrence, detection and detoxification of mycotoxins.\",\n \"abstract\": \"Mycotoxins have been identified as important toxins affecting animal species and humans ever since the discovery of aflatoxin B1 in 1960. Mycotoxigenic fungi are ubiquitous in nature and are held responsible for economic loss as they decrease crop yield and quality of food. The presence of fungi and their mycotoxins are reported not only in food grains but also in medicinal herbs and processed foods. Since prevention is not always possible, detoxification of mycotoxins have been attempted using several means; however, only few have been accepted for practical use, e.g. ammonia in the corn industry. Organizations such as the World Health Organization, US Food and Drug Administration and European Union have set regulations and safety limits of important mycotoxins, viz. aflatoxins, fusarium toxins, ochratoxin, patulin zearalenone, etc., to ensure the safety of the consumers. This review article is a brief and up-to-date account of the occurrence, detection and detoxification of mycotoxins for those interested in and considering research in this area.\",\n \"corpus_id\": 16871258,\n \"score\": 2\n },\n {\n \"doc_id\": \"26786025\",\n \"title\": \"Environment contamination by mycotoxins and their occurrence in food and feed: Physiological aspects and economical approach.\",\n \"abstract\": \"The contamination of food and feed by mycotoxins as toxic metabolites of fungi is a risk not only for consumers resulting in various embarrassment regarding health status and well-being, but also for producers, companies and export market on the ground of economic losses and ruined stability of economic trade. As it is given in historical evidence, the contamination of food by mycotoxins is a topic as old as a history of mankind, finding some evidence even in the ancient books and records. Nowadays, the mycotoxins are used in modern biotechnological laboratories and are considered an agent for targeting the specific cells (e.g., defected cells to eliminate them). However, this promising procedure is only the beginning. More concern is focused on mycotoxins as abiotic hazard agents. The dealing with them, systematic monitoring, and development of techniques for their elimination from agricultural commodities are worldwide issues concerning all countries. They can be found alone or in co-occurrence with other mycotoxins. Thus, this review aims to provide widened information regarding mycotoxins contamination in environment with the consequences on health of animals and humans. The inevitability for more data that correctly determine the risk points linked to mycotoxins occurrence and their specific reactions in the environment is demonstrated. This review includes various symptoms in animals and humans that result from mycotoxin exposure. For better understanding of mycotoxin's impact on animals, the sensitivities of various animal species to various mycotoxins are listed. Strategies for elimination and preventing the risks of mycotoxins contamination as well as economical approach are discussed. To complete the topic, some data from past as historical evidences are presented.\",\n \"corpus_id\": 1251615,\n \"score\": 2\n },\n {\n \"doc_id\": \"27554261\",\n \"title\": \"Impact of food processing and detoxification treatments on mycotoxin contamination.\",\n \"abstract\": \"Mycotoxins are fungal metabolites commonly occurring in food, which pose a health risk to the consumer. Maximum levels for major mycotoxins allowed in food have been established worldwide. Good agricultural practices, plant disease management, and adequate storage conditions limit mycotoxin levels in the food chain yet do not eliminate mycotoxins completely. Food processing can further reduce mycotoxin levels by physical removal and decontamination by chemical or enzymatic transformation of mycotoxins into less toxic products. Physical removal of mycotoxins is very efficient: manual sorting of grains, nuts, and fruits by farmers as well as automatic sorting by the industry significantly lowers the mean mycotoxin content. Further processing such as milling, steeping, and extrusion can also reduce mycotoxin content. Mycotoxins can be detoxified chemically by reacting with food components and technical aids; these reactions are facilitated by high temperature and alkaline or acidic conditions. Detoxification of mycotoxins can also be achieved enzymatically. Some enzymes able to transform mycotoxins naturally occur in food commodities or are produced during fermentation but more efficient detoxification can be achieved by deliberate introduction of purified enzymes. We recommend integrating evaluation of processing technologies for their impact on mycotoxins into risk management. Processing steps proven to mitigate mycotoxin contamination should be used whenever necessary. Development of detoxification technologies for high-risk commodities should be a priority for research. While physical techniques currently offer the most efficient post-harvest reduction of mycotoxin content in food, biotechnology possesses the largest potential for future developments.\",\n \"corpus_id\": 6887962,\n \"score\": 2\n },\n {\n \"doc_id\": \"27933870\",\n \"title\": \"Tools for Defusing a Major Global Food and Feed Safety Risk: Nonbiological Postharvest Procedures To Decontaminate Mycotoxins in Foods and Feeds.\",\n \"abstract\": \"Mycotoxin contamination of foods and animal feeds is a worldwide problem for human and animal health. Controlling mycotoxin contamination has drawn the attention of scientists and other food and feed stakeholders all over the world. Despite best efforts targeting field and storage preventive measures, environmental conditions can still lead to mycotoxin contamination. This raises a need for developing decontamination methods to inactivate or remove the toxins from contaminated products. At present, decontamination methods applied include an array of both biological and nonbiological methods. The targeted use of nonbiological methods spans from the latter half of last century, when ammoniation and ozonation were first used to inactivate mycotoxins in animal feeds, to the novel techniques being developed today such as photosensitization. Effectiveness and drawbacks of different nonbiological methods have been reported in the literature, and this review examines the utility of these methods in addressing food safety. Particular consideration is given to the application of such methods in the developing world, where mycotoxin contamination is a serious food safety issue in staple crops such as maize and rice.\",\n \"corpus_id\": 21386600,\n \"score\": 2\n },\n {\n \"doc_id\": \"28298196\",\n \"title\": \"Microbial detoxification of eleven food and feed contaminating trichothecene mycotoxins.\",\n \"abstract\": \"BACKGROUND: Contamination of agricultural commodities with multiple trichothecene mycotoxins, produced by toxigenic Fusarium species, is a food safety issue, which greatly affects grain production and marketing worldwide. Importantly, exposure to multiple trichothecenes may increase toxicity in animals due to their synergistic and/or additive effects. To address the problem this study aimed to achieve a novel biological trait capable of detoxifying various food and feed contaminating trichothecenes under aerobic and anaerobic conditions and wide range of temperatures. RESULTS: A highly enriched microbial consortium (called DX100) capable of transforming eleven trichothecenes to significantly less toxic de-epoxy forms was achieved after prolonged incubation of soil microbial culture with 200 μg/mL deoxynivalenol (DON). DX100 demonstrated de-epoxidation activity under aerobic and anaerobic conditions, a greater range of temperatures and around neutral pH. The consortium contains 70% known and 30% unknown bacterial species, dominated by Stenotrophomonas species. Probably novel bacteria including strains of Stenotrophomonas and Alkaliphilus-Blautia species complex could be involved in aerobic and anaerobic de-epoxidation of trichothecenes, respectively. DX100 showed rapid and stable activity by de-epoxidizing 100% of 50 μg/mL deoxynivalenol at 48 h of incubation and retaining de-epoxidation ability after 100 subcultures in mineral salts broth (MSB). It was able to de-epoxidize high concentration of DON (500 μg/mL), and transformed ten more food contaminating trichothecenes into de-epoxy forms and/or other known/unknown compounds. Microbial de-epoxidation rate increased with increasing trichothecene concentrations in the broth media, suggesting that DX100 maintains a robust trichothecene detoxifying mechanism. Furthermore, the nature of microbial de-epoxidation reaction and inhibition of the reaction by sodium azide and the finding that bacterial cell culture lysate retained activity suggests that certain cytoplasmic reductases may be responsible for the de-epoxidation activity. CONCLUSIONS: This study reports the enrichment procedure for obtaining an effective and stable microbial consortium DX100 capable of de-epoxidizing several food contaminating trichothecene mycotoxins. DX100, which has de-epoxidation ability under wide range of conditions, represents a unique enzymatic source which has great industrial potential for reducing contamination of foods/feeds with multiple trichothecenes, and minimizing their synergistic/additive cytotoxic effects on consumer health.\",\n \"corpus_id\": 18627367,\n \"score\": 2\n },\n {\n \"doc_id\": \"28387743\",\n \"title\": \"Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins.\",\n \"abstract\": \"Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.\",\n \"corpus_id\": 1641676,\n \"score\": 2\n },\n {\n \"doc_id\": \"28720287\",\n \"title\": \"Occurrence, toxicity, bioaccessibility and mitigation strategies of beauvericin, a minor Fusarium mycotoxin.\",\n \"abstract\": \"Emerging Fusarium mycotoxins include the toxic secondary metabolites fusaproliferin, enniatins, beauvericin (BEA), and moniliform. BEA is produced by some entomo- and phytopathogenic Fusarium species and occurs naturally on corn and corn-based foods and feeds infected by Fusarium spp. BEA has shown various biological activities (antibacterial, antifungal, and insecticidal) and possesses toxic activity, including the induction of apoptosis, increase cytoplasmic calcium concentration and lead to DNA fragmentation in mammalian cell lines. Cereals food processing has an important effect on mycotoxin stability, leading to less-contaminated food compared to the raw materials. Different industrial processes have shown to be effective practices to reduce BEA contents due to thermal food processing applied, such as cooking, boiling, baking, frying, roasting and pasteurization. Some studies demonstrated the capacity of lactic acid bacteria to reduce the presence of the BEA in model solution and in food chain through fermentation processes, modifying this mycotoxin in a less toxic derivate. Prebiotic and probiotic ingredient can modulate the bioaccessibility of BEA reducing the risk of intake of this minor Fusarium mycotoxin. This review summarizes the existing data on occurrence, toxicity and especially on BEA reduction strategies in food and feed such as chemical reduction, biocontrol and food processing.\",\n \"corpus_id\": 11637397,\n \"score\": 2\n },\n {\n \"doc_id\": \"18258326\",\n \"title\": \"Mycotoxin problem in Africa: current status, implications to food safety and health and possible management strategies.\",\n \"abstract\": \"Mycotoxins are toxic secondary metabolites of fungal origin and contaminate agricultural commodities before or under post-harvest conditions. They are mainly produced by fungi in the Aspergillus, Penicillium and Fusarium genera. When ingested, inhaled or absorbed through the skin, mycotoxins will cause lowered performance, sickness or death on humans and animals. Factors that contribute to mycotoxin contamination of food and feed in Africa include environmental, socio-economic and food production. Environmental conditions especially high humidity and temperatures favour fungal proliferation resulting in contamination of food and feed. The socio-economic status of majority of inhabitants of sub-Saharan Africa predisposes them to consumption of mycotoxin contaminated products either directly or at various points in the food chain. The resulting implications include immuno-suppression, impaired growth, various cancers and death depending on the type, period and amount of exposure. A synergistic effect between mycotoxin exposure and some important diseases in the continent such as malaria, kwashiorkor and HIV/AIDS have been suggested. Mycotoxin concerns have grown during the last few decades because of their implications to human and animal health, productivity, economics of their management and trade. This has led to development of maximum tolerated limits for mycotoxins in various countries. Even with the standards in place, the greatest recorded fatal mycotoxin-poisoning outbreak caused by contamination of maize with aflatoxins occurred in Africa in 2004. Pre-harvest practices; time of harvesting; handling of produce during harvesting; moisture levels at harvesting, transportation, marketing and processing; insect damage all contribute to mycotoxin contamination. Possible intervention strategies include good agricultural practices such as early harvesting, proper drying, sanitation, proper storage and insect management among others. Other possible interventions include biological control, chemical control, decontamination, breeding for resistance as well as surveillance and awareness creation. There is need for efficient, cost-effective sampling and analytical methods that can be used for detection analysis of mycotoxins in developing countries.\",\n \"corpus_id\": 31564911,\n \"score\": 1\n },\n {\n \"doc_id\": \"18274964\",\n \"title\": \"Emerging fusarium-mycotoxins fusaproliferin, beauvericin, enniatins, and moniliformin: a review.\",\n \"abstract\": \"The contamination of foods and feed with mycotoxins is a commonly known problem. Intense investigations have been conducted to study the occurrence, toxicity, and recently also the prevention and detoxification strategies of mycotoxins in human and animal food chains. Most of the studies have emphasized on \\\"traditional\\\" mycotoxins, such as aflatoxins, ochratoxin A, and trichothecenes. However, one of the most common grain-contaminating genus of fungi, Fusarium spp., is also capable of producing other toxic secondary metabolites - the so-called emerging mycotoxins such as fusaproliferin, beauvericin, enniatins, and moniliformin. So far, only limited data is available on these metabolites. This is not only due to their late recognition but especially the late understanding of their role as mycotoxins. This paper summarizes the existing data on the chemistry, analytical techniques, biosynthesis, production, toxicity, and occurrence data on fusaproliferin, beauvericin, enniatins, and moniliformin. Based on the available studies, attention should be paid to the studies on the distinct significance of these compounds in the human and animal food chains.\",\n \"corpus_id\": 21330571,\n \"score\": 1\n },\n {\n \"doc_id\": \"18936919\",\n \"title\": \"Rapid test strips for analysis of mycotoxins in food and feed.\",\n \"abstract\": \"An overview is given on recent trends and applications of rapid immunodiagnostic tests for screening of food and feed for mycotoxins. Different test formats are discussed, and challenges in the development of lateral-flow devices for on-site determination of mycotoxins, with requirements such as being robust, fast, and cost-effective, are briefly elucidated.\",\n \"corpus_id\": 43915454,\n \"score\": 1\n },\n {\n \"doc_id\": \"18949120\",\n \"title\": \"Determination of mycotoxins in human foods.\",\n \"abstract\": \"This tutorial review deals with the analytical methods available for the determination of mycotoxins in food commodities. As the secondary metabolites of a range of fungal species, mycotoxins possess diverse chemical structures, presenting analytical chemists with a unique set of challenges in the microg kg(-1) (ppb) range. A number of analytical methods have been applied to mycotoxin analysis. These include widely applicable HPLC methods with UV or fluorimetric detection, which are extensively used both in research and for legal enforcement of food safety legislation and for regulations in international agricultural trade. Other chromatographic methods, such as TLC and GC, are also employed for the determination of mycotoxins, whereas recent advances in analytical instrumentation have highlighted the potential of LC-MS methods, especially for multi-toxin determination and for confirmation purposes. Conventional chromatographic methods are generally time consuming and capital intensive, and hence a range of methods, mostly based on immunological principles, have been developed and commercialised for rapid analysis. These methods include, among others, enzyme-linked immunosorbent analysis (ELISA), direct fluorimetry, fluorescence polarization, and various biosensors and strip methods.\",\n \"corpus_id\": 36851512,\n \"score\": 1\n },\n {\n \"doc_id\": \"20339844\",\n \"title\": \"Determination of mycotoxins in foods: current state of analytical methods and limitations.\",\n \"abstract\": \"Mycotoxins are natural contaminants produced by a range of fungal species. Their common occurrence in food and feed poses a threat to the health of humans and animals. This threat is caused either by the direct contamination of agricultural commodities or by a \\\"carry-over\\\" of mycotoxins and their metabolites into animal tissues, milk, and eggs after feeding of contaminated hay or corn. As a consequence of their diverse chemical structures and varying physical properties, mycotoxins exhibit a wide range of biological effects. Individual mycotoxins can be genotoxic, mutagenic, carcinogenic, teratogenic, and oestrogenic. To protect consumer health and to reduce economic losses, surveillance and control of mycotoxins in food and feed has become a major objective for producers, regulatory authorities and researchers worldwide. However, the variety of chemical structures makes it impossible to use one single technique for mycotoxin analysis. Hence, a vast number of analytical methods has been developed and validated. The heterogeneity of food matrices combined with the demand for a fast, simultaneous and accurate determination of multiple mycotoxins creates enormous challenges for routine analysis. The most crucial issues will be discussed in this review. These are (1) the collection of representative samples, (2) the performance of classical and emerging analytical methods based on chromatographic or immunochemical techniques, (3) the validation of official methods for enforcement, and (4) the limitations and future prospects of the current methods.\",\n \"corpus_id\": 24974696,\n \"score\": 1\n },\n {\n \"doc_id\": \"20358681\",\n \"title\": \"Toxicology of mycotoxins.\",\n \"abstract\": \"Humans are exposed to mycotoxins via ingestion, contact and inhalation. This must have occurred throughout human history and led to severe outbreaks. Potential diseases range from akakabio-byo to stachybotryotoxicosis and cancer. The known molecular bases of toxicology run the gamut of 23 compounds, from aflatoxins (AFs) to zearalenone, ochratoxin A and deoxynivalenol. Ergotism is one of the oldest recognized mycotoxicosis, although mycotoxin science only commenced in the 1960s with the discovery of AFs in turkey feed. AFs are carcinogenic. Some others are suspected carcinogens. The effects of mycotoxins are acute or chronic in nature. Mycotoxins are well known in the scientific community, although they have a low profile in the general population. An incongruous situation occurs in United States where mycotoxins from \\\"moldy homes\\\" are considered to be a significant problem, although there is a general debate about seriousness. This contrasts with the thousands of deaths from mycotoxins that occur, even now, in the technologically less developed countries (e.g., Indonesia, China, and Africa). Mycotoxins are more toxic than pesticides. Studies are moving from whole animal work to investigating the biochemical mechanisms in isolated cells, and the mechanisms of toxicity at the molecular level are being elucidated. The stereochemical nature of AFs has been shown to be important. In addition, the effect of multiple mycotoxins is being increasingly investigated, which will more accurately represent the situation in nature. It is anticipated that more fungal metabolites will be recognized as dangerous toxins and permitted statutory levels will decrease in the future.\",\n \"corpus_id\": 22945774,\n \"score\": 1\n },\n {\n \"doc_id\": \"20376161\",\n \"title\": \"[Mycotoxins in food: legislation and thresholds.].\",\n \"abstract\": \"Micotossine negli alimenti: normative e limiti di legge. Mycotoxins are chemical substances produced by fungal species belonging mostly to Aspergillus, Penicillium and Fusarium , and having a toxic effect on humans and farm animals. In recent years health authorities have dedicated much attention to food contamination by mycotoxins, especially with regards to aflatoxins, fumonisin, ocratoxin A, patulin, trichothecenes e zearalenone. The current European legislation CE n. 1881/2006 and n. 1126/2007 establish the maximum levels of mycotoxins allowed in human food. Despite the existence of such legislation, regulations regarding certain products are not very clear (i.e. milk products). More interest should be paid to these food products in terms of regulations and testing.\",\n \"corpus_id\": 34067960,\n \"score\": 1\n },\n {\n \"doc_id\": \"21641127\",\n \"title\": \"Ochratoxin A in feed of food-producing animals: an undesirable mycotoxin with health and performance effects.\",\n \"abstract\": \"Mycotoxins are secondary fungal metabolites, whose presence in feed- and foodstuffs is unavoidable. Ochratoxin A (OTA) is one of the known mycotoxins with greatest public health and agro-economic significance. Several toxic effects have been ascribed following exposure, namely nephrotoxicity, as well negative impacts in the performance of farm animals, resulting in major economic implications. Of no less importance for the route of human exposure that can also embody the carry-over of OTA from feed into animal-derived products is also a concern. For all these reasons the present article updates the worldwide occurrence of OTA in different raw ingredients and finished feed destined to food-producing animals. After that a brief characterization of specie susceptibility and the major rationales is made. An historical overview of field outbreaks linked to OTA exposure in farm animals, concerning the implicated feeds, contamination levels and major clinical and productivity effects is presented. Finally a review of the major animal health and performance potential impacts of animals being reared on contaminated feed is made allied to a perspective regarding its co-occurrence with other mycotoxins, and simultaneous parasitic and bacterial infections. Ultimately, this article aims to be instructive and draw attention to a mycotoxin so often neglected and elapsed from the list of differential diagnosis in farm practice. For the unpredictability and unavoidability of occurrence, OTA will definitely be an enduring problem in animal production.\",\n \"corpus_id\": 43819175,\n \"score\": 1\n },\n {\n \"doc_id\": \"21643911\",\n \"title\": \"Analysis of multiple mycotoxins in food.\",\n \"abstract\": \"Mycotoxins are secondary metabolites of microscopic filamentous fungi. With regard to the widespread distribution of fungi in the environment, mycotoxins are considered to be one of the most important natural contaminants in foods and feeds. To protect consumers' health and reduce economic losses, surveillance and control of mycotoxins in food and feed has become a major objective for producers, regulatory authorities, and researchers worldwide. In this context, availability of reliable analytical methods applicable for this purpose is essential. Since the variety of chemical structures of mycotoxins makes impossible to use one single technique for their analysis, a vast number of analytical methods has been developed and validated. Both a large variability of food matrices and growing demands for a fast, cost-saving and accurate determination of multiple mycotoxins by a single method outline new challenges for analytical research. This strong effort is facilitated by technical developments in mass spectrometry allowing decreasing the influence of matrix effects in spite of omitting sample clean-up step. The current state-of-the-art together with future trends is presented in this chapter. Attention is focused mainly on instrumental method; advances in biosensors and other screening bioanalytical approaches enabling analysis of multiple mycotoxins are not discussed in detail.\",\n \"corpus_id\": 21505019,\n \"score\": 1\n },\n {\n \"doc_id\": \"22069600\",\n \"title\": \"Real and perceived risks for mycotoxin contamination in foods and feeds: challenges for food safety control.\",\n \"abstract\": \"Mycotoxins are toxic compounds, produced by the secondary metabolism of toxigenic moulds in the Aspergillus, Alternaria, Claviceps, Fusarium, Penicillium and Stachybotrys genera occurring in food and feed commodities both pre- and post-harvest. Adverse human health effects from the consumption of mycotoxins have occurred for many centuries. When ingested, mycotoxins may cause a mycotoxicosis which can result in an acute or chronic disease episode. Chronic conditions have a much greater impact, numerically, on human health in general, and induce diverse and powerful toxic effects in test systems: some are carcinogenic, mutagenic, teratogenic, estrogenic, hemorrhagic, immunotoxic, nephrotoxic, hepatotoxic, dermotoxic and neurotoxic. Although mycotoxin contamination of agricultural products still occurs in the developed world, the application of modern agricultural practices and the presence of a legislatively regulated food processing and marketing system have greatly reduced mycotoxin exposure in these populations. However, in developing countries, where climatic and crop storage conditions are frequently conducive to fungal growth and mycotoxin production, much of the population relies on subsistence farming or on unregulated local markets. Therefore both producers and governmental control authorities are directing their efforts toward the implementation of a correct and reliable evaluation of the real status of contamination of a lot of food commodity and, consequently, of the impact of mycotoxins on human and animal health.\",\n \"corpus_id\": 5878422,\n \"score\": 1\n },\n {\n \"doc_id\": \"22725671\",\n \"title\": \"Fungal and bacterial metabolites in commercial poultry feed from Nigeria.\",\n \"abstract\": \"Metabolites of toxigenic fungi and bacteria occur as natural contaminants (e.g. mycotoxins) in feedstuffs making them unsafe to animals. The multi-toxin profiles in 58 commercial poultry feed samples collected from 19 districts in 17 states of Nigeria were determined by LC/ESI-MS/MS with a single extraction step and no clean-up. Sixty-three (56 fungal and seven bacterial) metabolites were detected with concentrations ranging up to 10,200 µg kg⁻¹ in the case of aurofusarin. Fusarium toxins were the most prevalent group of fungal metabolites, whereas valinomycin occurred in more than 50% of the samples. Twelve non-regulatory fungal and seven bacterial metabolites detected and quantified in this study have never been reported previously in naturally contaminated stored grains or finished feed. Among the regulatory toxins in poultry feed, aflatoxin concentrations in 62% of samples were above 20 µg kg⁻¹, demonstrating high prevalence of unsafe levels of aflatoxins in Nigeria. Deoxynivalenol concentrations exceeded 1000 µg kg⁻¹ in 10.3% of samples. Actions are required to reduce the consequences from regulatory mycotoxins and understand the risks of the single or co-occurrence of non-regulatory metabolites for the benefit of the poultry industry.\",\n \"corpus_id\": 35148398,\n \"score\": 1\n },\n {\n \"doc_id\": \"23047235\",\n \"title\": \"Masked mycotoxins: a review.\",\n \"abstract\": \"The aim of this review is to give a comprehensive overview of the current knowledge on plant metabolites of mycotoxins, also called masked mycotoxins. Mycotoxins are secondary fungal metabolites, toxic to human and animals. Toxigenic fungi often grow on edible plants, thus contaminating food and feed. Plants, as living organisms, can alter the chemical structure of mycotoxins as part of their defence against xenobiotics. The extractable conjugated or non-extractable bound mycotoxins formed remain present in the plant tissue but are currently neither routinely screened for in food nor regulated by legislation, thus they may be considered masked. Fusarium mycotoxins (deoxynivalenol, zearalenone, fumonisins, nivalenol, fusarenon-X, T-2 toxin, HT-2 toxin, fusaric acid) are prone to metabolisation or binding by plants, but transformation of other mycotoxins by plants (ochratoxin A, patulin, destruxins) has also been described. Toxicological data are scarce, but several studies highlight the potential threat to consumer safety from these substances. In particular, the possible hydrolysis of masked mycotoxins back to their toxic parents during mammalian digestion raises concerns. Dedicated chapters of this article address plant metabolism as well as the occurrence of masked mycotoxins in food, analytical aspects for their determination, toxicology and their impact on stakeholders.\",\n \"corpus_id\": 15401052,\n \"score\": 1\n },\n {\n \"doc_id\": \"23162698\",\n \"title\": \"Current situation of mycotoxin contamination and co-occurrence in animal feed--focus on Europe.\",\n \"abstract\": \"Mycotoxins are secondary metabolites produced by fungi especially those belonging to the genus Aspergillus, Penicillum and Fusarium. Mycotoxin contamination can occur in all agricultural commodities in the field and/or during storage, if conditions are favourable to fungal growth. Regarding animal feed, five mycotoxins (aflatoxins, deoxynivalenol, zearalenone, fumonisins and ochratoxin A) are covered by EU legislation (regulation or recommendation). Transgressions of these limits are rarely observed in official monitoring programs. However, low level contamination by Fusarium toxins is very common (e.g., deoxynivalenol (DON) is typically found in more than 50% of the samples) and co-contamination is frequently observed. Multi-mycotoxin studies reported 75%-100% of the samples to contain more than one mycotoxin which could impact animal health at already low doses. Co-occurrence of mycotoxins is likely to arise for at least three different reasons (i) most fungi are able to simultaneously produce a number of mycotoxins, (ii) commodities can be contaminated by several fungi, and (iii) completed feed is made from various commodities. In the present paper, we reviewed the data published since 2004 concerning the contamination of animal feed with single or combinations of mycotoxins and highlighted the occurrence of these co-contaminations.\",\n \"corpus_id\": 43725891,\n \"score\": 1\n },\n {\n \"doc_id\": \"23605238\",\n \"title\": \"Mycotoxins in horse feed.\",\n \"abstract\": \"A total of 62 samples of commercial horse feed preparations (complementary feeds) containing cereal mixtures (\\\"muesli\\\" or mash, n = 39; pelleted feeds, n = 12), and plain horse feed grains (maize, n = 5; oats, n = 4; barley, n = 2) were purchased from 21 different producers/distributors from the German market. All samples were analysed by competitive enzyme immunoassays (EIA) for six different mycotoxins (mycotoxin groups). Analytes (detection limit, mean recovery) were: deoxynivalenol (DON, 10 µg/kg, 84%), zearalenone (ZEA, 5 µg/kg, 93%), fumonisin B1 (FB1, 2 µg/kg, 113%), T-2 toxin (T-2, 0.1 µg/kg, 71%), sum of T-2 + HT-2 toxin (T-2/HT2, 0.2 µg/kg, 97%), ochratoxin A (OTA, 0.2 µg/kg, 67%), and total ergot alkaloids (Generic Ergot Alkaloids \\\"GEA\\\", 30 µg/kg, 132%). All samples contained DON (16-4,900 µg/kg, median 220 µg/kg), T-2/HT-2 (0.8-230 µg/kg, median 24 µg/kg), and T-2 (0.3-91 µg/kg, median 7 µg/kg). ZEA was detected in 98% of the samples (7-310 µg/kg, median 61 µg/kg). Most samples (94%) were positive for FB1 (2-2,200 µg/kg, median 27 µg/kg). Ergot alkaloids were detected in 61% of samples (28-1,200 µg/kg, median 97 µg/kg), OTA was found in 42% of samples (0.2-4 µg/kg, median 0.35 µg/kg). The results demonstrate that a co-contamination with several mycotoxins is very common in commercial horse feed from the German market. The toxin concentrations were in most cases well below the levels which are usually considered as critical or even toxic. The highest mycotoxin concentrations were mostly found in single-grain cereal feed: the maximum values for DON and FB1 were found in maize, the highest T-2/HT-2 toxin concentrations were found in oats, and the highest concentration of ergot alkaloids was found in barley. In composed feeds, no correlation between cereal composition and mycotoxin levels could be found.\",\n \"corpus_id\": 11697229,\n \"score\": 1\n },\n {\n \"doc_id\": \"23606076\",\n \"title\": \"Mycotoxins in feedstuffs in Portugal: an overview.\",\n \"abstract\": \"Mycotoxins are secondary metabolites produced by many genera of fungi in many commodities, under certain conditions. Mycotoxicological control of feed is a procedure that aims to protect human and animal health, avoiding the adverse effects of these undesirable substances. This component of the sanitary control of feed and food is essential to prevent the presence of those substances which can seriously affect the health of the animals. In Portugal, there is relatively few information related to the natural occurrence of mycotoxins in feed. In this context, the authors present results and data compilation concerning the occurrence of mycotoxins in raw materials and also feed for dairy cattle, swine, poultry, horses, fish, laboratory rats and pet; making a generic qualitative appreciation of the risks associated to the presence of mycotoxins in these feedstuffs. The mycotoxins studied: aflatoxins (AFs), ochratoxin A (OTA), fumonisin B1 and B2 (FB1, FB2) were analysed by High Performance Liquid Chromatoghraphy (HPLC). Deoxynivalenol (DON) and zearalenone (ZEN) were determined by Thin-Layer Chromatography (TLC). The results suggest that contaminations with these mycotoxins in feed are quite common, revealing the need for surveillance and monitoring programs for the prevention of the sanitary impacts of these \\\"non desirable substances\\\".\",\n \"corpus_id\": 1735613,\n \"score\": 1\n },\n {\n \"doc_id\": \"23612752\",\n \"title\": \"From the gut to the brain: journey and pathophysiological effects of the food-associated trichothecene mycotoxin deoxynivalenol.\",\n \"abstract\": \"Mycotoxins are fungal secondary metabolites contaminating food and causing toxicity to animals and humans. Among the various mycotoxins found in crops used for food and feed production, the trichothecene toxin deoxynivalenol (DON or vomitoxin) is one of the most prevalent and hazardous. In addition to native toxins, food also contains a large amount of plant and fungal derivatives of DON, including acetyl-DON (3 and 15ADON), glucoside-DON (D3G), and potentially animal derivatives such as glucuronide metabolites (D3 and D15GA) present in animal tissues (e.g., blood, muscle and liver tissue). The present review summarizes previous and very recent experimental data collected in vivo and in vitro regarding the transport, detoxification/metabolism and physiological impact of DON and its derivatives on intestinal, immune, endocrine and neurologic functions during their journey from the gut to the brain.\",\n \"corpus_id\": 10276932,\n \"score\": 1\n },\n {\n \"doc_id\": \"23768181\",\n \"title\": \"Food safety and increasing hazard of mycotoxin occurrence in foods and feeds.\",\n \"abstract\": \"The possible hazard of mycotoxin occurrence in foods and feeds and some food-borne mycotoxicoses is reviewed. Management of the risk of mycotoxin contamination using some useful preventive measures against mycotoxin contamination of foods/feeds during pre- and post-harvesting periods is considered. The physical and chemical methods of mycotoxin decontamination of foods/feeds are briefly described. The use of various feed additives as a method for prevention of the adverse effects of mycotoxins is reviewed. The processing of various foods and feeds is considered in a view to possible mycotoxin decontamination. The necessary hygiene control and risk assessment in regard to mycotoxin contamination of foods and feeds in addition to some useful prophylactic measures are briefly described. A short reference is made concerning the most successful methods of veterinary hygiene control in order to prevent a possible entering of some mycotoxins in commercial channels with a view to human health.\",\n \"corpus_id\": 2305869,\n \"score\": 1\n },\n {\n \"doc_id\": \"24162094\",\n \"title\": \"Fusarial toxins: secondary metabolites of Fusarium fungi.\",\n \"abstract\": \"Exposure to mycotoxins occurs worldwide, even though there are geographic and climatic differences in the amounts produced and occurrence of these substances. Mycotoxins are secondary chemical metabolites of different fungi. They are natural contaminants of cereals, so their presence is often inevitable. Among many genera that produce mycotoxins, Fusarium fungi are the most widespread in cereal-growing areas of the planet. Fusarium fungi produce a diversity of mycotoxin types, whose distributions are also diverse. What is produced and where it is produced is influenced primarily by environmental conditions, and crop production and storage methods. The amount of toxin produced depends on physical (viz., moisture, relative humidity, temperature, and mechanical damage), chemical (viz., carbon dioxide,oxygen, composition of substrate, insecticides and fungicides), and biological factors (viz., plant variety, stress, insects, spore load, etc.). Moisture and temperature have a major influence on mold growth rate and mycotoxin production. Among the most toxic and prevalent fusaria) toxins are the following: zearalenone,fumonisins, moniliformin and trichothecenes (T-2/HT-2 toxin, deoxynivalenol,diacetoxyscirpenol, nivalenol). Zearalenone (ZEA; ZON, F-2 toxin) isaphy to estrogenic compound, primarily a field contaminant, which exhibits estrogenic activity and has been implicated in numerous mycotoxicoses of farm animals,especially pigs. Recently, evidence suggests that ZEA has potential to stimulate the growth of human breast cancer cells. Fumonisins are also cancer-promoting metabolites,of which Fumonisin 8 I (FBI) is the most important. Moniliformin (MON) isalso highly toxic to both animals and humans. Trichothecenes are classified as gastrointestinal toxins, dermatotoxins, immunotoxins, hematotoxins, and gene toxins. T-2 and HT-2 toxin, and diacetoxyscirpenol (DAS, anguidine) are the most toxic mycotoxins among the trichothecene group. Deoxynivalenol (DON, vomitoxin) and nivalenol although less toxic are important because they frequently occur at levels high enough to cause adverse effects. The presence of mycotoxins in the animal diet can produce significant production losses. Any considerable presence of mycotoxins, in major dietary components,confirms the need to adopt a continuous prevention and control program. Such programs are usually based on several common approaches to minimize mycotoxin contamination in the food chain. Major strategies include preventing fungal growth and therefore mycotoxin formation, reducing or eliminating mycotoxins from contaminated feedstuffs, or diverting contaminated products to low risk uses. Because of the complexity of their chemical structures, mycotoxins also present a major analytical challenge. They are also found in a vast array of feed matrices. Analysis is essential for determining the extent of mycotoxin contamination, for risk analysis, confirming the diagnosis of a mycotoxicosis and for monitoring mycotoxin mitigation strategies. For the future, adequately controlling the mycotoxin problem in the livestock economy will depend on implementing appropriate agricultural management policies,as well as augmenting production and storage systems and analysis methods. Only such policies offer the opportunity to bring solid and long-lasting economical results to the livestock industry that is afflicted with the mycotoxin problem.\",\n \"corpus_id\": 44438391,\n \"score\": 1\n },\n {\n \"doc_id\": \"24377857\",\n \"title\": \"Upstream regulation of mycotoxin biosynthesis.\",\n \"abstract\": \"Mycotoxins are natural contaminants of food and feed products, posing a substantial health risk to humans and animals throughout the world. A plethora of filamentous fungi has been identified as mycotoxin producers and most of these fungal species belong to the genera Aspergillus, Fusarium, and Penicillium. A number of studies have been conducted to better understand the molecular mechanisms of biosynthesis of key mycotoxins and the regulatory cascades controlling toxigenesis. In many cases, the mycotoxin biosynthetic genes are clustered and regulated by one or more pathway-specific transcription factor(s). In addition, as biosynthesis of many secondary metabolites is coordinated with fungal growth and development, there are a number of upstream regulators affecting biosynthesis of mycotoxins in fungi. This review presents a concise summary of the regulation of mycotoxin biosynthesis, focusing on the roles of the upstream regulatory elements governing biosynthesis of aflatoxin and sterigmatocystin in Aspergillus.\",\n \"corpus_id\": 8249845,\n \"score\": 1\n },\n {\n \"doc_id\": \"24572628\",\n \"title\": \"An overview on mycotoxin contamination of foods in Africa.\",\n \"abstract\": \"Mycotoxins are fungal secondary metabolites that contaminate various feedstuffs and agricultural crops. The contamination of food by mycotoxins can occur before production, during storage, processing, transportation or marketing of the food products. High temperature, moisture content and water activity are among the predisposing factors that facilitate the production of mycotoxins in food. Aflatoxins, ochratoxins, fumonisins, deoxynivalenol and zearalenone are all considered the major mycotoxins produced in food and feedstuffs. In Africa, mycotoxin contamination is considered to be a major problem with implications that affect human and animal health and economy. Aflatoxin-related hepatic diseases are reported in many African countries. Ochratoxin and fumonisin toxicity in humans and animals is widespread in Africa. The available, updated information on the incidence of mycotoxin contamination, decontamination and its public health importance in Africa is lacking. The aim of this review is to highlight, update and discuss the available information on the incidence of mycotoxins in African countries. The public health implications and the recommended strategies for control of mycotoxins in food and agricultural crops are also discussed.\",\n \"corpus_id\": 16654472,\n \"score\": 1\n },\n {\n \"doc_id\": \"24769018\",\n \"title\": \"Mycotoxins in a changing global environment--a review.\",\n \"abstract\": \"Mycotoxins are toxic metabolites produced by fungal species that commonly contaminate staple foods and feeds. They represent an unavoidable problem due to their presence in globally consumed cereals such as rice, maize and wheat. Most mycotoxins are immunosuppressive agents and some are carcinogens, hepatotoxins, nephrotoxins, and neurotoxins. Worldwide trends envision a stricter control of mycotoxins, however, the changing global environment may not be the ideal setting to control and reduce the exposure to these toxins. Although new technologies allow us to inspect the multi-mycotoxin presence in foods, new sources of exposure, gaps in knowledge of mycotoxins interactions, appearance of \\\"emergent\\\" mycotoxins and elucidation of consequent health effects can complicate their control even more. While humans are adapting to cope with environmental changes, such as food scarcity, decreased food quality, mycotoxin regulations, crop production and seasonality, and other climate related modifications, fungal species are also adapting and increased cases of mycotoxin adverse health effects are likely to occur in the future. To guarantee access to quality food for all, we need a way to balance global mycotoxin standards with the realistic feasibility of reaching them, considering limitations of producers and designing strategies to reduce mycotoxin exposure based on sound research.\",\n \"corpus_id\": 22508699,\n \"score\": 1\n },\n {\n \"doc_id\": \"24987806\",\n \"title\": \"A Review of Mycotoxins in Food and Feed Products in Portugal and Estimation of Probable Daily Intakes.\",\n \"abstract\": \"Mycotoxins are toxic secondary metabolites produced by filamentous fungi that occur naturally in agricultural commodities worldwide. Aflatoxins, ochratoxin A, patulin, fumonisins, zearalenone, trichothecenes, and ergot alkaloids are presently the most important for food and feed safety. These compounds are produced by several species that belong to the Aspergillus, Penicillium, Fusarium, and Claviceps genera and can be carcinogenic, mutagenic, teratogenic, cytotoxic, neurotoxic, nephrotoxic, estrogenic, and immunosuppressant. Human and animal exposure to mycotoxins is generally assessed by taking into account data on the occurrence of mycotoxins in food and feed as well as data on the consumption patterns of the concerned population. This evaluation is crucial to support measures to reduce consumer exposure to mycotoxins. This work reviews the occurrence and levels of mycotoxins in Portuguese food and feed to provide a global overview of this issue in Portugal. With the information collected, the exposure of the Portuguese population to those mycotoxins is assessed, and the estimated dietary intakes are presented.\",\n \"corpus_id\": 39180109,\n \"score\": 1\n },\n {\n \"doc_id\": \"25126610\",\n \"title\": \"Mycotoxins and mycotoxigenic fungi in poultry feed for food-producing animals.\",\n \"abstract\": \"Moulds are capable of reducing the nutritional value of feedstuff as well as elaborating several mycotoxins. Mycotoxin-contaminated feed has adverse effects on animal health and productivity. Also, mycotoxins may be carried over into meat and eggs when poultry are fed with contaminated feed. In a point prevalence study feedstuff used for poultry nutrition in Argentina was analyzed for fungal flora, natural incidence of selected mycotoxins, and nutritional quality. Ten mould genera were recovered, six of them known to be mycotoxigenic. More than 28 species were determined. Fumonisins were detected in all the samples (median 1,750 ppb). Forty-four out of 49 samples (90%) were contaminated with DON (median 222 ppb) and OTA (median 5 ppb). Also, 44 out of 49 samples were contaminated with aflatoxins (median 2.685 ppb), 42 samples (86%) with ZEA (median 50 ppb), and 38 samples (78%) with T2-toxin (median 50 ppb). Ninety percent of the samples had at least one type of nutritional deficiency. This study indicates the need for continuous assessment of the mycological status of animal feed production, in order to feed animals for optimal performance ensuring food safety.\",\n \"corpus_id\": 18439326,\n \"score\": 1\n },\n {\n \"doc_id\": \"25898143\",\n \"title\": \"Keeping Mycotoxins Away from the Food: Does the Existence of Regulations Have any Impact in Africa?\",\n \"abstract\": \"Following the discovery of aflatoxins in the early 1960s, there have been many studies leading to the uncovering of many mycotoxins and the understanding of associated health effects in animals and humans. Consequently, there has been a global increase in the number of countries with mycotoxin regulations in foods. However, many African countries have only regulations for aflatoxins (or a few other mycotoxins) in specific foods or no regulations at all. This article critically reviews the challenges thwarting the establishment of mycotoxin regulations and their impacts on human dietary mycotoxin exposure in Africa. Mycotoxin regulatory limits for different countries are compared with mycotoxin tolerable daily intakes established by international food safety bodies taking into account consumption patterns. The agrarian setup, food insecurity and mycotoxin analytical challenges in African countries are discussed; and more feasible mycotoxin dietary exposure reduction strategies proposed.\",\n \"corpus_id\": 205692168,\n \"score\": 1\n },\n {\n \"doc_id\": \"26001087\",\n \"title\": \"Emerging nanotechnology for detection of mycotoxins in food and feed.\",\n \"abstract\": \"The term mycotoxin was coined for toxic metabolites secreted by some fungi in food, food products and feed. The most prominent mycotoxins include aflatoxins (AFs), deoxynivalenol, zearalenone, ochratoxin, fumonisin and patulin. Among these some are proved to be strong carcinogenic agents such as AFs B1 while others are under suspicion to have carcinogenic effects. Ingestion of such mycotoxin-contaminated food and feed pose to a threat, mycotoxicoses. Various conventional techniques are available for the detection of mycotoxins, but unfortunately as a consequence of their constraint, the development of new and rapid techniques is the need of the hour. The use of nanotechnology for the development of nanobiosensors would be the alternative sensitive methods for the rapid detection of mycotoxins. Implementation of nanomaterials in the fabrication of nanobiosensors and their use for the detection of the mycotoxins in food and feed is the centre of interest of this review. We have inventoried nanomaterials applied for weaving nanobiosensors, which includes carbon nanotubes, nanowires, nanoparticles, quantum dots, nanorods and nanofibers. In addition, we have extensively reviewed available nanobiosensors specific for different mycotoxins, their advantages and challenges.\",\n \"corpus_id\": 21214332,\n \"score\": 1\n },\n {\n \"doc_id\": \"26449927\",\n \"title\": \"Determination of the Mycotoxin Content in Distiller's Dried Grain with Solubles Using a Multianalyte UHPLC-MS/MS Method.\",\n \"abstract\": \"There are more than 300 potential mycotoxins that can contaminate food and feed and cause adverse effects in humans and animals. The data on the co-occurrence of mycotoxins in novel animal feed materials, such as distiller's dried grain with solubles (DDGS), are limited. Thus, a UHPLC-MS/MS method for the quantitation of 77 mycotoxins and other fungal metabolites was used to analyze 169 DDGS samples produced from wheat, maize, and barley and 61 grain samples. All DDGS samples analyzed were contaminated with 13-34 different mycotoxins. Fumonisins were present in all 52 maize DDGS samples (81.0-6890 μg/kg for fumonisin B1), and deoxynivalenol was present in all 99 wheat DDGS samples (39.3-1120 μg/kg). A number of co-occurring mycotoxins were also identified. Due to the high co-occurrence of mycotoxins, routine screening of the animal feed ingredients is highly recommended to allow the highlighted risks to be effectively managed.\",\n \"corpus_id\": 22575964,\n \"score\": 1\n },\n {\n \"doc_id\": \"26529017\",\n \"title\": \"Effects of Mycotoxins on Mucosal Microbial Infection and Related Pathogenesis.\",\n \"abstract\": \"Mycotoxins are fungal secondary metabolites detected in many agricultural commodities and water-damaged indoor environments. Susceptibility to mucosal infectious diseases is closely associated with immune dysfunction caused by mycotoxin exposure in humans and other animals. Many mycotoxins suppress immune function by decreasing the proliferation of activated lymphocytes, impairing phagocytic function of macrophages, and suppressing cytokine production, but some induce hypersensitive responses in different dose regimes. The present review describes various mycotoxin responses to infectious pathogens that trigger mucosa-associated diseases in the gastrointestinal and respiratory tracts of humans and other animals. In particular, it focuses on the effects of mycotoxin exposure on invasion, pathogen clearance, the production of cytokines and immunoglobulins, and the prognostic implications of interactions between infectious pathogens and mycotoxin exposure.\",\n \"corpus_id\": 2751434,\n \"score\": 1\n },\n {\n \"doc_id\": \"26725999\",\n \"title\": \"Overall internal exposure to mycotoxins and their occurrence in occupational and residential settings - An overview.\",\n \"abstract\": \"Mycotoxins are toxic secondary metabolites of various fungal species that can contaminate food and feed, as well as indoor environments. Numerous studies have summarized the adverse health effects of mycotoxins and described severe intoxications of humans and animals. The major health concerns are caused via the alimentary route which unambiguously is the main source for human internal exposure; however, the relevance of other pathways under environmental and occupational conditions should also be considered. Thus firstly, this review aims in summarizing literature data on potentially inhalable mycotoxins occurring in dusts or air in residences and in working environments. Secondly, it gives an overview of the overall internal body burden of mycotoxins in humans in an attempt to characterize total human exposure. These data are also discussed in relation to the current toxicologically based values used for risk assessment.\",\n \"corpus_id\": 24068429,\n \"score\": 1\n },\n {\n \"doc_id\": \"26891326\",\n \"title\": \"Mycotoxin Contamination in the EU Feed Supply Chain: A Focus on Cereal Byproducts.\",\n \"abstract\": \"Mycotoxins represent a risk to the feed supply chain with an impact on economies and international trade. A high percentage of feed samples have been reported to be contaminated with more than one mycotoxin. In most cases, the concentrations were low enough to ensure compliance with the European Union (EU) guidance values or maximum admitted levels. However, mycotoxin co-contamination might still exert adverse effects on animals due to additive/synergistic interactions. Studies on the fate of mycotoxins during cereal processing, such as milling, production of ethanol fuels, and beer brewing, have shown that mycotoxins are concentrated into fractions that are commonly used as animal feed. Published data show a high variability in mycotoxin repartitioning, mainly due to the type of mycotoxins, the level and extent of fungal contamination, and a failure to understand the complexity of food processing technologies. Precise knowledge of mycotoxin repartitioning during technological processes is critical and may provide a sound technical basis for feed managers to conform to legislation requirements and reduce the risk of severe adverse market and trade repercussions. Regular, economical and straightforward feed testing is critical to reach a quick and accurate diagnosis of feed quality. The use of rapid methods represents a future challenge.\",\n \"corpus_id\": 5093889,\n \"score\": 1\n },\n {\n \"doc_id\": \"27417439\",\n \"title\": \"The intestinal barrier as an emerging target in the toxicological assessment of mycotoxins.\",\n \"abstract\": \"Mycotoxins, the secondary metabolites of fungal species, are the most frequently occurring natural food contaminants in human and animal diets. Risk assessment of mycotoxins focused as yet on their mutagenic, genotoxic and potential carcinogenic effects. Recently, there is an increasing awareness of the adverse effects of various mycotoxins on vulnerable structures in the intestines. In particular, an impairment of the barrier function of the epithelial lining cells and the sealing tight junction proteins has been noted, as this could result in an increased translocation of luminal antigens and pathogens and an excessive activation of the immune system. The current review aims to provide a summary of the available evidence regarding direct effects of various mycotoxins on the intestinal epithelial barrier. Available data, based on different cellular and animal studies, show that food-associated exposure to certain mycotoxins, especially trichothecenes and patulin, affects the intestinal barrier integrity and can result in an increased translocation of harmful stressors. It is therefore hypothesized that human exposure to certain mycotoxins, particularly deoxynivalenol, as the major trichothecene, may play an important role in etiology of various chronic intestinal inflammatory diseases, such as inflammatory bowel disease, and in the prevalence of food allergies, particularly in children.\",\n \"corpus_id\": 11253120,\n \"score\": 1\n },\n {\n \"doc_id\": \"27886128\",\n \"title\": \"Worldwide Mycotoxins Exposure in Pig and Poultry Feed Formulations.\",\n \"abstract\": \"The purpose of this review is to present information about raw materials that can be used in pig and poultry diets and the factors responsible for variations in their mycotoxin contents. The levels of mycotoxins in pig and poultry feeds are calculated based on mycotoxin contamination levels of the raw materials with different diet formulations, to highlight the important role the stage of production and the raw materials used can have on mycotoxins levels in diets. Our analysis focuses on mycotoxins for which maximum tolerated levels or regulatory guidelines exist, and for which sufficient contamination data are available. Raw materials used in feed formulation vary considerably depending on the species of animal, and the stage of production. Mycotoxins are secondary fungal metabolites whose frequency and levels also vary considerably depending on the raw materials used and on the geographic location where they were produced. Although several reviews of existing data and of the literature on worldwide mycotoxin contamination of food and feed are available, the impact of the different raw materials used on feed formulation has not been widely studied.\",\n \"corpus_id\": 14369542,\n \"score\": 1\n },\n {\n \"doc_id\": \"27924528\",\n \"title\": \"Mycotoxins: An Underhand Food Problem.\",\n \"abstract\": \"Among the food safety issues, the occurrence of fungal species able to produce toxic metabolites on the agro-food products has acquired a general attention. These compounds, the mycotoxins, generally provided of low molecular weight, are the result of the secondary metabolism of the toxigenic fungi. They may have toxic activity toward the plants, but mostly represent a serious risk for human and animal health worldwide, since they can be accumulated on many final crop products and they have a broad range of toxic biological activities. In particular, mainly cereals are the most sensitive crops to the colonization of toxigenic fungal species which accumulate in the grains the related mycotoxins both in the field, until the harvest stage, and in the storage. According to a Food and Agriculture Organization study, approximately 25 % of the global food and feed output is contaminated by mycotoxins. Therefore, since a large proportion of the world's population consumes, as a staple food, the cereals, the consumption of mycotoxin-contaminated cereals is a main issue for health risk worldwide. Furthermore, mycotoxin contamination can have a huge economic and social impact, especially when mycotoxin occurrence on the food commodities is over the regulation limits established by different national and transnational institutions, implying that contaminated products must be discarded. Finally, the climate change due to the global warming can alter stages and rates of toxigenic fungi development and modify host-resistance and host-pathogen interactions, influencing deeply also the conditions for mycotoxin production that vary for each individual pathogen. New combinations of mycotoxins/host plants/geographical areas are arising to the attention of the scientific community and require new diagnostic tools and deeper knowledge of both biology and genetics of toxigenic fungi. Moreover, to spread awareness and knowledge at international level on both the hazard that mycotoxins represent for consumers and costs for stakeholders is of key importance for developing all possible measures aimed to control such dangerous contaminants worldwide.\",\n \"corpus_id\": 8001329,\n \"score\": 1\n },\n {\n \"doc_id\": \"27929415\",\n \"title\": \"Co-Occurrence of Regulated, Masked and Emerging Mycotoxins and Secondary Metabolites in Finished Feed and Maize-An Extensive Survey.\",\n \"abstract\": \"Global trade of agricultural commodities (e.g., animal feed) requires monitoring for fungal toxins. Also, little is known about masked and emerging toxins and metabolites. 1926 samples from 52 countries were analysed for toxins and metabolites. Of 162 compounds detected, up to 68 metabolites were found in a single sample. A subset of 1113 finished feed, maize and maize silage samples containing 57 compounds from 2012 to 2015 from 44 countries was investigated using liquid chromatography and mass spectrometry. Deoxynivalenol (DON), zearalenone (ZEN) and fumonisins showed large increases of annual medians in Europe. Within a region, distinct trends were observed, suggesting importance of local meteorology and cultivars. In 2015, median DON concentrations increased to 1400 μ g·kg - 1 in Austria, but were stable in Germany at 350 μ g·kg - 1 . In 2014, enniatins occurred at median concentrations of 250 μ g·kg - 1 in Europe, at levels similar to DON and ZEN. The latter were frequently correlated with DON-3-glucoside and ZEN-14-sulfate. Co-occurrence of regulated toxins was frequent with e.g., enniatins, and moniliformin. Correlation was observed between DON and DON-3-glucoside and with beauvericin. Results indicate that considerably more than 25% of agricultural commodities could be contaminated with mycotoxins as suggested by FAO, although this is at least partly due to the lower limits of detection in the current survey. Observed contamination percentages ranged from 7.1 to 79% for B trichothecenes and 88% for ZEN.\",\n \"corpus_id\": 790135,\n \"score\": 1\n },\n {\n \"doc_id\": \"28067768\",\n \"title\": \"The Status of Fusarium Mycotoxins in Sub-Saharan Africa: A Review of Emerging Trends and Post-Harvest Mitigation Strategies towards Food Control.\",\n \"abstract\": \"Fusarium fungi are common plant pathogens causing several plant diseases. The presence of these molds in plants exposes crops to toxic secondary metabolites called Fusarium mycotoxins. The most studied Fusarium mycotoxins include fumonisins, zearalenone, and trichothecenes. Studies have highlighted the economic impact of mycotoxins produced by Fusarium. These arrays of toxins have been implicated as the causal agents of wide varieties of toxic health effects in humans and animals ranging from acute to chronic. Global surveillance of Fusarium mycotoxins has recorded significant progress in its control; however, little attention has been paid to Fusarium mycotoxins in sub-Saharan Africa, thus translating to limited occurrence data. In addition, legislative regulation is virtually non-existent. The emergence of modified Fusarium mycotoxins, which may contribute to additional toxic effects, worsens an already precarious situation. This review highlights the status of Fusarium mycotoxins in sub-Saharan Africa, the possible food processing mitigation strategies, as well as future perspectives.\",\n \"corpus_id\": 17214000,\n \"score\": 1\n },\n {\n \"doc_id\": \"28125272\",\n \"title\": \"Mechanisms of cell death induction by food-borne mycotoxins.\",\n \"abstract\": \"Mycotoxins are secondary metabolites of fungi that contaminate a wide range of foods and feeds. Mycotoxin contamination is considered to be an important risk factor for food safety which poses serious threat to human and animal health. Cell death induction is suggested to be the key cellular event contributed to the pleiotropically toxic effects of mycotoxins. During the past decades, substantial progress has been made in uncovering the mechanisms of cell death induction by mycotoxins. Understanding of the mechanisms underlying mycotoxin-induced cytotoxicity will benefit the development of effective strategies for the management of mycotoxin-associated health issues. The current review will discuss the types of cell death induced by mycotoxins and summarize the present understanding of signaling pathways involved in mycotoxin-mediated cytotoxicities.\",\n \"corpus_id\": 13767530,\n \"score\": 1\n },\n {\n \"doc_id\": \"28244108\",\n \"title\": \"Occurrence of multiple mycotoxins and other fungal metabolites in animal feed and maize samples from Egypt using LC-MS/MS.\",\n \"abstract\": \"BACKGROUND: The present study aimed to investigate the occurrence of multiple toxic fungal and bacterial metabolites in 156 animal feed (n = 77) and maize (n = 79) samples collected from three regions in Upper Egypt. The target analytes were quantified using the 'dilute and shoot' approach, followed by a liquid chromatography tandem mass spectrometry analysis. RESULTS: In total, 115 fungal and bacterial metabolites were detected in both matrices, including the regulated mycotoxins in the European Union, in addition to the modified forms such as deoxynivalenol-3-glucosid. Furthermore, some Fusarium, Alternaria, Aspergillus and Penicillum metabolites beside other fungal and bacterial metabolites were detected for the first time in Egypt. All of the samples were contaminated with at least four toxins. On average, 26 different metabolites were detected per sample with a trend of more metabolites in feed than in maize. The maximum number of analytes observed per samples was 54 analytes at maximum concentrations ranging from 0.04 µg kg(-1) for tentoxin to 25 040 µg kg(-1) for kojic acid. CONCLUSION: According to the international standards, the contamination rates in the investigated regions were not alarming, except for AFB1 in maize. The necessity of further and continuous monitoring is highly recommended to establish a database for mycotoxin occurrence. © 2017 Society of Chemical Industry.\",\n \"corpus_id\": 34085555,\n \"score\": 1\n },\n {\n \"doc_id\": \"28608841\",\n \"title\": \"Occurrence, Toxicity, and Analysis of Major Mycotoxins in Food.\",\n \"abstract\": \"Mycotoxins are toxic secondary metabolites produced by certain filamentous fungi (molds). These low molecular weight compounds (usually less than 1000 Daltons) are naturally occurring and practically unavoidable. They can enter our food chain either directly from plant-based food components contaminated with mycotoxins or by indirect contamination from the growth of toxigenic fungi on food. Mycotoxins can accumulate in maturing corn, cereals, soybeans, sorghum, peanuts, and other food and feed crops in the field and in grain during transportation. Consumption of mycotoxin-contaminated food or feed can cause acute or chronic toxicity in human and animals. In addition to concerns over adverse effects from direct consumption of mycotoxin-contaminated foods and feeds, there is also public health concern over the potential ingestion of animal-derived food products, such as meat, milk, or eggs, containing residues or metabolites of mycotoxins. Members of three fungal genera, Aspergillus, Fusarium, and Penicillium, are the major mycotoxin producers. While over 300 mycotoxins have been identified, six (aflatoxins, trichothecenes, zearalenone, fumonisins, ochratoxins, and patulin) are regularly found in food, posing unpredictable and ongoing food safety problems worldwide. This review summarizes the toxicity of the six mycotoxins, foods commonly contaminated by one or more of them, and the current methods for detection and analysis of these mycotoxins.\",\n \"corpus_id\": 5398472,\n \"score\": 1\n },\n {\n \"doc_id\": \"29243648\",\n \"title\": \"Recent developments and applications of surface plasmon resonance biosensors for the detection of mycotoxins in foodstuffs.\",\n \"abstract\": \"Over the past 10years, great efforts on the development of methods for rapid mycotoxin detection in foodstuffs have been made. As one of the relatively new analytical techniques, surface plasmon resonance (SPR) has been proven particularly advantageous for rapid, label-free, sensitive analyte detection. Using SPR, qualitative and quantitative analysis can be performed in real-time. Mycotoxins are a group of small, toxic products formed as secondary metabolites by a few fungal species. They can contaminate foodstuffs on a large scale and consequently threaten human health through food chain. Thus, rapid, sensitive, and selective determination of mycotoxin is of great significance for the food safety. This contribution addresses the basic principle of SPR, the existing detection methods, and the progress on mycotoxin detection using SPR biosensor.\",\n \"corpus_id\": 29689230,\n \"score\": 1\n },\n {\n \"doc_id\": \"29384153\",\n \"title\": \"Advances, challenges and opportunities for point-of-need screening of mycotoxins in foods and feeds.\",\n \"abstract\": \"The assurance of food and feed safety, including the identification and effective monitoring of multiple biological and chemical hazards, is a major societal challenge, given the increasing pace at which food commodities are demanded, produced and traded across the globe. Within this context, mycotoxins are globally widespread secondary fungal metabolites, which can contaminate crops either in the field or during storage and have serious human and animal health impacts such as carcinogenic, teratogenic and hepatotoxic effects. Therefore, their presence in a wide range of foods and feeds is strictly regulated, particularly in the European Union. In order to perform effective and routine monitoring of mycotoxin levels in the field prior to further processing, during transport or during processing, rapid, simple, portable and sensitive means of screening of regulated mycotoxins are in high demand. This review focuses on (1) discussing the relevance of mycotoxins and the standard approaches for their sampling and monitoring; and (2) compiling and discussing recent advances in miniaturized analytical tools for mycotoxin detection. This provides insights into current research efforts and opportunities to develop a truly integrated and fit-for-purpose analytical tool, suitable for use at critical points of the food, feed and raw material processing and distribution chains.\",\n \"corpus_id\": 3542968,\n \"score\": 1\n },\n {\n \"doc_id\": \"29685276\",\n \"title\": \"Silage review: Mycotoxins in silage: Occurrence, effects, prevention, and mitigation.\",\n \"abstract\": \"Ensiled forage, particularly corn silage, is an important component of dairy cow diets worldwide. Forages can be contaminated with several mycotoxins in the field pre-harvest, during storage, or after ensiling during feed-out. Exposure to dietary mycotoxins adversely affects the performance and health of livestock and can compromise human health. Several studies and surveys indicate that ruminants are often exposed to mycotoxins such as aflatoxins, trichothecenes, ochratoxin A, fumonisins, zearalenone, and many other fungal secondary metabolites, via the silage they ingest. Problems associated with mycotoxins in silage can be minimized by preventing fungal growth before and after ensiling. Proper silage management is essential to reduce mycotoxin contamination of dairy cow feeds, and certain mold-inhibiting chemical additives or microbial inoculants can also reduce the contamination levels. Several sequestering agents also can be added to diets to reduce mycotoxin levels, but their efficacy varies with the type and level of mycotoxin contamination. This article gives an overview of the types, prevalence, and levels of mycotoxin contamination in ensiled forages in different countries, and describes their adverse effects on health of ruminants, and effective prevention and mitigation strategies for dairy cow diets. Future research priorities discussed include research efforts to develop silage additives or rumen microbial innocula that degrade mycotoxins.\",\n \"corpus_id\": 13811861,\n \"score\": 1\n },\n {\n \"doc_id\": \"29766989\",\n \"title\": \"Mycotoxins and the intestine.\",\n \"abstract\": \"Fungal biochemical pathways can yield various compounds that are not considered to be necessary for their growth and are thus referred to as secondary metabolites. These compounds have been found to have wide ranging biological effects and include potent poisons (mycotoxins). Mycotoxins invariably contaminate crops and (thus) animal feeds. The intestine is the key link between ingested mycotoxins and their detrimental effects on the animal. Effects on the intestine, or intestinal environment, and immune system have been reported with various mycotoxins. These effects are almost certainly occurring across species. Most, if not all, of the reported effects of mycotoxins are negative in terms of intestinal health, for example, decreased intestinal cell viability, reductions in short chain fatty acid (SCFA) concentrations and elimination of beneficial bacteria, increased expression of genes involved in promoting inflammation and counteracting oxidative stress. This challenge to intestinal health will predispose the animal to intestinal (and systemic) infections and impair efficient digestion and absorption of nutrients, with the associated effect on animal productivity.\",\n \"corpus_id\": 21706057,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":62,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29681764\",\n \"title\": \"Galaxy rotation curves via conformal factors.\",\n \"abstract\": \"We propose a new formula to explain circular velocity profiles of spiral galaxies obtained from the Starobinsky model in the Palatini formalism. It is based on the assumption that the gravity can be described by two conformally related metrics: one of them is responsible for the measurement of distances, while the other, the so-called dark metric, is responsible for a geodesic equation and therefore can be used for the description of the velocity profile. The formula is tested against a subset of galaxies taken from the HI Nearby Galaxy Survey (THINGS).\",\n \"corpus_id\": 4991752\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"21517292","title":"Impact of a global quadratic potential on galactic rotation curves.","abstract":"We present a conformal gravity fit to the 20 largest of a sample of 110 spiral galaxies. We identify the presence of a universal quadratic potential V(κ)(r)=-κc²r²/2 with κ=9.54×10⁻⁵⁴ cm⁻² induced by cosmic inhomogeneities. When V(κ)(r) is taken in conjunction with both a universal linear potential V(γ₀)(r)=γ₀c²r/2 with γ₀=3.06×10⁻³⁰ cm⁻¹ generated by the homogeneous cosmic background and the contribution generated by the local luminous matter in galaxies, the theory then accounts for the rotation curve systematics observed in the entire 110 galaxies, without the need for any dark matter whatsoever. Our study suggests that using dark matter may be nothing more than an attempt to describe global effects in purely local galactic terms. With V(κ)(r) being negative, galaxies can only support bound orbits up to distances of order γ₀/κ=100kpc, with global physics imposing a limit on the size of galaxies.","corpus_id":18044816,"score":2},{"doc_id":"23931350","title":"Testing the MOND paradigm of modified dynamics with galaxy-galaxy gravitational lensing.","abstract":"The MOND paradigm of modified dynamics predicts that the asymptotic gravitational potential of an isolated, bounded (baryonic) mass, M, is ϕ(r)=(MGa0)1/2ln(r). Relativistic MOND theories predict that the lensing effects of M are dictated by ϕ(r) as general-relativity lensing is dictated by the Newtonian potential. Thus MOND predicts that the asymptotic Newtonian potential deduced from galaxy-galaxy gravitational lensing will have (1) a logarithmic r dependence, and (2) a normalization (parametrized standardly as 2σ2) that depends only on M: σ=(MGa0/4)1/4. I compare these predictions with recent results of galaxy-galaxy lensing, and find agreement on all counts. For the “blue”-lenses subsample (“spiral” galaxies) MOND reproduces the observations well with an r′-band M/Lr′∼(1–3)(M/L)⊙, and for “red” lenses (“elliptical” galaxies) with M/Lr′∼(3–6)(M/L)⊙, both consistent with baryons only. In contradistinction, Newtonian analysis requires, typically, M/Lr′∼130(M/L)⊙, bespeaking a mass discrepancy of a factor ∼40. Compared with the staple, rotation-curve tests, MOND is here tested in a wider population of galaxies, through a different phenomenon, using relativistic test objects, and is probed to several-times-lower accelerations–as low as a few percent of a0.","corpus_id":37710554,"score":2},{"doc_id":"19892973","title":"Einstein's theory of gravity and the problem of missing mass.","abstract":"The observed matter in the universe accounts for just 5% of the observed gravity. A possible explanation is that Newton's and Einstein's theories of gravity fail where gravity is either weak or enhanced. The modified theory of Newtonian dynamics (MOND) reproduces, without dark matter, spiral-galaxy orbital motions and the relation between luminosity and rotation in galaxies, although not in clusters. Recent extensions of Einstein's theory are theoretically more complete. They inevitably include dark fields that seed structure growth, and they may explain recent weak lensing data. However, the presence of dark fields reduces calculability and comes at the expense of the original MOND premise, that the matter we see is the sole source of gravity. Observational tests of the relic radiation, weak lensing, and the growth of structure may distinguish modified gravity from dark matter.","corpus_id":889826,"score":1},{"doc_id":"20220843","title":"Confirmation of general relativity on large scales from weak lensing and galaxy velocities.","abstract":"Although general relativity underlies modern cosmology, its applicability on cosmological length scales has yet to be stringently tested. Such a test has recently been proposed, using a quantity, E(G), that combines measures of large-scale gravitational lensing, galaxy clustering and structure growth rate. The combination is insensitive to 'galaxy bias' (the difference between the clustering of visible galaxies and invisible dark matter) and is thus robust to the uncertainty in this parameter. Modified theories of gravity generally predict values of E(G) different from the general relativistic prediction because, in these theories, the 'gravitational slip' (the difference between the two potentials that describe perturbations in the gravitational metric) is non-zero, which leads to changes in the growth of structure and the strength of the gravitational lensing effect. Here we report that E(G) = 0.39 +/- 0.06 on length scales of tens of megaparsecs, in agreement with the general relativistic prediction of E(G) approximately 0.4. The measured value excludes a model within the tensor-vector-scalar gravity theory, which modifies both Newtonian and Einstein gravity. However, the relatively large uncertainty still permits models within f(R) theory, which is an extension of general relativity. A fivefold decrease in uncertainty is needed to rule out these models.","corpus_id":205219902,"score":1},{"doc_id":"21517295","title":"Novel test of modified Newtonian dynamics with gas rich galaxies.","abstract":"The current cosmological paradigm, the cold dark matter model with a cosmological constant, requires that the mass-energy of the Universe be dominated by invisible components: dark matter and dark energy. An alternative to these dark components is that the law of gravity be modified on the relevant scales. A test of these ideas is provided by the baryonic Tully-Fisher relation (BTFR), an empirical relation between the observed mass of a galaxy and its rotation velocity. Here, I report a test using gas rich galaxies for which both axes of the BTFR can be measured independently of the theories being tested and without the systematic uncertainty in stellar mass that affects the same test with star dominated spirals. The data fall precisely where predicted a priori by the modified Newtonian dynamics. The scatter in the BTFR is attributable entirely to observational uncertainty, consistent with a single effective force law.","corpus_id":263792143,"score":1},{"doc_id":"22810697","title":"High velocity dispersion in a rare grand-design spiral galaxy at redshift z = 2.18.","abstract":"Although grand-design spiral galaxies are relatively common in the local Universe, only one has been spectroscopically confirmed to lie at redshift z > 2 (HDFX 28; z = 2.011); and it may prove to be a major merger that simply resembles a spiral in projection. The rarity of spirals has been explained as a result of disks being dynamically 'hot' at z > 2 (refs 2-5), which may instead favour the formation of commonly observed clumpy structures. Alternatively, current instrumentation may simply not be sensitive enough to detect spiral structures comparable to those in the modern Universe. At z < 2, the velocity dispersion of disks decreases, and spiral galaxies are more numerous by z ≈ 1 (refs 7, 13-15). Here we report observations of the grand-design spiral galaxy Q2343-BX442 at z = 2.18. Spectroscopy of ionized gas shows that the disk is dynamically hot, implying an uncertain origin for the spiral structure. The kinematics of the galaxy are consistent with a thick disk undergoing a minor merger, which can drive the formation of short-lived spiral structure. A duty cycle of <100 Myr for such tidally induced spiral structure in a hot massive disk is consistent with its rarity.","corpus_id":205229562,"score":1},{"doc_id":"24949751","title":"Clear and measurable signature of modified gravity in the galaxy velocity field.","abstract":"The velocity field of dark matter and galaxies reflects the continued action of gravity throughout cosmic history. We show that the low-order moments of the pairwise velocity distribution v_{12} are a powerful diagnostic of the laws of gravity on cosmological scales. In particular, the projected line-of-sight galaxy pairwise velocity dispersion σ_{12}(r) is very sensitive to the presence of modified gravity. Using a set of high-resolution N-body simulations, we compute the pairwise velocity distribution and its projected line-of-sight dispersion for a class of modified gravity theories: the chameleon f(R) gravity and Galileon gravity (cubic and quartic). The velocities of dark matter halos with a wide range of masses would exhibit deviations from general relativity at the (5-10)σ level. We examine strategies for detecting these deviations in galaxy redshift and peculiar velocity surveys. If detected, this signature would be a \"smoking gun\" for modified gravity.","corpus_id":7074456,"score":1},{"doc_id":"27274704","title":"The different baryonic Tully-Fisher relations at low masses.","abstract":"We compare the Baryonic Tully-Fisher relation (BTFR) of simulations and observations of galaxies ranging from dwarfs to spirals, using various measures of rotational velocity Vrot. We explore the BTFR when measuring Vrot at the flat part of the rotation curve, Vflat, at the extent of H i gas, Vlast, and using 20 per cent (W20) and 50 per cent (W50) of the width of H i line profiles. We also compare with the maximum circular velocity of the parent halo, [Formula: see text], within dark matter only simulations. The different BTFRs increasingly diverge as galaxy mass decreases. Using Vlast one obtains a power law over four orders of magnitude in baryonic mass, with slope similar to the observed BTFR. Measuring Vflat gives similar results as Vlast when galaxies with rising rotation curves are excluded. However, higher rotation velocities would be found for low-mass galaxies if the cold gas extended far enough for Vrot to reach a maximum. W20 gives a similar slope as Vlast but with slightly lower values of Vrot for low-mass galaxies, although this may depend on the extent of the gas in your galaxy sample. W50 bends away from these other relations towards low velocities at low masses. By contrast, [Formula: see text] bends towards high velocities for low-mass galaxies, as cold gas does not extend out to the radius at which haloes reach [Formula: see text]. Our study highlights the need for careful comparisons between observations and models: one needs to be consistent about the particular method of measuring Vrot, and precise about the radius at which velocities are measured.","corpus_id":41639803,"score":1},{"doc_id":"27279784","title":"Modelling galaxy clustering: halo occupation distribution versus subhalo matching.","abstract":"We model the luminosity-dependent projected and redshift-space two-point correlation functions (2PCFs) of the Sloan Digital Sky Survey (SDSS) Data Release 7 Main galaxy sample, using the halo occupation distribution (HOD) model and the subhalo abundance matching (SHAM) model and its extension. All the models are built on the same high-resolution N-body simulations. We find that the HOD model generally provides the best performance in reproducing the clustering measurements in both projected and redshift spaces. The SHAM model with the same halo-galaxy relation for central and satellite galaxies (or distinct haloes and subhaloes), when including scatters, has a best-fitting χ(2)/dof around 2-3. We therefore extend the SHAM model to the subhalo clustering and abundance matching (SCAM) by allowing the central and satellite galaxies to have different galaxy-halo relations. We infer the corresponding halo/subhalo parameters by jointly fitting the galaxy 2PCFs and abundances and consider subhaloes selected based on three properties, the mass Macc at the time of accretion, the maximum circular velocity Vacc at the time of accretion, and the peak maximum circular velocity Vpeak over the history of the subhaloes. The three subhalo models work well for luminous galaxy samples (with luminosity above L*). For low-luminosity samples, the Vacc model stands out in reproducing the data, with the Vpeak model slightly worse, while the Macc model fails to fit the data. We discuss the implications of the modelling results.","corpus_id":25248798,"score":1},{"doc_id":"28474932","title":"Mass-Discrepancy Acceleration Relation: A Natural Outcome of Galaxy Formation in Cold Dark Matter Halos.","abstract":"We analyze the total and baryonic acceleration profiles of a set of well-resolved galaxies identified in the eagle suite of hydrodynamic simulations. Our runs start from the same initial conditions but adopt different prescriptions for unresolved stellar and active galactic nuclei feedback, resulting in diverse populations of galaxies by the present day. Some of them reproduce observed galaxy scaling relations, while others do not. However, regardless of the feedback implementation, all of our galaxies follow closely a simple relationship between the total and baryonic acceleration profiles, consistent with recent observations of rotationally supported galaxies. The relation has small scatter: Different feedback implementations-which produce different galaxy populations-mainly shift galaxies along the relation rather than perpendicular to it. Furthermore, galaxies exhibit a characteristic acceleration g_{†}, above which baryons dominate the mass budget, as observed. These observations, consistent with simple modified Newtonian dynamics, can be accommodated within the standard cold dark matter paradigm.","corpus_id":38545116,"score":1},{"doc_id":"28949220","title":"Self-Interacting Dark Matter Can Explain Diverse Galactic Rotation Curves.","abstract":"The rotation curves of spiral galaxies exhibit a diversity that has been difficult to understand in the cold dark matter (CDM) paradigm. We show that the self-interacting dark matter (SIDM) model provides excellent fits to the rotation curves of a sample of galaxies with asymptotic velocities in the 25-300 km/s range that exemplify the full range of diversity. We assume only the halo concentration-mass relation predicted by the CDM model and a fixed value of the self-interaction cross section. In dark-matter-dominated galaxies, thermalization due to self-interactions creates large cores and reduces dark matter densities. In contrast, thermalization leads to denser and smaller cores in more luminous galaxies and naturally explains the flatness of rotation curves of the highly luminous galaxies at small radii. Our results demonstrate that the impact of the baryons on the SIDM halo profile and the scatter from the assembly history of halos as encoded in the concentration-mass relation can explain the diverse rotation curves of spiral galaxies.","corpus_id":38659240,"score":1},{"doc_id":"18235494","title":"A test of the nature of cosmic acceleration using galaxy redshift distortions.","abstract":"Observations of distant supernovae indicate that the Universe is now in a phase of accelerated expansion the physical cause of which is a mystery. Formally, this requires the inclusion of a term acting as a negative pressure in the equations of cosmic expansion, accounting for about 75 per cent of the total energy density in the Universe. The simplest option for this 'dark energy' corresponds to a 'cosmological constant', perhaps related to the quantum vacuum energy. Physically viable alternatives invoke either the presence of a scalar field with an evolving equation of state, or extensions of general relativity involving higher-order curvature terms or extra dimensions. Although they produce similar expansion rates, different models predict measurable differences in the growth rate of large-scale structure with cosmic time. A fingerprint of this growth is provided by coherent galaxy motions, which introduce a radial anisotropy in the clustering pattern reconstructed by galaxy redshift surveys. Here we report a measurement of this effect at a redshift of 0.8. Using a new survey of more than 10,000 faint galaxies, we measure the anisotropy parameter beta = 0.70 +/- 0.26, which corresponds to a growth rate of structure at that time of f = 0.91 +/- 0.36. This is consistent with the standard cosmological-constant model with low matter density and flat geometry, although the error bars are still too large to distinguish among alternative origins for the accelerated expansion. The correct origin could be determined with a further factor-of-ten increase in the sampled volume at similar redshift.","corpus_id":4403989,"score":0},{"doc_id":"18352285","title":"Conformal curves on the WO3 surface.","abstract":"We have studied the isoheight lines on the WO3 surface as a physical candidate for conformally invariant curves. We have shown that these lines are conformally invariant with the same statistics of domain walls in the critical Ising model. They belong to the family of conformal invariant curves called Schramm-Loewner evolution (or SLE(kappa)), with diffusivity of kappa approximately 3. This can be regarded as the first experimental observation of SLE curves. We have also argued that Ballistic Deposition (BD) can serve as a growth model giving rise to contours with similar statistics at large scales.","corpus_id":39009580,"score":0},{"doc_id":"18756252","title":"A common mass scale for satellite galaxies of the Milky Way.","abstract":"The Milky Way has at least twenty-three known satellite galaxies that shine with luminosities ranging from about a thousand to a billion times that of the Sun. Half of these galaxies were discovered in the past few years in the Sloan Digital Sky Survey, and they are among the least luminous galaxies in the known Universe. A determination of the mass of these galaxies provides a test of galaxy formation at the smallest scales and probes the nature of the dark matter that dominates the mass density of the Universe. Here we use new measurements of the velocities of the stars in these galaxies to show that they are consistent with them having a common mass of about 10(7) within their central 300 parsecs. This result demonstrates that the faintest of the Milky Way satellites are the most dark-matter-dominated galaxies known, and could be a hint of a new scale in galaxy formation or a characteristic scale for the clustering of dark matter.","corpus_id":4373541,"score":0},{"doc_id":"18843363","title":"The formation and assembly of a typical star-forming galaxy at redshift z approximately 3.","abstract":"Recent studies of galaxies approximately 2-3 Gyr after the Big Bang have revealed large, rotating disks, similar to those of galaxies today. The existence of well-ordered rotation in galaxies during this peak epoch of cosmic star formation indicates that gas accretion is likely to be the dominant mode by which galaxies grow, because major mergers of galaxies would completely disrupt the observed velocity fields. But poor spatial resolution and sensitivity have hampered this interpretation; such studies have been limited to the largest and most luminous galaxies, which may have fundamentally different modes of assembly from those of more typical galaxies (which are thought to grow into the spheroidal components at the centres of galaxies similar to the Milky Way). Here we report observations of a typical star-forming galaxy at z = 3.07, with a linear resolution of approximately 100 parsecs. We find a well-ordered compact source in which molecular gas is being converted efficiently into stars, likely to be assembling a spheroidal bulge similar to those seen in spiral galaxies at the present day. The presence of undisrupted rotation may indicate that galaxies such as the Milky Way gain much of their mass by accretion rather than major mergers.","corpus_id":4422629,"score":0},{"doc_id":"19340075","title":"Early assembly of the most massive galaxies.","abstract":"The current consensus is that galaxies begin as small density fluctuations in the early Universe and grow by in situ star formation and hierarchical merging. Stars begin to form relatively quickly in sub-galactic-sized building blocks called haloes which are subsequently assembled into galaxies. However, exactly when this assembly takes place is a matter of some debate. Here we report that the stellar masses of brightest cluster galaxies, which are the most luminous objects emitting stellar light, some 9 billion years ago are not significantly different from their stellar masses today. Brightest cluster galaxies are almost fully assembled 4-5 billion years after the Big Bang, having grown to more than 90 per cent of their final stellar mass by this time. Our data conflict with the most recent galaxy formation models based on the largest simulations of dark-matter halo development. These models predict protracted formation of brightest cluster galaxies over a Hubble time, with only 22 per cent of the stellar mass assembled at the epoch probed by our sample. Our findings suggest a new picture in which brightest cluster galaxies experience an early period of rapid growth rather than prolonged hierarchical assembly.","corpus_id":4386728,"score":0},{"doc_id":"19661911","title":"A high stellar velocity dispersion for a compact massive galaxy at redshift z = 2.186.","abstract":"Recent studies have found that the oldest and most luminous galaxies in the early Universe are surprisingly compact, having stellar masses similar to present-day elliptical galaxies but much smaller sizes. This finding has attracted considerable attention, as it suggests that massive galaxies have grown in size by a factor of about five over the past ten billion years (10 Gyr). A key test of these results is a determination of the stellar kinematics of one of the compact galaxies: if the sizes of these objects are as extreme as has been claimed, their stars are expected to have much higher velocities than those in present-day galaxies of the same mass. Here we report a measurement of the stellar velocity dispersion of a massive compact galaxy at redshift z = 2.186, corresponding to a look-back time of 10.7 Gyr. The velocity dispersion is very high at km s(-1), consistent with the mass and compactness of the galaxy inferred from photometric data. This would indicate significant recent structural and dynamical evolution of massive galaxies over the past 10 Gyr. The uncertainty in the dispersion was determined from simulations that include the effects of noise and template mismatch. However, we cannot exclude the possibility that some subtle systematic effect may have influenced the analysis, given the low signal-to-noise ratio of our spectrum.","corpus_id":4429718,"score":0},{"doc_id":"19792482","title":"Size bias in galaxy surveys.","abstract":"Only certain galaxies are included in surveys: those bright and large enough to be detectable as extended sources. Because gravitational lensing can make galaxies appear both brighter and larger, the presence of foreground inhomogeneities can scatter galaxies across not only magnitude cuts but also size cuts, changing the statistical properties of the resulting catalog. Here we explore this size bias and how it combines with magnification bias to affect galaxy statistics. We demonstrate that photometric galaxy samples from current and upcoming surveys can be even more affected by size bias than by magnification bias.","corpus_id":38220338,"score":0},{"doc_id":"20161594","title":"Automatic morphological classification of galaxy images.","abstract":"We describe an image analysis supervised learning algorithm that can automatically classify galaxy images. The algorithm is first trained using a manually classified images of elliptical, spiral, and edge-on galaxies. A large set of image features is extracted from each image, and the most informative features are selected using Fisher scores. Test images can then be classified using a simple Weighted Nearest Neighbor rule such that the Fisher scores are used as the feature weights. Experimental results show that galaxy images from Galaxy Zoo can be classified automatically to spiral, elliptical and edge-on galaxies with accuracy of ~90% compared to classifications carried out by the author. Full compilable source code of the algorithm is available for free download, and its general-purpose nature makes it suitable for other uses that involve automatic image analysis of celestial objects.","corpus_id":1389063,"score":0},{"doc_id":"20520705","title":"Nearby galaxies as pointers to a better theory of cosmic evolution.","abstract":"The great advances in the network of cosmological tests show that the relativistic Big Bang theory is a good description of our expanding Universe. However, the properties of nearby galaxies that can be observed in greatest detail suggest that a better theory would describe a mechanism by which matter is more rapidly gathered into galaxies and groups of galaxies. This more rapid growth occurs in some theoretical ideas now under discussion.","corpus_id":43767061,"score":0},{"doc_id":"20724628","title":"Cosmological constraints from strong gravitational lensing in clusters of galaxies.","abstract":"Current efforts in observational cosmology are focused on characterizing the mass-energy content of the universe. We present results from a geometric test based on strong lensing in galaxy clusters. Based on Hubble Space Telescope images and extensive ground-based spectroscopic follow-up of the massive galaxy cluster Abell 1689, we used a parametric model to simultaneously constrain the cluster mass distribution and dark energy equation of state. Combining our cosmological constraints with those from x-ray clusters and the Wilkinson Microwave Anisotropy Probe 5-year data gives Omega(m) = 0.25 +/- 0.05 and w(x) = -0.97 +/- 0.07, which are consistent with results from other methods. Inclusion of our method with all other available techniques brings down the current 2sigma contours on the dark energy equation-of-state parameter w(x) by approximately 30%.","corpus_id":7832717,"score":0},{"doc_id":"21107424","title":"A geometric measure of dark energy with pairs of galaxies.","abstract":"Observations indicate that the expansion of the Universe is accelerating, which is attributed to a ‘dark energy’ component that opposes gravity. There is a purely geometric test of the expansion of the Universe (the Alcock–Paczynski test), which would provide an independent way of investigating the abundance (Ω(X)) and equation of state (W(X)) of dark energy. It is based on an analysis of the geometrical distortions expected from comparing the real-space and redshift-space shape of distant cosmic structures, but it has proved difficult to implement. Here we report an analysis of the symmetry properties of distant pairs of galaxies from archival data. This allows us to determine that the Universe is flat. By alternately fixing its spatial geometry at Ω(k)≡0 and the dark energy equation-of-state parameter at W(X)≡-1, and using the results of baryon acoustic oscillations, we can establish at the 68.3% confidence level that and -0.85>W(X)>-1.12 and 0.60<Ω(X)<0.80.","corpus_id":4426871,"score":0},{"doc_id":"21228776","title":"A massive protocluster of galaxies at a redshift of z ≈ 5.3.","abstract":"Massive clusters of galaxies have been found that date from as early as 3.9 billion years (3.9 Gyr; z = 1.62) after the Big Bang, containing stars that formed at even earlier epochs. Cosmological simulations using the current cold dark matter model predict that these systems should descend from 'protoclusters'-early overdensities of massive galaxies that merge hierarchically to form a cluster. These protocluster regions themselves are built up hierarchically and so are expected to contain extremely massive galaxies that can be observed as luminous quasars and starbursts. Observational evidence for this picture, however, is sparse because high-redshift protoclusters are rare and difficult to observe. Here we report a protocluster region that dates from 1 Gyr (z = 5.3) after the Big Bang. This cluster of massive galaxies extends over more than 13 megaparsecs and contains a luminous quasar as well as a system rich in molecular gas. These massive galaxies place a lower limit of more than 4 × 10(11) solar masses of dark and luminous matter in this region, consistent with that expected from cosmological simulations for the earliest galaxy clusters.","corpus_id":205223398,"score":0},{"doc_id":"21552608","title":"Analysis and modeling of flow in rotating spiral microchannels: towards math-aided design of microfluidic systems using centrifugal pumping.","abstract":"This paper describes the experimental measurement and mathematical modeling of centrifugally-pumped flow in spiral microchannels. Here, the liquid is delivered by the rotation of a circular microchip as depicted before (X. Y. Peng, P. C. H. Li, H. Z. Yu, M. Parameswaran and W. L. Chou, Sens. Actuators, B, 2007, 128, 64-69). The spiral microchannel in it was specially designed to produce a constant centrifugal force component. From experimental measurements, it was found that the flow velocity inside the spiral microchannels was associated with the rotation speed only, but not with the length of the liquid column. The mathematical modeling of liquid flow was constructed based on solving the Navier-Stokes equations of incompressible flow formulated in a new orthogonal curvilinear coordinate system aligned with the channel geometry. The governing equations were simplified under various assumptions, rendering a mathematically-tractable physical model. In addition, a commercial computational fluid dynamics (CFD) program was used to simulate the flow in the spiral microchannel. The predicted liquid flow velocities from the mathematical model and the CFD program showed reasonable agreement with the experimental data. Under proper assumptions, the mathematical model gave a flexible and rather accurate analytical solution using much less computing power. The proposed study demonstrated the effectiveness of the spiral microchannel design in microfluidic applications using centrifugal force. With modifications, this study could be adapted to the simulation and modeling of other centrifugal-pumping microflow systems.","corpus_id":35720599,"score":0},{"doc_id":"21635025","title":"Cores in dwarf galaxies from dark matter with a Yukawa potential.","abstract":"We show that cold dark matter particles interacting through a Yukawa potential could naturally explain the recently observed cores in dwarf galaxies without affecting the dynamics of objects with a much larger velocity dispersion, such as clusters of galaxies. The velocity dependence of the associated cross section as well as the possible exothermic nature of the interaction alleviates earlier concerns about strongly interacting dark matter. Dark matter evaporation in low-mass objects might explain the observed deficit of satellite galaxies in the Milky Way halo and have important implications for the first galaxies and reionization.","corpus_id":29767392,"score":0},{"doc_id":"21737732","title":"Galaxy evolution. Galactic paleontology.","abstract":"Individual low-mass stars have very long lives, comparable to the age of the universe, and can thus be used to probe ancient star formation. At present, such stars can be identified and studied only in the Milky Way and in the very closest of our neighboring galaxies, which are predominantly small dwarf galaxies. These nearby ancient stars are a fossil record that can provide detailed information about the physical processes that dominated the epoch of galaxy formation and subsequent evolution.","corpus_id":33882128,"score":0},{"doc_id":"21881560","title":"A close nuclear black-hole pair in the spiral galaxy NGC 3393.","abstract":"The current picture of galaxy evolution advocates co-evolution of galaxies and their nuclear massive black holes, through accretion and galactic merging. Pairs of quasars, each with a massive black hole at the centre of its galaxy, have separations of 6,000 to 300,000 light years (refs 2 and 3; 1 parsec = 3.26 light years) and exemplify the first stages of this gravitational interaction. The final stages of the black-hole merging process, through binary black holes and final collapse into a single black hole with gravitational wave emission, are consistent with the sub-light-year separation inferred from the optical spectra and light-variability of two such quasars. The double active nuclei of a few nearby galaxies with disrupted morphology and intense star formation (such as NGC 6240 with a separation of about 2,600 light years and Mrk 463 with a separation of about 13,000 light years between the nuclei) demonstrate the importance of major mergers of equal-mass spiral galaxies in this evolution; such mergers lead to an elliptical galaxy, as in the case of the double-radio-nucleus elliptical galaxy 0402+379 (with a separation of about 24 light years between the nuclei). Minor mergers of a spiral galaxy with a smaller companion should be a more common occurrence, evolving into spiral galaxies with active massive black-hole pairs, but have hitherto not been seen. Here we report the presence of two active massive black holes, separated by about 490 light years, in the Seyfert galaxy NGC 3393 (50 Mpc, about 160 million light years). The regular spiral morphology and predominantly old circum-nuclear stellar population of this galaxy, and the closeness of the black holes embedded in the bulge, provide a hitherto missing observational point to the study of galaxy/black hole evolution. Comparison of our observations with current theoretical models of mergers suggests that they are the result of minor merger evolution.","corpus_id":205226065,"score":0},{"doc_id":"21956329","title":"Gravitational redshift of galaxies in clusters as predicted by general relativity.","abstract":"The theoretical framework of cosmology is mainly defined by gravity, of which general relativity is the current model. Recent tests of general relativity within the Lambda Cold Dark Matter (ΛCDM) model have found a concordance between predictions and the observations of the growth rate and clustering of the cosmic web. General relativity has not hitherto been tested on cosmological scales independently of the assumptions of the ΛCDM model. Here we report an observation of the gravitational redshift of light coming from galaxies in clusters at the 99 per cent confidence level, based on archival data. Our measurement agrees with the predictions of general relativity and its modification created to explain cosmic acceleration without the need for dark energy (the f(R) theory), but is inconsistent with alternative models designed to avoid the presence of dark matter.","corpus_id":4373051,"score":0},{"doc_id":"22084285","title":"One gravitational potential or two? Forecasts and tests.","abstract":"The metric of a perturbed Robertson-Walker space-time is characterized by three functions: a scale-factor giving the expansion history and two potentials that generalize the single potential of Newtonian gravity. The Newtonian potential induces peculiar velocities and, from these, the growth of matter fluctuations. Massless particles respond equally to the Newtonian potential and to a curvature potential. The difference of the two potentials, called the gravitational slip, is predicted to be very small in general relativity, but can be substantial in modified gravity theories. The two potentials can be measured, and gravity tested on cosmological scales, by combining weak gravitational lensing or the integrated Sachs-Wolfe effect with galaxy peculiar velocities or clustering.","corpus_id":299978,"score":0},{"doc_id":"22084295","title":"Designing surveys for tests of gravity.","abstract":"Modified gravity theories may provide an alternative to dark energy to explain cosmic acceleration. We argue that the observational programme developed to test dark energy needs to be augmented to capture new tests of gravity on astrophysical scales. Several distinct signatures of gravity theories exist outside the 'linear' regime, especially owing to the screening mechanism that operates inside halos such as the Milky Way to ensure that gravity tests in the solar system are satisfied. This opens up several decades in length scale and classes of galaxies at low redshift that can be exploited by surveys. While theoretical work on models of gravity is in the early stages, we can already identify new regimes that cosmological surveys could target to test gravity. These include: (i) a small-scale component that focuses on the interior and vicinity of galaxy and cluster halos, (ii) spectroscopy of low-redshift galaxies, especially galaxies smaller than the Milky Way, in environments that range from voids to clusters, and (iii) a programme of combining lensing and dynamical information, from imaging and spectroscopic surveys, respectively, on the same (or statistically identical) sample of galaxies.","corpus_id":27953932,"score":0},{"doc_id":"22258612","title":"Gravitational detection of a low-mass dark satellite galaxy at cosmological distance.","abstract":"The mass function of dwarf satellite galaxies that are observed around Local Group galaxies differs substantially from simulations based on cold dark matter: the simulations predict many more dwarf galaxies than are seen. The Local Group, however, may be anomalous in this regard. A massive dark satellite in an early-type lens galaxy at a redshift of 0.222 was recently found using a method based on gravitational lensing, suggesting that the mass fraction contained in substructure could be higher than is predicted from simulations. The lack of very low-mass detections, however, prohibited any constraint on their mass function. Here we report the presence of a (1.9 ± 0.1) × 10(8) M dark satellite galaxy in the Einstein ring system JVAS B1938+666 (ref. 11) at a redshift of 0.881, where M denotes the solar mass. This satellite galaxy has a mass similar to that of the Sagittarius galaxy, which is a satellite of the Milky Way. We determine the logarithmic slope of the mass function for substructure beyond the local Universe to be 1.1(+0.6)(-0.4), with an average mass fraction of 3.3(+3.6)(-1.8) per cent, by combining data on both of these recently discovered galaxies. Our results are consistent with the predictions from cold dark matter simulations at the 95 per cent confidence level, and therefore agree with the view that galaxies formed hierarchically in a Universe composed of cold dark matter.","corpus_id":205227095,"score":0},{"doc_id":"22281178","title":"Specific rotation as a property to validate monosaccharide conformations.","abstract":"Specific rotation ([α](D)) values were calculated for the 15 conformations of xylopyranose that are the most stable in the gas phase and in aqueous solution. The effects of different theoretical descriptions and the medium on the geometry of the conformers and the [α](D) values are evaluated. Differences in [α](D) values found for the same conformer in all descriptions used were smaller than those found between any two different conformers in the same description. The difference between [α](D) values is prominent, even for two conformations that are distinguished from each other only by the orientation of one secondary hydroxyl group. This finding suggests that [α](D) values may potentially be used in the validation of monosaccharide conformations that are theoretically sampled.","corpus_id":44351059,"score":0},{"doc_id":"23006162","title":"Testing gravity with the stacked phase space around galaxy clusters.","abstract":"In general relativity, the average velocity field of dark matter around galaxy clusters is uniquely determined by the mass profile. The latter can be measured through weak lensing. We propose a new method of measuring the velocity field (phase space density) by stacking redshifts of surrounding galaxies from a spectroscopic sample. In combination with lensing, this yields a direct test of gravity on scales of 1-30 Mpc. Using N-body simulations, we show that this method can improve upon current constraints on f(R) and Dvali-Gabadadze-Porrati model parameters by several orders of magnitude when applied to upcoming imaging and redshift surveys.","corpus_id":29852776,"score":0},{"doc_id":"23099405","title":"Near-infrared background anisotropies from diffuse intrahalo light of galaxies.","abstract":"Unresolved anisotropies of the cosmic near-infrared background radiation are expected to have contributions from the earliest galaxies during the epoch of reionization and from faint, dwarf galaxies at intermediate redshifts. Previous measurements were unable to pinpoint conclusively the dominant origin because they did not sample spatial scales that were sufficiently large to distinguish between these two possibilities. Here we report a measurement of the anisotropy power spectrum from subarcminute to one-degree angular scales, and find the clustering amplitude to be larger than predicted by the models based on the two existing explanations. As the shot-noise level of the power spectrum is consistent with that expected from faint galaxies, a new source population on the sky is not necessary to explain the observations. However, a physical mechanism that increases the clustering amplitude is needed. Motivated by recent results related to the extended stellar light profile in dark-matter haloes, we consider the possibility that the fluctuations originate from intrahalo stars of all galaxies. We find that the measured power spectrum can be explained by an intrahalo light fraction of 0.07 to 0.2 per cent relative to the total luminosity in dark-matter haloes of 10(9) to 10(12) solar masses at redshifts of about 1 to 4.","corpus_id":205230649,"score":0},{"doc_id":"23282362","title":"A vast, thin plane of corotating dwarf galaxies orbiting the Andromeda galaxy.","abstract":"Dwarf satellite galaxies are thought to be the remnants of the population of primordial structures that coalesced to form giant galaxies like the Milky Way. It has previously been suspected that dwarf galaxies may not be isotropically distributed around our Galaxy, because several are correlated with streams of H I emission, and may form coplanar groups. These suspicions are supported by recent analyses. It has been claimed that the apparently planar distribution of satellites is not predicted within standard cosmology, and cannot simply represent a memory of past coherent accretion. However, other studies dispute this conclusion. Here we report the existence of a planar subgroup of satellites in the Andromeda galaxy (M 31), comprising about half of the population. The structure is at least 400 kiloparsecs in diameter, but also extremely thin, with a perpendicular scatter of less than 14.1 kiloparsecs. Radial velocity measurements reveal that the satellites in this structure have the same sense of rotation about their host. This shows conclusively that substantial numbers of dwarf satellite galaxies share the same dynamical orbital properties and direction of angular momentum. Intriguingly, the plane we identify is approximately aligned with the pole of the Milky Way's disk and with the vector between the Milky Way and Andromeda.","corpus_id":4404711,"score":0},{"doc_id":"23739604","title":"[A man with a 'galaxy sign'].","abstract":"Een man met het 'galaxy sign'. This brief report describes the radiographic images of a 29-year-old man with asymptomatic sarcoidosis. On a CT-scan a coalescent granuloma with a central core and peripheral nodules mimics a globular cluster galaxy; therefore it is called 'galaxy sign'. This is a classic finding in a granulomatous disease like sarcoidosis.","corpus_id":13068459,"score":0},{"doc_id":"24580436","title":"Cosmology with void-galaxy correlations.","abstract":"Galaxy bias, the unknown relationship between the clustering of galaxies and the underlying dark matter density field is a major hurdle for cosmological inference from large-scale structure. While traditional analyses focus on the absolute clustering amplitude of high-density regions mapped out by galaxy surveys, we propose a relative measurement that compares those to the underdense regions, cosmic voids. On the basis of realistic mock catalogs we demonstrate that cross correlating galaxies and voids opens up the possibility to calibrate galaxy bias and to define a static ruler thanks to the observable geometric nature of voids. We illustrate how the clustering of voids is related to mass compensation and show that volume-exclusion significantly reduces the degree of stochasticity in their spatial distribution. Extracting the spherically averaged distribution of galaxies inside voids from their cross correlations reveals a remarkable concordance with the mass-density profile of voids.","corpus_id":5518892,"score":0},{"doc_id":"24702345","title":"Conformal gravity holography in four dimensions.","abstract":"We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a \"partially massless response\". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair.","corpus_id":12853206,"score":0},{"doc_id":"24928211","title":"BioBlend.objects: metacomputing with Galaxy.","abstract":"SUMMARY: BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows. AVAILABILITY AND IMPLEMENTATION: BioBlend.objects is available online at https://github.com/afgane/bioblend. The new object-oriented API is implemented by the galaxy/objects subpackage.","corpus_id":15973453,"score":0},{"doc_id":"25186900","title":"The Laniakea supercluster of galaxies.","abstract":"Galaxies congregate in clusters and along filaments, and are missing from large regions referred to as voids. These structures are seen in maps derived from spectroscopic surveys that reveal networks of structure that are interconnected with no clear boundaries. Extended regions with a high concentration of galaxies are called 'superclusters', although this term is not precise. There is, however, another way to analyse the structure. If the distance to each galaxy from Earth is directly measured, then the peculiar velocity can be derived from the subtraction of the mean cosmic expansion, the product of distance times the Hubble constant, from observed velocity. The peculiar velocity is the line-of-sight departure from the cosmic expansion and arises from gravitational perturbations; a map of peculiar velocities can be translated into a map of the distribution of matter. Here we report a map of structure made using a catalogue of peculiar velocities. We find locations where peculiar velocity flows diverge, as water does at watershed divides, and we trace the surface of divergent points that surrounds us. Within the volume enclosed by this surface, the motions of galaxies are inward after removal of the mean cosmic expansion and long range flows. We define a supercluster to be the volume within such a surface, and so we are defining the extent of our home supercluster, which we call Laniakea.","corpus_id":205240232,"score":0},{"doc_id":"25309716","title":"Executing SADI services in Galaxy.","abstract":"BACKGROUND: In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. RESULTS: SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. CONCLUSIONS: SADI-Galaxy bridges the gap between Galaxy, an easy to use but \"static\" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.","corpus_id":783717,"score":0},{"doc_id":"25646464","title":"Cold dark matter: Controversies on small scales.","abstract":"The cold dark matter (CDM) cosmological model has been remarkably successful in explaining cosmic structure over an enormous span of redshift, but it has faced persistent challenges from observations that probe the innermost regions of dark matter halos and the properties of the Milky Way's dwarf galaxy satellites. We review the current observational and theoretical status of these \"small-scale controversies.\" Cosmological simulations that incorporate only gravity and collisionless CDM predict halos with abundant substructure and central densities that are too high to match constraints from galaxy dynamics. The solution could lie in baryonic physics: Recent numerical simulations and analytical models suggest that gravitational potential fluctuations tied to efficient supernova feedback can flatten the central cusps of halos in massive galaxies, and a combination of feedback and low star formation efficiency could explain why most of the dark matter subhalos orbiting the Milky Way do not host visible galaxies. However, it is not clear that this solution can work in the lowest mass galaxies, where discrepancies are observed. Alternatively, the small-scale conflicts could be evidence of more complex physics in the dark sector itself. For example, elastic scattering from strong dark matter self-interactions can alter predicted halo mass profiles, leading to good agreement with observations across a wide range of galaxy mass. Gravitational lensing and dynamical perturbations of tidal streams in the stellar halo provide evidence for an abundant population of low-mass subhalos in accord with CDM predictions. These observational approaches will get more powerful over the next few years.","corpus_id":30473661,"score":0},{"doc_id":"25988504","title":"The concept of geodesic curvature applied to optical surfaces.","abstract":"PURPOSE: To propose geodesic curvature as a metric to characterise how an optical surface locally differs from axial symmetry. To derive equations to evaluate geodesic curvatures of arbitrary surfaces expressed in polar coordinates. METHODS: The concept of geodesic curvature is explained in detail as compared to other curvature-based metrics. Starting with the formula representing a surface as function of polar coordinates, an equation for the geodesic curvature is obtained depending only on first and second radial and first order angular derivatives of the surface function. The potential of the geodesic curvature is illustrated using different surface tests. RESULTS: Geodesic curvature reveals local axial asymmetries more sharply than other types of curvatures such as normal curvatures. CONCLUSION: Geodesic curvature maps could be used to characterise local axial asymmetries for relevant optometry applications such as corneal topography anomalies (keratoconus) or ophthalmic lens metrology.","corpus_id":30375053,"score":0},{"doc_id":"26017450","title":"A kiloparsec-scale internal shock collision in the jet of a nearby radio galaxy.","abstract":"Jets of highly energized plasma with relativistic velocities are associated with black holes ranging in mass from a few times that of the Sun to the billion-solar-mass black holes at the centres of galaxies. A popular but unconfirmed hypothesis to explain how the plasma is energized is the 'internal shock model', in which the relativistic flow is unsteady. Faster components in the jet catch up to and collide with slower ones, leading to internal shocks that accelerate particles and generate magnetic fields. This mechanism can explain the variable, high-energy emission from a diverse set of objects, with the best indirect evidence being the unseen fast relativistic flow inferred to energize slower components in X-ray binary jets. Mapping of the kinematic profiles in resolved jets has revealed precessing and helical patterns in X-ray binaries, apparent superluminal motions, and the ejection of knots (bright components) from standing shocks in the jets of active galaxies. Observations revealing the structure and evolution of an internal shock in action have, however, remained elusive, hindering measurement of the physical parameters and ultimate efficiency of the mechanism. Here we report observations of a collision between two knots in the jet of nearby radio galaxy 3C 264. A bright knot with an apparent speed of (7.0 ± 0.8)c, where c is the speed of light in a vacuum, is in the incipient stages of a collision with a slower-moving knot of speed (1.8 ± 0.5)c just downstream, resulting in brightening of both knots--as seen in the most recent epoch of imaging.","corpus_id":4451677,"score":0},{"doc_id":"26182087","title":"Growth Rate of Cosmological Perturbations at z∼0.1 from a New Observational Test.","abstract":"Spatial variations in the distribution of galaxy luminosities, estimated from redshifts as distance proxies, are correlated with the peculiar velocity field. Comparing these variations with the peculiar velocities inferred from galaxy redshift surveys is a powerful test of gravity and dark-energy theories on cosmological scales. Using ∼2×10(5) galaxies from the SDSS Data Release 7, we perform this test in the framework of gravitational instability to estimate the normalized growth rate of density perturbations fσ8=0.37±0.13 at z∼0.1, which is in agreement with the cold dark matter model with a cosmological constant. This unique measurement is complementary to those obtained with more traditional methods, including clustering analysis. The estimated accuracy at z∼0.1 is competitive with other methods when applied to similar data sets.","corpus_id":30013989,"score":0},{"doc_id":"26382671","title":"New Test of the Friedmann-Lemaître-Robertson-Walker Metric Using the Distance Sum Rule.","abstract":"We present a new test of the validity of the Friedmann-Lemaître-Robertson-Walker (FLRW) metric, based on comparing the distance from redshift 0 to z(1) and from z(1) to z(2) to the distance from 0 to z(2). If the Universe is described by the FLRW metric, the comparison provides a model-independent measurement of spatial curvature. The test relies on geometrical optics, it is independent of the matter content of the Universe and the applicability of the Einstein equation on cosmological scales. We apply the test to observations, using the Union2.1 compilation of supernova distances and Sloan Lens ACS Survey galaxy strong lensing data. The FLRW metric is consistent with the data, and the spatial curvature parameter is constrained to be -1.22<Ω(K0)<0.63, or -0.08<Ω(K0)<0.97 with a prior from the cosmic microwave background and the local Hubble constant, though modeling of the lenses is a source of significant systematic uncertainty.","corpus_id":22551992,"score":0},{"doc_id":"26762455","title":"Eight per cent leakage of Lyman continuum photons from a compact, star-forming dwarf galaxy.","abstract":"One of the key questions in observational cosmology is the identification of the sources responsible for ionization of the Universe after the cosmic 'Dark Ages', when the baryonic matter was neutral. The currently identified distant galaxies are insufficient to fully reionize the Universe by redshift z ≈ 6 (refs 1-3), but low-mass, star-forming galaxies are thought to be responsible for the bulk of the ionizing radiation. As direct observations at high redshift are difficult for a variety of reasons, one solution is to identify local proxies of this galaxy population. Starburst galaxies at low redshifts, however, generally are opaque to Lyman continuum photons. Small escape fractions of about 1 to 3 per cent, insufficient to ionize much surrounding gas, have been detected only in three low-redshift galaxies. Here we report far-ultraviolet observations of the nearby low-mass star-forming galaxy J0925+1403. The galaxy is leaking ionizing radiation with an escape fraction of about 8 per cent. The total number of photons emitted during the starburst phase is sufficient to ionize intergalactic medium material that is about 40 times as massive as the stellar mass of the galaxy.","corpus_id":3033749,"score":0},{"doc_id":"26829789","title":"Geometry-Aware Neighborhood Search for Learning Local Models for Image Superresolution.","abstract":"Local learning of sparse image models has proved to be very effective to solve inverse problems in many computer vision applications. To learn such models, the data samples are often clustered using the K-means algorithm with the Euclidean distance as a dissimilarity metric. However, the Euclidean distance may not always be a good dissimilarity measure for comparing data samples lying on a manifold. In this paper, we propose two algorithms for determining a local subset of training samples from which a good local model can be computed for reconstructing a given input test sample, where we consider the underlying geometry of the data. The first algorithm, called adaptive geometry-driven nearest neighbor search (AGNN), is an adaptive scheme, which can be seen as an out-of-sample extension of the replicator graph clustering method for local model learning. The second method, called geometry-driven overlapping clusters (GOCs), is a less complex nonadaptive alternative for training subset selection. The proposed AGNN and GOC methods are evaluated in image superresolution and shown to outperform spectral clustering, soft clustering, and geodesic distance-based subset selection in most settings.","corpus_id":7924419,"score":0},{"doc_id":"27007681","title":"Cosmological tests of modified gravity.","abstract":"We review recent progress in the construction of modified gravity models as alternatives to dark energy as well as the development of cosmological tests of gravity. Einstein's theory of general relativity (GR) has been tested accurately within the local universe i.e. the Solar System, but this leaves the possibility open that it is not a good description of gravity at the largest scales in the Universe. This being said, the standard model of cosmology assumes GR on all scales. In 1998, astronomers made the surprising discovery that the expansion of the Universe is accelerating, not slowing down. This late-time acceleration of the Universe has become the most challenging problem in theoretical physics. Within the framework of GR, the acceleration would originate from an unknown dark energy. Alternatively, it could be that there is no dark energy and GR itself is in error on cosmological scales. In this review, we first give an overview of recent developments in modified gravity theories including f(R) gravity, braneworld gravity, Horndeski theory and massive/bigravity theory. We then focus on common properties these models share, such as screening mechanisms they use to evade the stringent Solar System tests. Once armed with a theoretical knowledge of modified gravity models, we move on to discuss how we can test modifications of gravity on cosmological scales. We present tests of gravity using linear cosmological perturbations and review the latest constraints on deviations from the standard [Formula: see text]CDM model. Since screening mechanisms leave distinct signatures in the non-linear structure formation, we also review novel astrophysical tests of gravity using clusters, dwarf galaxies and stars. The last decade has seen a number of new constraints placed on gravity from astrophysical to cosmological scales. Thanks to on-going and future surveys, cosmological tests of gravity will enjoy another, possibly even more, exciting ten years.","corpus_id":20161785,"score":0},{"doc_id":"27929014","title":"A massive, quiescent, population II galaxy at a redshift of 2.1.","abstract":"Unlike spiral galaxies such as the Milky Way, the majority of the stars in massive elliptical galaxies were formed in a short period early in the history of the Universe. The duration of this formation period can be measured using the ratio of magnesium to iron abundance ([Mg/Fe]) in spectra, which reflects the relative enrichment by core-collapse and type Ia supernovae. For local galaxies, [Mg/Fe] probes the combined formation history of all stars currently in the galaxy, including younger and metal-poor stars that were added during late-time mergers. Therefore, to directly constrain the initial star-formation period, we must study galaxies at earlier epochs. The most distant galaxy for which [Mg/Fe] had previously been measured is at a redshift of z ≈ 1.4, with [Mg/Fe] = . A slightly earlier epoch (z ≈ 1.6) was probed by combining the spectra of 24 massive quiescent galaxies, yielding an average [Mg/Fe] = 0.31 ± 0.12 (ref. 7). However, the relatively low signal-to-noise ratio of the data and the use of index analysis techniques for both of these studies resulted in measurement errors that are too large to allow us to form strong conclusions. Deeper spectra at even earlier epochs in combination with analysis techniques based on full spectral fitting are required to precisely measure the abundance pattern shortly after the major star-forming phase (z > 2). Here we report a measurement of [Mg/Fe] for a massive quiescent galaxy at a redshift of z = 2.1, when the Universe was three billion years old. With [Mg/Fe] = 0.59 ± 0.11, this galaxy is the most Mg-enhanced massive galaxy found so far, having twice the Mg enhancement of similar-mass galaxies today. The abundance pattern of the galaxy is consistent with enrichment exclusively by core-collapse supernovae and with a star-formation timescale of 0.1 to 0.5 billion years-characteristics that are similar to population II stars in the Milky Way. With an average past star-formation rate of 600 to 3,000 solar masses per year, this galaxy was among the most vigorous star-forming galaxies in the Universe.","corpus_id":4383112,"score":0},{"doc_id":"28300118","title":"Strongly baryon-dominated disk galaxies at the peak of galaxy formation ten billion years ago.","abstract":"In the cold dark matter cosmology, the baryonic components of galaxies-stars and gas-are thought to be mixed with and embedded in non-baryonic and non-relativistic dark matter, which dominates the total mass of the galaxy and its dark-matter halo. In the local (low-redshift) Universe, the mass of dark matter within a galactic disk increases with disk radius, becoming appreciable and then dominant in the outer, baryonic regions of the disks of star-forming galaxies. This results in rotation velocities of the visible matter within the disk that are constant or increasing with disk radius-a hallmark of the dark-matter model. Comparisons between the dynamical mass, inferred from these velocities in rotational equilibrium, and the sum of the stellar and cold-gas mass at the peak epoch of galaxy formation ten billion years ago, inferred from ancillary data, suggest high baryon fractions in the inner, star-forming regions of the disks. Although this implied baryon fraction may be larger than in the local Universe, the systematic uncertainties (owing to the chosen stellar initial-mass function and the calibration of gas masses) render such comparisons inconclusive in terms of the mass of dark matter. Here we report rotation curves (showing rotation velocity as a function of disk radius) for the outer disks of six massive star-forming galaxies, and find that the rotation velocities are not constant, but decrease with radius. We propose that this trend arises because of a combination of two main factors: first, a large fraction of the massive high-redshift galaxy population was strongly baryon-dominated, with dark matter playing a smaller part than in the local Universe; and second, the large velocity dispersion in high-redshift disks introduces a substantial pressure term that leads to a decrease in rotation velocity with increasing radius. The effect of both factors appears to increase with redshift. Qualitatively, the observations suggest that baryons in the early (high-redshift) Universe efficiently condensed at the centres of dark-matter haloes when gas fractions were high and dark matter was less concentrated.","corpus_id":205254567,"score":0},{"doc_id":"28382981","title":"A massive, quiescent galaxy at a redshift of 3.717.","abstract":"Finding massive galaxies that stopped forming stars in the early Universe presents an observational challenge because their rest-frame ultraviolet emission is negligible and they can only be reliably identified by extremely deep near-infrared surveys. These surveys have revealed the presence of massive, quiescent early-type galaxies appearing as early as redshift z ≈ 2, an epoch three billion years after the Big Bang. Their age and formation processes have now been explained by an improved generation of galaxy-formation models, in which they form rapidly at z ≈ 3-4, consistent with the typical masses and ages derived from their observations. Deeper surveys have reported evidence for populations of massive, quiescent galaxies at even higher redshifts and earlier times, using coarsely sampled photometry. However, these early, massive, quiescent galaxies are not predicted by the latest generation of theoretical models. Here we report the spectroscopic confirmation of one such galaxy at redshift z = 3.717, with a stellar mass of 1.7 × 10(11) solar masses. We derive its age to be nearly half the age of the Universe at this redshift and the absorption line spectrum shows no current star formation. These observations demonstrate that the galaxy must have formed the majority of its stars quickly, within the first billion years of cosmic history in a short, extreme starburst. This ancestral starburst appears similar to those being found by submillimetre-wavelength surveys. The early formation of such massive systems implies that our picture of early galaxy assembly requires substantial revision.","corpus_id":205254535,"score":0},{"doc_id":"28474927","title":"Measurement of a Cosmographic Distance Ratio with Galaxy and Cosmic Microwave Background Lensing.","abstract":"We measure the gravitational lensing shear signal around dark matter halos hosting constant mass galaxies using light sources at z∼1 (background galaxies) and at the surface of last scattering at z∼1100 (the cosmic microwave background). The galaxy shear measurement uses data from the CFHTLenS survey, and the microwave background shear measurement uses data from the Planck satellite. The ratio of shears from these cross-correlations provides a purely geometric distance measurement across the longest possible cosmological lever arm. This is because the matter distribution around the halos, including uncertainties in galaxy bias and systematic errors such as miscentering, cancels in the ratio for halos in thin redshift slices. We measure this distance ratio in three different redshift slices of the constant mass (CMASS) sample and combine them to obtain a 17% measurement of the distance ratio, r=0.390_{-0.062}^{+0.070}, at an effective redshift of z=0.53. This is consistent with the predicted ratio from the Planck best-fit cold dark matter model with a cosmological constant cosmology of r=0.419.","corpus_id":46765856,"score":0},{"doc_id":"28607526","title":"A unified framework for constructing, tuning and assessing photometric redshift density estimates in a selection bias setting.","abstract":"Photometric redshift estimation is an indispensable tool of precision cosmology. One problem that plagues the use of this tool in the era of large-scale sky surveys is that the bright galaxies that are selected for spectroscopic observation do not have properties that match those of (far more numerous) dimmer galaxies; thus, ill-designed empirical methods that produce accurate and precise redshift estimates for the former generally will not produce good estimates for the latter. In this paper, we provide a principled framework for generating conditional density estimates (i.e. photometric redshift PDFs) that takes into account selection bias and the covariate shift that this bias induces. We base our approach on the assumption that the probability that astronomers label a galaxy (i.e. determine its spectroscopic redshift) depends only on its measured (photometric and perhaps other) properties [Formula: see text] and not on its true redshift. With this assumption, we can explicitly write down risk functions that allow us to both tune and compare methods for estimating importance weights (i.e. the ratio of densities of unlabelled and labelled galaxies for different values of [Formula: see text]) and conditional densities. We also provide a method for combining multiple conditional density estimates for the same galaxy into a single estimate with better properties. We apply our risk functions to an analysis of ≈10(6) galaxies, mostly observed by Sloan Digital Sky Survey, and demonstrate through multiple diagnostic tests that our method achieves good conditional density estimates for the unlabelled galaxies.","corpus_id":11728899,"score":0},{"doc_id":"28667318","title":"Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach.","abstract":"This paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.","corpus_id":3318257,"score":0},{"doc_id":"29097690","title":"Ruling out dark matter interpretation of the galactic GeV excess by gamma-ray data of galaxy clusters.","abstract":"Recently, some very tight constraints of annihilating dark matter have been obtained from gamma-ray data of the Milky Way and Milky Way dwarf spheroidal satellite galaxies. In this article, we report that there are two excellent galaxy clusters (A2877 and Fornax) which can provide interesting constraints for annihilating dark matter. The lower limits of the dark matter mass for the thermal relic annihilation cross section are 25 GeV, 6 GeV, 130 GeV and 100 GeV respectively for the e + e -, μ + μ -, τ + τ - and [Formula: see text] channels. For some configuration of our working assumptions, our results improve the Fermi-LAT upper limits of annihilation cross sections by a factor of 1.3 - 1.8 for wide ranges of dark matter mass for e + e -, μ + μ - and [Formula: see text] channels, and a factor of 1.2-1.8 for τ + τ - channel with dark matter mass ≤100 GeV. These limits basically rule out most of the existing popular dark matter interpretation of the GeV excess in the Milky Way.","corpus_id":21176026,"score":0},{"doc_id":"29323299","title":"Rotation in [C ii]-emitting gas in two galaxies at a redshift of 6.8.","abstract":"The earliest galaxies are thought to have emerged during the first billion years of cosmic history, initiating the ionization of the neutral hydrogen that pervaded the Universe at this time. Studying this 'epoch of reionization' involves looking for the spectral signatures of ancient galaxies that are, owing to the expansion of the Universe, now very distant from Earth and therefore exhibit large redshifts. However, finding these spectral fingerprints is challenging. One spectral characteristic of ancient and distant galaxies is strong hydrogen-emission lines (known as Lyman-α lines), but the neutral intergalactic medium that was present early in the epoch of reionization scatters such Lyman-α photons. Another potential spectral identifier is the line at wavelength 157.4 micrometres of the singly ionized state of carbon (the [C ii] λ = 157.74 μm line), which signifies cooling gas and is expected to have been bright in the early Universe. However, so far Lyman-α-emitting galaxies from the epoch of reionization have demonstrated much fainter [C ii] luminosities than would be expected from local scaling relations, and searches for the [C ii] line in sources without Lyman-α emission but with photometric redshifts greater than 6 (corresponding to the first billion years of the Universe) have been unsuccessful. Here we identify [C ii] λ = 157.74 μm emission from two sources that we selected as high-redshift candidates on the basis of near-infrared photometry; we confirm that these sources are two galaxies at redshifts of z = 6.8540 ± 0.0003 and z = 6.8076 ± 0.0002. Notably, the luminosity of the [C ii] line from these galaxies is higher than that found previously in star-forming galaxies with redshifts greater than 6.5. The luminous and extended [C ii] lines reveal clear velocity gradients that, if interpreted as rotation, would indicate that these galaxies have similar dynamic properties to the turbulent yet rotation-dominated disks that have been observed in Hα-emitting galaxies two billion years later, at 'cosmic noon'.","corpus_id":205261958,"score":0},{"doc_id":"29420285","title":"A whirling plane of satellite galaxies around Centaurus A challenges cold dark matter cosmology.","abstract":"The Milky Way and Andromeda galaxies are each surrounded by a thin plane of satellite dwarf galaxies that may be corotating. Cosmological simulations predict that most satellite galaxy systems are close to isotropic with random motions, so those two well-studied systems are often interpreted as rare statistical outliers. We test this assumption using the kinematics of satellite galaxies around the Centaurus A galaxy. Our statistical analysis reveals evidence for corotation in a narrow plane: Of the 16 Centaurus A satellites with kinematic data, 14 follow a coherent velocity pattern aligned with the long axis of their spatial distribution. In standard cosmological simulations, <0.5% of Centaurus A-like systems show such behavior. Corotating satellite systems may be common in the universe, challenging small-scale structure formation in the prevailing cosmological paradigm.","corpus_id":4924232,"score":0},{"doc_id":"29531319","title":"A single population of red globular clusters around the massive compact galaxy NGC 1277.","abstract":"Massive galaxies are thought to form in two phases: an initial collapse of gas and giant burst of central star formation, followed by the later accretion of material that builds up their stellar and dark-matter haloes. The systems of globular clusters within such galaxies are believed to form in a similar manner. The initial central burst forms metal-rich (spectrally red) clusters, whereas more metal-poor (spectrally blue) clusters are brought in by the later accretion of less-massive satellites. This formation process is thought to result in the multimodal optical colour distributions that are seen in the globular cluster systems of massive galaxies. Here we report optical observations of the massive relic-galaxy candidate NGC 1277-a nearby, un-evolved example of a high-redshift 'red nugget' galaxy. We find that the optical colour distribution of the cluster system of NGC 1277 is unimodal and entirely red. This finding is in strong contrast to other galaxies of similar and larger stellar mass, the cluster systems of which always exhibit (and are generally dominated by) blue clusters. We argue that the colour distribution of the cluster system of NGC 1277 indicates that the galaxy has undergone little (if any) mass accretion after its initial collapse, and use simulations of possible merger histories to show that the stellar mass due to accretion is probably at most ten per cent of the total stellar mass of the galaxy. These results confirm that NGC 1277 is a genuine relic galaxy and demonstrate that blue clusters constitute an accreted population in present-day massive galaxies.","corpus_id":4440393,"score":0},{"doc_id":"29595770","title":"A galaxy lacking dark matter.","abstract":"Studies of galaxy surveys in the context of the cold dark matter paradigm have shown that the mass of the dark matter halo and the total stellar mass are coupled through a function that varies smoothly with mass. Their average ratio Mhalo/Mstars has a minimum of about 30 for galaxies with stellar masses near that of the Milky Way (approximately 5 × 1010 solar masses) and increases both towards lower masses and towards higher masses. The scatter in this relation is not well known; it is generally thought to be less than a factor of two for massive galaxies but much larger for dwarf galaxies. Here we report the radial velocities of ten luminous globular-cluster-like objects in the ultra-diffuse galaxy NGC1052-DF2, which has a stellar mass of approximately 2 × 108 solar masses. We infer that its velocity dispersion is less than 10.5 kilometres per second with 90 per cent confidence, and we determine from this that its total mass within a radius of 7.6 kiloparsecs is less than 3.4 × 108 solar masses. This implies that the ratio Mhalo/Mstars is of order unity (and consistent with zero), a factor of at least 400 lower than expected. NGC1052-DF2 demonstrates that dark matter is not always coupled with baryonic matter on galactic scales.","corpus_id":-1,"score":0}],"string":"[\n {\n \"doc_id\": \"21517292\",\n \"title\": \"Impact of a global quadratic potential on galactic rotation curves.\",\n \"abstract\": \"We present a conformal gravity fit to the 20 largest of a sample of 110 spiral galaxies. We identify the presence of a universal quadratic potential V(κ)(r)=-κc²r²/2 with κ=9.54×10⁻⁵⁴ cm⁻² induced by cosmic inhomogeneities. When V(κ)(r) is taken in conjunction with both a universal linear potential V(γ₀)(r)=γ₀c²r/2 with γ₀=3.06×10⁻³⁰ cm⁻¹ generated by the homogeneous cosmic background and the contribution generated by the local luminous matter in galaxies, the theory then accounts for the rotation curve systematics observed in the entire 110 galaxies, without the need for any dark matter whatsoever. Our study suggests that using dark matter may be nothing more than an attempt to describe global effects in purely local galactic terms. With V(κ)(r) being negative, galaxies can only support bound orbits up to distances of order γ₀/κ=100kpc, with global physics imposing a limit on the size of galaxies.\",\n \"corpus_id\": 18044816,\n \"score\": 2\n },\n {\n \"doc_id\": \"23931350\",\n \"title\": \"Testing the MOND paradigm of modified dynamics with galaxy-galaxy gravitational lensing.\",\n \"abstract\": \"The MOND paradigm of modified dynamics predicts that the asymptotic gravitational potential of an isolated, bounded (baryonic) mass, M, is ϕ(r)=(MGa0)1/2ln(r). Relativistic MOND theories predict that the lensing effects of M are dictated by ϕ(r) as general-relativity lensing is dictated by the Newtonian potential. Thus MOND predicts that the asymptotic Newtonian potential deduced from galaxy-galaxy gravitational lensing will have (1) a logarithmic r dependence, and (2) a normalization (parametrized standardly as 2σ2) that depends only on M: σ=(MGa0/4)1/4. I compare these predictions with recent results of galaxy-galaxy lensing, and find agreement on all counts. For the “blue”-lenses subsample (“spiral” galaxies) MOND reproduces the observations well with an r′-band M/Lr′∼(1–3)(M/L)⊙, and for “red” lenses (“elliptical” galaxies) with M/Lr′∼(3–6)(M/L)⊙, both consistent with baryons only. In contradistinction, Newtonian analysis requires, typically, M/Lr′∼130(M/L)⊙, bespeaking a mass discrepancy of a factor ∼40. Compared with the staple, rotation-curve tests, MOND is here tested in a wider population of galaxies, through a different phenomenon, using relativistic test objects, and is probed to several-times-lower accelerations–as low as a few percent of a0.\",\n \"corpus_id\": 37710554,\n \"score\": 2\n },\n {\n \"doc_id\": \"19892973\",\n \"title\": \"Einstein's theory of gravity and the problem of missing mass.\",\n \"abstract\": \"The observed matter in the universe accounts for just 5% of the observed gravity. A possible explanation is that Newton's and Einstein's theories of gravity fail where gravity is either weak or enhanced. The modified theory of Newtonian dynamics (MOND) reproduces, without dark matter, spiral-galaxy orbital motions and the relation between luminosity and rotation in galaxies, although not in clusters. Recent extensions of Einstein's theory are theoretically more complete. They inevitably include dark fields that seed structure growth, and they may explain recent weak lensing data. However, the presence of dark fields reduces calculability and comes at the expense of the original MOND premise, that the matter we see is the sole source of gravity. Observational tests of the relic radiation, weak lensing, and the growth of structure may distinguish modified gravity from dark matter.\",\n \"corpus_id\": 889826,\n \"score\": 1\n },\n {\n \"doc_id\": \"20220843\",\n \"title\": \"Confirmation of general relativity on large scales from weak lensing and galaxy velocities.\",\n \"abstract\": \"Although general relativity underlies modern cosmology, its applicability on cosmological length scales has yet to be stringently tested. Such a test has recently been proposed, using a quantity, E(G), that combines measures of large-scale gravitational lensing, galaxy clustering and structure growth rate. The combination is insensitive to 'galaxy bias' (the difference between the clustering of visible galaxies and invisible dark matter) and is thus robust to the uncertainty in this parameter. Modified theories of gravity generally predict values of E(G) different from the general relativistic prediction because, in these theories, the 'gravitational slip' (the difference between the two potentials that describe perturbations in the gravitational metric) is non-zero, which leads to changes in the growth of structure and the strength of the gravitational lensing effect. Here we report that E(G) = 0.39 +/- 0.06 on length scales of tens of megaparsecs, in agreement with the general relativistic prediction of E(G) approximately 0.4. The measured value excludes a model within the tensor-vector-scalar gravity theory, which modifies both Newtonian and Einstein gravity. However, the relatively large uncertainty still permits models within f(R) theory, which is an extension of general relativity. A fivefold decrease in uncertainty is needed to rule out these models.\",\n \"corpus_id\": 205219902,\n \"score\": 1\n },\n {\n \"doc_id\": \"21517295\",\n \"title\": \"Novel test of modified Newtonian dynamics with gas rich galaxies.\",\n \"abstract\": \"The current cosmological paradigm, the cold dark matter model with a cosmological constant, requires that the mass-energy of the Universe be dominated by invisible components: dark matter and dark energy. An alternative to these dark components is that the law of gravity be modified on the relevant scales. A test of these ideas is provided by the baryonic Tully-Fisher relation (BTFR), an empirical relation between the observed mass of a galaxy and its rotation velocity. Here, I report a test using gas rich galaxies for which both axes of the BTFR can be measured independently of the theories being tested and without the systematic uncertainty in stellar mass that affects the same test with star dominated spirals. The data fall precisely where predicted a priori by the modified Newtonian dynamics. The scatter in the BTFR is attributable entirely to observational uncertainty, consistent with a single effective force law.\",\n \"corpus_id\": 263792143,\n \"score\": 1\n },\n {\n \"doc_id\": \"22810697\",\n \"title\": \"High velocity dispersion in a rare grand-design spiral galaxy at redshift z = 2.18.\",\n \"abstract\": \"Although grand-design spiral galaxies are relatively common in the local Universe, only one has been spectroscopically confirmed to lie at redshift z > 2 (HDFX 28; z = 2.011); and it may prove to be a major merger that simply resembles a spiral in projection. The rarity of spirals has been explained as a result of disks being dynamically 'hot' at z > 2 (refs 2-5), which may instead favour the formation of commonly observed clumpy structures. Alternatively, current instrumentation may simply not be sensitive enough to detect spiral structures comparable to those in the modern Universe. At z < 2, the velocity dispersion of disks decreases, and spiral galaxies are more numerous by z ≈ 1 (refs 7, 13-15). Here we report observations of the grand-design spiral galaxy Q2343-BX442 at z = 2.18. Spectroscopy of ionized gas shows that the disk is dynamically hot, implying an uncertain origin for the spiral structure. The kinematics of the galaxy are consistent with a thick disk undergoing a minor merger, which can drive the formation of short-lived spiral structure. A duty cycle of <100 Myr for such tidally induced spiral structure in a hot massive disk is consistent with its rarity.\",\n \"corpus_id\": 205229562,\n \"score\": 1\n },\n {\n \"doc_id\": \"24949751\",\n \"title\": \"Clear and measurable signature of modified gravity in the galaxy velocity field.\",\n \"abstract\": \"The velocity field of dark matter and galaxies reflects the continued action of gravity throughout cosmic history. We show that the low-order moments of the pairwise velocity distribution v_{12} are a powerful diagnostic of the laws of gravity on cosmological scales. In particular, the projected line-of-sight galaxy pairwise velocity dispersion σ_{12}(r) is very sensitive to the presence of modified gravity. Using a set of high-resolution N-body simulations, we compute the pairwise velocity distribution and its projected line-of-sight dispersion for a class of modified gravity theories: the chameleon f(R) gravity and Galileon gravity (cubic and quartic). The velocities of dark matter halos with a wide range of masses would exhibit deviations from general relativity at the (5-10)σ level. We examine strategies for detecting these deviations in galaxy redshift and peculiar velocity surveys. If detected, this signature would be a \\\"smoking gun\\\" for modified gravity.\",\n \"corpus_id\": 7074456,\n \"score\": 1\n },\n {\n \"doc_id\": \"27274704\",\n \"title\": \"The different baryonic Tully-Fisher relations at low masses.\",\n \"abstract\": \"We compare the Baryonic Tully-Fisher relation (BTFR) of simulations and observations of galaxies ranging from dwarfs to spirals, using various measures of rotational velocity Vrot. We explore the BTFR when measuring Vrot at the flat part of the rotation curve, Vflat, at the extent of H i gas, Vlast, and using 20 per cent (W20) and 50 per cent (W50) of the width of H i line profiles. We also compare with the maximum circular velocity of the parent halo, [Formula: see text], within dark matter only simulations. The different BTFRs increasingly diverge as galaxy mass decreases. Using Vlast one obtains a power law over four orders of magnitude in baryonic mass, with slope similar to the observed BTFR. Measuring Vflat gives similar results as Vlast when galaxies with rising rotation curves are excluded. However, higher rotation velocities would be found for low-mass galaxies if the cold gas extended far enough for Vrot to reach a maximum. W20 gives a similar slope as Vlast but with slightly lower values of Vrot for low-mass galaxies, although this may depend on the extent of the gas in your galaxy sample. W50 bends away from these other relations towards low velocities at low masses. By contrast, [Formula: see text] bends towards high velocities for low-mass galaxies, as cold gas does not extend out to the radius at which haloes reach [Formula: see text]. Our study highlights the need for careful comparisons between observations and models: one needs to be consistent about the particular method of measuring Vrot, and precise about the radius at which velocities are measured.\",\n \"corpus_id\": 41639803,\n \"score\": 1\n },\n {\n \"doc_id\": \"27279784\",\n \"title\": \"Modelling galaxy clustering: halo occupation distribution versus subhalo matching.\",\n \"abstract\": \"We model the luminosity-dependent projected and redshift-space two-point correlation functions (2PCFs) of the Sloan Digital Sky Survey (SDSS) Data Release 7 Main galaxy sample, using the halo occupation distribution (HOD) model and the subhalo abundance matching (SHAM) model and its extension. All the models are built on the same high-resolution N-body simulations. We find that the HOD model generally provides the best performance in reproducing the clustering measurements in both projected and redshift spaces. The SHAM model with the same halo-galaxy relation for central and satellite galaxies (or distinct haloes and subhaloes), when including scatters, has a best-fitting χ(2)/dof around 2-3. We therefore extend the SHAM model to the subhalo clustering and abundance matching (SCAM) by allowing the central and satellite galaxies to have different galaxy-halo relations. We infer the corresponding halo/subhalo parameters by jointly fitting the galaxy 2PCFs and abundances and consider subhaloes selected based on three properties, the mass Macc at the time of accretion, the maximum circular velocity Vacc at the time of accretion, and the peak maximum circular velocity Vpeak over the history of the subhaloes. The three subhalo models work well for luminous galaxy samples (with luminosity above L*). For low-luminosity samples, the Vacc model stands out in reproducing the data, with the Vpeak model slightly worse, while the Macc model fails to fit the data. We discuss the implications of the modelling results.\",\n \"corpus_id\": 25248798,\n \"score\": 1\n },\n {\n \"doc_id\": \"28474932\",\n \"title\": \"Mass-Discrepancy Acceleration Relation: A Natural Outcome of Galaxy Formation in Cold Dark Matter Halos.\",\n \"abstract\": \"We analyze the total and baryonic acceleration profiles of a set of well-resolved galaxies identified in the eagle suite of hydrodynamic simulations. Our runs start from the same initial conditions but adopt different prescriptions for unresolved stellar and active galactic nuclei feedback, resulting in diverse populations of galaxies by the present day. Some of them reproduce observed galaxy scaling relations, while others do not. However, regardless of the feedback implementation, all of our galaxies follow closely a simple relationship between the total and baryonic acceleration profiles, consistent with recent observations of rotationally supported galaxies. The relation has small scatter: Different feedback implementations-which produce different galaxy populations-mainly shift galaxies along the relation rather than perpendicular to it. Furthermore, galaxies exhibit a characteristic acceleration g_{†}, above which baryons dominate the mass budget, as observed. These observations, consistent with simple modified Newtonian dynamics, can be accommodated within the standard cold dark matter paradigm.\",\n \"corpus_id\": 38545116,\n \"score\": 1\n },\n {\n \"doc_id\": \"28949220\",\n \"title\": \"Self-Interacting Dark Matter Can Explain Diverse Galactic Rotation Curves.\",\n \"abstract\": \"The rotation curves of spiral galaxies exhibit a diversity that has been difficult to understand in the cold dark matter (CDM) paradigm. We show that the self-interacting dark matter (SIDM) model provides excellent fits to the rotation curves of a sample of galaxies with asymptotic velocities in the 25-300 km/s range that exemplify the full range of diversity. We assume only the halo concentration-mass relation predicted by the CDM model and a fixed value of the self-interaction cross section. In dark-matter-dominated galaxies, thermalization due to self-interactions creates large cores and reduces dark matter densities. In contrast, thermalization leads to denser and smaller cores in more luminous galaxies and naturally explains the flatness of rotation curves of the highly luminous galaxies at small radii. Our results demonstrate that the impact of the baryons on the SIDM halo profile and the scatter from the assembly history of halos as encoded in the concentration-mass relation can explain the diverse rotation curves of spiral galaxies.\",\n \"corpus_id\": 38659240,\n \"score\": 1\n },\n {\n \"doc_id\": \"18235494\",\n \"title\": \"A test of the nature of cosmic acceleration using galaxy redshift distortions.\",\n \"abstract\": \"Observations of distant supernovae indicate that the Universe is now in a phase of accelerated expansion the physical cause of which is a mystery. Formally, this requires the inclusion of a term acting as a negative pressure in the equations of cosmic expansion, accounting for about 75 per cent of the total energy density in the Universe. The simplest option for this 'dark energy' corresponds to a 'cosmological constant', perhaps related to the quantum vacuum energy. Physically viable alternatives invoke either the presence of a scalar field with an evolving equation of state, or extensions of general relativity involving higher-order curvature terms or extra dimensions. Although they produce similar expansion rates, different models predict measurable differences in the growth rate of large-scale structure with cosmic time. A fingerprint of this growth is provided by coherent galaxy motions, which introduce a radial anisotropy in the clustering pattern reconstructed by galaxy redshift surveys. Here we report a measurement of this effect at a redshift of 0.8. Using a new survey of more than 10,000 faint galaxies, we measure the anisotropy parameter beta = 0.70 +/- 0.26, which corresponds to a growth rate of structure at that time of f = 0.91 +/- 0.36. This is consistent with the standard cosmological-constant model with low matter density and flat geometry, although the error bars are still too large to distinguish among alternative origins for the accelerated expansion. The correct origin could be determined with a further factor-of-ten increase in the sampled volume at similar redshift.\",\n \"corpus_id\": 4403989,\n \"score\": 0\n },\n {\n \"doc_id\": \"18352285\",\n \"title\": \"Conformal curves on the WO3 surface.\",\n \"abstract\": \"We have studied the isoheight lines on the WO3 surface as a physical candidate for conformally invariant curves. We have shown that these lines are conformally invariant with the same statistics of domain walls in the critical Ising model. They belong to the family of conformal invariant curves called Schramm-Loewner evolution (or SLE(kappa)), with diffusivity of kappa approximately 3. This can be regarded as the first experimental observation of SLE curves. We have also argued that Ballistic Deposition (BD) can serve as a growth model giving rise to contours with similar statistics at large scales.\",\n \"corpus_id\": 39009580,\n \"score\": 0\n },\n {\n \"doc_id\": \"18756252\",\n \"title\": \"A common mass scale for satellite galaxies of the Milky Way.\",\n \"abstract\": \"The Milky Way has at least twenty-three known satellite galaxies that shine with luminosities ranging from about a thousand to a billion times that of the Sun. Half of these galaxies were discovered in the past few years in the Sloan Digital Sky Survey, and they are among the least luminous galaxies in the known Universe. A determination of the mass of these galaxies provides a test of galaxy formation at the smallest scales and probes the nature of the dark matter that dominates the mass density of the Universe. Here we use new measurements of the velocities of the stars in these galaxies to show that they are consistent with them having a common mass of about 10(7) within their central 300 parsecs. This result demonstrates that the faintest of the Milky Way satellites are the most dark-matter-dominated galaxies known, and could be a hint of a new scale in galaxy formation or a characteristic scale for the clustering of dark matter.\",\n \"corpus_id\": 4373541,\n \"score\": 0\n },\n {\n \"doc_id\": \"18843363\",\n \"title\": \"The formation and assembly of a typical star-forming galaxy at redshift z approximately 3.\",\n \"abstract\": \"Recent studies of galaxies approximately 2-3 Gyr after the Big Bang have revealed large, rotating disks, similar to those of galaxies today. The existence of well-ordered rotation in galaxies during this peak epoch of cosmic star formation indicates that gas accretion is likely to be the dominant mode by which galaxies grow, because major mergers of galaxies would completely disrupt the observed velocity fields. But poor spatial resolution and sensitivity have hampered this interpretation; such studies have been limited to the largest and most luminous galaxies, which may have fundamentally different modes of assembly from those of more typical galaxies (which are thought to grow into the spheroidal components at the centres of galaxies similar to the Milky Way). Here we report observations of a typical star-forming galaxy at z = 3.07, with a linear resolution of approximately 100 parsecs. We find a well-ordered compact source in which molecular gas is being converted efficiently into stars, likely to be assembling a spheroidal bulge similar to those seen in spiral galaxies at the present day. The presence of undisrupted rotation may indicate that galaxies such as the Milky Way gain much of their mass by accretion rather than major mergers.\",\n \"corpus_id\": 4422629,\n \"score\": 0\n },\n {\n \"doc_id\": \"19340075\",\n \"title\": \"Early assembly of the most massive galaxies.\",\n \"abstract\": \"The current consensus is that galaxies begin as small density fluctuations in the early Universe and grow by in situ star formation and hierarchical merging. Stars begin to form relatively quickly in sub-galactic-sized building blocks called haloes which are subsequently assembled into galaxies. However, exactly when this assembly takes place is a matter of some debate. Here we report that the stellar masses of brightest cluster galaxies, which are the most luminous objects emitting stellar light, some 9 billion years ago are not significantly different from their stellar masses today. Brightest cluster galaxies are almost fully assembled 4-5 billion years after the Big Bang, having grown to more than 90 per cent of their final stellar mass by this time. Our data conflict with the most recent galaxy formation models based on the largest simulations of dark-matter halo development. These models predict protracted formation of brightest cluster galaxies over a Hubble time, with only 22 per cent of the stellar mass assembled at the epoch probed by our sample. Our findings suggest a new picture in which brightest cluster galaxies experience an early period of rapid growth rather than prolonged hierarchical assembly.\",\n \"corpus_id\": 4386728,\n \"score\": 0\n },\n {\n \"doc_id\": \"19661911\",\n \"title\": \"A high stellar velocity dispersion for a compact massive galaxy at redshift z = 2.186.\",\n \"abstract\": \"Recent studies have found that the oldest and most luminous galaxies in the early Universe are surprisingly compact, having stellar masses similar to present-day elliptical galaxies but much smaller sizes. This finding has attracted considerable attention, as it suggests that massive galaxies have grown in size by a factor of about five over the past ten billion years (10 Gyr). A key test of these results is a determination of the stellar kinematics of one of the compact galaxies: if the sizes of these objects are as extreme as has been claimed, their stars are expected to have much higher velocities than those in present-day galaxies of the same mass. Here we report a measurement of the stellar velocity dispersion of a massive compact galaxy at redshift z = 2.186, corresponding to a look-back time of 10.7 Gyr. The velocity dispersion is very high at km s(-1), consistent with the mass and compactness of the galaxy inferred from photometric data. This would indicate significant recent structural and dynamical evolution of massive galaxies over the past 10 Gyr. The uncertainty in the dispersion was determined from simulations that include the effects of noise and template mismatch. However, we cannot exclude the possibility that some subtle systematic effect may have influenced the analysis, given the low signal-to-noise ratio of our spectrum.\",\n \"corpus_id\": 4429718,\n \"score\": 0\n },\n {\n \"doc_id\": \"19792482\",\n \"title\": \"Size bias in galaxy surveys.\",\n \"abstract\": \"Only certain galaxies are included in surveys: those bright and large enough to be detectable as extended sources. Because gravitational lensing can make galaxies appear both brighter and larger, the presence of foreground inhomogeneities can scatter galaxies across not only magnitude cuts but also size cuts, changing the statistical properties of the resulting catalog. Here we explore this size bias and how it combines with magnification bias to affect galaxy statistics. We demonstrate that photometric galaxy samples from current and upcoming surveys can be even more affected by size bias than by magnification bias.\",\n \"corpus_id\": 38220338,\n \"score\": 0\n },\n {\n \"doc_id\": \"20161594\",\n \"title\": \"Automatic morphological classification of galaxy images.\",\n \"abstract\": \"We describe an image analysis supervised learning algorithm that can automatically classify galaxy images. The algorithm is first trained using a manually classified images of elliptical, spiral, and edge-on galaxies. A large set of image features is extracted from each image, and the most informative features are selected using Fisher scores. Test images can then be classified using a simple Weighted Nearest Neighbor rule such that the Fisher scores are used as the feature weights. Experimental results show that galaxy images from Galaxy Zoo can be classified automatically to spiral, elliptical and edge-on galaxies with accuracy of ~90% compared to classifications carried out by the author. Full compilable source code of the algorithm is available for free download, and its general-purpose nature makes it suitable for other uses that involve automatic image analysis of celestial objects.\",\n \"corpus_id\": 1389063,\n \"score\": 0\n },\n {\n \"doc_id\": \"20520705\",\n \"title\": \"Nearby galaxies as pointers to a better theory of cosmic evolution.\",\n \"abstract\": \"The great advances in the network of cosmological tests show that the relativistic Big Bang theory is a good description of our expanding Universe. However, the properties of nearby galaxies that can be observed in greatest detail suggest that a better theory would describe a mechanism by which matter is more rapidly gathered into galaxies and groups of galaxies. This more rapid growth occurs in some theoretical ideas now under discussion.\",\n \"corpus_id\": 43767061,\n \"score\": 0\n },\n {\n \"doc_id\": \"20724628\",\n \"title\": \"Cosmological constraints from strong gravitational lensing in clusters of galaxies.\",\n \"abstract\": \"Current efforts in observational cosmology are focused on characterizing the mass-energy content of the universe. We present results from a geometric test based on strong lensing in galaxy clusters. Based on Hubble Space Telescope images and extensive ground-based spectroscopic follow-up of the massive galaxy cluster Abell 1689, we used a parametric model to simultaneously constrain the cluster mass distribution and dark energy equation of state. Combining our cosmological constraints with those from x-ray clusters and the Wilkinson Microwave Anisotropy Probe 5-year data gives Omega(m) = 0.25 +/- 0.05 and w(x) = -0.97 +/- 0.07, which are consistent with results from other methods. Inclusion of our method with all other available techniques brings down the current 2sigma contours on the dark energy equation-of-state parameter w(x) by approximately 30%.\",\n \"corpus_id\": 7832717,\n \"score\": 0\n },\n {\n \"doc_id\": \"21107424\",\n \"title\": \"A geometric measure of dark energy with pairs of galaxies.\",\n \"abstract\": \"Observations indicate that the expansion of the Universe is accelerating, which is attributed to a ‘dark energy’ component that opposes gravity. There is a purely geometric test of the expansion of the Universe (the Alcock–Paczynski test), which would provide an independent way of investigating the abundance (Ω(X)) and equation of state (W(X)) of dark energy. It is based on an analysis of the geometrical distortions expected from comparing the real-space and redshift-space shape of distant cosmic structures, but it has proved difficult to implement. Here we report an analysis of the symmetry properties of distant pairs of galaxies from archival data. This allows us to determine that the Universe is flat. By alternately fixing its spatial geometry at Ω(k)≡0 and the dark energy equation-of-state parameter at W(X)≡-1, and using the results of baryon acoustic oscillations, we can establish at the 68.3% confidence level that and -0.85>W(X)>-1.12 and 0.60<Ω(X)<0.80.\",\n \"corpus_id\": 4426871,\n \"score\": 0\n },\n {\n \"doc_id\": \"21228776\",\n \"title\": \"A massive protocluster of galaxies at a redshift of z ≈ 5.3.\",\n \"abstract\": \"Massive clusters of galaxies have been found that date from as early as 3.9 billion years (3.9 Gyr; z = 1.62) after the Big Bang, containing stars that formed at even earlier epochs. Cosmological simulations using the current cold dark matter model predict that these systems should descend from 'protoclusters'-early overdensities of massive galaxies that merge hierarchically to form a cluster. These protocluster regions themselves are built up hierarchically and so are expected to contain extremely massive galaxies that can be observed as luminous quasars and starbursts. Observational evidence for this picture, however, is sparse because high-redshift protoclusters are rare and difficult to observe. Here we report a protocluster region that dates from 1 Gyr (z = 5.3) after the Big Bang. This cluster of massive galaxies extends over more than 13 megaparsecs and contains a luminous quasar as well as a system rich in molecular gas. These massive galaxies place a lower limit of more than 4 × 10(11) solar masses of dark and luminous matter in this region, consistent with that expected from cosmological simulations for the earliest galaxy clusters.\",\n \"corpus_id\": 205223398,\n \"score\": 0\n },\n {\n \"doc_id\": \"21552608\",\n \"title\": \"Analysis and modeling of flow in rotating spiral microchannels: towards math-aided design of microfluidic systems using centrifugal pumping.\",\n \"abstract\": \"This paper describes the experimental measurement and mathematical modeling of centrifugally-pumped flow in spiral microchannels. Here, the liquid is delivered by the rotation of a circular microchip as depicted before (X. Y. Peng, P. C. H. Li, H. Z. Yu, M. Parameswaran and W. L. Chou, Sens. Actuators, B, 2007, 128, 64-69). The spiral microchannel in it was specially designed to produce a constant centrifugal force component. From experimental measurements, it was found that the flow velocity inside the spiral microchannels was associated with the rotation speed only, but not with the length of the liquid column. The mathematical modeling of liquid flow was constructed based on solving the Navier-Stokes equations of incompressible flow formulated in a new orthogonal curvilinear coordinate system aligned with the channel geometry. The governing equations were simplified under various assumptions, rendering a mathematically-tractable physical model. In addition, a commercial computational fluid dynamics (CFD) program was used to simulate the flow in the spiral microchannel. The predicted liquid flow velocities from the mathematical model and the CFD program showed reasonable agreement with the experimental data. Under proper assumptions, the mathematical model gave a flexible and rather accurate analytical solution using much less computing power. The proposed study demonstrated the effectiveness of the spiral microchannel design in microfluidic applications using centrifugal force. With modifications, this study could be adapted to the simulation and modeling of other centrifugal-pumping microflow systems.\",\n \"corpus_id\": 35720599,\n \"score\": 0\n },\n {\n \"doc_id\": \"21635025\",\n \"title\": \"Cores in dwarf galaxies from dark matter with a Yukawa potential.\",\n \"abstract\": \"We show that cold dark matter particles interacting through a Yukawa potential could naturally explain the recently observed cores in dwarf galaxies without affecting the dynamics of objects with a much larger velocity dispersion, such as clusters of galaxies. The velocity dependence of the associated cross section as well as the possible exothermic nature of the interaction alleviates earlier concerns about strongly interacting dark matter. Dark matter evaporation in low-mass objects might explain the observed deficit of satellite galaxies in the Milky Way halo and have important implications for the first galaxies and reionization.\",\n \"corpus_id\": 29767392,\n \"score\": 0\n },\n {\n \"doc_id\": \"21737732\",\n \"title\": \"Galaxy evolution. Galactic paleontology.\",\n \"abstract\": \"Individual low-mass stars have very long lives, comparable to the age of the universe, and can thus be used to probe ancient star formation. At present, such stars can be identified and studied only in the Milky Way and in the very closest of our neighboring galaxies, which are predominantly small dwarf galaxies. These nearby ancient stars are a fossil record that can provide detailed information about the physical processes that dominated the epoch of galaxy formation and subsequent evolution.\",\n \"corpus_id\": 33882128,\n \"score\": 0\n },\n {\n \"doc_id\": \"21881560\",\n \"title\": \"A close nuclear black-hole pair in the spiral galaxy NGC 3393.\",\n \"abstract\": \"The current picture of galaxy evolution advocates co-evolution of galaxies and their nuclear massive black holes, through accretion and galactic merging. Pairs of quasars, each with a massive black hole at the centre of its galaxy, have separations of 6,000 to 300,000 light years (refs 2 and 3; 1 parsec = 3.26 light years) and exemplify the first stages of this gravitational interaction. The final stages of the black-hole merging process, through binary black holes and final collapse into a single black hole with gravitational wave emission, are consistent with the sub-light-year separation inferred from the optical spectra and light-variability of two such quasars. The double active nuclei of a few nearby galaxies with disrupted morphology and intense star formation (such as NGC 6240 with a separation of about 2,600 light years and Mrk 463 with a separation of about 13,000 light years between the nuclei) demonstrate the importance of major mergers of equal-mass spiral galaxies in this evolution; such mergers lead to an elliptical galaxy, as in the case of the double-radio-nucleus elliptical galaxy 0402+379 (with a separation of about 24 light years between the nuclei). Minor mergers of a spiral galaxy with a smaller companion should be a more common occurrence, evolving into spiral galaxies with active massive black-hole pairs, but have hitherto not been seen. Here we report the presence of two active massive black holes, separated by about 490 light years, in the Seyfert galaxy NGC 3393 (50 Mpc, about 160 million light years). The regular spiral morphology and predominantly old circum-nuclear stellar population of this galaxy, and the closeness of the black holes embedded in the bulge, provide a hitherto missing observational point to the study of galaxy/black hole evolution. Comparison of our observations with current theoretical models of mergers suggests that they are the result of minor merger evolution.\",\n \"corpus_id\": 205226065,\n \"score\": 0\n },\n {\n \"doc_id\": \"21956329\",\n \"title\": \"Gravitational redshift of galaxies in clusters as predicted by general relativity.\",\n \"abstract\": \"The theoretical framework of cosmology is mainly defined by gravity, of which general relativity is the current model. Recent tests of general relativity within the Lambda Cold Dark Matter (ΛCDM) model have found a concordance between predictions and the observations of the growth rate and clustering of the cosmic web. General relativity has not hitherto been tested on cosmological scales independently of the assumptions of the ΛCDM model. Here we report an observation of the gravitational redshift of light coming from galaxies in clusters at the 99 per cent confidence level, based on archival data. Our measurement agrees with the predictions of general relativity and its modification created to explain cosmic acceleration without the need for dark energy (the f(R) theory), but is inconsistent with alternative models designed to avoid the presence of dark matter.\",\n \"corpus_id\": 4373051,\n \"score\": 0\n },\n {\n \"doc_id\": \"22084285\",\n \"title\": \"One gravitational potential or two? Forecasts and tests.\",\n \"abstract\": \"The metric of a perturbed Robertson-Walker space-time is characterized by three functions: a scale-factor giving the expansion history and two potentials that generalize the single potential of Newtonian gravity. The Newtonian potential induces peculiar velocities and, from these, the growth of matter fluctuations. Massless particles respond equally to the Newtonian potential and to a curvature potential. The difference of the two potentials, called the gravitational slip, is predicted to be very small in general relativity, but can be substantial in modified gravity theories. The two potentials can be measured, and gravity tested on cosmological scales, by combining weak gravitational lensing or the integrated Sachs-Wolfe effect with galaxy peculiar velocities or clustering.\",\n \"corpus_id\": 299978,\n \"score\": 0\n },\n {\n \"doc_id\": \"22084295\",\n \"title\": \"Designing surveys for tests of gravity.\",\n \"abstract\": \"Modified gravity theories may provide an alternative to dark energy to explain cosmic acceleration. We argue that the observational programme developed to test dark energy needs to be augmented to capture new tests of gravity on astrophysical scales. Several distinct signatures of gravity theories exist outside the 'linear' regime, especially owing to the screening mechanism that operates inside halos such as the Milky Way to ensure that gravity tests in the solar system are satisfied. This opens up several decades in length scale and classes of galaxies at low redshift that can be exploited by surveys. While theoretical work on models of gravity is in the early stages, we can already identify new regimes that cosmological surveys could target to test gravity. These include: (i) a small-scale component that focuses on the interior and vicinity of galaxy and cluster halos, (ii) spectroscopy of low-redshift galaxies, especially galaxies smaller than the Milky Way, in environments that range from voids to clusters, and (iii) a programme of combining lensing and dynamical information, from imaging and spectroscopic surveys, respectively, on the same (or statistically identical) sample of galaxies.\",\n \"corpus_id\": 27953932,\n \"score\": 0\n },\n {\n \"doc_id\": \"22258612\",\n \"title\": \"Gravitational detection of a low-mass dark satellite galaxy at cosmological distance.\",\n \"abstract\": \"The mass function of dwarf satellite galaxies that are observed around Local Group galaxies differs substantially from simulations based on cold dark matter: the simulations predict many more dwarf galaxies than are seen. The Local Group, however, may be anomalous in this regard. A massive dark satellite in an early-type lens galaxy at a redshift of 0.222 was recently found using a method based on gravitational lensing, suggesting that the mass fraction contained in substructure could be higher than is predicted from simulations. The lack of very low-mass detections, however, prohibited any constraint on their mass function. Here we report the presence of a (1.9 ± 0.1) × 10(8) M dark satellite galaxy in the Einstein ring system JVAS B1938+666 (ref. 11) at a redshift of 0.881, where M denotes the solar mass. This satellite galaxy has a mass similar to that of the Sagittarius galaxy, which is a satellite of the Milky Way. We determine the logarithmic slope of the mass function for substructure beyond the local Universe to be 1.1(+0.6)(-0.4), with an average mass fraction of 3.3(+3.6)(-1.8) per cent, by combining data on both of these recently discovered galaxies. Our results are consistent with the predictions from cold dark matter simulations at the 95 per cent confidence level, and therefore agree with the view that galaxies formed hierarchically in a Universe composed of cold dark matter.\",\n \"corpus_id\": 205227095,\n \"score\": 0\n },\n {\n \"doc_id\": \"22281178\",\n \"title\": \"Specific rotation as a property to validate monosaccharide conformations.\",\n \"abstract\": \"Specific rotation ([α](D)) values were calculated for the 15 conformations of xylopyranose that are the most stable in the gas phase and in aqueous solution. The effects of different theoretical descriptions and the medium on the geometry of the conformers and the [α](D) values are evaluated. Differences in [α](D) values found for the same conformer in all descriptions used were smaller than those found between any two different conformers in the same description. The difference between [α](D) values is prominent, even for two conformations that are distinguished from each other only by the orientation of one secondary hydroxyl group. This finding suggests that [α](D) values may potentially be used in the validation of monosaccharide conformations that are theoretically sampled.\",\n \"corpus_id\": 44351059,\n \"score\": 0\n },\n {\n \"doc_id\": \"23006162\",\n \"title\": \"Testing gravity with the stacked phase space around galaxy clusters.\",\n \"abstract\": \"In general relativity, the average velocity field of dark matter around galaxy clusters is uniquely determined by the mass profile. The latter can be measured through weak lensing. We propose a new method of measuring the velocity field (phase space density) by stacking redshifts of surrounding galaxies from a spectroscopic sample. In combination with lensing, this yields a direct test of gravity on scales of 1-30 Mpc. Using N-body simulations, we show that this method can improve upon current constraints on f(R) and Dvali-Gabadadze-Porrati model parameters by several orders of magnitude when applied to upcoming imaging and redshift surveys.\",\n \"corpus_id\": 29852776,\n \"score\": 0\n },\n {\n \"doc_id\": \"23099405\",\n \"title\": \"Near-infrared background anisotropies from diffuse intrahalo light of galaxies.\",\n \"abstract\": \"Unresolved anisotropies of the cosmic near-infrared background radiation are expected to have contributions from the earliest galaxies during the epoch of reionization and from faint, dwarf galaxies at intermediate redshifts. Previous measurements were unable to pinpoint conclusively the dominant origin because they did not sample spatial scales that were sufficiently large to distinguish between these two possibilities. Here we report a measurement of the anisotropy power spectrum from subarcminute to one-degree angular scales, and find the clustering amplitude to be larger than predicted by the models based on the two existing explanations. As the shot-noise level of the power spectrum is consistent with that expected from faint galaxies, a new source population on the sky is not necessary to explain the observations. However, a physical mechanism that increases the clustering amplitude is needed. Motivated by recent results related to the extended stellar light profile in dark-matter haloes, we consider the possibility that the fluctuations originate from intrahalo stars of all galaxies. We find that the measured power spectrum can be explained by an intrahalo light fraction of 0.07 to 0.2 per cent relative to the total luminosity in dark-matter haloes of 10(9) to 10(12) solar masses at redshifts of about 1 to 4.\",\n \"corpus_id\": 205230649,\n \"score\": 0\n },\n {\n \"doc_id\": \"23282362\",\n \"title\": \"A vast, thin plane of corotating dwarf galaxies orbiting the Andromeda galaxy.\",\n \"abstract\": \"Dwarf satellite galaxies are thought to be the remnants of the population of primordial structures that coalesced to form giant galaxies like the Milky Way. It has previously been suspected that dwarf galaxies may not be isotropically distributed around our Galaxy, because several are correlated with streams of H I emission, and may form coplanar groups. These suspicions are supported by recent analyses. It has been claimed that the apparently planar distribution of satellites is not predicted within standard cosmology, and cannot simply represent a memory of past coherent accretion. However, other studies dispute this conclusion. Here we report the existence of a planar subgroup of satellites in the Andromeda galaxy (M 31), comprising about half of the population. The structure is at least 400 kiloparsecs in diameter, but also extremely thin, with a perpendicular scatter of less than 14.1 kiloparsecs. Radial velocity measurements reveal that the satellites in this structure have the same sense of rotation about their host. This shows conclusively that substantial numbers of dwarf satellite galaxies share the same dynamical orbital properties and direction of angular momentum. Intriguingly, the plane we identify is approximately aligned with the pole of the Milky Way's disk and with the vector between the Milky Way and Andromeda.\",\n \"corpus_id\": 4404711,\n \"score\": 0\n },\n {\n \"doc_id\": \"23739604\",\n \"title\": \"[A man with a 'galaxy sign'].\",\n \"abstract\": \"Een man met het 'galaxy sign'. This brief report describes the radiographic images of a 29-year-old man with asymptomatic sarcoidosis. On a CT-scan a coalescent granuloma with a central core and peripheral nodules mimics a globular cluster galaxy; therefore it is called 'galaxy sign'. This is a classic finding in a granulomatous disease like sarcoidosis.\",\n \"corpus_id\": 13068459,\n \"score\": 0\n },\n {\n \"doc_id\": \"24580436\",\n \"title\": \"Cosmology with void-galaxy correlations.\",\n \"abstract\": \"Galaxy bias, the unknown relationship between the clustering of galaxies and the underlying dark matter density field is a major hurdle for cosmological inference from large-scale structure. While traditional analyses focus on the absolute clustering amplitude of high-density regions mapped out by galaxy surveys, we propose a relative measurement that compares those to the underdense regions, cosmic voids. On the basis of realistic mock catalogs we demonstrate that cross correlating galaxies and voids opens up the possibility to calibrate galaxy bias and to define a static ruler thanks to the observable geometric nature of voids. We illustrate how the clustering of voids is related to mass compensation and show that volume-exclusion significantly reduces the degree of stochasticity in their spatial distribution. Extracting the spherically averaged distribution of galaxies inside voids from their cross correlations reveals a remarkable concordance with the mass-density profile of voids.\",\n \"corpus_id\": 5518892,\n \"score\": 0\n },\n {\n \"doc_id\": \"24702345\",\n \"title\": \"Conformal gravity holography in four dimensions.\",\n \"abstract\": \"We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a \\\"partially massless response\\\". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair.\",\n \"corpus_id\": 12853206,\n \"score\": 0\n },\n {\n \"doc_id\": \"24928211\",\n \"title\": \"BioBlend.objects: metacomputing with Galaxy.\",\n \"abstract\": \"SUMMARY: BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows. AVAILABILITY AND IMPLEMENTATION: BioBlend.objects is available online at https://github.com/afgane/bioblend. The new object-oriented API is implemented by the galaxy/objects subpackage.\",\n \"corpus_id\": 15973453,\n \"score\": 0\n },\n {\n \"doc_id\": \"25186900\",\n \"title\": \"The Laniakea supercluster of galaxies.\",\n \"abstract\": \"Galaxies congregate in clusters and along filaments, and are missing from large regions referred to as voids. These structures are seen in maps derived from spectroscopic surveys that reveal networks of structure that are interconnected with no clear boundaries. Extended regions with a high concentration of galaxies are called 'superclusters', although this term is not precise. There is, however, another way to analyse the structure. If the distance to each galaxy from Earth is directly measured, then the peculiar velocity can be derived from the subtraction of the mean cosmic expansion, the product of distance times the Hubble constant, from observed velocity. The peculiar velocity is the line-of-sight departure from the cosmic expansion and arises from gravitational perturbations; a map of peculiar velocities can be translated into a map of the distribution of matter. Here we report a map of structure made using a catalogue of peculiar velocities. We find locations where peculiar velocity flows diverge, as water does at watershed divides, and we trace the surface of divergent points that surrounds us. Within the volume enclosed by this surface, the motions of galaxies are inward after removal of the mean cosmic expansion and long range flows. We define a supercluster to be the volume within such a surface, and so we are defining the extent of our home supercluster, which we call Laniakea.\",\n \"corpus_id\": 205240232,\n \"score\": 0\n },\n {\n \"doc_id\": \"25309716\",\n \"title\": \"Executing SADI services in Galaxy.\",\n \"abstract\": \"BACKGROUND: In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. RESULTS: SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. CONCLUSIONS: SADI-Galaxy bridges the gap between Galaxy, an easy to use but \\\"static\\\" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.\",\n \"corpus_id\": 783717,\n \"score\": 0\n },\n {\n \"doc_id\": \"25646464\",\n \"title\": \"Cold dark matter: Controversies on small scales.\",\n \"abstract\": \"The cold dark matter (CDM) cosmological model has been remarkably successful in explaining cosmic structure over an enormous span of redshift, but it has faced persistent challenges from observations that probe the innermost regions of dark matter halos and the properties of the Milky Way's dwarf galaxy satellites. We review the current observational and theoretical status of these \\\"small-scale controversies.\\\" Cosmological simulations that incorporate only gravity and collisionless CDM predict halos with abundant substructure and central densities that are too high to match constraints from galaxy dynamics. The solution could lie in baryonic physics: Recent numerical simulations and analytical models suggest that gravitational potential fluctuations tied to efficient supernova feedback can flatten the central cusps of halos in massive galaxies, and a combination of feedback and low star formation efficiency could explain why most of the dark matter subhalos orbiting the Milky Way do not host visible galaxies. However, it is not clear that this solution can work in the lowest mass galaxies, where discrepancies are observed. Alternatively, the small-scale conflicts could be evidence of more complex physics in the dark sector itself. For example, elastic scattering from strong dark matter self-interactions can alter predicted halo mass profiles, leading to good agreement with observations across a wide range of galaxy mass. Gravitational lensing and dynamical perturbations of tidal streams in the stellar halo provide evidence for an abundant population of low-mass subhalos in accord with CDM predictions. These observational approaches will get more powerful over the next few years.\",\n \"corpus_id\": 30473661,\n \"score\": 0\n },\n {\n \"doc_id\": \"25988504\",\n \"title\": \"The concept of geodesic curvature applied to optical surfaces.\",\n \"abstract\": \"PURPOSE: To propose geodesic curvature as a metric to characterise how an optical surface locally differs from axial symmetry. To derive equations to evaluate geodesic curvatures of arbitrary surfaces expressed in polar coordinates. METHODS: The concept of geodesic curvature is explained in detail as compared to other curvature-based metrics. Starting with the formula representing a surface as function of polar coordinates, an equation for the geodesic curvature is obtained depending only on first and second radial and first order angular derivatives of the surface function. The potential of the geodesic curvature is illustrated using different surface tests. RESULTS: Geodesic curvature reveals local axial asymmetries more sharply than other types of curvatures such as normal curvatures. CONCLUSION: Geodesic curvature maps could be used to characterise local axial asymmetries for relevant optometry applications such as corneal topography anomalies (keratoconus) or ophthalmic lens metrology.\",\n \"corpus_id\": 30375053,\n \"score\": 0\n },\n {\n \"doc_id\": \"26017450\",\n \"title\": \"A kiloparsec-scale internal shock collision in the jet of a nearby radio galaxy.\",\n \"abstract\": \"Jets of highly energized plasma with relativistic velocities are associated with black holes ranging in mass from a few times that of the Sun to the billion-solar-mass black holes at the centres of galaxies. A popular but unconfirmed hypothesis to explain how the plasma is energized is the 'internal shock model', in which the relativistic flow is unsteady. Faster components in the jet catch up to and collide with slower ones, leading to internal shocks that accelerate particles and generate magnetic fields. This mechanism can explain the variable, high-energy emission from a diverse set of objects, with the best indirect evidence being the unseen fast relativistic flow inferred to energize slower components in X-ray binary jets. Mapping of the kinematic profiles in resolved jets has revealed precessing and helical patterns in X-ray binaries, apparent superluminal motions, and the ejection of knots (bright components) from standing shocks in the jets of active galaxies. Observations revealing the structure and evolution of an internal shock in action have, however, remained elusive, hindering measurement of the physical parameters and ultimate efficiency of the mechanism. Here we report observations of a collision between two knots in the jet of nearby radio galaxy 3C 264. A bright knot with an apparent speed of (7.0 ± 0.8)c, where c is the speed of light in a vacuum, is in the incipient stages of a collision with a slower-moving knot of speed (1.8 ± 0.5)c just downstream, resulting in brightening of both knots--as seen in the most recent epoch of imaging.\",\n \"corpus_id\": 4451677,\n \"score\": 0\n },\n {\n \"doc_id\": \"26182087\",\n \"title\": \"Growth Rate of Cosmological Perturbations at z∼0.1 from a New Observational Test.\",\n \"abstract\": \"Spatial variations in the distribution of galaxy luminosities, estimated from redshifts as distance proxies, are correlated with the peculiar velocity field. Comparing these variations with the peculiar velocities inferred from galaxy redshift surveys is a powerful test of gravity and dark-energy theories on cosmological scales. Using ∼2×10(5) galaxies from the SDSS Data Release 7, we perform this test in the framework of gravitational instability to estimate the normalized growth rate of density perturbations fσ8=0.37±0.13 at z∼0.1, which is in agreement with the cold dark matter model with a cosmological constant. This unique measurement is complementary to those obtained with more traditional methods, including clustering analysis. The estimated accuracy at z∼0.1 is competitive with other methods when applied to similar data sets.\",\n \"corpus_id\": 30013989,\n \"score\": 0\n },\n {\n \"doc_id\": \"26382671\",\n \"title\": \"New Test of the Friedmann-Lemaître-Robertson-Walker Metric Using the Distance Sum Rule.\",\n \"abstract\": \"We present a new test of the validity of the Friedmann-Lemaître-Robertson-Walker (FLRW) metric, based on comparing the distance from redshift 0 to z(1) and from z(1) to z(2) to the distance from 0 to z(2). If the Universe is described by the FLRW metric, the comparison provides a model-independent measurement of spatial curvature. The test relies on geometrical optics, it is independent of the matter content of the Universe and the applicability of the Einstein equation on cosmological scales. We apply the test to observations, using the Union2.1 compilation of supernova distances and Sloan Lens ACS Survey galaxy strong lensing data. The FLRW metric is consistent with the data, and the spatial curvature parameter is constrained to be -1.22<Ω(K0)<0.63, or -0.08<Ω(K0)<0.97 with a prior from the cosmic microwave background and the local Hubble constant, though modeling of the lenses is a source of significant systematic uncertainty.\",\n \"corpus_id\": 22551992,\n \"score\": 0\n },\n {\n \"doc_id\": \"26762455\",\n \"title\": \"Eight per cent leakage of Lyman continuum photons from a compact, star-forming dwarf galaxy.\",\n \"abstract\": \"One of the key questions in observational cosmology is the identification of the sources responsible for ionization of the Universe after the cosmic 'Dark Ages', when the baryonic matter was neutral. The currently identified distant galaxies are insufficient to fully reionize the Universe by redshift z ≈ 6 (refs 1-3), but low-mass, star-forming galaxies are thought to be responsible for the bulk of the ionizing radiation. As direct observations at high redshift are difficult for a variety of reasons, one solution is to identify local proxies of this galaxy population. Starburst galaxies at low redshifts, however, generally are opaque to Lyman continuum photons. Small escape fractions of about 1 to 3 per cent, insufficient to ionize much surrounding gas, have been detected only in three low-redshift galaxies. Here we report far-ultraviolet observations of the nearby low-mass star-forming galaxy J0925+1403. The galaxy is leaking ionizing radiation with an escape fraction of about 8 per cent. The total number of photons emitted during the starburst phase is sufficient to ionize intergalactic medium material that is about 40 times as massive as the stellar mass of the galaxy.\",\n \"corpus_id\": 3033749,\n \"score\": 0\n },\n {\n \"doc_id\": \"26829789\",\n \"title\": \"Geometry-Aware Neighborhood Search for Learning Local Models for Image Superresolution.\",\n \"abstract\": \"Local learning of sparse image models has proved to be very effective to solve inverse problems in many computer vision applications. To learn such models, the data samples are often clustered using the K-means algorithm with the Euclidean distance as a dissimilarity metric. However, the Euclidean distance may not always be a good dissimilarity measure for comparing data samples lying on a manifold. In this paper, we propose two algorithms for determining a local subset of training samples from which a good local model can be computed for reconstructing a given input test sample, where we consider the underlying geometry of the data. The first algorithm, called adaptive geometry-driven nearest neighbor search (AGNN), is an adaptive scheme, which can be seen as an out-of-sample extension of the replicator graph clustering method for local model learning. The second method, called geometry-driven overlapping clusters (GOCs), is a less complex nonadaptive alternative for training subset selection. The proposed AGNN and GOC methods are evaluated in image superresolution and shown to outperform spectral clustering, soft clustering, and geodesic distance-based subset selection in most settings.\",\n \"corpus_id\": 7924419,\n \"score\": 0\n },\n {\n \"doc_id\": \"27007681\",\n \"title\": \"Cosmological tests of modified gravity.\",\n \"abstract\": \"We review recent progress in the construction of modified gravity models as alternatives to dark energy as well as the development of cosmological tests of gravity. Einstein's theory of general relativity (GR) has been tested accurately within the local universe i.e. the Solar System, but this leaves the possibility open that it is not a good description of gravity at the largest scales in the Universe. This being said, the standard model of cosmology assumes GR on all scales. In 1998, astronomers made the surprising discovery that the expansion of the Universe is accelerating, not slowing down. This late-time acceleration of the Universe has become the most challenging problem in theoretical physics. Within the framework of GR, the acceleration would originate from an unknown dark energy. Alternatively, it could be that there is no dark energy and GR itself is in error on cosmological scales. In this review, we first give an overview of recent developments in modified gravity theories including f(R) gravity, braneworld gravity, Horndeski theory and massive/bigravity theory. We then focus on common properties these models share, such as screening mechanisms they use to evade the stringent Solar System tests. Once armed with a theoretical knowledge of modified gravity models, we move on to discuss how we can test modifications of gravity on cosmological scales. We present tests of gravity using linear cosmological perturbations and review the latest constraints on deviations from the standard [Formula: see text]CDM model. Since screening mechanisms leave distinct signatures in the non-linear structure formation, we also review novel astrophysical tests of gravity using clusters, dwarf galaxies and stars. The last decade has seen a number of new constraints placed on gravity from astrophysical to cosmological scales. Thanks to on-going and future surveys, cosmological tests of gravity will enjoy another, possibly even more, exciting ten years.\",\n \"corpus_id\": 20161785,\n \"score\": 0\n },\n {\n \"doc_id\": \"27929014\",\n \"title\": \"A massive, quiescent, population II galaxy at a redshift of 2.1.\",\n \"abstract\": \"Unlike spiral galaxies such as the Milky Way, the majority of the stars in massive elliptical galaxies were formed in a short period early in the history of the Universe. The duration of this formation period can be measured using the ratio of magnesium to iron abundance ([Mg/Fe]) in spectra, which reflects the relative enrichment by core-collapse and type Ia supernovae. For local galaxies, [Mg/Fe] probes the combined formation history of all stars currently in the galaxy, including younger and metal-poor stars that were added during late-time mergers. Therefore, to directly constrain the initial star-formation period, we must study galaxies at earlier epochs. The most distant galaxy for which [Mg/Fe] had previously been measured is at a redshift of z ≈ 1.4, with [Mg/Fe] = . A slightly earlier epoch (z ≈ 1.6) was probed by combining the spectra of 24 massive quiescent galaxies, yielding an average [Mg/Fe] = 0.31 ± 0.12 (ref. 7). However, the relatively low signal-to-noise ratio of the data and the use of index analysis techniques for both of these studies resulted in measurement errors that are too large to allow us to form strong conclusions. Deeper spectra at even earlier epochs in combination with analysis techniques based on full spectral fitting are required to precisely measure the abundance pattern shortly after the major star-forming phase (z > 2). Here we report a measurement of [Mg/Fe] for a massive quiescent galaxy at a redshift of z = 2.1, when the Universe was three billion years old. With [Mg/Fe] = 0.59 ± 0.11, this galaxy is the most Mg-enhanced massive galaxy found so far, having twice the Mg enhancement of similar-mass galaxies today. The abundance pattern of the galaxy is consistent with enrichment exclusively by core-collapse supernovae and with a star-formation timescale of 0.1 to 0.5 billion years-characteristics that are similar to population II stars in the Milky Way. With an average past star-formation rate of 600 to 3,000 solar masses per year, this galaxy was among the most vigorous star-forming galaxies in the Universe.\",\n \"corpus_id\": 4383112,\n \"score\": 0\n },\n {\n \"doc_id\": \"28300118\",\n \"title\": \"Strongly baryon-dominated disk galaxies at the peak of galaxy formation ten billion years ago.\",\n \"abstract\": \"In the cold dark matter cosmology, the baryonic components of galaxies-stars and gas-are thought to be mixed with and embedded in non-baryonic and non-relativistic dark matter, which dominates the total mass of the galaxy and its dark-matter halo. In the local (low-redshift) Universe, the mass of dark matter within a galactic disk increases with disk radius, becoming appreciable and then dominant in the outer, baryonic regions of the disks of star-forming galaxies. This results in rotation velocities of the visible matter within the disk that are constant or increasing with disk radius-a hallmark of the dark-matter model. Comparisons between the dynamical mass, inferred from these velocities in rotational equilibrium, and the sum of the stellar and cold-gas mass at the peak epoch of galaxy formation ten billion years ago, inferred from ancillary data, suggest high baryon fractions in the inner, star-forming regions of the disks. Although this implied baryon fraction may be larger than in the local Universe, the systematic uncertainties (owing to the chosen stellar initial-mass function and the calibration of gas masses) render such comparisons inconclusive in terms of the mass of dark matter. Here we report rotation curves (showing rotation velocity as a function of disk radius) for the outer disks of six massive star-forming galaxies, and find that the rotation velocities are not constant, but decrease with radius. We propose that this trend arises because of a combination of two main factors: first, a large fraction of the massive high-redshift galaxy population was strongly baryon-dominated, with dark matter playing a smaller part than in the local Universe; and second, the large velocity dispersion in high-redshift disks introduces a substantial pressure term that leads to a decrease in rotation velocity with increasing radius. The effect of both factors appears to increase with redshift. Qualitatively, the observations suggest that baryons in the early (high-redshift) Universe efficiently condensed at the centres of dark-matter haloes when gas fractions were high and dark matter was less concentrated.\",\n \"corpus_id\": 205254567,\n \"score\": 0\n },\n {\n \"doc_id\": \"28382981\",\n \"title\": \"A massive, quiescent galaxy at a redshift of 3.717.\",\n \"abstract\": \"Finding massive galaxies that stopped forming stars in the early Universe presents an observational challenge because their rest-frame ultraviolet emission is negligible and they can only be reliably identified by extremely deep near-infrared surveys. These surveys have revealed the presence of massive, quiescent early-type galaxies appearing as early as redshift z ≈ 2, an epoch three billion years after the Big Bang. Their age and formation processes have now been explained by an improved generation of galaxy-formation models, in which they form rapidly at z ≈ 3-4, consistent with the typical masses and ages derived from their observations. Deeper surveys have reported evidence for populations of massive, quiescent galaxies at even higher redshifts and earlier times, using coarsely sampled photometry. However, these early, massive, quiescent galaxies are not predicted by the latest generation of theoretical models. Here we report the spectroscopic confirmation of one such galaxy at redshift z = 3.717, with a stellar mass of 1.7 × 10(11) solar masses. We derive its age to be nearly half the age of the Universe at this redshift and the absorption line spectrum shows no current star formation. These observations demonstrate that the galaxy must have formed the majority of its stars quickly, within the first billion years of cosmic history in a short, extreme starburst. This ancestral starburst appears similar to those being found by submillimetre-wavelength surveys. The early formation of such massive systems implies that our picture of early galaxy assembly requires substantial revision.\",\n \"corpus_id\": 205254535,\n \"score\": 0\n },\n {\n \"doc_id\": \"28474927\",\n \"title\": \"Measurement of a Cosmographic Distance Ratio with Galaxy and Cosmic Microwave Background Lensing.\",\n \"abstract\": \"We measure the gravitational lensing shear signal around dark matter halos hosting constant mass galaxies using light sources at z∼1 (background galaxies) and at the surface of last scattering at z∼1100 (the cosmic microwave background). The galaxy shear measurement uses data from the CFHTLenS survey, and the microwave background shear measurement uses data from the Planck satellite. The ratio of shears from these cross-correlations provides a purely geometric distance measurement across the longest possible cosmological lever arm. This is because the matter distribution around the halos, including uncertainties in galaxy bias and systematic errors such as miscentering, cancels in the ratio for halos in thin redshift slices. We measure this distance ratio in three different redshift slices of the constant mass (CMASS) sample and combine them to obtain a 17% measurement of the distance ratio, r=0.390_{-0.062}^{+0.070}, at an effective redshift of z=0.53. This is consistent with the predicted ratio from the Planck best-fit cold dark matter model with a cosmological constant cosmology of r=0.419.\",\n \"corpus_id\": 46765856,\n \"score\": 0\n },\n {\n \"doc_id\": \"28607526\",\n \"title\": \"A unified framework for constructing, tuning and assessing photometric redshift density estimates in a selection bias setting.\",\n \"abstract\": \"Photometric redshift estimation is an indispensable tool of precision cosmology. One problem that plagues the use of this tool in the era of large-scale sky surveys is that the bright galaxies that are selected for spectroscopic observation do not have properties that match those of (far more numerous) dimmer galaxies; thus, ill-designed empirical methods that produce accurate and precise redshift estimates for the former generally will not produce good estimates for the latter. In this paper, we provide a principled framework for generating conditional density estimates (i.e. photometric redshift PDFs) that takes into account selection bias and the covariate shift that this bias induces. We base our approach on the assumption that the probability that astronomers label a galaxy (i.e. determine its spectroscopic redshift) depends only on its measured (photometric and perhaps other) properties [Formula: see text] and not on its true redshift. With this assumption, we can explicitly write down risk functions that allow us to both tune and compare methods for estimating importance weights (i.e. the ratio of densities of unlabelled and labelled galaxies for different values of [Formula: see text]) and conditional densities. We also provide a method for combining multiple conditional density estimates for the same galaxy into a single estimate with better properties. We apply our risk functions to an analysis of ≈10(6) galaxies, mostly observed by Sloan Digital Sky Survey, and demonstrate through multiple diagnostic tests that our method achieves good conditional density estimates for the unlabelled galaxies.\",\n \"corpus_id\": 11728899,\n \"score\": 0\n },\n {\n \"doc_id\": \"28667318\",\n \"title\": \"Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach.\",\n \"abstract\": \"This paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.\",\n \"corpus_id\": 3318257,\n \"score\": 0\n },\n {\n \"doc_id\": \"29097690\",\n \"title\": \"Ruling out dark matter interpretation of the galactic GeV excess by gamma-ray data of galaxy clusters.\",\n \"abstract\": \"Recently, some very tight constraints of annihilating dark matter have been obtained from gamma-ray data of the Milky Way and Milky Way dwarf spheroidal satellite galaxies. In this article, we report that there are two excellent galaxy clusters (A2877 and Fornax) which can provide interesting constraints for annihilating dark matter. The lower limits of the dark matter mass for the thermal relic annihilation cross section are 25 GeV, 6 GeV, 130 GeV and 100 GeV respectively for the e + e -, μ + μ -, τ + τ - and [Formula: see text] channels. For some configuration of our working assumptions, our results improve the Fermi-LAT upper limits of annihilation cross sections by a factor of 1.3 - 1.8 for wide ranges of dark matter mass for e + e -, μ + μ - and [Formula: see text] channels, and a factor of 1.2-1.8 for τ + τ - channel with dark matter mass ≤100 GeV. These limits basically rule out most of the existing popular dark matter interpretation of the GeV excess in the Milky Way.\",\n \"corpus_id\": 21176026,\n \"score\": 0\n },\n {\n \"doc_id\": \"29323299\",\n \"title\": \"Rotation in [C ii]-emitting gas in two galaxies at a redshift of 6.8.\",\n \"abstract\": \"The earliest galaxies are thought to have emerged during the first billion years of cosmic history, initiating the ionization of the neutral hydrogen that pervaded the Universe at this time. Studying this 'epoch of reionization' involves looking for the spectral signatures of ancient galaxies that are, owing to the expansion of the Universe, now very distant from Earth and therefore exhibit large redshifts. However, finding these spectral fingerprints is challenging. One spectral characteristic of ancient and distant galaxies is strong hydrogen-emission lines (known as Lyman-α lines), but the neutral intergalactic medium that was present early in the epoch of reionization scatters such Lyman-α photons. Another potential spectral identifier is the line at wavelength 157.4 micrometres of the singly ionized state of carbon (the [C ii] λ = 157.74 μm line), which signifies cooling gas and is expected to have been bright in the early Universe. However, so far Lyman-α-emitting galaxies from the epoch of reionization have demonstrated much fainter [C ii] luminosities than would be expected from local scaling relations, and searches for the [C ii] line in sources without Lyman-α emission but with photometric redshifts greater than 6 (corresponding to the first billion years of the Universe) have been unsuccessful. Here we identify [C ii] λ = 157.74 μm emission from two sources that we selected as high-redshift candidates on the basis of near-infrared photometry; we confirm that these sources are two galaxies at redshifts of z = 6.8540 ± 0.0003 and z = 6.8076 ± 0.0002. Notably, the luminosity of the [C ii] line from these galaxies is higher than that found previously in star-forming galaxies with redshifts greater than 6.5. The luminous and extended [C ii] lines reveal clear velocity gradients that, if interpreted as rotation, would indicate that these galaxies have similar dynamic properties to the turbulent yet rotation-dominated disks that have been observed in Hα-emitting galaxies two billion years later, at 'cosmic noon'.\",\n \"corpus_id\": 205261958,\n \"score\": 0\n },\n {\n \"doc_id\": \"29420285\",\n \"title\": \"A whirling plane of satellite galaxies around Centaurus A challenges cold dark matter cosmology.\",\n \"abstract\": \"The Milky Way and Andromeda galaxies are each surrounded by a thin plane of satellite dwarf galaxies that may be corotating. Cosmological simulations predict that most satellite galaxy systems are close to isotropic with random motions, so those two well-studied systems are often interpreted as rare statistical outliers. We test this assumption using the kinematics of satellite galaxies around the Centaurus A galaxy. Our statistical analysis reveals evidence for corotation in a narrow plane: Of the 16 Centaurus A satellites with kinematic data, 14 follow a coherent velocity pattern aligned with the long axis of their spatial distribution. In standard cosmological simulations, <0.5% of Centaurus A-like systems show such behavior. Corotating satellite systems may be common in the universe, challenging small-scale structure formation in the prevailing cosmological paradigm.\",\n \"corpus_id\": 4924232,\n \"score\": 0\n },\n {\n \"doc_id\": \"29531319\",\n \"title\": \"A single population of red globular clusters around the massive compact galaxy NGC 1277.\",\n \"abstract\": \"Massive galaxies are thought to form in two phases: an initial collapse of gas and giant burst of central star formation, followed by the later accretion of material that builds up their stellar and dark-matter haloes. The systems of globular clusters within such galaxies are believed to form in a similar manner. The initial central burst forms metal-rich (spectrally red) clusters, whereas more metal-poor (spectrally blue) clusters are brought in by the later accretion of less-massive satellites. This formation process is thought to result in the multimodal optical colour distributions that are seen in the globular cluster systems of massive galaxies. Here we report optical observations of the massive relic-galaxy candidate NGC 1277-a nearby, un-evolved example of a high-redshift 'red nugget' galaxy. We find that the optical colour distribution of the cluster system of NGC 1277 is unimodal and entirely red. This finding is in strong contrast to other galaxies of similar and larger stellar mass, the cluster systems of which always exhibit (and are generally dominated by) blue clusters. We argue that the colour distribution of the cluster system of NGC 1277 indicates that the galaxy has undergone little (if any) mass accretion after its initial collapse, and use simulations of possible merger histories to show that the stellar mass due to accretion is probably at most ten per cent of the total stellar mass of the galaxy. These results confirm that NGC 1277 is a genuine relic galaxy and demonstrate that blue clusters constitute an accreted population in present-day massive galaxies.\",\n \"corpus_id\": 4440393,\n \"score\": 0\n },\n {\n \"doc_id\": \"29595770\",\n \"title\": \"A galaxy lacking dark matter.\",\n \"abstract\": \"Studies of galaxy surveys in the context of the cold dark matter paradigm have shown that the mass of the dark matter halo and the total stellar mass are coupled through a function that varies smoothly with mass. Their average ratio Mhalo/Mstars has a minimum of about 30 for galaxies with stellar masses near that of the Milky Way (approximately 5 × 1010 solar masses) and increases both towards lower masses and towards higher masses. The scatter in this relation is not well known; it is generally thought to be less than a factor of two for massive galaxies but much larger for dwarf galaxies. Here we report the radial velocities of ten luminous globular-cluster-like objects in the ultra-diffuse galaxy NGC1052-DF2, which has a stellar mass of approximately 2 × 108 solar masses. We infer that its velocity dispersion is less than 10.5 kilometres per second with 90 per cent confidence, and we determine from this that its total mass within a radius of 7.6 kiloparsecs is less than 3.4 × 108 solar masses. This implies that the ratio Mhalo/Mstars is of order unity (and consistent with zero), a factor of at least 400 lower than expected. NGC1052-DF2 demonstrates that dark matter is not always coupled with baryonic matter on galactic scales.\",\n \"corpus_id\": -1,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":63,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29723187\",\n \"title\": \"Ebolaviruses: New roles for old proteins.\",\n \"abstract\": \"In 2014, the world witnessed the largest Ebolavirus outbreak in recorded history. The subsequent humanitarian effort spurred extensive research, significantly enhancing our understanding of ebolavirus replication and pathogenicity. The main functions of each ebolavirus protein have been studied extensively since the discovery of the virus in 1976; however, the recent expansion of ebolavirus research has led to the discovery of new protein functions. These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Many of these new functions appear to be unrelated to the protein's primary function during virus replication. Such new functions range from bystander T-lymphocyte death caused by VP40-secreted exosomes to new roles for VP24 in viral particle formation. This review highlights the newly discovered roles of ebolavirus proteins in order to provide a more encompassing view of ebolavirus replication and pathogenicity.\",\n \"corpus_id\": 13716608\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20164217","title":"Role of the GTPase Rab1b in ebolavirus particle formation.","abstract":"The Ebolavirus matrix protein VP40 is essential for virion assembly and egress. Recently, we reported that the coat protein complex II (COPII) transport system plays an important role in the transport of VP40 to the plasma membrane. Here, we show that dominant-negative mutants of the GTPase Rab1b interfere with VP40-mediated particle formation. Rab1b activates GBF1 (Golgi-specific BFA [brefeldin A] resistance factor 1), a critical factor in the assembly of COPI vesicles. Activated GBF1 stimulates ARF1 (ADP ribosylation factor 1), which recruits coat protein to cellular membranes for the assembly of COPI vesicles. Here, we demonstrate that GBF1 and ARF1 are involved in Ebolavirus virion formation, suggesting that both the COPII and COPI transport systems play a role in Ebolavirus VP40-mediated particle formation. These findings provide new insights into the cellular pathways employed for Ebolavirus virion formation.","corpus_id":1252067,"score":2},{"doc_id":"20444481","title":"Both matrix proteins of Ebola virus contribute to the regulation of viral genome replication and transcription.","abstract":"Ebola virus (EBOV) causes severe hemorrhagic fevers in humans and non-human primates. While the role of the EBOV major matrix protein VP40 in morphogenesis is well understood, nothing is known about its contributions to the regulation of viral genome replication and/or transcription. Similarly, while it was reported that the minor matrix protein VP24 impairs viral genome replication, it remains unclear whether it also regulates transcription, since all common experimental systems measure the combined products of replication and transcription. We have developed systems that allow the independent monitoring of viral transcription and replication, based on qRT-PCR and a replication-deficient minigenome. Using these systems we show that VP24 regulates not only viral genome replication, but also transcription. Further, we show for the first time that VP40 is also involved in regulating these processes. These functions are conserved among EBOV species and, in the case of VP40, independent of its budding or RNA-binding functions.","corpus_id":20603860,"score":2},{"doc_id":"21697477","title":"Ebolavirus delta-peptide immunoadhesins inhibit marburgvirus and ebolavirus cell entry.","abstract":"With the exception of Reston and Lloviu viruses, filoviruses (marburgviruses, ebolaviruses, and \"cuevaviruses\") cause severe viral hemorrhagic fevers in humans. Filoviruses use a class I fusion protein, GP(1,2), to bind to an unknown, but shared, cell surface receptor to initiate virus-cell fusion. In addition to GP(1,2), ebolaviruses and cuevaviruses, but not marburgviruses, express two secreted glycoproteins, soluble GP (sGP) and small soluble GP (ssGP). All three glycoproteins have identical N termini that include the receptor-binding region (RBR) but differ in their C termini. We evaluated the effect of the secreted ebolavirus glycoproteins on marburgvirus and ebolavirus cell entry, using Fc-tagged recombinant proteins. Neither sGP-Fc nor ssGP-Fc bound to filovirus-permissive cells or inhibited GP(1,2)-mediated cell entry of pseudotyped retroviruses. Surprisingly, several Fc-tagged Δ-peptides, which are small C-terminal cleavage products of sGP secreted by ebolavirus-infected cells, inhibited entry of retroviruses pseudotyped with Marburg virus GP(1,2), as well as Marburg virus and Ebola virus infection in a dose-dependent manner and at low molarity despite absence of sequence similarity to filovirus RBRs. Fc-tagged Δ-peptides from three ebolaviruses (Ebola virus, Sudan virus, and Taï Forest virus) inhibited GP(1,2)-mediated entry and infection of viruses comparably to or better than the Fc-tagged RBRs, whereas the Δ-peptide-Fc of an ebolavirus nonpathogenic for humans (Reston virus) and that of an ebolavirus with lower lethality for humans (Bundibugyo virus) had little effect. These data indicate that Δ-peptides are functional components of ebolavirus proteomes. They join cathepsins and integrins as novel modulators of filovirus cell entry, might play important roles in pathogenesis, and could be exploited for the synthesis of powerful new antivirals.","corpus_id":35118269,"score":2},{"doc_id":"21987759","title":"Unconventional secretion of Ebola virus matrix protein VP40.","abstract":"The Ebola virus matrix protein VP40 plays an essential role in virus assembly and budding. In this study we reveal that transient VP40 expression results in the release into the culture medium of substantial amounts of soluble monomeric VP40 in addition to the release of virus-like particles containing an oligomeric form of this protein as previously described. We show that VP40 secretion is endoplasmic reticulum/Golgi-independent and is not associated with cell death. Soluble VP40 was observed during Ebola virus infection of cells and was also found in the serum of virus-infected animals albeit in lower amounts. Unconventional secretion of VP40 may therefore play a role in Ebola virus pathogenicity.","corpus_id":26940897,"score":2},{"doc_id":"22371572","title":"Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.","abstract":"Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.","corpus_id":21640245,"score":2},{"doc_id":"22485110","title":"Ebolavirus Replication and Tetherin/BST-2.","abstract":"Ebolavirus (EBOV) is an enveloped, non-segmented, negative-stranded RNA virus, which consists of five species: Zaire ebolavirus, Sudan ebolavirus, Tai Forest ebolavirus, Bundibugyo ebolavirus, and Reston ebolavirus. EBOV causes a lethal hemorrhagic fever in both humans and non-human primates. The EBOV RNA genome encodes seven viral proteins: NP, VP35, VP40, GP, VP30, VP24, and L. VP40 is a matrix protein and is essential for virus assembly and release from host cells. Expression of VP40 in mammalian cells is sufficient to generate extracellular virus-like particles, which resemble authentic virions. Tetherin/BST-2, which was identified as an effective cellular factor that prevents human immunodeficiency virus-1 release in the absence of viral accessory protein Vpu, has been reported to inhibit ZEBOV VP40-induced VLP release. Tetherin/BST-2 appears to inhibit virus release by physically tethering viral particles to the cell surface via its N-terminal transmembrane domain and C-terminal glycosylphosphatidylinositol anchor. Replication of ZEBOV is not inhibited by tetherin/BST-2 expression, although tetherin/BST-2 was expected to inhibit EBOV release as well as VLP release. Recently, it was reported that viral glycoprotein of EBOV, GP, antagonizes the antiviral effect of tetherin/BST-2. However, the mechanism by which GP antagonizes the antiviral activity of tetherin/BST-2 and whether GP of the other EBOV species function as antagonists of tetherin/BST-2 remain unclear.","corpus_id":1557593,"score":2},{"doc_id":"23076242","title":"The ebolavirus VP24 interferon antagonist: know your enemy.","abstract":"Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways. The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation. A more recent discovery is that VP24 also binds STAT1 directly, suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses.","corpus_id":38317375,"score":2},{"doc_id":"23383374","title":"The spatio-temporal distribution dynamics of Ebola virus proteins and RNA in infected cells.","abstract":"Here, we used a biologically contained Ebola virus system to characterize the spatio-temporal distribution of Ebola virus proteins and RNA during virus replication. We found that viral nucleoprotein (NP), the polymerase cofactor VP35, the major matrix protein VP40, the transcription activator VP30, and the minor matrix protein VP24 were distributed in cytoplasmic inclusions. These inclusions enlarged near the nucleus, became smaller pieces, and subsequently localized near the plasma membrane. GP was distributed in the cytoplasm and transported to the plasma membrane independent of the other viral proteins. We also found that viral RNA synthesis occurred within the inclusions. Newly synthesized negative-sense RNA was distributed inside the inclusions, whereas positive-sense RNA was distributed both inside and outside. These findings provide useful insights into Ebola virus replication.","corpus_id":840522,"score":2},{"doc_id":"23953110","title":"Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle.","abstract":"Proteins, particularly viral proteins, can be multifunctional, but the mechanisms behind multifunctionality are not fully understood. Here, we illustrate through multiple crystal structures, biochemistry, and cellular microscopy that VP40 rearranges into different structures, each with a distinct function required for the ebolavirus life cycle. A butterfly-shaped VP40 dimer traffics to the cellular membrane. Once there, electrostatic interactions trigger rearrangement of the polypeptide into a linear hexamer. These hexamers construct a multilayered, filamentous matrix structure that is critical for budding and resembles tomograms of authentic virions. A third structure of VP40, formed by a different rearrangement, is not involved in virus assembly but instead uniquely binds RNA to regulate viral transcription inside infected cells. These results provide a functional model for ebolavirus matrix assembly and the other roles of VP40 in the virus life cycle and demonstrate how a single wild-type, unmodified polypeptide can assemble into different structures for different functions.","corpus_id":14669246,"score":2},{"doc_id":"24965473","title":"A novel life cycle modeling system for Ebola virus shows a genome length-dependent role of VP24 in virus infectivity.","abstract":"UNLABELLED: Work with infectious Ebola viruses is restricted to biosafety level 4 (BSL4) laboratories, presenting a significant barrier for studying these viruses. Life cycle modeling systems, including minigenome systems and transcription- and replication-competent virus-like particle (trVLP) systems, allow modeling of the virus life cycle under BSL2 conditions; however, all current systems model only certain aspects of the virus life cycle, rely on plasmid-based viral protein expression, and have been used to model only single infectious cycles. We have developed a novel life cycle modeling system allowing continuous passaging of infectious trVLPs containing a tetracistronic minigenome that encodes a reporter and the viral proteins VP40, VP24, and GP1,2. This system is ideally suited for studying morphogenesis, budding, and entry, in addition to genome replication and transcription. Importantly, the specific infectivity of trVLPs in this system was ∼ 500-fold higher than that in previous systems. Using this system for functional studies of VP24, we showed that, contrary to previous reports, VP24 only very modestly inhibits genome replication and transcription when expressed in a regulated fashion, which we confirmed using infectious Ebola viruses. Interestingly, we also discovered a genome length-dependent effect of VP24 on particle infectivity, which was previously undetected due to the short length of monocistronic minigenomes and which is due at least partially to a previously unknown function of VP24 in RNA packaging. Based on our findings, we propose a model for the function of VP24 that reconciles all currently available data regarding the role of VP24 in nucleocapsid assembly as well as genome replication and transcription. IMPORTANCE: Ebola viruses cause severe hemorrhagic fevers in humans, with no countermeasures currently being available, and must be studied in maximum-containment laboratories. Only a few of these laboratories exist worldwide, limiting our ability to study Ebola viruses and develop countermeasures. Here we report the development of a novel reverse genetics-based system that allows the study of Ebola viruses without maximum-containment laboratories. We used this system to investigate the Ebola virus protein VP24, showing that, contrary to previous reports, it only modestly inhibits virus genome replication and transcription but is important for packaging of genomes into virus particles, which constitutes a previously unknown function of VP24 and a potential antiviral target. We further propose a comprehensive model for the function of VP24 in nucleocapsid assembly. Importantly, on the basis of this approach, it should easily be possible to develop similar experimental systems for other viruses that are currently restricted to maximum-containment laboratories.","corpus_id":28102686,"score":2},{"doc_id":"25957961","title":"High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.","abstract":"Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly.","corpus_id":24874326,"score":2},{"doc_id":"26034199","title":"Interferon-Induced Transmembrane Protein-Mediated Inhibition of Host Cell Entry of Ebolaviruses.","abstract":"Ebolaviruses are highly pathogenic in humans and nonhuman primates and pose a severe threat to public health. The interferon-induced transmembrane (IFITM) proteins can restrict entry of ebolaviruses, influenza A viruses, and other enveloped viruses. However, the breadth and mechanism of the antiviral activity of IFITM proteins are incompletely understood. Here, we employed ebolavirus glycoprotein-pseudotyped vectors and ebolavirus-like particles to address this question. We show that IFITM proteins inhibit the cellular entry of diverse ebolaviruses and demonstrate that type I interferon induces IFITM protein expression in macrophages, major viral targets. Moreover, we show that IFITM proteins block entry of influenza A viruses and ebolaviruses by different mechanisms and provide evidence that antibodies and IFITM proteins can synergistically inhibit cellular entry of ebolaviruses. These results provide insights into the role of IFITM proteins in infection by ebolaviruses and suggest a mechanism by which antibodies, though poorly neutralizing in vitro, might contribute to viral control in vivo.","corpus_id":17790537,"score":2},{"doc_id":"26753796","title":"The Ebola Virus matrix protein, VP40, requires phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) for extensive oligomerization at the plasma membrane and viral egress.","abstract":"VP40 is one of eight proteins encoded by the Ebola Virus (EBOV) and serves as the primary matrix protein, forming virus like particles (VLPs) from mammalian cells without the need for other EBOV proteins. While VP40 is required for viral assembly and budding from host cells during infection, the mechanisms that target VP40 to the plasma membrane are not well understood. Phosphatidylserine is required for VP40 plasma membrane binding, VP40 hexamer formation, and VLP egress, However, PS also becomes exposed on the outer membrane leaflet at sites of VP40 budding, raising the question of how VP40 maintains an interaction with the plasma membrane inner leaflet when PS is flipped to the opposite side. To address this question, cellular and in vitro assays were employed to determine if phosphoinositides are important for efficient VP40 localization to the plasma membrane. Cellular studies demonstrated that PI(4,5)P2 was an important component of VP40 assembly at the plasma membrane and subsequent virus like particle formation. Additionally, PI(4,5)P2 was required for formation of extensive oligomers of VP40, suggesting PS and PI(4,5)P2 have different roles in VP40 assembly where PS regulates formation of hexamers from VP40 dimers and PI(4,5)P2 stabilizes and/or induces extensive VP40 oligomerization at the plasma membrane.","corpus_id":41372364,"score":2},{"doc_id":"27009368","title":"Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses.","abstract":"Reston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts, and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission.","corpus_id":11578096,"score":2},{"doc_id":"27757455","title":"The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane.","abstract":"The Ebola virus is a lipid-enveloped virus that obtains its lipid coat from the plasma membrane of the host cell it infects during the budding process. The Ebola virus protein VP40 localizes to the inner leaflet of the plasma membrane and forms the viral matrix, which provides the major structure for the Ebola virus particles. VP40 is initially a dimer that rearranges to a hexameric structure that mediates budding. VP40 hexamers and larger filaments have been shown to be stabilized by PI(4,5)P2 in the plasma membrane inner leaflet. Reduction in the plasma membrane levels of PI(4,5)P2 significantly reduce formation of VP40 oligomers and virus-like particles. We investigated the lipid-protein interactions in VP40 hexamers at the plasma membrane. We quantified lipid-lipid self-clustering by calculating the fractional interaction matrix and found that the VP40 hexamer significantly enhances the PI(4,5)P2 clustering. The radial pair distribution functions suggest a strong interaction between PI(4,5)P2 and the VP40 hexamer. The cationic Lys side chains are found to mediate the PIP2 clustering around the protein, with cholesterol filling the space between the interacting PIP2 molecules. These computational studies support recent experimental data and provide new insights into the mechanisms by which VP40 assembles at the plasma membrane inner leaflet, alters membrane curvature, and forms new virus-like particles.","corpus_id":24549981,"score":2},{"doc_id":"27847361","title":"Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak.","abstract":"The Ebola virus (EBOV) outbreak in West Africa started in December 2013, claimed more than 11,000 lives, threatened to destabilize a whole region, and showed how easily health crises can turn into humanitarian disasters. EBOV genomic sequences of the West African outbreak revealed nonsynonymous mutations, which induced considerable public attention, but their role in virus spread and disease remains obscure. In this study, we investigated the functional significance of three nonsynonymous mutations that emerged early during the West African EBOV outbreak. Almost 90% of more than 1,000 EBOV genomes sequenced during the outbreak carried the signature of three mutations: a D759G substitution in the active center of the L polymerase, an A82V substitution in the receptor binding domain of surface glycoprotein GP, and an R111C substitution in the self-assembly domain of RNA-encapsidating nucleoprotein NP. Using a newly developed virus-like particle system and reverse genetics, we found that the mutations have an impact on the functions of the respective viral proteins and on the growth of recombinant EBOVs. The mutation in L increased viral transcription and replication, whereas the mutation in NP decreased viral transcription and replication. The mutation in the receptor binding domain of the glycoprotein GP improved the efficiency of GP-mediated viral entry into target cells. Recombinant EBOVs with combinations of the three mutations showed a growth advantage over the prototype isolate Makona C7 lacking the mutations. This study showed that virus variants with improved fitness emerged early during the West African EBOV outbreak. IMPORTANCE: The dimension of the Ebola virus outbreak in West Africa was unprecedented. Amino acid substitutions in the viral L polymerase, surface glycoprotein GP, and nucleocapsid protein NP emerged, were fixed early in the outbreak, and were found in almost 90% of the sequences. Here we showed that these mutations affected the functional activity of viral proteins and improved viral growth in cell culture. Our results demonstrate emergence of adaptive changes in the Ebola virus genome during virus circulation in humans and prompt further studies on the potential role of these changes in virus transmissibility and pathogenicity.","corpus_id":34739793,"score":2},{"doc_id":"27849047","title":"Regulation of Ebola virus VP40 matrix protein by SUMO.","abstract":"The matrix protein of Ebola virus (EBOV) VP40 regulates viral budding, nucleocapsid recruitment, virus structure and stability, viral genome replication and transcription, and has an intrinsic ability to form virus-like particles. The elucidation of the regulation of VP40 functions is essential to identify mechanisms to inhibit viral replication and spread. Post-translational modifications of proteins with ubiquitin-like family members are common mechanisms for the regulation of host and virus multifunctional proteins. Thus far, no SUMOylation of VP40 has been described. Here we demonstrate that VP40 is modified by SUMO and that SUMO is included into the viral like particles (VLPs). We demonstrate that lysine residue 326 in VP40 is involved in SUMOylation, and by analyzing a mutant in this residue we show that SUMO conjugation regulates the stability of VP40 and the incorporation of SUMO into the VLPs. Our study indicates for the first time, to the best of our knowledge, that EBOV hijacks the cellular SUMOylation system in order to modify its own proteins. Modulation of the VP40-SUMO interaction may represent a novel target for the therapy of Ebola virus infection.","corpus_id":18876818,"score":2},{"doc_id":"27853993","title":"The roles of ebolavirus glycoproteins in viral pathogenesis.","abstract":"Ebolaviruses are highly dangerous pathogens exhibiting extreme virulence in humans and nonhuman primates. The majority of ebolavirus species, most notably Zaire ebolavirus, can cause Ebola virus disease (EVD), formerly known as Ebola hemorrhagic fever, in humans. EVD is associated with case-fatality rates as high as 90%, and there is currently no specific treatment or licensed vaccine available against EVD. Understanding the molecular biology and pathogenesis of ebolaviruses is important for the development of antiviral therapeutics. Ebolavirus encodes several forms of glycoproteins (GPs), which have some interesting characteristics, including the transcriptional editing coding strategy and extensive O-glycosylation modification, clustered in the mucin-like domain of GP1, full-length GP (GP1,2), and shed GP. In addition to the canonical role of the spike protein, GP1,2, in viral entry, ebolavirus GPs appear to have multiple additional functions, likely contributing to the complex pathogenesis of the virus. Here, we review the roles of ebolavirus GPs in viral pathogenesis.","corpus_id":20856805,"score":2},{"doc_id":"27872619","title":"Ebola VP40 in Exosomes Can Cause Immune Cell Dysfunction.","abstract":"Ebola virus (EBOV) is an enveloped, ssRNA virus from the family Filoviridae capable of causing severe hemorrhagic fever with up to 80-90% mortality rates. The most recent outbreak of EBOV in West Africa starting in 2014 resulted in over 11,300 deaths; however, long-lasting persistence and recurrence in survivors has been documented, potentially leading to further transmission of the virus. We have previously shown that exosomes from cells infected with HIV-1, HTLV-1 and Rift Valley Fever virus are able to transfer viral proteins and non-coding RNAs to naïve recipient cells, resulting in an altered cellular activity. In the current manuscript, we examined the effect of Ebola structural proteins VP40, GP, NP and VLPs on recipient immune cells, as well as the effect of exosomes containing these proteins on naïve immune cells. We found that VP40-transfected cells packaged VP40 into exosomes, and that these exosomes were capable of inducing apoptosis in recipient immune cells. Additionally, we show that presence of VP40 within parental cells or in exosomes delivered to naïve cells could result in the regulation of RNAi machinery including Dicer, Drosha, and Ago 1, which may play a role in the induction of cell death in recipient immune cells. Exosome biogenesis was regulated by VP40 in transfected cells by increasing levels of ESCRT-II proteins EAP20 and EAP45, and exosomal marker proteins CD63 and Alix. VP40 was phosphorylated by Cdk2/Cyclin complexes at Serine 233 which could be reversed with r-Roscovitine treatment. The level of VP40-containing exosomes could also be regulated by treated cells with FDA-approved Oxytetracycline. Additionally, we utilized novel nanoparticles to safely capture VP40 and other viral proteins from Ebola VLPs spiked into human samples using SDS/reducing agents, thus minimizing the need for BSL-4 conditions for most downstream assays. Collectively, our data indicates that VP40 packaged into exosomes may be responsible for the deregulation and eventual destruction of the T-cell and myeloid arms of the immune system (bystander lymphocyte apoptosis), allowing the virus to replicate to high titers in the immunocompromised host. Moreover, our results suggest that the use of drugs such as Oxytetracycline to modulate the levels of exosomes exiting EBOV-infected cells may be able to prevent the devastation of the adaptive immune system and allow for an improved rate of survival.","corpus_id":49381955,"score":2},{"doc_id":"28066813","title":"Risks Posed by Reston, the Forgotten Ebolavirus.","abstract":"Out of the five members of the Ebolavirus family, four cause life-threatening disease, whereas the fifth, Reston virus (RESTV), is nonpathogenic in humans. The reasons for this discrepancy remain unclear. In this review, we analyze the currently available information to provide a state-of-the-art summary of the factors that determine the human pathogenicity of Ebolaviruses. RESTV causes sporadic infections in cynomolgus monkeys and is found in domestic pigs throughout the Philippines and China. Phylogenetic analyses revealed that RESTV is most closely related to the Sudan virus, which causes a high mortality rate in humans. Amino acid sequence differences between RESTV and the other Ebolaviruses are found in all nine Ebolavirus proteins, though no one residue appears sufficient to confer pathogenicity. Changes in the glycoprotein contribute to differences in Ebolavirus pathogenicity but are not sufficient to confer pathogenicity on their own. Similarly, differences in VP24 and VP35 affect viral immune evasion and are associated with changes in human pathogenicity. A recent in silico analysis systematically determined the functional consequences of sequence variations between RESTV and human-pathogenic Ebolaviruses. Multiple positions in VP24 were differently conserved between RESTV and the other Ebolaviruses and may alter human pathogenicity. In conclusion, the factors that determine the pathogenicity of Ebolaviruses in humans remain insufficiently understood. An improved understanding of these pathogenicity-determining factors is of crucial importance for disease prevention and for the early detection of emergent and potentially human-pathogenic RESTVs.","corpus_id":5248937,"score":2},{"doc_id":"28177658","title":"The Role of Exosomal VP40 in Ebola Virus Disease.","abstract":"Ebola virus (EBOV) can cause a devastating hemorrhagic disease, leading to death in a short period of time. After infection, the resulting EBOV disease results in high levels of circulating cytokines, endothelial dysfunction, coagulopathy, and bystander lymphocyte apoptosis in humans and nonhuman primates. The VP40 matrix protein of EBOV is essential for viral assembly and budding from the host cell. Recent data have shown that VP40 exists in the extracellular environment, including in exosomes, and exosomal VP40 can impact the viability of recipient immune cells, including myeloid and T cells, through the regulation of the RNAi and endosomal sorting complexes required for transport pathways. In this study, we discuss the latest findings of the impact of exosomal VP40 on immune cells in vitro and its potential implications for pathogenesis in vivo.","corpus_id":196628327,"score":2},{"doc_id":"28573615","title":"Modeling the Ebolavirus Life Cycle with Transcription and Replication-Competent Viruslike Particle Assays.","abstract":"Ebolaviruses are the causative agent of a severe hemorrhagic fever with high case fatality rates, for which no approved specific therapy is available. As biosafety level 4 (BSL4) agents, work with live ebolaviruses is restricted to maximum containment laboratories. Transcription and replication-competent viruslike particle (trVLP) systems are reverse genetics-based life cycle modeling systems that allow researchers to model virtually the entire ebolavirus life cycle outside of a maximum containment laboratory. These systems can be used to dissect the virus life cycle, and thus increase our understanding of virus biology, as well as for more applied uses such as the screening and development of novel antivirals, and thus represent powerful tools for work on ebolaviruses.","corpus_id":9774325,"score":2},{"doc_id":"28595092","title":"Ebolavirus protein VP24 interferes with innate immune responses by inhibiting interferon-λ1 gene expression.","abstract":"Ebolaviruses (EBOV) cause severe disease with a recent outbreak in West Africa in 2014-2015 leading to more than 28 000 cases and 11 300 fatalities. This emphasizes the urgent need for better knowledge on these highly pathogenic RNA viruses. Host innate immune responses play a key role in restricting the spread of a viral disease. In this study we systematically analyzed the effects of cloned EBOV genes on the main host immune response to RNA viruses: the activation of RIG-I pathway and type I and III interferon (IFN) gene expression. EBOV VP24, in addition of inhibiting IFN-induced antiviral responses, was found to efficiently inhibit type III IFN-λ1 gene expression. This inhibition was found to occur downstream of IRF3 activation and to be dependent on VP24 importin binding residues. These results emphasize the importance of VP24 in EBOV infection cycle, making VP24 as an excellent target for drug development.","corpus_id":27740318,"score":2},{"doc_id":"28878074","title":"Cooperation of the Ebola Virus Proteins VP40 and GP1,2 with BST2 To Activate NF-κB Independently of Virus-Like Particle Trapping.","abstract":"BST2 is a host protein with dual functions in response to viral infections: it traps newly assembled enveloped virions at the plasma membrane in infected cells, and it induces NF-κB activity, especially in the context of retroviral assembly. In this study, we examined whether Ebola virus proteins affect BST2-mediated induction of NF-κB. We found that the Ebola virus matrix protein, VP40, and envelope glycoprotein, GP, each cooperate with BST2 to induce NF-κB activity, with maximal activity when all three proteins are expressed. Unlike human immunodeficiency virus type 1 Vpu protein, which antagonizes both virion entrapment and the activation of NF-κB by BST2, Ebola virus GP does not inhibit NF-κB signaling even while it antagonizes the entrapment of virus-like particles. GP from Reston ebolavirus, a nonpathogenic species in humans, showed a phenotype similar to that of GP from Zaire ebolavirus, a highly pathogenic species, in terms of both the activation of NF-κB and the antagonism of virion entrapment. Although Ebola virus VP40 and GP both activate NF-κB independently of BST2, VP40 is the more potent activator. Activation of NF-κB by the Ebola virus proteins either alone or together with BST2 requires the canonical NF-κB signaling pathway. Mechanistically, the maximal NF-κB activation by GP, VP40, and BST2 together requires the ectodomain cysteines needed for BST2 dimerization, the putative BST2 tetramerization residue L70, and Y6 of a potential hemi-ITAM motif in BST2's cytoplasmic domain. BST2 with a glycosylphosphatidylinositol (GPI) anchor signal deletion, which is not expressed at the plasma membrane and is unable to entrap virions, activated NF-κB in concert with the Ebola virus proteins at least as effectively as wild-type BST2. Signaling by the GPI anchor mutant also depended on Y6 of BST2. Overall, our data show that activation of NF-κB by BST2 is independent of virion entrapment in the case of Ebola virus. Nonetheless, BST2 may induce or amplify proinflammatory signaling during Ebola virus infection, potentially contributing to the dysregulated cytokine response that is a hallmark of Ebola virus disease. IMPORTANCE Understanding how the host responds to viral infections informs the development of therapeutics and vaccines. We asked how proinflammatory signaling by the host protein BST2/tetherin, which is mediated by the transcription factor NF-κB, responds to Ebola virus proteins. Although the Ebola virus envelope glycoprotein (GP1,2) antagonizes the trapping of newly formed virions at the plasma membrane by BST2, we found that it does not inhibit BST2's ability to induce NF-κB activity. This distinguishes GP1,2 from the HIV-1 protein Vpu, the prototype BST2 antagonist, which inhibits both virion entrapment and the induction of NF-κB activity. Ebola virus GP1,2, the Ebola virus matrix protein VP40, and BST2 are at least additive with respect to the induction of NF-κB activity. The effects of these proteins converge on an intracellular signaling pathway that depends on a protein modification termed neddylation. Better mechanistic understanding of these phenomena could provide targets for therapies that modulate the inflammatory response during Ebola virus disease.","corpus_id":41339762,"score":2},{"doc_id":"19023410","title":"Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda.","abstract":"Over the past 30 years, Zaire and Sudan ebolaviruses have been responsible for large hemorrhagic fever (HF) outbreaks with case fatalities ranging from 53% to 90%, while a third species, Côte d'Ivoire ebolavirus, caused a single non-fatal HF case. In November 2007, HF cases were reported in Bundibugyo District, Western Uganda. Laboratory investigation of the initial 29 suspect-case blood specimens by classic methods (antigen capture, IgM and IgG ELISA) and a recently developed random-primed pyrosequencing approach quickly identified this to be an Ebola HF outbreak associated with a newly discovered ebolavirus species (Bundibugyo ebolavirus) distantly related to the Côte d'Ivoire ebolavirus found in western Africa. Due to the sequence divergence of this new virus relative to all previously recognized ebolaviruses, these findings have important implications for design of future diagnostic assays to monitor Ebola HF disease in humans and animals, and ongoing efforts to develop effective antivirals and vaccines.","corpus_id":-1,"score":1},{"doc_id":"19091859","title":"Vacuolar protein sorting pathway contributes to the release of Marburg virus.","abstract":"VP40, the major matrix protein of Marburg virus, is the main driving force for viral budding. Additionally, cellular factors are likely to play an important role in the release of progeny virus. In the present study, we characterized the influence of the vacuolar protein sorting (VPS) pathway on the release of virus-like particles (VLPs), which are induced by Marburg virus VP40. In the supernatants of HEK 293 cells expressing VP40, different populations of VLPs with either a vesicular or a filamentous morphology were detected. While the filaments were almost completely composed of VP40, the vesicular particles additionally contained considerable amounts of cellular proteins. In contrast to that in the vesicles, the VP40 in the filaments was regularly organized, probably inducing the elimination of cellular proteins from the released VLPs. Vesicular particles were observed in the supernatants of cells even in the absence of VP40. Mutation of the late-domain motif in VP40 resulted in reduced release of filamentous particles, and likewise, inhibition of the VPS pathway by expression of a dominant-negative (DN) form of VPS4 inhibited the release of filamentous particles. In contrast, the release of vesicular particles did not respond significantly to the expression of DN VPS4. Like the budding of VLPs, the budding of Marburg virus particles was partially inhibited by the expression of DN VPS4. While the release of VLPs from VP40-expressing cells is a valuable tool with which to investigate the budding of Marburg virus particles, it is important to separate filamentous VLPs from vesicular particles, which contain many cellular proteins and use a different budding mechanism.","corpus_id":36420798,"score":1},{"doc_id":"20394957","title":"Reduced virus replication, proinflammatory cytokine production, and delayed macrophage cell death in human PBMCs infected with the newly discovered Bundibugyo ebolavirus relative to Zaire ebolavirus.","abstract":"Bundibugyo ebolavirus is a newly identified Ebolavirus species. The virus was responsible for a recent hemorrhagic fever outbreak in Uganda with an approximate 30% case fatality rate. In this study, we compared the pathogenesis of Bundibugyo with highly lethal Zaire Ebolavirus by using in vitro human PBMCs. We found that PBMCs infected with Bundibugyo ebolaviruses resulted in 1 to 2 log lower virus yields compared to Zaire ebolavirus and produced 2- to 10-fold lower levels of TNF-alpha, MCP-1, IL-1beta, MIP1-alpha and IL-10 than PBMCs infected with Zaire ebolavirus. In addition, flow cytometric studies have shown lower levels and delay of the macrophage cell death in Bundibugyo ebolavirus compared to Zaire ebolavirus infection. The findings of slower Bundibugyo ebolavirus replication, lower production of proinflammatory cytokines and delay in macrophage cell death provide insight into the basis of the lower case fatality observed with Bundibugyo ebolavirus.","corpus_id":42682193,"score":1},{"doc_id":"21073307","title":"Towards broad protection against Ebolaviruses.","abstract":"The Ebola and Marburg viruses (from the filovirus family) induce deadly hemorrhagic fevers for which there is currently no licensed vaccine or treatment. Frequent outbreaks have occurred in sub-Saharan Africa, in humans and nonhuman primates over the last 15 years or so and constitute a major public health problem. Of particular concern, a new species of Ebolavirus recently emerged in Uganda, highlighting the high potential of these viruses to evolve and the need to develop 'broad-spectrum' vaccines against filoviruses. Hensley et al. used their well studied vaccine platform based on DNA vectors and recombinant, replication-defective, adenoviruses producing Ebolavirus glycoproteins to protect cynomolgus monkeys against a heterologous challenge with the new species. Further developments are required before this experimental approach could be adapted for field use in humans, but this study nevertheless constitutes a proof-of-concept for broad protection against Ebolaviruses.","corpus_id":31774927,"score":1},{"doc_id":"21349211","title":"Tackling Ebola: new insights into prophylactic and therapeutic intervention strategies.","abstract":"Since its discovery in 1976, Ebolavirus has caused periodic outbreaks of viral hemorrhagic fever associated with severe and often fatal disease. Ebolavirus is endemic in Central Africa and the Philippines. Although there is currently no approved treatment available, the past 10 years has seen remarkable progress in our understanding of the pathogenicity of Ebolavirus and the development of prophylactic and post-exposure therapies against it. In vitro and in vivo experiments have shown that Ebolavirus pathogenicity is multifactorial, including viral and host determinants. Besides their function in the virus replication cycle, the viral glycoprotein, nucleoprotein, minor matrix protein and polymerase cofactor are viral determinants of pathogenicity, with evasion of the host innate and adaptive immune responses as the main mechanism. Although no licensed Ebolavirus vaccines are currently available, vaccine research in non-human primates, the 'gold standard' animal model for Ebolavirus, has produced several promising candidates. A combination of DNA vaccination and a recombinant adenovirus serotype 5 boost resulted in cross-protective immunity in non-human primates. A recombinant vesicular stomatitis vaccine vector protected non-human primates in pre- and post-exposure challenge studies. Several antiviral therapies are currently under investigation, but only a few of these have been tested in non-human primate models. Antisense therapies, in which oligonucleotides inhibit viral replication, have shown promising results in non-human primates following post-exposure treatment. In light of the severity of Ebolavirus disease and the observed increase in Ebolavirus outbreaks over the past decade, the expedited translation of potential candidate therapeutics and vaccines from bench to bedside is currently the most challenging task for the field. Here, we review the current state of Ebolavirus research, with emphasis on prophylactic and therapeutic intervention strategies.","corpus_id":6243897,"score":1},{"doc_id":"21742058","title":"Current perspectives on the phylogeny of Filoviridae.","abstract":"Sporadic fatal outbreaks of disease in humans and non-human primates caused by Ebola or Marburg viruses have driven research into the characterization of these viruses with the hopes of identifying host tropisms and potential reservoirs. Such an understanding of the relatedness of newly discovered filoviruses may help to predict risk factors for outbreaks of hemorrhagic disease in humans and/or non-human primates. Recent discoveries such as three distinct genotypes of Reston ebolavirus, unexpectedly discovered in domestic swine in the Philippines; as well as a new species, Bundibugyo ebolavirus; the recent discovery of Lloviu virus as a potential new genus, Cuevavirus, within Filoviridae; and germline integrations of filovirus-like sequences in some animal species bring new insights into the relatedness of filoviruses, their prevalence and potential for transmission to humans. These new findings reveal that filoviruses are more diverse and may have had a greater influence on the evolution of animals than previously thought. Herein we review these findings with regard to the implications for understanding the host range, prevalence and transmission of Filoviridae.","corpus_id":19609341,"score":1},{"doc_id":"21987741","title":"Advances in virus-like particle vaccines for filoviruses.","abstract":"Ebola virus (EBOV) and Marburg virus (MARV) are among the deadliest human pathogens, with no vaccines or therapeutics available. Multiple vaccine platforms have been tested for efficacy as prophylactic pretreatments or therapeutics for prevention of filovirus hemorrhagic fever. Most successful vaccines are based on a virus-vectored approach expressing the protective glycoprotein (GP); protein-based subunit and DNA vaccines have been tested with moderate success. Virus-like particle (VLP) vaccines have realized promising results when tested in both rodents and nonhuman primates. VLPs rely on the natural properties of the viral matrix protein (VP) 40 to drive budding of filamentous particles that can also incorporate ≥ 1 other filovirus protein, including GP, VP24, and nucleoprotein (NP). Filovirus VLP vaccines have used particles containing 2 or 3 (GP and VP40, with or without NP) viral proteins generated in either mammalian or insect cells. Early studies successfully demonstrated efficacy of bivalent VLP vaccines in rodents; more recent studies have shown the ability of the VLP vaccines containing GP, NP, and VP40 to confer complete homologous protection against Ebola virus and Marburg virus in a prophylactic setting against in macaques. This review will discuss published work to date regarding development of the VLP vaccines for prevention of lethal filovirus hemorrhagic fever.","corpus_id":44556002,"score":1},{"doc_id":"25260583","title":"Clinical features and pathobiology of Ebolavirus infection.","abstract":"There has clearly been a deluge of international press coverage of the recent outbreak of Ebolavirus in Africa and is partly related to the \"fear factor\" that comes across when one is confronted with the fact that once infected, not only is the speed of death in a majority of cases rapid but also the images of the cause of death such as bleeding from various orifices gruesome and frightening. The fact that it leads to infection and death of health care providers (10% during the current epidemic) and the visualization of protective gear worn by these individuals to contain such infection adds to this \"fear factor\". Finally, there is a clear perceived notion that such an agent can be utilized as a bioterrorism agent that adds to the apprehension. Thus, in efforts to gain an objective view of the growing threat Ebolavirus poses to the general public, it is important to provide some basic understanding for the lethality of Ebolavirus infection that is highlighted in Fig. 1. This virus infection first appears to disable the immune system (the very system needed to fight the infection) and subsequently disables the vascular system that leads to blood leakage (hemorrhage), hypotension, drop in blood pressure, followed by shock and death. The virus appears to sequentially infect dendritic cells disabling the interferon system (one of the major host anti-viral immune systems) then macrophages (that trigger the formation of blood clots, release of inflammatory proteins and nitric oxide damaging the lining of blood vessels leading to blood leakage) and finally endothelial cells that contribute to blood leakage. The virus also affects organs such as the liver (that dysregulates the formation of coagulation proteins), the adrenal gland (that destroys the ability of the patient to synthesize steroids and leads to circulation failure and disabling of regulators of blood pressure) and the gastro-intestinal tract (leading to diarrhea). The ability of the virus to disable such major mechanisms in the body facilitates the ability of the virus to replicate in an uncontrolled fashion leading to the rapidity by which the virus can cause lethality. Various laboratories have been working on defining such mechanisms utilizing in vitro culture systems, a variety of animal models including inbred strains of normal and select gene knock out mice, guinea pigs and nonhuman primates that have led to a better understanding of the potential mechanisms involved. There have also been some major advances made in the identification of therapies from the very simple (major supportive type of therapy), to the identification of a number of highly effective chemotherapeutic agents, a variety of highly effective preventive (demonstrating 100% effectiveness in nonhuman primate models) recombinant formulations (adenovirus based, VSV-based, rabies virus based), therapeutic candidate vaccines (cocktail of monoclonal antibodies such as ZMAPP) and alternate approaches (RNAi-based such as TKM-Ebola and antisense based such as AVI-7537) that show great promise and at an unprecedented rate of discovery that speaks well for the scientific research community at large.","corpus_id":27779475,"score":1},{"doc_id":"25387613","title":"Ebola virus disease: a review on epidemiology, symptoms, treatment and pathogenesis.","abstract":"Currently, West Africa is facing the largest outbreak of Ebola virus disease (EVD) in history. The virus causing this outbreak, the Zaire Ebolavirus (EBOV), belongs to the genus Ebolavirus which together with the genus Marburgvirus forms the family of the Filoviridae. EBOV is one of the most virulent pathogens among the viral haemorrhagic fevers, and case fatality rates up to 90% have been reported. Mortality is the result of multi-organ failure and severe bleeding complications. By 18 September 2014, the WHO reported of 5335 cases (confirmed, suspected and probable) with 2622 deaths, resulting in a case fatality rate of around 50%. This review aims to provide an overview of EVD for clinicians, with the emphasis on pathogenesis, clinical manifestations, and treatment options.","corpus_id":27706777,"score":1},{"doc_id":"25803489","title":"Ebolavirus classification based on natural vectors.","abstract":"According to the WHO, ebolaviruses have resulted in 8818 human deaths in West Africa as of January 2015. To better understand the evolutionary relationship of the ebolaviruses and infer virulence from the relationship, we applied the alignment-free natural vector method to classify the newest ebolaviruses. The dataset includes three new Guinea viruses as well as 99 viruses from Sierra Leone. For the viruses of the family of Filoviridae, both genus label classification and species label classification achieve an accuracy rate of 100%. We represented the relationships among Filoviridae viruses by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) phylogenetic trees and found that the filoviruses can be separated well by three genera. We performed the phylogenetic analysis on the relationship among different species of Ebolavirus by their coding-complete genomes and seven viral protein genes (glycoprotein [GP], nucleoprotein [NP], VP24, VP30, VP35, VP40, and RNA polymerase [L]). The topology of the phylogenetic tree by the viral protein VP24 shows consistency with the variations of virulence of ebolaviruses. The result suggests that VP24 be a pharmaceutical target for treating or preventing ebolaviruses.","corpus_id":22865000,"score":1},{"doc_id":"27190508","title":"Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses.","abstract":"Ebola Virus Disease (EVD) is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB) and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus. The genomic analyses of ebolaviruses will provide important clues for locating the essential and core functional genes. The aim of EDB is to act as an integrated resource for ebolaviruses and we strongly believe that the database will be a useful tool for clinicians, microbiologists, health care workers, and bioscience researchers.","corpus_id":17087473,"score":1},{"doc_id":"27528741","title":"Computational analysis of Ebolavirus data: prospects, promises and challenges.","abstract":"The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches.","corpus_id":1361715,"score":1},{"doc_id":"27974555","title":"VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability.","abstract":"Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Reston ebolavirus (RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA binding affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. These data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability. IMPORTANCE: The interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the interactions of VP24 proteins from EBOV and two members of the Ebolavirus genus, Bundibugyo virus (BDBV) and Reston virus (RESTV). The data reveal lower binding affinity of the BDBV VP24 (bVP24) for KPNAs and demonstrate that the interaction with KPNA modulates inhibition of IFN signaling and VP24 stability. The effect of KPNA interaction on VP24 stability is a novel functional consequence of this virus-host interaction, and the differences identified between viral species may contribute to differences in pathogenesis.","corpus_id":4603661,"score":1},{"doc_id":"28331091","title":"Ebolaviruses Associated with Differential Pathogenicity Induce Distinct Host Responses in Human Macrophages.","abstract":"Ebola virus (EBOV) and Reston virus (RESTV) are members of the Ebolavirus genus which greatly differ in their pathogenicity. While EBOV causes a severe disease in humans characterized by a dysregulated inflammatory response and elevated cytokine and chemokine production, there are no reported disease-associated human cases of RESTV infection, suggesting that RESTV is nonpathogenic for humans. The underlying mechanisms determining the pathogenicity of different ebolavirus species are not yet known. In this study, we dissected the host response to EBOV and RESTV infection in primary human monocyte-derived macrophages (MDMs). As expected, EBOV infection led to a profound proinflammatory response, including strong induction of type I and type III interferons (IFNs). In contrast, RESTV-infected macrophages remained surprisingly silent. Early activation of IFN regulatory factor 3 (IRF3) and NF-κB was observed in EBOV-infected, but not in RESTV-infected, MDMs. In concordance with previous results, MDMs treated with inactivated EBOV and Ebola virus-like particles (VLPs) induced NF-κB activation mediated by Toll-like receptor 4 (TLR4) in a glycoprotein (GP)-dependent manner. This was not the case in cells exposed to live RESTV, inactivated RESTV, or VLPs containing RESTV GP, indicating that RESTV GP does not trigger TLR4 signaling. Our results suggest that the lack of immune activation in RESTV-infected MDMs contributes to lower pathogenicity by preventing the cytokine storm observed in EBOV infection. We further demonstrate that inhibition of TLR4 signaling abolishes EBOV GP-mediated NF-κB activation. This finding indicates that limiting the excessive TLR4-mediated proinflammatory response in EBOV infection should be considered as a potential supportive treatment option for EBOV disease. IMPORTANCE Emerging infectious diseases are a major public health concern, as exemplified by the recent devastating Ebola virus (EBOV) outbreak. Different ebolavirus species are associated with widely varying pathogenicity in humans, ranging from asymptomatic infections for Reston virus (RESTV) to severe disease with fatal outcomes for EBOV. In this comparative study of EBOV- and RESTV-infected human macrophages, we identified key differences in host cell responses. Consistent with previous data, EBOV infection is associated with a proinflammatory signature triggered by the surface glycoprotein (GP), which can be inhibited by blocking TLR4 signaling. In contrast, infection with RESTV failed to stimulate a strong host response in infected macrophages due to the inability of RESTV GP to stimulate TLR4. We propose that disparate proinflammatory host signatures contribute to the differences in pathogenicity reported for ebolavirus species and suggest that proinflammatory pathways represent an intriguing target for the development of novel therapeutics.","corpus_id":4619931,"score":1},{"doc_id":"28396469","title":"The Ebola outbreak, 2013-2016: old lessons for new epidemics.","abstract":"Ebola virus causes a severe haemorrhagic fever in humans with high case fatality and significant epidemic potential. The 2013-2016 outbreak in West Africa was unprecedented in scale, being larger than all previous outbreaks combined, with 28 646 reported cases and 11 323 reported deaths. It was also unique in its geographical distribution and multicountry spread. It is vital that the lessons learned from the world's largest Ebola outbreak are not lost. This article aims to provide a detailed description of the evolution of the outbreak. We contextualize this outbreak in relation to previous Ebola outbreaks and outline the theories regarding its origins and emergence. The outbreak is described by country, in chronological order, including epidemiological parameters and implementation of outbreak containment strategies. We then summarize the factors that led to rapid and extensive propagation, as well as highlight the key successes, failures and lessons learned from this outbreak and the response. This article is part of the themed issue 'The 2013-2016 West African Ebola epidemic: data, decision-making and disease control'.","corpus_id":8159817,"score":1},{"doc_id":"28539437","title":"Spontaneous Mutation at Amino Acid 544 of the Ebola Virus Glycoprotein Potentiates Virus Entry and Selection in Tissue Culture.","abstract":"Ebolaviruses have a surface glycoprotein (GP1,2) that is required for virus attachment and entry into cells. Mutations affecting GP1,2 functions can alter virus growth properties. We generated a recombinant vesicular stomatitis virus encoding Ebola virus Makona variant GP1,2 (rVSV-MAK-GP) and observed emergence of a T544I mutation in the Makona GP1,2 gene during tissue culture passage in certain cell lines. The T544I mutation emerged within two passages when VSV-MAK-GP was grown on Vero E6, Vero, and BS-C-1 cells but not when it was passaged on Huh7 and HepG2 cells. The mutation led to a marked increase in virus growth kinetics and conferred a robust growth advantage over wild-type rVSV-MAK-GP on Vero E6 cells. Analysis of complete viral genomes collected from patients in western Africa indicated that this mutation was not found in Ebola virus clinical samples. However, we observed the emergence of T544I during serial passage of various Ebola Makona isolates on Vero E6 cells. Three independent isolates showed emergence of T544I from undetectable levels in nonpassaged virus or virus passaged once to frequencies of greater than 60% within a single passage, consistent with it being a tissue culture adaptation. Intriguingly, T544I is not found in any Sudan, Bundibugyo, or Tai Forest ebolavirus sequences. Furthermore, T544I did not emerge when we serially passaged recombinant VSV encoding GP1,2 from these ebolaviruses. This report provides experimental evidence that the spontaneous mutation T544I is a tissue culture adaptation in certain cell lines and that it may be unique for the species Zaire ebolavirusIMPORTANCE The Ebola virus (Zaire) species is the most lethal species of all ebolaviruses in terms of mortality rate and number of deaths. Understanding how the Ebola virus surface glycoprotein functions to facilitate entry in cells is an area of intense research. Recently, three groups independently identified a polymorphism in the Ebola glycoprotein (I544) that enhanced virus entry, but they did not agree in their conclusions regarding its impact on pathogenesis. Our findings here address the origins of this polymorphism and provide experimental evidence showing that it is the result of a spontaneous mutation (T544I) specific to tissue culture conditions, suggesting that it has no role in pathogenesis. We further show that this mutation may be unique to the species Zaire ebolavirus, as it does not occur in Sudan, Bundibugyo, and Tai Forest ebolaviruses. Understanding the mechanism behind this mutation can provide insight into functional differences that exist in culture conditions and among ebolavirus glycoproteins.","corpus_id":4529248,"score":1},{"doc_id":"28573607","title":"Marburg- and Ebolaviruses: A Look Back and Lessons for the Future.","abstract":"Since the discovery of Marburg virus 50 years ago, filoviruses have reemerged in the human population more than 40 times. Already the first episode was as dramatic as most of the subsequent ones, but none of them was as devastating as the West-African Ebola virus outbreak in 2013-2015. Although progress toward a better understanding of the viruses is impressive, there is clearly a need to improve and strengthen the measures to detect and control these deadly infections.","corpus_id":3790352,"score":1},{"doc_id":"28812539","title":"Investigating Ebola virus pathogenicity using molecular dynamics.","abstract":"BACKGROUND: Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. RESULTS: As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. CONCLUSION: Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.","corpus_id":4378814,"score":1},{"doc_id":"29140409","title":"Ebolavirus interferon antagonists-protein interaction perspectives to combat pathogenesis.","abstract":"Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories. As an alternative, computational techniques have also been adopted to improve the success rate of drug discovery. This article elaborates on the interactions between viral and human IFN proteins that lead to IFN antagonism. A computational framework is proposed after evaluating existing computational studies. This protein interaction and protein design-based computational framework identified critical interacting residues of the VP (VP24) responsible for the formation of a stable complex with the human KPNA5 (karyopherin alpha proteins 5). The mutations of those critical residues, as demonstrated in this article, affected the overall stability of the complex because of a sharp decrease in both the number of hydrogen bonds and possible charge-charge interactions. Therefore, we proposed that the framework could be an effective alternative to experimental work for destabilizing interactions between the VPs and human proteins responsible for IFN induction and response.","corpus_id":206335112,"score":1},{"doc_id":"18487121","title":"Something old, something new.","abstract":"Some thoughts on the development of theoretical fluid dynamics in this century and some reflections on the developments of the past century were provided as an introduction to a broad-ranging conference. A written synopsis of these remarks is provided here.","corpus_id":43643881,"score":0},{"doc_id":"18729235","title":"Oncogenesis by retroviruses: old and new paradigms.","abstract":"Retroviruses are associated with a variety of diseases including an array of malignancies, immunodeficiencies and neurological disorders. In particular, studies of oncogenic retroviruses established fundamental principles of modern molecular cancer biology. Studies of avian Rous sarcoma virus (RSV) led to the discovery of the viral oncogene src, and this was followed by the discovery of other viral oncogenes in retroviruses of mammals including rodents, cats, monkeys and so forth. Studies of the viral oncogenes in turn led to the discovery of cellular proto-oncogenes in the host genome; cellular oncogenes have been shown to be activated in a variety of human cancers, including those with no viral involvement. Oncogenic animal retroviruses can be divided into two groups based on their mechanisms of tumourigenesis, acute transforming retroviruses and nonacute retroviruses. Acute transforming retroviruses are typically replication defective and they induce tumours rapidly due to expression of their viral oncogenes. Nonacute retroviruses are replication competent and they induce tumours with longer latencies, by activating cellular proto-oncogenes in the tumour cells; this results from insertion of proviral DNA in the vicinity of the activated proto-oncogene. More recently, human T-cell leukaemia virus type I (HTLV-I) was discovered as an etiological agent of human cancer (adult T-cell leukaemia [ATL]); this virus also encodes regulatory genes some of which are important for its oncogenic potential. Most recently, the retroviral structural protein Envelope (Env) has been shown to be directly involved in oncogenic transformation for certain retroviruses. Env-induced transformation is a new paradigm for retroviral oncogenesis. In this review, we will summarise research on retrovirus oncogenic transformation over the past 100 years since the first published report of an oncogenic virus with particular attention to Env-induced transformation.","corpus_id":24766664,"score":0},{"doc_id":"18849653","title":"Old proteins, developing roles: The regulation of calcium channels by synaptic proteins.","abstract":"Coupling of presynaptic voltage-gated calcium channels to the synaptic release machinery is critical for neurotransmission. It was traditionally believed that anchoring calcium channels close to the calcium microdomain dependent release machinery was the main reason for the physical interactions between channels and synaptic proteins, however in recent years, it is becoming clear that these proteins additionally regulate channel activity, and such processes as channel targeting and alternative splicing, to orchestrate a much broader regulatory role in controlling calcium channel function, calcium influx and hence neurotransmission. Calcium signalling serves a multitude of cellular functions and therefore requires tight regulation. Specific, often calcium-dependent interactions between synaptic proteins and calcium channels appear to play a significant role in fine-tuning of the synaptic response over development. While it is clear that investigation of a few of the multitude of synaptic proteins will not provide a complete understanding of calcium channel regulation, consideration of the emerging mechanisms by which synaptic protein interactions might regulate calcium channel function is important in order to understand their possible contributions to synaptic transmission. Here, we review the current state of knowledge of the molecular mechanisms by which synaptic proteins regulate presynaptic calcium channel activity.","corpus_id":11374601,"score":0},{"doc_id":"19527723","title":"Physiological responses to protein aggregates: fibrinolysis, coagulation and inflammation (new roles for old factors).","abstract":"Misfolding is an inherent and potentially problematic propensity of proteins. Misfolded proteins tend to aggregate and the deposition of aggregated proteins is associated with a variety of highly debilitating diseases known as amyloidoses. Protein misfolding and aggregation is also increasingly recognized as the underlying cause of other health problems, including atherosclerosis and immunogenicity of biopharmaceuticals. This raises the question how nature deals with the removal of obsolete proteins in order to avoid their accumulation and disease. In recent years two proteases, tPA and factor XII, have been identified that specifically recognize aggregates of misfolded proteins. We here review these discoveries that have uncovered new roles for the fibrinolytic system and the contact activation system beyond haemostasis.","corpus_id":207561992,"score":0},{"doc_id":"20074144","title":"Flavonoids: new roles for old molecules.","abstract":"Flavonoids are ubiquitous in the plant kingdom and have many diverse functions including defense, UV protection, auxin transport inhibition, allelopathy, and flower coloring. Interestingly, these compounds also have considerable biological activity in plant, animal and bacterial systems - such broad activity is accomplished by few compounds. Yet, for all the research over the last three decades, many of the cellular targets of these secondary metabolites are unknown. The many mutants available in model plant species such as Arabidopsis thaliana and Medicago truncatula are enabling the intricacies of the physiology of these compounds to be deduced. In the present review, we cover recent advances in flavonoid research, discuss deficiencies in our understanding of the physiological processes, and suggest approaches to identify the cellular targets of flavonoids.","corpus_id":205903893,"score":0},{"doc_id":"20842205","title":"Clarifying the role of G protein signaling in HIV infection: new approaches to an old question.","abstract":"Whether or not HIV gp120-elicited signal transduction through the coreceptors CCR5 and CXCR4 is required for productive viral replication has long been a subject of controversy. The complexity and diversity of G protein signal transduction initiated by chemokine receptor activation has hindered efforts to understand the contributions of these pathways to the HIV life cycle. Several recent studies have demonstrated an important role for G proteins in mediating signaling events through both CCR5 and CXCR4 that are necessary for productive HIV infection. In addition to gp120-mediated G protein activation, there is still much to learn about the impact of G protein signaling during HIV infection, including the role of T-cell receptor/CXCR4 cross-talk, regulation of G protein expression during infection and the contribution of G protein subunit genetic polymorphisms to disease progression. This review will describe the effects of G protein signaling in immune cells, summarize the current understanding of CCR5 and CXCR4-initiated signal transduction in HIV replication, and discuss important gaps that still remain in our understanding of G protein signaling and its contribution to HIV pathogenesis.","corpus_id":45736224,"score":0},{"doc_id":"21478633","title":"New targets for old hormones: inhibins clinical role revisited.","abstract":"Inhibins are gonadal peptide hormones belonging to the transforming growth factor-β (TGF-β) superfamily that regulate the pituitary follicle stimulating hormone (FSH) secretion by negative feedback mechanisms. It is evident that the understanding of inhibins function in the hypothalamic-pituitary-gonadal axis will provide insights into physiology and pathology of the gonadal function. In recent years, a great deal of attention has been focussed on clinical relevance of measuring circulating inhibins in normal and disease state. The past few years also have witnessed the emergence and discovery of extra pituitary action of inhibins that might provide further insights into the underlying diseases like cancer especially in the reproductive axis and various other new endocrine target organs. In this review after systematic analysis of literature, we discuss briefly the known and recent advances in function of these hormones highlighting also its structure, production and mechanisms of signal transduction. Also this review discusses about the physiological relevance of inhibin association in the normal function to the development of reproductive cancers. Finally, we describe evidence from various emerging studies that inhibins make an important contribution to other physiological functions apart from reproduction which reveals new endocrine target organs of inhibins. The emerging view is inhibin participates in multiple ways to regulate the function in different cell types and still complete repertoire of its actions is under investigation.","corpus_id":7879977,"score":0},{"doc_id":"21607083","title":"AMPylation: Something Old is New Again.","abstract":"The post-translational modification AMPylation is emerging as a significant regulatory mechanism in both prokaryotic and eukaryotic biology. This process involves the covalent addition of an adenosine monophosphate to a protein resulting in a modified protein with altered activity. Proteins capable of catalyzing AMPylation, termed AMPylators, are comparable to kinases in that they both hydrolyze ATP and reversibly transfer a part of this primary metabolite to a hydroxyl side chain of the protein substrate. To date, only four AMPylators have been characterized, though many more potential candidates have been identified through amino acid sequence analysis and preliminary in vitro studies. This modification was first discovered over 40 years ago by Earl Stadtman and colleagues through the modification of glutamine synthetase by adenylyl transferase; however research into this mechanism has only just been reenergized by the studies on bacterial effectors. New AMPylators were revealed due to the discovery that a bacterial effector having a conserved Fic domain transfers an AMP group to protein substrates. Current research focuses on identifying and characterizing various types of AMPylators homologous to Fic domains and adenylyl transferase domains and their respective substrates. While all AMPylators characterized thus far are bacterial proteins, the conservation of the Fic domain in eukaryotic organisms suggests that AMPylation is omnipresent in various forms of life and has significant impact on a wide range of regulatory processes.","corpus_id":2274552,"score":0},{"doc_id":"21976651","title":"Microvesicles and viral infection.","abstract":"Cells secrete various membrane-enclosed microvesicles from their cell surface (shedding microvesicles) and from internal, endosome-derived membranes (exosomes). Intriguingly, these vesicles have many characteristics in common with enveloped viruses, including biophysical properties, biogenesis, and uptake by cells. Recent discoveries describing the microvesicle-mediated intercellular transfer of functional cellular proteins, RNAs, and mRNAs have revealed additional similarities between viruses and cellular microvesicles. Apparent differences include the complexity of viral entry, temporally regulated viral expression, and self-replication proceeding to infection of new cells. Interestingly, many virally infected cells secrete microvesicles that differ in content from their virion counterparts but may contain various viral proteins and RNAs. For the most part, these particles have not been analyzed for their content or functions during viral infection. However, early studies of microvesicles (L-particles) secreted from herpes simplex virus-infected cells provided the first evidence of microvesicle-mediated intercellular communication. In the case of Epstein-Barr virus, recent evidence suggests that this tumorigenic herpesvirus also utilizes exosomes as a mechanism of cell-to-cell communication through the transfer of signaling competent proteins and functional microRNAs to uninfected cells. This review focuses on aspects of the biology of microvesicles with an emphasis on their potential contributions to viral infection and pathogenesis.","corpus_id":24866739,"score":0},{"doc_id":"23170177","title":"Uncovering viral protein-protein interactions and their role in arenavirus life cycle.","abstract":"The Arenaviridae family includes widely distributed pathogens that cause severe hemorrhagic fever in humans. Replication and packaging of their single-stranded RNA genome involve RNA recognition by viral proteins and a number of key protein-protein interactions. Viral RNA synthesis is directed by the virus-encoded RNA dependent-RNA polymerase (L protein) and requires viral RNA encapsidation by the Nucleoprotein. In addition to the role that the interaction between L and the Nucleoprotein may have in the replication process, polymerase activity appears to be modulated by the association between L and the small multifunctional Z protein. Z is also a structural component of the virions that plays an essential role in viral morphogenesis. Indeed, interaction of the Z protein with the Nucleoprotein is critical for genome packaging. Furthermore, current evidence suggests that binding between Z and the viral envelope glycoprotein complex is required for virion infectivity, and that Z homo-oligomerization is an essential step for particle assembly and budding. Efforts to understand the molecular basis of arenavirus life cycle have revealed important details on these viral protein-protein interactions that will be reviewed in this article.","corpus_id":2369714,"score":0},{"doc_id":"25125715","title":"A novel T cell evasion mechanism in persistent RNA virus infection.","abstract":"Hepatitis C virus (HCV) and GB virus type C (GBV-C) are associated with impaired T cell function despite the fact that HCV replicates in hepatocytes and GBV-C in a small proportion of lymphocytes. Recently, we showed that HCV and GBV-C E2-envelope proteins reduce T cell activation via the T cell receptor (TCR) by competing for phosphorylation with a critical kinase in the TCR signaling cascade (Lck). E2 interfered with TCR signaling in E2 expressing cells and in bystander cells. The bystander effect was mediated by virus particles and extracellular microvesicular particles (exosomes). Multiple kinase substrate sites are predicted to reside on viral structural proteins and based on bioinformatic predictions, many RNA virus pathogens may interfere with TCR signaling via a similar mechanism. Identification of T cell inhibitory effects of virus structural proteins may provide novel approaches to enhance the immunogenicity and memory of viral vaccines.","corpus_id":30483357,"score":0},{"doc_id":"25206336","title":"Glutathione: new roles in redox signaling for an old antioxidant.","abstract":"The physiological roles played by the tripeptide glutathione have greatly advanced over the past decades superimposing the research on free radicals, oxidative stress and, more recently, redox signaling. In particular, GSH is involved in nutrient metabolism, antioxidant defense, and regulation of cellular metabolic functions ranging from gene expression, DNA and protein synthesis to signal transduction, cell proliferation and apoptosis. This review will be focused on the role of GSH in cell signaling by analysing the more recent advancements about its capability to modulate nitroxidative stress, autophagy, and viral infection.","corpus_id":14294863,"score":0},{"doc_id":"26320628","title":"Antimicrobial proteins: From old proteins, new tricks.","abstract":"This review describes the main types of antimicrobial peptides (AMPs) synthesised by crustaceans, primarily those identified in shrimp, crayfish, crab and lobster. It includes an overview of their range of microbicidal activities and the current landscape of our understanding of their gene expression patterns in different body tissues. It further summarises how their expression might change following various types of immune challenges. The review further considers proteins or protein fragments from crustaceans that have antimicrobial properties but are more usually associated with other biological functions, or are derived from such proteins. It discusses how these unconventional AMPs might be generated at, or delivered to, sites of infection and how they might contribute to crustacean host defence in vivo. It also highlights recent work that is starting to reveal the extent of multi-functionality displayed by some decapod AMPs, particularly their participation in other aspects of host protection. Examples of such activities include proteinase inhibition, phagocytosis, antiviral activity and haematopoiesis.","corpus_id":40012153,"score":0},{"doc_id":"28009816","title":"The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport.","abstract":"The pleiotropic serine/threonine protein kinase CK2 was the first kinase discovered. It is renowned for its role in cell proliferation and anti-apoptosis. The complexity of this kinase is well reflected by the findings of past decades in terms of its heterotetrameric structure, subcellular location, constitutive activity and the extensive catalogue of substrates. With the advent of non-biased high-throughput functional genomics such as genome-wide deletion mutant screening, novel aspects of CK2 functionality have been revealed. Our recent discoveries using the model organism Saccharomyces cerevisiae and mammalian cells demonstrate that CK2 regulates metal toxicity. Extensive literature search reveals that there are few but elegant works on the role of CK2 in regulating the sodium and zinc channels. As both CK2 and metal ions are key players in cell biology and oncogenesis, understanding the details of CK2's regulation of metal ion homeostasis has a direct bearing on cancer research. In this review, we aim to garner the recent data and gain insights into the role of CK2 in metal ion transport.","corpus_id":526485,"score":0},{"doc_id":"29280156","title":"The Many Roles of Type II Phosphatidylinositol 4-Kinases in Membrane Trafficking: New Tricks for Old Dogs.","abstract":"The type II phosphatidylinositol 4-kinases (PI4KIIs) produce the lipid phosphatidylinositol 4-phosphate (PtdIns4P) and participate in a confusing variety of membrane trafficking and signaling roles. This review argues that both historical and contemporary evidence supports the function of the PI4KIIs in numerous trafficking pathways, and that the key to understanding the enzymatic regulation is through membrane interaction and the intrinsic membrane environment. By summarizing new research and examining the trafficking roles of the PI4KIIs in the context of recently solved molecular structures, I highlight how mechanisms of PI4KII function and regulation are providing insights into the development of cancer and in neurological disease. I present an integrated view connecting the cell biology, molecular regulation, and roles in whole animal systems of these increasingly important proteins.","corpus_id":33556894,"score":0},{"doc_id":"29307596","title":"An \"Old\" protein with a new story: Coronavirus endoribonuclease is important for evading host antiviral defenses.","abstract":"Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses.","corpus_id":4874123,"score":0},{"doc_id":"29514907","title":"Distinct Immunogenicity and Efficacy of Poxvirus-Based Vaccine Candidates against Ebola Virus Expressing GP and VP40 Proteins.","abstract":"Zaire and Sudan ebolavirus species cause a severe disease in humans and nonhuman primates (NHPs) characterized by a high mortality rate. There are no licensed therapies or vaccines against Ebola virus disease (EVD), and the recent 2013 to 2016 outbreak in West Africa highlighted the need for EVD-specific medical countermeasures. Here, we generated and characterized head-to-head the immunogenicity and efficacy of five vaccine candidates against Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV) based on the highly attenuated poxvirus vector modified vaccinia virus Ankara (MVA) expressing either the virus glycoprotein (GP) or GP together with the virus protein 40 (VP40) forming virus-like particles (VLPs). In a human monocytic cell line, the different MVA vectors (termed MVA-EBOVs and MVA-SUDVs) triggered robust innate immune responses, with production of beta interferon (IFN-β), proinflammatory cytokines, and chemokines. Additionally, several innate immune cells, such as dendritic cells, neutrophils, and natural killer cells, were differentially recruited in the peritoneal cavity of mice inoculated with MVA-EBOVs. After immunization of mice with a homologous prime/boost protocol (MVA/MVA), total IgG antibodies against GP or VP40 from Zaire and Sudan ebolavirus were differentially induced by these vectors, which were mainly of the IgG1 and IgG3 isotypes. Remarkably, an MVA-EBOV construct coexpressing GP and VP40 protected chimeric mice challenged with EBOV to a greater extent than a vector expressing GP alone. These results support the consideration of MVA-EBOVs and MVA-SUDVs expressing GP and VP40 and producing VLPs as best-in-class potential vaccine candidates against EBOV and SUDV.IMPORTANCE EBOV and SUDV cause a severe hemorrhagic fever affecting humans and NHPs. Since their discovery in 1976, they have caused several sporadic epidemics, with the recent outbreak in West Africa from 2013 to 2016 being the largest and most severe, with more than 11,000 deaths being reported. Although some vaccines are in advanced clinical phases, less expensive, safer, and more effective licensed vaccines are desirable. We generated and characterized head-to-head the immunogenicity and efficacy of five novel vaccines against EBOV and SUDV based on the poxvirus MVA expressing GP or GP and VP40. The expression of GP and VP40 leads to the formation of VLPs. These MVA-EBOV and MVA-SUDV recombinants triggered robust innate and humoral immune responses in mice. Furthermore, MVA-EBOV recombinants expressing GP and VP40 induced high protection against EBOV in a mouse challenge model. Thus, MVA expressing GP and VP40 and producing VLPs is a promising vaccine candidate against EBOV and SUDV.","corpus_id":3781897,"score":0}],"string":"[\n {\n \"doc_id\": \"20164217\",\n \"title\": \"Role of the GTPase Rab1b in ebolavirus particle formation.\",\n \"abstract\": \"The Ebolavirus matrix protein VP40 is essential for virion assembly and egress. Recently, we reported that the coat protein complex II (COPII) transport system plays an important role in the transport of VP40 to the plasma membrane. Here, we show that dominant-negative mutants of the GTPase Rab1b interfere with VP40-mediated particle formation. Rab1b activates GBF1 (Golgi-specific BFA [brefeldin A] resistance factor 1), a critical factor in the assembly of COPI vesicles. Activated GBF1 stimulates ARF1 (ADP ribosylation factor 1), which recruits coat protein to cellular membranes for the assembly of COPI vesicles. Here, we demonstrate that GBF1 and ARF1 are involved in Ebolavirus virion formation, suggesting that both the COPII and COPI transport systems play a role in Ebolavirus VP40-mediated particle formation. These findings provide new insights into the cellular pathways employed for Ebolavirus virion formation.\",\n \"corpus_id\": 1252067,\n \"score\": 2\n },\n {\n \"doc_id\": \"20444481\",\n \"title\": \"Both matrix proteins of Ebola virus contribute to the regulation of viral genome replication and transcription.\",\n \"abstract\": \"Ebola virus (EBOV) causes severe hemorrhagic fevers in humans and non-human primates. While the role of the EBOV major matrix protein VP40 in morphogenesis is well understood, nothing is known about its contributions to the regulation of viral genome replication and/or transcription. Similarly, while it was reported that the minor matrix protein VP24 impairs viral genome replication, it remains unclear whether it also regulates transcription, since all common experimental systems measure the combined products of replication and transcription. We have developed systems that allow the independent monitoring of viral transcription and replication, based on qRT-PCR and a replication-deficient minigenome. Using these systems we show that VP24 regulates not only viral genome replication, but also transcription. Further, we show for the first time that VP40 is also involved in regulating these processes. These functions are conserved among EBOV species and, in the case of VP40, independent of its budding or RNA-binding functions.\",\n \"corpus_id\": 20603860,\n \"score\": 2\n },\n {\n \"doc_id\": \"21697477\",\n \"title\": \"Ebolavirus delta-peptide immunoadhesins inhibit marburgvirus and ebolavirus cell entry.\",\n \"abstract\": \"With the exception of Reston and Lloviu viruses, filoviruses (marburgviruses, ebolaviruses, and \\\"cuevaviruses\\\") cause severe viral hemorrhagic fevers in humans. Filoviruses use a class I fusion protein, GP(1,2), to bind to an unknown, but shared, cell surface receptor to initiate virus-cell fusion. In addition to GP(1,2), ebolaviruses and cuevaviruses, but not marburgviruses, express two secreted glycoproteins, soluble GP (sGP) and small soluble GP (ssGP). All three glycoproteins have identical N termini that include the receptor-binding region (RBR) but differ in their C termini. We evaluated the effect of the secreted ebolavirus glycoproteins on marburgvirus and ebolavirus cell entry, using Fc-tagged recombinant proteins. Neither sGP-Fc nor ssGP-Fc bound to filovirus-permissive cells or inhibited GP(1,2)-mediated cell entry of pseudotyped retroviruses. Surprisingly, several Fc-tagged Δ-peptides, which are small C-terminal cleavage products of sGP secreted by ebolavirus-infected cells, inhibited entry of retroviruses pseudotyped with Marburg virus GP(1,2), as well as Marburg virus and Ebola virus infection in a dose-dependent manner and at low molarity despite absence of sequence similarity to filovirus RBRs. Fc-tagged Δ-peptides from three ebolaviruses (Ebola virus, Sudan virus, and Taï Forest virus) inhibited GP(1,2)-mediated entry and infection of viruses comparably to or better than the Fc-tagged RBRs, whereas the Δ-peptide-Fc of an ebolavirus nonpathogenic for humans (Reston virus) and that of an ebolavirus with lower lethality for humans (Bundibugyo virus) had little effect. These data indicate that Δ-peptides are functional components of ebolavirus proteomes. They join cathepsins and integrins as novel modulators of filovirus cell entry, might play important roles in pathogenesis, and could be exploited for the synthesis of powerful new antivirals.\",\n \"corpus_id\": 35118269,\n \"score\": 2\n },\n {\n \"doc_id\": \"21987759\",\n \"title\": \"Unconventional secretion of Ebola virus matrix protein VP40.\",\n \"abstract\": \"The Ebola virus matrix protein VP40 plays an essential role in virus assembly and budding. In this study we reveal that transient VP40 expression results in the release into the culture medium of substantial amounts of soluble monomeric VP40 in addition to the release of virus-like particles containing an oligomeric form of this protein as previously described. We show that VP40 secretion is endoplasmic reticulum/Golgi-independent and is not associated with cell death. Soluble VP40 was observed during Ebola virus infection of cells and was also found in the serum of virus-infected animals albeit in lower amounts. Unconventional secretion of VP40 may therefore play a role in Ebola virus pathogenicity.\",\n \"corpus_id\": 26940897,\n \"score\": 2\n },\n {\n \"doc_id\": \"22371572\",\n \"title\": \"Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.\",\n \"abstract\": \"Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.\",\n \"corpus_id\": 21640245,\n \"score\": 2\n },\n {\n \"doc_id\": \"22485110\",\n \"title\": \"Ebolavirus Replication and Tetherin/BST-2.\",\n \"abstract\": \"Ebolavirus (EBOV) is an enveloped, non-segmented, negative-stranded RNA virus, which consists of five species: Zaire ebolavirus, Sudan ebolavirus, Tai Forest ebolavirus, Bundibugyo ebolavirus, and Reston ebolavirus. EBOV causes a lethal hemorrhagic fever in both humans and non-human primates. The EBOV RNA genome encodes seven viral proteins: NP, VP35, VP40, GP, VP30, VP24, and L. VP40 is a matrix protein and is essential for virus assembly and release from host cells. Expression of VP40 in mammalian cells is sufficient to generate extracellular virus-like particles, which resemble authentic virions. Tetherin/BST-2, which was identified as an effective cellular factor that prevents human immunodeficiency virus-1 release in the absence of viral accessory protein Vpu, has been reported to inhibit ZEBOV VP40-induced VLP release. Tetherin/BST-2 appears to inhibit virus release by physically tethering viral particles to the cell surface via its N-terminal transmembrane domain and C-terminal glycosylphosphatidylinositol anchor. Replication of ZEBOV is not inhibited by tetherin/BST-2 expression, although tetherin/BST-2 was expected to inhibit EBOV release as well as VLP release. Recently, it was reported that viral glycoprotein of EBOV, GP, antagonizes the antiviral effect of tetherin/BST-2. However, the mechanism by which GP antagonizes the antiviral activity of tetherin/BST-2 and whether GP of the other EBOV species function as antagonists of tetherin/BST-2 remain unclear.\",\n \"corpus_id\": 1557593,\n \"score\": 2\n },\n {\n \"doc_id\": \"23076242\",\n \"title\": \"The ebolavirus VP24 interferon antagonist: know your enemy.\",\n \"abstract\": \"Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways. The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation. A more recent discovery is that VP24 also binds STAT1 directly, suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses.\",\n \"corpus_id\": 38317375,\n \"score\": 2\n },\n {\n \"doc_id\": \"23383374\",\n \"title\": \"The spatio-temporal distribution dynamics of Ebola virus proteins and RNA in infected cells.\",\n \"abstract\": \"Here, we used a biologically contained Ebola virus system to characterize the spatio-temporal distribution of Ebola virus proteins and RNA during virus replication. We found that viral nucleoprotein (NP), the polymerase cofactor VP35, the major matrix protein VP40, the transcription activator VP30, and the minor matrix protein VP24 were distributed in cytoplasmic inclusions. These inclusions enlarged near the nucleus, became smaller pieces, and subsequently localized near the plasma membrane. GP was distributed in the cytoplasm and transported to the plasma membrane independent of the other viral proteins. We also found that viral RNA synthesis occurred within the inclusions. Newly synthesized negative-sense RNA was distributed inside the inclusions, whereas positive-sense RNA was distributed both inside and outside. These findings provide useful insights into Ebola virus replication.\",\n \"corpus_id\": 840522,\n \"score\": 2\n },\n {\n \"doc_id\": \"23953110\",\n \"title\": \"Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle.\",\n \"abstract\": \"Proteins, particularly viral proteins, can be multifunctional, but the mechanisms behind multifunctionality are not fully understood. Here, we illustrate through multiple crystal structures, biochemistry, and cellular microscopy that VP40 rearranges into different structures, each with a distinct function required for the ebolavirus life cycle. A butterfly-shaped VP40 dimer traffics to the cellular membrane. Once there, electrostatic interactions trigger rearrangement of the polypeptide into a linear hexamer. These hexamers construct a multilayered, filamentous matrix structure that is critical for budding and resembles tomograms of authentic virions. A third structure of VP40, formed by a different rearrangement, is not involved in virus assembly but instead uniquely binds RNA to regulate viral transcription inside infected cells. These results provide a functional model for ebolavirus matrix assembly and the other roles of VP40 in the virus life cycle and demonstrate how a single wild-type, unmodified polypeptide can assemble into different structures for different functions.\",\n \"corpus_id\": 14669246,\n \"score\": 2\n },\n {\n \"doc_id\": \"24965473\",\n \"title\": \"A novel life cycle modeling system for Ebola virus shows a genome length-dependent role of VP24 in virus infectivity.\",\n \"abstract\": \"UNLABELLED: Work with infectious Ebola viruses is restricted to biosafety level 4 (BSL4) laboratories, presenting a significant barrier for studying these viruses. Life cycle modeling systems, including minigenome systems and transcription- and replication-competent virus-like particle (trVLP) systems, allow modeling of the virus life cycle under BSL2 conditions; however, all current systems model only certain aspects of the virus life cycle, rely on plasmid-based viral protein expression, and have been used to model only single infectious cycles. We have developed a novel life cycle modeling system allowing continuous passaging of infectious trVLPs containing a tetracistronic minigenome that encodes a reporter and the viral proteins VP40, VP24, and GP1,2. This system is ideally suited for studying morphogenesis, budding, and entry, in addition to genome replication and transcription. Importantly, the specific infectivity of trVLPs in this system was ∼ 500-fold higher than that in previous systems. Using this system for functional studies of VP24, we showed that, contrary to previous reports, VP24 only very modestly inhibits genome replication and transcription when expressed in a regulated fashion, which we confirmed using infectious Ebola viruses. Interestingly, we also discovered a genome length-dependent effect of VP24 on particle infectivity, which was previously undetected due to the short length of monocistronic minigenomes and which is due at least partially to a previously unknown function of VP24 in RNA packaging. Based on our findings, we propose a model for the function of VP24 that reconciles all currently available data regarding the role of VP24 in nucleocapsid assembly as well as genome replication and transcription. IMPORTANCE: Ebola viruses cause severe hemorrhagic fevers in humans, with no countermeasures currently being available, and must be studied in maximum-containment laboratories. Only a few of these laboratories exist worldwide, limiting our ability to study Ebola viruses and develop countermeasures. Here we report the development of a novel reverse genetics-based system that allows the study of Ebola viruses without maximum-containment laboratories. We used this system to investigate the Ebola virus protein VP24, showing that, contrary to previous reports, it only modestly inhibits virus genome replication and transcription but is important for packaging of genomes into virus particles, which constitutes a previously unknown function of VP24 and a potential antiviral target. We further propose a comprehensive model for the function of VP24 in nucleocapsid assembly. Importantly, on the basis of this approach, it should easily be possible to develop similar experimental systems for other viruses that are currently restricted to maximum-containment laboratories.\",\n \"corpus_id\": 28102686,\n \"score\": 2\n },\n {\n \"doc_id\": \"25957961\",\n \"title\": \"High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.\",\n \"abstract\": \"Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly.\",\n \"corpus_id\": 24874326,\n \"score\": 2\n },\n {\n \"doc_id\": \"26034199\",\n \"title\": \"Interferon-Induced Transmembrane Protein-Mediated Inhibition of Host Cell Entry of Ebolaviruses.\",\n \"abstract\": \"Ebolaviruses are highly pathogenic in humans and nonhuman primates and pose a severe threat to public health. The interferon-induced transmembrane (IFITM) proteins can restrict entry of ebolaviruses, influenza A viruses, and other enveloped viruses. However, the breadth and mechanism of the antiviral activity of IFITM proteins are incompletely understood. Here, we employed ebolavirus glycoprotein-pseudotyped vectors and ebolavirus-like particles to address this question. We show that IFITM proteins inhibit the cellular entry of diverse ebolaviruses and demonstrate that type I interferon induces IFITM protein expression in macrophages, major viral targets. Moreover, we show that IFITM proteins block entry of influenza A viruses and ebolaviruses by different mechanisms and provide evidence that antibodies and IFITM proteins can synergistically inhibit cellular entry of ebolaviruses. These results provide insights into the role of IFITM proteins in infection by ebolaviruses and suggest a mechanism by which antibodies, though poorly neutralizing in vitro, might contribute to viral control in vivo.\",\n \"corpus_id\": 17790537,\n \"score\": 2\n },\n {\n \"doc_id\": \"26753796\",\n \"title\": \"The Ebola Virus matrix protein, VP40, requires phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) for extensive oligomerization at the plasma membrane and viral egress.\",\n \"abstract\": \"VP40 is one of eight proteins encoded by the Ebola Virus (EBOV) and serves as the primary matrix protein, forming virus like particles (VLPs) from mammalian cells without the need for other EBOV proteins. While VP40 is required for viral assembly and budding from host cells during infection, the mechanisms that target VP40 to the plasma membrane are not well understood. Phosphatidylserine is required for VP40 plasma membrane binding, VP40 hexamer formation, and VLP egress, However, PS also becomes exposed on the outer membrane leaflet at sites of VP40 budding, raising the question of how VP40 maintains an interaction with the plasma membrane inner leaflet when PS is flipped to the opposite side. To address this question, cellular and in vitro assays were employed to determine if phosphoinositides are important for efficient VP40 localization to the plasma membrane. Cellular studies demonstrated that PI(4,5)P2 was an important component of VP40 assembly at the plasma membrane and subsequent virus like particle formation. Additionally, PI(4,5)P2 was required for formation of extensive oligomers of VP40, suggesting PS and PI(4,5)P2 have different roles in VP40 assembly where PS regulates formation of hexamers from VP40 dimers and PI(4,5)P2 stabilizes and/or induces extensive VP40 oligomerization at the plasma membrane.\",\n \"corpus_id\": 41372364,\n \"score\": 2\n },\n {\n \"doc_id\": \"27009368\",\n \"title\": \"Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses.\",\n \"abstract\": \"Reston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts, and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission.\",\n \"corpus_id\": 11578096,\n \"score\": 2\n },\n {\n \"doc_id\": \"27757455\",\n \"title\": \"The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane.\",\n \"abstract\": \"The Ebola virus is a lipid-enveloped virus that obtains its lipid coat from the plasma membrane of the host cell it infects during the budding process. The Ebola virus protein VP40 localizes to the inner leaflet of the plasma membrane and forms the viral matrix, which provides the major structure for the Ebola virus particles. VP40 is initially a dimer that rearranges to a hexameric structure that mediates budding. VP40 hexamers and larger filaments have been shown to be stabilized by PI(4,5)P2 in the plasma membrane inner leaflet. Reduction in the plasma membrane levels of PI(4,5)P2 significantly reduce formation of VP40 oligomers and virus-like particles. We investigated the lipid-protein interactions in VP40 hexamers at the plasma membrane. We quantified lipid-lipid self-clustering by calculating the fractional interaction matrix and found that the VP40 hexamer significantly enhances the PI(4,5)P2 clustering. The radial pair distribution functions suggest a strong interaction between PI(4,5)P2 and the VP40 hexamer. The cationic Lys side chains are found to mediate the PIP2 clustering around the protein, with cholesterol filling the space between the interacting PIP2 molecules. These computational studies support recent experimental data and provide new insights into the mechanisms by which VP40 assembles at the plasma membrane inner leaflet, alters membrane curvature, and forms new virus-like particles.\",\n \"corpus_id\": 24549981,\n \"score\": 2\n },\n {\n \"doc_id\": \"27847361\",\n \"title\": \"Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak.\",\n \"abstract\": \"The Ebola virus (EBOV) outbreak in West Africa started in December 2013, claimed more than 11,000 lives, threatened to destabilize a whole region, and showed how easily health crises can turn into humanitarian disasters. EBOV genomic sequences of the West African outbreak revealed nonsynonymous mutations, which induced considerable public attention, but their role in virus spread and disease remains obscure. In this study, we investigated the functional significance of three nonsynonymous mutations that emerged early during the West African EBOV outbreak. Almost 90% of more than 1,000 EBOV genomes sequenced during the outbreak carried the signature of three mutations: a D759G substitution in the active center of the L polymerase, an A82V substitution in the receptor binding domain of surface glycoprotein GP, and an R111C substitution in the self-assembly domain of RNA-encapsidating nucleoprotein NP. Using a newly developed virus-like particle system and reverse genetics, we found that the mutations have an impact on the functions of the respective viral proteins and on the growth of recombinant EBOVs. The mutation in L increased viral transcription and replication, whereas the mutation in NP decreased viral transcription and replication. The mutation in the receptor binding domain of the glycoprotein GP improved the efficiency of GP-mediated viral entry into target cells. Recombinant EBOVs with combinations of the three mutations showed a growth advantage over the prototype isolate Makona C7 lacking the mutations. This study showed that virus variants with improved fitness emerged early during the West African EBOV outbreak. IMPORTANCE: The dimension of the Ebola virus outbreak in West Africa was unprecedented. Amino acid substitutions in the viral L polymerase, surface glycoprotein GP, and nucleocapsid protein NP emerged, were fixed early in the outbreak, and were found in almost 90% of the sequences. Here we showed that these mutations affected the functional activity of viral proteins and improved viral growth in cell culture. Our results demonstrate emergence of adaptive changes in the Ebola virus genome during virus circulation in humans and prompt further studies on the potential role of these changes in virus transmissibility and pathogenicity.\",\n \"corpus_id\": 34739793,\n \"score\": 2\n },\n {\n \"doc_id\": \"27849047\",\n \"title\": \"Regulation of Ebola virus VP40 matrix protein by SUMO.\",\n \"abstract\": \"The matrix protein of Ebola virus (EBOV) VP40 regulates viral budding, nucleocapsid recruitment, virus structure and stability, viral genome replication and transcription, and has an intrinsic ability to form virus-like particles. The elucidation of the regulation of VP40 functions is essential to identify mechanisms to inhibit viral replication and spread. Post-translational modifications of proteins with ubiquitin-like family members are common mechanisms for the regulation of host and virus multifunctional proteins. Thus far, no SUMOylation of VP40 has been described. Here we demonstrate that VP40 is modified by SUMO and that SUMO is included into the viral like particles (VLPs). We demonstrate that lysine residue 326 in VP40 is involved in SUMOylation, and by analyzing a mutant in this residue we show that SUMO conjugation regulates the stability of VP40 and the incorporation of SUMO into the VLPs. Our study indicates for the first time, to the best of our knowledge, that EBOV hijacks the cellular SUMOylation system in order to modify its own proteins. Modulation of the VP40-SUMO interaction may represent a novel target for the therapy of Ebola virus infection.\",\n \"corpus_id\": 18876818,\n \"score\": 2\n },\n {\n \"doc_id\": \"27853993\",\n \"title\": \"The roles of ebolavirus glycoproteins in viral pathogenesis.\",\n \"abstract\": \"Ebolaviruses are highly dangerous pathogens exhibiting extreme virulence in humans and nonhuman primates. The majority of ebolavirus species, most notably Zaire ebolavirus, can cause Ebola virus disease (EVD), formerly known as Ebola hemorrhagic fever, in humans. EVD is associated with case-fatality rates as high as 90%, and there is currently no specific treatment or licensed vaccine available against EVD. Understanding the molecular biology and pathogenesis of ebolaviruses is important for the development of antiviral therapeutics. Ebolavirus encodes several forms of glycoproteins (GPs), which have some interesting characteristics, including the transcriptional editing coding strategy and extensive O-glycosylation modification, clustered in the mucin-like domain of GP1, full-length GP (GP1,2), and shed GP. In addition to the canonical role of the spike protein, GP1,2, in viral entry, ebolavirus GPs appear to have multiple additional functions, likely contributing to the complex pathogenesis of the virus. Here, we review the roles of ebolavirus GPs in viral pathogenesis.\",\n \"corpus_id\": 20856805,\n \"score\": 2\n },\n {\n \"doc_id\": \"27872619\",\n \"title\": \"Ebola VP40 in Exosomes Can Cause Immune Cell Dysfunction.\",\n \"abstract\": \"Ebola virus (EBOV) is an enveloped, ssRNA virus from the family Filoviridae capable of causing severe hemorrhagic fever with up to 80-90% mortality rates. The most recent outbreak of EBOV in West Africa starting in 2014 resulted in over 11,300 deaths; however, long-lasting persistence and recurrence in survivors has been documented, potentially leading to further transmission of the virus. We have previously shown that exosomes from cells infected with HIV-1, HTLV-1 and Rift Valley Fever virus are able to transfer viral proteins and non-coding RNAs to naïve recipient cells, resulting in an altered cellular activity. In the current manuscript, we examined the effect of Ebola structural proteins VP40, GP, NP and VLPs on recipient immune cells, as well as the effect of exosomes containing these proteins on naïve immune cells. We found that VP40-transfected cells packaged VP40 into exosomes, and that these exosomes were capable of inducing apoptosis in recipient immune cells. Additionally, we show that presence of VP40 within parental cells or in exosomes delivered to naïve cells could result in the regulation of RNAi machinery including Dicer, Drosha, and Ago 1, which may play a role in the induction of cell death in recipient immune cells. Exosome biogenesis was regulated by VP40 in transfected cells by increasing levels of ESCRT-II proteins EAP20 and EAP45, and exosomal marker proteins CD63 and Alix. VP40 was phosphorylated by Cdk2/Cyclin complexes at Serine 233 which could be reversed with r-Roscovitine treatment. The level of VP40-containing exosomes could also be regulated by treated cells with FDA-approved Oxytetracycline. Additionally, we utilized novel nanoparticles to safely capture VP40 and other viral proteins from Ebola VLPs spiked into human samples using SDS/reducing agents, thus minimizing the need for BSL-4 conditions for most downstream assays. Collectively, our data indicates that VP40 packaged into exosomes may be responsible for the deregulation and eventual destruction of the T-cell and myeloid arms of the immune system (bystander lymphocyte apoptosis), allowing the virus to replicate to high titers in the immunocompromised host. Moreover, our results suggest that the use of drugs such as Oxytetracycline to modulate the levels of exosomes exiting EBOV-infected cells may be able to prevent the devastation of the adaptive immune system and allow for an improved rate of survival.\",\n \"corpus_id\": 49381955,\n \"score\": 2\n },\n {\n \"doc_id\": \"28066813\",\n \"title\": \"Risks Posed by Reston, the Forgotten Ebolavirus.\",\n \"abstract\": \"Out of the five members of the Ebolavirus family, four cause life-threatening disease, whereas the fifth, Reston virus (RESTV), is nonpathogenic in humans. The reasons for this discrepancy remain unclear. In this review, we analyze the currently available information to provide a state-of-the-art summary of the factors that determine the human pathogenicity of Ebolaviruses. RESTV causes sporadic infections in cynomolgus monkeys and is found in domestic pigs throughout the Philippines and China. Phylogenetic analyses revealed that RESTV is most closely related to the Sudan virus, which causes a high mortality rate in humans. Amino acid sequence differences between RESTV and the other Ebolaviruses are found in all nine Ebolavirus proteins, though no one residue appears sufficient to confer pathogenicity. Changes in the glycoprotein contribute to differences in Ebolavirus pathogenicity but are not sufficient to confer pathogenicity on their own. Similarly, differences in VP24 and VP35 affect viral immune evasion and are associated with changes in human pathogenicity. A recent in silico analysis systematically determined the functional consequences of sequence variations between RESTV and human-pathogenic Ebolaviruses. Multiple positions in VP24 were differently conserved between RESTV and the other Ebolaviruses and may alter human pathogenicity. In conclusion, the factors that determine the pathogenicity of Ebolaviruses in humans remain insufficiently understood. An improved understanding of these pathogenicity-determining factors is of crucial importance for disease prevention and for the early detection of emergent and potentially human-pathogenic RESTVs.\",\n \"corpus_id\": 5248937,\n \"score\": 2\n },\n {\n \"doc_id\": \"28177658\",\n \"title\": \"The Role of Exosomal VP40 in Ebola Virus Disease.\",\n \"abstract\": \"Ebola virus (EBOV) can cause a devastating hemorrhagic disease, leading to death in a short period of time. After infection, the resulting EBOV disease results in high levels of circulating cytokines, endothelial dysfunction, coagulopathy, and bystander lymphocyte apoptosis in humans and nonhuman primates. The VP40 matrix protein of EBOV is essential for viral assembly and budding from the host cell. Recent data have shown that VP40 exists in the extracellular environment, including in exosomes, and exosomal VP40 can impact the viability of recipient immune cells, including myeloid and T cells, through the regulation of the RNAi and endosomal sorting complexes required for transport pathways. In this study, we discuss the latest findings of the impact of exosomal VP40 on immune cells in vitro and its potential implications for pathogenesis in vivo.\",\n \"corpus_id\": 196628327,\n \"score\": 2\n },\n {\n \"doc_id\": \"28573615\",\n \"title\": \"Modeling the Ebolavirus Life Cycle with Transcription and Replication-Competent Viruslike Particle Assays.\",\n \"abstract\": \"Ebolaviruses are the causative agent of a severe hemorrhagic fever with high case fatality rates, for which no approved specific therapy is available. As biosafety level 4 (BSL4) agents, work with live ebolaviruses is restricted to maximum containment laboratories. Transcription and replication-competent viruslike particle (trVLP) systems are reverse genetics-based life cycle modeling systems that allow researchers to model virtually the entire ebolavirus life cycle outside of a maximum containment laboratory. These systems can be used to dissect the virus life cycle, and thus increase our understanding of virus biology, as well as for more applied uses such as the screening and development of novel antivirals, and thus represent powerful tools for work on ebolaviruses.\",\n \"corpus_id\": 9774325,\n \"score\": 2\n },\n {\n \"doc_id\": \"28595092\",\n \"title\": \"Ebolavirus protein VP24 interferes with innate immune responses by inhibiting interferon-λ1 gene expression.\",\n \"abstract\": \"Ebolaviruses (EBOV) cause severe disease with a recent outbreak in West Africa in 2014-2015 leading to more than 28 000 cases and 11 300 fatalities. This emphasizes the urgent need for better knowledge on these highly pathogenic RNA viruses. Host innate immune responses play a key role in restricting the spread of a viral disease. In this study we systematically analyzed the effects of cloned EBOV genes on the main host immune response to RNA viruses: the activation of RIG-I pathway and type I and III interferon (IFN) gene expression. EBOV VP24, in addition of inhibiting IFN-induced antiviral responses, was found to efficiently inhibit type III IFN-λ1 gene expression. This inhibition was found to occur downstream of IRF3 activation and to be dependent on VP24 importin binding residues. These results emphasize the importance of VP24 in EBOV infection cycle, making VP24 as an excellent target for drug development.\",\n \"corpus_id\": 27740318,\n \"score\": 2\n },\n {\n \"doc_id\": \"28878074\",\n \"title\": \"Cooperation of the Ebola Virus Proteins VP40 and GP1,2 with BST2 To Activate NF-κB Independently of Virus-Like Particle Trapping.\",\n \"abstract\": \"BST2 is a host protein with dual functions in response to viral infections: it traps newly assembled enveloped virions at the plasma membrane in infected cells, and it induces NF-κB activity, especially in the context of retroviral assembly. In this study, we examined whether Ebola virus proteins affect BST2-mediated induction of NF-κB. We found that the Ebola virus matrix protein, VP40, and envelope glycoprotein, GP, each cooperate with BST2 to induce NF-κB activity, with maximal activity when all three proteins are expressed. Unlike human immunodeficiency virus type 1 Vpu protein, which antagonizes both virion entrapment and the activation of NF-κB by BST2, Ebola virus GP does not inhibit NF-κB signaling even while it antagonizes the entrapment of virus-like particles. GP from Reston ebolavirus, a nonpathogenic species in humans, showed a phenotype similar to that of GP from Zaire ebolavirus, a highly pathogenic species, in terms of both the activation of NF-κB and the antagonism of virion entrapment. Although Ebola virus VP40 and GP both activate NF-κB independently of BST2, VP40 is the more potent activator. Activation of NF-κB by the Ebola virus proteins either alone or together with BST2 requires the canonical NF-κB signaling pathway. Mechanistically, the maximal NF-κB activation by GP, VP40, and BST2 together requires the ectodomain cysteines needed for BST2 dimerization, the putative BST2 tetramerization residue L70, and Y6 of a potential hemi-ITAM motif in BST2's cytoplasmic domain. BST2 with a glycosylphosphatidylinositol (GPI) anchor signal deletion, which is not expressed at the plasma membrane and is unable to entrap virions, activated NF-κB in concert with the Ebola virus proteins at least as effectively as wild-type BST2. Signaling by the GPI anchor mutant also depended on Y6 of BST2. Overall, our data show that activation of NF-κB by BST2 is independent of virion entrapment in the case of Ebola virus. Nonetheless, BST2 may induce or amplify proinflammatory signaling during Ebola virus infection, potentially contributing to the dysregulated cytokine response that is a hallmark of Ebola virus disease. IMPORTANCE Understanding how the host responds to viral infections informs the development of therapeutics and vaccines. We asked how proinflammatory signaling by the host protein BST2/tetherin, which is mediated by the transcription factor NF-κB, responds to Ebola virus proteins. Although the Ebola virus envelope glycoprotein (GP1,2) antagonizes the trapping of newly formed virions at the plasma membrane by BST2, we found that it does not inhibit BST2's ability to induce NF-κB activity. This distinguishes GP1,2 from the HIV-1 protein Vpu, the prototype BST2 antagonist, which inhibits both virion entrapment and the induction of NF-κB activity. Ebola virus GP1,2, the Ebola virus matrix protein VP40, and BST2 are at least additive with respect to the induction of NF-κB activity. The effects of these proteins converge on an intracellular signaling pathway that depends on a protein modification termed neddylation. Better mechanistic understanding of these phenomena could provide targets for therapies that modulate the inflammatory response during Ebola virus disease.\",\n \"corpus_id\": 41339762,\n \"score\": 2\n },\n {\n \"doc_id\": \"19023410\",\n \"title\": \"Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda.\",\n \"abstract\": \"Over the past 30 years, Zaire and Sudan ebolaviruses have been responsible for large hemorrhagic fever (HF) outbreaks with case fatalities ranging from 53% to 90%, while a third species, Côte d'Ivoire ebolavirus, caused a single non-fatal HF case. In November 2007, HF cases were reported in Bundibugyo District, Western Uganda. Laboratory investigation of the initial 29 suspect-case blood specimens by classic methods (antigen capture, IgM and IgG ELISA) and a recently developed random-primed pyrosequencing approach quickly identified this to be an Ebola HF outbreak associated with a newly discovered ebolavirus species (Bundibugyo ebolavirus) distantly related to the Côte d'Ivoire ebolavirus found in western Africa. Due to the sequence divergence of this new virus relative to all previously recognized ebolaviruses, these findings have important implications for design of future diagnostic assays to monitor Ebola HF disease in humans and animals, and ongoing efforts to develop effective antivirals and vaccines.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"19091859\",\n \"title\": \"Vacuolar protein sorting pathway contributes to the release of Marburg virus.\",\n \"abstract\": \"VP40, the major matrix protein of Marburg virus, is the main driving force for viral budding. Additionally, cellular factors are likely to play an important role in the release of progeny virus. In the present study, we characterized the influence of the vacuolar protein sorting (VPS) pathway on the release of virus-like particles (VLPs), which are induced by Marburg virus VP40. In the supernatants of HEK 293 cells expressing VP40, different populations of VLPs with either a vesicular or a filamentous morphology were detected. While the filaments were almost completely composed of VP40, the vesicular particles additionally contained considerable amounts of cellular proteins. In contrast to that in the vesicles, the VP40 in the filaments was regularly organized, probably inducing the elimination of cellular proteins from the released VLPs. Vesicular particles were observed in the supernatants of cells even in the absence of VP40. Mutation of the late-domain motif in VP40 resulted in reduced release of filamentous particles, and likewise, inhibition of the VPS pathway by expression of a dominant-negative (DN) form of VPS4 inhibited the release of filamentous particles. In contrast, the release of vesicular particles did not respond significantly to the expression of DN VPS4. Like the budding of VLPs, the budding of Marburg virus particles was partially inhibited by the expression of DN VPS4. While the release of VLPs from VP40-expressing cells is a valuable tool with which to investigate the budding of Marburg virus particles, it is important to separate filamentous VLPs from vesicular particles, which contain many cellular proteins and use a different budding mechanism.\",\n \"corpus_id\": 36420798,\n \"score\": 1\n },\n {\n \"doc_id\": \"20394957\",\n \"title\": \"Reduced virus replication, proinflammatory cytokine production, and delayed macrophage cell death in human PBMCs infected with the newly discovered Bundibugyo ebolavirus relative to Zaire ebolavirus.\",\n \"abstract\": \"Bundibugyo ebolavirus is a newly identified Ebolavirus species. The virus was responsible for a recent hemorrhagic fever outbreak in Uganda with an approximate 30% case fatality rate. In this study, we compared the pathogenesis of Bundibugyo with highly lethal Zaire Ebolavirus by using in vitro human PBMCs. We found that PBMCs infected with Bundibugyo ebolaviruses resulted in 1 to 2 log lower virus yields compared to Zaire ebolavirus and produced 2- to 10-fold lower levels of TNF-alpha, MCP-1, IL-1beta, MIP1-alpha and IL-10 than PBMCs infected with Zaire ebolavirus. In addition, flow cytometric studies have shown lower levels and delay of the macrophage cell death in Bundibugyo ebolavirus compared to Zaire ebolavirus infection. The findings of slower Bundibugyo ebolavirus replication, lower production of proinflammatory cytokines and delay in macrophage cell death provide insight into the basis of the lower case fatality observed with Bundibugyo ebolavirus.\",\n \"corpus_id\": 42682193,\n \"score\": 1\n },\n {\n \"doc_id\": \"21073307\",\n \"title\": \"Towards broad protection against Ebolaviruses.\",\n \"abstract\": \"The Ebola and Marburg viruses (from the filovirus family) induce deadly hemorrhagic fevers for which there is currently no licensed vaccine or treatment. Frequent outbreaks have occurred in sub-Saharan Africa, in humans and nonhuman primates over the last 15 years or so and constitute a major public health problem. Of particular concern, a new species of Ebolavirus recently emerged in Uganda, highlighting the high potential of these viruses to evolve and the need to develop 'broad-spectrum' vaccines against filoviruses. Hensley et al. used their well studied vaccine platform based on DNA vectors and recombinant, replication-defective, adenoviruses producing Ebolavirus glycoproteins to protect cynomolgus monkeys against a heterologous challenge with the new species. Further developments are required before this experimental approach could be adapted for field use in humans, but this study nevertheless constitutes a proof-of-concept for broad protection against Ebolaviruses.\",\n \"corpus_id\": 31774927,\n \"score\": 1\n },\n {\n \"doc_id\": \"21349211\",\n \"title\": \"Tackling Ebola: new insights into prophylactic and therapeutic intervention strategies.\",\n \"abstract\": \"Since its discovery in 1976, Ebolavirus has caused periodic outbreaks of viral hemorrhagic fever associated with severe and often fatal disease. Ebolavirus is endemic in Central Africa and the Philippines. Although there is currently no approved treatment available, the past 10 years has seen remarkable progress in our understanding of the pathogenicity of Ebolavirus and the development of prophylactic and post-exposure therapies against it. In vitro and in vivo experiments have shown that Ebolavirus pathogenicity is multifactorial, including viral and host determinants. Besides their function in the virus replication cycle, the viral glycoprotein, nucleoprotein, minor matrix protein and polymerase cofactor are viral determinants of pathogenicity, with evasion of the host innate and adaptive immune responses as the main mechanism. Although no licensed Ebolavirus vaccines are currently available, vaccine research in non-human primates, the 'gold standard' animal model for Ebolavirus, has produced several promising candidates. A combination of DNA vaccination and a recombinant adenovirus serotype 5 boost resulted in cross-protective immunity in non-human primates. A recombinant vesicular stomatitis vaccine vector protected non-human primates in pre- and post-exposure challenge studies. Several antiviral therapies are currently under investigation, but only a few of these have been tested in non-human primate models. Antisense therapies, in which oligonucleotides inhibit viral replication, have shown promising results in non-human primates following post-exposure treatment. In light of the severity of Ebolavirus disease and the observed increase in Ebolavirus outbreaks over the past decade, the expedited translation of potential candidate therapeutics and vaccines from bench to bedside is currently the most challenging task for the field. Here, we review the current state of Ebolavirus research, with emphasis on prophylactic and therapeutic intervention strategies.\",\n \"corpus_id\": 6243897,\n \"score\": 1\n },\n {\n \"doc_id\": \"21742058\",\n \"title\": \"Current perspectives on the phylogeny of Filoviridae.\",\n \"abstract\": \"Sporadic fatal outbreaks of disease in humans and non-human primates caused by Ebola or Marburg viruses have driven research into the characterization of these viruses with the hopes of identifying host tropisms and potential reservoirs. Such an understanding of the relatedness of newly discovered filoviruses may help to predict risk factors for outbreaks of hemorrhagic disease in humans and/or non-human primates. Recent discoveries such as three distinct genotypes of Reston ebolavirus, unexpectedly discovered in domestic swine in the Philippines; as well as a new species, Bundibugyo ebolavirus; the recent discovery of Lloviu virus as a potential new genus, Cuevavirus, within Filoviridae; and germline integrations of filovirus-like sequences in some animal species bring new insights into the relatedness of filoviruses, their prevalence and potential for transmission to humans. These new findings reveal that filoviruses are more diverse and may have had a greater influence on the evolution of animals than previously thought. Herein we review these findings with regard to the implications for understanding the host range, prevalence and transmission of Filoviridae.\",\n \"corpus_id\": 19609341,\n \"score\": 1\n },\n {\n \"doc_id\": \"21987741\",\n \"title\": \"Advances in virus-like particle vaccines for filoviruses.\",\n \"abstract\": \"Ebola virus (EBOV) and Marburg virus (MARV) are among the deadliest human pathogens, with no vaccines or therapeutics available. Multiple vaccine platforms have been tested for efficacy as prophylactic pretreatments or therapeutics for prevention of filovirus hemorrhagic fever. Most successful vaccines are based on a virus-vectored approach expressing the protective glycoprotein (GP); protein-based subunit and DNA vaccines have been tested with moderate success. Virus-like particle (VLP) vaccines have realized promising results when tested in both rodents and nonhuman primates. VLPs rely on the natural properties of the viral matrix protein (VP) 40 to drive budding of filamentous particles that can also incorporate ≥ 1 other filovirus protein, including GP, VP24, and nucleoprotein (NP). Filovirus VLP vaccines have used particles containing 2 or 3 (GP and VP40, with or without NP) viral proteins generated in either mammalian or insect cells. Early studies successfully demonstrated efficacy of bivalent VLP vaccines in rodents; more recent studies have shown the ability of the VLP vaccines containing GP, NP, and VP40 to confer complete homologous protection against Ebola virus and Marburg virus in a prophylactic setting against in macaques. This review will discuss published work to date regarding development of the VLP vaccines for prevention of lethal filovirus hemorrhagic fever.\",\n \"corpus_id\": 44556002,\n \"score\": 1\n },\n {\n \"doc_id\": \"25260583\",\n \"title\": \"Clinical features and pathobiology of Ebolavirus infection.\",\n \"abstract\": \"There has clearly been a deluge of international press coverage of the recent outbreak of Ebolavirus in Africa and is partly related to the \\\"fear factor\\\" that comes across when one is confronted with the fact that once infected, not only is the speed of death in a majority of cases rapid but also the images of the cause of death such as bleeding from various orifices gruesome and frightening. The fact that it leads to infection and death of health care providers (10% during the current epidemic) and the visualization of protective gear worn by these individuals to contain such infection adds to this \\\"fear factor\\\". Finally, there is a clear perceived notion that such an agent can be utilized as a bioterrorism agent that adds to the apprehension. Thus, in efforts to gain an objective view of the growing threat Ebolavirus poses to the general public, it is important to provide some basic understanding for the lethality of Ebolavirus infection that is highlighted in Fig. 1. This virus infection first appears to disable the immune system (the very system needed to fight the infection) and subsequently disables the vascular system that leads to blood leakage (hemorrhage), hypotension, drop in blood pressure, followed by shock and death. The virus appears to sequentially infect dendritic cells disabling the interferon system (one of the major host anti-viral immune systems) then macrophages (that trigger the formation of blood clots, release of inflammatory proteins and nitric oxide damaging the lining of blood vessels leading to blood leakage) and finally endothelial cells that contribute to blood leakage. The virus also affects organs such as the liver (that dysregulates the formation of coagulation proteins), the adrenal gland (that destroys the ability of the patient to synthesize steroids and leads to circulation failure and disabling of regulators of blood pressure) and the gastro-intestinal tract (leading to diarrhea). The ability of the virus to disable such major mechanisms in the body facilitates the ability of the virus to replicate in an uncontrolled fashion leading to the rapidity by which the virus can cause lethality. Various laboratories have been working on defining such mechanisms utilizing in vitro culture systems, a variety of animal models including inbred strains of normal and select gene knock out mice, guinea pigs and nonhuman primates that have led to a better understanding of the potential mechanisms involved. There have also been some major advances made in the identification of therapies from the very simple (major supportive type of therapy), to the identification of a number of highly effective chemotherapeutic agents, a variety of highly effective preventive (demonstrating 100% effectiveness in nonhuman primate models) recombinant formulations (adenovirus based, VSV-based, rabies virus based), therapeutic candidate vaccines (cocktail of monoclonal antibodies such as ZMAPP) and alternate approaches (RNAi-based such as TKM-Ebola and antisense based such as AVI-7537) that show great promise and at an unprecedented rate of discovery that speaks well for the scientific research community at large.\",\n \"corpus_id\": 27779475,\n \"score\": 1\n },\n {\n \"doc_id\": \"25387613\",\n \"title\": \"Ebola virus disease: a review on epidemiology, symptoms, treatment and pathogenesis.\",\n \"abstract\": \"Currently, West Africa is facing the largest outbreak of Ebola virus disease (EVD) in history. The virus causing this outbreak, the Zaire Ebolavirus (EBOV), belongs to the genus Ebolavirus which together with the genus Marburgvirus forms the family of the Filoviridae. EBOV is one of the most virulent pathogens among the viral haemorrhagic fevers, and case fatality rates up to 90% have been reported. Mortality is the result of multi-organ failure and severe bleeding complications. By 18 September 2014, the WHO reported of 5335 cases (confirmed, suspected and probable) with 2622 deaths, resulting in a case fatality rate of around 50%. This review aims to provide an overview of EVD for clinicians, with the emphasis on pathogenesis, clinical manifestations, and treatment options.\",\n \"corpus_id\": 27706777,\n \"score\": 1\n },\n {\n \"doc_id\": \"25803489\",\n \"title\": \"Ebolavirus classification based on natural vectors.\",\n \"abstract\": \"According to the WHO, ebolaviruses have resulted in 8818 human deaths in West Africa as of January 2015. To better understand the evolutionary relationship of the ebolaviruses and infer virulence from the relationship, we applied the alignment-free natural vector method to classify the newest ebolaviruses. The dataset includes three new Guinea viruses as well as 99 viruses from Sierra Leone. For the viruses of the family of Filoviridae, both genus label classification and species label classification achieve an accuracy rate of 100%. We represented the relationships among Filoviridae viruses by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) phylogenetic trees and found that the filoviruses can be separated well by three genera. We performed the phylogenetic analysis on the relationship among different species of Ebolavirus by their coding-complete genomes and seven viral protein genes (glycoprotein [GP], nucleoprotein [NP], VP24, VP30, VP35, VP40, and RNA polymerase [L]). The topology of the phylogenetic tree by the viral protein VP24 shows consistency with the variations of virulence of ebolaviruses. The result suggests that VP24 be a pharmaceutical target for treating or preventing ebolaviruses.\",\n \"corpus_id\": 22865000,\n \"score\": 1\n },\n {\n \"doc_id\": \"27190508\",\n \"title\": \"Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses.\",\n \"abstract\": \"Ebola Virus Disease (EVD) is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB) and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus. The genomic analyses of ebolaviruses will provide important clues for locating the essential and core functional genes. The aim of EDB is to act as an integrated resource for ebolaviruses and we strongly believe that the database will be a useful tool for clinicians, microbiologists, health care workers, and bioscience researchers.\",\n \"corpus_id\": 17087473,\n \"score\": 1\n },\n {\n \"doc_id\": \"27528741\",\n \"title\": \"Computational analysis of Ebolavirus data: prospects, promises and challenges.\",\n \"abstract\": \"The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches.\",\n \"corpus_id\": 1361715,\n \"score\": 1\n },\n {\n \"doc_id\": \"27974555\",\n \"title\": \"VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability.\",\n \"abstract\": \"Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Reston ebolavirus (RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA binding affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. These data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability. IMPORTANCE: The interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the interactions of VP24 proteins from EBOV and two members of the Ebolavirus genus, Bundibugyo virus (BDBV) and Reston virus (RESTV). The data reveal lower binding affinity of the BDBV VP24 (bVP24) for KPNAs and demonstrate that the interaction with KPNA modulates inhibition of IFN signaling and VP24 stability. The effect of KPNA interaction on VP24 stability is a novel functional consequence of this virus-host interaction, and the differences identified between viral species may contribute to differences in pathogenesis.\",\n \"corpus_id\": 4603661,\n \"score\": 1\n },\n {\n \"doc_id\": \"28331091\",\n \"title\": \"Ebolaviruses Associated with Differential Pathogenicity Induce Distinct Host Responses in Human Macrophages.\",\n \"abstract\": \"Ebola virus (EBOV) and Reston virus (RESTV) are members of the Ebolavirus genus which greatly differ in their pathogenicity. While EBOV causes a severe disease in humans characterized by a dysregulated inflammatory response and elevated cytokine and chemokine production, there are no reported disease-associated human cases of RESTV infection, suggesting that RESTV is nonpathogenic for humans. The underlying mechanisms determining the pathogenicity of different ebolavirus species are not yet known. In this study, we dissected the host response to EBOV and RESTV infection in primary human monocyte-derived macrophages (MDMs). As expected, EBOV infection led to a profound proinflammatory response, including strong induction of type I and type III interferons (IFNs). In contrast, RESTV-infected macrophages remained surprisingly silent. Early activation of IFN regulatory factor 3 (IRF3) and NF-κB was observed in EBOV-infected, but not in RESTV-infected, MDMs. In concordance with previous results, MDMs treated with inactivated EBOV and Ebola virus-like particles (VLPs) induced NF-κB activation mediated by Toll-like receptor 4 (TLR4) in a glycoprotein (GP)-dependent manner. This was not the case in cells exposed to live RESTV, inactivated RESTV, or VLPs containing RESTV GP, indicating that RESTV GP does not trigger TLR4 signaling. Our results suggest that the lack of immune activation in RESTV-infected MDMs contributes to lower pathogenicity by preventing the cytokine storm observed in EBOV infection. We further demonstrate that inhibition of TLR4 signaling abolishes EBOV GP-mediated NF-κB activation. This finding indicates that limiting the excessive TLR4-mediated proinflammatory response in EBOV infection should be considered as a potential supportive treatment option for EBOV disease. IMPORTANCE Emerging infectious diseases are a major public health concern, as exemplified by the recent devastating Ebola virus (EBOV) outbreak. Different ebolavirus species are associated with widely varying pathogenicity in humans, ranging from asymptomatic infections for Reston virus (RESTV) to severe disease with fatal outcomes for EBOV. In this comparative study of EBOV- and RESTV-infected human macrophages, we identified key differences in host cell responses. Consistent with previous data, EBOV infection is associated with a proinflammatory signature triggered by the surface glycoprotein (GP), which can be inhibited by blocking TLR4 signaling. In contrast, infection with RESTV failed to stimulate a strong host response in infected macrophages due to the inability of RESTV GP to stimulate TLR4. We propose that disparate proinflammatory host signatures contribute to the differences in pathogenicity reported for ebolavirus species and suggest that proinflammatory pathways represent an intriguing target for the development of novel therapeutics.\",\n \"corpus_id\": 4619931,\n \"score\": 1\n },\n {\n \"doc_id\": \"28396469\",\n \"title\": \"The Ebola outbreak, 2013-2016: old lessons for new epidemics.\",\n \"abstract\": \"Ebola virus causes a severe haemorrhagic fever in humans with high case fatality and significant epidemic potential. The 2013-2016 outbreak in West Africa was unprecedented in scale, being larger than all previous outbreaks combined, with 28 646 reported cases and 11 323 reported deaths. It was also unique in its geographical distribution and multicountry spread. It is vital that the lessons learned from the world's largest Ebola outbreak are not lost. This article aims to provide a detailed description of the evolution of the outbreak. We contextualize this outbreak in relation to previous Ebola outbreaks and outline the theories regarding its origins and emergence. The outbreak is described by country, in chronological order, including epidemiological parameters and implementation of outbreak containment strategies. We then summarize the factors that led to rapid and extensive propagation, as well as highlight the key successes, failures and lessons learned from this outbreak and the response. This article is part of the themed issue 'The 2013-2016 West African Ebola epidemic: data, decision-making and disease control'.\",\n \"corpus_id\": 8159817,\n \"score\": 1\n },\n {\n \"doc_id\": \"28539437\",\n \"title\": \"Spontaneous Mutation at Amino Acid 544 of the Ebola Virus Glycoprotein Potentiates Virus Entry and Selection in Tissue Culture.\",\n \"abstract\": \"Ebolaviruses have a surface glycoprotein (GP1,2) that is required for virus attachment and entry into cells. Mutations affecting GP1,2 functions can alter virus growth properties. We generated a recombinant vesicular stomatitis virus encoding Ebola virus Makona variant GP1,2 (rVSV-MAK-GP) and observed emergence of a T544I mutation in the Makona GP1,2 gene during tissue culture passage in certain cell lines. The T544I mutation emerged within two passages when VSV-MAK-GP was grown on Vero E6, Vero, and BS-C-1 cells but not when it was passaged on Huh7 and HepG2 cells. The mutation led to a marked increase in virus growth kinetics and conferred a robust growth advantage over wild-type rVSV-MAK-GP on Vero E6 cells. Analysis of complete viral genomes collected from patients in western Africa indicated that this mutation was not found in Ebola virus clinical samples. However, we observed the emergence of T544I during serial passage of various Ebola Makona isolates on Vero E6 cells. Three independent isolates showed emergence of T544I from undetectable levels in nonpassaged virus or virus passaged once to frequencies of greater than 60% within a single passage, consistent with it being a tissue culture adaptation. Intriguingly, T544I is not found in any Sudan, Bundibugyo, or Tai Forest ebolavirus sequences. Furthermore, T544I did not emerge when we serially passaged recombinant VSV encoding GP1,2 from these ebolaviruses. This report provides experimental evidence that the spontaneous mutation T544I is a tissue culture adaptation in certain cell lines and that it may be unique for the species Zaire ebolavirusIMPORTANCE The Ebola virus (Zaire) species is the most lethal species of all ebolaviruses in terms of mortality rate and number of deaths. Understanding how the Ebola virus surface glycoprotein functions to facilitate entry in cells is an area of intense research. Recently, three groups independently identified a polymorphism in the Ebola glycoprotein (I544) that enhanced virus entry, but they did not agree in their conclusions regarding its impact on pathogenesis. Our findings here address the origins of this polymorphism and provide experimental evidence showing that it is the result of a spontaneous mutation (T544I) specific to tissue culture conditions, suggesting that it has no role in pathogenesis. We further show that this mutation may be unique to the species Zaire ebolavirus, as it does not occur in Sudan, Bundibugyo, and Tai Forest ebolaviruses. Understanding the mechanism behind this mutation can provide insight into functional differences that exist in culture conditions and among ebolavirus glycoproteins.\",\n \"corpus_id\": 4529248,\n \"score\": 1\n },\n {\n \"doc_id\": \"28573607\",\n \"title\": \"Marburg- and Ebolaviruses: A Look Back and Lessons for the Future.\",\n \"abstract\": \"Since the discovery of Marburg virus 50 years ago, filoviruses have reemerged in the human population more than 40 times. Already the first episode was as dramatic as most of the subsequent ones, but none of them was as devastating as the West-African Ebola virus outbreak in 2013-2015. Although progress toward a better understanding of the viruses is impressive, there is clearly a need to improve and strengthen the measures to detect and control these deadly infections.\",\n \"corpus_id\": 3790352,\n \"score\": 1\n },\n {\n \"doc_id\": \"28812539\",\n \"title\": \"Investigating Ebola virus pathogenicity using molecular dynamics.\",\n \"abstract\": \"BACKGROUND: Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. RESULTS: As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. CONCLUSION: Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.\",\n \"corpus_id\": 4378814,\n \"score\": 1\n },\n {\n \"doc_id\": \"29140409\",\n \"title\": \"Ebolavirus interferon antagonists-protein interaction perspectives to combat pathogenesis.\",\n \"abstract\": \"Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories. As an alternative, computational techniques have also been adopted to improve the success rate of drug discovery. This article elaborates on the interactions between viral and human IFN proteins that lead to IFN antagonism. A computational framework is proposed after evaluating existing computational studies. This protein interaction and protein design-based computational framework identified critical interacting residues of the VP (VP24) responsible for the formation of a stable complex with the human KPNA5 (karyopherin alpha proteins 5). The mutations of those critical residues, as demonstrated in this article, affected the overall stability of the complex because of a sharp decrease in both the number of hydrogen bonds and possible charge-charge interactions. Therefore, we proposed that the framework could be an effective alternative to experimental work for destabilizing interactions between the VPs and human proteins responsible for IFN induction and response.\",\n \"corpus_id\": 206335112,\n \"score\": 1\n },\n {\n \"doc_id\": \"18487121\",\n \"title\": \"Something old, something new.\",\n \"abstract\": \"Some thoughts on the development of theoretical fluid dynamics in this century and some reflections on the developments of the past century were provided as an introduction to a broad-ranging conference. A written synopsis of these remarks is provided here.\",\n \"corpus_id\": 43643881,\n \"score\": 0\n },\n {\n \"doc_id\": \"18729235\",\n \"title\": \"Oncogenesis by retroviruses: old and new paradigms.\",\n \"abstract\": \"Retroviruses are associated with a variety of diseases including an array of malignancies, immunodeficiencies and neurological disorders. In particular, studies of oncogenic retroviruses established fundamental principles of modern molecular cancer biology. Studies of avian Rous sarcoma virus (RSV) led to the discovery of the viral oncogene src, and this was followed by the discovery of other viral oncogenes in retroviruses of mammals including rodents, cats, monkeys and so forth. Studies of the viral oncogenes in turn led to the discovery of cellular proto-oncogenes in the host genome; cellular oncogenes have been shown to be activated in a variety of human cancers, including those with no viral involvement. Oncogenic animal retroviruses can be divided into two groups based on their mechanisms of tumourigenesis, acute transforming retroviruses and nonacute retroviruses. Acute transforming retroviruses are typically replication defective and they induce tumours rapidly due to expression of their viral oncogenes. Nonacute retroviruses are replication competent and they induce tumours with longer latencies, by activating cellular proto-oncogenes in the tumour cells; this results from insertion of proviral DNA in the vicinity of the activated proto-oncogene. More recently, human T-cell leukaemia virus type I (HTLV-I) was discovered as an etiological agent of human cancer (adult T-cell leukaemia [ATL]); this virus also encodes regulatory genes some of which are important for its oncogenic potential. Most recently, the retroviral structural protein Envelope (Env) has been shown to be directly involved in oncogenic transformation for certain retroviruses. Env-induced transformation is a new paradigm for retroviral oncogenesis. In this review, we will summarise research on retrovirus oncogenic transformation over the past 100 years since the first published report of an oncogenic virus with particular attention to Env-induced transformation.\",\n \"corpus_id\": 24766664,\n \"score\": 0\n },\n {\n \"doc_id\": \"18849653\",\n \"title\": \"Old proteins, developing roles: The regulation of calcium channels by synaptic proteins.\",\n \"abstract\": \"Coupling of presynaptic voltage-gated calcium channels to the synaptic release machinery is critical for neurotransmission. It was traditionally believed that anchoring calcium channels close to the calcium microdomain dependent release machinery was the main reason for the physical interactions between channels and synaptic proteins, however in recent years, it is becoming clear that these proteins additionally regulate channel activity, and such processes as channel targeting and alternative splicing, to orchestrate a much broader regulatory role in controlling calcium channel function, calcium influx and hence neurotransmission. Calcium signalling serves a multitude of cellular functions and therefore requires tight regulation. Specific, often calcium-dependent interactions between synaptic proteins and calcium channels appear to play a significant role in fine-tuning of the synaptic response over development. While it is clear that investigation of a few of the multitude of synaptic proteins will not provide a complete understanding of calcium channel regulation, consideration of the emerging mechanisms by which synaptic protein interactions might regulate calcium channel function is important in order to understand their possible contributions to synaptic transmission. Here, we review the current state of knowledge of the molecular mechanisms by which synaptic proteins regulate presynaptic calcium channel activity.\",\n \"corpus_id\": 11374601,\n \"score\": 0\n },\n {\n \"doc_id\": \"19527723\",\n \"title\": \"Physiological responses to protein aggregates: fibrinolysis, coagulation and inflammation (new roles for old factors).\",\n \"abstract\": \"Misfolding is an inherent and potentially problematic propensity of proteins. Misfolded proteins tend to aggregate and the deposition of aggregated proteins is associated with a variety of highly debilitating diseases known as amyloidoses. Protein misfolding and aggregation is also increasingly recognized as the underlying cause of other health problems, including atherosclerosis and immunogenicity of biopharmaceuticals. This raises the question how nature deals with the removal of obsolete proteins in order to avoid their accumulation and disease. In recent years two proteases, tPA and factor XII, have been identified that specifically recognize aggregates of misfolded proteins. We here review these discoveries that have uncovered new roles for the fibrinolytic system and the contact activation system beyond haemostasis.\",\n \"corpus_id\": 207561992,\n \"score\": 0\n },\n {\n \"doc_id\": \"20074144\",\n \"title\": \"Flavonoids: new roles for old molecules.\",\n \"abstract\": \"Flavonoids are ubiquitous in the plant kingdom and have many diverse functions including defense, UV protection, auxin transport inhibition, allelopathy, and flower coloring. Interestingly, these compounds also have considerable biological activity in plant, animal and bacterial systems - such broad activity is accomplished by few compounds. Yet, for all the research over the last three decades, many of the cellular targets of these secondary metabolites are unknown. The many mutants available in model plant species such as Arabidopsis thaliana and Medicago truncatula are enabling the intricacies of the physiology of these compounds to be deduced. In the present review, we cover recent advances in flavonoid research, discuss deficiencies in our understanding of the physiological processes, and suggest approaches to identify the cellular targets of flavonoids.\",\n \"corpus_id\": 205903893,\n \"score\": 0\n },\n {\n \"doc_id\": \"20842205\",\n \"title\": \"Clarifying the role of G protein signaling in HIV infection: new approaches to an old question.\",\n \"abstract\": \"Whether or not HIV gp120-elicited signal transduction through the coreceptors CCR5 and CXCR4 is required for productive viral replication has long been a subject of controversy. The complexity and diversity of G protein signal transduction initiated by chemokine receptor activation has hindered efforts to understand the contributions of these pathways to the HIV life cycle. Several recent studies have demonstrated an important role for G proteins in mediating signaling events through both CCR5 and CXCR4 that are necessary for productive HIV infection. In addition to gp120-mediated G protein activation, there is still much to learn about the impact of G protein signaling during HIV infection, including the role of T-cell receptor/CXCR4 cross-talk, regulation of G protein expression during infection and the contribution of G protein subunit genetic polymorphisms to disease progression. This review will describe the effects of G protein signaling in immune cells, summarize the current understanding of CCR5 and CXCR4-initiated signal transduction in HIV replication, and discuss important gaps that still remain in our understanding of G protein signaling and its contribution to HIV pathogenesis.\",\n \"corpus_id\": 45736224,\n \"score\": 0\n },\n {\n \"doc_id\": \"21478633\",\n \"title\": \"New targets for old hormones: inhibins clinical role revisited.\",\n \"abstract\": \"Inhibins are gonadal peptide hormones belonging to the transforming growth factor-β (TGF-β) superfamily that regulate the pituitary follicle stimulating hormone (FSH) secretion by negative feedback mechanisms. It is evident that the understanding of inhibins function in the hypothalamic-pituitary-gonadal axis will provide insights into physiology and pathology of the gonadal function. In recent years, a great deal of attention has been focussed on clinical relevance of measuring circulating inhibins in normal and disease state. The past few years also have witnessed the emergence and discovery of extra pituitary action of inhibins that might provide further insights into the underlying diseases like cancer especially in the reproductive axis and various other new endocrine target organs. In this review after systematic analysis of literature, we discuss briefly the known and recent advances in function of these hormones highlighting also its structure, production and mechanisms of signal transduction. Also this review discusses about the physiological relevance of inhibin association in the normal function to the development of reproductive cancers. Finally, we describe evidence from various emerging studies that inhibins make an important contribution to other physiological functions apart from reproduction which reveals new endocrine target organs of inhibins. The emerging view is inhibin participates in multiple ways to regulate the function in different cell types and still complete repertoire of its actions is under investigation.\",\n \"corpus_id\": 7879977,\n \"score\": 0\n },\n {\n \"doc_id\": \"21607083\",\n \"title\": \"AMPylation: Something Old is New Again.\",\n \"abstract\": \"The post-translational modification AMPylation is emerging as a significant regulatory mechanism in both prokaryotic and eukaryotic biology. This process involves the covalent addition of an adenosine monophosphate to a protein resulting in a modified protein with altered activity. Proteins capable of catalyzing AMPylation, termed AMPylators, are comparable to kinases in that they both hydrolyze ATP and reversibly transfer a part of this primary metabolite to a hydroxyl side chain of the protein substrate. To date, only four AMPylators have been characterized, though many more potential candidates have been identified through amino acid sequence analysis and preliminary in vitro studies. This modification was first discovered over 40 years ago by Earl Stadtman and colleagues through the modification of glutamine synthetase by adenylyl transferase; however research into this mechanism has only just been reenergized by the studies on bacterial effectors. New AMPylators were revealed due to the discovery that a bacterial effector having a conserved Fic domain transfers an AMP group to protein substrates. Current research focuses on identifying and characterizing various types of AMPylators homologous to Fic domains and adenylyl transferase domains and their respective substrates. While all AMPylators characterized thus far are bacterial proteins, the conservation of the Fic domain in eukaryotic organisms suggests that AMPylation is omnipresent in various forms of life and has significant impact on a wide range of regulatory processes.\",\n \"corpus_id\": 2274552,\n \"score\": 0\n },\n {\n \"doc_id\": \"21976651\",\n \"title\": \"Microvesicles and viral infection.\",\n \"abstract\": \"Cells secrete various membrane-enclosed microvesicles from their cell surface (shedding microvesicles) and from internal, endosome-derived membranes (exosomes). Intriguingly, these vesicles have many characteristics in common with enveloped viruses, including biophysical properties, biogenesis, and uptake by cells. Recent discoveries describing the microvesicle-mediated intercellular transfer of functional cellular proteins, RNAs, and mRNAs have revealed additional similarities between viruses and cellular microvesicles. Apparent differences include the complexity of viral entry, temporally regulated viral expression, and self-replication proceeding to infection of new cells. Interestingly, many virally infected cells secrete microvesicles that differ in content from their virion counterparts but may contain various viral proteins and RNAs. For the most part, these particles have not been analyzed for their content or functions during viral infection. However, early studies of microvesicles (L-particles) secreted from herpes simplex virus-infected cells provided the first evidence of microvesicle-mediated intercellular communication. In the case of Epstein-Barr virus, recent evidence suggests that this tumorigenic herpesvirus also utilizes exosomes as a mechanism of cell-to-cell communication through the transfer of signaling competent proteins and functional microRNAs to uninfected cells. This review focuses on aspects of the biology of microvesicles with an emphasis on their potential contributions to viral infection and pathogenesis.\",\n \"corpus_id\": 24866739,\n \"score\": 0\n },\n {\n \"doc_id\": \"23170177\",\n \"title\": \"Uncovering viral protein-protein interactions and their role in arenavirus life cycle.\",\n \"abstract\": \"The Arenaviridae family includes widely distributed pathogens that cause severe hemorrhagic fever in humans. Replication and packaging of their single-stranded RNA genome involve RNA recognition by viral proteins and a number of key protein-protein interactions. Viral RNA synthesis is directed by the virus-encoded RNA dependent-RNA polymerase (L protein) and requires viral RNA encapsidation by the Nucleoprotein. In addition to the role that the interaction between L and the Nucleoprotein may have in the replication process, polymerase activity appears to be modulated by the association between L and the small multifunctional Z protein. Z is also a structural component of the virions that plays an essential role in viral morphogenesis. Indeed, interaction of the Z protein with the Nucleoprotein is critical for genome packaging. Furthermore, current evidence suggests that binding between Z and the viral envelope glycoprotein complex is required for virion infectivity, and that Z homo-oligomerization is an essential step for particle assembly and budding. Efforts to understand the molecular basis of arenavirus life cycle have revealed important details on these viral protein-protein interactions that will be reviewed in this article.\",\n \"corpus_id\": 2369714,\n \"score\": 0\n },\n {\n \"doc_id\": \"25125715\",\n \"title\": \"A novel T cell evasion mechanism in persistent RNA virus infection.\",\n \"abstract\": \"Hepatitis C virus (HCV) and GB virus type C (GBV-C) are associated with impaired T cell function despite the fact that HCV replicates in hepatocytes and GBV-C in a small proportion of lymphocytes. Recently, we showed that HCV and GBV-C E2-envelope proteins reduce T cell activation via the T cell receptor (TCR) by competing for phosphorylation with a critical kinase in the TCR signaling cascade (Lck). E2 interfered with TCR signaling in E2 expressing cells and in bystander cells. The bystander effect was mediated by virus particles and extracellular microvesicular particles (exosomes). Multiple kinase substrate sites are predicted to reside on viral structural proteins and based on bioinformatic predictions, many RNA virus pathogens may interfere with TCR signaling via a similar mechanism. Identification of T cell inhibitory effects of virus structural proteins may provide novel approaches to enhance the immunogenicity and memory of viral vaccines.\",\n \"corpus_id\": 30483357,\n \"score\": 0\n },\n {\n \"doc_id\": \"25206336\",\n \"title\": \"Glutathione: new roles in redox signaling for an old antioxidant.\",\n \"abstract\": \"The physiological roles played by the tripeptide glutathione have greatly advanced over the past decades superimposing the research on free radicals, oxidative stress and, more recently, redox signaling. In particular, GSH is involved in nutrient metabolism, antioxidant defense, and regulation of cellular metabolic functions ranging from gene expression, DNA and protein synthesis to signal transduction, cell proliferation and apoptosis. This review will be focused on the role of GSH in cell signaling by analysing the more recent advancements about its capability to modulate nitroxidative stress, autophagy, and viral infection.\",\n \"corpus_id\": 14294863,\n \"score\": 0\n },\n {\n \"doc_id\": \"26320628\",\n \"title\": \"Antimicrobial proteins: From old proteins, new tricks.\",\n \"abstract\": \"This review describes the main types of antimicrobial peptides (AMPs) synthesised by crustaceans, primarily those identified in shrimp, crayfish, crab and lobster. It includes an overview of their range of microbicidal activities and the current landscape of our understanding of their gene expression patterns in different body tissues. It further summarises how their expression might change following various types of immune challenges. The review further considers proteins or protein fragments from crustaceans that have antimicrobial properties but are more usually associated with other biological functions, or are derived from such proteins. It discusses how these unconventional AMPs might be generated at, or delivered to, sites of infection and how they might contribute to crustacean host defence in vivo. It also highlights recent work that is starting to reveal the extent of multi-functionality displayed by some decapod AMPs, particularly their participation in other aspects of host protection. Examples of such activities include proteinase inhibition, phagocytosis, antiviral activity and haematopoiesis.\",\n \"corpus_id\": 40012153,\n \"score\": 0\n },\n {\n \"doc_id\": \"28009816\",\n \"title\": \"The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport.\",\n \"abstract\": \"The pleiotropic serine/threonine protein kinase CK2 was the first kinase discovered. It is renowned for its role in cell proliferation and anti-apoptosis. The complexity of this kinase is well reflected by the findings of past decades in terms of its heterotetrameric structure, subcellular location, constitutive activity and the extensive catalogue of substrates. With the advent of non-biased high-throughput functional genomics such as genome-wide deletion mutant screening, novel aspects of CK2 functionality have been revealed. Our recent discoveries using the model organism Saccharomyces cerevisiae and mammalian cells demonstrate that CK2 regulates metal toxicity. Extensive literature search reveals that there are few but elegant works on the role of CK2 in regulating the sodium and zinc channels. As both CK2 and metal ions are key players in cell biology and oncogenesis, understanding the details of CK2's regulation of metal ion homeostasis has a direct bearing on cancer research. In this review, we aim to garner the recent data and gain insights into the role of CK2 in metal ion transport.\",\n \"corpus_id\": 526485,\n \"score\": 0\n },\n {\n \"doc_id\": \"29280156\",\n \"title\": \"The Many Roles of Type II Phosphatidylinositol 4-Kinases in Membrane Trafficking: New Tricks for Old Dogs.\",\n \"abstract\": \"The type II phosphatidylinositol 4-kinases (PI4KIIs) produce the lipid phosphatidylinositol 4-phosphate (PtdIns4P) and participate in a confusing variety of membrane trafficking and signaling roles. This review argues that both historical and contemporary evidence supports the function of the PI4KIIs in numerous trafficking pathways, and that the key to understanding the enzymatic regulation is through membrane interaction and the intrinsic membrane environment. By summarizing new research and examining the trafficking roles of the PI4KIIs in the context of recently solved molecular structures, I highlight how mechanisms of PI4KII function and regulation are providing insights into the development of cancer and in neurological disease. I present an integrated view connecting the cell biology, molecular regulation, and roles in whole animal systems of these increasingly important proteins.\",\n \"corpus_id\": 33556894,\n \"score\": 0\n },\n {\n \"doc_id\": \"29307596\",\n \"title\": \"An \\\"Old\\\" protein with a new story: Coronavirus endoribonuclease is important for evading host antiviral defenses.\",\n \"abstract\": \"Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses.\",\n \"corpus_id\": 4874123,\n \"score\": 0\n },\n {\n \"doc_id\": \"29514907\",\n \"title\": \"Distinct Immunogenicity and Efficacy of Poxvirus-Based Vaccine Candidates against Ebola Virus Expressing GP and VP40 Proteins.\",\n \"abstract\": \"Zaire and Sudan ebolavirus species cause a severe disease in humans and nonhuman primates (NHPs) characterized by a high mortality rate. There are no licensed therapies or vaccines against Ebola virus disease (EVD), and the recent 2013 to 2016 outbreak in West Africa highlighted the need for EVD-specific medical countermeasures. Here, we generated and characterized head-to-head the immunogenicity and efficacy of five vaccine candidates against Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV) based on the highly attenuated poxvirus vector modified vaccinia virus Ankara (MVA) expressing either the virus glycoprotein (GP) or GP together with the virus protein 40 (VP40) forming virus-like particles (VLPs). In a human monocytic cell line, the different MVA vectors (termed MVA-EBOVs and MVA-SUDVs) triggered robust innate immune responses, with production of beta interferon (IFN-β), proinflammatory cytokines, and chemokines. Additionally, several innate immune cells, such as dendritic cells, neutrophils, and natural killer cells, were differentially recruited in the peritoneal cavity of mice inoculated with MVA-EBOVs. After immunization of mice with a homologous prime/boost protocol (MVA/MVA), total IgG antibodies against GP or VP40 from Zaire and Sudan ebolavirus were differentially induced by these vectors, which were mainly of the IgG1 and IgG3 isotypes. Remarkably, an MVA-EBOV construct coexpressing GP and VP40 protected chimeric mice challenged with EBOV to a greater extent than a vector expressing GP alone. These results support the consideration of MVA-EBOVs and MVA-SUDVs expressing GP and VP40 and producing VLPs as best-in-class potential vaccine candidates against EBOV and SUDV.IMPORTANCE EBOV and SUDV cause a severe hemorrhagic fever affecting humans and NHPs. Since their discovery in 1976, they have caused several sporadic epidemics, with the recent outbreak in West Africa from 2013 to 2016 being the largest and most severe, with more than 11,000 deaths being reported. Although some vaccines are in advanced clinical phases, less expensive, safer, and more effective licensed vaccines are desirable. We generated and characterized head-to-head the immunogenicity and efficacy of five novel vaccines against EBOV and SUDV based on the poxvirus MVA expressing GP or GP and VP40. The expression of GP and VP40 leads to the formation of VLPs. These MVA-EBOV and MVA-SUDV recombinants triggered robust innate and humoral immune responses in mice. Furthermore, MVA-EBOV recombinants expressing GP and VP40 induced high protection against EBOV in a mouse challenge model. Thus, MVA expressing GP and VP40 and producing VLPs is a promising vaccine candidate against EBOV and SUDV.\",\n \"corpus_id\": 3781897,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":64,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29715316\",\n \"title\": \"Useful field of view test performance throughout adulthood in subjects without ocular disorders.\",\n \"abstract\": \"Previous research has shown an age-related decline in Useful Field of View (UFOV) test performance, which measures the duration required to extract relevant information from a scene in three subtasks. However, these results are mostly based on data that may have been confounded by (age-related) ocular diseases. We examined UFOV performance in subjects aged 19.5 to 70.3 years to investigate how UFOV performance changes throughout adulthood. All subjects underwent a thorough ophthalmological examination to exclude ocular disorders. We also examined some elementary visual functions, i.e., near and far visual acuity, crowding and contrast sensitivity. We investigated whether these functions were related to age and whether they could explain a possible age-related decline in UFOV performance. The subjects (n = 41) performed very well on almost every measure and reached far better UFOV and visual acuity scores than those reported by other studies that relied on self-reported absence of ocular pathology. We did not find significant relationships between age and any of the elementary visual functions or the first two UFOV subtasks (R2UFOV1 = 0.03, p = 0.25; R2UFOV2 = 0.07, p = 0.10). However, we found an age-related decline in performance on the third UFOV subtask (R2UFOV3 = 0.36, p < 0.001), which was unrelated to performance on the elementary visual function tasks. Our results show that performance on the first two UFOV subtasks as well as central elementary visual functions may remain high in the absence of obvious ophthalmological pathology.\",\n \"corpus_id\": 13705773\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19140660","title":"What predicts changes in useful field of view test performance?","abstract":"The Useful Field of View Test (UFOV) has been used as an examination of age-related changes in visual processing and cognition and as an indicator of everyday performance outcomes, particularly driving, for over 20 years. How UFOV performance changes with age and what may impact such changes have not previously been investigated longitudinally. Predictors of change in UFOV performance over a 5-year period among control group participants (N=690) from the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) study were examined. Random effects models were estimated with 4-subtest-total UFOV as the outcome and with baseline age, education, gender, race, visual acuity, depressive symptoms, mental status, and self-rated health, as well as attrition, as predictors. UFOV performance generally followed a curvilinear pattern, improving and then declining over time. Only increased age was consistently related to greater declines in UFOV performance over time. UFOV and Digit Symbol Substitution subtest, a standard measure of cognitive speed, had similar trajectories of change. The implications of these results are discussed.","corpus_id":38937595,"score":2},{"doc_id":"22048613","title":"Impaired attentional disengagement in older adults with useful field of view decline.","abstract":"OBJECTIVES: Typical measures of the useful field of view (UFOV) involve many components of attention. The objective of the current research was to examine the attentional operations that might underlie declines in the UFOV. METHOD AND RESULTS: We used 2 basic attention tasks to characterize the profile of visual attention in UFOV-impaired and -unimpaired observers. Our results suggested that declines in the UFOV result from a deficit in attentional disengagement, not a decrease in attentional breadth or scope. DISCUSSION: The results suggested that UFOV decline in normal aging can be associated with a specific attentional operation, namely attentional disengagement. These results suggest that the underlying cause of UFOV decline may not be a restriction in the breadth or scope of attention. Because the UFOV is a reliable predictor of driving safety, our results point to attentional components that are critical for the visual behavior of older adults.","corpus_id":14147187,"score":2},{"doc_id":"22830667","title":"Visual search for features and conjunctions following declines in the useful field of view.","abstract":"UNLABELLED: BACKGROUND/STUDY CONTEXT: Typical measures for assessing the useful field (UFOV) of view involve many components of attention. The objective of the current experiment was to examine differences in visual search efficiency for older individuals with and without UFOV impairment. METHODS: The authors used a computerized screening instrument to assess the useful field of view and to characterize participants as having an impaired or normal UFOV. Participants also performed two visual search tasks, a feature search (e.g., search for a green target among red distractors) or a conjunction search (e.g., a green target with a gap on its left or right side among red distractors with gaps on the left or right and green distractors with gaps on the top or bottom). RESULTS: Visual search performance did not differ between UFOV impaired and unimpaired individuals when searching for a basic feature. However, search efficiency was lower for impaired individuals than unimpaired individuals when searching for a conjunction of features. CONCLUSION: The results suggest that UFOV decline in normal aging is associated with conjunction search. This finding suggests that the underlying cause of UFOV decline may arise from an overall decline in attentional efficiency. Because the useful field of view is a reliable predictor of driving safety, the results suggest that decline in the everyday visual behavior of older adults might arise from attentional declines.","corpus_id":17481692,"score":2},{"doc_id":"24642933","title":"Useful field of view test.","abstract":"The useful field of view test was developed to reflect the visual difficulties that older adults experience with everyday tasks. Importantly, the useful field of view test (UFOV) is one of the most extensively researched and promising predictor tests for a range of driving outcomes measures, including driving ability and crash risk as well as other everyday tasks. Currently available commercial versions of the test can be administered using personal computers; these measure the speed of visual processing for rapid detection and localization of targets under conditions of divided visual attention and in the presence and absence of visual clutter. The test is believed to assess higher-order cognitive abilities, but performance also relies on visual sensory function because in order for targets to be attended to, they must be visible. The format of the UFOV has been modified over the years; the original version estimated the spatial extent of useful field of view, while the latest version measures visual processing speed. While deficits in the useful field of view are associated with functional impairments in everyday activities in older adults, there is also emerging evidence from several research groups that improvements in visual processing speed can be achieved through training. These improvements have been shown to reduce crash risk, and can have a positive impact on health and functional well-being, with the potential to increase the mobility and hence the independence of older adults.","corpus_id":38955211,"score":2},{"doc_id":"24705277","title":"Cognitive and visual predictors of UFOV performance in older adults.","abstract":"Eighty two community dwelling older adults (52 females) aged 62-92 years (mean=75) completed a battery of cognitive and visual tests selected to assess functions relevant to driving performance. These were visual acuity, contrast sensitivity, general mental competence (Mini Mental State Examination, MMSE), processing speed (Inspection Time, IT), crowding across the visual field (Proficiency of Peripheral Vision Processing, ProPerVis) and change detection (DriverScan). These six tasks provided predictor variables for performance on the Useful Field of View test (UFOV), a well validated test of fitness to drive that includes subtests for (i) processing speed; (ii) divided attention; and (iii) selective attention. Relative importance regression analyses confirmed that UFOV is sensitive to attentional and speed processes but suggested that subtest (i) primarily reflects visual acuity and contrast sensitivity; subtest (ii) is better explained by change detection and processing speed; and subtest (iii) predominantly reflects crowding and contrast sensitivity. Unexpectedly, given no evidence of substantial cognitive decline, MMSE contributed significantly to performance on the more complex subtests (ii) and (iii).","corpus_id":29207146,"score":2},{"doc_id":"25976135","title":"[Principle of the useful field of view and normative data].","abstract":"Principes de réalisation du champ visuel attentionnel et élaboration de normes. PURPOSE: The useful field of view is a test which takes into account the influence of patient attention during the evaluation of the visual field. This study aims to generate normative data for an adaptation of the useful field of view (UFOV) test. These normative data are essential to judge, in a clinical setting, whether patients' performance is normal or not across demographically similar peers, in order to advise whether or not to resume driving after a brain injury (traumatic brain injury, stroke or cerebral tumour). PATIENTS AND METHODS: This study examined demographic influences on an UFOV adaptation in a sample of 52 control participants (17 males and 35 females, aged 19 to 69) with no prior ophthalmologic or neurologic history. This adaptation used three visual attention tasks. In a simple task (ST), the participant had to detect, as fast as (s)he could, a single target in a visual display; in a double task (DT,) (s)he had to detect both a central and a lateral target in a double task with visual distractions present on the screen. The number of missed targets and the time needed to detect them are measured. RESULTS: Time to detect target was found to differ by gender and by age. Men and young people (from 19 to 29 years) are faster at detecting central and lateral targets. However, no demographic influence was observed on the number of missed targets. CONCLUSIONS: A normative table for this French UFOV adaptation is provided. This will allow clinicians to compare patient performance with similar peers and may help in identifying persons who would benefit from training on a driving simulator or having a road test with a driving-school.","corpus_id":32947812,"score":2},{"doc_id":"26236026","title":"Perceptual and cognitive neural correlates of the useful field of view test in older adults.","abstract":"The Useful Field of View Test (UFOV) is often used as a behavioral assessment of age-related decline in visual perception and cognition. Poor performance may reflect slowed processing speed, difficulty dividing attention, and difficulty ignoring irrelevant information. However, the underlying neural correlates of UFOV performance have not been identified. The relationship between older adults׳ UFOV performance and event-related potential (ERP) components reflecting visual processing was examined. P1 amplitude increased with better UFOV performance involving object identification (subtest 1), suggesting that this task is associated with stimulus processing at an early perceptual level. Better performance in all UFOV subtests was associated with faster speed of processing, as reflected by decreases in P3b latency. Current evidence supports the hypothesis that the UFOV recruits both early perceptual and later cognitive processing involved in attentional control. The implications of these results are discussed.","corpus_id":3971047,"score":2},{"doc_id":"26782018","title":"Incremental validity of Useful Field of View subtests for the prediction of instrumental activities of daily living.","abstract":"INTRODUCTION: The Useful Field of View Test (UFOV®) is a cognitive measure that predicts older adults' ability to perform a range of everyday activities. However, little is known about the individual contribution of each subtest to these predictions, and the underlying constructs of UFOV performance remain a topic of debate. METHOD: We investigated the incremental validity of UFOV subtests for the prediction of Instrumental Activities of Daily Living (IADL) performance in two independent datasets, the SKILL (n = 828) and ACTIVE (n = 2426) studies. We then explored the cognitive and visual abilities assessed by UFOV using a range of neuropsychological and vision tests administered in the SKILL study. RESULTS: In the four subtest variant of UFOV, only Subtests 2 and 3 consistently made independent contributions to the prediction of IADL performance across three different behavioral measures. In all cases, the incremental validity of UFOV Subtests 1 and 4 was negligible. Furthermore, we found that UFOV was related to processing speed, general nonspeeded cognition, and visual function; the omission of Subtests 1 and 4 from the test score did not affect these associations. CONCLUSIONS: UFOV Subtests 1 and 4 appear to be of limited use to predict IADL and possibly other everyday activities. Future research should investigate whether shortening UFOV by omitting these subtests is a reliable and valid assessment approach.","corpus_id":24804625,"score":2},{"doc_id":"26808364","title":"Relationship between Functional Visual Acuity and Useful Field of View in Elderly Drivers.","abstract":"PURPOSE: To investigate the relationship between the functional visual acuity (FVA) and useful field of view (UFOV) in elderly drivers and assess the usefulness of the FVA test to screen driving aptitude in elderly drivers. METHODS: This study included 45 elderly drivers (31 men, 14 women; mean age, 68.1 years) and 30 younger drivers (26 men, 4 women; mean age, 34.2 years) who drive regularly. All participants underwent measurement of the binocular corrected distant visual acuity (CDVA), binocular corrected distant FVA (CDFVA), and Visual Field with Inhibitory Tasks Elderly Version (VFIT-EV) to measure UFOV. The tear function and cognitive status also were evaluated. RESULTS: The CDVA, the CDFVA, cognitive status, and the correct response rate (CAR) of the VFIT-EV were significantly worse in the elderly group than in the control group (P = 0.000 for all parameters). The cognitive status was correlated significantly with the CDVA (r = -0.301, P = 0.009), CDFVA (r = -0.402, P = 0.000), and the CAR of the VFIT-EV (r = 0.348, P = 0.002) in all subjects. The results of the tear function tests were not correlated with the CDVA, CDFVA, or VFIT-EV in any subjects. Stepwise regression analysis for all subjects in the elderly and control groups showed that the CDFVA predicted the CAR most significantly among the clinical factors evaluated. CONCLUSION: The FVA test is a promising method to screen the driving aptitude, including both visual and cognitive functions, in a short time.","corpus_id":16380182,"score":2},{"doc_id":"29270605","title":"A meta-analysis of perceptual and cognitive functions involved in useful-field-of-view test performance.","abstract":"The useful-field-of-view (UFOV) test measures the amount of information someone can extract from a visual scene in one glance. Its scores show relatively strong relationships with everyday activities. The UFOV test consists of three computer tests, suggested to measure processing speed and central vision, divided attention, and selective attention. However, other functions seem to be involved as well. In order to investigate the contribution of these suggested and other perceptual and cognitive functions, we performed a meta-analysis of 116 Pearson's correlation coefficients between UFOV scores and other test scores reported in 18 peer-reviewed articles. We divided these correlations into nine domains: attention, executive functioning, general cognition, memory, spatial ability, visual closure, contrast sensitivity, visual processing speed, and visual acuity. A multivariate mixed-effects model analysis revealed that each domain correlated significantly with each of the UFOV subtest scores. These correlations were stronger for Subtests 2 and 3 than for Subtest 1. Furthermore, some domains were more strongly correlated to the UFOV than others across subtests. We did not find interaction effects between subtest and domain, indicating that none of the UFOV subtests is more selectively sensitive to a particular domain than the others. Thus, none of the three UFOV subtests seem to measure one clear construct. Instead, a range of visual and cognitive functions is involved. Perhaps this is the reason for the UFOV's high ecological validity, as it involves many functions at once, making it harder to compensate if one of them fails.","corpus_id":114413,"score":2},{"doc_id":"17962396","title":"Assessing visual fields for driving in patients with paracentral scotomata.","abstract":"BACKGROUND: The binocular Esterman visual field test (EVFT) is the current visual field test for driving in the UK. Merging of monocular field tests (Integrated Visual Field, IVF) has been proposed as an alternative for glaucoma patients. AIMS: To examine the level of agreement between the EVFT and IVF for patients with binocular paracentral scotomata, caused by either ophthalmological or neurological conditions, and to compare outcomes with useful field of view (UFOV) performance, a test of visual attention thought to be important in driving. METHODS: 60 patients with binocular paracentral scotomata but normal visual acuity (VA) were recruited prospectively. Subjects completed and were classified as \"pass\" or \"fail\" for the EVFT, IVF and UFOV. RESULTS: Good agreement occurred between the EVFT and IVF in classifying subjects as \"pass\" or \"fail\" (kappa = 0.84). Classifications disagreed for four subjects with paracentral scotomata of neurological origin (three \"passed\" IVF yet \"failed\" EVFT). Mean UFOV scores did not differ between those who \"passed\" and those who \"failed\" both visual field tests (p = 0.11). Agreement between the visual field tests and UFOV was limited (EVFT kappa = 0.22, IVF kappa 0.32). CONCLUSIONS: Although the IVF and EVFT agree well in classifying visual fields with regard to legal fitness to drive in the UK, the IVF \"passes\" some individuals currently classed as unfit to drive due to paracentral scotomata of non-glaucomatous origin. The suitability of the UFOV for assessing crash risk in those with visual field loss is questionable.","corpus_id":9887632,"score":1},{"doc_id":"18081908","title":"Effect of driver distraction and low alcohol concentrations on useful field of view and frequency-doubling technology perimetry.","abstract":"PURPOSE: To investigate the effects of a mental psychometric task that simulates the distraction effect of a hands-free mobile phone and of low alcohol concentrations (0.3-0.5 g/l) on two tests: the useful field of view (UFOV) and frequency-doubling technology (FDT) perimetry. METHODS: Thirty-seven healthy young vehicle drivers aged 22 +/- 3 years were subjected to a computer version of the UFOV test and FDT perimetry, undertaken according to a counterbalanced within-subject design. The tests were performed in two sessions (an 'alcohol session' and a 'sober session'), while undertaking or not undertaking a psychometric test [the Paced Auditory Serial Addition Test (PASAT)] to simulate the effect of distraction. Each subject was instructed to concentrate on the PASAT while taking each test. RESULTS: UFOV scores were affected when the PASAT was performed simultaneously (P < 0.0001) in that longer times were required to identify a central target and the location of a peripheral target. FDT perimetry was affected by the addition of the PASAT, with a significant reduction in mean sensitivity and a localized sensitivity loss [pattern standard deviation (PSD) >6 dB]. Test times, false-positive and negative catch trial responses were all increased. However, the UFOV test and FDT perimetry results were not significantly affected by a low alcohol concentration. CONCLUSION: Distraction significantly affects performance in the UFOV test and frequency-doubling technology perimetry. Our findings suggest that using a hands-free mobile phone while driving may lead to a low-to-moderate crash risk in young adults with normal visual function.","corpus_id":20846986,"score":1},{"doc_id":"18307055","title":"[Evaluation of the capacity to drive in patients diagnosed of mild cognitive impairment and dementia].","abstract":"Valoración de la capacidad de conducción de vehículos en pacientes con diagnóstico de deterioro cognitivo leve y demencia. INTRODUCTION: Mild cognitive impairment (MCI) and dementia involve cognitive changes that may influence driving capacity. OBJECTIVES: a) To study if the tests used for renewing the driver's licence are appropriate; b) to study the MCI patient's driving capacity according to ASDE Driver-Test and Useful Field of View (UFOV) test; c) to study mild dementia (MD) patient's driving capacity according to ASDE and UFOV tests; d) to determine which neuropsychological tests may be useful to make decisions on driving capacity in MCI and MD; e) to study the difference in the evaluation of each neuropsychological test between patients who are able to drive and those who are not, in each MCI subgroups, and f) we will establish the correlation between the neuropsychological tests and driving tests used for licence renewal. METHOD: A total of 184 people were included: 92 MCI, 55 MD and 40 healthy controls. Cognitive functioning was evaluated by Repeatable Battery Assessment for Neuropsychological Status (RBANS), Trail Making Test (TMT) and Kohs' Block Design. Driving capacity was assessed by ASDE and UFOV test. RESULTS: We established the cut-off points for ASDE and UFOV tests. Sensitivity and specificity for the MD on the ASDE test was 86% and 95%, respectively for concentrated attention and monotony resistance subtest. The UFOV test sensitivity was 88%, specificity 81%. For MCI, both tests showed a sensitivity and specificity lower than 70 %. According to the performance on the test only a half of the MCI group could drive. They showed different driving profiles according to MCI subtype. Neuropsychological tests showing the best correlations with performance on driving test were: Kohs' Block Design, Immediate Memory, Delayed Memory and TMT-A. CONCLUSIONS: a) People with MD should not drive; b) both ASDE and UFOV tests can detect driving difficulties in people with dementia; c) according to the UFOV and ASDE, half of those diagnosed of MCI should not drive; d) there are significant differences in memory test (RBANS) between Amnesic MCI patients who are able to drive and those who are not (according to ASDE/UFOV tests); e) there are significant differences in TMT-A between multiple functions MCI patients who are able to drive and those who are not (according to ASDE/UFOV tests), and f) the neuropsychological tests that correlate with the driving test were: Kohs' Block Design, Immediate Memory, Delayed Memory and TMT-A.","corpus_id":26038109,"score":1},{"doc_id":"18808255","title":"Cognition, but not sensation, mediates age-related changes in the ability to monitor the environment.","abstract":"The objective of the study was to determine which age-related changes in sensation and cognition are associated with age-related changes in the ability to monitor the environment. To that end, a proxy measure of the ability to monitor the environment (useful field of view, UFOV) and measures of sensation and cognition were collected from young adult (N = 61) and older adult subjects (N = 79). Although UFOV performance was expected to be mediated primarily by cognition rather than by sensation, it was somewhat unexpected to find no reliable associations between UFOV and sensory functioning beyond those of age and cognition.","corpus_id":7526694,"score":1},{"doc_id":"19280448","title":"The effects of chemotherapy on Useful Field of View (UFOV) in younger and older breast cancer patients.","abstract":"Chemotherapy is thought to cause cognitive deficits in some breast cancer patients, but the relative effects on older and younger breast cancer patients are unknown. The effects of chemotherapy on everyday cognitive tasks have not been examined. Thirty-eight female breast cancer survivors (3 to 45 months post chemotherapy) were compared to 55 age-matched control participants. Participants completed the Useful Field of View (UFOV), a computerized test of visual information processing that has been shown to decline with age, and which has been used to predict older adults' driving performance. Older chemotherapy patients performed more poorly than controls on the UFOV speed of processing, but not on the other two components. They also performed more poorly than younger chemotherapy patients. On the divided attention and selective attention components of the UFOV, older participants performed more poorly than younger participants, but there were no significant differences between chemotherapy patients and controls. These findings are explained in terms of brain changes thought to be caused by chemotherapy, which might have the most impact on older adults, already at risk for behavioral slowing.","corpus_id":23286679,"score":1},{"doc_id":"19369744","title":"Comparing visual performance and useful field of view of older and younger drivers - biomed 2009.","abstract":"Older licensed drivers are involved in more crash deaths than any other age group. A critical issue in reducing these accident numbers is to improve our understanding of the association between the visual performance of these older drivers and their useful field of view (UFOV) when driving. We estimated driver saccadic amplitudes and fixation durations for ten different traffic scenarios using a driving simulator. Six traffic situations presented dangerous or other relevant events to the drivers, with the other four having no dangerous or relevant events. To estimate saccadic amplitudes and fixation durations, eye position data was analyzed during the five seconds before and five seconds after the traffic situations. Results imply that eye movements, fixation durations and number of fixation change as a function of the visual stimuli presented in each traffic situation. The difference in age was found to be significant for number of fixations and fixation time, but not for the total eye movement. Based on these results, we expressed UFOV as a function of saccadic amplitude between fixation points and durations, and estimated the ranges of a sequence UFOVs during the 10-second period for each traffic situation. Our findings suggests that UFOV radius depends on driving scenario, time of event, age-group, driving course, two factor and three-factor interactions among these variables.","corpus_id":21615848,"score":1},{"doc_id":"19417701","title":"The useful field of view test, normative data in children of school age.","abstract":"PURPOSE: The incidence of early brain injury in children is rising, mainly because of changing reproductive demographics and better perinatal care. Early brain injury may be associated with altered visual perception and visuospatial attention. The useful field of view test (UFOV) has been developed to assess visual attention and processing speed in the elderly. The UFOV may have utility in the evaluation of children with early brain injury. The aim of this study was to collect age-specific normative data for the UFOV test. METHODS: Subjects were recruited from visitors at Glasgow Science Centre. One hundred thirty-five healthy children and young adults were tested (range: 5-22 years). After a comprehensive visual screening to establish normal visual function, all three subtests of the UFOV (1: Processing Speed; 2: Divided Attention; 3: Selective Attention) were performed. RESULTS.: All the children were able to understand and complete all subtests. UFOV scores improved monotonically with age, for all subtests, throughout the primary school years, with subtest 3 showing the greatest improvement. By age 14, UFOV scores had reached adult levels. DISCUSSION: UFOV performance shows measurable improvement during middle to late childhood, as has been previously found for abilities such as visual acuity. This is a simple test, which was easily understood and performed by all children in the study. Thus, we believe that our results are suggestive of continuing development in visual attention and processing during this period. CONCLUSIONS: The UFOV is an objective, standardized computer-based test of visual attention. This study indicates suitability for use with children. It remains to be determined how successful this test proves to be in discriminating between normal children and those with early brain injury.","corpus_id":205907637,"score":1},{"doc_id":"19462009","title":"Is visual selective attention in deaf individuals enhanced or deficient? The case of the useful field of view.","abstract":"BACKGROUND: Early deafness leads to enhanced attention in the visual periphery. Yet, whether this enhancement confers advantages in everyday life remains unknown, as deaf individuals have been shown to be more distracted by irrelevant information in the periphery than their hearing peers. Here, we show that, in a complex attentional task, a performance advantage results for deaf individuals. METHODOLOGY/PRINCIPAL FINDINGS: We employed the Useful Field of View (UFOV) which requires central target identification concurrent with peripheral target localization in the presence of distractors - a divided, selective attention task. First, the comparison of deaf and hearing adults with or without sign language skills establishes that deafness and not sign language use drives UFOV enhancement. Second, UFOV performance was enhanced in deaf children, but only after 11 years of age. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that, following early auditory deprivation, visual attention resources toward the periphery slowly get augmented to eventually result in a clear behavioral advantage by pre-adolescence on a selective visual attention task.","corpus_id":210343,"score":1},{"doc_id":"19916131","title":"Useful field of view as a reliable screening measure of driving performance in people with Parkinson's disease: results of a pilot study.","abstract":"PURPOSE: To determine the correlations of the Useful Field of View (UFOV), compared to other clinical tests of Parkinson's disease (PD); vision; and cognition with measures of on-road driving assessments and to quantify the UFOV's ability to indicate passing/failing an on-road test in people with PD. METHODS: Nineteen randomly selected people with idiopathic PD, mean age = 74.8 (6.1), 14 (73.7%) men, 18 (94.7%) Caucasians, were age-matched to 104 controls without PD. The controls had a mean age of 75.4 (6.4), 59 (56.7%) men, 96 (92.3%) Caucasians. Both groups were referred for a driving evaluation after institutional review board approval. RESULTS: Compared to neuropsychological and clinical tests of vision and cognition, the UFOV showed the strongest correlations (r > .75, p < 0.05) with measures of failing a standardized road test and number of driving errors. Among PD patients, the UFOV Risk Index score of 3 (range 1-5) was established as the optimal cutoff value for passing the on-road test, with sensitivity 87 percent and specificity 82 percent, AUC = 92 percent (SE 0.61, p = .002). Similarly, the UFOV 2 (divided attention) optimum cutoff value is 223 ms (range 16-500 ms), sensitivity 87.5 percent, specificity 81.8 percent, AUC = 91 percent (SE 0.73, p = .003). The UFOV 3 (selected attention) optimal cutoff value is 273 ms (range 16-500 ms), sensitivity 75 percent, specificity 72.7 percent, AUC = 87 percent (SE 0.81, p = .007). CONCLUSION: In this pilot study among PD patients, the UFOV may be a superior screening measure (compared to other measures of disease, cognition, and vision) for predicting on-road driving performance but its rigor must be verified in a larger sample of people with PD.","corpus_id":24995547,"score":1},{"doc_id":"22269568","title":"The role of cognitive and visual abilities as predictors in the Multifactorial Model of Driving Safety.","abstract":"OBJECTIVE: The current study evaluated part of the Multifactorial Model of Driving Safety to elucidate the relative importance of cognitive function and a limited range of standard measures of visual function in relation to the Capacity to Drive Safely. Capacity to Drive Safely was operationalized using three validated screening measures for older drivers. These included an adaptation of the well validated Useful Field of View (UFOV) and two newer measures, namely a Hazard Perception Test (HPT), and a Hazard Change Detection Task (HCDT). METHOD: Community dwelling drivers (n=297) aged 65-96 were assessed using a battery of measures of cognitive and visual function. RESULTS: Factor analysis of these predictor variables yielded factors including Executive/Speed, Vision (measured by visual acuity and contrast sensitivity), Spatial, Visual Closure, and Working Memory. Cognitive and Vision factors explained 83-95% of age-related variance in the Capacity to Drive Safely. Spatial and Working Memory were associated with UFOV, HPT and HCDT, Executive/Speed was associated with UFOV and HCDT and Vision was associated with HPT. CONCLUSION: The Capacity to Drive Safely declines with chronological age, and this decline is associated with age-related declines in several higher order cognitive abilities involving manipulation and storage of visuospatial information under speeded conditions. There are also age-independent effects of cognitive function and vision that determine driving safety.","corpus_id":25292002,"score":1},{"doc_id":"22366710","title":"Useful field of view predicts driving in the presence of distracters.","abstract":"PURPOSE: The Useful Field of View (UFOV) test has been shown to be highly effective in predicting crash risk among older adults. An important question which we examined in this study is whether this association is due to the ability of the UFOV to predict difficulties in attention-demanding driving situations that involve either visual or auditory distracters. METHODS: Participants included 92 community-living adults (mean age 73.6 ± 5.4 years; range 65-88 years) who completed all three subtests of the UFOV involving assessment of visual processing speed (subtest 1), divided attention (subtest 2), and selective attention (subtest 3); driving safety risk was also classified using the UFOV scoring system. Driving performance was assessed separately on a closed-road circuit while driving under three conditions: no distracters, visual distracters, and auditory distracters. Driving outcome measures included road sign recognition, hazard detection, gap perception, time to complete the course, and performance on the distracter tasks. RESULTS: Those rated as safe on the UFOV (safety rating categories 1 and 2), as well as those responding faster than the recommended cut-off on the selective attention subtest (350 msec), performed significantly better in terms of overall driving performance and also experienced less interference from distracters. Of the three UFOV subtests, the selective attention subtest best predicted overall driving performance in the presence of distracters. CONCLUSIONS: Older adults who were rated as higher risk on the UFOV, particularly on the selective attention subtest, demonstrated poorest driving performance in the presence of distracters. This finding suggests that the selective attention subtest of the UFOV may be differentially more effective in predicting driving difficulties in situations of divided attention which are commonly associated with crashes.","corpus_id":5116383,"score":1},{"doc_id":"22878441","title":"Using the real-life vision test to assess the functional vision of age-related cataract patients.","abstract":"PURPOSE: (1) To describe and validate a newly developed, timed performance-based measures of functional vision-the real-life vision test (RLVT). ( 2) To determine how RLVT relates to clinical measures and self-report assessment of visual function and the complex interactions among visual impairment, psychosocial status, and demographic factors. METHODS: A total of 64 patients with age-related cataract and 45 age-matched controls were evaluated by four types of measurements: (1) demographic, medical, cognitive, and depressive evaluation and the reaction time (RT) testing; (2) clinical measures (visual acuity, contrast sensitivity, stereopsis, and the color perception); (3) the 25-item National Eye Institute's Visual Functioning Questionnaire; and (4) the RLVT. Spearman's coefficients, partial correlation, and multiple regression analysis were conducted to determine the relationship among RLVT, clinical measures, and self-report assessment of visual function while controlling for confounders. RESULTS: Control subjects performed RLVT significantly better than the cataract patients. RLVT correlated well with both clinical and self-report assessments of visual function. All subscales of RLVT remained highly associated with most of the clinical measures, even after adjusting for age, years of education, depression, cognitive status, and the RT. Distance, intermediate and near visual acuity, and binocular contrast sensitivity were significant predictors of the RLVT performances. CONCLUSIONS: Given the strong relationship among RLVT, clinical measures, and the self-report assessments, our results highlight the potential usefulness of RLVT for assessing the functional vision of cataract patients. RLVT may provide information not obtainable from clinical measures or surveys and therefore it is essential to be incorporated into future ophthalmological practice.","corpus_id":205139749,"score":1},{"doc_id":"23954688","title":"Can we improve clinical prediction of at-risk older drivers?","abstract":"OBJECTIVES: To conduct a pilot study to evaluate the predictive value of the Montreal Cognitive Assessment test (MoCA) and a brief test of multiple object tracking (MOT) relative to other tests of cognition and attention in identifying at-risk older drivers, and to determine which combination of tests provided the best overall prediction. METHODS: Forty-seven currently licensed drivers (58-95 years), primarily from a clinical driving evaluation program, participated. Their performance was measured on: (1) a screening test battery, comprising MoCA, MOT, Mini-Mental State Examination (MMSE), Trail-Making Test, visual acuity, contrast sensitivity, and Useful Field of View (UFOV) and (2) a standardized road test. RESULTS: Eighteen participants were rated at-risk on the road test. UFOV subtest 2 was the best single predictor with an area under the curve (AUC) of .84. Neither MoCA nor MOT was a better predictor of the at-risk outcome than either MMSE or UFOV, respectively. The best four-test combination (MMSE, UFOV subtest 2, visual acuity and contrast sensitivity) was able to identify at-risk drivers with 95% specificity and 80% sensitivity (.91 AUC). CONCLUSIONS: Although the best four-test combination was much better than a single test in identifying at-risk drivers, there is still much work to do in this field to establish test batteries that have both high sensitivity and specificity.","corpus_id":31681055,"score":1},{"doc_id":"23968796","title":"Predicting older driver on-road performance by means of the useful field of view and trail making test part B.","abstract":"The Useful Field of View(®) (UFOV) and Trail Making Test Part B (Trails B) are measures of divided attention. We determined which measure was more accurate in predicting on-road outcomes among drivers (N = 198, mean age = 73.86, standard deviation = 6.05). Receiver operating characteristic curves for the UFOV (Risk Index [RI] and Subtests 1-3) and Trails B significantly predicted on-road outcomes. Contrasting Trails B with the UFOV RI and subtests, the only difference was found between the UFOV RI and Trails B, indicating the UFOV RI was the best predictor of on-road outcomes. Misclassifications of drivers totaled 28 for the UFOV RI, 62 for Trails B, and 58 for UFOV Subtest 2. The UFOV RI is a superior test in predicting on-road outcomes, but the Trails B has acceptable accuracy and is comparable to the other UFOV subtests.","corpus_id":26669258,"score":1},{"doc_id":"24211819","title":"The Efficacy of InSight Cognitive Training to Improve Useful Field of View Performance: A Brief Report.","abstract":"OBJECTIVE: It is well established that cognitive speed of processing training (SOPT) improves Useful Field of View (UFOV) performance and transfers to enhanced performance of instrumental activities of daily living, including driving. InSight is a recently developed version of SOPT formatted for self-administration by older adults with exercises translated into a gaming format. The goal was to examine whether InSight training improves UFOV performance. METHOD: Participants ranged in age between 59-95 years and were randomized to InSight cognitive training or a control condition. Cognitive performance and self-perceptions were measured pre- and post-training, or for controls, after an equivalent delay. Participants completed training twice a week over a 12-week period with the goal of completing 20 sessions. RESULTS: Participants randomized to InSight training experienced greater improvements in their UFOV performance relative to the control condition, F(1, 58) = 4.26, p = .043, but no changes in cognitive self-perceptions were found. CONCLUSIONS: The InSight program is a viable tool for enhancing older adults' UFOV performance. Future research should examine if training gains from the program endure and transfer to improved everyday function.","corpus_id":13567409,"score":1},{"doc_id":"24273754","title":"USEFUL FIELD OF VIEW IMPAIRMENTS IN DRIVERS WITH OBSTRUCTIVE SLEEP APNEA.","abstract":"As a group, drivers with obstructive sleep apnea (OSA) have an increased risk for motor vehicle crashes, but determining individual crash risk is difficult. We tested the hypothesis that drivers with OSA have impaired visual attention, as indexed by reduced useful field of view (UFOV), a predictor of high-risk driving. Forty-one drivers with untreated OSA and 50 comparison drivers were assessed by UFOV. OSA drivers performed significantly worse than controls on all UFOV subtests and had reduced UFOV as indicated by a higher mean total UFOV score (p = 0.0017). However, only 4 OSA and 2 control drivers had values indicative of high crash risk (UFOV reduction >23%). Drivers with OSA have reduced UFOV compared to drivers without neurological or sleep disorders. However, as UFOV identifies few high-risk drivers, its role in assessing crash risk in an unselected population of drivers with OSA appears to be limited.","corpus_id":11282436,"score":1},{"doc_id":"24558495","title":"Visual attention measures predict pedestrian detection in central field loss: a pilot study.","abstract":"PURPOSE: The ability of visually impaired people to deploy attention effectively to maximize use of their residual vision in dynamic situations is fundamental to safe mobility. We conducted a pilot study to evaluate whether tests of dynamic attention (multiple object tracking; MOT) and static attention (Useful Field of View; UFOV) were predictive of the ability of people with central field loss (CFL) to detect pedestrian hazards in simulated driving. METHODS: 11 people with bilateral CFL (visual acuity 20/30-20/200) and 11 age-similar normally-sighted drivers participated. Dynamic and static attention were evaluated with brief, computer-based MOT and UFOV tasks, respectively. Dependent variables were the log speed threshold for 60% correct identification of targets (MOT) and the increase in the presentation duration for 75% correct identification of a central target when a concurrent peripheral task was added (UFOV divided and selective attention subtests). Participants drove in a simulator and pressed the horn whenever they detected pedestrians that walked or ran toward the road. The dependent variable was the proportion of timely reactions (could have stopped in time to avoid a collision). RESULTS: UFOV and MOT performance of CFL participants was poorer than that of controls, and the proportion of timely reactions was also lower (worse) (84% and 97%, respectively; p = 0.001). For CFL participants, higher proportions of timely reactions correlated significantly with higher (better) MOT speed thresholds (r = 0.73, p = 0.01), with better performance on the UFOV divided and selective attention subtests (r = -0.66 and -0.62, respectively, p<0.04), with better contrast sensitivity scores (r = 0.54, p = 0.08) and smaller scotomas (r = -0.60, p = 0.05). CONCLUSIONS: Our results suggest that brief laboratory-based tests of visual attention may provide useful measures of functional visual ability of individuals with CFL relevant to more complex mobility tasks.","corpus_id":1563571,"score":1},{"doc_id":"24582906","title":"Is the size of the useful field of view affected by postural demands associated with standing and stepping?","abstract":"The useful field of view (UFOV) is the visual area from which information is obtained at a brief glance. While studies have examined the effects of increased cognitive load on the visual field, no one has specifically looked at the effects of postural control or locomotor activity on the UFOV. The current study aimed to examine the effects of postural demand and locomotor activity on UFOV performance in healthy young adults. Eleven participants were tested on three modified UFOV tasks (central processing, peripheral processing, and divided-attention) while seated, standing, and stepping in place. Across all postural conditions, participants showed no difference in their central or peripheral processing. However, in the divided-attention task (reporting the letter in central vision and target location in peripheral vision amongst distracter items) a main effect of posture condition on peripheral target accuracy was found for targets at 57° of eccentricity (p=.037). The mean accuracy reduced from 80.5% (standing) to 74% (seated) to 56.3% (stepping). These findings show that postural demands do affect UFOV divided-attention performance. In particular, the size of the useful field of view significantly decreases when stepping. This finding has important implications for how the results of a UFOV test are used to evaluate the general size of the UFOV during varying activities, as the traditional seated test procedure may overestimate the size of the UFOV during locomotor activities.","corpus_id":33906709,"score":1},{"doc_id":"24985476","title":"The effect of aging on crowded letter recognition in the peripheral visual field.","abstract":"PURPOSE: Crowding describes the increased difficulty in identifying a target object when it is surrounded by nearby objects (flankers). A recent study investigated the effect of age on visual crowding and found equivocal results: Although crowded visual acuity was worse in older participants, crowding expressed as a ratio did not change with age. However, the spatial extent of crowding is a better index of crowding effects and remains unknown. In the present study, we used established psychophysical methods to characterize the effect of age on visual crowding (magnitude and extent) in a letter recognition task. METHODS: Letter recognition thresholds were determined for three different flanker separations in 54 adults (aged 18-76 years) with normal vision. Additionally, the spatial extent of crowding was established by measuring spacing thresholds: the flanker-to-target separation required to produce a given reduction in performance. Uncrowded visual acuity, crowded visual acuity, and spacing thresholds were expressed as a function of age, avoiding arbitrary categorization of young and old participants. RESULTS: Our results showed that uncrowded and crowded visual acuities do not change significantly as a function of age. Furthermore, spacing thresholds did not change with age and approximated Bouma's law (half eccentricity). CONCLUSIONS: These data show that crowding in adults is unaffected by senescence and provide additional evidence for distinct neural mechanisms mediating surround suppression and visual crowding, since the former shows a significant age effect. Finally, our data suggest that the well-documented age-related decline in peripheral reading ability is not due to age-related changes in visual crowding.","corpus_id":12232054,"score":1},{"doc_id":"25110186","title":"Is the useful field of view a good predictor of at-fault crash risk in elderly Japanese drivers?","abstract":"AIM: Although age-related decline in the useful field of view (UFOV) is well recognized as a risk factor for at-fault crash involvement in elderly drivers, there is still room to study its applicability to elderly Japanese drivers. In the current study, we thus examined the relationship between UFOV and at-fault crash history in an elderly Japanese population. We also explored whether potential factors that create awareness of reduced driving fitness could be a trigger for the self-regulation of driving in elderly drivers. METHODS: We measured UFOV and at-fault crash history from 151 community-dwelling Japanese aged 60 years or older, and compared UFOV of at-fault crash-free and crash-involved drivers. We also measured self-evaluated driving style using a questionnaire. RESULTS: UFOV in crash-involved drivers was significantly lower than that in crash-free drivers. No significant difference was found in self-evaluated driving style between crash-free and crash-involved drivers. In addition, there was no significant association between UFOV and self-evaluated driving style. CONCLUSIONS: The present study showed that UFOV is a good predictor of at-fault crash risk in elderly Japanese drivers. Furthermore, our data imply that it might be difficult for elderly drivers to adopt appropriate driving strategies commensurate with their current driving competence.","corpus_id":1522429,"score":1},{"doc_id":"25160890","title":"Cognitive speed of processing training in older adults with visual impairments.","abstract":"PURPOSE: To examine whether older adults with vision impairment differentially benefit from cognitive speed of processing training (SPT) relative to healthy older adults. METHODS: Secondary data analyses were conducted from a randomised trial on the effects of SPT among older adults. The effects of vision impairment as indicated by (1) near visual acuity, (2) contrast sensitivity, (3) self-reported cataracts and (4) self-reported other eye conditions (e.g., glaucoma, macular degeneration, diabetic retinopathy, optic neuritis, and retinopathy) among participants randomised to either SPT or a social- and computer-contact control group was assessed. The primary outcome was Useful Field of View Test (UFOV) performance. RESULTS: Mixed repeated-measures ancovas demonstrated that those randomized to SPT experienced greater baseline to post-test improvements in UFOV performance relative to controls (p's < 0.001), regardless of impairments in near visual acuity, contrast sensitivity or presence of cataracts. Those with other eye conditions significantly benefitted from training (p = 0.044), but to a lesser degree than those without such conditions. Covariates included age and baseline measures of balance and depressive symptoms, which were significantly correlated with baseline UFOV performance. CONCLUSIONS: Among a community-based sample of older adults with and without visual impairment and eye disease, the SPT intervention was effective in enhancing participants' UFOV performance. The analyses presented here indicate the potential for SPT to enhance UFOV performance among a community-based sample of older adults with visual impairment and potentially for some with self-reported eye disease; further research to explore this area is warranted, particularly to determine the effects of eye diseases on SPT benefits.","corpus_id":2889824,"score":1},{"doc_id":"26046007","title":"Relationship Between Motor Vehicle Collisions and Results of Perimetry, Useful Field of View, and Driving Simulation in Drivers With Glaucoma.","abstract":"PURPOSE: To examine the relationship between Motor Vehicle Collisions (MVCs) in drivers with glaucoma and standard automated perimetry (SAP), Useful Field of View (UFOV), and driving simulator assessment of divided attention. METHODS: A cross-sectional study of 153 drivers from the Diagnostic Innovations in Glaucoma Study. All subjects had SAP and divided attention was assessed using UFOV and driving simulation using low-, medium-, and high-contrast peripheral stimuli presented during curve negotiation and car following tasks. Self-reported history of MVCs and average mileage driven were recorded. RESULTS: Eighteen of 153 subjects (11.8%) reported a MVC. There was no difference in visual acuity but the MVC group was older, drove fewer miles, and had worse binocular SAP sensitivity, contrast sensitivity, and ability to divide attention (UFOV and driving simulation). Low contrast driving simulator tasks were the best discriminators of MVC (AUC 0.80 for curve negotiation versus 0.69 for binocular SAP and 0.59 for UFOV). Adjusting for confounding factors, longer reaction times to driving simulator divided attention tasks provided additional value compared with SAP and UFOV, with a 1 standard deviation (SD) increase in reaction time (approximately 0.75 s) associated with almost two-fold increased odds of MVC. CONCLUSIONS: Reaction times to low contrast divided attention tasks during driving simulation were significantly associated with history of MVC, performing better than conventional perimetric tests and UFOV. TRANSLATIONAL RELEVANCE: The association between conventional tests of visual function and MVCs in drivers with glaucoma is weak, however, tests of divided attention, particularly using driving simulation, may improve risk assessment.","corpus_id":12842198,"score":1},{"doc_id":"26122710","title":"Sensorimotor and cognitive factors associated with the age-related increase of visual field dependence: a cross-sectional study.","abstract":"Reliance on the visual frame of reference for spatial orientation (or visual field dependence) has been reported to increase with age. This has implications on old adults' daily living tasks as it affects stability, attention, and adaptation capacities. However, the nature and underlying mechanisms of this increase are not well defined. We investigated sensorimotor and cognitive factors possibly associated with increased visual field dependence in old age, by considering functions that are both known to degrade with age and important for spatial orientation and sensorimotor control: reliance on the (somatosensory-based) egocentric frame of reference, visual fixation stability, and attentional processing of complex visual scenes (useful field of view, UFOV). Twenty young, 18 middle-aged, and 20 old adults completed a visual examination, three tests of visual field dependence (RFT, RDT, and GEFT), a test of egocentric dependence (subjective vertical estimation with the body erect and tilted at 70°), a visual fixation task, and a test of visual attentional processing (UFOV®). Increased visual field dependence with age was associated with reduced egocentric dependence, visual fixation stability, and visual attentional processing. In addition, visual fixation instability and reduced UFOV were correlated. Results of middle-aged adults fell between those of the young and old, revealing the progressive nature of the age effects we evaluated. We discuss results in terms of reference frame selection with respect to ageing as well as visual and non-visual information processing. Inter-individual differences amongst old adults are highlighted and discussed with respect to the functionality of increased visual field dependence.","corpus_id":16251004,"score":1},{"doc_id":"26426342","title":"Predicting Risk of Motor Vehicle Collisions in Patients with Glaucoma: A Longitudinal Study.","abstract":"PURPOSE: To evaluate the ability of longitudinal Useful Field of View (UFOV) and simulated driving measurements to predict future occurrence of motor vehicle collision (MVC) in drivers with glaucoma. DESIGN: Prospective observational cohort study. PARTICIPANTS: 117 drivers with glaucoma followed for an average of 2.1 ± 0.5 years. METHODS: All subjects had standard automated perimetry (SAP), UFOV, driving simulator, and cognitive assessment obtained at baseline and every 6 months during follow-up. The driving simulator evaluated reaction times to high and low contrast peripheral divided attention stimuli presented while negotiating a winding country road, with central driving task performance assessed as \"curve coherence\". Drivers with MVC during follow-up were identified from Department of Motor Vehicle records. MAIN OUTCOME MEASURES: Survival models were used to evaluate the ability of driving simulator and UFOV to predict MVC over time, adjusting for potential confounding factors. RESULTS: Mean age at baseline was 64.5 ± 12.6 years. 11 of 117 (9.4%) drivers had a MVC during follow-up. In the multivariable models, low contrast reaction time was significantly predictive of MVC, with a hazard ratio (HR) of 2.19 per 1 SD slower reaction time (95% CI, 1.30 to 3.69; P = 0.003). UFOV divided attention was also significantly predictive of MVC with a HR of 1.98 per 1 SD worse (95% CI, 1.10 to 3.57; P = 0.022). Global SAP visual field indices in the better or worse eye were not predictive of MVC. The longitudinal model including driving simulator performance was a better predictor of MVC compared to UFOV (R2 = 0.41 vs R2 = 0.18). CONCLUSIONS: Longitudinal divided attention metrics on the UFOV test and during simulated driving were significantly predictive of risk of MVC in glaucoma patients. These findings may help improve the understanding of factors associated with driving impairment related to glaucoma.","corpus_id":15675655,"score":1},{"doc_id":"26890935","title":"The useful field of view assessment predicts simulated commercial motor vehicle driving safety.","abstract":"OBJECTIVE: The Useful Field of View (UFOV) assessment, a measure of visual speed of processing, has been shown to be a predictive measure of motor vehicle collision (MVC) involvement in an older adult population, but it remains unknown whether UFOV predicts commercial motor vehicle (CMV) driving safety during secondary task engagement. The purpose of this study is to determine whether the UFOV assessment predicts simulated MVCs in long-haul CMV drivers. METHOD: Fifty licensed CMV drivers (Mage = 39.80, SD = 8.38, 98% male, 56% Caucasian) were administered the 3-subtest version of the UFOV assessment, where lower scores measured in milliseconds indicated better performance. CMV drivers completed 4 simulated drives, each spanning approximately a 22.50-mile distance. Four secondary tasks were presented to participants in a counterbalanced order during the drives: (a) no secondary task, (b) cell phone conversation, (c) text messaging interaction, and (d) e-mailing interaction with an on-board dispatch device. RESULTS: The selective attention subtest significantly predicted simulated MVCs regardless of secondary task. Each 20 ms slower on subtest 3 was associated with a 25% increase in the risk of an MVC in the simulated drive. The e-mail interaction secondary task significantly predicted simulated MVCs with a 4.14 times greater risk of an MVC compared to the no secondary task condition. Subtest 3, a measure of visual speed of processing, significantly predicted MVCs in the email interaction task. Each 20 ms slower on subtest 3 was associated with a 25% increase in the risk of an MVC during the email interaction task. CONCLUSIONS: The UFOV subtest 3 may be a promising measure to identify CMV drivers who may be at risk for MVCs or in need of cognitive training aimed at improving speed of processing. Subtest 3 may also identify CMV drivers who are particularly at risk when engaged in secondary tasks while driving.","corpus_id":26591968,"score":1},{"doc_id":"27050950","title":"Impairing the useful field of view in natural scenes: Tunnel vision versus general interference.","abstract":"A fundamental issue in visual attention is the relationship between the useful field of view (UFOV), the region of visual space where information is encoded within a single fixation, and eccentricity. A common assumption is that impairing attentional resources reduces the size of the UFOV (i.e., tunnel vision). However, most research has not accounted for eccentricity-dependent changes in spatial resolution, potentially conflating fixed visual properties with flexible changes in visual attention. Williams (1988, 1989) argued that foveal loads are necessary to reduce the size of the UFOV, producing tunnel vision. Without a foveal load, it is argued that the attentional decrement is constant across the visual field (i.e., general interference). However, other research asserts that auditory working memory (WM) loads produce tunnel vision. To date, foveal versus auditory WM loads have not been compared to determine if they differentially change the size of the UFOV. In two experiments, we tested the effects of a foveal (rotated L vs. T discrimination) task and an auditory WM (N-back) task on an extrafoveal (Gabor) discrimination task. Gabor patches were scaled for size and processing time to produce equal performance across the visual field under single-task conditions, thus removing the confound of eccentricity-dependent differences in visual sensitivity. The results showed that although both foveal and auditory loads reduced Gabor orientation sensitivity, only the foveal load interacted with retinal eccentricity to produce tunnel vision, clearly demonstrating task-specific changes to the form of the UFOV. This has theoretical implications for understanding the UFOV.","corpus_id":15751029,"score":1},{"doc_id":"27091370","title":"Measuring the Useful Field of View During Simulated Driving With Gaze-Contingent Displays.","abstract":"OBJECTIVE: We aimed to develop and test a new dynamic measure of transient changes to the useful field of view (UFOV), utilizing a gaze-contingent paradigm for use in realistic simulated environments. BACKGROUND: The UFOV, the area from which an observer can extract visual information during a single fixation, has been correlated with driving performance and crash risk. However, some existing measures of the UFOV cannot be used dynamically in realistic simulators, and other UFOV measures involve constant stimuli at fixed locations. We propose a gaze-contingent UFOV measure (the GC-UFOV) that solves the above problems. METHODS: Twenty-five participants completed four simulated drives while they concurrently performed an occasional gaze-contingent Gabor orientation discrimination task. Gabors appeared randomly at one of three retinal eccentricities (5°, 10°, or 15°). Cognitive workload was manipulated both with a concurrent auditory working memory task and with driving task difficulty (via presence/absence of lateral wind). RESULTS: Cognitive workload had a detrimental effect on Gabor discrimination accuracy at all three retinal eccentricities. Interestingly, this accuracy cost was equivalent across eccentricities, consistent with previous findings of \"general interference\" rather than \"tunnel vision.\" CONCLUSION: The results showed that the GC-UFOV method was able to measure transient changes in UFOV due to cognitive load in a realistic simulated environment. APPLICATION: The GC-UFOV paradigm developed and tested in this study is a novel and effective tool for studying transient changes in the UFOV due to cognitive load in the context of complex real-world tasks such as simulated driving.","corpus_id":3806385,"score":1},{"doc_id":"27315540","title":"A Preliminary Study on Normalized Pattern-Reversal Peripheral Field SSVEPs as a Potential Objective Indicator of Useful Field of View Performance.","abstract":"PURPOSE: Currently, the test for useful field of view (UFOV) typically relies on subjective feedback for detecting peripheral targets while attending to a central target. Steady-state visual evoked potential (SSVEP) recorded from the occipital region of the brain has been frequently used as an objective alternative to replace subjective responses. Our aim was to investigate if a short screening test can approximate UFOV performance objectively. METHODS: We recorded SSVEPs during a simple peripheral task and a UFOV task with and without distractors as well as 30-second offline SSVEPs for eight participants. In all tasks, a peripheral annulus ring of checkered reversal pattern was concurrently presented to the participants to elicit SSVEPs. RESULTS: Orthogonal linear regression analysis found that normalized SSVEP during the UFOV task is predictive of peripheral target detection accuracy (F(1,6) = 16.250, P < 0.01, n = 8) for a task with peripheral distractors. However, this is not the case for a task without distractors (F(1,6) = 0.397, P = 0.552), possibly due to near-perfect accuracy across most participants. Offline normalized SSVEPs also only predicted the peripheral target detection accuracy (F(1,6) = 26.799, P < 0.01) for the UFOV task with peripheral distractors. CONCLUSIONS: Difficult peripheral target detection with distractors is required to differentiate UFOV performance in healthy young adults. The results suggested that offline normalized SSVEPs elicited by 30 seconds of pattern-reversal checkered annulus from the peripheral vision field can identify individuals with good UFOV performance under the stress of a difficult peripheral task.","corpus_id":20984809,"score":1},{"doc_id":"27353969","title":"Association of visual sensory function and higher-order visual processing skills with incident driving cessation.","abstract":"BACKGROUND: Many studies on vision and driving cessation have relied on measures of sensory function, which are insensitive to the higher-order cognitive aspects of visual processing. The purpose of this study was to examine the association between traditional measures of visual sensory function and higher-order visual processing skills with incident driving cessation in a population-based sample of older drivers. METHODS: Two thousand licensed drivers aged 70 years or older were enrolled and followed for three years. Tests for central vision and visual processing were administered at baseline and included visual acuity, contrast sensitivity, sensitivity in the driving visual field, visual processing speed (useful field of view [UFOV] Subtest 2 and Trails B) and spatial ability measured by the Visual Closure Subtest of the Motor-free Visual Perception Test. Participants self-reported the month and year of driving cessation and provided a reason for cessation. Cox proportional hazards models were used to generate crude and adjusted hazard ratios with 95% confidence intervals between visual functioning characteristics and risk of driving cessation over a three-year period. RESULTS: During the study period, 164 participants stopped driving, which corresponds to a cumulative incidence of 8.5 per cent. Impaired contrast sensitivity, visual fields, visual processing speed (UFOV and Trails B) and spatial ability were significant risk factors for subsequent driving cessation after adjusting for age, gender, marital status, number of medical conditions and miles driven. Visual acuity impairment was not associated with driving cessation. Medical problems (63 per cent), specifically musculoskeletal and neurological problems, as well as visual problems (17 per cent) were cited most frequently as the reason for driving cessation. CONCLUSION: Assessment of cognitive and visual functioning can provide useful information about subsequent risk of driving cessation among older drivers. In addition, a variety of factors, not just vision, influenced the decision to stop driving and may be amenable to intervention.","corpus_id":27929347,"score":1},{"doc_id":"27764828","title":"Driving Characteristics of Older Drivers and Their Relationship to the Useful Field of View Test.","abstract":"BACKGROUND: To maintain the mobility of older people in later life, it is essential to sustain their autonomy; however, driving is a complex task, requiring a large range of visual, psychomotor and cognitive abilities. Subsequently, a key issue is to measure and evaluate the fitness to drive of older drivers. Several methods have been proposed, among them the useful field of view (UFOV) test. OBJECTIVE: The present study aimed to identify driving characteristics in older drivers and the relationship between the UFOV test and the on-road driving results. METHOD: A total of 80 drivers aged 70 years or older performed both the UFOV test and the on-road driving assessment. The 'B On-Road' (Behaviour On-Road) protocol was used for the fitness-to-drive assessment. RESULTS: 'Driving too fast' was the item reported most often during the on-road assessment, followed by problems with the manual gearbox and 'attention to signs, road lines and traffic lights'. Overall, the results showed that the older the driver, the more errors were reported during the on-road driving assessment, as well as the slower the performance on the UFOV test. A significant relationship between the total number of on-road errors, as measured by the B On-Road protocol, and the UFOV 3, which stresses the capacity of selective attention, was found. CONCLUSION: The recommendation is still to use on-road driving assessment to fully assess fitness to drive for older drivers whose ability to drive requires assessment. However, to supplement this, the UFOV test, in particular the UFOV 3, is a valuable complement in selecting those drivers requiring to be assessed.","corpus_id":24652979,"score":1},{"doc_id":"28446144","title":"Association of physical activity and appetite with visual function related to driving competence in older adults.","abstract":"BACKGROUND: Older people are at greater risk of traffic accidents, partially because of age-related declines in visual function, including reduced useful field of view (UFOV). However, lifestyle factors which cause age-related decline in UFOV remain poorly understood. We conducted a study to investigate whether physical activity and appetite status were related to UFOV test performance in healthy older adults. METHODS: Thirty community-dwelling older people (age 68.6 ± 3.1 years, 15 females) were enrolled in this study. Each participant completed the Council on Nutrition appetite questionnaire (CNAQ) and a UFOV test. They then wore a tri-axial accelerometer (Active style Pro HJA-350IT) for 3-6 consecutive days to objectively measure their PA in free-living conditions. RESULTS: Longer time spent in vigorous physical activity was significantly associated with better UFOV test performance when adjusted for age and accelerometer wear time (non-locomotive: r = -0.435, locomotive: r = -0.449; n = 25). In addition, male, but not female, participants with a higher CNAQ score had significantly better UFOV test performance in both an unadjusted model (r = -0.560; n = 15) and a model adjusted for age (r = -0.635; n = 15). CONCLUSIONS: The results suggest that appetite status among males and time spent in high intensity PA are associated with visual function related to driving competence in older adults.","corpus_id":16962845,"score":1},{"doc_id":"28450973","title":"The Field of View is More Useful in Golfers than Regular Exercisers.","abstract":"Superior visual attention skills are vital for excellent sports performance. This study used a cognitive skills approach to examine expert and novice differences in a visual spatial attention task. Thirty-two males aged 18 to 42 years completed this study in return for course credit or monetary incentive. Participants were expert golfers (N = 18) or exercise controls (N = 14). Spatial attention was assessed using the useful field of view task which required participants to locate a target shown 10°, 20°, and 30° of eccentricity from centre in very brief presentations. At each degree of eccentricity, golfers were more accurate at locating the target than the exercise controls. These results provide support for the broad transfer hypothesis by demonstrating a link between golf expertise and better performance on an objective measure of spatial attention skills. Therefore, it appears that sports expertise can transfer to expertise in non-sport related tasks.","corpus_id":14817790,"score":1},{"doc_id":"28802451","title":"More than the Useful Field: Considering peripheral vision in driving.","abstract":"Applied research on driving and basic vision research have held similar views on central, fovea-based vision as the core of visual perception. In applied work, the concept of the Useful Field, as determined by the Useful Field of View (UFOV) test, divides vision between a \"useful\" region towards the center of the visual field, and the rest of the visual field. While compelling, this dichotomization is at odds with findings in vision science which demonstrate the capabilities of peripheral vision. In this paper, we examine driving research from this new perspective, and argue for the need for an updated understanding of how drivers acquire information about their operating environment using peripheral vision. The concept of the Useful Field and the UFOV test are not discarded; instead we discuss their strengths, limitations, and future directions. We discuss key findings from vision science on peripheral vision, and a theory that provides insights into its capabilities and limitations. This more complete basic science understanding of peripheral vision informs appropriate use of the UFOV and the Useful Field in driving research going forward.","corpus_id":10042446,"score":1},{"doc_id":"29089888","title":"Effect of Speed of Processing Training on Older Driver Screening Measures.","abstract":"Objective: Computerized training for cognitive enhancement is of great public interest, however, there is inconsistent evidence for the transfer of training gains to every day activity. Several large trials have focused on speed of processing (SOP) training with some promising findings for long-term effects on daily activity, but no immediate transfer to other cognitive tests. Here, we examine the transfer of SOP training gains to cognitive measures that are known predictors of driving safety in older adults. Methods: Fifty-three adults aged 65-87 years who were current drivers participated in a two group non-randomized design with repeated measures and a no-contact matched control group. The Intervention group completed an average of 7.9 (SD = 3.0) hours of self-administered online SOP training at home. Control group was matched on age, gender and test-re-test interval. Measures included the Useful Field of View (UFOV) test, a Hazard Perception test, choice reaction time (Cars RT), Trail Making Test B, a Maze test, visual motion threshold, as well as road craft and road knowledge tests. Results: Speed of processing training resulted in significant improvement in processing speed on the UFOV test relative to controls, with an average change of -45.8 ms (SE = 14.5), and effect size of ω2 = 0.21. Performance on the Maze test also improved, but significant slowing on the Hazard Perception test was observed after SOP training. Training effects on the UFOV task was associated with similar effects on the Cars RT, but not the Hazard Perception and Maze tests, suggesting transfer to some but not all driving related measures. There were no effects of training on any of the other measures examined. Conclusion: Speed of processing training effects on the UFOV task can be achieved with self-administered, online training at home, with some transfer to other cognitive tests. However, differential effects of training may be observed for tasks requiring goal-directed search strategies rather than diffuse attention.","corpus_id":941361,"score":1},{"doc_id":"29175362","title":"Systematic review and meta-analyses of useful field of view cognitive training.","abstract":"Systematic review and meta-analyses were conducted of Useful Field of View (UFOV) training, which was evaluated by Institute of Medicine criteria. Forty-four studies of UFOV training from 17 randomized trials conducted among adults were identified in systematic review. Results addressing the Institute of Medicine criteria indicated that: (a) UFOV training enhanced neural outcomes, speed of processing, and attention. ( b) UFOV training effects were equivalent when compared to active- or no-contact control conditions. ( c) UFOV training showed far transfer to everyday function. ( d) Improvements on the trained skills endured across ten years. ( e) Half of the clinical trials identified were conducted by researchers without financial interests in UFOV training. Results indicated that UFOV training effects were larger for adaptive- than non-adaptive training techniques, and in community-based as compared to clinical samples. UFOV training did not transfer to other neuropsychological outcomes, but positively enhanced well-being, health, and quality of life longitudinally. Criticisms of cognitive training are addressed. UFOV training should be implemented among older adults to improve real-world functional outcomes and well-being.","corpus_id":31077579,"score":1},{"doc_id":"29241017","title":"Older Adult Multitasking Performance Using a Gaze-Contingent Useful Field of View.","abstract":"Objective We implemented a gaze-contingent useful field of view paradigm to examine older adult multitasking performance in a simulated driving environment. Background Multitasking refers to the ability to manage multiple simultaneous streams of information. Recent work suggests that multitasking declines with age, yet the mechanisms supporting these declines are still debated. One possible framework to better understand this phenomenon is the useful field of view, or the area in the visual field where information can be attended and processed. In particular, the useful field of view allows for the discrimination of two competing theories of real-time multitasking, a general interference account and a tunneling account. Methods Twenty-five older adult subjects completed a useful field of view task that involved discriminating the orientation of lines in gaze-contingent Gabor patches appearing at varying eccentricities (based on distance from the fovea) as they operated a vehicle in a driving simulator. In half of the driving scenarios, subjects also completed an auditory two-back task to manipulate cognitive workload, and during some trials, wind was introduced as a means to alter general driving difficulty. Results Consistent with prior work, indices of driving performance were sensitive to both wind and workload. Interestingly, we also observed a decline in Gabor patch discrimination accuracy under high cognitive workload regardless of eccentricity, which provides support for a general interference account of multitasking. Conclusion The results showed that our gaze-contingent useful field of view paradigm was able to successfully examine older adult multitasking performance in a simulated driving environment. Application This study represents the first attempt to successfully measure dynamic changes in the useful field of view for older adults completing a multitasking scenario involving driving.","corpus_id":3340095,"score":1},{"doc_id":"29460955","title":"A pilot study: Can the UFOV assessment be used as a repeated measure to determine timing of on-road assessment in stroke?","abstract":"BACKGROUND/AIMS: Useful Field of View scores are predictive of on-road performance post-stroke. No objective data exist to determine if the Useful Field of View (UFOV) assessment can be used as a repeated measure in the post-stroke population to determine timing of occupational therapy on-road assessment as recovery occurs. The aims of this study were to determine whether there is a practice effect if the UFOV is administered at one, two and three months' post-stroke and to assess optimal time post-stroke to refer to an on-road assessment. METHOD: Forty-two participants, 17 men (40.5%), with a mean age of 71 years (SD 9.33) were randomly allocated to 1. Assessment group - UFOV at one, two and three months' post-stroke, 2. Control group-UFOV at three months' post-stroke. Parametric and non-parametric tests were utilised depending on data distribution. RESULTS: No significance was found between; three months' subtest 1 (P = 0.463), three months' subtest 2 (P = 0.729) and three months' subtest 3 (P = 0.534) between the assessment and control groups. Both group's scores were combined to examine pass/fail rates of UFOV assessment to indicate timing of referral to on-road assessments. At one month, 16.9% stroke survivors passed the UFOV, when reassessed at three months 69.1% passed and 28.6% again failed. CONCLUSION: Improvements in scores at one month intervals over three months are due to improvements in abilities assessed by the UFOV as no practice effect was found to influence scores. UFOV scores performed at monthly intervals post-stroke can be used to guide the timing of an occupational therapy on-road assessment, with an increased likelihood of passing, as recovery occurs. This repeated use of the UFOV assessment can assist referral practices that best utilise driving rehabilitation programmes. Larger studies need to be conducted to confirm these results.","corpus_id":3399996,"score":1},{"doc_id":"18455935","title":"Results of ocular dominance testing depend on assessment method.","abstract":"PURPOSE: We developed a near ocular dominance test modeled after the distance hole-in-the-card test and assessed both test-retest reliability of four tests of ocular dominance and agreement between tests. METHODS: Forty-six subjects aged 18 to 78 years with visual acuity 20/40 or better in each eye were enrolled from a primary care practice. All subjects had normal eye examinations, with the exception of refractive error, and were examined in their habitual correction. Subjects were tested twice each with the distance hole-in-the-card test, new near hole-in-the-card test, near convergence test, and the Pediatric Eye Disease Investigator Group fixation preference test. RESULTS: There was excellent test-retest reliability for each ocular dominance test. Nevertheless, there was only moderate to slight agreement between each possible pairing of tests. CONCLUSIONS: Results of ocular dominance tests vary depending on both the testing distance and the specific activity performed as part of the testing procedure.","corpus_id":2021507,"score":0},{"doc_id":"18711290","title":"Ocular disorders in renal transplant patients.","abstract":"This cross-sectional study was performed to determine ocular findings in renal transplant recipients and to correlate them with certain clinical characteristics related to transplantation. The study was performed on 150 patients who had received a renal transplant at least three months earlier and had serum creatinine levels < 3 mg/dL. All patients underwent a complete ophthalmologic examination. Clinical variables studied related to the transplant included cause of renal failure, duration of hemodialysis prior to transplantation and immunosuppressive regimen. Overall, 91 male and 59 female subjects with a mean age of 39.9 +/- 17.7 years were included. At least one ocular abnormality could be detected in 89.3% including impaired visual acuity < or = 20/25 (48.6%), conjunctival degeneration in the palpebral fissure (36.6%), posterior sub-capsular cataracts (24%), pinguecula (17.3%), retinal pigment epitheliopathy (14%), arteriovenous crossing changes (8.6%), proliferative diabetic retinopathy (6%), central serous chorioretinopathy and retinal vein occlusions (each in 3.3%), and non-proliferative diabetic retinopathy, optic nerve atrophy and diabetic macular edema (each in 2.7%). Abnormal ocular findings were not correlated with the underlying renal disorder or use of cyclosporine and prednisolone; however, they were positively correlated with transplant duration, pre-transplant dialysis duration and usage of azathioprine or mycophenolate mofetil. Our study suggests that ocular disorders are frequent among renal transplant patients especially with older transplants and those with a longer period of pre-transplant hemodialysis.","corpus_id":38530063,"score":0},{"doc_id":"18854790","title":"Assessing age-related macular degeneration with the ADREV performance-based measure.","abstract":"PURPOSE: To validate a new third-generation performance-based measure titled the \"assessment of disability related to vision\" (ADREV) in a study population of individuals with age-related macular degeneration. METHODS: Patients with either exudative or nonexudative age-related macular degeneration, but without ocular comorbidity, completed the ADREV, the 25-item National Eye Institute's visual functioning questionnaire, and a range of clinical assessments. Correlations were calculated between the data provided by the ADREV, visual functioning questionnaire, and clinical ophthalmic measures. Regression and bootstrap analysis were preformed to determine the relative relationship between specific clinical measures and ADREV performance, while controlling for a range of potentially confounding factors. RESULTS: One hundred twelve patients completed the study and correlative analysis showed that ADREV total and subscale scores were more related to nearly all measures of clinical ophthalmic status in comparison with the data provided by the visual functioning questionnaire. Significant correlative relationships between ADREV and visual functioning questionnaire scores showed moderate to high correlation. Central visual acuity and contrast sensitivity shared the strongest association with performance of activities. CONCLUSIONS: The ADREV is a valid instrument for the assessment of visual disability in patients with age-related macular degeneration. Furthermore, the data provided by this performance measure had stronger relationships with clinical indicators of visual impairment in comparison with self-report.","corpus_id":38646701,"score":0},{"doc_id":"21367570","title":"School performance and alcohol use problems in early adulthood: a longitudinal study.","abstract":"There is inconsistent evidence about the association between school performance and subsequent use of alcohol and alcohol problems in adolescents and young adults. This study examines whether school performance at 14 years is associated with drinking problems in early adulthood; and whether this association is explained by family and individual factors in childhood and adolescence. Data were from a 21-year follow-up of 3,478 Australian young adults from birth to the age of 21 years when data on use of alcohol were collected. Child school performance (CSP) was assessed at 14 years via self- and maternal report. Alcohol consumption at 21 years was measured via self-report, and alcohol abuse and dependence were assessed by the computerized version of Composite International Diagnostic Interview (CIDI-Auto). Potential confounding factors were prospectively measured between the child's birth and age of 14 years. School performance at 14 years predicted young adults' alcohol consumption and alcohol use disorders (AUDs). After controlling for confounding, children who had lower school performance had increased risk of drinking more than two glasses of alcohol per day in early adulthood (odds ratio=1.7; 95% confidence interval: 1.1-2.6). There was a similar pattern of association between CSP and young adults' alcohol abuse and dependence (AUD) measured by CIDI-Auto. Level of academic performance in high school children predicts their drinking problems as young adults, independently of a selected group of individual and family confounders. Exploration of the pathway linking school performance and alcohol problems in young people may help identify opportunities for preventive interventions.","corpus_id":46340596,"score":0},{"doc_id":"22008883","title":"Performance-based tests in subjects with stroke: outcome scores, reliability and measurement errors.","abstract":"OBJECTIVES: To assess the intra- and inter-rater reliabilities and measurement errors of seven widely applied performance-based tests for stroke subjects (comfortable/maximal gait speeds and both stair ascending/descending cadences, as well as the Timed 'Up and Go' test) and to verify whether the use of different types of outcome scores (one trial, the means of two and three trials, and the best and the worst values of the three trials) affected the score values, as well as their reliability and measurement errors. DESIGN: Intra- and inter-rater reliability study. SETTING: Research laboratory. SUBJECTS: Sixteen stroke subjects with a mean age of 52 ± 17.9 years. MAIN MEASURES: Seven performance-based tests, over two sessions, seven days apart, evaluated by two independent examiners. A third examiner recorded all data. One-way ANOVAs, intra-class correlation coefficients (ICCs) and percentages of the standard errors of measurement (SEM%) were used for analyses. RESULTS: For all tests, similar results were found for all types of outcome scores (0.01 ≤ F ≤ 0.56; 0.34 ≤ p ≤ 0.99). For instance, at the comfortable gait speed, the means (SD) values for the first trial, the means of two and three trials and the best and worst of three trials were, respectively, 1.04 (0.25), 1.04(0.24), 1.05 (0.24), 1.10 (0.26), 1.02 (0.24) seconds. Significant and adequate values of intra- (0.75 ≤ ICC ≤ 0.96; p ≤ 0.002) and inter-rater (0.75 ≤ ICC ≤ 0.97; p ≤ 0.001) reliabilities were found for all tests and outcome scores. Measurement errors were considered low (5.01 ≤ SEM% ≤14.78) and were also similar between all outcome scores. CONCLUSIONS: For the seven tests, only one trial was necessary to provide consistent and reliable results regarding the functional performances of stroke subjects.","corpus_id":39839412,"score":0},{"doc_id":"23307969","title":"Association between higher order visual processing abilities and a history of motor vehicle collision involvement by drivers ages 70 and over.","abstract":"PURPOSE: To examine in a population-based sample of 2000 drivers aged 70 years and older, the independent association between higher order visual processing impairment and motor vehicle collision (MVC) rate during the prior 5 years. METHODS: Three higher order visual processing screening tests were administered since previous research found associations between impaired performance on these screens and MVC involvement. They included an estimate of visual processing speed under divided attention conditions (useful field of view [UFOV] subset 2); Trails B, a paper and pencil test of visual processing speed also involving problem solving, executive function, and working memory; and the visual closure subtest of the Motor Free Visual Perception Test (MVPT) examining the ability to recognize objects only partially visible. Potentially confounding variables were also assessed including demographics, general cognitive status, visual acuity, and contrast sensitivity. MVC involvement was determined by accident reports from the Alabama Department of Public Safety, and driving exposure was estimated from the Driving Habits Questionnaire. RESULTS: MVC rates (for at fault and all MVCs) were significantly higher for those older drivers with impairments in any of the three visual processing screening tests. After adjustment for potentially confounding influences, the association between MVC rate and Trails B remained significant, whereas the association with MVPT and UFOV did not. CONCLUSIONS: This population-based study of drivers aged 70 years and older suggests that a paper and pencil test assessing higher order visual processing skills is independently associated with a recent history of MVC involvement.","corpus_id":46722452,"score":0},{"doc_id":"24106477","title":"Co-morbidity of depression and anxiety in common age-related eye diseases: a population-based study of 662 adults.","abstract":"This study examined the prevalence of co-morbid age-related eye disease and symptoms of depression and anxiety in late life, and the relative roles of visual function and disease in explaining symptoms of depression and anxiety. A community-based sample of 662 individuals aged over 70 years was recruited through the electoral roll. Vision was measured using a battery of tests including high and low contrast visual acuity, contrast sensitivity, motion sensitivity, stereoacuity, Useful Field of View, and visual fields. Depression and anxiety symptoms were measured using the Goldberg scales. The prevalence of self-reported eye disease [cataract, glaucoma, or age-related macular degeneration (AMD)] in the sample was 43.4%, with 7.7% reporting more than one form of ocular pathology. Of those with no eye disease, 3.7% had clinically significant depressive symptoms. This rate was 6.7% among cataract patients, 4.3% among those with glaucoma, and 10.5% for AMD. Generalized linear models adjusting for demographics, general health, treatment, and disability examined self-reported eye disease and visual function as correlates of depression and anxiety. Depressive symptoms were associated with cataract only, AMD, comorbid eye diseases and reduced low contrast visual acuity. Anxiety was significantly associated with self-reported cataract, and reduced low contrast visual acuity, motion sensitivity and contrast sensitivity. We found no evidence for elevated rates of depressive or anxiety symptoms associated with self-reported glaucoma. The results support previous findings of high rates of depression and anxiety in cataract and AMD, and in addition show that mood and anxiety are associated with objective measures of visual function independently of self-reported eye disease. The findings have implications for the assessment and treatment of mental health in the context of late-life visual impairment.","corpus_id":2053348,"score":0},{"doc_id":"24184091","title":"Objective and subjective visual performance of multifocal contact lenses: pilot study.","abstract":"PURPOSE: The aim of the present study was to compare the objective and subjective visual performance of three different soft multifocal contact lenses. METHODS: 10 subjects (habitual soft contact lens wearers) between the ages of 40 and 45 years participated in the study. Three different multifocal silicone hydrogel contact lenses (Acuvue Oasys, Air Optix and Biofinity) were fit within the same visit. All the lenses were fit according to the manufacturers' recommendation using the respective fitting guide. Visual performance tests included low and high contrast distance and near visual acuity, contrast sensitivity, range of clear vision and through-focus curve. Objective visual performance tests included measurement of open field accommodative response at different defocus levels and optical aberrations at different viewing distances. RESULTS: Accommodative response was not significantly different between the three types of multifocal contact lenses at each of the accommodative stimulus levels (p>0.05). Accommodative lag increased for higher stimulus levels for all 3 types of contact lenses. Ocular aberrations were not significantly different between these 3 contact lens designs at each of the different viewing distances (p>0.05). In addition, optical aberrations did not significantly differ between different viewing distances for any of these lenses (p>0.05). ANOVA revealed no significant difference in high and low contrast distance visual acuity as well as near visual acuity and contrast sensitivity function between the 3 multifocal contact lenses and spectacles (p>0.05). CONCLUSIONS: There was no statistically significant difference in accommodative response, optical aberrations or visual performance between the 3 multifocal contact lenses in early presbyopes.","corpus_id":7449008,"score":0},{"doc_id":"25282251","title":"Prosthetic replacement of the ocular surface ecosystem as treatment for ocular surface disease in patients with a history of Stevens-Johnson syndrome/toxic epidermal necrolysis.","abstract":"PURPOSE: To report the visual outcomes of prosthetic replacement of the ocular surface ecosystem (PROSE) treatment in patients with ocular surface disease related to Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN). DESIGN: Retrospective cohort study. SUBJECTS: We included 86 patients (167 eyes) with history of SJS/TEN who underwent PROSE treatment from January 1, 2006, to January 1, 2011. METHODS: Etiology, previous interventions, change in visual acuity, change in visual function, and duration of follow-up are reported. Paired t test and Friedman test with Dunn's post hoc test for multiple comparisons were used for statistical analysis. MAIN OUTCOME MEASURES: Visual acuity at last follow-up and visual function based on the National Eye Institute 25-item Visual Functioning Questionnaire (NEI VFQ-25) at 6 months. RESULTS: We treated 35 males and 51 females with a history of SJS/TENS; median age was 36 years. The most common reported etiologies for SJS/TENS were antibiotics (n = 25), ibuprofen (n = 15), and lamotrigine (n = 11). The median visual acuity at the initial visit was 20/60 (range, 20/400-20/25; 0.48 logarithm of the minimum angle of resolution [logMAR]), and the visual acuity at completion of customization was 20/25 (range, 20/200-20/20; 0.096 logMAR; P < 0.001), with no decline in median acuity at the end of follow-up. Median duration of follow-up was 16 months. There was a significant improvement in the visual function of the patients based on the NEI VFQ-25 questionnaire (mean of 48 points at baseline vs. mean of 72 points at 6 months; P < 0.001). In addition, there was also an improvement in the self-reported general health of the patients (mean of 57 points at baseline vs. mean of 65 points at 6 months; P < 0.01). CONCLUSIONS: In a large cohort of patients with chronic ocular surface disease related to SJS/TEN, PROSE treatment offers sustained and significant large improvement in visual function and acuity.","corpus_id":1809606,"score":0},{"doc_id":"25680247","title":"Effectiveness of measuring the central field with the Berkeley field test.","abstract":"INTRODUCTION: There are several limitations of the Amsler chart as a screening tool due to its low sensitivity and high false-negative results. The Berkeley central visual field test (BCFT), which is a simple power-point presentation of a 50-point scoring system for the central 10-degree of the visual field, was devised as an alternative to the Amsler chart. OBJECTIVES: To compare the efficacy of measuring the central visual field using the Berkeley central field test (BCFT) and the Amsler grid test. MATERIALS AND METHODS: In a comparative and validity study, 30 subjects with maculopathy and 35 controls were recruited. The maculopathy subjects with the best corrected visual acuity of 20/200 or better and 2.5M for distant and near vision respectively, were included. All the subjects under went a complete eye examination where visual assessment was done using the distant and near vision Log MAR Chart. The subjects were assessed with the Amsler chart-II at a distance of 30 cm. The BCFT was used as a 50- point scoring system. The effectiveness of BCFT was compared with that of the Amsler grid regarding the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). RESULTS: Out of 65 subjects, 30 subjects had maculopathy and 35 were normal. The mean age of the 65 subjects was 49.8±9.1 years. Of the 30 subjects with maculopathy, the majority (54%) had age- related macular degeneration. The sensitivity, specificity, PPV and NPV of the Amsler grid test were found to be 80%, 100%, 100% and 87%, respectively, whereas those of the BCFT were 71%, 99%, 98% and 82% (p=0.37). CONCLUSION: The BCFT test was as good as the Amsler grid test at detecting the presence of maculopathy.","corpus_id":31281796,"score":0},{"doc_id":"26272444","title":"Impact of cataract surgery on vision-related life performances: the usefulness of Real-Life Vision Test for cataract surgery outcomes evaluation.","abstract":"PurposeReal-Life Vision Test (RLVT) is a newly developed performance-based measures of functional vision. This present study is designed to determine whether it could be a meaningful assessment for cataract surgery outcomes evaluation. Patients and methodsAge-related cataract patients (56) who scheduled for bilateral cataract surgery and 44 age-matched controls were evaluated by four types of measurements: (1) demographic, medical, cognitive and depressive evaluation, and the reaction time testing; (2) clinical measures (visual acuity, contrast sensitivity, stereopsis, and color perception); (3) the 25-item National Eye Institute's Visual Functioning Questionnaire (NEI-VFQ); (4) the RLVT. Spearman's coefficients and multiple regression analysis were conducted to investigate the relationship among RLVT, clinical measures, and self-report assessment of visual function. ResultsThe results of RLVT, clinical measures, and NEI-VFQ total scores were improved significantly after cataract surgery. There were no differences between control subjects and post-surgery patients with respect to NEI-VFQ-25 total scores, self-rating depression scale scores and three tasks of RLVT. Change of RLVT was significantly associated with the change of clinical measures in the cataract group. Multiple regression analysis demonstrated that change of distance, intermediate, and near visual acuity, and binocular contrast sensitivity were significant predictors of improvements of RLVT.ConclusionsCataract surgery could improve real-world visual ability effectively for cataract patients. Our study highlights the potential usefulness of RLVT as an adjunct to the current outcomes evaluation system for cataract surgery. The use of RLVT combined with clinical and self-survey methods may be the comprehensive strategy to manifest the impact of cataract surgery on patients' overall vision-related quality of life.","corpus_id":32528470,"score":0},{"doc_id":"26664798","title":"Trail Making Test performance contributes to subjective judgment of visual efficiency in older adults.","abstract":"Introduction. The determinant factors that influence self-reported quality of vision have yet to be fully elucidated. This study evaluated a range of contextual information, established psychophysical tests, and in particular, a series of cognitive tests as potentially novel determinant factors. Materials & Methods. Community dwelling adults (aged 50+) recruited to Wave 1 of The Irish Longitudinal Study on Ageing, excluding those registered blind, participated in this study (N = 5,021). Self-reports of vision were analysed in relation to visual acuity and contrast sensitivity, ocular pathology, visual (Choice Response Time task; Trail Making Test) and global cognition. Contextual factors such as having visited an optometrist and wearing glasses were also considered. Ordinal logistic regression was used to determine univariate and multivariate associations. Results and Discussion. Poor Trail Making Test performance (Odds ratio, OR = 1.36), visual acuity (OR = 1.72) and ocular pathology (OR = 2.25) were determinant factors for poor versus excellent vision in self-reports. Education, wealth, age, depressive symptoms and general cognitive fitness also contributed to determining self-reported vision. Conclusions. Trail Making Test contribution to self-reports may capture higher level visual processing and should be considered when using self-reports to assess vision and its role in cognitive and functional health.","corpus_id":5707903,"score":0},{"doc_id":"29386615","title":"Corneal sensitivity and subjective complaints of ocular pain in patients with fibromyalgia.","abstract":"PurposeFibromyalgia (FM) is a chronic pain disorder associated with pain and hypersensitivity in various parts of the body. The aim of this study was to understand whether changes in corneal sensitivity were associated with the subjective complaints of these patients. Patients and methodsIn this study, we included 36 patients with FM (30 female, 6 male, mean age: 46.7±9.2 years) and 39 healthy control subjects (33 females, 6 males, mean age: 44.3±7.6 years). We performed a detailed ophthalmological examination, measured tear film breakup time (TBUT), and performed Schirmer I test without anesthetic (SIT). Only patients that did not have any eye disease were included in this study. Subjective complaints of the patients were evaluated with ocular surface disease index (OSDI) scores and the corneal sensation was evaluated with Cochet-Bonnet esthesiometer. ResultsThere was no significant difference between the groups for age, sex, and visual acuity. Both SIT (16.1 mm vs 15.3 mm, P=0.36) and TBUT results (17.8 s vs 18.8 s, P=0.40) were similar in FM group and the controls subjects. However, corneal sensations in central (60.0 mm vs 55.0 mm, P=0.03), superior (57.5 mm vs 50.0 mm, P=0.005), and inferior (53.89 mm vs 46.03 mm, P<0.001) regions were significantly increased in FM patients. There was a significant positive correlation between corneal sensation and OSDI scores. ConclusionIn this study, we have demonstrated that the patients with FM have increased corneal sensitivity and have related ocular surface complaints similar to dry eye disease in the absence of it.","corpus_id":4713527,"score":0}],"string":"[\n {\n \"doc_id\": \"19140660\",\n \"title\": \"What predicts changes in useful field of view test performance?\",\n \"abstract\": \"The Useful Field of View Test (UFOV) has been used as an examination of age-related changes in visual processing and cognition and as an indicator of everyday performance outcomes, particularly driving, for over 20 years. How UFOV performance changes with age and what may impact such changes have not previously been investigated longitudinally. Predictors of change in UFOV performance over a 5-year period among control group participants (N=690) from the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) study were examined. Random effects models were estimated with 4-subtest-total UFOV as the outcome and with baseline age, education, gender, race, visual acuity, depressive symptoms, mental status, and self-rated health, as well as attrition, as predictors. UFOV performance generally followed a curvilinear pattern, improving and then declining over time. Only increased age was consistently related to greater declines in UFOV performance over time. UFOV and Digit Symbol Substitution subtest, a standard measure of cognitive speed, had similar trajectories of change. The implications of these results are discussed.\",\n \"corpus_id\": 38937595,\n \"score\": 2\n },\n {\n \"doc_id\": \"22048613\",\n \"title\": \"Impaired attentional disengagement in older adults with useful field of view decline.\",\n \"abstract\": \"OBJECTIVES: Typical measures of the useful field of view (UFOV) involve many components of attention. The objective of the current research was to examine the attentional operations that might underlie declines in the UFOV. METHOD AND RESULTS: We used 2 basic attention tasks to characterize the profile of visual attention in UFOV-impaired and -unimpaired observers. Our results suggested that declines in the UFOV result from a deficit in attentional disengagement, not a decrease in attentional breadth or scope. DISCUSSION: The results suggested that UFOV decline in normal aging can be associated with a specific attentional operation, namely attentional disengagement. These results suggest that the underlying cause of UFOV decline may not be a restriction in the breadth or scope of attention. Because the UFOV is a reliable predictor of driving safety, our results point to attentional components that are critical for the visual behavior of older adults.\",\n \"corpus_id\": 14147187,\n \"score\": 2\n },\n {\n \"doc_id\": \"22830667\",\n \"title\": \"Visual search for features and conjunctions following declines in the useful field of view.\",\n \"abstract\": \"UNLABELLED: BACKGROUND/STUDY CONTEXT: Typical measures for assessing the useful field (UFOV) of view involve many components of attention. The objective of the current experiment was to examine differences in visual search efficiency for older individuals with and without UFOV impairment. METHODS: The authors used a computerized screening instrument to assess the useful field of view and to characterize participants as having an impaired or normal UFOV. Participants also performed two visual search tasks, a feature search (e.g., search for a green target among red distractors) or a conjunction search (e.g., a green target with a gap on its left or right side among red distractors with gaps on the left or right and green distractors with gaps on the top or bottom). RESULTS: Visual search performance did not differ between UFOV impaired and unimpaired individuals when searching for a basic feature. However, search efficiency was lower for impaired individuals than unimpaired individuals when searching for a conjunction of features. CONCLUSION: The results suggest that UFOV decline in normal aging is associated with conjunction search. This finding suggests that the underlying cause of UFOV decline may arise from an overall decline in attentional efficiency. Because the useful field of view is a reliable predictor of driving safety, the results suggest that decline in the everyday visual behavior of older adults might arise from attentional declines.\",\n \"corpus_id\": 17481692,\n \"score\": 2\n },\n {\n \"doc_id\": \"24642933\",\n \"title\": \"Useful field of view test.\",\n \"abstract\": \"The useful field of view test was developed to reflect the visual difficulties that older adults experience with everyday tasks. Importantly, the useful field of view test (UFOV) is one of the most extensively researched and promising predictor tests for a range of driving outcomes measures, including driving ability and crash risk as well as other everyday tasks. Currently available commercial versions of the test can be administered using personal computers; these measure the speed of visual processing for rapid detection and localization of targets under conditions of divided visual attention and in the presence and absence of visual clutter. The test is believed to assess higher-order cognitive abilities, but performance also relies on visual sensory function because in order for targets to be attended to, they must be visible. The format of the UFOV has been modified over the years; the original version estimated the spatial extent of useful field of view, while the latest version measures visual processing speed. While deficits in the useful field of view are associated with functional impairments in everyday activities in older adults, there is also emerging evidence from several research groups that improvements in visual processing speed can be achieved through training. These improvements have been shown to reduce crash risk, and can have a positive impact on health and functional well-being, with the potential to increase the mobility and hence the independence of older adults.\",\n \"corpus_id\": 38955211,\n \"score\": 2\n },\n {\n \"doc_id\": \"24705277\",\n \"title\": \"Cognitive and visual predictors of UFOV performance in older adults.\",\n \"abstract\": \"Eighty two community dwelling older adults (52 females) aged 62-92 years (mean=75) completed a battery of cognitive and visual tests selected to assess functions relevant to driving performance. These were visual acuity, contrast sensitivity, general mental competence (Mini Mental State Examination, MMSE), processing speed (Inspection Time, IT), crowding across the visual field (Proficiency of Peripheral Vision Processing, ProPerVis) and change detection (DriverScan). These six tasks provided predictor variables for performance on the Useful Field of View test (UFOV), a well validated test of fitness to drive that includes subtests for (i) processing speed; (ii) divided attention; and (iii) selective attention. Relative importance regression analyses confirmed that UFOV is sensitive to attentional and speed processes but suggested that subtest (i) primarily reflects visual acuity and contrast sensitivity; subtest (ii) is better explained by change detection and processing speed; and subtest (iii) predominantly reflects crowding and contrast sensitivity. Unexpectedly, given no evidence of substantial cognitive decline, MMSE contributed significantly to performance on the more complex subtests (ii) and (iii).\",\n \"corpus_id\": 29207146,\n \"score\": 2\n },\n {\n \"doc_id\": \"25976135\",\n \"title\": \"[Principle of the useful field of view and normative data].\",\n \"abstract\": \"Principes de réalisation du champ visuel attentionnel et élaboration de normes. PURPOSE: The useful field of view is a test which takes into account the influence of patient attention during the evaluation of the visual field. This study aims to generate normative data for an adaptation of the useful field of view (UFOV) test. These normative data are essential to judge, in a clinical setting, whether patients' performance is normal or not across demographically similar peers, in order to advise whether or not to resume driving after a brain injury (traumatic brain injury, stroke or cerebral tumour). PATIENTS AND METHODS: This study examined demographic influences on an UFOV adaptation in a sample of 52 control participants (17 males and 35 females, aged 19 to 69) with no prior ophthalmologic or neurologic history. This adaptation used three visual attention tasks. In a simple task (ST), the participant had to detect, as fast as (s)he could, a single target in a visual display; in a double task (DT,) (s)he had to detect both a central and a lateral target in a double task with visual distractions present on the screen. The number of missed targets and the time needed to detect them are measured. RESULTS: Time to detect target was found to differ by gender and by age. Men and young people (from 19 to 29 years) are faster at detecting central and lateral targets. However, no demographic influence was observed on the number of missed targets. CONCLUSIONS: A normative table for this French UFOV adaptation is provided. This will allow clinicians to compare patient performance with similar peers and may help in identifying persons who would benefit from training on a driving simulator or having a road test with a driving-school.\",\n \"corpus_id\": 32947812,\n \"score\": 2\n },\n {\n \"doc_id\": \"26236026\",\n \"title\": \"Perceptual and cognitive neural correlates of the useful field of view test in older adults.\",\n \"abstract\": \"The Useful Field of View Test (UFOV) is often used as a behavioral assessment of age-related decline in visual perception and cognition. Poor performance may reflect slowed processing speed, difficulty dividing attention, and difficulty ignoring irrelevant information. However, the underlying neural correlates of UFOV performance have not been identified. The relationship between older adults׳ UFOV performance and event-related potential (ERP) components reflecting visual processing was examined. P1 amplitude increased with better UFOV performance involving object identification (subtest 1), suggesting that this task is associated with stimulus processing at an early perceptual level. Better performance in all UFOV subtests was associated with faster speed of processing, as reflected by decreases in P3b latency. Current evidence supports the hypothesis that the UFOV recruits both early perceptual and later cognitive processing involved in attentional control. The implications of these results are discussed.\",\n \"corpus_id\": 3971047,\n \"score\": 2\n },\n {\n \"doc_id\": \"26782018\",\n \"title\": \"Incremental validity of Useful Field of View subtests for the prediction of instrumental activities of daily living.\",\n \"abstract\": \"INTRODUCTION: The Useful Field of View Test (UFOV®) is a cognitive measure that predicts older adults' ability to perform a range of everyday activities. However, little is known about the individual contribution of each subtest to these predictions, and the underlying constructs of UFOV performance remain a topic of debate. METHOD: We investigated the incremental validity of UFOV subtests for the prediction of Instrumental Activities of Daily Living (IADL) performance in two independent datasets, the SKILL (n = 828) and ACTIVE (n = 2426) studies. We then explored the cognitive and visual abilities assessed by UFOV using a range of neuropsychological and vision tests administered in the SKILL study. RESULTS: In the four subtest variant of UFOV, only Subtests 2 and 3 consistently made independent contributions to the prediction of IADL performance across three different behavioral measures. In all cases, the incremental validity of UFOV Subtests 1 and 4 was negligible. Furthermore, we found that UFOV was related to processing speed, general nonspeeded cognition, and visual function; the omission of Subtests 1 and 4 from the test score did not affect these associations. CONCLUSIONS: UFOV Subtests 1 and 4 appear to be of limited use to predict IADL and possibly other everyday activities. Future research should investigate whether shortening UFOV by omitting these subtests is a reliable and valid assessment approach.\",\n \"corpus_id\": 24804625,\n \"score\": 2\n },\n {\n \"doc_id\": \"26808364\",\n \"title\": \"Relationship between Functional Visual Acuity and Useful Field of View in Elderly Drivers.\",\n \"abstract\": \"PURPOSE: To investigate the relationship between the functional visual acuity (FVA) and useful field of view (UFOV) in elderly drivers and assess the usefulness of the FVA test to screen driving aptitude in elderly drivers. METHODS: This study included 45 elderly drivers (31 men, 14 women; mean age, 68.1 years) and 30 younger drivers (26 men, 4 women; mean age, 34.2 years) who drive regularly. All participants underwent measurement of the binocular corrected distant visual acuity (CDVA), binocular corrected distant FVA (CDFVA), and Visual Field with Inhibitory Tasks Elderly Version (VFIT-EV) to measure UFOV. The tear function and cognitive status also were evaluated. RESULTS: The CDVA, the CDFVA, cognitive status, and the correct response rate (CAR) of the VFIT-EV were significantly worse in the elderly group than in the control group (P = 0.000 for all parameters). The cognitive status was correlated significantly with the CDVA (r = -0.301, P = 0.009), CDFVA (r = -0.402, P = 0.000), and the CAR of the VFIT-EV (r = 0.348, P = 0.002) in all subjects. The results of the tear function tests were not correlated with the CDVA, CDFVA, or VFIT-EV in any subjects. Stepwise regression analysis for all subjects in the elderly and control groups showed that the CDFVA predicted the CAR most significantly among the clinical factors evaluated. CONCLUSION: The FVA test is a promising method to screen the driving aptitude, including both visual and cognitive functions, in a short time.\",\n \"corpus_id\": 16380182,\n \"score\": 2\n },\n {\n \"doc_id\": \"29270605\",\n \"title\": \"A meta-analysis of perceptual and cognitive functions involved in useful-field-of-view test performance.\",\n \"abstract\": \"The useful-field-of-view (UFOV) test measures the amount of information someone can extract from a visual scene in one glance. Its scores show relatively strong relationships with everyday activities. The UFOV test consists of three computer tests, suggested to measure processing speed and central vision, divided attention, and selective attention. However, other functions seem to be involved as well. In order to investigate the contribution of these suggested and other perceptual and cognitive functions, we performed a meta-analysis of 116 Pearson's correlation coefficients between UFOV scores and other test scores reported in 18 peer-reviewed articles. We divided these correlations into nine domains: attention, executive functioning, general cognition, memory, spatial ability, visual closure, contrast sensitivity, visual processing speed, and visual acuity. A multivariate mixed-effects model analysis revealed that each domain correlated significantly with each of the UFOV subtest scores. These correlations were stronger for Subtests 2 and 3 than for Subtest 1. Furthermore, some domains were more strongly correlated to the UFOV than others across subtests. We did not find interaction effects between subtest and domain, indicating that none of the UFOV subtests is more selectively sensitive to a particular domain than the others. Thus, none of the three UFOV subtests seem to measure one clear construct. Instead, a range of visual and cognitive functions is involved. Perhaps this is the reason for the UFOV's high ecological validity, as it involves many functions at once, making it harder to compensate if one of them fails.\",\n \"corpus_id\": 114413,\n \"score\": 2\n },\n {\n \"doc_id\": \"17962396\",\n \"title\": \"Assessing visual fields for driving in patients with paracentral scotomata.\",\n \"abstract\": \"BACKGROUND: The binocular Esterman visual field test (EVFT) is the current visual field test for driving in the UK. Merging of monocular field tests (Integrated Visual Field, IVF) has been proposed as an alternative for glaucoma patients. AIMS: To examine the level of agreement between the EVFT and IVF for patients with binocular paracentral scotomata, caused by either ophthalmological or neurological conditions, and to compare outcomes with useful field of view (UFOV) performance, a test of visual attention thought to be important in driving. METHODS: 60 patients with binocular paracentral scotomata but normal visual acuity (VA) were recruited prospectively. Subjects completed and were classified as \\\"pass\\\" or \\\"fail\\\" for the EVFT, IVF and UFOV. RESULTS: Good agreement occurred between the EVFT and IVF in classifying subjects as \\\"pass\\\" or \\\"fail\\\" (kappa = 0.84). Classifications disagreed for four subjects with paracentral scotomata of neurological origin (three \\\"passed\\\" IVF yet \\\"failed\\\" EVFT). Mean UFOV scores did not differ between those who \\\"passed\\\" and those who \\\"failed\\\" both visual field tests (p = 0.11). Agreement between the visual field tests and UFOV was limited (EVFT kappa = 0.22, IVF kappa 0.32). CONCLUSIONS: Although the IVF and EVFT agree well in classifying visual fields with regard to legal fitness to drive in the UK, the IVF \\\"passes\\\" some individuals currently classed as unfit to drive due to paracentral scotomata of non-glaucomatous origin. The suitability of the UFOV for assessing crash risk in those with visual field loss is questionable.\",\n \"corpus_id\": 9887632,\n \"score\": 1\n },\n {\n \"doc_id\": \"18081908\",\n \"title\": \"Effect of driver distraction and low alcohol concentrations on useful field of view and frequency-doubling technology perimetry.\",\n \"abstract\": \"PURPOSE: To investigate the effects of a mental psychometric task that simulates the distraction effect of a hands-free mobile phone and of low alcohol concentrations (0.3-0.5 g/l) on two tests: the useful field of view (UFOV) and frequency-doubling technology (FDT) perimetry. METHODS: Thirty-seven healthy young vehicle drivers aged 22 +/- 3 years were subjected to a computer version of the UFOV test and FDT perimetry, undertaken according to a counterbalanced within-subject design. The tests were performed in two sessions (an 'alcohol session' and a 'sober session'), while undertaking or not undertaking a psychometric test [the Paced Auditory Serial Addition Test (PASAT)] to simulate the effect of distraction. Each subject was instructed to concentrate on the PASAT while taking each test. RESULTS: UFOV scores were affected when the PASAT was performed simultaneously (P < 0.0001) in that longer times were required to identify a central target and the location of a peripheral target. FDT perimetry was affected by the addition of the PASAT, with a significant reduction in mean sensitivity and a localized sensitivity loss [pattern standard deviation (PSD) >6 dB]. Test times, false-positive and negative catch trial responses were all increased. However, the UFOV test and FDT perimetry results were not significantly affected by a low alcohol concentration. CONCLUSION: Distraction significantly affects performance in the UFOV test and frequency-doubling technology perimetry. Our findings suggest that using a hands-free mobile phone while driving may lead to a low-to-moderate crash risk in young adults with normal visual function.\",\n \"corpus_id\": 20846986,\n \"score\": 1\n },\n {\n \"doc_id\": \"18307055\",\n \"title\": \"[Evaluation of the capacity to drive in patients diagnosed of mild cognitive impairment and dementia].\",\n \"abstract\": \"Valoración de la capacidad de conducción de vehículos en pacientes con diagnóstico de deterioro cognitivo leve y demencia. INTRODUCTION: Mild cognitive impairment (MCI) and dementia involve cognitive changes that may influence driving capacity. OBJECTIVES: a) To study if the tests used for renewing the driver's licence are appropriate; b) to study the MCI patient's driving capacity according to ASDE Driver-Test and Useful Field of View (UFOV) test; c) to study mild dementia (MD) patient's driving capacity according to ASDE and UFOV tests; d) to determine which neuropsychological tests may be useful to make decisions on driving capacity in MCI and MD; e) to study the difference in the evaluation of each neuropsychological test between patients who are able to drive and those who are not, in each MCI subgroups, and f) we will establish the correlation between the neuropsychological tests and driving tests used for licence renewal. METHOD: A total of 184 people were included: 92 MCI, 55 MD and 40 healthy controls. Cognitive functioning was evaluated by Repeatable Battery Assessment for Neuropsychological Status (RBANS), Trail Making Test (TMT) and Kohs' Block Design. Driving capacity was assessed by ASDE and UFOV test. RESULTS: We established the cut-off points for ASDE and UFOV tests. Sensitivity and specificity for the MD on the ASDE test was 86% and 95%, respectively for concentrated attention and monotony resistance subtest. The UFOV test sensitivity was 88%, specificity 81%. For MCI, both tests showed a sensitivity and specificity lower than 70 %. According to the performance on the test only a half of the MCI group could drive. They showed different driving profiles according to MCI subtype. Neuropsychological tests showing the best correlations with performance on driving test were: Kohs' Block Design, Immediate Memory, Delayed Memory and TMT-A. CONCLUSIONS: a) People with MD should not drive; b) both ASDE and UFOV tests can detect driving difficulties in people with dementia; c) according to the UFOV and ASDE, half of those diagnosed of MCI should not drive; d) there are significant differences in memory test (RBANS) between Amnesic MCI patients who are able to drive and those who are not (according to ASDE/UFOV tests); e) there are significant differences in TMT-A between multiple functions MCI patients who are able to drive and those who are not (according to ASDE/UFOV tests), and f) the neuropsychological tests that correlate with the driving test were: Kohs' Block Design, Immediate Memory, Delayed Memory and TMT-A.\",\n \"corpus_id\": 26038109,\n \"score\": 1\n },\n {\n \"doc_id\": \"18808255\",\n \"title\": \"Cognition, but not sensation, mediates age-related changes in the ability to monitor the environment.\",\n \"abstract\": \"The objective of the study was to determine which age-related changes in sensation and cognition are associated with age-related changes in the ability to monitor the environment. To that end, a proxy measure of the ability to monitor the environment (useful field of view, UFOV) and measures of sensation and cognition were collected from young adult (N = 61) and older adult subjects (N = 79). Although UFOV performance was expected to be mediated primarily by cognition rather than by sensation, it was somewhat unexpected to find no reliable associations between UFOV and sensory functioning beyond those of age and cognition.\",\n \"corpus_id\": 7526694,\n \"score\": 1\n },\n {\n \"doc_id\": \"19280448\",\n \"title\": \"The effects of chemotherapy on Useful Field of View (UFOV) in younger and older breast cancer patients.\",\n \"abstract\": \"Chemotherapy is thought to cause cognitive deficits in some breast cancer patients, but the relative effects on older and younger breast cancer patients are unknown. The effects of chemotherapy on everyday cognitive tasks have not been examined. Thirty-eight female breast cancer survivors (3 to 45 months post chemotherapy) were compared to 55 age-matched control participants. Participants completed the Useful Field of View (UFOV), a computerized test of visual information processing that has been shown to decline with age, and which has been used to predict older adults' driving performance. Older chemotherapy patients performed more poorly than controls on the UFOV speed of processing, but not on the other two components. They also performed more poorly than younger chemotherapy patients. On the divided attention and selective attention components of the UFOV, older participants performed more poorly than younger participants, but there were no significant differences between chemotherapy patients and controls. These findings are explained in terms of brain changes thought to be caused by chemotherapy, which might have the most impact on older adults, already at risk for behavioral slowing.\",\n \"corpus_id\": 23286679,\n \"score\": 1\n },\n {\n \"doc_id\": \"19369744\",\n \"title\": \"Comparing visual performance and useful field of view of older and younger drivers - biomed 2009.\",\n \"abstract\": \"Older licensed drivers are involved in more crash deaths than any other age group. A critical issue in reducing these accident numbers is to improve our understanding of the association between the visual performance of these older drivers and their useful field of view (UFOV) when driving. We estimated driver saccadic amplitudes and fixation durations for ten different traffic scenarios using a driving simulator. Six traffic situations presented dangerous or other relevant events to the drivers, with the other four having no dangerous or relevant events. To estimate saccadic amplitudes and fixation durations, eye position data was analyzed during the five seconds before and five seconds after the traffic situations. Results imply that eye movements, fixation durations and number of fixation change as a function of the visual stimuli presented in each traffic situation. The difference in age was found to be significant for number of fixations and fixation time, but not for the total eye movement. Based on these results, we expressed UFOV as a function of saccadic amplitude between fixation points and durations, and estimated the ranges of a sequence UFOVs during the 10-second period for each traffic situation. Our findings suggests that UFOV radius depends on driving scenario, time of event, age-group, driving course, two factor and three-factor interactions among these variables.\",\n \"corpus_id\": 21615848,\n \"score\": 1\n },\n {\n \"doc_id\": \"19417701\",\n \"title\": \"The useful field of view test, normative data in children of school age.\",\n \"abstract\": \"PURPOSE: The incidence of early brain injury in children is rising, mainly because of changing reproductive demographics and better perinatal care. Early brain injury may be associated with altered visual perception and visuospatial attention. The useful field of view test (UFOV) has been developed to assess visual attention and processing speed in the elderly. The UFOV may have utility in the evaluation of children with early brain injury. The aim of this study was to collect age-specific normative data for the UFOV test. METHODS: Subjects were recruited from visitors at Glasgow Science Centre. One hundred thirty-five healthy children and young adults were tested (range: 5-22 years). After a comprehensive visual screening to establish normal visual function, all three subtests of the UFOV (1: Processing Speed; 2: Divided Attention; 3: Selective Attention) were performed. RESULTS.: All the children were able to understand and complete all subtests. UFOV scores improved monotonically with age, for all subtests, throughout the primary school years, with subtest 3 showing the greatest improvement. By age 14, UFOV scores had reached adult levels. DISCUSSION: UFOV performance shows measurable improvement during middle to late childhood, as has been previously found for abilities such as visual acuity. This is a simple test, which was easily understood and performed by all children in the study. Thus, we believe that our results are suggestive of continuing development in visual attention and processing during this period. CONCLUSIONS: The UFOV is an objective, standardized computer-based test of visual attention. This study indicates suitability for use with children. It remains to be determined how successful this test proves to be in discriminating between normal children and those with early brain injury.\",\n \"corpus_id\": 205907637,\n \"score\": 1\n },\n {\n \"doc_id\": \"19462009\",\n \"title\": \"Is visual selective attention in deaf individuals enhanced or deficient? The case of the useful field of view.\",\n \"abstract\": \"BACKGROUND: Early deafness leads to enhanced attention in the visual periphery. Yet, whether this enhancement confers advantages in everyday life remains unknown, as deaf individuals have been shown to be more distracted by irrelevant information in the periphery than their hearing peers. Here, we show that, in a complex attentional task, a performance advantage results for deaf individuals. METHODOLOGY/PRINCIPAL FINDINGS: We employed the Useful Field of View (UFOV) which requires central target identification concurrent with peripheral target localization in the presence of distractors - a divided, selective attention task. First, the comparison of deaf and hearing adults with or without sign language skills establishes that deafness and not sign language use drives UFOV enhancement. Second, UFOV performance was enhanced in deaf children, but only after 11 years of age. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that, following early auditory deprivation, visual attention resources toward the periphery slowly get augmented to eventually result in a clear behavioral advantage by pre-adolescence on a selective visual attention task.\",\n \"corpus_id\": 210343,\n \"score\": 1\n },\n {\n \"doc_id\": \"19916131\",\n \"title\": \"Useful field of view as a reliable screening measure of driving performance in people with Parkinson's disease: results of a pilot study.\",\n \"abstract\": \"PURPOSE: To determine the correlations of the Useful Field of View (UFOV), compared to other clinical tests of Parkinson's disease (PD); vision; and cognition with measures of on-road driving assessments and to quantify the UFOV's ability to indicate passing/failing an on-road test in people with PD. METHODS: Nineteen randomly selected people with idiopathic PD, mean age = 74.8 (6.1), 14 (73.7%) men, 18 (94.7%) Caucasians, were age-matched to 104 controls without PD. The controls had a mean age of 75.4 (6.4), 59 (56.7%) men, 96 (92.3%) Caucasians. Both groups were referred for a driving evaluation after institutional review board approval. RESULTS: Compared to neuropsychological and clinical tests of vision and cognition, the UFOV showed the strongest correlations (r > .75, p < 0.05) with measures of failing a standardized road test and number of driving errors. Among PD patients, the UFOV Risk Index score of 3 (range 1-5) was established as the optimal cutoff value for passing the on-road test, with sensitivity 87 percent and specificity 82 percent, AUC = 92 percent (SE 0.61, p = .002). Similarly, the UFOV 2 (divided attention) optimum cutoff value is 223 ms (range 16-500 ms), sensitivity 87.5 percent, specificity 81.8 percent, AUC = 91 percent (SE 0.73, p = .003). The UFOV 3 (selected attention) optimal cutoff value is 273 ms (range 16-500 ms), sensitivity 75 percent, specificity 72.7 percent, AUC = 87 percent (SE 0.81, p = .007). CONCLUSION: In this pilot study among PD patients, the UFOV may be a superior screening measure (compared to other measures of disease, cognition, and vision) for predicting on-road driving performance but its rigor must be verified in a larger sample of people with PD.\",\n \"corpus_id\": 24995547,\n \"score\": 1\n },\n {\n \"doc_id\": \"22269568\",\n \"title\": \"The role of cognitive and visual abilities as predictors in the Multifactorial Model of Driving Safety.\",\n \"abstract\": \"OBJECTIVE: The current study evaluated part of the Multifactorial Model of Driving Safety to elucidate the relative importance of cognitive function and a limited range of standard measures of visual function in relation to the Capacity to Drive Safely. Capacity to Drive Safely was operationalized using three validated screening measures for older drivers. These included an adaptation of the well validated Useful Field of View (UFOV) and two newer measures, namely a Hazard Perception Test (HPT), and a Hazard Change Detection Task (HCDT). METHOD: Community dwelling drivers (n=297) aged 65-96 were assessed using a battery of measures of cognitive and visual function. RESULTS: Factor analysis of these predictor variables yielded factors including Executive/Speed, Vision (measured by visual acuity and contrast sensitivity), Spatial, Visual Closure, and Working Memory. Cognitive and Vision factors explained 83-95% of age-related variance in the Capacity to Drive Safely. Spatial and Working Memory were associated with UFOV, HPT and HCDT, Executive/Speed was associated with UFOV and HCDT and Vision was associated with HPT. CONCLUSION: The Capacity to Drive Safely declines with chronological age, and this decline is associated with age-related declines in several higher order cognitive abilities involving manipulation and storage of visuospatial information under speeded conditions. There are also age-independent effects of cognitive function and vision that determine driving safety.\",\n \"corpus_id\": 25292002,\n \"score\": 1\n },\n {\n \"doc_id\": \"22366710\",\n \"title\": \"Useful field of view predicts driving in the presence of distracters.\",\n \"abstract\": \"PURPOSE: The Useful Field of View (UFOV) test has been shown to be highly effective in predicting crash risk among older adults. An important question which we examined in this study is whether this association is due to the ability of the UFOV to predict difficulties in attention-demanding driving situations that involve either visual or auditory distracters. METHODS: Participants included 92 community-living adults (mean age 73.6 ± 5.4 years; range 65-88 years) who completed all three subtests of the UFOV involving assessment of visual processing speed (subtest 1), divided attention (subtest 2), and selective attention (subtest 3); driving safety risk was also classified using the UFOV scoring system. Driving performance was assessed separately on a closed-road circuit while driving under three conditions: no distracters, visual distracters, and auditory distracters. Driving outcome measures included road sign recognition, hazard detection, gap perception, time to complete the course, and performance on the distracter tasks. RESULTS: Those rated as safe on the UFOV (safety rating categories 1 and 2), as well as those responding faster than the recommended cut-off on the selective attention subtest (350 msec), performed significantly better in terms of overall driving performance and also experienced less interference from distracters. Of the three UFOV subtests, the selective attention subtest best predicted overall driving performance in the presence of distracters. CONCLUSIONS: Older adults who were rated as higher risk on the UFOV, particularly on the selective attention subtest, demonstrated poorest driving performance in the presence of distracters. This finding suggests that the selective attention subtest of the UFOV may be differentially more effective in predicting driving difficulties in situations of divided attention which are commonly associated with crashes.\",\n \"corpus_id\": 5116383,\n \"score\": 1\n },\n {\n \"doc_id\": \"22878441\",\n \"title\": \"Using the real-life vision test to assess the functional vision of age-related cataract patients.\",\n \"abstract\": \"PURPOSE: (1) To describe and validate a newly developed, timed performance-based measures of functional vision-the real-life vision test (RLVT). ( 2) To determine how RLVT relates to clinical measures and self-report assessment of visual function and the complex interactions among visual impairment, psychosocial status, and demographic factors. METHODS: A total of 64 patients with age-related cataract and 45 age-matched controls were evaluated by four types of measurements: (1) demographic, medical, cognitive, and depressive evaluation and the reaction time (RT) testing; (2) clinical measures (visual acuity, contrast sensitivity, stereopsis, and the color perception); (3) the 25-item National Eye Institute's Visual Functioning Questionnaire; and (4) the RLVT. Spearman's coefficients, partial correlation, and multiple regression analysis were conducted to determine the relationship among RLVT, clinical measures, and self-report assessment of visual function while controlling for confounders. RESULTS: Control subjects performed RLVT significantly better than the cataract patients. RLVT correlated well with both clinical and self-report assessments of visual function. All subscales of RLVT remained highly associated with most of the clinical measures, even after adjusting for age, years of education, depression, cognitive status, and the RT. Distance, intermediate and near visual acuity, and binocular contrast sensitivity were significant predictors of the RLVT performances. CONCLUSIONS: Given the strong relationship among RLVT, clinical measures, and the self-report assessments, our results highlight the potential usefulness of RLVT for assessing the functional vision of cataract patients. RLVT may provide information not obtainable from clinical measures or surveys and therefore it is essential to be incorporated into future ophthalmological practice.\",\n \"corpus_id\": 205139749,\n \"score\": 1\n },\n {\n \"doc_id\": \"23954688\",\n \"title\": \"Can we improve clinical prediction of at-risk older drivers?\",\n \"abstract\": \"OBJECTIVES: To conduct a pilot study to evaluate the predictive value of the Montreal Cognitive Assessment test (MoCA) and a brief test of multiple object tracking (MOT) relative to other tests of cognition and attention in identifying at-risk older drivers, and to determine which combination of tests provided the best overall prediction. METHODS: Forty-seven currently licensed drivers (58-95 years), primarily from a clinical driving evaluation program, participated. Their performance was measured on: (1) a screening test battery, comprising MoCA, MOT, Mini-Mental State Examination (MMSE), Trail-Making Test, visual acuity, contrast sensitivity, and Useful Field of View (UFOV) and (2) a standardized road test. RESULTS: Eighteen participants were rated at-risk on the road test. UFOV subtest 2 was the best single predictor with an area under the curve (AUC) of .84. Neither MoCA nor MOT was a better predictor of the at-risk outcome than either MMSE or UFOV, respectively. The best four-test combination (MMSE, UFOV subtest 2, visual acuity and contrast sensitivity) was able to identify at-risk drivers with 95% specificity and 80% sensitivity (.91 AUC). CONCLUSIONS: Although the best four-test combination was much better than a single test in identifying at-risk drivers, there is still much work to do in this field to establish test batteries that have both high sensitivity and specificity.\",\n \"corpus_id\": 31681055,\n \"score\": 1\n },\n {\n \"doc_id\": \"23968796\",\n \"title\": \"Predicting older driver on-road performance by means of the useful field of view and trail making test part B.\",\n \"abstract\": \"The Useful Field of View(®) (UFOV) and Trail Making Test Part B (Trails B) are measures of divided attention. We determined which measure was more accurate in predicting on-road outcomes among drivers (N = 198, mean age = 73.86, standard deviation = 6.05). Receiver operating characteristic curves for the UFOV (Risk Index [RI] and Subtests 1-3) and Trails B significantly predicted on-road outcomes. Contrasting Trails B with the UFOV RI and subtests, the only difference was found between the UFOV RI and Trails B, indicating the UFOV RI was the best predictor of on-road outcomes. Misclassifications of drivers totaled 28 for the UFOV RI, 62 for Trails B, and 58 for UFOV Subtest 2. The UFOV RI is a superior test in predicting on-road outcomes, but the Trails B has acceptable accuracy and is comparable to the other UFOV subtests.\",\n \"corpus_id\": 26669258,\n \"score\": 1\n },\n {\n \"doc_id\": \"24211819\",\n \"title\": \"The Efficacy of InSight Cognitive Training to Improve Useful Field of View Performance: A Brief Report.\",\n \"abstract\": \"OBJECTIVE: It is well established that cognitive speed of processing training (SOPT) improves Useful Field of View (UFOV) performance and transfers to enhanced performance of instrumental activities of daily living, including driving. InSight is a recently developed version of SOPT formatted for self-administration by older adults with exercises translated into a gaming format. The goal was to examine whether InSight training improves UFOV performance. METHOD: Participants ranged in age between 59-95 years and were randomized to InSight cognitive training or a control condition. Cognitive performance and self-perceptions were measured pre- and post-training, or for controls, after an equivalent delay. Participants completed training twice a week over a 12-week period with the goal of completing 20 sessions. RESULTS: Participants randomized to InSight training experienced greater improvements in their UFOV performance relative to the control condition, F(1, 58) = 4.26, p = .043, but no changes in cognitive self-perceptions were found. CONCLUSIONS: The InSight program is a viable tool for enhancing older adults' UFOV performance. Future research should examine if training gains from the program endure and transfer to improved everyday function.\",\n \"corpus_id\": 13567409,\n \"score\": 1\n },\n {\n \"doc_id\": \"24273754\",\n \"title\": \"USEFUL FIELD OF VIEW IMPAIRMENTS IN DRIVERS WITH OBSTRUCTIVE SLEEP APNEA.\",\n \"abstract\": \"As a group, drivers with obstructive sleep apnea (OSA) have an increased risk for motor vehicle crashes, but determining individual crash risk is difficult. We tested the hypothesis that drivers with OSA have impaired visual attention, as indexed by reduced useful field of view (UFOV), a predictor of high-risk driving. Forty-one drivers with untreated OSA and 50 comparison drivers were assessed by UFOV. OSA drivers performed significantly worse than controls on all UFOV subtests and had reduced UFOV as indicated by a higher mean total UFOV score (p = 0.0017). However, only 4 OSA and 2 control drivers had values indicative of high crash risk (UFOV reduction >23%). Drivers with OSA have reduced UFOV compared to drivers without neurological or sleep disorders. However, as UFOV identifies few high-risk drivers, its role in assessing crash risk in an unselected population of drivers with OSA appears to be limited.\",\n \"corpus_id\": 11282436,\n \"score\": 1\n },\n {\n \"doc_id\": \"24558495\",\n \"title\": \"Visual attention measures predict pedestrian detection in central field loss: a pilot study.\",\n \"abstract\": \"PURPOSE: The ability of visually impaired people to deploy attention effectively to maximize use of their residual vision in dynamic situations is fundamental to safe mobility. We conducted a pilot study to evaluate whether tests of dynamic attention (multiple object tracking; MOT) and static attention (Useful Field of View; UFOV) were predictive of the ability of people with central field loss (CFL) to detect pedestrian hazards in simulated driving. METHODS: 11 people with bilateral CFL (visual acuity 20/30-20/200) and 11 age-similar normally-sighted drivers participated. Dynamic and static attention were evaluated with brief, computer-based MOT and UFOV tasks, respectively. Dependent variables were the log speed threshold for 60% correct identification of targets (MOT) and the increase in the presentation duration for 75% correct identification of a central target when a concurrent peripheral task was added (UFOV divided and selective attention subtests). Participants drove in a simulator and pressed the horn whenever they detected pedestrians that walked or ran toward the road. The dependent variable was the proportion of timely reactions (could have stopped in time to avoid a collision). RESULTS: UFOV and MOT performance of CFL participants was poorer than that of controls, and the proportion of timely reactions was also lower (worse) (84% and 97%, respectively; p = 0.001). For CFL participants, higher proportions of timely reactions correlated significantly with higher (better) MOT speed thresholds (r = 0.73, p = 0.01), with better performance on the UFOV divided and selective attention subtests (r = -0.66 and -0.62, respectively, p<0.04), with better contrast sensitivity scores (r = 0.54, p = 0.08) and smaller scotomas (r = -0.60, p = 0.05). CONCLUSIONS: Our results suggest that brief laboratory-based tests of visual attention may provide useful measures of functional visual ability of individuals with CFL relevant to more complex mobility tasks.\",\n \"corpus_id\": 1563571,\n \"score\": 1\n },\n {\n \"doc_id\": \"24582906\",\n \"title\": \"Is the size of the useful field of view affected by postural demands associated with standing and stepping?\",\n \"abstract\": \"The useful field of view (UFOV) is the visual area from which information is obtained at a brief glance. While studies have examined the effects of increased cognitive load on the visual field, no one has specifically looked at the effects of postural control or locomotor activity on the UFOV. The current study aimed to examine the effects of postural demand and locomotor activity on UFOV performance in healthy young adults. Eleven participants were tested on three modified UFOV tasks (central processing, peripheral processing, and divided-attention) while seated, standing, and stepping in place. Across all postural conditions, participants showed no difference in their central or peripheral processing. However, in the divided-attention task (reporting the letter in central vision and target location in peripheral vision amongst distracter items) a main effect of posture condition on peripheral target accuracy was found for targets at 57° of eccentricity (p=.037). The mean accuracy reduced from 80.5% (standing) to 74% (seated) to 56.3% (stepping). These findings show that postural demands do affect UFOV divided-attention performance. In particular, the size of the useful field of view significantly decreases when stepping. This finding has important implications for how the results of a UFOV test are used to evaluate the general size of the UFOV during varying activities, as the traditional seated test procedure may overestimate the size of the UFOV during locomotor activities.\",\n \"corpus_id\": 33906709,\n \"score\": 1\n },\n {\n \"doc_id\": \"24985476\",\n \"title\": \"The effect of aging on crowded letter recognition in the peripheral visual field.\",\n \"abstract\": \"PURPOSE: Crowding describes the increased difficulty in identifying a target object when it is surrounded by nearby objects (flankers). A recent study investigated the effect of age on visual crowding and found equivocal results: Although crowded visual acuity was worse in older participants, crowding expressed as a ratio did not change with age. However, the spatial extent of crowding is a better index of crowding effects and remains unknown. In the present study, we used established psychophysical methods to characterize the effect of age on visual crowding (magnitude and extent) in a letter recognition task. METHODS: Letter recognition thresholds were determined for three different flanker separations in 54 adults (aged 18-76 years) with normal vision. Additionally, the spatial extent of crowding was established by measuring spacing thresholds: the flanker-to-target separation required to produce a given reduction in performance. Uncrowded visual acuity, crowded visual acuity, and spacing thresholds were expressed as a function of age, avoiding arbitrary categorization of young and old participants. RESULTS: Our results showed that uncrowded and crowded visual acuities do not change significantly as a function of age. Furthermore, spacing thresholds did not change with age and approximated Bouma's law (half eccentricity). CONCLUSIONS: These data show that crowding in adults is unaffected by senescence and provide additional evidence for distinct neural mechanisms mediating surround suppression and visual crowding, since the former shows a significant age effect. Finally, our data suggest that the well-documented age-related decline in peripheral reading ability is not due to age-related changes in visual crowding.\",\n \"corpus_id\": 12232054,\n \"score\": 1\n },\n {\n \"doc_id\": \"25110186\",\n \"title\": \"Is the useful field of view a good predictor of at-fault crash risk in elderly Japanese drivers?\",\n \"abstract\": \"AIM: Although age-related decline in the useful field of view (UFOV) is well recognized as a risk factor for at-fault crash involvement in elderly drivers, there is still room to study its applicability to elderly Japanese drivers. In the current study, we thus examined the relationship between UFOV and at-fault crash history in an elderly Japanese population. We also explored whether potential factors that create awareness of reduced driving fitness could be a trigger for the self-regulation of driving in elderly drivers. METHODS: We measured UFOV and at-fault crash history from 151 community-dwelling Japanese aged 60 years or older, and compared UFOV of at-fault crash-free and crash-involved drivers. We also measured self-evaluated driving style using a questionnaire. RESULTS: UFOV in crash-involved drivers was significantly lower than that in crash-free drivers. No significant difference was found in self-evaluated driving style between crash-free and crash-involved drivers. In addition, there was no significant association between UFOV and self-evaluated driving style. CONCLUSIONS: The present study showed that UFOV is a good predictor of at-fault crash risk in elderly Japanese drivers. Furthermore, our data imply that it might be difficult for elderly drivers to adopt appropriate driving strategies commensurate with their current driving competence.\",\n \"corpus_id\": 1522429,\n \"score\": 1\n },\n {\n \"doc_id\": \"25160890\",\n \"title\": \"Cognitive speed of processing training in older adults with visual impairments.\",\n \"abstract\": \"PURPOSE: To examine whether older adults with vision impairment differentially benefit from cognitive speed of processing training (SPT) relative to healthy older adults. METHODS: Secondary data analyses were conducted from a randomised trial on the effects of SPT among older adults. The effects of vision impairment as indicated by (1) near visual acuity, (2) contrast sensitivity, (3) self-reported cataracts and (4) self-reported other eye conditions (e.g., glaucoma, macular degeneration, diabetic retinopathy, optic neuritis, and retinopathy) among participants randomised to either SPT or a social- and computer-contact control group was assessed. The primary outcome was Useful Field of View Test (UFOV) performance. RESULTS: Mixed repeated-measures ancovas demonstrated that those randomized to SPT experienced greater baseline to post-test improvements in UFOV performance relative to controls (p's < 0.001), regardless of impairments in near visual acuity, contrast sensitivity or presence of cataracts. Those with other eye conditions significantly benefitted from training (p = 0.044), but to a lesser degree than those without such conditions. Covariates included age and baseline measures of balance and depressive symptoms, which were significantly correlated with baseline UFOV performance. CONCLUSIONS: Among a community-based sample of older adults with and without visual impairment and eye disease, the SPT intervention was effective in enhancing participants' UFOV performance. The analyses presented here indicate the potential for SPT to enhance UFOV performance among a community-based sample of older adults with visual impairment and potentially for some with self-reported eye disease; further research to explore this area is warranted, particularly to determine the effects of eye diseases on SPT benefits.\",\n \"corpus_id\": 2889824,\n \"score\": 1\n },\n {\n \"doc_id\": \"26046007\",\n \"title\": \"Relationship Between Motor Vehicle Collisions and Results of Perimetry, Useful Field of View, and Driving Simulation in Drivers With Glaucoma.\",\n \"abstract\": \"PURPOSE: To examine the relationship between Motor Vehicle Collisions (MVCs) in drivers with glaucoma and standard automated perimetry (SAP), Useful Field of View (UFOV), and driving simulator assessment of divided attention. METHODS: A cross-sectional study of 153 drivers from the Diagnostic Innovations in Glaucoma Study. All subjects had SAP and divided attention was assessed using UFOV and driving simulation using low-, medium-, and high-contrast peripheral stimuli presented during curve negotiation and car following tasks. Self-reported history of MVCs and average mileage driven were recorded. RESULTS: Eighteen of 153 subjects (11.8%) reported a MVC. There was no difference in visual acuity but the MVC group was older, drove fewer miles, and had worse binocular SAP sensitivity, contrast sensitivity, and ability to divide attention (UFOV and driving simulation). Low contrast driving simulator tasks were the best discriminators of MVC (AUC 0.80 for curve negotiation versus 0.69 for binocular SAP and 0.59 for UFOV). Adjusting for confounding factors, longer reaction times to driving simulator divided attention tasks provided additional value compared with SAP and UFOV, with a 1 standard deviation (SD) increase in reaction time (approximately 0.75 s) associated with almost two-fold increased odds of MVC. CONCLUSIONS: Reaction times to low contrast divided attention tasks during driving simulation were significantly associated with history of MVC, performing better than conventional perimetric tests and UFOV. TRANSLATIONAL RELEVANCE: The association between conventional tests of visual function and MVCs in drivers with glaucoma is weak, however, tests of divided attention, particularly using driving simulation, may improve risk assessment.\",\n \"corpus_id\": 12842198,\n \"score\": 1\n },\n {\n \"doc_id\": \"26122710\",\n \"title\": \"Sensorimotor and cognitive factors associated with the age-related increase of visual field dependence: a cross-sectional study.\",\n \"abstract\": \"Reliance on the visual frame of reference for spatial orientation (or visual field dependence) has been reported to increase with age. This has implications on old adults' daily living tasks as it affects stability, attention, and adaptation capacities. However, the nature and underlying mechanisms of this increase are not well defined. We investigated sensorimotor and cognitive factors possibly associated with increased visual field dependence in old age, by considering functions that are both known to degrade with age and important for spatial orientation and sensorimotor control: reliance on the (somatosensory-based) egocentric frame of reference, visual fixation stability, and attentional processing of complex visual scenes (useful field of view, UFOV). Twenty young, 18 middle-aged, and 20 old adults completed a visual examination, three tests of visual field dependence (RFT, RDT, and GEFT), a test of egocentric dependence (subjective vertical estimation with the body erect and tilted at 70°), a visual fixation task, and a test of visual attentional processing (UFOV®). Increased visual field dependence with age was associated with reduced egocentric dependence, visual fixation stability, and visual attentional processing. In addition, visual fixation instability and reduced UFOV were correlated. Results of middle-aged adults fell between those of the young and old, revealing the progressive nature of the age effects we evaluated. We discuss results in terms of reference frame selection with respect to ageing as well as visual and non-visual information processing. Inter-individual differences amongst old adults are highlighted and discussed with respect to the functionality of increased visual field dependence.\",\n \"corpus_id\": 16251004,\n \"score\": 1\n },\n {\n \"doc_id\": \"26426342\",\n \"title\": \"Predicting Risk of Motor Vehicle Collisions in Patients with Glaucoma: A Longitudinal Study.\",\n \"abstract\": \"PURPOSE: To evaluate the ability of longitudinal Useful Field of View (UFOV) and simulated driving measurements to predict future occurrence of motor vehicle collision (MVC) in drivers with glaucoma. DESIGN: Prospective observational cohort study. PARTICIPANTS: 117 drivers with glaucoma followed for an average of 2.1 ± 0.5 years. METHODS: All subjects had standard automated perimetry (SAP), UFOV, driving simulator, and cognitive assessment obtained at baseline and every 6 months during follow-up. The driving simulator evaluated reaction times to high and low contrast peripheral divided attention stimuli presented while negotiating a winding country road, with central driving task performance assessed as \\\"curve coherence\\\". Drivers with MVC during follow-up were identified from Department of Motor Vehicle records. MAIN OUTCOME MEASURES: Survival models were used to evaluate the ability of driving simulator and UFOV to predict MVC over time, adjusting for potential confounding factors. RESULTS: Mean age at baseline was 64.5 ± 12.6 years. 11 of 117 (9.4%) drivers had a MVC during follow-up. In the multivariable models, low contrast reaction time was significantly predictive of MVC, with a hazard ratio (HR) of 2.19 per 1 SD slower reaction time (95% CI, 1.30 to 3.69; P = 0.003). UFOV divided attention was also significantly predictive of MVC with a HR of 1.98 per 1 SD worse (95% CI, 1.10 to 3.57; P = 0.022). Global SAP visual field indices in the better or worse eye were not predictive of MVC. The longitudinal model including driving simulator performance was a better predictor of MVC compared to UFOV (R2 = 0.41 vs R2 = 0.18). CONCLUSIONS: Longitudinal divided attention metrics on the UFOV test and during simulated driving were significantly predictive of risk of MVC in glaucoma patients. These findings may help improve the understanding of factors associated with driving impairment related to glaucoma.\",\n \"corpus_id\": 15675655,\n \"score\": 1\n },\n {\n \"doc_id\": \"26890935\",\n \"title\": \"The useful field of view assessment predicts simulated commercial motor vehicle driving safety.\",\n \"abstract\": \"OBJECTIVE: The Useful Field of View (UFOV) assessment, a measure of visual speed of processing, has been shown to be a predictive measure of motor vehicle collision (MVC) involvement in an older adult population, but it remains unknown whether UFOV predicts commercial motor vehicle (CMV) driving safety during secondary task engagement. The purpose of this study is to determine whether the UFOV assessment predicts simulated MVCs in long-haul CMV drivers. METHOD: Fifty licensed CMV drivers (Mage = 39.80, SD = 8.38, 98% male, 56% Caucasian) were administered the 3-subtest version of the UFOV assessment, where lower scores measured in milliseconds indicated better performance. CMV drivers completed 4 simulated drives, each spanning approximately a 22.50-mile distance. Four secondary tasks were presented to participants in a counterbalanced order during the drives: (a) no secondary task, (b) cell phone conversation, (c) text messaging interaction, and (d) e-mailing interaction with an on-board dispatch device. RESULTS: The selective attention subtest significantly predicted simulated MVCs regardless of secondary task. Each 20 ms slower on subtest 3 was associated with a 25% increase in the risk of an MVC in the simulated drive. The e-mail interaction secondary task significantly predicted simulated MVCs with a 4.14 times greater risk of an MVC compared to the no secondary task condition. Subtest 3, a measure of visual speed of processing, significantly predicted MVCs in the email interaction task. Each 20 ms slower on subtest 3 was associated with a 25% increase in the risk of an MVC during the email interaction task. CONCLUSIONS: The UFOV subtest 3 may be a promising measure to identify CMV drivers who may be at risk for MVCs or in need of cognitive training aimed at improving speed of processing. Subtest 3 may also identify CMV drivers who are particularly at risk when engaged in secondary tasks while driving.\",\n \"corpus_id\": 26591968,\n \"score\": 1\n },\n {\n \"doc_id\": \"27050950\",\n \"title\": \"Impairing the useful field of view in natural scenes: Tunnel vision versus general interference.\",\n \"abstract\": \"A fundamental issue in visual attention is the relationship between the useful field of view (UFOV), the region of visual space where information is encoded within a single fixation, and eccentricity. A common assumption is that impairing attentional resources reduces the size of the UFOV (i.e., tunnel vision). However, most research has not accounted for eccentricity-dependent changes in spatial resolution, potentially conflating fixed visual properties with flexible changes in visual attention. Williams (1988, 1989) argued that foveal loads are necessary to reduce the size of the UFOV, producing tunnel vision. Without a foveal load, it is argued that the attentional decrement is constant across the visual field (i.e., general interference). However, other research asserts that auditory working memory (WM) loads produce tunnel vision. To date, foveal versus auditory WM loads have not been compared to determine if they differentially change the size of the UFOV. In two experiments, we tested the effects of a foveal (rotated L vs. T discrimination) task and an auditory WM (N-back) task on an extrafoveal (Gabor) discrimination task. Gabor patches were scaled for size and processing time to produce equal performance across the visual field under single-task conditions, thus removing the confound of eccentricity-dependent differences in visual sensitivity. The results showed that although both foveal and auditory loads reduced Gabor orientation sensitivity, only the foveal load interacted with retinal eccentricity to produce tunnel vision, clearly demonstrating task-specific changes to the form of the UFOV. This has theoretical implications for understanding the UFOV.\",\n \"corpus_id\": 15751029,\n \"score\": 1\n },\n {\n \"doc_id\": \"27091370\",\n \"title\": \"Measuring the Useful Field of View During Simulated Driving With Gaze-Contingent Displays.\",\n \"abstract\": \"OBJECTIVE: We aimed to develop and test a new dynamic measure of transient changes to the useful field of view (UFOV), utilizing a gaze-contingent paradigm for use in realistic simulated environments. BACKGROUND: The UFOV, the area from which an observer can extract visual information during a single fixation, has been correlated with driving performance and crash risk. However, some existing measures of the UFOV cannot be used dynamically in realistic simulators, and other UFOV measures involve constant stimuli at fixed locations. We propose a gaze-contingent UFOV measure (the GC-UFOV) that solves the above problems. METHODS: Twenty-five participants completed four simulated drives while they concurrently performed an occasional gaze-contingent Gabor orientation discrimination task. Gabors appeared randomly at one of three retinal eccentricities (5°, 10°, or 15°). Cognitive workload was manipulated both with a concurrent auditory working memory task and with driving task difficulty (via presence/absence of lateral wind). RESULTS: Cognitive workload had a detrimental effect on Gabor discrimination accuracy at all three retinal eccentricities. Interestingly, this accuracy cost was equivalent across eccentricities, consistent with previous findings of \\\"general interference\\\" rather than \\\"tunnel vision.\\\" CONCLUSION: The results showed that the GC-UFOV method was able to measure transient changes in UFOV due to cognitive load in a realistic simulated environment. APPLICATION: The GC-UFOV paradigm developed and tested in this study is a novel and effective tool for studying transient changes in the UFOV due to cognitive load in the context of complex real-world tasks such as simulated driving.\",\n \"corpus_id\": 3806385,\n \"score\": 1\n },\n {\n \"doc_id\": \"27315540\",\n \"title\": \"A Preliminary Study on Normalized Pattern-Reversal Peripheral Field SSVEPs as a Potential Objective Indicator of Useful Field of View Performance.\",\n \"abstract\": \"PURPOSE: Currently, the test for useful field of view (UFOV) typically relies on subjective feedback for detecting peripheral targets while attending to a central target. Steady-state visual evoked potential (SSVEP) recorded from the occipital region of the brain has been frequently used as an objective alternative to replace subjective responses. Our aim was to investigate if a short screening test can approximate UFOV performance objectively. METHODS: We recorded SSVEPs during a simple peripheral task and a UFOV task with and without distractors as well as 30-second offline SSVEPs for eight participants. In all tasks, a peripheral annulus ring of checkered reversal pattern was concurrently presented to the participants to elicit SSVEPs. RESULTS: Orthogonal linear regression analysis found that normalized SSVEP during the UFOV task is predictive of peripheral target detection accuracy (F(1,6) = 16.250, P < 0.01, n = 8) for a task with peripheral distractors. However, this is not the case for a task without distractors (F(1,6) = 0.397, P = 0.552), possibly due to near-perfect accuracy across most participants. Offline normalized SSVEPs also only predicted the peripheral target detection accuracy (F(1,6) = 26.799, P < 0.01) for the UFOV task with peripheral distractors. CONCLUSIONS: Difficult peripheral target detection with distractors is required to differentiate UFOV performance in healthy young adults. The results suggested that offline normalized SSVEPs elicited by 30 seconds of pattern-reversal checkered annulus from the peripheral vision field can identify individuals with good UFOV performance under the stress of a difficult peripheral task.\",\n \"corpus_id\": 20984809,\n \"score\": 1\n },\n {\n \"doc_id\": \"27353969\",\n \"title\": \"Association of visual sensory function and higher-order visual processing skills with incident driving cessation.\",\n \"abstract\": \"BACKGROUND: Many studies on vision and driving cessation have relied on measures of sensory function, which are insensitive to the higher-order cognitive aspects of visual processing. The purpose of this study was to examine the association between traditional measures of visual sensory function and higher-order visual processing skills with incident driving cessation in a population-based sample of older drivers. METHODS: Two thousand licensed drivers aged 70 years or older were enrolled and followed for three years. Tests for central vision and visual processing were administered at baseline and included visual acuity, contrast sensitivity, sensitivity in the driving visual field, visual processing speed (useful field of view [UFOV] Subtest 2 and Trails B) and spatial ability measured by the Visual Closure Subtest of the Motor-free Visual Perception Test. Participants self-reported the month and year of driving cessation and provided a reason for cessation. Cox proportional hazards models were used to generate crude and adjusted hazard ratios with 95% confidence intervals between visual functioning characteristics and risk of driving cessation over a three-year period. RESULTS: During the study period, 164 participants stopped driving, which corresponds to a cumulative incidence of 8.5 per cent. Impaired contrast sensitivity, visual fields, visual processing speed (UFOV and Trails B) and spatial ability were significant risk factors for subsequent driving cessation after adjusting for age, gender, marital status, number of medical conditions and miles driven. Visual acuity impairment was not associated with driving cessation. Medical problems (63 per cent), specifically musculoskeletal and neurological problems, as well as visual problems (17 per cent) were cited most frequently as the reason for driving cessation. CONCLUSION: Assessment of cognitive and visual functioning can provide useful information about subsequent risk of driving cessation among older drivers. In addition, a variety of factors, not just vision, influenced the decision to stop driving and may be amenable to intervention.\",\n \"corpus_id\": 27929347,\n \"score\": 1\n },\n {\n \"doc_id\": \"27764828\",\n \"title\": \"Driving Characteristics of Older Drivers and Their Relationship to the Useful Field of View Test.\",\n \"abstract\": \"BACKGROUND: To maintain the mobility of older people in later life, it is essential to sustain their autonomy; however, driving is a complex task, requiring a large range of visual, psychomotor and cognitive abilities. Subsequently, a key issue is to measure and evaluate the fitness to drive of older drivers. Several methods have been proposed, among them the useful field of view (UFOV) test. OBJECTIVE: The present study aimed to identify driving characteristics in older drivers and the relationship between the UFOV test and the on-road driving results. METHOD: A total of 80 drivers aged 70 years or older performed both the UFOV test and the on-road driving assessment. The 'B On-Road' (Behaviour On-Road) protocol was used for the fitness-to-drive assessment. RESULTS: 'Driving too fast' was the item reported most often during the on-road assessment, followed by problems with the manual gearbox and 'attention to signs, road lines and traffic lights'. Overall, the results showed that the older the driver, the more errors were reported during the on-road driving assessment, as well as the slower the performance on the UFOV test. A significant relationship between the total number of on-road errors, as measured by the B On-Road protocol, and the UFOV 3, which stresses the capacity of selective attention, was found. CONCLUSION: The recommendation is still to use on-road driving assessment to fully assess fitness to drive for older drivers whose ability to drive requires assessment. However, to supplement this, the UFOV test, in particular the UFOV 3, is a valuable complement in selecting those drivers requiring to be assessed.\",\n \"corpus_id\": 24652979,\n \"score\": 1\n },\n {\n \"doc_id\": \"28446144\",\n \"title\": \"Association of physical activity and appetite with visual function related to driving competence in older adults.\",\n \"abstract\": \"BACKGROUND: Older people are at greater risk of traffic accidents, partially because of age-related declines in visual function, including reduced useful field of view (UFOV). However, lifestyle factors which cause age-related decline in UFOV remain poorly understood. We conducted a study to investigate whether physical activity and appetite status were related to UFOV test performance in healthy older adults. METHODS: Thirty community-dwelling older people (age 68.6 ± 3.1 years, 15 females) were enrolled in this study. Each participant completed the Council on Nutrition appetite questionnaire (CNAQ) and a UFOV test. They then wore a tri-axial accelerometer (Active style Pro HJA-350IT) for 3-6 consecutive days to objectively measure their PA in free-living conditions. RESULTS: Longer time spent in vigorous physical activity was significantly associated with better UFOV test performance when adjusted for age and accelerometer wear time (non-locomotive: r = -0.435, locomotive: r = -0.449; n = 25). In addition, male, but not female, participants with a higher CNAQ score had significantly better UFOV test performance in both an unadjusted model (r = -0.560; n = 15) and a model adjusted for age (r = -0.635; n = 15). CONCLUSIONS: The results suggest that appetite status among males and time spent in high intensity PA are associated with visual function related to driving competence in older adults.\",\n \"corpus_id\": 16962845,\n \"score\": 1\n },\n {\n \"doc_id\": \"28450973\",\n \"title\": \"The Field of View is More Useful in Golfers than Regular Exercisers.\",\n \"abstract\": \"Superior visual attention skills are vital for excellent sports performance. This study used a cognitive skills approach to examine expert and novice differences in a visual spatial attention task. Thirty-two males aged 18 to 42 years completed this study in return for course credit or monetary incentive. Participants were expert golfers (N = 18) or exercise controls (N = 14). Spatial attention was assessed using the useful field of view task which required participants to locate a target shown 10°, 20°, and 30° of eccentricity from centre in very brief presentations. At each degree of eccentricity, golfers were more accurate at locating the target than the exercise controls. These results provide support for the broad transfer hypothesis by demonstrating a link between golf expertise and better performance on an objective measure of spatial attention skills. Therefore, it appears that sports expertise can transfer to expertise in non-sport related tasks.\",\n \"corpus_id\": 14817790,\n \"score\": 1\n },\n {\n \"doc_id\": \"28802451\",\n \"title\": \"More than the Useful Field: Considering peripheral vision in driving.\",\n \"abstract\": \"Applied research on driving and basic vision research have held similar views on central, fovea-based vision as the core of visual perception. In applied work, the concept of the Useful Field, as determined by the Useful Field of View (UFOV) test, divides vision between a \\\"useful\\\" region towards the center of the visual field, and the rest of the visual field. While compelling, this dichotomization is at odds with findings in vision science which demonstrate the capabilities of peripheral vision. In this paper, we examine driving research from this new perspective, and argue for the need for an updated understanding of how drivers acquire information about their operating environment using peripheral vision. The concept of the Useful Field and the UFOV test are not discarded; instead we discuss their strengths, limitations, and future directions. We discuss key findings from vision science on peripheral vision, and a theory that provides insights into its capabilities and limitations. This more complete basic science understanding of peripheral vision informs appropriate use of the UFOV and the Useful Field in driving research going forward.\",\n \"corpus_id\": 10042446,\n \"score\": 1\n },\n {\n \"doc_id\": \"29089888\",\n \"title\": \"Effect of Speed of Processing Training on Older Driver Screening Measures.\",\n \"abstract\": \"Objective: Computerized training for cognitive enhancement is of great public interest, however, there is inconsistent evidence for the transfer of training gains to every day activity. Several large trials have focused on speed of processing (SOP) training with some promising findings for long-term effects on daily activity, but no immediate transfer to other cognitive tests. Here, we examine the transfer of SOP training gains to cognitive measures that are known predictors of driving safety in older adults. Methods: Fifty-three adults aged 65-87 years who were current drivers participated in a two group non-randomized design with repeated measures and a no-contact matched control group. The Intervention group completed an average of 7.9 (SD = 3.0) hours of self-administered online SOP training at home. Control group was matched on age, gender and test-re-test interval. Measures included the Useful Field of View (UFOV) test, a Hazard Perception test, choice reaction time (Cars RT), Trail Making Test B, a Maze test, visual motion threshold, as well as road craft and road knowledge tests. Results: Speed of processing training resulted in significant improvement in processing speed on the UFOV test relative to controls, with an average change of -45.8 ms (SE = 14.5), and effect size of ω2 = 0.21. Performance on the Maze test also improved, but significant slowing on the Hazard Perception test was observed after SOP training. Training effects on the UFOV task was associated with similar effects on the Cars RT, but not the Hazard Perception and Maze tests, suggesting transfer to some but not all driving related measures. There were no effects of training on any of the other measures examined. Conclusion: Speed of processing training effects on the UFOV task can be achieved with self-administered, online training at home, with some transfer to other cognitive tests. However, differential effects of training may be observed for tasks requiring goal-directed search strategies rather than diffuse attention.\",\n \"corpus_id\": 941361,\n \"score\": 1\n },\n {\n \"doc_id\": \"29175362\",\n \"title\": \"Systematic review and meta-analyses of useful field of view cognitive training.\",\n \"abstract\": \"Systematic review and meta-analyses were conducted of Useful Field of View (UFOV) training, which was evaluated by Institute of Medicine criteria. Forty-four studies of UFOV training from 17 randomized trials conducted among adults were identified in systematic review. Results addressing the Institute of Medicine criteria indicated that: (a) UFOV training enhanced neural outcomes, speed of processing, and attention. ( b) UFOV training effects were equivalent when compared to active- or no-contact control conditions. ( c) UFOV training showed far transfer to everyday function. ( d) Improvements on the trained skills endured across ten years. ( e) Half of the clinical trials identified were conducted by researchers without financial interests in UFOV training. Results indicated that UFOV training effects were larger for adaptive- than non-adaptive training techniques, and in community-based as compared to clinical samples. UFOV training did not transfer to other neuropsychological outcomes, but positively enhanced well-being, health, and quality of life longitudinally. Criticisms of cognitive training are addressed. UFOV training should be implemented among older adults to improve real-world functional outcomes and well-being.\",\n \"corpus_id\": 31077579,\n \"score\": 1\n },\n {\n \"doc_id\": \"29241017\",\n \"title\": \"Older Adult Multitasking Performance Using a Gaze-Contingent Useful Field of View.\",\n \"abstract\": \"Objective We implemented a gaze-contingent useful field of view paradigm to examine older adult multitasking performance in a simulated driving environment. Background Multitasking refers to the ability to manage multiple simultaneous streams of information. Recent work suggests that multitasking declines with age, yet the mechanisms supporting these declines are still debated. One possible framework to better understand this phenomenon is the useful field of view, or the area in the visual field where information can be attended and processed. In particular, the useful field of view allows for the discrimination of two competing theories of real-time multitasking, a general interference account and a tunneling account. Methods Twenty-five older adult subjects completed a useful field of view task that involved discriminating the orientation of lines in gaze-contingent Gabor patches appearing at varying eccentricities (based on distance from the fovea) as they operated a vehicle in a driving simulator. In half of the driving scenarios, subjects also completed an auditory two-back task to manipulate cognitive workload, and during some trials, wind was introduced as a means to alter general driving difficulty. Results Consistent with prior work, indices of driving performance were sensitive to both wind and workload. Interestingly, we also observed a decline in Gabor patch discrimination accuracy under high cognitive workload regardless of eccentricity, which provides support for a general interference account of multitasking. Conclusion The results showed that our gaze-contingent useful field of view paradigm was able to successfully examine older adult multitasking performance in a simulated driving environment. Application This study represents the first attempt to successfully measure dynamic changes in the useful field of view for older adults completing a multitasking scenario involving driving.\",\n \"corpus_id\": 3340095,\n \"score\": 1\n },\n {\n \"doc_id\": \"29460955\",\n \"title\": \"A pilot study: Can the UFOV assessment be used as a repeated measure to determine timing of on-road assessment in stroke?\",\n \"abstract\": \"BACKGROUND/AIMS: Useful Field of View scores are predictive of on-road performance post-stroke. No objective data exist to determine if the Useful Field of View (UFOV) assessment can be used as a repeated measure in the post-stroke population to determine timing of occupational therapy on-road assessment as recovery occurs. The aims of this study were to determine whether there is a practice effect if the UFOV is administered at one, two and three months' post-stroke and to assess optimal time post-stroke to refer to an on-road assessment. METHOD: Forty-two participants, 17 men (40.5%), with a mean age of 71 years (SD 9.33) were randomly allocated to 1. Assessment group - UFOV at one, two and three months' post-stroke, 2. Control group-UFOV at three months' post-stroke. Parametric and non-parametric tests were utilised depending on data distribution. RESULTS: No significance was found between; three months' subtest 1 (P = 0.463), three months' subtest 2 (P = 0.729) and three months' subtest 3 (P = 0.534) between the assessment and control groups. Both group's scores were combined to examine pass/fail rates of UFOV assessment to indicate timing of referral to on-road assessments. At one month, 16.9% stroke survivors passed the UFOV, when reassessed at three months 69.1% passed and 28.6% again failed. CONCLUSION: Improvements in scores at one month intervals over three months are due to improvements in abilities assessed by the UFOV as no practice effect was found to influence scores. UFOV scores performed at monthly intervals post-stroke can be used to guide the timing of an occupational therapy on-road assessment, with an increased likelihood of passing, as recovery occurs. This repeated use of the UFOV assessment can assist referral practices that best utilise driving rehabilitation programmes. Larger studies need to be conducted to confirm these results.\",\n \"corpus_id\": 3399996,\n \"score\": 1\n },\n {\n \"doc_id\": \"18455935\",\n \"title\": \"Results of ocular dominance testing depend on assessment method.\",\n \"abstract\": \"PURPOSE: We developed a near ocular dominance test modeled after the distance hole-in-the-card test and assessed both test-retest reliability of four tests of ocular dominance and agreement between tests. METHODS: Forty-six subjects aged 18 to 78 years with visual acuity 20/40 or better in each eye were enrolled from a primary care practice. All subjects had normal eye examinations, with the exception of refractive error, and were examined in their habitual correction. Subjects were tested twice each with the distance hole-in-the-card test, new near hole-in-the-card test, near convergence test, and the Pediatric Eye Disease Investigator Group fixation preference test. RESULTS: There was excellent test-retest reliability for each ocular dominance test. Nevertheless, there was only moderate to slight agreement between each possible pairing of tests. CONCLUSIONS: Results of ocular dominance tests vary depending on both the testing distance and the specific activity performed as part of the testing procedure.\",\n \"corpus_id\": 2021507,\n \"score\": 0\n },\n {\n \"doc_id\": \"18711290\",\n \"title\": \"Ocular disorders in renal transplant patients.\",\n \"abstract\": \"This cross-sectional study was performed to determine ocular findings in renal transplant recipients and to correlate them with certain clinical characteristics related to transplantation. The study was performed on 150 patients who had received a renal transplant at least three months earlier and had serum creatinine levels < 3 mg/dL. All patients underwent a complete ophthalmologic examination. Clinical variables studied related to the transplant included cause of renal failure, duration of hemodialysis prior to transplantation and immunosuppressive regimen. Overall, 91 male and 59 female subjects with a mean age of 39.9 +/- 17.7 years were included. At least one ocular abnormality could be detected in 89.3% including impaired visual acuity < or = 20/25 (48.6%), conjunctival degeneration in the palpebral fissure (36.6%), posterior sub-capsular cataracts (24%), pinguecula (17.3%), retinal pigment epitheliopathy (14%), arteriovenous crossing changes (8.6%), proliferative diabetic retinopathy (6%), central serous chorioretinopathy and retinal vein occlusions (each in 3.3%), and non-proliferative diabetic retinopathy, optic nerve atrophy and diabetic macular edema (each in 2.7%). Abnormal ocular findings were not correlated with the underlying renal disorder or use of cyclosporine and prednisolone; however, they were positively correlated with transplant duration, pre-transplant dialysis duration and usage of azathioprine or mycophenolate mofetil. Our study suggests that ocular disorders are frequent among renal transplant patients especially with older transplants and those with a longer period of pre-transplant hemodialysis.\",\n \"corpus_id\": 38530063,\n \"score\": 0\n },\n {\n \"doc_id\": \"18854790\",\n \"title\": \"Assessing age-related macular degeneration with the ADREV performance-based measure.\",\n \"abstract\": \"PURPOSE: To validate a new third-generation performance-based measure titled the \\\"assessment of disability related to vision\\\" (ADREV) in a study population of individuals with age-related macular degeneration. METHODS: Patients with either exudative or nonexudative age-related macular degeneration, but without ocular comorbidity, completed the ADREV, the 25-item National Eye Institute's visual functioning questionnaire, and a range of clinical assessments. Correlations were calculated between the data provided by the ADREV, visual functioning questionnaire, and clinical ophthalmic measures. Regression and bootstrap analysis were preformed to determine the relative relationship between specific clinical measures and ADREV performance, while controlling for a range of potentially confounding factors. RESULTS: One hundred twelve patients completed the study and correlative analysis showed that ADREV total and subscale scores were more related to nearly all measures of clinical ophthalmic status in comparison with the data provided by the visual functioning questionnaire. Significant correlative relationships between ADREV and visual functioning questionnaire scores showed moderate to high correlation. Central visual acuity and contrast sensitivity shared the strongest association with performance of activities. CONCLUSIONS: The ADREV is a valid instrument for the assessment of visual disability in patients with age-related macular degeneration. Furthermore, the data provided by this performance measure had stronger relationships with clinical indicators of visual impairment in comparison with self-report.\",\n \"corpus_id\": 38646701,\n \"score\": 0\n },\n {\n \"doc_id\": \"21367570\",\n \"title\": \"School performance and alcohol use problems in early adulthood: a longitudinal study.\",\n \"abstract\": \"There is inconsistent evidence about the association between school performance and subsequent use of alcohol and alcohol problems in adolescents and young adults. This study examines whether school performance at 14 years is associated with drinking problems in early adulthood; and whether this association is explained by family and individual factors in childhood and adolescence. Data were from a 21-year follow-up of 3,478 Australian young adults from birth to the age of 21 years when data on use of alcohol were collected. Child school performance (CSP) was assessed at 14 years via self- and maternal report. Alcohol consumption at 21 years was measured via self-report, and alcohol abuse and dependence were assessed by the computerized version of Composite International Diagnostic Interview (CIDI-Auto). Potential confounding factors were prospectively measured between the child's birth and age of 14 years. School performance at 14 years predicted young adults' alcohol consumption and alcohol use disorders (AUDs). After controlling for confounding, children who had lower school performance had increased risk of drinking more than two glasses of alcohol per day in early adulthood (odds ratio=1.7; 95% confidence interval: 1.1-2.6). There was a similar pattern of association between CSP and young adults' alcohol abuse and dependence (AUD) measured by CIDI-Auto. Level of academic performance in high school children predicts their drinking problems as young adults, independently of a selected group of individual and family confounders. Exploration of the pathway linking school performance and alcohol problems in young people may help identify opportunities for preventive interventions.\",\n \"corpus_id\": 46340596,\n \"score\": 0\n },\n {\n \"doc_id\": \"22008883\",\n \"title\": \"Performance-based tests in subjects with stroke: outcome scores, reliability and measurement errors.\",\n \"abstract\": \"OBJECTIVES: To assess the intra- and inter-rater reliabilities and measurement errors of seven widely applied performance-based tests for stroke subjects (comfortable/maximal gait speeds and both stair ascending/descending cadences, as well as the Timed 'Up and Go' test) and to verify whether the use of different types of outcome scores (one trial, the means of two and three trials, and the best and the worst values of the three trials) affected the score values, as well as their reliability and measurement errors. DESIGN: Intra- and inter-rater reliability study. SETTING: Research laboratory. SUBJECTS: Sixteen stroke subjects with a mean age of 52 ± 17.9 years. MAIN MEASURES: Seven performance-based tests, over two sessions, seven days apart, evaluated by two independent examiners. A third examiner recorded all data. One-way ANOVAs, intra-class correlation coefficients (ICCs) and percentages of the standard errors of measurement (SEM%) were used for analyses. RESULTS: For all tests, similar results were found for all types of outcome scores (0.01 ≤ F ≤ 0.56; 0.34 ≤ p ≤ 0.99). For instance, at the comfortable gait speed, the means (SD) values for the first trial, the means of two and three trials and the best and worst of three trials were, respectively, 1.04 (0.25), 1.04(0.24), 1.05 (0.24), 1.10 (0.26), 1.02 (0.24) seconds. Significant and adequate values of intra- (0.75 ≤ ICC ≤ 0.96; p ≤ 0.002) and inter-rater (0.75 ≤ ICC ≤ 0.97; p ≤ 0.001) reliabilities were found for all tests and outcome scores. Measurement errors were considered low (5.01 ≤ SEM% ≤14.78) and were also similar between all outcome scores. CONCLUSIONS: For the seven tests, only one trial was necessary to provide consistent and reliable results regarding the functional performances of stroke subjects.\",\n \"corpus_id\": 39839412,\n \"score\": 0\n },\n {\n \"doc_id\": \"23307969\",\n \"title\": \"Association between higher order visual processing abilities and a history of motor vehicle collision involvement by drivers ages 70 and over.\",\n \"abstract\": \"PURPOSE: To examine in a population-based sample of 2000 drivers aged 70 years and older, the independent association between higher order visual processing impairment and motor vehicle collision (MVC) rate during the prior 5 years. METHODS: Three higher order visual processing screening tests were administered since previous research found associations between impaired performance on these screens and MVC involvement. They included an estimate of visual processing speed under divided attention conditions (useful field of view [UFOV] subset 2); Trails B, a paper and pencil test of visual processing speed also involving problem solving, executive function, and working memory; and the visual closure subtest of the Motor Free Visual Perception Test (MVPT) examining the ability to recognize objects only partially visible. Potentially confounding variables were also assessed including demographics, general cognitive status, visual acuity, and contrast sensitivity. MVC involvement was determined by accident reports from the Alabama Department of Public Safety, and driving exposure was estimated from the Driving Habits Questionnaire. RESULTS: MVC rates (for at fault and all MVCs) were significantly higher for those older drivers with impairments in any of the three visual processing screening tests. After adjustment for potentially confounding influences, the association between MVC rate and Trails B remained significant, whereas the association with MVPT and UFOV did not. CONCLUSIONS: This population-based study of drivers aged 70 years and older suggests that a paper and pencil test assessing higher order visual processing skills is independently associated with a recent history of MVC involvement.\",\n \"corpus_id\": 46722452,\n \"score\": 0\n },\n {\n \"doc_id\": \"24106477\",\n \"title\": \"Co-morbidity of depression and anxiety in common age-related eye diseases: a population-based study of 662 adults.\",\n \"abstract\": \"This study examined the prevalence of co-morbid age-related eye disease and symptoms of depression and anxiety in late life, and the relative roles of visual function and disease in explaining symptoms of depression and anxiety. A community-based sample of 662 individuals aged over 70 years was recruited through the electoral roll. Vision was measured using a battery of tests including high and low contrast visual acuity, contrast sensitivity, motion sensitivity, stereoacuity, Useful Field of View, and visual fields. Depression and anxiety symptoms were measured using the Goldberg scales. The prevalence of self-reported eye disease [cataract, glaucoma, or age-related macular degeneration (AMD)] in the sample was 43.4%, with 7.7% reporting more than one form of ocular pathology. Of those with no eye disease, 3.7% had clinically significant depressive symptoms. This rate was 6.7% among cataract patients, 4.3% among those with glaucoma, and 10.5% for AMD. Generalized linear models adjusting for demographics, general health, treatment, and disability examined self-reported eye disease and visual function as correlates of depression and anxiety. Depressive symptoms were associated with cataract only, AMD, comorbid eye diseases and reduced low contrast visual acuity. Anxiety was significantly associated with self-reported cataract, and reduced low contrast visual acuity, motion sensitivity and contrast sensitivity. We found no evidence for elevated rates of depressive or anxiety symptoms associated with self-reported glaucoma. The results support previous findings of high rates of depression and anxiety in cataract and AMD, and in addition show that mood and anxiety are associated with objective measures of visual function independently of self-reported eye disease. The findings have implications for the assessment and treatment of mental health in the context of late-life visual impairment.\",\n \"corpus_id\": 2053348,\n \"score\": 0\n },\n {\n \"doc_id\": \"24184091\",\n \"title\": \"Objective and subjective visual performance of multifocal contact lenses: pilot study.\",\n \"abstract\": \"PURPOSE: The aim of the present study was to compare the objective and subjective visual performance of three different soft multifocal contact lenses. METHODS: 10 subjects (habitual soft contact lens wearers) between the ages of 40 and 45 years participated in the study. Three different multifocal silicone hydrogel contact lenses (Acuvue Oasys, Air Optix and Biofinity) were fit within the same visit. All the lenses were fit according to the manufacturers' recommendation using the respective fitting guide. Visual performance tests included low and high contrast distance and near visual acuity, contrast sensitivity, range of clear vision and through-focus curve. Objective visual performance tests included measurement of open field accommodative response at different defocus levels and optical aberrations at different viewing distances. RESULTS: Accommodative response was not significantly different between the three types of multifocal contact lenses at each of the accommodative stimulus levels (p>0.05). Accommodative lag increased for higher stimulus levels for all 3 types of contact lenses. Ocular aberrations were not significantly different between these 3 contact lens designs at each of the different viewing distances (p>0.05). In addition, optical aberrations did not significantly differ between different viewing distances for any of these lenses (p>0.05). ANOVA revealed no significant difference in high and low contrast distance visual acuity as well as near visual acuity and contrast sensitivity function between the 3 multifocal contact lenses and spectacles (p>0.05). CONCLUSIONS: There was no statistically significant difference in accommodative response, optical aberrations or visual performance between the 3 multifocal contact lenses in early presbyopes.\",\n \"corpus_id\": 7449008,\n \"score\": 0\n },\n {\n \"doc_id\": \"25282251\",\n \"title\": \"Prosthetic replacement of the ocular surface ecosystem as treatment for ocular surface disease in patients with a history of Stevens-Johnson syndrome/toxic epidermal necrolysis.\",\n \"abstract\": \"PURPOSE: To report the visual outcomes of prosthetic replacement of the ocular surface ecosystem (PROSE) treatment in patients with ocular surface disease related to Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN). DESIGN: Retrospective cohort study. SUBJECTS: We included 86 patients (167 eyes) with history of SJS/TEN who underwent PROSE treatment from January 1, 2006, to January 1, 2011. METHODS: Etiology, previous interventions, change in visual acuity, change in visual function, and duration of follow-up are reported. Paired t test and Friedman test with Dunn's post hoc test for multiple comparisons were used for statistical analysis. MAIN OUTCOME MEASURES: Visual acuity at last follow-up and visual function based on the National Eye Institute 25-item Visual Functioning Questionnaire (NEI VFQ-25) at 6 months. RESULTS: We treated 35 males and 51 females with a history of SJS/TENS; median age was 36 years. The most common reported etiologies for SJS/TENS were antibiotics (n = 25), ibuprofen (n = 15), and lamotrigine (n = 11). The median visual acuity at the initial visit was 20/60 (range, 20/400-20/25; 0.48 logarithm of the minimum angle of resolution [logMAR]), and the visual acuity at completion of customization was 20/25 (range, 20/200-20/20; 0.096 logMAR; P < 0.001), with no decline in median acuity at the end of follow-up. Median duration of follow-up was 16 months. There was a significant improvement in the visual function of the patients based on the NEI VFQ-25 questionnaire (mean of 48 points at baseline vs. mean of 72 points at 6 months; P < 0.001). In addition, there was also an improvement in the self-reported general health of the patients (mean of 57 points at baseline vs. mean of 65 points at 6 months; P < 0.01). CONCLUSIONS: In a large cohort of patients with chronic ocular surface disease related to SJS/TEN, PROSE treatment offers sustained and significant large improvement in visual function and acuity.\",\n \"corpus_id\": 1809606,\n \"score\": 0\n },\n {\n \"doc_id\": \"25680247\",\n \"title\": \"Effectiveness of measuring the central field with the Berkeley field test.\",\n \"abstract\": \"INTRODUCTION: There are several limitations of the Amsler chart as a screening tool due to its low sensitivity and high false-negative results. The Berkeley central visual field test (BCFT), which is a simple power-point presentation of a 50-point scoring system for the central 10-degree of the visual field, was devised as an alternative to the Amsler chart. OBJECTIVES: To compare the efficacy of measuring the central visual field using the Berkeley central field test (BCFT) and the Amsler grid test. MATERIALS AND METHODS: In a comparative and validity study, 30 subjects with maculopathy and 35 controls were recruited. The maculopathy subjects with the best corrected visual acuity of 20/200 or better and 2.5M for distant and near vision respectively, were included. All the subjects under went a complete eye examination where visual assessment was done using the distant and near vision Log MAR Chart. The subjects were assessed with the Amsler chart-II at a distance of 30 cm. The BCFT was used as a 50- point scoring system. The effectiveness of BCFT was compared with that of the Amsler grid regarding the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). RESULTS: Out of 65 subjects, 30 subjects had maculopathy and 35 were normal. The mean age of the 65 subjects was 49.8±9.1 years. Of the 30 subjects with maculopathy, the majority (54%) had age- related macular degeneration. The sensitivity, specificity, PPV and NPV of the Amsler grid test were found to be 80%, 100%, 100% and 87%, respectively, whereas those of the BCFT were 71%, 99%, 98% and 82% (p=0.37). CONCLUSION: The BCFT test was as good as the Amsler grid test at detecting the presence of maculopathy.\",\n \"corpus_id\": 31281796,\n \"score\": 0\n },\n {\n \"doc_id\": \"26272444\",\n \"title\": \"Impact of cataract surgery on vision-related life performances: the usefulness of Real-Life Vision Test for cataract surgery outcomes evaluation.\",\n \"abstract\": \"PurposeReal-Life Vision Test (RLVT) is a newly developed performance-based measures of functional vision. This present study is designed to determine whether it could be a meaningful assessment for cataract surgery outcomes evaluation. Patients and methodsAge-related cataract patients (56) who scheduled for bilateral cataract surgery and 44 age-matched controls were evaluated by four types of measurements: (1) demographic, medical, cognitive and depressive evaluation, and the reaction time testing; (2) clinical measures (visual acuity, contrast sensitivity, stereopsis, and color perception); (3) the 25-item National Eye Institute's Visual Functioning Questionnaire (NEI-VFQ); (4) the RLVT. Spearman's coefficients and multiple regression analysis were conducted to investigate the relationship among RLVT, clinical measures, and self-report assessment of visual function. ResultsThe results of RLVT, clinical measures, and NEI-VFQ total scores were improved significantly after cataract surgery. There were no differences between control subjects and post-surgery patients with respect to NEI-VFQ-25 total scores, self-rating depression scale scores and three tasks of RLVT. Change of RLVT was significantly associated with the change of clinical measures in the cataract group. Multiple regression analysis demonstrated that change of distance, intermediate, and near visual acuity, and binocular contrast sensitivity were significant predictors of improvements of RLVT.ConclusionsCataract surgery could improve real-world visual ability effectively for cataract patients. Our study highlights the potential usefulness of RLVT as an adjunct to the current outcomes evaluation system for cataract surgery. The use of RLVT combined with clinical and self-survey methods may be the comprehensive strategy to manifest the impact of cataract surgery on patients' overall vision-related quality of life.\",\n \"corpus_id\": 32528470,\n \"score\": 0\n },\n {\n \"doc_id\": \"26664798\",\n \"title\": \"Trail Making Test performance contributes to subjective judgment of visual efficiency in older adults.\",\n \"abstract\": \"Introduction. The determinant factors that influence self-reported quality of vision have yet to be fully elucidated. This study evaluated a range of contextual information, established psychophysical tests, and in particular, a series of cognitive tests as potentially novel determinant factors. Materials & Methods. Community dwelling adults (aged 50+) recruited to Wave 1 of The Irish Longitudinal Study on Ageing, excluding those registered blind, participated in this study (N = 5,021). Self-reports of vision were analysed in relation to visual acuity and contrast sensitivity, ocular pathology, visual (Choice Response Time task; Trail Making Test) and global cognition. Contextual factors such as having visited an optometrist and wearing glasses were also considered. Ordinal logistic regression was used to determine univariate and multivariate associations. Results and Discussion. Poor Trail Making Test performance (Odds ratio, OR = 1.36), visual acuity (OR = 1.72) and ocular pathology (OR = 2.25) were determinant factors for poor versus excellent vision in self-reports. Education, wealth, age, depressive symptoms and general cognitive fitness also contributed to determining self-reported vision. Conclusions. Trail Making Test contribution to self-reports may capture higher level visual processing and should be considered when using self-reports to assess vision and its role in cognitive and functional health.\",\n \"corpus_id\": 5707903,\n \"score\": 0\n },\n {\n \"doc_id\": \"29386615\",\n \"title\": \"Corneal sensitivity and subjective complaints of ocular pain in patients with fibromyalgia.\",\n \"abstract\": \"PurposeFibromyalgia (FM) is a chronic pain disorder associated with pain and hypersensitivity in various parts of the body. The aim of this study was to understand whether changes in corneal sensitivity were associated with the subjective complaints of these patients. Patients and methodsIn this study, we included 36 patients with FM (30 female, 6 male, mean age: 46.7±9.2 years) and 39 healthy control subjects (33 females, 6 males, mean age: 44.3±7.6 years). We performed a detailed ophthalmological examination, measured tear film breakup time (TBUT), and performed Schirmer I test without anesthetic (SIT). Only patients that did not have any eye disease were included in this study. Subjective complaints of the patients were evaluated with ocular surface disease index (OSDI) scores and the corneal sensation was evaluated with Cochet-Bonnet esthesiometer. ResultsThere was no significant difference between the groups for age, sex, and visual acuity. Both SIT (16.1 mm vs 15.3 mm, P=0.36) and TBUT results (17.8 s vs 18.8 s, P=0.40) were similar in FM group and the controls subjects. However, corneal sensations in central (60.0 mm vs 55.0 mm, P=0.03), superior (57.5 mm vs 50.0 mm, P=0.005), and inferior (53.89 mm vs 46.03 mm, P<0.001) regions were significantly increased in FM patients. There was a significant positive correlation between corneal sensation and OSDI scores. ConclusionIn this study, we have demonstrated that the patients with FM have increased corneal sensitivity and have related ocular surface complaints similar to dry eye disease in the absence of it.\",\n \"corpus_id\": 4713527,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":65,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28918260\",\n \"title\": \"Organization of sensory feature selectivity in the whisker system.\",\n \"abstract\": \"Our sensory receptors are faced with an onslaught of different environmental inputs. Each sensory event or encounter with an object involves a distinct combination of physical energy sources impinging upon receptors. In the rodent whisker system, each primary afferent neuron located in the trigeminal ganglion innervates and responds to a single whisker and encodes a distinct set of physical stimulus properties - features - corresponding to changes in whisker angle and shape and the consequent forces acting on the whisker follicle. Here we review the nature of the features encoded by successive stages of processing along the whisker pathway. At each stage different neurons respond to distinct features, such that the population as a whole represents diverse properties. Different neuronal types also have distinct feature selectivity. Thus, neurons at the same stage of processing and responding to the same whisker nevertheless play different roles in representing objects contacted by the whisker. This diversity, combined with the precise timing and high reliability of responses, enables populations at each stage to represent a wide range of stimuli. Cortical neurons respond to more complex stimulus properties - such as correlated motion across whiskers - than those at early subcortical stages. Temporal integration along the pathway is comparatively weak: neurons up to barrel cortex (BC) are sensitive mainly to fast (tens of milliseconds) fluctuations in whisker motion. The topographic organization of whisker sensitivity is paralleled by systematic organization of neuronal selectivity to certain other physical features, but selectivity to touch and to dynamic stimulus properties is distributed in \\\"salt-and-pepper\\\" fashion.\",\n \"corpus_id\": 5343820\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"17989240","title":"Development of thalamocortical response transformations in the rat whisker-barrel system.","abstract":"Extracellular single-unit recordings were used to characterize responses of thalamic barreloid and cortical barrel neurons to controlled whisker deflections in 2, 3-, and 4-wk-old and adult rats in vivo under fentanyl analgesia. Results indicate that response properties of thalamic and cortical neurons diverge during development. Responses to deflection onsets and offsets among thalamic neurons mature in parallel, whereas among cortical neurons responses to deflection offsets become disproportionately smaller with age. Thalamic neuron receptive fields become more multiwhisker, whereas those of cortical neurons become more single-whisker. Thalamic neurons develop a higher degree of angular selectivity, whereas that of cortical neurons remains constant. In the temporal domain, response latencies decrease both in thalamic and cortical neurons, but the maturation time-course differs between the two populations. Response latencies of thalamic cells decrease primarily between 2 and 3 wk of life, whereas response latencies of cortical neurons decrease in two distinct steps--the first between 2 and 3 wk of life and the second between the fourth postnatal week and adulthood. Although the first step likely reflects similar subcortical changes, the second phase likely corresponds to developmental myelination of thalamocortical fibers. Divergent development of thalamic and cortical response properties indicates that thalamocortical circuits in the whisker-to-barrel pathway undergo protracted maturation after 2 wk of life and provides a potential substrate for experience-dependent plasticity during this time.","corpus_id":8364990,"score":2},{"doc_id":"18491159","title":"Object localization with whiskers.","abstract":"Rats use their large facial hairs (whiskers) to detect, localize and identify objects in their proximal three-dimensional (3D) space. Here, we focus on recent evidence of how object location is encoded in the neural sensory pathways of the rat whisker system. Behavioral and neuronal observations have recently converged to the point where object location in 3D appears to be encoded by an efficient orthogonal scheme supported by primary sensory-afferents: each primary-afferent can signal object location by a spatial (labeled-line) code for the vertical axis (along whisker arcs), a temporal code for the horizontal axis (along whisker rows), and an intensity code for the radial axis (from the face out). Neuronal evidence shows that (i) the identities of activated sensory neurons convey information about the vertical coordinate of an object, (ii) the timing of their firing, in relation to other reference signals, conveys information about the horizontal object coordinate, and (iii) the intensity of firing conveys information about the radial object coordinate. Such a triple-coding scheme allows for efficient multiplexing of 3D object location information in the activity of single neurons. Also, this scheme provides redundancy since the same information may be represented in the activity of many neurons. These features of orthogonal coding increase accuracy and reliability. We propose that the multiplexed information is conveyed in parallel to different readout circuits, each decoding a specific spatial variable. Such decoding reduces ambiguity, and simplifies the required decoding algorithms, since different readout circuits can be optimized for a particular variable.","corpus_id":16829392,"score":2},{"doc_id":"18641667","title":"'Where' and 'what' in the whisker sensorimotor system.","abstract":"In the visual system of primates, different neuronal pathways are specialized for processing information about the spatial coordinates of objects and their identity - that is, 'where' and 'what'. By contrast, rats and other nocturnal animals build up a neuronal representation of 'where' and 'what' by seeking out and palpating objects with their whiskers. We present recent evidence about how the brain constructs a representation of the surrounding world through whisker-mediated sense of touch. While considerable knowledge exists about the representation of the physical properties of stimuli - like texture, shape and position - we know little about how the brain represents their meaning. Future research may elucidate this and show how the transformation of one representation to another is achieved.","corpus_id":6450408,"score":2},{"doc_id":"18684907","title":"Responses of rat trigeminal ganglion neurons to longitudinal whisker stimulation.","abstract":"Responses of rat trigeminal ganglion neurons to longitudinal whisker stimulation. Rats use their mobile set of whiskers to actively explore their environment. Parameters that play a role to generate movement dynamics of the whisker shaft within the follicle, thus activating primary afferents, are manifold: among them are mechanical properties of the whiskers (curvature, elasticity and taper), active movements (head, body, and whiskers), and finally, object characteristics (surface, geometry, position, and orientation). Hence the whisker system is confronted with forces along all three axes in space. Movements along the two latitudinal axes of the whisker (horizontal and vertical) have been well studied. Here we focus on movement along the whisker's longitudinal axis that has been neglected so far. We employed ramp-and-hold movements that pushed the whisker shaft toward the skin and quantified the resulting activity in trigeminal first-order afferents in anesthetized rats. Virtually all recorded neurons were highly sensitive to longitudinal movement. Neurons could be perfectly segregated into two groups according to their modulation by stimulus amplitude and velocity, respectively. This classification regimen correlated perfectly with the presence or absence of slowly adapting responses in longitudinal stimulation but agreed with classification derived from latitudinal stimulation only if the whisker was engaged in its optimal direction and set point. We conclude that longitudinal stimulation is an extremely effective means to activate the tactile pathway and thus is highly likely to play an important role in tactile coding on the ascending somatosensory pathway. In addition, compared with latitudinal stimulation, it provides a reliable and easy to use method to classify trigeminal first-order afferents.","corpus_id":13381930,"score":2},{"doc_id":"18971458","title":"Rapid changes in thalamic firing synchrony during repetitive whisker stimulation.","abstract":"Thalamic firing synchrony is thought to ensure selective transmission of relevant sensory information to the recipient cortical neurons by rendering them more responsive to temporally correlated input spikes. However, direct evidence for a synchrony code in the thalamus is limited. Here, we directly measure thalamic firing synchrony and its stimulus-induced modulation over time, using simultaneous single unit recordings from individual thalamic barreloids in the rat somatosensory whisker/barrel system. Employing whisker deflections varying in velocity or frequency and a cross-correlation approach, we find systematic changes in both time course and strength of thalamic firing synchrony as a function of stimulus parameters and sensory adaptation. Synchrony develops faster and is greater with higher velocity deflections. Greater firing synchrony reflects stimulus-dependent increases in instantaneous firing rates, greater spike time precision relative to stimulus onset as well as common input that likely arises from divergent trigeminothalamic and corticothalamic neurons. With adaptation, synchrony decreases and takes longer to develop but is more dependent on the cells' common inputs. Rapid, sharp increases in thalamic synchrony mirroring quick increases in whisker velocity occur also during ongoing random, high-frequency whisker vibrations. Together, results demonstrate millisecond by millisecond changes in thalamic near-synchronous firing during complex patterns of ongoing vibrissa movements that may ensure transmission of preferred sensory information in local thalamocortical circuits during whisking and active touch.","corpus_id":1207178,"score":2},{"doc_id":"19081382","title":"Diverse and temporally precise kinetic feature selectivity in the VPm thalamic nucleus.","abstract":"The thalamo-cortical pathway is the crucial sensory gateway into the cerebral cortex. We aimed to determine the nature of the tactile information encoded by neurons in the whisker somatosensory relay nucleus (VPm). We wanted to distinguish whether VPm neurons encode similar stimulus features, acting as a single information channel, or encode diverse features. We recorded responses to whisker deflections that thoroughly explored the space of temporal stimulus variables and identified features to which neurons were selective by reverse correlation. The timescale of the features was typically 1-2 ms, at the limit imposed by our experimental conditions, indicating highly acute feature selectivity. Sensitivity to stimulus kinetics was strikingly diverse. Some neurons (25%) only encoded velocity; others were sensitive to position, acceleration, or more complex features. A minority (19%) encoded two or more features. These results indicate that VPm contains a distributed representation of whisker motion, based on high-resolution kinetic features.","corpus_id":14611328,"score":2},{"doc_id":"19189120","title":"Neural coding and contextual influences in the whisker system.","abstract":"A fundamental problem in neuroscience, to which Prof. Segundo has made seminal contributions, is to understand how action potentials represent events in the external world. The aim of this paper is to review the issue of neural coding in the context of the rodent whiskers, an increasingly popular model system. Key issues we consider are: the role of spike timing; mechanisms of spike timing; decoding and context-dependence. Significant insight has come from the development of rigorous, information theoretic frameworks for tackling these questions, in conjunction with suitably designed experiments. We review both the theory and experimental studies. In contrast to the classical view that neurons are noisy and unreliable, it is becoming clear that many neurons in the subcortical whisker pathway are remarkably reliable and, by virtue of spike timing with millisecond-precision, have high bandwidth for conveying sensory information. In this way, even small (approximately 200 neuron) subcortical modules are able to support the sensory processing underlying sophisticated whisker-dependent behaviours. Future work on neural coding in cortex will need to consider new findings that responses are highly dependent on context, including behavioural and internal states.","corpus_id":1954837,"score":2},{"doc_id":"19430473","title":"Sparse temporal coding of elementary tactile features during active whisker sensation.","abstract":"How the brain encodes relevant sensory stimuli in the context of active, natural sensation is not known. During active tactile sensation by rodents, whisker movement across surfaces generates complex whisker micro-motion, including discrete, transient slip-stick events, which carry information about surface properties. We simultaneously measured whisker motion and neural activity in somatosensory cortex (S1) in rats whisking across surfaces. Slip-stick motion events were prominently encoded by one or two low-probability, precisely timed spikes in S1 neurons, resulting in a probabilistically sparse ensemble code. Slips could be efficiently decoded from transient, correlated spiking (approximately 20-ms time scale) in small (approximately 100 neuron) populations. Slip responses contributed substantially to increased firing rate and transient firing synchrony on surfaces, and firing synchrony was an important cue for surface texture. Slips are thus a fundamental encoded tactile feature in natural whisker input streams and are represented by sparse, temporally precise, synchronous spiking in S1.","corpus_id":1662194,"score":2},{"doc_id":"19741100","title":"Transformation in the neural code for whisker deflection direction along the lemniscal pathway.","abstract":"A prominent characteristic of neurons in the whisker system is their selectivity to the direction in which a whisker is deflected. The aim of this study was to determine how information about whisker direction is encoded at successive levels of the lemniscal pathway. We made extracellular recordings under identical conditions from the trigeminal ganglion, ventro-posterior medial thalamus (VPM), and barrel cortex while varying the direction of whisker deflection. We found a marked increase in the variability of single unit responses along the pathway. To study the consequences of this for information processing, we quantified the responses using mutual information. VPM units conveyed 48% of the mutual information conveyed by ganglion units, and cortical units conveyed 12%. The fraction of neuronal bandwidth used for transmitting direction information decreased from 40% in the ganglion to 24% in VPM and 5% in barrel cortex. To test whether, in cortex, population coding might compensate for this information loss, we made simultaneous recordings. We found that cortical neuron pairs conveyed 2.1 times the mutual information conveyed by single neurons. Overall, these findings indicate a marked transformation from a subcortical neural code based on small numbers of reliable neurons to a cortical code based on populations of unreliable neurons. However, the basic form of the neural code in ganglion, thalamus, and cortex was similar-at each stage, the first poststimulus spike carried the majority of the information.","corpus_id":2599968,"score":2},{"doc_id":"20107500","title":"Modeling the emergence of whisker direction maps in rat barrel cortex.","abstract":"Based on measuring responses to rat whiskers as they are mechanically stimulated, one recent study suggests that barrel-related areas in layer 2/3 rat primary somatosensory cortex (S1) contain a pinwheel map of whisker motion directions. Because this map is reminiscent of topographic organization for visual direction in primary visual cortex (V1) of higher mammals, we asked whether the S1 pinwheels could be explained by an input-driven developmental process as is often suggested for V1. We developed a computational model to capture how whisker stimuli are conveyed to supragranular S1, and simulate lateral cortical interactions using an established self-organizing algorithm. Inputs to the model each represent the deflection of a subset of 25 whiskers as they are contacted by a moving stimulus object. The subset of deflected whiskers corresponds with the shape of the stimulus, and the deflection direction corresponds with the movement direction of the stimulus. If these two features of the inputs are correlated during the training of the model, a somatotopically aligned map of direction emerges for each whisker in S1. Predictions of the model that are immediately testable include (1) that somatotopic pinwheel maps of whisker direction exist in adult layer 2/3 barrel cortex for every large whisker on the rat's face, even peripheral whiskers; and (2) in the adult, neurons with similar directional tuning are interconnected by a network of horizontal connections, spanning distances of many whisker representations. We also propose specific experiments for testing the predictions of the model by manipulating patterns of whisker inputs experienced during early development. The results suggest that similar intracortical mechanisms guide the development of primate V1 and rat S1.","corpus_id":6508740,"score":2},{"doc_id":"20610783","title":"Behavioral state dependency of neural activity and sensory (whisker) responses in superior colliculus.","abstract":"Rats use their vibrissa (whiskers) to explore and navigate the environment. These sensory signals are distributed within the brain stem by the trigeminal complex and are also relayed to the superior colliculus in the midbrain and to the thalamus (and subsequently barrel cortex) in the forebrain. In the intermediate layers of the superior colliculus, whisker-evoked responses are driven by direct inputs from the trigeminal complex (trigeminotectal) and feedback from the barrel cortex (corticotectal). But the effects of the behavioral state of the animal on the spontaneous firing and sensory responses of these neurons are unknown. By recording from freely behaving rats, we show that the spontaneous firing of whisker sensitive neurons in superior colliculus is higher, or in an activated mode, during active exploration and paradoxical sleep and much lower, or in a quiescent/deactivated mode, during awake immobility and slow-wave sleep. Sensory evoked responses in superior colliculus also depend on behavioral state. Most notably, feedback corticotectal responses are significantly larger during the quiescent/deactivated mode, which tracks the barrel cortex responses on which they depend. Finally, sensory evoked responses depend not only on the state of the animal but also on the orienting response elicited by the stimulus, which agrees with the well known role of the superior colliculus in orienting about salient stimuli.","corpus_id":10330093,"score":2},{"doc_id":"21068262","title":"A comparison of neuronal and behavioral detection and discrimination performances in rat whisker system.","abstract":"We used the rat whisker touch as a model system to investigate the correlation between the response function of cortical neurons and the behavior of rats in a sensory detection versus discrimination task. The rat whisker-barrel system is structurally well characterized and represents one of the main channels through which rodents collect information about the environment. In experiment 1, we recorded neuronal activity (n = 235) in the whisker area of the rat somatosensory cortex in anesthetized rats while applying vibrotactile stimuli of varying amplitudes to the whiskers. Neurons showed a characteristic sigmoidal input-output function, with an accelerating nonlinearity at low stimulus amplitudes and a compressive nonlinearity at high stimulus amplitudes. We further quantified the performance of individual neurons for stimulus detection and for discrimination across different stimulus pairs with identical amplitude differences. For near-threshold stimuli, the neuronal discrimination performance surpassed the detection performance despite the fact that detection and discrimination represented identical amplitude differences. This is consistent with the accelerating nonlinearity observed at low stimulus intensities. In the second stage of the experiment, four rats were trained to select the higher-amplitude stimulus between two vibrations applied to their whiskers. Similar to neuronal results, the rats' performance was better for the discrimination task compared with the detection task. The behavioral performance followed the same trend as that of the population of individual neurons. Both behavioral and neuronal data are consistent with the \"pedestal effect\" previously reported in human psychophysics.","corpus_id":13157806,"score":2},{"doc_id":"21423503","title":"Information Carried by Population Spike Times in the Whisker Sensory Cortex can be Decoded Without Knowledge of Stimulus Time.","abstract":"Computational analyses have revealed that precisely timed spikes emitted by somatosensory cortical neuronal populations encode basic stimulus features in the rat's whisker sensory system. Efficient spike time based decoding schemes both for the spatial location of a stimulus and for the kinetic features of complex whisker movements have been defined. To date, these decoding schemes have been based upon spike times referenced to an external temporal frame - the time of the stimulus itself. Such schemes are limited by the requirement of precise knowledge of the stimulus time signal, and it is not clear whether stimulus times are known to rats making sensory judgments. Here, we first review studies of the information obtained from spike timing referenced to the stimulus time. Then we explore new methods for extracting spike train information independently of any external temporal reference frame. These proposed methods are based on the detection of stimulus-dependent differences in the firing time within a neuronal population. We apply them to a data set using single-whisker stimulation in anesthetized rats and find that stimulus site can be decoded based on the millisecond-range relative differences in spike times even without knowledge of stimulus time. If spike counts alone are measured over tens or hundreds of milliseconds rather than milliseconds, such decoders are much less effective. These results suggest that decoding schemes based on millisecond-precise spike times are likely to subserve robust and information-rich transmission of information in the somatosensory system.","corpus_id":-1,"score":2},{"doc_id":"21490724","title":"The morphology of the rat vibrissal array: a model for quantifying spatiotemporal patterns of whisker-object contact.","abstract":"In all sensory modalities, the data acquired by the nervous system is shaped by the biomechanics, material properties, and the morphology of the peripheral sensory organs. The rat vibrissal (whisker) system is one of the premier models in neuroscience to study the relationship between physical embodiment of the sensor array and the neural circuits underlying perception. To date, however, the three-dimensional morphology of the vibrissal array has not been characterized. Quantifying array morphology is important because it directly constrains the mechanosensory inputs that will be generated during behavior. These inputs in turn shape all subsequent neural processing in the vibrissal-trigeminal system, from the trigeminal ganglion to primary somatosensory (\"barrel\") cortex. Here we develop a set of equations for the morphology of the vibrissal array that accurately describes the location of every point on every whisker to within ±5% of the whisker length. Given only a whisker's identity (row and column location within the array), the equations establish the whisker's two-dimensional (2D) shape as well as three-dimensional (3D) position and orientation. The equations were developed via parameterization of 2D and 3D scans of six rat vibrissal arrays, and the parameters were specifically chosen to be consistent with those commonly measured in behavioral studies. The final morphological model was used to simulate the contact patterns that would be generated as a rat uses its whiskers to tactually explore objects with varying curvatures. The simulations demonstrate that altering the morphology of the array changes the relationship between the sensory signals acquired and the curvature of the object. The morphology of the vibrissal array thus directly constrains the nature of the neural computations that can be associated with extraction of a particular object feature. These results illustrate the key role that the physical embodiment of the sensor array plays in the sensing process.","corpus_id":12613675,"score":2},{"doc_id":"21653730","title":"Spatial structure of multiwhisker receptive fields in the barrel cortex is stimulus dependent.","abstract":"The tactile sensations mediated by the whisker-trigeminal system allow rodents to efficiently detect and discriminate objects. These capabilities rely strongly on the temporal and spatial structure of whisker deflections. Subthreshold but also spiking receptive fields in the barrel cortex encompass a large number of vibrissae, and it seems likely that the functional properties of these multiwhisker receptive fields reflect the multiple-whisker interactions encountered by the animal during exploration of its environment. The aim of this study was to examine the dependence of the spatial structure of cortical receptive fields on stimulus parameters. Using a newly developed 24-whisker stimulation matrix, we applied a forward correlation analysis of spiking activity to randomized whisker deflections (sparse noise) to characterize the receptive fields that result from caudal and rostral directions of whisker deflection. We observed that the functionally determined principal whisker, the whisker eliciting the strongest response with the shortest latency, differed according to the direction of whisker deflection. Thus, for a given neuron, maximal responses to opposite directions of whisker deflections could be spatially separated. This spatial separation resulted in a displacement of the center of mass between the rostral and caudal subfields and was accompanied by differences between response latencies in rostral and caudal directions of whisker deflection. Such direction-dependent receptive field organization was observed in every cortical layer. We conclude that the spatial structure of receptive fields in the barrel cortex is not an intrinsic property of the neuron but depends on the properties of sensory input.","corpus_id":5676335,"score":2},{"doc_id":"21653856","title":"A unifying framework underlying mechanotransduction in the somatosensory system.","abstract":"Rodents use their whiskers to sense their surroundings. As most of the information available to the somatosensory system originates in whiskers' primary afferents, it is essential to understand the transformation of whisker motion into neuronal activity. Here, we combined in vivo recordings in anesthetized rats with mathematical modeling to ascertain the mechanical and electrical characteristics of mechanotransduction. We found that only two synergistic processes, which reflect the dynamic interactions between (1) receptor and whisker and (2) receptor and surrounding tissue, are needed to describe mechanotransduction during passive whiskers deflection. Interactions between these processes may account for stimulus-dependent changes in the magnitude and temporal pattern of tactile responses on multiple scales. Thus, we are able to explain complex electromechanical processes underlying sensory transduction using a simple model, which captures the responses of a wide range of mechanoreceptor types to diverse sensory stimuli. This compact and precise model allows for a ubiquitous description of how mechanoreceptors encode tactile stimulus.","corpus_id":2268624,"score":2},{"doc_id":"22399756","title":"Coding of apparent motion in the thalamic nucleus of the rat vibrissal somatosensory system.","abstract":"While exploring objects, rats make multiple contacts using their whiskers, thereby generating complex patterns of sensory information. The cerebral structures that process this information in the somatosensory system show discrete patterns of anatomically distinct units, each corresponding to one whisker. Moreover, the feedforward and feedback connections are remarkably topographic, with little cross-whisker divergence before reaching the cortical network. Despite this parallel design, information processing from several whiskers has been reported in subcortical nuclei. Here, we explored whether sensory neurons in the ventral posterior medial nucleus (VPM) of the thalamus encode emergent properties of complex multiwhisker stimulations. Using a 24-whisker stimulator, we tested the responses of VPM neurons to sequences of caudal deflections that generated an apparent motion in eight different directions across the whiskerpad. Overall, 45% of neurons exhibited an evoked increase in firing rate significantly selective to the direction of apparent motion of the global stimulus. Periods of suppression of firing rate were often observed, but were generally not selective. Global motion selectivity of VPM neurons could occur regardless of the extent and spatial organization of their receptive fields, and of their selectivity for the direction of motion of their principal whisker. To investigate whether the global selectivity could be due to corticothalamic feedback connections, we inactivated the barrel cortex while repeating the stimulation protocol. For most VPM neurons, the direction selectivity decreased but was still present. These results suggest that nonlinear processing of stimuli from different whiskers emerges in subcortical nuclei and is amplified by the corticofugal feedback.","corpus_id":6452092,"score":2},{"doc_id":"22683381","title":"Whisker sensory system - from receptor to decision.","abstract":"One of the great challenges of systems neuroscience is to understand how the neocortex transforms neuronal representations of the physical characteristics of sensory stimuli into the percepts which can guide the animal's decisions. Here we present progress made in understanding behavioral and neurophysiological aspects of a highly efficient sensory apparatus, the rat whisker system. Beginning with the 1970s discovery of \"barrels\" in the rat and mouse brain, one line of research has focused on unraveling the circuits that transmit information from the whiskers to the sensory cortex, together with the cellular mechanisms that underlie sensory responses. A second, more recent line of research has focused on tactile psychophysics, that is, quantification of the behavioral capacities supported by whisker sensation. The opportunity to join these two lines of investigation makes whisker-mediated sensation an exciting platform for the study of the neuronal bases of perception and decision-making. Even more appealing is the beginning-to-end prospective offered by this system: the inquiry can start at the level of the sensory receptor and conclude with the animal's choice. We argue that rats can switch between two modes of operation of the whisker sensory system: (1) generative mode and (2) receptive mode. In the generative mode, the rat moves its whiskers forward and backward to actively seek contact with objects and to palpate the object after initial contact. In the receptive mode, the rat immobilizes its whiskers to optimize the collection of signals from an object that is moving by its own power. We describe behavioral tasks that rats perform in these different modes. Next, we explore which neuronal codes in sensory cortex account for the rats' discrimination capacities. Finally, we present hypotheses for mechanisms through which \"downstream\" brain regions may read out the activity of sensory cortex in order to extract the significance of sensory stimuli and, ultimately, to select the appropriate action.","corpus_id":14521360,"score":2},{"doc_id":"22912602","title":"Functional diversity of supragranular GABAergic neurons in the barrel cortex.","abstract":"Although the neocortex forms a distributed system comprised of several functional areas, its vertical columnar organization is largely conserved across areas and species, suggesting the existence of a canonical neocortical microcircuit. In order to elucidate the principles governing the organization of such a cortical diagram, a detailed understanding of the dynamics binding different types of cortical neurons into a coherent algorithm is essential. Within this complex circuitry, GABAergic interneurons, while forming approximately only 15-20% of all cortical neurons, appear critical in maintaining a dynamic balance between excitation and inhibition. Despite their importance, cortical GABAergic neurons have not been extensively studied in vivo and their precise role in shaping the local microcircuit sensory response still remains to be determined. Their paucity, combined with their molecular, anatomical, and physiological diversity, has made it difficult to even establish a consensual nomenclature. However, recent technological advances in microscopy and mouse genetics have fostered a renewed interest in neocortical interneurons by putting them within \"visible\" reach of experimenters. The anatomically well-defined whisker-to-barrel pathway of the rodent is particularly amenable to studies attempting to link cortical circuit dynamics to behavior. To each whisker corresponds a discrete cortical unit equivalent to a single column, specialized in the encoding and processing of the sensory information it receives. In this review, we will focus on the functional role that each subtype of supragranular GABAergic neuron embedded within such a single neocortical unit may play in shaping the dynamics of the local circuit during somatosensory integration.","corpus_id":5413840,"score":2},{"doc_id":"22922646","title":"Activity in motor-sensory projections reveals distributed coding in somatosensation.","abstract":"Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide ‘contextual’ information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1-->vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.","corpus_id":2364419,"score":2},{"doc_id":"23486952","title":"Structure, function, and cortical representation of the rat submandibular whisker trident.","abstract":"Although the neurobiology of rodent facial whiskers has been studied intensively, little is known about sensing in other vibrissae. Here we describe the under-investigated submandibular \"whisker trident\" on the rat's chin. In this three-whisker array, a unique unpaired midline whisker is laterally flanked by two slightly shorter whiskers. All three whiskers point to the ground and are curved backwards. Unlike other whiskers, the trident is not located on an exposed body part. Trident vibrissae are not whisked and do not touch anything over long stretches of time. However, trident whiskers engage in sustained ground contact during head-down running while the animal is exploring or foraging. In biomechanical experiments, trident whiskers follow caudal ground movement more smoothly than facial whiskers. Remarkably, deflection angles decrease with increasing ground velocity. We identified one putative trident barrel in the left somatosensory cortex and two barrels in the right somatosensory cortex. The elongated putative trident-midline barrel is the longest and largest whisker barrel, suggesting that the midline trident whisker is of great functional significance. Cortical postsynaptic air-puff responses in the trident representation show much less temporal precision than facial whisker responses. Trident whiskers do not provide as much high-resolution information about object contacts as facial whiskers. Instead, our observations suggest an idiothetic function: their biomechanics allow trident whiskers to derive continuous measurements about ego motion from ground contacts. The midline position offers unique advantages in sensing heading direction in a laterally symmetric manner. The changes in trident deflection angle with velocity suggest that trident whiskers might function as a tactile speedometer.","corpus_id":16459116,"score":2},{"doc_id":"23864687","title":"Low-dimensional sensory feature representation by trigeminal primary afferents.","abstract":"In any sensory system, the primary afferents constitute the first level of sensory representation and fundamentally constrain all subsequent information processing. Here, we show that the spike timing, reliability, and stimulus selectivity of primary afferents in the whisker system can be accurately described by a simple model consisting of linear stimulus filtering combined with spike feedback. We fitted the parameters of the model by recording the responses of primary afferents to filtered, white noise whisker motion in anesthetized rats. The model accurately predicted not only the response of primary afferents to white noise whisker motion (median correlation coefficient 0.92) but also to naturalistic, texture-induced whisker motion. The model accounted both for submillisecond spike-timing precision and for non-Poisson spike train structure. We found substantial diversity in the responses of the afferent population, but this diversity was accurately captured by the model: a 2D filter subspace, corresponding to different mixtures of position and velocity sensitivity, captured 94% of the variance in the stimulus selectivity. Our results suggest that the first stage of the whisker system can be well approximated as a bank of linear filters, forming an overcomplete representation of a low-dimensional feature space.","corpus_id":14227142,"score":2},{"doc_id":"24097038","title":"Membrane potential correlates of sensory perception in mouse barrel cortex.","abstract":"Neocortical activity can evoke sensory percepts, but the cellular mechanisms remain poorly understood. We trained mice to detect single brief whisker stimuli and report perceived stimuli by licking to obtain a reward. Pharmacological inactivation and optogenetic stimulation demonstrated a causal role for the primary somatosensory barrel cortex. Whole-cell recordings from barrel cortex neurons revealed membrane potential correlates of sensory perception. Sensory responses depended strongly on prestimulus cortical state, but both slow-wave and desynchronized cortical states were compatible with task performance. Whisker deflection evoked an early (<50 ms) reliable sensory response that was encoded through cell-specific reversal potentials. A secondary late (50-400 ms) depolarization was enhanced on hit trials compared to misses. Optogenetic inactivation revealed a causal role for late excitation. Our data reveal dynamic processing in the sensory cortex during task performance, with an early sensory response reliably encoding the stimulus and later secondary activity contributing to driving the subjective percept.","corpus_id":23919226,"score":2},{"doc_id":"24349279","title":"Transformation of adaptation and gain rescaling along the whisker sensory pathway.","abstract":"Neurons in all sensory systems have a remarkable ability to adapt their sensitivity to the statistical structure of the sensory signals to which they are tuned. In the barrel cortex, firing rate adapts to the variance of a whisker stimulus and neuronal sensitivity (gain) adjusts in inverse proportion to the stimulus standard deviation. To determine how adaptation might be transformed across the ascending lemniscal pathway, we measured the responses of single units in the first and last subcortical stages, the trigeminal ganglion (TRG) and ventral posterior medial thalamic nucleus (VPM), to controlled whisker stimulation in urethane-anesthetized rats. We probed adaptation using a filtered white noise stimulus that switched between low- and high-variance epochs. We found that the firing rate of both TRG and VPM neurons adapted to stimulus variance. By fitting the responses of each unit to a Linear-Nonlinear-Poisson model, we tested whether adaptation changed feature selectivity and/or sensitivity. We found that, whereas feature selectivity was unaffected by stimulus variance, units often exhibited a marked change in sensitivity. The extent of these sensitivity changes increased systematically along the pathway from TRG to barrel cortex. However, there was marked variability across units, especially in VPM. In sum, in the whisker system, the adaptation properties of subcortical neurons are surprisingly diverse. The significance of this diversity may be that it contributes to a rich population representation of whisker dynamics.","corpus_id":11525820,"score":2},{"doc_id":"24361064","title":"The representation of social facial touch in rat barrel cortex.","abstract":"Controlled presentation of stimuli to anesthetized [1] or awake [2] animals suggested that neurons in sensory cortices respond to elementary features [3, 4], but we know little about neuronal responses evoked by social interactions. Here we investigate processing in the barrel cortex of rats engaging in social facial touch [5, 6]. Sensory stimulation by conspecifics differs from classic whisker stimuli such as deflections, contact poles [7, 8], or textures [9, 10]. A large fraction of barrel cortex neurons responded to facial touch. Social touch responses peaked when animals aligned their faces and contacted each other by multiple whiskers with small, irregular whisker movements. Object touch was associated with larger, more regular whisker movements, and object responses were weaker than social responses. Whisker trimming abolished responses. During social touch, neurons in males increased their firing on average by 44%, while neurons in females increased their firing by only 19%. In females, socially evoked and ongoing firing rates were more than 1.5-fold higher in nonestrus than in estrus. Barrel cortex represented socially different contacts by distinct firing rates, and the variation of activity with sex and sexual status could contribute to the generation of gender-specific neural constructs of conspecifics.","corpus_id":17495746,"score":2},{"doc_id":"24821429","title":"Cortical control of whisker movement.","abstract":"Facial muscles drive whisker movements, which are important for active tactile sensory perception in mice and rats. These whisker muscles are innervated by cholinergic motor neurons located in the lateral facial nucleus. The whisker motor neurons receive synaptic inputs from premotor neurons, which are located within the brain stem, the midbrain, and the neocortex. Complex, distributed neural circuits therefore regulate whisker movement during behavior. This review focuses specifically on cortical whisker motor control. The whisker primary motor cortex (M1) strongly innervates brain stem reticular nuclei containing whisker premotor neurons, which might form a central pattern generator for rhythmic whisker protraction. In a parallel analogous pathway, the whisker primary somatosensory cortex (S1) strongly projects to the brain stem spinal trigeminal interpolaris nucleus, which contains whisker premotor neurons innervating muscles for whisker retraction. These anatomical pathways may play important functional roles, since stimulation of M1 drives exploratory rhythmic whisking, whereas stimulation of S1 drives whisker retraction.","corpus_id":21063946,"score":2},{"doc_id":"25339711","title":"Tactile object localization by anticipatory whisker motion.","abstract":"Rodents use rhythmic protractions of their whiskers to locate objects in space. The amplitude of these protractions is reduced when whiskers contact objects, leading to a tendency of whiskers to only lightly touch the environment. While the impact of this process on the sensory input has been studied, little is known about how sensory input causes this change in the motor pattern. Here, using high-speed imaging of whisking in mice, we simultaneously measured whisker contacts and the resulting whisking motion. We found that mice precisely target their whisker protractions to the distance at which they expect objects. This modulation does not depend on the current sensory input and remains stable for at least one whisking cycle when there is no object contact or when the object position is changed. As a result, the timing and other information carried by whisker contacts encodes how well each protraction was matched to the object, functioning as an error signal. Whisker contacts can thus encode a mismatch between expected object locations and the actual environment.","corpus_id":2451110,"score":2},{"doc_id":"25934471","title":"Sparse, reliable, and long-term stable representation of periodic whisker deflections in the mouse barrel cortex.","abstract":"The rodent whisker system is a preferred model for studying plasticity in the somatosensory cortex (barrel cortex). Contrarily, only a small amount of research has been conducted to characterize the stability of neuronal population activity in the barrel cortex. We used the mouse whisker system to address the neuronal basis of stable perception in the somatosensory cortex. Cortical representation of periodic whisker deflections was studied in populations of neurons in supragranular layers over extended time periods (up to 3 months) with long-term two-photon Ca(2+) imaging in anesthetized mice. We found that in most of the neurons (87%), Ca(2+) responses increased sublinearly with increasing number of contralateral whisker deflections. The imaged population of neurons was activated in a stereotypic way over days and for different deflection rates (pulse frequencies). Thus, pulse frequencies are coded by response strength rather than by distinct neuronal sub-populations. A small population of highly responsive neurons (~3%) was sufficient to decode the whisker stimulus. This conserved functional map, led by a small set of highly responsive neurons, might form the foundation of stable sensory percepts.","corpus_id":6178321,"score":2},{"doc_id":"26126800","title":"Wideband phase locking to modulated whisker vibration point to a temporal code for texture in the rat's barrel cortex.","abstract":"Rats probe objects with their whiskers and make decisions about sizes, shapes, textures and distances within a few tens of milliseconds. This perceptual analysis requires the processing of tactile high-frequency object components reflecting surface roughness. We have shown that neurons in the barrel cortex of rats encode high-frequency sinusoidal vibrations of whiskers for sustained periods when presented with constant amplitudes and frequencies. In a natural situation, however, stimulus parameters change rapidly when whiskers are brushing across objects. In this study, we therefore analysed cortical responses to vibratory movements of single whiskers with rapidly changing amplitudes and frequencies. The results show that different neural codes are employed for a processing of stimulus parameters. The frequency of whisker vibration is encoded by the temporal pattern of spike discharges, i.e., the phase-locked responses of barrel cortex neurons. In addition, oscillatory gamma band activity was induced during high-frequency stimulation. The pivotal descriptor of the amplitude of whisker displacement, the velocity, is reflected in the rate of spike discharges. While phase-locked discharges occurred over the entire range of frequencies tested (10-600 Hz), the discharge rate increased with stimulus velocity only up to about 60 µm/ms, saturating at a mean rate of ~117 spikes/s. In addition, the results show that whisker movements of more than 500 Hz bandwidth may be encoded by phase-locked responses of small groups of cortical neurons. Thus, even single whiskers may transmit information about wide ranges of textural components owing to their set of different types of hair follicle mechanoreceptors.","corpus_id":14913640,"score":2},{"doc_id":"26441549","title":"Efficient population coding of naturalistic whisker motion in the ventro-posterior medial thalamus based on precise spike timing.","abstract":"The rodent whisker-associated thalamic nucleus (VPM) contains a somatotopic map where whisker representation is divided into distinct neuronal sub-populations, called \"barreloids\". Each barreloid projects to its associated cortical barrel column and so forms a gateway for incoming sensory stimuli to the barrel cortex. We aimed to determine how the population of neurons within one barreloid encodes naturalistic whisker motion. In rats, we recorded the extracellular activity of up to nine single neurons within a single barreloid, by implanting silicon probes parallel to the longitudinal axis of the barreloids. We found that play-back of texture-induced whisker motion evoked sparse responses, timed with millisecond precision. At the population level, there was synchronous activity: however, different subsets of neurons were synchronously active at different times. Mutual information between population responses and whisker motion increased near linearly with population size. When normalized to factor out firing rate differences, we found that texture was encoded with greater informational-efficiency than white noise. These results indicate that, within each VPM barreloid, there is a rich and efficient population code for naturalistic whisker motion based on precisely timed, population spike patterns.","corpus_id":5712901,"score":2},{"doc_id":"26864754","title":"Whisker-related afferents in superior colliculus.","abstract":"Rodents use their whiskers to explore the environment, and the superior colliculus is part of the neural circuits that process this sensorimotor information. Cells in the intermediate layers of the superior colliculus integrate trigeminotectal afferents from trigeminal complex and corticotectal afferents from barrel cortex. Using histological methods in mice, we found that trigeminotectal and corticotectal synapses overlap somewhat as they innervate the lower and upper portions of the intermediate granular layer, respectively. Using electrophysiological recordings and optogenetics in anesthetized mice in vivo, we showed that, similar to rats, whisker deflections produce two successive responses that are driven by trigeminotectal and corticotectal afferents. We then employed in vivo and slice experiments to characterize the response properties of these afferents. In vivo, corticotectal responses triggered by electrical stimulation of the barrel cortex evoke activity in the superior colliculus that increases with stimulus intensity and depresses with increasing frequency. In slices from adult mice, optogenetic activation of channelrhodopsin-expressing trigeminotectal and corticotectal fibers revealed that cells in the intermediate layers receive more efficacious trigeminotectal, than corticotectal, synaptic inputs. Moreover, the efficacy of trigeminotectal inputs depresses more strongly with increasing frequency than that of corticotectal inputs. The intermediate layers of superior colliculus appear to be tuned to process strong but infrequent trigeminal inputs and weak but more persistent cortical inputs, which explains features of sensory responsiveness, such as the robust rapid sensory adaptation of whisker responses in the superior colliculus.","corpus_id":22307626,"score":2},{"doc_id":"27098555","title":"The evolution of whisker-mediated somatosensation in mammals: Sensory processing in barrelless S1 cortex of a marsupial, Monodelphis domestica.","abstract":"Movable tactile sensors in the form of whiskers are present in most mammals, but sensory coding in the cortical whisker representation has been studied almost exclusively in mice and rats. Many species that possess whiskers lack the modular \"barrel\" organization found in the primary somatosensory cortex (S1) of mice and rats, but it is unclear how whisker-related input is represented in these species. We used single-unit extracellular recording techniques to characterize receptive fields and response properties in S1 of Monodelphis domestica (short-tailed opossum), a nocturnal, terrestrial marsupial that shared its last common ancestor with placental mammals over 160 million years ago. Short-tailed opossums lack barrels and septa in S1 but show active whisking behavior similar to that of mice and rats. Most neurons in short-tailed opossum S1 exhibited multiwhisker receptive fields, including a single best whisker (BW) and lower magnitude responses to the deflection of surrounding whiskers. Mean tuning width was similar to that reported for mice and rats. Both symmetrical and asymmetrical receptive fields were present. Neurons tuned to ventral whiskers tended to show broad tuning along the rostrocaudal axis. Thus, despite the absence of barrels, most receptive field properties were similar to those reported for mice and rats. However, unlike those species, S1 neuronal responses to BW and surround whisker deflection showed comparable latencies in short-tailed opossums. This dissimilarity suggests that some aspects of barrel cortex function may not generalize to tactile processing across mammalian species and may be related to differences in the architecture of the whisker-to-cortex pathway. J. Comp. Neurol. 524:3587-3613, 2016. © 2016 Wiley Periodicals, Inc.","corpus_id":13842932,"score":2},{"doc_id":"27463524","title":"Representation of Stimulus Speed and Direction in Vibrissal-Sensitive Regions of the Trigeminal Nuclei: A Comparison of Single Unit and Population Responses.","abstract":"The rat vibrissal (whisker) system is one of the oldest and most important models for the study of active tactile sensing and sensorimotor integration. It is well established that primary sensory neurons in the trigeminal ganglion respond to deflections of one and only one whisker, and that these neurons are strongly tuned for both the speed and direction of individual whisker deflections. During active whisking behavior, however, multiple whiskers will be deflected simultaneously. Very little is known about how neurons at central levels of the trigeminal pathway integrate direction and speed information across multiple whiskers. In the present work, we investigated speed and direction coding in the trigeminal brainstem nuclei, the first stage of neural processing that exhibits multi-whisker receptive fields. Specifically, we recorded both single-unit spikes and local field potentials from fifteen sites in spinal trigeminal nucleus interpolaris and oralis while systematically varying the speed and direction of coherent whisker deflections delivered across the whisker array. For 12/15 neurons, spike rate was higher when the whisker array was stimulated from caudal to rostral rather than rostral to caudal. In addition, 10/15 neurons exhibited higher firing rates for slower stimulus speeds. Interestingly, using a simple decoding strategy for the local field potentials and spike trains, classification of speed and direction was higher for field potentials than for single unit spike trains, suggesting that the field potential is a robust reflection of population activity. Taken together, these results point to the idea that population responses in these brainstem regions in the awake animal will be strongest during behaviors that stimulate a population of whiskers with a directionally coherent motion.","corpus_id":7485983,"score":2},{"doc_id":"27574970","title":"Short Time-Scale Sensory Coding in S1 during Discrimination of Whisker Vibrotactile Sequences.","abstract":"Rodent whisker input consists of dense microvibration sequences that are often temporally integrated for perceptual discrimination. Whether primary somatosensory cortex (S1) participates in temporal integration is unknown. We trained rats to discriminate whisker impulse sequences that varied in single-impulse kinematics (5-20-ms time scale) and mean speed (150-ms time scale). Rats appeared to use the integrated feature, mean speed, to guide discrimination in this task, consistent with similar prior studies. Despite this, 52% of S1 units, including 73% of units in L4 and L2/3, encoded sequences at fast time scales (≤20 ms, mostly 5-10 ms), accurately reflecting single impulse kinematics. 17% of units, mostly in L5, showed weaker impulse responses and a slow firing rate increase during sequences. However, these units did not effectively integrate whisker impulses, but instead combined weak impulse responses with a distinct, slow signal correlated to behavioral choice. A neural decoder could identify sequences from fast unit spike trains and behavioral choice from slow units. Thus, S1 encoded fast time scale whisker input without substantial temporal integration across whisker impulses.","corpus_id":16616768,"score":2},{"doc_id":"27707809","title":"Whisker row deprivation affects the flow of sensory information through rat barrel cortex.","abstract":"Whisker trimming causes substantial reorganization of neuronal response properties in barrel cortex. However, little is known about experience-dependent rerouting of sensory processing following sensory deprivation. To address this, we performed in vivo intracellular recordings from layers 2/3 (L2/3), layer 4 (L4), layer 5 regular-spiking (L5RS), and L5 intrinsically bursting (L5IB) neurons and measured their multiwhisker receptive field at the level of spiking activity, membrane potential, and synaptic conductance before and after sensory deprivation. We used Chernoff information to quantify the \"sensory information\" contained in the firing patterns of cells in response to spared and deprived whisker stimulation. In the control condition, information for flanking-row and same-row whiskers decreased in the order L4, L2/3, L5IB, L5RS. However, after whisker-row deprivation, spared flanking-row whisker information was reordered to L4, L5RS, L5IB, L2/3. Sensory information from the trimmed whiskers was reduced and delayed in L2/3 and L5IB neurons, whereas sensory information from spared whiskers was increased and advanced in L4 and L5RS neurons. Sensory information from spared whiskers was increased in L5IB neurons without a latency change. L5RS cells exhibited the largest changes in sensory information content through an atypical plasticity combining a significant decrease in spontaneous activity and an increase in a short-latency excitatory conductance. NEW & NOTEWORTHY: Sensory cortical plasticity is usually quantified by changes in evoked firing rate. In this study we quantified plasticity by changes in sensory detection performance using Chernoff information and receiver operating characteristic analysis. We found that whisker deprivation causes a change in information flow within the cortical layers and that layer 5 regular-spiking cells, despite showing only a small potentiation of short-latency input, show the greatest increase in information content for the spared input partly by decreasing their spontaneous activity.","corpus_id":14014559,"score":2},{"doc_id":"27869114","title":"A radial map of multi-whisker correlation selectivity in the rat barrel cortex.","abstract":"In the barrel cortex, several features of single-whisker stimuli are organized in functional maps. The barrel cortex also encodes spatio-temporal correlation patterns of multi-whisker inputs, but so far the cortical mapping of neurons tuned to such input statistics is unknown. Here we report that layer 2/3 of the rat barrel cortex contains an additional functional map based on neuronal tuning to correlated versus uncorrelated multi-whisker stimuli: neuron responses to uncorrelated multi-whisker stimulation are strongest above barrel centres, whereas neuron responses to correlated and anti-correlated multi-whisker stimulation peak above the barrel-septal borders, forming rings of multi-whisker synchrony-preferring cells.","corpus_id":854174,"score":2},{"doc_id":"28334121","title":"Interspersed Distribution of Selectivity to Kinematic Stimulus Features in Supragranular Layers of Mouse Barrel Cortex.","abstract":"Neurons in the primary sensory regions of neocortex have heterogeneous response properties. The spatial arrangement of neurons with particular response properties is a key aspect of population representations and can shed light on how local circuits are wired. Here, we investigated how neurons with sensitivity to different kinematic features of whisker stimuli are distributed across local circuits in supragranular layers of the barrel cortex. Using 2-photon calcium population imaging in anesthetized mice, we found that nearby neurons represent diverse kinematic features, providing a rich population representation at the local scale. Neurons interspersed in space therefore responded differently to a common stimulus kinematic feature. Conversely, neurons with similar feature selectivity were located no closer to each other than predicted by a random distribution null hypothesis. This finding relied on defining a null hypothesis that was specific for testing the spatial distribution of tuning across neurons. We also measured how neurons sensitive to specific features were distributed relative to barrel boundaries, and found no systematic organization. Our results are compatible with randomly distributed selectivity to kinematic features, with no systematic ordering superimposed upon the whisker map.","corpus_id":24343609,"score":2},{"doc_id":"28827090","title":"Organization of orientation-specific whisker deflection responses in layer 2/3 of mouse somatosensory cortex.","abstract":"The rodent whisker-barrel system is characterized by its patterned somatotopic mapping between the sensory periphery and multiple regions of the brain. While somatotopy in the whisker system is established, we know far less about how preferences for stimulus orientation or other features are organized. Mouse somatosensation is an increasingly popular model for circuit-based dissection of perceptual decision making and learning, yet our understanding of how stimulus feature representations are organized in the cortex is incomplete. Here, we used in vivo two-photon calcium imaging to monitor activity of populations of layer (L) 2/3 neurons in the mouse primary somatosensory cortex during deflections of a single whisker in two orthogonal orientations (azimuthal or elevational). We split the population response to whisker deflections into an orientation-specific component and a non-specific component that reflected overall excitability in response to deflection of a single whisker. Orientation-specific responses were organized in a locally heterogeneous and spatially distributed manner. Correlations in the stimulus-independent trial-to-trial variability of pairs of neurons were higher among neurons that preferred the same orientation. These correlations depended on similarity in both orientation-specific and non-specific components of responses to single-whisker deflections. Our results shed light on L2/3 organization in mouse somatosensory cortex, and lay a foundation for dissecting circuit mechanisms of perceptual learning and decision-making during orientation discrimination tasks.","corpus_id":23636932,"score":2},{"doc_id":"28843997","title":"Representation of tactile scenes in the rodent barrel cortex.","abstract":"After half a century of research, the sensory features coded by neurons of the rodent barrel cortex remain poorly understood. Still, views of the sensory representation of whisker information are increasingly shifting from a labeled line representation of single whisker deflections to a selectivity for specific elements of the complex statistics of the multi-whisker deflection patterns that take place during spontaneous rodent behavior - so called natural tactile scenes. Here we review the current knowledge regarding the coding of patterns of whisker stimuli by barrel cortex neurons, from responses to single whisker deflections to the representation of complex tactile scenes. A number of multi-whisker tunings have already been identified, including center-surround feature extraction, angular tuning during edge-like multi-whisker deflections, and even tuning to specific statistical properties of the tactile scene such as the level of correlation across whiskers. However, a more general model of the representation of multi-whisker information in the barrel cortex is still missing. This is in part because of the lack of a human intuition regarding the perception emerging from a whisker system, but also because in contrast to other primary sensory cortices such as the visual cortex, the spatial feature selectivity of barrel cortex neurons rests on highly nonlinear interactions that remained hidden to classical receptive-field approaches.","corpus_id":21058087,"score":2},{"doc_id":"28843998","title":"What the whiskers tell the brain.","abstract":"A fundamental question in the investigation of any sensory system is what physical signals drive its sensory neurons during natural behaviour. Surprisingly, in the whisker system, it is only recently that answers to this question have emerged. Here, we review the key developments, focussing mainly on the first stage of the ascending pathway - the primary whisker afferents (PWAs). We first consider a biomechanical framework, which describes the fundamental mechanical forces acting on the whiskers during active sensation. We then discuss technical progress that has allowed such mechanical variables to be estimated in awake, behaving animals. We discuss past electrophysiological evidence concerning how PWAs function and reinterpret it within the biomechanical framework. Finally, we consider recent studies of PWAs in awake, behaving animals and compare the results to related studies of the cortex. We argue that understanding 'what the whiskers tell the brain' sheds valuable light on the computational functions of downstream neural circuits, in particular, the barrel cortex.","corpus_id":19060461,"score":2},{"doc_id":"28919043","title":"Neocortical dynamics during whisker-based sensory discrimination in head-restrained mice.","abstract":"A fundamental task frequently encountered by brains is to rapidly and reliably discriminate between sensory stimuli of the same modality, be it distinct auditory sounds, odors, visual patterns, or tactile textures. A key mammalian brain structure involved in discrimination behavior is the neocortex. Sensory processing not only involves the respective primary sensory area, which is crucial for perceptual detection, but additionally relies on cortico-cortical communication among several regions including higher-order sensory areas as well as frontal cortical areas. It remains elusive how these regions exchange information to process neural representations of distinct stimuli to bring about a decision and initiate appropriate behavioral responses. Likewise, it is poorly understood how these neural computations are conjured during task learning. In this review, we discuss recent studies investigating cortical dynamics during discrimination behaviors that utilize head-fixed behavioral tasks in combination with in vivo electrophysiology, two-photon calcium imaging, and cell-type-specific targeting. We particularly focus on information flow in distinct cortico-cortical pathways when mice use their whiskers to discriminate between different objects or different locations. Within the primary and secondary somatosensory cortices (S1 and S2, respectively) as well as vibrissae motor cortex (M1), intermingled functional representations of touch, whisking, and licking were found, which partially re-organized during discrimination learning. These findings provide first glimpses of cortico-cortical communication but emphasize that for understanding the complete process of discrimination it will be crucial to elucidate the details of how neural processing is coordinated across brain-wide neuronal networks including the S1-S2-M1 triangle and cortical areas beyond.","corpus_id":11910957,"score":2},{"doc_id":"28929510","title":"Laminar-specific encoding of texture elements in rat barrel cortex.","abstract":"KEY POINTS: For rats texture discrimination is signalled by the large face whiskers by stick-slip events. Neural encoding of repetitive stick-slip events will be influenced by intrinsic properties of adaptation. We show that texture coding in the barrel cortex is laminar specific and follows a power function. Our results also show layer 2 codes for novel feature elements via robust firing rates and temporal fidelity. We conclude that texture coding relies on a subtle neural ensemble to provide important object information. ABSTRACT: Texture discrimination by rats is exquisitely guided by fine-grain mechanical stick-slip motions of the face whiskers as they encounter, stick to and slip past successive texture-defining surface features such as bumps and grooves. Neural encoding of successive stick-slip texture events will be shaped by adaptation, common to all sensory systems, whereby receptor and neural responses to a stimulus are affected by responses to preceding stimuli, allowing resetting to signal novel information. Additionally, when a whisker is actively moved to contact and brush over surfaces, that motion itself generates neural responses that could cause adaptation of responses to subsequent stick-slip events. Nothing is known about encoding in the rat whisker system of stick-slip events defining textures of different grain or the influence of adaptation from whisker protraction or successive texture-defining stick-slip events. Here we recorded responses from halothane-anaesthetized rats in response to texture-defining stimuli applied to passive whiskers. We demonstrate that: across the columnar network of the whisker-recipient barrel cortex, adaptation in response to repetitive stick-slip events is strongest in uppermost layers and equally lower thereafter; neither whisker protraction speed nor stick-slip frequency impede encoding of stick-slip events at rates up to 34.08 Hz; and layer 2 normalizes responses to whisker protraction to resist effects on texture signalling. Thus, within laminar-specific response patterns, barrel cortex reliably encodes texture-defining elements even to high frequencies.","corpus_id":38446113,"score":2},{"doc_id":"29265375","title":"Millisecond precision temporal encoding of stimulus features during cortically generated gamma oscillations in the rat somatosensory cortex.","abstract":"KEY POINTS: Rodents explore their immediate environment using their whiskers. Such exploration leads to micromotions, which contain many high-frequency (50-200 Hz) components. High-frequency whisker motion is represented faithfully in the temporal structure of the spike trains of trigeminal neurons. However, the representation of high-frequency sensory inputs in cortex is not fully understood. By combining extracellular and intracellular recordings in the rat somatosensory cortex and thalamus, we show that high-frequency sensory inputs, either sinusoidal or white noise, elicit internally generated gamma (20-60 Hz) band oscillations in cortical networks. Gamma oscillations modulate cortical spike probability while preserving sub-millisecond phase relations with high-frequency sensory inputs. Consequently, our results indicate that millisecond precision stimulus-locked spiking activity and sensory-induced gamma oscillation can constitute independent multiplexed coding schemes at the single-cell level. ABSTRACT: In the natural environment, tactile exploration often leads to high-frequency vibrations at the level of the sensory organs. Single-unit recordings of cortical neurons have pointed towards either a rate or a temporal code for representing high-frequency tactile signals. In cortical networks, sensory processing results from the interaction between feedforward inputs relayed from the thalamus and internally generated activity. However, how the emergent activity represents high-frequency sensory input is not fully understood. Using multisite single-unit, local field potential and intracellular recordings in the somatosensory cortex and thalamus of lightly sedated male rats, we measured neuronal responses evoked by sinusoidal and band-pass white noise whisker stimulation at frequencies that encompass those observed during texture exploration (50-200 Hz). We found that high-frequency sensory inputs relayed from the thalamus elicit both sub-millisecond stimulus-locked responses and internally generated gamma (20-60 Hz) band oscillations in cortical networks. Gamma oscillations modulate spike probability while preserving sub-millisecond phase relations with sensory inputs. Therefore, precise stimulus-locked spiking activity and sensory-induced gamma oscillations can constitute independent multiplexed coding schemes at the single-cell level.","corpus_id":4920462,"score":2},{"doc_id":"29584719","title":"Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.","abstract":"Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks.","corpus_id":4644792,"score":2},{"doc_id":"22022245","title":"Neural computation via neural geometry: a place code for inter-whisker timing in the barrel cortex?","abstract":"The place theory proposed by Jeffress (1948) is still the dominant model of how the brain represents the movement of sensory stimuli between sensory receptors. According to the place theory, delays in signalling between neurons, dependent on the distances between them, compensate for time differences in the stimulation of sensory receptors. Hence the location of neurons, activated by the coincident arrival of multiple signals, reports the stimulus movement velocity. Despite its generality, most evidence for the place theory has been provided by studies of the auditory system of auditory specialists like the barn owl, but in the study of mammalian auditory systems the evidence is inconclusive. We ask to what extent the somatosensory systems of tactile specialists like rats and mice use distance dependent delays between neurons to compute the motion of tactile stimuli between the facial whiskers (or 'vibrissae'). We present a model in which synaptic inputs evoked by whisker deflections arrive at neurons in layer 2/3 (L2/3) somatosensory 'barrel' cortex at different times. The timing of synaptic inputs to each neuron depends on its location relative to sources of input in layer 4 (L4) that represent stimulation of each whisker. Constrained by the geometry and timing of projections from L4 to L2/3, the model can account for a range of experimentally measured responses to two-whisker stimuli. Consistent with that data, responses of model neurons located between the barrels to paired stimulation of two whiskers are greater than the sum of the responses to either whisker input alone. The model predicts that for neurons located closer to either barrel these supralinear responses are tuned for longer inter-whisker stimulation intervals, yielding a topographic map for the inter-whisker deflection interval across the surface of L2/3. This map constitutes a neural place code for the relative timing of sensory stimuli.","corpus_id":18707403,"score":1},{"doc_id":"22537827","title":"Barrel cortical neurons and astrocytes coordinately respond to an increased whisker stimulus frequency.","abstract":"BACKGROUND: Nerve cells program the brain codes to manage well-organized cognitions and behaviors. It remains unclear how a population of neurons and astrocytes work coordinately to encode their spatial and temporal activity patterns in response to frequency and intensity signals from sensory inputs. RESULTS: With two-photon imaging and electrophysiology to record cellular functions in the barrel cortex in vivo, we analyzed the activity patterns of neurons and astrocytes in response to whisker stimuli with increasing frequency, an environmental stimulus pattern that rodents experience in the accelerated motion. Compared to the resting state, whisker stimulation caused barrel neurons and astrocytes to be activated more synchronously. An increased stimulus frequency up-regulated the activity strength of neurons and astrocytes as well as coordinated their interaction. The coordination among the barrel neurons and astrocytes was fulfilled by increasing their functional connections. CONCLUSIONS: Our study reveals that the nerve cells in the barrel cortex encode frequency messages in whisker tactile inputs through setting their activity coordination.","corpus_id":5743731,"score":1},{"doc_id":"24305831","title":"Independent population coding of speech with sub-millisecond precision.","abstract":"To understand the strategies used by the brain to analyze complex environments, we must first characterize how the features of sensory stimuli are encoded in the spiking of neuronal populations. Characterizing a population code requires identifying the temporal precision of spiking and the extent to which spiking is correlated, both between cells and over time. In this study, we characterize the population code for speech in the gerbil inferior colliculus (IC), the hub of the auditory system where inputs from parallel brainstem pathways are integrated for transmission to the cortex. We find that IC spike trains can carry information about speech with sub-millisecond precision, and, consequently, that the temporal correlations imposed by refractoriness can play a significant role in shaping spike patterns. We also find that, in contrast to most other brain areas, the noise correlations between IC cells are extremely weak, indicating that spiking in the population is conditionally independent. These results demonstrate that the problem of understanding the population coding of speech can be reduced to the problem of understanding the stimulus-driven spiking of individual cells, suggesting that a comprehensive model of the subcortical processing of speech may be attainable in the near future.","corpus_id":23377470,"score":1},{"doc_id":"24472465","title":"[What the whiskers tell the tactile brain].","abstract":"Ce que les vibrisses disent au cerveau tactile. The rodent whisker system became one of the main system models for the study of the functional properties of sensory neurons. This is due on one hand to the detailed knowledge that we have on the afferent pathways linking the mechanoreceptors in the follicles to the primary somatosensory cortex and on the other hand to the possibility of controlling the sensory input at a micrometer and millisecond scale. The observation of the natural use of the whiskers by rodents indicates that exploration of objects and textures imply multiple contacts with tens of whiskers simultaneously. We have studied the neural code in the barrel cortex, which receives tactile information from the whiskers. By combining multi-electrode recordings and controlled multiwhisker tactile stimulation with theoretical analysis, we have observed a dependence of neural responses on the statistics of the sensory input. Several classes of neuronal responses, similar to those described in a number of cortical visual areas, were observed in the same cortical volume, indicating that various coding schemes are implemented in the same cortical network and can be put into play differentially to cope with the changing statistics of the peripheral stimuli.","corpus_id":196595761,"score":1},{"doc_id":"24695456","title":"Optogenetic patterning of whisker-barrel cortical system in transgenic rat expressing channelrhodopsin-2.","abstract":"The rodent whisker-barrel system has been an ideal model for studying somatosensory representations in the cortex. However, it remains a challenge to experimentally stimulate whiskers with a given pattern under spatiotemporal precision. Recently the optogenetic manipulation of neuronal activity has made possible the analysis of the neuronal network with precise spatiotemporal resolution. Here we identified the selective expression of channelrhodopsin-2 (ChR2), an algal light-driven cation channel, in the large mechanoreceptive neurons in the trigeminal ganglion (TG) as well as their peripheral nerve endings innervating the whisker follicles of a transgenic rat. The spatiotemporal pattern of whisker irradiation thus produced a barrel-cortical response with a specific spatiotemporal pattern as evidenced by electrophysiological and functional MRI (fMRI) studies. Our methods of generating an optogenetic tactile pattern (OTP) can be expected to facilitate studies on how the spatiotemporal pattern of touch is represented in the somatosensory cortex, as Hubel and Wiesel did in the visual cortex.","corpus_id":881274,"score":1},{"doc_id":"25100857","title":"Imprecise Whisker Map in the Neonatal Rat Barrel Cortex.","abstract":"The somatosensory barrel cortex in rodents contains a topographic map of the facial whiskers where each cortical barrel is tuned to a corresponding whisker. However, exactly when this correspondence is established during development and how precise the functional topography of the whisker protomap is at birth, before the anatomical formation of barrels, are questions that remain unresolved. Here, using extracellular and whole-cell recordings from the barrel cortex of 0- to 7-day-old (P0-7; P0 = day of birth) rat pups in vivo, we report a low level of tuning to the principal whisker at P0-1, with multiple adjacent whiskers evoking large multi- and single-unit responses and excitatory postsynaptic currents in cortical neurons. Additionally, we found broad and largely overlapping projection fields (PFs) for neighboring whiskers in the barrel cortex at P0-1. Starting from P2-3, a segregated whisker map emerged, characterized by preferential single whisker tuning and segregated whisker PFs. These results indicate that the functional whisker protomap in the somatosensory cortex is imprecise at birth, that for 2-3 days after birth, whiskers compete for the cortical target territories, and that formation of a segregated functional whisker map coincides with emergence of the anatomical barrel map.","corpus_id":16959113,"score":1},{"doc_id":"26217194","title":"Emergence of spatiotemporal invariance in large neuronal ensembles in rat barrel cortex.","abstract":"Invariant sensory coding is the robust coding of some sensory information (e.g., stimulus type) despite major changes in other sensory parameters (e.g., stimulus strength). The contribution of large populations of neurons (ensembles) to invariant sensory coding is not well understood, but could offer distinct advantages over invariance in single cell receptive fields. To test invariant sensory coding in neuronal ensembles evoked by single whisker stimulation as early as primary sensory cortex, we recorded detailed spatiotemporal movies of evoked ensemble activity through the depth of rat barrel cortex using microelectrode arrays. We found that an emergent property of whisker evoked ensemble activity, its spatiotemporal profile, was notably invariant across major changes in stimulus amplitude (up to >200-fold). Such ensemble-based invariance was found for single whisker stimulation as well as for the integrated profile of activity evoked by the more naturalistic stimulation of the entire whisker array. Further, the integrated profile of whisker array evoked ensemble activity and its invariance to stimulus amplitude shares striking similarities to \"funneled\" tactile perception in humans. We therefore suggest that ensemble-based invariance could provide a robust neurobiological substrate for invariant sensory coding and integration at an early stage of cortical sensory processing already in primary sensory cortex.","corpus_id":6911368,"score":1},{"doc_id":"26417040","title":"Facial whisker pattern is not sufficient to instruct a whisker-related topographic map in the mouse somatosensory brainstem.","abstract":"Facial somatosensory input is relayed by trigeminal ganglion (TG) neurons and serially wired to brainstem, thalamus and cortex. Spatially ordered sets of target neurons generate central topographic maps reproducing the spatial arrangement of peripheral facial receptors. Facial pattern provides a necessary template for map formation, but may be insufficient to impose a brain somatotopic pattern. In mice, lower jaw sensory information is relayed by the trigeminal nerve mandibular branch, whose axons target the brainstem dorsal principal sensory trigeminal nucleus (dPrV). Input from mystacial whiskers is relayed by the maxillary branch and forms a topographic representation of rows and whiskers in the ventral PrV (vPrV). To investigate peripheral organisation in imposing a brain topographic pattern, we analysed Edn1(-/-) mice, which present ectopic whisker rows on the lower jaw. We found that these whiskers were innervated by mandibular TG neurons which initially targeted dPrV. Unlike maxillary TG neurons, the ectopic whisker-innervating mandibular neuron cell bodies and pre-target central axons did not segregate into a row-specific pattern nor target the dPrV with a topographic pattern. Following periphery-driven molecular repatterning to a maxillary-like identity, mandibular neurons partially redirected their central projections from dPrV to vPrV. Thus, while able to induce maxillary-like molecular features resulting in vPrV final targeting, a spatially ordered lower jaw ectopic whisker pattern is insufficient to impose row-specific pre-target organisation of the central mandibular tract or a whisker-related matching pattern of afferents in dPrV. These results provide novel insights into periphery-dependent versus periphery-independent mechanisms of trigeminal ganglion and brainstem patterning in matching whisker topography.","corpus_id":8192621,"score":1},{"doc_id":"27242445","title":"Push-Pull Receptive Field Organization and Synaptic Depression: Mechanisms for Reliably Encoding Naturalistic Stimuli in V1.","abstract":"Neurons in the primary visual cortex are known for responding vigorously but with high variability to classical stimuli such as drifting bars or gratings. By contrast, natural scenes are encoded more efficiently by sparse and temporal precise spiking responses. We used a conductance-based model of the visual system in higher mammals to investigate how two specific features of the thalamo-cortical pathway, namely push-pull receptive field organization and fast synaptic depression, can contribute to this contextual reshaping of V1 responses. By comparing cortical dynamics evoked respectively by natural vs. artificial stimuli in a comprehensive parametric space analysis, we demonstrate that the reliability and sparseness of the spiking responses during natural vision is not a mere consequence of the increased bandwidth in the sensory input spectrum. Rather, it results from the combined impacts of fast synaptic depression and push-pull inhibition, the later acting for natural scenes as a form of \"effective\" feed-forward inhibition as demonstrated in other sensory systems. Thus, the combination of feedforward-like inhibition with fast thalamo-cortical synaptic depression by simple cells receiving a direct structured input from thalamus composes a generic computational mechanism for generating a sparse and reliable encoding of natural sensory events.","corpus_id":8808505,"score":1},{"doc_id":"27334956","title":"Neural mechanisms of selective attention in the somatosensory system.","abstract":"Selective attention allows organisms to extract behaviorally relevant information while ignoring distracting stimuli that compete for the limited resources of their central nervous systems. Attention is highly flexible, and it can be harnessed to select information based on sensory modality, within-modality feature(s), spatial location, object identity, and/or temporal properties. In this review, we discuss the body of work devoted to understanding mechanisms of selective attention in the somatosensory system. In particular, we describe the effects of attention on tactile behavior and corresponding neural activity in somatosensory cortex. Our focus is on neural mechanisms that select tactile stimuli based on their location on the body (somatotopic-based attention) or their sensory feature (feature-based attention). We highlight parallels between selection mechanisms in touch and other sensory systems and discuss several putative neural coding schemes employed by cortical populations to signal the behavioral relevance of sensory inputs. Specifically, we contrast the advantages and disadvantages of using a gain vs. spike-spike correlation code for representing attended sensory stimuli. We favor a neural network model of tactile attention that is composed of frontal, parietal, and subcortical areas that controls somatosensory cells encoding the relevant stimulus features to enable preferential processing throughout the somatosensory hierarchy. Our review is based on data from noninvasive electrophysiological and imaging data in humans as well as single-unit recordings in nonhuman primates.","corpus_id":13530488,"score":1},{"doc_id":"27921067","title":"Parallel pathways from whisker and visual sensory cortices to distinct frontal regions of mouse neocortex.","abstract":"The spatial organization of mouse frontal cortex is poorly understood. Here, we used voltage-sensitive dye to image electrical activity in the dorsal cortex of awake head-restrained mice. Whisker-deflection evoked the earliest sensory response in a localized region of primary somatosensory cortex and visual stimulation evoked the earliest responses in a localized region of primary visual cortex. Over the next milliseconds, the initial sensory response spread within the respective primary sensory cortex and into the surrounding higher order sensory cortices. In addition, secondary hotspots in the frontal cortex were evoked by whisker and visual stimulation, with the frontal hotspot for whisker deflection being more anterior and lateral compared to the frontal hotspot evoked by visual stimulation. Investigating axonal projections, we found that the somatosensory whisker cortex and the visual cortex directly innervated frontal cortex, with visual cortex axons innervating a region medial and posterior to the innervation from somatosensory cortex, consistent with the location of sensory responses in frontal cortex. In turn, the axonal outputs of these two frontal cortical areas innervate distinct regions of striatum, superior colliculus, and brainstem. Sensory input, therefore, appears to map onto modality-specific regions of frontal cortex, perhaps participating in distinct sensorimotor transformations, and directing distinct motor outputs.","corpus_id":23885467,"score":1},{"doc_id":"28243518","title":"Study of the cortical representation of whisker frequency selectivity using voltage-sensitive dye optical imaging.","abstract":"The facial whiskers of rodents act as a high-resolution tactile apparatus that allow the animal to detect the finest details of its environment. Previously it was shown that whisker-sensitive neurons in the somatosensory cortex show frequency selectivity to small amplitude stimuli, An intravital voltage-sensitive dye optical imaging (VSDi) method in combination with the different frequency whisker stimulation was used in order to visualize neural activity in the mice somatosensory cortex in response to the stimulation of a single whisker by different frequencies. Using the intravital voltage-sensitive dye optical imaging (VSDi) method in combination with the different frequency whisker stimulation we visualized neural activity in the mice somatosensory cortex in response to the stimulation of a single whisker by different frequencies. We found that whisker stimuli with different frequencies led to different optical signals in the barrel field. Our results provide evidence that different neurons of the barrel cortex have different frequency preferences. This supports prior research that whisker deflections cause responses in cortical neurons within the barrel field according to the frequency of the stimulation. Many studies of the whisker frequency selectivity were performed using unit recording but to map spatial organization, imaging methods are essential. In the work described in the present paper, we take a serious step toward detailed functional mapping of the somatosensory cortex using VSDi. To our knowledge, this is the first demonstration of whisker frequency sensitivity and selectivity of barrel cortex neurons with optical imaging methods.","corpus_id":205967503,"score":1},{"doc_id":"28663199","title":"Behavioral Consequences of a Bifacial Map in the Mouse Somatosensory Cortex.","abstract":"The whisker system is an important sensory organ with extensive neural representations in the brain of the mouse. Patterned neural modules (barrelettes) in the ipsilateral principal sensory nucleus of the trigeminal nerve (PrV) correspond to the whiskers. Axons of the PrV barrelette neurons cross the midline and confer the whisker-related patterning to the contralateral ventroposteromedial nucleus of the thalamus, and subsequently to the cortex. In this way, specific neural modules called barreloids and barrels in the contralateral thalamus and cortex represent each whisker. Partial midline crossing of the PrV axons, in a conditional Robo3 mutant (Robo3(R3-5)cKO) mouse line, leads to the formation of bilateral whisker maps in the ventroposteromedial, as well as the barrel cortex. We used voltage-sensitive dye optical imaging and somatosensory and motor behavioral tests to characterize the consequences of bifacial maps in the thalamocortical system. Voltage-sensitive dye optical imaging verified functional, bilateral whisker representation in the barrel cortex and activation of distinct cortical loci following ipsilateral and contralateral stimulation of the specific whiskers. The mutant animals were comparable with the control animals in sensorimotor tests. However, they showed noticeable deficits in all of the whisker-dependent or -related tests, including Y-maze exploration, horizontal surface approach, bridge crossing, gap crossing, texture discrimination, floating in water, and whisking laterality. Our results indicate that bifacial maps along the thalamocortical system do not offer a functional advantage. Instead, they lead to impairments, possibly due to the smaller size of the whisker-related modules and interference between the ipsilateral and contralateral whisker representations in the same thalamus and cortex. SIGNIFICANCE STATEMENT The whisker sensory system plays a quintessentially important role in exploratory behavior of mice and other nocturnal rodents. Here, we studied a novel mutant mouse line, in which the projections from the brainstem to the thalamus are disrupted. This led to formation of bilateral whisker maps in both the thalamus and the cortex. The two whisker maps crowd in a space normally devoted to the contralateral map alone and in a nonoverlapping fashion. Stimulation of the whiskers on either side activates the corresponding region of the map. Mice with bilateral whisker maps perform well in general sensorimotor tasks but show poor performance in specific tests that require whisker-dependent tactile discrimination. These observations indicate that contralateral, instead of bilateral, representation of the sensory space plays a critical role in acuity and fine discrimination during somesthesis.","corpus_id":207511300,"score":1},{"doc_id":"29738998","title":"Development of the whisker-to-barrel cortex system.","abstract":"This review provides an overview on the development of the rodent whisker-to-barrel cortex system from late embryonic stage to the end of the first postnatal month. During this period the system shows a remarkable transition from a mostly genetic-molecular driven generation of crude connectivity, providing the template for activity-dependent structural and functional maturation and plasticity, to the manifestation of a complex behavioral repertoire including social interactions. Spontaneous and sensory-evoked activity is present in neonatal barrel cortex and control the generation of the cortical architecture. Half a century after its first description by Woolsey and van der Loos the whisker-to-barrel cortex system with its unique and clear topographic organization still offers the exceptional opportunity to study sensory processing and complex behavior.","corpus_id":13705465,"score":1},{"doc_id":"29807911","title":"Neural Coding of Whisker-Mediated Touch in Primary Somatosensory Cortex Is Altered Following Early Blindness.","abstract":"Sensory systems do not develop and function independently of one another, yet they are typically studied in isolation. Effects of multisensory interactions on the developing neocortex can be revealed by altering the ratios of incoming sensory inputs associated with different modalities. We investigated neural responses in primary somatosensory cortex (S1) of short-tailed opossums (Monodelphis domestica; either sex) after the elimination of visual input through bilateral enucleation very early in development. To assess the influence of tactile experience after vision loss, we also examined naturally occurring patterns of exploratory behavior. In early blind (EB) animals, overall levels of tactile experience were similar to those of sighted controls (SC); locomotor activity was unimpaired and accompanied by whisking. Using extracellular single-unit recording techniques under anesthesia, we found that EB animals exhibited a reduction in the magnitude of neural responses to whisker stimuli in S1, coupled with spatial sharpening of receptive fields, in comparison to SC animals. These alterations manifested as two different effects on sensory processing in S1 of EB animals: the ability of neurons to detect single whisker stimulation was decreased, whereas their ability to discriminate between stimulation of neighboring whiskers was enhanced. The increased selectivity of S1 neurons in EB animals was reflected in improved population decoding performance for whisker stimulus position, particularly along the rostrocaudal axis of the snout, which aligns with the primary axis of natural whisker motion. These findings suggest that a functionally distinct form of somatosensory plasticity occurs when vision is lost early in development. SIGNIFICANCE STATEMENT After sensory loss, compensatory behavior mediated through the spared senses could be generated entirely through the recruitment of brain areas associated with the deprived sense. Alternatively, functional compensation in spared modalities may be achieved through a combination of plasticity in brain areas corresponding to both spared and deprived sensory modalities. Although activation of neurons in cortex associated with a deprived sense has been described frequently, it is unclear whether this is the only substrate available for compensation or if plasticity within cortical fields corresponding to spared modalities, particularly primary sensory cortices, may also contribute. Here, we demonstrate empirically that early loss of vision alters coding of sensory inputs in primary somatosensory cortex in a manner that supports enhanced tactile discrimination.","corpus_id":44092505,"score":1}],"string":"[\n {\n \"doc_id\": \"17989240\",\n \"title\": \"Development of thalamocortical response transformations in the rat whisker-barrel system.\",\n \"abstract\": \"Extracellular single-unit recordings were used to characterize responses of thalamic barreloid and cortical barrel neurons to controlled whisker deflections in 2, 3-, and 4-wk-old and adult rats in vivo under fentanyl analgesia. Results indicate that response properties of thalamic and cortical neurons diverge during development. Responses to deflection onsets and offsets among thalamic neurons mature in parallel, whereas among cortical neurons responses to deflection offsets become disproportionately smaller with age. Thalamic neuron receptive fields become more multiwhisker, whereas those of cortical neurons become more single-whisker. Thalamic neurons develop a higher degree of angular selectivity, whereas that of cortical neurons remains constant. In the temporal domain, response latencies decrease both in thalamic and cortical neurons, but the maturation time-course differs between the two populations. Response latencies of thalamic cells decrease primarily between 2 and 3 wk of life, whereas response latencies of cortical neurons decrease in two distinct steps--the first between 2 and 3 wk of life and the second between the fourth postnatal week and adulthood. Although the first step likely reflects similar subcortical changes, the second phase likely corresponds to developmental myelination of thalamocortical fibers. Divergent development of thalamic and cortical response properties indicates that thalamocortical circuits in the whisker-to-barrel pathway undergo protracted maturation after 2 wk of life and provides a potential substrate for experience-dependent plasticity during this time.\",\n \"corpus_id\": 8364990,\n \"score\": 2\n },\n {\n \"doc_id\": \"18491159\",\n \"title\": \"Object localization with whiskers.\",\n \"abstract\": \"Rats use their large facial hairs (whiskers) to detect, localize and identify objects in their proximal three-dimensional (3D) space. Here, we focus on recent evidence of how object location is encoded in the neural sensory pathways of the rat whisker system. Behavioral and neuronal observations have recently converged to the point where object location in 3D appears to be encoded by an efficient orthogonal scheme supported by primary sensory-afferents: each primary-afferent can signal object location by a spatial (labeled-line) code for the vertical axis (along whisker arcs), a temporal code for the horizontal axis (along whisker rows), and an intensity code for the radial axis (from the face out). Neuronal evidence shows that (i) the identities of activated sensory neurons convey information about the vertical coordinate of an object, (ii) the timing of their firing, in relation to other reference signals, conveys information about the horizontal object coordinate, and (iii) the intensity of firing conveys information about the radial object coordinate. Such a triple-coding scheme allows for efficient multiplexing of 3D object location information in the activity of single neurons. Also, this scheme provides redundancy since the same information may be represented in the activity of many neurons. These features of orthogonal coding increase accuracy and reliability. We propose that the multiplexed information is conveyed in parallel to different readout circuits, each decoding a specific spatial variable. Such decoding reduces ambiguity, and simplifies the required decoding algorithms, since different readout circuits can be optimized for a particular variable.\",\n \"corpus_id\": 16829392,\n \"score\": 2\n },\n {\n \"doc_id\": \"18641667\",\n \"title\": \"'Where' and 'what' in the whisker sensorimotor system.\",\n \"abstract\": \"In the visual system of primates, different neuronal pathways are specialized for processing information about the spatial coordinates of objects and their identity - that is, 'where' and 'what'. By contrast, rats and other nocturnal animals build up a neuronal representation of 'where' and 'what' by seeking out and palpating objects with their whiskers. We present recent evidence about how the brain constructs a representation of the surrounding world through whisker-mediated sense of touch. While considerable knowledge exists about the representation of the physical properties of stimuli - like texture, shape and position - we know little about how the brain represents their meaning. Future research may elucidate this and show how the transformation of one representation to another is achieved.\",\n \"corpus_id\": 6450408,\n \"score\": 2\n },\n {\n \"doc_id\": \"18684907\",\n \"title\": \"Responses of rat trigeminal ganglion neurons to longitudinal whisker stimulation.\",\n \"abstract\": \"Responses of rat trigeminal ganglion neurons to longitudinal whisker stimulation. Rats use their mobile set of whiskers to actively explore their environment. Parameters that play a role to generate movement dynamics of the whisker shaft within the follicle, thus activating primary afferents, are manifold: among them are mechanical properties of the whiskers (curvature, elasticity and taper), active movements (head, body, and whiskers), and finally, object characteristics (surface, geometry, position, and orientation). Hence the whisker system is confronted with forces along all three axes in space. Movements along the two latitudinal axes of the whisker (horizontal and vertical) have been well studied. Here we focus on movement along the whisker's longitudinal axis that has been neglected so far. We employed ramp-and-hold movements that pushed the whisker shaft toward the skin and quantified the resulting activity in trigeminal first-order afferents in anesthetized rats. Virtually all recorded neurons were highly sensitive to longitudinal movement. Neurons could be perfectly segregated into two groups according to their modulation by stimulus amplitude and velocity, respectively. This classification regimen correlated perfectly with the presence or absence of slowly adapting responses in longitudinal stimulation but agreed with classification derived from latitudinal stimulation only if the whisker was engaged in its optimal direction and set point. We conclude that longitudinal stimulation is an extremely effective means to activate the tactile pathway and thus is highly likely to play an important role in tactile coding on the ascending somatosensory pathway. In addition, compared with latitudinal stimulation, it provides a reliable and easy to use method to classify trigeminal first-order afferents.\",\n \"corpus_id\": 13381930,\n \"score\": 2\n },\n {\n \"doc_id\": \"18971458\",\n \"title\": \"Rapid changes in thalamic firing synchrony during repetitive whisker stimulation.\",\n \"abstract\": \"Thalamic firing synchrony is thought to ensure selective transmission of relevant sensory information to the recipient cortical neurons by rendering them more responsive to temporally correlated input spikes. However, direct evidence for a synchrony code in the thalamus is limited. Here, we directly measure thalamic firing synchrony and its stimulus-induced modulation over time, using simultaneous single unit recordings from individual thalamic barreloids in the rat somatosensory whisker/barrel system. Employing whisker deflections varying in velocity or frequency and a cross-correlation approach, we find systematic changes in both time course and strength of thalamic firing synchrony as a function of stimulus parameters and sensory adaptation. Synchrony develops faster and is greater with higher velocity deflections. Greater firing synchrony reflects stimulus-dependent increases in instantaneous firing rates, greater spike time precision relative to stimulus onset as well as common input that likely arises from divergent trigeminothalamic and corticothalamic neurons. With adaptation, synchrony decreases and takes longer to develop but is more dependent on the cells' common inputs. Rapid, sharp increases in thalamic synchrony mirroring quick increases in whisker velocity occur also during ongoing random, high-frequency whisker vibrations. Together, results demonstrate millisecond by millisecond changes in thalamic near-synchronous firing during complex patterns of ongoing vibrissa movements that may ensure transmission of preferred sensory information in local thalamocortical circuits during whisking and active touch.\",\n \"corpus_id\": 1207178,\n \"score\": 2\n },\n {\n \"doc_id\": \"19081382\",\n \"title\": \"Diverse and temporally precise kinetic feature selectivity in the VPm thalamic nucleus.\",\n \"abstract\": \"The thalamo-cortical pathway is the crucial sensory gateway into the cerebral cortex. We aimed to determine the nature of the tactile information encoded by neurons in the whisker somatosensory relay nucleus (VPm). We wanted to distinguish whether VPm neurons encode similar stimulus features, acting as a single information channel, or encode diverse features. We recorded responses to whisker deflections that thoroughly explored the space of temporal stimulus variables and identified features to which neurons were selective by reverse correlation. The timescale of the features was typically 1-2 ms, at the limit imposed by our experimental conditions, indicating highly acute feature selectivity. Sensitivity to stimulus kinetics was strikingly diverse. Some neurons (25%) only encoded velocity; others were sensitive to position, acceleration, or more complex features. A minority (19%) encoded two or more features. These results indicate that VPm contains a distributed representation of whisker motion, based on high-resolution kinetic features.\",\n \"corpus_id\": 14611328,\n \"score\": 2\n },\n {\n \"doc_id\": \"19189120\",\n \"title\": \"Neural coding and contextual influences in the whisker system.\",\n \"abstract\": \"A fundamental problem in neuroscience, to which Prof. Segundo has made seminal contributions, is to understand how action potentials represent events in the external world. The aim of this paper is to review the issue of neural coding in the context of the rodent whiskers, an increasingly popular model system. Key issues we consider are: the role of spike timing; mechanisms of spike timing; decoding and context-dependence. Significant insight has come from the development of rigorous, information theoretic frameworks for tackling these questions, in conjunction with suitably designed experiments. We review both the theory and experimental studies. In contrast to the classical view that neurons are noisy and unreliable, it is becoming clear that many neurons in the subcortical whisker pathway are remarkably reliable and, by virtue of spike timing with millisecond-precision, have high bandwidth for conveying sensory information. In this way, even small (approximately 200 neuron) subcortical modules are able to support the sensory processing underlying sophisticated whisker-dependent behaviours. Future work on neural coding in cortex will need to consider new findings that responses are highly dependent on context, including behavioural and internal states.\",\n \"corpus_id\": 1954837,\n \"score\": 2\n },\n {\n \"doc_id\": \"19430473\",\n \"title\": \"Sparse temporal coding of elementary tactile features during active whisker sensation.\",\n \"abstract\": \"How the brain encodes relevant sensory stimuli in the context of active, natural sensation is not known. During active tactile sensation by rodents, whisker movement across surfaces generates complex whisker micro-motion, including discrete, transient slip-stick events, which carry information about surface properties. We simultaneously measured whisker motion and neural activity in somatosensory cortex (S1) in rats whisking across surfaces. Slip-stick motion events were prominently encoded by one or two low-probability, precisely timed spikes in S1 neurons, resulting in a probabilistically sparse ensemble code. Slips could be efficiently decoded from transient, correlated spiking (approximately 20-ms time scale) in small (approximately 100 neuron) populations. Slip responses contributed substantially to increased firing rate and transient firing synchrony on surfaces, and firing synchrony was an important cue for surface texture. Slips are thus a fundamental encoded tactile feature in natural whisker input streams and are represented by sparse, temporally precise, synchronous spiking in S1.\",\n \"corpus_id\": 1662194,\n \"score\": 2\n },\n {\n \"doc_id\": \"19741100\",\n \"title\": \"Transformation in the neural code for whisker deflection direction along the lemniscal pathway.\",\n \"abstract\": \"A prominent characteristic of neurons in the whisker system is their selectivity to the direction in which a whisker is deflected. The aim of this study was to determine how information about whisker direction is encoded at successive levels of the lemniscal pathway. We made extracellular recordings under identical conditions from the trigeminal ganglion, ventro-posterior medial thalamus (VPM), and barrel cortex while varying the direction of whisker deflection. We found a marked increase in the variability of single unit responses along the pathway. To study the consequences of this for information processing, we quantified the responses using mutual information. VPM units conveyed 48% of the mutual information conveyed by ganglion units, and cortical units conveyed 12%. The fraction of neuronal bandwidth used for transmitting direction information decreased from 40% in the ganglion to 24% in VPM and 5% in barrel cortex. To test whether, in cortex, population coding might compensate for this information loss, we made simultaneous recordings. We found that cortical neuron pairs conveyed 2.1 times the mutual information conveyed by single neurons. Overall, these findings indicate a marked transformation from a subcortical neural code based on small numbers of reliable neurons to a cortical code based on populations of unreliable neurons. However, the basic form of the neural code in ganglion, thalamus, and cortex was similar-at each stage, the first poststimulus spike carried the majority of the information.\",\n \"corpus_id\": 2599968,\n \"score\": 2\n },\n {\n \"doc_id\": \"20107500\",\n \"title\": \"Modeling the emergence of whisker direction maps in rat barrel cortex.\",\n \"abstract\": \"Based on measuring responses to rat whiskers as they are mechanically stimulated, one recent study suggests that barrel-related areas in layer 2/3 rat primary somatosensory cortex (S1) contain a pinwheel map of whisker motion directions. Because this map is reminiscent of topographic organization for visual direction in primary visual cortex (V1) of higher mammals, we asked whether the S1 pinwheels could be explained by an input-driven developmental process as is often suggested for V1. We developed a computational model to capture how whisker stimuli are conveyed to supragranular S1, and simulate lateral cortical interactions using an established self-organizing algorithm. Inputs to the model each represent the deflection of a subset of 25 whiskers as they are contacted by a moving stimulus object. The subset of deflected whiskers corresponds with the shape of the stimulus, and the deflection direction corresponds with the movement direction of the stimulus. If these two features of the inputs are correlated during the training of the model, a somatotopically aligned map of direction emerges for each whisker in S1. Predictions of the model that are immediately testable include (1) that somatotopic pinwheel maps of whisker direction exist in adult layer 2/3 barrel cortex for every large whisker on the rat's face, even peripheral whiskers; and (2) in the adult, neurons with similar directional tuning are interconnected by a network of horizontal connections, spanning distances of many whisker representations. We also propose specific experiments for testing the predictions of the model by manipulating patterns of whisker inputs experienced during early development. The results suggest that similar intracortical mechanisms guide the development of primate V1 and rat S1.\",\n \"corpus_id\": 6508740,\n \"score\": 2\n },\n {\n \"doc_id\": \"20610783\",\n \"title\": \"Behavioral state dependency of neural activity and sensory (whisker) responses in superior colliculus.\",\n \"abstract\": \"Rats use their vibrissa (whiskers) to explore and navigate the environment. These sensory signals are distributed within the brain stem by the trigeminal complex and are also relayed to the superior colliculus in the midbrain and to the thalamus (and subsequently barrel cortex) in the forebrain. In the intermediate layers of the superior colliculus, whisker-evoked responses are driven by direct inputs from the trigeminal complex (trigeminotectal) and feedback from the barrel cortex (corticotectal). But the effects of the behavioral state of the animal on the spontaneous firing and sensory responses of these neurons are unknown. By recording from freely behaving rats, we show that the spontaneous firing of whisker sensitive neurons in superior colliculus is higher, or in an activated mode, during active exploration and paradoxical sleep and much lower, or in a quiescent/deactivated mode, during awake immobility and slow-wave sleep. Sensory evoked responses in superior colliculus also depend on behavioral state. Most notably, feedback corticotectal responses are significantly larger during the quiescent/deactivated mode, which tracks the barrel cortex responses on which they depend. Finally, sensory evoked responses depend not only on the state of the animal but also on the orienting response elicited by the stimulus, which agrees with the well known role of the superior colliculus in orienting about salient stimuli.\",\n \"corpus_id\": 10330093,\n \"score\": 2\n },\n {\n \"doc_id\": \"21068262\",\n \"title\": \"A comparison of neuronal and behavioral detection and discrimination performances in rat whisker system.\",\n \"abstract\": \"We used the rat whisker touch as a model system to investigate the correlation between the response function of cortical neurons and the behavior of rats in a sensory detection versus discrimination task. The rat whisker-barrel system is structurally well characterized and represents one of the main channels through which rodents collect information about the environment. In experiment 1, we recorded neuronal activity (n = 235) in the whisker area of the rat somatosensory cortex in anesthetized rats while applying vibrotactile stimuli of varying amplitudes to the whiskers. Neurons showed a characteristic sigmoidal input-output function, with an accelerating nonlinearity at low stimulus amplitudes and a compressive nonlinearity at high stimulus amplitudes. We further quantified the performance of individual neurons for stimulus detection and for discrimination across different stimulus pairs with identical amplitude differences. For near-threshold stimuli, the neuronal discrimination performance surpassed the detection performance despite the fact that detection and discrimination represented identical amplitude differences. This is consistent with the accelerating nonlinearity observed at low stimulus intensities. In the second stage of the experiment, four rats were trained to select the higher-amplitude stimulus between two vibrations applied to their whiskers. Similar to neuronal results, the rats' performance was better for the discrimination task compared with the detection task. The behavioral performance followed the same trend as that of the population of individual neurons. Both behavioral and neuronal data are consistent with the \\\"pedestal effect\\\" previously reported in human psychophysics.\",\n \"corpus_id\": 13157806,\n \"score\": 2\n },\n {\n \"doc_id\": \"21423503\",\n \"title\": \"Information Carried by Population Spike Times in the Whisker Sensory Cortex can be Decoded Without Knowledge of Stimulus Time.\",\n \"abstract\": \"Computational analyses have revealed that precisely timed spikes emitted by somatosensory cortical neuronal populations encode basic stimulus features in the rat's whisker sensory system. Efficient spike time based decoding schemes both for the spatial location of a stimulus and for the kinetic features of complex whisker movements have been defined. To date, these decoding schemes have been based upon spike times referenced to an external temporal frame - the time of the stimulus itself. Such schemes are limited by the requirement of precise knowledge of the stimulus time signal, and it is not clear whether stimulus times are known to rats making sensory judgments. Here, we first review studies of the information obtained from spike timing referenced to the stimulus time. Then we explore new methods for extracting spike train information independently of any external temporal reference frame. These proposed methods are based on the detection of stimulus-dependent differences in the firing time within a neuronal population. We apply them to a data set using single-whisker stimulation in anesthetized rats and find that stimulus site can be decoded based on the millisecond-range relative differences in spike times even without knowledge of stimulus time. If spike counts alone are measured over tens or hundreds of milliseconds rather than milliseconds, such decoders are much less effective. These results suggest that decoding schemes based on millisecond-precise spike times are likely to subserve robust and information-rich transmission of information in the somatosensory system.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"21490724\",\n \"title\": \"The morphology of the rat vibrissal array: a model for quantifying spatiotemporal patterns of whisker-object contact.\",\n \"abstract\": \"In all sensory modalities, the data acquired by the nervous system is shaped by the biomechanics, material properties, and the morphology of the peripheral sensory organs. The rat vibrissal (whisker) system is one of the premier models in neuroscience to study the relationship between physical embodiment of the sensor array and the neural circuits underlying perception. To date, however, the three-dimensional morphology of the vibrissal array has not been characterized. Quantifying array morphology is important because it directly constrains the mechanosensory inputs that will be generated during behavior. These inputs in turn shape all subsequent neural processing in the vibrissal-trigeminal system, from the trigeminal ganglion to primary somatosensory (\\\"barrel\\\") cortex. Here we develop a set of equations for the morphology of the vibrissal array that accurately describes the location of every point on every whisker to within ±5% of the whisker length. Given only a whisker's identity (row and column location within the array), the equations establish the whisker's two-dimensional (2D) shape as well as three-dimensional (3D) position and orientation. The equations were developed via parameterization of 2D and 3D scans of six rat vibrissal arrays, and the parameters were specifically chosen to be consistent with those commonly measured in behavioral studies. The final morphological model was used to simulate the contact patterns that would be generated as a rat uses its whiskers to tactually explore objects with varying curvatures. The simulations demonstrate that altering the morphology of the array changes the relationship between the sensory signals acquired and the curvature of the object. The morphology of the vibrissal array thus directly constrains the nature of the neural computations that can be associated with extraction of a particular object feature. These results illustrate the key role that the physical embodiment of the sensor array plays in the sensing process.\",\n \"corpus_id\": 12613675,\n \"score\": 2\n },\n {\n \"doc_id\": \"21653730\",\n \"title\": \"Spatial structure of multiwhisker receptive fields in the barrel cortex is stimulus dependent.\",\n \"abstract\": \"The tactile sensations mediated by the whisker-trigeminal system allow rodents to efficiently detect and discriminate objects. These capabilities rely strongly on the temporal and spatial structure of whisker deflections. Subthreshold but also spiking receptive fields in the barrel cortex encompass a large number of vibrissae, and it seems likely that the functional properties of these multiwhisker receptive fields reflect the multiple-whisker interactions encountered by the animal during exploration of its environment. The aim of this study was to examine the dependence of the spatial structure of cortical receptive fields on stimulus parameters. Using a newly developed 24-whisker stimulation matrix, we applied a forward correlation analysis of spiking activity to randomized whisker deflections (sparse noise) to characterize the receptive fields that result from caudal and rostral directions of whisker deflection. We observed that the functionally determined principal whisker, the whisker eliciting the strongest response with the shortest latency, differed according to the direction of whisker deflection. Thus, for a given neuron, maximal responses to opposite directions of whisker deflections could be spatially separated. This spatial separation resulted in a displacement of the center of mass between the rostral and caudal subfields and was accompanied by differences between response latencies in rostral and caudal directions of whisker deflection. Such direction-dependent receptive field organization was observed in every cortical layer. We conclude that the spatial structure of receptive fields in the barrel cortex is not an intrinsic property of the neuron but depends on the properties of sensory input.\",\n \"corpus_id\": 5676335,\n \"score\": 2\n },\n {\n \"doc_id\": \"21653856\",\n \"title\": \"A unifying framework underlying mechanotransduction in the somatosensory system.\",\n \"abstract\": \"Rodents use their whiskers to sense their surroundings. As most of the information available to the somatosensory system originates in whiskers' primary afferents, it is essential to understand the transformation of whisker motion into neuronal activity. Here, we combined in vivo recordings in anesthetized rats with mathematical modeling to ascertain the mechanical and electrical characteristics of mechanotransduction. We found that only two synergistic processes, which reflect the dynamic interactions between (1) receptor and whisker and (2) receptor and surrounding tissue, are needed to describe mechanotransduction during passive whiskers deflection. Interactions between these processes may account for stimulus-dependent changes in the magnitude and temporal pattern of tactile responses on multiple scales. Thus, we are able to explain complex electromechanical processes underlying sensory transduction using a simple model, which captures the responses of a wide range of mechanoreceptor types to diverse sensory stimuli. This compact and precise model allows for a ubiquitous description of how mechanoreceptors encode tactile stimulus.\",\n \"corpus_id\": 2268624,\n \"score\": 2\n },\n {\n \"doc_id\": \"22399756\",\n \"title\": \"Coding of apparent motion in the thalamic nucleus of the rat vibrissal somatosensory system.\",\n \"abstract\": \"While exploring objects, rats make multiple contacts using their whiskers, thereby generating complex patterns of sensory information. The cerebral structures that process this information in the somatosensory system show discrete patterns of anatomically distinct units, each corresponding to one whisker. Moreover, the feedforward and feedback connections are remarkably topographic, with little cross-whisker divergence before reaching the cortical network. Despite this parallel design, information processing from several whiskers has been reported in subcortical nuclei. Here, we explored whether sensory neurons in the ventral posterior medial nucleus (VPM) of the thalamus encode emergent properties of complex multiwhisker stimulations. Using a 24-whisker stimulator, we tested the responses of VPM neurons to sequences of caudal deflections that generated an apparent motion in eight different directions across the whiskerpad. Overall, 45% of neurons exhibited an evoked increase in firing rate significantly selective to the direction of apparent motion of the global stimulus. Periods of suppression of firing rate were often observed, but were generally not selective. Global motion selectivity of VPM neurons could occur regardless of the extent and spatial organization of their receptive fields, and of their selectivity for the direction of motion of their principal whisker. To investigate whether the global selectivity could be due to corticothalamic feedback connections, we inactivated the barrel cortex while repeating the stimulation protocol. For most VPM neurons, the direction selectivity decreased but was still present. These results suggest that nonlinear processing of stimuli from different whiskers emerges in subcortical nuclei and is amplified by the corticofugal feedback.\",\n \"corpus_id\": 6452092,\n \"score\": 2\n },\n {\n \"doc_id\": \"22683381\",\n \"title\": \"Whisker sensory system - from receptor to decision.\",\n \"abstract\": \"One of the great challenges of systems neuroscience is to understand how the neocortex transforms neuronal representations of the physical characteristics of sensory stimuli into the percepts which can guide the animal's decisions. Here we present progress made in understanding behavioral and neurophysiological aspects of a highly efficient sensory apparatus, the rat whisker system. Beginning with the 1970s discovery of \\\"barrels\\\" in the rat and mouse brain, one line of research has focused on unraveling the circuits that transmit information from the whiskers to the sensory cortex, together with the cellular mechanisms that underlie sensory responses. A second, more recent line of research has focused on tactile psychophysics, that is, quantification of the behavioral capacities supported by whisker sensation. The opportunity to join these two lines of investigation makes whisker-mediated sensation an exciting platform for the study of the neuronal bases of perception and decision-making. Even more appealing is the beginning-to-end prospective offered by this system: the inquiry can start at the level of the sensory receptor and conclude with the animal's choice. We argue that rats can switch between two modes of operation of the whisker sensory system: (1) generative mode and (2) receptive mode. In the generative mode, the rat moves its whiskers forward and backward to actively seek contact with objects and to palpate the object after initial contact. In the receptive mode, the rat immobilizes its whiskers to optimize the collection of signals from an object that is moving by its own power. We describe behavioral tasks that rats perform in these different modes. Next, we explore which neuronal codes in sensory cortex account for the rats' discrimination capacities. Finally, we present hypotheses for mechanisms through which \\\"downstream\\\" brain regions may read out the activity of sensory cortex in order to extract the significance of sensory stimuli and, ultimately, to select the appropriate action.\",\n \"corpus_id\": 14521360,\n \"score\": 2\n },\n {\n \"doc_id\": \"22912602\",\n \"title\": \"Functional diversity of supragranular GABAergic neurons in the barrel cortex.\",\n \"abstract\": \"Although the neocortex forms a distributed system comprised of several functional areas, its vertical columnar organization is largely conserved across areas and species, suggesting the existence of a canonical neocortical microcircuit. In order to elucidate the principles governing the organization of such a cortical diagram, a detailed understanding of the dynamics binding different types of cortical neurons into a coherent algorithm is essential. Within this complex circuitry, GABAergic interneurons, while forming approximately only 15-20% of all cortical neurons, appear critical in maintaining a dynamic balance between excitation and inhibition. Despite their importance, cortical GABAergic neurons have not been extensively studied in vivo and their precise role in shaping the local microcircuit sensory response still remains to be determined. Their paucity, combined with their molecular, anatomical, and physiological diversity, has made it difficult to even establish a consensual nomenclature. However, recent technological advances in microscopy and mouse genetics have fostered a renewed interest in neocortical interneurons by putting them within \\\"visible\\\" reach of experimenters. The anatomically well-defined whisker-to-barrel pathway of the rodent is particularly amenable to studies attempting to link cortical circuit dynamics to behavior. To each whisker corresponds a discrete cortical unit equivalent to a single column, specialized in the encoding and processing of the sensory information it receives. In this review, we will focus on the functional role that each subtype of supragranular GABAergic neuron embedded within such a single neocortical unit may play in shaping the dynamics of the local circuit during somatosensory integration.\",\n \"corpus_id\": 5413840,\n \"score\": 2\n },\n {\n \"doc_id\": \"22922646\",\n \"title\": \"Activity in motor-sensory projections reveals distributed coding in somatosensation.\",\n \"abstract\": \"Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide ‘contextual’ information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1-->vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.\",\n \"corpus_id\": 2364419,\n \"score\": 2\n },\n {\n \"doc_id\": \"23486952\",\n \"title\": \"Structure, function, and cortical representation of the rat submandibular whisker trident.\",\n \"abstract\": \"Although the neurobiology of rodent facial whiskers has been studied intensively, little is known about sensing in other vibrissae. Here we describe the under-investigated submandibular \\\"whisker trident\\\" on the rat's chin. In this three-whisker array, a unique unpaired midline whisker is laterally flanked by two slightly shorter whiskers. All three whiskers point to the ground and are curved backwards. Unlike other whiskers, the trident is not located on an exposed body part. Trident vibrissae are not whisked and do not touch anything over long stretches of time. However, trident whiskers engage in sustained ground contact during head-down running while the animal is exploring or foraging. In biomechanical experiments, trident whiskers follow caudal ground movement more smoothly than facial whiskers. Remarkably, deflection angles decrease with increasing ground velocity. We identified one putative trident barrel in the left somatosensory cortex and two barrels in the right somatosensory cortex. The elongated putative trident-midline barrel is the longest and largest whisker barrel, suggesting that the midline trident whisker is of great functional significance. Cortical postsynaptic air-puff responses in the trident representation show much less temporal precision than facial whisker responses. Trident whiskers do not provide as much high-resolution information about object contacts as facial whiskers. Instead, our observations suggest an idiothetic function: their biomechanics allow trident whiskers to derive continuous measurements about ego motion from ground contacts. The midline position offers unique advantages in sensing heading direction in a laterally symmetric manner. The changes in trident deflection angle with velocity suggest that trident whiskers might function as a tactile speedometer.\",\n \"corpus_id\": 16459116,\n \"score\": 2\n },\n {\n \"doc_id\": \"23864687\",\n \"title\": \"Low-dimensional sensory feature representation by trigeminal primary afferents.\",\n \"abstract\": \"In any sensory system, the primary afferents constitute the first level of sensory representation and fundamentally constrain all subsequent information processing. Here, we show that the spike timing, reliability, and stimulus selectivity of primary afferents in the whisker system can be accurately described by a simple model consisting of linear stimulus filtering combined with spike feedback. We fitted the parameters of the model by recording the responses of primary afferents to filtered, white noise whisker motion in anesthetized rats. The model accurately predicted not only the response of primary afferents to white noise whisker motion (median correlation coefficient 0.92) but also to naturalistic, texture-induced whisker motion. The model accounted both for submillisecond spike-timing precision and for non-Poisson spike train structure. We found substantial diversity in the responses of the afferent population, but this diversity was accurately captured by the model: a 2D filter subspace, corresponding to different mixtures of position and velocity sensitivity, captured 94% of the variance in the stimulus selectivity. Our results suggest that the first stage of the whisker system can be well approximated as a bank of linear filters, forming an overcomplete representation of a low-dimensional feature space.\",\n \"corpus_id\": 14227142,\n \"score\": 2\n },\n {\n \"doc_id\": \"24097038\",\n \"title\": \"Membrane potential correlates of sensory perception in mouse barrel cortex.\",\n \"abstract\": \"Neocortical activity can evoke sensory percepts, but the cellular mechanisms remain poorly understood. We trained mice to detect single brief whisker stimuli and report perceived stimuli by licking to obtain a reward. Pharmacological inactivation and optogenetic stimulation demonstrated a causal role for the primary somatosensory barrel cortex. Whole-cell recordings from barrel cortex neurons revealed membrane potential correlates of sensory perception. Sensory responses depended strongly on prestimulus cortical state, but both slow-wave and desynchronized cortical states were compatible with task performance. Whisker deflection evoked an early (<50 ms) reliable sensory response that was encoded through cell-specific reversal potentials. A secondary late (50-400 ms) depolarization was enhanced on hit trials compared to misses. Optogenetic inactivation revealed a causal role for late excitation. Our data reveal dynamic processing in the sensory cortex during task performance, with an early sensory response reliably encoding the stimulus and later secondary activity contributing to driving the subjective percept.\",\n \"corpus_id\": 23919226,\n \"score\": 2\n },\n {\n \"doc_id\": \"24349279\",\n \"title\": \"Transformation of adaptation and gain rescaling along the whisker sensory pathway.\",\n \"abstract\": \"Neurons in all sensory systems have a remarkable ability to adapt their sensitivity to the statistical structure of the sensory signals to which they are tuned. In the barrel cortex, firing rate adapts to the variance of a whisker stimulus and neuronal sensitivity (gain) adjusts in inverse proportion to the stimulus standard deviation. To determine how adaptation might be transformed across the ascending lemniscal pathway, we measured the responses of single units in the first and last subcortical stages, the trigeminal ganglion (TRG) and ventral posterior medial thalamic nucleus (VPM), to controlled whisker stimulation in urethane-anesthetized rats. We probed adaptation using a filtered white noise stimulus that switched between low- and high-variance epochs. We found that the firing rate of both TRG and VPM neurons adapted to stimulus variance. By fitting the responses of each unit to a Linear-Nonlinear-Poisson model, we tested whether adaptation changed feature selectivity and/or sensitivity. We found that, whereas feature selectivity was unaffected by stimulus variance, units often exhibited a marked change in sensitivity. The extent of these sensitivity changes increased systematically along the pathway from TRG to barrel cortex. However, there was marked variability across units, especially in VPM. In sum, in the whisker system, the adaptation properties of subcortical neurons are surprisingly diverse. The significance of this diversity may be that it contributes to a rich population representation of whisker dynamics.\",\n \"corpus_id\": 11525820,\n \"score\": 2\n },\n {\n \"doc_id\": \"24361064\",\n \"title\": \"The representation of social facial touch in rat barrel cortex.\",\n \"abstract\": \"Controlled presentation of stimuli to anesthetized [1] or awake [2] animals suggested that neurons in sensory cortices respond to elementary features [3, 4], but we know little about neuronal responses evoked by social interactions. Here we investigate processing in the barrel cortex of rats engaging in social facial touch [5, 6]. Sensory stimulation by conspecifics differs from classic whisker stimuli such as deflections, contact poles [7, 8], or textures [9, 10]. A large fraction of barrel cortex neurons responded to facial touch. Social touch responses peaked when animals aligned their faces and contacted each other by multiple whiskers with small, irregular whisker movements. Object touch was associated with larger, more regular whisker movements, and object responses were weaker than social responses. Whisker trimming abolished responses. During social touch, neurons in males increased their firing on average by 44%, while neurons in females increased their firing by only 19%. In females, socially evoked and ongoing firing rates were more than 1.5-fold higher in nonestrus than in estrus. Barrel cortex represented socially different contacts by distinct firing rates, and the variation of activity with sex and sexual status could contribute to the generation of gender-specific neural constructs of conspecifics.\",\n \"corpus_id\": 17495746,\n \"score\": 2\n },\n {\n \"doc_id\": \"24821429\",\n \"title\": \"Cortical control of whisker movement.\",\n \"abstract\": \"Facial muscles drive whisker movements, which are important for active tactile sensory perception in mice and rats. These whisker muscles are innervated by cholinergic motor neurons located in the lateral facial nucleus. The whisker motor neurons receive synaptic inputs from premotor neurons, which are located within the brain stem, the midbrain, and the neocortex. Complex, distributed neural circuits therefore regulate whisker movement during behavior. This review focuses specifically on cortical whisker motor control. The whisker primary motor cortex (M1) strongly innervates brain stem reticular nuclei containing whisker premotor neurons, which might form a central pattern generator for rhythmic whisker protraction. In a parallel analogous pathway, the whisker primary somatosensory cortex (S1) strongly projects to the brain stem spinal trigeminal interpolaris nucleus, which contains whisker premotor neurons innervating muscles for whisker retraction. These anatomical pathways may play important functional roles, since stimulation of M1 drives exploratory rhythmic whisking, whereas stimulation of S1 drives whisker retraction.\",\n \"corpus_id\": 21063946,\n \"score\": 2\n },\n {\n \"doc_id\": \"25339711\",\n \"title\": \"Tactile object localization by anticipatory whisker motion.\",\n \"abstract\": \"Rodents use rhythmic protractions of their whiskers to locate objects in space. The amplitude of these protractions is reduced when whiskers contact objects, leading to a tendency of whiskers to only lightly touch the environment. While the impact of this process on the sensory input has been studied, little is known about how sensory input causes this change in the motor pattern. Here, using high-speed imaging of whisking in mice, we simultaneously measured whisker contacts and the resulting whisking motion. We found that mice precisely target their whisker protractions to the distance at which they expect objects. This modulation does not depend on the current sensory input and remains stable for at least one whisking cycle when there is no object contact or when the object position is changed. As a result, the timing and other information carried by whisker contacts encodes how well each protraction was matched to the object, functioning as an error signal. Whisker contacts can thus encode a mismatch between expected object locations and the actual environment.\",\n \"corpus_id\": 2451110,\n \"score\": 2\n },\n {\n \"doc_id\": \"25934471\",\n \"title\": \"Sparse, reliable, and long-term stable representation of periodic whisker deflections in the mouse barrel cortex.\",\n \"abstract\": \"The rodent whisker system is a preferred model for studying plasticity in the somatosensory cortex (barrel cortex). Contrarily, only a small amount of research has been conducted to characterize the stability of neuronal population activity in the barrel cortex. We used the mouse whisker system to address the neuronal basis of stable perception in the somatosensory cortex. Cortical representation of periodic whisker deflections was studied in populations of neurons in supragranular layers over extended time periods (up to 3 months) with long-term two-photon Ca(2+) imaging in anesthetized mice. We found that in most of the neurons (87%), Ca(2+) responses increased sublinearly with increasing number of contralateral whisker deflections. The imaged population of neurons was activated in a stereotypic way over days and for different deflection rates (pulse frequencies). Thus, pulse frequencies are coded by response strength rather than by distinct neuronal sub-populations. A small population of highly responsive neurons (~3%) was sufficient to decode the whisker stimulus. This conserved functional map, led by a small set of highly responsive neurons, might form the foundation of stable sensory percepts.\",\n \"corpus_id\": 6178321,\n \"score\": 2\n },\n {\n \"doc_id\": \"26126800\",\n \"title\": \"Wideband phase locking to modulated whisker vibration point to a temporal code for texture in the rat's barrel cortex.\",\n \"abstract\": \"Rats probe objects with their whiskers and make decisions about sizes, shapes, textures and distances within a few tens of milliseconds. This perceptual analysis requires the processing of tactile high-frequency object components reflecting surface roughness. We have shown that neurons in the barrel cortex of rats encode high-frequency sinusoidal vibrations of whiskers for sustained periods when presented with constant amplitudes and frequencies. In a natural situation, however, stimulus parameters change rapidly when whiskers are brushing across objects. In this study, we therefore analysed cortical responses to vibratory movements of single whiskers with rapidly changing amplitudes and frequencies. The results show that different neural codes are employed for a processing of stimulus parameters. The frequency of whisker vibration is encoded by the temporal pattern of spike discharges, i.e., the phase-locked responses of barrel cortex neurons. In addition, oscillatory gamma band activity was induced during high-frequency stimulation. The pivotal descriptor of the amplitude of whisker displacement, the velocity, is reflected in the rate of spike discharges. While phase-locked discharges occurred over the entire range of frequencies tested (10-600 Hz), the discharge rate increased with stimulus velocity only up to about 60 µm/ms, saturating at a mean rate of ~117 spikes/s. In addition, the results show that whisker movements of more than 500 Hz bandwidth may be encoded by phase-locked responses of small groups of cortical neurons. Thus, even single whiskers may transmit information about wide ranges of textural components owing to their set of different types of hair follicle mechanoreceptors.\",\n \"corpus_id\": 14913640,\n \"score\": 2\n },\n {\n \"doc_id\": \"26441549\",\n \"title\": \"Efficient population coding of naturalistic whisker motion in the ventro-posterior medial thalamus based on precise spike timing.\",\n \"abstract\": \"The rodent whisker-associated thalamic nucleus (VPM) contains a somatotopic map where whisker representation is divided into distinct neuronal sub-populations, called \\\"barreloids\\\". Each barreloid projects to its associated cortical barrel column and so forms a gateway for incoming sensory stimuli to the barrel cortex. We aimed to determine how the population of neurons within one barreloid encodes naturalistic whisker motion. In rats, we recorded the extracellular activity of up to nine single neurons within a single barreloid, by implanting silicon probes parallel to the longitudinal axis of the barreloids. We found that play-back of texture-induced whisker motion evoked sparse responses, timed with millisecond precision. At the population level, there was synchronous activity: however, different subsets of neurons were synchronously active at different times. Mutual information between population responses and whisker motion increased near linearly with population size. When normalized to factor out firing rate differences, we found that texture was encoded with greater informational-efficiency than white noise. These results indicate that, within each VPM barreloid, there is a rich and efficient population code for naturalistic whisker motion based on precisely timed, population spike patterns.\",\n \"corpus_id\": 5712901,\n \"score\": 2\n },\n {\n \"doc_id\": \"26864754\",\n \"title\": \"Whisker-related afferents in superior colliculus.\",\n \"abstract\": \"Rodents use their whiskers to explore the environment, and the superior colliculus is part of the neural circuits that process this sensorimotor information. Cells in the intermediate layers of the superior colliculus integrate trigeminotectal afferents from trigeminal complex and corticotectal afferents from barrel cortex. Using histological methods in mice, we found that trigeminotectal and corticotectal synapses overlap somewhat as they innervate the lower and upper portions of the intermediate granular layer, respectively. Using electrophysiological recordings and optogenetics in anesthetized mice in vivo, we showed that, similar to rats, whisker deflections produce two successive responses that are driven by trigeminotectal and corticotectal afferents. We then employed in vivo and slice experiments to characterize the response properties of these afferents. In vivo, corticotectal responses triggered by electrical stimulation of the barrel cortex evoke activity in the superior colliculus that increases with stimulus intensity and depresses with increasing frequency. In slices from adult mice, optogenetic activation of channelrhodopsin-expressing trigeminotectal and corticotectal fibers revealed that cells in the intermediate layers receive more efficacious trigeminotectal, than corticotectal, synaptic inputs. Moreover, the efficacy of trigeminotectal inputs depresses more strongly with increasing frequency than that of corticotectal inputs. The intermediate layers of superior colliculus appear to be tuned to process strong but infrequent trigeminal inputs and weak but more persistent cortical inputs, which explains features of sensory responsiveness, such as the robust rapid sensory adaptation of whisker responses in the superior colliculus.\",\n \"corpus_id\": 22307626,\n \"score\": 2\n },\n {\n \"doc_id\": \"27098555\",\n \"title\": \"The evolution of whisker-mediated somatosensation in mammals: Sensory processing in barrelless S1 cortex of a marsupial, Monodelphis domestica.\",\n \"abstract\": \"Movable tactile sensors in the form of whiskers are present in most mammals, but sensory coding in the cortical whisker representation has been studied almost exclusively in mice and rats. Many species that possess whiskers lack the modular \\\"barrel\\\" organization found in the primary somatosensory cortex (S1) of mice and rats, but it is unclear how whisker-related input is represented in these species. We used single-unit extracellular recording techniques to characterize receptive fields and response properties in S1 of Monodelphis domestica (short-tailed opossum), a nocturnal, terrestrial marsupial that shared its last common ancestor with placental mammals over 160 million years ago. Short-tailed opossums lack barrels and septa in S1 but show active whisking behavior similar to that of mice and rats. Most neurons in short-tailed opossum S1 exhibited multiwhisker receptive fields, including a single best whisker (BW) and lower magnitude responses to the deflection of surrounding whiskers. Mean tuning width was similar to that reported for mice and rats. Both symmetrical and asymmetrical receptive fields were present. Neurons tuned to ventral whiskers tended to show broad tuning along the rostrocaudal axis. Thus, despite the absence of barrels, most receptive field properties were similar to those reported for mice and rats. However, unlike those species, S1 neuronal responses to BW and surround whisker deflection showed comparable latencies in short-tailed opossums. This dissimilarity suggests that some aspects of barrel cortex function may not generalize to tactile processing across mammalian species and may be related to differences in the architecture of the whisker-to-cortex pathway. J. Comp. Neurol. 524:3587-3613, 2016. © 2016 Wiley Periodicals, Inc.\",\n \"corpus_id\": 13842932,\n \"score\": 2\n },\n {\n \"doc_id\": \"27463524\",\n \"title\": \"Representation of Stimulus Speed and Direction in Vibrissal-Sensitive Regions of the Trigeminal Nuclei: A Comparison of Single Unit and Population Responses.\",\n \"abstract\": \"The rat vibrissal (whisker) system is one of the oldest and most important models for the study of active tactile sensing and sensorimotor integration. It is well established that primary sensory neurons in the trigeminal ganglion respond to deflections of one and only one whisker, and that these neurons are strongly tuned for both the speed and direction of individual whisker deflections. During active whisking behavior, however, multiple whiskers will be deflected simultaneously. Very little is known about how neurons at central levels of the trigeminal pathway integrate direction and speed information across multiple whiskers. In the present work, we investigated speed and direction coding in the trigeminal brainstem nuclei, the first stage of neural processing that exhibits multi-whisker receptive fields. Specifically, we recorded both single-unit spikes and local field potentials from fifteen sites in spinal trigeminal nucleus interpolaris and oralis while systematically varying the speed and direction of coherent whisker deflections delivered across the whisker array. For 12/15 neurons, spike rate was higher when the whisker array was stimulated from caudal to rostral rather than rostral to caudal. In addition, 10/15 neurons exhibited higher firing rates for slower stimulus speeds. Interestingly, using a simple decoding strategy for the local field potentials and spike trains, classification of speed and direction was higher for field potentials than for single unit spike trains, suggesting that the field potential is a robust reflection of population activity. Taken together, these results point to the idea that population responses in these brainstem regions in the awake animal will be strongest during behaviors that stimulate a population of whiskers with a directionally coherent motion.\",\n \"corpus_id\": 7485983,\n \"score\": 2\n },\n {\n \"doc_id\": \"27574970\",\n \"title\": \"Short Time-Scale Sensory Coding in S1 during Discrimination of Whisker Vibrotactile Sequences.\",\n \"abstract\": \"Rodent whisker input consists of dense microvibration sequences that are often temporally integrated for perceptual discrimination. Whether primary somatosensory cortex (S1) participates in temporal integration is unknown. We trained rats to discriminate whisker impulse sequences that varied in single-impulse kinematics (5-20-ms time scale) and mean speed (150-ms time scale). Rats appeared to use the integrated feature, mean speed, to guide discrimination in this task, consistent with similar prior studies. Despite this, 52% of S1 units, including 73% of units in L4 and L2/3, encoded sequences at fast time scales (≤20 ms, mostly 5-10 ms), accurately reflecting single impulse kinematics. 17% of units, mostly in L5, showed weaker impulse responses and a slow firing rate increase during sequences. However, these units did not effectively integrate whisker impulses, but instead combined weak impulse responses with a distinct, slow signal correlated to behavioral choice. A neural decoder could identify sequences from fast unit spike trains and behavioral choice from slow units. Thus, S1 encoded fast time scale whisker input without substantial temporal integration across whisker impulses.\",\n \"corpus_id\": 16616768,\n \"score\": 2\n },\n {\n \"doc_id\": \"27707809\",\n \"title\": \"Whisker row deprivation affects the flow of sensory information through rat barrel cortex.\",\n \"abstract\": \"Whisker trimming causes substantial reorganization of neuronal response properties in barrel cortex. However, little is known about experience-dependent rerouting of sensory processing following sensory deprivation. To address this, we performed in vivo intracellular recordings from layers 2/3 (L2/3), layer 4 (L4), layer 5 regular-spiking (L5RS), and L5 intrinsically bursting (L5IB) neurons and measured their multiwhisker receptive field at the level of spiking activity, membrane potential, and synaptic conductance before and after sensory deprivation. We used Chernoff information to quantify the \\\"sensory information\\\" contained in the firing patterns of cells in response to spared and deprived whisker stimulation. In the control condition, information for flanking-row and same-row whiskers decreased in the order L4, L2/3, L5IB, L5RS. However, after whisker-row deprivation, spared flanking-row whisker information was reordered to L4, L5RS, L5IB, L2/3. Sensory information from the trimmed whiskers was reduced and delayed in L2/3 and L5IB neurons, whereas sensory information from spared whiskers was increased and advanced in L4 and L5RS neurons. Sensory information from spared whiskers was increased in L5IB neurons without a latency change. L5RS cells exhibited the largest changes in sensory information content through an atypical plasticity combining a significant decrease in spontaneous activity and an increase in a short-latency excitatory conductance. NEW & NOTEWORTHY: Sensory cortical plasticity is usually quantified by changes in evoked firing rate. In this study we quantified plasticity by changes in sensory detection performance using Chernoff information and receiver operating characteristic analysis. We found that whisker deprivation causes a change in information flow within the cortical layers and that layer 5 regular-spiking cells, despite showing only a small potentiation of short-latency input, show the greatest increase in information content for the spared input partly by decreasing their spontaneous activity.\",\n \"corpus_id\": 14014559,\n \"score\": 2\n },\n {\n \"doc_id\": \"27869114\",\n \"title\": \"A radial map of multi-whisker correlation selectivity in the rat barrel cortex.\",\n \"abstract\": \"In the barrel cortex, several features of single-whisker stimuli are organized in functional maps. The barrel cortex also encodes spatio-temporal correlation patterns of multi-whisker inputs, but so far the cortical mapping of neurons tuned to such input statistics is unknown. Here we report that layer 2/3 of the rat barrel cortex contains an additional functional map based on neuronal tuning to correlated versus uncorrelated multi-whisker stimuli: neuron responses to uncorrelated multi-whisker stimulation are strongest above barrel centres, whereas neuron responses to correlated and anti-correlated multi-whisker stimulation peak above the barrel-septal borders, forming rings of multi-whisker synchrony-preferring cells.\",\n \"corpus_id\": 854174,\n \"score\": 2\n },\n {\n \"doc_id\": \"28334121\",\n \"title\": \"Interspersed Distribution of Selectivity to Kinematic Stimulus Features in Supragranular Layers of Mouse Barrel Cortex.\",\n \"abstract\": \"Neurons in the primary sensory regions of neocortex have heterogeneous response properties. The spatial arrangement of neurons with particular response properties is a key aspect of population representations and can shed light on how local circuits are wired. Here, we investigated how neurons with sensitivity to different kinematic features of whisker stimuli are distributed across local circuits in supragranular layers of the barrel cortex. Using 2-photon calcium population imaging in anesthetized mice, we found that nearby neurons represent diverse kinematic features, providing a rich population representation at the local scale. Neurons interspersed in space therefore responded differently to a common stimulus kinematic feature. Conversely, neurons with similar feature selectivity were located no closer to each other than predicted by a random distribution null hypothesis. This finding relied on defining a null hypothesis that was specific for testing the spatial distribution of tuning across neurons. We also measured how neurons sensitive to specific features were distributed relative to barrel boundaries, and found no systematic organization. Our results are compatible with randomly distributed selectivity to kinematic features, with no systematic ordering superimposed upon the whisker map.\",\n \"corpus_id\": 24343609,\n \"score\": 2\n },\n {\n \"doc_id\": \"28827090\",\n \"title\": \"Organization of orientation-specific whisker deflection responses in layer 2/3 of mouse somatosensory cortex.\",\n \"abstract\": \"The rodent whisker-barrel system is characterized by its patterned somatotopic mapping between the sensory periphery and multiple regions of the brain. While somatotopy in the whisker system is established, we know far less about how preferences for stimulus orientation or other features are organized. Mouse somatosensation is an increasingly popular model for circuit-based dissection of perceptual decision making and learning, yet our understanding of how stimulus feature representations are organized in the cortex is incomplete. Here, we used in vivo two-photon calcium imaging to monitor activity of populations of layer (L) 2/3 neurons in the mouse primary somatosensory cortex during deflections of a single whisker in two orthogonal orientations (azimuthal or elevational). We split the population response to whisker deflections into an orientation-specific component and a non-specific component that reflected overall excitability in response to deflection of a single whisker. Orientation-specific responses were organized in a locally heterogeneous and spatially distributed manner. Correlations in the stimulus-independent trial-to-trial variability of pairs of neurons were higher among neurons that preferred the same orientation. These correlations depended on similarity in both orientation-specific and non-specific components of responses to single-whisker deflections. Our results shed light on L2/3 organization in mouse somatosensory cortex, and lay a foundation for dissecting circuit mechanisms of perceptual learning and decision-making during orientation discrimination tasks.\",\n \"corpus_id\": 23636932,\n \"score\": 2\n },\n {\n \"doc_id\": \"28843997\",\n \"title\": \"Representation of tactile scenes in the rodent barrel cortex.\",\n \"abstract\": \"After half a century of research, the sensory features coded by neurons of the rodent barrel cortex remain poorly understood. Still, views of the sensory representation of whisker information are increasingly shifting from a labeled line representation of single whisker deflections to a selectivity for specific elements of the complex statistics of the multi-whisker deflection patterns that take place during spontaneous rodent behavior - so called natural tactile scenes. Here we review the current knowledge regarding the coding of patterns of whisker stimuli by barrel cortex neurons, from responses to single whisker deflections to the representation of complex tactile scenes. A number of multi-whisker tunings have already been identified, including center-surround feature extraction, angular tuning during edge-like multi-whisker deflections, and even tuning to specific statistical properties of the tactile scene such as the level of correlation across whiskers. However, a more general model of the representation of multi-whisker information in the barrel cortex is still missing. This is in part because of the lack of a human intuition regarding the perception emerging from a whisker system, but also because in contrast to other primary sensory cortices such as the visual cortex, the spatial feature selectivity of barrel cortex neurons rests on highly nonlinear interactions that remained hidden to classical receptive-field approaches.\",\n \"corpus_id\": 21058087,\n \"score\": 2\n },\n {\n \"doc_id\": \"28843998\",\n \"title\": \"What the whiskers tell the brain.\",\n \"abstract\": \"A fundamental question in the investigation of any sensory system is what physical signals drive its sensory neurons during natural behaviour. Surprisingly, in the whisker system, it is only recently that answers to this question have emerged. Here, we review the key developments, focussing mainly on the first stage of the ascending pathway - the primary whisker afferents (PWAs). We first consider a biomechanical framework, which describes the fundamental mechanical forces acting on the whiskers during active sensation. We then discuss technical progress that has allowed such mechanical variables to be estimated in awake, behaving animals. We discuss past electrophysiological evidence concerning how PWAs function and reinterpret it within the biomechanical framework. Finally, we consider recent studies of PWAs in awake, behaving animals and compare the results to related studies of the cortex. We argue that understanding 'what the whiskers tell the brain' sheds valuable light on the computational functions of downstream neural circuits, in particular, the barrel cortex.\",\n \"corpus_id\": 19060461,\n \"score\": 2\n },\n {\n \"doc_id\": \"28919043\",\n \"title\": \"Neocortical dynamics during whisker-based sensory discrimination in head-restrained mice.\",\n \"abstract\": \"A fundamental task frequently encountered by brains is to rapidly and reliably discriminate between sensory stimuli of the same modality, be it distinct auditory sounds, odors, visual patterns, or tactile textures. A key mammalian brain structure involved in discrimination behavior is the neocortex. Sensory processing not only involves the respective primary sensory area, which is crucial for perceptual detection, but additionally relies on cortico-cortical communication among several regions including higher-order sensory areas as well as frontal cortical areas. It remains elusive how these regions exchange information to process neural representations of distinct stimuli to bring about a decision and initiate appropriate behavioral responses. Likewise, it is poorly understood how these neural computations are conjured during task learning. In this review, we discuss recent studies investigating cortical dynamics during discrimination behaviors that utilize head-fixed behavioral tasks in combination with in vivo electrophysiology, two-photon calcium imaging, and cell-type-specific targeting. We particularly focus on information flow in distinct cortico-cortical pathways when mice use their whiskers to discriminate between different objects or different locations. Within the primary and secondary somatosensory cortices (S1 and S2, respectively) as well as vibrissae motor cortex (M1), intermingled functional representations of touch, whisking, and licking were found, which partially re-organized during discrimination learning. These findings provide first glimpses of cortico-cortical communication but emphasize that for understanding the complete process of discrimination it will be crucial to elucidate the details of how neural processing is coordinated across brain-wide neuronal networks including the S1-S2-M1 triangle and cortical areas beyond.\",\n \"corpus_id\": 11910957,\n \"score\": 2\n },\n {\n \"doc_id\": \"28929510\",\n \"title\": \"Laminar-specific encoding of texture elements in rat barrel cortex.\",\n \"abstract\": \"KEY POINTS: For rats texture discrimination is signalled by the large face whiskers by stick-slip events. Neural encoding of repetitive stick-slip events will be influenced by intrinsic properties of adaptation. We show that texture coding in the barrel cortex is laminar specific and follows a power function. Our results also show layer 2 codes for novel feature elements via robust firing rates and temporal fidelity. We conclude that texture coding relies on a subtle neural ensemble to provide important object information. ABSTRACT: Texture discrimination by rats is exquisitely guided by fine-grain mechanical stick-slip motions of the face whiskers as they encounter, stick to and slip past successive texture-defining surface features such as bumps and grooves. Neural encoding of successive stick-slip texture events will be shaped by adaptation, common to all sensory systems, whereby receptor and neural responses to a stimulus are affected by responses to preceding stimuli, allowing resetting to signal novel information. Additionally, when a whisker is actively moved to contact and brush over surfaces, that motion itself generates neural responses that could cause adaptation of responses to subsequent stick-slip events. Nothing is known about encoding in the rat whisker system of stick-slip events defining textures of different grain or the influence of adaptation from whisker protraction or successive texture-defining stick-slip events. Here we recorded responses from halothane-anaesthetized rats in response to texture-defining stimuli applied to passive whiskers. We demonstrate that: across the columnar network of the whisker-recipient barrel cortex, adaptation in response to repetitive stick-slip events is strongest in uppermost layers and equally lower thereafter; neither whisker protraction speed nor stick-slip frequency impede encoding of stick-slip events at rates up to 34.08 Hz; and layer 2 normalizes responses to whisker protraction to resist effects on texture signalling. Thus, within laminar-specific response patterns, barrel cortex reliably encodes texture-defining elements even to high frequencies.\",\n \"corpus_id\": 38446113,\n \"score\": 2\n },\n {\n \"doc_id\": \"29265375\",\n \"title\": \"Millisecond precision temporal encoding of stimulus features during cortically generated gamma oscillations in the rat somatosensory cortex.\",\n \"abstract\": \"KEY POINTS: Rodents explore their immediate environment using their whiskers. Such exploration leads to micromotions, which contain many high-frequency (50-200 Hz) components. High-frequency whisker motion is represented faithfully in the temporal structure of the spike trains of trigeminal neurons. However, the representation of high-frequency sensory inputs in cortex is not fully understood. By combining extracellular and intracellular recordings in the rat somatosensory cortex and thalamus, we show that high-frequency sensory inputs, either sinusoidal or white noise, elicit internally generated gamma (20-60 Hz) band oscillations in cortical networks. Gamma oscillations modulate cortical spike probability while preserving sub-millisecond phase relations with high-frequency sensory inputs. Consequently, our results indicate that millisecond precision stimulus-locked spiking activity and sensory-induced gamma oscillation can constitute independent multiplexed coding schemes at the single-cell level. ABSTRACT: In the natural environment, tactile exploration often leads to high-frequency vibrations at the level of the sensory organs. Single-unit recordings of cortical neurons have pointed towards either a rate or a temporal code for representing high-frequency tactile signals. In cortical networks, sensory processing results from the interaction between feedforward inputs relayed from the thalamus and internally generated activity. However, how the emergent activity represents high-frequency sensory input is not fully understood. Using multisite single-unit, local field potential and intracellular recordings in the somatosensory cortex and thalamus of lightly sedated male rats, we measured neuronal responses evoked by sinusoidal and band-pass white noise whisker stimulation at frequencies that encompass those observed during texture exploration (50-200 Hz). We found that high-frequency sensory inputs relayed from the thalamus elicit both sub-millisecond stimulus-locked responses and internally generated gamma (20-60 Hz) band oscillations in cortical networks. Gamma oscillations modulate spike probability while preserving sub-millisecond phase relations with sensory inputs. Therefore, precise stimulus-locked spiking activity and sensory-induced gamma oscillations can constitute independent multiplexed coding schemes at the single-cell level.\",\n \"corpus_id\": 4920462,\n \"score\": 2\n },\n {\n \"doc_id\": \"29584719\",\n \"title\": \"Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.\",\n \"abstract\": \"Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks.\",\n \"corpus_id\": 4644792,\n \"score\": 2\n },\n {\n \"doc_id\": \"22022245\",\n \"title\": \"Neural computation via neural geometry: a place code for inter-whisker timing in the barrel cortex?\",\n \"abstract\": \"The place theory proposed by Jeffress (1948) is still the dominant model of how the brain represents the movement of sensory stimuli between sensory receptors. According to the place theory, delays in signalling between neurons, dependent on the distances between them, compensate for time differences in the stimulation of sensory receptors. Hence the location of neurons, activated by the coincident arrival of multiple signals, reports the stimulus movement velocity. Despite its generality, most evidence for the place theory has been provided by studies of the auditory system of auditory specialists like the barn owl, but in the study of mammalian auditory systems the evidence is inconclusive. We ask to what extent the somatosensory systems of tactile specialists like rats and mice use distance dependent delays between neurons to compute the motion of tactile stimuli between the facial whiskers (or 'vibrissae'). We present a model in which synaptic inputs evoked by whisker deflections arrive at neurons in layer 2/3 (L2/3) somatosensory 'barrel' cortex at different times. The timing of synaptic inputs to each neuron depends on its location relative to sources of input in layer 4 (L4) that represent stimulation of each whisker. Constrained by the geometry and timing of projections from L4 to L2/3, the model can account for a range of experimentally measured responses to two-whisker stimuli. Consistent with that data, responses of model neurons located between the barrels to paired stimulation of two whiskers are greater than the sum of the responses to either whisker input alone. The model predicts that for neurons located closer to either barrel these supralinear responses are tuned for longer inter-whisker stimulation intervals, yielding a topographic map for the inter-whisker deflection interval across the surface of L2/3. This map constitutes a neural place code for the relative timing of sensory stimuli.\",\n \"corpus_id\": 18707403,\n \"score\": 1\n },\n {\n \"doc_id\": \"22537827\",\n \"title\": \"Barrel cortical neurons and astrocytes coordinately respond to an increased whisker stimulus frequency.\",\n \"abstract\": \"BACKGROUND: Nerve cells program the brain codes to manage well-organized cognitions and behaviors. It remains unclear how a population of neurons and astrocytes work coordinately to encode their spatial and temporal activity patterns in response to frequency and intensity signals from sensory inputs. RESULTS: With two-photon imaging and electrophysiology to record cellular functions in the barrel cortex in vivo, we analyzed the activity patterns of neurons and astrocytes in response to whisker stimuli with increasing frequency, an environmental stimulus pattern that rodents experience in the accelerated motion. Compared to the resting state, whisker stimulation caused barrel neurons and astrocytes to be activated more synchronously. An increased stimulus frequency up-regulated the activity strength of neurons and astrocytes as well as coordinated their interaction. The coordination among the barrel neurons and astrocytes was fulfilled by increasing their functional connections. CONCLUSIONS: Our study reveals that the nerve cells in the barrel cortex encode frequency messages in whisker tactile inputs through setting their activity coordination.\",\n \"corpus_id\": 5743731,\n \"score\": 1\n },\n {\n \"doc_id\": \"24305831\",\n \"title\": \"Independent population coding of speech with sub-millisecond precision.\",\n \"abstract\": \"To understand the strategies used by the brain to analyze complex environments, we must first characterize how the features of sensory stimuli are encoded in the spiking of neuronal populations. Characterizing a population code requires identifying the temporal precision of spiking and the extent to which spiking is correlated, both between cells and over time. In this study, we characterize the population code for speech in the gerbil inferior colliculus (IC), the hub of the auditory system where inputs from parallel brainstem pathways are integrated for transmission to the cortex. We find that IC spike trains can carry information about speech with sub-millisecond precision, and, consequently, that the temporal correlations imposed by refractoriness can play a significant role in shaping spike patterns. We also find that, in contrast to most other brain areas, the noise correlations between IC cells are extremely weak, indicating that spiking in the population is conditionally independent. These results demonstrate that the problem of understanding the population coding of speech can be reduced to the problem of understanding the stimulus-driven spiking of individual cells, suggesting that a comprehensive model of the subcortical processing of speech may be attainable in the near future.\",\n \"corpus_id\": 23377470,\n \"score\": 1\n },\n {\n \"doc_id\": \"24472465\",\n \"title\": \"[What the whiskers tell the tactile brain].\",\n \"abstract\": \"Ce que les vibrisses disent au cerveau tactile. The rodent whisker system became one of the main system models for the study of the functional properties of sensory neurons. This is due on one hand to the detailed knowledge that we have on the afferent pathways linking the mechanoreceptors in the follicles to the primary somatosensory cortex and on the other hand to the possibility of controlling the sensory input at a micrometer and millisecond scale. The observation of the natural use of the whiskers by rodents indicates that exploration of objects and textures imply multiple contacts with tens of whiskers simultaneously. We have studied the neural code in the barrel cortex, which receives tactile information from the whiskers. By combining multi-electrode recordings and controlled multiwhisker tactile stimulation with theoretical analysis, we have observed a dependence of neural responses on the statistics of the sensory input. Several classes of neuronal responses, similar to those described in a number of cortical visual areas, were observed in the same cortical volume, indicating that various coding schemes are implemented in the same cortical network and can be put into play differentially to cope with the changing statistics of the peripheral stimuli.\",\n \"corpus_id\": 196595761,\n \"score\": 1\n },\n {\n \"doc_id\": \"24695456\",\n \"title\": \"Optogenetic patterning of whisker-barrel cortical system in transgenic rat expressing channelrhodopsin-2.\",\n \"abstract\": \"The rodent whisker-barrel system has been an ideal model for studying somatosensory representations in the cortex. However, it remains a challenge to experimentally stimulate whiskers with a given pattern under spatiotemporal precision. Recently the optogenetic manipulation of neuronal activity has made possible the analysis of the neuronal network with precise spatiotemporal resolution. Here we identified the selective expression of channelrhodopsin-2 (ChR2), an algal light-driven cation channel, in the large mechanoreceptive neurons in the trigeminal ganglion (TG) as well as their peripheral nerve endings innervating the whisker follicles of a transgenic rat. The spatiotemporal pattern of whisker irradiation thus produced a barrel-cortical response with a specific spatiotemporal pattern as evidenced by electrophysiological and functional MRI (fMRI) studies. Our methods of generating an optogenetic tactile pattern (OTP) can be expected to facilitate studies on how the spatiotemporal pattern of touch is represented in the somatosensory cortex, as Hubel and Wiesel did in the visual cortex.\",\n \"corpus_id\": 881274,\n \"score\": 1\n },\n {\n \"doc_id\": \"25100857\",\n \"title\": \"Imprecise Whisker Map in the Neonatal Rat Barrel Cortex.\",\n \"abstract\": \"The somatosensory barrel cortex in rodents contains a topographic map of the facial whiskers where each cortical barrel is tuned to a corresponding whisker. However, exactly when this correspondence is established during development and how precise the functional topography of the whisker protomap is at birth, before the anatomical formation of barrels, are questions that remain unresolved. Here, using extracellular and whole-cell recordings from the barrel cortex of 0- to 7-day-old (P0-7; P0 = day of birth) rat pups in vivo, we report a low level of tuning to the principal whisker at P0-1, with multiple adjacent whiskers evoking large multi- and single-unit responses and excitatory postsynaptic currents in cortical neurons. Additionally, we found broad and largely overlapping projection fields (PFs) for neighboring whiskers in the barrel cortex at P0-1. Starting from P2-3, a segregated whisker map emerged, characterized by preferential single whisker tuning and segregated whisker PFs. These results indicate that the functional whisker protomap in the somatosensory cortex is imprecise at birth, that for 2-3 days after birth, whiskers compete for the cortical target territories, and that formation of a segregated functional whisker map coincides with emergence of the anatomical barrel map.\",\n \"corpus_id\": 16959113,\n \"score\": 1\n },\n {\n \"doc_id\": \"26217194\",\n \"title\": \"Emergence of spatiotemporal invariance in large neuronal ensembles in rat barrel cortex.\",\n \"abstract\": \"Invariant sensory coding is the robust coding of some sensory information (e.g., stimulus type) despite major changes in other sensory parameters (e.g., stimulus strength). The contribution of large populations of neurons (ensembles) to invariant sensory coding is not well understood, but could offer distinct advantages over invariance in single cell receptive fields. To test invariant sensory coding in neuronal ensembles evoked by single whisker stimulation as early as primary sensory cortex, we recorded detailed spatiotemporal movies of evoked ensemble activity through the depth of rat barrel cortex using microelectrode arrays. We found that an emergent property of whisker evoked ensemble activity, its spatiotemporal profile, was notably invariant across major changes in stimulus amplitude (up to >200-fold). Such ensemble-based invariance was found for single whisker stimulation as well as for the integrated profile of activity evoked by the more naturalistic stimulation of the entire whisker array. Further, the integrated profile of whisker array evoked ensemble activity and its invariance to stimulus amplitude shares striking similarities to \\\"funneled\\\" tactile perception in humans. We therefore suggest that ensemble-based invariance could provide a robust neurobiological substrate for invariant sensory coding and integration at an early stage of cortical sensory processing already in primary sensory cortex.\",\n \"corpus_id\": 6911368,\n \"score\": 1\n },\n {\n \"doc_id\": \"26417040\",\n \"title\": \"Facial whisker pattern is not sufficient to instruct a whisker-related topographic map in the mouse somatosensory brainstem.\",\n \"abstract\": \"Facial somatosensory input is relayed by trigeminal ganglion (TG) neurons and serially wired to brainstem, thalamus and cortex. Spatially ordered sets of target neurons generate central topographic maps reproducing the spatial arrangement of peripheral facial receptors. Facial pattern provides a necessary template for map formation, but may be insufficient to impose a brain somatotopic pattern. In mice, lower jaw sensory information is relayed by the trigeminal nerve mandibular branch, whose axons target the brainstem dorsal principal sensory trigeminal nucleus (dPrV). Input from mystacial whiskers is relayed by the maxillary branch and forms a topographic representation of rows and whiskers in the ventral PrV (vPrV). To investigate peripheral organisation in imposing a brain topographic pattern, we analysed Edn1(-/-) mice, which present ectopic whisker rows on the lower jaw. We found that these whiskers were innervated by mandibular TG neurons which initially targeted dPrV. Unlike maxillary TG neurons, the ectopic whisker-innervating mandibular neuron cell bodies and pre-target central axons did not segregate into a row-specific pattern nor target the dPrV with a topographic pattern. Following periphery-driven molecular repatterning to a maxillary-like identity, mandibular neurons partially redirected their central projections from dPrV to vPrV. Thus, while able to induce maxillary-like molecular features resulting in vPrV final targeting, a spatially ordered lower jaw ectopic whisker pattern is insufficient to impose row-specific pre-target organisation of the central mandibular tract or a whisker-related matching pattern of afferents in dPrV. These results provide novel insights into periphery-dependent versus periphery-independent mechanisms of trigeminal ganglion and brainstem patterning in matching whisker topography.\",\n \"corpus_id\": 8192621,\n \"score\": 1\n },\n {\n \"doc_id\": \"27242445\",\n \"title\": \"Push-Pull Receptive Field Organization and Synaptic Depression: Mechanisms for Reliably Encoding Naturalistic Stimuli in V1.\",\n \"abstract\": \"Neurons in the primary visual cortex are known for responding vigorously but with high variability to classical stimuli such as drifting bars or gratings. By contrast, natural scenes are encoded more efficiently by sparse and temporal precise spiking responses. We used a conductance-based model of the visual system in higher mammals to investigate how two specific features of the thalamo-cortical pathway, namely push-pull receptive field organization and fast synaptic depression, can contribute to this contextual reshaping of V1 responses. By comparing cortical dynamics evoked respectively by natural vs. artificial stimuli in a comprehensive parametric space analysis, we demonstrate that the reliability and sparseness of the spiking responses during natural vision is not a mere consequence of the increased bandwidth in the sensory input spectrum. Rather, it results from the combined impacts of fast synaptic depression and push-pull inhibition, the later acting for natural scenes as a form of \\\"effective\\\" feed-forward inhibition as demonstrated in other sensory systems. Thus, the combination of feedforward-like inhibition with fast thalamo-cortical synaptic depression by simple cells receiving a direct structured input from thalamus composes a generic computational mechanism for generating a sparse and reliable encoding of natural sensory events.\",\n \"corpus_id\": 8808505,\n \"score\": 1\n },\n {\n \"doc_id\": \"27334956\",\n \"title\": \"Neural mechanisms of selective attention in the somatosensory system.\",\n \"abstract\": \"Selective attention allows organisms to extract behaviorally relevant information while ignoring distracting stimuli that compete for the limited resources of their central nervous systems. Attention is highly flexible, and it can be harnessed to select information based on sensory modality, within-modality feature(s), spatial location, object identity, and/or temporal properties. In this review, we discuss the body of work devoted to understanding mechanisms of selective attention in the somatosensory system. In particular, we describe the effects of attention on tactile behavior and corresponding neural activity in somatosensory cortex. Our focus is on neural mechanisms that select tactile stimuli based on their location on the body (somatotopic-based attention) or their sensory feature (feature-based attention). We highlight parallels between selection mechanisms in touch and other sensory systems and discuss several putative neural coding schemes employed by cortical populations to signal the behavioral relevance of sensory inputs. Specifically, we contrast the advantages and disadvantages of using a gain vs. spike-spike correlation code for representing attended sensory stimuli. We favor a neural network model of tactile attention that is composed of frontal, parietal, and subcortical areas that controls somatosensory cells encoding the relevant stimulus features to enable preferential processing throughout the somatosensory hierarchy. Our review is based on data from noninvasive electrophysiological and imaging data in humans as well as single-unit recordings in nonhuman primates.\",\n \"corpus_id\": 13530488,\n \"score\": 1\n },\n {\n \"doc_id\": \"27921067\",\n \"title\": \"Parallel pathways from whisker and visual sensory cortices to distinct frontal regions of mouse neocortex.\",\n \"abstract\": \"The spatial organization of mouse frontal cortex is poorly understood. Here, we used voltage-sensitive dye to image electrical activity in the dorsal cortex of awake head-restrained mice. Whisker-deflection evoked the earliest sensory response in a localized region of primary somatosensory cortex and visual stimulation evoked the earliest responses in a localized region of primary visual cortex. Over the next milliseconds, the initial sensory response spread within the respective primary sensory cortex and into the surrounding higher order sensory cortices. In addition, secondary hotspots in the frontal cortex were evoked by whisker and visual stimulation, with the frontal hotspot for whisker deflection being more anterior and lateral compared to the frontal hotspot evoked by visual stimulation. Investigating axonal projections, we found that the somatosensory whisker cortex and the visual cortex directly innervated frontal cortex, with visual cortex axons innervating a region medial and posterior to the innervation from somatosensory cortex, consistent with the location of sensory responses in frontal cortex. In turn, the axonal outputs of these two frontal cortical areas innervate distinct regions of striatum, superior colliculus, and brainstem. Sensory input, therefore, appears to map onto modality-specific regions of frontal cortex, perhaps participating in distinct sensorimotor transformations, and directing distinct motor outputs.\",\n \"corpus_id\": 23885467,\n \"score\": 1\n },\n {\n \"doc_id\": \"28243518\",\n \"title\": \"Study of the cortical representation of whisker frequency selectivity using voltage-sensitive dye optical imaging.\",\n \"abstract\": \"The facial whiskers of rodents act as a high-resolution tactile apparatus that allow the animal to detect the finest details of its environment. Previously it was shown that whisker-sensitive neurons in the somatosensory cortex show frequency selectivity to small amplitude stimuli, An intravital voltage-sensitive dye optical imaging (VSDi) method in combination with the different frequency whisker stimulation was used in order to visualize neural activity in the mice somatosensory cortex in response to the stimulation of a single whisker by different frequencies. Using the intravital voltage-sensitive dye optical imaging (VSDi) method in combination with the different frequency whisker stimulation we visualized neural activity in the mice somatosensory cortex in response to the stimulation of a single whisker by different frequencies. We found that whisker stimuli with different frequencies led to different optical signals in the barrel field. Our results provide evidence that different neurons of the barrel cortex have different frequency preferences. This supports prior research that whisker deflections cause responses in cortical neurons within the barrel field according to the frequency of the stimulation. Many studies of the whisker frequency selectivity were performed using unit recording but to map spatial organization, imaging methods are essential. In the work described in the present paper, we take a serious step toward detailed functional mapping of the somatosensory cortex using VSDi. To our knowledge, this is the first demonstration of whisker frequency sensitivity and selectivity of barrel cortex neurons with optical imaging methods.\",\n \"corpus_id\": 205967503,\n \"score\": 1\n },\n {\n \"doc_id\": \"28663199\",\n \"title\": \"Behavioral Consequences of a Bifacial Map in the Mouse Somatosensory Cortex.\",\n \"abstract\": \"The whisker system is an important sensory organ with extensive neural representations in the brain of the mouse. Patterned neural modules (barrelettes) in the ipsilateral principal sensory nucleus of the trigeminal nerve (PrV) correspond to the whiskers. Axons of the PrV barrelette neurons cross the midline and confer the whisker-related patterning to the contralateral ventroposteromedial nucleus of the thalamus, and subsequently to the cortex. In this way, specific neural modules called barreloids and barrels in the contralateral thalamus and cortex represent each whisker. Partial midline crossing of the PrV axons, in a conditional Robo3 mutant (Robo3(R3-5)cKO) mouse line, leads to the formation of bilateral whisker maps in the ventroposteromedial, as well as the barrel cortex. We used voltage-sensitive dye optical imaging and somatosensory and motor behavioral tests to characterize the consequences of bifacial maps in the thalamocortical system. Voltage-sensitive dye optical imaging verified functional, bilateral whisker representation in the barrel cortex and activation of distinct cortical loci following ipsilateral and contralateral stimulation of the specific whiskers. The mutant animals were comparable with the control animals in sensorimotor tests. However, they showed noticeable deficits in all of the whisker-dependent or -related tests, including Y-maze exploration, horizontal surface approach, bridge crossing, gap crossing, texture discrimination, floating in water, and whisking laterality. Our results indicate that bifacial maps along the thalamocortical system do not offer a functional advantage. Instead, they lead to impairments, possibly due to the smaller size of the whisker-related modules and interference between the ipsilateral and contralateral whisker representations in the same thalamus and cortex. SIGNIFICANCE STATEMENT The whisker sensory system plays a quintessentially important role in exploratory behavior of mice and other nocturnal rodents. Here, we studied a novel mutant mouse line, in which the projections from the brainstem to the thalamus are disrupted. This led to formation of bilateral whisker maps in both the thalamus and the cortex. The two whisker maps crowd in a space normally devoted to the contralateral map alone and in a nonoverlapping fashion. Stimulation of the whiskers on either side activates the corresponding region of the map. Mice with bilateral whisker maps perform well in general sensorimotor tasks but show poor performance in specific tests that require whisker-dependent tactile discrimination. These observations indicate that contralateral, instead of bilateral, representation of the sensory space plays a critical role in acuity and fine discrimination during somesthesis.\",\n \"corpus_id\": 207511300,\n \"score\": 1\n },\n {\n \"doc_id\": \"29738998\",\n \"title\": \"Development of the whisker-to-barrel cortex system.\",\n \"abstract\": \"This review provides an overview on the development of the rodent whisker-to-barrel cortex system from late embryonic stage to the end of the first postnatal month. During this period the system shows a remarkable transition from a mostly genetic-molecular driven generation of crude connectivity, providing the template for activity-dependent structural and functional maturation and plasticity, to the manifestation of a complex behavioral repertoire including social interactions. Spontaneous and sensory-evoked activity is present in neonatal barrel cortex and control the generation of the cortical architecture. Half a century after its first description by Woolsey and van der Loos the whisker-to-barrel cortex system with its unique and clear topographic organization still offers the exceptional opportunity to study sensory processing and complex behavior.\",\n \"corpus_id\": 13705465,\n \"score\": 1\n },\n {\n \"doc_id\": \"29807911\",\n \"title\": \"Neural Coding of Whisker-Mediated Touch in Primary Somatosensory Cortex Is Altered Following Early Blindness.\",\n \"abstract\": \"Sensory systems do not develop and function independently of one another, yet they are typically studied in isolation. Effects of multisensory interactions on the developing neocortex can be revealed by altering the ratios of incoming sensory inputs associated with different modalities. We investigated neural responses in primary somatosensory cortex (S1) of short-tailed opossums (Monodelphis domestica; either sex) after the elimination of visual input through bilateral enucleation very early in development. To assess the influence of tactile experience after vision loss, we also examined naturally occurring patterns of exploratory behavior. In early blind (EB) animals, overall levels of tactile experience were similar to those of sighted controls (SC); locomotor activity was unimpaired and accompanied by whisking. Using extracellular single-unit recording techniques under anesthesia, we found that EB animals exhibited a reduction in the magnitude of neural responses to whisker stimuli in S1, coupled with spatial sharpening of receptive fields, in comparison to SC animals. These alterations manifested as two different effects on sensory processing in S1 of EB animals: the ability of neurons to detect single whisker stimulation was decreased, whereas their ability to discriminate between stimulation of neighboring whiskers was enhanced. The increased selectivity of S1 neurons in EB animals was reflected in improved population decoding performance for whisker stimulus position, particularly along the rostrocaudal axis of the snout, which aligns with the primary axis of natural whisker motion. These findings suggest that a functionally distinct form of somatosensory plasticity occurs when vision is lost early in development. SIGNIFICANCE STATEMENT After sensory loss, compensatory behavior mediated through the spared senses could be generated entirely through the recruitment of brain areas associated with the deprived sense. Alternatively, functional compensation in spared modalities may be achieved through a combination of plasticity in brain areas corresponding to both spared and deprived sensory modalities. Although activation of neurons in cortex associated with a deprived sense has been described frequently, it is unclear whether this is the only substrate available for compensation or if plasticity within cortical fields corresponding to spared modalities, particularly primary sensory cortices, may also contribute. Here, we demonstrate empirically that early loss of vision alters coding of sensory inputs in primary somatosensory cortex in a manner that supports enhanced tactile discrimination.\",\n \"corpus_id\": 44092505,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":66,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29596343\",\n \"title\": \"Antipruritic Effects of Botulinum Neurotoxins.\",\n \"abstract\": \"This review explores current evidence to demonstrate that botulinum neurotoxins (BoNTs) exert antipruritic effects. Both experimental and clinical conditions in which botulinum neurotoxins have been applied for pruritus relief will be presented and significant findings will be highlighted. Potential mechanisms underlying antipruritic effects will also be discussed and ongoing challenges and unmet needs will be addressed.\",\n \"corpus_id\": 4516269\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18357364","title":"Novel agents for intractable itch.","abstract":"There exists a multitude of medical conditions that cause intractable itch, or pruritus. The successful management of this symptom depends explicitly on establishing the underlying cause. Studies have shown that drugs not traditionally used in the treatment of cutaneous disorders, such as opiate receptor antagonists, antidepressants, and antiepileptics, can provide symptomatic relief of intractable itch. These novel antipruritic agents will be explored in this review.","corpus_id":25646667,"score":2},{"doc_id":"18836352","title":"Relief of intractable pruritus after administration of botulinum toxin A (botox): a case report.","abstract":"A 55-year-old woman sought assistance for intractable pruritus of 6-year duration, affecting the right side of the forehead. She had surgery on the right frontal area for treatment of a frontal sinus condition, a few years earlier. The itch failed to respond to a variety of medical interventions, including oral antipruritic agents and local injections of anesthetic. Administration of botulinum toxin A (Allergan Inc, Irvine, CA) into the pruritic area resulted in a significant relief of pruritus in this patient.","corpus_id":27104400,"score":2},{"doc_id":"19887944","title":"Botulinum neurotoxin A for benign prostatic hyperplasia.","abstract":"PURPOSE OF REVIEW: The injection of botulinum neurotoxin A (BoNT-A) into the prostate represents an alternative, minimal invasive treatment for lower urinary tract symptoms suggestive of benign prostatic hyperplasia (BPH), which gained the interest of urologists during the last years, although it is not yet licensed. The purpose of this review is to summarize the mechanisms through which BoNT-A could inhibit the progression of BPH and eliminate the lower urinary tract symptoms according to the findings of animal studies. Furthermore, we review clinical studies to report the efficacy and safety of intraprostatic BoNT-A injection according to various injection protocols. RECENT FINDINGS: The experimental studies report induced relaxation of the prostate, atrophy, and reduction in its size through inhibition of the trophic effect of the autonomic system on the prostate gland. Also, a possible mechanism of reduction in lower urinary tract symptoms might take place through inhibition of sensory afferents from the prostate to the spinal cord. Clinical studies report symptomatic relief and improvement in the measured parameters during the follow-up period, whereas local or systematic side-effects are rare. SUMMARY: We should recognize that, at present, this therapy is still experimental. Although the results of the clinical studies are encouraging, the level of evidence is low. Clearly, we need large-scale, clinical, placebo-controlled, randomized studies, including long-term surveillance to document the evidence of this therapy and, eventually, to register BoNT-A for this indication.","corpus_id":23180726,"score":2},{"doc_id":"20950328","title":"Role of spinal neurotransmitter receptors in itch: new insights into therapies and drug development.","abstract":"Targets for antipruritic therapies are now expanding from the skin to the central nervous system. Recent studies demonstrate that various neuronal receptors in the spinal cord are involved in pruritus. The spinal opioid receptor is one of the best-known examples. Spinal administration of morphine is frequently accompanied by segmental pruritus. In addition to μ-opioid receptor antagonists, κ-opioid receptor agonists have recently come into usage as novel antipruritic drugs, and are expected to suppress certain subtypes of itch such as hemodialysis- and cholestasis-associated itch that are difficult to treat with antihistamines. The gastrin-releasing peptide receptor in the superficial dorsal horn of the spinal cord has also received recent attention as a novel pathway of itch-selective neural transmission. The NMDA glutamate receptor appears to be another potential target for the treatment of itch, especially in terms of central sensitization. The development of NMDA receptor antagonists with less undesirable side effects on the central nervous system might be beneficial for antipruritic therapies. Drugs suppressing presynaptic glutamate-release such as gabapentin and pregabalin also reportedly inhibit certain subtypes of itch such as brachioradial pruritus. Spinal receptors of other neuromediators such as bradykinin, substance P, serotonin, and histamine may also be potential targets for antipruritic therapies, given that most of these molecules interfere not only with pain, but also with itch transmission or regulation. Thus, the identification of itch-specific receptors and understanding itch-related circuits in the spinal cord may be innovative strategies for the development of novel antipruritic drugs.","corpus_id":30072228,"score":2},{"doc_id":"23162705","title":"Clinical uses of botulinum neurotoxins: current indications, limitations and future developments.","abstract":"Botulinum neurotoxins (BoNTs) cause flaccid paralysis by interfering with vesicle fusion and neurotransmitter release in the neuronal cells. BoNTs are the most widely used therapeutic proteins. BoNT/A was approved by the U.S. FDA to treat strabismus, blepharospam, and hemificial spasm as early as 1989 and then for treatment of cervical dystonia, glabellar facial lines, axillary hyperhidrosis, chronic migraine and for cosmetic use. Due to its high efficacy, longevity of action and satisfactory safety profile, it has been used empirically in a variety of ophthalmological, gastrointestinal, urological, orthopedic, dermatological, secretory, and painful disorders. Currently available BoNT therapies are limited to neuronal indications with the requirement of periodic injections resulting in immune-resistance for some indications. Recent understanding of the structure-function relationship of BoNTs prompted the engineering of novel BoNTs to extend therapeutic interventions in non-neuronal systems and to overcome the immune-resistance issue. Much research still needs to be done to improve and extend the medical uses of BoNTs.","corpus_id":34697296,"score":2},{"doc_id":"24685845","title":"Understanding itch: an update on mediators and mechanisms of pruritus.","abstract":"Pruritus is the most common symptom secondary to skin diseases. Advances in the fields of neurobiology, immunology and physiology have made it possible for us to understand and unravel the deeper pathophysiological basis of pruritus. This review aims to update our current understanding of the mechanisms and mediators of pruritus. Special attention is paid to endogenous itch mediators particularly newly identified ones like endovanilloids, opioids, neurotrophins, cannabinoids, proteases and cytokines. Various theories explaining the peripheral encoding of itch are reviewed. Multiple neural pathways including the central itch pathways as well as supraspinal processing of itch and brain areas involved in pruritus are highlighted. Apart from peripheral itch mediators, spinal neural receptors are also involved in control of itch and should form part of the development of a novel antipruritic strategy. Further studies are required to fill the lacunae in our current understanding of the pathophysiology of pruritus.","corpus_id":19338172,"score":2},{"doc_id":"26556371","title":"Current Status and Future Directions of Botulinum Neurotoxins for Targeting Pain Processing.","abstract":"Current evidence suggests that botulinum neurotoxins (BoNTs) A1 and B1, given locally into peripheral tissues such as skin, muscles, and joints, alter nociceptive processing otherwise initiated by inflammation or nerve injury in animal models and humans. Recent data indicate that such locally delivered BoNTs exert not only local action on sensory afferent terminals but undergo transport to central afferent cell bodies (dorsal root ganglia) and spinal dorsal horn terminals, where they cleave SNAREs and block transmitter release. Increasing evidence supports the possibility of a trans-synaptic movement to alter postsynaptic function in neuronal and possibly non-neuronal (glial) cells. The vast majority of these studies have been conducted on BoNT/A1 and BoNT/B1, the only two pharmaceutically developed variants. However, now over 40 different subtypes of botulinum neurotoxins (BoNTs) have been identified. By combining our existing and rapidly growing understanding of BoNT/A1 and /B1 in altering nociceptive processing with explorations of the specific characteristics of the various toxins from this family, we may be able to discover or design novel, effective, and long-lasting pain therapeutics. This review will focus on our current understanding of the molecular mechanisms whereby BoNTs alter pain processing, and future directions in the development of these agents as pain therapeutics.","corpus_id":16243194,"score":2},{"doc_id":"27421250","title":"Non-cosmetic dermatological uses of botulinum neurotoxin.","abstract":"Botulinum neurotoxin (BoNT) is renowned for its inhibitory effects on the neuromuscular junction. The evidence for its use in cosmetic dermatology and in non-dermatological indications is well established. We have systemically analysed the evidence for the non-cosmetic dermatological uses of BoNT. This review presents the many small studies showing promising results for the use of BoNT in a multitude of dermatological diseases, including (but not limited to) hyperhidrosis, Darier's disease, Hailey-Hailey disease, pompholyx and hidradenitis suppurativa. There is, however, the need for larger, double-blinded randomized control trials against established treatments to cement the evidence base underlying the use of BoNT in dermatology.","corpus_id":206043331,"score":2},{"doc_id":"27578080","title":"Neurologic Itch Management.","abstract":"Neurologic itch is defined as pruritus resulting from any dysfunction of the nervous system. Itch arising due to a neuroanatomic pathology is seen to be neuropathic. Causes of neuropathic itch range from localized entrapment of a peripheral nerve to generalized degeneration of small nerve fibers. Antipruritic medications commonly used for other types of itch such as antihistamines and corticosteroids lack efficacy in neuropathic itch. Currently there are no therapeutic options that offer relief in all types of neuropathic pruritus, and treatment strategies vary according to etiology. It is best to decide on the appropriate tests and procedures in collaboration with a neurologist during the initial work-up. Treatment of neuropathic itch includes general antipruritic measures, local or systemic pharmacotherapy, various physical modalities, and surgery. Surgical intervention is the obvious choice of therapy in cases of spinal or cerebral mass, abscess, or hemorrhagic stroke, and may provide decompression in entrapment neuropathies. Symptomatic treatment is needed in the vast majority of patients. General antipruritic measures should be encouraged. Local treatment agents with at least some antipruritic effect include capsaicin, local anesthetics, doxepin, tacrolimus, and botulinum toxin A. Current systemic therapy relies on anticonvulsants such as gabapentin and pregabalin. Phototherapy, transcutaneous electrical nerve stimulation, and physical therapy have also been of value in selected cases. Among the avenues to be explored are transcranial magnetic stimulation of the brain, new topical cannabinoid receptor agonists, various modes of acupuncture, a holistic approach with healing touch, and cell transplantation to the spinal cord.","corpus_id":21276723,"score":2},{"doc_id":"29570628","title":"A Study and Review of Effects of Botulinum Toxins on Mast Cell Dependent and Independent Pruritus.","abstract":"Pruriceptive itch originates following activation of peripheral sensory nerve terminals when pruritogens come in contact with the skin. The ability of botulinum neurotoxins (BoNTs) to attenuate transmitter release from afferent terminals provides a rationale for studying its effect on pruritus. This study investigated the effects of BoNT/A1 and BoNT/B1 on mast cell dependent (Compound 48/80:48/80) and independent (Chloroquine:CQ) scratching. C57Bl/6 male mice received intradermal injection of 1.5 U of BoNT/A1, BoNT/B1 or saline 2, 7, 14 and 21 days prior to ipsilateral 48/80 or CQ at the nape of the neck. Ipsilateral hind paw scratching was determined using an automated recording device. The effect of BoNTs on 48/80 mediated mast cell degranulation was analyzed in human and murine mast cells and the presence of SNAREs was determined using qPCR, immunostaining and Western blot. Pre-treatment with BoNT/A1 and BoNT/B1 reduced 48/80 and CQ induced scratching behavior starting on day 2 with reversal by day 21. Both serotypes inhibited 48/80 induced mast cell degranulation. qPCR and immunostaining detected SNAP-25 mRNA and protein, respectively, in mast cells, however, Western blots did not. This study demonstrates the long-lasting anti-pruritic effects of two BoNT serotypes, in a murine pruritus model using two different mechanistically driven pruritogens. These data also indicate that BoNTs may have a direct effect upon mast cell degranulation.","corpus_id":4229209,"score":2},{"doc_id":"29783676","title":"The Expanding Therapeutic Utility of Botulinum Neurotoxins.","abstract":"Botulinum neurotoxin (BoNT) is a major therapeutic agent that is licensed in neurological indications, such as dystonia and spasticity. The BoNT family, which is produced in nature by clostridial bacteria, comprises several pharmacologically distinct proteins with distinct properties. In this review, we present an overview of the current therapeutic landscape and explore the diversity of BoNT proteins as future therapeutics. In recent years, novel indications have emerged in the fields of pain, migraine, overactive bladder, osteoarthritis, and wound healing. The study of biological effects distal to the injection site could provide future opportunities for disease-tailored BoNT therapies. However, there are some challenges in the pharmaceutical development of BoNTs, such as liquid and slow-release BoNT formulations; and, transdermal, transurothelial, and transepithelial delivery. Innovative approaches in the areas of formulation and delivery, together with highly sensitive analytical tools, will be key for the success of next generation BoNT clinical products.","corpus_id":29151386,"score":2},{"doc_id":"18385327","title":"Long-distance retrograde effects of botulinum neurotoxin A.","abstract":"Botulinum neurotoxins (designated BoNT/A-BoNT/G) are bacterial enzymes that block neurotransmitter release by cleaving essential components of the vesicle fusion machinery. BoNT/A, which cleaves SNAP-25 (synaptosomal-associated protein of 25 kDa), is extensively exploited in clinical medicine to treat neuromuscular pathologies, facial wrinkles, and various types of pain. It is widely assumed that BoNT/A remains at the synaptic terminal and its effects are confined to the injection site. Here we demonstrate that catalytically active BoNT/A is retrogradely transported by central neurons and motoneurons and is then transcytosed to afferent synapses, in which it cleaves SNAP-25. SNAP-25 cleavage by BoNT/A was observed in the contralateral hemisphere after unilateral BoNT/A delivery to the hippocampus. Appearance of cleaved SNAP-25 resulted in blockade of hippocampal activity in the untreated hemisphere. Injections of BoNT/A into the optic tectum led to the appearance of BoNT/A-truncated SNAP-25 in synaptic terminals within the retina. Cleaved SNAP-25 also appeared in the facial nucleus after injection of the toxin into rat whisker muscles. Experiments excluded passive spread of the toxin and demonstrated axonal migration and neuronal transcytosis of BoNT/A. These findings reveal a novel pathway of BoNT/A trafficking in neurons and have important implications for the clinical uses of this neurotoxin.","corpus_id":16689610,"score":1},{"doc_id":"18543757","title":"[Mechanism of therapy effects by botulinum neurotoxin].","abstract":"Mehanizam djelovanja i terapija botulinum toksinom. Botulinum neurotoxin (BoNT) is produced by Clostridium botulinum as a complex of proteins containing the neurotoxin itself and other nontoxic proteins. Activation of the neurotoxin occurs upon proteolytic cleavage into the heavy and light chains. This di-chain moiety is essential for neurotoxin and each chain is playing a unique role; the heavy chain mediates neurospecifics cell binding and entry, whereas the light chain, a protease, catalyzes the cleavage and inactivation of neuronal proteins that mediate neurotransmitter release. There are seven BoNT serotypes (A,B,CI,D,E,F, and G), all of which inhibit acetylcholine release, though their intracellular target proteins, the characteristics of their actions, and their potencies vary substantially. BoNT type A has been the most widely studied and applied serotype for therapeutic purposes. It has been a mainstay in the treatment of cervical dystonia, blepharospasm, and hemifacial spasm for years. BoNT has more recently emerged as an increasingly important therapeutic option in the clinical management of a broad array of conditions, including other focal dystonias, spasticity, cerebral palsy, equinovarus, gastrointestinal (GI) and urogenital disorders, hypersecretory disorders, facial lines due to hyperfunctional facial muscles and recently, musculoskeletal pain disorders and headache.","corpus_id":22843456,"score":1},{"doc_id":"18784598","title":"Clinical comparisons of botulinum neurotoxin formulations.","abstract":"BACKGROUND: The expanding uses of botulinum neurotoxin (BoNT) for a growing number of clinical indications, including cervical and other dystonias, adult and childhood spasticity, and hyperhidrosis, in conjunction with the emergence of new formulations of BoNT, prompt discussion of the differences in formulations, serotypes, and indications for different neurologic diseases. REVIEW SUMMARY: This review will evaluate evidence from preclinical studies, prospective treatment studies, and direct comparative trials to discuss the differences among BoNTs and the clinical implications of using these different drugs. Data from these sources indicate that formulations of BoNT are distinct; even the same serotype formulations of BoNT serotype A have different molecular structures and sizes and therapeutic indices (reflected in different safety and efficacy profiles). CONCLUSION: Taken together, these findings confirm that the different BoNT serotypes, including the different BoNTA formulations, are distinct therapeutic entities.","corpus_id":2604853,"score":1},{"doc_id":"19154335","title":"A reappraisal of the central effects of botulinum neurotoxin type A: by what mechanism?","abstract":"Botulinum neurotoxin A (BoNT/A) is a metalloprotease that enters peripheral motor nerve terminals and blocks the release of acetylcholine via the specific cleavage of the synaptosomal-associated protein of 25-kDa. Localized injections of BoNT/A are widely employed in clinical neurology to treat several human diseases characterized by muscle hyperactivity. It is generally assumed that the effects of BoNT/A remain localized to the injection site. However, several neurophysiological studies have provided evidence for central effects of BoNT/A, raising the issue of how these actions arise. Here we review these data and discuss the possibility that retrograde axonal transport of catalytically active BoNT/A may explain at least some of its effects at the level of central circuits.","corpus_id":33068721,"score":1},{"doc_id":"19264088","title":"Central effects of tetanus and botulinum neurotoxins.","abstract":"Tetanus neurotoxin (TeNT) and botulinum neurotoxins (BoNTs; from A to G) are metalloproteases that act on nerve terminals to prevent exocytosis. They are extensively exploited for the study of cellular physiology. Moreover, BoNTs are also employed in clinical neurology for the treatment of several disorders characterized by hyperexcitability of peripheral nerve terminals. This review summarizes recent studies that have provided a deeper understanding of the mode of action of TeNT and BoNTs. TeNT and BoNTs bind with extreme specificity and are internalized at the neuromuscular junction. We first examine the retrograde transport mechanisms by which TeNT gains access to the central nervous system. We also discuss recent findings indicating that, besides their well known local actions at the neuromuscular junction, BoNTs can also affect central circuits.","corpus_id":515573,"score":1},{"doc_id":"19365125","title":"Botulinum neurotoxin: the ugly duckling.","abstract":"This review presents a brief account of the most significant biological effects and clinical applications of botulinum neurotoxins, in a way comprehensive even for casual readers who are not familiar with the subject. The most toxic known substances in botulinum neurotoxins are polypeptides naturally synthesized by bacteria of the genus Clostridium. These polypeptides inhibit acetylcholine release at neuromuscular junctions, thus causing muscle paralysis involving both somatic and autonomic innervation. There is substantial evidence that this muscle-paralyzing feature of botulinum neurotoxins is useful for their beneficial influence on more than 50 pathological conditions such as spastic paralysis, cerebral palsy, focal dystonia, essential tremor, headache, incontinence and a variety of cosmetic interventions. Injection of adequate quantities of botulinum toxins in spastic muscles is considered as a highly hopeful procedure for the treatment of people who suffer from dystonia, cerebral palsy or have experienced a stroke. So far, numerous and reliable studies have established the safety and efficacy of botulinum neurotoxins and advocate wider clinical therapeutic and cosmetic applications.","corpus_id":38608385,"score":1},{"doc_id":"19846187","title":"[Botulinum neurotoxin].","abstract":"La neurotoxine botulinique. Botulinum toxin is a multi-molecular complex comprised of a neuro-active moiety (i.e. botulinum neurotoxin) and several associated non-toxic proteins. The toxin dissociates rapidly at plasmatic pH, thereby releasing neurotoxin. Nerve terminals only take up the neurotoxin. In the peripheral nerve system, the neurotoxin mainly blocks acetylcholine release. When acting at the neuromuscular junctions, this results in paralysis of the muscle fibers. The duration of the neurotoxin action is mainly determined by the life-time of neurotoxin molecules inside the nerve terminals. Inhibition of cholinergic transmission induces rapid atrophy of the muscle fibres, and, sometimes, sprouting from poisoned nerve terminals. These effects, as well as the acetylcholine release blockade are entirely reversible. When injected in the periphery, a direct action of botulinum neurotoxin in the central nervous system remains unlikely despite its retrograde ascent demonstrated in animal models. However, indirect effects are numerous. The constituting proteins of the toxin complex can lead to immunisation against the non-toxic associated proteins and neurotoxin. Only the antibodies directed against neurotoxin are potentially neutralizing.","corpus_id":23299996,"score":1},{"doc_id":"20462283","title":"Re-engineering clostridial neurotoxins for the treatment of chronic pain: current status and future prospects.","abstract":"Clostridial neurotoxins from the botulinum neurotoxin (BoNT) family are protein complexes, derived from the bacterium Clostridium botulinum, which potently inhibit acetylcholine release and result in a reversible blockade of the neuromuscular junction. This feature led to the clinical development of BoNT-A for a number of neuromuscular disorders. BoNT-A toxins are commercially available as three different preparations: Dysport/Azzalure, Botox/Vistabel, and Xeomin/Bocouture. Although BoNT-A preparations have not yet been approved for the treatment of pain, a substantial body of preclinical and clinical evidence shows that BoNT-A is effective in treating a number of different types of pain. It is thought to exert an analgesic effect both via muscle-relaxant properties and also directly, via inhibition of nociceptive neuropeptides. This review explores the mechanistic basis of this analgesic effect, summarizing current knowledge of the structure-function relationship of BoNT and discussing effects on both motor and pain neurons. For a complete picture of the analgesic properties of BoNT-A, clinical evidence of efficacy in myofascial pain and neuropathic pain is considered in tandem with a mechanistic rationale for activity. Patients experiencing chronic pain are clear candidates for treatment with a modified clostridial endopeptidase that would provide enduring inhibition of neurotransmitter release. A strong preclinical evidence base underpins the concept that re-engineering of BoNT could be used to enhance the analgesic potential of this neurotoxin, and it is hoped that the first clinical studies examining re-engineered BoNT-A will confirm this potential.","corpus_id":2016651,"score":1},{"doc_id":"20462660","title":"Antipruritic treatment with systemic μ-opioid receptor antagonists: a review.","abstract":"During the past two decades, systemic μ-opioid receptor antagonists (MORA) have been used in the treatment of various forms of chronic pruritus. In a number of case reports, case series, and controlled trials, treatment with MORA has demonstrated considerable antipruritic effects. In double-blind controlled studies, significant antipruritic relief has been achieved by MORA in cholestatic pruritus, chronic urticaria, and atopic dermatitis. In case reports and case series, antipruritic efficacy of MORA has been reported in prurigo nodularis, mycosis fungoides, postburn pruritus, aquagenic pruritus, hydroxyethyl starch-induced pruritus, and pruritus of unknown origin. However, most of the evidence remains anecdotal, the design of these trials varies, and comparison of results is difficult. In this review we aim to present an overview of these reports and to assess the evidence for the antipruritic action of the drugs naloxone, nalmefene, and naltrexone, which are currently in use for the treatment of chronic pruritus of different origins. We will also evaluate recommendations for the use of MORA in daily medical practice.","corpus_id":22721145,"score":1},{"doc_id":"20585245","title":"The role of botulinum toxin in management of pain: an evidence-based review.","abstract":"PURPOSE OF REVIEW: In the present review we discuss the role of botulinum neurotoxins (BoNTs) in the management of different pain conditions, with evidence-based data on the toxins' efficacy on pain and its mechanisms. RECENT FINDINGS: Experimental in-vitro studies have reported promising results of a novel recombinant chimera of BoNT A and E that inhibits the calcitonin gene-related peptide exocytosis from brainstem sensory neurons. Animal studies in neuropathic pain rat models have reported an analgesic effect of BoNT A given after the neuropathic procedure and a bilateral antinociceptive effect to the unilateral noxious stimuli. There is a growing body of evidence that BoNTs are effective in myofascial pain syndrome, neuropathic pain, and joint pain. The pre-existing evidence that BoNTs are ineffective in migraine or other headache disorders has not yet been challenged. In other pain syndromes, studies published in the last review year have not contributed significantly in either demonstrating or invalidating the research that has so far proved inconclusive. SUMMARY: The role of BoNTs in management of pain is not yet well established. Larger studies in neuropathic pain, joint pain, and myofascial pain syndrome are needed to fully ascertain the role for BoNT therapy in those areas.","corpus_id":205448184,"score":1},{"doc_id":"21747148","title":"[Use of botulinum neurotoxin therapy].","abstract":"Botulinum neurotoxins (BoNTs), produced by the gram-positive anaerobic bacterium Clostridium botulinum, act on motor nerve endings and induce muscle relaxation. BoNT type A and B are used as therapeutic agents. Several preparations of BoNT type A are commercially available; Botox®, Dysport®, and Xeomin® are popular. They differ in the manufacturing method used, for example, BoNT consists of neurotoxin and a complex protein, Botox® and Dysport® contain a complex protein, whereas Xeomin® is free from the protein. However, when applied clinically, there is no significant difference in the efficacy and adverse effects between these BoNT products. Intramuscular BoNT injection is widely recognized as a safe and effective treatment for blepharospasm, hemifacial spasm, cervical dystonia, spasticity, squint, migraine, hyperhidrosis, wrinkles (cosmetic purpose), achalasia, hyperactive bladder, etc. BoNT preparations are used in more than 70 countries. In Japan, BoNT is used to treat blepharospasm, hemifacial spasm, cervical dystonia, and spasticity in addition to being used to treat wrinkles. However, its use is not yet widespread in Japan. This article reviews the structure and characteristics of BoNT, and throws light upon the technique of injecting BoNT.","corpus_id":22206368,"score":1},{"doc_id":"22069581","title":"Botulinum neurotoxin for pain management: insights from animal models.","abstract":"The action of botulinum neurotoxins (BoNTs) at the neuromuscular junction has been extensively investigated and knowledge gained in this field laid the foundation for the use of BoNTs in human pathologies characterized by excessive muscle contractions. Although much more is known about the action of BoNTs on the peripheral system, growing evidence has demonstrated several effects also at the central level. Pain conditions, with special regard to neuropathic and intractable pain, are some of the pathological states that have been recently treated with BoNTs with beneficial effects. The knowledge of the action and potentiality of BoNTs utilization against pain, with emphasis for its possible use in modulation and alleviation of chronic pain, still represents an outstanding challenge for experimental research. This review highlights recent findings on the effects of BoNTs in animal pain models.","corpus_id":17691216,"score":1},{"doc_id":"22552262","title":"Botulinum neurotoxin A: a review.","abstract":"Despite its ubiquity in cosmetic circles and broad general awareness, a literature search of botulinum neurotoxin in JPRAS and BJPS yielded a mere 4 articles germane to cosmesis. A pair each detailing its application in masseteric hypertrophy(1,2) and the use of cryoanalgesia.(3,4) Given that botulinum neurotoxin A is the most commonly used cosmetic treatment, with American figures being most accurate,(5) a review of the background, development and scientific evidence would be perhaps useful, if not overdue, as Plastic Surgeons increasingly incorporate non-surgical interventions into their practices as part of a comprehensive facial rejuvenation strategy.","corpus_id":30053642,"score":1},{"doc_id":"23201505","title":"Botulinum neurotoxins: mechanism of action.","abstract":"Botulinum neurotoxins are used clinically for conditions characterized by hyperexcitability of peripheral nerve terminals and hypersecretory syndromes. These neurotoxins are synthesized as precursor proteins with low activity, but their effects are mediated by the active form of the neurotoxin through a multistep mechanism. Following a high-affinity interaction with a protein receptor and polysialogangliosides on the synaptic membrane, botulinum neurotoxins enter the neuron and causes a sustained inhibition of synaptic transmission. The active neurotoxin is part of a high-molecular-weight complex that protects the neurotoxin from proteolytic degradation. Although complexing proteins do not affect diffusion of therapeutic neurotoxin, they may lead to the development of neutralizing antibodies that block responsiveness to it. Nerve terminal intoxication is reversible and its duration varies for different BoNT serotypes. Although it was previously assumed that botulinum neurotoxins exert effects only on the peripheral synapses, such as the neuromuscular junction, there is now substantial evidence that these neurotoxins affect neurotransmission at distal central nervous system sites as well.","corpus_id":1603007,"score":1},{"doc_id":"23202312","title":"Emerging opportunities for serotypes of botulinum neurotoxins.","abstract":"BACKGROUND: Two decades ago, botulinum neurotoxin (BoNT) type A was introduced to the commercial market. Subsequently, the toxin was approved by the FDA to address several neurological syndromes, involving muscle, nerve, and gland hyperactivity. These syndromes have typically been associated with abnormalities in cholinergic transmission. Despite the multiplicity of botulinal serotypes (designated as types A through G), therapeutic preparations are currently only available for BoNT types A and B. However, other BoNT serotypes are under study for possible clinical use and new clinical indications; OBJECTIVE: To review the current research on botulinum neurotoxin serotypes A-G, and to analyze potential applications within basic science and clinical settings; CONCLUSIONS: The increasing understanding of botulinal neurotoxin pathophysiology, including the neurotoxin's effects on specific neuronal populations, will help us in tailoring treatments for specific diagnoses, symptoms and patients. Scientists and clinicians should be aware of the full range of available data involving neurotoxin subtypes A-G.","corpus_id":34629468,"score":1},{"doc_id":"23222890","title":"The brain circuitry mediating antipruritic effects of acupuncture.","abstract":"Itch is an aversive sensory experience and while systemic therapies, such as acupuncture, have shown promise in alleviating itch in patients suffering from chronic itch, their antipruritic mechanisms are unknown. As several lines of evidence implicate brain-focused mechanisms, we applied functional magnetic resonance imaging and our validated temperature-modulation itch model to evaluate the underlying brain circuitry supporting allergen-induced itch reduction in atopic dermatitis patients by acupuncture, antihistamine, and respective placebo treatments. Brain response to allergen itch demonstrated phase dependency. During an increasing itch phase, activation was localized in anterior insula and striatum, regions associated with salience/interoception and motivation processing. Once itch reached peak plateau, robust activation was noted in prefrontal cognitive and premotor areas. Acupuncture reduced itch and itch-evoked activation in the insula, putamen, and premotor and prefrontal cortical areas. Neither itch sensation nor itch-evoked brain response was altered following antihistamine or placebo acupuncture. Greater itch reduction following acupuncture was associated with greater reduction in putamen response, a region implicated in motivation and habitual behavior underlying the urge to scratch, specifically implicating this region in acupuncture's antipruritic effects. Understanding brain circuitry underlying itch reduction following acupuncture and related neuromodulatory therapies will significantly impact the development and applicability of novel therapies to reduce an itch.","corpus_id":8928190,"score":1},{"doc_id":"23375537","title":"Clinical utility of different botulinum neurotoxin preparations.","abstract":"Comparative literature assessing the relative safety and efficacy of different BoNT products is limited. The quantity and quality of data vary by preparation and indication. Clinicians seeking data relevant to the care of patients with specific conditions may find only reports about small numbers of patients with varying symptoms. While a literature search for \"botulinum neurotoxins\" will yield a large number of publications; only a fraction of these meet criteria for an academic evidence-based review. Patients may have been treated with a different BoNT formulation than that with which the physician is familiar, or there may be little or no clinical data on the use of a specific BoNT product for the proposed intervention. This paper is an introduction to a series of papers (which follow) in which an expert panel reviewed the BoNT clinical trial literature in order to provide evidence-based recommendations regarding the clinical use and efficacy of available BoNT preparations for four major therapeutic areas: movement disorders, spasticity, urology, and secretory disorders. Expert opinion is also included to address practical issues where more evidence and further research is needed.","corpus_id":24982165,"score":1},{"doc_id":"23747735","title":"A closer look to botulinum neurotoxin type A-induced analgesia.","abstract":"Chronic pain indicates a type of pain that lasts over time and is accompanied by diagnostic and therapeutic difficulties. It follows that treatment failures are common and patients roam from doctor to doctor in search of an effective care program. So there is an urgent need for long-acting and effective therapeutics to alleviate symptoms of the varied forms of chronic pain. During the past few years, a good success has been achieved with a derivative of a neurotoxin. It has been shown that administration of this toxin can block the release of neurotransmitters and pain mediators. Botulinum neurotoxin type A (BoNT/A) is well known as a treatment for neuromuscular conditions such as dystonia and spasticity. However, the clinical application for BoNT/A has continued to expand. Its analgesic effect has been used in clinical practice with satisfactory results. This review provides an introduction of a hypothesis for the mechanism by which BoNT/A eases chronic pain. It also summarizes the clinical therapeutic effects of BoNT/A in different types of chronic pain and its potential prospects.","corpus_id":22384674,"score":1},{"doc_id":"23980845","title":"Chronic pruritus associated with dermatologic disease in infancy and childhood: update from an interdisciplinary group of dermatologists and pediatricians.","abstract":"An effective treatment strategy for chronic pruritus in children with dermatologic disorders should consider the multidimensional aspects of pruritus, the unique challenges associated with treating pruritic skin disorders in the pediatric population, and evidence-based therapies with demonstrated antipruritic benefits and clinically relevant effects on patient/family quality of life (QoL). The Course of Advanced Learning for the Management of ITch (CALM-IT) Task Force is an interdisciplinary group of experts specializing in core aspects of pruritus treatment, integrating pediatrics, dermatology, psychotherapy, pruritus management, and sleep. CALM-IT recently convened to provide updated guidance on managing chronic pruritus associated with dermatologic diseases in pediatric patients, with a special focus on atopic dermatitis (AD) and chronic spontaneous urticaria (csU). This review highlights the updated concepts and best practices, which were built upon international PRACTALL consensus and modified for children and infants with AD and csU. CALM-IT supports the routine use of basic skin therapy and the escalation of topical medications, according to severity and focused on rapid itch control. Anti-inflammatory agents should be appropriate for infants and children (i.e., with an optimized therapeutic index) and have proven antipruritic properties, such as those demonstrated by methylprednisolone aceponate. New experimental findings do not support the use of non-sedating oral antihistamines as adjuvant antipruritic therapy for AD. In csU, oral H1 -antihistamine use is justified, consistent with the distinct pathophysiologic mechanisms of itch underlying AD and csU. All encompassing QoL assessments should consider the burden of both patient and caregiver and should address outstanding unmet clinical needs of pediatric patients. Future research areas include integrated QoL assessments and multidisciplinary treatment programs with pediatric-targeted pruritic therapies providing rapid itch control.","corpus_id":189736,"score":1},{"doc_id":"24576870","title":"More than at the neuromuscular synapse: actions of botulinum neurotoxin A in the central nervous system.","abstract":"Botulinum neurotoxin type A (BoNT/A) is a metalloprotease that produces a sustained yet transitory blockade of transmitter release from peripheral nerve terminals. Local delivery of this neurotoxin is successfully employed in clinical practice to reduce muscle hyperactivity such as in spasticity and dystonia, and to relieve pain with long-lasting therapeutic effects. However, not all BoNT/A effects can be explained by an action at peripheral nerve terminals. Indeed, it appears that BoNT/A is endowed with trafficking properties similar to the parental tetanus neurotoxin and thus be able to directly affect the CNS. In this review, we present and discuss novel compelling evidence for a direct central effect of BoNT/A in both dorsal and ventral horns of the animal and human spinal cord after peripheral injection of the neurotoxin, with important consequences on pain and motor control. This new knowledge is expected to radically change the approach to the use of BoNT/A in the future. As BoNT/A central action appears to also contribute to functional improvement, for instance in human spastic gait, the challenge will be to develop new subtypes or BoNT derivatives with deliberate, cell-specific central effects in order to fully exploit the spectrum of BoNT/A therapeutic activity.","corpus_id":5237512,"score":1},{"doc_id":"25842964","title":"Novel therapeutic uses and formulations of botulinum neurotoxins: a patent review (2012 - 2014).","abstract":"INTRODUCTION: Botulinum neurotoxins (BoNTs) are among the most toxic of known biological molecules and function as acetylcholine release inhibitors and neuromuscular blocking agents. Paradoxically, these properties also make them valuable therapeutic agents for the treatment of movement disorders, urological conditions and hypersecretory disorders. Greater understanding of their molecular mechanism of action and advances in protein engineering has led to significant efforts to improve and expand their function with a view towards broadening their therapeutic potential. AREAS COVERED: Searches of Espacenet and Google Patent have revealed a number of patents related to BoNTs. This review will focus on novel therapeutic uses and formulations disclosed during 2012 - 2014. The seven patents discussed will include nanoformulations of FDA-approved BoNTs, additional BoNT subtypes and novel BoNT variants and chimeras created through protein engineering. Supporting patents and related publications are also briefly discussed. EXPERT OPINION: The clinical and commercial success of BoNTs has prompted investigation into novel BoNTs or BoNT-mediated chimeras with promising in vitro results. Distinct strategies including the use of nanoformulations and targeted delivery have been implemented to identify new indication and improved functionality. Greater understanding of their systemic exposure, efficacy and safety profiles will be required for further development.","corpus_id":46238953,"score":1},{"doc_id":"26169827","title":"Botulinum neurotoxin type A: Actions beyond SNAP-25?","abstract":"Botulinum neurotoxin type A (BoNT/A), the most potent toxin known in nature which causes botulism, is a commonly used therapeutic protein. It prevents synaptic vesicle neuroexocytosis by proteolytic cleavage of synaptosomal-associated protein of 25 kDa (SNAP-25). It is widely believed that BoNT/A therapeutic or toxic actions are exclusively mediated by SNAP-25 cleavage. On the other hand, in vitro and in vivo findings suggest that several BoNT/A actions related to neuroexocytosis, cell cycle and apoptosis, neuritogenesis and gene expression are not necessarily mediated by this widely accepted mechanism of action. In present review we summarize the literature evidence which point to the existence of unknown BoNT/A molecular target(s) and modulation of unknown signaling pathways. The effects of BoNT/A apparently independent of SNAP-25 occur at similar doses/concentrations known to induce SNAP-25 cleavage and prevention of neurotransmitter release. Accordingly, these effects might be pharmacologically significant. Potentially the most interesting are observations of antimitotic and antitumor activity of BoNT/A. However, the exact mechanisms require further studies.","corpus_id":21369081,"score":1},{"doc_id":"26260691","title":"Clinical differences between botulinum neurotoxin type A and B.","abstract":"In humans, the therapeutic use of botulinum neurotoxin A (BoNT/A) is well recognized and continuously expanding. Four BoNTs are widely available for clinical practice: three are serotype A and one is serotype B: onabotulinumtoxinA (A/Ona), abobotulinumtoxinA (A/Abo) and incobotulinumtoxinA (A/Inco), rimabotulinumtoxinB (B/Rima). A/Abo, A/Inco, A/Ona and B/Rima are all licensed worldwide for cervical dystonia. In addition, the three BoNT/A products are approved for blepharospasm and focal dystonias, spasticity, hemifacial spasm, hyperhidrosis and facial lines, with remarkable regional differences. These toxin brands differ for specific activity, packaging, constituents, excipient, and storage. Comparative literature assessing the relative safety and efficacy of different BoNT products is limited, most data come from reports on small samples, and only a few studies meet criteria of evidence-based medicine. One study compared the effects of BoNT/A and BoNT/B on muscle activity of healthy volunteers, showing similar neurophysiological effects with a dose ratio of 1:100. In cervical dystonia, when comparing the effects of BoNT/A and BoNT/B, results are more variable, some studies reporting roughly similar peak effect and overall duration (at a ratio of 1:66, others reporting substantially shorter duration of BoNT/B than BoNT/A (at a ratio 1/24). Although the results of clinical studies are difficult to compare for methodological differences (dose ratio, study design, outcome measures), it is widely accepted that: BoNT/B is clinically effective using appropriate doses as BoNT/A (1:40-50), injections are generally more painful, in most of the studies on muscular conditions, efficacy is shorter, and immunogenicity higher. Since the earliest clinical trials, it has been reported that autonomic side effects are more frequent after BoNT/B injections, and this observation encouraged the use of BoNT/B for sialorrhea, hyperhidrosis and other non-motor symptoms. In these indications the efficacy of toxins A and B are comparable and dose ratio is 1:25-30.","corpus_id":664189,"score":1},{"doc_id":"26745805","title":"Structural and Functional Interactions between Transient Receptor Potential Vanilloid Subfamily 1 and Botulinum Neurotoxin Serotype A.","abstract":"BACKGROUND: Botulinum neurotoxins are produced by Clostridium botulinum bacteria. There are eight serologically distinct botulinum neurotoxin isoforms (serotypes A-H). Currently, botulinum neurotoxin serotype A (BoNT⁄A) is commonly used for the treatment of many disorders, such as hyperactive musculoskeletal disorders, dystonia, and pain. However, the effectiveness of BoNT⁄A for pain alleviation and the mechanisms that mediate the analgesic effects of BoNT⁄A remain unclear. To define the antinociceptive mechanisms by which BoNT/A functions, the interactions between BoNT⁄A and the transient receptor potential vanilloid subfamily 1 (TRPV1) were investigated using immunofluorescence, co-immunoprecipitation, and western blot analysis in primary mouse embryonic dorsal root ganglion neuronal cultures. RESULTS: 1) Three-week-old cultured dorsal root ganglion neurons highly expressed transient TRPV1, synaptic vesicle 2A (SV2A) and synaptosomal-associated protein 25 (SNAP-25). SV2A and SNAP-25 are the binding receptor and target protein, respectively, of BoNT⁄A. 2) TRPV1 colocalized with both BoNT⁄A and cleaved SNAP-25 when BoNT⁄A was added to dorsal root ganglia neuronal cultures. 3) After 24 hours of BoNT⁄A treatment (1 nmol⁄l), both TRPV1 and BoNT⁄A positive bands were detected in western blots of immunoprecipitated pellets. 4) Blocking TRPV1 with a specific antibody decreased the cleavage of SNAP-25 by BoNT⁄A. CONCLUSION: BoNT/A interacts with TRPV1 both structurally and functionally in cultured mouse embryonic dorsal root ganglion neurons. These results suggest that an alternative mechanism is used by BoNT⁄A to mediate pain relief.","corpus_id":1768054,"score":1},{"doc_id":"28324318","title":"Botulinum neurotoxin type A for the treatment of pain: not just in migraine and trigeminal neuralgia.","abstract":"BACKGROUND: Despite their huge epidemiological impact, primary headaches, trigeminal neuralgia and other chronic pain conditions still receive suboptimal medical approach, even in developed countries. The limited efficacy of current pain-killers and prophylactic treatments stands among the main reasons for this phenomenon. Botulinum neurotoxin (BoNT) represents a well-established and licensed treatment for chronic migraine, but also an emerging treatment for other types of primary headache, trigeminal neuralgia, neuropathic pain, and an increasing number of pain conditions. METHODS: We searched and critically reviewed evidence for the efficacy of BoNT for the treatment of chronic pain. RESULTS: Meta-analyses and randomized controlled trials (RCTs) suggest that BoNT potentially represents a multi-purpose drug for the treatment of pain in several disorders due to a favorable safety profile and a long-lasting relief after a single injection. CONCLUSIONS: BoNT is an emerging treatment in different pain conditions. Future RCTs should explore the use of BoNT injection therapy combined with systemic drugs and/or physical therapies as new pain treatment strategies.","corpus_id":10989660,"score":1},{"doc_id":"28770820","title":"Identification and characterization of a novel botulinum neurotoxin.","abstract":"Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Remarkably, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5 and Ykt6. To validate its activity, a small amount of full-length BoNT/X was assembled by linking two non-toxic fragments using a transpeptidase (sortase). Assembled BoNT/X cleaves VAMP2 and VAMP4 in cultured neurons and causes flaccid paralysis in mice. Thus, BoNT/X is a novel BoNT with a unique substrate profile. Its discovery posts a challenge to develop effective countermeasures, provides a novel tool for studying intracellular membrane trafficking, and presents a new potential therapeutic toxin for modulating secretions in cells.","corpus_id":-1,"score":1},{"doc_id":"29111119","title":"Direct central nervous system effects of botulinum neurotoxin.","abstract":"Local intramuscular injections of botulinum neurotoxin type A (BoNT/A) are effective in the treatment of focal dystonias, muscle spasms, and spasticity. However, not all clinical effects of BoNT/A may be explained by its action at peripheral nerve terminals. For example, the therapeutic benefit may exceed the duration of the peripheral neuroparalysis induced by the neurotoxin. In cellular and animal models, evidence demonstrates retrograde transport of catalytically active BoNT/A in projection neurons. This process of long-range trafficking is followed by transcytosis and action at second-order synapses. In humans, several physiological changes have been described following intramuscular delivery of BoNT/A. In particular, clinical studies have documented a decrease in Renshaw cell-mediated inhibition (i.e., recurrent inhibition), which may be important therapeutically for normalizing uncoordinated movements and overflow of muscle activity. In this review, we present data obtained in animal and experimental models that support direct central actions of BoNT/A mediated via retrograde axonal trafficking. We also discuss the reorganization of central circuitry induced by BoNT/A in patients, and the potential contribution of these effects to the therapeutic efficacy of the neurotoxin.","corpus_id":5009015,"score":1},{"doc_id":"29456150","title":"Antidepressants as antipruritic agents: A review.","abstract":"Pruritus is a concomitant symptom of various underlying disorders viz. dermatological, systemic and psychiatric disorders that provoke the person to scratch the skin. Many natural as well as, antipruritic therapies are usually practiced in the treatment of pruritus including general preventive measures, topical therapies such as cooling agents, antihistamines, anesthetics, capsaicin, corticosteroids, immunomodulators and; systemic therapies including administration of antihistamines, opioid antagonists/agonists, antiepileptic drugs/neuroleptics (e.g., gabapentin and pregabalin), antidepressants (e.g., doxepin, amitriptyline, paroxetine, fluvoxamine, sertraline, escitalopram and mirtazapine) (Patel and Yosipovitch, 2010; Reich et al., 2011; Martín and Padilla, 2015; Eskeland et al., 2016). Topical therapies are the mainstay of treatment of delicate and localized pruritus while other systemic drug therapies are used to treat stern and generalized pruritus. The reported antipruritic activity of some antidepressant drugs has intrigued this review to focus on the types of pruritus, pruritus mechanism, the antipruritic mechanism of antidepressants and to comprehend the role of antidepressants in the management of pruritus.","corpus_id":3380505,"score":1},{"doc_id":"18322639","title":"The use of botulinum neurotoxin type A (BoNTA) in urology.","abstract":"The use of Botulinum neurotoxin type A (BoNT/A) in the lower urinary tract was pioneered as early as 20 years ago with injections into the urethral sphincter reducing bladder voiding pressures, urethral pressures, and post-void residual urine. Over the past 9 years, the use of BoNT/A has revolutionised the treatment of intractable symptoms associated with the neurogenic or idiopathic overactive bladder, both in adults and children. The duration of clinical improvement is 6-11 months, is accompanied by significant amelioration of patients' quality of life and repeat bladder treatments appear to have sustained effects. Despite evidence for an effect on the afferent pathways, its mode of action in the human bladder remains largely unknown. The use of BoNT/A has also expanded into the painful bladder syndrome and in benign prostatic diseases, with promising preliminary results. This review aims to provide an insight of the use of BoNT/A in the lower urinary tract, addressing issues such as treatment outcomes and safety, mechanisms of action and potential for future research.","corpus_id":6972948,"score":0},{"doc_id":"18538461","title":"Effects of purification on the bioavailability of botulinum neurotoxin type A.","abstract":"Botulinum neurotoxins (BoNTs) are among the most potent biological toxins for humans. They are primarily produced by the gram-positive, anaerobic spore-forming bacterium, Clostridium botulinum. In bacterial cultures, secreted BoNTs are associated with non-toxic accessory proteins forming large complexes. Neurotoxin-associated proteins have been shown to play an important role in the oral toxicity of BoNTs by protecting them from degradation and digestion by gastric acid and enzymes. Most toxicity studies using BoNTs have been performed using highly purified toxin. In this study, the toxicities of purified and crude BoNT/A toxin preparations were compared. Protein components secreted into culture supernatants along with BoNT/A were identified by mass spectrometry and the contribution of extra proteins found in the soluble crude toxin extracts to the toxicity of BoNTs was determined in mouse models of oral and parenteral botulinum intoxication. Analysis of crude toxin composition permitted assessment of the impact of accessory proteins on the oral bioavailability of BoNT/A toxin in food matrices.","corpus_id":34021406,"score":0},{"doc_id":"19110753","title":"[Use of botulinum neurotoxin for spasticity].","abstract":"Spasticity is characterized by increased muscle resistance. It is usually associated with muscle weakness or poor motor control. This condition not only reduces activities of daily living (ADLs), but also interferes personal hygiere and causes caregiuer's difficulty. The use of botulinum neurotoxin (BoNT) intramuscular injections is a simple and effective therapy for spasticity. The use of BoNT to treat adult patients with spasticity was first reported in 1989, since then, using the neurotoxin to treat spasticity became popular in some European countries. Now in Japan, BoNT can be used to treat only torticollis, blepharospasm and hemifacial spasm because of the legal limitation on its use. However, clinical research on the use of BoNT in spasticity caused by stroke is presently underway, and an adaptation of the toxin may be available in the near future. This article reviews the characteristics of BoNT and the techniques for injecting this neurotoxin.","corpus_id":31781392,"score":0},{"doc_id":"19118561","title":"Domain organization in Clostridium botulinum neurotoxin type E is unique: its implication in faster translocation.","abstract":"Clostridium botulinum produces seven antigenically distinct neurotoxins [C. botulinum neurotoxins (BoNTs) A-G] sharing a significant sequence homology. Based on sequence and functional similarity, it was believed that their three-dimensional structures will also be similar. Indeed, the crystal structures of BoNTs A and B exhibit similar fold and domain association where the translocation domain is flanked on either side by binding and catalytic domains. Here, we report the crystal structure of BoNT E holotoxin and show that the domain association is different and unique, although the individual domains are similar to those of BoNTs A and B. In BoNT E, both the binding domain and the catalytic domain are on the same side of the translocation domain, and all three have mutual interfaces. This unique association may have an effect on the rate of translocation, with the molecule strategically positioned in the vesicle for quick entry into cytosol. Botulism, the disease caused by BoNT E, sets in faster than any other serotype because of its speedy internalization and translocation, and the present structure offers a credible explanation. We propose that the translocation domain in other BoNTs follows a two-step process to attain translocation-competent conformation as in BoNT E. We also suggest that this translocation-competent conformation in BoNT E is a probable reason for its faster toxic rate compared to BoNT A. However, this needs further experimental elucidation.","corpus_id":26420703,"score":0},{"doc_id":"19327377","title":"Investigations into small molecule non-peptidic inhibitors of the botulinum neurotoxins.","abstract":"Botulinum neurotoxins (BoNTs), proteins secreted by the bacteria genus Clostridium, represent a group of extremely lethal toxins and a potential bioterrorism threat. As the current therapeutic options are of a predominantly prophylactic nature and cannot be used en masse, new strategies and ultimately potential treatments are desperately needed to combat any widespread release of these neurotoxins. In these regards, our laboratory has been working on developing new alternatives to treat botulinum intoxication through the development of inhibitors of the light chain proteases, the etiological agent which causes BoNT intoxication. Such a strategy has required the construction of two high-throughput screens and small molecule non-peptidic libraries; excitingly, inhibitors of the BoNT/A protease have been uncovered and are being optimized via structure activity relationship studies.","corpus_id":13790000,"score":0},{"doc_id":"20552020","title":"Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum.","abstract":"BACKGROUND: Clostridium botulinum produces seven distinct serotypes of botulinum neurotoxins (BoNTs). The genes encoding different subtype neurotoxins of serotypes A, B, F and several dual neurotoxin-producing strains have been shown to reside on plasmids, suggesting that intra- and interspecies transfer of BoNT-encoding plasmids may occur. The objective of the present study was to determine whether these C. botulinum BoNT-encoding plasmids are conjugative. METHODOLOGY/PRINCIPAL FINDINGS: C. botulinum BoNT-encoding plasmids pBotCDC-A3 (strain CDC-A3), pCLJ (strain 657Ba) and pCLL (strain Eklund 17B) were tagged with the erythromycin resistance marker (Erm) using the ClosTron mutagenesis system by inserting a group II intron into the neurotoxin genes carried on these plasmids. Transfer of the tagged plasmids from the donor strains CDC-A3, 657Ba and Eklund 17B to tetracycline-resistant recipient C. botulinum strains was evaluated in mating experiments. Erythromycin and tetracycline resistant transconjugants were isolated from donor:recipient mating pairs tested. Transfer of the plasmids to the transconjugants was confirmed by pulsed-field gel electrophoresis (PFGE) and Southern hybridizations. Transfer required cell-to-cell contact and was DNase resistant. This indicates that transfer of these plasmids occurs via a conjugation mechanism. CONCLUSIONS/SIGNIFICANCE: This is the first evidence supporting conjugal transfer of native botulinum neurotoxin-encoding plasmids in C. botulinum, and provides a probable mechanism for the lateral distribution of BoNT-encoding plasmids to other C. botulinum strains. The potential transfer of C. botulinum BoNT-encoding plasmids to other bacterial hosts in the environment or within the human intestine is of great concern for human pathogenicity and necessitates further characterization of these plasmids.","corpus_id":16361363,"score":0},{"doc_id":"20600570","title":"Development and preclinical evaluation of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A.","abstract":"Concern about the malicious applications of botulinum neurotoxin has highlighted the need for a new generation of safe and highly potent antitoxins. In this study, we developed and evaluated the preclinical pharmacology and safety of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A (BoNT/A). As an alternative to formalin-inactivated toxoid, the recombinant Hc domain of botulinum neurotoxin serotype A (rAHc) was used to immunize horses, and the IgGs from the hyperimmune sera were digested to obtain F(ab')₂ antitoxin. The protective effect of the new F(ab')₂ antitoxin against BoNT/A was determined both in vitro and in vivo. The results showed that the F(ab')₂ antitoxin could prevent botulism in mice challenged with BoNT/A and effectively delayed progression of paralysis from botulism in the therapeutic setting. The preclinical safety of the new F(ab')₂ antitoxin was also evaluated, and it showed neither harmful effects on vital functions nor adverse effects such as acute toxicity, or immunological reactions in mice and dogs. Thus, our results provide valuable experimental data for this new antitoxin as a potential candidate for treatment of botulism caused by BoNT/A, and our findings support the safety of the new F(ab')₂ antitoxin for clinical use. Our study further demonstrates the proof of concept for development of a similar strategy for obtaining potent antitoxin against other BoNT serotypes.","corpus_id":22581463,"score":0},{"doc_id":"20731382","title":"Identification of a unique ganglioside binding loop within botulinum neurotoxins C and D-SA .","abstract":"The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A-G) based on a lack of cross antiserum neutralization. BoNTs utilize gangliosides as components of the host receptors for binding and entry into neurons. Members of BoNT/C and BoNT/D serotypes include mosaic toxins that are organized in D/C and C/D toxins. One D/C mosaic toxin, BoNT/D-South Africa (BoNT/D-SA), was not fully neutralized by immunization with BoNT serotype C or D, which stimulated this study. Here the crystal structures of the receptor binding domains of BoNT/C, BoNT/D, and BoNT/D-SA are presented. Biochemical and cell binding studies show that BoNT/C and BoNT/D-SA possess unique mechanisms for ganglioside binding. These studies provide new information about how the BoNTs can enter host cells as well as a basis for understanding the immunological diversity of these neurotoxins.","corpus_id":23554795,"score":0},{"doc_id":"21053906","title":"Clostridium botulinum neurotoxin type B is heat-stable in milk and not inactivated by pasteurization.","abstract":"Foodborne botulism is caused by the ingestion of foods containing botulinum neurotoxins (BoNTs). To study the heat stability of Clostridium botulinum neurotoxins, we needed to measure and compare the activity of botulinum neurotoxins, serotypes A and B, under various pasteurization conditions. Currently, the only accepted assay to detect active C. botulinum neurotoxin is an in vivo mouse bioassay, which raises ethical concerns with regard to the use of experimental animals. In this study, noninvasive methods were used to simultaneously detect and distinguish between active BoNT serotypes A and B in one reaction and sample. We developed an enzymatic activity assay employing internally quenched fluorogenic peptides corresponding to SNAP-25, for BoNT-A, and VAMP2, for BoNT-B, as an alternative method to the mouse bioassay. Because each peptide is labeled with different fluorophores, we were able to distinguish between these two toxins. We used this method to analyze the heat stability of BoNT-A and BoNT-B. This study reports that conventional milk pasteurization (63 °C, 30 min) inactivated BoNT serotype A; however, serotype B is heat-stable in milk and not inactivated by pasteurization. Using this activity assay, we also showed that the commonly used food processes such as acidity and pasteurization, which are known to inhibit C. botulinum growth and toxin production, are more effective in inactivating BoNT serotype A than serotype B when conventional pasteurization (63 °C, 30 min) is used.","corpus_id":5450345,"score":0},{"doc_id":"22676403","title":"Botulinum neurotoxin: where are we with detection technologies?","abstract":"Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current \"gold standard\". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.","corpus_id":19534609,"score":0},{"doc_id":"22882378","title":"Is there a direct antimicrobial effect of botulinum neurotoxin type A?","abstract":"UNLABELLED: Study Type--Therapy (case series) Level of Evidence 4. What's known on the subject? and What does the study add? Several studies describe a reduction of symptomatic urinary tract infections in patients with neurogenic detrusor overactivity after intradetrusor injections of botulinum neurotoxin A (BoNT/A). It was, however, unclear if a direct antibacterial effect of BoNT/A plays a role in this clinical observation. This is the first study to investigate a potential antibacterial effect of two frequently used BoNT/A formulations (i.e. Botox® and Dysport®), providing evidence that BoNT/A does not exert an antibacterial effect on lower urinary tract pathogens. OBJECTIVE: • To determine a potential direct antimicrobial effect of botulinum neurotoxin type A (BoNT/A). MATERIALS AND METHODS: • A prospective study was carried out using onabotulinumtoxin A (Botox®) and abobotulinumtoxin A (Dypsort®) in agar diffusion and broth microdilution assays with various clinical urinary tract isolates (Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca and Bacillus subtilis). • Inhibition zones (mm) of bacteria around a disc containing 20 µL saline with 4 IU of Botox® were measured in the agar diffusion assay. • Minimal inhibitory concentrations (MICs, IU/mL) of both toxins for all bacteria were determined in the broth microdilution assay after overnight incubation at 35 °C. RESULTS: • There was no inhibition zone in the agar diffusion assays with any bacterial strain. • The microdilution test using Botox® and Dysport® showed bacterial growth in all dilutions, i.e. MICs > 20 and >100 IU/mL for Botox® and Dysport®, respectively. CONCLUSIONS: • BoNT/A has no direct antimicrobial effect. • The reduced frequency of symptomatic urinary tract infections (sUTIs) in patients with neurogenic detrusor overactivity (NDO) after BoNT/A intradetrusor injections seems to be caused by different indirect mechanisms, which are still not completely understood.","corpus_id":20453964,"score":0},{"doc_id":"23239348","title":"Uptake of botulinum neurotoxin in the intestine.","abstract":"Foodborne and intestinal botulism are the most common forms of human botulism; both result from the absorption of botulinum neurotoxin (BoNT) from the digestive tract into the circulation. BoNT is a large protein toxin (approximately 150 kDa), but it is able to pass through the epithelial barrier in the digestive tract. Recent cellular and molecular biology studies have begun to unravel the mechanisms by which this large protein toxin crosses the intestinal epithelial barrier. This review provides an overview of current knowledge relating to the absorption of botulinum toxins (BoNT and BoNT complex) from the gastrointestinal tract, with particular emphasis on the interaction of these toxins with the intestinal epithelial barrier.","corpus_id":21230102,"score":0},{"doc_id":"23239356","title":"Complexity of botulinum neurotoxins: challenges for detection technology.","abstract":"The detection of botulinum neurotoxins (BoNT) is extremely challenging due to their high toxicity and the multiple BoNT variants. To date, seven serotypes with more than 30 subtypes have been described, and even more subtypes are expected to be discovered. The fact that the BoNT molecules are released as large complexes of different size and composition adds further complexity to the issue. Currently, in the diagnostics of botulism, the mouse bioassay (MBA) is still considered as gold standard for the detection of BoNT in complex sample materials. Over the years, different functional, immunological, and spectrometric assays or combinations thereof have been developed, supplemented by DNA-based assays for the detection of the organism. In this review, advantages and limitations of the current technologies will be discussed, highlighting some of the intricacies of real sample analysis.","corpus_id":22955562,"score":0},{"doc_id":"25564463","title":"On botulinum neurotoxin variability.","abstract":"The rapidly growing number of botulinum neurotoxin sequences poses the problem of the possible evolutionary significance of the variability of these superpotent neurotoxins for toxin-producing Clostridium species. To progress in the understanding of this remarkable phenomenon, we suggest that researchers should (i) abandon an anthropocentric view of these neurotoxins as human botulism-causing agents or as human therapeutics, (ii) begin to investigate in depth the role of botulinum neurotoxins in animal botulism in the wilderness, and (iii) devote large efforts to next-generation sequencing of soil samples to identify novel botulinum neurotoxins. In order to compare the fitness of the different toxins, we suggest that assays of all the steps from toxin production to animal death should be performed.","corpus_id":6983148,"score":0},{"doc_id":"26350137","title":"New Elements To Consider When Modeling the Hazards Associated with Botulinum Neurotoxin in Food.","abstract":"Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most potent biological substances known to mankind. BoNTs are the agents responsible for botulism, a rare condition affecting the neuromuscular junction and causing a spectrum of diseases ranging from mild cranial nerve palsies to acute respiratory failure and death. BoNTs are a potential biowarfare threat and a public health hazard, since outbreaks of foodborne botulism are caused by the ingestion of preformed BoNTs in food. Currently, mathematical models relating to the hazards associated with C. botulinum, which are largely empirical, make major contributions to botulinum risk assessment. Evaluated using statistical techniques, these models simulate the response of the bacterium to environmental conditions. Though empirical models have been successfully incorporated into risk assessments to support food safety decision making, this process includes significant uncertainties so that relevant decision making is frequently conservative and inflexible. Progression involves encoding into the models cellular processes at a molecular level, especially the details of the genetic and molecular machinery. This addition drives the connection between biological mechanisms and botulism risk assessment and hazard management strategies. This review brings together elements currently described in the literature that will be useful in building quantitative models of C. botulinum neurotoxin production. Subsequently, it outlines how the established form of modeling could be extended to include these new elements. Ultimately, this can offer further contributions to risk assessments to support food safety decision making.","corpus_id":3879734,"score":0},{"doc_id":"26368006","title":"Genetic diversity within the botulinum neurotoxin-producing bacteria and their neurotoxins.","abstract":"The recent availability of multiple Clostridium botulinum genomic sequences has initiated a new genomics era that strengthens our understanding of the bacterial species that produce botulinum neurotoxins (BoNTs). Analysis of the genomes has reinforced the historical Group I-VI designations and provided evidence that the bont genes can be located within the chromosome, phage or plasmids. The sequences provide the opportunity to examine closely the variation among the toxin genes, the composition and organization of the toxin complex, the regions flanking the toxin complex and the location of the toxin within different bacterial strains. These comparisons provide evidence of horizontal gene transfer and site-specific insertion and recombination events that have contributed to the variation observed among the neurotoxins. Here, examples that have contributed to the variation observed in serotypes A-H strains are presented to illustrate the mechanisms that have contributed to their variation.","corpus_id":25495666,"score":0},{"doc_id":"27130373","title":"Serological identification of botulinum neurotoxins: A critical overview.","abstract":"The reasons that gave rise to the controversy over the serological method (SerM) and genetics regarding the identification of an alleged novel botulinum neurotoxin (BoNT), type H, have been concisely examined. This discussion will remain opened inasmuch as the SerM is not performed according to the recommended procedures outlined in this overview and thoroughly discussed on previous publications. If correctly performed and interpreted, the SerM will keep its preeminence in the identification, typing and taxonomy of BoNTs.","corpus_id":30112372,"score":0},{"doc_id":"27153088","title":"Zebrafish Sensitivity to Botulinum Neurotoxins.","abstract":"Botulinum neurotoxins (BoNT) are the most potent known toxins. The mouse LD50 assay is the gold standard for testing BoNT potency, but is not sensitive enough to detect the extremely low levels of neurotoxin that may be present in the serum of sensitive animal species that are showing the effects of BoNT toxicity, such as channel catfish affected by visceral toxicosis of catfish. Since zebrafish are an important animal model for diverse biomedical and basic research, they are readily available and have defined genetic lines that facilitate reproducibility. This makes them attractive for use as an alternative bioassay organism. The utility of zebrafish as a bioassay model organism for BoNT was investigated. The 96 h median immobilizing doses of BoNT/A, BoNT/C, BoNT/E, and BoNT/F for adult male Tübingen strain zebrafish (0.32 g mean weight) at 25 °C were 16.31, 124.6, 4.7, and 0.61 picograms (pg)/fish, respectively. These findings support the use of the zebrafish-based bioassays for evaluating the presence of BoNT/A, BoNT/E, and BoNT/F. Evaluating the basis of the relatively high resistance of zebrafish to BoNT/C and the extreme sensitivity to BoNT/F may reveal unique functional patterns to the action of these neurotoxins.","corpus_id":14507697,"score":0},{"doc_id":"28271909","title":"Challenges in searching for therapeutics against Botulinum Neurotoxins.","abstract":"INTRODUCTION: Botulinum neurotoxins (BoNTs) are the most potent toxins known. BoNTs are responsible for botulism, a deadly neuroparalytic syndrome caused by the inactivation of neurotransmitter release at peripheral nerve terminals. Thanks to their specificity and potency, BoNTs are both considered potential bio-weapons and therapeutics of choice for a variety of medical syndromes. Several variants of BoNTs have been identified with individual biological properties and little antigenic relation. This expands greatly the potential of BoNTs as therapeutics but poses a major safety problem, increasing the need for finding appropriate antidotes. Areas covered: The authors describe the multi-step molecular mechanism through which BoNTs enter nerve terminals and discuss the many levels at which the toxins can be inhibited. They review the outcomes of the different strategies adopted to limit neurotoxicity and counter intoxication. Potential new targets arising from the last discoveries of the mechanism of action and the approaches to promote neuromuscular junction recovery are also discussed. Expert opinion: Current drug discovery efforts have mainly focused on BoNT type A and addressed primarily light chain proteolytic activity. Development of pan-BoNT inhibitors acting independently of BoNT immunological properties and targeting a common step of the intoxication process should be encouraged.","corpus_id":27539897,"score":0},{"doc_id":"28843941","title":"Botulinum Neurotoxin and Its Potential Role in the Treatment of Erectile Dysfunction.","abstract":"INTRODUCTION: Botulinum toxin type A (BoNT-A) has been used to treat several striated and smooth muscle disorders. During the past year, human and animal studies conducted in Egypt and Canada by two different groups of investigators have suggested a possible role for the intracavernosal injection of BoNT-A in the treatment of erectile dysfunction (ED). AIM: To discuss BoNT-A and its current medical uses, the rationale for its new potential use in the treatment of ED, and the available evidence and concerns. METHODS: A literature search was conducted. This review was based on the available studies presented at the European Society for Sexual Medicine, Sexual Medicine Society of North America, and International Society for Sexual Medicine meetings in 2016 by the two groups. MAIN OUTCOME MEASURES: Sinusoidal diameter; penile color Doppler study; Erection Hardness Score; Sexual Health Inventory for Men questionnaire; and Sexual Encounter Profile questions 2 and 3. RESULTS: Two human studies conducted by the authors and two animal studies (one from the authors' group and one from Canada) were reviewed. These seemed to suggest generally favorable outcomes with the use of BoNT-A in the treatment of ED. CONCLUSION: BoNT-A could be a potential therapy for ED. In addition to the findings of the three pilot studies, larger multicenter trials need to be conducted to further explore the true therapeutic efficacy and clinical safety of BoNT-A in the treatment of ED. Ghanem H, Raheem AA, AbdelRahman IFS, et al. Botulinum Neurotoxin and Its Potential Role in the Treatment of Erectile Dysfunction. Sex Med Rev 2017;X:XXX-XXX.","corpus_id":20815518,"score":0},{"doc_id":"29447689","title":"Botulinum Neurotoxins: Still a Privilege of Clostridia?","abstract":"Botulinum neurotoxins (BoNTs) are potent bacterial toxins mostly produced by genetically diverse clostridial strains. Recently, BoNT variants have been reported in non-clostridial strains. In this issue of Cell Host & Microbe, Zhang et al. (2018) describe a novel BoNT in Entecoccus faecium.","corpus_id":3511791,"score":0}],"string":"[\n {\n \"doc_id\": \"18357364\",\n \"title\": \"Novel agents for intractable itch.\",\n \"abstract\": \"There exists a multitude of medical conditions that cause intractable itch, or pruritus. The successful management of this symptom depends explicitly on establishing the underlying cause. Studies have shown that drugs not traditionally used in the treatment of cutaneous disorders, such as opiate receptor antagonists, antidepressants, and antiepileptics, can provide symptomatic relief of intractable itch. These novel antipruritic agents will be explored in this review.\",\n \"corpus_id\": 25646667,\n \"score\": 2\n },\n {\n \"doc_id\": \"18836352\",\n \"title\": \"Relief of intractable pruritus after administration of botulinum toxin A (botox): a case report.\",\n \"abstract\": \"A 55-year-old woman sought assistance for intractable pruritus of 6-year duration, affecting the right side of the forehead. She had surgery on the right frontal area for treatment of a frontal sinus condition, a few years earlier. The itch failed to respond to a variety of medical interventions, including oral antipruritic agents and local injections of anesthetic. Administration of botulinum toxin A (Allergan Inc, Irvine, CA) into the pruritic area resulted in a significant relief of pruritus in this patient.\",\n \"corpus_id\": 27104400,\n \"score\": 2\n },\n {\n \"doc_id\": \"19887944\",\n \"title\": \"Botulinum neurotoxin A for benign prostatic hyperplasia.\",\n \"abstract\": \"PURPOSE OF REVIEW: The injection of botulinum neurotoxin A (BoNT-A) into the prostate represents an alternative, minimal invasive treatment for lower urinary tract symptoms suggestive of benign prostatic hyperplasia (BPH), which gained the interest of urologists during the last years, although it is not yet licensed. The purpose of this review is to summarize the mechanisms through which BoNT-A could inhibit the progression of BPH and eliminate the lower urinary tract symptoms according to the findings of animal studies. Furthermore, we review clinical studies to report the efficacy and safety of intraprostatic BoNT-A injection according to various injection protocols. RECENT FINDINGS: The experimental studies report induced relaxation of the prostate, atrophy, and reduction in its size through inhibition of the trophic effect of the autonomic system on the prostate gland. Also, a possible mechanism of reduction in lower urinary tract symptoms might take place through inhibition of sensory afferents from the prostate to the spinal cord. Clinical studies report symptomatic relief and improvement in the measured parameters during the follow-up period, whereas local or systematic side-effects are rare. SUMMARY: We should recognize that, at present, this therapy is still experimental. Although the results of the clinical studies are encouraging, the level of evidence is low. Clearly, we need large-scale, clinical, placebo-controlled, randomized studies, including long-term surveillance to document the evidence of this therapy and, eventually, to register BoNT-A for this indication.\",\n \"corpus_id\": 23180726,\n \"score\": 2\n },\n {\n \"doc_id\": \"20950328\",\n \"title\": \"Role of spinal neurotransmitter receptors in itch: new insights into therapies and drug development.\",\n \"abstract\": \"Targets for antipruritic therapies are now expanding from the skin to the central nervous system. Recent studies demonstrate that various neuronal receptors in the spinal cord are involved in pruritus. The spinal opioid receptor is one of the best-known examples. Spinal administration of morphine is frequently accompanied by segmental pruritus. In addition to μ-opioid receptor antagonists, κ-opioid receptor agonists have recently come into usage as novel antipruritic drugs, and are expected to suppress certain subtypes of itch such as hemodialysis- and cholestasis-associated itch that are difficult to treat with antihistamines. The gastrin-releasing peptide receptor in the superficial dorsal horn of the spinal cord has also received recent attention as a novel pathway of itch-selective neural transmission. The NMDA glutamate receptor appears to be another potential target for the treatment of itch, especially in terms of central sensitization. The development of NMDA receptor antagonists with less undesirable side effects on the central nervous system might be beneficial for antipruritic therapies. Drugs suppressing presynaptic glutamate-release such as gabapentin and pregabalin also reportedly inhibit certain subtypes of itch such as brachioradial pruritus. Spinal receptors of other neuromediators such as bradykinin, substance P, serotonin, and histamine may also be potential targets for antipruritic therapies, given that most of these molecules interfere not only with pain, but also with itch transmission or regulation. Thus, the identification of itch-specific receptors and understanding itch-related circuits in the spinal cord may be innovative strategies for the development of novel antipruritic drugs.\",\n \"corpus_id\": 30072228,\n \"score\": 2\n },\n {\n \"doc_id\": \"23162705\",\n \"title\": \"Clinical uses of botulinum neurotoxins: current indications, limitations and future developments.\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs) cause flaccid paralysis by interfering with vesicle fusion and neurotransmitter release in the neuronal cells. BoNTs are the most widely used therapeutic proteins. BoNT/A was approved by the U.S. FDA to treat strabismus, blepharospam, and hemificial spasm as early as 1989 and then for treatment of cervical dystonia, glabellar facial lines, axillary hyperhidrosis, chronic migraine and for cosmetic use. Due to its high efficacy, longevity of action and satisfactory safety profile, it has been used empirically in a variety of ophthalmological, gastrointestinal, urological, orthopedic, dermatological, secretory, and painful disorders. Currently available BoNT therapies are limited to neuronal indications with the requirement of periodic injections resulting in immune-resistance for some indications. Recent understanding of the structure-function relationship of BoNTs prompted the engineering of novel BoNTs to extend therapeutic interventions in non-neuronal systems and to overcome the immune-resistance issue. Much research still needs to be done to improve and extend the medical uses of BoNTs.\",\n \"corpus_id\": 34697296,\n \"score\": 2\n },\n {\n \"doc_id\": \"24685845\",\n \"title\": \"Understanding itch: an update on mediators and mechanisms of pruritus.\",\n \"abstract\": \"Pruritus is the most common symptom secondary to skin diseases. Advances in the fields of neurobiology, immunology and physiology have made it possible for us to understand and unravel the deeper pathophysiological basis of pruritus. This review aims to update our current understanding of the mechanisms and mediators of pruritus. Special attention is paid to endogenous itch mediators particularly newly identified ones like endovanilloids, opioids, neurotrophins, cannabinoids, proteases and cytokines. Various theories explaining the peripheral encoding of itch are reviewed. Multiple neural pathways including the central itch pathways as well as supraspinal processing of itch and brain areas involved in pruritus are highlighted. Apart from peripheral itch mediators, spinal neural receptors are also involved in control of itch and should form part of the development of a novel antipruritic strategy. Further studies are required to fill the lacunae in our current understanding of the pathophysiology of pruritus.\",\n \"corpus_id\": 19338172,\n \"score\": 2\n },\n {\n \"doc_id\": \"26556371\",\n \"title\": \"Current Status and Future Directions of Botulinum Neurotoxins for Targeting Pain Processing.\",\n \"abstract\": \"Current evidence suggests that botulinum neurotoxins (BoNTs) A1 and B1, given locally into peripheral tissues such as skin, muscles, and joints, alter nociceptive processing otherwise initiated by inflammation or nerve injury in animal models and humans. Recent data indicate that such locally delivered BoNTs exert not only local action on sensory afferent terminals but undergo transport to central afferent cell bodies (dorsal root ganglia) and spinal dorsal horn terminals, where they cleave SNAREs and block transmitter release. Increasing evidence supports the possibility of a trans-synaptic movement to alter postsynaptic function in neuronal and possibly non-neuronal (glial) cells. The vast majority of these studies have been conducted on BoNT/A1 and BoNT/B1, the only two pharmaceutically developed variants. However, now over 40 different subtypes of botulinum neurotoxins (BoNTs) have been identified. By combining our existing and rapidly growing understanding of BoNT/A1 and /B1 in altering nociceptive processing with explorations of the specific characteristics of the various toxins from this family, we may be able to discover or design novel, effective, and long-lasting pain therapeutics. This review will focus on our current understanding of the molecular mechanisms whereby BoNTs alter pain processing, and future directions in the development of these agents as pain therapeutics.\",\n \"corpus_id\": 16243194,\n \"score\": 2\n },\n {\n \"doc_id\": \"27421250\",\n \"title\": \"Non-cosmetic dermatological uses of botulinum neurotoxin.\",\n \"abstract\": \"Botulinum neurotoxin (BoNT) is renowned for its inhibitory effects on the neuromuscular junction. The evidence for its use in cosmetic dermatology and in non-dermatological indications is well established. We have systemically analysed the evidence for the non-cosmetic dermatological uses of BoNT. This review presents the many small studies showing promising results for the use of BoNT in a multitude of dermatological diseases, including (but not limited to) hyperhidrosis, Darier's disease, Hailey-Hailey disease, pompholyx and hidradenitis suppurativa. There is, however, the need for larger, double-blinded randomized control trials against established treatments to cement the evidence base underlying the use of BoNT in dermatology.\",\n \"corpus_id\": 206043331,\n \"score\": 2\n },\n {\n \"doc_id\": \"27578080\",\n \"title\": \"Neurologic Itch Management.\",\n \"abstract\": \"Neurologic itch is defined as pruritus resulting from any dysfunction of the nervous system. Itch arising due to a neuroanatomic pathology is seen to be neuropathic. Causes of neuropathic itch range from localized entrapment of a peripheral nerve to generalized degeneration of small nerve fibers. Antipruritic medications commonly used for other types of itch such as antihistamines and corticosteroids lack efficacy in neuropathic itch. Currently there are no therapeutic options that offer relief in all types of neuropathic pruritus, and treatment strategies vary according to etiology. It is best to decide on the appropriate tests and procedures in collaboration with a neurologist during the initial work-up. Treatment of neuropathic itch includes general antipruritic measures, local or systemic pharmacotherapy, various physical modalities, and surgery. Surgical intervention is the obvious choice of therapy in cases of spinal or cerebral mass, abscess, or hemorrhagic stroke, and may provide decompression in entrapment neuropathies. Symptomatic treatment is needed in the vast majority of patients. General antipruritic measures should be encouraged. Local treatment agents with at least some antipruritic effect include capsaicin, local anesthetics, doxepin, tacrolimus, and botulinum toxin A. Current systemic therapy relies on anticonvulsants such as gabapentin and pregabalin. Phototherapy, transcutaneous electrical nerve stimulation, and physical therapy have also been of value in selected cases. Among the avenues to be explored are transcranial magnetic stimulation of the brain, new topical cannabinoid receptor agonists, various modes of acupuncture, a holistic approach with healing touch, and cell transplantation to the spinal cord.\",\n \"corpus_id\": 21276723,\n \"score\": 2\n },\n {\n \"doc_id\": \"29570628\",\n \"title\": \"A Study and Review of Effects of Botulinum Toxins on Mast Cell Dependent and Independent Pruritus.\",\n \"abstract\": \"Pruriceptive itch originates following activation of peripheral sensory nerve terminals when pruritogens come in contact with the skin. The ability of botulinum neurotoxins (BoNTs) to attenuate transmitter release from afferent terminals provides a rationale for studying its effect on pruritus. This study investigated the effects of BoNT/A1 and BoNT/B1 on mast cell dependent (Compound 48/80:48/80) and independent (Chloroquine:CQ) scratching. C57Bl/6 male mice received intradermal injection of 1.5 U of BoNT/A1, BoNT/B1 or saline 2, 7, 14 and 21 days prior to ipsilateral 48/80 or CQ at the nape of the neck. Ipsilateral hind paw scratching was determined using an automated recording device. The effect of BoNTs on 48/80 mediated mast cell degranulation was analyzed in human and murine mast cells and the presence of SNAREs was determined using qPCR, immunostaining and Western blot. Pre-treatment with BoNT/A1 and BoNT/B1 reduced 48/80 and CQ induced scratching behavior starting on day 2 with reversal by day 21. Both serotypes inhibited 48/80 induced mast cell degranulation. qPCR and immunostaining detected SNAP-25 mRNA and protein, respectively, in mast cells, however, Western blots did not. This study demonstrates the long-lasting anti-pruritic effects of two BoNT serotypes, in a murine pruritus model using two different mechanistically driven pruritogens. These data also indicate that BoNTs may have a direct effect upon mast cell degranulation.\",\n \"corpus_id\": 4229209,\n \"score\": 2\n },\n {\n \"doc_id\": \"29783676\",\n \"title\": \"The Expanding Therapeutic Utility of Botulinum Neurotoxins.\",\n \"abstract\": \"Botulinum neurotoxin (BoNT) is a major therapeutic agent that is licensed in neurological indications, such as dystonia and spasticity. The BoNT family, which is produced in nature by clostridial bacteria, comprises several pharmacologically distinct proteins with distinct properties. In this review, we present an overview of the current therapeutic landscape and explore the diversity of BoNT proteins as future therapeutics. In recent years, novel indications have emerged in the fields of pain, migraine, overactive bladder, osteoarthritis, and wound healing. The study of biological effects distal to the injection site could provide future opportunities for disease-tailored BoNT therapies. However, there are some challenges in the pharmaceutical development of BoNTs, such as liquid and slow-release BoNT formulations; and, transdermal, transurothelial, and transepithelial delivery. Innovative approaches in the areas of formulation and delivery, together with highly sensitive analytical tools, will be key for the success of next generation BoNT clinical products.\",\n \"corpus_id\": 29151386,\n \"score\": 2\n },\n {\n \"doc_id\": \"18385327\",\n \"title\": \"Long-distance retrograde effects of botulinum neurotoxin A.\",\n \"abstract\": \"Botulinum neurotoxins (designated BoNT/A-BoNT/G) are bacterial enzymes that block neurotransmitter release by cleaving essential components of the vesicle fusion machinery. BoNT/A, which cleaves SNAP-25 (synaptosomal-associated protein of 25 kDa), is extensively exploited in clinical medicine to treat neuromuscular pathologies, facial wrinkles, and various types of pain. It is widely assumed that BoNT/A remains at the synaptic terminal and its effects are confined to the injection site. Here we demonstrate that catalytically active BoNT/A is retrogradely transported by central neurons and motoneurons and is then transcytosed to afferent synapses, in which it cleaves SNAP-25. SNAP-25 cleavage by BoNT/A was observed in the contralateral hemisphere after unilateral BoNT/A delivery to the hippocampus. Appearance of cleaved SNAP-25 resulted in blockade of hippocampal activity in the untreated hemisphere. Injections of BoNT/A into the optic tectum led to the appearance of BoNT/A-truncated SNAP-25 in synaptic terminals within the retina. Cleaved SNAP-25 also appeared in the facial nucleus after injection of the toxin into rat whisker muscles. Experiments excluded passive spread of the toxin and demonstrated axonal migration and neuronal transcytosis of BoNT/A. These findings reveal a novel pathway of BoNT/A trafficking in neurons and have important implications for the clinical uses of this neurotoxin.\",\n \"corpus_id\": 16689610,\n \"score\": 1\n },\n {\n \"doc_id\": \"18543757\",\n \"title\": \"[Mechanism of therapy effects by botulinum neurotoxin].\",\n \"abstract\": \"Mehanizam djelovanja i terapija botulinum toksinom. Botulinum neurotoxin (BoNT) is produced by Clostridium botulinum as a complex of proteins containing the neurotoxin itself and other nontoxic proteins. Activation of the neurotoxin occurs upon proteolytic cleavage into the heavy and light chains. This di-chain moiety is essential for neurotoxin and each chain is playing a unique role; the heavy chain mediates neurospecifics cell binding and entry, whereas the light chain, a protease, catalyzes the cleavage and inactivation of neuronal proteins that mediate neurotransmitter release. There are seven BoNT serotypes (A,B,CI,D,E,F, and G), all of which inhibit acetylcholine release, though their intracellular target proteins, the characteristics of their actions, and their potencies vary substantially. BoNT type A has been the most widely studied and applied serotype for therapeutic purposes. It has been a mainstay in the treatment of cervical dystonia, blepharospasm, and hemifacial spasm for years. BoNT has more recently emerged as an increasingly important therapeutic option in the clinical management of a broad array of conditions, including other focal dystonias, spasticity, cerebral palsy, equinovarus, gastrointestinal (GI) and urogenital disorders, hypersecretory disorders, facial lines due to hyperfunctional facial muscles and recently, musculoskeletal pain disorders and headache.\",\n \"corpus_id\": 22843456,\n \"score\": 1\n },\n {\n \"doc_id\": \"18784598\",\n \"title\": \"Clinical comparisons of botulinum neurotoxin formulations.\",\n \"abstract\": \"BACKGROUND: The expanding uses of botulinum neurotoxin (BoNT) for a growing number of clinical indications, including cervical and other dystonias, adult and childhood spasticity, and hyperhidrosis, in conjunction with the emergence of new formulations of BoNT, prompt discussion of the differences in formulations, serotypes, and indications for different neurologic diseases. REVIEW SUMMARY: This review will evaluate evidence from preclinical studies, prospective treatment studies, and direct comparative trials to discuss the differences among BoNTs and the clinical implications of using these different drugs. Data from these sources indicate that formulations of BoNT are distinct; even the same serotype formulations of BoNT serotype A have different molecular structures and sizes and therapeutic indices (reflected in different safety and efficacy profiles). CONCLUSION: Taken together, these findings confirm that the different BoNT serotypes, including the different BoNTA formulations, are distinct therapeutic entities.\",\n \"corpus_id\": 2604853,\n \"score\": 1\n },\n {\n \"doc_id\": \"19154335\",\n \"title\": \"A reappraisal of the central effects of botulinum neurotoxin type A: by what mechanism?\",\n \"abstract\": \"Botulinum neurotoxin A (BoNT/A) is a metalloprotease that enters peripheral motor nerve terminals and blocks the release of acetylcholine via the specific cleavage of the synaptosomal-associated protein of 25-kDa. Localized injections of BoNT/A are widely employed in clinical neurology to treat several human diseases characterized by muscle hyperactivity. It is generally assumed that the effects of BoNT/A remain localized to the injection site. However, several neurophysiological studies have provided evidence for central effects of BoNT/A, raising the issue of how these actions arise. Here we review these data and discuss the possibility that retrograde axonal transport of catalytically active BoNT/A may explain at least some of its effects at the level of central circuits.\",\n \"corpus_id\": 33068721,\n \"score\": 1\n },\n {\n \"doc_id\": \"19264088\",\n \"title\": \"Central effects of tetanus and botulinum neurotoxins.\",\n \"abstract\": \"Tetanus neurotoxin (TeNT) and botulinum neurotoxins (BoNTs; from A to G) are metalloproteases that act on nerve terminals to prevent exocytosis. They are extensively exploited for the study of cellular physiology. Moreover, BoNTs are also employed in clinical neurology for the treatment of several disorders characterized by hyperexcitability of peripheral nerve terminals. This review summarizes recent studies that have provided a deeper understanding of the mode of action of TeNT and BoNTs. TeNT and BoNTs bind with extreme specificity and are internalized at the neuromuscular junction. We first examine the retrograde transport mechanisms by which TeNT gains access to the central nervous system. We also discuss recent findings indicating that, besides their well known local actions at the neuromuscular junction, BoNTs can also affect central circuits.\",\n \"corpus_id\": 515573,\n \"score\": 1\n },\n {\n \"doc_id\": \"19365125\",\n \"title\": \"Botulinum neurotoxin: the ugly duckling.\",\n \"abstract\": \"This review presents a brief account of the most significant biological effects and clinical applications of botulinum neurotoxins, in a way comprehensive even for casual readers who are not familiar with the subject. The most toxic known substances in botulinum neurotoxins are polypeptides naturally synthesized by bacteria of the genus Clostridium. These polypeptides inhibit acetylcholine release at neuromuscular junctions, thus causing muscle paralysis involving both somatic and autonomic innervation. There is substantial evidence that this muscle-paralyzing feature of botulinum neurotoxins is useful for their beneficial influence on more than 50 pathological conditions such as spastic paralysis, cerebral palsy, focal dystonia, essential tremor, headache, incontinence and a variety of cosmetic interventions. Injection of adequate quantities of botulinum toxins in spastic muscles is considered as a highly hopeful procedure for the treatment of people who suffer from dystonia, cerebral palsy or have experienced a stroke. So far, numerous and reliable studies have established the safety and efficacy of botulinum neurotoxins and advocate wider clinical therapeutic and cosmetic applications.\",\n \"corpus_id\": 38608385,\n \"score\": 1\n },\n {\n \"doc_id\": \"19846187\",\n \"title\": \"[Botulinum neurotoxin].\",\n \"abstract\": \"La neurotoxine botulinique. Botulinum toxin is a multi-molecular complex comprised of a neuro-active moiety (i.e. botulinum neurotoxin) and several associated non-toxic proteins. The toxin dissociates rapidly at plasmatic pH, thereby releasing neurotoxin. Nerve terminals only take up the neurotoxin. In the peripheral nerve system, the neurotoxin mainly blocks acetylcholine release. When acting at the neuromuscular junctions, this results in paralysis of the muscle fibers. The duration of the neurotoxin action is mainly determined by the life-time of neurotoxin molecules inside the nerve terminals. Inhibition of cholinergic transmission induces rapid atrophy of the muscle fibres, and, sometimes, sprouting from poisoned nerve terminals. These effects, as well as the acetylcholine release blockade are entirely reversible. When injected in the periphery, a direct action of botulinum neurotoxin in the central nervous system remains unlikely despite its retrograde ascent demonstrated in animal models. However, indirect effects are numerous. The constituting proteins of the toxin complex can lead to immunisation against the non-toxic associated proteins and neurotoxin. Only the antibodies directed against neurotoxin are potentially neutralizing.\",\n \"corpus_id\": 23299996,\n \"score\": 1\n },\n {\n \"doc_id\": \"20462283\",\n \"title\": \"Re-engineering clostridial neurotoxins for the treatment of chronic pain: current status and future prospects.\",\n \"abstract\": \"Clostridial neurotoxins from the botulinum neurotoxin (BoNT) family are protein complexes, derived from the bacterium Clostridium botulinum, which potently inhibit acetylcholine release and result in a reversible blockade of the neuromuscular junction. This feature led to the clinical development of BoNT-A for a number of neuromuscular disorders. BoNT-A toxins are commercially available as three different preparations: Dysport/Azzalure, Botox/Vistabel, and Xeomin/Bocouture. Although BoNT-A preparations have not yet been approved for the treatment of pain, a substantial body of preclinical and clinical evidence shows that BoNT-A is effective in treating a number of different types of pain. It is thought to exert an analgesic effect both via muscle-relaxant properties and also directly, via inhibition of nociceptive neuropeptides. This review explores the mechanistic basis of this analgesic effect, summarizing current knowledge of the structure-function relationship of BoNT and discussing effects on both motor and pain neurons. For a complete picture of the analgesic properties of BoNT-A, clinical evidence of efficacy in myofascial pain and neuropathic pain is considered in tandem with a mechanistic rationale for activity. Patients experiencing chronic pain are clear candidates for treatment with a modified clostridial endopeptidase that would provide enduring inhibition of neurotransmitter release. A strong preclinical evidence base underpins the concept that re-engineering of BoNT could be used to enhance the analgesic potential of this neurotoxin, and it is hoped that the first clinical studies examining re-engineered BoNT-A will confirm this potential.\",\n \"corpus_id\": 2016651,\n \"score\": 1\n },\n {\n \"doc_id\": \"20462660\",\n \"title\": \"Antipruritic treatment with systemic μ-opioid receptor antagonists: a review.\",\n \"abstract\": \"During the past two decades, systemic μ-opioid receptor antagonists (MORA) have been used in the treatment of various forms of chronic pruritus. In a number of case reports, case series, and controlled trials, treatment with MORA has demonstrated considerable antipruritic effects. In double-blind controlled studies, significant antipruritic relief has been achieved by MORA in cholestatic pruritus, chronic urticaria, and atopic dermatitis. In case reports and case series, antipruritic efficacy of MORA has been reported in prurigo nodularis, mycosis fungoides, postburn pruritus, aquagenic pruritus, hydroxyethyl starch-induced pruritus, and pruritus of unknown origin. However, most of the evidence remains anecdotal, the design of these trials varies, and comparison of results is difficult. In this review we aim to present an overview of these reports and to assess the evidence for the antipruritic action of the drugs naloxone, nalmefene, and naltrexone, which are currently in use for the treatment of chronic pruritus of different origins. We will also evaluate recommendations for the use of MORA in daily medical practice.\",\n \"corpus_id\": 22721145,\n \"score\": 1\n },\n {\n \"doc_id\": \"20585245\",\n \"title\": \"The role of botulinum toxin in management of pain: an evidence-based review.\",\n \"abstract\": \"PURPOSE OF REVIEW: In the present review we discuss the role of botulinum neurotoxins (BoNTs) in the management of different pain conditions, with evidence-based data on the toxins' efficacy on pain and its mechanisms. RECENT FINDINGS: Experimental in-vitro studies have reported promising results of a novel recombinant chimera of BoNT A and E that inhibits the calcitonin gene-related peptide exocytosis from brainstem sensory neurons. Animal studies in neuropathic pain rat models have reported an analgesic effect of BoNT A given after the neuropathic procedure and a bilateral antinociceptive effect to the unilateral noxious stimuli. There is a growing body of evidence that BoNTs are effective in myofascial pain syndrome, neuropathic pain, and joint pain. The pre-existing evidence that BoNTs are ineffective in migraine or other headache disorders has not yet been challenged. In other pain syndromes, studies published in the last review year have not contributed significantly in either demonstrating or invalidating the research that has so far proved inconclusive. SUMMARY: The role of BoNTs in management of pain is not yet well established. Larger studies in neuropathic pain, joint pain, and myofascial pain syndrome are needed to fully ascertain the role for BoNT therapy in those areas.\",\n \"corpus_id\": 205448184,\n \"score\": 1\n },\n {\n \"doc_id\": \"21747148\",\n \"title\": \"[Use of botulinum neurotoxin therapy].\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs), produced by the gram-positive anaerobic bacterium Clostridium botulinum, act on motor nerve endings and induce muscle relaxation. BoNT type A and B are used as therapeutic agents. Several preparations of BoNT type A are commercially available; Botox®, Dysport®, and Xeomin® are popular. They differ in the manufacturing method used, for example, BoNT consists of neurotoxin and a complex protein, Botox® and Dysport® contain a complex protein, whereas Xeomin® is free from the protein. However, when applied clinically, there is no significant difference in the efficacy and adverse effects between these BoNT products. Intramuscular BoNT injection is widely recognized as a safe and effective treatment for blepharospasm, hemifacial spasm, cervical dystonia, spasticity, squint, migraine, hyperhidrosis, wrinkles (cosmetic purpose), achalasia, hyperactive bladder, etc. BoNT preparations are used in more than 70 countries. In Japan, BoNT is used to treat blepharospasm, hemifacial spasm, cervical dystonia, and spasticity in addition to being used to treat wrinkles. However, its use is not yet widespread in Japan. This article reviews the structure and characteristics of BoNT, and throws light upon the technique of injecting BoNT.\",\n \"corpus_id\": 22206368,\n \"score\": 1\n },\n {\n \"doc_id\": \"22069581\",\n \"title\": \"Botulinum neurotoxin for pain management: insights from animal models.\",\n \"abstract\": \"The action of botulinum neurotoxins (BoNTs) at the neuromuscular junction has been extensively investigated and knowledge gained in this field laid the foundation for the use of BoNTs in human pathologies characterized by excessive muscle contractions. Although much more is known about the action of BoNTs on the peripheral system, growing evidence has demonstrated several effects also at the central level. Pain conditions, with special regard to neuropathic and intractable pain, are some of the pathological states that have been recently treated with BoNTs with beneficial effects. The knowledge of the action and potentiality of BoNTs utilization against pain, with emphasis for its possible use in modulation and alleviation of chronic pain, still represents an outstanding challenge for experimental research. This review highlights recent findings on the effects of BoNTs in animal pain models.\",\n \"corpus_id\": 17691216,\n \"score\": 1\n },\n {\n \"doc_id\": \"22552262\",\n \"title\": \"Botulinum neurotoxin A: a review.\",\n \"abstract\": \"Despite its ubiquity in cosmetic circles and broad general awareness, a literature search of botulinum neurotoxin in JPRAS and BJPS yielded a mere 4 articles germane to cosmesis. A pair each detailing its application in masseteric hypertrophy(1,2) and the use of cryoanalgesia.(3,4) Given that botulinum neurotoxin A is the most commonly used cosmetic treatment, with American figures being most accurate,(5) a review of the background, development and scientific evidence would be perhaps useful, if not overdue, as Plastic Surgeons increasingly incorporate non-surgical interventions into their practices as part of a comprehensive facial rejuvenation strategy.\",\n \"corpus_id\": 30053642,\n \"score\": 1\n },\n {\n \"doc_id\": \"23201505\",\n \"title\": \"Botulinum neurotoxins: mechanism of action.\",\n \"abstract\": \"Botulinum neurotoxins are used clinically for conditions characterized by hyperexcitability of peripheral nerve terminals and hypersecretory syndromes. These neurotoxins are synthesized as precursor proteins with low activity, but their effects are mediated by the active form of the neurotoxin through a multistep mechanism. Following a high-affinity interaction with a protein receptor and polysialogangliosides on the synaptic membrane, botulinum neurotoxins enter the neuron and causes a sustained inhibition of synaptic transmission. The active neurotoxin is part of a high-molecular-weight complex that protects the neurotoxin from proteolytic degradation. Although complexing proteins do not affect diffusion of therapeutic neurotoxin, they may lead to the development of neutralizing antibodies that block responsiveness to it. Nerve terminal intoxication is reversible and its duration varies for different BoNT serotypes. Although it was previously assumed that botulinum neurotoxins exert effects only on the peripheral synapses, such as the neuromuscular junction, there is now substantial evidence that these neurotoxins affect neurotransmission at distal central nervous system sites as well.\",\n \"corpus_id\": 1603007,\n \"score\": 1\n },\n {\n \"doc_id\": \"23202312\",\n \"title\": \"Emerging opportunities for serotypes of botulinum neurotoxins.\",\n \"abstract\": \"BACKGROUND: Two decades ago, botulinum neurotoxin (BoNT) type A was introduced to the commercial market. Subsequently, the toxin was approved by the FDA to address several neurological syndromes, involving muscle, nerve, and gland hyperactivity. These syndromes have typically been associated with abnormalities in cholinergic transmission. Despite the multiplicity of botulinal serotypes (designated as types A through G), therapeutic preparations are currently only available for BoNT types A and B. However, other BoNT serotypes are under study for possible clinical use and new clinical indications; OBJECTIVE: To review the current research on botulinum neurotoxin serotypes A-G, and to analyze potential applications within basic science and clinical settings; CONCLUSIONS: The increasing understanding of botulinal neurotoxin pathophysiology, including the neurotoxin's effects on specific neuronal populations, will help us in tailoring treatments for specific diagnoses, symptoms and patients. Scientists and clinicians should be aware of the full range of available data involving neurotoxin subtypes A-G.\",\n \"corpus_id\": 34629468,\n \"score\": 1\n },\n {\n \"doc_id\": \"23222890\",\n \"title\": \"The brain circuitry mediating antipruritic effects of acupuncture.\",\n \"abstract\": \"Itch is an aversive sensory experience and while systemic therapies, such as acupuncture, have shown promise in alleviating itch in patients suffering from chronic itch, their antipruritic mechanisms are unknown. As several lines of evidence implicate brain-focused mechanisms, we applied functional magnetic resonance imaging and our validated temperature-modulation itch model to evaluate the underlying brain circuitry supporting allergen-induced itch reduction in atopic dermatitis patients by acupuncture, antihistamine, and respective placebo treatments. Brain response to allergen itch demonstrated phase dependency. During an increasing itch phase, activation was localized in anterior insula and striatum, regions associated with salience/interoception and motivation processing. Once itch reached peak plateau, robust activation was noted in prefrontal cognitive and premotor areas. Acupuncture reduced itch and itch-evoked activation in the insula, putamen, and premotor and prefrontal cortical areas. Neither itch sensation nor itch-evoked brain response was altered following antihistamine or placebo acupuncture. Greater itch reduction following acupuncture was associated with greater reduction in putamen response, a region implicated in motivation and habitual behavior underlying the urge to scratch, specifically implicating this region in acupuncture's antipruritic effects. Understanding brain circuitry underlying itch reduction following acupuncture and related neuromodulatory therapies will significantly impact the development and applicability of novel therapies to reduce an itch.\",\n \"corpus_id\": 8928190,\n \"score\": 1\n },\n {\n \"doc_id\": \"23375537\",\n \"title\": \"Clinical utility of different botulinum neurotoxin preparations.\",\n \"abstract\": \"Comparative literature assessing the relative safety and efficacy of different BoNT products is limited. The quantity and quality of data vary by preparation and indication. Clinicians seeking data relevant to the care of patients with specific conditions may find only reports about small numbers of patients with varying symptoms. While a literature search for \\\"botulinum neurotoxins\\\" will yield a large number of publications; only a fraction of these meet criteria for an academic evidence-based review. Patients may have been treated with a different BoNT formulation than that with which the physician is familiar, or there may be little or no clinical data on the use of a specific BoNT product for the proposed intervention. This paper is an introduction to a series of papers (which follow) in which an expert panel reviewed the BoNT clinical trial literature in order to provide evidence-based recommendations regarding the clinical use and efficacy of available BoNT preparations for four major therapeutic areas: movement disorders, spasticity, urology, and secretory disorders. Expert opinion is also included to address practical issues where more evidence and further research is needed.\",\n \"corpus_id\": 24982165,\n \"score\": 1\n },\n {\n \"doc_id\": \"23747735\",\n \"title\": \"A closer look to botulinum neurotoxin type A-induced analgesia.\",\n \"abstract\": \"Chronic pain indicates a type of pain that lasts over time and is accompanied by diagnostic and therapeutic difficulties. It follows that treatment failures are common and patients roam from doctor to doctor in search of an effective care program. So there is an urgent need for long-acting and effective therapeutics to alleviate symptoms of the varied forms of chronic pain. During the past few years, a good success has been achieved with a derivative of a neurotoxin. It has been shown that administration of this toxin can block the release of neurotransmitters and pain mediators. Botulinum neurotoxin type A (BoNT/A) is well known as a treatment for neuromuscular conditions such as dystonia and spasticity. However, the clinical application for BoNT/A has continued to expand. Its analgesic effect has been used in clinical practice with satisfactory results. This review provides an introduction of a hypothesis for the mechanism by which BoNT/A eases chronic pain. It also summarizes the clinical therapeutic effects of BoNT/A in different types of chronic pain and its potential prospects.\",\n \"corpus_id\": 22384674,\n \"score\": 1\n },\n {\n \"doc_id\": \"23980845\",\n \"title\": \"Chronic pruritus associated with dermatologic disease in infancy and childhood: update from an interdisciplinary group of dermatologists and pediatricians.\",\n \"abstract\": \"An effective treatment strategy for chronic pruritus in children with dermatologic disorders should consider the multidimensional aspects of pruritus, the unique challenges associated with treating pruritic skin disorders in the pediatric population, and evidence-based therapies with demonstrated antipruritic benefits and clinically relevant effects on patient/family quality of life (QoL). The Course of Advanced Learning for the Management of ITch (CALM-IT) Task Force is an interdisciplinary group of experts specializing in core aspects of pruritus treatment, integrating pediatrics, dermatology, psychotherapy, pruritus management, and sleep. CALM-IT recently convened to provide updated guidance on managing chronic pruritus associated with dermatologic diseases in pediatric patients, with a special focus on atopic dermatitis (AD) and chronic spontaneous urticaria (csU). This review highlights the updated concepts and best practices, which were built upon international PRACTALL consensus and modified for children and infants with AD and csU. CALM-IT supports the routine use of basic skin therapy and the escalation of topical medications, according to severity and focused on rapid itch control. Anti-inflammatory agents should be appropriate for infants and children (i.e., with an optimized therapeutic index) and have proven antipruritic properties, such as those demonstrated by methylprednisolone aceponate. New experimental findings do not support the use of non-sedating oral antihistamines as adjuvant antipruritic therapy for AD. In csU, oral H1 -antihistamine use is justified, consistent with the distinct pathophysiologic mechanisms of itch underlying AD and csU. All encompassing QoL assessments should consider the burden of both patient and caregiver and should address outstanding unmet clinical needs of pediatric patients. Future research areas include integrated QoL assessments and multidisciplinary treatment programs with pediatric-targeted pruritic therapies providing rapid itch control.\",\n \"corpus_id\": 189736,\n \"score\": 1\n },\n {\n \"doc_id\": \"24576870\",\n \"title\": \"More than at the neuromuscular synapse: actions of botulinum neurotoxin A in the central nervous system.\",\n \"abstract\": \"Botulinum neurotoxin type A (BoNT/A) is a metalloprotease that produces a sustained yet transitory blockade of transmitter release from peripheral nerve terminals. Local delivery of this neurotoxin is successfully employed in clinical practice to reduce muscle hyperactivity such as in spasticity and dystonia, and to relieve pain with long-lasting therapeutic effects. However, not all BoNT/A effects can be explained by an action at peripheral nerve terminals. Indeed, it appears that BoNT/A is endowed with trafficking properties similar to the parental tetanus neurotoxin and thus be able to directly affect the CNS. In this review, we present and discuss novel compelling evidence for a direct central effect of BoNT/A in both dorsal and ventral horns of the animal and human spinal cord after peripheral injection of the neurotoxin, with important consequences on pain and motor control. This new knowledge is expected to radically change the approach to the use of BoNT/A in the future. As BoNT/A central action appears to also contribute to functional improvement, for instance in human spastic gait, the challenge will be to develop new subtypes or BoNT derivatives with deliberate, cell-specific central effects in order to fully exploit the spectrum of BoNT/A therapeutic activity.\",\n \"corpus_id\": 5237512,\n \"score\": 1\n },\n {\n \"doc_id\": \"25842964\",\n \"title\": \"Novel therapeutic uses and formulations of botulinum neurotoxins: a patent review (2012 - 2014).\",\n \"abstract\": \"INTRODUCTION: Botulinum neurotoxins (BoNTs) are among the most toxic of known biological molecules and function as acetylcholine release inhibitors and neuromuscular blocking agents. Paradoxically, these properties also make them valuable therapeutic agents for the treatment of movement disorders, urological conditions and hypersecretory disorders. Greater understanding of their molecular mechanism of action and advances in protein engineering has led to significant efforts to improve and expand their function with a view towards broadening their therapeutic potential. AREAS COVERED: Searches of Espacenet and Google Patent have revealed a number of patents related to BoNTs. This review will focus on novel therapeutic uses and formulations disclosed during 2012 - 2014. The seven patents discussed will include nanoformulations of FDA-approved BoNTs, additional BoNT subtypes and novel BoNT variants and chimeras created through protein engineering. Supporting patents and related publications are also briefly discussed. EXPERT OPINION: The clinical and commercial success of BoNTs has prompted investigation into novel BoNTs or BoNT-mediated chimeras with promising in vitro results. Distinct strategies including the use of nanoformulations and targeted delivery have been implemented to identify new indication and improved functionality. Greater understanding of their systemic exposure, efficacy and safety profiles will be required for further development.\",\n \"corpus_id\": 46238953,\n \"score\": 1\n },\n {\n \"doc_id\": \"26169827\",\n \"title\": \"Botulinum neurotoxin type A: Actions beyond SNAP-25?\",\n \"abstract\": \"Botulinum neurotoxin type A (BoNT/A), the most potent toxin known in nature which causes botulism, is a commonly used therapeutic protein. It prevents synaptic vesicle neuroexocytosis by proteolytic cleavage of synaptosomal-associated protein of 25 kDa (SNAP-25). It is widely believed that BoNT/A therapeutic or toxic actions are exclusively mediated by SNAP-25 cleavage. On the other hand, in vitro and in vivo findings suggest that several BoNT/A actions related to neuroexocytosis, cell cycle and apoptosis, neuritogenesis and gene expression are not necessarily mediated by this widely accepted mechanism of action. In present review we summarize the literature evidence which point to the existence of unknown BoNT/A molecular target(s) and modulation of unknown signaling pathways. The effects of BoNT/A apparently independent of SNAP-25 occur at similar doses/concentrations known to induce SNAP-25 cleavage and prevention of neurotransmitter release. Accordingly, these effects might be pharmacologically significant. Potentially the most interesting are observations of antimitotic and antitumor activity of BoNT/A. However, the exact mechanisms require further studies.\",\n \"corpus_id\": 21369081,\n \"score\": 1\n },\n {\n \"doc_id\": \"26260691\",\n \"title\": \"Clinical differences between botulinum neurotoxin type A and B.\",\n \"abstract\": \"In humans, the therapeutic use of botulinum neurotoxin A (BoNT/A) is well recognized and continuously expanding. Four BoNTs are widely available for clinical practice: three are serotype A and one is serotype B: onabotulinumtoxinA (A/Ona), abobotulinumtoxinA (A/Abo) and incobotulinumtoxinA (A/Inco), rimabotulinumtoxinB (B/Rima). A/Abo, A/Inco, A/Ona and B/Rima are all licensed worldwide for cervical dystonia. In addition, the three BoNT/A products are approved for blepharospasm and focal dystonias, spasticity, hemifacial spasm, hyperhidrosis and facial lines, with remarkable regional differences. These toxin brands differ for specific activity, packaging, constituents, excipient, and storage. Comparative literature assessing the relative safety and efficacy of different BoNT products is limited, most data come from reports on small samples, and only a few studies meet criteria of evidence-based medicine. One study compared the effects of BoNT/A and BoNT/B on muscle activity of healthy volunteers, showing similar neurophysiological effects with a dose ratio of 1:100. In cervical dystonia, when comparing the effects of BoNT/A and BoNT/B, results are more variable, some studies reporting roughly similar peak effect and overall duration (at a ratio of 1:66, others reporting substantially shorter duration of BoNT/B than BoNT/A (at a ratio 1/24). Although the results of clinical studies are difficult to compare for methodological differences (dose ratio, study design, outcome measures), it is widely accepted that: BoNT/B is clinically effective using appropriate doses as BoNT/A (1:40-50), injections are generally more painful, in most of the studies on muscular conditions, efficacy is shorter, and immunogenicity higher. Since the earliest clinical trials, it has been reported that autonomic side effects are more frequent after BoNT/B injections, and this observation encouraged the use of BoNT/B for sialorrhea, hyperhidrosis and other non-motor symptoms. In these indications the efficacy of toxins A and B are comparable and dose ratio is 1:25-30.\",\n \"corpus_id\": 664189,\n \"score\": 1\n },\n {\n \"doc_id\": \"26745805\",\n \"title\": \"Structural and Functional Interactions between Transient Receptor Potential Vanilloid Subfamily 1 and Botulinum Neurotoxin Serotype A.\",\n \"abstract\": \"BACKGROUND: Botulinum neurotoxins are produced by Clostridium botulinum bacteria. There are eight serologically distinct botulinum neurotoxin isoforms (serotypes A-H). Currently, botulinum neurotoxin serotype A (BoNT⁄A) is commonly used for the treatment of many disorders, such as hyperactive musculoskeletal disorders, dystonia, and pain. However, the effectiveness of BoNT⁄A for pain alleviation and the mechanisms that mediate the analgesic effects of BoNT⁄A remain unclear. To define the antinociceptive mechanisms by which BoNT/A functions, the interactions between BoNT⁄A and the transient receptor potential vanilloid subfamily 1 (TRPV1) were investigated using immunofluorescence, co-immunoprecipitation, and western blot analysis in primary mouse embryonic dorsal root ganglion neuronal cultures. RESULTS: 1) Three-week-old cultured dorsal root ganglion neurons highly expressed transient TRPV1, synaptic vesicle 2A (SV2A) and synaptosomal-associated protein 25 (SNAP-25). SV2A and SNAP-25 are the binding receptor and target protein, respectively, of BoNT⁄A. 2) TRPV1 colocalized with both BoNT⁄A and cleaved SNAP-25 when BoNT⁄A was added to dorsal root ganglia neuronal cultures. 3) After 24 hours of BoNT⁄A treatment (1 nmol⁄l), both TRPV1 and BoNT⁄A positive bands were detected in western blots of immunoprecipitated pellets. 4) Blocking TRPV1 with a specific antibody decreased the cleavage of SNAP-25 by BoNT⁄A. CONCLUSION: BoNT/A interacts with TRPV1 both structurally and functionally in cultured mouse embryonic dorsal root ganglion neurons. These results suggest that an alternative mechanism is used by BoNT⁄A to mediate pain relief.\",\n \"corpus_id\": 1768054,\n \"score\": 1\n },\n {\n \"doc_id\": \"28324318\",\n \"title\": \"Botulinum neurotoxin type A for the treatment of pain: not just in migraine and trigeminal neuralgia.\",\n \"abstract\": \"BACKGROUND: Despite their huge epidemiological impact, primary headaches, trigeminal neuralgia and other chronic pain conditions still receive suboptimal medical approach, even in developed countries. The limited efficacy of current pain-killers and prophylactic treatments stands among the main reasons for this phenomenon. Botulinum neurotoxin (BoNT) represents a well-established and licensed treatment for chronic migraine, but also an emerging treatment for other types of primary headache, trigeminal neuralgia, neuropathic pain, and an increasing number of pain conditions. METHODS: We searched and critically reviewed evidence for the efficacy of BoNT for the treatment of chronic pain. RESULTS: Meta-analyses and randomized controlled trials (RCTs) suggest that BoNT potentially represents a multi-purpose drug for the treatment of pain in several disorders due to a favorable safety profile and a long-lasting relief after a single injection. CONCLUSIONS: BoNT is an emerging treatment in different pain conditions. Future RCTs should explore the use of BoNT injection therapy combined with systemic drugs and/or physical therapies as new pain treatment strategies.\",\n \"corpus_id\": 10989660,\n \"score\": 1\n },\n {\n \"doc_id\": \"28770820\",\n \"title\": \"Identification and characterization of a novel botulinum neurotoxin.\",\n \"abstract\": \"Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Remarkably, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5 and Ykt6. To validate its activity, a small amount of full-length BoNT/X was assembled by linking two non-toxic fragments using a transpeptidase (sortase). Assembled BoNT/X cleaves VAMP2 and VAMP4 in cultured neurons and causes flaccid paralysis in mice. Thus, BoNT/X is a novel BoNT with a unique substrate profile. Its discovery posts a challenge to develop effective countermeasures, provides a novel tool for studying intracellular membrane trafficking, and presents a new potential therapeutic toxin for modulating secretions in cells.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"29111119\",\n \"title\": \"Direct central nervous system effects of botulinum neurotoxin.\",\n \"abstract\": \"Local intramuscular injections of botulinum neurotoxin type A (BoNT/A) are effective in the treatment of focal dystonias, muscle spasms, and spasticity. However, not all clinical effects of BoNT/A may be explained by its action at peripheral nerve terminals. For example, the therapeutic benefit may exceed the duration of the peripheral neuroparalysis induced by the neurotoxin. In cellular and animal models, evidence demonstrates retrograde transport of catalytically active BoNT/A in projection neurons. This process of long-range trafficking is followed by transcytosis and action at second-order synapses. In humans, several physiological changes have been described following intramuscular delivery of BoNT/A. In particular, clinical studies have documented a decrease in Renshaw cell-mediated inhibition (i.e., recurrent inhibition), which may be important therapeutically for normalizing uncoordinated movements and overflow of muscle activity. In this review, we present data obtained in animal and experimental models that support direct central actions of BoNT/A mediated via retrograde axonal trafficking. We also discuss the reorganization of central circuitry induced by BoNT/A in patients, and the potential contribution of these effects to the therapeutic efficacy of the neurotoxin.\",\n \"corpus_id\": 5009015,\n \"score\": 1\n },\n {\n \"doc_id\": \"29456150\",\n \"title\": \"Antidepressants as antipruritic agents: A review.\",\n \"abstract\": \"Pruritus is a concomitant symptom of various underlying disorders viz. dermatological, systemic and psychiatric disorders that provoke the person to scratch the skin. Many natural as well as, antipruritic therapies are usually practiced in the treatment of pruritus including general preventive measures, topical therapies such as cooling agents, antihistamines, anesthetics, capsaicin, corticosteroids, immunomodulators and; systemic therapies including administration of antihistamines, opioid antagonists/agonists, antiepileptic drugs/neuroleptics (e.g., gabapentin and pregabalin), antidepressants (e.g., doxepin, amitriptyline, paroxetine, fluvoxamine, sertraline, escitalopram and mirtazapine) (Patel and Yosipovitch, 2010; Reich et al., 2011; Martín and Padilla, 2015; Eskeland et al., 2016). Topical therapies are the mainstay of treatment of delicate and localized pruritus while other systemic drug therapies are used to treat stern and generalized pruritus. The reported antipruritic activity of some antidepressant drugs has intrigued this review to focus on the types of pruritus, pruritus mechanism, the antipruritic mechanism of antidepressants and to comprehend the role of antidepressants in the management of pruritus.\",\n \"corpus_id\": 3380505,\n \"score\": 1\n },\n {\n \"doc_id\": \"18322639\",\n \"title\": \"The use of botulinum neurotoxin type A (BoNTA) in urology.\",\n \"abstract\": \"The use of Botulinum neurotoxin type A (BoNT/A) in the lower urinary tract was pioneered as early as 20 years ago with injections into the urethral sphincter reducing bladder voiding pressures, urethral pressures, and post-void residual urine. Over the past 9 years, the use of BoNT/A has revolutionised the treatment of intractable symptoms associated with the neurogenic or idiopathic overactive bladder, both in adults and children. The duration of clinical improvement is 6-11 months, is accompanied by significant amelioration of patients' quality of life and repeat bladder treatments appear to have sustained effects. Despite evidence for an effect on the afferent pathways, its mode of action in the human bladder remains largely unknown. The use of BoNT/A has also expanded into the painful bladder syndrome and in benign prostatic diseases, with promising preliminary results. This review aims to provide an insight of the use of BoNT/A in the lower urinary tract, addressing issues such as treatment outcomes and safety, mechanisms of action and potential for future research.\",\n \"corpus_id\": 6972948,\n \"score\": 0\n },\n {\n \"doc_id\": \"18538461\",\n \"title\": \"Effects of purification on the bioavailability of botulinum neurotoxin type A.\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs) are among the most potent biological toxins for humans. They are primarily produced by the gram-positive, anaerobic spore-forming bacterium, Clostridium botulinum. In bacterial cultures, secreted BoNTs are associated with non-toxic accessory proteins forming large complexes. Neurotoxin-associated proteins have been shown to play an important role in the oral toxicity of BoNTs by protecting them from degradation and digestion by gastric acid and enzymes. Most toxicity studies using BoNTs have been performed using highly purified toxin. In this study, the toxicities of purified and crude BoNT/A toxin preparations were compared. Protein components secreted into culture supernatants along with BoNT/A were identified by mass spectrometry and the contribution of extra proteins found in the soluble crude toxin extracts to the toxicity of BoNTs was determined in mouse models of oral and parenteral botulinum intoxication. Analysis of crude toxin composition permitted assessment of the impact of accessory proteins on the oral bioavailability of BoNT/A toxin in food matrices.\",\n \"corpus_id\": 34021406,\n \"score\": 0\n },\n {\n \"doc_id\": \"19110753\",\n \"title\": \"[Use of botulinum neurotoxin for spasticity].\",\n \"abstract\": \"Spasticity is characterized by increased muscle resistance. It is usually associated with muscle weakness or poor motor control. This condition not only reduces activities of daily living (ADLs), but also interferes personal hygiere and causes caregiuer's difficulty. The use of botulinum neurotoxin (BoNT) intramuscular injections is a simple and effective therapy for spasticity. The use of BoNT to treat adult patients with spasticity was first reported in 1989, since then, using the neurotoxin to treat spasticity became popular in some European countries. Now in Japan, BoNT can be used to treat only torticollis, blepharospasm and hemifacial spasm because of the legal limitation on its use. However, clinical research on the use of BoNT in spasticity caused by stroke is presently underway, and an adaptation of the toxin may be available in the near future. This article reviews the characteristics of BoNT and the techniques for injecting this neurotoxin.\",\n \"corpus_id\": 31781392,\n \"score\": 0\n },\n {\n \"doc_id\": \"19118561\",\n \"title\": \"Domain organization in Clostridium botulinum neurotoxin type E is unique: its implication in faster translocation.\",\n \"abstract\": \"Clostridium botulinum produces seven antigenically distinct neurotoxins [C. botulinum neurotoxins (BoNTs) A-G] sharing a significant sequence homology. Based on sequence and functional similarity, it was believed that their three-dimensional structures will also be similar. Indeed, the crystal structures of BoNTs A and B exhibit similar fold and domain association where the translocation domain is flanked on either side by binding and catalytic domains. Here, we report the crystal structure of BoNT E holotoxin and show that the domain association is different and unique, although the individual domains are similar to those of BoNTs A and B. In BoNT E, both the binding domain and the catalytic domain are on the same side of the translocation domain, and all three have mutual interfaces. This unique association may have an effect on the rate of translocation, with the molecule strategically positioned in the vesicle for quick entry into cytosol. Botulism, the disease caused by BoNT E, sets in faster than any other serotype because of its speedy internalization and translocation, and the present structure offers a credible explanation. We propose that the translocation domain in other BoNTs follows a two-step process to attain translocation-competent conformation as in BoNT E. We also suggest that this translocation-competent conformation in BoNT E is a probable reason for its faster toxic rate compared to BoNT A. However, this needs further experimental elucidation.\",\n \"corpus_id\": 26420703,\n \"score\": 0\n },\n {\n \"doc_id\": \"19327377\",\n \"title\": \"Investigations into small molecule non-peptidic inhibitors of the botulinum neurotoxins.\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs), proteins secreted by the bacteria genus Clostridium, represent a group of extremely lethal toxins and a potential bioterrorism threat. As the current therapeutic options are of a predominantly prophylactic nature and cannot be used en masse, new strategies and ultimately potential treatments are desperately needed to combat any widespread release of these neurotoxins. In these regards, our laboratory has been working on developing new alternatives to treat botulinum intoxication through the development of inhibitors of the light chain proteases, the etiological agent which causes BoNT intoxication. Such a strategy has required the construction of two high-throughput screens and small molecule non-peptidic libraries; excitingly, inhibitors of the BoNT/A protease have been uncovered and are being optimized via structure activity relationship studies.\",\n \"corpus_id\": 13790000,\n \"score\": 0\n },\n {\n \"doc_id\": \"20552020\",\n \"title\": \"Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum.\",\n \"abstract\": \"BACKGROUND: Clostridium botulinum produces seven distinct serotypes of botulinum neurotoxins (BoNTs). The genes encoding different subtype neurotoxins of serotypes A, B, F and several dual neurotoxin-producing strains have been shown to reside on plasmids, suggesting that intra- and interspecies transfer of BoNT-encoding plasmids may occur. The objective of the present study was to determine whether these C. botulinum BoNT-encoding plasmids are conjugative. METHODOLOGY/PRINCIPAL FINDINGS: C. botulinum BoNT-encoding plasmids pBotCDC-A3 (strain CDC-A3), pCLJ (strain 657Ba) and pCLL (strain Eklund 17B) were tagged with the erythromycin resistance marker (Erm) using the ClosTron mutagenesis system by inserting a group II intron into the neurotoxin genes carried on these plasmids. Transfer of the tagged plasmids from the donor strains CDC-A3, 657Ba and Eklund 17B to tetracycline-resistant recipient C. botulinum strains was evaluated in mating experiments. Erythromycin and tetracycline resistant transconjugants were isolated from donor:recipient mating pairs tested. Transfer of the plasmids to the transconjugants was confirmed by pulsed-field gel electrophoresis (PFGE) and Southern hybridizations. Transfer required cell-to-cell contact and was DNase resistant. This indicates that transfer of these plasmids occurs via a conjugation mechanism. CONCLUSIONS/SIGNIFICANCE: This is the first evidence supporting conjugal transfer of native botulinum neurotoxin-encoding plasmids in C. botulinum, and provides a probable mechanism for the lateral distribution of BoNT-encoding plasmids to other C. botulinum strains. The potential transfer of C. botulinum BoNT-encoding plasmids to other bacterial hosts in the environment or within the human intestine is of great concern for human pathogenicity and necessitates further characterization of these plasmids.\",\n \"corpus_id\": 16361363,\n \"score\": 0\n },\n {\n \"doc_id\": \"20600570\",\n \"title\": \"Development and preclinical evaluation of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A.\",\n \"abstract\": \"Concern about the malicious applications of botulinum neurotoxin has highlighted the need for a new generation of safe and highly potent antitoxins. In this study, we developed and evaluated the preclinical pharmacology and safety of a new F(ab')₂ antitoxin against botulinum neurotoxin serotype A (BoNT/A). As an alternative to formalin-inactivated toxoid, the recombinant Hc domain of botulinum neurotoxin serotype A (rAHc) was used to immunize horses, and the IgGs from the hyperimmune sera were digested to obtain F(ab')₂ antitoxin. The protective effect of the new F(ab')₂ antitoxin against BoNT/A was determined both in vitro and in vivo. The results showed that the F(ab')₂ antitoxin could prevent botulism in mice challenged with BoNT/A and effectively delayed progression of paralysis from botulism in the therapeutic setting. The preclinical safety of the new F(ab')₂ antitoxin was also evaluated, and it showed neither harmful effects on vital functions nor adverse effects such as acute toxicity, or immunological reactions in mice and dogs. Thus, our results provide valuable experimental data for this new antitoxin as a potential candidate for treatment of botulism caused by BoNT/A, and our findings support the safety of the new F(ab')₂ antitoxin for clinical use. Our study further demonstrates the proof of concept for development of a similar strategy for obtaining potent antitoxin against other BoNT serotypes.\",\n \"corpus_id\": 22581463,\n \"score\": 0\n },\n {\n \"doc_id\": \"20731382\",\n \"title\": \"Identification of a unique ganglioside binding loop within botulinum neurotoxins C and D-SA .\",\n \"abstract\": \"The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A-G) based on a lack of cross antiserum neutralization. BoNTs utilize gangliosides as components of the host receptors for binding and entry into neurons. Members of BoNT/C and BoNT/D serotypes include mosaic toxins that are organized in D/C and C/D toxins. One D/C mosaic toxin, BoNT/D-South Africa (BoNT/D-SA), was not fully neutralized by immunization with BoNT serotype C or D, which stimulated this study. Here the crystal structures of the receptor binding domains of BoNT/C, BoNT/D, and BoNT/D-SA are presented. Biochemical and cell binding studies show that BoNT/C and BoNT/D-SA possess unique mechanisms for ganglioside binding. These studies provide new information about how the BoNTs can enter host cells as well as a basis for understanding the immunological diversity of these neurotoxins.\",\n \"corpus_id\": 23554795,\n \"score\": 0\n },\n {\n \"doc_id\": \"21053906\",\n \"title\": \"Clostridium botulinum neurotoxin type B is heat-stable in milk and not inactivated by pasteurization.\",\n \"abstract\": \"Foodborne botulism is caused by the ingestion of foods containing botulinum neurotoxins (BoNTs). To study the heat stability of Clostridium botulinum neurotoxins, we needed to measure and compare the activity of botulinum neurotoxins, serotypes A and B, under various pasteurization conditions. Currently, the only accepted assay to detect active C. botulinum neurotoxin is an in vivo mouse bioassay, which raises ethical concerns with regard to the use of experimental animals. In this study, noninvasive methods were used to simultaneously detect and distinguish between active BoNT serotypes A and B in one reaction and sample. We developed an enzymatic activity assay employing internally quenched fluorogenic peptides corresponding to SNAP-25, for BoNT-A, and VAMP2, for BoNT-B, as an alternative method to the mouse bioassay. Because each peptide is labeled with different fluorophores, we were able to distinguish between these two toxins. We used this method to analyze the heat stability of BoNT-A and BoNT-B. This study reports that conventional milk pasteurization (63 °C, 30 min) inactivated BoNT serotype A; however, serotype B is heat-stable in milk and not inactivated by pasteurization. Using this activity assay, we also showed that the commonly used food processes such as acidity and pasteurization, which are known to inhibit C. botulinum growth and toxin production, are more effective in inactivating BoNT serotype A than serotype B when conventional pasteurization (63 °C, 30 min) is used.\",\n \"corpus_id\": 5450345,\n \"score\": 0\n },\n {\n \"doc_id\": \"22676403\",\n \"title\": \"Botulinum neurotoxin: where are we with detection technologies?\",\n \"abstract\": \"Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current \\\"gold standard\\\". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.\",\n \"corpus_id\": 19534609,\n \"score\": 0\n },\n {\n \"doc_id\": \"22882378\",\n \"title\": \"Is there a direct antimicrobial effect of botulinum neurotoxin type A?\",\n \"abstract\": \"UNLABELLED: Study Type--Therapy (case series) Level of Evidence 4. What's known on the subject? and What does the study add? Several studies describe a reduction of symptomatic urinary tract infections in patients with neurogenic detrusor overactivity after intradetrusor injections of botulinum neurotoxin A (BoNT/A). It was, however, unclear if a direct antibacterial effect of BoNT/A plays a role in this clinical observation. This is the first study to investigate a potential antibacterial effect of two frequently used BoNT/A formulations (i.e. Botox® and Dysport®), providing evidence that BoNT/A does not exert an antibacterial effect on lower urinary tract pathogens. OBJECTIVE: • To determine a potential direct antimicrobial effect of botulinum neurotoxin type A (BoNT/A). MATERIALS AND METHODS: • A prospective study was carried out using onabotulinumtoxin A (Botox®) and abobotulinumtoxin A (Dypsort®) in agar diffusion and broth microdilution assays with various clinical urinary tract isolates (Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca and Bacillus subtilis). • Inhibition zones (mm) of bacteria around a disc containing 20 µL saline with 4 IU of Botox® were measured in the agar diffusion assay. • Minimal inhibitory concentrations (MICs, IU/mL) of both toxins for all bacteria were determined in the broth microdilution assay after overnight incubation at 35 °C. RESULTS: • There was no inhibition zone in the agar diffusion assays with any bacterial strain. • The microdilution test using Botox® and Dysport® showed bacterial growth in all dilutions, i.e. MICs > 20 and >100 IU/mL for Botox® and Dysport®, respectively. CONCLUSIONS: • BoNT/A has no direct antimicrobial effect. • The reduced frequency of symptomatic urinary tract infections (sUTIs) in patients with neurogenic detrusor overactivity (NDO) after BoNT/A intradetrusor injections seems to be caused by different indirect mechanisms, which are still not completely understood.\",\n \"corpus_id\": 20453964,\n \"score\": 0\n },\n {\n \"doc_id\": \"23239348\",\n \"title\": \"Uptake of botulinum neurotoxin in the intestine.\",\n \"abstract\": \"Foodborne and intestinal botulism are the most common forms of human botulism; both result from the absorption of botulinum neurotoxin (BoNT) from the digestive tract into the circulation. BoNT is a large protein toxin (approximately 150 kDa), but it is able to pass through the epithelial barrier in the digestive tract. Recent cellular and molecular biology studies have begun to unravel the mechanisms by which this large protein toxin crosses the intestinal epithelial barrier. This review provides an overview of current knowledge relating to the absorption of botulinum toxins (BoNT and BoNT complex) from the gastrointestinal tract, with particular emphasis on the interaction of these toxins with the intestinal epithelial barrier.\",\n \"corpus_id\": 21230102,\n \"score\": 0\n },\n {\n \"doc_id\": \"23239356\",\n \"title\": \"Complexity of botulinum neurotoxins: challenges for detection technology.\",\n \"abstract\": \"The detection of botulinum neurotoxins (BoNT) is extremely challenging due to their high toxicity and the multiple BoNT variants. To date, seven serotypes with more than 30 subtypes have been described, and even more subtypes are expected to be discovered. The fact that the BoNT molecules are released as large complexes of different size and composition adds further complexity to the issue. Currently, in the diagnostics of botulism, the mouse bioassay (MBA) is still considered as gold standard for the detection of BoNT in complex sample materials. Over the years, different functional, immunological, and spectrometric assays or combinations thereof have been developed, supplemented by DNA-based assays for the detection of the organism. In this review, advantages and limitations of the current technologies will be discussed, highlighting some of the intricacies of real sample analysis.\",\n \"corpus_id\": 22955562,\n \"score\": 0\n },\n {\n \"doc_id\": \"25564463\",\n \"title\": \"On botulinum neurotoxin variability.\",\n \"abstract\": \"The rapidly growing number of botulinum neurotoxin sequences poses the problem of the possible evolutionary significance of the variability of these superpotent neurotoxins for toxin-producing Clostridium species. To progress in the understanding of this remarkable phenomenon, we suggest that researchers should (i) abandon an anthropocentric view of these neurotoxins as human botulism-causing agents or as human therapeutics, (ii) begin to investigate in depth the role of botulinum neurotoxins in animal botulism in the wilderness, and (iii) devote large efforts to next-generation sequencing of soil samples to identify novel botulinum neurotoxins. In order to compare the fitness of the different toxins, we suggest that assays of all the steps from toxin production to animal death should be performed.\",\n \"corpus_id\": 6983148,\n \"score\": 0\n },\n {\n \"doc_id\": \"26350137\",\n \"title\": \"New Elements To Consider When Modeling the Hazards Associated with Botulinum Neurotoxin in Food.\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most potent biological substances known to mankind. BoNTs are the agents responsible for botulism, a rare condition affecting the neuromuscular junction and causing a spectrum of diseases ranging from mild cranial nerve palsies to acute respiratory failure and death. BoNTs are a potential biowarfare threat and a public health hazard, since outbreaks of foodborne botulism are caused by the ingestion of preformed BoNTs in food. Currently, mathematical models relating to the hazards associated with C. botulinum, which are largely empirical, make major contributions to botulinum risk assessment. Evaluated using statistical techniques, these models simulate the response of the bacterium to environmental conditions. Though empirical models have been successfully incorporated into risk assessments to support food safety decision making, this process includes significant uncertainties so that relevant decision making is frequently conservative and inflexible. Progression involves encoding into the models cellular processes at a molecular level, especially the details of the genetic and molecular machinery. This addition drives the connection between biological mechanisms and botulism risk assessment and hazard management strategies. This review brings together elements currently described in the literature that will be useful in building quantitative models of C. botulinum neurotoxin production. Subsequently, it outlines how the established form of modeling could be extended to include these new elements. Ultimately, this can offer further contributions to risk assessments to support food safety decision making.\",\n \"corpus_id\": 3879734,\n \"score\": 0\n },\n {\n \"doc_id\": \"26368006\",\n \"title\": \"Genetic diversity within the botulinum neurotoxin-producing bacteria and their neurotoxins.\",\n \"abstract\": \"The recent availability of multiple Clostridium botulinum genomic sequences has initiated a new genomics era that strengthens our understanding of the bacterial species that produce botulinum neurotoxins (BoNTs). Analysis of the genomes has reinforced the historical Group I-VI designations and provided evidence that the bont genes can be located within the chromosome, phage or plasmids. The sequences provide the opportunity to examine closely the variation among the toxin genes, the composition and organization of the toxin complex, the regions flanking the toxin complex and the location of the toxin within different bacterial strains. These comparisons provide evidence of horizontal gene transfer and site-specific insertion and recombination events that have contributed to the variation observed among the neurotoxins. Here, examples that have contributed to the variation observed in serotypes A-H strains are presented to illustrate the mechanisms that have contributed to their variation.\",\n \"corpus_id\": 25495666,\n \"score\": 0\n },\n {\n \"doc_id\": \"27130373\",\n \"title\": \"Serological identification of botulinum neurotoxins: A critical overview.\",\n \"abstract\": \"The reasons that gave rise to the controversy over the serological method (SerM) and genetics regarding the identification of an alleged novel botulinum neurotoxin (BoNT), type H, have been concisely examined. This discussion will remain opened inasmuch as the SerM is not performed according to the recommended procedures outlined in this overview and thoroughly discussed on previous publications. If correctly performed and interpreted, the SerM will keep its preeminence in the identification, typing and taxonomy of BoNTs.\",\n \"corpus_id\": 30112372,\n \"score\": 0\n },\n {\n \"doc_id\": \"27153088\",\n \"title\": \"Zebrafish Sensitivity to Botulinum Neurotoxins.\",\n \"abstract\": \"Botulinum neurotoxins (BoNT) are the most potent known toxins. The mouse LD50 assay is the gold standard for testing BoNT potency, but is not sensitive enough to detect the extremely low levels of neurotoxin that may be present in the serum of sensitive animal species that are showing the effects of BoNT toxicity, such as channel catfish affected by visceral toxicosis of catfish. Since zebrafish are an important animal model for diverse biomedical and basic research, they are readily available and have defined genetic lines that facilitate reproducibility. This makes them attractive for use as an alternative bioassay organism. The utility of zebrafish as a bioassay model organism for BoNT was investigated. The 96 h median immobilizing doses of BoNT/A, BoNT/C, BoNT/E, and BoNT/F for adult male Tübingen strain zebrafish (0.32 g mean weight) at 25 °C were 16.31, 124.6, 4.7, and 0.61 picograms (pg)/fish, respectively. These findings support the use of the zebrafish-based bioassays for evaluating the presence of BoNT/A, BoNT/E, and BoNT/F. Evaluating the basis of the relatively high resistance of zebrafish to BoNT/C and the extreme sensitivity to BoNT/F may reveal unique functional patterns to the action of these neurotoxins.\",\n \"corpus_id\": 14507697,\n \"score\": 0\n },\n {\n \"doc_id\": \"28271909\",\n \"title\": \"Challenges in searching for therapeutics against Botulinum Neurotoxins.\",\n \"abstract\": \"INTRODUCTION: Botulinum neurotoxins (BoNTs) are the most potent toxins known. BoNTs are responsible for botulism, a deadly neuroparalytic syndrome caused by the inactivation of neurotransmitter release at peripheral nerve terminals. Thanks to their specificity and potency, BoNTs are both considered potential bio-weapons and therapeutics of choice for a variety of medical syndromes. Several variants of BoNTs have been identified with individual biological properties and little antigenic relation. This expands greatly the potential of BoNTs as therapeutics but poses a major safety problem, increasing the need for finding appropriate antidotes. Areas covered: The authors describe the multi-step molecular mechanism through which BoNTs enter nerve terminals and discuss the many levels at which the toxins can be inhibited. They review the outcomes of the different strategies adopted to limit neurotoxicity and counter intoxication. Potential new targets arising from the last discoveries of the mechanism of action and the approaches to promote neuromuscular junction recovery are also discussed. Expert opinion: Current drug discovery efforts have mainly focused on BoNT type A and addressed primarily light chain proteolytic activity. Development of pan-BoNT inhibitors acting independently of BoNT immunological properties and targeting a common step of the intoxication process should be encouraged.\",\n \"corpus_id\": 27539897,\n \"score\": 0\n },\n {\n \"doc_id\": \"28843941\",\n \"title\": \"Botulinum Neurotoxin and Its Potential Role in the Treatment of Erectile Dysfunction.\",\n \"abstract\": \"INTRODUCTION: Botulinum toxin type A (BoNT-A) has been used to treat several striated and smooth muscle disorders. During the past year, human and animal studies conducted in Egypt and Canada by two different groups of investigators have suggested a possible role for the intracavernosal injection of BoNT-A in the treatment of erectile dysfunction (ED). AIM: To discuss BoNT-A and its current medical uses, the rationale for its new potential use in the treatment of ED, and the available evidence and concerns. METHODS: A literature search was conducted. This review was based on the available studies presented at the European Society for Sexual Medicine, Sexual Medicine Society of North America, and International Society for Sexual Medicine meetings in 2016 by the two groups. MAIN OUTCOME MEASURES: Sinusoidal diameter; penile color Doppler study; Erection Hardness Score; Sexual Health Inventory for Men questionnaire; and Sexual Encounter Profile questions 2 and 3. RESULTS: Two human studies conducted by the authors and two animal studies (one from the authors' group and one from Canada) were reviewed. These seemed to suggest generally favorable outcomes with the use of BoNT-A in the treatment of ED. CONCLUSION: BoNT-A could be a potential therapy for ED. In addition to the findings of the three pilot studies, larger multicenter trials need to be conducted to further explore the true therapeutic efficacy and clinical safety of BoNT-A in the treatment of ED. Ghanem H, Raheem AA, AbdelRahman IFS, et al. Botulinum Neurotoxin and Its Potential Role in the Treatment of Erectile Dysfunction. Sex Med Rev 2017;X:XXX-XXX.\",\n \"corpus_id\": 20815518,\n \"score\": 0\n },\n {\n \"doc_id\": \"29447689\",\n \"title\": \"Botulinum Neurotoxins: Still a Privilege of Clostridia?\",\n \"abstract\": \"Botulinum neurotoxins (BoNTs) are potent bacterial toxins mostly produced by genetically diverse clostridial strains. Recently, BoNT variants have been reported in non-clostridial strains. In this issue of Cell Host & Microbe, Zhang et al. (2018) describe a novel BoNT in Entecoccus faecium.\",\n \"corpus_id\": 3511791,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":67,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29713497\",\n \"title\": \"Patient-derived orthotopic xenograft models for cancer of unknown primary precisely distinguish chemotherapy, and tumor-targeting S. typhimurium A1-R is superior to first-line chemotherapy.\",\n \"abstract\": \"Cancer of unknown primary (CUP) is a recalcitrant disease with poor prognosis because it lacks standard first-line therapy. CUP consists of diverse malignancy groups, making personalized precision therapy essential. The present study aimed to identify an effective therapy for a CUP patient using a patient-derived orthotopic xenograft (PDOX) model. This paper reports the usefulness of the PDOX model to precisely identify effective and ineffective chemotherapy and to compare the efficacy of S. typhimurium A1-R with first-line chemotherapy using the CUP PDOX model. The present study is the first to use a CUP PDOX model, which was able to precisely distinguish the chemotherapeutic course. We found that a carboplatinum (CAR)-based regimen was effective for this CUP patient. We also demonstrated that S. typhimurium A1-R was more effective against the CUP tumor than first-line chemotherapy. Our results indicate that S. typhimurium A1-R has clinical potential for CUP, a resistant disease that requires effective therapy.\",\n \"corpus_id\": 13974194\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19291366","title":"Tumor-targeting amino acid auxotrophic Salmonella typhimurium.","abstract":"We have developed an effective bacterial cancer therapy strategy by targeting viable tumor tissue using Salmonella typhimurium auxotrophs that we have generated which grow in viable as well as necrotic areas of tumors. However, the auxotrophy severely restricts growth of these bacteria in normal tissue. The S. typhimurium A1-R mutant, which is auxotrophic for leu-arg and has high anti-tumor virulence, was developed in our laboratory. In vitro, A1-R infects tumor cells and causes nuclear destruction. A1-R was initially used to treat metastatic human prostate and breast tumors that had been orthotopically implanted in nude mice. Forty percent of treated mice were cured completely and survived as long as non-tumor-bearing mice. A1-R administered i.v. to nude mice with primary osteosarcoma and lung metastasis was highly effective, especially against metastasis. A1-R was also targeted to both axillary lymph and popliteal lymph node metastasis of human pancreatic cancer and fibrosarcoma, respectively, as well as lung metastasis of the fibrosarcoma in nude mice. The bacteria were delivered via a lymphatic channel to target the lymph node metastases and systemically via the tail vein to target the lung metastasis. The metastases were cured without the need of chemotherapy or any other treatment. A1-R was administered intratumorally to nude mice with an orthotopically transplanted human pancreatic tumor. The primary pancreatic cancer regressed without additional chemotherapy or any other treatment. A1-R was also effective against pancreatic cancer liver metastasis when administered intrasplenically to nude mice. The approach described here, where bacterial monotherapy effectively treats primary and metastatic tumors, is a significant improvement over previous bacterial tumor-therapy strategies that require combination with toxic chemotherapy. Three promoter clones engineered in S. enterica typhimurium were identified to have enhanced expression in bacteria growing in tumors relative to those growing in the spleen. The expression of therapeutics in Salmonella under the regulation of one or more promoters that are activated preferentially in tumors has the potential to improve the efficacy of Salmonella tumor therapy. Exploitation of the tumor-killing capability of Salmonella has great promise for a new paradigm of cancer therapy.","corpus_id":23144815,"score":2},{"doc_id":"20179238","title":"Patient-derived first generation xenografts of non-small cell lung cancers: promising tools for predicting drug responses for personalized chemotherapy.","abstract":"PURPOSE: Current chemotherapeutic regimens have only modest benefit for non-small cell lung cancer (NSCLC) patients. Cumulative toxicities/drug resistance limit chemotherapy given after the first-line regimen. For personalized chemotherapy, clinically relevant NSCLC models are needed for quickly predicting the most effective regimens for therapy with curative intent. In this study, first generation subrenal capsule xenografts of primary NSCLCs were examined for (a) determining responses to conventional chemotherapeutic regimens and (b) selecting regimens most effective for individual patients. EXPERIMENTAL DESIGN: Pieces (1x3x3 mm(3)) of 32 nontreated, completely resected patients' NSCLCs were grafted under renal capsules of nonobese diabetic/severe combined immunodeficient mice and treated with (A) cisplatin+vinorelbine, (B) cisplatin+docetaxel, (C) cisplatin+gemcitabine, and positive responses (treated tumor area <or=50% of control, P < 0.05) were determined. Clinical outcomes of treated patients were acquired. RESULTS: Xenografts from all NSCLCs were established (engraftment rate, 90%) with the retention of major biological characteristics of the original cancers. The entire process of drug assessment took 8 weeks. Response rates to regimens A, B, and C were 28% (9 of 32), 42% (8 of 19), and 44% (7 of 16), respectively. Certain cancers that were resistant to a particular regimen were sensitive to others. The majority of responsive tumors contained foci of nonresponding cancer cells, indicative of tumor heterogeneity and potential drug resistance. Xenografts from six of seven patients who developed recurrence/metastasis were nonresponsive. CONCLUSIONS: Models based on first generation NSCLC subrenal capsule xenografts have been developed, which are suitable for quick assessment (6-8 weeks) of the chemosensitivity of patients' cancers and selection of the most effective regimens. They hold promise for application in personalized chemotherapy of NSCLC patients.","corpus_id":31387377,"score":2},{"doc_id":"21559815","title":"Second-line chemotherapy in patients with primary unknown cancer.","abstract":"PURPOSE: There are few existing reports on the efficacy of second-line chemotherapy in patients with cancer of unknown primary site (CUP). The aim of this study was to identify characteristics of CUP patients linked to a positive response to chemotherapy. METHODS: We retrospectively studied the clinical outcomes of second-line chemotherapy in patients with CUP who had previously been treated with platinum-based first-line chemotherapy. RESULTS: A total of 27 patients received second-line chemotherapy. Of these patients, 5 (19%) showed an objective response to second-line chemotherapy; 4 of these patients had shown a favorable response to first-line chemotherapy and had a chemotherapy-free interval (CFI) of more than 4.5 months. Among the 8 patients in whom the CFI was more than 4.5 months, 4 (50%) showed an objective response to platinum-based second-line chemotherapy, whereas among the 16 patients with a CFI of less than 4.5 months, only 1 (6%) showed a response to any chemotherapeutic regimen. CONCLUSIONS: The response to second-line chemotherapy in CUP patients who had received platinum-based first-line treatment seemed to be associated with the response to first-line chemotherapy and the CFI. Although it remains unclear whether second-line chemotherapy might contribute to a survival benefit in patients with CUP, patients who show a favorable response to first-line chemotherapy and also a relatively prolonged CFI appear to be likely to benefit from second-line chemotherapy.","corpus_id":21088307,"score":2},{"doc_id":"22584324","title":"[Treatment of patients with cancer of an unknown primary site].","abstract":"Cancer of unknown primary(CUP)is a heterogenous group of tumors that accounts for 3 to 5 percent of all malignancies. Due to CUP's heterogeneity, clinical trials are difficult to perform and articles published on the disease require careful interpretation. Among CUP's, there are several clinical groups that are treated with specific treatment modalities. Each clinical group has similar treatment effects and prognoses with common malignancies that arise in adjacent locations, such as breast cancer and head/neck cancer. Therefore, accurate histological diagnosis and careful clinical staging are important. However, many CUP's do not belong to these specific clinical groups and generally have a poor prognosis. The treatment is usually directed based upon histology, location of the tumor, and stage. Platinum agents, taxanes and other new cytotoxic drugs are often used for systemic therapy, but their efficacy is often limited. Currently, specific molecular markers and targeted therapy are being explored.","corpus_id":12206628,"score":2},{"doc_id":"24435915","title":"Efficacy of Salmonella typhimurium A1-R versus chemotherapy on a pancreatic cancer patient-derived orthotopic xenograft (PDOX).","abstract":"The aim of this study is to determine the efficacy of tumor-targeting Salmonella typhimurium A1-R (A1-R) on pancreatic cancer patient-derived orthotopic xenografts (PDOX). The PDOX model was originally established from a pancreatic cancer patient in SCID-NOD mice. The pancreatic cancer PDOX was subsequently transplanted by surgical orthotopic implantation (SOI) in transgenic nude red fluorescent protein (RFP) mice in order that the PDOX stably acquired red fluorescent protein (RFP)-expressing stroma for the purpose of imaging the tumor after passage to non-transgenic nude mice in order to visualize tumor growth and drug efficacy. The nude mice with human pancreatic PDOX were treated with A1-R or standard chemotherapy, including gemcitabine (GEM), which is first-line therapy for pancreatic cancer, for comparison of efficacy. A1-R treatment significantly reduced tumor weight, as well as tumor fluorescence area, compared to untreated control (P = 0.011), with comparable efficacy of GEM, CDDP, and 5-FU. Histopathological response to treatment was defined according to Evans's criteria and A1-R had increased efficacy compared to standard chemotherapy. The present report is the first to show that A1-R is effective against a very low-passage patient tumor, in this case, pancreatic cancer. The data of the present report suggest A1-1 will have clinical activity in pancreatic cancer, a highly lethal and treatment-resistant disease and may be most effectively used in combination with other agents.","corpus_id":6899767,"score":2},{"doc_id":"24924355","title":"Efficacy of tumor-targeting Salmonella typhimurium A1-R on nude mouse models of metastatic and disseminated human ovarian cancer.","abstract":"We report here the efficacy of tumor-targeting Salmonella typhimurium A1-R (A1-R) on mouse models of disseminated and metastatic ovarian cancer. The proliferation-inhibitory efficacy of A1-R on human ovarian cancer cell lines (SKOV-3-GFP, OVCAR-3-RFP) was initially demonstrated in vitro. Orthotopic and dissemination mouse models of ovarian cancer were made with the human ovarian cancer cell line SKOV-3-GFP. After tumor implantation, the mice were treated with A1-R (5 × 10(7) colony-forming units [CFU], i.v.), and there were no severe adverse events observed. In the orthotopic model, tumor volume after treatment was 276 ± 60.8 mm(3), compared to 930 ± 342 mm(3) in the untreated control group (P = 0.022). There was also a significant difference in survival between treated mice and untreated mice in a peritoneal dissemination model (P = 0.005). The results of this report demonstrate that A1-R is effective for highly aggressive human ovarian cancer in metastatic and dissemination mouse models and suggest its clinical potential for this highly treatment-resistant disease.","corpus_id":45208730,"score":2},{"doc_id":"25394368","title":"Selective efficacy of zoledronic acid on metastasis in a patient-derived orthotopic xenograph (PDOX) nude-mouse model of human pancreatic cancer.","abstract":"BACKGROUND AND OBJECTIVES: Patient-derived orthotopic xenograft (PDOX) nude-mouse models replicate the behavior of clinical cancer, including metastasis. The objective of the study was to determine the efficacy of zoledronic acid (ZA) on metastasis of a patient-derived orthotopic xenograft (PDOX) nude-mouse model of pancreatic cancer. METHODS: In the present study, we examined the efficacy of ZA on pancreatic cancer growth and metastasis in a PDOX nude-mouse model. RESULTS: ZA monotherapy did not significantly suppress primary tumor growth. However, the primary tumor weight of gemcitabine (GEM) and combination GEM + ZA-treated mice was significantly decreased compared to the control group (GEM: P = 0.003; GEM + ZA: P = 0.002). The primary tumor weight of GEM + ZA-treated mice was significantly decreased compared to GEM-treated mice (P = 0.016). The metastasis weight decreased in ZA- or GEM-treated mice compared to the control group (ZA: P = 0.009; GEM: P = 0.007. No metastasis was detected in combination GEM + ZA-treated mice compared to the control group (GEM + ZA; P = 0.005). CONCLUSIONS: The results of the present study indicate that ZA can selectively target metastasis in a pancreatic cancer PDOX model and that the combination of ZA and GEM should be evaluated clinically in the near future for this highly treatment-resistant disease.","corpus_id":206175793,"score":2},{"doc_id":"25402324","title":"Efficacy of tumor-targeting Salmonella typhimurium A1-R in combination with anti-angiogenesis therapy on a pancreatic cancer patient-derived orthotopic xenograft (PDOX) and cell line mouse models.","abstract":"The aim of the present study was to examine the efficacy of tumor-targeting Salmonella typhimurium A1-R treatment following anti-vascular endothelial growth factor (VEGF) therapy on VEGF-positive human pancreatic cancer. A pancreatic cancer patient-derived orthotopic xenograft (PDOX) that was VEGF-positive and an orthotopic VEGF-positive human pancreatic cancer cell line (MiaPaCa-2-GFP) as well as a VEGF-negative cell line (Panc-1) were tested. Nude mice with these tumors were treated with gemcitabine (GEM), bevacizumab (BEV), and S. typhimurium A1-R. BEV/GEM followed by S. typhimurium A1-R significantly reduced tumor weight compared to BEV/GEM treatment alone in the PDOX and MiaPaCa-2 models. Neither treatment was as effective in the VEGF-negative model as in the VEGF-positive models. These results demonstrate that S. typhimurium A1-R following anti-angiogenic therapy is effective on pancreatic cancer including the PDOX model, suggesting its clinical potential.","corpus_id":18010924,"score":2},{"doc_id":"25483077","title":"Tumor-targeting Salmonella typhimurium A1-R decoys quiescent cancer cells to cycle as visualized by FUCCI imaging and become sensitive to chemotherapy.","abstract":"Quiescent cancer cells are resistant to cytotoxic agents which target only proliferating cancer cells. Time-lapse imaging demonstrated that tumor-targeting Salmonella typhimurium A1-R (A1-R) decoyed cancer cells in monolayer culture and in tumor spheres to cycle from G0/G1 to S/G2/M, as demonstrated by fluorescence ubiquitination-based cell cycle indicator (FUCCI) imaging. A1-R infection of FUCCI-expressing subcutaneous tumors growing in nude mice also decoyed quiescent cancer cells, which were the majority of the cells in the tumors, to cycle from G0/G1 to S/G2/M, thereby making them sensitive to cytotoxic agents. The combination of A1-R and cisplatinum or paclitaxel reduced tumor size compared with A1-R monotherapy or cisplatinum or paclitaxel alone. The results of this study demonstrate that A1-R can decoy quiescent cancer cells to cycle to S/G2/M and sensitize them to cytotoxic chemotherapy. These results suggest a new paradigm of bacterial-decoy chemotherapy of cancer.","corpus_id":34911807,"score":2},{"doc_id":"25689852","title":"Establishment of a patient-derived orthotopic Xenograft (PDOX) model of HER-2-positive cervical cancer expressing the clinical metastatic pattern.","abstract":"Squamous cell carcinoma of the cervix, highly prevalent in the developing world, is often metastatic and treatment resistant with no standard treatment protocol. Our laboratory pioneered the patient-derived orthotopic xenograft (PDOX) nude mouse model with the technique of surgical orthotopic implantation (SOI). Unlike subcutaneous transplant patient-derived xenograft (PDX) models, PDOX models metastasize. Most importantly, the metastasis pattern correlates to the patient. In the present report, we describe the development of a PDOX model of HER-2-positive cervical cancer. Metastasis after SOI in nude mice included peritoneal dissemination, liver metastasis, lung metastasis as well as lymph node metastasis reflecting the metastatic pattern in the donor patient. Metastasis was detected in 4 of 6 nude mice with primary tumors. Primary tumors and metastases in the nude mice had histological structures similar to the original tumor and were stained by an anti-HER-2 antibody in the same pattern as the patient's cancer. The metastatic pattern, histology and HER-2 tumor expression of the patient were thus preserved in the PDOX model. In contrast, subcutaneous transplantation of the patient's cervical tumors resulted in primary growth but not metastasis.","corpus_id":8546713,"score":2},{"doc_id":"25800176","title":"Fluorescence-guided surgery, but not bright-light surgery, prevents local recurrence in a pancreatic cancer patient derived orthotopic xenograft (PDOX) model resistant to neoadjuvant chemotherapy (NAC).","abstract":"BACKGROUND: The aim of this study is to determine the efficacy of neoadjuvant chemotherapy (NAC) with gemcitabine (GEM) in combination with fluorescence-guided surgery (FGS) on a pancreatic cancer patient derived orthotopic xenograft (PDOX) model. METHODS: A PDOX model was established from a CEA-positive tumor from a patient who had undergone a pancreaticoduodenectomy for pancreatic adenocarcinoma. Mice were randomized to 4 groups: bright light surgery (BLS) only; BLS + NAC; FGS only; and FGS + NAC. An anti-CEA antibody conjugated to DyLight 650 was administered intravenously via the tail vein of mice with a pancreatic cancer PDOX 24 h before surgery. RESULTS: The PDOX was clearly labeled with fluorophore-conjugated anti-CEA antibody. Only one out of 8 mice had local recurrence in the FGS only group and zero out of 8 mice had local recurrence in the FGS + NAC which was significantly lower than BLS only or BLS + NAC mice, where local disease recurred in 6 out of 8 mice in each treatment group (p = 0.041 and p = 0.007, respectively). NAC did not significantly reduce recurrence rates when combined with either FGS or BLS. CONCLUSION: These results indicate that FGS can significantly reduce local recurrence compared to BLS in pancreatic cancer resistant to NAC.","corpus_id":44325772,"score":2},{"doc_id":"25957417","title":"Intraperitoneal administration of tumor-targeting Salmonella typhimurium A1-R inhibits disseminated human ovarian cancer and extends survival in nude mice.","abstract":"UNLABELLED: Peritoneal disseminated cancer is highly treatment resistant. We here report the efficacy of intraperitoneal (i.p.) administration of tumor-targeting Salmonella typhimurium A1-R in a nude mouse model of disseminated human ovarian cancer. The mouse model was established by intraperitoneal injection of the human ovarian cancer cell line SKOV3-GFP. Seven days after implantation, mice were treated with S. typhimurium A1-R via intravenous (i.v.) or i.p. administration at the same dose, 5 × 10(7) CFU, once per week. Both i.v. and i.p. treatments effected prolonged survival compared with the untreated control group (P=0.025 and P<0.001, respectively). However, i.p. treatment was less toxic than i.v. TREATMENT: Tumor-specific targeting of S. typhimurium A1-R was confirmed with bacterial culture from tumors and various organs and tumor or organ colony formation after i.v. or i.p. injection. Selective tumor targeting was most effective with i.p. administration. The results of the present study show S. typhimurium A1-R has promising clinical potential for disseminated ovarian cancer, especially via i.p. administration.","corpus_id":7133817,"score":2},{"doc_id":"26047477","title":"Tumor-Targeting Salmonella typhimurium A1-R in Combination with Trastuzumab Eradicates HER-2-Positive Cervical Cancer Cells in Patient-Derived Mouse Models.","abstract":"We have previously developed mouse models of HER-2-positive cervical cancer. Tumors in nude mice had histological structures similar to the original tumor and were stained by anti-HER-2 antibody in the same pattern as the patient's cancer. We have also previously developed tumor-targeting Salmonella typhimurium A1-R and have demonstrated its efficacy against patient-derived tumor mouse models, both alone and in combination. In the current study, we determined the efficacy of S. typhimurium A1-R in combination with trastuzumab on a patient-cancer nude-mouse model of HER-2 positive cervical cancer. Mice were randomized to 5 groups and treated as follows: (1) no treatment; (2) carboplatinum (30 mg/kg, ip, weekly, 5 weeks); (3) trastuzumab (20 mg/kg, ip, weekly, 5 weeks); (4) S. typhimurium A1-R (5 × 107 CFU/body, ip, weekly, 5 weeks); (5) S. typhimurium A1-R (5 × 107 CFU/body, ip, weekly, 5 weeks) + trastuzumab (20 mg/kg, ip, weekly, 5 weeks). All regimens had significant efficacy compared to the untreated mice. The relative tumor volume of S. typhimurium A1-R + trastuzumab-treated mice was smaller compared to trastuzumab alone (p = 0.007) and S. typhimurium A1-R alone (p = 0.039). No significant body weight loss was found compared to the no treatment group except for carboplatinum-treated mice (p = 0.021). Upon histological examination, viable tumor cells were not detected, and replaced by stromal cells in the tumors treated with S. typhimurium A1-R + trastuzumab. The results of the present study suggest that S. typhimurium A1-R and trastuzumab in combination are highly effective against HER-2-expressing cervical cancer.","corpus_id":17513596,"score":2},{"doc_id":"26088297","title":"Color-coding cancer and stromal cells with genetic reporters in a patient-derived orthotopic xenograft (PDOX) model of pancreatic cancer enhances fluorescence-guided surgery.","abstract":"Precise fluorescence-guided surgery (FGS) for pancreatic cancer has the potential to greatly improve the outcome in this recalcitrant disease. To achieve this goal, we have used genetic reporters to color code cancer and stroma cells in a patient-derived orthotopic xenograft (PDOX) model. The telomerase-dependent green fluorescent protein (GFP)-containing adenovirus OBP-401 was used to label the cancer cells of a pancreatic cancer PDOX. The PDOX was previously grown in a red fluorescent protein (RFP) transgenic mouse that stably labeled the PDOX stroma cells bright red. The color-coded PDOX model enabled FGS to completely resect the pancreatic tumors including stroma. Dual-colored FGS significantly prevented local recurrence, which bright-light surgery or single-color FGS could not. FGS, with color-coded cancer and stroma cells has important potential for improving the outcome of recalcitrant-cancer surgery.","corpus_id":14631190,"score":2},{"doc_id":"26375054","title":"Therapeutic efficacy of tumor-targeting Salmonella typhimurium A1-R on human colorectal cancer liver metastasis in orthotopic nude-mouse models.","abstract":"Liver metastasis is the most frequent cause of death from colon and other cancers. Generally, liver metastasis is recalcitrant to treatment. The aim of this study is to determine the efficacy of tumor-targeting Salmonella typhimurium A1-R on liver metastasis in orthotopic mouse models. HT-29 human colon cancer cells expressing red fluorescent protein (RFP) were used in the present study. S. typhimurium A1-R infected HT-29 cells in a time-dependent manner, inhibiting cancer-cell proliferation in vitro. S. typhimurium A1-R promoted tumor necrosis and inhibited tumor growth in a subcutaneous tumor mouse model of HT-29-RFP. In orthotopic mouse models, S. typhimurium A1-R targeted liver metastases and significantly reduced their growth. The results of this study demonstrate the future clinical potential of S. typhimurium A1-R targeting of liver metastasis.","corpus_id":2516025,"score":2},{"doc_id":"26431498","title":"Tumor-targeting Salmonella typhimurium A1-R inhibits human prostate cancer experimental bone metastasis in mouse models.","abstract":"Bone metastasis is a frequent occurrence in prostate cancer patients and often is lethal. Zoledronic acid (ZOL) is often used for bone metastasis with limited efficacy. More effective models and treatment methods are required to improve the outcome of prostate cancer patients. In the present study, the effects of tumor-targeting Salmonella typhimurium A1-R were analyzed in vitro and in vivo on prostate cancer cells and experimental bone metastasis. Both ZOL and S. typhimurium A1-R inhibited the growth of PC-3 cells expressing red fluorescent protien in vitro. To investigate the efficacy of S. typhimurium A1-R on prostate cancer experimental bone metastasis, we established models of both early and advanced stage bone metastasis. The mice were treated with ZOL, S. typhimurium A1-R, and combination therapy of both ZOL and S. typhimurium A1-R. ZOL and S. typhimurium A1-R inhibited the growth of solitary bone metastases. S. typhimurium A1-R treatment significantly decreased bone metastasis and delayed the appearance of PC-3 bone metastases of multiple mouse models. Additionally, S. typhimurium A1-R treatment significantly improved the overall survival of the mice with multiple bone metastases. The results of the present study indicate that S. typhimurium A1-R is useful to prevent and inhibit prostate cancer bone metastasis and has potential for future clinical use in the adjuvant setting.","corpus_id":29988503,"score":2},{"doc_id":"26846797","title":"Tumor-Targeting Salmonella typhimurium A1-R: An Overview.","abstract":"The present chapter reviews the development of the tumor-targeting amino-acid auxotrophic strain S. typhimurium A1 and the in vivo selection and characterization of the high-tumor-targeting strain S. typhimurium A1-R. Efficacy of S. typhimurium A1-R in nude-mouse models of prostate, breast, pancreatic, and ovarian cancer, as well as sarcoma and glioma in orthotopic mouse models is described. Also reviewed is efficacy of S. typhimurium A1-R targeting of primary bone tumor and lung metastasis of high-grade osteosarcoma, breast-cancer brain metastasis, and experimental breast-cancer bone metastasis in orthotopic mouse models. The efficacy of S. typhimurium A1-R on pancreatic cancer stem cells, on pancreatic cancer in combination with anti-angiogenic agents, as well as on cervical cancer, soft-tissue sarcoma, and pancreatic cancer patient-derived orthotopic xenograft (PDOX) mouse models, is also described.","corpus_id":34206699,"score":2},{"doc_id":"26846809","title":"Methods for Tumor Targeting with Salmonella typhimurium A1-R.","abstract":"Salmonella typhimurium A1-R (S. typhimurium A1-R) has shown great preclinical promise as a broad-based anti-cancer therapeutic (please see Chapter 1 ). The present chapter describes materials and methods for the preclinical study of S. typhimurium A1-R in clinically-relevant mouse models. Establishment of orthotopic metastatic mouse models of the major cancer types is described, as well as other useful models, for efficacy studies of S. typhimurium A1-R or other tumor-targeting bacteria, as well. Imaging methods are described to visualize GFP-labeled S. typhimurium A1-R, as well as GFP- and/or RFP-labeled cancer cells in vitro and in vivo, which S. typhimurium A1-R targets. The mouse models include metastasis to major organs that are life-threatening to cancer patients including the liver, lung, bone, and brain and how to target these metastases with S. typhimurium A1-R. Various routes of administration of S. typhimurium A1-R are described with the advantages and disadvantages of each. Basic experiments to determine toxic effects of S. typhimurium A1-R are also described. Also described are methodologies for combining S. typhimurium A1-R and chemotherapy. The testing of S. typhimurium A1-R on patient tumors in patient-derived orthotopic xenograft (PDOX) mouse models is also described. The major methodologies described in this chapter should be translatable for clinical studies.","corpus_id":19597283,"score":2},{"doc_id":"26846810","title":"Salmonella typhimurium A1-R and Cell-Cycle Decoy Therapy of Cancer.","abstract":"Cancer cells in G0/G1 are resistant to cytotoxic chemotherapy agents which kill only cycling cancer cells. Salmonella typhimurium A1-R (S. typhimurium A1-R) decoyed cancer cells in monolayer culture and in tumor spheres to cycle from G0/G1 to S/G2/M, as demonstrated by fluorescence ubiquitination-based cell cycle indicator (FUCCI) imaging. S. typhimurium A1-R targeted FUCCI-expressing subcutaneous tumors, and tumors growing on the liver, growing in nude mice and also decoyed quiescent cancer cells, which were the majority of the cells in the tumors, to cycle from G0/G1 to S/G2/M. The S. typhimurium A1-R-decoyed cancer cells became sensitive to cytotoxic agents.","corpus_id":45367328,"score":2},{"doc_id":"26846811","title":"Future of Bacterial Therapy of Cancer.","abstract":"Bacterial therapy of cancer has a centuries-long history and was first-line therapy at the hospital in New York City that would become Memorial Sloan-Kettering Cancer Center, under Dr. William B. Coley. However, after Coley's death in 1936, bacterial therapy of cancer ceased in the clinic until the present century. Clinical trials have been recently carried out for strains of the obligate anaerobe Clostridium novyi with the toxin gene deleted, and on an attenuated strain of Salmonella typhimurium (S. typhimurium), which is a facultative anaerobe that can grow in viable, as well as necrotic, areas of tumors, unlike Clostridium, which can only grow in the hypoxic areas. Our laboratory has developed the novel strain S. typhimurium A1-R that is effective against all tumor types in clinically-relevant mouse models, including patient-derived orthotopic xenograft (PDOX) mouse models. This chapter suggests future clinical applications for S. typhimurium A1-R.","corpus_id":10295493,"score":2},{"doc_id":"26859573","title":"Tumor-targeting Salmonella typhimurium A1-R in combination with doxorubicin eradicate soft tissue sarcoma in a patient-derived orthotopic xenograft (PDOX) model.","abstract":"A patient with high grade undifferentiated pleomorphic soft-tissue sarcoma from a striated muscle was grown orthotopically in the right biceps femoris muscle of mice to establish a patient-derived orthotopic xenograft (PDOX) model. Twenty PDOX mice were divided into 4 groups: G1, control without treatment; G2, Salmonella typhimurium (S. typhimurium)A1-R administered by intratumoral (i.t.) injection once a week for 4 weeks; G3, doxorubicin (DOX) administered by intraperitoneal (i.p.) injection once a week for 4 weeks; G4, S. typhimurium A1-R (i.t.) administered once a week for 2 weeks followed by i.p. doxorubicin once a week for 2 weeks. On day 25 from the initiation of treatment, tumor volume in G2, G3, and G4 was significantly lower than G1. Mice found without gross tumor included one mouse (20%) in G2; one mouse (20%) in G3; and 3 mice (60%) in G4. Body weight loss did not significantly differ between the 3 treated groups or from the untreated control. Histological examination revealed eradication of tumor only in G4 where mice were treated with S. typhimurium A1-R followed by DOX. Our present study indicates future clinical potential of combining S. typhimurium A1-R with chemotherapy such as DOX for soft tissue sarcoma patients.","corpus_id":252170,"score":2},{"doc_id":"27105519","title":"High efficacy of tumor-targeting Salmonella typhimurium A1-R on a doxorubicin- and dactolisib-resistant follicular dendritic-cell sarcoma in a patient-derived orthotopic xenograft PDOX nude mouse model.","abstract":"Follicular dendritic-cell sarcoma (FDCS) is a rare and recalcitrant disease. In the present study, a patient-derived orthotopic xenograft (PDOX) mouse model of FDCS was established in the biceps muscle of nude mice. The FDCS PDOX was resistant to both doxorubicin (DOX) and NVP-BEZ235, dactolisib (BEZ) an experimental agent which is a dual pan-phosphoinositide 3-kinase-mammalian target of rapamycin inhibitor. However, in contrast to DOX and BEZ, the FDCS PDOX was sensitive to the tumor-targeting bacterial strain, Salmonella typhimurium A1-R (S. typhimurium A1-R). The combination of S. typhimurium A1-R and either DOX or BEZ did not increase the antitumor efficacy of S. typhimurium A1-R, indicating that DOX and BEZ were not active in this PDOX model. The efficacy of S. typhimurium A1-R in this recalcitrant FDCS gives strong impetus to move bacterial therapy to clinical trials for this disease. The findings of the present study are of particular importance since it demonstrates that S. typhimurium A1-R is effective in a PDOX model of FDCS established from a patient who failed DOX therapy.","corpus_id":16203307,"score":2},{"doc_id":"27286459","title":"Effective molecular targeting of CDK4/6 and IGF-1R in a rare FUS-ERG fusion CDKN2A-deletion doxorubicin-resistant Ewing's sarcoma patient-derived orthotopic xenograft (PDOX) nude-mouse model.","abstract":"Ewing's sarcoma is a rare and aggressive malignancy. In the present study, tumor from a patient with a Ewing's sarcoma with cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) loss and FUS-ERG fusion was implanted in the right chest wall of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. The aim of the present study was to determine efficacy of cyclin-dependent kinase 4/6 (CDK4/6) and insulin-like growth factor-1 receptor (IGF-1R) inhibitors on the Ewing's sarcoma PDOX. The PDOX models were randomized into the following groups when tumor volume reached 50 mm3: G1, untreated control; G2, doxorubicin (DOX) (intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, CDK4/6 inhibitor (palbociclib, PD0332991, per oral (p.o.), daily, for 14 days); G4, IGF-1R inhibitor (linsitinib, OSI-906, p.o., daily, for 14 days). Tumor growth was significantly suppressed both in G3 (palbociclib) and in G4 (linsitinib) compared to G1 (untreated control) at all measured time points. In contrast, DOX did not inhibit tumor growth at any time point, which is consistent with the failure of DOX to control tumor growth in the patient. The results of the present study demonstrate the power of the PDOX model to identify effective targeted molecular therapy of a recalcitrant DOX-resistant Ewing's sarcoma with specific genetic alterations. The results of this study suggest the potential of PDOX models for individually-tailored, effective targeted therapy for recalcitrant cancer.","corpus_id":7280485,"score":2},{"doc_id":"27500926","title":"Efficacy of Tumor-Targeting Salmonella A1-R on a Melanoma Patient-Derived Orthotopic Xenograft (PDOX) Nude-Mouse Model.","abstract":"Tumor-targeting Salmonella enterica serovar Typhimurium A1-R (Salmonella A1-R) had strong efficacy on a melanoma patient-derived orthotopic xenograft (PDOX) nude-mouse model. GFP-expressing Salmonella A1-R highly and selectively colonized the PDOX melanoma and significantly suppressed tumor growth (p = 0.021). The combination of Salmonella A1-R and cisplatinum (CDDP), both at low-dose, also significantly suppressed the growth of the melanoma PDOX (P = 0.001). Salmonella A1-R has future clinical potential for combination chemotherapy with CDDP of melanoma, a highly-recalcitrant cancer.","corpus_id":15528318,"score":2},{"doc_id":"27683127","title":"High-efficacy targeting of colon-cancer liver metastasis with Salmonella typhimurium A1-R via intra-portal-vein injection in orthotopic nude-mouse models.","abstract":"Liver metastasis is the main cause of colon cancer-related death and is a recalcitrant disease. We report here the efficacy and safety of intra-portal-vein (iPV) targeting of Salmonella typhimurium A1-R on colon cancer liver metastasis in a nude-mouse orthotopic model. Nude mice with HT29 human colon cancer cells, expressing red fluorescent protein (RFP) (HT29-RFP), growing in the liver were administered S. typhimurium A1-R by either iPV (1×104 colony forming units (CFU)/100 μl) or, for comparison, intra-venous injection (iv; 5×107 CFU/100 μl). Similar amounts of bacteria were delivered to the liver with the two doses, indicating that iPV delivery is 5×103 times more efficient than iv delivery. Treatment efficacy was evaluated by tumor fluorescent area (mm2) and total fluorescence intensity. Tumor fluorescent area and fluorescence intensity highly correlated (p<0.0001). iPV treatment was more effective compared to both untreated control and iv treatment (p<0.01 and p<0.05, respectively with iPV treatment with S. typhimurium arresting metastatic growth). There were no significant differences in body weight between all groups. The results of this study suggest that S. typhimurium A1-R administered iPV has potential for peri-operative adjuvant treatment of colon cancer liver metastasis.","corpus_id":12291312,"score":2},{"doc_id":"27690220","title":"Vemurafenib-resistant BRAF-V600E-mutated melanoma is regressed by MEK-targeting drug trametinib, but not cobimetinib in a patient-derived orthotopic xenograft (PDOX) mouse model.","abstract":"Melanoma is a recalcitrant disease. The present study used a patient-derived orthotopic xenograft (PDOX) model of melanoma to test sensitivity to three molecularly-targeted drugs and one standard chemotherapeutic. A BRAF-V600E-mutant melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a PDOX model. Two weeks after implantation, 50 PDOX nude mice were divided into 5 groups: G1, control without treatment; G2, vemurafenib (VEM) (30 mg/kg); G3; temozolomide (TEM) (25 mg/kg); G4, trametinib (TRA) (0.3 mg/kg); and G5, cobimetinib (COB) (5 mg/kg). Each drug was administered orally, daily for 14 consecutive days. Tumor sizes were measured with calipers twice a week. On day 14 from initiation of treatment, TRA, an MEK inhibitor, was the only agent of the 4 tested that caused tumor regression (P < 0.001 at day 14). In contrast, another MEK inhibitor, COB, could slow but not arrest growth or cause regression of the melanoma. First-line therapy TEM could slow but not arrest tumor growth or cause regression. The patient in this study had a BRAF-V600E-mutant melanoma and would be considered to be a strong candidate for VEM as first-line therapy, since VEM targets this mutation. However, VEM was not effective. The PDOX model thus helped identify the very-high efficacy of TRA against the melanoma PDOX and is a promising drug for this patient. These results demonstrate the powerful precision of the PDOX model for cancer therapy, not achievable by genomic analysis alone.","corpus_id":16003329,"score":2},{"doc_id":"27765934","title":"Patient-derived mouse models of cancer need to be orthotopic in order to evaluate targeted anti-metastatic therapy.","abstract":"Patient-derived xenograft (PDX) mouse models of cancer are emerging as an important component of personalized precision cancer therapy. However, most models currently offered to patients have their tumors subcutaneously-transplanted in immunodeficient mice, which rarely metastasize. In contrast, orthotopic-transplant patient-derived models, termed patient-derived orthotopic xenografts (PDOX), usually metastasize as in the patient. We demonstrate in the present report why orthotopic models are so important for the patient, since primary and metastatic tumors developed in an orthotopic model can have differential chemosensitivity, not detectable in standard subcutaneous tumor models. A subcutaneous nude mouse model of HER-2 expressing cervical carcinoma was not sensitive to entinostat (a benzamide histone deactylase inhibitor), which also did not inhibit primary tumor growth in a PDOX model of the same tumor. However, in the PDOX model, entinostat alone significantly reduced the metastatic tumor burden, compared to the control. Thus, only the PDOX model could be used to discover the anti-metastatic activity of entinostat for this patient. The results of the present report indicate the importance of using mouse models that can recapitulate metastatic cancer for precisely individualizing cancer therapy.","corpus_id":6976813,"score":2},{"doc_id":"27830986","title":"Patient-derived orthotopic xenograft (PDOX) mouse model of adult rhabdomyosarcoma invades and recurs after resection in contrast to the subcutaneous ectopic model.","abstract":"Rhabdomyosarcoma (RMS) is a rare mesenchymal tumor. The aim of the present study was to develop a patient-derived orthotopic xenograft (PDOX) mouse model of RMS and compare the PDOX model to a subcutaneous (s.c.)-transplant model. A patient RMS from a striated muscle was grown orthotopically in the right biceps femoris muscle and right quadriceps muscle of nude mice to establish a PDOX model, as well as under the skin to establish an s.c. MODEL: PDOX tumors grew at a statistically-significant faster rate compared to the s.c. tumors. Recurrence after surgical resection occurred only in PDOX tumors, not in the s.c. MODEL: Histologically, only the PDOX model was shown to be invasive. In conclusion, these results indicate that the PDOX model of adult RMS is malignant and the subcutaneous model is benign. These results emphasize that a proper tumor microenvironment is necessary for patient-like behavior of a tumor in a mouse model.","corpus_id":26074344,"score":2},{"doc_id":"27835903","title":"Tumor-targeting Salmonella typhimurium A1-R combined with temozolomide regresses malignant melanoma with a BRAF-V600E mutation in a patient-derived orthotopic xenograft (PDOX) model.","abstract":"Melanoma is a recalcitrant disease in need of transformative therapuetics. The present study used a patient-derived orthotopic xenograft (PDOX) nude-mouse model of melanoma with a BRAF-V600E mutation to determine the efficacy of temozolomide (TEM) combined with tumor-targeting Salmonella typhimurium A1-R. A melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a PDOX model. Two weeks after implantation, 40 PDOX nude mice were divided into 4 groups: G1, control without treatment (n = 10); G2, TEM (25 mg/kg, administrated orally daily for 14 consecutive days, n = 10); G3, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., once a week for 2 weeks, n = 10); G4, TEM combined with S. typhimurium A1-R (25 mg/kg, administrated orally daily for 14 consecutive days and 5 × 107 CFU/100 μl, i.v., once a week for 2 weeks, respectively, n = 10). Tumor sizes were measured with calipers twice a week. On day 14 from initiation of treatment, all treatments significantly inhibited tumor growth compared to untreated control (TEM: p < 0.0001; S. typhimurium A1-R: p < 0.0001; TEM combined with S. typhimurium A1-R: p < 0.0001). TEM combined with S. typhimurium A1-R was significantly more effective than either S. typhimurium A1-R (p = 0.0004) alone or TEM alone (p = 0.0017). TEM combined with S. typhimurium A1-R could regress the melanoma in the PDOX model and has important future clinical potential for melanoma patients.","corpus_id":3491201,"score":2},{"doc_id":"28011474","title":"Cervical Cancer Patient-Derived Orthotopic Xenograft (PDOX) Is Sensitive to Cisplatinum and Resistant to Nab-paclitaxel.","abstract":"BACKGROUND: Cervical cancer is a world-wide problem that requires transformative therapeutic strategies. We have previously developed patient-derived orthotopic xenograft (PDOX) nude-mouse models of this disease. In the present report, we demonstrate that the standard drug, cisplatinum (CDDP), is highly-effective while the new, highly-touted agent, nab-paclitaxel (NAB-PTX) is ineffective. MATERIALS AND METHODS: Cervical PDOX tumors were grown on the cervix of nude mice for 4 weeks after surgical orthotopic implantation (SOI). Tumors were treated with CDDP or NAB-PTX. RESULTS: H&E staining demonstrated that the PDOX tumor recapitulated the original patient tumor. CDDP was highly-effective. One tumor that was treated with CDDP completely regressed. CDDP-treated tumors were smaller (tumor volume ratio: 0.42±0.36) than the control group (tumor volume ratio: 3.47±1.66) (p<0.01). In contrast, NAB-PTX did not show significant efficacy on the cervical cancer PDOX model (tumor volume ratio: 2.85±1.45) (p=0.47). CDDP-treated tumor weight (50±50 mg) was significantly less than control (238±114 mg) (p<0.01). NAB-PTX-treated tumors were not reduced in weight (246±136 mg) compared to control (p=0.91). There were no significant differences in mouse body weight between groups. Histological evaluation demonstrated that CDDP-treated tumors were fibrotic with scattered squamous cell nests compared to control or NAB-PTX-treated tumors. CONCLUSION: The results of the present study demonstrate the power of PDOX models of cervical cancer to distinguish efficacy of potential therapeutics for individual patients with this disease.","corpus_id":3679912,"score":2},{"doc_id":"28030831","title":"Tumor-targeting Salmonella typhimurium A1-R regresses an osteosarcoma in a patient-derived xenograft model resistant to a molecular-targeting drug.","abstract":"Osteosarcoma occurs mostly in children and young adults, who are treated with multiple agents in combination with limb-salvage surgery. However, the overall 5-year survival rate for patients with recurrent or metastatic osteosarcoma is 20-30% which has not improved significantly over 30 years. Refractory patients would benefit from precise individualized therapy. We report here that a patient-derived osteosarcoma growing in a subcutaneous nude-mouse model was regressed by tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R, p<0.001 compared to untreated control). The osteosarcoma was only partially sensitive to the molecular-targeting drug sorafenib, which did not arrest its growth. S. typhimurium A1-R was significantly more effective than sorafenib (P <0.001). S. typhimurium grew in the treated tumors and caused extensive necrosis of the tumor tissue. These data show that S. typhimurium A1-R is powerful therapy for an osteosarcoma patient-derived xenograft model.","corpus_id":3701566,"score":2},{"doc_id":"28106277","title":"Tumor-Targeting Salmonella typhimurium A1-R Sensitizes Melanoma With a BRAF-V600E Mutation to Vemurafenib in a Patient-Derived Orthotopic Xenograft (PDOX) Nude Mouse Model.","abstract":"Previously, a BRAF-V600E-mutant melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. Trametinib (TRA), an MEK inhibitor, caused tumor regression. In contrast, another MEK inhibitor, cobimetinib (COB) could slow but not arrest growth or cause regression of the melanoma PDOX. First-line therapy temozolomide (TEM) could slow but not arrest tumor growth or cause regression. In addition, vemurafenib (VEM) was not effective even though VEM is supposed to target the BRAF-V600E mutation. We also previously demonstrated that tumor-targeting with S. typhimurium A1-R combined with TEM was significantly more effective than either S. typhimurium A1-R alone or TEM alone on the melanoma PDOX with the BRAF-V600E mutation. The present study used this PDOX model of melanoma to test its sensitivity to VEM combined with S. typhimurium A1-R compared to VEM alone and VEM combined with COB. VEM combined with S. typhimurium A1-R was significantly more effective than VEM alone or VEM combined with COB (P = 0.0216) which is currently first line therapy for advanced melanoma with a BRAF-V600E mutation. J. Cell. Biochem. 118: 2314-2319, 2017. © 2017 Wiley Periodicals, Inc.","corpus_id":3898060,"score":2},{"doc_id":"28176365","title":"High Efficacy of Pazopanib on an Undifferentiated Spindle-Cell Sarcoma Resistant to First-Line Therapy Is Identified With a Patient-Derived Orthotopic Xenograft (PDOX) Nude Mouse Model.","abstract":"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant -cancer. Our laboratory pioneered the patient-derived orthotopic xenograft (PDOX) nude mouse model with the technique of surgical orthotopic implantation (SOI). In the present study, we evaluated the efficacy of standard first-line chemistry of doxorubicin (DOX), gemcitabine (GEM) combined with docetaxel (DOC), compared to pazopanib (PAZ), a multi-targeting tyrosine-kinase inhibitor, in an USCS PDOX model. A high-grade USCS from a striated muscle of the patients was grown orthotopically in the right biceps femoris muscle of nude mice to establish the PDOX model. The PDOX models were randomized into the following groups when tumor volume reached 100 mm(3) : G1, control without treatment; G2, DOX (3 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, GEM (100 mg/kg, i.p., weekly, for 2 weeks) combined with DOC (20 mg/kg, i.p., once); G4, PAZ (100 mg/kg, p.o., daily, for 14 days). All treatments except DOX significantly inhibited tumor growth compared to untreated control on day 14 after treatment initiation. Tumor sizes were as fallows: control (G1): 332.0 ± 58.7 mm(3) ; DOX (G2): 316.9 ± 55.9 mm(3) , P = 0.605; GEM + DOC (G3): 228.9 ± 39.8 mm(3) , P = 0.001; PAZ (G4): 173.8 ± 23.3 mm(3) , P < 0.0001. PAZ showed significantly more efficacy compared to other therapies evaluated: DOX (P < 0.0001), GEM + DOC (P = 0.006). There were no animal deaths in any group and body weight of treated mice was not significantly different in each group. The present results demonstrate that the PDOX model of USCS can identify a promising novel agent with significantly greater efficacy than first-line therapy for this recalcitrant disease. J. Cell. Biochem. 118: 2739-2743, 2017. © 2017 Wiley Periodicals, Inc.","corpus_id":3928172,"score":2},{"doc_id":"28296559","title":"The irony of highly-effective bacterial therapy of a patient-derived orthotopic xenograft (PDOX) model of Ewing's sarcoma, which was blocked by Ewing himself 80 years ago.","abstract":"William B. Coley developed bacterial therapy of cancer more than 100 years ago and had clinical success. James Ewing, a very famous cancer pathologist for whom the Ewing sarcoma is named, was Coley's boss at Memorial Hospital in New York and terminated Coley's bacterial therapy of cancer. A tumor from a patient with soft-tissue Ewing's sarcoma, who failed doxorubicin (DOX) therapy, was previously implanted in nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. In the present study, the Ewing's sarcoma PDOX was treated with tumor-targeting S. typhimurium A1-R expressing green fluorescent (GFP), alone and in combination with DOX. S. typhimurium A1-R-GFP was detected in the tumors after intratumor (i.t.) or intravenous (i.v.) injection. The combination of S. typhimurium A1-R and DOX significantly reduced tumor weight (37.8 ± 15.6 mg) compared to the untreated control (73.8 ± 10.1 mg, P < 0.01). S. typhimurium A1-R monotherapy-treated tumors tended to be smaller (50.9 ± 17.8 mg, P = 0.051). DOX monotherapy did not show efficacy (66.3 ± 26.4 mg, P = 0.82), as was the case with the patient. The PDOX model faithfully replicated the DOX resistance the Ewing's sarcoma had in the patient. S. typhimurium A1-R converted the Ewing's sarcoma from DOX resistant to sensitive. One can only wonder how bacterial therapy and immunotherapy of cancer would have developed over the past 80 years if Ewing did not stop Coley.","corpus_id":205881832,"score":2},{"doc_id":"28404944","title":"Recombinant methioninase effectively targets a Ewing's sarcoma in a patient-derived orthotopic xenograft (PDOX) nude-mouse model.","abstract":"Methionine dependence is due to the overuse of methionine for aberrant transmethylation reactions in cancer. Methionine dependence may be the only general metabolic defect in cancer. In order to exploit methionine dependence for therapy, our laboratory previously cloned L-methionine α-deamino-γ-mercaptomethane lyase [EC 4.4.1.11]). The cloned methioninase, termed recombinant methioninase, or rMETase, has been tested in mouse models of human cancer cell lines. Ewing's sarcoma is recalcitrant disease even though development of multimodal therapy has improved patients'outcome. Here we report efficacy of rMETase against Ewing's sarcoma in a patient-derived orthotopic xenograft (PDOX) model. The Ewing's sarcoma was implanted in the right chest wall of nude mice to establish a PDOX model. Eight Ewing's sarcoma PDOX mice were randomized into untreated control group (n = 4) and rMETase treatment group (n = 4). rMETase (100 units) was injected intraperitoneally (i.p.) every 24 hours for 14 consecutive days. All mice were sacrificed on day-15, 24 hours after the last rMETase administration. rMETase effectively reduced tumor growth compared to untreated control. The methionine level both of plasma and supernatants derived from sonicated tumors was lower in the rMETase group. Body weight did not significantly differ at any time points between the 2 groups. The present study is the first demonstrating rMETase efficacy in a PDOX model, suggesting potential clinical development, especially in recalcitrant cancers such as Ewing's sarcoma.","corpus_id":4320744,"score":2},{"doc_id":"28426279","title":"Combination of gemcitabine and docetaxel regresses both gastric leiomyosarcoma proliferation and invasion in an imageable patient-derived orthotopic xenograft (iPDOX) model.","abstract":"Gastric leiomyosarcoma is a recalcitrant cancer and the chemotherapy strategy is controversial. The present study used a patient-derived orthotopic xenograft (PDOX) nude mouse model of gastric leiomyosarcoma to identify an effective therapeutic regimen to develop individualized precision medicine for this disease. The gastric leiomyosarcoma obtained from a patient was first grown in transgenic nude mice ubiquitously expressing red fluorescent protein (RFP) to stably label the tumor stroma. The RFP-expressing tumor was then passaged orthotopically in the gastric wall of non-transgenic nude mice to establish an imageable PDOX (iPDOX) model. The bright fluorescent tumor was readily imaged over time to determine drug efficacy. Four weeks after implantation, 70 PDOX nude mice were divided into 7 groups: control without treatment (n = 10); doxorubicin (DOX) (2.4 mg/kg, intraperitoneally (i.p.), once a week for 2 weeks, n = 10); gemcitabine (GEM)/ docetaxel (DOC) (GEM: 100 mg/kg, DOC: 20 mg/kg, i.p., once a week for 2 weeks, n = 10); cyclophosphamide (CPA) (140 mg/kg, i.p., once a week for 2 weeks, n = 10); temozolomide (TEM) (25 mg/kg, orally, daily for 14 consecutive days, n = 10); yondelis (YON) (0.15 mg/kg, i.v., once a week for 2 weeks, n = 10); pazopanib (PAZ) (100 mg/kg, orally, daily for 14 consecutive days, n = 10). On day 14 from initiation of treatment, all treatments except PAZ significantly inhibited tumor growth compared with untreated control (DOX: p < 0.01, GEM/DOC: p < 0.01, CPA: p < 0.01, TEM: p < 0.01, YON: p < 0.01) on day 14 after initiation. In addition, only GEM/DOC was more significantly effective than DOX (p < 0.05). GEM/DOC could regress the leimyosarcoma in the PDOX model and has important clinical potential for precision individual treatment of leiomyosarcoma patients.","corpus_id":205881880,"score":2},{"doc_id":"28494180","title":"Intra-arterial administration of tumor-targeting Salmonella typhimurium A1-R regresses a cisplatin-resistant relapsed osteosarcoma in a patient-derived orthotopic xenograft (PDOX) mouse model.","abstract":"Previously, a patient-derived orthotopic xenograft (PDOX) model was established with a lung metastasis from an osteosarcoma patient which developed after adjuvant cisplatinum (CDDP) treatment. In this model, we previously demonstrated the efficacy of trabectedin (TRAB) and temozolomide (TEM) compared with CDDP. In the present report, osteosarcoma tissue was implanted orthotopically in the distal femur of mice which were randomized into the following groups when tumor volume reached approximately 100 mm(3); On day 14 after initiation of treatment, all but CDDP significantly inhibited tumor volume growth compared with untreated controls. Control (G1): 793.7 ± 215.0 mm(3); CDDP (G2): 588.1 ± 176.9 mm(3); Salmonella typhimurium A1-R (S. typhimurium A1-R) intravenous (i.v.) ( G3): 269.7 ± 72.7 mm(3); S. typhimurium A1-R intra-arterial (i.a.) ( G4): 70.2 ± 18.9 mm(3) (CDDP: p = 0.056; S. typhimurium A1-R i.v.: p = 0.0001; S. typhimurium A1-R i.a.: p = 0.00003, all vs. untreated controls). i.a. administration of S. typhimurium A1-R was significantly more effective than either CDDP (p = 0.00007), or i.v. administration of S. typhimurium A1-R (p = 0.00007) and significantly regressed the tumor volume compared with day 0 (p = 0.001). The new model of i.a. administration of S. typhimurium A1-R has great promise for the treatment of recalcitrant osteosarcoma.","corpus_id":4768952,"score":2},{"doc_id":"28622068","title":"Salmonella typhimurium A1-R targeting of a chemotherapy-resistant BRAF-V600E melanoma in a patient-derived orthotopic xenograft (PDOX) model is enhanced in combination with either vemurafenib or temozolomide.","abstract":"A metastatic melanoma obtained from the right chest wall of a patient was previously established orthotopically in the right chest wall of nude mice as a patient-derived orthotopic xenograft (PDOX) model. We previously showed that the combination of tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R) and chemotherapy was highly effective against the melanoma PDOX. In the present study, we investigated the mechanism of the high efficacy of this combination. Two weeks after implantation, 40 PDOX mouse models were randomized into 4 groups of 10 mice each: untreated control (n = 10); treated with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks, n = 10); treated with temozolomide (TEM) (25 mg/kg, p.o. for 14 consecutive days) combined with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks, n = 10); treated with vemurafenib (VEM) (30 mg/kg, p.o., for 14 consecutive days) combined with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks) (n = 10). On day 14 from initiation, all treatments significantly inhibited tumor growth compared with untreated control (S. typhimurium A1-R: p < 0.01; TEM combined with S. typhimurium A1-R: p < 0.01; VEM combined with S. typhimurium A1-R: p < 0.01). Combination therapy with S. typhimurium A1-R was significantly more effective on tumor growth than S. typhimurium A1-R alone (with TEM: p < 0.01; with VEM: p < 0.01). Combination therapy significantly increased S. typhimurium A1-R tumor targeting alone (S. typhimurium A1-R + TEM: p < 0.01, S. typhimurium A1-R + VEM: p < 0.01), relative to S. typhimurium A1-R alone, respectively. In conclusion, chemotherapy drugs promoted targeting of S. typhimurium A1-R of melanoma, thereby enhancing efficacy against the melanoma PDOX.","corpus_id":4583281,"score":2},{"doc_id":"28681998","title":"Eribulin regresses a doxorubicin-resistant Ewing's sarcoma with a FUS-ERG fusion and CDKN2A-deletion for the patient-derived orthotopic xenograft (PDOX) nude mouse model.","abstract":"Ewing's sarcoma is a recalcitrant tumor greatly in need of more effective therapy. The aim of this study was to determine the efficacy of eribulin on a doxorubicin (DOX)-resistant Ewing's sarcoma patient derived orthotopic xenograft (PDOX) model. The Ewing's sarcoma PDOX model was previously established in the right chest wall of nude mice from the patient's right chest wall. In the previous study, the Ewing's sarcoma PDOX was resistant to DOX and sensitive to palbociclib and linsitinib. In the present study, the PDOX models were randomized into 3 groups when the tumor volume reached 60 mm(3) : G1, untreated control (n = 6); G2, DOX treated (n = 6), intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, Eribulin treated (n = 6, intravenous (i.v.) injection, weekly for 2 weeks). All mice were sacrificed on day 15. Changes in body weight and tumor volume were assessed 2 times per week. Tumor weight was measured after sacrifice. DOX did not suppress tumor growth compared to the control group (p = 0.589), consistent with the previous results in the patient and PDOX. Eribulin regressed tumor size significantly compared to G1 and G2 (p = 0.006, p = 0.017). No significant difference was observed in body weight. Our results demonstrate that eribulin is a novel therapeutic possibility for Ewing's sarcoma. This article is protected by copyright. All rights reserved.","corpus_id":19065571,"score":2},{"doc_id":"28858204","title":"Patient-Derived Orthotopic Xenograft (PDOX) Models of Melanoma.","abstract":"Metastatic melanoma is a recalcitrant tumor. Although \"targeted\" and immune therapies have been highly touted, only relatively few patients have had durable responses. To overcome this problem, our laboratory has established the melanoma patient-derived orthotopic xenograft (PDOX) model with the use of surgical orthotopic implantation (SOI). Promising results have been obtained with regard to identifying effective approved agents and experimental therapeutics, as well as combinations of the two using the melanoma PDOX model.","corpus_id":869376,"score":2},{"doc_id":"28977930","title":"A patient-derived orthotopic xenograft (PDOX) mouse model of a cisplatinum-resistant osteosarcoma lung metastasis that was sensitive to temozolomide and trabectedin: implications for precision oncology.","abstract":"In the present study, we evaluated the efficacy of trabectedin (TRAB) and temozolomide (TEM) compared to cisplatinum (CDDP) on a patient-derived orthotopic xenogrraft (PDOX) of a lung-metastasis from an osteosarcoma of a patient who failed CDDP therapy. Osteosarcoma resected from the patient was implanted orthotopically in the distal femur of mice to establish PDOX models which were randomized into the following groups when tumor volume reached approximately 100 mm3: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal injection, weekly, for 2 weeks); G3, TRAB (0.15 mg/kg, intravenous injection, weekly, for 2 weeks); G4, TEM (25 mg/kg, oral, daily, for 14 days). Tumor size and body weight were measured with calipers and a digital balance, respectively, twice a week. On day 14 after initiation of treatment, TEM and TRAB, but not CDDP, significantly inhibited tumor volume compared to untreated control: control (G1): 814.5±258.8 mm3; CDDP (G2): 608.6±126.9 mm3; TRAB (G3): 286.6±133.0 mm3; TEM (G4): 182.9±69.1 mm3. CDDP vs. control, p=0.07; TRAB vs. control, p=0.0004; TEM vs. control p =0.0002; TRAB vs. CDDP, p =0.0002; TEM vs. CDDP, p =0.00003. The results of the present study show that a PDOX model of an osteosarcoma lung-metastasis that recurred after adjuvant CDDP-treatment has identified potentially, highly-effective drugs for this recalcitrant disease, while accurately maintaining the CDDP resistance of the tumor in the patient, thereby demonstrating the potential of the osteosarcoma PDOX model for precision oncology.","corpus_id":-1,"score":2},{"doc_id":"29061220","title":"[Advances in Patient Derived Tumor Xenograft (PDTX) Model from Lung Cancer].","abstract":"With the development of tumor molecular biology and genomics, it has been recognized that there are great heterogeneity in the biological characteristics, molecular typing and reactivity of the same tumor species among different individuals. In order to achieve true tumor individualized and precise therapy, a new concept of human tumor tissue xenograft model (patient derived tumor xenograft, PDTX) is proposed. The previous study has revealed that PDTX model can truly reflect the biological characteristics of tumor tissue and drug efficacy. And PDTX model could be used to select individual chemotherapy regime, evaluate drug resistance and explore efficacy and safety of new drug. PDTX model has been used in clinical practice of several type of cancer including lung cancer. In this paper, the current research progress of lung cancer PDTX is reviewed.","corpus_id":3885909,"score":2},{"doc_id":"29143983","title":"Growth of doxorubicin-resistant undifferentiated spindle-cell sarcoma PDOX is arrested by metabolic targeting with recombinant methioninase.","abstract":"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant -cancer in need of individualized therapy. A high-grade USCS from a striated muscle of a patient was grown orthotopically in the right biceps femoris muscle of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. In a previous study, we evaluated the efficacy of standard first-line chemotherapy of doxorubicin (DOX), gemcitabine (GEM) combined with docetaxel (DOC), compared to pazopanib (PAZ), a multi-targeting tyrosine-kinase inhibitor, in an USCS PDOX model. In the present study, mice-bearing the USCS PDOX tumors were randomized into the following groups when tumor volume reached 100 mm3 : G1, untreated control without treatment; G2, DOX (3 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, L-methionine α-deamino-γ-mercaptomethane lyase (recombinant methioninase [rMETase]) (100 U/mouse, i.p., daily, for 2 weeks). Tumor size and body weight were measured with calipers and a digital balance twice a week. The methionine level of supernatants derived from sonicated tumors was also measured. rMETase inhibited tumor growth, measured by tumor volume, compared to untreated controls and the DOX-treated group on day 14 after initiation of treatment: control (G1): 347.6 ± 88 mm3 ; DOX (G2): 329.5 ± 79 mm3 , P = 0.670; rMETase (G3): 162.6 ± 51 mm3 , P = 0.0003. The mouse body weight of the treated mice was not significantly different from the untreated controls. Tumor L-methionine levels were reduced after the rMETase-treatment compared to untreated control and pre-rMETase treatment. We previously reported efficacy of rMETase against Ewing's sarcoma and melanoma in a PDOX models. These studies suggest clinical development of rMETase, especially in recalcitrant cancers such as sarcoma.","corpus_id":3570136,"score":2},{"doc_id":"29156737","title":"Combination treatment with recombinant methioninase enables temozolomide to arrest a BRAF V600E melanoma in a patient-derived orthotopic xenograft (PDOX) mouse model.","abstract":"An excessive requirement for methionine termed methionine dependence, appears to be a general metabolic defect in cancer. We have previously shown that cancer-cell growth can be selectively arrested by methionine deprivation such as with recombinant methioninase (rMETase). The present study used a previously-established patient-derived orthotopic xenograft (PDOX) nude mouse model of BRAF V600E-mutant melanoma to determine the efficacy of rMETase in combination with a first-line melanoma drug, temozolomide (TEM). In the present study 40 melanoma PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n=10); TEM (25 mg/kg, oral 14 consecutive days, n=10); rMETase (100 units, intraperitoneal 14 consecutive days, n=10); combination TEM + rMETase (TEM: 25 mg/kg, oral rMETase: 100 units, intraperitoneal 14 consecutive days, n=10). All treatments inhibited tumor growth compared to untreated control (TEM: p=0.0081, rMETase: p=0.0037, TEM-rMETase: p=0.0024) on day 14 after initiation. However, the combination therapy of TEM and rMETase was significantly more efficacious than either mono-therapy (TEM: p=0.0051, rMETase: p=0.0051). The present study is the first demonstrating the efficacy of rMETase combination therapy in a PDOX model, suggesting potential clinical development, especially in recalcitrant cancers such as melanoma, where rMETase may enhance first-line therapy.","corpus_id":22244271,"score":2},{"doc_id":"29262551","title":"The combination of temozolomide-irinotecan regresses a doxorubicin-resistant patient-derived orthotopic xenograft (PDOX) nude-mouse model of recurrent Ewing's sarcoma with a FUS-ERG fusion and CDKN2A deletion: Direction for third-line patient therapy.","abstract":"The aim of the present study was to determine the usefulness of a patient-derived orthotopic xenograft (PDOX) nude-mouse model of a doxorubicin-resistant metastatic Ewing's sarcoma, with a unique combination of a FUS-ERG fusion and CDKN2A deletion, to identify effective drugs for third-line chemotherapy of the patient. Our previous study showed that cyclin-dependent kinase 4/6 (CDK4/6) and insulin-like growth factor-1 receptor (IGF-1R) inhibitors were effective on the Ewing's sarcoma PDOX, but not doxorubicin, similar to the patient's resistance to doxorubicin. The results of the previous PDOX study were successfully used for second-line therapy of the patiend. In the present study, the PDOX mice established with the Ewing's sarcoma in the right chest wall were randomized into 5 groups when the tumor volume reached 60 mm3: untreated control; gemcitabine combined with docetaxel (intraperitoneal [i.p.] injection, weekly, for 2 weeks); irinotecan combined with temozolomide (irinotecan: i.p. injection; temozolomide: oral administration, daily, for 2 weeks); pazopanib (oral administration, daily, for 2 weeks); yondelis (intravenous injection, weekly, for 2 weeks). All mice were sacrificed on day 15. Body weight and tumor volume were assessed 2 times per week. Tumor weight was measured after sacrifice. Irinotecan combined with temozolomide was the most effective regimen compared to the untreated control group (p=0.022). Gemcitabine combined with docetaxel was also effective (p=0.026). Pazopanib and yondelis did not have significant efficacy compared to the untreated control (p=0.130, p=0.818). These results could be obtained within two months after the physician's request and were used for third-line therapy of the patient.","corpus_id":21746767,"score":2},{"doc_id":"29306021","title":"Recombinant methioninase in combination with doxorubicin (DOX) overcomes first-line DOX resistance in a patient-derived orthotopic xenograft nude-mouse model of undifferentiated spindle-cell sarcoma.","abstract":"We have previously established a patient-derived orthotopic xenograft (PDOX) model of undifferentiated spindle cell sarcoma (USCS). Recombinant methioninase (rMETase) has previously demonstrated efficacy in PDOX mouse models of human cancers. In the present study, we determined if rMETase in combination with doxorubicin (DOX) can overcome first-line DOX resistance in a PDOX models of USCS. The USCS PDOX mouse models were randomized into the following groups when tumor volume reached 100 mm3: G1, control without treatment; G2, doxorubicin (DOX) (3 mg/kg, intraperitoneal [i.p.] injection, weekly, for 2 weeks); G3, rMETase (100 units/mouse, i.p., daily, for 2 weeks); G4, DOX (3 mg/kg, i.p., weekly, for 2 weeks) combined with rMETase (100 units/mouse, i.p., daily, for 2 weeks). Tumor size and body weight were measured twice a week. On day 14 after initiation, the USCS PDOX tumor sizes were (G1): 360 ± 85 mm3; DOX (G2): 355 ± 111 mm3, p = .927; rMETase (G3): 182 ± 57 mm3, p = .0003; DOX + rMETase (G4): 134 ± 29 mm3, p = .00001. These results indicate that rMETase can overcome USCS resistance to DOX, which is first line therapy for this disease. The body weight of treated mice was not significantly different in any group. The present results demonstrate the power of the PDOX model to identify effective therapy for recalcitrant cancer and the potential of rMETase to overcome DOX resistance.","corpus_id":206431780,"score":2},{"doc_id":"29374999","title":"Tumor-targeting Salmonella typhimurium A1-R combined with recombinant methioninase and cisplatinum eradicates an osteosarcoma cisplatinum-resistant lung metastasis in a patient-derived orthotopic xenograft (PDOX) mouse model: decoy, trap and kill chemotherapy moves toward the clinic.","abstract":"In the present study, a patient-derived orthotopic xenograft (PDOX) model of recurrent cisplatinum (CDDP)-resistant metastatic osteosarcoma was treated with Salmonella typhimurium A1-R (S. typhimurium A1-R), which decoys chemoresistant quiescent cancer cells to cycle, and recombinant methioninase (rMETase), which selectively traps cancer cells in late S/G2, and chemotherapy. The PDOX models were randomized into the following groups 14 days after implantation: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, rMETase (100 unit/mouse, i.p., daily, for 2 weeks). G4, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks); G5, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks); G6, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks) and CDDP (6 mg/kg, i.p. injection, weekly, for 2 weeks). On day 14 after initiation, all treatments except CDDP alone, significantly inhibited tumor growth compared to untreated control: (CDDP: p = 0.586; rMETase: p = 0.002; S. typhimurium A1-R: p = 0.002; S. typhimurium A1-R combined with rMETase: p = 0.0004; rMETase combined with both S. typhimurium A1-R and CDDP: p = 0.0001). The decoy, trap and kill combination of S. typhimurium A1-R, rMETase and CDDP was the most effective of all therapies and was able to eradicate the metastatic osteosarcoma PDOX.","corpus_id":4735278,"score":2},{"doc_id":"29384032","title":"Individualized doxorubicin sensitivity testing of undifferentiated soft tissue sarcoma (USTS) in a patient-derived orthotopic xenograft (PDOX) model demonstrates large differences between patients.","abstract":"Doxorubicin (DOX) is often first-line treatment of undifferentiated/unclassified soft tissue sarcoma (USTS). However, the DOX response rate for USTS patients is low. Individualized precision-medicine technology that could identify DOX responders as well as non-responders would be of high value to cancer patients. In the present study, we established 5 patient-derived orthotopic xenograft (PDOX) nude mouse models from 5 USTS patients and evaluated the efficacy of DOX in each PDOX model. USTS's were grown orthotopically in the right thigh of nude mice to establish the PDOX models. Two weeks after implantation, the mouse models were randomized into two groups of 8 mice each: untreated control; and DOX (3 mg/kg, i.p., once a week for 2 weeks). DOX showed significant growth inhibition in only 2 USTS PDOX models out of 5 (p = 0.0054, p = 0.0055, respectively) on day 14 after initiation. DOX was ineffective in the other 3 PDOX models. However, even in the DOX-sensitive cases, DOX could not regress the PDOX tumors responding to treatment. The present study has important implications since this is the first in vivo study to compare the DOX sensitivity for USTS on multiple patient tumors. We showed that only two of five USTS were responsive to DOX, despite DOX being first line chemotherapy for USTS. The 3 resistant cases should not be treated with DOX clinically, in order to spare the patients' unnecessary toxicity. This PDOX model is useful for precise individualized drug sensitivity testing, especially for rare heterogeneous recalcitrant sarcomas such as USTS.","corpus_id":13767379,"score":2},{"doc_id":"29416666","title":"Recombinant methioninase (rMETase) is an effective therapeutic for BRAF-V600E-negative as well as -positive melanoma in patient-derived orthotopic xenograft (PDOX) mouse models.","abstract":"Melanoma is a recalcitrant disease. Melanoma patients with the BRAF-V600E mutation have been treated with the drug vemurafenib (VEM) which targets this mutation. However, we previously showed that VEM is not very effective against a BRAF-V600E melanoma mutant in a patient-derived orthotopic xenograft (PDOX) model. In contrast, we demonstrated that recombinant methioninase (rMETase) which targets the general metabolic defect in cancer of methionine dependence, was effective against the BRAF-V600E mutant melanoma PDOX model. In the present study, we demonstrate that rMETase is effective against a BRAF-V600E-negative melanoma PDOX which we established. Forty BRAF-V600E-negative melanoma PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n = 10); temozolomide (TEM) (25 mg/kg, p.o., 14 consecutive days, n = 10); rMETase (100 units, i.p., 14 consecutive days, n = 10); TEM + rMETase (TEM: 25 mg/kg, p.o., rMETase: 100 units, i.p., 14 consecutive days, n = 10). All treatments inhibited tumor growth compared to untreated control (TEM: p = 0.0003, rMETase: p = 0.0006, TEM/rMETase: p = 0.0002) on day 14 after initiation. Combination therapy of TEM and rMETase was significantly more effective than either mono-therapy (TEM: p = 0.0113, rMETase: p = 0.0173). The present study shows that TEM combined with rMETase is effective for BRAF-V600E-negative melanoma PDOX similar to the BRAF-V600E-positive mutation melanoma. These results suggest rMETase in combination with first-line chemotherapy can be highly effective in both BRAF-V600E-negative as well as BRAF-V600E-positive melanoma and has clinical potential for this recalcitrant disease.","corpus_id":21163866,"score":2},{"doc_id":"29481803","title":"Tumor-targeting Salmonella typhimurium A1-R is a highly effective general therapeutic for undifferentiated soft tissue sarcoma patient-derived orthotopic xenograft nude-mouse models.","abstract":"Undifferentiated soft tissue sarcoma (USTS) is a recalcitrant and heterogeneous subgroup of soft tissue sarcoma with high risk of metastasis and recurrence. Due to heterogeneity of USTS, there is no reliably effective first-line therapy. We have generated tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R), which previously showed strong efficacy on single patient-derived orthotopic xenograft (PDOX) models of Ewing's sarcoma and follicular dendritic cell sarcoma. In the present study, tumor resected from 4 patients with a biopsy-proven USTS (2 undifferentiated pleomorphic sarcoma [UPS], 1 undifferentiated sarcoma not otherwise specified [NOS] and 1 undifferentiated spindle cell sarcoma [USS]) were grown orthotopically in the biceps femoris muscle of mice to establish PDOX models. One USS model and one UPS model were doxorubicin (DOX) resistant. One UPS and the NOS model were partially sensitive to DOX. DOX is first-line therapy for these diseases. S. typhimurium A1-R arrested tumor growth all 4 models. In addition to arresting tumor growth in each case, S. typhimurium A1-R was significantly more efficacious than DOX in each case, thereby surpassing first-line therapy. These results suggest that S. typhimurium A1-R can be a general therapeutic for USTS and possibly sarcoma in general.","corpus_id":4768154,"score":2},{"doc_id":"29487690","title":"Temozolomide combined with irinotecan regresses a cisplatinum-resistant relapsed osteosarcoma in a patient-derived orthotopic xenograft (PDOX) precision-oncology mouse model.","abstract":"Relapsed osteosarcoma is a recalcitrant tumor. A patient's cisplatinum (CDDP)-resistant relapsed osteosarcoma lung metastasis was previously established orthotopically in the distal femur of mice to establish a patient-derived orthotopic xenograft (PDOX) model. In the present study, the PDOX models were randomized into the following groups when tumor volume reached 100 mm3: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); gemcitabine (GEM) (100 mg/kg, i.p., weekly, for 2 weeks) combined with docetaxel (DOC) (20 mg/kg, i.p., once); temozolomide (TEM) (25 mg/kg, p.o., daily, for 2 weeks) combined with irinotecan (IRN) (4 mg/kg i.p., daily for 2 weeks). Tumor size and body weight were measured with calipers and a digital balance twice a week. After 2 weeks, all treatments significantly inhibited tumor growth except CDDP compared to the untreated control: CDDP: p = 0.093; GEM+DOC: p = 0.0002, TEM+IRN: p < 0.0001. TEM combined with IRN was significantly more effective than either CDDP (p = 0.0001) or GEM combined with DOC (p = 0.0003) and significantly regressed the tumor volume compared to day 0 (p = 0.003). Thus the PDOX model precisely identified the combination of TEM-IRN that could regress the CDDP-resistant relapsed metastatic osteosarcoma PDOX.","corpus_id":3584333,"score":2},{"doc_id":"29491256","title":"Establishment of a Patient-Derived Tumor Xenograft Model and Application for Precision Cancer Medicine.","abstract":"Patient-derived xenograft (PDX) models can be created with the transplantation of cancerous cells or tissues from patients' primary tumors into immunodeficient mice. PDXs are now in the spotlight as more accurate human cancer models compared with mouse tumor and human cancer cell lines transplanted into mice. PDX technology leads to breakthroughs with the introduction of novel, highly immunodeficient mice such as NOG (NOD/Scid/IL2Rγnull), NSG (NOD/Scid/IL2Rγnull), and NOJ (NOD/Scid/Jak3null) mice. Xenograft efficiency differs by type of tumor, site of implantation, and tumor aggressiveness. Subcutaneous implantation is a standard method for PDX, and renal capsule or orthotropic implantation improves the efficiency. Despite positive test results in animal cancer models, significant numbers of novel drug candidates fail in clinical trials because conventional animal models such as murine tumor and human cancer cell line transplantation models do not always reflect the nature of human cancers. Since PDXs conserve the original tumor characteristics such as heterogeneous histology, clinical biomolecular signatures, malignant phenotypes and genotypes, tumor architecture, and tumor vasculature, they are currently believed to offer relevant predictive insights into clinical outcomes when evaluating the efficacy of novel cancer therapies. PDX banks with integrated genomic signatures are now established in many organizations including pharmaceutical companies. These PDX databases are becoming powerful tools for advancing precision cancer medicine.","corpus_id":4399747,"score":2},{"doc_id":"29541401","title":"Intra-tumor L-methionine level highly correlates with tumor size in both pancreatic cancer and melanoma patient-derived orthotopic xenograft (PDOX) nude-mouse models.","abstract":"An excessive requirement for methionine (MET) for growth, termed MET dependence, appears to be a general metabolic defect in cancer. We have previously shown that cancer-cell growth can be selectively arrested by MET restriction such as with recombinant methioninase (rMETase). In the present study, we utilized patient-derived orthotopic xenograft (PDOX) nude mouse models with pancreatic cancer or melanoma to determine the relationship between intra-tumor MET level and tumor size. After the tumors grew to 100 mm3, the PDOX nude mice were divided into two groups: untreated control and treated with rMETase (100 units, i.p., 14 consecutive days). On day 14 from initiation of treatment, intra-tumor MET levels were measured and found to highly correlate with tumor volume, both in the pancreatic cancer PDOX (p<0.0001, R2=0.89016) and melanoma PDOX (p<0.0001, R2=0.88114). Tumors with low concentration of MET were smaller. The present results demonstrates that patient tumors are highly dependent on MET for growth and that rMETase effectively lowers tumor MET.","corpus_id":3849509,"score":2},{"doc_id":"29623758","title":"Targeting altered cancer methionine metabolism with recombinant methioninase (rMETase) overcomes partial gemcitabine-resistance and regresses a patient-derived orthotopic xenograft (PDOX) nude mouse model of pancreatic cancer.","abstract":"Pancreatic cancer is a recalcitrant disease. Gemcitabine (GEM) is the most widely-used first-line therapy for pancreatic cancer, but most patients eventually fail. Transformative therapy is necessary to significantly improve the outcome of pancreatic cancer patients. Tumors have an elevated requirement for methionine and are susceptible to methionine restriction. The present study used a patient-derived orthotopic xenograft (PDOX) nude mouse model of pancreatic cancer to determine the efficacy of recombinant methioninase (rMETase) to effect methionine restriction and thereby overcome GEM-resistance. A pancreatic cancer obtained from a patient was grown orthotopically in the pancreatic tail of nude mice to establish the PDOX model. Five weeks after implantation, 40 pancreatic cancer PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n = 10); GEM (100 mg/kg, i.p., once a week for 5 weeks, n = 10); rMETase (100 units, i.p., 14 consecutive days, n = 10); GEM+rMETase (GEM: 100 mg/kg, i.p., once a week for 5 weeks, rMETase: 100 units, i.p., 14 consecutive days, n = 10). Although GEM partially inhibited PDOX tumor growth, combination therapy (GEM+rMETase) was significantly more effective than mono therapy (GEM: p = 0.0025, rMETase: p = 0.0010). The present study is the first demonstrating the efficacy of rMETase combination therapy in a pancreatic cancer PDOX model to overcome first-line therapy resistance in this recalcitrant disease.","corpus_id":4639569,"score":2},{"doc_id":"29737543","title":"Temozolomide regresses a doxorubicin-resistant undifferentiated spindle-cell sarcoma patient-derived orthotopic xenograft (PDOX): precision-oncology nude-mouse model matching the patient with effective therapy.","abstract":"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant cancer, resistant to conventional chemotherapy. A patient with high-grade USCS from a striated muscle was implanted orthotopically in the right biceps femoris muscle of mice to establish a patient-derived orthotopic xenograft (PDOX) model. The PDOX models were randomized into the following groups when tumor volume reached 100 mm3 : G1, control without treatment; G2, doxorubicin (DOX) (3 mg/kg, intraperitoneal [i.p.] injection, weekly, for 2 weeks); G3, temozolomide (TEM) (25 mg/kg, p.o., daily, for 14 days). Tumor size and body weight were measured with calipers and a digital balance twice a week. TEM significantly inhibited tumor volume growth compared to the untreated control and the DOX-treated group on day 14 after treatment initiation: control (G1): 343 ± 78 mm3 ; DOX (G2): 308 ± 31 mm3 , P = 0.272; TEM (G3): 85 ± 21 mm3 , P < 0.0001. TEM significantly regressed the tumor volume compared to day 0 (P = 0.019). There were no animal deaths in any group. The body weight of treated mice was not significantly different in any group. Tumors treated with DOX were comprised of spindle-shaped viable cells without apparent necrosis or inflammatory changes. In contrast, tumors treated with TEM showed extensive tumor necrosis. The present study demonstrates the potential power of matching the patient with an effective drug and saving the patient needless toxicity from ineffective drugs.","corpus_id":13684406,"score":2},{"doc_id":"29857821","title":"MEK inhibitor trametinib in combination with gemcitabine regresses a patient-derived orthotopic xenograft (PDOX) pancreatic cancer nude mouse model.","abstract":"Pancreatic cancer is resistant to treatment and needs precision individualized therapy to improve the outcome of this disease. Previously, we demonstrated that trametinib (TRA), a MEK inhibitor, could inhibit a pancreatic cancer patient-derived orthotopic xenograft (PDOX). In the present study, we show that gemcitabine (GEM) in combination with TRA was more effective than TRA alone. We implanted a patient pancreatic cancer orthotopically in the pancreatic tail of nude mice to establish the PDOX model. After seven weeks of tumor growth, we divided 32 pancreatic-cancer PDOX nude mice into 4 groups of eight: untreated control; GEM (once a week for 2 weeks); TRA (14 consecutive days); GEM + TRA (GEM: once a week for 2 weeks, TRA:14 consecutive days). We found that treated mice on day 14 had significantly reduced tumor volume in comparison to untreated control. TRA and the combination of GEM + TRA therapy significantly inhibited tumor development in comparison to GEM alone. However, GEM + TRA inhibited the PDOX tumor growth significantly greater than TRA alone. These results suggest the clinical potential of the combination of TRA and GEM for pancreatic cancer.","corpus_id":46923111,"score":2},{"doc_id":"23877869","title":"Sonoporation-enhanced chemotherapy significantly reduces primary tumour burden in an orthotopic pancreatic cancer xenograft.","abstract":"PURPOSE: Adenocarcinoma of the pancreas remains one of the most lethal human cancers. The high mortality rates associated with this form of cancer are subsequent to late-stage clinical presentation and diagnosis, when surgery is rarely possible and of modest chemotherapeutic impact. Survival rates following diagnosis with advanced pancreatic cancer are very low; typical mortality rates of 50% are expected within 3 months of diagnosis. However, adjuvant chemotherapy improves the prognosis of patients even after palliative surgery, and successful newer neoadjuvant chemotherapeutical modalities have recently been reported. For patients whose tumours appear unresectable, chemotherapy remains the only option. During the past two decades, the nucleoside analogue gemcitabine has become the first-line chemotherapy for pancreatic adenocarcinoma. In this study, we aim to increase the delivery of gemcitabine to pancreatic tumours by exploring the effect of sonoporation for localised drug delivery of gemcitabine in an orthotopic xenograft mouse model of pancreatic cancer. EXPERIMENTAL DESIGN: An orthotopic xenograft mouse model of luciferase expressing MIA PaCa-2 cells was developed, exhibiting disease development similar to human pancreatic adenocarcinoma. Subsequently, two groups of mice were treated with gemcitabine alone and gemcitabine combined with sonoporation; saline-treated mice were used as a control group. A custom-made focused ultrasound transducer using clinically safe acoustic conditions in combination with SonoVue® ultrasound contrast agent was used to induce sonoporation in the localised region of the primary tumour only. Whole-body disease development was measured using bioluminescence imaging, and primary tumour development was measured using 3D ultrasound. RESULTS: Following just two treatments combining sonoporation and gemcitabine, primary tumour volumes were significantly lower than control groups. Additional therapy dramatically inhibited primary tumour growth throughout the course of the disease, with median survival increases of up to 10% demonstrated in comparison to the control groups. CONCLUSION: Combined sonoporation and gemcitabine therapy significantly impedes primary tumour development in an orthotopic xenograft model of human pancreatic cancer, suggesting additional clinical benefits for patients treated with gemcitabine in combination with sonoporation.","corpus_id":23094615,"score":1},{"doc_id":"24507750","title":"Generation of orthotopic patient-derived xenografts from gastrointestinal stromal tumor.","abstract":"BACKGROUND: Gastrointestinal stromal tumor (GIST) is the most common sarcoma and its treatment with imatinib has served as the paradigm for developing targeted anti-cancer therapies. Despite this success, imatinib-resistance has emerged as a major problem and therefore, the clinical efficacy of other drugs has been investigated. Unfortunately, most clinical trials have failed to identify efficacious drugs despite promising in vitro data and pathological responses in subcutaneous xenografts. We hypothesized that it was feasible to develop orthotopic patient-derived xenografts (PDXs) from resected GIST that could recapitulate the genetic heterogeneity and biology of the human disease. METHODS: Fresh tumor tissue from three patients with pathologically confirmed GISTs was obtained immediately following tumor resection. Tumor fragments (4.2-mm3) were surgically xenografted into the liver, gastric wall, renal capsule, and pancreas of immunodeficient mice. Tumor growth was serially assessed with ultrasonography (US) every 3-4 weeks. Tumors were also evaluated with positron emission tomography (PET). Animals were sacrificed when they became moribund or their tumors reached a threshold size of 2500-mm3. Tumors were subsequently passaged, as well as immunohistochemically and histologically analyzed. RESULTS: Herein, we describe the first model for generating orthotopic GIST PDXs. We have successfully xenografted three unique KIT-mutated tumors into a total of 25 mice with an overall success rate of 84% (21/25). We serially followed tumor growth with US to describe the natural history of PDX growth. Successful PDXs resulted in 12 primary xenografts in NOD-scid gamma or NOD-scid mice while subsequent successful passages resulted in 9 tumors. At a median of 7.9 weeks (range 2.9-33.1 weeks), tumor size averaged 473 ± 695-mm³ (median 199-mm3, range 12.6-2682.5-mm³) by US. Furthermore, tumor size on US within 14 days of death correlated with gross tumor size on necropsy. We also demonstrated that these tumors are FDG-avid on PET imaging, while immunohistochemically and histologically the PDXs resembled the primary tumors. CONCLUSIONS: We report the first orthotopic model of human GIST using patient-derived tumor tissue. This novel, reproducible in vivo model of human GIST may enhance the study of GIST biology, biomarkers, personalized cancer treatments, and provide a preclinical platform to evaluate new therapeutic agents for GIST.","corpus_id":1548936,"score":1},{"doc_id":"25348321","title":"Establishment of orthotopic primary cervix cancer xenografts.","abstract":"Standard treatment for women who are diagnosed with stage IIB through IVA cervical cancer consists of cisplatin-based chemotherapy and radiation. Current options for patients with recurrent and metastatic disease are limited, and their median overall survival is <12 months. To date, biologic therapy has had little impact on survival, so identification of potential new targets is urgently required to develop novel therapeutic strategies. Developing relevant animal models for human cervix cancer is important to further enhance our understanding of the characteristics of these tumors and for identification and assessment of novel therapies. We have established a panel of orthotopically passaged xenografts (OCICx) by implanting cervix tumor pieces from patient biopsies directly into the cervix of mice. The tumors have been passaged up to five generations, were characterized histologically for tumor and stromal content and, where possible, related to similar measurements in the original patient biopsy. The tumors were found to metastasize to the para-aortic lymphnodes allowing assessment of their metastatic potential. Preliminary studies demonstrate aberrant expression of genes in the Hedgehog (Hh) pathway in the xenografts similar to findings in primary cervix cancers. The OCICx xenografts represent unique models to test strategies for targeting essential pathways in cervix cancer and metastasis.","corpus_id":26616109,"score":1},{"doc_id":"29487698","title":"Genetic and metabolic comparison of orthotopic and heterotopic patient-derived pancreatic-cancer xenografts to the original patient tumors.","abstract":"Tumors from 25 patients with pancreatic cancer were used to establish two patient-derived xenograft (PDX) models: orthotopic PDX (PDOX) and heterotopic (subcutaneous) PDX (PDHX). We compared gene expression by immunohistochemistry, single-nucleotide polymorphism (SNP), DNA methylation, and metabolite levels. The 4 cases, of the total of 13 in which simultaneous PDHX & PDOX models were established, were randomly selected. The molecular-genetic characteristics of the patient's tumor were well maintained in the two PDX models. SNP analysis demonstrated that both groups were more than 90% identical to the original patient's tumor, and there was little difference between the two models. DNA methylation of most genes was similar among the two models and the original patients tumor, but some gene sets were hypermethylated the in PDOX model and hypomethylated in the PDHX model. Most of the metabolites had a similar pattern to those of the original patient tumor in both PDX tumor models, but some metabolites were more prominent in the PDOX and PDHX models. This is the first simultaneous molecular-genetic and metabolite comparison of patient tumors and their tumors established in PDOX and PDHX models. The results indicate high fidelity of these critical properties of the patient tumors in the two models.","corpus_id":3588878,"score":1}],"string":"[\n {\n \"doc_id\": \"19291366\",\n \"title\": \"Tumor-targeting amino acid auxotrophic Salmonella typhimurium.\",\n \"abstract\": \"We have developed an effective bacterial cancer therapy strategy by targeting viable tumor tissue using Salmonella typhimurium auxotrophs that we have generated which grow in viable as well as necrotic areas of tumors. However, the auxotrophy severely restricts growth of these bacteria in normal tissue. The S. typhimurium A1-R mutant, which is auxotrophic for leu-arg and has high anti-tumor virulence, was developed in our laboratory. In vitro, A1-R infects tumor cells and causes nuclear destruction. A1-R was initially used to treat metastatic human prostate and breast tumors that had been orthotopically implanted in nude mice. Forty percent of treated mice were cured completely and survived as long as non-tumor-bearing mice. A1-R administered i.v. to nude mice with primary osteosarcoma and lung metastasis was highly effective, especially against metastasis. A1-R was also targeted to both axillary lymph and popliteal lymph node metastasis of human pancreatic cancer and fibrosarcoma, respectively, as well as lung metastasis of the fibrosarcoma in nude mice. The bacteria were delivered via a lymphatic channel to target the lymph node metastases and systemically via the tail vein to target the lung metastasis. The metastases were cured without the need of chemotherapy or any other treatment. A1-R was administered intratumorally to nude mice with an orthotopically transplanted human pancreatic tumor. The primary pancreatic cancer regressed without additional chemotherapy or any other treatment. A1-R was also effective against pancreatic cancer liver metastasis when administered intrasplenically to nude mice. The approach described here, where bacterial monotherapy effectively treats primary and metastatic tumors, is a significant improvement over previous bacterial tumor-therapy strategies that require combination with toxic chemotherapy. Three promoter clones engineered in S. enterica typhimurium were identified to have enhanced expression in bacteria growing in tumors relative to those growing in the spleen. The expression of therapeutics in Salmonella under the regulation of one or more promoters that are activated preferentially in tumors has the potential to improve the efficacy of Salmonella tumor therapy. Exploitation of the tumor-killing capability of Salmonella has great promise for a new paradigm of cancer therapy.\",\n \"corpus_id\": 23144815,\n \"score\": 2\n },\n {\n \"doc_id\": \"20179238\",\n \"title\": \"Patient-derived first generation xenografts of non-small cell lung cancers: promising tools for predicting drug responses for personalized chemotherapy.\",\n \"abstract\": \"PURPOSE: Current chemotherapeutic regimens have only modest benefit for non-small cell lung cancer (NSCLC) patients. Cumulative toxicities/drug resistance limit chemotherapy given after the first-line regimen. For personalized chemotherapy, clinically relevant NSCLC models are needed for quickly predicting the most effective regimens for therapy with curative intent. In this study, first generation subrenal capsule xenografts of primary NSCLCs were examined for (a) determining responses to conventional chemotherapeutic regimens and (b) selecting regimens most effective for individual patients. EXPERIMENTAL DESIGN: Pieces (1x3x3 mm(3)) of 32 nontreated, completely resected patients' NSCLCs were grafted under renal capsules of nonobese diabetic/severe combined immunodeficient mice and treated with (A) cisplatin+vinorelbine, (B) cisplatin+docetaxel, (C) cisplatin+gemcitabine, and positive responses (treated tumor area <or=50% of control, P < 0.05) were determined. Clinical outcomes of treated patients were acquired. RESULTS: Xenografts from all NSCLCs were established (engraftment rate, 90%) with the retention of major biological characteristics of the original cancers. The entire process of drug assessment took 8 weeks. Response rates to regimens A, B, and C were 28% (9 of 32), 42% (8 of 19), and 44% (7 of 16), respectively. Certain cancers that were resistant to a particular regimen were sensitive to others. The majority of responsive tumors contained foci of nonresponding cancer cells, indicative of tumor heterogeneity and potential drug resistance. Xenografts from six of seven patients who developed recurrence/metastasis were nonresponsive. CONCLUSIONS: Models based on first generation NSCLC subrenal capsule xenografts have been developed, which are suitable for quick assessment (6-8 weeks) of the chemosensitivity of patients' cancers and selection of the most effective regimens. They hold promise for application in personalized chemotherapy of NSCLC patients.\",\n \"corpus_id\": 31387377,\n \"score\": 2\n },\n {\n \"doc_id\": \"21559815\",\n \"title\": \"Second-line chemotherapy in patients with primary unknown cancer.\",\n \"abstract\": \"PURPOSE: There are few existing reports on the efficacy of second-line chemotherapy in patients with cancer of unknown primary site (CUP). The aim of this study was to identify characteristics of CUP patients linked to a positive response to chemotherapy. METHODS: We retrospectively studied the clinical outcomes of second-line chemotherapy in patients with CUP who had previously been treated with platinum-based first-line chemotherapy. RESULTS: A total of 27 patients received second-line chemotherapy. Of these patients, 5 (19%) showed an objective response to second-line chemotherapy; 4 of these patients had shown a favorable response to first-line chemotherapy and had a chemotherapy-free interval (CFI) of more than 4.5 months. Among the 8 patients in whom the CFI was more than 4.5 months, 4 (50%) showed an objective response to platinum-based second-line chemotherapy, whereas among the 16 patients with a CFI of less than 4.5 months, only 1 (6%) showed a response to any chemotherapeutic regimen. CONCLUSIONS: The response to second-line chemotherapy in CUP patients who had received platinum-based first-line treatment seemed to be associated with the response to first-line chemotherapy and the CFI. Although it remains unclear whether second-line chemotherapy might contribute to a survival benefit in patients with CUP, patients who show a favorable response to first-line chemotherapy and also a relatively prolonged CFI appear to be likely to benefit from second-line chemotherapy.\",\n \"corpus_id\": 21088307,\n \"score\": 2\n },\n {\n \"doc_id\": \"22584324\",\n \"title\": \"[Treatment of patients with cancer of an unknown primary site].\",\n \"abstract\": \"Cancer of unknown primary(CUP)is a heterogenous group of tumors that accounts for 3 to 5 percent of all malignancies. Due to CUP's heterogeneity, clinical trials are difficult to perform and articles published on the disease require careful interpretation. Among CUP's, there are several clinical groups that are treated with specific treatment modalities. Each clinical group has similar treatment effects and prognoses with common malignancies that arise in adjacent locations, such as breast cancer and head/neck cancer. Therefore, accurate histological diagnosis and careful clinical staging are important. However, many CUP's do not belong to these specific clinical groups and generally have a poor prognosis. The treatment is usually directed based upon histology, location of the tumor, and stage. Platinum agents, taxanes and other new cytotoxic drugs are often used for systemic therapy, but their efficacy is often limited. Currently, specific molecular markers and targeted therapy are being explored.\",\n \"corpus_id\": 12206628,\n \"score\": 2\n },\n {\n \"doc_id\": \"24435915\",\n \"title\": \"Efficacy of Salmonella typhimurium A1-R versus chemotherapy on a pancreatic cancer patient-derived orthotopic xenograft (PDOX).\",\n \"abstract\": \"The aim of this study is to determine the efficacy of tumor-targeting Salmonella typhimurium A1-R (A1-R) on pancreatic cancer patient-derived orthotopic xenografts (PDOX). The PDOX model was originally established from a pancreatic cancer patient in SCID-NOD mice. The pancreatic cancer PDOX was subsequently transplanted by surgical orthotopic implantation (SOI) in transgenic nude red fluorescent protein (RFP) mice in order that the PDOX stably acquired red fluorescent protein (RFP)-expressing stroma for the purpose of imaging the tumor after passage to non-transgenic nude mice in order to visualize tumor growth and drug efficacy. The nude mice with human pancreatic PDOX were treated with A1-R or standard chemotherapy, including gemcitabine (GEM), which is first-line therapy for pancreatic cancer, for comparison of efficacy. A1-R treatment significantly reduced tumor weight, as well as tumor fluorescence area, compared to untreated control (P = 0.011), with comparable efficacy of GEM, CDDP, and 5-FU. Histopathological response to treatment was defined according to Evans's criteria and A1-R had increased efficacy compared to standard chemotherapy. The present report is the first to show that A1-R is effective against a very low-passage patient tumor, in this case, pancreatic cancer. The data of the present report suggest A1-1 will have clinical activity in pancreatic cancer, a highly lethal and treatment-resistant disease and may be most effectively used in combination with other agents.\",\n \"corpus_id\": 6899767,\n \"score\": 2\n },\n {\n \"doc_id\": \"24924355\",\n \"title\": \"Efficacy of tumor-targeting Salmonella typhimurium A1-R on nude mouse models of metastatic and disseminated human ovarian cancer.\",\n \"abstract\": \"We report here the efficacy of tumor-targeting Salmonella typhimurium A1-R (A1-R) on mouse models of disseminated and metastatic ovarian cancer. The proliferation-inhibitory efficacy of A1-R on human ovarian cancer cell lines (SKOV-3-GFP, OVCAR-3-RFP) was initially demonstrated in vitro. Orthotopic and dissemination mouse models of ovarian cancer were made with the human ovarian cancer cell line SKOV-3-GFP. After tumor implantation, the mice were treated with A1-R (5 × 10(7) colony-forming units [CFU], i.v.), and there were no severe adverse events observed. In the orthotopic model, tumor volume after treatment was 276 ± 60.8 mm(3), compared to 930 ± 342 mm(3) in the untreated control group (P = 0.022). There was also a significant difference in survival between treated mice and untreated mice in a peritoneal dissemination model (P = 0.005). The results of this report demonstrate that A1-R is effective for highly aggressive human ovarian cancer in metastatic and dissemination mouse models and suggest its clinical potential for this highly treatment-resistant disease.\",\n \"corpus_id\": 45208730,\n \"score\": 2\n },\n {\n \"doc_id\": \"25394368\",\n \"title\": \"Selective efficacy of zoledronic acid on metastasis in a patient-derived orthotopic xenograph (PDOX) nude-mouse model of human pancreatic cancer.\",\n \"abstract\": \"BACKGROUND AND OBJECTIVES: Patient-derived orthotopic xenograft (PDOX) nude-mouse models replicate the behavior of clinical cancer, including metastasis. The objective of the study was to determine the efficacy of zoledronic acid (ZA) on metastasis of a patient-derived orthotopic xenograft (PDOX) nude-mouse model of pancreatic cancer. METHODS: In the present study, we examined the efficacy of ZA on pancreatic cancer growth and metastasis in a PDOX nude-mouse model. RESULTS: ZA monotherapy did not significantly suppress primary tumor growth. However, the primary tumor weight of gemcitabine (GEM) and combination GEM + ZA-treated mice was significantly decreased compared to the control group (GEM: P = 0.003; GEM + ZA: P = 0.002). The primary tumor weight of GEM + ZA-treated mice was significantly decreased compared to GEM-treated mice (P = 0.016). The metastasis weight decreased in ZA- or GEM-treated mice compared to the control group (ZA: P = 0.009; GEM: P = 0.007. No metastasis was detected in combination GEM + ZA-treated mice compared to the control group (GEM + ZA; P = 0.005). CONCLUSIONS: The results of the present study indicate that ZA can selectively target metastasis in a pancreatic cancer PDOX model and that the combination of ZA and GEM should be evaluated clinically in the near future for this highly treatment-resistant disease.\",\n \"corpus_id\": 206175793,\n \"score\": 2\n },\n {\n \"doc_id\": \"25402324\",\n \"title\": \"Efficacy of tumor-targeting Salmonella typhimurium A1-R in combination with anti-angiogenesis therapy on a pancreatic cancer patient-derived orthotopic xenograft (PDOX) and cell line mouse models.\",\n \"abstract\": \"The aim of the present study was to examine the efficacy of tumor-targeting Salmonella typhimurium A1-R treatment following anti-vascular endothelial growth factor (VEGF) therapy on VEGF-positive human pancreatic cancer. A pancreatic cancer patient-derived orthotopic xenograft (PDOX) that was VEGF-positive and an orthotopic VEGF-positive human pancreatic cancer cell line (MiaPaCa-2-GFP) as well as a VEGF-negative cell line (Panc-1) were tested. Nude mice with these tumors were treated with gemcitabine (GEM), bevacizumab (BEV), and S. typhimurium A1-R. BEV/GEM followed by S. typhimurium A1-R significantly reduced tumor weight compared to BEV/GEM treatment alone in the PDOX and MiaPaCa-2 models. Neither treatment was as effective in the VEGF-negative model as in the VEGF-positive models. These results demonstrate that S. typhimurium A1-R following anti-angiogenic therapy is effective on pancreatic cancer including the PDOX model, suggesting its clinical potential.\",\n \"corpus_id\": 18010924,\n \"score\": 2\n },\n {\n \"doc_id\": \"25483077\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R decoys quiescent cancer cells to cycle as visualized by FUCCI imaging and become sensitive to chemotherapy.\",\n \"abstract\": \"Quiescent cancer cells are resistant to cytotoxic agents which target only proliferating cancer cells. Time-lapse imaging demonstrated that tumor-targeting Salmonella typhimurium A1-R (A1-R) decoyed cancer cells in monolayer culture and in tumor spheres to cycle from G0/G1 to S/G2/M, as demonstrated by fluorescence ubiquitination-based cell cycle indicator (FUCCI) imaging. A1-R infection of FUCCI-expressing subcutaneous tumors growing in nude mice also decoyed quiescent cancer cells, which were the majority of the cells in the tumors, to cycle from G0/G1 to S/G2/M, thereby making them sensitive to cytotoxic agents. The combination of A1-R and cisplatinum or paclitaxel reduced tumor size compared with A1-R monotherapy or cisplatinum or paclitaxel alone. The results of this study demonstrate that A1-R can decoy quiescent cancer cells to cycle to S/G2/M and sensitize them to cytotoxic chemotherapy. These results suggest a new paradigm of bacterial-decoy chemotherapy of cancer.\",\n \"corpus_id\": 34911807,\n \"score\": 2\n },\n {\n \"doc_id\": \"25689852\",\n \"title\": \"Establishment of a patient-derived orthotopic Xenograft (PDOX) model of HER-2-positive cervical cancer expressing the clinical metastatic pattern.\",\n \"abstract\": \"Squamous cell carcinoma of the cervix, highly prevalent in the developing world, is often metastatic and treatment resistant with no standard treatment protocol. Our laboratory pioneered the patient-derived orthotopic xenograft (PDOX) nude mouse model with the technique of surgical orthotopic implantation (SOI). Unlike subcutaneous transplant patient-derived xenograft (PDX) models, PDOX models metastasize. Most importantly, the metastasis pattern correlates to the patient. In the present report, we describe the development of a PDOX model of HER-2-positive cervical cancer. Metastasis after SOI in nude mice included peritoneal dissemination, liver metastasis, lung metastasis as well as lymph node metastasis reflecting the metastatic pattern in the donor patient. Metastasis was detected in 4 of 6 nude mice with primary tumors. Primary tumors and metastases in the nude mice had histological structures similar to the original tumor and were stained by an anti-HER-2 antibody in the same pattern as the patient's cancer. The metastatic pattern, histology and HER-2 tumor expression of the patient were thus preserved in the PDOX model. In contrast, subcutaneous transplantation of the patient's cervical tumors resulted in primary growth but not metastasis.\",\n \"corpus_id\": 8546713,\n \"score\": 2\n },\n {\n \"doc_id\": \"25800176\",\n \"title\": \"Fluorescence-guided surgery, but not bright-light surgery, prevents local recurrence in a pancreatic cancer patient derived orthotopic xenograft (PDOX) model resistant to neoadjuvant chemotherapy (NAC).\",\n \"abstract\": \"BACKGROUND: The aim of this study is to determine the efficacy of neoadjuvant chemotherapy (NAC) with gemcitabine (GEM) in combination with fluorescence-guided surgery (FGS) on a pancreatic cancer patient derived orthotopic xenograft (PDOX) model. METHODS: A PDOX model was established from a CEA-positive tumor from a patient who had undergone a pancreaticoduodenectomy for pancreatic adenocarcinoma. Mice were randomized to 4 groups: bright light surgery (BLS) only; BLS + NAC; FGS only; and FGS + NAC. An anti-CEA antibody conjugated to DyLight 650 was administered intravenously via the tail vein of mice with a pancreatic cancer PDOX 24 h before surgery. RESULTS: The PDOX was clearly labeled with fluorophore-conjugated anti-CEA antibody. Only one out of 8 mice had local recurrence in the FGS only group and zero out of 8 mice had local recurrence in the FGS + NAC which was significantly lower than BLS only or BLS + NAC mice, where local disease recurred in 6 out of 8 mice in each treatment group (p = 0.041 and p = 0.007, respectively). NAC did not significantly reduce recurrence rates when combined with either FGS or BLS. CONCLUSION: These results indicate that FGS can significantly reduce local recurrence compared to BLS in pancreatic cancer resistant to NAC.\",\n \"corpus_id\": 44325772,\n \"score\": 2\n },\n {\n \"doc_id\": \"25957417\",\n \"title\": \"Intraperitoneal administration of tumor-targeting Salmonella typhimurium A1-R inhibits disseminated human ovarian cancer and extends survival in nude mice.\",\n \"abstract\": \"UNLABELLED: Peritoneal disseminated cancer is highly treatment resistant. We here report the efficacy of intraperitoneal (i.p.) administration of tumor-targeting Salmonella typhimurium A1-R in a nude mouse model of disseminated human ovarian cancer. The mouse model was established by intraperitoneal injection of the human ovarian cancer cell line SKOV3-GFP. Seven days after implantation, mice were treated with S. typhimurium A1-R via intravenous (i.v.) or i.p. administration at the same dose, 5 × 10(7) CFU, once per week. Both i.v. and i.p. treatments effected prolonged survival compared with the untreated control group (P=0.025 and P<0.001, respectively). However, i.p. treatment was less toxic than i.v. TREATMENT: Tumor-specific targeting of S. typhimurium A1-R was confirmed with bacterial culture from tumors and various organs and tumor or organ colony formation after i.v. or i.p. injection. Selective tumor targeting was most effective with i.p. administration. The results of the present study show S. typhimurium A1-R has promising clinical potential for disseminated ovarian cancer, especially via i.p. administration.\",\n \"corpus_id\": 7133817,\n \"score\": 2\n },\n {\n \"doc_id\": \"26047477\",\n \"title\": \"Tumor-Targeting Salmonella typhimurium A1-R in Combination with Trastuzumab Eradicates HER-2-Positive Cervical Cancer Cells in Patient-Derived Mouse Models.\",\n \"abstract\": \"We have previously developed mouse models of HER-2-positive cervical cancer. Tumors in nude mice had histological structures similar to the original tumor and were stained by anti-HER-2 antibody in the same pattern as the patient's cancer. We have also previously developed tumor-targeting Salmonella typhimurium A1-R and have demonstrated its efficacy against patient-derived tumor mouse models, both alone and in combination. In the current study, we determined the efficacy of S. typhimurium A1-R in combination with trastuzumab on a patient-cancer nude-mouse model of HER-2 positive cervical cancer. Mice were randomized to 5 groups and treated as follows: (1) no treatment; (2) carboplatinum (30 mg/kg, ip, weekly, 5 weeks); (3) trastuzumab (20 mg/kg, ip, weekly, 5 weeks); (4) S. typhimurium A1-R (5 × 107 CFU/body, ip, weekly, 5 weeks); (5) S. typhimurium A1-R (5 × 107 CFU/body, ip, weekly, 5 weeks) + trastuzumab (20 mg/kg, ip, weekly, 5 weeks). All regimens had significant efficacy compared to the untreated mice. The relative tumor volume of S. typhimurium A1-R + trastuzumab-treated mice was smaller compared to trastuzumab alone (p = 0.007) and S. typhimurium A1-R alone (p = 0.039). No significant body weight loss was found compared to the no treatment group except for carboplatinum-treated mice (p = 0.021). Upon histological examination, viable tumor cells were not detected, and replaced by stromal cells in the tumors treated with S. typhimurium A1-R + trastuzumab. The results of the present study suggest that S. typhimurium A1-R and trastuzumab in combination are highly effective against HER-2-expressing cervical cancer.\",\n \"corpus_id\": 17513596,\n \"score\": 2\n },\n {\n \"doc_id\": \"26088297\",\n \"title\": \"Color-coding cancer and stromal cells with genetic reporters in a patient-derived orthotopic xenograft (PDOX) model of pancreatic cancer enhances fluorescence-guided surgery.\",\n \"abstract\": \"Precise fluorescence-guided surgery (FGS) for pancreatic cancer has the potential to greatly improve the outcome in this recalcitrant disease. To achieve this goal, we have used genetic reporters to color code cancer and stroma cells in a patient-derived orthotopic xenograft (PDOX) model. The telomerase-dependent green fluorescent protein (GFP)-containing adenovirus OBP-401 was used to label the cancer cells of a pancreatic cancer PDOX. The PDOX was previously grown in a red fluorescent protein (RFP) transgenic mouse that stably labeled the PDOX stroma cells bright red. The color-coded PDOX model enabled FGS to completely resect the pancreatic tumors including stroma. Dual-colored FGS significantly prevented local recurrence, which bright-light surgery or single-color FGS could not. FGS, with color-coded cancer and stroma cells has important potential for improving the outcome of recalcitrant-cancer surgery.\",\n \"corpus_id\": 14631190,\n \"score\": 2\n },\n {\n \"doc_id\": \"26375054\",\n \"title\": \"Therapeutic efficacy of tumor-targeting Salmonella typhimurium A1-R on human colorectal cancer liver metastasis in orthotopic nude-mouse models.\",\n \"abstract\": \"Liver metastasis is the most frequent cause of death from colon and other cancers. Generally, liver metastasis is recalcitrant to treatment. The aim of this study is to determine the efficacy of tumor-targeting Salmonella typhimurium A1-R on liver metastasis in orthotopic mouse models. HT-29 human colon cancer cells expressing red fluorescent protein (RFP) were used in the present study. S. typhimurium A1-R infected HT-29 cells in a time-dependent manner, inhibiting cancer-cell proliferation in vitro. S. typhimurium A1-R promoted tumor necrosis and inhibited tumor growth in a subcutaneous tumor mouse model of HT-29-RFP. In orthotopic mouse models, S. typhimurium A1-R targeted liver metastases and significantly reduced their growth. The results of this study demonstrate the future clinical potential of S. typhimurium A1-R targeting of liver metastasis.\",\n \"corpus_id\": 2516025,\n \"score\": 2\n },\n {\n \"doc_id\": \"26431498\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R inhibits human prostate cancer experimental bone metastasis in mouse models.\",\n \"abstract\": \"Bone metastasis is a frequent occurrence in prostate cancer patients and often is lethal. Zoledronic acid (ZOL) is often used for bone metastasis with limited efficacy. More effective models and treatment methods are required to improve the outcome of prostate cancer patients. In the present study, the effects of tumor-targeting Salmonella typhimurium A1-R were analyzed in vitro and in vivo on prostate cancer cells and experimental bone metastasis. Both ZOL and S. typhimurium A1-R inhibited the growth of PC-3 cells expressing red fluorescent protien in vitro. To investigate the efficacy of S. typhimurium A1-R on prostate cancer experimental bone metastasis, we established models of both early and advanced stage bone metastasis. The mice were treated with ZOL, S. typhimurium A1-R, and combination therapy of both ZOL and S. typhimurium A1-R. ZOL and S. typhimurium A1-R inhibited the growth of solitary bone metastases. S. typhimurium A1-R treatment significantly decreased bone metastasis and delayed the appearance of PC-3 bone metastases of multiple mouse models. Additionally, S. typhimurium A1-R treatment significantly improved the overall survival of the mice with multiple bone metastases. The results of the present study indicate that S. typhimurium A1-R is useful to prevent and inhibit prostate cancer bone metastasis and has potential for future clinical use in the adjuvant setting.\",\n \"corpus_id\": 29988503,\n \"score\": 2\n },\n {\n \"doc_id\": \"26846797\",\n \"title\": \"Tumor-Targeting Salmonella typhimurium A1-R: An Overview.\",\n \"abstract\": \"The present chapter reviews the development of the tumor-targeting amino-acid auxotrophic strain S. typhimurium A1 and the in vivo selection and characterization of the high-tumor-targeting strain S. typhimurium A1-R. Efficacy of S. typhimurium A1-R in nude-mouse models of prostate, breast, pancreatic, and ovarian cancer, as well as sarcoma and glioma in orthotopic mouse models is described. Also reviewed is efficacy of S. typhimurium A1-R targeting of primary bone tumor and lung metastasis of high-grade osteosarcoma, breast-cancer brain metastasis, and experimental breast-cancer bone metastasis in orthotopic mouse models. The efficacy of S. typhimurium A1-R on pancreatic cancer stem cells, on pancreatic cancer in combination with anti-angiogenic agents, as well as on cervical cancer, soft-tissue sarcoma, and pancreatic cancer patient-derived orthotopic xenograft (PDOX) mouse models, is also described.\",\n \"corpus_id\": 34206699,\n \"score\": 2\n },\n {\n \"doc_id\": \"26846809\",\n \"title\": \"Methods for Tumor Targeting with Salmonella typhimurium A1-R.\",\n \"abstract\": \"Salmonella typhimurium A1-R (S. typhimurium A1-R) has shown great preclinical promise as a broad-based anti-cancer therapeutic (please see Chapter 1 ). The present chapter describes materials and methods for the preclinical study of S. typhimurium A1-R in clinically-relevant mouse models. Establishment of orthotopic metastatic mouse models of the major cancer types is described, as well as other useful models, for efficacy studies of S. typhimurium A1-R or other tumor-targeting bacteria, as well. Imaging methods are described to visualize GFP-labeled S. typhimurium A1-R, as well as GFP- and/or RFP-labeled cancer cells in vitro and in vivo, which S. typhimurium A1-R targets. The mouse models include metastasis to major organs that are life-threatening to cancer patients including the liver, lung, bone, and brain and how to target these metastases with S. typhimurium A1-R. Various routes of administration of S. typhimurium A1-R are described with the advantages and disadvantages of each. Basic experiments to determine toxic effects of S. typhimurium A1-R are also described. Also described are methodologies for combining S. typhimurium A1-R and chemotherapy. The testing of S. typhimurium A1-R on patient tumors in patient-derived orthotopic xenograft (PDOX) mouse models is also described. The major methodologies described in this chapter should be translatable for clinical studies.\",\n \"corpus_id\": 19597283,\n \"score\": 2\n },\n {\n \"doc_id\": \"26846810\",\n \"title\": \"Salmonella typhimurium A1-R and Cell-Cycle Decoy Therapy of Cancer.\",\n \"abstract\": \"Cancer cells in G0/G1 are resistant to cytotoxic chemotherapy agents which kill only cycling cancer cells. Salmonella typhimurium A1-R (S. typhimurium A1-R) decoyed cancer cells in monolayer culture and in tumor spheres to cycle from G0/G1 to S/G2/M, as demonstrated by fluorescence ubiquitination-based cell cycle indicator (FUCCI) imaging. S. typhimurium A1-R targeted FUCCI-expressing subcutaneous tumors, and tumors growing on the liver, growing in nude mice and also decoyed quiescent cancer cells, which were the majority of the cells in the tumors, to cycle from G0/G1 to S/G2/M. The S. typhimurium A1-R-decoyed cancer cells became sensitive to cytotoxic agents.\",\n \"corpus_id\": 45367328,\n \"score\": 2\n },\n {\n \"doc_id\": \"26846811\",\n \"title\": \"Future of Bacterial Therapy of Cancer.\",\n \"abstract\": \"Bacterial therapy of cancer has a centuries-long history and was first-line therapy at the hospital in New York City that would become Memorial Sloan-Kettering Cancer Center, under Dr. William B. Coley. However, after Coley's death in 1936, bacterial therapy of cancer ceased in the clinic until the present century. Clinical trials have been recently carried out for strains of the obligate anaerobe Clostridium novyi with the toxin gene deleted, and on an attenuated strain of Salmonella typhimurium (S. typhimurium), which is a facultative anaerobe that can grow in viable, as well as necrotic, areas of tumors, unlike Clostridium, which can only grow in the hypoxic areas. Our laboratory has developed the novel strain S. typhimurium A1-R that is effective against all tumor types in clinically-relevant mouse models, including patient-derived orthotopic xenograft (PDOX) mouse models. This chapter suggests future clinical applications for S. typhimurium A1-R.\",\n \"corpus_id\": 10295493,\n \"score\": 2\n },\n {\n \"doc_id\": \"26859573\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R in combination with doxorubicin eradicate soft tissue sarcoma in a patient-derived orthotopic xenograft (PDOX) model.\",\n \"abstract\": \"A patient with high grade undifferentiated pleomorphic soft-tissue sarcoma from a striated muscle was grown orthotopically in the right biceps femoris muscle of mice to establish a patient-derived orthotopic xenograft (PDOX) model. Twenty PDOX mice were divided into 4 groups: G1, control without treatment; G2, Salmonella typhimurium (S. typhimurium)A1-R administered by intratumoral (i.t.) injection once a week for 4 weeks; G3, doxorubicin (DOX) administered by intraperitoneal (i.p.) injection once a week for 4 weeks; G4, S. typhimurium A1-R (i.t.) administered once a week for 2 weeks followed by i.p. doxorubicin once a week for 2 weeks. On day 25 from the initiation of treatment, tumor volume in G2, G3, and G4 was significantly lower than G1. Mice found without gross tumor included one mouse (20%) in G2; one mouse (20%) in G3; and 3 mice (60%) in G4. Body weight loss did not significantly differ between the 3 treated groups or from the untreated control. Histological examination revealed eradication of tumor only in G4 where mice were treated with S. typhimurium A1-R followed by DOX. Our present study indicates future clinical potential of combining S. typhimurium A1-R with chemotherapy such as DOX for soft tissue sarcoma patients.\",\n \"corpus_id\": 252170,\n \"score\": 2\n },\n {\n \"doc_id\": \"27105519\",\n \"title\": \"High efficacy of tumor-targeting Salmonella typhimurium A1-R on a doxorubicin- and dactolisib-resistant follicular dendritic-cell sarcoma in a patient-derived orthotopic xenograft PDOX nude mouse model.\",\n \"abstract\": \"Follicular dendritic-cell sarcoma (FDCS) is a rare and recalcitrant disease. In the present study, a patient-derived orthotopic xenograft (PDOX) mouse model of FDCS was established in the biceps muscle of nude mice. The FDCS PDOX was resistant to both doxorubicin (DOX) and NVP-BEZ235, dactolisib (BEZ) an experimental agent which is a dual pan-phosphoinositide 3-kinase-mammalian target of rapamycin inhibitor. However, in contrast to DOX and BEZ, the FDCS PDOX was sensitive to the tumor-targeting bacterial strain, Salmonella typhimurium A1-R (S. typhimurium A1-R). The combination of S. typhimurium A1-R and either DOX or BEZ did not increase the antitumor efficacy of S. typhimurium A1-R, indicating that DOX and BEZ were not active in this PDOX model. The efficacy of S. typhimurium A1-R in this recalcitrant FDCS gives strong impetus to move bacterial therapy to clinical trials for this disease. The findings of the present study are of particular importance since it demonstrates that S. typhimurium A1-R is effective in a PDOX model of FDCS established from a patient who failed DOX therapy.\",\n \"corpus_id\": 16203307,\n \"score\": 2\n },\n {\n \"doc_id\": \"27286459\",\n \"title\": \"Effective molecular targeting of CDK4/6 and IGF-1R in a rare FUS-ERG fusion CDKN2A-deletion doxorubicin-resistant Ewing's sarcoma patient-derived orthotopic xenograft (PDOX) nude-mouse model.\",\n \"abstract\": \"Ewing's sarcoma is a rare and aggressive malignancy. In the present study, tumor from a patient with a Ewing's sarcoma with cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) loss and FUS-ERG fusion was implanted in the right chest wall of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. The aim of the present study was to determine efficacy of cyclin-dependent kinase 4/6 (CDK4/6) and insulin-like growth factor-1 receptor (IGF-1R) inhibitors on the Ewing's sarcoma PDOX. The PDOX models were randomized into the following groups when tumor volume reached 50 mm3: G1, untreated control; G2, doxorubicin (DOX) (intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, CDK4/6 inhibitor (palbociclib, PD0332991, per oral (p.o.), daily, for 14 days); G4, IGF-1R inhibitor (linsitinib, OSI-906, p.o., daily, for 14 days). Tumor growth was significantly suppressed both in G3 (palbociclib) and in G4 (linsitinib) compared to G1 (untreated control) at all measured time points. In contrast, DOX did not inhibit tumor growth at any time point, which is consistent with the failure of DOX to control tumor growth in the patient. The results of the present study demonstrate the power of the PDOX model to identify effective targeted molecular therapy of a recalcitrant DOX-resistant Ewing's sarcoma with specific genetic alterations. The results of this study suggest the potential of PDOX models for individually-tailored, effective targeted therapy for recalcitrant cancer.\",\n \"corpus_id\": 7280485,\n \"score\": 2\n },\n {\n \"doc_id\": \"27500926\",\n \"title\": \"Efficacy of Tumor-Targeting Salmonella A1-R on a Melanoma Patient-Derived Orthotopic Xenograft (PDOX) Nude-Mouse Model.\",\n \"abstract\": \"Tumor-targeting Salmonella enterica serovar Typhimurium A1-R (Salmonella A1-R) had strong efficacy on a melanoma patient-derived orthotopic xenograft (PDOX) nude-mouse model. GFP-expressing Salmonella A1-R highly and selectively colonized the PDOX melanoma and significantly suppressed tumor growth (p = 0.021). The combination of Salmonella A1-R and cisplatinum (CDDP), both at low-dose, also significantly suppressed the growth of the melanoma PDOX (P = 0.001). Salmonella A1-R has future clinical potential for combination chemotherapy with CDDP of melanoma, a highly-recalcitrant cancer.\",\n \"corpus_id\": 15528318,\n \"score\": 2\n },\n {\n \"doc_id\": \"27683127\",\n \"title\": \"High-efficacy targeting of colon-cancer liver metastasis with Salmonella typhimurium A1-R via intra-portal-vein injection in orthotopic nude-mouse models.\",\n \"abstract\": \"Liver metastasis is the main cause of colon cancer-related death and is a recalcitrant disease. We report here the efficacy and safety of intra-portal-vein (iPV) targeting of Salmonella typhimurium A1-R on colon cancer liver metastasis in a nude-mouse orthotopic model. Nude mice with HT29 human colon cancer cells, expressing red fluorescent protein (RFP) (HT29-RFP), growing in the liver were administered S. typhimurium A1-R by either iPV (1×104 colony forming units (CFU)/100 μl) or, for comparison, intra-venous injection (iv; 5×107 CFU/100 μl). Similar amounts of bacteria were delivered to the liver with the two doses, indicating that iPV delivery is 5×103 times more efficient than iv delivery. Treatment efficacy was evaluated by tumor fluorescent area (mm2) and total fluorescence intensity. Tumor fluorescent area and fluorescence intensity highly correlated (p<0.0001). iPV treatment was more effective compared to both untreated control and iv treatment (p<0.01 and p<0.05, respectively with iPV treatment with S. typhimurium arresting metastatic growth). There were no significant differences in body weight between all groups. The results of this study suggest that S. typhimurium A1-R administered iPV has potential for peri-operative adjuvant treatment of colon cancer liver metastasis.\",\n \"corpus_id\": 12291312,\n \"score\": 2\n },\n {\n \"doc_id\": \"27690220\",\n \"title\": \"Vemurafenib-resistant BRAF-V600E-mutated melanoma is regressed by MEK-targeting drug trametinib, but not cobimetinib in a patient-derived orthotopic xenograft (PDOX) mouse model.\",\n \"abstract\": \"Melanoma is a recalcitrant disease. The present study used a patient-derived orthotopic xenograft (PDOX) model of melanoma to test sensitivity to three molecularly-targeted drugs and one standard chemotherapeutic. A BRAF-V600E-mutant melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a PDOX model. Two weeks after implantation, 50 PDOX nude mice were divided into 5 groups: G1, control without treatment; G2, vemurafenib (VEM) (30 mg/kg); G3; temozolomide (TEM) (25 mg/kg); G4, trametinib (TRA) (0.3 mg/kg); and G5, cobimetinib (COB) (5 mg/kg). Each drug was administered orally, daily for 14 consecutive days. Tumor sizes were measured with calipers twice a week. On day 14 from initiation of treatment, TRA, an MEK inhibitor, was the only agent of the 4 tested that caused tumor regression (P < 0.001 at day 14). In contrast, another MEK inhibitor, COB, could slow but not arrest growth or cause regression of the melanoma. First-line therapy TEM could slow but not arrest tumor growth or cause regression. The patient in this study had a BRAF-V600E-mutant melanoma and would be considered to be a strong candidate for VEM as first-line therapy, since VEM targets this mutation. However, VEM was not effective. The PDOX model thus helped identify the very-high efficacy of TRA against the melanoma PDOX and is a promising drug for this patient. These results demonstrate the powerful precision of the PDOX model for cancer therapy, not achievable by genomic analysis alone.\",\n \"corpus_id\": 16003329,\n \"score\": 2\n },\n {\n \"doc_id\": \"27765934\",\n \"title\": \"Patient-derived mouse models of cancer need to be orthotopic in order to evaluate targeted anti-metastatic therapy.\",\n \"abstract\": \"Patient-derived xenograft (PDX) mouse models of cancer are emerging as an important component of personalized precision cancer therapy. However, most models currently offered to patients have their tumors subcutaneously-transplanted in immunodeficient mice, which rarely metastasize. In contrast, orthotopic-transplant patient-derived models, termed patient-derived orthotopic xenografts (PDOX), usually metastasize as in the patient. We demonstrate in the present report why orthotopic models are so important for the patient, since primary and metastatic tumors developed in an orthotopic model can have differential chemosensitivity, not detectable in standard subcutaneous tumor models. A subcutaneous nude mouse model of HER-2 expressing cervical carcinoma was not sensitive to entinostat (a benzamide histone deactylase inhibitor), which also did not inhibit primary tumor growth in a PDOX model of the same tumor. However, in the PDOX model, entinostat alone significantly reduced the metastatic tumor burden, compared to the control. Thus, only the PDOX model could be used to discover the anti-metastatic activity of entinostat for this patient. The results of the present report indicate the importance of using mouse models that can recapitulate metastatic cancer for precisely individualizing cancer therapy.\",\n \"corpus_id\": 6976813,\n \"score\": 2\n },\n {\n \"doc_id\": \"27830986\",\n \"title\": \"Patient-derived orthotopic xenograft (PDOX) mouse model of adult rhabdomyosarcoma invades and recurs after resection in contrast to the subcutaneous ectopic model.\",\n \"abstract\": \"Rhabdomyosarcoma (RMS) is a rare mesenchymal tumor. The aim of the present study was to develop a patient-derived orthotopic xenograft (PDOX) mouse model of RMS and compare the PDOX model to a subcutaneous (s.c.)-transplant model. A patient RMS from a striated muscle was grown orthotopically in the right biceps femoris muscle and right quadriceps muscle of nude mice to establish a PDOX model, as well as under the skin to establish an s.c. MODEL: PDOX tumors grew at a statistically-significant faster rate compared to the s.c. tumors. Recurrence after surgical resection occurred only in PDOX tumors, not in the s.c. MODEL: Histologically, only the PDOX model was shown to be invasive. In conclusion, these results indicate that the PDOX model of adult RMS is malignant and the subcutaneous model is benign. These results emphasize that a proper tumor microenvironment is necessary for patient-like behavior of a tumor in a mouse model.\",\n \"corpus_id\": 26074344,\n \"score\": 2\n },\n {\n \"doc_id\": \"27835903\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R combined with temozolomide regresses malignant melanoma with a BRAF-V600E mutation in a patient-derived orthotopic xenograft (PDOX) model.\",\n \"abstract\": \"Melanoma is a recalcitrant disease in need of transformative therapuetics. The present study used a patient-derived orthotopic xenograft (PDOX) nude-mouse model of melanoma with a BRAF-V600E mutation to determine the efficacy of temozolomide (TEM) combined with tumor-targeting Salmonella typhimurium A1-R. A melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a PDOX model. Two weeks after implantation, 40 PDOX nude mice were divided into 4 groups: G1, control without treatment (n = 10); G2, TEM (25 mg/kg, administrated orally daily for 14 consecutive days, n = 10); G3, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., once a week for 2 weeks, n = 10); G4, TEM combined with S. typhimurium A1-R (25 mg/kg, administrated orally daily for 14 consecutive days and 5 × 107 CFU/100 μl, i.v., once a week for 2 weeks, respectively, n = 10). Tumor sizes were measured with calipers twice a week. On day 14 from initiation of treatment, all treatments significantly inhibited tumor growth compared to untreated control (TEM: p < 0.0001; S. typhimurium A1-R: p < 0.0001; TEM combined with S. typhimurium A1-R: p < 0.0001). TEM combined with S. typhimurium A1-R was significantly more effective than either S. typhimurium A1-R (p = 0.0004) alone or TEM alone (p = 0.0017). TEM combined with S. typhimurium A1-R could regress the melanoma in the PDOX model and has important future clinical potential for melanoma patients.\",\n \"corpus_id\": 3491201,\n \"score\": 2\n },\n {\n \"doc_id\": \"28011474\",\n \"title\": \"Cervical Cancer Patient-Derived Orthotopic Xenograft (PDOX) Is Sensitive to Cisplatinum and Resistant to Nab-paclitaxel.\",\n \"abstract\": \"BACKGROUND: Cervical cancer is a world-wide problem that requires transformative therapeutic strategies. We have previously developed patient-derived orthotopic xenograft (PDOX) nude-mouse models of this disease. In the present report, we demonstrate that the standard drug, cisplatinum (CDDP), is highly-effective while the new, highly-touted agent, nab-paclitaxel (NAB-PTX) is ineffective. MATERIALS AND METHODS: Cervical PDOX tumors were grown on the cervix of nude mice for 4 weeks after surgical orthotopic implantation (SOI). Tumors were treated with CDDP or NAB-PTX. RESULTS: H&E staining demonstrated that the PDOX tumor recapitulated the original patient tumor. CDDP was highly-effective. One tumor that was treated with CDDP completely regressed. CDDP-treated tumors were smaller (tumor volume ratio: 0.42±0.36) than the control group (tumor volume ratio: 3.47±1.66) (p<0.01). In contrast, NAB-PTX did not show significant efficacy on the cervical cancer PDOX model (tumor volume ratio: 2.85±1.45) (p=0.47). CDDP-treated tumor weight (50±50 mg) was significantly less than control (238±114 mg) (p<0.01). NAB-PTX-treated tumors were not reduced in weight (246±136 mg) compared to control (p=0.91). There were no significant differences in mouse body weight between groups. Histological evaluation demonstrated that CDDP-treated tumors were fibrotic with scattered squamous cell nests compared to control or NAB-PTX-treated tumors. CONCLUSION: The results of the present study demonstrate the power of PDOX models of cervical cancer to distinguish efficacy of potential therapeutics for individual patients with this disease.\",\n \"corpus_id\": 3679912,\n \"score\": 2\n },\n {\n \"doc_id\": \"28030831\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R regresses an osteosarcoma in a patient-derived xenograft model resistant to a molecular-targeting drug.\",\n \"abstract\": \"Osteosarcoma occurs mostly in children and young adults, who are treated with multiple agents in combination with limb-salvage surgery. However, the overall 5-year survival rate for patients with recurrent or metastatic osteosarcoma is 20-30% which has not improved significantly over 30 years. Refractory patients would benefit from precise individualized therapy. We report here that a patient-derived osteosarcoma growing in a subcutaneous nude-mouse model was regressed by tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R, p<0.001 compared to untreated control). The osteosarcoma was only partially sensitive to the molecular-targeting drug sorafenib, which did not arrest its growth. S. typhimurium A1-R was significantly more effective than sorafenib (P <0.001). S. typhimurium grew in the treated tumors and caused extensive necrosis of the tumor tissue. These data show that S. typhimurium A1-R is powerful therapy for an osteosarcoma patient-derived xenograft model.\",\n \"corpus_id\": 3701566,\n \"score\": 2\n },\n {\n \"doc_id\": \"28106277\",\n \"title\": \"Tumor-Targeting Salmonella typhimurium A1-R Sensitizes Melanoma With a BRAF-V600E Mutation to Vemurafenib in a Patient-Derived Orthotopic Xenograft (PDOX) Nude Mouse Model.\",\n \"abstract\": \"Previously, a BRAF-V600E-mutant melanoma obtained from the right chest wall of a patient was grown orthotopically in the right chest wall of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. Trametinib (TRA), an MEK inhibitor, caused tumor regression. In contrast, another MEK inhibitor, cobimetinib (COB) could slow but not arrest growth or cause regression of the melanoma PDOX. First-line therapy temozolomide (TEM) could slow but not arrest tumor growth or cause regression. In addition, vemurafenib (VEM) was not effective even though VEM is supposed to target the BRAF-V600E mutation. We also previously demonstrated that tumor-targeting with S. typhimurium A1-R combined with TEM was significantly more effective than either S. typhimurium A1-R alone or TEM alone on the melanoma PDOX with the BRAF-V600E mutation. The present study used this PDOX model of melanoma to test its sensitivity to VEM combined with S. typhimurium A1-R compared to VEM alone and VEM combined with COB. VEM combined with S. typhimurium A1-R was significantly more effective than VEM alone or VEM combined with COB (P = 0.0216) which is currently first line therapy for advanced melanoma with a BRAF-V600E mutation. J. Cell. Biochem. 118: 2314-2319, 2017. © 2017 Wiley Periodicals, Inc.\",\n \"corpus_id\": 3898060,\n \"score\": 2\n },\n {\n \"doc_id\": \"28176365\",\n \"title\": \"High Efficacy of Pazopanib on an Undifferentiated Spindle-Cell Sarcoma Resistant to First-Line Therapy Is Identified With a Patient-Derived Orthotopic Xenograft (PDOX) Nude Mouse Model.\",\n \"abstract\": \"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant -cancer. Our laboratory pioneered the patient-derived orthotopic xenograft (PDOX) nude mouse model with the technique of surgical orthotopic implantation (SOI). In the present study, we evaluated the efficacy of standard first-line chemistry of doxorubicin (DOX), gemcitabine (GEM) combined with docetaxel (DOC), compared to pazopanib (PAZ), a multi-targeting tyrosine-kinase inhibitor, in an USCS PDOX model. A high-grade USCS from a striated muscle of the patients was grown orthotopically in the right biceps femoris muscle of nude mice to establish the PDOX model. The PDOX models were randomized into the following groups when tumor volume reached 100 mm(3) : G1, control without treatment; G2, DOX (3 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, GEM (100 mg/kg, i.p., weekly, for 2 weeks) combined with DOC (20 mg/kg, i.p., once); G4, PAZ (100 mg/kg, p.o., daily, for 14 days). All treatments except DOX significantly inhibited tumor growth compared to untreated control on day 14 after treatment initiation. Tumor sizes were as fallows: control (G1): 332.0 ± 58.7 mm(3) ; DOX (G2): 316.9 ± 55.9 mm(3) , P = 0.605; GEM + DOC (G3): 228.9 ± 39.8 mm(3) , P = 0.001; PAZ (G4): 173.8 ± 23.3 mm(3) , P < 0.0001. PAZ showed significantly more efficacy compared to other therapies evaluated: DOX (P < 0.0001), GEM + DOC (P = 0.006). There were no animal deaths in any group and body weight of treated mice was not significantly different in each group. The present results demonstrate that the PDOX model of USCS can identify a promising novel agent with significantly greater efficacy than first-line therapy for this recalcitrant disease. J. Cell. Biochem. 118: 2739-2743, 2017. © 2017 Wiley Periodicals, Inc.\",\n \"corpus_id\": 3928172,\n \"score\": 2\n },\n {\n \"doc_id\": \"28296559\",\n \"title\": \"The irony of highly-effective bacterial therapy of a patient-derived orthotopic xenograft (PDOX) model of Ewing's sarcoma, which was blocked by Ewing himself 80 years ago.\",\n \"abstract\": \"William B. Coley developed bacterial therapy of cancer more than 100 years ago and had clinical success. James Ewing, a very famous cancer pathologist for whom the Ewing sarcoma is named, was Coley's boss at Memorial Hospital in New York and terminated Coley's bacterial therapy of cancer. A tumor from a patient with soft-tissue Ewing's sarcoma, who failed doxorubicin (DOX) therapy, was previously implanted in nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. In the present study, the Ewing's sarcoma PDOX was treated with tumor-targeting S. typhimurium A1-R expressing green fluorescent (GFP), alone and in combination with DOX. S. typhimurium A1-R-GFP was detected in the tumors after intratumor (i.t.) or intravenous (i.v.) injection. The combination of S. typhimurium A1-R and DOX significantly reduced tumor weight (37.8 ± 15.6 mg) compared to the untreated control (73.8 ± 10.1 mg, P < 0.01). S. typhimurium A1-R monotherapy-treated tumors tended to be smaller (50.9 ± 17.8 mg, P = 0.051). DOX monotherapy did not show efficacy (66.3 ± 26.4 mg, P = 0.82), as was the case with the patient. The PDOX model faithfully replicated the DOX resistance the Ewing's sarcoma had in the patient. S. typhimurium A1-R converted the Ewing's sarcoma from DOX resistant to sensitive. One can only wonder how bacterial therapy and immunotherapy of cancer would have developed over the past 80 years if Ewing did not stop Coley.\",\n \"corpus_id\": 205881832,\n \"score\": 2\n },\n {\n \"doc_id\": \"28404944\",\n \"title\": \"Recombinant methioninase effectively targets a Ewing's sarcoma in a patient-derived orthotopic xenograft (PDOX) nude-mouse model.\",\n \"abstract\": \"Methionine dependence is due to the overuse of methionine for aberrant transmethylation reactions in cancer. Methionine dependence may be the only general metabolic defect in cancer. In order to exploit methionine dependence for therapy, our laboratory previously cloned L-methionine α-deamino-γ-mercaptomethane lyase [EC 4.4.1.11]). The cloned methioninase, termed recombinant methioninase, or rMETase, has been tested in mouse models of human cancer cell lines. Ewing's sarcoma is recalcitrant disease even though development of multimodal therapy has improved patients'outcome. Here we report efficacy of rMETase against Ewing's sarcoma in a patient-derived orthotopic xenograft (PDOX) model. The Ewing's sarcoma was implanted in the right chest wall of nude mice to establish a PDOX model. Eight Ewing's sarcoma PDOX mice were randomized into untreated control group (n = 4) and rMETase treatment group (n = 4). rMETase (100 units) was injected intraperitoneally (i.p.) every 24 hours for 14 consecutive days. All mice were sacrificed on day-15, 24 hours after the last rMETase administration. rMETase effectively reduced tumor growth compared to untreated control. The methionine level both of plasma and supernatants derived from sonicated tumors was lower in the rMETase group. Body weight did not significantly differ at any time points between the 2 groups. The present study is the first demonstrating rMETase efficacy in a PDOX model, suggesting potential clinical development, especially in recalcitrant cancers such as Ewing's sarcoma.\",\n \"corpus_id\": 4320744,\n \"score\": 2\n },\n {\n \"doc_id\": \"28426279\",\n \"title\": \"Combination of gemcitabine and docetaxel regresses both gastric leiomyosarcoma proliferation and invasion in an imageable patient-derived orthotopic xenograft (iPDOX) model.\",\n \"abstract\": \"Gastric leiomyosarcoma is a recalcitrant cancer and the chemotherapy strategy is controversial. The present study used a patient-derived orthotopic xenograft (PDOX) nude mouse model of gastric leiomyosarcoma to identify an effective therapeutic regimen to develop individualized precision medicine for this disease. The gastric leiomyosarcoma obtained from a patient was first grown in transgenic nude mice ubiquitously expressing red fluorescent protein (RFP) to stably label the tumor stroma. The RFP-expressing tumor was then passaged orthotopically in the gastric wall of non-transgenic nude mice to establish an imageable PDOX (iPDOX) model. The bright fluorescent tumor was readily imaged over time to determine drug efficacy. Four weeks after implantation, 70 PDOX nude mice were divided into 7 groups: control without treatment (n = 10); doxorubicin (DOX) (2.4 mg/kg, intraperitoneally (i.p.), once a week for 2 weeks, n = 10); gemcitabine (GEM)/ docetaxel (DOC) (GEM: 100 mg/kg, DOC: 20 mg/kg, i.p., once a week for 2 weeks, n = 10); cyclophosphamide (CPA) (140 mg/kg, i.p., once a week for 2 weeks, n = 10); temozolomide (TEM) (25 mg/kg, orally, daily for 14 consecutive days, n = 10); yondelis (YON) (0.15 mg/kg, i.v., once a week for 2 weeks, n = 10); pazopanib (PAZ) (100 mg/kg, orally, daily for 14 consecutive days, n = 10). On day 14 from initiation of treatment, all treatments except PAZ significantly inhibited tumor growth compared with untreated control (DOX: p < 0.01, GEM/DOC: p < 0.01, CPA: p < 0.01, TEM: p < 0.01, YON: p < 0.01) on day 14 after initiation. In addition, only GEM/DOC was more significantly effective than DOX (p < 0.05). GEM/DOC could regress the leimyosarcoma in the PDOX model and has important clinical potential for precision individual treatment of leiomyosarcoma patients.\",\n \"corpus_id\": 205881880,\n \"score\": 2\n },\n {\n \"doc_id\": \"28494180\",\n \"title\": \"Intra-arterial administration of tumor-targeting Salmonella typhimurium A1-R regresses a cisplatin-resistant relapsed osteosarcoma in a patient-derived orthotopic xenograft (PDOX) mouse model.\",\n \"abstract\": \"Previously, a patient-derived orthotopic xenograft (PDOX) model was established with a lung metastasis from an osteosarcoma patient which developed after adjuvant cisplatinum (CDDP) treatment. In this model, we previously demonstrated the efficacy of trabectedin (TRAB) and temozolomide (TEM) compared with CDDP. In the present report, osteosarcoma tissue was implanted orthotopically in the distal femur of mice which were randomized into the following groups when tumor volume reached approximately 100 mm(3); On day 14 after initiation of treatment, all but CDDP significantly inhibited tumor volume growth compared with untreated controls. Control (G1): 793.7 ± 215.0 mm(3); CDDP (G2): 588.1 ± 176.9 mm(3); Salmonella typhimurium A1-R (S. typhimurium A1-R) intravenous (i.v.) ( G3): 269.7 ± 72.7 mm(3); S. typhimurium A1-R intra-arterial (i.a.) ( G4): 70.2 ± 18.9 mm(3) (CDDP: p = 0.056; S. typhimurium A1-R i.v.: p = 0.0001; S. typhimurium A1-R i.a.: p = 0.00003, all vs. untreated controls). i.a. administration of S. typhimurium A1-R was significantly more effective than either CDDP (p = 0.00007), or i.v. administration of S. typhimurium A1-R (p = 0.00007) and significantly regressed the tumor volume compared with day 0 (p = 0.001). The new model of i.a. administration of S. typhimurium A1-R has great promise for the treatment of recalcitrant osteosarcoma.\",\n \"corpus_id\": 4768952,\n \"score\": 2\n },\n {\n \"doc_id\": \"28622068\",\n \"title\": \"Salmonella typhimurium A1-R targeting of a chemotherapy-resistant BRAF-V600E melanoma in a patient-derived orthotopic xenograft (PDOX) model is enhanced in combination with either vemurafenib or temozolomide.\",\n \"abstract\": \"A metastatic melanoma obtained from the right chest wall of a patient was previously established orthotopically in the right chest wall of nude mice as a patient-derived orthotopic xenograft (PDOX) model. We previously showed that the combination of tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R) and chemotherapy was highly effective against the melanoma PDOX. In the present study, we investigated the mechanism of the high efficacy of this combination. Two weeks after implantation, 40 PDOX mouse models were randomized into 4 groups of 10 mice each: untreated control (n = 10); treated with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks, n = 10); treated with temozolomide (TEM) (25 mg/kg, p.o. for 14 consecutive days) combined with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks, n = 10); treated with vemurafenib (VEM) (30 mg/kg, p.o., for 14 consecutive days) combined with S. typhimurium A1-R (5 × 10(7) CFU/100 μl, i.v., once a week for 2 weeks) (n = 10). On day 14 from initiation, all treatments significantly inhibited tumor growth compared with untreated control (S. typhimurium A1-R: p < 0.01; TEM combined with S. typhimurium A1-R: p < 0.01; VEM combined with S. typhimurium A1-R: p < 0.01). Combination therapy with S. typhimurium A1-R was significantly more effective on tumor growth than S. typhimurium A1-R alone (with TEM: p < 0.01; with VEM: p < 0.01). Combination therapy significantly increased S. typhimurium A1-R tumor targeting alone (S. typhimurium A1-R + TEM: p < 0.01, S. typhimurium A1-R + VEM: p < 0.01), relative to S. typhimurium A1-R alone, respectively. In conclusion, chemotherapy drugs promoted targeting of S. typhimurium A1-R of melanoma, thereby enhancing efficacy against the melanoma PDOX.\",\n \"corpus_id\": 4583281,\n \"score\": 2\n },\n {\n \"doc_id\": \"28681998\",\n \"title\": \"Eribulin regresses a doxorubicin-resistant Ewing's sarcoma with a FUS-ERG fusion and CDKN2A-deletion for the patient-derived orthotopic xenograft (PDOX) nude mouse model.\",\n \"abstract\": \"Ewing's sarcoma is a recalcitrant tumor greatly in need of more effective therapy. The aim of this study was to determine the efficacy of eribulin on a doxorubicin (DOX)-resistant Ewing's sarcoma patient derived orthotopic xenograft (PDOX) model. The Ewing's sarcoma PDOX model was previously established in the right chest wall of nude mice from the patient's right chest wall. In the previous study, the Ewing's sarcoma PDOX was resistant to DOX and sensitive to palbociclib and linsitinib. In the present study, the PDOX models were randomized into 3 groups when the tumor volume reached 60 mm(3) : G1, untreated control (n = 6); G2, DOX treated (n = 6), intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, Eribulin treated (n = 6, intravenous (i.v.) injection, weekly for 2 weeks). All mice were sacrificed on day 15. Changes in body weight and tumor volume were assessed 2 times per week. Tumor weight was measured after sacrifice. DOX did not suppress tumor growth compared to the control group (p = 0.589), consistent with the previous results in the patient and PDOX. Eribulin regressed tumor size significantly compared to G1 and G2 (p = 0.006, p = 0.017). No significant difference was observed in body weight. Our results demonstrate that eribulin is a novel therapeutic possibility for Ewing's sarcoma. This article is protected by copyright. All rights reserved.\",\n \"corpus_id\": 19065571,\n \"score\": 2\n },\n {\n \"doc_id\": \"28858204\",\n \"title\": \"Patient-Derived Orthotopic Xenograft (PDOX) Models of Melanoma.\",\n \"abstract\": \"Metastatic melanoma is a recalcitrant tumor. Although \\\"targeted\\\" and immune therapies have been highly touted, only relatively few patients have had durable responses. To overcome this problem, our laboratory has established the melanoma patient-derived orthotopic xenograft (PDOX) model with the use of surgical orthotopic implantation (SOI). Promising results have been obtained with regard to identifying effective approved agents and experimental therapeutics, as well as combinations of the two using the melanoma PDOX model.\",\n \"corpus_id\": 869376,\n \"score\": 2\n },\n {\n \"doc_id\": \"28977930\",\n \"title\": \"A patient-derived orthotopic xenograft (PDOX) mouse model of a cisplatinum-resistant osteosarcoma lung metastasis that was sensitive to temozolomide and trabectedin: implications for precision oncology.\",\n \"abstract\": \"In the present study, we evaluated the efficacy of trabectedin (TRAB) and temozolomide (TEM) compared to cisplatinum (CDDP) on a patient-derived orthotopic xenogrraft (PDOX) of a lung-metastasis from an osteosarcoma of a patient who failed CDDP therapy. Osteosarcoma resected from the patient was implanted orthotopically in the distal femur of mice to establish PDOX models which were randomized into the following groups when tumor volume reached approximately 100 mm3: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal injection, weekly, for 2 weeks); G3, TRAB (0.15 mg/kg, intravenous injection, weekly, for 2 weeks); G4, TEM (25 mg/kg, oral, daily, for 14 days). Tumor size and body weight were measured with calipers and a digital balance, respectively, twice a week. On day 14 after initiation of treatment, TEM and TRAB, but not CDDP, significantly inhibited tumor volume compared to untreated control: control (G1): 814.5±258.8 mm3; CDDP (G2): 608.6±126.9 mm3; TRAB (G3): 286.6±133.0 mm3; TEM (G4): 182.9±69.1 mm3. CDDP vs. control, p=0.07; TRAB vs. control, p=0.0004; TEM vs. control p =0.0002; TRAB vs. CDDP, p =0.0002; TEM vs. CDDP, p =0.00003. The results of the present study show that a PDOX model of an osteosarcoma lung-metastasis that recurred after adjuvant CDDP-treatment has identified potentially, highly-effective drugs for this recalcitrant disease, while accurately maintaining the CDDP resistance of the tumor in the patient, thereby demonstrating the potential of the osteosarcoma PDOX model for precision oncology.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"29061220\",\n \"title\": \"[Advances in Patient Derived Tumor Xenograft (PDTX) Model from Lung Cancer].\",\n \"abstract\": \"With the development of tumor molecular biology and genomics, it has been recognized that there are great heterogeneity in the biological characteristics, molecular typing and reactivity of the same tumor species among different individuals. In order to achieve true tumor individualized and precise therapy, a new concept of human tumor tissue xenograft model (patient derived tumor xenograft, PDTX) is proposed. The previous study has revealed that PDTX model can truly reflect the biological characteristics of tumor tissue and drug efficacy. And PDTX model could be used to select individual chemotherapy regime, evaluate drug resistance and explore efficacy and safety of new drug. PDTX model has been used in clinical practice of several type of cancer including lung cancer. In this paper, the current research progress of lung cancer PDTX is reviewed.\",\n \"corpus_id\": 3885909,\n \"score\": 2\n },\n {\n \"doc_id\": \"29143983\",\n \"title\": \"Growth of doxorubicin-resistant undifferentiated spindle-cell sarcoma PDOX is arrested by metabolic targeting with recombinant methioninase.\",\n \"abstract\": \"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant -cancer in need of individualized therapy. A high-grade USCS from a striated muscle of a patient was grown orthotopically in the right biceps femoris muscle of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. In a previous study, we evaluated the efficacy of standard first-line chemotherapy of doxorubicin (DOX), gemcitabine (GEM) combined with docetaxel (DOC), compared to pazopanib (PAZ), a multi-targeting tyrosine-kinase inhibitor, in an USCS PDOX model. In the present study, mice-bearing the USCS PDOX tumors were randomized into the following groups when tumor volume reached 100 mm3 : G1, untreated control without treatment; G2, DOX (3 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, L-methionine α-deamino-γ-mercaptomethane lyase (recombinant methioninase [rMETase]) (100 U/mouse, i.p., daily, for 2 weeks). Tumor size and body weight were measured with calipers and a digital balance twice a week. The methionine level of supernatants derived from sonicated tumors was also measured. rMETase inhibited tumor growth, measured by tumor volume, compared to untreated controls and the DOX-treated group on day 14 after initiation of treatment: control (G1): 347.6 ± 88 mm3 ; DOX (G2): 329.5 ± 79 mm3 , P = 0.670; rMETase (G3): 162.6 ± 51 mm3 , P = 0.0003. The mouse body weight of the treated mice was not significantly different from the untreated controls. Tumor L-methionine levels were reduced after the rMETase-treatment compared to untreated control and pre-rMETase treatment. We previously reported efficacy of rMETase against Ewing's sarcoma and melanoma in a PDOX models. These studies suggest clinical development of rMETase, especially in recalcitrant cancers such as sarcoma.\",\n \"corpus_id\": 3570136,\n \"score\": 2\n },\n {\n \"doc_id\": \"29156737\",\n \"title\": \"Combination treatment with recombinant methioninase enables temozolomide to arrest a BRAF V600E melanoma in a patient-derived orthotopic xenograft (PDOX) mouse model.\",\n \"abstract\": \"An excessive requirement for methionine termed methionine dependence, appears to be a general metabolic defect in cancer. We have previously shown that cancer-cell growth can be selectively arrested by methionine deprivation such as with recombinant methioninase (rMETase). The present study used a previously-established patient-derived orthotopic xenograft (PDOX) nude mouse model of BRAF V600E-mutant melanoma to determine the efficacy of rMETase in combination with a first-line melanoma drug, temozolomide (TEM). In the present study 40 melanoma PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n=10); TEM (25 mg/kg, oral 14 consecutive days, n=10); rMETase (100 units, intraperitoneal 14 consecutive days, n=10); combination TEM + rMETase (TEM: 25 mg/kg, oral rMETase: 100 units, intraperitoneal 14 consecutive days, n=10). All treatments inhibited tumor growth compared to untreated control (TEM: p=0.0081, rMETase: p=0.0037, TEM-rMETase: p=0.0024) on day 14 after initiation. However, the combination therapy of TEM and rMETase was significantly more efficacious than either mono-therapy (TEM: p=0.0051, rMETase: p=0.0051). The present study is the first demonstrating the efficacy of rMETase combination therapy in a PDOX model, suggesting potential clinical development, especially in recalcitrant cancers such as melanoma, where rMETase may enhance first-line therapy.\",\n \"corpus_id\": 22244271,\n \"score\": 2\n },\n {\n \"doc_id\": \"29262551\",\n \"title\": \"The combination of temozolomide-irinotecan regresses a doxorubicin-resistant patient-derived orthotopic xenograft (PDOX) nude-mouse model of recurrent Ewing's sarcoma with a FUS-ERG fusion and CDKN2A deletion: Direction for third-line patient therapy.\",\n \"abstract\": \"The aim of the present study was to determine the usefulness of a patient-derived orthotopic xenograft (PDOX) nude-mouse model of a doxorubicin-resistant metastatic Ewing's sarcoma, with a unique combination of a FUS-ERG fusion and CDKN2A deletion, to identify effective drugs for third-line chemotherapy of the patient. Our previous study showed that cyclin-dependent kinase 4/6 (CDK4/6) and insulin-like growth factor-1 receptor (IGF-1R) inhibitors were effective on the Ewing's sarcoma PDOX, but not doxorubicin, similar to the patient's resistance to doxorubicin. The results of the previous PDOX study were successfully used for second-line therapy of the patiend. In the present study, the PDOX mice established with the Ewing's sarcoma in the right chest wall were randomized into 5 groups when the tumor volume reached 60 mm3: untreated control; gemcitabine combined with docetaxel (intraperitoneal [i.p.] injection, weekly, for 2 weeks); irinotecan combined with temozolomide (irinotecan: i.p. injection; temozolomide: oral administration, daily, for 2 weeks); pazopanib (oral administration, daily, for 2 weeks); yondelis (intravenous injection, weekly, for 2 weeks). All mice were sacrificed on day 15. Body weight and tumor volume were assessed 2 times per week. Tumor weight was measured after sacrifice. Irinotecan combined with temozolomide was the most effective regimen compared to the untreated control group (p=0.022). Gemcitabine combined with docetaxel was also effective (p=0.026). Pazopanib and yondelis did not have significant efficacy compared to the untreated control (p=0.130, p=0.818). These results could be obtained within two months after the physician's request and were used for third-line therapy of the patient.\",\n \"corpus_id\": 21746767,\n \"score\": 2\n },\n {\n \"doc_id\": \"29306021\",\n \"title\": \"Recombinant methioninase in combination with doxorubicin (DOX) overcomes first-line DOX resistance in a patient-derived orthotopic xenograft nude-mouse model of undifferentiated spindle-cell sarcoma.\",\n \"abstract\": \"We have previously established a patient-derived orthotopic xenograft (PDOX) model of undifferentiated spindle cell sarcoma (USCS). Recombinant methioninase (rMETase) has previously demonstrated efficacy in PDOX mouse models of human cancers. In the present study, we determined if rMETase in combination with doxorubicin (DOX) can overcome first-line DOX resistance in a PDOX models of USCS. The USCS PDOX mouse models were randomized into the following groups when tumor volume reached 100 mm3: G1, control without treatment; G2, doxorubicin (DOX) (3 mg/kg, intraperitoneal [i.p.] injection, weekly, for 2 weeks); G3, rMETase (100 units/mouse, i.p., daily, for 2 weeks); G4, DOX (3 mg/kg, i.p., weekly, for 2 weeks) combined with rMETase (100 units/mouse, i.p., daily, for 2 weeks). Tumor size and body weight were measured twice a week. On day 14 after initiation, the USCS PDOX tumor sizes were (G1): 360 ± 85 mm3; DOX (G2): 355 ± 111 mm3, p = .927; rMETase (G3): 182 ± 57 mm3, p = .0003; DOX + rMETase (G4): 134 ± 29 mm3, p = .00001. These results indicate that rMETase can overcome USCS resistance to DOX, which is first line therapy for this disease. The body weight of treated mice was not significantly different in any group. The present results demonstrate the power of the PDOX model to identify effective therapy for recalcitrant cancer and the potential of rMETase to overcome DOX resistance.\",\n \"corpus_id\": 206431780,\n \"score\": 2\n },\n {\n \"doc_id\": \"29374999\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R combined with recombinant methioninase and cisplatinum eradicates an osteosarcoma cisplatinum-resistant lung metastasis in a patient-derived orthotopic xenograft (PDOX) mouse model: decoy, trap and kill chemotherapy moves toward the clinic.\",\n \"abstract\": \"In the present study, a patient-derived orthotopic xenograft (PDOX) model of recurrent cisplatinum (CDDP)-resistant metastatic osteosarcoma was treated with Salmonella typhimurium A1-R (S. typhimurium A1-R), which decoys chemoresistant quiescent cancer cells to cycle, and recombinant methioninase (rMETase), which selectively traps cancer cells in late S/G2, and chemotherapy. The PDOX models were randomized into the following groups 14 days after implantation: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, rMETase (100 unit/mouse, i.p., daily, for 2 weeks). G4, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks); G5, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks); G6, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks) and CDDP (6 mg/kg, i.p. injection, weekly, for 2 weeks). On day 14 after initiation, all treatments except CDDP alone, significantly inhibited tumor growth compared to untreated control: (CDDP: p = 0.586; rMETase: p = 0.002; S. typhimurium A1-R: p = 0.002; S. typhimurium A1-R combined with rMETase: p = 0.0004; rMETase combined with both S. typhimurium A1-R and CDDP: p = 0.0001). The decoy, trap and kill combination of S. typhimurium A1-R, rMETase and CDDP was the most effective of all therapies and was able to eradicate the metastatic osteosarcoma PDOX.\",\n \"corpus_id\": 4735278,\n \"score\": 2\n },\n {\n \"doc_id\": \"29384032\",\n \"title\": \"Individualized doxorubicin sensitivity testing of undifferentiated soft tissue sarcoma (USTS) in a patient-derived orthotopic xenograft (PDOX) model demonstrates large differences between patients.\",\n \"abstract\": \"Doxorubicin (DOX) is often first-line treatment of undifferentiated/unclassified soft tissue sarcoma (USTS). However, the DOX response rate for USTS patients is low. Individualized precision-medicine technology that could identify DOX responders as well as non-responders would be of high value to cancer patients. In the present study, we established 5 patient-derived orthotopic xenograft (PDOX) nude mouse models from 5 USTS patients and evaluated the efficacy of DOX in each PDOX model. USTS's were grown orthotopically in the right thigh of nude mice to establish the PDOX models. Two weeks after implantation, the mouse models were randomized into two groups of 8 mice each: untreated control; and DOX (3 mg/kg, i.p., once a week for 2 weeks). DOX showed significant growth inhibition in only 2 USTS PDOX models out of 5 (p = 0.0054, p = 0.0055, respectively) on day 14 after initiation. DOX was ineffective in the other 3 PDOX models. However, even in the DOX-sensitive cases, DOX could not regress the PDOX tumors responding to treatment. The present study has important implications since this is the first in vivo study to compare the DOX sensitivity for USTS on multiple patient tumors. We showed that only two of five USTS were responsive to DOX, despite DOX being first line chemotherapy for USTS. The 3 resistant cases should not be treated with DOX clinically, in order to spare the patients' unnecessary toxicity. This PDOX model is useful for precise individualized drug sensitivity testing, especially for rare heterogeneous recalcitrant sarcomas such as USTS.\",\n \"corpus_id\": 13767379,\n \"score\": 2\n },\n {\n \"doc_id\": \"29416666\",\n \"title\": \"Recombinant methioninase (rMETase) is an effective therapeutic for BRAF-V600E-negative as well as -positive melanoma in patient-derived orthotopic xenograft (PDOX) mouse models.\",\n \"abstract\": \"Melanoma is a recalcitrant disease. Melanoma patients with the BRAF-V600E mutation have been treated with the drug vemurafenib (VEM) which targets this mutation. However, we previously showed that VEM is not very effective against a BRAF-V600E melanoma mutant in a patient-derived orthotopic xenograft (PDOX) model. In contrast, we demonstrated that recombinant methioninase (rMETase) which targets the general metabolic defect in cancer of methionine dependence, was effective against the BRAF-V600E mutant melanoma PDOX model. In the present study, we demonstrate that rMETase is effective against a BRAF-V600E-negative melanoma PDOX which we established. Forty BRAF-V600E-negative melanoma PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n = 10); temozolomide (TEM) (25 mg/kg, p.o., 14 consecutive days, n = 10); rMETase (100 units, i.p., 14 consecutive days, n = 10); TEM + rMETase (TEM: 25 mg/kg, p.o., rMETase: 100 units, i.p., 14 consecutive days, n = 10). All treatments inhibited tumor growth compared to untreated control (TEM: p = 0.0003, rMETase: p = 0.0006, TEM/rMETase: p = 0.0002) on day 14 after initiation. Combination therapy of TEM and rMETase was significantly more effective than either mono-therapy (TEM: p = 0.0113, rMETase: p = 0.0173). The present study shows that TEM combined with rMETase is effective for BRAF-V600E-negative melanoma PDOX similar to the BRAF-V600E-positive mutation melanoma. These results suggest rMETase in combination with first-line chemotherapy can be highly effective in both BRAF-V600E-negative as well as BRAF-V600E-positive melanoma and has clinical potential for this recalcitrant disease.\",\n \"corpus_id\": 21163866,\n \"score\": 2\n },\n {\n \"doc_id\": \"29481803\",\n \"title\": \"Tumor-targeting Salmonella typhimurium A1-R is a highly effective general therapeutic for undifferentiated soft tissue sarcoma patient-derived orthotopic xenograft nude-mouse models.\",\n \"abstract\": \"Undifferentiated soft tissue sarcoma (USTS) is a recalcitrant and heterogeneous subgroup of soft tissue sarcoma with high risk of metastasis and recurrence. Due to heterogeneity of USTS, there is no reliably effective first-line therapy. We have generated tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R), which previously showed strong efficacy on single patient-derived orthotopic xenograft (PDOX) models of Ewing's sarcoma and follicular dendritic cell sarcoma. In the present study, tumor resected from 4 patients with a biopsy-proven USTS (2 undifferentiated pleomorphic sarcoma [UPS], 1 undifferentiated sarcoma not otherwise specified [NOS] and 1 undifferentiated spindle cell sarcoma [USS]) were grown orthotopically in the biceps femoris muscle of mice to establish PDOX models. One USS model and one UPS model were doxorubicin (DOX) resistant. One UPS and the NOS model were partially sensitive to DOX. DOX is first-line therapy for these diseases. S. typhimurium A1-R arrested tumor growth all 4 models. In addition to arresting tumor growth in each case, S. typhimurium A1-R was significantly more efficacious than DOX in each case, thereby surpassing first-line therapy. These results suggest that S. typhimurium A1-R can be a general therapeutic for USTS and possibly sarcoma in general.\",\n \"corpus_id\": 4768154,\n \"score\": 2\n },\n {\n \"doc_id\": \"29487690\",\n \"title\": \"Temozolomide combined with irinotecan regresses a cisplatinum-resistant relapsed osteosarcoma in a patient-derived orthotopic xenograft (PDOX) precision-oncology mouse model.\",\n \"abstract\": \"Relapsed osteosarcoma is a recalcitrant tumor. A patient's cisplatinum (CDDP)-resistant relapsed osteosarcoma lung metastasis was previously established orthotopically in the distal femur of mice to establish a patient-derived orthotopic xenograft (PDOX) model. In the present study, the PDOX models were randomized into the following groups when tumor volume reached 100 mm3: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); gemcitabine (GEM) (100 mg/kg, i.p., weekly, for 2 weeks) combined with docetaxel (DOC) (20 mg/kg, i.p., once); temozolomide (TEM) (25 mg/kg, p.o., daily, for 2 weeks) combined with irinotecan (IRN) (4 mg/kg i.p., daily for 2 weeks). Tumor size and body weight were measured with calipers and a digital balance twice a week. After 2 weeks, all treatments significantly inhibited tumor growth except CDDP compared to the untreated control: CDDP: p = 0.093; GEM+DOC: p = 0.0002, TEM+IRN: p < 0.0001. TEM combined with IRN was significantly more effective than either CDDP (p = 0.0001) or GEM combined with DOC (p = 0.0003) and significantly regressed the tumor volume compared to day 0 (p = 0.003). Thus the PDOX model precisely identified the combination of TEM-IRN that could regress the CDDP-resistant relapsed metastatic osteosarcoma PDOX.\",\n \"corpus_id\": 3584333,\n \"score\": 2\n },\n {\n \"doc_id\": \"29491256\",\n \"title\": \"Establishment of a Patient-Derived Tumor Xenograft Model and Application for Precision Cancer Medicine.\",\n \"abstract\": \"Patient-derived xenograft (PDX) models can be created with the transplantation of cancerous cells or tissues from patients' primary tumors into immunodeficient mice. PDXs are now in the spotlight as more accurate human cancer models compared with mouse tumor and human cancer cell lines transplanted into mice. PDX technology leads to breakthroughs with the introduction of novel, highly immunodeficient mice such as NOG (NOD/Scid/IL2Rγnull), NSG (NOD/Scid/IL2Rγnull), and NOJ (NOD/Scid/Jak3null) mice. Xenograft efficiency differs by type of tumor, site of implantation, and tumor aggressiveness. Subcutaneous implantation is a standard method for PDX, and renal capsule or orthotropic implantation improves the efficiency. Despite positive test results in animal cancer models, significant numbers of novel drug candidates fail in clinical trials because conventional animal models such as murine tumor and human cancer cell line transplantation models do not always reflect the nature of human cancers. Since PDXs conserve the original tumor characteristics such as heterogeneous histology, clinical biomolecular signatures, malignant phenotypes and genotypes, tumor architecture, and tumor vasculature, they are currently believed to offer relevant predictive insights into clinical outcomes when evaluating the efficacy of novel cancer therapies. PDX banks with integrated genomic signatures are now established in many organizations including pharmaceutical companies. These PDX databases are becoming powerful tools for advancing precision cancer medicine.\",\n \"corpus_id\": 4399747,\n \"score\": 2\n },\n {\n \"doc_id\": \"29541401\",\n \"title\": \"Intra-tumor L-methionine level highly correlates with tumor size in both pancreatic cancer and melanoma patient-derived orthotopic xenograft (PDOX) nude-mouse models.\",\n \"abstract\": \"An excessive requirement for methionine (MET) for growth, termed MET dependence, appears to be a general metabolic defect in cancer. We have previously shown that cancer-cell growth can be selectively arrested by MET restriction such as with recombinant methioninase (rMETase). In the present study, we utilized patient-derived orthotopic xenograft (PDOX) nude mouse models with pancreatic cancer or melanoma to determine the relationship between intra-tumor MET level and tumor size. After the tumors grew to 100 mm3, the PDOX nude mice were divided into two groups: untreated control and treated with rMETase (100 units, i.p., 14 consecutive days). On day 14 from initiation of treatment, intra-tumor MET levels were measured and found to highly correlate with tumor volume, both in the pancreatic cancer PDOX (p<0.0001, R2=0.89016) and melanoma PDOX (p<0.0001, R2=0.88114). Tumors with low concentration of MET were smaller. The present results demonstrates that patient tumors are highly dependent on MET for growth and that rMETase effectively lowers tumor MET.\",\n \"corpus_id\": 3849509,\n \"score\": 2\n },\n {\n \"doc_id\": \"29623758\",\n \"title\": \"Targeting altered cancer methionine metabolism with recombinant methioninase (rMETase) overcomes partial gemcitabine-resistance and regresses a patient-derived orthotopic xenograft (PDOX) nude mouse model of pancreatic cancer.\",\n \"abstract\": \"Pancreatic cancer is a recalcitrant disease. Gemcitabine (GEM) is the most widely-used first-line therapy for pancreatic cancer, but most patients eventually fail. Transformative therapy is necessary to significantly improve the outcome of pancreatic cancer patients. Tumors have an elevated requirement for methionine and are susceptible to methionine restriction. The present study used a patient-derived orthotopic xenograft (PDOX) nude mouse model of pancreatic cancer to determine the efficacy of recombinant methioninase (rMETase) to effect methionine restriction and thereby overcome GEM-resistance. A pancreatic cancer obtained from a patient was grown orthotopically in the pancreatic tail of nude mice to establish the PDOX model. Five weeks after implantation, 40 pancreatic cancer PDOX mouse models were randomized into four groups of 10 mice each: untreated control (n = 10); GEM (100 mg/kg, i.p., once a week for 5 weeks, n = 10); rMETase (100 units, i.p., 14 consecutive days, n = 10); GEM+rMETase (GEM: 100 mg/kg, i.p., once a week for 5 weeks, rMETase: 100 units, i.p., 14 consecutive days, n = 10). Although GEM partially inhibited PDOX tumor growth, combination therapy (GEM+rMETase) was significantly more effective than mono therapy (GEM: p = 0.0025, rMETase: p = 0.0010). The present study is the first demonstrating the efficacy of rMETase combination therapy in a pancreatic cancer PDOX model to overcome first-line therapy resistance in this recalcitrant disease.\",\n \"corpus_id\": 4639569,\n \"score\": 2\n },\n {\n \"doc_id\": \"29737543\",\n \"title\": \"Temozolomide regresses a doxorubicin-resistant undifferentiated spindle-cell sarcoma patient-derived orthotopic xenograft (PDOX): precision-oncology nude-mouse model matching the patient with effective therapy.\",\n \"abstract\": \"Undifferentiated spindle-cell sarcoma (USCS) is a recalcitrant cancer, resistant to conventional chemotherapy. A patient with high-grade USCS from a striated muscle was implanted orthotopically in the right biceps femoris muscle of mice to establish a patient-derived orthotopic xenograft (PDOX) model. The PDOX models were randomized into the following groups when tumor volume reached 100 mm3 : G1, control without treatment; G2, doxorubicin (DOX) (3 mg/kg, intraperitoneal [i.p.] injection, weekly, for 2 weeks); G3, temozolomide (TEM) (25 mg/kg, p.o., daily, for 14 days). Tumor size and body weight were measured with calipers and a digital balance twice a week. TEM significantly inhibited tumor volume growth compared to the untreated control and the DOX-treated group on day 14 after treatment initiation: control (G1): 343 ± 78 mm3 ; DOX (G2): 308 ± 31 mm3 , P = 0.272; TEM (G3): 85 ± 21 mm3 , P < 0.0001. TEM significantly regressed the tumor volume compared to day 0 (P = 0.019). There were no animal deaths in any group. The body weight of treated mice was not significantly different in any group. Tumors treated with DOX were comprised of spindle-shaped viable cells without apparent necrosis or inflammatory changes. In contrast, tumors treated with TEM showed extensive tumor necrosis. The present study demonstrates the potential power of matching the patient with an effective drug and saving the patient needless toxicity from ineffective drugs.\",\n \"corpus_id\": 13684406,\n \"score\": 2\n },\n {\n \"doc_id\": \"29857821\",\n \"title\": \"MEK inhibitor trametinib in combination with gemcitabine regresses a patient-derived orthotopic xenograft (PDOX) pancreatic cancer nude mouse model.\",\n \"abstract\": \"Pancreatic cancer is resistant to treatment and needs precision individualized therapy to improve the outcome of this disease. Previously, we demonstrated that trametinib (TRA), a MEK inhibitor, could inhibit a pancreatic cancer patient-derived orthotopic xenograft (PDOX). In the present study, we show that gemcitabine (GEM) in combination with TRA was more effective than TRA alone. We implanted a patient pancreatic cancer orthotopically in the pancreatic tail of nude mice to establish the PDOX model. After seven weeks of tumor growth, we divided 32 pancreatic-cancer PDOX nude mice into 4 groups of eight: untreated control; GEM (once a week for 2 weeks); TRA (14 consecutive days); GEM + TRA (GEM: once a week for 2 weeks, TRA:14 consecutive days). We found that treated mice on day 14 had significantly reduced tumor volume in comparison to untreated control. TRA and the combination of GEM + TRA therapy significantly inhibited tumor development in comparison to GEM alone. However, GEM + TRA inhibited the PDOX tumor growth significantly greater than TRA alone. These results suggest the clinical potential of the combination of TRA and GEM for pancreatic cancer.\",\n \"corpus_id\": 46923111,\n \"score\": 2\n },\n {\n \"doc_id\": \"23877869\",\n \"title\": \"Sonoporation-enhanced chemotherapy significantly reduces primary tumour burden in an orthotopic pancreatic cancer xenograft.\",\n \"abstract\": \"PURPOSE: Adenocarcinoma of the pancreas remains one of the most lethal human cancers. The high mortality rates associated with this form of cancer are subsequent to late-stage clinical presentation and diagnosis, when surgery is rarely possible and of modest chemotherapeutic impact. Survival rates following diagnosis with advanced pancreatic cancer are very low; typical mortality rates of 50% are expected within 3 months of diagnosis. However, adjuvant chemotherapy improves the prognosis of patients even after palliative surgery, and successful newer neoadjuvant chemotherapeutical modalities have recently been reported. For patients whose tumours appear unresectable, chemotherapy remains the only option. During the past two decades, the nucleoside analogue gemcitabine has become the first-line chemotherapy for pancreatic adenocarcinoma. In this study, we aim to increase the delivery of gemcitabine to pancreatic tumours by exploring the effect of sonoporation for localised drug delivery of gemcitabine in an orthotopic xenograft mouse model of pancreatic cancer. EXPERIMENTAL DESIGN: An orthotopic xenograft mouse model of luciferase expressing MIA PaCa-2 cells was developed, exhibiting disease development similar to human pancreatic adenocarcinoma. Subsequently, two groups of mice were treated with gemcitabine alone and gemcitabine combined with sonoporation; saline-treated mice were used as a control group. A custom-made focused ultrasound transducer using clinically safe acoustic conditions in combination with SonoVue® ultrasound contrast agent was used to induce sonoporation in the localised region of the primary tumour only. Whole-body disease development was measured using bioluminescence imaging, and primary tumour development was measured using 3D ultrasound. RESULTS: Following just two treatments combining sonoporation and gemcitabine, primary tumour volumes were significantly lower than control groups. Additional therapy dramatically inhibited primary tumour growth throughout the course of the disease, with median survival increases of up to 10% demonstrated in comparison to the control groups. CONCLUSION: Combined sonoporation and gemcitabine therapy significantly impedes primary tumour development in an orthotopic xenograft model of human pancreatic cancer, suggesting additional clinical benefits for patients treated with gemcitabine in combination with sonoporation.\",\n \"corpus_id\": 23094615,\n \"score\": 1\n },\n {\n \"doc_id\": \"24507750\",\n \"title\": \"Generation of orthotopic patient-derived xenografts from gastrointestinal stromal tumor.\",\n \"abstract\": \"BACKGROUND: Gastrointestinal stromal tumor (GIST) is the most common sarcoma and its treatment with imatinib has served as the paradigm for developing targeted anti-cancer therapies. Despite this success, imatinib-resistance has emerged as a major problem and therefore, the clinical efficacy of other drugs has been investigated. Unfortunately, most clinical trials have failed to identify efficacious drugs despite promising in vitro data and pathological responses in subcutaneous xenografts. We hypothesized that it was feasible to develop orthotopic patient-derived xenografts (PDXs) from resected GIST that could recapitulate the genetic heterogeneity and biology of the human disease. METHODS: Fresh tumor tissue from three patients with pathologically confirmed GISTs was obtained immediately following tumor resection. Tumor fragments (4.2-mm3) were surgically xenografted into the liver, gastric wall, renal capsule, and pancreas of immunodeficient mice. Tumor growth was serially assessed with ultrasonography (US) every 3-4 weeks. Tumors were also evaluated with positron emission tomography (PET). Animals were sacrificed when they became moribund or their tumors reached a threshold size of 2500-mm3. Tumors were subsequently passaged, as well as immunohistochemically and histologically analyzed. RESULTS: Herein, we describe the first model for generating orthotopic GIST PDXs. We have successfully xenografted three unique KIT-mutated tumors into a total of 25 mice with an overall success rate of 84% (21/25). We serially followed tumor growth with US to describe the natural history of PDX growth. Successful PDXs resulted in 12 primary xenografts in NOD-scid gamma or NOD-scid mice while subsequent successful passages resulted in 9 tumors. At a median of 7.9 weeks (range 2.9-33.1 weeks), tumor size averaged 473 ± 695-mm³ (median 199-mm3, range 12.6-2682.5-mm³) by US. Furthermore, tumor size on US within 14 days of death correlated with gross tumor size on necropsy. We also demonstrated that these tumors are FDG-avid on PET imaging, while immunohistochemically and histologically the PDXs resembled the primary tumors. CONCLUSIONS: We report the first orthotopic model of human GIST using patient-derived tumor tissue. This novel, reproducible in vivo model of human GIST may enhance the study of GIST biology, biomarkers, personalized cancer treatments, and provide a preclinical platform to evaluate new therapeutic agents for GIST.\",\n \"corpus_id\": 1548936,\n \"score\": 1\n },\n {\n \"doc_id\": \"25348321\",\n \"title\": \"Establishment of orthotopic primary cervix cancer xenografts.\",\n \"abstract\": \"Standard treatment for women who are diagnosed with stage IIB through IVA cervical cancer consists of cisplatin-based chemotherapy and radiation. Current options for patients with recurrent and metastatic disease are limited, and their median overall survival is <12 months. To date, biologic therapy has had little impact on survival, so identification of potential new targets is urgently required to develop novel therapeutic strategies. Developing relevant animal models for human cervix cancer is important to further enhance our understanding of the characteristics of these tumors and for identification and assessment of novel therapies. We have established a panel of orthotopically passaged xenografts (OCICx) by implanting cervix tumor pieces from patient biopsies directly into the cervix of mice. The tumors have been passaged up to five generations, were characterized histologically for tumor and stromal content and, where possible, related to similar measurements in the original patient biopsy. The tumors were found to metastasize to the para-aortic lymphnodes allowing assessment of their metastatic potential. Preliminary studies demonstrate aberrant expression of genes in the Hedgehog (Hh) pathway in the xenografts similar to findings in primary cervix cancers. The OCICx xenografts represent unique models to test strategies for targeting essential pathways in cervix cancer and metastasis.\",\n \"corpus_id\": 26616109,\n \"score\": 1\n },\n {\n \"doc_id\": \"29487698\",\n \"title\": \"Genetic and metabolic comparison of orthotopic and heterotopic patient-derived pancreatic-cancer xenografts to the original patient tumors.\",\n \"abstract\": \"Tumors from 25 patients with pancreatic cancer were used to establish two patient-derived xenograft (PDX) models: orthotopic PDX (PDOX) and heterotopic (subcutaneous) PDX (PDHX). We compared gene expression by immunohistochemistry, single-nucleotide polymorphism (SNP), DNA methylation, and metabolite levels. The 4 cases, of the total of 13 in which simultaneous PDHX & PDOX models were established, were randomly selected. The molecular-genetic characteristics of the patient's tumor were well maintained in the two PDX models. SNP analysis demonstrated that both groups were more than 90% identical to the original patient's tumor, and there was little difference between the two models. DNA methylation of most genes was similar among the two models and the original patients tumor, but some gene sets were hypermethylated the in PDOX model and hypomethylated in the PDHX model. Most of the metabolites had a similar pattern to those of the original patient tumor in both PDX tumor models, but some metabolites were more prominent in the PDOX and PDHX models. This is the first simultaneous molecular-genetic and metabolite comparison of patient tumors and their tumors established in PDOX and PDHX models. The results indicate high fidelity of these critical properties of the patient tumors in the two models.\",\n \"corpus_id\": 3588878,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":68,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29576637\",\n \"title\": \"Complications Associated with Locking Plate of Proximal Humerus Fractures.\",\n \"abstract\": \"Proximal humerus fractures constitute a significant percentage of fragility fractures. The growing use of locking plate has helped treat this problem, but at the same time has brought about complications. Past systematic reviews have documented these complications, however a large number of recent studies have been published since, reporting their own complication rates with different techniques. This study reviews the current complications associated with locking plate of proximal humerus fractures as well as methods to reduce them. A systematic review, following the PRISMA guidelines, was conducted in November 2013 and repeated in March 2015, using PubMed, Scopus, and Cochrane databases, to evaluate locking plate fixation (and complications) of traumatic proximal humerus fractures. Inclusion criteria included adults (>18 years), minimum of 12-month postoperative followup, articles within the last 5 years, and studies with >10 participants. Exclusion criteria included pathologic fractures, cadaveric studies, and nonhuman subjects. Eligible studies were graded using a quality scoring system. Articles with a minimum of 7/10 score were included and assessed regarding their level of evidence per the Journal of Bone and Joint Surgery and Centre for Evidence-Based Medicine guidelines. The initial query identified 51,206 articles from multiple databases. These records were thoroughly screened and resulted in 57 articles, consisting of seven Level 1, three Level 2, 10 Level 3, and 37 Level 4 studies, totaling 3422 proximal humerus fractures treated with locking plates. Intraarticular screw penetration was the most reported complication (9.5%), followed by varus collapse (6.8%), subacromial impingement (5.0%), avascular necrosis (4.6%), adhesive capsulitis (4.0%), nonunion (1.5%), and deep infection (1.4%). Reoperation occurred at a rate of 13.8%. Collapse at the fracture site contributed to a majority of the implant-related complications, which in turn were the main reasons for reoperation. The authors of these studies discussed different techniques that could be used to address these issues. Expanding use of locking plate in the proximal humerus fractures leads to improvements and advancements in surgical technique. Further research is necessary to outline indications to decrease complications, further.\",\n \"corpus_id\": 4190285\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18317048","title":"Early complications in proximal humerus fractures (OTA Types 11) treated with locked plates.","abstract":"PURPOSE: To examine our incidence of early complications that occur using the Proximal Humeral Internal Locking System (PHILOS) and to determine the contributing factors. SETTING: Academic medical center. PATIENTS: Fifty-one consecutive patients treated with a proximal humerus locking plate. OUTCOME: Development of an intraoperative, acute postoperative, or delayed postoperative complication. METHODS: A retrospective analysis was undertaken of a consecutive series of proximal humerus fractures treated with a locking plate between February 2003 and January 2006 at our institution. Fifty-one fractures or fracture nonunions were identified in 18 male and 33 female patients with an average age of 61. All acute injuries were treated with a similar protocol of open reduction internal fixation with the PHILOS plate followed by early range of shoulder motion. Nonunions were treated in a similar manner with the addition of iliac crest bone graft placement. Patients were objectively assessed on their outcome by physical as well as radiological examination. All complications were recorded. Statistical analyses were performed to determine if patient age, fracture type, or number of screws placed in the humeral head contributed to complications. RESULTS: Fifty-one patients were available for minimum 6-month follow-up (mean, 16 months; range, 6 to 45 months). Radiographically, 92% of the cases united at 3 months after surgery, and 2 fractures had signs of osteonecrosis at latest follow-up. Sixteen complications were seen in 12 patients (24%). Eight shoulders in eight patients (16%) had screws that penetrated the humeral head. Two patients developed osteonecrosis at latest follow-up. One acute fracture and one nonunion failed to unite after index surgery. Significant heterotopic bone developed in 1 patient. Early implant failure occurred in 2 patients; one was revised to a longer plate, and one underwent resection arthroplasty. There was one acute postoperative infection. CONCLUSION: The major complication reported in this study was screw penetration, suggesting that exceptional vigilance must be taken in estimating the appropriate number and length of screws used to prevent articular penetration; although the device provides exceptional fixation stability, its indication must be scrutinized for each individual patient, taking the extent of trauma/fracture and age into consideration and carefully weighing it against other forms of treatment.","corpus_id":1356340,"score":2},{"doc_id":"18552530","title":"[The results of internal fixation of proximal humeral fractures with the PHILOS locking plate].","abstract":"Proksimal humerus kiriklarinda kilitli plak PHILOS ile internal tespit sonuçlari. OBJECTIVES: Proximal and diaphyseal humeral fractures are common especially in the elderly, presenting as a challenging problem due to their high complication rates following surgical treatment. In this prospective study, we evaluated the results of patients treated with the PHILOS (Proximal Humeral Internal Locking System) locking plate, a new technique recently developed by the AO/ASIF. METHODS: Forty-one patients who were treated with the PHILOS plate for proximal humeral fractures were evaluated in two age groups. Group A included 24 patients (12 males, 12 females; mean age 47 years; range 24 to 64 years) younger than 65 years, and group B involved 17 patients (4 males, 13 females; mean age 78 years; range 67 to 90 years) at or above 65 years. Radiographically, all fractures were classified according to the AO/ASIF system. Surgery was performed with the deltopectoral approach in 10 and two patients, and with a deltoid split in 14 and 15 patients in group A and B, respectively. Functional and radiographic results were evaluated after a mean follow-up of 15 months (range 6 to 28 months). RESULTS: The mean Constant scores were 95.0 (range 74 to 100) and 92.8 (range 72 to 100) in group A and B, respectively (p>0.05). After six months of surgery, Constant scores and functional outcomes were similar in patients operated on with the deltopectoral approach or deltoid split. There was neither nonunion nor implant failure. Complications included intra-articular screw penetration (n=1), displacement of the greater tuberculum (n=1) with oblique placement of the plate (n=1), insufficient reduction (n=4), and varus displacement of the humeral head (n=3). No avascular necrosis was seen. CONCLUSION: Locking plate system is superior over other means of fixation methods, particularly in osteoporotic fractures, because it allows early rehabilitation and does not result in implant failure.","corpus_id":19621118,"score":2},{"doc_id":"18716427","title":"[Early results of treatment of proximal humerus fractures with the PHILOS locking plate].","abstract":"Proksimal humerus kiriklarin PHILOS plaği ile tedavisinde erken dönem sonuçlarimiz. OBJECTIVES: The aim of this study was to evaluate early results of proximal humerus fractures treated with the PHILOS locking plate. METHODS: Proximal humerus fractures of 22 patients (13 males, 9 females; mean age 57 years; range 35 to 83 years) were treated with the PHILOS locking plate. According to the Neer classification, 13 patients had comminuted fractures, four patients had valgus impact injuries, two patients had fracture-dislocations, and three patients had fractures involving the proximal 1/3 of the humerus. The fractures were reduced by the transdeltoid lateral approach (n=8) using minimally invasive surgery, and by the anterior deltopectoral approach (n=14) using open surgery. Passive and active exercises were initiated on the second postoperative day and after 4 to 6 weeks, respectively. The results were assessed using the Constant-Murley shoulder scoring system. The mean follow up was 14 months (range 12 to 19 months). RESULTS: Radiographically, union was observed in 20 patients at the end of 10 weeks. In one patient, time to union was 16 weeks. One patient underwent autogenous bone grafting because of nonunion after 16 weeks. The mean Constant-Murley score was 75.5 (range 51 to 93). There was no significant difference between Constant-Murley scores of patients undergoing the transdeltoid lateral and anterior deltopectoral approaches (p>0.05). Plate fixation was associated with minimal varus deformity in two patients, and subacromial impingement in one patient. Implant failure did not occur. Reflex sympathetic dystrophy and avascular necrosis were observed in two patients, respectively. CONCLUSION: Fixation with the PHILOS plate is a near-ideal technique with a high union rate in the treatment of proximal humeral fractures.","corpus_id":21437563,"score":2},{"doc_id":"19431978","title":"[Long PHILOS locking compression plate for treatment of proximal humerus and humeral shaft fractures].","abstract":"OBJECTIVE: To investigate the therapeutic effect of long PHILOS locking compression plate on the proximal humerus and humeral shaft fractures. METHODS: From March 2005 to December 2007, 35 cases with the proximal humerus and humeral shaft fractures were treated with long PHILOS locking compression plate, including 16 males and 19 females aged 29-68 years old (average 54.5 years old). There were 34 cases of fresh and close fracture, and the time from injury to operation was 3-9 days. One case had delayed union of fracture 5 months after receiving T-plates and internal fixation with steel plate. For the proximal humerus fracture, 7 cases had 2 parts of fracture, 19 had 3 parts of fracture, and 9 had 4 parts of fracture according to Neer classification; while for the humeral shaft fracture, 3 cases were classified as A1, 5 as A2, 10 as B1, 3 as B2, 6 as B3, 7 as C1 and 1 as C3 according to AO classification. Postoperatively, Neer scoring system was employed to evaluate the function of shoulder joint and HSS scoring system was adopted to evaluate the function of elbow joint. RESULTS: All incisions healed by first intension, and 30 cases were followed up for 12-33 months (average 18.2 months). Postoperatively, 2 cases had symptoms of radial nerve paralysis, which disappeared within 3 weeks; 1 case suffered from humeral head necrosis and received the secondary operation of humeral head replacement; humeral head was reduced evenly in 1 case, and 2 cases felt chronic slight pain in shoulder joints and received no further treatment. X-ray films showed 29 cases had fracture healing 6 months after operation, and all the patients had bone union 12 months after operation except 1 case receiving humeral head replacement. No such complications as screw loosening and internal fixation loosening occurred. By Neer scoring system, 6 cases were graded as excellent, 19 as good, 3 as fair, 2 as poor, and the excellent and good rate was 83.3%. By HSS scoring system, 16 cases were graded as excellent, 14 as good, and the excellent and good rate was 100%. CONCLUSION: Applying long PHILOS locking compression plate in the treatment of the proximal humerus and humeral shaft fractures provides a solid fixation and high satisfactory rate with minor complications.","corpus_id":38426029,"score":2},{"doc_id":"19487508","title":"Open reduction and internal fixation of proximal humeral fractures with use of the locking proximal humerus plate. Results of a prospective, multicenter, observational study.","abstract":"BACKGROUND: The treatment of unstable displaced proximal humeral fractures, especially in the elderly, remains controversial. The objective of the present prospective, multicenter, observational study was to evaluate the functional outcome and the complication rate after open reduction and internal fixation of proximal humeral fractures with use of a locking proximal humeral plate. METHODS: One hundred and eighty-seven patients (mean age, 62.9 +/- 15.7 years) with an acute proximal humeral fracture were managed with open reduction and internal fixation with a locking proximal humeral plate. At the three-month, six-month, and one-year follow-up examinations, 165 (88%), 158 (84%), and 155 (83%) of the 187 patients were assessed with regard to pain, shoulder mobility, and strength. The Constant score was determined at each interval, and the Disabilities of the Arm, Shoulder and Hand (DASH) score was determined for the injured and contralateral extremities at the time of the one-year follow-up. RESULTS: Between three months and one year, the mean range of motion and the mean Constant score for the injured shoulders improved substantially. Twelve months after surgery, the mean Constant score for the injured side was 70.6 +/- 13.7 points, corresponding to 85.1% +/- 14.0% of the score for the contralateral side. The mean DASH score at the time of the one-year follow-up was 15.2 +/- 16.8 points. Sixty-two complications were encountered in fifty-two (34%) of 155 patients at the time of the one-year follow-up. Twenty-five complications (40%) were related to incorrect surgical technique and were present at the end of the operative procedure. The most common complication, noted in twenty-one (14%) of 155 patients, was intraoperative screw perforation of the humeral head. Twenty-nine patients (19%) had an unplanned second operation within twelve months after the fracture. CONCLUSIONS: Surgical treatment of displaced proximal humeral fractures with use of the locking proximal humeral plate that was evaluated in the present study can lead to a good functional outcome provided that the correct surgical technique is used. Because many of the complications were related to incorrect surgical technique, it behooves the treating surgeon to perform the operation correctly to avoid iatrogenic errors.","corpus_id":26028870,"score":2},{"doc_id":"19748802","title":"Treatment of proximal humerus fractures with locking plates: a systematic review.","abstract":"HYPOTHESIS: Locking plates with special configuration for the anatomic region of the proximal humerus have been introduced recently to address the difficulties of stabilizing proximal humeral fractures. The purpose of this study was to carry out a systematic review of the literature on the efficacy and early to medium term functional results of locking plates for stabilization of proximal humeral fractures. METHODS: Using the PubMed database, a systematic review of the English and German literature was carried out in order to assess the efficacy and complications related to the use of these plates and the patients' functional outcome, using the key words \"locking plates proximal humeral fractures,\" \"angular stability plates proximal humeral fractures,\" \"PHILOS plate,\" and \"LPHP plate.\" Our criteria for eligibility were clinical studies with more than ten cases followed-up, adult patients, and adequate data provided at least in terms of implant related complications. Articles written in English and German language were included. Exclusion criteria were: studies dealing exclusively with 2-part fractures (since this category has a more favorable outcome); experimental studies; case reports; and, literature other than English or German. Each one of the articles was evaluated for quality of the study using the Structured Effectiveness Quality Evaluation Scale (SEQES). RESULTS: Twelve studies including 791 patients met the inclusion criteria. Patients in these studies continued to improve up to one year, achieving a mean Constant score of 74.3. The incidence of the reported complications was: avascular necrosis 7.9%, screw cut-out 11.6% and re-operation rate 13.7%. DISCUSSION: The high incidence of cut-out may be secondary to the rigidity of the implant in combination with medial inadequate support, in cases compromised by severe underlying osteoporotic bone. Definition of indications for the use of locking plates and attention on technical aspects of applying them would help optimization of the results. LEVEL OF EVIDENCE: Systematic Review.","corpus_id":10818409,"score":2},{"doc_id":"19995683","title":"Pitfalls and complications with locking plate for proximal humerus fracture.","abstract":"PURPOSE: The aim of this study was to identify specific complications of locking plate fixation of proximal humerus fractures. PATIENTS AND METHODS: Seventy-three adult patients with a displaced 3- (24%) or 4-part (76%) fracture of the proximal humerus were treated over a period of 2 years under the supervision of a trauma surgeon. Fourty-four patients came back for a clinical and radiographic examinations at least 18 months after the trauma; the others were evaluated at 6 weeks and 3 and 6 months. RESULTS: Out of the 73 patients (64.4% females, mean age of 65), 11 patients needed a second surgery and 18 were lost for follow-up after 6 months. Mean final constant score was 62.3 points. The incidence of secondary displacement was 8.2%. Nonunion rate was 5.5%, affecting the constant score (P = .018). 16.4% of the patients developed a partial necrosis of the humeral head at the latest follow-up, which influenced on the constant score (P = .029). Quality of the reduction of the greater tuberosity influenced final results (P = .037). Screw cutout rate was 13.7%, with an influence to the constant score (P = .001). A too high plate positioning influenced the constant score (P = .002). CONCLUSION: Locked screw-plates provide more secure fixation of fractures, especially in weak bone. Complications rate remains high. Two complications are to be distinguished: 1) technical complications in plate positioning, length of the screws or secondary screw cutout strongly influence the final clinical result; and 2) specific complications related to this technology such as pseudarthrosis or plate fracture.","corpus_id":2705321,"score":2},{"doc_id":"20188270","title":"Use of locking plates in the treatment of proximal humerus fractures.","abstract":"BACKGROUND/HYPOTHESIS: Open reduction and internal fixation (ORIF) using locked plating has demonstrated promise in the treatment of displaced proximal humerus fractures. The purpose of this article is to describe the surgical technique and to report early clinical results with this technique. METHODS: Important surgical principles to follow include adequate use of locking screws in the humeral head, bone graft or bone graft substitutes when needed, rotator cuff sutures to assist with reduction and augment fixation, and sufficient use of intraoperative fluoroscopic imaging. A review was performed to evaluate early outcomes of ORIF with proximal humerus locking plates. All cases were fixed with the described surgical technique. Postoperative assessment included radiographic imaging, PENN/ASES Shoulder Scores, range-of-motion (ROM), and complications. RESULTS: Fifty-two patients (54 shoulders) had minimum 6-month follow-up (13-month mean follow-up). Mean age was 65.5 years. Postoperatively, mean active forward elevation was 130.1 degrees, and mean active external rotation was 27.7 degrees. Mean post-op PENN shoulder score was 68.9 and mean post-op ASES score was 70.8. There were 11 (20.4%) complications in 10 (18.5%) shoulders after treatment with a proximal humerus locking plate. Three complications were classified as minor (5.6%), 8 as major (14.8%). Two shoulders (3.7%) required reoperation to address the complications. CONCLUSION: The use of locking plates in the treatment of displaced proximal humerus fractures is becoming more widespread. With precise knowledge of and experience with the surgical technique, locked plating can be performed safely with good results. However, surgeons should be aware that complications can arise.","corpus_id":30658678,"score":2},{"doc_id":"20415404","title":"Fixed-angle locking plating of displaced proximal humerus fractures.","abstract":"Proximal humerus fractures are common, especially among patients older than 60 years who have osteoporosis. Several techniques have been used within the past several decades to treat displaced proximal humerus fractures. Many different implants have been investigated and tested, all with inadequate results; debate continues as to the best method of fixation. Fixed-angle locking plates offer a relatively new treatment option for these complicated fractures, especially in patients with osteoporosis. The use of locking plates for treating comminuted proximal humerus fractures has biologic and biomechanical advantages over conventional fixation techniques. Complications including varus fracture collapse and screw penetration of the articular surface nonetheless remain problematic. Although the locking plate technique provides exceptional fixation stability, its use must be tailored to the individual patient, taking into account the extent of trauma, the fracture characteristics, and the patient's age and expectations; therefore, it must be carefully weighed against other forms of treatment. Prospective clinical trials and further study are necessary to generate data comparing locking plate fixation and alternative surgical treatments.","corpus_id":20754137,"score":2},{"doc_id":"20577069","title":"Clinical results for minimally invasive locked plating of proximal humerus fractures.","abstract":"OBJECTIVES: To describe the minimally invasive treatment of fractures of the proximal humerus using the Non-Contact-Bridging (NCB) plate. The system allows secondary locking of screws to the plate with a locking cap and polyaxial (30 degrees radius) screw placement. DESIGN: Prospective cohort study. SETTING: University Level I trauma center. PATIENTS: Fifty-four patients with unstable fractures of the proximal humerus. INTERVENTION: Minimal anterolateral acromial approach to the proximal humerus, percutaneous fracture reduction, and minimally invasive application of the NCB plate. MAIN OUTCOME MEASUREMENTS: Constant Score and radiologic follow-up (anteroposterior and transscapular). Visual Analog Scale for subjective evaluation of pain and function. RESULTS: After 17 months, the average Constant Score was 66.8 points (87% of the age- and sex-related normal values). Implant-related complications (plate impingement, screw perforation into the glenohumeral joint, loosening of screws) occurred in nine cases (17%). The rate of avascular necrosis was low (5.5%) and no cases of nonunion were seen. CONCLUSIONS: The effectiveness of the NCB is similar to other published methods of treatment for fractures of the proximal humerus and potentially provides a less invasive option for this problem. Complication rates and functional outcome in this series are comparable to the literature. An important factor in this technique is the process of percutaneous fracture reduction. The NCB plate is suitable for both a minimally invasive technique or standard open reduction and internal fixation through a deltopectoral approach; the surgeon must decide which approach is best for each particular fracture pattern and should be comfortable with both techniques.","corpus_id":205491196,"score":2},{"doc_id":"20676009","title":"Complications encountered in proximal humerus fractures treated with locking plate fixation.","abstract":"OBJECTIVES: We evaluated the complications encountered following locking plate fixation of proximal humerus fractures. METHODS: The study included 103 patients (70 females, 33 males; mean age 62 years; range 21 to 90 years) who were treated with open reduction and locking plate fixation for proximal humerus fractures between September 2005 and April 2009. Fixation was performed using the PHILOS locking plate in 93 patients, and S3 humerus plate in 10 patients. Postoperatively, a shoulder-arm sling was applied for six weeks and a standard rehabilitation program was used in all the patients. Intraoperative, acute postoperative, and late postoperative complications were assessed on radiographs. Varus inclination was defined as less than 120 degrees of the inclination angle on immediate postoperative radiographs, and varus displacement as postoperative increases in the varus angle. The mean follow-up period was 19 months (range 2 weeks to 43 months). RESULTS: Complications were seen in 10 patients (9.7%; mean age 67 years). The PHILOS plate was used in nine patients and S3 plate was used in one patient. Five patients (4.9%) had varus inclination with a mean inclination angle of 112.6 degrees (range 105 degrees to 118 degrees), four patients (3.9%) developed varus displacement with a mean inclination angle of 102.5 degrees (range 95 degrees to 110 degrees), and intra-articular screw penetration was seen in five patients (4.9%). The remaining complications were fixation failure (n=1, 1%), implant fracture (n=1), and deep infection (n=1). Screw penetration exceeded 3 mm in three patients, requiring revision surgery. The mean ages of patients with varus inclination, varus displacement, and screw penetration were 76.6, 74.4, and 71 years, respectively. Three patients with varus inclination (60%) developed varus displacement. Screw penetration was observed in three patients (60%) with varus inclination, and in all patients with varus displacement. The mean Constant-Murley shoulder score was 67.8 (range 50 to 90) in patients who developed a complication. CONCLUSION: Our findings show that locking plate and screw systems represent a significant treatment option in the treatment of comminuted and displaced humerus fractures, with low complication rates. Accurate indication, protection of the head's inclination angle through appropriate surgical approach and proper technique, and fine calculation of screw length are essential for successful functional results.","corpus_id":31556230,"score":2},{"doc_id":"20731844","title":"Displaced proximal humeral fractures: an Indian experience with locking plates.","abstract":"BACKGROUND: The treatment of displaced proximal humerus fractures, especially in elderly, remains controversial. The objective of this study was to evaluate functional outcome of locking plate used for fixation of these fractures after open reduction. We also attempted to evaluate the complications and predictors of loss of fixation for such an implant. METHODS: Over two and a half years, 56 patients with an acute proximal humerus fracture were managed with locking plate osteosynthesis. 47 of these patients who completed a minimum follow up of 1 year were evaluated using Constant score calculation. Statistical analysis was done using SPSS 16 and a p value of less than 0.05 was taken as statistically significant. RESULTS: The average follow up period was around 21.5 months. Outcomes were excellent in 17%, good in 38.5%, moderate in 34% while poor in 10.5%. The Constant score was poorer for AO-OTA type 3 fractures as compared to other types. The scores were also inferior for older patients (> 65 years old). Complications included screw perforation of head, AVN, subacromial impingement, loss of fixation, axillary nerve palsy and infection. A varus malalignment was found to be a strong predictor of loss of fixation. CONCLUSION: Locking plate osteosynthesis leads to satisfactory functional outcomes in all the patients. Results are better than non locking plates in osteoporotic fractures of the elderly. However the surgery has steep learning curve and various complications could be associated with its use. Nevertheless we believe that a strict adherence to the principles of locking plate use can ensure good result in such challenging fractures.","corpus_id":1128503,"score":2},{"doc_id":"21085030","title":"A prospective clinical study of proximal humerus fractures treated with a locking proximal humerus plate.","abstract":"OBJECTIVES: The purpose of this prospective study was to evaluate the safety, efficacy, and functional outcome of the locked proximal humerus plate (LPHP) to treat proximal humerus fractures. DESIGN: Prospective clinical trial. SETTING: University orthopedic center. PATIENTS: Over a 25-month period, 64 consecutive patients were treated with a LPHP for an unstable or displaced proximal humerus fracture. INTERVENTION: Demographic data, trauma mechanisms, surgical approaches, and postoperative complications were collected from medical records. Fracture classification according to the Neer classification, radiographic head-shaft angle, and screw tip-articular surface distance in true anteroposterior and axillary lateral radiographs of the shoulder were measured postoperatively. MAIN OUTCOME MEASUREMENTS: The functional outcome was evaluated with a Constant-Murley (CM) evaluation. The CM score is a validated shoulder-specific scoring system in which patients report subjective findings. The physician reported the objective measurements of the shoulder. RESULTS: Follow-ups were completed for all of the patients. The overall complication rate was 35.9%, with screw penetration into the glenohumeral joint as the most frequent problem (7.6%). Deep wound infections were observed in 3.1% (n = 2) of the cases and avascular necrosis in 3.1% (n = 2). All complications occurred in 4-part fractures. Subacromial impingement, frozen shoulder, rotator cuff rupture, and wound dehiscence were observed in 3.1% (n = 2), 3.1% (n = 2), 1.6% (n = 1), and 1.6% (n = 1) of the cases, respectively. Multivariate linear regression analysis revealed that the fracture pattern and the presence or absence of medial support were significant predictors of functional outcome (P = 0.026 and P = 0.003, respectively). Patient age (P = 0.581), sex (P = 0.325), and initial tuberosity displacement (varus/extension or valgus/impaction; P = 0.059) were not significantly associated with the CM score. CONCLUSIONS: The LPHP seems to be a promising implant for the fixation of proximal humerus fractures. However, there are certain limitations that should be mentioned. The number of cases in our study was small, and no safe conclusions can be extracted regarding the rate of avascular necrosis. Additional studies with larger cohorts and longer follow-ups are necessary to better define the appropriate indications for and expected outcomes of this technology.","corpus_id":22812713,"score":2},{"doc_id":"21176833","title":"A systematic review of locking plate fixation of proximal humerus fractures.","abstract":"PURPOSE: Technique for the fixation of two, three, and four part proximal humerus fractures has rapidly shifted towards the use of specially contoured proximal humerus locking plates. The purpose of this study is to evaluate the short to medium term functional results and common complications associated with the fixation of proximal humerus fractures with locking plates. METHODS: The PubMed and EMBASE databases were used to perform a systematic review of the English literature to assess the functional results and complications associated with proximal humerus locking plates. Our inclusion criteria were proximal humerus fracture due to trauma (excluding pathologic fractures), patients greater than 18 years of age, more than 15 patients in the study or subgroup of interest, at least 18 months follow-up, at least one relevant functional outcome score, and quality outcome score of at least 5/10. Studies that did not meet these criteria were excluded. All institutional, author, and journal information was concealed to minimize reviewer bias. RESULTS: Twelve studies including 514 patients met the inclusion criteria. At most recent follow-up patients achieved a mean Constant score of 74 and a mean DASH score of 27. The overall rate of complications was 49% including varus malunion, 33% excluding varus malunion, and reoperation rate was 14%. The most common complications included varus malunion 16%, AVN 10%, screw perforation of the humeral head into the joint 8%, subacromial impingement 6%, and infection 4%. DISCUSSION: Fixation of proximal humerus fractures with proximal humerus locking plates is associated with a high rate of complications and reoperation. Further study is needed to determine what technical errors and patient characteristics are risk factors for failure of this now common fixation technique.","corpus_id":21207722,"score":2},{"doc_id":"21691909","title":"Endosteal strut augment reduces complications associated with proximal humeral locking plates.","abstract":"BACKGROUND: Locking-plate technology has renewed interest in plate fixation for treating proximal humerus fractures. Complications associated with these devices, including loss of reduction, screw cutout, and intra-articular penetration, are frequent. Establishing a second column of support may reduce complications and improve clinical outcome scores. QUESTIONS/PURPOSES: We asked whether addition of an endosteal cortical allograft strut, used as an augment to locking-plate fixation for displaced proximal humerus fractures, would reduce complications and improve clinical outcome scores. PATIENTS AND METHODS: We retrospectively reviewed the charts and radiographs of 38 patients treated by this method. All patients were evaluated with serial radiographs, as well as the Disabilities of the Arm, Shoulder, and Hand and Constant-Murley scores. There were seven two-part, 19 three-part, and 12 four-part fractures. The minimum followup was 49 weeks (average, 75 weeks; range, 49-155 weeks). RESULTS: No patient had intra-articular screw penetration or cutout. No patient had complete osteonecrosis, but one had partial osteonecrosis. The reduction was lost in one patient. The mean Disabilities of the Arm, Shoulder, and Hand score was 15 (range, 0-66.4). The mean Constant-Murley score was 87 (range, 51-95). CONCLUSIONS: Low rates of complication and high clinical outcome scores can be achieved when treating complex proximal humerus fractures with locking-plate fixation and an endosteal strut augment. LEVEL OF EVIDENCE: Level IV, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.","corpus_id":23539102,"score":2},{"doc_id":"21814772","title":"Rate of avascular necrosis following proximal humerus fractures treated with a lateral locking plate and endosteal implant.","abstract":"INTRODUCTION: Treatment of displaced proximal humerus fractures remains challenging. The introduction of locking plates has renewed interest in treating these fractures with joint-preserving techniques rather than hemiarthroplasty, but high complication rates are still reported. Avascular necrosis is not solely dependent on the initial fracture pattern, but can also result from intraoperative and postoperative vascular insults. METHOD: We describe a technique to minimize disruption of humeral head blood supply and maximize fracture fixation. A total of 34 patients with complex proximal humerus fractures were treated with a locking plate and endosteal implant through an anterolateral approach and followed for an average of 66 weeks to determine the rates of avascular necrosis. RESULTS: No patient suffered complete osteonecrosis (0%) and only one patient suffered partial necrosis (2.8%) of the humeral head. The length of the posteromedial hinge was not predictive of this complication. CONCLUSION: Use of the anterolateral approach and endosteal augment of a lateral locking plate can minimize avascular necrosis following proximal humerus fracture.","corpus_id":8733025,"score":2},{"doc_id":"21837232","title":"Results of 131 consecutive operated patients with a displaced proximal humerus fracture: an analysis with more than two years follow-up.","abstract":"OBJECTIVE: The purpose of this study is to determine the efficacy of the open reduction and fixation of a dislocated proximal humerus fracture with a locking plate, also evaluating the incidence of complications and functional recovery of the shoulder. A retrospective study focusing on patients who had suffered a fracture of the proximal humerus and were treated by means of an open reduction and internal fixation with a locking plate, using either the Philos or the LPHP plate. We have also included a comparison of these two plates. METHOD: Ninety-two patients were found to be eligible and were included in our study. These patients had all been treated for a proximal humerus fracture between 2002 and 2008. We included those patients who could be classified as a class 2, 3, or 4 according to the Neer classification. Demographic data, surgical technique, and peri/post-operative complications were collected from medical records. Patients were followed-up and the Oxford Shoulder Score (OSS) was filled in by phone. The mean age of our patient population was 66.2 (15-97), with a male: female ratio of 1:5 (15:77). ( The median follow-up was 2.4 years (0.2-5.8). Fourteen of our patients died during follow-up, while 25 patients were otherwise lost to follow-up. For this study, out of the original 131 patients, this finally resulted in 92 patients whom we followed-up post-operatively. RESULTS: Ninety-two patients (70%, 92/131) were interviewed. The mean Oxford Shoulder Score (OSS) was 19.76 (11-54). The overall complication rate was 39.1% (36/92). The most frequently occurring complications in our patient population were hemorrhage 3.3%; dislocation of the caput humeri and/or tuberculum majus 2.2%; persistent pain 3.3%; Avascular necrosis (AVN) of the humeral head 0%; Loss of reduction and screw cutout 6.5%; Plate breakout 6.5%; Subacromial Impingement 11.9%; Frozen shoulder 3.3%; rotator cuff rupture 1.1%, and infection 1.1%. Of the entire group of patients originally included in this study, 29% was re-operated due to one of the above-mentioned complications. CONCLUSION: In conclusion, the locking plate provides satisfactory functional outcomes after a mid-term follow-up in patients with displaced proximal humerus fractures. The incidence of complications and subsequent re-operation is relatively high, however, comparable to or slightly better when compared to data found in literature. Subacromial Impingement seems to occur more frequently when a Philos plate is implemented. We therefore suggest that randomized clinical trials determining the possible superiority of one specific type of plate in patients with a displaced proximal humerus fracture are to be performed in future.","corpus_id":14239158,"score":2},{"doc_id":"21968245","title":"Benefits and harms of locking plate osteosynthesis in intraarticular (OTA Type C) fractures of the proximal humerus: a systematic review.","abstract":"INTRODUCTION: Locking plate osteosynthesis of proximal humeral fractures are widely recommended and used, even in complex intraarticular fracture patterns such as AO/OTA Type C fractures. We systematically reviewed clinical studies assessing the benefits and harms of osteosynthesis with angle stable plates in AO/OTA Type C fractures of the proximal humerus. METHODS: We conducted an iterative search in PubMed, Embase, Cochrane Library, Web of Science, Cinahl, and PEDro in all languages from 1999 to November 2010. Eligible studies should study the outcome for Type C fractures after primary osteosynthesis with locking plate within two weeks of injury, and a follow-up period of six months or more. Patients should be evaluated with the Constant-Murley Score (CS). Two observers extracted data independently. RESULTS: Twelve studies and 282 Type C fractures were included. Results were categorised according to study type and synthesised qualitatively. No randomised clinical trials were identified. Two comparative, observational studies reported a mean CS of 71 (relative to contralateral shoulder) and 75 (non-adjusted Constant Score) for Type C fractures. For all studies mean non-adjusted CS ranged from 53 to 75. Mean age- and sex-adjusted CS ranged from 60 to 88. Mean CS relative to the contralateral shoulder ranged from 71 to 85. The most common complications were avascular necrosis (range, 4-33%), screw perforations (range, 5-20%), loss of fixation (range, 3-16%), impingement (range, 7-11%) and infections range 4-19%. Reoperation rate ranged from 6 to 44%. CONCLUSIONS: Insufficient study designs and unclear reporting preclude safe treatment recommendations. Complication and reoperation rates were unexpected high. Based on the studies included we cannot routinely recommend the use of locking plates in AO/OTA Type C fractures.","corpus_id":205442077,"score":2},{"doc_id":"22008672","title":"[Complication analysis of proximal humeral fractures treated with locking plate].","abstract":"OBJECTIVE: To analyze complications of surgically treated proximal humeral fractures with locking plate. METHODS: Eighty three (30 males and 53 females) coherent unstable proximal humeral fractures were treated with locking plate from January 2007 to January 2010 with a mean follow-up lasting 23.5 months ( 10-51 months ). Their mean age was 66.4 years (33-89 years). The patients were evaluated with outpatient physical examination, X-ray film, visual analogue scale (VAS), and Constant-Murley scores. Complications and functional outcome of the involved shoulders were recorded and estimated. Complications were diagnosed in 15 cases, varus malunion in 6, humeral head necrosis in 3, delayed union in 1, screw cut-out in 3, and subacromio-impingement in 3.Four cases were combined with two or more complications. RESULT: Four-part fractures had higher complication risks in implant related complications (P=0.009)and none implant related complications (P=0.003).Age and comobities had little influence on complication occurrence. CONCLUSION: Although locking plate provides optimal clinical results in proximal humeral fracture management, its complications should be highly considered. Preoperative evaluation, implant option, accurate reconstructions and rehabilitations are key points to restore the shoulder function.","corpus_id":41239727,"score":2},{"doc_id":"22287062","title":"Complex fractures of the proximal humerus in the elderly--outcome and complications after locking plate fixation.","abstract":"Open reduction and internal fixation (ORIF) with locking plates or primary arthroplasty remains a controversial issue in the management of complex proximal humerus fractures. Aim of this study was to evaluate the surgeon- and patient-based outcome of patients older than 65 years who underwent ORIF using locking plate fixation of a 3- or 4-part fracture of the proximal humerus. Twenty-seven patients older than 65 years were treated with locking plate fixation (PHILOS, Fa. Synthes, Umkirch, Germany). At an average follow-up of 44 months, the clinical and the subjective outcome were evaluated, and complications were analyzed. The mean age- and gender-related Constant score was 70% (30–100%) compared with 92% (47–108%) of the contralateral non-injured shoulder. The mean DASH score was 29 points (0–71). Five patients (18.5%) showed clinical signs of an impingement, which was related to malpositioning of the plate in 3 cases. Screw cutout was seen in 22.2% (6 patients). Avascular necrosis of the head or the tubercula was found in 8 patients (29.6%). The revision rate was 29.6%. However, the patients considered the functional status of their shoulder as “good” or “satisfactory.” The functional and patient-orientated results of the locking plate fixation of complex displaced proximal humerus fractures in the elderly are comparable to those of primary arthroplasty and minimally invasive treatment. Proper surgical technique (screw length, plate position) is mandatory for reducing the revision rate.","corpus_id":8859779,"score":2},{"doc_id":"22310414","title":"Locking plate fixation for proximal humerus fractures.","abstract":"Locking plates are increasingly used to surgically treat proximal humerus fractures. Knowledge of the bone quality of the proximal humerus is important. Studies have shown the medial and dorsal aspects of the proximal humeral head to have the highest bone strength, and this should be exploited by fixation techniques, particularly in elderly patients with osteoporosis. The goals of surgery for proximal humeral fractures should involve minimal soft tissue dissection and achieve anatomic reduction of the head complex with sufficient stability to allow for early shoulder mobilization. This article reviews various treatment options, in particular locking plate fixation. Locking plate fixation is associated with a high complication rate, such as avascular necrosis (7.9%), screw cutout (11.6%), and revision surgery (13.7%). These complications are frequently due to the varus deformation of the humeral head. Strategic screw placement in the humeral head would minimize the possibility of loss of fracture reduction and potential hardware complications. Locking plate fixation is a good surgical option for the management of proximal humerus fractures. Complications can be avoided by using better bone stock and by careful screw placement in the humeral head.","corpus_id":3035080,"score":2},{"doc_id":"22321162","title":"Hemiarthroplasty versus angle-stable locking compression plate osteosynthesis in the treatment of three- and four-part fractures of the proximal humerus in the elderly: design of a randomized controlled trial.","abstract":"BACKGROUND: The optimal surgical management of dislocated three- and four-part fractures of the proximal humerus in elderly patients remains unclear. Most used techniques are hemiarthroplasty and angle-stable locking compression plate osteosynthesis. In the current literature there is no evidence available presenting superior results between hemiarthroplasty and angle-stable locking compression plate osteosynthesis in terms of speed of recovery, pain, patient satisfaction, functional outcome, quality of life or complications. METHODS/DESIGN: A randomized controlled multicenter trial will be conducted. Patients older than 60 years of age with a dislocated three- or four-part fracture of the proximal humerus as diagnosed by X-rays and CT-scans will be included. Exclusion criteria are a fracture older than 14 days, multiple comorbidity, multitrauma, a pathological fracture, previous surgery on the injured shoulder, severely deranged function caused by a previous disease, \"head-split\" proximal humerus fracture and unwillingness or inability to follow instructions. Participants will be randomized between surgical treatment with hemiarthroplasty and angle-stable locking compression plate osteosynthesis. Measurements will take place preoperatively and 3 months, 6 months, 9 months, 12 months and 24 months postoperatively. Primary outcome measure is speed of recovery of functional capacity of the affected upper limb using the Disabilities of Arm, Shoulder and Hand score (DASH). Secondary outcome measures are pain, patient satisfaction, shoulder function, quality of life, radiological evaluation and complications. Data will be analyzed on an intention-to-treat basis, using univariate and multivariate analyses. DISCUSSION: Both hemiarthroplasty and angle-stable locking compression plate osteosynthesis are used in the current treatment of dislocated three-and four-part fractures of the proximal humerus. There is a lack of level-1 studies comparing these two most-used surgical treatment options. This randomized controlled multicenter trial has been designed to determine which surgical treatment option provides the fastest recovery of functional capacity of the affected upper limb, and will provide better outcomes in pain, satisfaction, shoulder function, quality of life, radiological evaluation and complications. TRIAL REGISTRATION NUMBER: The trial is registered in the Netherlands Trial Registry (NTR2461).","corpus_id":6582468,"score":2},{"doc_id":"22337487","title":"Locked plating of the proximal humerus using an endosteal implant.","abstract":"PURPOSE: To report on the use of a supplemental medial endosteal implant to prevent varus collapse and screw cutout in proximal humerus fractures treated with a laterally placed locking plate. METHODS: Twenty-seven patients meeting study inclusion criteria were included in the study. Follow-up averaged 63.1 weeks (minimum 37 weeks and maximum 120 weeks). All patients were either older than 70 years or had sustained a proximal humerus fracture with medial comminution. Using the anterolateral acromial approach, a proximal humeral locking plate augmented with a medial endosteal implant (fibular allograft in 23 patients and semitubular plate in 4 patients) was used for fixation. Intraoperative fluoroscopic images and the most recent follow-up radiographs were used to measure the head-shaft angle and loss of height between the implant and the articular surface. RESULTS: Only 1 of 27 patients had significant loss of reduction with collapse of the fracture into varus (4.2 mm change). Ninety-six percent of patients maintained their original reduction with an average loss of height of 1.2 mm and an average change in shaft-head angle of 2.2 degrees. There were no implant failures or screw perforations of the articular surface and no radiographic or clinical evidence of AVN. CONCLUSIONS: Use of a medial endosteal implant as a supplement to a lateral locking plate is effective in maintaining operative reduction, preventing varus collapse, and implant failure in fractures with medial comminution and/or poor bone quality. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.","corpus_id":12389893,"score":2},{"doc_id":"22959524","title":"Locking plate fixation of fractures of the proximal humerus: analysis of complications, revision strategies and outcome.","abstract":"BACKGROUND: Locking plates for open reduction-internal fixation (ORIF) of proximal humeral fractures are widely used. We observed an unusually high number of patients with complications referred to our institution. It was the purpose of this study to report these complications, as well as their treatment and outcome. MATERIALS AND METHODS: From 2003 to 2010, all patients treated for complications after ORIF with locking plates for proximal humeral fractures were prospectively collected and retrospectively analyzed. Patients were followed up clinically and radiographically. RESULTS: In total, 121 patients (67 women and 54 men; mean age, 59 years) were referred after primary locking plate ORIF; 80% had a 3- or 4-part fracture. A mean of 3 complications occurred per patient, including malreduction, primary screw cutout, malunion, nonunion, avascular necrosis, and infection. Secondary screw cutout was found in 57% of patients, causing glenoid destruction in 33% of patients. A mean of 1.5 revision surgeries were needed. Hemiarthroplasty, total shoulder arthroplasty, and reverse shoulder arthroplasty improved the mean Constant score (24 to 55 points, P < .05; 29 to 54 points, P = .3; and 25 to 48 points, P < .05, respectively) after a mean of 24 months. In 6 patients, glenoid implantation was no longer possible because of the destruction by perforated head screws. CONCLUSION: In this negatively selected series, complications resulted in secondary arthroplasties in over 50% of the patients. Shoulder function, though improved, remained substantially restricted even after revision surgery. Glenoid destruction by locking screws was the most devastating and previously almost unseen complication, which limited the options of treatment.","corpus_id":44522291,"score":2},{"doc_id":"23235575","title":"Interventions for treating proximal humeral fractures in adults.","abstract":"BACKGROUND: Fractures of the proximal humerus are common injuries. The management, including surgical intervention, of these fractures varies widely. This is an update of a Cochrane review first published in 2001 and last updated in 2010. OBJECTIVES: To review the evidence supporting the various treatment and rehabilitation interventions for proximal humeral fractures. SEARCH METHODS: We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE and other databases, and bibliographies of trial reports. The full search ended in January 2012. SELECTION CRITERIA: All randomised controlled trials pertinent to the management of proximal humeral fractures in adults were selected. DATA COLLECTION AND ANALYSIS: Two people performed independent study selection, risk of bias assessment and data extraction. Only limited meta-analysis was performed. MAIN RESULTS: Twenty-three small randomised trials with a total of 1238 participants were included. Bias in these trials could not be ruled out. Additionally there is a need for caution in interpreting the results of these small trials, which generally do not provide sufficient evidence to conclude that any non-statistically significant finding is 'evidence of no effect'.Eight trials evaluated conservative treatment. One trial found an arm sling was generally more comfortable than a less commonly used body bandage. There was some evidence that 'immediate' physiotherapy compared with that delayed until after three weeks of immobilisation resulted in less pain and potentially better recovery in people with undisplaced or other stable fractures. Similarly, there was evidence that mobilisation at one week instead of three weeks alleviated short term pain without compromising long term outcome. Two trials provided some evidence that unsupervised patients could generally achieve a satisfactory outcome when given sufficient instruction for an adequate self-directed exercise programme. Six heterogeneous trials, involving a total of 270 participants with displaced and/or complex fractures, compared surgical versus conservative treatment. Pooled results of patient-reported functional scores at one year from three trials (153 participants) showed no statistically significant difference between the two groups (standardised mean difference -0.10, 95% CI -0.42 to 0.22; negative results favour surgery). Quality of life based on the EuroQol results scores from three trials (153 participants) showed non-statistically significant differences between the two groups at three time points up to 12 months. However, the pooled EuroQol results at two years (101 participants) from two trials run concurrently from the same centre were significantly in favour of the surgical group. There was no significant difference between the two groups in mortality (8/98 versus 5/98; RR 1.55, 95% CI 0.55 to 4.36; 4 trials). Significantly more surgical group patients had additional or secondary surgery (18/112 versus 5/111; RR 3.36, 95% CI 1.33 to 8.49; 5 trials). This is equivalent to an extra operation in one of every nine surgically treated patients. Different methods of surgical management were tested in seven small trials. One trial comparing two types of locking plate versus a locking nail for treating two-part surgical neck fractures found some evidence of better function after plate fixation but also of a higher rate of surgically-related complications. One trial comparing a locking plate versus minimally invasive fixation with distally inserted intramedullary nails found some evidence of a short-term benefit for the nailing group. Compared with hemiarthroplasty, tension-band fixation of severe injuries using wires was associated with a higher re-operation rate in one trial. Two trials found no important differences between 'polyaxial' and 'monaxial' screws combined with locking plate fixation. One trial produced some preliminary evidence that tended to support the use of medial support locking screws in locking plate fixation. One trial found better functional results for one of two types of hemiarthroplasty. Very limited evidence suggested similar outcomes from early versus later mobilisation after either surgical fixation (one trial) or hemiarthroplasty (one trial). AUTHORS' CONCLUSIONS: There is insufficient evidence to inform the management of these fractures. Early physiotherapy, without immobilisation, may be sufficient for some types of undisplaced fractures. It remains unclear whether surgery, even for specific fracture types, will produce consistently better long term outcomes but it is likely to be associated with a higher risk of surgery-related complications and requirement for further surgery. There is insufficient evidence to establish what is the best method of surgical treatment, either in terms of the use of different categories of surgical intervention (such as plate versus nail fixation, or hemiarthroplasty versus tension-wire fixation) or different methods of performing an intervention in the same category (such as different methods of plate fixation). There is insufficient evidence to say when to start mobilisation after either surgical fixation or hemiarthroplasty.","corpus_id":38242239,"score":2},{"doc_id":"23412173","title":"Treatment of three- and four-part proximal humeral fractures with locking proximal humerus plate.","abstract":"OBJECTIVE: The purpose of this study was to evaluate the effectiveness and complications of the locking proximal humerus plate to treat proximal humerus fractures. DESIGN: A retrospective clinical trial. SETTING: Department of Orthopaedics, Tianjin Medical University General Hospital. PATIENTS: Sixty-eight consecutive patients with three- or four-part fractures of the proximal humerus were treated with locking proximal humerus plates. INTERVENTION: The deltopectoral anterolateral acromial approach was used to the proximal humerus; open reduction and locking proximal humerus plate were applied. MAIN OUTCOME MEASUREMENTS: Constant Score was used to measure the shoulder functional recovery, and Visual Analog Scale (VAS) was used to measure subjective evaluation of pain. The radiology was observed. RESULTS: After average 26.7 months, the average Constant Score was 72.6 ± 13.2 points and the average VAS was 1.2 ± 0.8 points. All the complications such as screw perforation into the glenohumeral joint, screws loosening, soft tissue infections, avascular necrosis and delayed union occurred in eight cases (11.8 %). CONCLUSIONS: The effectiveness of the locking proximal humerus plate was similar to other published literatures on treating fractures of the proximal humerus; however, a lower complications rate in short follow-up time was observed in this study. It may potentially provide a favorable option for treating three- or four-part fractures of the proximal humerus. Dealing with each particular fracture pattern, surgeons should have a decision of appropriate way to internal fixation.","corpus_id":25597316,"score":2},{"doc_id":"23682177","title":"Open reduction and locking plate fixation of displaced proximal humerus fractures.","abstract":"BACKGROUND: Treatment of proximal humerus fractures is controversial and various operative modalities have been tried in the literature. The aim of the present study was to evaluate functional outcome and complication rate after open reduction and internal fixation of displaced proximal humerus fractures by proximal humerus locking plate. MATERIALS AND METHODS: 52 patients with displaced proximal humerus fractures treated with proximal humerus locking plate between May 2008 and October 2010 were included in the study. Fractures were classified according to Neer's classification into displaced 2-part, 3-part, and 4-part fractures. Patients were followed for a minimum period of 1 year. 11 patients had less than 1 year of followup and were not considered in the evaluation of final results. Forty one patients were considered for final evaluation. Functional evaluation was done according to the Constant-Murley scoring system. Constant score was compared between 2-part, 3-part, and 4-part fractures at final up and also between young (≤60 yrs) and old (>60 yrs). RESULTS: 11 patients had 2-part fractures, 22 patients had 3-part fractures, and 19 patients had 4-part fractures. The mean followup period was 15.21 ± 2.59 months. 65.8% (n = 27) patients had good to excellent result, 19.5% (n = 8) had fair, and 14.7% (n = 6) had poor result. Constant scores for 2-part (79.83 ± 6.95) and 3-part fractures (74.22 ± 12.53) were significantly superior to those of 4-part fractures (61.09 ± 14.29) (P value = 0.002 and 0.018, respectively). Difference between 2-part and 3-part fractures was not significant (P value = 0.623). There was no significant difference between younger (≤60) and older patients (>60). Complications encountered in this series were varus malreduction in 17% (n = 7), screw perforation in 10% (n = 4), plate impingement in 12% (n = 5), infection in 2% (n = 1), and nonunion in 2% (n = 1) of cases. CONCLUSION: Proximal humerus locking plate gives reliable fixation for 2-part and 3-part fractures. Its use in more complicated fracture patterns of 4-part fractures is associated with poor clinical outcome.","corpus_id":5376232,"score":2},{"doc_id":"24003839","title":"Fixed-angle locking proximal humerus plate: an evaluation of functional results and implant-related outcomes.","abstract":"BACKGROUND: Displaced and unstable proximal humeral fractures are challenging injuries to treat. Proximal humeral locking plates are a recent development for the treatment of these complex fractures. METHODS: Retrospective analysis of 23 patients with 23 proximal humeral fractures treated with the Synthes locking proximal humerus plate. These were Neer two-, three- and four-part fractures. Follow-up was at a mean of 22 months and included clinical assessment using the Constant score (CS) and the Short Form-12 health questionnaire. Radiographic assessment was performed to assess implant-related complication in relation to the initial fracture pattern and the presence of adequate medial support. RESULTS: The mean CS for all patients was 60.4 (range, 29-85). The mean adjusted CS was 82% (range, 30-117), active forward flexion 127 degrees and the active abduction 115 degrees. Initial fracture pattern, the presence or absence of adequate medial support and age did not significantly influence the clinical scores. Complications included one infection, two cases of avascular necrosis, two cases of varus collapse with screw penetration and one non-union. The overall reoperation rate was 26%. There was an increased rate of complications in those with inadequate medial support (P = 0.0183) and a trend to higher complication rates in four-part fractures. CONCLUSION: Using the locking proximal humerus plate for the treatment of proximal humeral fractures is an acceptable procedure with comparable outcomes with historical controls, but with a complication rate of 30%. More important than implant selection, however, is the ability to achieve a stable reduction with calcar support.","corpus_id":22980777,"score":2},{"doc_id":"24296598","title":"The impact of preoperative coronal plane deformity on proximal humerus fixation with endosteal augmentation.","abstract":"OBJECTIVES: To examine the impact of preoperative coronal plane deformity on functional and radiographic outcomes on endosteal strut augmentation of proximal humerus fracture fixation. DESIGN: Single surgeon, retrospective analysis of a prospective database. Case series. SETTING: Academic level 1 trauma center. PATIENTS/PARTICIPANTS: Seventy-two patients with isolated proximal humerus fractures fulfilled all inclusion/exclusion criteria with a minimum follow-up of 12 months. INTERVENTION: Proximal humerus open reduction internal fixation with a laterally placed proximal humeral locking plate and endosteal placement of an allograft fibula treated through the anterolateral approach. MAIN OUTCOME MEASUREMENTS: Global functional outcome as determined by the Disabilities of the Arm, Shoulder and Hand (DASH) score and Short Form 36 physical function. Shoulder-specific functional outcome as determined by the Constant-Murley and the University of California Los Angeles shoulder scores. RESULTS: The mean age was 62 years old (range, 26-90 years). There were 32 varus fractures (neck-shaft angle, 110.8 degrees) and 40 valgus fractures (neck-shaft angle, 168.9 degrees). There was no significant difference in the initial postoperative (varus: 132.5 degrees, valgus: 135.5 degrees) and final (varus: 129.9 degrees, valgus: 132.2 degrees) neck-shaft angles or change in humeral height (varus: 0.94 mm, valgus: 1.48 mm). There were no significant differences in functional outcomes [Constant (varus: 85.2, valgus: 88.7) DASH (varus: 21.4, valgus: 13.9), University of California Los Angeles (28.6, varus 30.4), and Short Form 36 (varus: 66.8, valgus: 59.1)]. There were 2 patients in the valgus group and 3 patients in the varus group with an asymptomatic humeral head screw penetration (mean Constant 84.5, DASH 9.5). There was 1 deep infection in the varus group and 2 in the valgus group necessitating implant removal after fracture union. There was 1 case of avascular necrosis in the valgus group (DASH 19.4, Constant 73). CONCLUSIONS: There were no significant differences in complication rates, radiographic, or clinical outcomes between fractures presenting with preoperative varus coronal displacement compared with those presenting with valgus coronal displacement. The equivalent outcomes may be attributed to the uniform operative technique and fibular strut augmentation used by the primary surgeon. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.","corpus_id":46543591,"score":2},{"doc_id":"24781604","title":"Outcome of locking compression plating for proximal humeral fractures: a prospective study.","abstract":"PURPOSE: To evaluate the outcome of open reduction and internal fixation using locking compression plates for proximal humeral fractures. METHODS: 54 men and 16 women aged 28 to 79 (mean, 54) years underwent open reduction and internal fixation using a locking compression plate for closed 2-part (n=22), 3-part (n=38), and 4-part (n=10) proximal humeral fractures. 10 of the patients also had dislocation of the humeral head; 4 had fractures extending to the shaft. Wound condition, functional outcome, bone union, amount of collapse, and malalignment were assessed. Functional outcome was assessed using the Constant-Murley score. RESULTS; The mean follow-up period was 15 (range, 6-24) months. All fractures achieved union after a mean of 9 (range, 6-12) weeks. The mean Constant-Murley scores for the injured and normal shoulders were 72 and 82, respectively (88% of normal). The final outcome was excellent in 14 patients, good in 28, moderate in 22, and poor in 6. In the latter 6 patients, 2 had screw penetration, 2 had plate impingement, one had a mal-reduced greater tuberosity, and one had adhesive capsulitis. All were preventable. In all, 18 patients had 20 complications: subacromial impingement of the plate (n=6), mal-reduction of the greater tuberosity (n=6), screw penetration (n=2), adhesive capsulitis (n=2), superficial infection (n=2), and haematoma (n=2); 12 of these complications were technique-related. CONCLUSION: Locking proximal humeral plates enabled stable fixation in all Neer-type proximal humeral fractures. Most complications were technique-related.","corpus_id":8503619,"score":2},{"doc_id":"24791873","title":"Locking plate fixation combined with iliac crest bone autologous graft for proximal humerus comminuted fracture.","abstract":"BACKGROUND: Although the use of an intramedullary fibular allograft together with locking plate fixation can provide additional medial support and prevent varus malalignment in displaced proximal humeral fractures with promising results, the fibular autograft donor site often sustains significant trauma and cannot restore the articular surface of comminuted fractures. The aim of this study was to evaluate the clinical and radiographic outcomes of a locking plate and crest bone autologous graft for treating proximal humerus comminuted fractures. METHODS: We assessed the functional outcomes and complication rates in 40 patients with proximal humerus comminuted fractures. Eighteen patients were treated with a locking plate and an autologous crest bone graft (experimental group), and 22 were treated with only the locking plate and no bone graft (control group). Postoperative assessments included radiographic imaging, range of motion analysis, pain level based on the visual analogue scale (VAS), and the SF-36 (Short Form (36) Health Survey), as well as whether patients could return to their previous occupation. RESULTS: All fractures healed both clinically and radiologically in the experimental group. There was no more than 2 mm collapse of the humeral head, and no osteonecrosis or screw penetration of the articular surface. In contrast, two patients had a nonunion in the control group, and they eventually accepted total shoulder replacements. The average time from surgery to radiographic union was significantly shorter in the experimental group ((4.66±1.63) months) compared with the control group ((5.98±1.57) months) (P < 0.05). For the experimental versus controls groups, the mean shoulder active flexion (148.00±18.59 vs. 121.73±17.20) degrees, extension (49.00±2.22 vs. 42.06±2.06) degrees, internal rotation (45.00±5.61 vs. 35.00±3.55) degrees, external rotation (64.00±9.17 vs. 52.14±5.73) degrees, and abduction (138.00±28.78 vs. 105.95±15.66) degrees were all significantly higher (all P < 0.001). The median SF-36 in the experimental group ((88.00±5.71) points) was significantly higher than that of the control group ((69.45±9.45) points; P < 0.001). The median VAS pain level (mean rank, 10.50) in the experimental group was lower than that (mean rank, 47.19) of the control group (P < 0.001). All but one patient (17 of 18, 94.4%) in the experimental group returned to their previous activities or occupations, and that one patient changed to a different occupation because of slight restrictions to activities. On the other hand, four patients could not return to their previous activities or occupations in the control group. CONCLUSION: Locking plate fixation combined with an iliac crest bone graft is an effective technique for treating proximal humerus comminuted fractures.","corpus_id":7911624,"score":2},{"doc_id":"25293898","title":"Surgical treatment of proximal humerus fractures using PHILOS plate.","abstract":"OBJECTIVE: To evaluate functional outcome and complications of open reduction and internal fixation with proximal humeral internal locking system (PHILOS) plate for proximal humerus fractures. METHODS: We reviewed 51 patients who underwent open reduction and internal fixation with PHILOS plate between the years 2007 to 2012. There were 35 men and 16 women with a mean age of 38 years (range 24-68). There were 41 patients in the age group of <60 years and 10 patients in the age group of >60 years. According to Neer classification system, 8, 15 and 23 patients had 2-part, 3-part, and 4-part fractures, respectively and 5 patients had 4-part fracture dislocation. All surgeries were carried out at our tertiary care trauma centre. Functional evaluation of the shoulder at final follow-up was done using Constant-Murley score. RESULTS: The mean follow-up period was 30 months (range 12-44 months). Two patients were lost to follow-up. Of the remaining 49 patients, all fractures were united clinically and radiologically. The mean time for radiological union was 12 weeks (range 8-20 weeks). At the final follow-up the mean Constant-Murley score was 79 (range 50-100). The results were excellent in 25 patients, good in 13 patients, fair in 6 patients and poor in 5 patients. During the follow-up, four cases of varus malunion, one case of subacromial impingement, one case of deep infection, one case of intraarticular screw penetration and one case of failure of fixation were noted. No cases of avascular necrosis, hardware failure, locking screw loosening or nonunion were noted. CONCLUSION: PHILOS provides stable fixation in proximal humerus fractures. To prevent potential complications like avascular necrosis, meticulous surgical dissection to preserve vascularity of humeral head is necessary.","corpus_id":36408736,"score":2},{"doc_id":"25350626","title":"Early outcomes of proximal humerus fracture fixation with locking plate and intramedullary fibular strut graft.","abstract":"Proximal humerus fractures are commonly encountered in elderly patients. Surgical treatment demonstrates high complication rates, including varus construct collapse and screw cutout. In this study, the authors evaluate the clinical outcome of locking plate fixation with intramedullary fibular strut graft augmentation as a primary surgical treatment in the prevention of early collapse and screw cutout. A total of 9 patients were evaluated. Surgery was performed for displaced proximal humerus fractures between April and December 2011. Patients were either class 2, 3, or 4, according to Neer classification. Mean patient age was 75.4 years. Preoperative and immediate, 6-week, and 3-month postoperative radiographs were evaluated. Head-shaft angles were measured to assess for varus collapse and displacement. Range of motion, complication rates, and functional recovery were also evaluated. Patients underwent open reduction and internal fixation with placement of an intramedullary fibular strut graft. Fixation was achieved with a Philos plate (Synthes, Oberdorf, Switzerland). Reduction and fixation were evaluated with radiographs. Passive exercises and range of motion were allowed immediately postoperatively, and all patients achieved active abduction and forward flexion 6 weeks postoperatively. Shoulder radiographs taken 12 weeks postoperatively revealed no loss of reduction or screw cutout. The introduction of the locking plate has improved outcomes. The addition of an intramedullary strut graft has shown improved preliminary results. Maintained reduction was observed in all 9 patients in the early postoperative period, and good functional motion was achieved. No incidence of screw cutout was recorded.","corpus_id":10065894,"score":2},{"doc_id":"25433318","title":"The Results of Internal Fixation of Proximal Humeral Osteoporotic Fractures with PHILOS Locking Plate.","abstract":"BACKGROUND: In the last fifty years since plate and screw osteosynthesis has been implemented in fracture treatment, osteosporotic bone fractures were observed as a special problem. Due to special histologic, anatomic, physical and biomehanic properties of osteoporotic changed bone the laws of biomechanics suggest that stable osteosynthesis for osteoporotic bone is necessary to increase the contact surface of metallic implants and bone and the stability of the screw-plate-bone compound. There are numerous surgical techniques and methods for treatment of osteoporotic proximal humeral fractures. Every surgical procedure has to establish anatomical reduction and stable fixation that will enable early mobilisation. SUBJECTS AND METHODS: The aim of this study was to present results of internal fixation of proximal humeral osteoporotic fractures with PHILOS locking plate. Between 2007 and 2012, a total of 67 patients older than 65 years with closed proximal humerus fractures underwent surgical treatment with PHILOS plate system (Synthes, Switzerland). 42 patients were operated with deltopectoral approach and 25 with deltoid split approach. After a mean follow up period of 14.68 (6-28) months functional and radiologic results were assessed. RESULTS: We noted 9 postoperative complications related to surgical technique (1 intraarticular screw placement, 1 displacement in major tuberculum fragment, 1 displacement in major tuberculum fragment along with oblique placement of the plate, 2 cases of inadequate reduction, 1 case of humeral head avascular necrosis, varus humeral head fixation in 3 cases). None of the patients developed superficial or deep surgical infection. There was no nonunions. In the final evaluation, the Constant shoulder score was 91.75 (72-100). CONCLUSIONS: In this study PHILOS locking plate showed good applicability, respecting bone biologic properties because of negligible interference with blood supply of the humeral head. There was no requirement to shape the plate enabling stabilization at constant angles as clear benefit of this plate. All that enables early mobilisation, and no implant insufficiency resulting in satisfactory treatment results and high Constant shoulder scores.","corpus_id":36475215,"score":2},{"doc_id":"25457318","title":"Fractures and fracture-dislocations of the proximal humerus: A retrospective analysis of 82 cases treated with the Philos(®) locking plate.","abstract":"OBJECTIVE: To present the experience in a single institution of the management of 82 consecutive fractures and fracture-dislocations of the proximal humerus treated with the Proximal Humeral Internal Locking System (Philos(®)) plate. MATERIALS AND METHODS: A total of 81 patients with 82 proximal humerus fractures (one patient had bilateral fracture) were treated at our institution with open reduction and internal fixation with Philos(®) plate from January 2008 to December 2012 and the clinico-radiological outcome was analysed. Twelve of these patients also had a dislocation of the proximal humerus. According to the Neer classification, there were seven two-part fractures, 40 three-part fractures and 35 four-part fractures. All patients received a similar physical therapy programme following internal fixation. Mean final follow-up was 32 months. Functional outcome was evaluated for each patient using the Constant-Murley score; radiographic evaluation was also conducted and complications were recorded. RESULTS: At the end of the follow-up period, the mean Constant-Murley score for the injured side was 75 points (range 42-92); results were graded as excellent for eight patients, good for 52, moderate for 17 and poor for five. Twenty-three patients (28%) had complications during the follow-up period. Reoperation was required in 12 patients. Complications included avascular necrosis of the humeral head in 10 patients (12%), varus positioning of the head in four patients (4.8%), impingement syndrome in three patients (3.6%), secondary screw perforation in three patients (3.6%), non-union of the fracture in two patients (2.4%) and infection in one patient (1.2%). CONCLUSIONS: Open reduction and internal fixation of proximal humeral fractures with the Philos(®) plate was associated with good clinical outcomes provided the correct surgical technique was used. To better evaluate the real incidence of complications, it is important to follow patients for more than one year after surgery as some complications may arise after this time.","corpus_id":35160685,"score":2},{"doc_id":"25978864","title":"How to enhance the stability of locking plate fixation of proximal humerus fractures? An overview of current biomechanical and clinical data.","abstract":"BACKGROUND: The complication rate after locking plate fixation of proximal humerus fractures is high. In addition to low bone mineral density, a lack of medial support has been identified as one of the most important factors accounting for mechanical instability. As a result of the high failure rate, different strategies have been developed to enhance the mechanical stability of locking plate fixation of proximal humerus fractures. The aim of the present article is to give an overview of the current biomechanical and clinical studies that focus on how to increase the stability of locking plate fixation of proximal humerus fractures. METHODS: A comprehensive search of the Medline databases using specific search terms with regard to the stability of locking plate fixation of proximal humerus fractures was performed. After screening of the articles for eligibility, they were subdivided according to clinical and biomechanical aspects. RESULTS: Medial support screws, filling of bone voids and screw-tip augmentation with bone cement as well as the application of bone grafts are currently the most frequently assessed and performed methods. Although the evidence is weak, all of the mentioned strategies appear to have a positive effect on achieving and maintaining a stable reduction even of complex fractures. CONCLUSION: Further clinical studies with a higher number of patients and a higher level of evidence are required to develop a standardised treatment algorithm with regard to cement augmentation and bone grafting. Although these measures are likely to have a stabilising effect on locking plate fixation, its general use cannot be fully recommended yet.","corpus_id":37222526,"score":2},{"doc_id":"26161759","title":"Reducing Postoperative Fracture Displacement After Locked Plating of Proximal Humerus Fractures: Current Concepts.","abstract":"The incidence of proximal humerus fractures in the elderly has been rising. Concomitantly, operative fixation with use of locking plates has been increasing. Postoperative complications of locking plate fixation, particularly in the setting of osteoporotic bone, include screw penetration of the articular surface, progressive fracture displacement, and avascular necrosis. Intraoperative techniques to enhance the fixation construct and reduce complications include use of rotator cuff sutures, bone void fillers (fibular strut allograft, cancellous allograft, autograft, bone cement), appropriate placement of divergent and shorter locking screws, and medial calcar reduction and support. More recent clinical and biomechanical studies suggest that use of these strategies may reduce complications after locked plating of osteoporotic proximal humerus fractures. Furthermore, a multidisciplinary approach to the evaluation and treatment of osteoporosis may be beneficial in these patients.","corpus_id":19987527,"score":2},{"doc_id":"26445824","title":"Additional calcar support using a blade device reduces secondary varus displacement following reconstruction of the proximal humerus: a prospective study.","abstract":"BACKGROUND: Locking plate fixation of displaced fractures of the proximal humerus is still accompanied by a distinct complication rate, especially in case of osteoporotic bone, short-segment fracture length and comminution of the medial calcar. Secondary loss of reduction leading to varus deformity and screw cutout most frequently lead to surgical revision. The aim of the present study was to evaluate the clinical and radiological outcome of a recently developed polyaxial locking plate that allows for the additional placement of a helical blade device, aiming for support of the medial calcar. METHODS: In this prospective study, 17 patients with a mean age of 63.0 ± 16.0 years suffering from displaced fractures of the proximal humerus (Neer type two-, three- and four-part) were enrolled. All patients were surgically treated using a polyaxial locking plate with additional blade device (group PAB, n = 12) or without blade device (group PA, n = 5). Functional outcome was recorded using the Munich Shoulder Questionnaire allowing for qualitative self-assessment of the Shoulder Pain and Disability Index (SPADI), the Disability of the Arm, Shoulder and Hand (DASH score) and the Constant Score. Radiological outcome was assessed by analyzing standardized true anterior-posterior and outlet-view radiographs with respect to radiographic evidence of secondary varus displacement, cutout of screws and hardware failure. Results were compared to an age-, gender- and fracture type-matched collective treated by monoaxial locking plate fixation (group MA, n = 15). RESULTS: The mean follow-up was 12.4 ± 2.9 months after surgery. There were no statistical significant differences in clinical outcome in all three groups. Group MA and group PA revealed significant secondary varus displacement in comparison to group PAB at the final follow-up compared to postoperative analysis (p < 0.001). The distance between the blade and the articular surface showed no significant increase in group PAB at the final follow-up compared to postoperative analysis. Not-implant-related complications were seen in one and implant-related complications were seen in two patients in group PAB. CONCLUSIONS: Polyaxial locking plate fixation with a blade device to restore medial cortical support reduces the risk of secondary varus displacement even in proximal humeral fractures of the elderly in comparison to monoaxial and polyaxial locking plate fixation without blade insertion.","corpus_id":12850095,"score":2},{"doc_id":"26535597","title":"Analysis of Failure with the Use of Locked Plates for Stabilization of Proximal Humerus Fractures.","abstract":"OBJECTIVE: To evaluate factors associated with complicationsin a series of patients with proximal humerus fracturestreated with locked plating. DESIGN: Retrospective chart review. SETTING: Level 1 Trauma Center. PATIENTS AND METHODS: A retrospective review was performedon patients older than 18 years of age treated with alocked plate for a proximal humerus fracture between June2007 and December 2011 in order to identify any factorsassociated with failure. Patients had a minimum of 6 monthsof clinical follow-up. RESULTS: 78 proximal humerus fractures in 78 patientswere stabilized using a locked plate. Twenty-four patientswere lost to follow-up, while 54 patients were available for6-month minimum follow-up and comprised the study group. A healing complication occurred in 20 patients (37%) andconsisted of loss of reduction (16), varus malunion (16),avascular necrosis (6) or implant penetration (1). Elevenof 54 patients (20%) required secondary surgery. Factorsassociated with a healing complication were number offracture parts (p < 0.029), one or more comorbidities (p <0.016), three or more comorbidities (p < 0.038), and varusmalreduction (p < 0.001). CONCLUSION: An overall complication rate of 37% wasfound in patients stabilized using a locked plate after sustaininga proximal humerus fracture. Factors associatedwith healing complications included increased number offracture parts, increasing number of comorbidities, and initialvarus malreduction. Patient selection for locked platingafter proximal humerus fracture should incorporate manyfactors with meticulous attention to surgical technique.","corpus_id":19574384,"score":2},{"doc_id":"26560014","title":"Interventions for treating proximal humeral fractures in adults.","abstract":"BACKGROUND: Fracture of the proximal humerus, often termed shoulder fracture, is a common injury in older people. The management of these fractures varies widely. This is an update of a Cochrane Review first published in 2001 and last updated in 2012. OBJECTIVES: To assess the effects (benefits and harms) of treatment and rehabilitation interventions for proximal humeral fractures in adults. SEARCH METHODS: We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and other databases, conference proceedings and bibliographies of trial reports. The full search ended in November 2014. SELECTION CRITERIA: We considered all randomised controlled trials (RCTs) and quasi-randomised controlled trials pertinent to the management of proximal humeral fractures in adults. DATA COLLECTION AND ANALYSIS: Both review authors performed independent study selection, risk of bias assessment and data extraction. Only limited meta-analysis was performed. MAIN RESULTS: We included 31 heterogeneous RCTs (1941 participants). Most of the 18 separate treatment comparisons were tested by small single-centre trials. The main exception was the surgical versus non-surgical treatment comparison tested by eight trials. Except for a large multicentre trial, bias in these trials could not be ruled out. The quality of the evidence was either low or very low for all comparisons except the largest comparison. Nine trials evaluated non-surgical treatment in mainly minimally displaced fractures. Four trials compared early (usually one week) versus delayed (three or four weeks) mobilisation after fracture but only limited pooling was possible and most of the data were from one trial (86 participants). This found some evidence that early mobilisation resulted in better recovery and less pain in people with mainly minimally displaced fractures. There was evidence of little difference between the two groups in shoulder complications (2/127 early mobilisation versus 3/132 delayed mobilisation; 4 trials) and fracture displacement and non-union (2/52 versus 1/54; 2 trials).One quasi-randomised trial (28 participants) found the Gilchrist-type sling was generally more comfortable than the Desault-type sling (body bandage). One trial (48 participants) testing pulsed electromagnetic high-frequency energy provided no evidence. Two trials (62 participants) provided evidence indicating little difference in outcome between instruction for home exercises versus supervised physiotherapy. One trial (48 participants) reported, without presentable data, that home exercise alone gave better early and comparable long-term results than supervised exercise in a swimming pool plus home exercise. Eight trials, involving 567 older participants, evaluated surgical intervention for displaced fractures. There was high quality evidence of no clinically important difference in patient-reported shoulder and upper-limb function at one- or two-year follow-up between surgical (primarily locking plate fixation or hemiarthroplasty) and non-surgical treatment (sling immobilisation) for the majority of displaced proximal humeral fractures; and moderate quality evidence of no clinically important difference between the two groups in quality of life at two years (and at interim follow-ups at six and 12 months). There was moderate quality evidence of little difference between groups in mortality in the surgery group (17/248 versus 12/248; risk ratio (RR) 1.40 favouring non-surgical treatment, 95% confidence interval (CI) 0.69 to 2.83; P = 0.35; 6 trials); only one death was explicitly linked with the treatment. There was moderate quality evidence of a higher risk of additional surgery in the surgery group (34/262 versus 16/261; RR 2.06, 95% CI 1.18 to 3.60; P = 0.01; 7 trials). Although there was moderate evidence of a higher risk of adverse events after surgery, the 95% confidence intervals for adverse events also included the potential for a greater risk of adverse events after non-surgical treatment. Different methods of surgical management were tested in 12 trials. One trial (57 participants) comparing two types of locking plate versus a locking nail for treating two-part surgical neck fractures found some evidence of slightly better function after plate fixation but also of a higher rate of surgically-related complications. One trial (61 participants) comparing a locking plate versus minimally invasive fixation with distally inserted intramedullary K-wires found little difference between the two implants at two years. Compared with hemiarthroplasty, one trial (32 participants) found similar results with locking plate fixation in function and re-operation rates, whereas another trial (30 participants) reported all five re-operations occurred in the tension-band fixation group. One trial (62 participants) found better patient-rated (Quick DASH) and composite shoulder function scores at a minimum of two years follow-up and a lower incidence of re-operation and complications after reverse shoulder arthroplasty (RSA) compared with hemiarthroplasty. No important between-group differences were found in one trial (120 participants) comparing the deltoid-split approach versus deltopectoral approach for non-contact bridging plate fixation, and two trials (180 participants) comparing 'polyaxial' and 'monaxial' screws in locking plate fixation. One trial (68 participants) produced some preliminary evidence that tended to support the use of medial support locking screws in locking plate fixation. One trial (54 participants) found fewer adverse events, including re-operations, for the newer of two types of intramedullary nail. One trial (35 participants) found better functional results for one of two types of hemiarthroplasty. One trial (45 participants) found no important effects of tenodesis of the long head of the biceps for people undergoing hemiarthroplasty. Very limited evidence suggested similar outcomes from early versus later mobilisation after either surgical fixation (one trial: 64 participants) or hemiarthroplasty (one trial: 49 participants). AUTHORS' CONCLUSIONS: There is high or moderate quality evidence that, compared with non-surgical treatment, surgery does not result in a better outcome at one and two years after injury for people with displaced proximal humeral fractures involving the humeral neck and is likely to result in a greater need for subsequent surgery. The evidence does not cover the treatment of two-part tuberosity fractures, fractures in young people, high energy trauma, nor the less common fractures such as fracture dislocations and head splitting fractures. There is insufficient evidence from RCTs to inform the choices between different non-surgical, surgical, or rehabilitation interventions for these fractures.","corpus_id":205161397,"score":2},{"doc_id":"26878816","title":"Initial varus displacement of proximal humerus fractures results in similar function but higher complication rates.","abstract":"PURPOSE: To investigate the effect of initial varus or valgus surgical neck alignment on outcomes of patients who sustained proximal humerus fractures treated with open reduction and internal fixation (ORIF). METHODS: An institutional review board approved database of proximal humerus fractures treated with locked plates was reviewed. Of 185 fractures in the database, 101 fractures were identified and met inclusion criteria. Initial varus displacement was seen in 47 fractures (OTA types 11.A2.2, A3.1, A3.3, B1.2, B2.2, C1.2, C2.2, or C2.3) and initial valgus displacement was observed in 54 fractures (OTA types 11.A2.3, B1.1, C1.1, or C2.1). All patients were treated in a similar manner and examined by the treating physician at standard intervals. Functional outcomes were quantified via the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire and physical examination data at 12 months. Radiographs were reviewed for complications of healing. Additionally, complication rate and reoperation rate were investigated. RESULTS: Patients who presented with initial varus displacement had an average age of 59.3 years, while patients in the valgus group had an average age of 62.4 years. Overall, there was no statistically significant difference in age, sex distribution, BMI, fracture parts, screws used, or implant plate type between the two groups. At a minimum 12 months follow up, there was no significant difference in DASH scores between those presenting with varus versus valgus fracture patterns. In addition, no significant differences were seen in final shoulder range of motion in any plane. Overall, 30 patients included in this study developed a complication. A significantly greater number of patients in the initial varus cohort developed complications (40.4%), as compared to 20.3% of patients in the initial valgus cohort (P=0.03). Fourteen patients in this study underwent reoperation. Nine of these patients were in the varus cohort, while 5 were in the valgus cohort (P=0.15). CONCLUSIONS: In this study, initial surgical neck displacement in varus or valgus was found to not significantly affect functional outcome. Based upon our findings, patients with varus displaced proximal humerus fractures are at a greater risk of developing postoperative complications than those who present with initial valgus displaced fracture patterns.","corpus_id":23617781,"score":2},{"doc_id":"27047867","title":"EVALUATION OF THE COMPLICATIONS OF SURGICAL TREATMENT OF FRACTURES OF THE PROXIMAL EXTREMITY OF THE HUMERUS USING A LOCKING PLATE.","abstract":"OBJECTIVE: To evaluate the complications from surgical treatment using a locking plate among patients with fractures of the proximal extremity of the humerus. METHODS: Between July 2004 and December 2009, 56 patients with fractures of the proximal extremity of the humerus were treated using the PHILOS(®) plate. There were 19 male patients and 37 female patients, with a mean age of 62 years (range: 30 to 92 years). All the cases had a mean postoperative followup period of 12 months. Thirteen fractures were classified as presenting in two parts, 28 as three, eight as four and seven as epiphyseal fractures. RESULTS: Among the patients operated, 26 were considered to have achieved excellent results, twelve good, ten fair and eight poor, according to the UCLA score. Thirty complications occurred in 20 patients (35.7%), among which the most frequent complication was inadequate reduction of the fracture, which occurred in eight cases. Subacromial impact, caused by the plate, occurred in seven cases, while inadequate fixation occurred in six cases. Other complications such as pseudarthrosis, adhesive capsulitis, avascular necrosis, loss of varus reduction and infection were also seen. CONCLUSION: The functional results from treating fractures of the proximal extremity of the humerus using a locking plate depended on correct anatomical reduction of the fracture and stable fixation of the implant. Complications still occur frequently, particularly because of intraoperative technical difficulty, fracture severity and possible inexperience of the surgeon.","corpus_id":17124313,"score":2},{"doc_id":"27079217","title":"Complications of locked plating for proximal humeral fractures-are we getting any better?","abstract":"BACKGROUND: Complication rates reported after locking plate fixation of proximal humeral fractures still range up to 40%. Whether modifications of surgical techniques, use of primary shoulder arthroplasty, or a fracture-specific management resulted in decreased complication rates during recent years remains unclear. Therefore, the aim of this long-term observation study was to analyze the incidence of complications and revision surgery after locked plating. METHODS: Between February 2002 and December 2013, 788 patients (aged 67.4 ± 17.3 years) with displaced proximal humeral fractures were treated with locking plate, primary hemiarthroplasty (HA), or reverse shoulder arthroplasty (RSA). Standardized follow-up included radiographs at 1 day, 6 weeks, and 3, 6, and 12 months. Complications and unplanned revision surgery were prospectively recorded over the complete follow-up. RESULTS: Of 788 patients, 646 (82%) were treated with locking plate, 82 (10.4%) with HA, and 60 (7.6%) with RSA. Mean follow-up was 14.8 ± 3.8 months. The mean complication rate associated with locked plating was 12.8%, and revision surgery was necessary in 11.6%. Within the last 5 years, the loss of fixation rate markedly decreased from 14.3% to 4.8%; simultaneously, an increased use of RSA was observed. CONCLUSION: The overall complication rate of locking plate osteosynthesis for proximal humeral fractures has been decreasing considerably within the last years. Among others, this might be due to an increased use of primary RSA for complex fracture types. In addition to a precise surgical technique, choosing the adequate treatment for each individual fracture to avoid complications and revision surgery is of utmost importance.","corpus_id":27836057,"score":2},{"doc_id":"27114810","title":"Least Possible Fixation Techniques of 4-Part Valgus Impacted Fractures of the Proximal Humerus: A Systematic Review.","abstract":"UNLABELLED: The valgus-impacted (VI) 4-part fractures are a subset of fractures of the proximal humerus with a unique anatomic configuration characterized by a relatively lower incidence of avascular necrosis after operative intervention. We systematically reviewed clinical studies assessing the benefits and harms of least possible fixation techniques (LPFT) for this unique fracture type. Such information would be potentially helpful in developing an evidence-based approach in the management of these complex injuries. We performed analytic searches of PubMed, Embase, Web of Science, Google Scholar and the Cochrane Library, restricting it to the years 1991-2014. Included studies had to describe outcomes and complications after primary osteosynthesis with any type of LPFT apart from plate-screws and intramedullary nailing. Eligibility criteria were also included English language, more than 5 cases, minimum follow up of one year and report of clinical outcome using at least one relevant score (Constant, Neer or ASES). Based on 292 database hits we identified 12 eligible studies including 190 four-part valgus impacted fractures in 188 patients. All eligible studies were case series composed of min 8 to max 45 patients per study. The gender distribution was 60% (112) female and 40% (76) male. The average age of the patients at the time of injury was 54.5 years. In 8/12 studies an open reduction was used for fracture fixation using different surgical techniques including KW, cerclage wires, cannulated screws and osteosutures. Closed reduction and percutaneous fixation was used in 4 studies. Mean follow-up time ranged from 24 to 69 months. A good functional outcome (constant score >80) was reported in 9/12 studies. The most common complication was avascular necrosis of the humeral head with an overall incidence of 11% (range, 0-26.3%). Total avascular necrosis (AVN) was found in 15/188 patients (7.9%) and was more common in percutaneous techniques and partial AVN in 6/188 (3.1%) being more common in open techniques. The overall re-operation rate was very low (3.7%). Insufficient study designs cannot provide definite treatment recommendations and quantitative data synthesis of outcome. In general, LPFT for 4-part VI fractures leads to satisfactory outcomes with low incidence of complications. A considerable risk of biases can be attributed to fracture classification, proper radiological control, mean age of patients, mixed types of fixation methods, nonage adjusted clinical scoring and small follow up periods. These factors are discussed in detail. LEVEL OF EVIDENCE: systematic review of literature (level IV) as most of the studies were level IV.","corpus_id":38649590,"score":2},{"doc_id":"27504463","title":"Fibular Strut Graft Augmentation for Open Reduction and Internal Fixation of Proximal Humerus Fractures: A Systematic Review and the Authors' Preferred Surgical Technique.","abstract":"BACKGROUND: Proximal humerus fractures are common problems plaguing the elderly population. PURPOSE: The purposes of this study were to determine the outcomes of fibular strut allografts in treatment of proximal humerus fractures with open reduction internal fixation (ORIF) and to present the authors' preferred surgical technique. The hypothesis was that the use of fibular strut allografts in treating proximal humerus fractures with ORIF will provide low reoperation rates with acceptable outcomes. STUDY DESIGN: Systematic review; Level of evidence, 4. METHODS: A systematic review was registered with PROSPERO and performed with PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines using 3 publicly available free databases. Therapeutic clinical outcome investigations reporting arthroscopic elbow outcomes with levels of evidence 1 through 4 were eligible for inclusion. All study, subject, and surgical technique demographics were analyzed and compared between continents and countries. Statistics were calculated using Student t tests, 1-way analysis of variance, chi-square tests, and 2-proportion Z tests. RESULTS: Four studies met the inclusion criteria. While there is great heterogeneity existing in the literature surrounding use of a fibular strut allograft as an adjunct to ORIF of proximal humerus fractures, current evidence shows a humeral head screw penetration rate of 3.7% with acceptable functional outcome scores, with a reoperation rate of 4.4% at a weighted mean 80.78 weeks (1.55 years) of postoperative follow-up. CONCLUSION: There is great heterogeneity that exists in the literature surrounding the use of a fibular strut allograft as an adjunct to ORIF of proximal humerus fractures. Current evidence shows a screw penetration rate of 3.7% with acceptable functional outcome scores, demonstrating fibular strut allograft is a viable option for treating proximal humerus fractures.","corpus_id":7256929,"score":2},{"doc_id":"27656515","title":"Outcome Analysis of Locking Plate Fixation in Proximal Humerus Fracture.","abstract":"INTRODUCTION: Proximal humerus fractures account for approximately 5% of all fractures. Stable minimally displaced fractures can be treated nonoperatively but the management of displaced fractures remain controversial with various modalities of treatment available. Locking plates provide stable fixation and enable early postoperative mobilization specially in osteoporotic proximal humerus fracture. AIM: To evaluate the functional outcome of locking plate fixation and to compare the results of two approaches used for fixation. MATERIALS AND METHODS: This prospective study was conducted at a tertiary level hospital between September 2011 to December 2013. PHILOS plates were used for internal fixation of displaced proximal humerus fractures Neer's type 2 part, 3 part and 4 part fractures on 26 patients (M/F ratio 1.36:1; mean age 46 years). According to Neer classification, 5,12 and 9 patients had displaced 2, 3 and 4 part fractures respectively. Deltopectoral and deltoid splitting approaches were used for fixation on 13 patients each. Functional outcome was assessed using Constant-Murley shoulder score. Graphpad software version 6.0 was used with Chi-square test and Fisher-exact test are used to compare data. The p-value< 0.05 is considered significant. RESULTS: Of the 26 patients, all fractures united radiologically and clinically and average constant score at final follow-up was 72.5. At the final follow-up 8 patients had good score, 10 patients had moderate score, 6 patients had excellent outcome and 2 patients had poor outcome according to Constant score. Mean time to union was 12.3 weeks (9 -15 weeks). Four complications (15.4%) were encountered, 2 cases of varus malunion, 1 case of wound infection which required wound debridement and 1 case of screw cut-out in which screw removal was done. Mean constant score in delto splitting approach was 70.9 and 74 in deltopectoral group (p-value= 0.54). No significant difference existed in constant score in 2 approaches. No significant difference existed between groups in terms of complications (P > .05) and all fractures were united. CONCLUSION: Our study demonstrates that locking plate fixation gives good functional outcomes in treatment of proximal humerus fractures. There was no significant difference in the two approaches used for exposure. Our results are comparable to various studies conducted by other authors which states that locking plates provide better functional and radiological outcomes as compared to other fixation methods like Tension band wiring, percutaneous K-wire fixation, non-locking plates, intramedullary nails.","corpus_id":23173609,"score":2},{"doc_id":"27818186","title":"Fixation of 4-part fractures of the proximal humerus: Can we identify radiological criteria that support locking plates or IM nailing? Comparative, retrospective study of 107 cases.","abstract":"INTRODUCTION: No objective criteria exist to help surgeons choose between IM nailing and plate fixation for 4-part fractures of the proximal humerus. The goal of this study was to identify radiological criteria that would make one technique a better choice than the other. MATERIAL AND METHODS: This was a comparative, multicentre, retrospective study of 54 cases of antegrade nailing and 53 cases of plating performed between 1st January 2009 and 31 December 2011 for 4-part fractures of the proximal humerus. All patients had a minimum radiological and clinical follow-up of 18 months. The functional outcomes were evaluated using the weighted Constant score; a poor result was defined as a weighted Constant score<70%. The following radiological criteria were evaluated during the preoperative assessment and at the last follow-up: initial displacement and reduction of humeral head and tuberosities; morphology of the medial column (i.e. calcar comminution, posteromedial hinge, size of metaphyseal head extension); occurrence of avascular necrosis (AVN). RESULTS: After an average follow-up of 42 months, the weighted Constant scores and rate of poor outcomes were 77% and 48% in the nail group and 81% and 38% in the plate group, respectively (ns). The humeral head was reduced into an anatomical position, valgus or varus in 57%, 30% and 13% of cases in the nail group, and 58%, 29% and 13% in the plate group, respectively. The tuberosities healed in an anatomical position in 72% of nail cases and 70% of plate cases (ns). Only the presence of a medial hinge preoperatively had an effect on the functional outcomes in the nail and plate groups: the weighted Constant scores (P=0.05) and rate of poor outcomes (P=0.02) were 82% and 52% in the nail group and 97% and 9% in the plate group, respectively. The complication rates were comparable: the rates of AVN and articular screw penetration were 17% and 11% in the nail group, and 15% and 11% in the plate group, respectively. The surgical revision rate was 18.5% in the nail group and 30% in the plate group. CONCLUSION: If the medial hinge is preserved, we recommend locking plate fixation. In other cases, either technique can be used as long as the general rules of internal fixation are applied: reduction of the tuberosities, varus correction and stabilization of the calcar area. LEVEL OF EVIDENCE: IV, retrospective study.","corpus_id":4018387,"score":2},{"doc_id":"27866913","title":"Minimally invasive plate osteosynthesis with PHILOS plate for proximal humerus fractures.","abstract":"OBJECTIVES: The aim of the present study was to evaluate results, including clinical and radiological outcomes and number of complications, following minimally invasive plate osteosynthesis (MIPO) of proximal humerus fractures, using the PHILOS® proximal humerus internal locking system (Synthes Holding AG, Solothurn, Switzerland). METHODS: Retrospectively evaluated were 31 patients treated with MIPO (12 male, 19 female; average age: 58.4 years). Four patients had 2-part fractures, 14 patients had 3-part fractures, and 13 patients had 4-part fractures, according to Neer classification. Healing, complications, and head-shaft angle (HSA) were radiographically evaluated. Clinical outcomes were assessed at 1-year follow-up with Constant score. RESULTS: Average Constant scores for fractured and normal shoulders were 73.2 ± 10.9 and 84.8 ± 5.1, respectively. Varus progression, fracture type, and age had no significant effect on functional outcome. Average postoperative and follow-up HSA's were 130.80 ± 7.70 and 128.80 ± 10.00, respectively. Significant varus progression was observed during follow-up (p = 0.01). Varus progression was more prominent in patients with postoperative HSA < 130° (p < 0.001). Inferomedial calcar screw usage, fracture type, and age had no significant effect on varus progression. Complications included 2 implant failures, 1 case of avascular necrosis (AVN), 1 primary screw cut-out, 1 axillary nerve injury, and 1 radial nerve injury (22.6% overall). CONCLUSION: MIPO is a safe and effective option for the treatment of proximal humerus fractures, with good functional recovery and fewer complications, which are typically technique dependent. Reduction may be difficult, resulting in varus progression. Another disadvantage is risk of axillary nerve injury. Careful surgical technique and correct implant selection is important in the prevention of nerve injury. LEVEL OF EVIDENCE: Level IV, Therapeutic study.","corpus_id":44932381,"score":2},{"doc_id":"28360490","title":"Postoperative outcomes of initial varus versus initial valgus proximal humerus fracture: A systematic review and meta-analysis.","abstract":"OBJECTIVES: Our objective was to perform a systematic review of the literature and conduct a meta-analysis to investigate the effect of initial varus or valgus displacement of proximal humerus on the outcomes of patients with proximal humerus fractures treated with open reduction and internal fixation. METHODS: In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement standards, we performed a systematic review. Electronic databases MEDLINE, EMBASE, CINAHL and the Cochrane Central Register of Controlled Trials (CENTRAL) were searched to identify randomised and non-randomised studies comparing postoperative outcomes associated with initial varus versus initial valgus displacement of proximal humerus fracture. The Newcastle-Ottawa scale was used to assess the methodological quality and risk of bias of the selected studies. Fixed-effect or random-effects models were applied to calculate pooled outcome data. RESULTS: We identified two retrospective cohort studies and one retrospective analysis of a prospective database, enrolling a total of 243 patients with proximal humerus fractures. Our analysis showed that initial varus displacement was associated with a higher risk of overall complication (RR 2.28, 95% CI 1.12-4.64, P = 0.02), screw penetration (RR 2.30, 95% CI 1.06-5.02, P = 0.04), varus displacement (RR 4.38, 95% CI 2.22-8.65, P < 0.0001), and reoperation (RR 3.01, 95% CI 1.80-5.03, P < 0.0001) compared to valgus displacement. There was no significant difference in avascular necrosis (RR 1.43, 95% CI 0.62-3.27, P = 0.40), infection (RR 1.49, 95% CI 0.46-4.84, P = 0.51), and non-union or malunion (RR 1.37, 95% CI 0.37-5.04, P = 0.64). CONCLUSIONS: The best available evidence demonstrates that initial varus displacement of proximal humerus fractures is associated with higher risk of overall complication, screw penetration, varus displacement, and reoperation compared to initial valgus displacement. The best available evidence is not adequately robust to make definitive conclusions. Further high quality studies, that are adequately powered, are required to investigate the outcomes of initial varus and valgus displacement in specific fracture types. LEVEL OF EVIDENCE: Level II.","corpus_id":23184574,"score":2},{"doc_id":"28467336","title":"Early results for treatment of two- and three-part fractures of the proximal humerus using Contours PHP (proximal humeral plate).","abstract":"BACKGROUND AND AIM OF THE WORK: The management of displaced 2- and 3-part fractures of the proximal humerus is controversial, both in younger and in elderly patients. The purpose of this paper is to evaluate the functional results of the Contours Proximal Humerus Plate (OrthofixR, Bussolengo,Verona, Italy), for the treatment of displaced 2- and 3-part fractures of the proximal humerus. METHODS: We retrospectively reviewed 55 patients with proximal humerus fractures, who underwent osteosynthesis with Contours Proximal Humerus Plate from December 2011 to March 2015. We had 21 patients with 2-part fractures and with an average age of 67.1 years and 34 patients with 3-part fractures, with average age of 63.6 years. RESULTS: The average union time was 3 months. The mean Constant score was 67 for 2-part fracture group and 64.9 for 3-part fracture group. The difference was not statistically significant (p = 0.18). The overall complication rate was 14.5 %. Six patients underwent additional surgery (10.9%). CONCLUSIONS: The most frequent major complication was secondary loss of reduction following varus collapse of the fracture (2 cases). In these patients, there was loss of medial hinge integrity due to impaction and osteoporosis. The placement of the main locking screw in the calcar area to provide inferomedial support is the rational of the Contours Proximal Humerus Plate. Osteosynthesis with Contours Proximal Humerus Plate is a safe system for treating displaced 2- and 3-part fractures of the proximal humerus, with good functional results and complication rates comparable to those reported in the literature.","corpus_id":43487,"score":2},{"doc_id":"28946902","title":"Current concepts in locking plate fixation of proximal humerus fractures.","abstract":"Despite numerous available treatment strategies, the management of complex proximal humeral fractures remains demanding. Impaired bone quality and considerable comorbidities pose special challenges in the growing aging population. Complications after operative treatment are frequent, in particular loss of reduction with varus malalignment and subsequent screw cutout. Locking plate fixation has become a standard in stabilizing these fractures, but surgical revision rates of up to 25% stagnate at high levels. Therefore, it seems of utmost importance to select the right treatment for the right patient. This article provides an overview of available classification systems, indications for operative treatment, important pathoanatomic principles, and latest surgical strategies in locking plate fixation. The importance of correct reduction of the medial cortices, the use of calcar screws, augmentation with bone cement, double-plate fixation, and auxiliary intramedullary bone graft stabilization are discussed in detail.","corpus_id":8777688,"score":2},{"doc_id":"29541270","title":"Early Results of the A.L.P.S. Proximal Humerus Locking Plate.","abstract":"Background: Open reduction internal fixation of displaced 3 and 4-part proximal humerus fractures is an effective treatment modality particularly for the younger age group, but it is not without complications. Fixed angled locking screw plates are the mainstay of fixation. The A.L.P.S. Proximal Humerus Plating System is a new implant that has smooth locking pegs in the place of humeral head screws to help reduce glenoid damage in the event of cut-out and is designed to sit low on the humerus in order to reduce the risk of subacromial impingement. Methods: Retrospective analysis of 15 consecutive patients who sustained closed displaced 3-part or 4-part fractures and had fixation surgery using the A.L.P.S. plate. Outcome measures were the time to radiographic and clinical union, Oxford Shoulder Score, quick DASH score and complications. Results: Average follow-up was 31.9 weeks. Union was achieved in 100% of patients with a mean time to union of 15.1 weeks. In terms of function, mean OSS was 33.6 and mean quick DASH was 32.5. There were no instances of AVN. Conclusion: Our preliminary results of 15 patients followed up for a mean of 31.9 weeks show equitable union rates and time to union as well as functional scores compared to other available plating systems. This is the first study to report on this implant to date.","corpus_id":3865855,"score":2},{"doc_id":"22754418","title":"Evidence for success with locking plates for fragility fractures.","abstract":"Fixation of fragility fractures with plates and screws often results in loss of fixation and need for revision surgery. Locking plates and screw were introduced to improve fixation of fragility fractures and have been in use for a decade. This review was conducted to compile evidence that locking plates and screws improve fixation of fragility fractures. A search of PubMed was performed to identify biomechanical studies as well as clinical series of fragility fractures treated with locking plates. Biomechanics papers had to use models of osteoporotic bone and had to directly compare locking plates with traditional plates. Clinical studies included case series in which locking plates were applied to elderly patients with fractures of the proximal humerus and periprosthetic distal femur fractures. Most studies are retrospective case series. Locking plates lead to greater stability and higher loads to failure than traditional plates. When applied to proximal humerus fractures, uncomplicated healing occurs in 85% of patients. Constant and Dash scores approach normal values. For distal femoral periprosthetic fractures, union rates of 75% are reported with a malunion rate of 10%. Early evidence suggests that locking plates improve results of treatment of proximal humerus fractures and distal femoral periprosthetic fractures in the elderly. Loss of fixation is associated with failure to achieve stability at the fracture site. Principles of fracture fixation in osteoporotic bone defined prior to the introduction of locking plates should still be applied.","corpus_id":8773498,"score":1},{"doc_id":"26012943","title":"Biomechanical effect of medial cortical support and medial screw support on locking plate fixation in proximal humeral fractures with a medial gap: a finite element analysis.","abstract":"OBJECTIVE: This finite element analysis aimed to examine the effect of medial cortical support and medial screw support on loads at the implant-bone interface of locking plate fixation of proximal humeral fractures with a medial gap. METHODS: An intact humerus from a healthy volunteer was used as the basis for a 3-dimensional (3D) computer-aided design (CAD) model. The 3D CAD model of the locking plate system was based on information in the manufacturer's catalogue. The proximal part of the humerus was osteotomized to create standard three-part fractures, which were then divided into a -MSC group (which lacked medial cortical support, and in which fractures with a 5-mm medial bone gap simulated this lack) and +MCS group (which had medial cortical support, and in which fractures with medial cortical-to-cortical contact simulated this). Both fracture groups were respectively fixed with either +MSS (in which medial screw support was simulated by the addition of two calcar screws to the locking plate system), or with -MSS (in which the lack of medial screw support was simulated by absence of the two additional calcar screws to the locking plate system). All the modeling was conducted to represent 90° arm abduction. RESULTS: On the screw-bone interface, medial screw support and medial cortical support decreased maximum shear stress by 17% and 23% respectively. On the locking plate, medial screw support and medial cortical support decreased maximum von Mises stress by 11% and 22% respectively. However, a combination of these two appeared to decrease maximum shear stress by 56% for the screw-bone interface, and maximum von Mises stress by 54% for the locking plate. CONCLUSION: Placement of calcar screws combined with good medial cortical contact in varus in locking plate fixation of proximal humeral fractures with a medial gap may provide optimal stability for the fixation.","corpus_id":35922538,"score":1},{"doc_id":"26165257","title":"Geometry of Proximal Humerus Locking Plates.","abstract":"OBJECTIVES: Proximal humerus fractures are commonly treated with open reduction and internal fixation with periarticular locking plates. This study compared the geometry of proximal humerus locking plate's screw distribution, amount of bone-screw interface, and the volume the screws occupy within the humeral head, as well as how leaving the screws short of the articular surface affects these measures. METHODS: Locking plates from 7 manufacturers were applied to foam humerus models. The entry and exit hole of each screw trajectory was digitized using a 3-dimensional motion tracking system. A trajectory for each screw was modeled, as well as the volume enclosed by the screw trajectories. The following outcome metrics were calculated: the bone-screw interface, the volume enclosed by the screws, and the effect of leaving the screws short of the articular surface. RESULTS: Biomet had the most bone-screw interface (7259 mm), whereas Zimmer had the least (3982 mm). The original Synthes plate had the largest screw volume, occupying 31.5% of the humeral head, whereas Smith & Nephew and Zimmer had the lowest volumes, occupying 21.2% and 12.6%, respectively. Leaving the screws 15 mm short of the articular surface resulted in the most reduction in volume for the Depuy plate (50%) and the least reduction for the new version of the Synthes plate (29%). CONCLUSIONS: Many different manufactured periarticular locking plates exist to stabilize a proximal humeral fracture. Clinicians need to be familiar with the different plate configurations, screw lengths, and trajectories, which affect potential biomechanical performance and can optimize fracture site maintenance.","corpus_id":25751172,"score":1},{"doc_id":"26631205","title":"Management of Proximal Humerus Fractures with the Equinoxe Locking Plate System.","abstract":"There is no consensus on surgical fixation and treatment of proximal humerus fractures, even though they are common fractures with several fixation techniques. This retrospective study quantifies the outcomes of patients who sustained a proximal humerus fracture and were treated with open re - duction and internal fixation by at a single academic center between December 2010 and December 2014 using the Equi - noxe ® proximal humerus locking plate. Following enrollment, injury and surgical data was recorded. Forty-nine patients (31 female, 18 male) with 50 fractures were identified who met the inclusion criteria. Mean follow-up period was 16.8 months (range: 6 to 44 months). Mean age was 60.7 years with no significant difference in mean age by gender. Mean age-adjusted Charlson Comorbidity Index (CCI) was 2.9 (range: 0 to 6). The overall complication rate was 10% (N = 5) with the most common complication being osteonecrosis (N = 3). Four patients required reoperation. At final follow- up, mean active forward flexion for the cohort was 140.8º ± 30.1º, mean passive forward flexion was 155.7º ± 25.2º, and mean active external rotation was 50.1º ± 17.9º. For patients with postoperative complications, mean active forward flexion was 106.0º ± 23.0º, mean passive forward flexion was 136.7º ± 23.1º, and mean active external rotation was 34.2º ± 24.4. Active forward flexion and external rotation were significantly different in the presence of a complication (p = 0.005 and p = 0.038, respectively). Mean DASH score for the cohort was 19.1 ± 20.9. Mean DASH score for patients who developed complications or underwent reoperations was 34.2 ± 24.3. This study demonstrates that the Equinoxe ® proximal humerus locking plate provides stable fracture treatment with excellent clinical results and a low complication rate when performed by experienced orthopaedic traumatologists.","corpus_id":43409475,"score":1},{"doc_id":"27793135","title":"Operative treatment of 2-part surgical neck fractures of the proximal humerus (AO 11-A3) in the elderly: Cement augmented locking plate Philos™ vs. proximal humerus nail MultiLoc®.","abstract":"BACKGROUND: Proximal humeral fractures are with an incidence of 4-5 % the third most common fractures in the elderly. In 20 % of humeral fractures there is an indication for surgical treatment according to the modified Neer-Criteria. A secondary varus dislocation of the head fragment and cutting-out are the most common complications of angle stable locking plates in AO11-A3 fractures of the elderly. One possibility to increase the stability of the screw-bone-interface is the cement augmentation of the screw tips. A second is the use of a multiplanar angle stablentramedullary nail that might provide better biomechanical properties after fixation of 2-part-fractures. A comparison of these two treatment options augmented locking plate versus multiplanar angle stable locking nail in 2-part surgical neck fractures of the proximal humerus has not been carried out up to now. METHODS/DESIGN: Forty patients (female/male, ≥60 years or female postmenopausal) with a 2-part-fracture of the proximal humerus (AO type 11-A3) will be randomized to either to augmented plate fixation group (PhilosAugment) or to multiplanar intramedullary nail group (MultiLoc). Outcome parameters are Disabilities of the Shoulder, Arm and Hand-Score (DASH) Constant Score (CS), American Shoulder and Elbow Score (ASES), Oxford Shoulder Score (OSS), Range of motion (ROM) and Short Form 36 (SF-36) after 3 weeks, 6 weeks, 3 months, 6 months, 12 and 24 months. DISCUSSION: Because of the lack of clinical studies that compare cement augmented locking plates with multiplanar humeral nail systems after 2-part surgical neck fractures of the proximal humerus, the decision of surgical method currently depends only on surgeons preference. Because only a randomized clinical trial (RCT) can sufficiently answer the question if one treatment option provides advantages compared to the other method we are planning to perform a RCT. TRIAL REGISTRATION: Clinical Trial ( NCT02609906 ), November 18, 2015, registered retrospectively.","corpus_id":662829,"score":1},{"doc_id":"18310691","title":"Results of polyaxial locked-plate fixation of periarticular fractures of the knee. Surgical technique.","abstract":"BACKGROUND: Locked-plate fracture-fixation techniques and designs continue to evolve. Polyaxial locking plates that allow screw angulation and end-point locking have become available; however, there are no clinical data documenting their strength and efficacy, to our knowledge. The purpose of this study was to evaluate the clinical performance of a variable-axis locking plate in a multicenter series of periarticular fractures about the knee. METHODS: Between 2003 and 2005, fifty-four patients with a total of fifty-six fractures were treated with a polyaxial locked-plate fixation system (DePuy, Warsaw, Indiana). There were twenty male patients and thirty-four female patients with a mean age of fifty-seven years. There were twenty-five distal femoral fractures and thirty-one proximal tibial fractures. Twelve of the fractures were open. Clinical and radiographic data, including changes in alignment, hardware breakage, or other mechanical complications of the device, were retrospectively reviewed. Function was assessed with use of the Knee Society scores. One patient with a bilateral fracture died less than three months postoperatively, and two patients were lost to follow-up prior to union. Fifty-two fractures in fifty-one patients were followed to union or for a minimum of six months; the mean duration of follow-up was nine months (range, six to twenty-five months). RESULTS: Forty-nine (94%) of the fifty-two fractures united. There were no mechanical complications. Most importantly, there was no evidence of varus collapse as a result of polyaxial screw failure. There were three deep infections and one aseptic nonunion. No plate fractured, and no screw cut out. CONCLUSIONS: The variable-axis locking plates performed well, with a high rate of fracture union and no evidence of varus collapse due to failure of the polyaxial screw fixation, in a series of complex fractures about the knee. Complication rates were similar to those for historical controls treated with fixed-trajectory locking plates. Polyaxial locking plates offer more fixation versatility without an apparent increase in mechanical complications or loss of reduction.","corpus_id":207281072,"score":0},{"doc_id":"24262583","title":"Complications following volar locking plate fixation for distal radial fractures: a systematic review.","abstract":"The purpose of this systematic review is to assess the prevalence of complications following volar locking plate fixation of distal radial fractures. A computer-based search was carried out using EMBASE and PUBMED/MEDLINE. Only prospective comparative and prospective cohort studies that presented data concerning complications after treatment of distal radial fractures with a volar locking plate in human adults with a minimal follow-up of 6 months were included. Two quality assessment tools were used to assess the methodological quality of the studies (level of evidence rating according to the Oxford Centre of Evidence Based Medicine and the modified version of the Cochrane Bone, Joint and Muscle Trauma Group's former quality assessment tool). Thirty three studies were eligible for final assessment. Most complications were problems with nerve and tendon function as well as complex regional pain syndrome. With an overall complication rate of 16.5%, most of which were 'minor' complications and low rates of nonunion and malunion, volar locking plate fixation can be considered a reasonably safe treatment option for patients with distal radial fractures.","corpus_id":23146646,"score":0},{"doc_id":"27144821","title":"Unstable Proximal Femur Fractures Treated With Proximal Femoral Locking Plates: A Retrospective, Multicenter Study of 111 Cases.","abstract":"OBJECTIVES: A few small case series have found that proximal femur fractures treated with a proximal femur locking plate (PFLP) have experienced more failures than expected. The purpose of this study was to review the clinical results of patients with acute, unstable proximal femur fractures treated with proximal femoral locking plates in a large, multicenter patient cohort. DESIGN: This is a retrospective clinical study. SETTING: The study included patients from 12 regional trauma centers and tertiary referral hospitals. PATIENTS: One hundred eleven consecutive patients with unstable proximal femur fractures stabilized with a PFLP and having required clinical and radiographic follow-up at a minimum of 12 months after injury. INTERVENTION: Surgical repair of an unstable proximal femur fracture with a PFLP. MAIN OUTCOME MEASUREMENTS: Treatment failures (failure of fixation, nonunion, and malunion) and need for revision surgery. RESULTS: Forty-six patients (41.4%) experienced a major treatment failure, including failed fixation with or without nonunion (39), surgical malalignment or malunion (18), deep infection (8), or a combination of these. Thirty-eight (34%) patients underwent secondary surgeries, including 30 for failed fixation, nonunion, or both. Treatment failure was found to occur at a significantly higher rate in patients with major comorbidities, in femurs repaired in varus malalignment, and using specific plate designs. CONCLUSIONS: Proximal femoral locking plates are associated with a high complication rate, frequently requiring revision or secondary surgeries in the treatment of unstable proximal femur fractures. Given the high complication rate with PFLPs, careful attention to reduction, use of a PFLP implant, and consideration should be given to alternative implants or fixation techniques when appropriate. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.","corpus_id":8259027,"score":0}],"string":"[\n {\n \"doc_id\": \"18317048\",\n \"title\": \"Early complications in proximal humerus fractures (OTA Types 11) treated with locked plates.\",\n \"abstract\": \"PURPOSE: To examine our incidence of early complications that occur using the Proximal Humeral Internal Locking System (PHILOS) and to determine the contributing factors. SETTING: Academic medical center. PATIENTS: Fifty-one consecutive patients treated with a proximal humerus locking plate. OUTCOME: Development of an intraoperative, acute postoperative, or delayed postoperative complication. METHODS: A retrospective analysis was undertaken of a consecutive series of proximal humerus fractures treated with a locking plate between February 2003 and January 2006 at our institution. Fifty-one fractures or fracture nonunions were identified in 18 male and 33 female patients with an average age of 61. All acute injuries were treated with a similar protocol of open reduction internal fixation with the PHILOS plate followed by early range of shoulder motion. Nonunions were treated in a similar manner with the addition of iliac crest bone graft placement. Patients were objectively assessed on their outcome by physical as well as radiological examination. All complications were recorded. Statistical analyses were performed to determine if patient age, fracture type, or number of screws placed in the humeral head contributed to complications. RESULTS: Fifty-one patients were available for minimum 6-month follow-up (mean, 16 months; range, 6 to 45 months). Radiographically, 92% of the cases united at 3 months after surgery, and 2 fractures had signs of osteonecrosis at latest follow-up. Sixteen complications were seen in 12 patients (24%). Eight shoulders in eight patients (16%) had screws that penetrated the humeral head. Two patients developed osteonecrosis at latest follow-up. One acute fracture and one nonunion failed to unite after index surgery. Significant heterotopic bone developed in 1 patient. Early implant failure occurred in 2 patients; one was revised to a longer plate, and one underwent resection arthroplasty. There was one acute postoperative infection. CONCLUSION: The major complication reported in this study was screw penetration, suggesting that exceptional vigilance must be taken in estimating the appropriate number and length of screws used to prevent articular penetration; although the device provides exceptional fixation stability, its indication must be scrutinized for each individual patient, taking the extent of trauma/fracture and age into consideration and carefully weighing it against other forms of treatment.\",\n \"corpus_id\": 1356340,\n \"score\": 2\n },\n {\n \"doc_id\": \"18552530\",\n \"title\": \"[The results of internal fixation of proximal humeral fractures with the PHILOS locking plate].\",\n \"abstract\": \"Proksimal humerus kiriklarinda kilitli plak PHILOS ile internal tespit sonuçlari. OBJECTIVES: Proximal and diaphyseal humeral fractures are common especially in the elderly, presenting as a challenging problem due to their high complication rates following surgical treatment. In this prospective study, we evaluated the results of patients treated with the PHILOS (Proximal Humeral Internal Locking System) locking plate, a new technique recently developed by the AO/ASIF. METHODS: Forty-one patients who were treated with the PHILOS plate for proximal humeral fractures were evaluated in two age groups. Group A included 24 patients (12 males, 12 females; mean age 47 years; range 24 to 64 years) younger than 65 years, and group B involved 17 patients (4 males, 13 females; mean age 78 years; range 67 to 90 years) at or above 65 years. Radiographically, all fractures were classified according to the AO/ASIF system. Surgery was performed with the deltopectoral approach in 10 and two patients, and with a deltoid split in 14 and 15 patients in group A and B, respectively. Functional and radiographic results were evaluated after a mean follow-up of 15 months (range 6 to 28 months). RESULTS: The mean Constant scores were 95.0 (range 74 to 100) and 92.8 (range 72 to 100) in group A and B, respectively (p>0.05). After six months of surgery, Constant scores and functional outcomes were similar in patients operated on with the deltopectoral approach or deltoid split. There was neither nonunion nor implant failure. Complications included intra-articular screw penetration (n=1), displacement of the greater tuberculum (n=1) with oblique placement of the plate (n=1), insufficient reduction (n=4), and varus displacement of the humeral head (n=3). No avascular necrosis was seen. CONCLUSION: Locking plate system is superior over other means of fixation methods, particularly in osteoporotic fractures, because it allows early rehabilitation and does not result in implant failure.\",\n \"corpus_id\": 19621118,\n \"score\": 2\n },\n {\n \"doc_id\": \"18716427\",\n \"title\": \"[Early results of treatment of proximal humerus fractures with the PHILOS locking plate].\",\n \"abstract\": \"Proksimal humerus kiriklarin PHILOS plaği ile tedavisinde erken dönem sonuçlarimiz. OBJECTIVES: The aim of this study was to evaluate early results of proximal humerus fractures treated with the PHILOS locking plate. METHODS: Proximal humerus fractures of 22 patients (13 males, 9 females; mean age 57 years; range 35 to 83 years) were treated with the PHILOS locking plate. According to the Neer classification, 13 patients had comminuted fractures, four patients had valgus impact injuries, two patients had fracture-dislocations, and three patients had fractures involving the proximal 1/3 of the humerus. The fractures were reduced by the transdeltoid lateral approach (n=8) using minimally invasive surgery, and by the anterior deltopectoral approach (n=14) using open surgery. Passive and active exercises were initiated on the second postoperative day and after 4 to 6 weeks, respectively. The results were assessed using the Constant-Murley shoulder scoring system. The mean follow up was 14 months (range 12 to 19 months). RESULTS: Radiographically, union was observed in 20 patients at the end of 10 weeks. In one patient, time to union was 16 weeks. One patient underwent autogenous bone grafting because of nonunion after 16 weeks. The mean Constant-Murley score was 75.5 (range 51 to 93). There was no significant difference between Constant-Murley scores of patients undergoing the transdeltoid lateral and anterior deltopectoral approaches (p>0.05). Plate fixation was associated with minimal varus deformity in two patients, and subacromial impingement in one patient. Implant failure did not occur. Reflex sympathetic dystrophy and avascular necrosis were observed in two patients, respectively. CONCLUSION: Fixation with the PHILOS plate is a near-ideal technique with a high union rate in the treatment of proximal humeral fractures.\",\n \"corpus_id\": 21437563,\n \"score\": 2\n },\n {\n \"doc_id\": \"19431978\",\n \"title\": \"[Long PHILOS locking compression plate for treatment of proximal humerus and humeral shaft fractures].\",\n \"abstract\": \"OBJECTIVE: To investigate the therapeutic effect of long PHILOS locking compression plate on the proximal humerus and humeral shaft fractures. METHODS: From March 2005 to December 2007, 35 cases with the proximal humerus and humeral shaft fractures were treated with long PHILOS locking compression plate, including 16 males and 19 females aged 29-68 years old (average 54.5 years old). There were 34 cases of fresh and close fracture, and the time from injury to operation was 3-9 days. One case had delayed union of fracture 5 months after receiving T-plates and internal fixation with steel plate. For the proximal humerus fracture, 7 cases had 2 parts of fracture, 19 had 3 parts of fracture, and 9 had 4 parts of fracture according to Neer classification; while for the humeral shaft fracture, 3 cases were classified as A1, 5 as A2, 10 as B1, 3 as B2, 6 as B3, 7 as C1 and 1 as C3 according to AO classification. Postoperatively, Neer scoring system was employed to evaluate the function of shoulder joint and HSS scoring system was adopted to evaluate the function of elbow joint. RESULTS: All incisions healed by first intension, and 30 cases were followed up for 12-33 months (average 18.2 months). Postoperatively, 2 cases had symptoms of radial nerve paralysis, which disappeared within 3 weeks; 1 case suffered from humeral head necrosis and received the secondary operation of humeral head replacement; humeral head was reduced evenly in 1 case, and 2 cases felt chronic slight pain in shoulder joints and received no further treatment. X-ray films showed 29 cases had fracture healing 6 months after operation, and all the patients had bone union 12 months after operation except 1 case receiving humeral head replacement. No such complications as screw loosening and internal fixation loosening occurred. By Neer scoring system, 6 cases were graded as excellent, 19 as good, 3 as fair, 2 as poor, and the excellent and good rate was 83.3%. By HSS scoring system, 16 cases were graded as excellent, 14 as good, and the excellent and good rate was 100%. CONCLUSION: Applying long PHILOS locking compression plate in the treatment of the proximal humerus and humeral shaft fractures provides a solid fixation and high satisfactory rate with minor complications.\",\n \"corpus_id\": 38426029,\n \"score\": 2\n },\n {\n \"doc_id\": \"19487508\",\n \"title\": \"Open reduction and internal fixation of proximal humeral fractures with use of the locking proximal humerus plate. Results of a prospective, multicenter, observational study.\",\n \"abstract\": \"BACKGROUND: The treatment of unstable displaced proximal humeral fractures, especially in the elderly, remains controversial. The objective of the present prospective, multicenter, observational study was to evaluate the functional outcome and the complication rate after open reduction and internal fixation of proximal humeral fractures with use of a locking proximal humeral plate. METHODS: One hundred and eighty-seven patients (mean age, 62.9 +/- 15.7 years) with an acute proximal humeral fracture were managed with open reduction and internal fixation with a locking proximal humeral plate. At the three-month, six-month, and one-year follow-up examinations, 165 (88%), 158 (84%), and 155 (83%) of the 187 patients were assessed with regard to pain, shoulder mobility, and strength. The Constant score was determined at each interval, and the Disabilities of the Arm, Shoulder and Hand (DASH) score was determined for the injured and contralateral extremities at the time of the one-year follow-up. RESULTS: Between three months and one year, the mean range of motion and the mean Constant score for the injured shoulders improved substantially. Twelve months after surgery, the mean Constant score for the injured side was 70.6 +/- 13.7 points, corresponding to 85.1% +/- 14.0% of the score for the contralateral side. The mean DASH score at the time of the one-year follow-up was 15.2 +/- 16.8 points. Sixty-two complications were encountered in fifty-two (34%) of 155 patients at the time of the one-year follow-up. Twenty-five complications (40%) were related to incorrect surgical technique and were present at the end of the operative procedure. The most common complication, noted in twenty-one (14%) of 155 patients, was intraoperative screw perforation of the humeral head. Twenty-nine patients (19%) had an unplanned second operation within twelve months after the fracture. CONCLUSIONS: Surgical treatment of displaced proximal humeral fractures with use of the locking proximal humeral plate that was evaluated in the present study can lead to a good functional outcome provided that the correct surgical technique is used. Because many of the complications were related to incorrect surgical technique, it behooves the treating surgeon to perform the operation correctly to avoid iatrogenic errors.\",\n \"corpus_id\": 26028870,\n \"score\": 2\n },\n {\n \"doc_id\": \"19748802\",\n \"title\": \"Treatment of proximal humerus fractures with locking plates: a systematic review.\",\n \"abstract\": \"HYPOTHESIS: Locking plates with special configuration for the anatomic region of the proximal humerus have been introduced recently to address the difficulties of stabilizing proximal humeral fractures. The purpose of this study was to carry out a systematic review of the literature on the efficacy and early to medium term functional results of locking plates for stabilization of proximal humeral fractures. METHODS: Using the PubMed database, a systematic review of the English and German literature was carried out in order to assess the efficacy and complications related to the use of these plates and the patients' functional outcome, using the key words \\\"locking plates proximal humeral fractures,\\\" \\\"angular stability plates proximal humeral fractures,\\\" \\\"PHILOS plate,\\\" and \\\"LPHP plate.\\\" Our criteria for eligibility were clinical studies with more than ten cases followed-up, adult patients, and adequate data provided at least in terms of implant related complications. Articles written in English and German language were included. Exclusion criteria were: studies dealing exclusively with 2-part fractures (since this category has a more favorable outcome); experimental studies; case reports; and, literature other than English or German. Each one of the articles was evaluated for quality of the study using the Structured Effectiveness Quality Evaluation Scale (SEQES). RESULTS: Twelve studies including 791 patients met the inclusion criteria. Patients in these studies continued to improve up to one year, achieving a mean Constant score of 74.3. The incidence of the reported complications was: avascular necrosis 7.9%, screw cut-out 11.6% and re-operation rate 13.7%. DISCUSSION: The high incidence of cut-out may be secondary to the rigidity of the implant in combination with medial inadequate support, in cases compromised by severe underlying osteoporotic bone. Definition of indications for the use of locking plates and attention on technical aspects of applying them would help optimization of the results. LEVEL OF EVIDENCE: Systematic Review.\",\n \"corpus_id\": 10818409,\n \"score\": 2\n },\n {\n \"doc_id\": \"19995683\",\n \"title\": \"Pitfalls and complications with locking plate for proximal humerus fracture.\",\n \"abstract\": \"PURPOSE: The aim of this study was to identify specific complications of locking plate fixation of proximal humerus fractures. PATIENTS AND METHODS: Seventy-three adult patients with a displaced 3- (24%) or 4-part (76%) fracture of the proximal humerus were treated over a period of 2 years under the supervision of a trauma surgeon. Fourty-four patients came back for a clinical and radiographic examinations at least 18 months after the trauma; the others were evaluated at 6 weeks and 3 and 6 months. RESULTS: Out of the 73 patients (64.4% females, mean age of 65), 11 patients needed a second surgery and 18 were lost for follow-up after 6 months. Mean final constant score was 62.3 points. The incidence of secondary displacement was 8.2%. Nonunion rate was 5.5%, affecting the constant score (P = .018). 16.4% of the patients developed a partial necrosis of the humeral head at the latest follow-up, which influenced on the constant score (P = .029). Quality of the reduction of the greater tuberosity influenced final results (P = .037). Screw cutout rate was 13.7%, with an influence to the constant score (P = .001). A too high plate positioning influenced the constant score (P = .002). CONCLUSION: Locked screw-plates provide more secure fixation of fractures, especially in weak bone. Complications rate remains high. Two complications are to be distinguished: 1) technical complications in plate positioning, length of the screws or secondary screw cutout strongly influence the final clinical result; and 2) specific complications related to this technology such as pseudarthrosis or plate fracture.\",\n \"corpus_id\": 2705321,\n \"score\": 2\n },\n {\n \"doc_id\": \"20188270\",\n \"title\": \"Use of locking plates in the treatment of proximal humerus fractures.\",\n \"abstract\": \"BACKGROUND/HYPOTHESIS: Open reduction and internal fixation (ORIF) using locked plating has demonstrated promise in the treatment of displaced proximal humerus fractures. The purpose of this article is to describe the surgical technique and to report early clinical results with this technique. METHODS: Important surgical principles to follow include adequate use of locking screws in the humeral head, bone graft or bone graft substitutes when needed, rotator cuff sutures to assist with reduction and augment fixation, and sufficient use of intraoperative fluoroscopic imaging. A review was performed to evaluate early outcomes of ORIF with proximal humerus locking plates. All cases were fixed with the described surgical technique. Postoperative assessment included radiographic imaging, PENN/ASES Shoulder Scores, range-of-motion (ROM), and complications. RESULTS: Fifty-two patients (54 shoulders) had minimum 6-month follow-up (13-month mean follow-up). Mean age was 65.5 years. Postoperatively, mean active forward elevation was 130.1 degrees, and mean active external rotation was 27.7 degrees. Mean post-op PENN shoulder score was 68.9 and mean post-op ASES score was 70.8. There were 11 (20.4%) complications in 10 (18.5%) shoulders after treatment with a proximal humerus locking plate. Three complications were classified as minor (5.6%), 8 as major (14.8%). Two shoulders (3.7%) required reoperation to address the complications. CONCLUSION: The use of locking plates in the treatment of displaced proximal humerus fractures is becoming more widespread. With precise knowledge of and experience with the surgical technique, locked plating can be performed safely with good results. However, surgeons should be aware that complications can arise.\",\n \"corpus_id\": 30658678,\n \"score\": 2\n },\n {\n \"doc_id\": \"20415404\",\n \"title\": \"Fixed-angle locking plating of displaced proximal humerus fractures.\",\n \"abstract\": \"Proximal humerus fractures are common, especially among patients older than 60 years who have osteoporosis. Several techniques have been used within the past several decades to treat displaced proximal humerus fractures. Many different implants have been investigated and tested, all with inadequate results; debate continues as to the best method of fixation. Fixed-angle locking plates offer a relatively new treatment option for these complicated fractures, especially in patients with osteoporosis. The use of locking plates for treating comminuted proximal humerus fractures has biologic and biomechanical advantages over conventional fixation techniques. Complications including varus fracture collapse and screw penetration of the articular surface nonetheless remain problematic. Although the locking plate technique provides exceptional fixation stability, its use must be tailored to the individual patient, taking into account the extent of trauma, the fracture characteristics, and the patient's age and expectations; therefore, it must be carefully weighed against other forms of treatment. Prospective clinical trials and further study are necessary to generate data comparing locking plate fixation and alternative surgical treatments.\",\n \"corpus_id\": 20754137,\n \"score\": 2\n },\n {\n \"doc_id\": \"20577069\",\n \"title\": \"Clinical results for minimally invasive locked plating of proximal humerus fractures.\",\n \"abstract\": \"OBJECTIVES: To describe the minimally invasive treatment of fractures of the proximal humerus using the Non-Contact-Bridging (NCB) plate. The system allows secondary locking of screws to the plate with a locking cap and polyaxial (30 degrees radius) screw placement. DESIGN: Prospective cohort study. SETTING: University Level I trauma center. PATIENTS: Fifty-four patients with unstable fractures of the proximal humerus. INTERVENTION: Minimal anterolateral acromial approach to the proximal humerus, percutaneous fracture reduction, and minimally invasive application of the NCB plate. MAIN OUTCOME MEASUREMENTS: Constant Score and radiologic follow-up (anteroposterior and transscapular). Visual Analog Scale for subjective evaluation of pain and function. RESULTS: After 17 months, the average Constant Score was 66.8 points (87% of the age- and sex-related normal values). Implant-related complications (plate impingement, screw perforation into the glenohumeral joint, loosening of screws) occurred in nine cases (17%). The rate of avascular necrosis was low (5.5%) and no cases of nonunion were seen. CONCLUSIONS: The effectiveness of the NCB is similar to other published methods of treatment for fractures of the proximal humerus and potentially provides a less invasive option for this problem. Complication rates and functional outcome in this series are comparable to the literature. An important factor in this technique is the process of percutaneous fracture reduction. The NCB plate is suitable for both a minimally invasive technique or standard open reduction and internal fixation through a deltopectoral approach; the surgeon must decide which approach is best for each particular fracture pattern and should be comfortable with both techniques.\",\n \"corpus_id\": 205491196,\n \"score\": 2\n },\n {\n \"doc_id\": \"20676009\",\n \"title\": \"Complications encountered in proximal humerus fractures treated with locking plate fixation.\",\n \"abstract\": \"OBJECTIVES: We evaluated the complications encountered following locking plate fixation of proximal humerus fractures. METHODS: The study included 103 patients (70 females, 33 males; mean age 62 years; range 21 to 90 years) who were treated with open reduction and locking plate fixation for proximal humerus fractures between September 2005 and April 2009. Fixation was performed using the PHILOS locking plate in 93 patients, and S3 humerus plate in 10 patients. Postoperatively, a shoulder-arm sling was applied for six weeks and a standard rehabilitation program was used in all the patients. Intraoperative, acute postoperative, and late postoperative complications were assessed on radiographs. Varus inclination was defined as less than 120 degrees of the inclination angle on immediate postoperative radiographs, and varus displacement as postoperative increases in the varus angle. The mean follow-up period was 19 months (range 2 weeks to 43 months). RESULTS: Complications were seen in 10 patients (9.7%; mean age 67 years). The PHILOS plate was used in nine patients and S3 plate was used in one patient. Five patients (4.9%) had varus inclination with a mean inclination angle of 112.6 degrees (range 105 degrees to 118 degrees), four patients (3.9%) developed varus displacement with a mean inclination angle of 102.5 degrees (range 95 degrees to 110 degrees), and intra-articular screw penetration was seen in five patients (4.9%). The remaining complications were fixation failure (n=1, 1%), implant fracture (n=1), and deep infection (n=1). Screw penetration exceeded 3 mm in three patients, requiring revision surgery. The mean ages of patients with varus inclination, varus displacement, and screw penetration were 76.6, 74.4, and 71 years, respectively. Three patients with varus inclination (60%) developed varus displacement. Screw penetration was observed in three patients (60%) with varus inclination, and in all patients with varus displacement. The mean Constant-Murley shoulder score was 67.8 (range 50 to 90) in patients who developed a complication. CONCLUSION: Our findings show that locking plate and screw systems represent a significant treatment option in the treatment of comminuted and displaced humerus fractures, with low complication rates. Accurate indication, protection of the head's inclination angle through appropriate surgical approach and proper technique, and fine calculation of screw length are essential for successful functional results.\",\n \"corpus_id\": 31556230,\n \"score\": 2\n },\n {\n \"doc_id\": \"20731844\",\n \"title\": \"Displaced proximal humeral fractures: an Indian experience with locking plates.\",\n \"abstract\": \"BACKGROUND: The treatment of displaced proximal humerus fractures, especially in elderly, remains controversial. The objective of this study was to evaluate functional outcome of locking plate used for fixation of these fractures after open reduction. We also attempted to evaluate the complications and predictors of loss of fixation for such an implant. METHODS: Over two and a half years, 56 patients with an acute proximal humerus fracture were managed with locking plate osteosynthesis. 47 of these patients who completed a minimum follow up of 1 year were evaluated using Constant score calculation. Statistical analysis was done using SPSS 16 and a p value of less than 0.05 was taken as statistically significant. RESULTS: The average follow up period was around 21.5 months. Outcomes were excellent in 17%, good in 38.5%, moderate in 34% while poor in 10.5%. The Constant score was poorer for AO-OTA type 3 fractures as compared to other types. The scores were also inferior for older patients (> 65 years old). Complications included screw perforation of head, AVN, subacromial impingement, loss of fixation, axillary nerve palsy and infection. A varus malalignment was found to be a strong predictor of loss of fixation. CONCLUSION: Locking plate osteosynthesis leads to satisfactory functional outcomes in all the patients. Results are better than non locking plates in osteoporotic fractures of the elderly. However the surgery has steep learning curve and various complications could be associated with its use. Nevertheless we believe that a strict adherence to the principles of locking plate use can ensure good result in such challenging fractures.\",\n \"corpus_id\": 1128503,\n \"score\": 2\n },\n {\n \"doc_id\": \"21085030\",\n \"title\": \"A prospective clinical study of proximal humerus fractures treated with a locking proximal humerus plate.\",\n \"abstract\": \"OBJECTIVES: The purpose of this prospective study was to evaluate the safety, efficacy, and functional outcome of the locked proximal humerus plate (LPHP) to treat proximal humerus fractures. DESIGN: Prospective clinical trial. SETTING: University orthopedic center. PATIENTS: Over a 25-month period, 64 consecutive patients were treated with a LPHP for an unstable or displaced proximal humerus fracture. INTERVENTION: Demographic data, trauma mechanisms, surgical approaches, and postoperative complications were collected from medical records. Fracture classification according to the Neer classification, radiographic head-shaft angle, and screw tip-articular surface distance in true anteroposterior and axillary lateral radiographs of the shoulder were measured postoperatively. MAIN OUTCOME MEASUREMENTS: The functional outcome was evaluated with a Constant-Murley (CM) evaluation. The CM score is a validated shoulder-specific scoring system in which patients report subjective findings. The physician reported the objective measurements of the shoulder. RESULTS: Follow-ups were completed for all of the patients. The overall complication rate was 35.9%, with screw penetration into the glenohumeral joint as the most frequent problem (7.6%). Deep wound infections were observed in 3.1% (n = 2) of the cases and avascular necrosis in 3.1% (n = 2). All complications occurred in 4-part fractures. Subacromial impingement, frozen shoulder, rotator cuff rupture, and wound dehiscence were observed in 3.1% (n = 2), 3.1% (n = 2), 1.6% (n = 1), and 1.6% (n = 1) of the cases, respectively. Multivariate linear regression analysis revealed that the fracture pattern and the presence or absence of medial support were significant predictors of functional outcome (P = 0.026 and P = 0.003, respectively). Patient age (P = 0.581), sex (P = 0.325), and initial tuberosity displacement (varus/extension or valgus/impaction; P = 0.059) were not significantly associated with the CM score. CONCLUSIONS: The LPHP seems to be a promising implant for the fixation of proximal humerus fractures. However, there are certain limitations that should be mentioned. The number of cases in our study was small, and no safe conclusions can be extracted regarding the rate of avascular necrosis. Additional studies with larger cohorts and longer follow-ups are necessary to better define the appropriate indications for and expected outcomes of this technology.\",\n \"corpus_id\": 22812713,\n \"score\": 2\n },\n {\n \"doc_id\": \"21176833\",\n \"title\": \"A systematic review of locking plate fixation of proximal humerus fractures.\",\n \"abstract\": \"PURPOSE: Technique for the fixation of two, three, and four part proximal humerus fractures has rapidly shifted towards the use of specially contoured proximal humerus locking plates. The purpose of this study is to evaluate the short to medium term functional results and common complications associated with the fixation of proximal humerus fractures with locking plates. METHODS: The PubMed and EMBASE databases were used to perform a systematic review of the English literature to assess the functional results and complications associated with proximal humerus locking plates. Our inclusion criteria were proximal humerus fracture due to trauma (excluding pathologic fractures), patients greater than 18 years of age, more than 15 patients in the study or subgroup of interest, at least 18 months follow-up, at least one relevant functional outcome score, and quality outcome score of at least 5/10. Studies that did not meet these criteria were excluded. All institutional, author, and journal information was concealed to minimize reviewer bias. RESULTS: Twelve studies including 514 patients met the inclusion criteria. At most recent follow-up patients achieved a mean Constant score of 74 and a mean DASH score of 27. The overall rate of complications was 49% including varus malunion, 33% excluding varus malunion, and reoperation rate was 14%. The most common complications included varus malunion 16%, AVN 10%, screw perforation of the humeral head into the joint 8%, subacromial impingement 6%, and infection 4%. DISCUSSION: Fixation of proximal humerus fractures with proximal humerus locking plates is associated with a high rate of complications and reoperation. Further study is needed to determine what technical errors and patient characteristics are risk factors for failure of this now common fixation technique.\",\n \"corpus_id\": 21207722,\n \"score\": 2\n },\n {\n \"doc_id\": \"21691909\",\n \"title\": \"Endosteal strut augment reduces complications associated with proximal humeral locking plates.\",\n \"abstract\": \"BACKGROUND: Locking-plate technology has renewed interest in plate fixation for treating proximal humerus fractures. Complications associated with these devices, including loss of reduction, screw cutout, and intra-articular penetration, are frequent. Establishing a second column of support may reduce complications and improve clinical outcome scores. QUESTIONS/PURPOSES: We asked whether addition of an endosteal cortical allograft strut, used as an augment to locking-plate fixation for displaced proximal humerus fractures, would reduce complications and improve clinical outcome scores. PATIENTS AND METHODS: We retrospectively reviewed the charts and radiographs of 38 patients treated by this method. All patients were evaluated with serial radiographs, as well as the Disabilities of the Arm, Shoulder, and Hand and Constant-Murley scores. There were seven two-part, 19 three-part, and 12 four-part fractures. The minimum followup was 49 weeks (average, 75 weeks; range, 49-155 weeks). RESULTS: No patient had intra-articular screw penetration or cutout. No patient had complete osteonecrosis, but one had partial osteonecrosis. The reduction was lost in one patient. The mean Disabilities of the Arm, Shoulder, and Hand score was 15 (range, 0-66.4). The mean Constant-Murley score was 87 (range, 51-95). CONCLUSIONS: Low rates of complication and high clinical outcome scores can be achieved when treating complex proximal humerus fractures with locking-plate fixation and an endosteal strut augment. LEVEL OF EVIDENCE: Level IV, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.\",\n \"corpus_id\": 23539102,\n \"score\": 2\n },\n {\n \"doc_id\": \"21814772\",\n \"title\": \"Rate of avascular necrosis following proximal humerus fractures treated with a lateral locking plate and endosteal implant.\",\n \"abstract\": \"INTRODUCTION: Treatment of displaced proximal humerus fractures remains challenging. The introduction of locking plates has renewed interest in treating these fractures with joint-preserving techniques rather than hemiarthroplasty, but high complication rates are still reported. Avascular necrosis is not solely dependent on the initial fracture pattern, but can also result from intraoperative and postoperative vascular insults. METHOD: We describe a technique to minimize disruption of humeral head blood supply and maximize fracture fixation. A total of 34 patients with complex proximal humerus fractures were treated with a locking plate and endosteal implant through an anterolateral approach and followed for an average of 66 weeks to determine the rates of avascular necrosis. RESULTS: No patient suffered complete osteonecrosis (0%) and only one patient suffered partial necrosis (2.8%) of the humeral head. The length of the posteromedial hinge was not predictive of this complication. CONCLUSION: Use of the anterolateral approach and endosteal augment of a lateral locking plate can minimize avascular necrosis following proximal humerus fracture.\",\n \"corpus_id\": 8733025,\n \"score\": 2\n },\n {\n \"doc_id\": \"21837232\",\n \"title\": \"Results of 131 consecutive operated patients with a displaced proximal humerus fracture: an analysis with more than two years follow-up.\",\n \"abstract\": \"OBJECTIVE: The purpose of this study is to determine the efficacy of the open reduction and fixation of a dislocated proximal humerus fracture with a locking plate, also evaluating the incidence of complications and functional recovery of the shoulder. A retrospective study focusing on patients who had suffered a fracture of the proximal humerus and were treated by means of an open reduction and internal fixation with a locking plate, using either the Philos or the LPHP plate. We have also included a comparison of these two plates. METHOD: Ninety-two patients were found to be eligible and were included in our study. These patients had all been treated for a proximal humerus fracture between 2002 and 2008. We included those patients who could be classified as a class 2, 3, or 4 according to the Neer classification. Demographic data, surgical technique, and peri/post-operative complications were collected from medical records. Patients were followed-up and the Oxford Shoulder Score (OSS) was filled in by phone. The mean age of our patient population was 66.2 (15-97), with a male: female ratio of 1:5 (15:77). ( The median follow-up was 2.4 years (0.2-5.8). Fourteen of our patients died during follow-up, while 25 patients were otherwise lost to follow-up. For this study, out of the original 131 patients, this finally resulted in 92 patients whom we followed-up post-operatively. RESULTS: Ninety-two patients (70%, 92/131) were interviewed. The mean Oxford Shoulder Score (OSS) was 19.76 (11-54). The overall complication rate was 39.1% (36/92). The most frequently occurring complications in our patient population were hemorrhage 3.3%; dislocation of the caput humeri and/or tuberculum majus 2.2%; persistent pain 3.3%; Avascular necrosis (AVN) of the humeral head 0%; Loss of reduction and screw cutout 6.5%; Plate breakout 6.5%; Subacromial Impingement 11.9%; Frozen shoulder 3.3%; rotator cuff rupture 1.1%, and infection 1.1%. Of the entire group of patients originally included in this study, 29% was re-operated due to one of the above-mentioned complications. CONCLUSION: In conclusion, the locking plate provides satisfactory functional outcomes after a mid-term follow-up in patients with displaced proximal humerus fractures. The incidence of complications and subsequent re-operation is relatively high, however, comparable to or slightly better when compared to data found in literature. Subacromial Impingement seems to occur more frequently when a Philos plate is implemented. We therefore suggest that randomized clinical trials determining the possible superiority of one specific type of plate in patients with a displaced proximal humerus fracture are to be performed in future.\",\n \"corpus_id\": 14239158,\n \"score\": 2\n },\n {\n \"doc_id\": \"21968245\",\n \"title\": \"Benefits and harms of locking plate osteosynthesis in intraarticular (OTA Type C) fractures of the proximal humerus: a systematic review.\",\n \"abstract\": \"INTRODUCTION: Locking plate osteosynthesis of proximal humeral fractures are widely recommended and used, even in complex intraarticular fracture patterns such as AO/OTA Type C fractures. We systematically reviewed clinical studies assessing the benefits and harms of osteosynthesis with angle stable plates in AO/OTA Type C fractures of the proximal humerus. METHODS: We conducted an iterative search in PubMed, Embase, Cochrane Library, Web of Science, Cinahl, and PEDro in all languages from 1999 to November 2010. Eligible studies should study the outcome for Type C fractures after primary osteosynthesis with locking plate within two weeks of injury, and a follow-up period of six months or more. Patients should be evaluated with the Constant-Murley Score (CS). Two observers extracted data independently. RESULTS: Twelve studies and 282 Type C fractures were included. Results were categorised according to study type and synthesised qualitatively. No randomised clinical trials were identified. Two comparative, observational studies reported a mean CS of 71 (relative to contralateral shoulder) and 75 (non-adjusted Constant Score) for Type C fractures. For all studies mean non-adjusted CS ranged from 53 to 75. Mean age- and sex-adjusted CS ranged from 60 to 88. Mean CS relative to the contralateral shoulder ranged from 71 to 85. The most common complications were avascular necrosis (range, 4-33%), screw perforations (range, 5-20%), loss of fixation (range, 3-16%), impingement (range, 7-11%) and infections range 4-19%. Reoperation rate ranged from 6 to 44%. CONCLUSIONS: Insufficient study designs and unclear reporting preclude safe treatment recommendations. Complication and reoperation rates were unexpected high. Based on the studies included we cannot routinely recommend the use of locking plates in AO/OTA Type C fractures.\",\n \"corpus_id\": 205442077,\n \"score\": 2\n },\n {\n \"doc_id\": \"22008672\",\n \"title\": \"[Complication analysis of proximal humeral fractures treated with locking plate].\",\n \"abstract\": \"OBJECTIVE: To analyze complications of surgically treated proximal humeral fractures with locking plate. METHODS: Eighty three (30 males and 53 females) coherent unstable proximal humeral fractures were treated with locking plate from January 2007 to January 2010 with a mean follow-up lasting 23.5 months ( 10-51 months ). Their mean age was 66.4 years (33-89 years). The patients were evaluated with outpatient physical examination, X-ray film, visual analogue scale (VAS), and Constant-Murley scores. Complications and functional outcome of the involved shoulders were recorded and estimated. Complications were diagnosed in 15 cases, varus malunion in 6, humeral head necrosis in 3, delayed union in 1, screw cut-out in 3, and subacromio-impingement in 3.Four cases were combined with two or more complications. RESULT: Four-part fractures had higher complication risks in implant related complications (P=0.009)and none implant related complications (P=0.003).Age and comobities had little influence on complication occurrence. CONCLUSION: Although locking plate provides optimal clinical results in proximal humeral fracture management, its complications should be highly considered. Preoperative evaluation, implant option, accurate reconstructions and rehabilitations are key points to restore the shoulder function.\",\n \"corpus_id\": 41239727,\n \"score\": 2\n },\n {\n \"doc_id\": \"22287062\",\n \"title\": \"Complex fractures of the proximal humerus in the elderly--outcome and complications after locking plate fixation.\",\n \"abstract\": \"Open reduction and internal fixation (ORIF) with locking plates or primary arthroplasty remains a controversial issue in the management of complex proximal humerus fractures. Aim of this study was to evaluate the surgeon- and patient-based outcome of patients older than 65 years who underwent ORIF using locking plate fixation of a 3- or 4-part fracture of the proximal humerus. Twenty-seven patients older than 65 years were treated with locking plate fixation (PHILOS, Fa. Synthes, Umkirch, Germany). At an average follow-up of 44 months, the clinical and the subjective outcome were evaluated, and complications were analyzed. The mean age- and gender-related Constant score was 70% (30–100%) compared with 92% (47–108%) of the contralateral non-injured shoulder. The mean DASH score was 29 points (0–71). Five patients (18.5%) showed clinical signs of an impingement, which was related to malpositioning of the plate in 3 cases. Screw cutout was seen in 22.2% (6 patients). Avascular necrosis of the head or the tubercula was found in 8 patients (29.6%). The revision rate was 29.6%. However, the patients considered the functional status of their shoulder as “good” or “satisfactory.” The functional and patient-orientated results of the locking plate fixation of complex displaced proximal humerus fractures in the elderly are comparable to those of primary arthroplasty and minimally invasive treatment. Proper surgical technique (screw length, plate position) is mandatory for reducing the revision rate.\",\n \"corpus_id\": 8859779,\n \"score\": 2\n },\n {\n \"doc_id\": \"22310414\",\n \"title\": \"Locking plate fixation for proximal humerus fractures.\",\n \"abstract\": \"Locking plates are increasingly used to surgically treat proximal humerus fractures. Knowledge of the bone quality of the proximal humerus is important. Studies have shown the medial and dorsal aspects of the proximal humeral head to have the highest bone strength, and this should be exploited by fixation techniques, particularly in elderly patients with osteoporosis. The goals of surgery for proximal humeral fractures should involve minimal soft tissue dissection and achieve anatomic reduction of the head complex with sufficient stability to allow for early shoulder mobilization. This article reviews various treatment options, in particular locking plate fixation. Locking plate fixation is associated with a high complication rate, such as avascular necrosis (7.9%), screw cutout (11.6%), and revision surgery (13.7%). These complications are frequently due to the varus deformation of the humeral head. Strategic screw placement in the humeral head would minimize the possibility of loss of fracture reduction and potential hardware complications. Locking plate fixation is a good surgical option for the management of proximal humerus fractures. Complications can be avoided by using better bone stock and by careful screw placement in the humeral head.\",\n \"corpus_id\": 3035080,\n \"score\": 2\n },\n {\n \"doc_id\": \"22321162\",\n \"title\": \"Hemiarthroplasty versus angle-stable locking compression plate osteosynthesis in the treatment of three- and four-part fractures of the proximal humerus in the elderly: design of a randomized controlled trial.\",\n \"abstract\": \"BACKGROUND: The optimal surgical management of dislocated three- and four-part fractures of the proximal humerus in elderly patients remains unclear. Most used techniques are hemiarthroplasty and angle-stable locking compression plate osteosynthesis. In the current literature there is no evidence available presenting superior results between hemiarthroplasty and angle-stable locking compression plate osteosynthesis in terms of speed of recovery, pain, patient satisfaction, functional outcome, quality of life or complications. METHODS/DESIGN: A randomized controlled multicenter trial will be conducted. Patients older than 60 years of age with a dislocated three- or four-part fracture of the proximal humerus as diagnosed by X-rays and CT-scans will be included. Exclusion criteria are a fracture older than 14 days, multiple comorbidity, multitrauma, a pathological fracture, previous surgery on the injured shoulder, severely deranged function caused by a previous disease, \\\"head-split\\\" proximal humerus fracture and unwillingness or inability to follow instructions. Participants will be randomized between surgical treatment with hemiarthroplasty and angle-stable locking compression plate osteosynthesis. Measurements will take place preoperatively and 3 months, 6 months, 9 months, 12 months and 24 months postoperatively. Primary outcome measure is speed of recovery of functional capacity of the affected upper limb using the Disabilities of Arm, Shoulder and Hand score (DASH). Secondary outcome measures are pain, patient satisfaction, shoulder function, quality of life, radiological evaluation and complications. Data will be analyzed on an intention-to-treat basis, using univariate and multivariate analyses. DISCUSSION: Both hemiarthroplasty and angle-stable locking compression plate osteosynthesis are used in the current treatment of dislocated three-and four-part fractures of the proximal humerus. There is a lack of level-1 studies comparing these two most-used surgical treatment options. This randomized controlled multicenter trial has been designed to determine which surgical treatment option provides the fastest recovery of functional capacity of the affected upper limb, and will provide better outcomes in pain, satisfaction, shoulder function, quality of life, radiological evaluation and complications. TRIAL REGISTRATION NUMBER: The trial is registered in the Netherlands Trial Registry (NTR2461).\",\n \"corpus_id\": 6582468,\n \"score\": 2\n },\n {\n \"doc_id\": \"22337487\",\n \"title\": \"Locked plating of the proximal humerus using an endosteal implant.\",\n \"abstract\": \"PURPOSE: To report on the use of a supplemental medial endosteal implant to prevent varus collapse and screw cutout in proximal humerus fractures treated with a laterally placed locking plate. METHODS: Twenty-seven patients meeting study inclusion criteria were included in the study. Follow-up averaged 63.1 weeks (minimum 37 weeks and maximum 120 weeks). All patients were either older than 70 years or had sustained a proximal humerus fracture with medial comminution. Using the anterolateral acromial approach, a proximal humeral locking plate augmented with a medial endosteal implant (fibular allograft in 23 patients and semitubular plate in 4 patients) was used for fixation. Intraoperative fluoroscopic images and the most recent follow-up radiographs were used to measure the head-shaft angle and loss of height between the implant and the articular surface. RESULTS: Only 1 of 27 patients had significant loss of reduction with collapse of the fracture into varus (4.2 mm change). Ninety-six percent of patients maintained their original reduction with an average loss of height of 1.2 mm and an average change in shaft-head angle of 2.2 degrees. There were no implant failures or screw perforations of the articular surface and no radiographic or clinical evidence of AVN. CONCLUSIONS: Use of a medial endosteal implant as a supplement to a lateral locking plate is effective in maintaining operative reduction, preventing varus collapse, and implant failure in fractures with medial comminution and/or poor bone quality. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.\",\n \"corpus_id\": 12389893,\n \"score\": 2\n },\n {\n \"doc_id\": \"22959524\",\n \"title\": \"Locking plate fixation of fractures of the proximal humerus: analysis of complications, revision strategies and outcome.\",\n \"abstract\": \"BACKGROUND: Locking plates for open reduction-internal fixation (ORIF) of proximal humeral fractures are widely used. We observed an unusually high number of patients with complications referred to our institution. It was the purpose of this study to report these complications, as well as their treatment and outcome. MATERIALS AND METHODS: From 2003 to 2010, all patients treated for complications after ORIF with locking plates for proximal humeral fractures were prospectively collected and retrospectively analyzed. Patients were followed up clinically and radiographically. RESULTS: In total, 121 patients (67 women and 54 men; mean age, 59 years) were referred after primary locking plate ORIF; 80% had a 3- or 4-part fracture. A mean of 3 complications occurred per patient, including malreduction, primary screw cutout, malunion, nonunion, avascular necrosis, and infection. Secondary screw cutout was found in 57% of patients, causing glenoid destruction in 33% of patients. A mean of 1.5 revision surgeries were needed. Hemiarthroplasty, total shoulder arthroplasty, and reverse shoulder arthroplasty improved the mean Constant score (24 to 55 points, P < .05; 29 to 54 points, P = .3; and 25 to 48 points, P < .05, respectively) after a mean of 24 months. In 6 patients, glenoid implantation was no longer possible because of the destruction by perforated head screws. CONCLUSION: In this negatively selected series, complications resulted in secondary arthroplasties in over 50% of the patients. Shoulder function, though improved, remained substantially restricted even after revision surgery. Glenoid destruction by locking screws was the most devastating and previously almost unseen complication, which limited the options of treatment.\",\n \"corpus_id\": 44522291,\n \"score\": 2\n },\n {\n \"doc_id\": \"23235575\",\n \"title\": \"Interventions for treating proximal humeral fractures in adults.\",\n \"abstract\": \"BACKGROUND: Fractures of the proximal humerus are common injuries. The management, including surgical intervention, of these fractures varies widely. This is an update of a Cochrane review first published in 2001 and last updated in 2010. OBJECTIVES: To review the evidence supporting the various treatment and rehabilitation interventions for proximal humeral fractures. SEARCH METHODS: We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE and other databases, and bibliographies of trial reports. The full search ended in January 2012. SELECTION CRITERIA: All randomised controlled trials pertinent to the management of proximal humeral fractures in adults were selected. DATA COLLECTION AND ANALYSIS: Two people performed independent study selection, risk of bias assessment and data extraction. Only limited meta-analysis was performed. MAIN RESULTS: Twenty-three small randomised trials with a total of 1238 participants were included. Bias in these trials could not be ruled out. Additionally there is a need for caution in interpreting the results of these small trials, which generally do not provide sufficient evidence to conclude that any non-statistically significant finding is 'evidence of no effect'.Eight trials evaluated conservative treatment. One trial found an arm sling was generally more comfortable than a less commonly used body bandage. There was some evidence that 'immediate' physiotherapy compared with that delayed until after three weeks of immobilisation resulted in less pain and potentially better recovery in people with undisplaced or other stable fractures. Similarly, there was evidence that mobilisation at one week instead of three weeks alleviated short term pain without compromising long term outcome. Two trials provided some evidence that unsupervised patients could generally achieve a satisfactory outcome when given sufficient instruction for an adequate self-directed exercise programme. Six heterogeneous trials, involving a total of 270 participants with displaced and/or complex fractures, compared surgical versus conservative treatment. Pooled results of patient-reported functional scores at one year from three trials (153 participants) showed no statistically significant difference between the two groups (standardised mean difference -0.10, 95% CI -0.42 to 0.22; negative results favour surgery). Quality of life based on the EuroQol results scores from three trials (153 participants) showed non-statistically significant differences between the two groups at three time points up to 12 months. However, the pooled EuroQol results at two years (101 participants) from two trials run concurrently from the same centre were significantly in favour of the surgical group. There was no significant difference between the two groups in mortality (8/98 versus 5/98; RR 1.55, 95% CI 0.55 to 4.36; 4 trials). Significantly more surgical group patients had additional or secondary surgery (18/112 versus 5/111; RR 3.36, 95% CI 1.33 to 8.49; 5 trials). This is equivalent to an extra operation in one of every nine surgically treated patients. Different methods of surgical management were tested in seven small trials. One trial comparing two types of locking plate versus a locking nail for treating two-part surgical neck fractures found some evidence of better function after plate fixation but also of a higher rate of surgically-related complications. One trial comparing a locking plate versus minimally invasive fixation with distally inserted intramedullary nails found some evidence of a short-term benefit for the nailing group. Compared with hemiarthroplasty, tension-band fixation of severe injuries using wires was associated with a higher re-operation rate in one trial. Two trials found no important differences between 'polyaxial' and 'monaxial' screws combined with locking plate fixation. One trial produced some preliminary evidence that tended to support the use of medial support locking screws in locking plate fixation. One trial found better functional results for one of two types of hemiarthroplasty. Very limited evidence suggested similar outcomes from early versus later mobilisation after either surgical fixation (one trial) or hemiarthroplasty (one trial). AUTHORS' CONCLUSIONS: There is insufficient evidence to inform the management of these fractures. Early physiotherapy, without immobilisation, may be sufficient for some types of undisplaced fractures. It remains unclear whether surgery, even for specific fracture types, will produce consistently better long term outcomes but it is likely to be associated with a higher risk of surgery-related complications and requirement for further surgery. There is insufficient evidence to establish what is the best method of surgical treatment, either in terms of the use of different categories of surgical intervention (such as plate versus nail fixation, or hemiarthroplasty versus tension-wire fixation) or different methods of performing an intervention in the same category (such as different methods of plate fixation). There is insufficient evidence to say when to start mobilisation after either surgical fixation or hemiarthroplasty.\",\n \"corpus_id\": 38242239,\n \"score\": 2\n },\n {\n \"doc_id\": \"23412173\",\n \"title\": \"Treatment of three- and four-part proximal humeral fractures with locking proximal humerus plate.\",\n \"abstract\": \"OBJECTIVE: The purpose of this study was to evaluate the effectiveness and complications of the locking proximal humerus plate to treat proximal humerus fractures. DESIGN: A retrospective clinical trial. SETTING: Department of Orthopaedics, Tianjin Medical University General Hospital. PATIENTS: Sixty-eight consecutive patients with three- or four-part fractures of the proximal humerus were treated with locking proximal humerus plates. INTERVENTION: The deltopectoral anterolateral acromial approach was used to the proximal humerus; open reduction and locking proximal humerus plate were applied. MAIN OUTCOME MEASUREMENTS: Constant Score was used to measure the shoulder functional recovery, and Visual Analog Scale (VAS) was used to measure subjective evaluation of pain. The radiology was observed. RESULTS: After average 26.7 months, the average Constant Score was 72.6 ± 13.2 points and the average VAS was 1.2 ± 0.8 points. All the complications such as screw perforation into the glenohumeral joint, screws loosening, soft tissue infections, avascular necrosis and delayed union occurred in eight cases (11.8 %). CONCLUSIONS: The effectiveness of the locking proximal humerus plate was similar to other published literatures on treating fractures of the proximal humerus; however, a lower complications rate in short follow-up time was observed in this study. It may potentially provide a favorable option for treating three- or four-part fractures of the proximal humerus. Dealing with each particular fracture pattern, surgeons should have a decision of appropriate way to internal fixation.\",\n \"corpus_id\": 25597316,\n \"score\": 2\n },\n {\n \"doc_id\": \"23682177\",\n \"title\": \"Open reduction and locking plate fixation of displaced proximal humerus fractures.\",\n \"abstract\": \"BACKGROUND: Treatment of proximal humerus fractures is controversial and various operative modalities have been tried in the literature. The aim of the present study was to evaluate functional outcome and complication rate after open reduction and internal fixation of displaced proximal humerus fractures by proximal humerus locking plate. MATERIALS AND METHODS: 52 patients with displaced proximal humerus fractures treated with proximal humerus locking plate between May 2008 and October 2010 were included in the study. Fractures were classified according to Neer's classification into displaced 2-part, 3-part, and 4-part fractures. Patients were followed for a minimum period of 1 year. 11 patients had less than 1 year of followup and were not considered in the evaluation of final results. Forty one patients were considered for final evaluation. Functional evaluation was done according to the Constant-Murley scoring system. Constant score was compared between 2-part, 3-part, and 4-part fractures at final up and also between young (≤60 yrs) and old (>60 yrs). RESULTS: 11 patients had 2-part fractures, 22 patients had 3-part fractures, and 19 patients had 4-part fractures. The mean followup period was 15.21 ± 2.59 months. 65.8% (n = 27) patients had good to excellent result, 19.5% (n = 8) had fair, and 14.7% (n = 6) had poor result. Constant scores for 2-part (79.83 ± 6.95) and 3-part fractures (74.22 ± 12.53) were significantly superior to those of 4-part fractures (61.09 ± 14.29) (P value = 0.002 and 0.018, respectively). Difference between 2-part and 3-part fractures was not significant (P value = 0.623). There was no significant difference between younger (≤60) and older patients (>60). Complications encountered in this series were varus malreduction in 17% (n = 7), screw perforation in 10% (n = 4), plate impingement in 12% (n = 5), infection in 2% (n = 1), and nonunion in 2% (n = 1) of cases. CONCLUSION: Proximal humerus locking plate gives reliable fixation for 2-part and 3-part fractures. Its use in more complicated fracture patterns of 4-part fractures is associated with poor clinical outcome.\",\n \"corpus_id\": 5376232,\n \"score\": 2\n },\n {\n \"doc_id\": \"24003839\",\n \"title\": \"Fixed-angle locking proximal humerus plate: an evaluation of functional results and implant-related outcomes.\",\n \"abstract\": \"BACKGROUND: Displaced and unstable proximal humeral fractures are challenging injuries to treat. Proximal humeral locking plates are a recent development for the treatment of these complex fractures. METHODS: Retrospective analysis of 23 patients with 23 proximal humeral fractures treated with the Synthes locking proximal humerus plate. These were Neer two-, three- and four-part fractures. Follow-up was at a mean of 22 months and included clinical assessment using the Constant score (CS) and the Short Form-12 health questionnaire. Radiographic assessment was performed to assess implant-related complication in relation to the initial fracture pattern and the presence of adequate medial support. RESULTS: The mean CS for all patients was 60.4 (range, 29-85). The mean adjusted CS was 82% (range, 30-117), active forward flexion 127 degrees and the active abduction 115 degrees. Initial fracture pattern, the presence or absence of adequate medial support and age did not significantly influence the clinical scores. Complications included one infection, two cases of avascular necrosis, two cases of varus collapse with screw penetration and one non-union. The overall reoperation rate was 26%. There was an increased rate of complications in those with inadequate medial support (P = 0.0183) and a trend to higher complication rates in four-part fractures. CONCLUSION: Using the locking proximal humerus plate for the treatment of proximal humeral fractures is an acceptable procedure with comparable outcomes with historical controls, but with a complication rate of 30%. More important than implant selection, however, is the ability to achieve a stable reduction with calcar support.\",\n \"corpus_id\": 22980777,\n \"score\": 2\n },\n {\n \"doc_id\": \"24296598\",\n \"title\": \"The impact of preoperative coronal plane deformity on proximal humerus fixation with endosteal augmentation.\",\n \"abstract\": \"OBJECTIVES: To examine the impact of preoperative coronal plane deformity on functional and radiographic outcomes on endosteal strut augmentation of proximal humerus fracture fixation. DESIGN: Single surgeon, retrospective analysis of a prospective database. Case series. SETTING: Academic level 1 trauma center. PATIENTS/PARTICIPANTS: Seventy-two patients with isolated proximal humerus fractures fulfilled all inclusion/exclusion criteria with a minimum follow-up of 12 months. INTERVENTION: Proximal humerus open reduction internal fixation with a laterally placed proximal humeral locking plate and endosteal placement of an allograft fibula treated through the anterolateral approach. MAIN OUTCOME MEASUREMENTS: Global functional outcome as determined by the Disabilities of the Arm, Shoulder and Hand (DASH) score and Short Form 36 physical function. Shoulder-specific functional outcome as determined by the Constant-Murley and the University of California Los Angeles shoulder scores. RESULTS: The mean age was 62 years old (range, 26-90 years). There were 32 varus fractures (neck-shaft angle, 110.8 degrees) and 40 valgus fractures (neck-shaft angle, 168.9 degrees). There was no significant difference in the initial postoperative (varus: 132.5 degrees, valgus: 135.5 degrees) and final (varus: 129.9 degrees, valgus: 132.2 degrees) neck-shaft angles or change in humeral height (varus: 0.94 mm, valgus: 1.48 mm). There were no significant differences in functional outcomes [Constant (varus: 85.2, valgus: 88.7) DASH (varus: 21.4, valgus: 13.9), University of California Los Angeles (28.6, varus 30.4), and Short Form 36 (varus: 66.8, valgus: 59.1)]. There were 2 patients in the valgus group and 3 patients in the varus group with an asymptomatic humeral head screw penetration (mean Constant 84.5, DASH 9.5). There was 1 deep infection in the varus group and 2 in the valgus group necessitating implant removal after fracture union. There was 1 case of avascular necrosis in the valgus group (DASH 19.4, Constant 73). CONCLUSIONS: There were no significant differences in complication rates, radiographic, or clinical outcomes between fractures presenting with preoperative varus coronal displacement compared with those presenting with valgus coronal displacement. The equivalent outcomes may be attributed to the uniform operative technique and fibular strut augmentation used by the primary surgeon. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.\",\n \"corpus_id\": 46543591,\n \"score\": 2\n },\n {\n \"doc_id\": \"24781604\",\n \"title\": \"Outcome of locking compression plating for proximal humeral fractures: a prospective study.\",\n \"abstract\": \"PURPOSE: To evaluate the outcome of open reduction and internal fixation using locking compression plates for proximal humeral fractures. METHODS: 54 men and 16 women aged 28 to 79 (mean, 54) years underwent open reduction and internal fixation using a locking compression plate for closed 2-part (n=22), 3-part (n=38), and 4-part (n=10) proximal humeral fractures. 10 of the patients also had dislocation of the humeral head; 4 had fractures extending to the shaft. Wound condition, functional outcome, bone union, amount of collapse, and malalignment were assessed. Functional outcome was assessed using the Constant-Murley score. RESULTS; The mean follow-up period was 15 (range, 6-24) months. All fractures achieved union after a mean of 9 (range, 6-12) weeks. The mean Constant-Murley scores for the injured and normal shoulders were 72 and 82, respectively (88% of normal). The final outcome was excellent in 14 patients, good in 28, moderate in 22, and poor in 6. In the latter 6 patients, 2 had screw penetration, 2 had plate impingement, one had a mal-reduced greater tuberosity, and one had adhesive capsulitis. All were preventable. In all, 18 patients had 20 complications: subacromial impingement of the plate (n=6), mal-reduction of the greater tuberosity (n=6), screw penetration (n=2), adhesive capsulitis (n=2), superficial infection (n=2), and haematoma (n=2); 12 of these complications were technique-related. CONCLUSION: Locking proximal humeral plates enabled stable fixation in all Neer-type proximal humeral fractures. Most complications were technique-related.\",\n \"corpus_id\": 8503619,\n \"score\": 2\n },\n {\n \"doc_id\": \"24791873\",\n \"title\": \"Locking plate fixation combined with iliac crest bone autologous graft for proximal humerus comminuted fracture.\",\n \"abstract\": \"BACKGROUND: Although the use of an intramedullary fibular allograft together with locking plate fixation can provide additional medial support and prevent varus malalignment in displaced proximal humeral fractures with promising results, the fibular autograft donor site often sustains significant trauma and cannot restore the articular surface of comminuted fractures. The aim of this study was to evaluate the clinical and radiographic outcomes of a locking plate and crest bone autologous graft for treating proximal humerus comminuted fractures. METHODS: We assessed the functional outcomes and complication rates in 40 patients with proximal humerus comminuted fractures. Eighteen patients were treated with a locking plate and an autologous crest bone graft (experimental group), and 22 were treated with only the locking plate and no bone graft (control group). Postoperative assessments included radiographic imaging, range of motion analysis, pain level based on the visual analogue scale (VAS), and the SF-36 (Short Form (36) Health Survey), as well as whether patients could return to their previous occupation. RESULTS: All fractures healed both clinically and radiologically in the experimental group. There was no more than 2 mm collapse of the humeral head, and no osteonecrosis or screw penetration of the articular surface. In contrast, two patients had a nonunion in the control group, and they eventually accepted total shoulder replacements. The average time from surgery to radiographic union was significantly shorter in the experimental group ((4.66±1.63) months) compared with the control group ((5.98±1.57) months) (P < 0.05). For the experimental versus controls groups, the mean shoulder active flexion (148.00±18.59 vs. 121.73±17.20) degrees, extension (49.00±2.22 vs. 42.06±2.06) degrees, internal rotation (45.00±5.61 vs. 35.00±3.55) degrees, external rotation (64.00±9.17 vs. 52.14±5.73) degrees, and abduction (138.00±28.78 vs. 105.95±15.66) degrees were all significantly higher (all P < 0.001). The median SF-36 in the experimental group ((88.00±5.71) points) was significantly higher than that of the control group ((69.45±9.45) points; P < 0.001). The median VAS pain level (mean rank, 10.50) in the experimental group was lower than that (mean rank, 47.19) of the control group (P < 0.001). All but one patient (17 of 18, 94.4%) in the experimental group returned to their previous activities or occupations, and that one patient changed to a different occupation because of slight restrictions to activities. On the other hand, four patients could not return to their previous activities or occupations in the control group. CONCLUSION: Locking plate fixation combined with an iliac crest bone graft is an effective technique for treating proximal humerus comminuted fractures.\",\n \"corpus_id\": 7911624,\n \"score\": 2\n },\n {\n \"doc_id\": \"25293898\",\n \"title\": \"Surgical treatment of proximal humerus fractures using PHILOS plate.\",\n \"abstract\": \"OBJECTIVE: To evaluate functional outcome and complications of open reduction and internal fixation with proximal humeral internal locking system (PHILOS) plate for proximal humerus fractures. METHODS: We reviewed 51 patients who underwent open reduction and internal fixation with PHILOS plate between the years 2007 to 2012. There were 35 men and 16 women with a mean age of 38 years (range 24-68). There were 41 patients in the age group of <60 years and 10 patients in the age group of >60 years. According to Neer classification system, 8, 15 and 23 patients had 2-part, 3-part, and 4-part fractures, respectively and 5 patients had 4-part fracture dislocation. All surgeries were carried out at our tertiary care trauma centre. Functional evaluation of the shoulder at final follow-up was done using Constant-Murley score. RESULTS: The mean follow-up period was 30 months (range 12-44 months). Two patients were lost to follow-up. Of the remaining 49 patients, all fractures were united clinically and radiologically. The mean time for radiological union was 12 weeks (range 8-20 weeks). At the final follow-up the mean Constant-Murley score was 79 (range 50-100). The results were excellent in 25 patients, good in 13 patients, fair in 6 patients and poor in 5 patients. During the follow-up, four cases of varus malunion, one case of subacromial impingement, one case of deep infection, one case of intraarticular screw penetration and one case of failure of fixation were noted. No cases of avascular necrosis, hardware failure, locking screw loosening or nonunion were noted. CONCLUSION: PHILOS provides stable fixation in proximal humerus fractures. To prevent potential complications like avascular necrosis, meticulous surgical dissection to preserve vascularity of humeral head is necessary.\",\n \"corpus_id\": 36408736,\n \"score\": 2\n },\n {\n \"doc_id\": \"25350626\",\n \"title\": \"Early outcomes of proximal humerus fracture fixation with locking plate and intramedullary fibular strut graft.\",\n \"abstract\": \"Proximal humerus fractures are commonly encountered in elderly patients. Surgical treatment demonstrates high complication rates, including varus construct collapse and screw cutout. In this study, the authors evaluate the clinical outcome of locking plate fixation with intramedullary fibular strut graft augmentation as a primary surgical treatment in the prevention of early collapse and screw cutout. A total of 9 patients were evaluated. Surgery was performed for displaced proximal humerus fractures between April and December 2011. Patients were either class 2, 3, or 4, according to Neer classification. Mean patient age was 75.4 years. Preoperative and immediate, 6-week, and 3-month postoperative radiographs were evaluated. Head-shaft angles were measured to assess for varus collapse and displacement. Range of motion, complication rates, and functional recovery were also evaluated. Patients underwent open reduction and internal fixation with placement of an intramedullary fibular strut graft. Fixation was achieved with a Philos plate (Synthes, Oberdorf, Switzerland). Reduction and fixation were evaluated with radiographs. Passive exercises and range of motion were allowed immediately postoperatively, and all patients achieved active abduction and forward flexion 6 weeks postoperatively. Shoulder radiographs taken 12 weeks postoperatively revealed no loss of reduction or screw cutout. The introduction of the locking plate has improved outcomes. The addition of an intramedullary strut graft has shown improved preliminary results. Maintained reduction was observed in all 9 patients in the early postoperative period, and good functional motion was achieved. No incidence of screw cutout was recorded.\",\n \"corpus_id\": 10065894,\n \"score\": 2\n },\n {\n \"doc_id\": \"25433318\",\n \"title\": \"The Results of Internal Fixation of Proximal Humeral Osteoporotic Fractures with PHILOS Locking Plate.\",\n \"abstract\": \"BACKGROUND: In the last fifty years since plate and screw osteosynthesis has been implemented in fracture treatment, osteosporotic bone fractures were observed as a special problem. Due to special histologic, anatomic, physical and biomehanic properties of osteoporotic changed bone the laws of biomechanics suggest that stable osteosynthesis for osteoporotic bone is necessary to increase the contact surface of metallic implants and bone and the stability of the screw-plate-bone compound. There are numerous surgical techniques and methods for treatment of osteoporotic proximal humeral fractures. Every surgical procedure has to establish anatomical reduction and stable fixation that will enable early mobilisation. SUBJECTS AND METHODS: The aim of this study was to present results of internal fixation of proximal humeral osteoporotic fractures with PHILOS locking plate. Between 2007 and 2012, a total of 67 patients older than 65 years with closed proximal humerus fractures underwent surgical treatment with PHILOS plate system (Synthes, Switzerland). 42 patients were operated with deltopectoral approach and 25 with deltoid split approach. After a mean follow up period of 14.68 (6-28) months functional and radiologic results were assessed. RESULTS: We noted 9 postoperative complications related to surgical technique (1 intraarticular screw placement, 1 displacement in major tuberculum fragment, 1 displacement in major tuberculum fragment along with oblique placement of the plate, 2 cases of inadequate reduction, 1 case of humeral head avascular necrosis, varus humeral head fixation in 3 cases). None of the patients developed superficial or deep surgical infection. There was no nonunions. In the final evaluation, the Constant shoulder score was 91.75 (72-100). CONCLUSIONS: In this study PHILOS locking plate showed good applicability, respecting bone biologic properties because of negligible interference with blood supply of the humeral head. There was no requirement to shape the plate enabling stabilization at constant angles as clear benefit of this plate. All that enables early mobilisation, and no implant insufficiency resulting in satisfactory treatment results and high Constant shoulder scores.\",\n \"corpus_id\": 36475215,\n \"score\": 2\n },\n {\n \"doc_id\": \"25457318\",\n \"title\": \"Fractures and fracture-dislocations of the proximal humerus: A retrospective analysis of 82 cases treated with the Philos(®) locking plate.\",\n \"abstract\": \"OBJECTIVE: To present the experience in a single institution of the management of 82 consecutive fractures and fracture-dislocations of the proximal humerus treated with the Proximal Humeral Internal Locking System (Philos(®)) plate. MATERIALS AND METHODS: A total of 81 patients with 82 proximal humerus fractures (one patient had bilateral fracture) were treated at our institution with open reduction and internal fixation with Philos(®) plate from January 2008 to December 2012 and the clinico-radiological outcome was analysed. Twelve of these patients also had a dislocation of the proximal humerus. According to the Neer classification, there were seven two-part fractures, 40 three-part fractures and 35 four-part fractures. All patients received a similar physical therapy programme following internal fixation. Mean final follow-up was 32 months. Functional outcome was evaluated for each patient using the Constant-Murley score; radiographic evaluation was also conducted and complications were recorded. RESULTS: At the end of the follow-up period, the mean Constant-Murley score for the injured side was 75 points (range 42-92); results were graded as excellent for eight patients, good for 52, moderate for 17 and poor for five. Twenty-three patients (28%) had complications during the follow-up period. Reoperation was required in 12 patients. Complications included avascular necrosis of the humeral head in 10 patients (12%), varus positioning of the head in four patients (4.8%), impingement syndrome in three patients (3.6%), secondary screw perforation in three patients (3.6%), non-union of the fracture in two patients (2.4%) and infection in one patient (1.2%). CONCLUSIONS: Open reduction and internal fixation of proximal humeral fractures with the Philos(®) plate was associated with good clinical outcomes provided the correct surgical technique was used. To better evaluate the real incidence of complications, it is important to follow patients for more than one year after surgery as some complications may arise after this time.\",\n \"corpus_id\": 35160685,\n \"score\": 2\n },\n {\n \"doc_id\": \"25978864\",\n \"title\": \"How to enhance the stability of locking plate fixation of proximal humerus fractures? An overview of current biomechanical and clinical data.\",\n \"abstract\": \"BACKGROUND: The complication rate after locking plate fixation of proximal humerus fractures is high. In addition to low bone mineral density, a lack of medial support has been identified as one of the most important factors accounting for mechanical instability. As a result of the high failure rate, different strategies have been developed to enhance the mechanical stability of locking plate fixation of proximal humerus fractures. The aim of the present article is to give an overview of the current biomechanical and clinical studies that focus on how to increase the stability of locking plate fixation of proximal humerus fractures. METHODS: A comprehensive search of the Medline databases using specific search terms with regard to the stability of locking plate fixation of proximal humerus fractures was performed. After screening of the articles for eligibility, they were subdivided according to clinical and biomechanical aspects. RESULTS: Medial support screws, filling of bone voids and screw-tip augmentation with bone cement as well as the application of bone grafts are currently the most frequently assessed and performed methods. Although the evidence is weak, all of the mentioned strategies appear to have a positive effect on achieving and maintaining a stable reduction even of complex fractures. CONCLUSION: Further clinical studies with a higher number of patients and a higher level of evidence are required to develop a standardised treatment algorithm with regard to cement augmentation and bone grafting. Although these measures are likely to have a stabilising effect on locking plate fixation, its general use cannot be fully recommended yet.\",\n \"corpus_id\": 37222526,\n \"score\": 2\n },\n {\n \"doc_id\": \"26161759\",\n \"title\": \"Reducing Postoperative Fracture Displacement After Locked Plating of Proximal Humerus Fractures: Current Concepts.\",\n \"abstract\": \"The incidence of proximal humerus fractures in the elderly has been rising. Concomitantly, operative fixation with use of locking plates has been increasing. Postoperative complications of locking plate fixation, particularly in the setting of osteoporotic bone, include screw penetration of the articular surface, progressive fracture displacement, and avascular necrosis. Intraoperative techniques to enhance the fixation construct and reduce complications include use of rotator cuff sutures, bone void fillers (fibular strut allograft, cancellous allograft, autograft, bone cement), appropriate placement of divergent and shorter locking screws, and medial calcar reduction and support. More recent clinical and biomechanical studies suggest that use of these strategies may reduce complications after locked plating of osteoporotic proximal humerus fractures. Furthermore, a multidisciplinary approach to the evaluation and treatment of osteoporosis may be beneficial in these patients.\",\n \"corpus_id\": 19987527,\n \"score\": 2\n },\n {\n \"doc_id\": \"26445824\",\n \"title\": \"Additional calcar support using a blade device reduces secondary varus displacement following reconstruction of the proximal humerus: a prospective study.\",\n \"abstract\": \"BACKGROUND: Locking plate fixation of displaced fractures of the proximal humerus is still accompanied by a distinct complication rate, especially in case of osteoporotic bone, short-segment fracture length and comminution of the medial calcar. Secondary loss of reduction leading to varus deformity and screw cutout most frequently lead to surgical revision. The aim of the present study was to evaluate the clinical and radiological outcome of a recently developed polyaxial locking plate that allows for the additional placement of a helical blade device, aiming for support of the medial calcar. METHODS: In this prospective study, 17 patients with a mean age of 63.0 ± 16.0 years suffering from displaced fractures of the proximal humerus (Neer type two-, three- and four-part) were enrolled. All patients were surgically treated using a polyaxial locking plate with additional blade device (group PAB, n = 12) or without blade device (group PA, n = 5). Functional outcome was recorded using the Munich Shoulder Questionnaire allowing for qualitative self-assessment of the Shoulder Pain and Disability Index (SPADI), the Disability of the Arm, Shoulder and Hand (DASH score) and the Constant Score. Radiological outcome was assessed by analyzing standardized true anterior-posterior and outlet-view radiographs with respect to radiographic evidence of secondary varus displacement, cutout of screws and hardware failure. Results were compared to an age-, gender- and fracture type-matched collective treated by monoaxial locking plate fixation (group MA, n = 15). RESULTS: The mean follow-up was 12.4 ± 2.9 months after surgery. There were no statistical significant differences in clinical outcome in all three groups. Group MA and group PA revealed significant secondary varus displacement in comparison to group PAB at the final follow-up compared to postoperative analysis (p < 0.001). The distance between the blade and the articular surface showed no significant increase in group PAB at the final follow-up compared to postoperative analysis. Not-implant-related complications were seen in one and implant-related complications were seen in two patients in group PAB. CONCLUSIONS: Polyaxial locking plate fixation with a blade device to restore medial cortical support reduces the risk of secondary varus displacement even in proximal humeral fractures of the elderly in comparison to monoaxial and polyaxial locking plate fixation without blade insertion.\",\n \"corpus_id\": 12850095,\n \"score\": 2\n },\n {\n \"doc_id\": \"26535597\",\n \"title\": \"Analysis of Failure with the Use of Locked Plates for Stabilization of Proximal Humerus Fractures.\",\n \"abstract\": \"OBJECTIVE: To evaluate factors associated with complicationsin a series of patients with proximal humerus fracturestreated with locked plating. DESIGN: Retrospective chart review. SETTING: Level 1 Trauma Center. PATIENTS AND METHODS: A retrospective review was performedon patients older than 18 years of age treated with alocked plate for a proximal humerus fracture between June2007 and December 2011 in order to identify any factorsassociated with failure. Patients had a minimum of 6 monthsof clinical follow-up. RESULTS: 78 proximal humerus fractures in 78 patientswere stabilized using a locked plate. Twenty-four patientswere lost to follow-up, while 54 patients were available for6-month minimum follow-up and comprised the study group. A healing complication occurred in 20 patients (37%) andconsisted of loss of reduction (16), varus malunion (16),avascular necrosis (6) or implant penetration (1). Elevenof 54 patients (20%) required secondary surgery. Factorsassociated with a healing complication were number offracture parts (p < 0.029), one or more comorbidities (p <0.016), three or more comorbidities (p < 0.038), and varusmalreduction (p < 0.001). CONCLUSION: An overall complication rate of 37% wasfound in patients stabilized using a locked plate after sustaininga proximal humerus fracture. Factors associatedwith healing complications included increased number offracture parts, increasing number of comorbidities, and initialvarus malreduction. Patient selection for locked platingafter proximal humerus fracture should incorporate manyfactors with meticulous attention to surgical technique.\",\n \"corpus_id\": 19574384,\n \"score\": 2\n },\n {\n \"doc_id\": \"26560014\",\n \"title\": \"Interventions for treating proximal humeral fractures in adults.\",\n \"abstract\": \"BACKGROUND: Fracture of the proximal humerus, often termed shoulder fracture, is a common injury in older people. The management of these fractures varies widely. This is an update of a Cochrane Review first published in 2001 and last updated in 2012. OBJECTIVES: To assess the effects (benefits and harms) of treatment and rehabilitation interventions for proximal humeral fractures in adults. SEARCH METHODS: We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and other databases, conference proceedings and bibliographies of trial reports. The full search ended in November 2014. SELECTION CRITERIA: We considered all randomised controlled trials (RCTs) and quasi-randomised controlled trials pertinent to the management of proximal humeral fractures in adults. DATA COLLECTION AND ANALYSIS: Both review authors performed independent study selection, risk of bias assessment and data extraction. Only limited meta-analysis was performed. MAIN RESULTS: We included 31 heterogeneous RCTs (1941 participants). Most of the 18 separate treatment comparisons were tested by small single-centre trials. The main exception was the surgical versus non-surgical treatment comparison tested by eight trials. Except for a large multicentre trial, bias in these trials could not be ruled out. The quality of the evidence was either low or very low for all comparisons except the largest comparison. Nine trials evaluated non-surgical treatment in mainly minimally displaced fractures. Four trials compared early (usually one week) versus delayed (three or four weeks) mobilisation after fracture but only limited pooling was possible and most of the data were from one trial (86 participants). This found some evidence that early mobilisation resulted in better recovery and less pain in people with mainly minimally displaced fractures. There was evidence of little difference between the two groups in shoulder complications (2/127 early mobilisation versus 3/132 delayed mobilisation; 4 trials) and fracture displacement and non-union (2/52 versus 1/54; 2 trials).One quasi-randomised trial (28 participants) found the Gilchrist-type sling was generally more comfortable than the Desault-type sling (body bandage). One trial (48 participants) testing pulsed electromagnetic high-frequency energy provided no evidence. Two trials (62 participants) provided evidence indicating little difference in outcome between instruction for home exercises versus supervised physiotherapy. One trial (48 participants) reported, without presentable data, that home exercise alone gave better early and comparable long-term results than supervised exercise in a swimming pool plus home exercise. Eight trials, involving 567 older participants, evaluated surgical intervention for displaced fractures. There was high quality evidence of no clinically important difference in patient-reported shoulder and upper-limb function at one- or two-year follow-up between surgical (primarily locking plate fixation or hemiarthroplasty) and non-surgical treatment (sling immobilisation) for the majority of displaced proximal humeral fractures; and moderate quality evidence of no clinically important difference between the two groups in quality of life at two years (and at interim follow-ups at six and 12 months). There was moderate quality evidence of little difference between groups in mortality in the surgery group (17/248 versus 12/248; risk ratio (RR) 1.40 favouring non-surgical treatment, 95% confidence interval (CI) 0.69 to 2.83; P = 0.35; 6 trials); only one death was explicitly linked with the treatment. There was moderate quality evidence of a higher risk of additional surgery in the surgery group (34/262 versus 16/261; RR 2.06, 95% CI 1.18 to 3.60; P = 0.01; 7 trials). Although there was moderate evidence of a higher risk of adverse events after surgery, the 95% confidence intervals for adverse events also included the potential for a greater risk of adverse events after non-surgical treatment. Different methods of surgical management were tested in 12 trials. One trial (57 participants) comparing two types of locking plate versus a locking nail for treating two-part surgical neck fractures found some evidence of slightly better function after plate fixation but also of a higher rate of surgically-related complications. One trial (61 participants) comparing a locking plate versus minimally invasive fixation with distally inserted intramedullary K-wires found little difference between the two implants at two years. Compared with hemiarthroplasty, one trial (32 participants) found similar results with locking plate fixation in function and re-operation rates, whereas another trial (30 participants) reported all five re-operations occurred in the tension-band fixation group. One trial (62 participants) found better patient-rated (Quick DASH) and composite shoulder function scores at a minimum of two years follow-up and a lower incidence of re-operation and complications after reverse shoulder arthroplasty (RSA) compared with hemiarthroplasty. No important between-group differences were found in one trial (120 participants) comparing the deltoid-split approach versus deltopectoral approach for non-contact bridging plate fixation, and two trials (180 participants) comparing 'polyaxial' and 'monaxial' screws in locking plate fixation. One trial (68 participants) produced some preliminary evidence that tended to support the use of medial support locking screws in locking plate fixation. One trial (54 participants) found fewer adverse events, including re-operations, for the newer of two types of intramedullary nail. One trial (35 participants) found better functional results for one of two types of hemiarthroplasty. One trial (45 participants) found no important effects of tenodesis of the long head of the biceps for people undergoing hemiarthroplasty. Very limited evidence suggested similar outcomes from early versus later mobilisation after either surgical fixation (one trial: 64 participants) or hemiarthroplasty (one trial: 49 participants). AUTHORS' CONCLUSIONS: There is high or moderate quality evidence that, compared with non-surgical treatment, surgery does not result in a better outcome at one and two years after injury for people with displaced proximal humeral fractures involving the humeral neck and is likely to result in a greater need for subsequent surgery. The evidence does not cover the treatment of two-part tuberosity fractures, fractures in young people, high energy trauma, nor the less common fractures such as fracture dislocations and head splitting fractures. There is insufficient evidence from RCTs to inform the choices between different non-surgical, surgical, or rehabilitation interventions for these fractures.\",\n \"corpus_id\": 205161397,\n \"score\": 2\n },\n {\n \"doc_id\": \"26878816\",\n \"title\": \"Initial varus displacement of proximal humerus fractures results in similar function but higher complication rates.\",\n \"abstract\": \"PURPOSE: To investigate the effect of initial varus or valgus surgical neck alignment on outcomes of patients who sustained proximal humerus fractures treated with open reduction and internal fixation (ORIF). METHODS: An institutional review board approved database of proximal humerus fractures treated with locked plates was reviewed. Of 185 fractures in the database, 101 fractures were identified and met inclusion criteria. Initial varus displacement was seen in 47 fractures (OTA types 11.A2.2, A3.1, A3.3, B1.2, B2.2, C1.2, C2.2, or C2.3) and initial valgus displacement was observed in 54 fractures (OTA types 11.A2.3, B1.1, C1.1, or C2.1). All patients were treated in a similar manner and examined by the treating physician at standard intervals. Functional outcomes were quantified via the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire and physical examination data at 12 months. Radiographs were reviewed for complications of healing. Additionally, complication rate and reoperation rate were investigated. RESULTS: Patients who presented with initial varus displacement had an average age of 59.3 years, while patients in the valgus group had an average age of 62.4 years. Overall, there was no statistically significant difference in age, sex distribution, BMI, fracture parts, screws used, or implant plate type between the two groups. At a minimum 12 months follow up, there was no significant difference in DASH scores between those presenting with varus versus valgus fracture patterns. In addition, no significant differences were seen in final shoulder range of motion in any plane. Overall, 30 patients included in this study developed a complication. A significantly greater number of patients in the initial varus cohort developed complications (40.4%), as compared to 20.3% of patients in the initial valgus cohort (P=0.03). Fourteen patients in this study underwent reoperation. Nine of these patients were in the varus cohort, while 5 were in the valgus cohort (P=0.15). CONCLUSIONS: In this study, initial surgical neck displacement in varus or valgus was found to not significantly affect functional outcome. Based upon our findings, patients with varus displaced proximal humerus fractures are at a greater risk of developing postoperative complications than those who present with initial valgus displaced fracture patterns.\",\n \"corpus_id\": 23617781,\n \"score\": 2\n },\n {\n \"doc_id\": \"27047867\",\n \"title\": \"EVALUATION OF THE COMPLICATIONS OF SURGICAL TREATMENT OF FRACTURES OF THE PROXIMAL EXTREMITY OF THE HUMERUS USING A LOCKING PLATE.\",\n \"abstract\": \"OBJECTIVE: To evaluate the complications from surgical treatment using a locking plate among patients with fractures of the proximal extremity of the humerus. METHODS: Between July 2004 and December 2009, 56 patients with fractures of the proximal extremity of the humerus were treated using the PHILOS(®) plate. There were 19 male patients and 37 female patients, with a mean age of 62 years (range: 30 to 92 years). All the cases had a mean postoperative followup period of 12 months. Thirteen fractures were classified as presenting in two parts, 28 as three, eight as four and seven as epiphyseal fractures. RESULTS: Among the patients operated, 26 were considered to have achieved excellent results, twelve good, ten fair and eight poor, according to the UCLA score. Thirty complications occurred in 20 patients (35.7%), among which the most frequent complication was inadequate reduction of the fracture, which occurred in eight cases. Subacromial impact, caused by the plate, occurred in seven cases, while inadequate fixation occurred in six cases. Other complications such as pseudarthrosis, adhesive capsulitis, avascular necrosis, loss of varus reduction and infection were also seen. CONCLUSION: The functional results from treating fractures of the proximal extremity of the humerus using a locking plate depended on correct anatomical reduction of the fracture and stable fixation of the implant. Complications still occur frequently, particularly because of intraoperative technical difficulty, fracture severity and possible inexperience of the surgeon.\",\n \"corpus_id\": 17124313,\n \"score\": 2\n },\n {\n \"doc_id\": \"27079217\",\n \"title\": \"Complications of locked plating for proximal humeral fractures-are we getting any better?\",\n \"abstract\": \"BACKGROUND: Complication rates reported after locking plate fixation of proximal humeral fractures still range up to 40%. Whether modifications of surgical techniques, use of primary shoulder arthroplasty, or a fracture-specific management resulted in decreased complication rates during recent years remains unclear. Therefore, the aim of this long-term observation study was to analyze the incidence of complications and revision surgery after locked plating. METHODS: Between February 2002 and December 2013, 788 patients (aged 67.4 ± 17.3 years) with displaced proximal humeral fractures were treated with locking plate, primary hemiarthroplasty (HA), or reverse shoulder arthroplasty (RSA). Standardized follow-up included radiographs at 1 day, 6 weeks, and 3, 6, and 12 months. Complications and unplanned revision surgery were prospectively recorded over the complete follow-up. RESULTS: Of 788 patients, 646 (82%) were treated with locking plate, 82 (10.4%) with HA, and 60 (7.6%) with RSA. Mean follow-up was 14.8 ± 3.8 months. The mean complication rate associated with locked plating was 12.8%, and revision surgery was necessary in 11.6%. Within the last 5 years, the loss of fixation rate markedly decreased from 14.3% to 4.8%; simultaneously, an increased use of RSA was observed. CONCLUSION: The overall complication rate of locking plate osteosynthesis for proximal humeral fractures has been decreasing considerably within the last years. Among others, this might be due to an increased use of primary RSA for complex fracture types. In addition to a precise surgical technique, choosing the adequate treatment for each individual fracture to avoid complications and revision surgery is of utmost importance.\",\n \"corpus_id\": 27836057,\n \"score\": 2\n },\n {\n \"doc_id\": \"27114810\",\n \"title\": \"Least Possible Fixation Techniques of 4-Part Valgus Impacted Fractures of the Proximal Humerus: A Systematic Review.\",\n \"abstract\": \"UNLABELLED: The valgus-impacted (VI) 4-part fractures are a subset of fractures of the proximal humerus with a unique anatomic configuration characterized by a relatively lower incidence of avascular necrosis after operative intervention. We systematically reviewed clinical studies assessing the benefits and harms of least possible fixation techniques (LPFT) for this unique fracture type. Such information would be potentially helpful in developing an evidence-based approach in the management of these complex injuries. We performed analytic searches of PubMed, Embase, Web of Science, Google Scholar and the Cochrane Library, restricting it to the years 1991-2014. Included studies had to describe outcomes and complications after primary osteosynthesis with any type of LPFT apart from plate-screws and intramedullary nailing. Eligibility criteria were also included English language, more than 5 cases, minimum follow up of one year and report of clinical outcome using at least one relevant score (Constant, Neer or ASES). Based on 292 database hits we identified 12 eligible studies including 190 four-part valgus impacted fractures in 188 patients. All eligible studies were case series composed of min 8 to max 45 patients per study. The gender distribution was 60% (112) female and 40% (76) male. The average age of the patients at the time of injury was 54.5 years. In 8/12 studies an open reduction was used for fracture fixation using different surgical techniques including KW, cerclage wires, cannulated screws and osteosutures. Closed reduction and percutaneous fixation was used in 4 studies. Mean follow-up time ranged from 24 to 69 months. A good functional outcome (constant score >80) was reported in 9/12 studies. The most common complication was avascular necrosis of the humeral head with an overall incidence of 11% (range, 0-26.3%). Total avascular necrosis (AVN) was found in 15/188 patients (7.9%) and was more common in percutaneous techniques and partial AVN in 6/188 (3.1%) being more common in open techniques. The overall re-operation rate was very low (3.7%). Insufficient study designs cannot provide definite treatment recommendations and quantitative data synthesis of outcome. In general, LPFT for 4-part VI fractures leads to satisfactory outcomes with low incidence of complications. A considerable risk of biases can be attributed to fracture classification, proper radiological control, mean age of patients, mixed types of fixation methods, nonage adjusted clinical scoring and small follow up periods. These factors are discussed in detail. LEVEL OF EVIDENCE: systematic review of literature (level IV) as most of the studies were level IV.\",\n \"corpus_id\": 38649590,\n \"score\": 2\n },\n {\n \"doc_id\": \"27504463\",\n \"title\": \"Fibular Strut Graft Augmentation for Open Reduction and Internal Fixation of Proximal Humerus Fractures: A Systematic Review and the Authors' Preferred Surgical Technique.\",\n \"abstract\": \"BACKGROUND: Proximal humerus fractures are common problems plaguing the elderly population. PURPOSE: The purposes of this study were to determine the outcomes of fibular strut allografts in treatment of proximal humerus fractures with open reduction internal fixation (ORIF) and to present the authors' preferred surgical technique. The hypothesis was that the use of fibular strut allografts in treating proximal humerus fractures with ORIF will provide low reoperation rates with acceptable outcomes. STUDY DESIGN: Systematic review; Level of evidence, 4. METHODS: A systematic review was registered with PROSPERO and performed with PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines using 3 publicly available free databases. Therapeutic clinical outcome investigations reporting arthroscopic elbow outcomes with levels of evidence 1 through 4 were eligible for inclusion. All study, subject, and surgical technique demographics were analyzed and compared between continents and countries. Statistics were calculated using Student t tests, 1-way analysis of variance, chi-square tests, and 2-proportion Z tests. RESULTS: Four studies met the inclusion criteria. While there is great heterogeneity existing in the literature surrounding use of a fibular strut allograft as an adjunct to ORIF of proximal humerus fractures, current evidence shows a humeral head screw penetration rate of 3.7% with acceptable functional outcome scores, with a reoperation rate of 4.4% at a weighted mean 80.78 weeks (1.55 years) of postoperative follow-up. CONCLUSION: There is great heterogeneity that exists in the literature surrounding the use of a fibular strut allograft as an adjunct to ORIF of proximal humerus fractures. Current evidence shows a screw penetration rate of 3.7% with acceptable functional outcome scores, demonstrating fibular strut allograft is a viable option for treating proximal humerus fractures.\",\n \"corpus_id\": 7256929,\n \"score\": 2\n },\n {\n \"doc_id\": \"27656515\",\n \"title\": \"Outcome Analysis of Locking Plate Fixation in Proximal Humerus Fracture.\",\n \"abstract\": \"INTRODUCTION: Proximal humerus fractures account for approximately 5% of all fractures. Stable minimally displaced fractures can be treated nonoperatively but the management of displaced fractures remain controversial with various modalities of treatment available. Locking plates provide stable fixation and enable early postoperative mobilization specially in osteoporotic proximal humerus fracture. AIM: To evaluate the functional outcome of locking plate fixation and to compare the results of two approaches used for fixation. MATERIALS AND METHODS: This prospective study was conducted at a tertiary level hospital between September 2011 to December 2013. PHILOS plates were used for internal fixation of displaced proximal humerus fractures Neer's type 2 part, 3 part and 4 part fractures on 26 patients (M/F ratio 1.36:1; mean age 46 years). According to Neer classification, 5,12 and 9 patients had displaced 2, 3 and 4 part fractures respectively. Deltopectoral and deltoid splitting approaches were used for fixation on 13 patients each. Functional outcome was assessed using Constant-Murley shoulder score. Graphpad software version 6.0 was used with Chi-square test and Fisher-exact test are used to compare data. The p-value< 0.05 is considered significant. RESULTS: Of the 26 patients, all fractures united radiologically and clinically and average constant score at final follow-up was 72.5. At the final follow-up 8 patients had good score, 10 patients had moderate score, 6 patients had excellent outcome and 2 patients had poor outcome according to Constant score. Mean time to union was 12.3 weeks (9 -15 weeks). Four complications (15.4%) were encountered, 2 cases of varus malunion, 1 case of wound infection which required wound debridement and 1 case of screw cut-out in which screw removal was done. Mean constant score in delto splitting approach was 70.9 and 74 in deltopectoral group (p-value= 0.54). No significant difference existed in constant score in 2 approaches. No significant difference existed between groups in terms of complications (P > .05) and all fractures were united. CONCLUSION: Our study demonstrates that locking plate fixation gives good functional outcomes in treatment of proximal humerus fractures. There was no significant difference in the two approaches used for exposure. Our results are comparable to various studies conducted by other authors which states that locking plates provide better functional and radiological outcomes as compared to other fixation methods like Tension band wiring, percutaneous K-wire fixation, non-locking plates, intramedullary nails.\",\n \"corpus_id\": 23173609,\n \"score\": 2\n },\n {\n \"doc_id\": \"27818186\",\n \"title\": \"Fixation of 4-part fractures of the proximal humerus: Can we identify radiological criteria that support locking plates or IM nailing? Comparative, retrospective study of 107 cases.\",\n \"abstract\": \"INTRODUCTION: No objective criteria exist to help surgeons choose between IM nailing and plate fixation for 4-part fractures of the proximal humerus. The goal of this study was to identify radiological criteria that would make one technique a better choice than the other. MATERIAL AND METHODS: This was a comparative, multicentre, retrospective study of 54 cases of antegrade nailing and 53 cases of plating performed between 1st January 2009 and 31 December 2011 for 4-part fractures of the proximal humerus. All patients had a minimum radiological and clinical follow-up of 18 months. The functional outcomes were evaluated using the weighted Constant score; a poor result was defined as a weighted Constant score<70%. The following radiological criteria were evaluated during the preoperative assessment and at the last follow-up: initial displacement and reduction of humeral head and tuberosities; morphology of the medial column (i.e. calcar comminution, posteromedial hinge, size of metaphyseal head extension); occurrence of avascular necrosis (AVN). RESULTS: After an average follow-up of 42 months, the weighted Constant scores and rate of poor outcomes were 77% and 48% in the nail group and 81% and 38% in the plate group, respectively (ns). The humeral head was reduced into an anatomical position, valgus or varus in 57%, 30% and 13% of cases in the nail group, and 58%, 29% and 13% in the plate group, respectively. The tuberosities healed in an anatomical position in 72% of nail cases and 70% of plate cases (ns). Only the presence of a medial hinge preoperatively had an effect on the functional outcomes in the nail and plate groups: the weighted Constant scores (P=0.05) and rate of poor outcomes (P=0.02) were 82% and 52% in the nail group and 97% and 9% in the plate group, respectively. The complication rates were comparable: the rates of AVN and articular screw penetration were 17% and 11% in the nail group, and 15% and 11% in the plate group, respectively. The surgical revision rate was 18.5% in the nail group and 30% in the plate group. CONCLUSION: If the medial hinge is preserved, we recommend locking plate fixation. In other cases, either technique can be used as long as the general rules of internal fixation are applied: reduction of the tuberosities, varus correction and stabilization of the calcar area. LEVEL OF EVIDENCE: IV, retrospective study.\",\n \"corpus_id\": 4018387,\n \"score\": 2\n },\n {\n \"doc_id\": \"27866913\",\n \"title\": \"Minimally invasive plate osteosynthesis with PHILOS plate for proximal humerus fractures.\",\n \"abstract\": \"OBJECTIVES: The aim of the present study was to evaluate results, including clinical and radiological outcomes and number of complications, following minimally invasive plate osteosynthesis (MIPO) of proximal humerus fractures, using the PHILOS® proximal humerus internal locking system (Synthes Holding AG, Solothurn, Switzerland). METHODS: Retrospectively evaluated were 31 patients treated with MIPO (12 male, 19 female; average age: 58.4 years). Four patients had 2-part fractures, 14 patients had 3-part fractures, and 13 patients had 4-part fractures, according to Neer classification. Healing, complications, and head-shaft angle (HSA) were radiographically evaluated. Clinical outcomes were assessed at 1-year follow-up with Constant score. RESULTS: Average Constant scores for fractured and normal shoulders were 73.2 ± 10.9 and 84.8 ± 5.1, respectively. Varus progression, fracture type, and age had no significant effect on functional outcome. Average postoperative and follow-up HSA's were 130.80 ± 7.70 and 128.80 ± 10.00, respectively. Significant varus progression was observed during follow-up (p = 0.01). Varus progression was more prominent in patients with postoperative HSA < 130° (p < 0.001). Inferomedial calcar screw usage, fracture type, and age had no significant effect on varus progression. Complications included 2 implant failures, 1 case of avascular necrosis (AVN), 1 primary screw cut-out, 1 axillary nerve injury, and 1 radial nerve injury (22.6% overall). CONCLUSION: MIPO is a safe and effective option for the treatment of proximal humerus fractures, with good functional recovery and fewer complications, which are typically technique dependent. Reduction may be difficult, resulting in varus progression. Another disadvantage is risk of axillary nerve injury. Careful surgical technique and correct implant selection is important in the prevention of nerve injury. LEVEL OF EVIDENCE: Level IV, Therapeutic study.\",\n \"corpus_id\": 44932381,\n \"score\": 2\n },\n {\n \"doc_id\": \"28360490\",\n \"title\": \"Postoperative outcomes of initial varus versus initial valgus proximal humerus fracture: A systematic review and meta-analysis.\",\n \"abstract\": \"OBJECTIVES: Our objective was to perform a systematic review of the literature and conduct a meta-analysis to investigate the effect of initial varus or valgus displacement of proximal humerus on the outcomes of patients with proximal humerus fractures treated with open reduction and internal fixation. METHODS: In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement standards, we performed a systematic review. Electronic databases MEDLINE, EMBASE, CINAHL and the Cochrane Central Register of Controlled Trials (CENTRAL) were searched to identify randomised and non-randomised studies comparing postoperative outcomes associated with initial varus versus initial valgus displacement of proximal humerus fracture. The Newcastle-Ottawa scale was used to assess the methodological quality and risk of bias of the selected studies. Fixed-effect or random-effects models were applied to calculate pooled outcome data. RESULTS: We identified two retrospective cohort studies and one retrospective analysis of a prospective database, enrolling a total of 243 patients with proximal humerus fractures. Our analysis showed that initial varus displacement was associated with a higher risk of overall complication (RR 2.28, 95% CI 1.12-4.64, P = 0.02), screw penetration (RR 2.30, 95% CI 1.06-5.02, P = 0.04), varus displacement (RR 4.38, 95% CI 2.22-8.65, P < 0.0001), and reoperation (RR 3.01, 95% CI 1.80-5.03, P < 0.0001) compared to valgus displacement. There was no significant difference in avascular necrosis (RR 1.43, 95% CI 0.62-3.27, P = 0.40), infection (RR 1.49, 95% CI 0.46-4.84, P = 0.51), and non-union or malunion (RR 1.37, 95% CI 0.37-5.04, P = 0.64). CONCLUSIONS: The best available evidence demonstrates that initial varus displacement of proximal humerus fractures is associated with higher risk of overall complication, screw penetration, varus displacement, and reoperation compared to initial valgus displacement. The best available evidence is not adequately robust to make definitive conclusions. Further high quality studies, that are adequately powered, are required to investigate the outcomes of initial varus and valgus displacement in specific fracture types. LEVEL OF EVIDENCE: Level II.\",\n \"corpus_id\": 23184574,\n \"score\": 2\n },\n {\n \"doc_id\": \"28467336\",\n \"title\": \"Early results for treatment of two- and three-part fractures of the proximal humerus using Contours PHP (proximal humeral plate).\",\n \"abstract\": \"BACKGROUND AND AIM OF THE WORK: The management of displaced 2- and 3-part fractures of the proximal humerus is controversial, both in younger and in elderly patients. The purpose of this paper is to evaluate the functional results of the Contours Proximal Humerus Plate (OrthofixR, Bussolengo,Verona, Italy), for the treatment of displaced 2- and 3-part fractures of the proximal humerus. METHODS: We retrospectively reviewed 55 patients with proximal humerus fractures, who underwent osteosynthesis with Contours Proximal Humerus Plate from December 2011 to March 2015. We had 21 patients with 2-part fractures and with an average age of 67.1 years and 34 patients with 3-part fractures, with average age of 63.6 years. RESULTS: The average union time was 3 months. The mean Constant score was 67 for 2-part fracture group and 64.9 for 3-part fracture group. The difference was not statistically significant (p = 0.18). The overall complication rate was 14.5 %. Six patients underwent additional surgery (10.9%). CONCLUSIONS: The most frequent major complication was secondary loss of reduction following varus collapse of the fracture (2 cases). In these patients, there was loss of medial hinge integrity due to impaction and osteoporosis. The placement of the main locking screw in the calcar area to provide inferomedial support is the rational of the Contours Proximal Humerus Plate. Osteosynthesis with Contours Proximal Humerus Plate is a safe system for treating displaced 2- and 3-part fractures of the proximal humerus, with good functional results and complication rates comparable to those reported in the literature.\",\n \"corpus_id\": 43487,\n \"score\": 2\n },\n {\n \"doc_id\": \"28946902\",\n \"title\": \"Current concepts in locking plate fixation of proximal humerus fractures.\",\n \"abstract\": \"Despite numerous available treatment strategies, the management of complex proximal humeral fractures remains demanding. Impaired bone quality and considerable comorbidities pose special challenges in the growing aging population. Complications after operative treatment are frequent, in particular loss of reduction with varus malalignment and subsequent screw cutout. Locking plate fixation has become a standard in stabilizing these fractures, but surgical revision rates of up to 25% stagnate at high levels. Therefore, it seems of utmost importance to select the right treatment for the right patient. This article provides an overview of available classification systems, indications for operative treatment, important pathoanatomic principles, and latest surgical strategies in locking plate fixation. The importance of correct reduction of the medial cortices, the use of calcar screws, augmentation with bone cement, double-plate fixation, and auxiliary intramedullary bone graft stabilization are discussed in detail.\",\n \"corpus_id\": 8777688,\n \"score\": 2\n },\n {\n \"doc_id\": \"29541270\",\n \"title\": \"Early Results of the A.L.P.S. Proximal Humerus Locking Plate.\",\n \"abstract\": \"Background: Open reduction internal fixation of displaced 3 and 4-part proximal humerus fractures is an effective treatment modality particularly for the younger age group, but it is not without complications. Fixed angled locking screw plates are the mainstay of fixation. The A.L.P.S. Proximal Humerus Plating System is a new implant that has smooth locking pegs in the place of humeral head screws to help reduce glenoid damage in the event of cut-out and is designed to sit low on the humerus in order to reduce the risk of subacromial impingement. Methods: Retrospective analysis of 15 consecutive patients who sustained closed displaced 3-part or 4-part fractures and had fixation surgery using the A.L.P.S. plate. Outcome measures were the time to radiographic and clinical union, Oxford Shoulder Score, quick DASH score and complications. Results: Average follow-up was 31.9 weeks. Union was achieved in 100% of patients with a mean time to union of 15.1 weeks. In terms of function, mean OSS was 33.6 and mean quick DASH was 32.5. There were no instances of AVN. Conclusion: Our preliminary results of 15 patients followed up for a mean of 31.9 weeks show equitable union rates and time to union as well as functional scores compared to other available plating systems. This is the first study to report on this implant to date.\",\n \"corpus_id\": 3865855,\n \"score\": 2\n },\n {\n \"doc_id\": \"22754418\",\n \"title\": \"Evidence for success with locking plates for fragility fractures.\",\n \"abstract\": \"Fixation of fragility fractures with plates and screws often results in loss of fixation and need for revision surgery. Locking plates and screw were introduced to improve fixation of fragility fractures and have been in use for a decade. This review was conducted to compile evidence that locking plates and screws improve fixation of fragility fractures. A search of PubMed was performed to identify biomechanical studies as well as clinical series of fragility fractures treated with locking plates. Biomechanics papers had to use models of osteoporotic bone and had to directly compare locking plates with traditional plates. Clinical studies included case series in which locking plates were applied to elderly patients with fractures of the proximal humerus and periprosthetic distal femur fractures. Most studies are retrospective case series. Locking plates lead to greater stability and higher loads to failure than traditional plates. When applied to proximal humerus fractures, uncomplicated healing occurs in 85% of patients. Constant and Dash scores approach normal values. For distal femoral periprosthetic fractures, union rates of 75% are reported with a malunion rate of 10%. Early evidence suggests that locking plates improve results of treatment of proximal humerus fractures and distal femoral periprosthetic fractures in the elderly. Loss of fixation is associated with failure to achieve stability at the fracture site. Principles of fracture fixation in osteoporotic bone defined prior to the introduction of locking plates should still be applied.\",\n \"corpus_id\": 8773498,\n \"score\": 1\n },\n {\n \"doc_id\": \"26012943\",\n \"title\": \"Biomechanical effect of medial cortical support and medial screw support on locking plate fixation in proximal humeral fractures with a medial gap: a finite element analysis.\",\n \"abstract\": \"OBJECTIVE: This finite element analysis aimed to examine the effect of medial cortical support and medial screw support on loads at the implant-bone interface of locking plate fixation of proximal humeral fractures with a medial gap. METHODS: An intact humerus from a healthy volunteer was used as the basis for a 3-dimensional (3D) computer-aided design (CAD) model. The 3D CAD model of the locking plate system was based on information in the manufacturer's catalogue. The proximal part of the humerus was osteotomized to create standard three-part fractures, which were then divided into a -MSC group (which lacked medial cortical support, and in which fractures with a 5-mm medial bone gap simulated this lack) and +MCS group (which had medial cortical support, and in which fractures with medial cortical-to-cortical contact simulated this). Both fracture groups were respectively fixed with either +MSS (in which medial screw support was simulated by the addition of two calcar screws to the locking plate system), or with -MSS (in which the lack of medial screw support was simulated by absence of the two additional calcar screws to the locking plate system). All the modeling was conducted to represent 90° arm abduction. RESULTS: On the screw-bone interface, medial screw support and medial cortical support decreased maximum shear stress by 17% and 23% respectively. On the locking plate, medial screw support and medial cortical support decreased maximum von Mises stress by 11% and 22% respectively. However, a combination of these two appeared to decrease maximum shear stress by 56% for the screw-bone interface, and maximum von Mises stress by 54% for the locking plate. CONCLUSION: Placement of calcar screws combined with good medial cortical contact in varus in locking plate fixation of proximal humeral fractures with a medial gap may provide optimal stability for the fixation.\",\n \"corpus_id\": 35922538,\n \"score\": 1\n },\n {\n \"doc_id\": \"26165257\",\n \"title\": \"Geometry of Proximal Humerus Locking Plates.\",\n \"abstract\": \"OBJECTIVES: Proximal humerus fractures are commonly treated with open reduction and internal fixation with periarticular locking plates. This study compared the geometry of proximal humerus locking plate's screw distribution, amount of bone-screw interface, and the volume the screws occupy within the humeral head, as well as how leaving the screws short of the articular surface affects these measures. METHODS: Locking plates from 7 manufacturers were applied to foam humerus models. The entry and exit hole of each screw trajectory was digitized using a 3-dimensional motion tracking system. A trajectory for each screw was modeled, as well as the volume enclosed by the screw trajectories. The following outcome metrics were calculated: the bone-screw interface, the volume enclosed by the screws, and the effect of leaving the screws short of the articular surface. RESULTS: Biomet had the most bone-screw interface (7259 mm), whereas Zimmer had the least (3982 mm). The original Synthes plate had the largest screw volume, occupying 31.5% of the humeral head, whereas Smith & Nephew and Zimmer had the lowest volumes, occupying 21.2% and 12.6%, respectively. Leaving the screws 15 mm short of the articular surface resulted in the most reduction in volume for the Depuy plate (50%) and the least reduction for the new version of the Synthes plate (29%). CONCLUSIONS: Many different manufactured periarticular locking plates exist to stabilize a proximal humeral fracture. Clinicians need to be familiar with the different plate configurations, screw lengths, and trajectories, which affect potential biomechanical performance and can optimize fracture site maintenance.\",\n \"corpus_id\": 25751172,\n \"score\": 1\n },\n {\n \"doc_id\": \"26631205\",\n \"title\": \"Management of Proximal Humerus Fractures with the Equinoxe Locking Plate System.\",\n \"abstract\": \"There is no consensus on surgical fixation and treatment of proximal humerus fractures, even though they are common fractures with several fixation techniques. This retrospective study quantifies the outcomes of patients who sustained a proximal humerus fracture and were treated with open re - duction and internal fixation by at a single academic center between December 2010 and December 2014 using the Equi - noxe ® proximal humerus locking plate. Following enrollment, injury and surgical data was recorded. Forty-nine patients (31 female, 18 male) with 50 fractures were identified who met the inclusion criteria. Mean follow-up period was 16.8 months (range: 6 to 44 months). Mean age was 60.7 years with no significant difference in mean age by gender. Mean age-adjusted Charlson Comorbidity Index (CCI) was 2.9 (range: 0 to 6). The overall complication rate was 10% (N = 5) with the most common complication being osteonecrosis (N = 3). Four patients required reoperation. At final follow- up, mean active forward flexion for the cohort was 140.8º ± 30.1º, mean passive forward flexion was 155.7º ± 25.2º, and mean active external rotation was 50.1º ± 17.9º. For patients with postoperative complications, mean active forward flexion was 106.0º ± 23.0º, mean passive forward flexion was 136.7º ± 23.1º, and mean active external rotation was 34.2º ± 24.4. Active forward flexion and external rotation were significantly different in the presence of a complication (p = 0.005 and p = 0.038, respectively). Mean DASH score for the cohort was 19.1 ± 20.9. Mean DASH score for patients who developed complications or underwent reoperations was 34.2 ± 24.3. This study demonstrates that the Equinoxe ® proximal humerus locking plate provides stable fracture treatment with excellent clinical results and a low complication rate when performed by experienced orthopaedic traumatologists.\",\n \"corpus_id\": 43409475,\n \"score\": 1\n },\n {\n \"doc_id\": \"27793135\",\n \"title\": \"Operative treatment of 2-part surgical neck fractures of the proximal humerus (AO 11-A3) in the elderly: Cement augmented locking plate Philos™ vs. proximal humerus nail MultiLoc®.\",\n \"abstract\": \"BACKGROUND: Proximal humeral fractures are with an incidence of 4-5 % the third most common fractures in the elderly. In 20 % of humeral fractures there is an indication for surgical treatment according to the modified Neer-Criteria. A secondary varus dislocation of the head fragment and cutting-out are the most common complications of angle stable locking plates in AO11-A3 fractures of the elderly. One possibility to increase the stability of the screw-bone-interface is the cement augmentation of the screw tips. A second is the use of a multiplanar angle stablentramedullary nail that might provide better biomechanical properties after fixation of 2-part-fractures. A comparison of these two treatment options augmented locking plate versus multiplanar angle stable locking nail in 2-part surgical neck fractures of the proximal humerus has not been carried out up to now. METHODS/DESIGN: Forty patients (female/male, ≥60 years or female postmenopausal) with a 2-part-fracture of the proximal humerus (AO type 11-A3) will be randomized to either to augmented plate fixation group (PhilosAugment) or to multiplanar intramedullary nail group (MultiLoc). Outcome parameters are Disabilities of the Shoulder, Arm and Hand-Score (DASH) Constant Score (CS), American Shoulder and Elbow Score (ASES), Oxford Shoulder Score (OSS), Range of motion (ROM) and Short Form 36 (SF-36) after 3 weeks, 6 weeks, 3 months, 6 months, 12 and 24 months. DISCUSSION: Because of the lack of clinical studies that compare cement augmented locking plates with multiplanar humeral nail systems after 2-part surgical neck fractures of the proximal humerus, the decision of surgical method currently depends only on surgeons preference. Because only a randomized clinical trial (RCT) can sufficiently answer the question if one treatment option provides advantages compared to the other method we are planning to perform a RCT. TRIAL REGISTRATION: Clinical Trial ( NCT02609906 ), November 18, 2015, registered retrospectively.\",\n \"corpus_id\": 662829,\n \"score\": 1\n },\n {\n \"doc_id\": \"18310691\",\n \"title\": \"Results of polyaxial locked-plate fixation of periarticular fractures of the knee. Surgical technique.\",\n \"abstract\": \"BACKGROUND: Locked-plate fracture-fixation techniques and designs continue to evolve. Polyaxial locking plates that allow screw angulation and end-point locking have become available; however, there are no clinical data documenting their strength and efficacy, to our knowledge. The purpose of this study was to evaluate the clinical performance of a variable-axis locking plate in a multicenter series of periarticular fractures about the knee. METHODS: Between 2003 and 2005, fifty-four patients with a total of fifty-six fractures were treated with a polyaxial locked-plate fixation system (DePuy, Warsaw, Indiana). There were twenty male patients and thirty-four female patients with a mean age of fifty-seven years. There were twenty-five distal femoral fractures and thirty-one proximal tibial fractures. Twelve of the fractures were open. Clinical and radiographic data, including changes in alignment, hardware breakage, or other mechanical complications of the device, were retrospectively reviewed. Function was assessed with use of the Knee Society scores. One patient with a bilateral fracture died less than three months postoperatively, and two patients were lost to follow-up prior to union. Fifty-two fractures in fifty-one patients were followed to union or for a minimum of six months; the mean duration of follow-up was nine months (range, six to twenty-five months). RESULTS: Forty-nine (94%) of the fifty-two fractures united. There were no mechanical complications. Most importantly, there was no evidence of varus collapse as a result of polyaxial screw failure. There were three deep infections and one aseptic nonunion. No plate fractured, and no screw cut out. CONCLUSIONS: The variable-axis locking plates performed well, with a high rate of fracture union and no evidence of varus collapse due to failure of the polyaxial screw fixation, in a series of complex fractures about the knee. Complication rates were similar to those for historical controls treated with fixed-trajectory locking plates. Polyaxial locking plates offer more fixation versatility without an apparent increase in mechanical complications or loss of reduction.\",\n \"corpus_id\": 207281072,\n \"score\": 0\n },\n {\n \"doc_id\": \"24262583\",\n \"title\": \"Complications following volar locking plate fixation for distal radial fractures: a systematic review.\",\n \"abstract\": \"The purpose of this systematic review is to assess the prevalence of complications following volar locking plate fixation of distal radial fractures. A computer-based search was carried out using EMBASE and PUBMED/MEDLINE. Only prospective comparative and prospective cohort studies that presented data concerning complications after treatment of distal radial fractures with a volar locking plate in human adults with a minimal follow-up of 6 months were included. Two quality assessment tools were used to assess the methodological quality of the studies (level of evidence rating according to the Oxford Centre of Evidence Based Medicine and the modified version of the Cochrane Bone, Joint and Muscle Trauma Group's former quality assessment tool). Thirty three studies were eligible for final assessment. Most complications were problems with nerve and tendon function as well as complex regional pain syndrome. With an overall complication rate of 16.5%, most of which were 'minor' complications and low rates of nonunion and malunion, volar locking plate fixation can be considered a reasonably safe treatment option for patients with distal radial fractures.\",\n \"corpus_id\": 23146646,\n \"score\": 0\n },\n {\n \"doc_id\": \"27144821\",\n \"title\": \"Unstable Proximal Femur Fractures Treated With Proximal Femoral Locking Plates: A Retrospective, Multicenter Study of 111 Cases.\",\n \"abstract\": \"OBJECTIVES: A few small case series have found that proximal femur fractures treated with a proximal femur locking plate (PFLP) have experienced more failures than expected. The purpose of this study was to review the clinical results of patients with acute, unstable proximal femur fractures treated with proximal femoral locking plates in a large, multicenter patient cohort. DESIGN: This is a retrospective clinical study. SETTING: The study included patients from 12 regional trauma centers and tertiary referral hospitals. PATIENTS: One hundred eleven consecutive patients with unstable proximal femur fractures stabilized with a PFLP and having required clinical and radiographic follow-up at a minimum of 12 months after injury. INTERVENTION: Surgical repair of an unstable proximal femur fracture with a PFLP. MAIN OUTCOME MEASUREMENTS: Treatment failures (failure of fixation, nonunion, and malunion) and need for revision surgery. RESULTS: Forty-six patients (41.4%) experienced a major treatment failure, including failed fixation with or without nonunion (39), surgical malalignment or malunion (18), deep infection (8), or a combination of these. Thirty-eight (34%) patients underwent secondary surgeries, including 30 for failed fixation, nonunion, or both. Treatment failure was found to occur at a significantly higher rate in patients with major comorbidities, in femurs repaired in varus malalignment, and using specific plate designs. CONCLUSIONS: Proximal femoral locking plates are associated with a high complication rate, frequently requiring revision or secondary surgeries in the treatment of unstable proximal femur fractures. Given the high complication rate with PFLPs, careful attention to reduction, use of a PFLP implant, and consideration should be given to alternative implants or fixation techniques when appropriate. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.\",\n \"corpus_id\": 8259027,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":69,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"10097113\",\n \"title\": \"Deletion of the loop region of Bcl-2 completely blocks paclitaxel-induced apoptosis.\",\n \"abstract\": \"At high concentrations, the tubule poison paclitaxel is able to kill cancer cells that express Bcl-2; it inhibits the antiapoptotic activity of Bcl-2 by inducing its phosphorylation. To localize the site on Bcl-2 regulated by phosphorylation, mutant forms of Bcl-2 were constructed. Mutant forms of Bcl-2 with an alteration in serine at amino acid 70 (S70A) or with deletion of a 60-aa loop region between the alpha1 and alpha2 helices (Deltaloop Bcl-2, which also deletes amino acid 70) were unable to be phosphorylated by paclitaxel treatment of MDA-MB-231 cells into which the genes for the mutant proteins were transfected. The Deltaloop mutant completely inhibited paclitaxel-induced apoptosis. In cells expressing the S70A mutant, paclitaxel induced about one-third the level of apoptosis seen with wild-type Bcl-2. To evaluate the role of mitogen-activated protein kinases (MAPKs) in Bcl-2 phosphorylation, the activation of c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK), and p38 was examined. Paclitaxel-induced apoptosis was associated with phosphorylation of Bcl-2 and activation of ERK and JNK MAPKs. If JNK activation was blocked by transfections with either a stress-activated protein kinase kinase dominant-negative (K-->R) gene (which prevents the activation of a kinase upstream of JNK) or MAPK phosphatase-1 gene (which dephosphorylates and inactivates JNK), Bcl-2 phosphorylation did not occur, and the cells were not killed by paclitaxel. By contrast, neither an ERK inhibitor (PD098059) nor p38 inhibitors (SB203580 and SB202190) had an effect on Bcl-2 phosphorylation. Thus, our data show that the antiapoptotic effects of Bcl-2 can be overcome by phosphorylation of Ser-70; forms of Bcl-2 lacking the loop region are much more effective at preventing apoptosis than wild-type Bcl-2 because they cannot be phosphorylated. JNK, but not ERK or p38 MAPK, appear to be involved in the phosphorylation of Bcl-2 induced by paclitaxel.\",\n \"corpus_id\": 21952950\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18201741","title":"The contribution of c-Jun N-terminal kinase activation and subsequent Bcl-2 phosphorylation to apoptosis induction in human B-cells is dependent on the mode of action of specific stresses.","abstract":"The c-Jun N-terminal kinase (JNK) pathway can play paradoxical roles as either a pro-survival or a pro-cell death pathway depending on type of stress and cell type. The goal of the present study was to determine the role of JNK pathway signaling for regulating B-cell apoptosis in two important but contrasting situations--global proteotoxic damage, induced by arsenite and hyperthermia, versus specific microtubule inhibition, induced by the anti-cancer drug vincristine, using the EW36 B-cell line. This cell line over-expresses the Bcl-2 protein and is a useful model to identify treatments that can overcome multi-drug resistance in lymphoid cells. Exposure of EW36 B-cells to arsenite or lethal hyperthermia resulted in activation of the JNK pathway and induction of apoptosis. However, pharmacological inhibition of the JNK pathway did not inhibit apoptosis, indicating that JNK pathway activation is not required for apoptosis induction by these treatments. In contrast, vincristine treatment of EW36 B-cells resulted in JNK activation and apoptosis that was suppressed by JNK inhibition. A critical difference between the two types of stress treatments was that only vincristine-induced JNK activation resulted in phosphorylation of Bcl-2 at threonine-56, a modification that can block its anti-apoptotic function. Importantly, Bcl-2 phosphorylation was attenuated by JNK inhibition implicating JNK as the upstream kinase. Furthermore, arsenite and hyperthermia treatments activated a p53/p21 pathway associated with apoptosis induction, whereas vincristine did not activate this pathway. These results reveal two stress-activated pathways, one JNK-dependent and another JNK-independent, either of which can bypass Bcl-2 mediated resistance, resulting in cell death.","corpus_id":19271563,"score":2},{"doc_id":"18412143","title":"The role of p38 MAPK and JNK in Arsenic trioxide-induced mitochondrial cell death in human cervical cancer cells.","abstract":"Previously, we have shown that the release of AIF from mitochondria is required for As2O3-induced cell death in human cervical cancer cells, and that reactive oxygen species (ROS) is necessary for AIF release from mitochondria. In this study, we further investigated the role of MAPKs in ROS-mediated mitochondrial apoptotic cell death triggered by As2O3. As2O3-induced apoptotic cell death in HeLa cells was associated with activation and mitochondrial translocation of Bax, a marked phosphorylation of Bcl-2, reduction of Bcl-2 and Bax interaction, dissipation of mitochondrial membrane potential. Using small interfering RNA, reduced Bax expression effectively attenuated As2O3-induced mitochondrial membrane potential loss and apoptotic cell death. Moreover, the phosphorylation of Bcl-2 induced by As2O3 diminished its ability to bind to Bax. Treatment of cells with As2O3 activated both the p38 MAPK and JNK pathways. Mitochondrial translocation of Bax was completely suppressed in the presence of p38 MAPK inhibitor PD169316 or si-p38 MAPK. The As2O3-induced Bcl-2 phosphorylation was attenuated largely by JNK inhibition using SP600125 or si-JNK and to some extent by p38 MAPK inhibition with PD169316 or si-p38 MAPK. In addition, N-acetyl-L-cystein (NAC), a thiol-containing anti-oxidant, completely blocked As2O3-induced p38 MAPK and JNK activations, mitochondria translocation of Bax, and phosphorylation of Bcl-2. These results support a notion that ROS-mediated activations of p38 MAPK and JNK in response to As2O3 treatment signals activation of Bax and phosphorylation of Bcl-2, resulting in mitochondrial apoptotic cell death in human cervical cancer cells.","corpus_id":25492988,"score":2},{"doc_id":"18534198","title":"Requirement of the JNK-associated Bcl-2 pathway for human lactoferrin-induced apoptosis in the Jurkat leukemia T cell line.","abstract":"The cell proliferation of p53-deficient Jurkat T cells is controlled after prolonged exposure to human lactoferrin (Lf). However, the molecular mechanism by which Lf influences these cellular responses remains unclear. In this study, we demonstrate that Lf-induced apoptosis in Jurkat T cells occurs in a dose- and time-dependent manner via the regulation of c-Jun N-terminal kinase (JNK) activity. Jurkat cells exposed to Lf for 1 day, especially at concentrations in excess of 500 microg/ml, showed typical apoptosis, as indicated by decreased cell viability and increased Annexin V binding. Our results also showed that Lf induced the activation of caspase 9 and caspase 3 activation, as demonstrated by our detection of cleaved caspases and PARP. Lf-induced apoptosis did not influence Bcl-2 expression via an ERK1/2 phosphorylation pathway, but was rather associated with the level of Bcl-2 phosphorylation. The treatment of cells with the specific JNK inhibitor SP600125, but not the p38 MAPK inhibitor SB203580, revealed that the JNK-Bcl-2 signaling cascade is required for Lf-induced apoptosis. When JNK activation was abolished by SP600125, no Bcl-2 phosphorylation was detected, and the Lf-treated Jurkat cells did not undergo cell death. These findings indicate that Lf functions as a biological mediator of apoptosis in the human leukemia Jurkat T-cell line, via the JNK-associated Bcl-2 signaling pathway.","corpus_id":205994478,"score":2},{"doc_id":"22262057","title":"Inactivation of Bcl-2 through IκB kinase (IKK)-dependent phosphorylation mediates apoptosis upon exposure to 4-hydroxynonenal (HNE).","abstract":"Apoptosis of macrophage foam cells loaded with modified/oxidized lipids is implicated in destabilization of advanced atherosclerotic plaques in humans. Concentration of HNE, main aldehydic product of plasma LDL peroxidation, elevates in atherosclerotic lesions as well as in cultured cells under oxidative stress. Although this reactive aldehyde has been shown to promote apoptosis with the involvement of p38 MAPK and JNK in various mammalian cell lines, roles of B-cell lymphoma 2 (Bcl-2) family proteins remain to be deciphered. We demonstrated that HNE-induced apoptosis was accompanied by concurrent downregulations of antiapoptotic Bcl-x(L) and Mcl-1 as well as upregulation of proapoptotic Bak. Furthermore, phoshorylation of Bcl-2 at Thr56, Ser70, and probably more phosphorylation sites located on N-terminal loop domain associated with HNE-induced apoptosis in both U937 and HeLa cells while ectopic expression of a phospho-defective Bcl-2 mutant significantly attenuated apoptosis. In parallel to this, HNE treatment caused release of proapoptotic Bax from Bcl-2. Pharmacological inhbition of IKK inhibited HNE-induced Bcl-2 phosphorylation. Similarly, silencing IKKα and -β both ended up with abrogation of Bcl-2 phosphorylation along with attenuation of apoptosis. Moreover, both IKKα and -β coimmunoprecipitated with Bcl-2 and in vitro kinase assay proved the ability of IKK to phosphorylate Bcl-2. In view of these findings and considering HNE inhibits DNA-binding activity of nuclear factor-κB (NF-κB) through prevention of IκB phosphorylation/ubiquitination/proteolysis, IKK appears to directly interfere with Bcl-2 activity through phosphorylation in HNE-mediated apoptosis independent of NF-κB signaling.","corpus_id":19923494,"score":2},{"doc_id":"22433870","title":"Tyrosine-phosphorylated caveolin-1 (Tyr-14) increases sensitivity to paclitaxel by inhibiting BCL2 and BCLxL proteins via c-Jun N-terminal kinase (JNK).","abstract":"Paclitaxel, an anti-microtubule agent, is an effective chemotherapeutic drug in breast cancer. Nonetheless, resistance to paclitaxel remains a major clinical challenge. The need to better understand the resistant phenotype and to find biomarkers that could predict tumor response to paclitaxel is evident. In estrogen receptor α-positive (ER(+)) breast cancer cells, phosphorylation of caveolin-1 (CAV1) on Tyr-14 facilitates mitochondrial apoptosis by increasing BCL2 phosphorylation in response to low dose paclitaxel (10 nM). However, two variants of CAV1 exist: the full-length form, CAV1α (wild-type CAV1 or wtCAV1), and a truncated form, CAV1β. Only wtCAV1 has the Tyr-14 region at the N terminus. The precise cellular functions of CAV1 variants are unknown. We now show that CAV1 variants play distinct roles in paclitaxel-mediated cell death/survival. CAV1β expression is increased in paclitaxel-resistant cells when compared with sensitive cells. Expression of CAV1β in sensitive cells significantly reduces their responsiveness to paclitaxel. These activities reflect an essential role for Tyr-14 phosphorylation because wtCAV1 expression, but not a phosphorylation-deficient mutant (Y14F), inactivates BCL2 and BCLxL through activation of c-Jun N-terminal kinase (JNK). MCF-7 cells that express Y14F are resistant to paclitaxel and are resensitized by co-treatment with ABT-737, a BH3-mimetic small molecule inhibitor. Using structural homology modeling, we propose that phosphorylation on Tyr-14 enables a favorable conformation for proteins to bind to the CAV1 scaffolding domain. Thus, we highlight novel roles for CAV1 variants in cell death; wtCAV1 promotes cell death, whereas CAV1β promotes cell survival by preventing inactivation of BCL2 and BCLxL via JNK in paclitaxel-mediated apoptosis.","corpus_id":25431731,"score":2},{"doc_id":"22953963","title":"Acanthoic acid induces cell apoptosis through activation of the p38 MAPK pathway in HL-60 human promyelocytic leukaemia.","abstract":"The present study was designed to evaluate the molecular mechanisms of the action of acanthoic acid (ACAN) from Acanthopanax koreanum (Araliaceae) against HL-60 human promyelocytic leukaemia cells. ACAN reduced the proliferation of HL-60 cells in a dose- and time-dependent manner accompanied by the induction of apoptosis. Possible mechanisms of ACAN-induced apoptosis were also examined. The results showed that ACAN-induced the phosphorylation of members of the mitogen-activated protein kinase (MAPK) family, c-Jun N-terminal kinase (JNK), p38 MAPK (p38), and extracellular signal-regulated kinase (ERK). A specific p38 MAPK inhibitor (SB203580) significantly blocked ACAN-induced apoptosis and cell viability, whereas an ERK inhibitor (PD98059) and JNK inhibitor (SP600125) had no effect. Moreover, ACAN induced the cleavage of caspase-3 and poly-ADP-ribose polymerase (PARP), and decreased the level of Bcl-xL, but these effects were inhibited by SB203580 pre-treatment. These results strongly suggest that ACAN may have cancer chemopreventive and therapeutic potential, due to its ability to activate the p38 MAPK-mediated signalling pathways.","corpus_id":22731309,"score":2},{"doc_id":"23272207","title":"The natively disordered loop of Bcl-2 undergoes phosphorylation-dependent conformational change and interacts with Pin1.","abstract":"Bcl-2 plays a central role in the regulation of apoptosis. Structural studies of Bcl-2 revealed the presence of a flexible and natively disordered loop that bridges the Bcl-2 homology motifs, BH3 and BH4. This loop is phosphorylated on multiple sites in response to a variety of external stimuli, including the microtubule-targeting drugs, paclitaxel and colchicine. Currently, the underlying molecular mechanism of Bcl-2 phosphorylation and its biological significance remain elusive. In this study, we investigated the molecular characteristics of this anti-apoptotic protein. To this end, we generated synthetic peptides derived from the Bcl-2 loop, and multiple Bcl-2 loop truncation mutants that include the phosphorylation sites. Our results demonstrate that S87 in the flexible loop of Bcl-2 is the primary phosphorylation site for JNK and ERK2, suggesting some sequence or structural specificity for the phosphorylation by these kinases. Our NMR studies and molecular dynamics simulation studies support indicate that phosphorylation of S87 induces a conformational change in the peptide. Finally, we show that the phosphorylated peptides of the Bcl-2 loop can bind Pin1, further substantiating the phosphorylation-mediated conformation change of Bcl-2.","corpus_id":14581799,"score":2},{"doc_id":"23415863","title":"Paclitaxel attenuates Bcl-2 resistance to apoptosis in breast cancer cells through an endoplasmic reticulum-mediated calcium release in a dosage dependent manner.","abstract":"To address the controversy regarding efficacy of paclitaxel in the presence of the anti-apoptotic protein Bcl-2, we investigated calcium stored in the endoplasmic reticulum as a potential factor. Our results showed that the ER calcium store is a common target for both paclitaxel and Bcl-2 protein. Paclitaxel directly associates with the endoplasmic reticulum to stimulate the release of calcium into the cytosol, contributing to the induction of apoptosis. However, Bcl-2 expression suppresses the cell's pro-apoptotic response of endoplasmic reticulum calcium release, thus inhibiting susceptibility of cancer cells to undergo apoptosis. Depending upon dosage, a paclitaxel-induced stimulatory effect can overcome the Bcl-2-mediated inhibitory effect on endoplasmic reticulum calcium release, thus attenuating the resistance of Bcl-2 to apoptosis. Our finding is the first to demonstrate that endoplasmic reticulum calcium plays a key role in the efficacy of paclitaxel in the presence of Bcl-2, thus providing insight into the complex but crucial paclitaxel-calcium-Bcl-2 relationship, which may impact breast cancer treatment.","corpus_id":2719810,"score":2},{"doc_id":"25815462","title":"Apoptosis of HL-60 human leukemia cells induced by Asiatic acid through modulation of B-cell lymphoma 2 family proteins and the mitogen-activated protein kinase signaling pathway.","abstract":"The toxicities of conventional chemotherapeutic agents to normal cells restrict their dosage and clinical efficacy in acute leukemia; therefore, it is important to develop novel chemotherapeutics, including natural products, which selectively target cancer-specific pathways. The present study aimed to explore the effect of the chemopreventive agent asiatic acid (AA) on the proliferation and apoptotic rate of the leukemia cell line HL-60 and investigated the mechanisms underlying its anti-tumor activity. The effect of AA on the proliferation of HL-60 cells was evaluated using the MTT assay. Annexin V-fluorescein isothiocyanate/propidium iodide double staining followed by flow cytometric analysis as well as Hoechst 33258 staining were used to analyze the apoptotic rate of the cells. Furthermore, changes of survivin, B-cell lymphoma 2 (Bcl-2), myeloid cell leukemia 1 (Mcl-1), extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK) and p38 expressions were detected by western blot analysis. AA blocked the growth of HL-60 cells in a dose- and time-dependent manner. The IC50-value of AA on HL-60 cells was 46.67 ± 5.08 µmol/l for 24 h. AA induced apoptosis in a dose-dependent manner, which was inhibited in the presence of Z-DEVD-FMK, a specific inhibitor of caspase. The anti-apoptotic proteins Bcl-2, Mcl-1 and survivin were downregulated by AA in a dose-dependent manner. Concurrently, AA inhibited ERK and p38 phosphorylation in a dose-dependent manner, while JNK phosphorylation was not affected. In conclusion, the present study indicated that the p38 and ERK pathways, as well as modulation of Bcl-2 family and survivin proteins were key regulators of apoptosis induced in HL-60 cells in response to AA.","corpus_id":14178799,"score":2},{"doc_id":"25876659","title":"Dominant negative form of alpha4 inhibits the BCR crosslinking-induced phosphorylation of Bcl-xL and apoptosis in an immature B cell line WEHI-231.","abstract":"We previously demonstrated that c-Jun N-terminal kinase (JNK) phosphorylates serine 62 of Bcl-xL to induce the degradation of Bcl-xL and apoptosis in WEHI-231 cells upon BCR crosslinking. In order to elucidate the regulatory mechanisms underlying the phosphorylation of Bcl-xL, we prepared an assay system in which JNK phosphorylated Bcl-xL in HEK293T cells. Consequently, we found that a signal transduction molecule, alpha4, enhanced the phosphorylation of Bcl-xL by JNK, while the co-expression of C-terminal alpha4 (220-340) diminished the phosphorylation of Bcl-xL induced by JNK. Furthermore, full-length alpha4 associated with both JNK and Bcl-xL, whereas C-terminal alpha4 (220-340) associated only with Bcl-xL, not JNK. In addition, WEHI-231 cells transfected with the cDNA of C-terminal alpha4 (220-340) exhibited decreased phosphorylation of Bcl-xL and stronger resistance to apoptosis induced by BCR crosslinking. These results indicate that alpha4 is an important regulatory molecule of apoptosis induced by BCR crosslinking in WEHI-231 cells and that C-terminal alpha4 (220-340) functions as a dominant negative form.","corpus_id":24270214,"score":2},{"doc_id":"28731137","title":"Phosphorylation of Bcl-2 plays an important role in glycochenodeoxycholate-induced survival and chemoresistance in HCC.","abstract":"Hepatocellular carcinoma (HCC) is a highly malignant tumor and can evolve rapidly to resistance to chemotherapies. Glycochenodeoxycholate (GCDA), which is toxic and hydrophobic, is the main ingredient in the bile and associated with carcinogenesis of gastrointenstinal tumors. Bcl-2 is the most important anti-apoptotic protein and overexpressed in various human tumors. In the present study, we found that GCDA can induce the chemoresistance of human liver cancer cells and specific depletion of Bcl-2 by RNA interference blocks GCDA-stimulated chemoresistance, which indicate the pivotal role of Bcl-2 in such process. Mechanistically, GCDA simultaneously stimulates phosphorylation of Bcl-2 at Ser70 site and activates extracellular signal-regulated kinase 1/2 (ERK1/2), and inhibition of ERK1/2 by PD98059 (MAPK/ERK1/2 inhibitor) or siRNA (targeting ERK1/2) suppresses GCDA-stimulated phosphorylation of Bcl-2 and significantly attenuates the survival and chemoresistance induced by GCDA in liver cancer cells. Thus, GCDA-induced survival and chemoresistance of liver cancer cells may occur through activation of Bcl-2 by phosphorylation at Ser70 site through MAPK/ERK1/2 pathway, which may contribute to the development of human liver cancer and chemoresistance.","corpus_id":22610268,"score":2},{"doc_id":"18021293","title":"MAPK and mTOR pathways are involved in cadmium-induced neuronal apoptosis.","abstract":"Cadmium (Cd) may be accumulated in human body through long-term exposure to Cd-polluted environment, resulting in neurodegeneration and other diseases. To study the mechanism of Cd-induced neurodegeneration, PC12 and SH-SY5Y cells were exposed to Cd. We observed that Cd-induced apoptosis in the cells in a time- and concentration-dependent manner. Cd rapidly activated the mitogen-activated protein kinases (MAPK) including extracellular signal-regulated kinase 1/2 (Erk1/2), c-Jun N-terminal kinase (JNK) and p38. Inhibition of Erk1/2 and JNK, but not p38, partially protected the cells from Cd-induced apoptosis. Consistently, over-expression of dominant negative c-Jun or down-regulation of Erk1/2, but not p38 MAPK, partially prevented Cd-induced apoptosis. To our surprise, Cd also activated mammalian target of rapamycin (mTOR)-mediated signaling pathways. Treatment with rapamycin, an mTOR inhibitor, blocked Cd-induced phosphorylation of S6K1 and eukaryotic initiation factor 4E binding protein 1, and markedly inhibited Cd-induced apoptosis. Down-regulation of mTOR by RNA interference also in part, rescued cells from Cd-induced death. These findings indicate that activation of the signaling network of MAPK and mTOR is associated with Cd-induced neuronal apoptosis. Our results strongly suggest that inhibitors of MAPK and mTOR may have a potential for prevention of Cd-induced neurodegeneration.","corpus_id":10910517,"score":1},{"doc_id":"18049903","title":"Acetylcholine inhibits long-term hypoxia-induced apoptosis by suppressing the oxidative stress-mediated MAPKs activation as well as regulation of Bcl-2, c-IAPs, and caspase-3 in mouse embryonic stem cells.","abstract":"This study examined the effect of acetylcholine (ACh) on the hypoxia-induced apoptosis of mouse embryonic stem (ES) cells. Hypoxia (60 h) decreased both the cell viability and level of [3H] thymidine incorporation, which were prevented by a pretreatment with ACh. However, the atropine (ACh receptor [AChR] inhibitor) treatment blocked the protective effect of ACh. Hypoxia (90 min) increased the intracellular level of reactive oxygen species (ROS). On the other hand, ACh inhibited the hypoxia-induced increase in ROS, which was blocked by an atropine treatment. Subsequently, the hypoxia-induced ROS increased the level of p38 mitogen activated protein kinase (MAPK) and Jun-N-terminal kinase (JNK) phosphorylation, which were inhibited by the ACh pretreatment. Moreover, hypoxic exposure (90 min) increased the level of nuclear factor-kappa B (NF-kappa B) phosphorylation, which was blocked by a pretreatment with SB 203580 (p38 MAPK inhibitor) or SP 600125 (JNK inhibitor). However, hypoxia (60 h) decreased the protein levels of Bcl-2 and c-IAPs (cellular inhibitor of apoptosis proteins) but increased the level of caspase-3 activation. All these effects were inhibited by a pretreatment with ACh. In conclusion, ACh prevented the hypoxia-induced apoptosis of mouse ES cells by inhibiting the ROS-mediated p38 MAPK and JNK activation as well as the regulation of Bcl-2, c-IAPs, and caspase-3.","corpus_id":1706453,"score":1},{"doc_id":"18059338","title":"p38 MAPK plays an essential role in apoptosis induced by photoactivation of a novel ethylene glycol porphyrin derivative.","abstract":"In this study, we provide evidence that photostimulation of various cancer cells preloaded with a new photosensitizing compound, tetrakis-meso-(4-ethyleneglycol-2,3,5,6-tetrafluorophenyl) porphyrin (PORF-TEG), results in rapid activation of the cell death machinery. PORF-TEG, although primarily localized in lysosomes, induces mitochondria-driven apoptosis. The induction of apoptosis is accompanied by immediate and sustained activation of p38 mitogen-activated protein kinase (MAPK) and transient activation of c-Jun N-terminal kinase (JNK). Conversely, the inhibition of p38 by PD 169316 or SB202190 and by the p38alpha dominant-negative mutant as well as the deletion of the p38alpha gene (MEFs-KO) protected cells from apoptosis, whereas inhibition of JNK did not. Activation of the p38 signaling pathway occurs upstream of caspase activation. In addition, preincubation of cells with scavengers of reactive oxygen species attenuated p38 and caspase activation and increased cell survival, thus connecting reactive oxygen species formation with the activation of the p38 pathway. Later events included degradation of Bcl-2, activation of tBid, and cleavage of Bad and Mcl-1. The data suggest a key role for p38 MAPK in PORF-TEG-photoinduced apoptosis.","corpus_id":12329087,"score":1},{"doc_id":"18222647","title":"Activation of c-Jun N-terminal kinase (JNK) by widely used specific p38 MAPK inhibitors SB202190 and SB203580: a MLK-3-MKK7-dependent mechanism.","abstract":"Mitogen-activated protein kinases (MAPKs) are key signaling molecules that respond to mitogenic stimulation or environmental stress, resulting in the expression of target proteins. c-Jun N-terminal kinase (JNK) and p38 MAPKs are activated by inflammatory cytokines or environmental stress. Specific p38 MAPK inhibitors, such as SB202190 or SB203580, are widely used to dissect p38 MAPK-related signal transduction mechanisms. While using SB202190 to inhibit p38 MAPK-related signaling, we observed that SB202190 treatment could activate JNK. Further experiments showed that treatment of cells with SB202190 could phosphorylate JNK and activating transcription factor 2 (ATF-2), and increased AP-1 DNA binding. Using multiple cell lines and primary endothelial cells, we demonstrated that specific p38 MAPK inhibitors SB202190 or SB203580 induces the activation of the JNK pathway. Further, using with RNA interference and kinase-inactive expression of intermediates of the JNK pathway, we demonstrated SB202190- or SB203580-induced JNK activation is dependent on the MLK-3-MKK4/MKK7-dependent signal transduction pathway. Finally, we demonstrate that treatment of cells with SB202190 or SB203580 induces the phosphorylation and activation of MLK3.","corpus_id":24351356,"score":1},{"doc_id":"18695917","title":"Role of p38 MAPK and JNK in enhanced cervical cancer cell killing by the combination of arsenic trioxide and ionizing radiation.","abstract":"Enhancement of radiation response is possible to be achieved by combination treatment with therapeutic drugs. Previously we have shown that As2O3 in combination with ionizing radiation enhanced radiation response in cervical cancer cells. In this study, we further investigated molecular mechanism of synergistic enhancement of radiation response in combination with As2O3. The combination treatment of HeLa cells induced translocation of Bax to the mitochondria and a marked phosphorylation of Bcl-2. p38 MAPK and JNK were also found to be activated in response to the combination treatment. Pretreatment of PD169316, a p38 MAPK specific inhibitor, completely attenuated the combination treatment-induced mitochondrial relocalization of Bax, and altered Bcl-2 phosphorylation. Moreover, pretreatment of SP600125, JNK specific inhibitor, clearly attenuated Bcl-2 phosphorylation, but did not affect Bax translocation to the mitochondria. In addition, N-acetyl-L-cysteine (NAC), a thiol-containing anti-oxidant, completely blocked p38 MAPK and JNK activations, Bax relocalization and Bcl-2 phosphorylation. These results indicate that activation of p38 MAPK is specifically required for translocation of Bax to the mitochondria, and both JNK and p38 MAPK are involved in phosphorylation of Bcl-2 in response to combination treatment with gamma-radiation and As2O3, and that ROS is a critical regulator of p38 MAPK and JNK activations. The molecular mechanism elucidated in this study may provide insight into the design of future combination cancer therapies to cells intrinsically less sensitive to radiation treatment.","corpus_id":19690706,"score":1},{"doc_id":"18718176","title":"Protein tyrosine kinase, JNK, and ERK involvement in pseudolaric acid B-induced apoptosis of human breast cancer MCF-7 cells.","abstract":"AIM: To investigate the apoptotic mechanism of pseudolaric acid B (PAB) in human breast cancer MCF-7 cells. METHODS: 3-(4,5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide analysis and morphological changes were applied to detect apoptosis. The percentage of apoptotic and necrotic cells were calculated by the lactate dehydrogenase activity-based cytotoxicity assay, and the protein expression was examined by Western blot analysis. RESULTS: PAB and/or the mitogen-activated protein kinases, including p38, c-Jun-N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK), did not participate in necrosis. P38 had no obvious function on apoptosis after 4 micromol/L PAB treatment for 36 h, but PAB induced JNK phosphorylation and inhibited ERK phosphorylation in the apoptotic process. In this study the inhibitor of protein tyrosine kinase (PTK) genistein inverted the inhibitory effect of PAB, instead promoting the survival of MCF-7 cells. Like genistein, another PTK inhibitor AG1024 had a similar effect on PAB-treated MCF-7 cells, indicating that PAB activated PTK to induce apoptosis. Together with PAB, genistein increased the expression of p-ERK, and decreased the expressions of JNK and p-JNK in PAB-treated MCF-7 cells at 36 h. And it is considered that the p-ERK and p-JNK were active patterns of ERK and JNK, respectively. CONCLUSION: PTK were upstream of ERK and JNK, and PTK induced apoptosis through activating JNK and inactivating ERK in PAB-treated MCF-7 cells.","corpus_id":22568742,"score":1},{"doc_id":"18930812","title":"ERK MAPK activation mediates the antiapoptotic signaling of melatonin in UVB-stressed U937 cells.","abstract":"The pineal gland hormone melatonin has been recently described to downregulate the intrinsic (or damage-induced) pathway of apoptosis in human leukocytes. These properties appear to depend on a specific mitochondrial signaling of melatonin which is associated with a lower generation of reactive oxygen species and a better control of redox-sensitive components such as the antiapoptotic protein Bcl-2. Other elements upstream in this signaling are expected to contribute regulatory roles that remain unexplored. The aim of this study was to investigate whether the extracellular signal-regulated kinase (ERK), which controls the balance between survival and death-promoting genes throughout the MAPK pathway, is involved in the antiapoptotic signaling of melatonin. Human monocytic U937 cells irradiated with UVB light were used as a model of stress-induced apoptosis. In this model we found that pharmacological concentrations of melatonin (1 mM) were able to decrease superoxide anion production, mitochondrial damage, and caspase-dependent apoptosis by improved Bcl-2 levels and decreased Cyt c release in the cytoplasm. Moreover, melatonin increased the phosphorylative activation of ERK 1/2 independently from the presence of UVB stress, and decreased the UVB-mediated activation of the stress kinases p38 MAPK and JNK. The ERK 1/2 inhibitor PD98059, but not the p38 MAPK inhibitor SB203580, abolished to different extents the effects that melatonin had on the UVB-induced ROS generation, mitochondrial dysfunction, and apoptosis. Using these inhibitors, a cross-talk effect between stress and survival-promoting kinases was tentatively identified, and confirmed the hierarchical role of ERK MAPK phosphorylation in the signaling of melatonin. In conclusion, melatonin sustains the activation of the survival-promoting pathway ERK MAPK which is required to antagonize UVB-induced apoptosis of U937 cells. This kinase mediates also the antioxidant and mitochondrial protection effects of this hormonal substance that may find therapeutic applications in inflammatory and immune diseases associated with leukocyte oxidative stress and accelerated apoptosis.","corpus_id":25270805,"score":1},{"doc_id":"19038359","title":"Hydrogen peroxide-induced neuronal apoptosis is associated with inhibition of protein phosphatase 2A and 5, leading to activation of MAPK pathway.","abstract":"Oxidative stress-induced neuronal apoptosis is a prominent feature found in neurodegenerative disorders. However, how oxidative stress induces neuronal apoptosis is not well understood. To address this question, undifferentiated and differentiated neuronal cell lines (PC12 and SH-SY5Y) were exposed to hydrogen peroxide (H(2)O(2)), a major oxidant generated when oxidative stress occurs. We observed that H(2)O(2) induced generation of reactive oxygen species (ROS), leading to apoptosis of the cells in a concentration- and time-dependent manner. H(2)O(2) rapidly activated the mitogen-activated protein kinases (MAPK) including extracellular signal-regulated kinase 1/2 (Erk1/2), c-Jun N-terminal kinase (JNK) and p38. Inhibition of Erk1/2, JNK or p38 with kinase inhibitors (U0126, SP600125 or PD169316, respectively), downregulation of Erk1/2 or p38 using RNA interference, or expression of dominant negative c-Jun partially prevented H(2)O(2)-induced apoptosis. Pretreatment with N-acetyl-L-cysteine (NAC) scavenged H(2)O(2)-induced ROS, blocking activation of MAPKs and cell death. Furthermore, we found that H(2)O(2)-induced ROS inhibited serine/threonine protein phosphatases 2A (PP2A) and 5 (PP5), which was abrogated by NAC. Overexpression of PP2A or PP5 partially prevented H(2)O(2)-activation of Erk/12, JNK and p38, as well as cell death. Similar results were observed in primary murine neurons as well. The results suggest that H(2)O(2)-induction of ROS inhibit PP2A and PP5, leading to activation of Erk1/2, JNK and p38 pathways thereby resulting in neuronal apoptosis. Our findings suggest that inhibitors of MAPKs (JNK, Erk1/2 and p38), activators of phosphatases (PP2A and PP5) or antioxidants may have potentials to prevent and treat oxidative stress-induced neurodegenerative diseases.","corpus_id":7016424,"score":1},{"doc_id":"19059215","title":"PKD prevents H2O2-induced apoptosis via NF-kappaB and p38 MAPK in RIE-1 cells.","abstract":"Previously, we demonstrated that protein kinase D (PKD) plays a protective role during H(2)O(2)-induced intestinal cell death. Here, we sought to determine whether this effect is mediated by nuclear factor-kappaB (NF-kappaB) and mitogen-activated protein kinases (MAPKs). Treatment with H(2)O(2) activated NF-kappaB in RIE-1 cells; H(2)O(2) also induced the translocation of NF-kappaB p65 as well as phosphorylation of IkappaB-alpha. PKD1 siRNA inhibited H(2)O(2)-induced activation, translocation of NF-kappaB, and phosphorylation of IkappaB-alpha. We also found that overexpression of wild type PKD1 attenuated H(2)O(2)-induced phosphorylation of p38 MAPK and its upstream activator, MAPK kinase (MKK) 3/6, whereas the phosphorylation was increased by PKD1 siRNA or kinase-dead PKD1. Phosphorylation of neither extracellular signal-regulated kinases (ERK) 1/2 nor c-Jun N-terminal kinases (JNK) was altered by PKD1 plasmids or siRNA. Our findings suggest that PKD protects intestinal cells through up-regulation of NF-kappaB and down-regulation of p38 MAPK.","corpus_id":41036670,"score":1},{"doc_id":"19259124","title":"Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through regulation of Bcl-2.","abstract":"The present study shows that double-stranded RNA-dependent protein kinase (PKR) regulates the protein expression level and phosphorylation of Bcl-2 and plays an anti-apoptotic role in human hepatocellular carcinoma cells (HepG2). In various types of cells, saturated free fatty acids (FFAs), such as palmitate, have been shown to induce cellular apoptosis by several mechanisms. Palmitate down-regulates the activity of PKR and thereby decreases the level of Bcl-2 protein, mediated in part by reduced activation of the NF-kappaB transcription factor. In addition to the level of Bcl-2 protein, the phosphorylation of Bcl-2 at different amino acid residues, such as Ser70 and Ser87, is also important in regulating cellular apoptosis. The decrease in the phosphorylation of Bcl-2 at Ser70 upon exposure to palmitate is mediated by inhibition of PKR and possibly by c-Jun N-terminal kinase (JNK), whereas the phosphorylation of Bcl-2 at Ser87 is unaffected by palmitate or PKR. In summary, PKR mediates the regulation of the protein level and the phosphorylation status of Bcl-2, providing a novel mechanism of palmitate-induced apoptosis in HepG2 cells.","corpus_id":14301260,"score":1},{"doc_id":"19433446","title":"Mcl-1 integrates the opposing actions of signaling pathways that mediate survival and apoptosis.","abstract":"Mcl-1 is a member of the Bcl2-related protein family that is a critical mediator of cell survival. Exposure of cells to stress causes inhibition of Mcl-1 mRNA translation and rapid destruction of Mcl-1 protein by proteasomal degradation mediated by a phosphodegron created by glycogen synthase kinase 3 (GSK3) phosphorylation of Mcl-1. Here we demonstrate that prior phosphorylation of Mcl-1 by the c-Jun N-terminal protein kinase (JNK) is essential for Mcl-1 phosphorylation by GSK3. Stress-induced Mcl-1 degradation therefore requires the coordinated activity of JNK and GSK3. Together, these data establish that Mcl-1 functions as a site of signal integration between the proapoptotic activity of JNK and the prosurvival activity of the AKT pathway that inhibits GSK3.","corpus_id":9049545,"score":1},{"doc_id":"19522739","title":"Melatonin induces apoptotic death in LNCaP cells via p38 and JNK pathways: therapeutic implications for prostate cancer.","abstract":"Apoptosis, a form of cell death, is a fundamental process for the development and maintenance of multicellular organisms that promotes the removal of damaged, senescent or unwanted cells. Induction of cancer cell apoptosis is an important strategy of anticancer therapy. In this study, we examined if melatonin, the main secretory product of the pineal gland, inhibited the growth of prostate cancer cells (LNCaP) and promoted apoptosis via mitogen-activated protein kinases (MAPKs), which are closely associated with apoptosis and survival. Melatonin treatment significantly inhibited the growth of LNCaP cells in a dose- and time-dependent manner. It clearly induced both an early stage of apoptosis (propidium iodide(-), FITC Annexin-V(+)) and a late apoptosis/secondary necrosis (propidium iodide(+) and FITC Annexin-V(+)), which indicated induction of serial stages of apoptosis in cells. Moreover, melatonin markedly activated c-JUN N-terminal kinase (JNK) and p38 kinase, whereas extracellular signal-regulated kinase (ERK) was not responsive to melatonin. Treatment with MAPK inhibitors, PD98059 (ERK inhibitor), SP600125 (JNK inhibitor) and SB202190 (p38 inhibitor), confirmed that melatonin-induced apoptosis was JNK- and p38-dependent, but ERK-independent. In the presence of PD98059, caspase-3 activity increased, while levels of Bax/cytochrome c (Cyt c) and Bcl-2 decreased. These effects were opposite to those observed with SP600125 and SB202190 treatments. Together, these results strongly suggest that JNK and p38 activation directly participate in apoptosis induced by melatonin. Thus, melatonin may be of promise for anti-prostate cancer strategies.","corpus_id":13054688,"score":1},{"doc_id":"19578154","title":"Inhibition of p38-MAPK potentiates cisplatin-induced apoptosis via GSH depletion and increases intracellular drug accumulation in growth-arrested kidney tubular epithelial cells.","abstract":"We were interested in analyzing the regulation by mitogen-activated protein kinases (MAPKs) of cisplatin-provoked toxicity in epithelial renal tubule cell lines, when assayed under culture conditions (cell confluence plus serum deprivation), which mimic the characteristics of a nonproliferating epithelium. Under these restrictive growth conditions, cisplatin induced apoptosis with lower efficacy than in exponentially growing cells, and decreased p38-MAPK phosphorylation in NRK-52E and other (LLC-PK1, MDCK, HK2) cell lines. Moreover, cisplatin-provoked apoptosis was potentiated by cotreatment with p38-MAPK-specific inhibitors (SB203580, SB220025) or transfection with a kinase-negative mutant of MKK6, whereas c-Jun NH2-terminal kinase or extracellular signal-regulated kinase/MAPK and ERK Kinase inhibitors were ineffective. By contrast, when applied to exponentially growing cells, cisplatin stimulated p38-MAPK phosphorylation and apoptosis, was attenuated by kinase inhibitors. Treatment of confluent/serum-deprived cells with cisplatin caused mitochondrial transmembrane potential disruption and activated the mitochondrial apoptotic pathway, as indicated by the decrease in Bcl-X(L) expression, increase in Bax expression and cytochrome c release, and these effects were potentiated by cotreatment with SB203580. Treatment of confluent/serum-deprived cells with cisplatin plus SB203580 decreased the intracellular reduced glutathione (GSH) content, and increased intracellular cisplatin accumulation as well as cisplatin binding to DNA. Cotreatment with the GSH-depleting agent D,L-buthionine-R,S-sulfoximine also potentiated cisplatin-provoked apoptosis. In summary, p38-MAPK inhibition potentiates cisplatin-provoked apoptosis in growth-arrested epithelial renal tubule cells, a result that may be explained at least in part by GSH depletion and drug transport alteration.","corpus_id":33818915,"score":1},{"doc_id":"19699753","title":"Novel indoloquinoline derivative, IQDMA, induces G(2)/M phase arrest and apoptosis in A549 cells through JNK/p38 MAPK signaling activation.","abstract":"AIMS: This study was performed to elucidate whether mitogen-activated protein kinases (MAPKs) are involved in the modulation of apoptosis and cell-cycle arrest by N'-(11H-indolo[3,2-c]quinolin-6-yl)-N,N-dimethylethane-1,2-diamine (IQDMA), in human lung adenocarcinoma A549 cells. MAIN METHODS: The effect of IQDMA on cell-cycle arrest and apoptosis was measured by flow cytometry, and phosphorylation levels of mitogen-activated protein kinases (MAPKs) and its regulatory molecules were studied by immunoblots. KEY FINDINGS: IQDMA-induced G(2)/M arrest was associated with a marked decrease in the protein expressions of cyclin A, cyclin B, and cyclin-dependent kinase (Cdk)1. IQDMA-induced apoptosis was accompanied with up-regulation of the protein expression of Bax and down-regulation of the protein levels of Bcl-2, Mcl-1, X-linked inhibitor of apoptosis (XIAP), and survivin, resulting in cytochrome c release and sequential activation of caspase-9 and caspase-3. IQDMA activated c-Jun N-terminal kinase (JNK), p38 MAPK (p38) and extracellular signal-regulated kinase (ERK) on A549 cells in a time-dependent manner. Unlike the ERK inhibitor (PD98059), inhibitors of JNK (SP600125) and p38 MAPK (SB203580) suppressed IQDMA-induced apoptosis and G(2)/M phase arrest in A549 cells. Both SP600125 and SB203580 attenuated the activation of Bax and cytochrome c release, and reversed down-regulation of Bcl-2, XIAP, survivin, cyclin A, cyclin B, and Cdk1 in IQDMA-treated cells. SIGNIFICANCE: These findings indicate that JNK/p38 MAPK pathways play an important role in IQDMA-induced G(2)/M arrest and apoptosis of A549 cells.","corpus_id":33315805,"score":1},{"doc_id":"19717209","title":"Potentiation of paclitaxel-induced apoptosis by galectin-13 overexpression via activation of Ask-1-p38-MAP kinase and JNK/SAPK pathways and suppression of Akt and ERK1/2 activation in U-937 human macrophage cells.","abstract":"Galectin-13 transcripts have been identified in several normal and malignant tissues, but the physiological function of galectin-13 is still poorly understood. Here, we present evidence for its possible role in promoting cell death in the U-937 human macrophage cell line. Transfection of U-937 human macrophages by a galectin-13 cDNA-containing mammalian expression vector increased the galectin-13 level and sensitized the cells to stress stimuli. Galectin-13 overexpression facilitated paclitaxel-induced cell death and nuclear translocation of apoptosis-inducing factor (AIF) and endonuclease-G without inducing mitochondrial cytochrome-c release or caspase-3 activation. Immunoblot and immunofluorescence data showed that overexpression of galectin-13 induced long-term activation of c-Jun N-terminal kinase (JNK) and p38-mitogen-activated protein kinase (MAPK) pathways, as well as activation of apoptosis signal-regulating kinase-1 (Ask-1) kinase while it suppressed paclitaxel-induced long-term activation of the phosphatidilylositol-3-kinase (PI-3K)-Akt and extracellular signal-regulated kinase (ERK1/2) cytoprotective pathways. In addition, pharmacological inhibition of JNK and p38-MAPK pathways protected the cells from paclitaxel-induced cell death. All this data indicate that galectin-13 overexpression promoted apoptosis presumably by activating the Ask-1 kinase-JNK and p38-MAPK pro-apoptotic pathways and by suppressing the PI-3K-Akt and ERK1/2 cytoprotective pathways.","corpus_id":9055248,"score":1},{"doc_id":"19747539","title":"Naphtho[1,2-b]furan-4,5-dione induces apoptosis and S-phase arrest of MDA-MB-231 cells through JNK and ERK signaling activation.","abstract":"Naphtho[1,2-b]furan-4,5-dione (NFD), prepared from 2-hydroxy-1,4-naphthoquinone and chloroacetaldehyde in an efficient one-pot reaction, exhibits anti-carcinogenic effect. The results of present study showed that NFD inhibited the proliferation of breast cancer MDA-MB-231 cells through the induction of S-phase arrest and apoptosis. NFD-induced S-phase arrest was associated with a marked decrease in the protein expression of cyclin A, cyclin B, and cyclin-dependent kinase (Cdk)2. NFD-induced apoptosis was characterized by increase of sub-G1 population, phosphatidylserine (PS) externalization, and activation of caspases. Moreover, up-regulation of Bad and down-regulation of Bcl-2, Bcl-X(L), and survivin led to the loss of mitochondrial membrane potential (DeltaPsim), the release of cytochrome c and sequential activation of caspase-9 and caspase-3. NFD activated c-Jun N-terminal kinase (JNK), p38 mitogen-activated protein kinase (p38 MAPK) and extracellular signal-regulated kinase (ERK) in MDA-MB-231 cells. Inhibitors of JNK (SP600125) and ERK (PD98059), but not p38 MAPK (SB203580) suppressed NFD-induced S-phase arrest and apoptosis in MDA-MB-231 cells. Both SP600125 and PD98059 attenuated Bad up-regulation, and reversed down-regulation of Bcl-2, Bcl-X(L), survivin, cyclin A, cyclin B, and Cdk2 in NFD-treated cells. Taken together, our data show that JNK and ERK-signaling pathways play important roles in NFD-mediated S-phase arrest and apoptosis of MDA-MB-231 cells.","corpus_id":8373336,"score":1},{"doc_id":"20359850","title":"Interaction of Pdcd4 with eIF4E inhibits the metastatic potential of hepatocellular carcinoma.","abstract":"Oxidative stress can contribute to the development of hepatocellular carcinoma (HCC) ability of the carcinoma. It has been found that oxidative stress stimulates the phosphorylation of eIF4E primarily through mitogen-activated protein kinase (MAPK) pathways resulting in increased protein translation. Utilizing specific inhibitors of MAPK pathways (SP600125 for c-Jun amino-terminal kinases [JNKs], PD098059 for extracellular signal-regulated kinases [ERKs], and SB203580 for p38 MAPK), we determined that it is primarily the inhibition of JNK that results in the suppression of the increase of p-eIF4E. We also found that PDCD4 inhibits JNK activity resulting in inhibition of the phosphorylation of c-Jun, one isoform of AP-1. We demonstrated that transfection with PDCD4 or inhibition of JNK by SP600125 alters the expression and phosphorylation of eIF4E in the presence of H(2)O(2). PDCD4 results in a stronger inhibitory effect than SP600125.","corpus_id":23767580,"score":1},{"doc_id":"21519792","title":"Lupulone triggers p38 MAPK-controlled activation of p53 and of the TRAIL receptor apoptotic pathway in human colon cancer-derived metastatic cells.","abstract":"We previously reported that the chemopreventive agent lupulone induces apoptosis through activation of the extrinsic pathway via TRAIL DR4/DR5 death receptors overcoming SW620 cell resistance to TRAIL. However, the underlying molecular mechanisms remain unknown. Since the mitogen-activated protein kinases (MAPKs), Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK) and p38 control fundamental cellular processes such as apoptosis, we determined the role of these MAPKs in lupulone-triggered apoptosis. We analyzed the effects of JNK, ERK and p38 MAPK inhibitors on lupulone-induced apoptosis by flow cytometry using specific antibodies and real-time RT-PCR. Our data showed that among the MAPKs, only p38 played a major role in lupulone-triggered apoptosis. In contrast to JNK and ERK inhibition, the specific inactivation of p38 inhibited the lupulone-triggered up-regulation of p53 and TRAIL-death receptor DR4/DR5 expression, and prevented DNA fragmentation. Lupulone treatment enhanced the expression of the anti-apoptotic Mcl-1 protein by 60% favoring the preservation of mitochondrial integrity. The inactivation of p38 initiated a 50% reduction in Mcl-1, Bcl-2 and Bax expression without changing the Mcl-1/Bax ratio suggesting that p38 was not involved in the protective effect of lupulone on mitochondria. Our data support the view that the lupulone-triggered enhanced expression of p38 plays a major role in the activation of p53 and of the TRAIL-death receptor apoptotic pathway in SW620 human colon cancer-derived metastatic cells.","corpus_id":25728436,"score":1},{"doc_id":"22678567","title":"Cyclosporin A induces apoptosis in H9c2 cardiomyoblast cells through calcium-sensing receptor-mediated activation of the ERK MAPK and p38 MAPK pathways.","abstract":"The cardiotoxicity of cyclosporine A (CsA) limits its clinical application in extensive and long-term therapies. Our group has shown that CsA induces myocardium cell apoptosis in vivo and increases calcium-sensing receptor (CaSR) expression. However, its molecular mechanism remains unknown. The purpose of this study was to determine whether CaSR plays an essential role in CsA-induced apoptosis in H9c2 cells and to investigate the role of the mitogen-activated protein kinase (MAPK) signaling cascade in this process. H9c2 cells were treated with CsA in a dose-dependent manner, and decreased Bcl-2 expression, increased Bax expression, and caspase-3 activation were observed. In a time-dependent manner, CsA increased CaSR expression, activated the extracellularly regulated kinase (ERK) and p38 MAPK pathways, and inactivated the c-Jun N-terminal kinase (JNK) MAPK signaling pathway. When H9c2 cardiomyoblast cells pretreated with gadolinium chloride (GdCl(3)), a CaSR activator, were treated with CsA, decreased phosphorylation of ERK1/2, increased phosphorylation of p38, decreased Bcl-2 expression, increased Bax expression, and activated caspase-3 were observed. Cells pretreated with the CaSR inhibitor NPS2390 inhibited this process. Furthermore, the MEK1/2 inhibitor U0126 and the p38 MAPK inhibitor SB203580 markedly blocked the effect of CsA on cell apoptosis, apoptotic-related protein expression, and caspase-3 activation. These findings showed that CsA induced apoptosis in H9c2 cells in vitro, and CaSR mediated the degradation of ERK MAPK and the upregulation of the p38 MAPK pathway involved in CsA-induced H9c2 cardiomyoblast cell apoptosis.","corpus_id":7955722,"score":1},{"doc_id":"23123629","title":"Role of JNK and p38 MAPK in Taiwanin A-induced cell death.","abstract":"AIM: The lignan compound Taiwanin A is cytotoxic for human cancer cells. Taiwanin A has been previously shown to damage microtubules, induce mitotic arrest and cause apoptosis in cancer cells. The goal of the current study is to identify intracellular signaling pathways that are involved in Taiwanin A-mediated apoptosis. MAIN METHODS: We examined the activation of three mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK), p38 and c-Jun N-terminal kinase (JNK), in HepG2 cells after Taiwanin A treatment. The role of MAPK activation in Taiwanin A-induced apoptosis was examined using Western blotting, caspase activity assays combined with specific MAPK inhibitors and shRNA treatment to knockdown JNK. KEY FINDINGS: Taiwanin A activated all three MAPKs (ERK, p38 and JNK). Cytotoxicity was blocked by the p38 MAPK inhibitor SB203580 and the JNK inhibitor SP600125 but not by the ERK inhibitor PD98059. A combined treatment of SB203580 and SP600125 showed increased effects on the inhibition of Taiwanin A cytotoxicity, suggesting that both JNK and p38 play a role in Taiwanin A-induced apoptosis. Inhibition of p38 activity reduced Taiwanin A-induced p53 phosphorylation on Ser15. Direct interaction of Taiwanin A-activated p38 and p53 was demonstrated by immunoprecipitation. In addition, inhibition of JNK by SP600125 or silencing of the JNK scaffold protein JIP2 reduced phosphorylation of Bcl-2, which may help to promote anti-apoptotic pathways. SIGNIFICANCE: We demonstrated for the first time that two distinct apoptotic pathways, the p38-p53 and JNK-Bcl-2 pathways, were triggered by the anti-microtubule compound Taiwanin A.","corpus_id":28896196,"score":1},{"doc_id":"23172806","title":"Apoptosis induced by para-phenylenediamine involves formation of ROS and activation of p38 and JNK in chang liver cells.","abstract":"para-Phenylenediamine (p-PD) is a suspected carcinogen, but it has been widely used as a component in permanent hair dyes. In this study, the mechanism of p-PD-induced cell death in normal Chang liver cells was investigated. The results demonstrated that p-PD decreased cell viability in a dose-dependent manner. Cell death via apoptosis was confirmed by enhanced DNA damage and increased cell number in the sub-G1 phase of the cell cycle, using Hoechst 33258 dye staining and flow cytometry analysis. Apoptosis via reactive oxygen species generation was detected by the dichlorofluorescin diacetate staining method. Mitogen-activated protein kinase (MAPK) activation was assessed by western blot analysis and revealed that p-PD activated not only stress-activated protein kinase (SAPK)/c-Jun N-terminal kinases (JNK) and p38 MAPK but also extracellular signal-regulated kinase (ERK). Cytotoxicity and apoptosis induced by p-PD were markedly enhanced by ERK activation and selectively inhibited by ERK inhibitor PD98059, thus indicating a negative role of ERK. In contrast, inhibition of p38 MAPK activity with the p38-specific inhibitor SB203580 moderately inhibited cytotoxicity and apoptosis induction by p-PD. Similarly, SP600125, an inhibitor of SAPK/JNK, moderately inhibited cytotoxicity and apoptosis induced by p-PD, thus implying that p38 MAPK and SAPK/JNK had a partial role in p-PD-induced apoptosis. Western blot analysis revealed that p-PD significantly increased phosphorylation of p38 and SAPK/JNK and decreased phosphorylation of ERK. In conclusion, the results demonstrated that SAPK/JNK and p38 cooperatively participate in apoptosis induced by p-PD and that a decreased ERK signal contributes to growth inhibition or apoptosis.","corpus_id":22951605,"score":1},{"doc_id":"23203057","title":"Apoptosis induction of human prostate carcinoma DU145 cells by diallyl disulfide via modulation of JNK and PI3K/AKT signaling pathways.","abstract":"Diallyl disulfide (DADS), a sulfur compound derived from garlic, has various biological properties, such as anticancer, antiangiogenic and anti-inflammatory effects. However, the mechanisms of action underlying the compound's anticancer activity have not been fully elucidated. In this study, the apoptotic effects of DADS were investigated in DU145 human prostate carcinoma cells. Our results showed that DADS markedly inhibited the growth of the DU145 cells by induction of apoptosis. Apoptosis was accompanied by modulation of Bcl-2 and inhibitor of apoptosis protein (IAP) family proteins, depolarization of the mitochondrial membrane potential (MMP, ΔΨm) and proteolytic activation of caspases. We also found that the expression of death-receptor 4 (DR4) and Fas ligand (FasL) proteins was increased and that the level of intact Bid proteins was down-regulated by DADS. Moreover, treatment with DADS induced phosphorylation of mitogen-activated protein kinases (MAPKs), including extracellular-signal regulating kinase (ERK), p38 MAPK and c-Jun N-terminal kinase (JNK). A specific JNK inhibitor, SP600125, significantly blocked DADS-induced-apoptosis, whereas inhibitors of the ERK (PD98059) and p38 MAPK (SB203580) had no effect. The induction of apoptosis was also accompanied by inactivation of phosphatidylinositol 3-kinase (PI3K)/Akt and the PI3K inhibitor LY29004 significantly increased DADS-induced cell death. These findings provide evidence demonstrating that the proapoptotic effect of DADS is mediated through the activation of JNK and the inhibition of the PI3K/Akt signaling pathway in DU145 cells.","corpus_id":11034222,"score":1},{"doc_id":"23681233","title":"Hypoxia counteracts taxol-induced apoptosis in MDA-MB-231 breast cancer cells: role of autophagy and JNK activation.","abstract":"Cancer cell resistance against chemotherapy is still a heavy burden to improve anticancer treatments. Autophagy activation and the development of hypoxic regions within the tumors are known to promote cancer cell resistance. Therefore, we sought to evaluate the role of autophagy and hypoxia on the taxol-induced apoptosis in MDA-MB-231 breast cancer cells. The results showed that taxol induced apoptosis after 16 h of incubation, and that hypoxia protected MDA-MB-231 cells from taxol-induced apoptosis. In parallel, taxol induced autophagy activation already after 2 h of incubation both under normoxia and hypoxia. Autophagy activation after taxol exposure was shown to be a protective mechanism against taxol-induced cell death both under normoxia and hypoxia. However, at longer incubation time, the autophagic process reached a saturation point under normoxia leading to cell death, whereas under hypoxia, autophagy flow still correctly took place allowing the cells to survive. Autophagy induction is induced after taxol exposure via mechanistic target of rapamycin (mTOR) inhibition, which is more important in cells exposed to hypoxia. Taxol also induced c-Jun N-terminal kinase (JNK) activation and phosphorylation of its substrates B-cell CLL/lymphoma 2 (Bcl2) and BCL2-like 1 (BclXL) under normoxia and hypoxia very early after taxol exposure. Bcl2 and BclXL phosphorylation was decreased more importantly under hypoxia after long incubation time. The role of JNK in autophagy and apoptosis induction was studied using siRNAs. The results showed that JNK activation promotes resistance against taxol-induced apoptosis under normoxia and hypoxia without being involved in induction of autophagy. In conclusion, the resistance against taxol-induced cell death observed under hypoxia can be explained by a more effective autophagic flow activated via the classical mTOR pathway and by a mechanism involving JNK, which could be dependent on Bcl2 and BclXL phosphorylation but independent of JNK-induced autophagy activation.","corpus_id":3758039,"score":1},{"doc_id":"23812630","title":"Olaquindox-induced apoptosis is suppressed through p38 MAPK and ROS-mediated JNK pathways in HepG2 cells.","abstract":"We investigated mitogen-activated protein kinase (MAPK) pathways as well as reactive oxygen species (ROS) in olaquindox-induced apoptosis. Exposure of HepG2 cells to olaquindox resulted in the phosphorylation of p38 MAPK and c-Jun N-terminal kinases (JNK). To confirm the role of p38 MAPK and JNK, HepG2 cells were pretreated with MAPKs-specific inhibitors prior to olaquindox treatment. Olaquindox-induced apoptosis was significantly potentiated by the JNK inhibitor (SP600125) or the p38 MAPK inhibitor (SB203580). Furthermore, we observed that olaquindox treatment led to ROS generation and that olaquindox-induced apoptosis and ROS generation were both significantly reduced by the antioxidants, superoxide dismutase and catalase. In addition, the levels of phosphorylation of JNK, but not p38 MAPK, were significantly suppressed after pretreatment of the antioxidants, while inhibition of the activations of JNK or p38 MAPK had no effect on ROS generation. This result suggested that ROS may be the upstream mediator for the activation of JNK. Conclusively, our results suggested that apoptosis in response to olaquindox treatment in HepG2 cells might be suppressed through p38 MAPK and ROS-JNK pathways.","corpus_id":12940772,"score":1},{"doc_id":"24173825","title":"Caffeine inhibits paclitaxel‑induced apoptosis in colorectal cancer cells through the upregulation of Mcl‑1 levels.","abstract":"Colorectal cancer (CRC) cells have been previously observed to be resistant to paclitaxel‑induced apoptosis by activation of the mitogen‑activated protein/extracellular signal‑regulated kinase (MEK)/ERK signaling pathway and increased expression of glucose‑regulated protein 78 (GRP78). Caffeine, the most widely used neuroactive compound, has antiproliferative activity and the ability to induce cell cycle arrest and apoptosis. In the current study, the effect of concomitant use of caffeine on paclitaxel‑induced apoptosis in CRC cells was investigated. The results revealed that treatment of Colo205 cells with varying caffeine concentrations did not induce apoptosis. Pretreatment of CRC cells with caffeine significantly inhibited paclitaxel‑induced cytotoxicity by increasing the levels of the antiapoptotic Bcl‑2 family member, Mcl‑1. This effect was inhibited by pretreatment of Colo205 cells with the MEK‑ERK chemical inhibitor, U0126. In addition to GRP78, these results indicated that Mcl‑1 may be a downstream target of the MEK‑ERK signaling pathway. Moreover, administration of caffeine may decrease chemotherapeutic responses to paclitaxel by the MEK‑ERK mediated upregulation of Mcl‑1. In conclusion, coadministration of cell cycle‑modifying agents, including caffeine should be avoided in CRC patients treated with paclitaxel.","corpus_id":207550025,"score":1},{"doc_id":"25187486","title":"Induction of Nur77-dependent apoptotic pathway by a coumarin derivative through activation of JNK and p38 MAPK.","abstract":"Coumarins are plant-derived natural products with a broad range of known pharmacological activities including anticancer effects. However, the molecular mechanisms by which this class of promising compounds exerts their anticancer effects remain largely unknown. We report here that a furanocoumarin named apaensin could effectively induce apoptosis of cancer cells through its activation of Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK). Apoptosis induction by apaensin in cancer cells was suppressed by chemical inhibitors of JNK and p38 MAPK. Inhibition of the expression of orphan nuclear receptor Nur77 by small interfering RNA (siRNA) approach also abrogated the death effect of apaensin. Molecular analysis demonstrated that JNK activation was required for the nuclear export of Nur77, a known apoptotic event in cancer cells. Although p38 MAPK activation was not involved in Nur77 nuclear export, it was essential for Nur77 mitochondrial targeting through induction of Nur77 interaction with Bcl-2, which is also known to convert Bcl-2 from an antiapoptotic to a proapoptotic molecule. Together, our results identify a new natural product that targets orphan nuclear receptor Nur77 through its unique activation of JNK and p38 MAPK and provide insight into the complex regulation of the Nur77-Bcl-2 apoptotic pathway.","corpus_id":37640174,"score":1},{"doc_id":"25236495","title":"MDA-7/IL-24 inhibits Nrf2-mediated antioxidant response through activation of p38 pathway and inhibition of ERK pathway involved in cancer cell apoptosis.","abstract":"Reactive oxygen species (ROS) have a crucial role in melanoma differentiation-associated gene-7 (MDA-7)/interleukin-24 (IL-24)-induced cancer cell apoptosis. However, cancer cell has a series of protective mechanisms to resist ROS damage. Nuclear factor erythroid 2-related factor 2 (Nrf2) activates antioxidant response element (ARE)-mediated gene expression involved in cellular protection against oxidative stress. As the Nrf2 repressor, Kelch-like ECH-associated protein-1 (Keap1) sequesters Nrf2 in cytoplasm to block Nrf2 nuclear translocation. In the present study, administration of MDA-7/IL-24 by means of tumor-selective replicating adenovirus (ZD55-IL-24) was used to investigate whether ZD55-IL-24 could attenuate Nrf2-mediated oxidative stress response in cancer cell. We found that ZD55-IL-24 effectively strengthened the association between Nrf2 and Keap1 to restrict Nrf2 nuclear translocation, thereby inhibiting ARE-dependent transcriptional response. To evaluate the detailed mechanism underlying the suppression of ZD55-IL-24 on Nrf2-mediated oxidative stress response, we further tested three different mitogen-activated protein kinase (MAPK) signaling pathways in A549 and HeLa cells transfected by ZD55-IL-24. Our data showed that ZD55-IL-24 inhibited extracellular signal-regulated kinase (ERK) signal pathway but activated p38 and c-Jun-NH2-kinase (JNK) signal pathways to exert the tumor-specific apoptosis. Moreover, ERK pathway inhibitor U0126 prevented Nrf2 phosphorylation at Ser40 to retard Nrf2 nuclear translocation, thus decreasing antioxidant gene transcription. In contrast, p38 pathway inhibitor SB203580 obviously promoted the dissociation of Nrf2 from Keap1 to promote antioxidant gene transcription. However, JNK pathway had no effect on Nrf2 subcellular localization or the association of Nrf2 with Keap1. Conclusively, our results indicate that ZD55-IL-24 inhibits Nrf2-mediated oxidative stress response not only by activating p38 signal pathway to potentiate the association of Nrf2 and Keap1 but also by suppressing ERK signal pathway to postpone Nrf2 nuclear translocation. Given the 'dark' side of Nrf2 on carcinoma cell survival and chemoresistance, our study provides a novel explanation about MDA-7/IL-24-induced cancer-specific apoptosis and therapeutic sensitization through suppression of the cytoprotective system.","corpus_id":7334566,"score":1},{"doc_id":"25753324","title":"Vincristine activates c-Jun N-terminal kinase in chronic lymphocytic leukaemia in vivo.","abstract":"AIMS: The authors' aim was to conduct a proof-of-principle study to test whether c-Jun N-terminal kinase (JNK) phosphorylation and Noxa induction occur in peripheral blood chronic lymphocytic leukaemia (CLL) cells in patients receiving a vincristine infusion. METHODS: Patients with CLL received 2 mg vincristine by a 5-min intravenous infusion. Blood samples were collected at baseline and up to 6 h after the vincristine infusion, and assayed for JNK activation, Noxa induction and vincristine plasma concentrations. RESULTS: Ex vivo treated peripheral CLL cells activated JNK in response to 10-100 nM vincristine in 6 h. Noxa protein expression, while variable, was also observed over this time frame. In CLL patients, vincristine infusion led to rapid (<1 h) JNK phosphorylation in peripheral blood CLL cells which was sustained for at least 4-6 h after the vincristine infusion. Noxa protein expression was not observed in response to vincristine infusion. CONCLUSIONS: This study confirmed that vincristine can activate JNK but not induce Noxa in CLL cells in vivo. The results suggest that novel JNK-dependent drug combinations with vincristine warrant further investigation.","corpus_id":34643335,"score":1},{"doc_id":"26961382","title":"Saikosaponin-D Reduces H2O2-Induced PC12 Cell Apoptosis by Removing ROS and Blocking MAPK-Dependent Oxidative Damage.","abstract":"Neuronal oxidative stress (OS) injury has been proven to be associated with many neurodegenerative diseases, and thus, antioxidation treatment is an effective method for treating these diseases. Saikosaponin-D (SSD) is a sapogenin extracted from Bupleurum falcatum and has been shown to have many pharmacological activities. The main purpose of this study was to investigate whether and how SSD protects PC12 cells from H2O2-induced apoptosis. The non-toxic level of SSD significantly mitigated the H2O2-induced decrease in cell viability, reduced the apoptosis rate, improved the nuclear morphology, and reduced caspase-3 activation and poly ADP-ribose polymerase (PARP) cleavage. Additionally, exogenous H2O2-induced apoptosis by damaging the intracellular antioxidation system. SSD significantly slowed the H2O2-induced release of malonic dialdehyde (MDA) and lactate dehydrogenase and increased the activity of superoxide dismutase (SOD) and the total antioxidant capacity, thereby reducing apoptosis. More importantly, SSD effectively blocked H2O2-induced phosphorylation of extracellular-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 mitogen-activated protein kinase (p38MAPK), and specific inhibitors of ERK, JNK, and p38-reduced OS injury and apoptosis, suggesting that SSD reduces OS injury and apoptosis via MAPK signalling pathways. Finally, we confirmed that SSD significantly reduced H2O2-induced reactive oxygen species (ROS) accumulation, and the ROS inhibitor blocked the apoptosis caused by MAPK activation and cellular oxidative damage. In short, our study confirmed that SSD reduces H2O2-induced PC12 cell apoptosis by removing ROS and blocking MAPK-dependent oxidative damage.","corpus_id":19197565,"score":1},{"doc_id":"27220839","title":"IL-1α induces apoptosis and inhibits the osteoblast differentiation of MC3T3-E1 cells through the JNK and p38 MAPK pathways.","abstract":"Interleukin (IL)-1 is a proinflammatory cytokine that plays important roles in inflammation and host responses to infection. The present study aimed to evaluate the effects of IL-1α on the apoptosis and differentiation of osteoblasts, and to elucidate the mechanism responsible for these effects in the osteoblast‑like cell line MC3T3-E1. The MC3T3-E1 cells were non-treated or treated with IL-1α. Following treatment, cell viability, alkaline phosphatase (ALP) activity and caspase-3 activity were evaluated. The expression of osteoblast-specific genes as well as Bax, Bcl-2 and caspase-3 were determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The protein levels of Bax, Bcl-2, caspase-3 and the phosphorylation of mitogen-activated protein kinases (MAPKs, also known as MAP kinases) were evaluated using western blot analysis. The MAPK signaling pathway was blocked by pre-treatment with MAPK inhibitors SB203580, PD98059 and SP600125. IL-1α treatment induced a significant decrease in cell viability and ALP activity in the MC3T3-E1 cells. IL-1α also significantly decreased the mRNA expression and protein levels of osteoblast-related genes in the MC3T3-E1 cells. On the other hand, IL-1α significantly upregulated the mRNA expression and protein levels of Bax and caspase-3 as well as caspase-3 activity, whereas Bcl-2 expression was decreased in the MC3T3-E1 cells. Furthermore, IL-1α activated the apoptotic signaling pathway by increasing the phosphorylation of c-Jun N-terminal kinase (JNK) and p38-MAPK, whereas it inhibited the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). Moreover, pre-treatment with MAPK inhibitors attenuated the phosphorylation of JNK, p38 and Bax expression enhanced by IL-1α. However, MAPK inhibitors markedly increased the protein expression of osteoblast-related genes and Bcl-xL in the MC3T3-E1 cells downregulated by IL-1α. Taken together, these findings suggest that IL-1α induces the apoptosis of osteoblasts and inhibits osteoblast differentiation by activating the JNK and the p38 MAPK pathways.","corpus_id":42103216,"score":1},{"doc_id":"27626409","title":"Kinase Signaling in Apoptosis Induced by Saturated Fatty Acids in Pancreatic β-Cells.","abstract":"Pancreatic β-cell failure and death is considered to be one of the main factors responsible for type 2 diabetes. It is caused by, in addition to hyperglycemia, chronic exposure to increased concentrations of fatty acids, mainly saturated fatty acids. Molecular mechanisms of apoptosis induction by saturated fatty acids in β-cells are not completely clear. It has been proposed that kinase signaling could be involved, particularly, c-Jun N-terminal kinase (JNK), protein kinase C (PKC), p38 mitogen-activated protein kinase (p38 MAPK), extracellular signal-regulated kinase (ERK), and Akt kinases and their pathways. In this review, we discuss these kinases and their signaling pathways with respect to their possible role in apoptosis induction by saturated fatty acids in pancreatic β-cells.","corpus_id":17403848,"score":1},{"doc_id":"29658576","title":"Paclitaxel suppresses proliferation and induces apoptosis through regulation of ROS and the AKT/MAPK signaling pathway in canine mammary gland tumor cells.","abstract":"Paclitaxel is a diterpenoid compound, derived from the pacific yew (Taxus brevifolia) berry, which exhibits antineoplastic effects against various types of cancer. However, the antitumor effects and the molecular mechanisms of paclitaxel on canine CHMm cells remain to be elucidated. The aim of the present study was to investigate the antitumor effects of paclitaxel on CHMm cells and identify relevant signal transduction pathways modulated by paclitaxel using multiple methods including MTT assay, flow cytometry, acridine orange/ethidium bromide staining, transmission electron microscopy, determination of cellular reactive oxygen species (ROS), superoxide dismutase (SOD) and malondiadehyde (MDA) and western blotting, the data indicated that paclitaxel decreased cell viability, induced G2/M‑phase cell cycle arrest, suppressed the expression of cyclin B1 and induced apoptosis in a dose‑dependent manner. In addition, paclitaxel upregulated the expression of Bax and cytochrome c, but reduced expression of apoptosis regulator Bcl‑2, resulting in activation of caspase‑3, chromatin condensation, karyopyknosis, intracellular vacuolization, increased production of ROS and MDA, and decreased activity of SOD. However, these effects were inhibited when CHMm cells were treated with N‑acetyl‑L‑cysteine. Furthermore, treatment with paclitaxel inhibited the level of of phospho (p)‑RAC‑α serine/threonine‑protein kinase (AKT) and p‑ribosomal protein S6 kinase proteins, and promoted phosphorylation of P38 mitogen‑activated protein kinase (MAPK) and p‑90 kDa ribosomal protein S6 kinase 1 proteins in CHMm cells. It was observed that paclitaxel in combination with pharmacological inhibitors of the P38 and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase (PI3K) signaling pathways (SB203580 and LY294002, respectively) exerted synergistic inhibitory effects on the proliferation of the CHMm cells. The results of the present study demonstrated that paclitaxel inhibited tumor cell proliferation by increasing intrinsic apoptosis through inhibition of the PI3K/AKT signaling pathway and activation of MAPK signaling pathway in CHMm cells.","corpus_id":4881550,"score":1},{"doc_id":"18186605","title":"Fermented Antrodia cinnamomea extract protects rat PC12 cells from serum deprivation-induced apoptosis: the role of the MAPK family.","abstract":"Antrodia cinnamomea (formerly A. camphorata) has recently and commercially been used in the formulation of nutraceuticals and functional foods in Taiwan. Because of its diverse properties, the neuroprotective effect was investigated using a fermented A. cinnamomea extract in this study. Serum deprivation-induced apoptosis in neuronal-like pheochromocytoma (PC12) cells was used as a cell stress model, and it was found that A. cinnamomea was effective in preventing serum-deprived apoptosis according to results of an MTT assay and Hoechst staining. Serum deprivation resulted in decreased phosphorylation of extracellular signal-regulated kinase (ERK) and increased phosphorylations of c-Jun NH2-terminal kinase (JNK) and p38, of the family of mitogen-activated protein kinases (MAPKs); however, A. cinnamomea reversed these phenomena, supporting the antagonistic effects between ERK and JNK-p38 in regulating cell survival. The previously identified active component of A. cinnamomea, adenosine (ADO), also exerted the same effects as A. cinnamomea in preventing apoptosis and regulating phosphorylations of MAPKs. Although an inhibitor of the ERK upstream activator blocked A. cinnamomea-induced ERK phosphorylations, it failed to block the protection of A. cinnamomea and ADO. A protein kinase A (PKA) inhibitor blocked the protection by both A. cinnamomea and ADO. Both JNK and p38 inhibitors were effective in preventing the phosphorylations of JNK and p38 and serum deprivation-induced apoptosis. Collectively, A. cinnamomea prevented serum deprivation-induced PC12 cell apoptosis through a PKA-dependent pathway and by suppression of JNK and p38 activities.","corpus_id":207197824,"score":0},{"doc_id":"18521846","title":"Mechanism of 2-methoxyestradiol-induced apoptosis and growth arrest in human breast cancer cells.","abstract":"2-Methoxyestradiol, a well-known nonpolar endogenous metabolite of 17beta-estradiol, has been shown to selectively induce apoptosis in a number of cancer cell lines, but not in normal cells. The mechanism of 2-methoxyestradiol-induced apoptosis appears to vary considerably in different cell lines examined. In the present study, we systematically analyzed the mechanisms of 2-methoxyestradiol-induced apoptosis in the estrogen receptor-negative MDA-MB-435s human breast cancer cells. We found that 2-methoxyestradiol induced the activation of JNK, ERK, and p38 MAPKs. 2-methoxyestradiol-induced JNK activation was associated with the induction of apoptosis through the mitochondrial pathways as a result of increased phosphorylation (inactivation) of the anti-apoptotic Bcl-2 and Bcl-xL proteins. In comparison, 2-methoxyestradiol-induced activation of ERK and p38 in these cells was found to have a protective effect against 2-MeO-E(2)-induced apoptosis. Consistent with this observation, the presence of pharmacological inhibitor of ERK or p38 enhanced 2-methoxyestradiol-induced apoptosis. Mechanistically, inhibition of ERK and p38 activity was associated with activation of various caspases and PARP cleavage, and it also stabilized the pro-apoptotic proteins Bax and Bim, thereby preventing them from degradation during 2-methoxyestradiol treatment. These results suggest that ERK and p38 MAPKs may serve as viable targets for the sensitization of human breast cancer cells to 2-methoxyestradiol-induced apoptosis.","corpus_id":37332405,"score":0},{"doc_id":"18690538","title":"Ran suppresses paclitaxel-induced apoptosis in human glioblastoma cells.","abstract":"Yeast-based functional screening of a human glioblastoma cDNA library identified ras-related nuclear protein (Ran) as a novel suppressor of Bcl-2-associated X protein (Bax), a pro-apoptotic member of the Bcl-2 family of proteins. Yeast cells that expressed human Ran were resistant to Bax-induced cell death. In U373MG glioblastoma cells, stable overexpression of Ran significantly attenuated apoptotic cell death induced by the chemotherapeutic agent paclitaxel. FACS analysis demonstrated that Ran is involved in paclitaxel-induced cell cycle arrest. Stable overexpression of Ran also markedly inhibited the phosphorylation of Bcl-2 by paclitaxel, and inhibited the translocation of Bax, the release of cytochrome c and activation of caspase-3. Paclitaxel-induced phosphorylation of c-JUN N-terminal kinase (JNK), but not p38, extracellular signal-regulated kinase and Akt, was markedly suppressed in U373MG cells that stably expressed Ran. These results suggest that Ran suppresses paclitaxel-induced cell death through the downregulation of JNK-mediated signal pathways.","corpus_id":32218347,"score":0},{"doc_id":"19493891","title":"NaF activates MAPKs and induces apoptosis in odontoblast-like cells.","abstract":"The cytotoxic effects of fluoride on odontoblasts are not clear. In this study, we examined whether NaF induces apoptosis in MDPC-23 odontoblast-like cells and the involvement of mitogen-activated protein kinase (MAPK) signaling pathways in NaF-induced apoptosis. MDPC-23 cells incubated with 5 mM NaF for 24 hrs exhibited caspase-3 activation, cleavage of poly(ADP-ribose) polymerase, DNA fragmentation, and an increase in cytoplasmic nucleosomes. Prior to the induction of apoptosis, all MAPKs examined were phosphorylated, but in a different manner. In contrast to the sustained phosphorylation of c-Jun NH(2)-terminal kinase (JNK) and p38, NaF exposure induced a biphasic phosphorylation of extracellular signal-regulated protein kinase (ERK). NaF-induced apoptosis was markedly suppressed by treatment with the JNK inhibitor, SP600125, and mildly suppressed by the MAPK/ERK kinase inhibitor, U0126. Inhibition of p38 activity did not protect cells from apoptosis. Thus, exposure to NaF induces apoptosis in odontoblast-like cells, depending on JNK and, less significantly, ERK pathways.","corpus_id":29316686,"score":0},{"doc_id":"19723051","title":"Activator protein-1 mediates docosahexaenoic acid-induced apoptosis of human gastric cancer cells.","abstract":"Docosahexaenoic acid (DHA) shows anti-inflammatory and/or anticancer effects in some cells. Activator protein-1 (AP-1) regulates cellular proliferation and apoptosis. Although recent studies demonstrate the association between gastric cancer risk and DHA, the exact molecular mechanism has not been clarified. We investigated whether AP-1 mediates DHA-induced apoptosis of gastric cancer cells. We found that DHA induced cell death and DNA fragmentation in parallel with the activation of extracellular signal-regulated kinases (ERK) and c-Jun N-terminal kinases (JNK) as well as AP-1. DHA increased the protein levels of p53, cytochrome c, and Bax in gastric cancer cells. DHA-induced DNA fragmentation and protein levels of p53, cytochrome c, and Bax were inhibited in the cells transfected with c-jun dominant-negative mutant (TAM67). Because JNK and ERK are upstream signaling for AP-1 activation, we suggest that DHA-induced activation of AP-1 may mediate apoptosis of gastric cancer cells by inducing the expression of apoptotic genes in gastric cancer cells.","corpus_id":25179794,"score":0},{"doc_id":"19747165","title":"Mesothelin inhibits paclitaxel-induced apoptosis through the PI3K pathway.","abstract":"Mesothelin, a secreted protein, is overexpressed in some cancers, but its exact function remains unclear. The aim of the present study was to evaluate the possible function of mesothelin. Real-time PCR, RT (reverse transcription)-PCR, cytotoxicity assays, proliferative assays, apoptotic assays by Hoechst staining, detection of active caspases 3 and 7 by flow cytometric analysis, and immunoprecipitation and immunoblotting were performed. Cancer tissues in paclitaxel-resistant ovarian cancer patients expressed higher levels of mesothelin as assessed using real-time PCR than paclitaxel-sensitive ovarian cancer patients (the mean crossing point value change of mesothelin was 26.9+/-0.4 in the resistant group and 34.3+/-0.7 for the sensitive group; P<0.001). Mesothelin also protected cells from paclitaxel-induced apoptosis. The protein expression of Bcl-2 family members, such as Bcl-2 and Mcl-1, was significantly increased regardless of whether cells were treated with exogenous mesothelin or were mesothelin-transfectants. Furthermore, mesothelin-treated cells revealed rapid tyrosine phosphorylation of the p85 subunit of PI3K (phosphoinositide 3-kinase) and ERK (extracellular-signal-regulated kinase) 1/2 for enhancing MAPK (mitogen-activated protein kinase) activity. The anti-apoptotic ability was suppressed and the expression of Bcl-2 family in response to mesothelin was altered by inhibiting PI3K activity, but not by inhibiting MAPK activity. Thus mesothelin can inhibit paclitaxel-induced cell death mainly by involving PI3K signalling in the regulation of Bcl-2 family expression. Mesothelin is a potential target in reducing resistance to cytotoxic drugs.","corpus_id":23918718,"score":0},{"doc_id":"20096139","title":"ABL-N-induced apoptosis in human breast cancer cells is partially mediated by c-Jun NH2-terminal kinase activation.","abstract":"INTRODUCTION: The present study was designed to determine the possibility of acetylbritannilactone (ABL) derivative 5-(5-(ethylperoxy)pentan-2-yl)-6-methyl-3-methylene-2-oxo-2,3,3a,4,7,7a-hexahydrobenzofuran-4-yl 2-(6-methoxynaphthalen-2-yl)propanoate (ABL-N) as a novel therapeutic agent in human breast cancers. METHODS: We investigated the effects of ABL-N on the induction of apoptosis in human breast cancer cells and further examined the underlying mechanisms. Moreover, tumor growth inhibition of ABL-N was done in xenograft models. RESULTS: ABL-N induced the activation of caspase-3 in estrogen receptor (ER)-negative cell lines MDA-MB-231 and MDA-MB-468, as evidenced by the cleavage of endogenous substrate Poly (ADP-ribose) polymerase (PARP). Pretreatment of cells with pan-caspase inhibitor z-VAD-fmk or caspase-3-specific inhibitor z-DEVD-fmk inhibited ABL-N-induced apoptosis. ABL-N treatment also resulted in an increase in the expression of pro-apoptotic members (Bax and Bad) with a concomitant decrease in Bcl-2. Furthermore, c-Jun-NH2-terminal kinase (JNK) and p38 mitogen-activated protein (MAP) kinase (p38) were activated in the apoptosis induced by ABL-N and JNK-specific inhibitor SP600125 and JNK small interfering RNA (siRNA) antagonized ABL-N-mediated apoptosis. However, the p38-specific inhibitor SB203580 had no effect upon these processes. Moreover, neither of the caspase inhibitors prevented ABL-N-induced JNK activation, indicating that JNK is upstream of caspases in ABL-N-initiated apoptosis. Additionally, in a nude mice xenograft experiment, ABL-N significantly inhibited the tumor growth of MDA-MB-231 cells. CONCLUSIONS: ABL-N induces apoptosis in breast cancer cells through the activation of caspases and JNK signaling pathways. Moreover, ABL-N treatment causes a significant inhibition of tumor growth in vivo. Therefore, it is thought that ABL-N might be a potential drug for use in breast cancer prevention and intervention.","corpus_id":3085133,"score":0},{"doc_id":"21468925","title":"Attenuated expression and function of the RECK tumor suppressor under hypoxic conditions is mediated by the MAPK signaling pathways.","abstract":"Downregulation of the tumor suppressor, reversion-inducing cysteine-rich protein with Kazal motifs (RECK) has been reported under hypoxic conditions (Lee et al., 2010); however, the signaling pathways involved in this downregulation have not yet been identified. Hypoxia causes the silencing of RECK mRNA expression, but treatment with inhibitors of extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 mitogen-activated kinase (MAPK) (PD98059, SP600125, and SB203580 respectively) or their dominant negative mutants recovered RECK suppression induced by hypoxia as analyzed with semiquantitative RT-PCR analysis and a RECK promoter luciferase assay. Hypoxia increased phosphorylation of ERK1/2, JNK and p38 MAPKs. The activities of matrix metalloproteinase (MMP)-9 and MMP-2 were increased under hypoxic conditions but treatment with PD98059, SP600125 and SB203580 inhibited their activation in cancer cells, as seen by zymography. Moreover, treatment with the inhibitors blocked cancer cell migration induced by hypoxia in H-Ras transformed MCF10A mammary cells. RECK suppression under hypoxic conditions was inversely related to HIF-1α expression; however, treatment with PD98059, SP600125 and SB203580 did not influence binding of HIF-1α to the reverse hypoxia responsive element site of the RECK promoter in a DNA precipitation assay. These results suggest that the ERK, JNK and p38 MAPK signaling pathways are indirectly involved in RECK suppression but are not involved in the binding activity of HIF-1α to the reverse hypoxia responsive element site on the RECK promoter under hypoxic conditions.","corpus_id":26013867,"score":0},{"doc_id":"21502402","title":"Phosphorylation of serine 68 of Twist1 by MAPKs stabilizes Twist1 protein and promotes breast cancer cell invasiveness.","abstract":"Twist1, a basic helix-loop-helix transcription factor, promotes breast tumor cell epithelial-mesenchymal transition (EMT), invasiveness, and metastasis. However, the mechanisms responsible for regulating Twist1 stability are unknown in these cells. We identified the serine 68 (Ser 68) as a major phosphorylation site of Twist1 by mass spectrometry and with specific antibodies. This Ser 68 is phosphorylated by p38, c-Jun N-terminal kinases (JNK), and extracellular signal-regulated kinases1/2 in vitro, and its phosphorylation levels positively correlate with Twist1 protein levels in human embryonic kidney 293 and breast cancer cells. Prevention of Ser 68 phosphorylation by an alanine (A) mutation (Ser 68A) dramatically accelerates Twist1 ubiquitination and degradation. Furthermore, activation of mitogen-activated protein kinases (MAPK) by an active Ras protein or TGF-β treatment significantly increases Ser 68 phosphorylation and Twist1 protein levels without altering Twist1 mRNA expression, whereas blocking of MAPK activities by either specific inhibitors or dominant negative inhibitory mutants effectively reduces the levels of both induced and uninduced Ser 68 phosphorylation and Twist protein. Accordingly, the mammary epithelial cells expressing Twist1 exhibit much higher degrees of EMT and invasiveness on stimulation with TGF-β or the active Ras and paclitaxel resistance compared with the same cells expressing the Ser 68A-Twist1 mutant. Importantly, the levels of Ser 68 phosphorylation in the invasive human breast ductal carcinomas positively correlate with the levels of Twist1 protein and JNK activity and are significantly higher in progesterone receptor-negative and HER2-positive breast cancers. These findings suggest that activation of MAPKs by tyrosine kinase receptors and Ras signaling pathways may substantially promote breast tumor cell EMT and metastasis via phoshorylation and stabilization of Twist1.","corpus_id":18469121,"score":0},{"doc_id":"22238304","title":"Varicella-Zoster virus ORF12 protein triggers phosphorylation of ERK1/2 and inhibits apoptosis.","abstract":"Mitogen-activated protein kinases (MAPKs) are a family of serine-threonine protein kinases involved in many cellular processes, including cell proliferation, differentiation, inflammation, and cell death. Activation of several MAPKs, including extracellular signal-regulated kinase 1 and 2 (ERK1/2), p38, and c-Jun N-terminal kinase (JNK), results in stimulation of activator protein 1 (AP-1), which promotes gene transcription. Previous studies have demonstrated that varicella-zoster virus (VZV) infection activates ERK1/2, p38, and JNK to promote viral replication, but the underlying mechanism(s) is unclear. To identify viral proteins responsible for the activation of MAPK, we used a proteomic approach to screen viral proteins for AP-1 promoter activation by an AP-1-luciferase reporter assay. We found that VZV ORF12 protein, located in the tegument of virions, enhances AP-1 reporter activity. This effect of ORF12 protein was markedly inhibited by a MAPK/ERK kinase 1 and 2 (MEK1/2) inhibitor (U0126), partially blocked by a p38 inhibitor (SB202190), but not inhibited by a JNK inhibitor (SP600125). Expression of VZV ORF12 protein in cells resulted in phosphorylation of ERK1/2 and p38 but not JNK. Infection of cells with a VZV ORF12 deletion mutant resulted in reduced levels of phosphorylated ERK1/2 (p-ERK1/2) compared to infection with wild-type VZV. Furthermore, deletion of ORF12 rendered VZV-infected cells more susceptible to staurosporine-induced apoptosis. In conclusion, VZV ORF12 protein activates the AP-1 pathway by selectively triggering the phosphorylation of ERK1/2 and p38. Cells infected with a VZV ORF12 deletion mutant have reduced levels of p-ERK1/2 and are more susceptible to apoptosis than cells infected with wild-type VZV.","corpus_id":7307015,"score":0},{"doc_id":"22258404","title":"ERK2 phosphorylation of serine 77 regulates Bmf pro-apoptotic activity.","abstract":"B-cell lymphoma 2 (Bcl-2) homology 3 (BH3)-only proteins represent a class of pro-apoptotic factors that neutralize pro-survival Bcl-2 proteins, and, in some cases, directly activate Bax. The mechanisms of control and the role of BH3-only proteins, such as Bcl-2 like protein 11 extra large and Bad are well studied. By contrast, relatively little is known about the regulation and role of Bcl-2 modifying factor (Bmf). The B-RAF oncogene is mutated in ∼8% of human tumors. We have previously shown that Bmf is upregulated at the transcript level and is required for apoptosis induced by targeting B-RAF signaling in tumor cells harboring mutant B-RAF. In this study, we show that Bmf is regulated at the post-translational level by mutant B-RAF-MEK-ERK2 signaling. Extracellular signal-regulated kinase (ERK2) directly phosphorylates Bmf on serine 74 and serine 77 residues with serine 77 being the predominant site. In addition, serine 77 phosphorylation reduces Bmf pro-apoptotic activity likely through a mechanism independent of altering Bmf localization to the mitochondria and/or interactions with dynein light chain 2 and the pro-survival proteins, B-cell lymphoma extra large, Bcl-2 and Mcl-1. These data identify a novel mode of regulation in Bmf that modulates its pro-apoptotic activity in mutant B-RAF tumor cells.","corpus_id":8660265,"score":0},{"doc_id":"23135225","title":"Vaspin attenuates the apoptosis of human osteoblasts through ERK signaling pathway.","abstract":"It has been hypothesized that adipocytokines originating from adipose tissue may have an important role in bone metabolism. Vaspin is a novel adipocytokine isolated from visceral white adipose tissue, which has been reported to have anti-apoptotic effects in vascular endothelial cells. However, to the best of our knowledge there is no information regarding the effects of vaspin on osteoblast apoptosis. This study therefore examined the possible effects of vaspin on apoptosis in human osteoblasts (hOBs). Our study established that vaspin inhibits hOBs apoptosis induced by serum deprivation, as determined by ELISA and TUNEL assays. Western blot analysis revealed that vaspin upregulates the expression of Bcl-2 and downregulates that of Bax in a dose-dependent manner. Vaspin stimulated the phosphorylation of ERK, and pretreatment of hOBs with the ERK inhibitor PD98059 blocked the vaspin-induced activation of ERK, however, vaspin did not stimulate the phosphorylation of p38, JNK or Akt. Vaspin protects hOBs from serum deprivation-induced apoptosis, which may be mediated by activating the MAPK/ERK signaling pathway.","corpus_id":1755050,"score":0},{"doc_id":"23577223","title":"Oxidative stress and mitogen-activated protein kinase pathways involved in cadmium-induced BRL 3A cell apoptosis.","abstract":"In this study, BRL 3A cells were treated with different Cd concentrations (0, 10, 20, and 40 μmol/L) for 12 h and preincubated with or without N-acetyl-L-cysteine (NAC) (2 mmol/L) for 30 min, and cells were treated with Cd (0 and 20 μmol/L), pretreated with p38 inhibitor (SB203580), JNK (c-Jun NH2-terminal kinases) inhibitor (SP600125), and extracellular signal-regulated kinase (ERK) inhibitor (U0126) for 30 min, and then treated with 20 μmol/L Cd for 12 h. Cd decreased cell viability, SOD, and GSH-Px activity in a concentration-dependent manner. Increased MDA level, ROS generation, nuclear condensation, shrinkage, and fragmentation in cell morphology were inhibited by NAC. Cd-induced apoptosis was attenuated by pretreatment with SB203580, SP600125, and U0126. The results of western blot showed that NAC preincubation affected Cd-activated MAPK pathways, p38 and ERK phosphorylation. Cd treatment elevated the mRNA levels of Bax and decreased the mRNA levels of Bcl-2, respectively. The same effect was found in their protein expression levels. These results suggest that oxidative stress and MAPK pathways participate in Cd-induced apoptosis and that the balance between pro- and antiapoptotic genes (Bax and Bcl-2) is important in Cd-induced apoptosis.","corpus_id":6233368,"score":0},{"doc_id":"23707804","title":"Brazilein suppresses migration and invasion of MDA-MB-231 breast cancer cells.","abstract":"Brazilein, a bioactive compound isolated from Caesalpinia sappan L., has long been used in oriental folk medicines. Cancer metastasis is a primary cause of cancer death. However, the anti-metastatic effects of brazilein remain elusive. In this study, we found that brazilein inhibited human breast cancer MDA-MB-231 cell migration and invasion using wound-healing assay and Boyden chamber assay. The results of Western blot, gelatin zymography and reversed transcription-PCR analysis showed that brazilein suppressed matrix metalloproteinase-2 (MMP-2) expression in a concentration-dependent manner. Brazilein also decreased the nuclear protein level of nuclear factor kappaB (NF-κB). Brazilein potently suppressed the phosphorylation of p38 mitogen-activated protein kinase (p38 MAPK), phosphatidylinositide-3-kinase (PI3K) and Akt, but did not affect phosphorylation of extracellular signal regulating kinase (ERK)1/2 and c-Jun N-terminal kinase (JNK). Additionally, treatment of SB203580 (p38 MAPK inhibitor) or wortmannin (PI3K inhibitor) resulted in a reduced activity and expression of MMP-2 as well as inhibition on cell migration and invasion in MDA-MB-231 cells. Taken together, these results suggest that brazilein inhibition of MDA-MB-231 cells may be mediated through inactivation of both PI3K/Akt and p38 MAPK signaling pathways, leading to inhibitory effect on NF-κB activation. Consequently, brazilein suppresses MMP-2 expression, and thus confers anti-migration and anti-invasion of MDA-MB-231 cells.","corpus_id":5435205,"score":0},{"doc_id":"24589734","title":"Differences in c-Jun N-terminal kinase recognition and phosphorylation of closely related stathmin-family members.","abstract":"The stathmin (STMN) family of tubulin-binding phosphoproteins are critical regulators of interphase microtubule dynamics and organization in a broad range of cellular processes. c-Jun N-terminal kinase (JNK) signalling to STMN family proteins has been implicated specifically in neuronal maturation, degeneration and cell stress responses more broadly. Previously, we characterized mechanisms underlying JNK phosphorylation of STMN at proline-flanked serine residues (Ser25 and Ser38) that are conserved across STMN-like proteins. In this study, we demonstrated using in vitro kinase assays and alanine replacement of serine residues that JNK phosphorylated the STMN-like domain (SLD) of SCG10 on Ser73, consistent with our previous finding that STMN Ser38 was the primary JNK target site. In addition, we confirmed that a JNK binding motif ((41)KKKDLSL(47)) that facilitates JNK targeting of STMN is conserved in SCG10. In contrast, SCLIP was phosphorylated by JNK primarily on Ser60 which corresponds to Ser25 on STMN. Moreover, although the JNK-binding motif identified in STMN and SCG10 was not conserved in SCLIP, JNK phosphorylation of SCLIP was inhibited by a substrate competitive peptide (TI-JIP) highlighting kinase-substrate interaction as required for JNK targeting. Thus, STMN and SCG10 are similarly targeted by JNK but there are clear differences in JNK recognition and phosphorylation of the closely related family member, SCLIP.","corpus_id":19988564,"score":0},{"doc_id":"28393288","title":"Differential effects of p38 MAP kinase inhibitors SB203580 and SB202190 on growth and migration of human MDA-MB-231 cancer cell line.","abstract":"p38 mitogen-activated protein kinase (MAPK) belongs to the MAPK superfamily, phosphorylating serine and/or threonine residues of the target proteins. The activation of p38 MAPK leads to cell growth, differentiation, inflammation, survival or apoptosis. In this study, we tested the effect of two highly specific and potent inhibitors of p38 MAPK (namely, SB203580 and SB202190) on human breast cancer cell line MDA-MB-231 to elucidate the controversial role of p38 MAPK on cell proliferation and/or cell migration/metastasis further. It was determined that the IC50 value of SB203580 was 85.1 µM, while that of SB202190 was 46.6 µM, suggesting that SB202190 is slightly more effective than SB203580. To verify the effect of each inhibitor on cell proliferation and cytotoxicity, the cells were treated with various doses of SB203580 and SB202190 and examined using iCELLigence system. No significant effect of 1 and 5 µM of both inhibitors were seen on cell proliferation as compared to the DMSO-treated control cells for up to 96 h. On the other hand, both SB203580 and SB202190 significantly prevented cell proliferation at a concentration of 50 µM. SB202190 was again more effective than SB203580. Afterwards, we tested the effect of each inhibitor on cell migration using wound assay. Both SB203580 and SB202190 significantly reduced cell migration in a time-dependent manner at a concentration of 50 µM. However, interestingly it was observed that a low and noncytotoxic dose of 5 µM of SB203580 and SB202190 also did cause significant cell migration inhibition at 48 h of the treatment, corroborating the fact that p38 MAPK pathway has a critical role in cell migration/metastasis. Then, we tested whether each p38 MAPK inhibitor has any effect on cell adhesion during a treatment period of 3 h using iCELLigence system. A concentration of only 50 µM of SB202190 reduced cell adhesion for about 1.5 h (p < 0.001); after that period of time, cell adhesion in 50 µM SB202190-treated cells returned to the level of the control cells. To determine the mechanism of growth and cell migration inhibitory effects of p38 MAPK inhibitors, the activation/inactivation of various proteins and enzymes was subsequently analyzed by PathScan(®) Intracellular Signaling Array kit. The ERK1/2 phosphorylation level was not modified by low concentrations (1 or 5 µM) of SB202190 and SB203580; while a high concentration (50 µM) of both inhibitors caused significant reductions in the ERK1/2 phosphorylation. In addition, it was determined that both p38 MAPK inhibitors caused significant increases on the Ser15 phosphorylation of mutant p53 in MDA-MB-231 under these experimental conditions; while SB202190 was more potent than SB203580.","corpus_id":44326135,"score":0},{"doc_id":"29022012","title":"Vanadate oxidative and apoptotic effects are mediated by the MAPK-Nrf2 pathway in layer oviduct magnum epithelial cells.","abstract":"Vanadium is a metal of high physiological, environmental and industrial importance. However, vanadium-induced oxidative stress can reduce the egg quality of poultry, and be potentially harmful to humans, and the underlying mechanism is not clear. In this study, we investigated the underlying relationship between the oxidant-sensitive mitogen-activated protein kinase (MAPK) signaling pathway and vanadium-induced oxidative stress in oviduct magnum epithelial (OME) cells. Cultured OME cells were treated with 100 μmol L-1 vanadium and/or MAPK inhibitors [P38 MAPK inhibitor, SB203580; extracellular regulated protein kinase 1 and 2 (ERK1/2) inhibitor, U0126; c-JUN N-terminal kinases (JNK) inhibitor, SP600125]. Cell viability, apoptosis, and generation of reactive oxygen species (ROS) were assessed using flow cytometry. The expression of oxidative stress-related genes and their proteins was measured by reverse transcription-polymerase chain reaction and western blotting. Vanadium treatment reduced cell viability, whereas pretreated OME cells with SB203580 and U0126 prevented the reducing effect of vanadium on cell viability (P < 0.05). Likewise, MAPK inhibitors effectively suppressed vanadium-induced apoptosis and ROS generation (P < 0.05). In the OME cells treated with vanadium, SB203580 (P < 0.05) and SP600125 (P = 0.08) increased catalase activity by 89.3% and 55.3%; SB203580 and U0126 increased (P < 0.05) glutathione peroxidase activity by 44.9% and 51.1%, respectively. Incubation of OME cells with MAPK inhibitors also prevents malondialdehyde concentration increase and lactic dehydrogenase activity decrease in response to vanadium (P < 0.05). Vanadium downregulated P38, ERK1/2, JNK, Nrf2, sMaf, GCLC, NQO1 and HO-1 mRNA expression (P < 0.05). In contrast, inhibition of JNK with SP600125 upregulated P38, ERK1/2, JNK, Nrf2, GCLC and HO-1 mRNA expression (P < 0.05); inhibition of P38 with SB203580 upregulated JNK, NQO1 and HO-1 mRNA expression (P < 0.05); and inhibition of ERK1/2 with U0126 upregulated ERK1/2, GCLC and HO-1 mRNA expression (P < 0.05). Moreover, phosphorylation of P38, ERK1/2, JNK, and Nrf2 proteins was enhanced by V incubation; however, SP600125 blocked the phosphorylation of these proteins, whereas SB203580 blocked the phosphorylation of P38 and Nrf2. These results indicate that vanadium inducing oxidative stress in OME cells might be, at least, associated with the phosphorylation of the P38MAPK/JNK-Nrf2 pathway, which reduces the expression of phase II detoxifying enzymes.","corpus_id":206096005,"score":0}],"string":"[\n {\n \"doc_id\": \"18201741\",\n \"title\": \"The contribution of c-Jun N-terminal kinase activation and subsequent Bcl-2 phosphorylation to apoptosis induction in human B-cells is dependent on the mode of action of specific stresses.\",\n \"abstract\": \"The c-Jun N-terminal kinase (JNK) pathway can play paradoxical roles as either a pro-survival or a pro-cell death pathway depending on type of stress and cell type. The goal of the present study was to determine the role of JNK pathway signaling for regulating B-cell apoptosis in two important but contrasting situations--global proteotoxic damage, induced by arsenite and hyperthermia, versus specific microtubule inhibition, induced by the anti-cancer drug vincristine, using the EW36 B-cell line. This cell line over-expresses the Bcl-2 protein and is a useful model to identify treatments that can overcome multi-drug resistance in lymphoid cells. Exposure of EW36 B-cells to arsenite or lethal hyperthermia resulted in activation of the JNK pathway and induction of apoptosis. However, pharmacological inhibition of the JNK pathway did not inhibit apoptosis, indicating that JNK pathway activation is not required for apoptosis induction by these treatments. In contrast, vincristine treatment of EW36 B-cells resulted in JNK activation and apoptosis that was suppressed by JNK inhibition. A critical difference between the two types of stress treatments was that only vincristine-induced JNK activation resulted in phosphorylation of Bcl-2 at threonine-56, a modification that can block its anti-apoptotic function. Importantly, Bcl-2 phosphorylation was attenuated by JNK inhibition implicating JNK as the upstream kinase. Furthermore, arsenite and hyperthermia treatments activated a p53/p21 pathway associated with apoptosis induction, whereas vincristine did not activate this pathway. These results reveal two stress-activated pathways, one JNK-dependent and another JNK-independent, either of which can bypass Bcl-2 mediated resistance, resulting in cell death.\",\n \"corpus_id\": 19271563,\n \"score\": 2\n },\n {\n \"doc_id\": \"18412143\",\n \"title\": \"The role of p38 MAPK and JNK in Arsenic trioxide-induced mitochondrial cell death in human cervical cancer cells.\",\n \"abstract\": \"Previously, we have shown that the release of AIF from mitochondria is required for As2O3-induced cell death in human cervical cancer cells, and that reactive oxygen species (ROS) is necessary for AIF release from mitochondria. In this study, we further investigated the role of MAPKs in ROS-mediated mitochondrial apoptotic cell death triggered by As2O3. As2O3-induced apoptotic cell death in HeLa cells was associated with activation and mitochondrial translocation of Bax, a marked phosphorylation of Bcl-2, reduction of Bcl-2 and Bax interaction, dissipation of mitochondrial membrane potential. Using small interfering RNA, reduced Bax expression effectively attenuated As2O3-induced mitochondrial membrane potential loss and apoptotic cell death. Moreover, the phosphorylation of Bcl-2 induced by As2O3 diminished its ability to bind to Bax. Treatment of cells with As2O3 activated both the p38 MAPK and JNK pathways. Mitochondrial translocation of Bax was completely suppressed in the presence of p38 MAPK inhibitor PD169316 or si-p38 MAPK. The As2O3-induced Bcl-2 phosphorylation was attenuated largely by JNK inhibition using SP600125 or si-JNK and to some extent by p38 MAPK inhibition with PD169316 or si-p38 MAPK. In addition, N-acetyl-L-cystein (NAC), a thiol-containing anti-oxidant, completely blocked As2O3-induced p38 MAPK and JNK activations, mitochondria translocation of Bax, and phosphorylation of Bcl-2. These results support a notion that ROS-mediated activations of p38 MAPK and JNK in response to As2O3 treatment signals activation of Bax and phosphorylation of Bcl-2, resulting in mitochondrial apoptotic cell death in human cervical cancer cells.\",\n \"corpus_id\": 25492988,\n \"score\": 2\n },\n {\n \"doc_id\": \"18534198\",\n \"title\": \"Requirement of the JNK-associated Bcl-2 pathway for human lactoferrin-induced apoptosis in the Jurkat leukemia T cell line.\",\n \"abstract\": \"The cell proliferation of p53-deficient Jurkat T cells is controlled after prolonged exposure to human lactoferrin (Lf). However, the molecular mechanism by which Lf influences these cellular responses remains unclear. In this study, we demonstrate that Lf-induced apoptosis in Jurkat T cells occurs in a dose- and time-dependent manner via the regulation of c-Jun N-terminal kinase (JNK) activity. Jurkat cells exposed to Lf for 1 day, especially at concentrations in excess of 500 microg/ml, showed typical apoptosis, as indicated by decreased cell viability and increased Annexin V binding. Our results also showed that Lf induced the activation of caspase 9 and caspase 3 activation, as demonstrated by our detection of cleaved caspases and PARP. Lf-induced apoptosis did not influence Bcl-2 expression via an ERK1/2 phosphorylation pathway, but was rather associated with the level of Bcl-2 phosphorylation. The treatment of cells with the specific JNK inhibitor SP600125, but not the p38 MAPK inhibitor SB203580, revealed that the JNK-Bcl-2 signaling cascade is required for Lf-induced apoptosis. When JNK activation was abolished by SP600125, no Bcl-2 phosphorylation was detected, and the Lf-treated Jurkat cells did not undergo cell death. These findings indicate that Lf functions as a biological mediator of apoptosis in the human leukemia Jurkat T-cell line, via the JNK-associated Bcl-2 signaling pathway.\",\n \"corpus_id\": 205994478,\n \"score\": 2\n },\n {\n \"doc_id\": \"22262057\",\n \"title\": \"Inactivation of Bcl-2 through IκB kinase (IKK)-dependent phosphorylation mediates apoptosis upon exposure to 4-hydroxynonenal (HNE).\",\n \"abstract\": \"Apoptosis of macrophage foam cells loaded with modified/oxidized lipids is implicated in destabilization of advanced atherosclerotic plaques in humans. Concentration of HNE, main aldehydic product of plasma LDL peroxidation, elevates in atherosclerotic lesions as well as in cultured cells under oxidative stress. Although this reactive aldehyde has been shown to promote apoptosis with the involvement of p38 MAPK and JNK in various mammalian cell lines, roles of B-cell lymphoma 2 (Bcl-2) family proteins remain to be deciphered. We demonstrated that HNE-induced apoptosis was accompanied by concurrent downregulations of antiapoptotic Bcl-x(L) and Mcl-1 as well as upregulation of proapoptotic Bak. Furthermore, phoshorylation of Bcl-2 at Thr56, Ser70, and probably more phosphorylation sites located on N-terminal loop domain associated with HNE-induced apoptosis in both U937 and HeLa cells while ectopic expression of a phospho-defective Bcl-2 mutant significantly attenuated apoptosis. In parallel to this, HNE treatment caused release of proapoptotic Bax from Bcl-2. Pharmacological inhbition of IKK inhibited HNE-induced Bcl-2 phosphorylation. Similarly, silencing IKKα and -β both ended up with abrogation of Bcl-2 phosphorylation along with attenuation of apoptosis. Moreover, both IKKα and -β coimmunoprecipitated with Bcl-2 and in vitro kinase assay proved the ability of IKK to phosphorylate Bcl-2. In view of these findings and considering HNE inhibits DNA-binding activity of nuclear factor-κB (NF-κB) through prevention of IκB phosphorylation/ubiquitination/proteolysis, IKK appears to directly interfere with Bcl-2 activity through phosphorylation in HNE-mediated apoptosis independent of NF-κB signaling.\",\n \"corpus_id\": 19923494,\n \"score\": 2\n },\n {\n \"doc_id\": \"22433870\",\n \"title\": \"Tyrosine-phosphorylated caveolin-1 (Tyr-14) increases sensitivity to paclitaxel by inhibiting BCL2 and BCLxL proteins via c-Jun N-terminal kinase (JNK).\",\n \"abstract\": \"Paclitaxel, an anti-microtubule agent, is an effective chemotherapeutic drug in breast cancer. Nonetheless, resistance to paclitaxel remains a major clinical challenge. The need to better understand the resistant phenotype and to find biomarkers that could predict tumor response to paclitaxel is evident. In estrogen receptor α-positive (ER(+)) breast cancer cells, phosphorylation of caveolin-1 (CAV1) on Tyr-14 facilitates mitochondrial apoptosis by increasing BCL2 phosphorylation in response to low dose paclitaxel (10 nM). However, two variants of CAV1 exist: the full-length form, CAV1α (wild-type CAV1 or wtCAV1), and a truncated form, CAV1β. Only wtCAV1 has the Tyr-14 region at the N terminus. The precise cellular functions of CAV1 variants are unknown. We now show that CAV1 variants play distinct roles in paclitaxel-mediated cell death/survival. CAV1β expression is increased in paclitaxel-resistant cells when compared with sensitive cells. Expression of CAV1β in sensitive cells significantly reduces their responsiveness to paclitaxel. These activities reflect an essential role for Tyr-14 phosphorylation because wtCAV1 expression, but not a phosphorylation-deficient mutant (Y14F), inactivates BCL2 and BCLxL through activation of c-Jun N-terminal kinase (JNK). MCF-7 cells that express Y14F are resistant to paclitaxel and are resensitized by co-treatment with ABT-737, a BH3-mimetic small molecule inhibitor. Using structural homology modeling, we propose that phosphorylation on Tyr-14 enables a favorable conformation for proteins to bind to the CAV1 scaffolding domain. Thus, we highlight novel roles for CAV1 variants in cell death; wtCAV1 promotes cell death, whereas CAV1β promotes cell survival by preventing inactivation of BCL2 and BCLxL via JNK in paclitaxel-mediated apoptosis.\",\n \"corpus_id\": 25431731,\n \"score\": 2\n },\n {\n \"doc_id\": \"22953963\",\n \"title\": \"Acanthoic acid induces cell apoptosis through activation of the p38 MAPK pathway in HL-60 human promyelocytic leukaemia.\",\n \"abstract\": \"The present study was designed to evaluate the molecular mechanisms of the action of acanthoic acid (ACAN) from Acanthopanax koreanum (Araliaceae) against HL-60 human promyelocytic leukaemia cells. ACAN reduced the proliferation of HL-60 cells in a dose- and time-dependent manner accompanied by the induction of apoptosis. Possible mechanisms of ACAN-induced apoptosis were also examined. The results showed that ACAN-induced the phosphorylation of members of the mitogen-activated protein kinase (MAPK) family, c-Jun N-terminal kinase (JNK), p38 MAPK (p38), and extracellular signal-regulated kinase (ERK). A specific p38 MAPK inhibitor (SB203580) significantly blocked ACAN-induced apoptosis and cell viability, whereas an ERK inhibitor (PD98059) and JNK inhibitor (SP600125) had no effect. Moreover, ACAN induced the cleavage of caspase-3 and poly-ADP-ribose polymerase (PARP), and decreased the level of Bcl-xL, but these effects were inhibited by SB203580 pre-treatment. These results strongly suggest that ACAN may have cancer chemopreventive and therapeutic potential, due to its ability to activate the p38 MAPK-mediated signalling pathways.\",\n \"corpus_id\": 22731309,\n \"score\": 2\n },\n {\n \"doc_id\": \"23272207\",\n \"title\": \"The natively disordered loop of Bcl-2 undergoes phosphorylation-dependent conformational change and interacts with Pin1.\",\n \"abstract\": \"Bcl-2 plays a central role in the regulation of apoptosis. Structural studies of Bcl-2 revealed the presence of a flexible and natively disordered loop that bridges the Bcl-2 homology motifs, BH3 and BH4. This loop is phosphorylated on multiple sites in response to a variety of external stimuli, including the microtubule-targeting drugs, paclitaxel and colchicine. Currently, the underlying molecular mechanism of Bcl-2 phosphorylation and its biological significance remain elusive. In this study, we investigated the molecular characteristics of this anti-apoptotic protein. To this end, we generated synthetic peptides derived from the Bcl-2 loop, and multiple Bcl-2 loop truncation mutants that include the phosphorylation sites. Our results demonstrate that S87 in the flexible loop of Bcl-2 is the primary phosphorylation site for JNK and ERK2, suggesting some sequence or structural specificity for the phosphorylation by these kinases. Our NMR studies and molecular dynamics simulation studies support indicate that phosphorylation of S87 induces a conformational change in the peptide. Finally, we show that the phosphorylated peptides of the Bcl-2 loop can bind Pin1, further substantiating the phosphorylation-mediated conformation change of Bcl-2.\",\n \"corpus_id\": 14581799,\n \"score\": 2\n },\n {\n \"doc_id\": \"23415863\",\n \"title\": \"Paclitaxel attenuates Bcl-2 resistance to apoptosis in breast cancer cells through an endoplasmic reticulum-mediated calcium release in a dosage dependent manner.\",\n \"abstract\": \"To address the controversy regarding efficacy of paclitaxel in the presence of the anti-apoptotic protein Bcl-2, we investigated calcium stored in the endoplasmic reticulum as a potential factor. Our results showed that the ER calcium store is a common target for both paclitaxel and Bcl-2 protein. Paclitaxel directly associates with the endoplasmic reticulum to stimulate the release of calcium into the cytosol, contributing to the induction of apoptosis. However, Bcl-2 expression suppresses the cell's pro-apoptotic response of endoplasmic reticulum calcium release, thus inhibiting susceptibility of cancer cells to undergo apoptosis. Depending upon dosage, a paclitaxel-induced stimulatory effect can overcome the Bcl-2-mediated inhibitory effect on endoplasmic reticulum calcium release, thus attenuating the resistance of Bcl-2 to apoptosis. Our finding is the first to demonstrate that endoplasmic reticulum calcium plays a key role in the efficacy of paclitaxel in the presence of Bcl-2, thus providing insight into the complex but crucial paclitaxel-calcium-Bcl-2 relationship, which may impact breast cancer treatment.\",\n \"corpus_id\": 2719810,\n \"score\": 2\n },\n {\n \"doc_id\": \"25815462\",\n \"title\": \"Apoptosis of HL-60 human leukemia cells induced by Asiatic acid through modulation of B-cell lymphoma 2 family proteins and the mitogen-activated protein kinase signaling pathway.\",\n \"abstract\": \"The toxicities of conventional chemotherapeutic agents to normal cells restrict their dosage and clinical efficacy in acute leukemia; therefore, it is important to develop novel chemotherapeutics, including natural products, which selectively target cancer-specific pathways. The present study aimed to explore the effect of the chemopreventive agent asiatic acid (AA) on the proliferation and apoptotic rate of the leukemia cell line HL-60 and investigated the mechanisms underlying its anti-tumor activity. The effect of AA on the proliferation of HL-60 cells was evaluated using the MTT assay. Annexin V-fluorescein isothiocyanate/propidium iodide double staining followed by flow cytometric analysis as well as Hoechst 33258 staining were used to analyze the apoptotic rate of the cells. Furthermore, changes of survivin, B-cell lymphoma 2 (Bcl-2), myeloid cell leukemia 1 (Mcl-1), extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK) and p38 expressions were detected by western blot analysis. AA blocked the growth of HL-60 cells in a dose- and time-dependent manner. The IC50-value of AA on HL-60 cells was 46.67 ± 5.08 µmol/l for 24 h. AA induced apoptosis in a dose-dependent manner, which was inhibited in the presence of Z-DEVD-FMK, a specific inhibitor of caspase. The anti-apoptotic proteins Bcl-2, Mcl-1 and survivin were downregulated by AA in a dose-dependent manner. Concurrently, AA inhibited ERK and p38 phosphorylation in a dose-dependent manner, while JNK phosphorylation was not affected. In conclusion, the present study indicated that the p38 and ERK pathways, as well as modulation of Bcl-2 family and survivin proteins were key regulators of apoptosis induced in HL-60 cells in response to AA.\",\n \"corpus_id\": 14178799,\n \"score\": 2\n },\n {\n \"doc_id\": \"25876659\",\n \"title\": \"Dominant negative form of alpha4 inhibits the BCR crosslinking-induced phosphorylation of Bcl-xL and apoptosis in an immature B cell line WEHI-231.\",\n \"abstract\": \"We previously demonstrated that c-Jun N-terminal kinase (JNK) phosphorylates serine 62 of Bcl-xL to induce the degradation of Bcl-xL and apoptosis in WEHI-231 cells upon BCR crosslinking. In order to elucidate the regulatory mechanisms underlying the phosphorylation of Bcl-xL, we prepared an assay system in which JNK phosphorylated Bcl-xL in HEK293T cells. Consequently, we found that a signal transduction molecule, alpha4, enhanced the phosphorylation of Bcl-xL by JNK, while the co-expression of C-terminal alpha4 (220-340) diminished the phosphorylation of Bcl-xL induced by JNK. Furthermore, full-length alpha4 associated with both JNK and Bcl-xL, whereas C-terminal alpha4 (220-340) associated only with Bcl-xL, not JNK. In addition, WEHI-231 cells transfected with the cDNA of C-terminal alpha4 (220-340) exhibited decreased phosphorylation of Bcl-xL and stronger resistance to apoptosis induced by BCR crosslinking. These results indicate that alpha4 is an important regulatory molecule of apoptosis induced by BCR crosslinking in WEHI-231 cells and that C-terminal alpha4 (220-340) functions as a dominant negative form.\",\n \"corpus_id\": 24270214,\n \"score\": 2\n },\n {\n \"doc_id\": \"28731137\",\n \"title\": \"Phosphorylation of Bcl-2 plays an important role in glycochenodeoxycholate-induced survival and chemoresistance in HCC.\",\n \"abstract\": \"Hepatocellular carcinoma (HCC) is a highly malignant tumor and can evolve rapidly to resistance to chemotherapies. Glycochenodeoxycholate (GCDA), which is toxic and hydrophobic, is the main ingredient in the bile and associated with carcinogenesis of gastrointenstinal tumors. Bcl-2 is the most important anti-apoptotic protein and overexpressed in various human tumors. In the present study, we found that GCDA can induce the chemoresistance of human liver cancer cells and specific depletion of Bcl-2 by RNA interference blocks GCDA-stimulated chemoresistance, which indicate the pivotal role of Bcl-2 in such process. Mechanistically, GCDA simultaneously stimulates phosphorylation of Bcl-2 at Ser70 site and activates extracellular signal-regulated kinase 1/2 (ERK1/2), and inhibition of ERK1/2 by PD98059 (MAPK/ERK1/2 inhibitor) or siRNA (targeting ERK1/2) suppresses GCDA-stimulated phosphorylation of Bcl-2 and significantly attenuates the survival and chemoresistance induced by GCDA in liver cancer cells. Thus, GCDA-induced survival and chemoresistance of liver cancer cells may occur through activation of Bcl-2 by phosphorylation at Ser70 site through MAPK/ERK1/2 pathway, which may contribute to the development of human liver cancer and chemoresistance.\",\n \"corpus_id\": 22610268,\n \"score\": 2\n },\n {\n \"doc_id\": \"18021293\",\n \"title\": \"MAPK and mTOR pathways are involved in cadmium-induced neuronal apoptosis.\",\n \"abstract\": \"Cadmium (Cd) may be accumulated in human body through long-term exposure to Cd-polluted environment, resulting in neurodegeneration and other diseases. To study the mechanism of Cd-induced neurodegeneration, PC12 and SH-SY5Y cells were exposed to Cd. We observed that Cd-induced apoptosis in the cells in a time- and concentration-dependent manner. Cd rapidly activated the mitogen-activated protein kinases (MAPK) including extracellular signal-regulated kinase 1/2 (Erk1/2), c-Jun N-terminal kinase (JNK) and p38. Inhibition of Erk1/2 and JNK, but not p38, partially protected the cells from Cd-induced apoptosis. Consistently, over-expression of dominant negative c-Jun or down-regulation of Erk1/2, but not p38 MAPK, partially prevented Cd-induced apoptosis. To our surprise, Cd also activated mammalian target of rapamycin (mTOR)-mediated signaling pathways. Treatment with rapamycin, an mTOR inhibitor, blocked Cd-induced phosphorylation of S6K1 and eukaryotic initiation factor 4E binding protein 1, and markedly inhibited Cd-induced apoptosis. Down-regulation of mTOR by RNA interference also in part, rescued cells from Cd-induced death. These findings indicate that activation of the signaling network of MAPK and mTOR is associated with Cd-induced neuronal apoptosis. Our results strongly suggest that inhibitors of MAPK and mTOR may have a potential for prevention of Cd-induced neurodegeneration.\",\n \"corpus_id\": 10910517,\n \"score\": 1\n },\n {\n \"doc_id\": \"18049903\",\n \"title\": \"Acetylcholine inhibits long-term hypoxia-induced apoptosis by suppressing the oxidative stress-mediated MAPKs activation as well as regulation of Bcl-2, c-IAPs, and caspase-3 in mouse embryonic stem cells.\",\n \"abstract\": \"This study examined the effect of acetylcholine (ACh) on the hypoxia-induced apoptosis of mouse embryonic stem (ES) cells. Hypoxia (60 h) decreased both the cell viability and level of [3H] thymidine incorporation, which were prevented by a pretreatment with ACh. However, the atropine (ACh receptor [AChR] inhibitor) treatment blocked the protective effect of ACh. Hypoxia (90 min) increased the intracellular level of reactive oxygen species (ROS). On the other hand, ACh inhibited the hypoxia-induced increase in ROS, which was blocked by an atropine treatment. Subsequently, the hypoxia-induced ROS increased the level of p38 mitogen activated protein kinase (MAPK) and Jun-N-terminal kinase (JNK) phosphorylation, which were inhibited by the ACh pretreatment. Moreover, hypoxic exposure (90 min) increased the level of nuclear factor-kappa B (NF-kappa B) phosphorylation, which was blocked by a pretreatment with SB 203580 (p38 MAPK inhibitor) or SP 600125 (JNK inhibitor). However, hypoxia (60 h) decreased the protein levels of Bcl-2 and c-IAPs (cellular inhibitor of apoptosis proteins) but increased the level of caspase-3 activation. All these effects were inhibited by a pretreatment with ACh. In conclusion, ACh prevented the hypoxia-induced apoptosis of mouse ES cells by inhibiting the ROS-mediated p38 MAPK and JNK activation as well as the regulation of Bcl-2, c-IAPs, and caspase-3.\",\n \"corpus_id\": 1706453,\n \"score\": 1\n },\n {\n \"doc_id\": \"18059338\",\n \"title\": \"p38 MAPK plays an essential role in apoptosis induced by photoactivation of a novel ethylene glycol porphyrin derivative.\",\n \"abstract\": \"In this study, we provide evidence that photostimulation of various cancer cells preloaded with a new photosensitizing compound, tetrakis-meso-(4-ethyleneglycol-2,3,5,6-tetrafluorophenyl) porphyrin (PORF-TEG), results in rapid activation of the cell death machinery. PORF-TEG, although primarily localized in lysosomes, induces mitochondria-driven apoptosis. The induction of apoptosis is accompanied by immediate and sustained activation of p38 mitogen-activated protein kinase (MAPK) and transient activation of c-Jun N-terminal kinase (JNK). Conversely, the inhibition of p38 by PD 169316 or SB202190 and by the p38alpha dominant-negative mutant as well as the deletion of the p38alpha gene (MEFs-KO) protected cells from apoptosis, whereas inhibition of JNK did not. Activation of the p38 signaling pathway occurs upstream of caspase activation. In addition, preincubation of cells with scavengers of reactive oxygen species attenuated p38 and caspase activation and increased cell survival, thus connecting reactive oxygen species formation with the activation of the p38 pathway. Later events included degradation of Bcl-2, activation of tBid, and cleavage of Bad and Mcl-1. The data suggest a key role for p38 MAPK in PORF-TEG-photoinduced apoptosis.\",\n \"corpus_id\": 12329087,\n \"score\": 1\n },\n {\n \"doc_id\": \"18222647\",\n \"title\": \"Activation of c-Jun N-terminal kinase (JNK) by widely used specific p38 MAPK inhibitors SB202190 and SB203580: a MLK-3-MKK7-dependent mechanism.\",\n \"abstract\": \"Mitogen-activated protein kinases (MAPKs) are key signaling molecules that respond to mitogenic stimulation or environmental stress, resulting in the expression of target proteins. c-Jun N-terminal kinase (JNK) and p38 MAPKs are activated by inflammatory cytokines or environmental stress. Specific p38 MAPK inhibitors, such as SB202190 or SB203580, are widely used to dissect p38 MAPK-related signal transduction mechanisms. While using SB202190 to inhibit p38 MAPK-related signaling, we observed that SB202190 treatment could activate JNK. Further experiments showed that treatment of cells with SB202190 could phosphorylate JNK and activating transcription factor 2 (ATF-2), and increased AP-1 DNA binding. Using multiple cell lines and primary endothelial cells, we demonstrated that specific p38 MAPK inhibitors SB202190 or SB203580 induces the activation of the JNK pathway. Further, using with RNA interference and kinase-inactive expression of intermediates of the JNK pathway, we demonstrated SB202190- or SB203580-induced JNK activation is dependent on the MLK-3-MKK4/MKK7-dependent signal transduction pathway. Finally, we demonstrate that treatment of cells with SB202190 or SB203580 induces the phosphorylation and activation of MLK3.\",\n \"corpus_id\": 24351356,\n \"score\": 1\n },\n {\n \"doc_id\": \"18695917\",\n \"title\": \"Role of p38 MAPK and JNK in enhanced cervical cancer cell killing by the combination of arsenic trioxide and ionizing radiation.\",\n \"abstract\": \"Enhancement of radiation response is possible to be achieved by combination treatment with therapeutic drugs. Previously we have shown that As2O3 in combination with ionizing radiation enhanced radiation response in cervical cancer cells. In this study, we further investigated molecular mechanism of synergistic enhancement of radiation response in combination with As2O3. The combination treatment of HeLa cells induced translocation of Bax to the mitochondria and a marked phosphorylation of Bcl-2. p38 MAPK and JNK were also found to be activated in response to the combination treatment. Pretreatment of PD169316, a p38 MAPK specific inhibitor, completely attenuated the combination treatment-induced mitochondrial relocalization of Bax, and altered Bcl-2 phosphorylation. Moreover, pretreatment of SP600125, JNK specific inhibitor, clearly attenuated Bcl-2 phosphorylation, but did not affect Bax translocation to the mitochondria. In addition, N-acetyl-L-cysteine (NAC), a thiol-containing anti-oxidant, completely blocked p38 MAPK and JNK activations, Bax relocalization and Bcl-2 phosphorylation. These results indicate that activation of p38 MAPK is specifically required for translocation of Bax to the mitochondria, and both JNK and p38 MAPK are involved in phosphorylation of Bcl-2 in response to combination treatment with gamma-radiation and As2O3, and that ROS is a critical regulator of p38 MAPK and JNK activations. The molecular mechanism elucidated in this study may provide insight into the design of future combination cancer therapies to cells intrinsically less sensitive to radiation treatment.\",\n \"corpus_id\": 19690706,\n \"score\": 1\n },\n {\n \"doc_id\": \"18718176\",\n \"title\": \"Protein tyrosine kinase, JNK, and ERK involvement in pseudolaric acid B-induced apoptosis of human breast cancer MCF-7 cells.\",\n \"abstract\": \"AIM: To investigate the apoptotic mechanism of pseudolaric acid B (PAB) in human breast cancer MCF-7 cells. METHODS: 3-(4,5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide analysis and morphological changes were applied to detect apoptosis. The percentage of apoptotic and necrotic cells were calculated by the lactate dehydrogenase activity-based cytotoxicity assay, and the protein expression was examined by Western blot analysis. RESULTS: PAB and/or the mitogen-activated protein kinases, including p38, c-Jun-N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK), did not participate in necrosis. P38 had no obvious function on apoptosis after 4 micromol/L PAB treatment for 36 h, but PAB induced JNK phosphorylation and inhibited ERK phosphorylation in the apoptotic process. In this study the inhibitor of protein tyrosine kinase (PTK) genistein inverted the inhibitory effect of PAB, instead promoting the survival of MCF-7 cells. Like genistein, another PTK inhibitor AG1024 had a similar effect on PAB-treated MCF-7 cells, indicating that PAB activated PTK to induce apoptosis. Together with PAB, genistein increased the expression of p-ERK, and decreased the expressions of JNK and p-JNK in PAB-treated MCF-7 cells at 36 h. And it is considered that the p-ERK and p-JNK were active patterns of ERK and JNK, respectively. CONCLUSION: PTK were upstream of ERK and JNK, and PTK induced apoptosis through activating JNK and inactivating ERK in PAB-treated MCF-7 cells.\",\n \"corpus_id\": 22568742,\n \"score\": 1\n },\n {\n \"doc_id\": \"18930812\",\n \"title\": \"ERK MAPK activation mediates the antiapoptotic signaling of melatonin in UVB-stressed U937 cells.\",\n \"abstract\": \"The pineal gland hormone melatonin has been recently described to downregulate the intrinsic (or damage-induced) pathway of apoptosis in human leukocytes. These properties appear to depend on a specific mitochondrial signaling of melatonin which is associated with a lower generation of reactive oxygen species and a better control of redox-sensitive components such as the antiapoptotic protein Bcl-2. Other elements upstream in this signaling are expected to contribute regulatory roles that remain unexplored. The aim of this study was to investigate whether the extracellular signal-regulated kinase (ERK), which controls the balance between survival and death-promoting genes throughout the MAPK pathway, is involved in the antiapoptotic signaling of melatonin. Human monocytic U937 cells irradiated with UVB light were used as a model of stress-induced apoptosis. In this model we found that pharmacological concentrations of melatonin (1 mM) were able to decrease superoxide anion production, mitochondrial damage, and caspase-dependent apoptosis by improved Bcl-2 levels and decreased Cyt c release in the cytoplasm. Moreover, melatonin increased the phosphorylative activation of ERK 1/2 independently from the presence of UVB stress, and decreased the UVB-mediated activation of the stress kinases p38 MAPK and JNK. The ERK 1/2 inhibitor PD98059, but not the p38 MAPK inhibitor SB203580, abolished to different extents the effects that melatonin had on the UVB-induced ROS generation, mitochondrial dysfunction, and apoptosis. Using these inhibitors, a cross-talk effect between stress and survival-promoting kinases was tentatively identified, and confirmed the hierarchical role of ERK MAPK phosphorylation in the signaling of melatonin. In conclusion, melatonin sustains the activation of the survival-promoting pathway ERK MAPK which is required to antagonize UVB-induced apoptosis of U937 cells. This kinase mediates also the antioxidant and mitochondrial protection effects of this hormonal substance that may find therapeutic applications in inflammatory and immune diseases associated with leukocyte oxidative stress and accelerated apoptosis.\",\n \"corpus_id\": 25270805,\n \"score\": 1\n },\n {\n \"doc_id\": \"19038359\",\n \"title\": \"Hydrogen peroxide-induced neuronal apoptosis is associated with inhibition of protein phosphatase 2A and 5, leading to activation of MAPK pathway.\",\n \"abstract\": \"Oxidative stress-induced neuronal apoptosis is a prominent feature found in neurodegenerative disorders. However, how oxidative stress induces neuronal apoptosis is not well understood. To address this question, undifferentiated and differentiated neuronal cell lines (PC12 and SH-SY5Y) were exposed to hydrogen peroxide (H(2)O(2)), a major oxidant generated when oxidative stress occurs. We observed that H(2)O(2) induced generation of reactive oxygen species (ROS), leading to apoptosis of the cells in a concentration- and time-dependent manner. H(2)O(2) rapidly activated the mitogen-activated protein kinases (MAPK) including extracellular signal-regulated kinase 1/2 (Erk1/2), c-Jun N-terminal kinase (JNK) and p38. Inhibition of Erk1/2, JNK or p38 with kinase inhibitors (U0126, SP600125 or PD169316, respectively), downregulation of Erk1/2 or p38 using RNA interference, or expression of dominant negative c-Jun partially prevented H(2)O(2)-induced apoptosis. Pretreatment with N-acetyl-L-cysteine (NAC) scavenged H(2)O(2)-induced ROS, blocking activation of MAPKs and cell death. Furthermore, we found that H(2)O(2)-induced ROS inhibited serine/threonine protein phosphatases 2A (PP2A) and 5 (PP5), which was abrogated by NAC. Overexpression of PP2A or PP5 partially prevented H(2)O(2)-activation of Erk/12, JNK and p38, as well as cell death. Similar results were observed in primary murine neurons as well. The results suggest that H(2)O(2)-induction of ROS inhibit PP2A and PP5, leading to activation of Erk1/2, JNK and p38 pathways thereby resulting in neuronal apoptosis. Our findings suggest that inhibitors of MAPKs (JNK, Erk1/2 and p38), activators of phosphatases (PP2A and PP5) or antioxidants may have potentials to prevent and treat oxidative stress-induced neurodegenerative diseases.\",\n \"corpus_id\": 7016424,\n \"score\": 1\n },\n {\n \"doc_id\": \"19059215\",\n \"title\": \"PKD prevents H2O2-induced apoptosis via NF-kappaB and p38 MAPK in RIE-1 cells.\",\n \"abstract\": \"Previously, we demonstrated that protein kinase D (PKD) plays a protective role during H(2)O(2)-induced intestinal cell death. Here, we sought to determine whether this effect is mediated by nuclear factor-kappaB (NF-kappaB) and mitogen-activated protein kinases (MAPKs). Treatment with H(2)O(2) activated NF-kappaB in RIE-1 cells; H(2)O(2) also induced the translocation of NF-kappaB p65 as well as phosphorylation of IkappaB-alpha. PKD1 siRNA inhibited H(2)O(2)-induced activation, translocation of NF-kappaB, and phosphorylation of IkappaB-alpha. We also found that overexpression of wild type PKD1 attenuated H(2)O(2)-induced phosphorylation of p38 MAPK and its upstream activator, MAPK kinase (MKK) 3/6, whereas the phosphorylation was increased by PKD1 siRNA or kinase-dead PKD1. Phosphorylation of neither extracellular signal-regulated kinases (ERK) 1/2 nor c-Jun N-terminal kinases (JNK) was altered by PKD1 plasmids or siRNA. Our findings suggest that PKD protects intestinal cells through up-regulation of NF-kappaB and down-regulation of p38 MAPK.\",\n \"corpus_id\": 41036670,\n \"score\": 1\n },\n {\n \"doc_id\": \"19259124\",\n \"title\": \"Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through regulation of Bcl-2.\",\n \"abstract\": \"The present study shows that double-stranded RNA-dependent protein kinase (PKR) regulates the protein expression level and phosphorylation of Bcl-2 and plays an anti-apoptotic role in human hepatocellular carcinoma cells (HepG2). In various types of cells, saturated free fatty acids (FFAs), such as palmitate, have been shown to induce cellular apoptosis by several mechanisms. Palmitate down-regulates the activity of PKR and thereby decreases the level of Bcl-2 protein, mediated in part by reduced activation of the NF-kappaB transcription factor. In addition to the level of Bcl-2 protein, the phosphorylation of Bcl-2 at different amino acid residues, such as Ser70 and Ser87, is also important in regulating cellular apoptosis. The decrease in the phosphorylation of Bcl-2 at Ser70 upon exposure to palmitate is mediated by inhibition of PKR and possibly by c-Jun N-terminal kinase (JNK), whereas the phosphorylation of Bcl-2 at Ser87 is unaffected by palmitate or PKR. In summary, PKR mediates the regulation of the protein level and the phosphorylation status of Bcl-2, providing a novel mechanism of palmitate-induced apoptosis in HepG2 cells.\",\n \"corpus_id\": 14301260,\n \"score\": 1\n },\n {\n \"doc_id\": \"19433446\",\n \"title\": \"Mcl-1 integrates the opposing actions of signaling pathways that mediate survival and apoptosis.\",\n \"abstract\": \"Mcl-1 is a member of the Bcl2-related protein family that is a critical mediator of cell survival. Exposure of cells to stress causes inhibition of Mcl-1 mRNA translation and rapid destruction of Mcl-1 protein by proteasomal degradation mediated by a phosphodegron created by glycogen synthase kinase 3 (GSK3) phosphorylation of Mcl-1. Here we demonstrate that prior phosphorylation of Mcl-1 by the c-Jun N-terminal protein kinase (JNK) is essential for Mcl-1 phosphorylation by GSK3. Stress-induced Mcl-1 degradation therefore requires the coordinated activity of JNK and GSK3. Together, these data establish that Mcl-1 functions as a site of signal integration between the proapoptotic activity of JNK and the prosurvival activity of the AKT pathway that inhibits GSK3.\",\n \"corpus_id\": 9049545,\n \"score\": 1\n },\n {\n \"doc_id\": \"19522739\",\n \"title\": \"Melatonin induces apoptotic death in LNCaP cells via p38 and JNK pathways: therapeutic implications for prostate cancer.\",\n \"abstract\": \"Apoptosis, a form of cell death, is a fundamental process for the development and maintenance of multicellular organisms that promotes the removal of damaged, senescent or unwanted cells. Induction of cancer cell apoptosis is an important strategy of anticancer therapy. In this study, we examined if melatonin, the main secretory product of the pineal gland, inhibited the growth of prostate cancer cells (LNCaP) and promoted apoptosis via mitogen-activated protein kinases (MAPKs), which are closely associated with apoptosis and survival. Melatonin treatment significantly inhibited the growth of LNCaP cells in a dose- and time-dependent manner. It clearly induced both an early stage of apoptosis (propidium iodide(-), FITC Annexin-V(+)) and a late apoptosis/secondary necrosis (propidium iodide(+) and FITC Annexin-V(+)), which indicated induction of serial stages of apoptosis in cells. Moreover, melatonin markedly activated c-JUN N-terminal kinase (JNK) and p38 kinase, whereas extracellular signal-regulated kinase (ERK) was not responsive to melatonin. Treatment with MAPK inhibitors, PD98059 (ERK inhibitor), SP600125 (JNK inhibitor) and SB202190 (p38 inhibitor), confirmed that melatonin-induced apoptosis was JNK- and p38-dependent, but ERK-independent. In the presence of PD98059, caspase-3 activity increased, while levels of Bax/cytochrome c (Cyt c) and Bcl-2 decreased. These effects were opposite to those observed with SP600125 and SB202190 treatments. Together, these results strongly suggest that JNK and p38 activation directly participate in apoptosis induced by melatonin. Thus, melatonin may be of promise for anti-prostate cancer strategies.\",\n \"corpus_id\": 13054688,\n \"score\": 1\n },\n {\n \"doc_id\": \"19578154\",\n \"title\": \"Inhibition of p38-MAPK potentiates cisplatin-induced apoptosis via GSH depletion and increases intracellular drug accumulation in growth-arrested kidney tubular epithelial cells.\",\n \"abstract\": \"We were interested in analyzing the regulation by mitogen-activated protein kinases (MAPKs) of cisplatin-provoked toxicity in epithelial renal tubule cell lines, when assayed under culture conditions (cell confluence plus serum deprivation), which mimic the characteristics of a nonproliferating epithelium. Under these restrictive growth conditions, cisplatin induced apoptosis with lower efficacy than in exponentially growing cells, and decreased p38-MAPK phosphorylation in NRK-52E and other (LLC-PK1, MDCK, HK2) cell lines. Moreover, cisplatin-provoked apoptosis was potentiated by cotreatment with p38-MAPK-specific inhibitors (SB203580, SB220025) or transfection with a kinase-negative mutant of MKK6, whereas c-Jun NH2-terminal kinase or extracellular signal-regulated kinase/MAPK and ERK Kinase inhibitors were ineffective. By contrast, when applied to exponentially growing cells, cisplatin stimulated p38-MAPK phosphorylation and apoptosis, was attenuated by kinase inhibitors. Treatment of confluent/serum-deprived cells with cisplatin caused mitochondrial transmembrane potential disruption and activated the mitochondrial apoptotic pathway, as indicated by the decrease in Bcl-X(L) expression, increase in Bax expression and cytochrome c release, and these effects were potentiated by cotreatment with SB203580. Treatment of confluent/serum-deprived cells with cisplatin plus SB203580 decreased the intracellular reduced glutathione (GSH) content, and increased intracellular cisplatin accumulation as well as cisplatin binding to DNA. Cotreatment with the GSH-depleting agent D,L-buthionine-R,S-sulfoximine also potentiated cisplatin-provoked apoptosis. In summary, p38-MAPK inhibition potentiates cisplatin-provoked apoptosis in growth-arrested epithelial renal tubule cells, a result that may be explained at least in part by GSH depletion and drug transport alteration.\",\n \"corpus_id\": 33818915,\n \"score\": 1\n },\n {\n \"doc_id\": \"19699753\",\n \"title\": \"Novel indoloquinoline derivative, IQDMA, induces G(2)/M phase arrest and apoptosis in A549 cells through JNK/p38 MAPK signaling activation.\",\n \"abstract\": \"AIMS: This study was performed to elucidate whether mitogen-activated protein kinases (MAPKs) are involved in the modulation of apoptosis and cell-cycle arrest by N'-(11H-indolo[3,2-c]quinolin-6-yl)-N,N-dimethylethane-1,2-diamine (IQDMA), in human lung adenocarcinoma A549 cells. MAIN METHODS: The effect of IQDMA on cell-cycle arrest and apoptosis was measured by flow cytometry, and phosphorylation levels of mitogen-activated protein kinases (MAPKs) and its regulatory molecules were studied by immunoblots. KEY FINDINGS: IQDMA-induced G(2)/M arrest was associated with a marked decrease in the protein expressions of cyclin A, cyclin B, and cyclin-dependent kinase (Cdk)1. IQDMA-induced apoptosis was accompanied with up-regulation of the protein expression of Bax and down-regulation of the protein levels of Bcl-2, Mcl-1, X-linked inhibitor of apoptosis (XIAP), and survivin, resulting in cytochrome c release and sequential activation of caspase-9 and caspase-3. IQDMA activated c-Jun N-terminal kinase (JNK), p38 MAPK (p38) and extracellular signal-regulated kinase (ERK) on A549 cells in a time-dependent manner. Unlike the ERK inhibitor (PD98059), inhibitors of JNK (SP600125) and p38 MAPK (SB203580) suppressed IQDMA-induced apoptosis and G(2)/M phase arrest in A549 cells. Both SP600125 and SB203580 attenuated the activation of Bax and cytochrome c release, and reversed down-regulation of Bcl-2, XIAP, survivin, cyclin A, cyclin B, and Cdk1 in IQDMA-treated cells. SIGNIFICANCE: These findings indicate that JNK/p38 MAPK pathways play an important role in IQDMA-induced G(2)/M arrest and apoptosis of A549 cells.\",\n \"corpus_id\": 33315805,\n \"score\": 1\n },\n {\n \"doc_id\": \"19717209\",\n \"title\": \"Potentiation of paclitaxel-induced apoptosis by galectin-13 overexpression via activation of Ask-1-p38-MAP kinase and JNK/SAPK pathways and suppression of Akt and ERK1/2 activation in U-937 human macrophage cells.\",\n \"abstract\": \"Galectin-13 transcripts have been identified in several normal and malignant tissues, but the physiological function of galectin-13 is still poorly understood. Here, we present evidence for its possible role in promoting cell death in the U-937 human macrophage cell line. Transfection of U-937 human macrophages by a galectin-13 cDNA-containing mammalian expression vector increased the galectin-13 level and sensitized the cells to stress stimuli. Galectin-13 overexpression facilitated paclitaxel-induced cell death and nuclear translocation of apoptosis-inducing factor (AIF) and endonuclease-G without inducing mitochondrial cytochrome-c release or caspase-3 activation. Immunoblot and immunofluorescence data showed that overexpression of galectin-13 induced long-term activation of c-Jun N-terminal kinase (JNK) and p38-mitogen-activated protein kinase (MAPK) pathways, as well as activation of apoptosis signal-regulating kinase-1 (Ask-1) kinase while it suppressed paclitaxel-induced long-term activation of the phosphatidilylositol-3-kinase (PI-3K)-Akt and extracellular signal-regulated kinase (ERK1/2) cytoprotective pathways. In addition, pharmacological inhibition of JNK and p38-MAPK pathways protected the cells from paclitaxel-induced cell death. All this data indicate that galectin-13 overexpression promoted apoptosis presumably by activating the Ask-1 kinase-JNK and p38-MAPK pro-apoptotic pathways and by suppressing the PI-3K-Akt and ERK1/2 cytoprotective pathways.\",\n \"corpus_id\": 9055248,\n \"score\": 1\n },\n {\n \"doc_id\": \"19747539\",\n \"title\": \"Naphtho[1,2-b]furan-4,5-dione induces apoptosis and S-phase arrest of MDA-MB-231 cells through JNK and ERK signaling activation.\",\n \"abstract\": \"Naphtho[1,2-b]furan-4,5-dione (NFD), prepared from 2-hydroxy-1,4-naphthoquinone and chloroacetaldehyde in an efficient one-pot reaction, exhibits anti-carcinogenic effect. The results of present study showed that NFD inhibited the proliferation of breast cancer MDA-MB-231 cells through the induction of S-phase arrest and apoptosis. NFD-induced S-phase arrest was associated with a marked decrease in the protein expression of cyclin A, cyclin B, and cyclin-dependent kinase (Cdk)2. NFD-induced apoptosis was characterized by increase of sub-G1 population, phosphatidylserine (PS) externalization, and activation of caspases. Moreover, up-regulation of Bad and down-regulation of Bcl-2, Bcl-X(L), and survivin led to the loss of mitochondrial membrane potential (DeltaPsim), the release of cytochrome c and sequential activation of caspase-9 and caspase-3. NFD activated c-Jun N-terminal kinase (JNK), p38 mitogen-activated protein kinase (p38 MAPK) and extracellular signal-regulated kinase (ERK) in MDA-MB-231 cells. Inhibitors of JNK (SP600125) and ERK (PD98059), but not p38 MAPK (SB203580) suppressed NFD-induced S-phase arrest and apoptosis in MDA-MB-231 cells. Both SP600125 and PD98059 attenuated Bad up-regulation, and reversed down-regulation of Bcl-2, Bcl-X(L), survivin, cyclin A, cyclin B, and Cdk2 in NFD-treated cells. Taken together, our data show that JNK and ERK-signaling pathways play important roles in NFD-mediated S-phase arrest and apoptosis of MDA-MB-231 cells.\",\n \"corpus_id\": 8373336,\n \"score\": 1\n },\n {\n \"doc_id\": \"20359850\",\n \"title\": \"Interaction of Pdcd4 with eIF4E inhibits the metastatic potential of hepatocellular carcinoma.\",\n \"abstract\": \"Oxidative stress can contribute to the development of hepatocellular carcinoma (HCC) ability of the carcinoma. It has been found that oxidative stress stimulates the phosphorylation of eIF4E primarily through mitogen-activated protein kinase (MAPK) pathways resulting in increased protein translation. Utilizing specific inhibitors of MAPK pathways (SP600125 for c-Jun amino-terminal kinases [JNKs], PD098059 for extracellular signal-regulated kinases [ERKs], and SB203580 for p38 MAPK), we determined that it is primarily the inhibition of JNK that results in the suppression of the increase of p-eIF4E. We also found that PDCD4 inhibits JNK activity resulting in inhibition of the phosphorylation of c-Jun, one isoform of AP-1. We demonstrated that transfection with PDCD4 or inhibition of JNK by SP600125 alters the expression and phosphorylation of eIF4E in the presence of H(2)O(2). PDCD4 results in a stronger inhibitory effect than SP600125.\",\n \"corpus_id\": 23767580,\n \"score\": 1\n },\n {\n \"doc_id\": \"21519792\",\n \"title\": \"Lupulone triggers p38 MAPK-controlled activation of p53 and of the TRAIL receptor apoptotic pathway in human colon cancer-derived metastatic cells.\",\n \"abstract\": \"We previously reported that the chemopreventive agent lupulone induces apoptosis through activation of the extrinsic pathway via TRAIL DR4/DR5 death receptors overcoming SW620 cell resistance to TRAIL. However, the underlying molecular mechanisms remain unknown. Since the mitogen-activated protein kinases (MAPKs), Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK) and p38 control fundamental cellular processes such as apoptosis, we determined the role of these MAPKs in lupulone-triggered apoptosis. We analyzed the effects of JNK, ERK and p38 MAPK inhibitors on lupulone-induced apoptosis by flow cytometry using specific antibodies and real-time RT-PCR. Our data showed that among the MAPKs, only p38 played a major role in lupulone-triggered apoptosis. In contrast to JNK and ERK inhibition, the specific inactivation of p38 inhibited the lupulone-triggered up-regulation of p53 and TRAIL-death receptor DR4/DR5 expression, and prevented DNA fragmentation. Lupulone treatment enhanced the expression of the anti-apoptotic Mcl-1 protein by 60% favoring the preservation of mitochondrial integrity. The inactivation of p38 initiated a 50% reduction in Mcl-1, Bcl-2 and Bax expression without changing the Mcl-1/Bax ratio suggesting that p38 was not involved in the protective effect of lupulone on mitochondria. Our data support the view that the lupulone-triggered enhanced expression of p38 plays a major role in the activation of p53 and of the TRAIL-death receptor apoptotic pathway in SW620 human colon cancer-derived metastatic cells.\",\n \"corpus_id\": 25728436,\n \"score\": 1\n },\n {\n \"doc_id\": \"22678567\",\n \"title\": \"Cyclosporin A induces apoptosis in H9c2 cardiomyoblast cells through calcium-sensing receptor-mediated activation of the ERK MAPK and p38 MAPK pathways.\",\n \"abstract\": \"The cardiotoxicity of cyclosporine A (CsA) limits its clinical application in extensive and long-term therapies. Our group has shown that CsA induces myocardium cell apoptosis in vivo and increases calcium-sensing receptor (CaSR) expression. However, its molecular mechanism remains unknown. The purpose of this study was to determine whether CaSR plays an essential role in CsA-induced apoptosis in H9c2 cells and to investigate the role of the mitogen-activated protein kinase (MAPK) signaling cascade in this process. H9c2 cells were treated with CsA in a dose-dependent manner, and decreased Bcl-2 expression, increased Bax expression, and caspase-3 activation were observed. In a time-dependent manner, CsA increased CaSR expression, activated the extracellularly regulated kinase (ERK) and p38 MAPK pathways, and inactivated the c-Jun N-terminal kinase (JNK) MAPK signaling pathway. When H9c2 cardiomyoblast cells pretreated with gadolinium chloride (GdCl(3)), a CaSR activator, were treated with CsA, decreased phosphorylation of ERK1/2, increased phosphorylation of p38, decreased Bcl-2 expression, increased Bax expression, and activated caspase-3 were observed. Cells pretreated with the CaSR inhibitor NPS2390 inhibited this process. Furthermore, the MEK1/2 inhibitor U0126 and the p38 MAPK inhibitor SB203580 markedly blocked the effect of CsA on cell apoptosis, apoptotic-related protein expression, and caspase-3 activation. These findings showed that CsA induced apoptosis in H9c2 cells in vitro, and CaSR mediated the degradation of ERK MAPK and the upregulation of the p38 MAPK pathway involved in CsA-induced H9c2 cardiomyoblast cell apoptosis.\",\n \"corpus_id\": 7955722,\n \"score\": 1\n },\n {\n \"doc_id\": \"23123629\",\n \"title\": \"Role of JNK and p38 MAPK in Taiwanin A-induced cell death.\",\n \"abstract\": \"AIM: The lignan compound Taiwanin A is cytotoxic for human cancer cells. Taiwanin A has been previously shown to damage microtubules, induce mitotic arrest and cause apoptosis in cancer cells. The goal of the current study is to identify intracellular signaling pathways that are involved in Taiwanin A-mediated apoptosis. MAIN METHODS: We examined the activation of three mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK), p38 and c-Jun N-terminal kinase (JNK), in HepG2 cells after Taiwanin A treatment. The role of MAPK activation in Taiwanin A-induced apoptosis was examined using Western blotting, caspase activity assays combined with specific MAPK inhibitors and shRNA treatment to knockdown JNK. KEY FINDINGS: Taiwanin A activated all three MAPKs (ERK, p38 and JNK). Cytotoxicity was blocked by the p38 MAPK inhibitor SB203580 and the JNK inhibitor SP600125 but not by the ERK inhibitor PD98059. A combined treatment of SB203580 and SP600125 showed increased effects on the inhibition of Taiwanin A cytotoxicity, suggesting that both JNK and p38 play a role in Taiwanin A-induced apoptosis. Inhibition of p38 activity reduced Taiwanin A-induced p53 phosphorylation on Ser15. Direct interaction of Taiwanin A-activated p38 and p53 was demonstrated by immunoprecipitation. In addition, inhibition of JNK by SP600125 or silencing of the JNK scaffold protein JIP2 reduced phosphorylation of Bcl-2, which may help to promote anti-apoptotic pathways. SIGNIFICANCE: We demonstrated for the first time that two distinct apoptotic pathways, the p38-p53 and JNK-Bcl-2 pathways, were triggered by the anti-microtubule compound Taiwanin A.\",\n \"corpus_id\": 28896196,\n \"score\": 1\n },\n {\n \"doc_id\": \"23172806\",\n \"title\": \"Apoptosis induced by para-phenylenediamine involves formation of ROS and activation of p38 and JNK in chang liver cells.\",\n \"abstract\": \"para-Phenylenediamine (p-PD) is a suspected carcinogen, but it has been widely used as a component in permanent hair dyes. In this study, the mechanism of p-PD-induced cell death in normal Chang liver cells was investigated. The results demonstrated that p-PD decreased cell viability in a dose-dependent manner. Cell death via apoptosis was confirmed by enhanced DNA damage and increased cell number in the sub-G1 phase of the cell cycle, using Hoechst 33258 dye staining and flow cytometry analysis. Apoptosis via reactive oxygen species generation was detected by the dichlorofluorescin diacetate staining method. Mitogen-activated protein kinase (MAPK) activation was assessed by western blot analysis and revealed that p-PD activated not only stress-activated protein kinase (SAPK)/c-Jun N-terminal kinases (JNK) and p38 MAPK but also extracellular signal-regulated kinase (ERK). Cytotoxicity and apoptosis induced by p-PD were markedly enhanced by ERK activation and selectively inhibited by ERK inhibitor PD98059, thus indicating a negative role of ERK. In contrast, inhibition of p38 MAPK activity with the p38-specific inhibitor SB203580 moderately inhibited cytotoxicity and apoptosis induction by p-PD. Similarly, SP600125, an inhibitor of SAPK/JNK, moderately inhibited cytotoxicity and apoptosis induced by p-PD, thus implying that p38 MAPK and SAPK/JNK had a partial role in p-PD-induced apoptosis. Western blot analysis revealed that p-PD significantly increased phosphorylation of p38 and SAPK/JNK and decreased phosphorylation of ERK. In conclusion, the results demonstrated that SAPK/JNK and p38 cooperatively participate in apoptosis induced by p-PD and that a decreased ERK signal contributes to growth inhibition or apoptosis.\",\n \"corpus_id\": 22951605,\n \"score\": 1\n },\n {\n \"doc_id\": \"23203057\",\n \"title\": \"Apoptosis induction of human prostate carcinoma DU145 cells by diallyl disulfide via modulation of JNK and PI3K/AKT signaling pathways.\",\n \"abstract\": \"Diallyl disulfide (DADS), a sulfur compound derived from garlic, has various biological properties, such as anticancer, antiangiogenic and anti-inflammatory effects. However, the mechanisms of action underlying the compound's anticancer activity have not been fully elucidated. In this study, the apoptotic effects of DADS were investigated in DU145 human prostate carcinoma cells. Our results showed that DADS markedly inhibited the growth of the DU145 cells by induction of apoptosis. Apoptosis was accompanied by modulation of Bcl-2 and inhibitor of apoptosis protein (IAP) family proteins, depolarization of the mitochondrial membrane potential (MMP, ΔΨm) and proteolytic activation of caspases. We also found that the expression of death-receptor 4 (DR4) and Fas ligand (FasL) proteins was increased and that the level of intact Bid proteins was down-regulated by DADS. Moreover, treatment with DADS induced phosphorylation of mitogen-activated protein kinases (MAPKs), including extracellular-signal regulating kinase (ERK), p38 MAPK and c-Jun N-terminal kinase (JNK). A specific JNK inhibitor, SP600125, significantly blocked DADS-induced-apoptosis, whereas inhibitors of the ERK (PD98059) and p38 MAPK (SB203580) had no effect. The induction of apoptosis was also accompanied by inactivation of phosphatidylinositol 3-kinase (PI3K)/Akt and the PI3K inhibitor LY29004 significantly increased DADS-induced cell death. These findings provide evidence demonstrating that the proapoptotic effect of DADS is mediated through the activation of JNK and the inhibition of the PI3K/Akt signaling pathway in DU145 cells.\",\n \"corpus_id\": 11034222,\n \"score\": 1\n },\n {\n \"doc_id\": \"23681233\",\n \"title\": \"Hypoxia counteracts taxol-induced apoptosis in MDA-MB-231 breast cancer cells: role of autophagy and JNK activation.\",\n \"abstract\": \"Cancer cell resistance against chemotherapy is still a heavy burden to improve anticancer treatments. Autophagy activation and the development of hypoxic regions within the tumors are known to promote cancer cell resistance. Therefore, we sought to evaluate the role of autophagy and hypoxia on the taxol-induced apoptosis in MDA-MB-231 breast cancer cells. The results showed that taxol induced apoptosis after 16 h of incubation, and that hypoxia protected MDA-MB-231 cells from taxol-induced apoptosis. In parallel, taxol induced autophagy activation already after 2 h of incubation both under normoxia and hypoxia. Autophagy activation after taxol exposure was shown to be a protective mechanism against taxol-induced cell death both under normoxia and hypoxia. However, at longer incubation time, the autophagic process reached a saturation point under normoxia leading to cell death, whereas under hypoxia, autophagy flow still correctly took place allowing the cells to survive. Autophagy induction is induced after taxol exposure via mechanistic target of rapamycin (mTOR) inhibition, which is more important in cells exposed to hypoxia. Taxol also induced c-Jun N-terminal kinase (JNK) activation and phosphorylation of its substrates B-cell CLL/lymphoma 2 (Bcl2) and BCL2-like 1 (BclXL) under normoxia and hypoxia very early after taxol exposure. Bcl2 and BclXL phosphorylation was decreased more importantly under hypoxia after long incubation time. The role of JNK in autophagy and apoptosis induction was studied using siRNAs. The results showed that JNK activation promotes resistance against taxol-induced apoptosis under normoxia and hypoxia without being involved in induction of autophagy. In conclusion, the resistance against taxol-induced cell death observed under hypoxia can be explained by a more effective autophagic flow activated via the classical mTOR pathway and by a mechanism involving JNK, which could be dependent on Bcl2 and BclXL phosphorylation but independent of JNK-induced autophagy activation.\",\n \"corpus_id\": 3758039,\n \"score\": 1\n },\n {\n \"doc_id\": \"23812630\",\n \"title\": \"Olaquindox-induced apoptosis is suppressed through p38 MAPK and ROS-mediated JNK pathways in HepG2 cells.\",\n \"abstract\": \"We investigated mitogen-activated protein kinase (MAPK) pathways as well as reactive oxygen species (ROS) in olaquindox-induced apoptosis. Exposure of HepG2 cells to olaquindox resulted in the phosphorylation of p38 MAPK and c-Jun N-terminal kinases (JNK). To confirm the role of p38 MAPK and JNK, HepG2 cells were pretreated with MAPKs-specific inhibitors prior to olaquindox treatment. Olaquindox-induced apoptosis was significantly potentiated by the JNK inhibitor (SP600125) or the p38 MAPK inhibitor (SB203580). Furthermore, we observed that olaquindox treatment led to ROS generation and that olaquindox-induced apoptosis and ROS generation were both significantly reduced by the antioxidants, superoxide dismutase and catalase. In addition, the levels of phosphorylation of JNK, but not p38 MAPK, were significantly suppressed after pretreatment of the antioxidants, while inhibition of the activations of JNK or p38 MAPK had no effect on ROS generation. This result suggested that ROS may be the upstream mediator for the activation of JNK. Conclusively, our results suggested that apoptosis in response to olaquindox treatment in HepG2 cells might be suppressed through p38 MAPK and ROS-JNK pathways.\",\n \"corpus_id\": 12940772,\n \"score\": 1\n },\n {\n \"doc_id\": \"24173825\",\n \"title\": \"Caffeine inhibits paclitaxel‑induced apoptosis in colorectal cancer cells through the upregulation of Mcl‑1 levels.\",\n \"abstract\": \"Colorectal cancer (CRC) cells have been previously observed to be resistant to paclitaxel‑induced apoptosis by activation of the mitogen‑activated protein/extracellular signal‑regulated kinase (MEK)/ERK signaling pathway and increased expression of glucose‑regulated protein 78 (GRP78). Caffeine, the most widely used neuroactive compound, has antiproliferative activity and the ability to induce cell cycle arrest and apoptosis. In the current study, the effect of concomitant use of caffeine on paclitaxel‑induced apoptosis in CRC cells was investigated. The results revealed that treatment of Colo205 cells with varying caffeine concentrations did not induce apoptosis. Pretreatment of CRC cells with caffeine significantly inhibited paclitaxel‑induced cytotoxicity by increasing the levels of the antiapoptotic Bcl‑2 family member, Mcl‑1. This effect was inhibited by pretreatment of Colo205 cells with the MEK‑ERK chemical inhibitor, U0126. In addition to GRP78, these results indicated that Mcl‑1 may be a downstream target of the MEK‑ERK signaling pathway. Moreover, administration of caffeine may decrease chemotherapeutic responses to paclitaxel by the MEK‑ERK mediated upregulation of Mcl‑1. In conclusion, coadministration of cell cycle‑modifying agents, including caffeine should be avoided in CRC patients treated with paclitaxel.\",\n \"corpus_id\": 207550025,\n \"score\": 1\n },\n {\n \"doc_id\": \"25187486\",\n \"title\": \"Induction of Nur77-dependent apoptotic pathway by a coumarin derivative through activation of JNK and p38 MAPK.\",\n \"abstract\": \"Coumarins are plant-derived natural products with a broad range of known pharmacological activities including anticancer effects. However, the molecular mechanisms by which this class of promising compounds exerts their anticancer effects remain largely unknown. We report here that a furanocoumarin named apaensin could effectively induce apoptosis of cancer cells through its activation of Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK). Apoptosis induction by apaensin in cancer cells was suppressed by chemical inhibitors of JNK and p38 MAPK. Inhibition of the expression of orphan nuclear receptor Nur77 by small interfering RNA (siRNA) approach also abrogated the death effect of apaensin. Molecular analysis demonstrated that JNK activation was required for the nuclear export of Nur77, a known apoptotic event in cancer cells. Although p38 MAPK activation was not involved in Nur77 nuclear export, it was essential for Nur77 mitochondrial targeting through induction of Nur77 interaction with Bcl-2, which is also known to convert Bcl-2 from an antiapoptotic to a proapoptotic molecule. Together, our results identify a new natural product that targets orphan nuclear receptor Nur77 through its unique activation of JNK and p38 MAPK and provide insight into the complex regulation of the Nur77-Bcl-2 apoptotic pathway.\",\n \"corpus_id\": 37640174,\n \"score\": 1\n },\n {\n \"doc_id\": \"25236495\",\n \"title\": \"MDA-7/IL-24 inhibits Nrf2-mediated antioxidant response through activation of p38 pathway and inhibition of ERK pathway involved in cancer cell apoptosis.\",\n \"abstract\": \"Reactive oxygen species (ROS) have a crucial role in melanoma differentiation-associated gene-7 (MDA-7)/interleukin-24 (IL-24)-induced cancer cell apoptosis. However, cancer cell has a series of protective mechanisms to resist ROS damage. Nuclear factor erythroid 2-related factor 2 (Nrf2) activates antioxidant response element (ARE)-mediated gene expression involved in cellular protection against oxidative stress. As the Nrf2 repressor, Kelch-like ECH-associated protein-1 (Keap1) sequesters Nrf2 in cytoplasm to block Nrf2 nuclear translocation. In the present study, administration of MDA-7/IL-24 by means of tumor-selective replicating adenovirus (ZD55-IL-24) was used to investigate whether ZD55-IL-24 could attenuate Nrf2-mediated oxidative stress response in cancer cell. We found that ZD55-IL-24 effectively strengthened the association between Nrf2 and Keap1 to restrict Nrf2 nuclear translocation, thereby inhibiting ARE-dependent transcriptional response. To evaluate the detailed mechanism underlying the suppression of ZD55-IL-24 on Nrf2-mediated oxidative stress response, we further tested three different mitogen-activated protein kinase (MAPK) signaling pathways in A549 and HeLa cells transfected by ZD55-IL-24. Our data showed that ZD55-IL-24 inhibited extracellular signal-regulated kinase (ERK) signal pathway but activated p38 and c-Jun-NH2-kinase (JNK) signal pathways to exert the tumor-specific apoptosis. Moreover, ERK pathway inhibitor U0126 prevented Nrf2 phosphorylation at Ser40 to retard Nrf2 nuclear translocation, thus decreasing antioxidant gene transcription. In contrast, p38 pathway inhibitor SB203580 obviously promoted the dissociation of Nrf2 from Keap1 to promote antioxidant gene transcription. However, JNK pathway had no effect on Nrf2 subcellular localization or the association of Nrf2 with Keap1. Conclusively, our results indicate that ZD55-IL-24 inhibits Nrf2-mediated oxidative stress response not only by activating p38 signal pathway to potentiate the association of Nrf2 and Keap1 but also by suppressing ERK signal pathway to postpone Nrf2 nuclear translocation. Given the 'dark' side of Nrf2 on carcinoma cell survival and chemoresistance, our study provides a novel explanation about MDA-7/IL-24-induced cancer-specific apoptosis and therapeutic sensitization through suppression of the cytoprotective system.\",\n \"corpus_id\": 7334566,\n \"score\": 1\n },\n {\n \"doc_id\": \"25753324\",\n \"title\": \"Vincristine activates c-Jun N-terminal kinase in chronic lymphocytic leukaemia in vivo.\",\n \"abstract\": \"AIMS: The authors' aim was to conduct a proof-of-principle study to test whether c-Jun N-terminal kinase (JNK) phosphorylation and Noxa induction occur in peripheral blood chronic lymphocytic leukaemia (CLL) cells in patients receiving a vincristine infusion. METHODS: Patients with CLL received 2 mg vincristine by a 5-min intravenous infusion. Blood samples were collected at baseline and up to 6 h after the vincristine infusion, and assayed for JNK activation, Noxa induction and vincristine plasma concentrations. RESULTS: Ex vivo treated peripheral CLL cells activated JNK in response to 10-100 nM vincristine in 6 h. Noxa protein expression, while variable, was also observed over this time frame. In CLL patients, vincristine infusion led to rapid (<1 h) JNK phosphorylation in peripheral blood CLL cells which was sustained for at least 4-6 h after the vincristine infusion. Noxa protein expression was not observed in response to vincristine infusion. CONCLUSIONS: This study confirmed that vincristine can activate JNK but not induce Noxa in CLL cells in vivo. The results suggest that novel JNK-dependent drug combinations with vincristine warrant further investigation.\",\n \"corpus_id\": 34643335,\n \"score\": 1\n },\n {\n \"doc_id\": \"26961382\",\n \"title\": \"Saikosaponin-D Reduces H2O2-Induced PC12 Cell Apoptosis by Removing ROS and Blocking MAPK-Dependent Oxidative Damage.\",\n \"abstract\": \"Neuronal oxidative stress (OS) injury has been proven to be associated with many neurodegenerative diseases, and thus, antioxidation treatment is an effective method for treating these diseases. Saikosaponin-D (SSD) is a sapogenin extracted from Bupleurum falcatum and has been shown to have many pharmacological activities. The main purpose of this study was to investigate whether and how SSD protects PC12 cells from H2O2-induced apoptosis. The non-toxic level of SSD significantly mitigated the H2O2-induced decrease in cell viability, reduced the apoptosis rate, improved the nuclear morphology, and reduced caspase-3 activation and poly ADP-ribose polymerase (PARP) cleavage. Additionally, exogenous H2O2-induced apoptosis by damaging the intracellular antioxidation system. SSD significantly slowed the H2O2-induced release of malonic dialdehyde (MDA) and lactate dehydrogenase and increased the activity of superoxide dismutase (SOD) and the total antioxidant capacity, thereby reducing apoptosis. More importantly, SSD effectively blocked H2O2-induced phosphorylation of extracellular-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 mitogen-activated protein kinase (p38MAPK), and specific inhibitors of ERK, JNK, and p38-reduced OS injury and apoptosis, suggesting that SSD reduces OS injury and apoptosis via MAPK signalling pathways. Finally, we confirmed that SSD significantly reduced H2O2-induced reactive oxygen species (ROS) accumulation, and the ROS inhibitor blocked the apoptosis caused by MAPK activation and cellular oxidative damage. In short, our study confirmed that SSD reduces H2O2-induced PC12 cell apoptosis by removing ROS and blocking MAPK-dependent oxidative damage.\",\n \"corpus_id\": 19197565,\n \"score\": 1\n },\n {\n \"doc_id\": \"27220839\",\n \"title\": \"IL-1α induces apoptosis and inhibits the osteoblast differentiation of MC3T3-E1 cells through the JNK and p38 MAPK pathways.\",\n \"abstract\": \"Interleukin (IL)-1 is a proinflammatory cytokine that plays important roles in inflammation and host responses to infection. The present study aimed to evaluate the effects of IL-1α on the apoptosis and differentiation of osteoblasts, and to elucidate the mechanism responsible for these effects in the osteoblast‑like cell line MC3T3-E1. The MC3T3-E1 cells were non-treated or treated with IL-1α. Following treatment, cell viability, alkaline phosphatase (ALP) activity and caspase-3 activity were evaluated. The expression of osteoblast-specific genes as well as Bax, Bcl-2 and caspase-3 were determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The protein levels of Bax, Bcl-2, caspase-3 and the phosphorylation of mitogen-activated protein kinases (MAPKs, also known as MAP kinases) were evaluated using western blot analysis. The MAPK signaling pathway was blocked by pre-treatment with MAPK inhibitors SB203580, PD98059 and SP600125. IL-1α treatment induced a significant decrease in cell viability and ALP activity in the MC3T3-E1 cells. IL-1α also significantly decreased the mRNA expression and protein levels of osteoblast-related genes in the MC3T3-E1 cells. On the other hand, IL-1α significantly upregulated the mRNA expression and protein levels of Bax and caspase-3 as well as caspase-3 activity, whereas Bcl-2 expression was decreased in the MC3T3-E1 cells. Furthermore, IL-1α activated the apoptotic signaling pathway by increasing the phosphorylation of c-Jun N-terminal kinase (JNK) and p38-MAPK, whereas it inhibited the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). Moreover, pre-treatment with MAPK inhibitors attenuated the phosphorylation of JNK, p38 and Bax expression enhanced by IL-1α. However, MAPK inhibitors markedly increased the protein expression of osteoblast-related genes and Bcl-xL in the MC3T3-E1 cells downregulated by IL-1α. Taken together, these findings suggest that IL-1α induces the apoptosis of osteoblasts and inhibits osteoblast differentiation by activating the JNK and the p38 MAPK pathways.\",\n \"corpus_id\": 42103216,\n \"score\": 1\n },\n {\n \"doc_id\": \"27626409\",\n \"title\": \"Kinase Signaling in Apoptosis Induced by Saturated Fatty Acids in Pancreatic β-Cells.\",\n \"abstract\": \"Pancreatic β-cell failure and death is considered to be one of the main factors responsible for type 2 diabetes. It is caused by, in addition to hyperglycemia, chronic exposure to increased concentrations of fatty acids, mainly saturated fatty acids. Molecular mechanisms of apoptosis induction by saturated fatty acids in β-cells are not completely clear. It has been proposed that kinase signaling could be involved, particularly, c-Jun N-terminal kinase (JNK), protein kinase C (PKC), p38 mitogen-activated protein kinase (p38 MAPK), extracellular signal-regulated kinase (ERK), and Akt kinases and their pathways. In this review, we discuss these kinases and their signaling pathways with respect to their possible role in apoptosis induction by saturated fatty acids in pancreatic β-cells.\",\n \"corpus_id\": 17403848,\n \"score\": 1\n },\n {\n \"doc_id\": \"29658576\",\n \"title\": \"Paclitaxel suppresses proliferation and induces apoptosis through regulation of ROS and the AKT/MAPK signaling pathway in canine mammary gland tumor cells.\",\n \"abstract\": \"Paclitaxel is a diterpenoid compound, derived from the pacific yew (Taxus brevifolia) berry, which exhibits antineoplastic effects against various types of cancer. However, the antitumor effects and the molecular mechanisms of paclitaxel on canine CHMm cells remain to be elucidated. The aim of the present study was to investigate the antitumor effects of paclitaxel on CHMm cells and identify relevant signal transduction pathways modulated by paclitaxel using multiple methods including MTT assay, flow cytometry, acridine orange/ethidium bromide staining, transmission electron microscopy, determination of cellular reactive oxygen species (ROS), superoxide dismutase (SOD) and malondiadehyde (MDA) and western blotting, the data indicated that paclitaxel decreased cell viability, induced G2/M‑phase cell cycle arrest, suppressed the expression of cyclin B1 and induced apoptosis in a dose‑dependent manner. In addition, paclitaxel upregulated the expression of Bax and cytochrome c, but reduced expression of apoptosis regulator Bcl‑2, resulting in activation of caspase‑3, chromatin condensation, karyopyknosis, intracellular vacuolization, increased production of ROS and MDA, and decreased activity of SOD. However, these effects were inhibited when CHMm cells were treated with N‑acetyl‑L‑cysteine. Furthermore, treatment with paclitaxel inhibited the level of of phospho (p)‑RAC‑α serine/threonine‑protein kinase (AKT) and p‑ribosomal protein S6 kinase proteins, and promoted phosphorylation of P38 mitogen‑activated protein kinase (MAPK) and p‑90 kDa ribosomal protein S6 kinase 1 proteins in CHMm cells. It was observed that paclitaxel in combination with pharmacological inhibitors of the P38 and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase (PI3K) signaling pathways (SB203580 and LY294002, respectively) exerted synergistic inhibitory effects on the proliferation of the CHMm cells. The results of the present study demonstrated that paclitaxel inhibited tumor cell proliferation by increasing intrinsic apoptosis through inhibition of the PI3K/AKT signaling pathway and activation of MAPK signaling pathway in CHMm cells.\",\n \"corpus_id\": 4881550,\n \"score\": 1\n },\n {\n \"doc_id\": \"18186605\",\n \"title\": \"Fermented Antrodia cinnamomea extract protects rat PC12 cells from serum deprivation-induced apoptosis: the role of the MAPK family.\",\n \"abstract\": \"Antrodia cinnamomea (formerly A. camphorata) has recently and commercially been used in the formulation of nutraceuticals and functional foods in Taiwan. Because of its diverse properties, the neuroprotective effect was investigated using a fermented A. cinnamomea extract in this study. Serum deprivation-induced apoptosis in neuronal-like pheochromocytoma (PC12) cells was used as a cell stress model, and it was found that A. cinnamomea was effective in preventing serum-deprived apoptosis according to results of an MTT assay and Hoechst staining. Serum deprivation resulted in decreased phosphorylation of extracellular signal-regulated kinase (ERK) and increased phosphorylations of c-Jun NH2-terminal kinase (JNK) and p38, of the family of mitogen-activated protein kinases (MAPKs); however, A. cinnamomea reversed these phenomena, supporting the antagonistic effects between ERK and JNK-p38 in regulating cell survival. The previously identified active component of A. cinnamomea, adenosine (ADO), also exerted the same effects as A. cinnamomea in preventing apoptosis and regulating phosphorylations of MAPKs. Although an inhibitor of the ERK upstream activator blocked A. cinnamomea-induced ERK phosphorylations, it failed to block the protection of A. cinnamomea and ADO. A protein kinase A (PKA) inhibitor blocked the protection by both A. cinnamomea and ADO. Both JNK and p38 inhibitors were effective in preventing the phosphorylations of JNK and p38 and serum deprivation-induced apoptosis. Collectively, A. cinnamomea prevented serum deprivation-induced PC12 cell apoptosis through a PKA-dependent pathway and by suppression of JNK and p38 activities.\",\n \"corpus_id\": 207197824,\n \"score\": 0\n },\n {\n \"doc_id\": \"18521846\",\n \"title\": \"Mechanism of 2-methoxyestradiol-induced apoptosis and growth arrest in human breast cancer cells.\",\n \"abstract\": \"2-Methoxyestradiol, a well-known nonpolar endogenous metabolite of 17beta-estradiol, has been shown to selectively induce apoptosis in a number of cancer cell lines, but not in normal cells. The mechanism of 2-methoxyestradiol-induced apoptosis appears to vary considerably in different cell lines examined. In the present study, we systematically analyzed the mechanisms of 2-methoxyestradiol-induced apoptosis in the estrogen receptor-negative MDA-MB-435s human breast cancer cells. We found that 2-methoxyestradiol induced the activation of JNK, ERK, and p38 MAPKs. 2-methoxyestradiol-induced JNK activation was associated with the induction of apoptosis through the mitochondrial pathways as a result of increased phosphorylation (inactivation) of the anti-apoptotic Bcl-2 and Bcl-xL proteins. In comparison, 2-methoxyestradiol-induced activation of ERK and p38 in these cells was found to have a protective effect against 2-MeO-E(2)-induced apoptosis. Consistent with this observation, the presence of pharmacological inhibitor of ERK or p38 enhanced 2-methoxyestradiol-induced apoptosis. Mechanistically, inhibition of ERK and p38 activity was associated with activation of various caspases and PARP cleavage, and it also stabilized the pro-apoptotic proteins Bax and Bim, thereby preventing them from degradation during 2-methoxyestradiol treatment. These results suggest that ERK and p38 MAPKs may serve as viable targets for the sensitization of human breast cancer cells to 2-methoxyestradiol-induced apoptosis.\",\n \"corpus_id\": 37332405,\n \"score\": 0\n },\n {\n \"doc_id\": \"18690538\",\n \"title\": \"Ran suppresses paclitaxel-induced apoptosis in human glioblastoma cells.\",\n \"abstract\": \"Yeast-based functional screening of a human glioblastoma cDNA library identified ras-related nuclear protein (Ran) as a novel suppressor of Bcl-2-associated X protein (Bax), a pro-apoptotic member of the Bcl-2 family of proteins. Yeast cells that expressed human Ran were resistant to Bax-induced cell death. In U373MG glioblastoma cells, stable overexpression of Ran significantly attenuated apoptotic cell death induced by the chemotherapeutic agent paclitaxel. FACS analysis demonstrated that Ran is involved in paclitaxel-induced cell cycle arrest. Stable overexpression of Ran also markedly inhibited the phosphorylation of Bcl-2 by paclitaxel, and inhibited the translocation of Bax, the release of cytochrome c and activation of caspase-3. Paclitaxel-induced phosphorylation of c-JUN N-terminal kinase (JNK), but not p38, extracellular signal-regulated kinase and Akt, was markedly suppressed in U373MG cells that stably expressed Ran. These results suggest that Ran suppresses paclitaxel-induced cell death through the downregulation of JNK-mediated signal pathways.\",\n \"corpus_id\": 32218347,\n \"score\": 0\n },\n {\n \"doc_id\": \"19493891\",\n \"title\": \"NaF activates MAPKs and induces apoptosis in odontoblast-like cells.\",\n \"abstract\": \"The cytotoxic effects of fluoride on odontoblasts are not clear. In this study, we examined whether NaF induces apoptosis in MDPC-23 odontoblast-like cells and the involvement of mitogen-activated protein kinase (MAPK) signaling pathways in NaF-induced apoptosis. MDPC-23 cells incubated with 5 mM NaF for 24 hrs exhibited caspase-3 activation, cleavage of poly(ADP-ribose) polymerase, DNA fragmentation, and an increase in cytoplasmic nucleosomes. Prior to the induction of apoptosis, all MAPKs examined were phosphorylated, but in a different manner. In contrast to the sustained phosphorylation of c-Jun NH(2)-terminal kinase (JNK) and p38, NaF exposure induced a biphasic phosphorylation of extracellular signal-regulated protein kinase (ERK). NaF-induced apoptosis was markedly suppressed by treatment with the JNK inhibitor, SP600125, and mildly suppressed by the MAPK/ERK kinase inhibitor, U0126. Inhibition of p38 activity did not protect cells from apoptosis. Thus, exposure to NaF induces apoptosis in odontoblast-like cells, depending on JNK and, less significantly, ERK pathways.\",\n \"corpus_id\": 29316686,\n \"score\": 0\n },\n {\n \"doc_id\": \"19723051\",\n \"title\": \"Activator protein-1 mediates docosahexaenoic acid-induced apoptosis of human gastric cancer cells.\",\n \"abstract\": \"Docosahexaenoic acid (DHA) shows anti-inflammatory and/or anticancer effects in some cells. Activator protein-1 (AP-1) regulates cellular proliferation and apoptosis. Although recent studies demonstrate the association between gastric cancer risk and DHA, the exact molecular mechanism has not been clarified. We investigated whether AP-1 mediates DHA-induced apoptosis of gastric cancer cells. We found that DHA induced cell death and DNA fragmentation in parallel with the activation of extracellular signal-regulated kinases (ERK) and c-Jun N-terminal kinases (JNK) as well as AP-1. DHA increased the protein levels of p53, cytochrome c, and Bax in gastric cancer cells. DHA-induced DNA fragmentation and protein levels of p53, cytochrome c, and Bax were inhibited in the cells transfected with c-jun dominant-negative mutant (TAM67). Because JNK and ERK are upstream signaling for AP-1 activation, we suggest that DHA-induced activation of AP-1 may mediate apoptosis of gastric cancer cells by inducing the expression of apoptotic genes in gastric cancer cells.\",\n \"corpus_id\": 25179794,\n \"score\": 0\n },\n {\n \"doc_id\": \"19747165\",\n \"title\": \"Mesothelin inhibits paclitaxel-induced apoptosis through the PI3K pathway.\",\n \"abstract\": \"Mesothelin, a secreted protein, is overexpressed in some cancers, but its exact function remains unclear. The aim of the present study was to evaluate the possible function of mesothelin. Real-time PCR, RT (reverse transcription)-PCR, cytotoxicity assays, proliferative assays, apoptotic assays by Hoechst staining, detection of active caspases 3 and 7 by flow cytometric analysis, and immunoprecipitation and immunoblotting were performed. Cancer tissues in paclitaxel-resistant ovarian cancer patients expressed higher levels of mesothelin as assessed using real-time PCR than paclitaxel-sensitive ovarian cancer patients (the mean crossing point value change of mesothelin was 26.9+/-0.4 in the resistant group and 34.3+/-0.7 for the sensitive group; P<0.001). Mesothelin also protected cells from paclitaxel-induced apoptosis. The protein expression of Bcl-2 family members, such as Bcl-2 and Mcl-1, was significantly increased regardless of whether cells were treated with exogenous mesothelin or were mesothelin-transfectants. Furthermore, mesothelin-treated cells revealed rapid tyrosine phosphorylation of the p85 subunit of PI3K (phosphoinositide 3-kinase) and ERK (extracellular-signal-regulated kinase) 1/2 for enhancing MAPK (mitogen-activated protein kinase) activity. The anti-apoptotic ability was suppressed and the expression of Bcl-2 family in response to mesothelin was altered by inhibiting PI3K activity, but not by inhibiting MAPK activity. Thus mesothelin can inhibit paclitaxel-induced cell death mainly by involving PI3K signalling in the regulation of Bcl-2 family expression. Mesothelin is a potential target in reducing resistance to cytotoxic drugs.\",\n \"corpus_id\": 23918718,\n \"score\": 0\n },\n {\n \"doc_id\": \"20096139\",\n \"title\": \"ABL-N-induced apoptosis in human breast cancer cells is partially mediated by c-Jun NH2-terminal kinase activation.\",\n \"abstract\": \"INTRODUCTION: The present study was designed to determine the possibility of acetylbritannilactone (ABL) derivative 5-(5-(ethylperoxy)pentan-2-yl)-6-methyl-3-methylene-2-oxo-2,3,3a,4,7,7a-hexahydrobenzofuran-4-yl 2-(6-methoxynaphthalen-2-yl)propanoate (ABL-N) as a novel therapeutic agent in human breast cancers. METHODS: We investigated the effects of ABL-N on the induction of apoptosis in human breast cancer cells and further examined the underlying mechanisms. Moreover, tumor growth inhibition of ABL-N was done in xenograft models. RESULTS: ABL-N induced the activation of caspase-3 in estrogen receptor (ER)-negative cell lines MDA-MB-231 and MDA-MB-468, as evidenced by the cleavage of endogenous substrate Poly (ADP-ribose) polymerase (PARP). Pretreatment of cells with pan-caspase inhibitor z-VAD-fmk or caspase-3-specific inhibitor z-DEVD-fmk inhibited ABL-N-induced apoptosis. ABL-N treatment also resulted in an increase in the expression of pro-apoptotic members (Bax and Bad) with a concomitant decrease in Bcl-2. Furthermore, c-Jun-NH2-terminal kinase (JNK) and p38 mitogen-activated protein (MAP) kinase (p38) were activated in the apoptosis induced by ABL-N and JNK-specific inhibitor SP600125 and JNK small interfering RNA (siRNA) antagonized ABL-N-mediated apoptosis. However, the p38-specific inhibitor SB203580 had no effect upon these processes. Moreover, neither of the caspase inhibitors prevented ABL-N-induced JNK activation, indicating that JNK is upstream of caspases in ABL-N-initiated apoptosis. Additionally, in a nude mice xenograft experiment, ABL-N significantly inhibited the tumor growth of MDA-MB-231 cells. CONCLUSIONS: ABL-N induces apoptosis in breast cancer cells through the activation of caspases and JNK signaling pathways. Moreover, ABL-N treatment causes a significant inhibition of tumor growth in vivo. Therefore, it is thought that ABL-N might be a potential drug for use in breast cancer prevention and intervention.\",\n \"corpus_id\": 3085133,\n \"score\": 0\n },\n {\n \"doc_id\": \"21468925\",\n \"title\": \"Attenuated expression and function of the RECK tumor suppressor under hypoxic conditions is mediated by the MAPK signaling pathways.\",\n \"abstract\": \"Downregulation of the tumor suppressor, reversion-inducing cysteine-rich protein with Kazal motifs (RECK) has been reported under hypoxic conditions (Lee et al., 2010); however, the signaling pathways involved in this downregulation have not yet been identified. Hypoxia causes the silencing of RECK mRNA expression, but treatment with inhibitors of extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 mitogen-activated kinase (MAPK) (PD98059, SP600125, and SB203580 respectively) or their dominant negative mutants recovered RECK suppression induced by hypoxia as analyzed with semiquantitative RT-PCR analysis and a RECK promoter luciferase assay. Hypoxia increased phosphorylation of ERK1/2, JNK and p38 MAPKs. The activities of matrix metalloproteinase (MMP)-9 and MMP-2 were increased under hypoxic conditions but treatment with PD98059, SP600125 and SB203580 inhibited their activation in cancer cells, as seen by zymography. Moreover, treatment with the inhibitors blocked cancer cell migration induced by hypoxia in H-Ras transformed MCF10A mammary cells. RECK suppression under hypoxic conditions was inversely related to HIF-1α expression; however, treatment with PD98059, SP600125 and SB203580 did not influence binding of HIF-1α to the reverse hypoxia responsive element site of the RECK promoter in a DNA precipitation assay. These results suggest that the ERK, JNK and p38 MAPK signaling pathways are indirectly involved in RECK suppression but are not involved in the binding activity of HIF-1α to the reverse hypoxia responsive element site on the RECK promoter under hypoxic conditions.\",\n \"corpus_id\": 26013867,\n \"score\": 0\n },\n {\n \"doc_id\": \"21502402\",\n \"title\": \"Phosphorylation of serine 68 of Twist1 by MAPKs stabilizes Twist1 protein and promotes breast cancer cell invasiveness.\",\n \"abstract\": \"Twist1, a basic helix-loop-helix transcription factor, promotes breast tumor cell epithelial-mesenchymal transition (EMT), invasiveness, and metastasis. However, the mechanisms responsible for regulating Twist1 stability are unknown in these cells. We identified the serine 68 (Ser 68) as a major phosphorylation site of Twist1 by mass spectrometry and with specific antibodies. This Ser 68 is phosphorylated by p38, c-Jun N-terminal kinases (JNK), and extracellular signal-regulated kinases1/2 in vitro, and its phosphorylation levels positively correlate with Twist1 protein levels in human embryonic kidney 293 and breast cancer cells. Prevention of Ser 68 phosphorylation by an alanine (A) mutation (Ser 68A) dramatically accelerates Twist1 ubiquitination and degradation. Furthermore, activation of mitogen-activated protein kinases (MAPK) by an active Ras protein or TGF-β treatment significantly increases Ser 68 phosphorylation and Twist1 protein levels without altering Twist1 mRNA expression, whereas blocking of MAPK activities by either specific inhibitors or dominant negative inhibitory mutants effectively reduces the levels of both induced and uninduced Ser 68 phosphorylation and Twist protein. Accordingly, the mammary epithelial cells expressing Twist1 exhibit much higher degrees of EMT and invasiveness on stimulation with TGF-β or the active Ras and paclitaxel resistance compared with the same cells expressing the Ser 68A-Twist1 mutant. Importantly, the levels of Ser 68 phosphorylation in the invasive human breast ductal carcinomas positively correlate with the levels of Twist1 protein and JNK activity and are significantly higher in progesterone receptor-negative and HER2-positive breast cancers. These findings suggest that activation of MAPKs by tyrosine kinase receptors and Ras signaling pathways may substantially promote breast tumor cell EMT and metastasis via phoshorylation and stabilization of Twist1.\",\n \"corpus_id\": 18469121,\n \"score\": 0\n },\n {\n \"doc_id\": \"22238304\",\n \"title\": \"Varicella-Zoster virus ORF12 protein triggers phosphorylation of ERK1/2 and inhibits apoptosis.\",\n \"abstract\": \"Mitogen-activated protein kinases (MAPKs) are a family of serine-threonine protein kinases involved in many cellular processes, including cell proliferation, differentiation, inflammation, and cell death. Activation of several MAPKs, including extracellular signal-regulated kinase 1 and 2 (ERK1/2), p38, and c-Jun N-terminal kinase (JNK), results in stimulation of activator protein 1 (AP-1), which promotes gene transcription. Previous studies have demonstrated that varicella-zoster virus (VZV) infection activates ERK1/2, p38, and JNK to promote viral replication, but the underlying mechanism(s) is unclear. To identify viral proteins responsible for the activation of MAPK, we used a proteomic approach to screen viral proteins for AP-1 promoter activation by an AP-1-luciferase reporter assay. We found that VZV ORF12 protein, located in the tegument of virions, enhances AP-1 reporter activity. This effect of ORF12 protein was markedly inhibited by a MAPK/ERK kinase 1 and 2 (MEK1/2) inhibitor (U0126), partially blocked by a p38 inhibitor (SB202190), but not inhibited by a JNK inhibitor (SP600125). Expression of VZV ORF12 protein in cells resulted in phosphorylation of ERK1/2 and p38 but not JNK. Infection of cells with a VZV ORF12 deletion mutant resulted in reduced levels of phosphorylated ERK1/2 (p-ERK1/2) compared to infection with wild-type VZV. Furthermore, deletion of ORF12 rendered VZV-infected cells more susceptible to staurosporine-induced apoptosis. In conclusion, VZV ORF12 protein activates the AP-1 pathway by selectively triggering the phosphorylation of ERK1/2 and p38. Cells infected with a VZV ORF12 deletion mutant have reduced levels of p-ERK1/2 and are more susceptible to apoptosis than cells infected with wild-type VZV.\",\n \"corpus_id\": 7307015,\n \"score\": 0\n },\n {\n \"doc_id\": \"22258404\",\n \"title\": \"ERK2 phosphorylation of serine 77 regulates Bmf pro-apoptotic activity.\",\n \"abstract\": \"B-cell lymphoma 2 (Bcl-2) homology 3 (BH3)-only proteins represent a class of pro-apoptotic factors that neutralize pro-survival Bcl-2 proteins, and, in some cases, directly activate Bax. The mechanisms of control and the role of BH3-only proteins, such as Bcl-2 like protein 11 extra large and Bad are well studied. By contrast, relatively little is known about the regulation and role of Bcl-2 modifying factor (Bmf). The B-RAF oncogene is mutated in ∼8% of human tumors. We have previously shown that Bmf is upregulated at the transcript level and is required for apoptosis induced by targeting B-RAF signaling in tumor cells harboring mutant B-RAF. In this study, we show that Bmf is regulated at the post-translational level by mutant B-RAF-MEK-ERK2 signaling. Extracellular signal-regulated kinase (ERK2) directly phosphorylates Bmf on serine 74 and serine 77 residues with serine 77 being the predominant site. In addition, serine 77 phosphorylation reduces Bmf pro-apoptotic activity likely through a mechanism independent of altering Bmf localization to the mitochondria and/or interactions with dynein light chain 2 and the pro-survival proteins, B-cell lymphoma extra large, Bcl-2 and Mcl-1. These data identify a novel mode of regulation in Bmf that modulates its pro-apoptotic activity in mutant B-RAF tumor cells.\",\n \"corpus_id\": 8660265,\n \"score\": 0\n },\n {\n \"doc_id\": \"23135225\",\n \"title\": \"Vaspin attenuates the apoptosis of human osteoblasts through ERK signaling pathway.\",\n \"abstract\": \"It has been hypothesized that adipocytokines originating from adipose tissue may have an important role in bone metabolism. Vaspin is a novel adipocytokine isolated from visceral white adipose tissue, which has been reported to have anti-apoptotic effects in vascular endothelial cells. However, to the best of our knowledge there is no information regarding the effects of vaspin on osteoblast apoptosis. This study therefore examined the possible effects of vaspin on apoptosis in human osteoblasts (hOBs). Our study established that vaspin inhibits hOBs apoptosis induced by serum deprivation, as determined by ELISA and TUNEL assays. Western blot analysis revealed that vaspin upregulates the expression of Bcl-2 and downregulates that of Bax in a dose-dependent manner. Vaspin stimulated the phosphorylation of ERK, and pretreatment of hOBs with the ERK inhibitor PD98059 blocked the vaspin-induced activation of ERK, however, vaspin did not stimulate the phosphorylation of p38, JNK or Akt. Vaspin protects hOBs from serum deprivation-induced apoptosis, which may be mediated by activating the MAPK/ERK signaling pathway.\",\n \"corpus_id\": 1755050,\n \"score\": 0\n },\n {\n \"doc_id\": \"23577223\",\n \"title\": \"Oxidative stress and mitogen-activated protein kinase pathways involved in cadmium-induced BRL 3A cell apoptosis.\",\n \"abstract\": \"In this study, BRL 3A cells were treated with different Cd concentrations (0, 10, 20, and 40 μmol/L) for 12 h and preincubated with or without N-acetyl-L-cysteine (NAC) (2 mmol/L) for 30 min, and cells were treated with Cd (0 and 20 μmol/L), pretreated with p38 inhibitor (SB203580), JNK (c-Jun NH2-terminal kinases) inhibitor (SP600125), and extracellular signal-regulated kinase (ERK) inhibitor (U0126) for 30 min, and then treated with 20 μmol/L Cd for 12 h. Cd decreased cell viability, SOD, and GSH-Px activity in a concentration-dependent manner. Increased MDA level, ROS generation, nuclear condensation, shrinkage, and fragmentation in cell morphology were inhibited by NAC. Cd-induced apoptosis was attenuated by pretreatment with SB203580, SP600125, and U0126. The results of western blot showed that NAC preincubation affected Cd-activated MAPK pathways, p38 and ERK phosphorylation. Cd treatment elevated the mRNA levels of Bax and decreased the mRNA levels of Bcl-2, respectively. The same effect was found in their protein expression levels. These results suggest that oxidative stress and MAPK pathways participate in Cd-induced apoptosis and that the balance between pro- and antiapoptotic genes (Bax and Bcl-2) is important in Cd-induced apoptosis.\",\n \"corpus_id\": 6233368,\n \"score\": 0\n },\n {\n \"doc_id\": \"23707804\",\n \"title\": \"Brazilein suppresses migration and invasion of MDA-MB-231 breast cancer cells.\",\n \"abstract\": \"Brazilein, a bioactive compound isolated from Caesalpinia sappan L., has long been used in oriental folk medicines. Cancer metastasis is a primary cause of cancer death. However, the anti-metastatic effects of brazilein remain elusive. In this study, we found that brazilein inhibited human breast cancer MDA-MB-231 cell migration and invasion using wound-healing assay and Boyden chamber assay. The results of Western blot, gelatin zymography and reversed transcription-PCR analysis showed that brazilein suppressed matrix metalloproteinase-2 (MMP-2) expression in a concentration-dependent manner. Brazilein also decreased the nuclear protein level of nuclear factor kappaB (NF-κB). Brazilein potently suppressed the phosphorylation of p38 mitogen-activated protein kinase (p38 MAPK), phosphatidylinositide-3-kinase (PI3K) and Akt, but did not affect phosphorylation of extracellular signal regulating kinase (ERK)1/2 and c-Jun N-terminal kinase (JNK). Additionally, treatment of SB203580 (p38 MAPK inhibitor) or wortmannin (PI3K inhibitor) resulted in a reduced activity and expression of MMP-2 as well as inhibition on cell migration and invasion in MDA-MB-231 cells. Taken together, these results suggest that brazilein inhibition of MDA-MB-231 cells may be mediated through inactivation of both PI3K/Akt and p38 MAPK signaling pathways, leading to inhibitory effect on NF-κB activation. Consequently, brazilein suppresses MMP-2 expression, and thus confers anti-migration and anti-invasion of MDA-MB-231 cells.\",\n \"corpus_id\": 5435205,\n \"score\": 0\n },\n {\n \"doc_id\": \"24589734\",\n \"title\": \"Differences in c-Jun N-terminal kinase recognition and phosphorylation of closely related stathmin-family members.\",\n \"abstract\": \"The stathmin (STMN) family of tubulin-binding phosphoproteins are critical regulators of interphase microtubule dynamics and organization in a broad range of cellular processes. c-Jun N-terminal kinase (JNK) signalling to STMN family proteins has been implicated specifically in neuronal maturation, degeneration and cell stress responses more broadly. Previously, we characterized mechanisms underlying JNK phosphorylation of STMN at proline-flanked serine residues (Ser25 and Ser38) that are conserved across STMN-like proteins. In this study, we demonstrated using in vitro kinase assays and alanine replacement of serine residues that JNK phosphorylated the STMN-like domain (SLD) of SCG10 on Ser73, consistent with our previous finding that STMN Ser38 was the primary JNK target site. In addition, we confirmed that a JNK binding motif ((41)KKKDLSL(47)) that facilitates JNK targeting of STMN is conserved in SCG10. In contrast, SCLIP was phosphorylated by JNK primarily on Ser60 which corresponds to Ser25 on STMN. Moreover, although the JNK-binding motif identified in STMN and SCG10 was not conserved in SCLIP, JNK phosphorylation of SCLIP was inhibited by a substrate competitive peptide (TI-JIP) highlighting kinase-substrate interaction as required for JNK targeting. Thus, STMN and SCG10 are similarly targeted by JNK but there are clear differences in JNK recognition and phosphorylation of the closely related family member, SCLIP.\",\n \"corpus_id\": 19988564,\n \"score\": 0\n },\n {\n \"doc_id\": \"28393288\",\n \"title\": \"Differential effects of p38 MAP kinase inhibitors SB203580 and SB202190 on growth and migration of human MDA-MB-231 cancer cell line.\",\n \"abstract\": \"p38 mitogen-activated protein kinase (MAPK) belongs to the MAPK superfamily, phosphorylating serine and/or threonine residues of the target proteins. The activation of p38 MAPK leads to cell growth, differentiation, inflammation, survival or apoptosis. In this study, we tested the effect of two highly specific and potent inhibitors of p38 MAPK (namely, SB203580 and SB202190) on human breast cancer cell line MDA-MB-231 to elucidate the controversial role of p38 MAPK on cell proliferation and/or cell migration/metastasis further. It was determined that the IC50 value of SB203580 was 85.1 µM, while that of SB202190 was 46.6 µM, suggesting that SB202190 is slightly more effective than SB203580. To verify the effect of each inhibitor on cell proliferation and cytotoxicity, the cells were treated with various doses of SB203580 and SB202190 and examined using iCELLigence system. No significant effect of 1 and 5 µM of both inhibitors were seen on cell proliferation as compared to the DMSO-treated control cells for up to 96 h. On the other hand, both SB203580 and SB202190 significantly prevented cell proliferation at a concentration of 50 µM. SB202190 was again more effective than SB203580. Afterwards, we tested the effect of each inhibitor on cell migration using wound assay. Both SB203580 and SB202190 significantly reduced cell migration in a time-dependent manner at a concentration of 50 µM. However, interestingly it was observed that a low and noncytotoxic dose of 5 µM of SB203580 and SB202190 also did cause significant cell migration inhibition at 48 h of the treatment, corroborating the fact that p38 MAPK pathway has a critical role in cell migration/metastasis. Then, we tested whether each p38 MAPK inhibitor has any effect on cell adhesion during a treatment period of 3 h using iCELLigence system. A concentration of only 50 µM of SB202190 reduced cell adhesion for about 1.5 h (p < 0.001); after that period of time, cell adhesion in 50 µM SB202190-treated cells returned to the level of the control cells. To determine the mechanism of growth and cell migration inhibitory effects of p38 MAPK inhibitors, the activation/inactivation of various proteins and enzymes was subsequently analyzed by PathScan(®) Intracellular Signaling Array kit. The ERK1/2 phosphorylation level was not modified by low concentrations (1 or 5 µM) of SB202190 and SB203580; while a high concentration (50 µM) of both inhibitors caused significant reductions in the ERK1/2 phosphorylation. In addition, it was determined that both p38 MAPK inhibitors caused significant increases on the Ser15 phosphorylation of mutant p53 in MDA-MB-231 under these experimental conditions; while SB202190 was more potent than SB203580.\",\n \"corpus_id\": 44326135,\n \"score\": 0\n },\n {\n \"doc_id\": \"29022012\",\n \"title\": \"Vanadate oxidative and apoptotic effects are mediated by the MAPK-Nrf2 pathway in layer oviduct magnum epithelial cells.\",\n \"abstract\": \"Vanadium is a metal of high physiological, environmental and industrial importance. However, vanadium-induced oxidative stress can reduce the egg quality of poultry, and be potentially harmful to humans, and the underlying mechanism is not clear. In this study, we investigated the underlying relationship between the oxidant-sensitive mitogen-activated protein kinase (MAPK) signaling pathway and vanadium-induced oxidative stress in oviduct magnum epithelial (OME) cells. Cultured OME cells were treated with 100 μmol L-1 vanadium and/or MAPK inhibitors [P38 MAPK inhibitor, SB203580; extracellular regulated protein kinase 1 and 2 (ERK1/2) inhibitor, U0126; c-JUN N-terminal kinases (JNK) inhibitor, SP600125]. Cell viability, apoptosis, and generation of reactive oxygen species (ROS) were assessed using flow cytometry. The expression of oxidative stress-related genes and their proteins was measured by reverse transcription-polymerase chain reaction and western blotting. Vanadium treatment reduced cell viability, whereas pretreated OME cells with SB203580 and U0126 prevented the reducing effect of vanadium on cell viability (P < 0.05). Likewise, MAPK inhibitors effectively suppressed vanadium-induced apoptosis and ROS generation (P < 0.05). In the OME cells treated with vanadium, SB203580 (P < 0.05) and SP600125 (P = 0.08) increased catalase activity by 89.3% and 55.3%; SB203580 and U0126 increased (P < 0.05) glutathione peroxidase activity by 44.9% and 51.1%, respectively. Incubation of OME cells with MAPK inhibitors also prevents malondialdehyde concentration increase and lactic dehydrogenase activity decrease in response to vanadium (P < 0.05). Vanadium downregulated P38, ERK1/2, JNK, Nrf2, sMaf, GCLC, NQO1 and HO-1 mRNA expression (P < 0.05). In contrast, inhibition of JNK with SP600125 upregulated P38, ERK1/2, JNK, Nrf2, GCLC and HO-1 mRNA expression (P < 0.05); inhibition of P38 with SB203580 upregulated JNK, NQO1 and HO-1 mRNA expression (P < 0.05); and inhibition of ERK1/2 with U0126 upregulated ERK1/2, GCLC and HO-1 mRNA expression (P < 0.05). Moreover, phosphorylation of P38, ERK1/2, JNK, and Nrf2 proteins was enhanced by V incubation; however, SP600125 blocked the phosphorylation of these proteins, whereas SB203580 blocked the phosphorylation of P38 and Nrf2. These results indicate that vanadium inducing oxidative stress in OME cells might be, at least, associated with the phosphorylation of the P38MAPK/JNK-Nrf2 pathway, which reduces the expression of phase II detoxifying enzymes.\",\n \"corpus_id\": 206096005,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":70,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29159452\",\n \"title\": \"Saprotrophic soil fungi to improve phosphorus solubilisation and release: In vitro abilities of several species.\",\n \"abstract\": \"Modern agriculture is dependent on phosphate rock (PR), which is a nonrenewable resource. Improvement of phosphorus (P) availability for crops in agricultural soils represents a key strategy to slow down the depletion of PR. The aim of this study was to identify potential P biofertilisers among saprotrophic fungal species. We tested 30 fungal strains belonging to 28 taxa (4 Zygomycota and 24 Ascomycota) and with different life strategies. The study showed that many saprotrophic fungi have the ability to mobilise P from insoluble forms according to a variety of mechanisms. Our results expand the pool of P solubilising fungal species, also suggesting a new solubilisation index and shedding light on parameters that could be basic in the selection of efficient soil P-biofertilisers fungi. Rhizopus stolonifer var. stolonifer, Aspergillus niger and Alternaria alternata were found to be the best performing strains in terms of amounts of TCP solubilisation.\",\n \"corpus_id\": 11749631\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19709342","title":"Comparing phosphorus mobilization strategies using Aspergillus niger for the mineral dissolution of three phosphate rocks.","abstract":"Phosphorus deficiencies are limiting crop production in agricultural soils worldwide. Locally available sources of raw phosphate rock (PR) are being recognized for their potential role in soil fertility improvement. Phosphorus bioavailability is essential for the efficiency of PRs and can be increased by acid treatments. The utilization of organic acid producing micro-organisms, notably Aspergillus niger, presents a sustainable alternative to the use of strong inorganic acids, but acid production of A. niger strongly depends on the mineral content of the growth media. This study compared the phosphorus mobilization efficiency of two biological treatments, namely addition of acidic cell-free supernatants from A. niger cultivations to PRs and the direct cultivation of A. niger with PRs. The results show that addition of PR to cultivations leads to significant differences in the profile of organic acids produced by A. niger. Additions of PR, especially igneous rocks containing high amounts of iron and manganese, lead to reduced citric acid concentrations. In spite of these differences, phosphorus mobilization was similar between treatments, suggesting that the simpler direct cultivation method was not inferior. In addition to citric acid, it is suggested that oxalic acid contributes to PR solubilization in direct cultivations with A. niger, which would benefit farmers in developing countries where conventional fertilizers are not adequately accessible.","corpus_id":9537394,"score":2},{"doc_id":"20705386","title":"The effectiveness of arbuscular-mycorrhizal fungi and Aspergillus niger or Phanerochaete chrysosporium treated organic amendments from olive residues upon plant growth in a semi-arid degraded soil.","abstract":"Arbuscular mycorrhizal (AM) fungi and a residue from dry olive cake (DOC) supplemented with rock phosphate (RP) and treated with either Aspergillus niger (DOC-A) or Phanerochaete chrysosporium (DOC-P), were assayed in a natural, semi-arid soil using Trifolium repens or Dorycnium pentaphyllum plants. The effects of the AM fungi and/or DOC-A were compared with P-fertilisation (P) over eleven successive harvests to evaluate the persistence of the effectiveness of the treatments. The biomass of dually-treated plants after four successive harvests was greater than that obtained for non-treated plants or those receiving the AM inoculum or DOC-A treatments after eleven yields. The AM inoculation was critical for obtaining plant growth benefit from the application of fermented DOC-A residue. The abilities of the treatments to prevent plant drought stress were also assayed. Drought-alleviating effects were evaluated in terms of plant growth, proline and total sugars concentration under alternative drought and re-watering conditions (8th and 9th harvests). The concentrations of both compounds in plant biomass increased under drought when DOC-A amendment and AM inoculation were employed together: they reinforced the plant drought-avoidance capabilities and anti-oxidative defence. Water stress was less compensated in P-fertilised than in DOC-A-treated plants. DOC-P increased D. pentaphyllum biomass, shoot P content, nodule number and AM colonisation, indicating the greater DOC-transforming ability of P. chrysosporium compared to A. niger. The lack of AM colonisation and nodulation in this soil was compensated by the application of DOC-P, particularly with AM inoculum. The management of natural resources (organic amendments and soil microorganisms) represents an important strategy that assured the growth, nutrition and plant establishment in arid, degraded soils, preventing the damage that arises from limited water and nutrient supply.","corpus_id":22384618,"score":2},{"doc_id":"23025081","title":"[Filamentous and phosphate solubilizing fungi relationships with some edaphic parameters and coffee plantations management].","abstract":"Relaciones entre los hongos filamentosos y solubilizadores de fosfatos con algunas variables edáficas y el manejo de cafetales. Soil properties and the environment have multiple outcomes on fungal communities. Although, the interaction effects between management intensity, pH, available phosphorus, organic carbon, soil texture and different fractions of water stable macro-aggregates on the communities of microscopic filamentous fungi (MFF), iron phosphate solubilizing fungi (PSF-Fe), and iron and calcium phosphate solubilizing fungi (PSF-(Fe+Ca)), have been previously evaluated in field conditions, this has never been performed in terms of their combined effects, neither with phosphate solubilizing fungi. To assess this, we collected 40 composite soil samples from eight Mexican and Colombian coffee plantations, with different management intensities and physico-chemical edaphic parameters, during 2008-2009. We isolated different communities of MFF, PSF-Fe and PSF-(Fe+Ca), by wet sieving and soil particles culture in Potato-Dextrose-Agar from soil samples, and we classified isolates in terms of their phosphate solubilizing ability. Following the principal component analysis results, we decided to analyze fungal communities and abiotic factors interactions for each country separately. Structural Equation Models revealed that organic carbon was positively associated to MFF richness and number of isolates (lambda>0.58), but its relationship with PSF-Fe and PSF-(Fe+Ca) were variable; while the available phosphorus, pH and water stable macro-aggregate fractions did not show a clear pattern. Management intensity was negatively related to PSF-Fe (lambda < or = -0.21) morphotype richness and the number of isolates in Colombian coffee plantations. We found that the relationships of clay and organic carbon content, and available phosphorus and soil pH, with the species richness and number of isolates of MFF, PSF-Fe and PSF-(Fe+Ca) were highly variable; this made impossible to generalize the responses between saprotrophic fungal groups and geographic zones. The management intensity was not related to species richness and number of isolates of MFF in any coffee areas, while for PSF the relationship could not be defined. The different water stable macro-aggregates fractions did not show a defined pattern in relation to the species richness and the number of isolates of saprophytic and phosphate solubilizing fungi (PSF). This study highlights the need to take into account edaphic and geographic context in order to reach a better understanding of the intensity management effects on MFF and PSF function in agroecosystems.","corpus_id":44553089,"score":2},{"doc_id":"23100719","title":"Isolation and characterisation of phosphate solubilising microorganisms from the cold desert habitat of Salix alba Linn. in trans Himalayan region of Himachal Pradesh.","abstract":"Phosphate solubilising microorganisms (PSM) (bacteria and fungi) associated with Salix alba Linn. from Lahaul and Spiti valleys of Himachal Pradesh were isolated on Pikovskaya (PVK), modified Pikovskaya (MPVK) and National Botanical Research Institute agar (NBRIP) media by spread plating. The viable colony count of P-solubilising bacteria (PSB) and fungi (PSF) was higher in rhizosphere than that of non-rhizosphere. The frequency of PSM was highest on MPVK followed by NBRIP and PVK agar. The maximum proportion of PSM out of total bacterial and fungal count was found in upper Keylong while the least in Rong Tong. The PSB frequently were Gram-positive, endosporeforming, motile rods and belonged to Bacillus sp. The PSF mainly belonged to Penicillium sp., Aspergillus fumigatus, A. niger, A. spp. and non-sporulating sterile. Amongst the isolates with high efficiency for tricalcium phosphate (TCP) solubilisation, seven bacterial and seven fungal isolates dissolved higher amount of P from North Carolina rock phosphate (NCRP) than Mussoorie rock phosphate (MRP) and Udaipur rock phosphate (URP). However, the organisms solubilised higher-P in NBRIP broth than PVK broth. SBC5 (Bacillus sp.) and SBC7 (Bacillus sp.) bacterial isolates exhibited maximun P solubilisation (40 and 33 μg ml(-1) respectively) whereas FC28 (Penicillium sp.) isolate (52.3 μg ml(-1)) amongst fungi while solubilising URP. The amount of P solubilised was positively correlated with the decrease in pH of medium. SBC5 (Bacillus sp.), SBC7 (Bacillus sp.) and SBC4 (Micrococcus) decreased the pH of medium from 6.8 to 6.08 while FC28 (Penicillium sp.) and FC39 (Penicillium sp.) isolates of fungi recorded maximum decrease in pH of medium from 6.8 to 5.96 in NBRIP broth.","corpus_id":9867654,"score":2},{"doc_id":"24560283","title":"Role of phosphate fertilizers in heavy metal uptake and detoxification of toxic metals.","abstract":"As a nonrenewable resource, phosphorus (P) is the second most important macronutrient for plant growth and nutrition. Demand of phosphorus application in the agricultural production is increasing fast throughout the globe. The bioavailability of phosphorus is distinctively low due to its slow diffusion and high fixation in soils which make phosphorus a key limiting factor for crop production. Applications of phosphorus-based fertilizers improve the soil fertility and agriculture yield but at the same time concerns over a number of factors that lead to environmental damage need to be addressed properly. Phosphate rock mining leads to reallocation and exposure of several heavy metals and radionuclides in crop fields and water bodies throughout the world. Proper management of phosphorus along with its fertilizers is required that may help the maximum utilization by plants and minimum run-off and wastage. Phosphorus solubilizing bacteria along with the root rhizosphere of plant integrated with root morphological and physiological adaptive strategies need to be explored further for utilization of this extremely valuable nonrenewable resource judiciously. The main objective of this review is to assess the role of phosphorus in fertilizers, their uptake along with other elements and signaling during P starvation.","corpus_id":41540557,"score":2},{"doc_id":"25561059","title":"Mechanisms for solubilization of various insoluble phosphates and activation of immobilized phosphates in different soils by an efficient and salinity-tolerant Aspergillus niger strain An2.","abstract":"Mechanisms for solubilization of different types of phosphates and activation of immobilized phosphates in different types of soils by an efficient fungal strain An2 were explored and evaluated in this study. An2 was isolated from a Chinese cabbage rhizosphere soil and identified as Aspergillus niger. It could fast release up to 1722, 2066, and 2356 mg L(-1) of soluble phosphorus (P) from 1 % Ca3(PO4)2, Mg3(PO4)2, and AlPO4 (Ca-P, Mg-P, and Al-P) and 215 and 179 mg L(-1) from 0.5 % FePO4 and rock phosphate (Fe-P and RP), respectively. HPLC assay demonstrated that An2 mainly secreted oxalic acid to solubilize Ca-P, Mg-P, Al-P, and Fe-P whereas secreted tartaric acid to solubilize RP. Furthermore, An2 could tolerate salinity up to 4 % NaCl without impairing its phosphate-solubilizing ability. The simulation experiments validated that An2 was able to effectively activate immobilized phosphates in general calcareous, acidic, as well as saline-alkali soils with high total P content. This study shows new insights into the mechanisms for microbial solubilization of different types of phosphates and supports the future application of strain An2 in different types of soils to effectively activate P for plants.","corpus_id":34638507,"score":2},{"doc_id":"25674415","title":"Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.","abstract":"Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05% (w/w) but only 0.1% of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8% of the plant dry weight. To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75-90% of added P is precipitated by metal-cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.","corpus_id":18845624,"score":2},{"doc_id":"26469739","title":"Phosphate solubilization and promotion of maize growth by Penicillium oxalicum P4 and Aspergillus niger P85 in a calcareous soil.","abstract":"Alternative tactics for improving phosphorus nutrition in crop production are needed in China and elsewhere, as the overapplication of phosphatic fertilizers can adversely impact agricultural sustainability. Penicillium oxalicum P4 and Aspergillus niger P85 were isolated from a calcareous soil in China that had been exposed to excessive application of phosphatic fertilizer for decades. Each isolate excreted a number of organic acids into, acidified, and solubilized phosphorus in a synthetic broth containing insoluble tricalcium phosphate or rock phosphate. Isolate P4, applied as a seed treatment, increased maize fresh mass per plant when rock phosphate was added to the calcareous soil in greenhouse pot studies. Isolate P85 did not increase maize fresh mass per plant but did significantly increase total phosphorus per plant when rock phosphate was added. Significant increases in 7 and 4 organic acids were detected in soil in association with isolates P4 and P85, respectively, relative to the soil-only control. The quantity and (or) number of organic acids produced by these isolates increased when rock phosphate was added to the soil. Both isolates also significantly increased available phosphorus in soil in the presence of added rock phosphate and effectively colonized the maize rhizosphere. Studies reported here indicate that isolate P4 is adapted to and capable of promoting maize growth in a calcareous soil. Plant-growth promotion by this isolate is likely due, at least in part, to increased phosphorus availability resulting from the excretion of organic acids into, and the resulting acidification of, this soil.","corpus_id":25397971,"score":2},{"doc_id":"26805616","title":"Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils.","abstract":"Intensive agricultural practices and cultivation of exhaustive crops has deteriorated soil fertility and its quality in agroecosystems. According to an estimate, such practices will convert 30% of the total world cultivated soil into degraded land by 2020. Soil structure and fertility loss are one of the main causes of soil degradation. They are also considered as a major threat to crop production and food security for future generations. Implementing safe and environmental friendly technology would be viable solution for achieving sustainable restoration of degraded soils. Bacterial and fungal inocula have a potential to reinstate the fertility of degraded land through various processes. These microorganisms increase the nutrient bioavailability through nitrogen fixation and mobilization of key nutrients (phosphorus, potassium and iron) to the crop plants while remediate soil structure by improving its aggregation and stability. Success rate of such inocula under field conditions depends on their antagonistic or synergistic interaction with indigenous microbes or their inoculation with organic fertilizers. Co-inoculation of bacteria and fungi with or without organic fertilizer are more beneficial for reinstating the soil fertility and organic matter content than single inoculum. Such factors are of great importance when considering bacteria and fungi inocula for restoration of degraded soils. The overview of presented mechanisms and interactions will help agriculturists in planning sustainable management strategy for reinstating the fertility of degraded soil and assist them in reducing the negative impact of artificial fertilizers on our environment.","corpus_id":206936928,"score":2},{"doc_id":"26850158","title":"Mycorrhizal fungal communities respond to experimental elevation of soil pH and P availability in temperate hardwood forests.","abstract":"Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.","corpus_id":37898479,"score":2},{"doc_id":"27102357","title":"Arbuscular mycorrhizal fungi in soil and roots respond differently to phosphorus inputs in an intensively managed calcareous agricultural soil.","abstract":"Understanding the diversity and community structure of arbuscular mycorrhizal fungi (AMF) is important for potentially optimizing their role in mining phosphorus (P) in agricultural ecosystems. Here, we conduct a comprehensive study to investigate the vertical distribution of AMF in a calcareous field and their temporal structure in maize-roots with fertilizer P application over a three-year period. The results showed that soil available-P response to P fertilization but maize yields did not. Phosphorus fertilization had no-significant effect on richness of AMF except at greater soil-depths. High P-supply reduced root colonization while optimum-P tended to increase colonization and fungal richness on all sampling occasions. Crop phenology might override P-supply in determining the community composition of active root inhabiting fungi. Significant differences in the community structure of soil AMF were observed between the controls and P treatments in surface soil and the community shift was attributable mainly to available-P, N/P and pH. Vertical distribution was related mainly to soil electrical conductivity and Na content. Our results indicate that the structure of AMF community assemblages is correlated with P fertilization, soil depth and crop phenology. Importantly, phosphorus management must be integrated with other agricultural-practices to ensure the sustainability of agricultural production in salinized soils.","corpus_id":14178968,"score":2},{"doc_id":"27688771","title":"Phosphate Solubilization Potential of Rhizosphere Fungi Isolated from Plants in Jimma Zone, Southwest Ethiopia.","abstract":"Phosphorus (P) is one of the major bioelements limiting agricultural production. Phosphate solubilizing fungi play a noteworthy role in increasing the bioavailability of soil phosphates for plants. The present study was aimed at isolating and characterizing phosphate solubilizing fungi from different rhizospheres using both solid and liquid Pikovskaya (PVK) medium. A total of 359 fungal isolates were obtained from 150 rhizosphere soil samples of haricot bean, faba bean, cabbage, tomato, and sugarcane. Among the isolates, 167 (46.52%) solubilized inorganic phosphate. The isolated phosphate solubilizing fungi belonged to genera of Aspergillus (55.69%), Penicillium spp. ( 23.35%), and Fusarium (9.58%). Solubilization index (SI) ranged from 1.10 to 3.05. Isolates designated as JUHbF95 (Aspergillus sp.) and JUFbF59 (Penicillium sp.) solubilized maximum amount of P 728.77 μg·mL(-1) and 514.44 μg mL(-1), respectively, from TCP (tricalcium phosphate) after 15 days of incubation. The highest (363 μg mL(-1)) soluble-P was released from RP with the inoculation of JUHbF95 in the PVK broth after 10 days of incubation. The present study indicated the presence of diverse plant associated P-solubilizing fungi that may serve as potential biofertilizers.","corpus_id":9160393,"score":2},{"doc_id":"27825490","title":"Phosphate dissolving fungi: Mechanism and application in alleviation of salt stress in wheat.","abstract":"The present investigation reveals the solubilization efficiency of tri-calcium phosphate (TCP), Udaipur rock phosphate (URP), aluminium phosphate (AP) and ferric phosphate (FP) by Aspergillus niger (ITCC 6719) and Trichoderma harzianum (ITCC 6721) as function of carbon concentrations. Increasing glucose concentration from 1 to 7% in the growth medium, though improved the phosphorus (P) solubilization significantly but each fungal strain preferred different optimum carbon concentrations for mediating solubilization of different P sources. The two fungi employed different mechanisms to reduce medium pH for release of P from TCP, AP and FP. However, URP was solubilized solely through fungal production of citric, succinic, propionic, malic and acetic acid. A linear increase in citric acid production with increasing carbon concentration was recorded during FP solubilization by T. harzianum. The cell free culture filtrate of A. niger detected high phytase and low acid phosphatase activity titre whereas results were vice versa for T. harzianum. Both the fungal strains possessed plant growth promoting attributes such as auxin and sidreophore production and could solubilize Zn. In hydroponic system (with 60mM of sodium chloride concentration), supplementation with culture filtrate from each fungal strain increased the shoot growth of wheat seedlings significantly compared to non culture filtrate control. Use of A.niger as bio-inoculant could be a sustainable approach to improve soil P availability, promote plant growth and alleviate adverse effect of salt stress.","corpus_id":35215601,"score":2},{"doc_id":"27872635","title":"Rhizosphere Organic Anions Play a Minor Role in Improving Crop Species' Ability to Take Up Residual Phosphorus (P) in Agricultural Soils Low in P Availability.","abstract":"Many arable lands have accumulated large reserves of residual phosphorus (P) and a relatively large proportion of soil P is less available for uptake by plants. Root released organic anions are widely documented as a key physiological strategy to enhance P availability, while limited information has been generated on the contribution of rhizosphere organic anions to P utilization by crops grown in agricultural soils that are low in available P and high in extractable Ca, Al, and Fe. We studied the role of rhizosphere organic anions in P uptake from residual P in four common crops Triticum aestivum, Avena sativa, Solanum tuberosum, and Brassica napus in low- and high-P availability agricultural soils from long-term fertilization field trials in a mini-rhizotron experiment with four replications. Malate was generally the dominant organic anion. More rhizosphere citrate was detected in low P soils than in high P soil. B. napus showed 74-103% increase of malate in low P loam, compared with clay loam. A. sativa had the greatest rhizosphere citrate concentration in all soils (5.3-15.2 μmol g(-1) root DW). A. sativa also showed the highest level of root colonization by arbuscular mycorrhizal fungi (AMF; 36 and 40%), the greatest root mass ratio (0.51 and 0.66) in the low-P clay loam and loam respectively, and the greatest total P uptake (5.92 mg P/mini-rhizotron) in the low-P loam. B. napus had 15-44% more rhizosphere acid phosphatase (APase) activity, ~0.1-0.4 units lower rhizosphere pH than other species, the greatest increase in rhizosphere water-soluble P in the low-P soils, and the greatest total P uptake in the low-P clay loam. Shoot P content was mainly explained by rhizosphere APase activity, water-soluble P and pH within low P soils across species. Within species, P uptake was mainly linked to rhizosphere water soluble P, APase, and pH in low P soils. The effects of rhizosphere organic anions varied among species and they appeared to play minor roles in improving P availability and uptake.","corpus_id":7775478,"score":2},{"doc_id":"28626450","title":"Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture.","abstract":"The use of excess conventional Phosphorus (P) fertilizers to improve agricultural productivity, in order to meet constantly increasing global food demand, potentially causes surface and ground water pollution, waterway eutrophication, soil fertility depletion, and accumulation of toxic elements such as high concentration of selenium (Se), arsenic (As) in the soil. Quite a number of soil microorganisms are capable of solubilizing/mineralizing insoluble soil phosphate to release soluble P and making it available to plants. These microorganisms improve the growth and yield of a wide variety of crops. Thus, inoculating seeds/crops/soil with Phosphate Solubilizing Microorganisms (PSM) is a promising strategy to improve world food production without causing any environmental hazard. Despite their great significance in soil fertility improvement, phosphorus-solubilizing microorganisms have yet to replace conventional chemical fertilizers in commercial agriculture. A better understanding of recent developments in PSM functional diversity, colonizing ability, mode of actions and judicious application should facilitate their use as reliable components of sustainable agricultural systems. In this review, we discussed various soil microorganisms that have the ability to solubilize phosphorus and hence have the potential to be used as bio fertilizers. The mechanisms of inorganic phosphate solubilization by PSM and the mechanisms of organic phosphorus mineralization are highlighted together with some factors that determine the success of this technology. Finally we provide some indications that the use of PSM will promote sustainable agriculture and conclude that this technology is ready for commercial exploitation in various regions worldwide.","corpus_id":1167346,"score":2},{"doc_id":"28769964","title":"Application of Mycorrhiza and Soil from a Permaculture System Improved Phosphorus Acquisition in Naranjilla.","abstract":"Naranjilla (Solanum quitoense) is a perennial shrub plant mainly cultivated in Ecuador, Colombia, and Central America where it represents an important cash crop. Current cultivation practices not only cause deforestation and large-scale soil degradation but also make plants highly susceptible to pests and diseases. The use of arbuscular mycorrhizal fungi (AMF) can offer a possibility to overcome these problems. AMF can act beneficially in various ways, for example by improving plant nutrition and growth, water relations, soil structure and stability and protection against biotic and abiotic stresses. In this study, the impact of AMF inoculation on growth and nutrition parameters of naranjilla has been assessed. For inoculation three European reference AMF strains (Rhizoglomus irregulare, Claroideoglomus claroideum, and Cetraspora helvetica) and soils originating from three differently managed naranjilla plantations in Ecuador (conventional, organic, and permaculture) have been used. This allowed for a comparison of the performance of exotic AMF strains (reference strains) versus native consortia contained in the three soils used as inocula. To study fungal communities present in the three soils, trap cultures have been established using naranjilla as host plant. The community structures of AMF and other fungi inhabiting the roots of trap cultured naranjilla were assessed using next generation sequencing (NGS) methods. The growth response experiment has shown that two of the three reference AMF strains, a mixture of the three and soil from a permaculture site led to significantly better acquisition of phosphorus (up to 104%) compared to uninoculated controls. These results suggest that the use of AMF strains and local soils as inoculants represent a valid approach to improve nutrient uptake efficiency of naranjilla and consequently to reduce inputs of mineral fertilizers in the cultivation process. Improved phosphorus acquisition after inoculation with permaculture soil might have been caused by a higher abundance of AMF and the presence of Piriformospora indica as revealed by NGS. A higher frequency of AMF and enhanced root colonization rates in the trap cultures supplemented with permaculture soil highlight the importance of diverse agricultural systems for soil quality and crop production.","corpus_id":19367198,"score":2},{"doc_id":"28865270","title":"Phosphorus activators contribute to legacy phosphorus availability in agricultural soils: A review.","abstract":"Phosphorus (P) is one of the most limiting macronutrients for crop productivity and P deficiency is a common phenomenon in agricultural soils worldwide. Despite long-term application of phosphate fertilizers to increase crop yields, P availability is often low, due to the high affinity of phosphate for the soil solid phase. It has been suggested that the accumulated (surplus) P in agricultural soils is sufficient to sustain crop yields worldwide for about 100years. In this paper, we try to clear up the potential for making use of legacy P in soils for crop growth potentially alleviating the global P resource shortage. Specifically, we try to clear up the potential of soil \"P activators\" for releasing fixed P. P activators accelerate and strengthen process which transform P into bio-available forms via a range of chemical reactions and biological interactions. They include phosphate solubilizing microorganisms, phosphatase enzymes and enzyme activators, low molecular weight organic acids, humic acids, lignin, crop residues, biochar and zeolites. Although reported performance is variable, there is growing evidence that P activators can promote the release of phosphate from soil and, hence, have potential for mitigating the impending global P crisis. Further basic and applied research is required to better understand the mechanisms of interaction of P activators with natural soils and to maximize activator efficacy.","corpus_id":205129053,"score":2},{"doc_id":"29679179","title":"Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities.","abstract":"Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger. High-performance liquid chromatography analysis revealed that the mechanism of phosphorus solubilization by CS-1 involved the synthesis and secretion of organic acids, mainly oxalic, tartaric, and citric acids. Furthermore, strain CS-1 exhibited other growth-promoting abilities, including efficient potassium release and degradation of crop straw cellulose. These properties help to returning crop residues to the soil, thereby increasing nutrient availability and sustaining organic matter concentration therein. A pot experiment revealed that CS-1 apparently increased the assessed biometric parameters of wheat seedlings, implying the potential of this strain to be developed as a commercial microbial agent. We used Illumina MiSeq sequencing to investigate the microbial community composition in the rhizosphere of uninoculated wheat plants and wheat plants inoculated with the CS-1 strain to obtain insight into the effect of the CS-1 strain inoculation. The data clearly demonstrated that CS-1 significantly reduced the content of pathogenic fungi, including Gibberella, Fusarium, Monographella, Bipolaris, and Volutella, which cause soil-borne diseases in various crops. Strain CS-1 may hence be developed into a microbial agent for plant growth improvement.","corpus_id":4974993,"score":2},{"doc_id":"19685081","title":"Ectomycorrhizal fungi and their enzymes in soils: is there enough evidence for their role as facultative soil saprotrophs?","abstract":"Although ectomycorrhizal (ECM) fungi are generally regarded as dependent upon the supply of carbon from their plant hosts, some recent papers have postulated a role for these fungi in the saprotrophic acquisition of carbon from soil. This theory was mainly based on the increase in enzymatic activity during periods of low photosynthate supply from tree hosts and emergence of the theory has led to a question about the overall influence of saprotrophy by ECM fungi on soil carbon turnover. However, I argue here that there is still not enough evidence to confirm this proposed function. My argument is based on inference from several lines of observation and concern over several aspects of the past studies. First, ECM fungi mainly inhabit deeper soil horizons, in which the availability of carbon compounds with positive energetic value is low. Second, the ability of ECM fungi to produce ligninolytic enzymes and cellulases is much weaker than that of saprotrophic basidiomycetes. This is most apparent in the low copy abundance of corresponding genes in the sequenced genomes of ECM species Laccaria bicolor and Amanita bisporigenes compared to the saprotrophic species Galerina marginata. I offer alternative hypotheses to explain the past observations of increased enzyme activity during starvation periods. These include, the induction of autolytic processes in ECM fungal mycelia or an attack on the host tissues to support escape from a dying root and to allow for a search for new hosts.","corpus_id":5806797,"score":1},{"doc_id":"22439851","title":"Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils.","abstract":"Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here, we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize vs. potato), soil type (sand vs. clay-textured soils) and habitat (plant root vs. bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species-poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive 'loss' from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass-cropping history together explained 32% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a 'bottleneck effect' on AMF communities through increased stochastic effects under environmental stress.","corpus_id":16670908,"score":1},{"doc_id":"23997599","title":"Ecological and physiological studies on soil fungi at Western region, libya.","abstract":"Sixty three species and 5 varieties belonging to 30 fungal genera were collected from 75 soil samples. Cultivated (29 genera and 58 species + 5 var.), desert (22 and 35 + 2 var.) and saline soil (21 and 41 + 1 var.) fungi were recovered on glucose-, cellulose- and 50% sucrose-Czapek's agar at 28℃. The most common genera were Alternaria, Aspergillus, Emericella, Fusarium, Mycosphaerella, Nectria and Penicillium. The most prevalent species from the three types of soils on the three types of media were Alternaria alternata, Aspergillus flavus, A. fumigatus, A. niger, A. terreus, Emericella nidulans, Fusarium oxysporum, Mycosphaerella tassiana, Nectria haematococca and Penicillium chrysogenum. Chaetomium globosum was in the top of fungi in producing endo-β-1,4-glucanases among the 42 tested isolates obtained from soils on cellulose-Czapek's agar. Maximum production of this enzyme by C. globosum obtained after 6 days of incubation at 30℃ with culture medium containing maltose as a carbon source and ammonium nitrate as a nitrogen source and pH initially adjusted to 6.","corpus_id":7982269,"score":1},{"doc_id":"24315210","title":"Does a rhizospheric microorganism enhance K⁺ availability in agricultural soils?","abstract":"The potassium solubilizing microorganisms (KSMs) are a rhizospheric microorganism which solubilizes the insoluble potassium (K) to soluble forms of K for plant growth and yield. K-solubilization is carried out by a large number of saprophytic bacteria (Bacillus mucilaginosus, Bacillus edaphicus, Bacillus circulans, Acidothiobacillus ferrooxidans, Paenibacillus spp.) and fungal strains (Aspergillus spp. and Aspergillus terreus). Major amounts of K containing minerals (muscovite, orthoclase, biotite, feldspar, illite, mica) are present in the soil as a fixed form which is not directly taken up by the plant. Nowadays most of the farmers use injudicious application of chemical fertilizers for achieving maximum productivity. However, the KSMs are most important microorganisms for solubilizing of fixed form of K in soil system. The KSMs are an indigenous rhizospheric microorganism which shows effective interaction between soil and plant systems. The main mechanism of KSMs is acidolysis, chelation, exchange reactions, complexolysis and production of organic acid. According to literature, currently negligible use of potassium fertilizer as a chemical form has been recorded in agriculture for enhancing crop yield. Most of the farmers use only nitrogen and phosphorus and not use the K fertilizer due to unawareness so that the problem of K deficiency occurs in rhizospheric soils. The K fertilizer is also costly as compared to other chemical fertilizers. Therefore, the efficient KSMs should be applied for solubilization of a fixed form of K to an available form of K in the soils. This available K can be easily taken up by the plant for growth and development. Our aim of this review is to elaborate on the studies of indigenous K-solubilizing microbes to develop efficient microbial consortia for solubilization of K in soil which enhances the plant growth and yield of crops. This review highlights the future need for research on potassium (K) in agriculture.","corpus_id":206936115,"score":1},{"doc_id":"24428372","title":"Survey of Aspergillus section Flavi presence in agricultural soils and effect of glyphosate on nontoxigenic A. flavus growth on soil-based medium.","abstract":"AIMS: To evaluate the cultivable mycobiota from agricultural soils exposed to pesticides, the aflatoxigenic capacity of Aspergillus section Flavi strains and the effect of glyphosate on lag phase and growth rates of native nontoxigenic Aspergillus flavus under different water potential (MPa) conditions on soil-based medium. METHODS AND RESULTS: Culturable mycobiota analysis from different agricultural soils was performed by the surface spread method. The effect of glyphosate (0-20 mmol l(-1)) on the growth of A. flavus strains was evaluated on a soil extract solid medium. Mycobiota analysis of crop soils showed the presence of twenty-one genera of filamentous fungi. Aspergillus flavus and Aspergillus niger aggregate strains were isolated from the three soil types. Ninety-two per cent of A. flavus strains were toxigenic. In vitro assay results showed that at -0·70 MPa, a significant increase in growth rate in all strains was recorded at 5 and 20 mmol l(-1) of glyphosate. At -2·78 MPa, this parameter remained constant at all glyphosate concentrations, except in GM4 strain where an increase in growth rate was recorded with increasing pesticide concentrations. At -7·06 MPa, a significant increase in growth rate has also been observed in GM 3 strain with 5 mmol l(-1) and in GM 4 strain with 10 and 20 mmol l(-1). CONCLUSIONS: This study showed that the imperfecti fungi Aspergillus spp., Penicillium spp., Trichoderma spp., Cladosporium spp. and Paecilomyces spp. are isolated as prevalent groups in agricultural soil exposed to pesticides, and the capacity of nontoxigenic A. flavus strains to tolerate different glyphosate concentrations under different water potential (MPa) conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This manuscript makes a contribution to the knowledge of cultivable fungal populations from agricultural soils exposed to pesticides and the glyphosate tolerance of A. flavus strains.","corpus_id":2270156,"score":1},{"doc_id":"26115994","title":"Arbuscular mycorrhizal fungal diversity, root colonization, and soil alkaline phosphatase activity in response to maize-wheat rotation and no-tillage in North China.","abstract":"Monitoring the effects of no-tillage (NT) in comparison with conventional tillage (CT) on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to compare the species composition and ecological function of soil arbuscular mycorrhizal (AM) fungi during the growth and rotation of crops under NT and CT. From late June 2009 to early June 2010, 32 topsoil (0-15 cm) samples from four individual plots per treatment (CT and NT) were collected at both the jointing and maturation stages of maize (Zea mays L.) and wheat (Triticum aestivum L.) from a long-term experimental field that was established in an Aquic Inceptisol in North China in June 2006. The AM fungal spores were isolated and identified and then used to calculate species diversity indices, including the Shannon- Wiener index (H'), Evenness (E), and Simpson's index (D). The root mycorrhizal colonization and soil alkaline phosphatase activity were also determined. A total of 34 species of AM fungi within nine genera were recorded. Compared with NT, CT negatively affected the soil AM fungal community at the maize sowing stage, leading to decreases in the average diversity indices (from 2.12, 0.79, and 0.82 to 1.79, 0.72, and 0.74 for H', E, and D, respectively), root mycorrhizal colonization (from 28% to 20%), soil alkaline phosphatase activity (from 0.24 to 0.19 mg/g/24 h) and available phosphorus concentration (from 17.4 to 10.5 mg/kg) at the maize jointing stage. However, reductions in diversity indices of H', E, and D were restored to 2.20, 0.81, and 0.84, respectively, at the maize maturation stage. CT should affect the community again at the wheat sowing stage; however, a similar restoration in the species diversity of AM fungi was completed before the wheat jointing stage, and the highest Jaccard index (0.800) for similarity in the species composition of soil AM fungi between CT and NT was recorded at the wheat maturation stage. Our results also demonstrated that NT resulted in the positive protection of the community structure of AM fungi and played an important role in maintaining their functionality especially for maize seedlings.","corpus_id":6222288,"score":1},{"doc_id":"26527297","title":"Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.","abstract":"Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.","corpus_id":7234128,"score":1},{"doc_id":"27429478","title":"Struvite: a slow-release fertiliser for sustainable phosphorus management?","abstract":"BACKGROUND AND AIM: Recycled sources of phosphorus (P), such as struvite extracted from wastewater, have potential to substitute for more soluble manufactured fertilisers and help reduce the long-term threat to food security from dwindling finite reserves of phosphate rock (PR). This study aimed to determine whether struvite could be a component of a sustainable P fertiliser management strategy for arable crops. METHODS: A combination of laboratory experiments, pot trials and mathematical modelling of the root system examined the P release properties of commercial fertiliser-grade struvite and patterns of P uptake from a low-P sandy soil by two different crop types, in comparison to more soluble inorganic P fertilisers (di-ammonium phosphate (DAP) and triple super phosphate (TSP)). RESULTS: Struvite had greatly enhanced solubility in the presence of organic acid anions; buckwheat, which exudes a high level of organic acids, was more effective at mobilising struvite P than the low level exuder, spring wheat. Struvite granules placed with the seed did not provide the same rate of P supply as placed DAP granules for early growth of spring wheat, but gave equivalent rates of P uptake, yield and apparent fertiliser recovery at harvest, even though only 26 % of struvite granules completely dissolved. Fertiliser mixes containing struvite and DAP applied to spring wheat have potential to provide both optimal early and late season P uptake and improve overall P use efficiency. CONCLUSIONS: We conclude that the potential resource savings and potential efficiency benefits of utilising a recycled slow release fertiliser like struvite offers a more sustainable alternative to only using conventional, high solubility, PR-based fertilisers.","corpus_id":10561990,"score":1},{"doc_id":"28087930","title":"Fungal Ecology: Principles and Mechanisms of Colonization and Competition by Saprotrophic Fungi.","abstract":"Decomposer fungi continually deplete the organic resources they inhabit, so successful colonization of new resources is a crucial part of their ecology. Colonization success can be split into (i) the ability to arrive at, gain entry into, and establish within a resource and (ii) the ability to persist within the resource until reproduction and dissemination. Fungi vary in their life history strategies, the three main drivers of which are stress (S-selected), disturbance (ruderal, or R-selected), and incidence of competitors (C-selected); however, fungi often have combinations of characteristics from different strategies. Arrival at a new resource may occur as spores or mycelium, with successful entry and establishment (primary resource capture) within the resource largely dependent on the enzymatic ability of the fungus. The communities that develop in a newly available resource depend on environmental conditions and, in particular, the levels of abiotic stress present (e.g., high temperature, low water availability). Community change occurs when these initial colonizers are replaced by species that are either more combative (secondary resource capture) or better able to tolerate conditions within the resource, either through changing abiotic conditions or due to modification of the resource by the initial colonizers. Competition for territory may involve highly specialized species-specific interactions such as mycoparasitism or may be more general; in both cases combat involves changes in morphology, metabolism, and reactive oxygen species production, and outcomes of these interactions can be altered under different environmental conditions. In summary, community development is not a simple ordered sequence, but a complex ever-changing mosaic.","corpus_id":3409003,"score":1},{"doc_id":"18365728","title":"[Diversity of facultatively anaerobic microscopic mycelial fungi in soils].","abstract":"The numbers of microscopic fungi isolated from soil samples after anaerobic incubation varied from tens to several hundreds of CFU per one gram of soil; a total of 30 species was found. This group is composed primarily of mitotic fungi of the ascomycete affinity belonging to the orders Hypocreales (Fusarium solani, F. oxysporum, Fusarium sp., Clonostachys grammicospora, C. rosea. Acremonium sp., Gliocladium penicilloides, Trichoderma aureoviride, T. harzianum, T. polysporum, T. viride. T. koningii, Lecanicillum lecanii, and Tolypocladium inflatum) and Eurotiales (Aspergillus terreus, A. niger, and Paecilomyces lilacimus), as well as to the phylum Zygomycota, to the order Mucorales (Actinomucor elegans, Absidia glauca, Mucor circinelloides, M. hiemalis, M. racemosus, Mucor sp., Rhizopus oryzae, Zygorrhynchus moelleri, Z. heterogamus, and Umbelopsis isabellina) and the order Mortierellales (Mortierella sp.). As much as 10-30% of the total amount of fungal mycelium remains viable for a long time (one month) under anaerobic conditions.","corpus_id":19715218,"score":0},{"doc_id":"19207833","title":"Antagonism of Microsporum species by soil fungi.","abstract":"Eighteen fungi isolated from soil by hair bating method were tested against soil inhabiting Microsporum equinum, Microsporum fulvum, Microsporum gypseum and Microsporum racemosum for their antagonistic interactions. Colony inhibition during dual cultures showed inhibition of all the four Microsporum species. The maximum inhibition of M. equinum, M. fulvum, M. gypseum and M. racemosum was caused by Chrysosporium keratinophilum, Chrysosporium tropicum, Curvularia lunata and Chrysosporium lucknowense in dual cultures. On the other hand, M. fulvum showed maximum inhibition of Macrophomina phaseolina (70.1%) while M. equinum, M. gypseum and M. racemosum showed maximum inhibition of Colletotrichum gloeosporoides. Staling products of C. lucknowense accelerated growth of all Microsporum species, C. keratinophilum 3 and Chrysosporium evolceaunui and M. phaseolina accelerated growth of two species of Microsporum. Staling product of Alternaria alternata was most inhibitory. Culture filtrates of Trichophyton vanbreseughemii accelerated the growth of all the four Microsporum species and C. tropicum, C. lucknowense accelerated growth of two species, while Botryotrichum piluliferum accelerated growth of three species of Microsporum. Volatiles showed inhibition of all the Microsporum species ranging from 0.33 to 57.2% except in case of M. fulvum. Lysis of Microsporum mycelium was the most common feature.","corpus_id":9016373,"score":0},{"doc_id":"19579778","title":"[Antagonistic interactions between saprotrophic fungi and geohelminths. 1. Saprotrophic fungi in the biological control of phytopathogenic geohelminths].","abstract":"Antagonistyczne interakcje miedzy grzybami saprotroficz- nymi a geohelmintami. 1. Grzyby saprotroficzne w walce biologicznej z nicieniami fitopatogenicznymi. The state of knowledge on the possible antagonism between soil saprotrophic fungi and phytopathogenic nematodes of the genera Meloidogyne, Heterodera, and Globodera is reviewed basing on the literature and our own research. Mycelial colonisation of various developmental stages of these geohelminths is the most common factor thought to reduce their populations in nature. The following parasitic fungi can be found on the cysts, eggs, as well as the larvae of the nematodes: Paecilomyces lilacinus, Verticillium chlamydosporium, Cylindrocarpon destructans, Pochonia chlamydosporia, Fusarium spp., and Penicillium spp. The fungi invade the nematodes, such as Heterodera, Globodera, or Meloidogyne, \"passively\" penetrating through the natural orifices of the cysts, eggs, and larvae of the host. Equally frequent, however, is a biochemical action of the fungi prior to colonisation, which is linked with production of mycotoxirls or hydrolytic enzymes. Such an active way of fungal penetration of various stages of the phytopathogenic nematodes has been observed in Pochonia chlamydosporia, Penicillium verrucosum var. cyclopium, P. frequentans, Sclerotinia rolfsii, Rhizoctonia solani, and Fusarium spp. Triacylglycerols (TAG), phenols, as well as trichothecene, T-2, have been found in the metabolites extracted from mycelia of these species. Predation by fungi is also a factor that may reduce a population of phytopathogenic nematodes. This form of antagonism is characteristic for nematicidal fungi of the genera Arthrobotrys and Dactylella. These fungi form shrinking rings and hooks in their mycelia by which the fungus entangles and paralyses a migrating form of nematode. Despite the fact that the antagonism between fungi and nematodes is a commonly occurring phenomenon observed in the soil, the nematicidal and nematotoxic properties of fungi have not a wide application in biological plant protection. Up till now, only the bionematicides based on Arthrobotrys robusta (Royal 300 and Royal 350) as well as Paecilomyces lilacinus (Biocon and PL Plus) have found its commercial application.","corpus_id":41740188,"score":0},{"doc_id":"19579779","title":"[Antagonistic interactions between saprotrophic fungi and geohelminths. 2. Saprotrophic fungi in biocontrol of parasitic geohelminths of humans and animals].","abstract":"Antagonistyczne interakcje miedzy grzybami saprotroficznymi a geohelmintami. 2. Grzyby saprotroficzne w bioregulacji pasozytniczych geohelmintów człowieka i zwierzat. The soils ecosystem plays an important role in the epidemiology of geohelminth diseases of humans and animals. Soil contamination with ova of the parasitic geohelminths represents a global public health-hazard issue. Biological agents have been thought to control the infective forms of parasites present in the soil. Biocontrol of geohelminths represents an alternative to pesticides (i.e., nematicides), which are not efficient in killing infective nematode forms and, additionally, result in the environment pollution and long-term disturbances in the soil ecosystem homeostasis. The degree of the inhibiting effect of soil saprotrophic fungi on geohelminth embryonic development varies and depends on the species. A number of fungi cause various morphological disorders in the embryos of developing parasitic nematodes, but also have an ovicidal effect. Although the nature of the antagonism between fungi and other living organisms has not been fully explained, it is certain that mycotoxins and fungal enzymes constitute its important components. Considering the studies carried out so far, the antagonistic effect of mold fungi against the infective stages of geohelminths can be fully recommended as a real control factor, especially as these saprotrophs represent a natural factor within the soil environment, that is of particular biochemical activity.","corpus_id":24760768,"score":0},{"doc_id":"19932506","title":"Phytoremediation of petroleum-polluted soils: application of Polygonum aviculare and its root-associated (penetrated) fungal strains for bioremediation of petroleum-polluted soils.","abstract":"Petroleum-polluted soils are a common disaster in many countries. Bioremediation of oil contamination in soils is based on the stimulation of petroleum-hydrocarbon-degrading fungal and microbial communities. A field study was conducted in a petroleum-contaminated site to find petroleum-resistant plants and their root-associated fungal strains for use in bioremediation of petroleum-polluted soils. Results and observations showed that the amounts of petroleum pollution in nonvegetated soils were several times higher than in vegetated soils. Plants collected from petroleum-polluted areas were identified using morphological characters. Results indicated that seven plant species were growing on the contaminated sites: Alhaji cameleron L. (Fabaceae), Amaranthus retroflexus L. var. retroflexus (Amaranthaceae), Convolvulus arvensis L. (Convolvulaceae), Chrozophora hierosolymitana Spreg. ( Euphorbiaceae), Noea mucronata L. (Boraginaceae), Poa sp. (Poaceae), and Polygonum aviculare L. (Polygonaceae). The root-associated fungi of each plant were determined and results showed the presence of 11 species that associated with and also penetrated the roots of plants growing in the polluted areas. Altenaria sp. was common to all of the plants and the others had species-specific distribution within the plants. The largest numbers of fungal species (six) were determined for P. aviculare and Poa sp. in polluted areas. However, the variation of fungal strains in the plants collected from petroleum-polluted areas was greater than for nonpolluted ones. Culture of fungi in oil-contaminated media showed that all the studied fungi were resistant to low petroleum pollution (1% v/v) and a few species, especially Fusarium species, showed resistance to higher petroleum pollution (10% v/v) and may be suitable for bioremediation in highly polluted areas. Bioremediation tests with P. aviculare, with and without fungal strains, showed that application of both the plant and its root-associated fungal strains was more effective than of the plant and fungi separately, and Fusarium species were the most effective. Results indicated that fungal strains had the main role in bioremediation of petroleum-polluted soils, but plant roots enhanced the process.","corpus_id":35676511,"score":0},{"doc_id":"21459413","title":"Biological removal of arsenic pollution by soil fungi.","abstract":"Fifteen fungal strains were isolated from arsenic contaminated (range 9.45-15.63 mg kg(-1)) agricultural soils from the state of West Bengal, India. Five fungal strains were belonged to the Aspergillus and Trichoderma group each, however, remaining five were identified as the Neocosmospora, Sordaria, Rhizopus, Penicillium and sterile mycelial strain. All these fungal strains were cultivated on medium supplemented with 100, 500, 1000, 5000 and 10,000 mg l(-1) of sodium arsenate. After 30-day cultivation under laboratory conditions, radial growth of these strains was determined and compared with control. Toxicity and tolerance of these strains to arsenate were evaluated on the basis of tolerance index. Out of fifteen, only five fungal strains were found resistant and survived with tolerance index pattern as 0.956 (sterile mycelial strain)>0.311 (Rhizopus sp.)>0.306 (Neocosmospora sp.)>0.212 (Penicillium sp.)>0.189 (Aspergillus sp.) at 10,000 mg l(-1) of arsenate. The arsenic removal efficacy of ten fungal strains, tolerant to 5000 mg l(-1) arsenate, was also assayed under laboratory conditions for 21 days. All these strains were cultivated individually on mycological broth enriched with 10 mg l(-1) of arsenic. The initial and final pH of cultivating medium, fungal biomass and removal of arsenic by each fungal strain were evaluated. Fungal biomass of ten strains removed arsenic biologically from the medium which were ranged from 10.92 to 65.81% depending on fungal species. The flux of biovolatilized arsenic was determined indirectly by estimating the sum of arsenic content in fungal biomass and medium. The mean percent removal as flux of biovolatilized arsenic ranged from 3.71 to 29.86%. The most effective removal of arsenic was observed in the Trichoderma sp., sterile mycelial strain, Neocosmospora sp. and Rhizopus sp. fungal strains. These fungal strains can be effectively used for the bioremediation of arsenic-contaminated agricultural soils.","corpus_id":45192270,"score":0},{"doc_id":"21470255","title":"Growth of saprotrophic fungi and bacteria in soil.","abstract":"Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed.","corpus_id":19771072,"score":0},{"doc_id":"21613136","title":"The fungi: 1, 2, 3 ... 5.1 million species?","abstract":"PREMISE OF THE STUDY: Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. METHODS: Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. KEY RESULTS: Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. CONCLUSIONS: Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.","corpus_id":24817330,"score":0},{"doc_id":"22022665","title":"Isolation and identification of microbes associated with mobile phones in Dammam in eastern Saudi Arabia.","abstract":"OBJECTIVE: This study was conducted to determine microbial contamination of mobile phones in the city of Dammam, in the eastern region of Saudi Arabia, and identify the most important microbial species associated with these phones in order to take the necessary remedial measures. MATERIALS AND METHODS: The analysis of a total of 202 samples was done to identify fungal and pathogenic bacteria isolates. Sterile swabs were firmly passed on the handset, the buttons and the screens of mobile phones, then inoculated into media of bacteria and fungi. Frequency distribution of isolates were calculated. RESULTS: There were 737 isolated of the following bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, Neisseria sicca, Micrococcus luteus, Proteus mirabilis, Bacillus subtilis, and Enterobacter aerogenes at the rate of 56.58, 13.57, 8.01, 7.73, 6.51, 3.66, 2.85 and 1.09% respectively. There were fungal isolates as follows: Alternaria alternata, Aspergillus niger, Cladosporium sp., Penicillium spp., Aspergillus flavus, Aspergillus fumigatus, Rhizopus stolonifer, Aspergillus ochraceus at the rate of 29.07, 26.74, 20.93, 10.47, 6.98, 2.33, 2.33, 1.16%, respectively. CONCLUSIONS: The study showed that all mobile phones under consideration were infected by several microbes, most of which belonged to the natural flora of the human body as well as airborne fungi and soil. This means that it is necessary to sterilize hands after contact with a phone since it is a source of disease transmission.","corpus_id":21588945,"score":0},{"doc_id":"22808743","title":"[Anaerobic growth ability and alcohol fermentation activity of microscopic fungi].","abstract":"The method proposed in this study was used to isolate fungi grown under anaerobic conditions and to reveal distinctions in their abundance and species composition in different habitats. The ability of micromycetes of different taxa to grow under anaerobic conditions and ensure alcohol fermentation was determined for a representative sample (344 strains belonging to more than 60 species). The group of fungi growing under anaerobic conditions included species with high, moderate, and low fermentation activity. The ability for anaerobic growth and fermentation depended on the taxonomic affiliation of fungi. In some cases, the expression of these characteristics depended on the habitat from which the strain was isolated. The maximum level of ethanol accumulation in culture liquid (1.2-4.7%) was detected for Absidia spinosa, Aspergillus sp. of group flavus, Aspergillus terreus, Acremonium sp., Mucor circinelloides, Mucor sp., Fusarium oxysporum, F. solani, F. sambucinum, Rhizopus arrhizus var. Arrhizus, Trichoderma atroviride, and Trichoderma sp.","corpus_id":19325427,"score":0},{"doc_id":"23115506","title":"Diversity of Culturable Soil Micro-fungi along Altitudinal Gradients of Eastern Himalayas.","abstract":"Very few studies have addressed the phylogenetic diversity of fungi from Northeast India under the Eastern Himalayan range. In the present study, an attempt has been made to study the phylogenetic diversity of culturable soil fungi along the altitudinal gradients of eastern Himalayas. Soil samples from 24 m above sea level to 2,000 m above sea level altitudes of North-East India were collected to investigate soil micro-fungal community structure and diversity. Molecular characterization of the isolates was done by PCR amplification of 18S rDNA using universal primers. Phylogenetic analysis using BLAST revealed variation in the distribution and richness of different fungal biodiversity over a wide range of altitudes. A total of 107 isolates were characterized belonging to the phyla Ascomycota and Zygomycota, corresponding to seven orders (Eurotiales, Hypocreales, Calosphaeriales, Capnodiales, Pleosporales, Mucorales, and Mortierellales) and Incertae sedis. The characterized isolates were analysed for richness, evenness and diversity indices. Fungal diversity had significant correlation with soil physico-chemical parameters and the altitude. Eurotiales and Hypocreales were most diverse and abundant group of fungi along the entire altitudinal stretch. Species of Penicillium (D = 1.44) and Aspergillus (D = 1.288) were found to have highest diversity index followed by Talaromyces (D = 1.26) and Fusarium (D = 1.26). Fungal distribution showed negative correlation with altitude and soil moisture content. Soil temperature, pH, humidity and ambient temperature showed positive correlation with fungal distribution.","corpus_id":10422794,"score":0},{"doc_id":"23143287","title":"Filamentous fungi transported by birds during migration across the mediterranean sea.","abstract":"The potential for the transport and diffusion of some pathogenic microorganisms by migratory birds is of concern. Migratory birds may be involved in the dispersal of microorganisms and may play a role of mechanical and biological vectors. The efficiency of dispersal of pathogenic microorganisms depends on a wide range of biotic and abiotic factors that influence the survival or disappearance of a given agent in a geographical area. In the present study, 349 migratory birds were captured in four sites (Mazara del Vallo, Lampedusa, Ustica and Linosa), representing the main stop-over points during spring and autumnal migration, and analyzed for the presence of filamentous fungi. A total of 2,337 filamentous fungi were isolated from 216 birds and identified by a combined phenotypic-genotypic approach to species level. Twelve species were identified in the study, with Cladosporium cladosporioides, Alternaria alternata, and Aspergillus niger as the most abundant. The transport of these fungal species isolated in this study is of considerable importance because some of these species can create dangers to human health.","corpus_id":15725008,"score":0},{"doc_id":"23410063","title":"In vitro antifungal activity of silver nanoparticles against ocular pathogenic filamentous fungi.","abstract":"PURPOSE: Fungal keratitis is emerging as a major cause of vision loss in a developing country such as China because of higher incidence and the unavailability of effective antifungals. It is urgent to explore broad-spectrum antifungals to effectively suppress ocular fungal pathogens, and to develop new antifungal eye drops to combat this vision-threatening infection. The aim of this study is to investigate the antifungal activity of silver nanoparticles (nano-Ag) in comparison with that of natamycin against ocular pathogenic filamentous fungi in vitro. METHODS: Susceptibility tests were performed against 216 strains of fungi isolated from patients with fungal keratitis from the Henan Eye Institute in China by broth dilution antifungal susceptibility test of filamentous fungi approved by the Clinical and Laboratory Standards Institute M38-A document. The isolates included 112 Fusarium isolates (82 Fusarium solani species complex, 20 Fusarium verticillioides species complex, and 10 Fusarium oxysporum species complex), 94 Aspergillus isolates (61 Aspergillus flavus species complex, 11 Aspergillus fumigatus species complex, 12 Aspergillus versicolor species complex, and 10 Aspergillus niger species complex), and 10 Alternaria alternata isolates. The minimum inhibitory concentration (MIC) range and mode, the MIC for 50% of the strains tested (MIC50 value), and the MIC90 value were provided for the isolates with the SPSS statistical package. RESULTS: MIC50 value of nano-Ag were 1, 0.5, and 0.5 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of nano-Ag were 1, 1, and 1 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC50 values of natamycin were 4, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of natamycin were 8, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. CONCLUSIONS: Nano-Ag, relative to natamycin, exhibits potent in vitro activity against ocular pathogenic filamentous fungi.","corpus_id":37031252,"score":0},{"doc_id":"23534981","title":"Biological interactions between soil saprotrophic fungi and Ascaris suum eggs.","abstract":"The in vitro effect of saprotrophic soil fungi on the embryonic development of Ascaris suum was evaluated. The fungi tested were Aspergillus fumigatus, Aspergillus terreus, Penicillium citrinum, Penicillium expansum, Fusarium oxysporum and Trichothecium roseum, isolated from children's recreation areas in the city of Lodz (Poland). Each species was co-cultured with A. suum egg suspension (6 × 10(3)eggs/ml) at 25 ± 2°C for 60 days. Each day, 100 eggs were randomly collected and their developmental stage was classified macroscopically. Additionally, at days 4, 7, 14, 28, 42 and 60 of incubation, the viability and the percentage of eggs with morphological altered embryo/larva were determined in each sample. Microscopic examination revealed that exposure of eggs to the mycelium of examined fungi inhibited embryogenesis of A. suum. All control culture eggs reached L2 larval stage after 26 days of incubation, while the experimental cultures did so after 32-51 days, depending on the fungal species. Three species were found to exhibit very high inhibitory activity on A. suum egg development: A. terreus, P. expansum and F. oxysporum. Embryopathies and non-viable embryos/larvae were observed significantly more frequently in the eggs co-cultured with fungal species than in control cultures. The fungus-exposed eggs revealed morphological alternations in the early zygotic cleavage, blastula, gastrula and larval stages. After 60 days of incubation with mycelia of P. expansum, A. terreus and F. oxysporum, the mortality of the larvae reached 55.3-60.3%. P. expansum and F. oxysporum showed hyphal penetration and internal egg colonization of A. suum eggs.","corpus_id":5744976,"score":0},{"doc_id":"23997619","title":"Effect of some food preservatives on the lipolytic activity of beef luncheon fungi.","abstract":"Beef luncheon meat is one of the most popular meals in several countries in the world including Egypt. Thirty one fungal species and 3 species varieties were recovered from 30 samples of beef luncheon meat collected from different supermarkets in Qena. Alternaria, Aspergillus, Emericella, Mucor, Mycosphaerella, Penicillium and Rhizopus were the most common genera on the two types of media. From the above genera, the most prevalent species were Alternaria alternate, Aspergillus flavus, A. fumigatus, A. niger, A. terreus, Emericella nidulans, Mucor racemosus, Mycosphaerella tassiana, Penicillium chrysogenum and Rhizopus stolonifer. Screening of fungi for their abilities to produce lipase enzyme showed that, ten isolates represented 32.26% of total isolates appeared high lipase production, while sixteen isolates (51.61%) were moderate and 5 isolates (16.13%) were low producers. Aspergillus niger, Fusarium oxysporum and Nectria haematococca produced the highest amount of lipase enzyme, so these fungi were used in further studies. The incorporation of five food preservatives (Disodium phosphate, sodium benzoate, citric acid, potassium sorbate and sodium citrate) individually in the culture medium of lipase production exhibited an inhibitive effect on the mycelial growth and enzyme production by Aspergillus niger, Fusarium oxysporum and Nectria haematococca.","corpus_id":7061271,"score":0},{"doc_id":"24263850","title":"Conjugation of deoxynivalenol by Alternaria alternata (54028 NRRL), Rhizopus microsporus var. rhizopodiformis (54029 NRRL) and Aspergillus oryzae (5509 NRRL).","abstract":"Deoxynivalenol (DON, vomitoxin) is a trichothecene mycotoxin which can be considered to be an indicator of Fusarium mycotoxin contamination in grain, feed and food. Recent studies have described the presence of glucose conjugated DON, which is a product of plant metabolism, but there is a lack of information available on DON conjugation by fungi. The aim of the current study was, therefore, to investigate the ability of fungi to metabolize DON into hydrolysable conjugated DON. Alternaria alternata (54028 NRRL) and Rhizopus microsporus var. rhizopodiformis (54029 NRRL) were found to be capable of metabolizing DON into hydrolysable conjugated DON. This ranged from 13-23 % conjugation of DON in potato dextrose agar media and from 11-36 % in corn-based media. There was, however, considerable variation between fungal strains in the ability to conjugate DON as only a slight increase in hydrolysable conjugated DON (1-6 %) was observed when incubating with A. oryzae (5509 NRRL). A. oryzae (5509 NRRL) was also shown to degrade DON (up to 92 %) over 21 days of incubation on corn-based media. The current study shows that conjugation of DON can be achieved through fungal metabolism in addition to being a product of plant metabolism.","corpus_id":5877764,"score":0},{"doc_id":"24494000","title":"Rye grains and the soil derived from under the organic and conventional rye crops as a potential source of biological agents causing respiratory diseases in farmers.","abstract":"INTRODUCTION: INTRODUCTION: Due to the specific work environment, farmers are exposed to various biological occupational hazard. Among these factors significant are fungi present in the grain and also in the soil. The fungi may be the cause of human diseases including skin infections, asthma, allergic rhinitis and many others. AIM: The aim of this study was to quantify and identify species of fungi colonizing rye grain samples and the soil under cultivation. MATERIAL AND METHODS: THE MATERIAL CONSISTED OF GRAIN AND SOIL SAMPLES FROM TWO AGRICULTURAL SYSTEMS: organic and conventional. To determine the concentration and composition of fungi in collected samples, two media: Malt Agar (MA, Becton, Dickinson and Company) and Potato Dextrose Agar (PDA, Becton, Dickinson and Company) were used. The composition of species in fungal flora was determined using macroscopic and microscopic methods. The isolates of fungi were ranked in the appropriate classes of biosafety BSL. RESULTS: THE MOST FREQUENTLY ISOLATED FUNGI FROM ORGANIC RYE GRAIN, REGARDLESS OF THE MEDIA USED, WERE SPECIES: Aureobasidium pullulans and Alternaria alternata. In conventional farms, most species isolated from rye grain were: Aureobasidium pullulans, Cladosporium oxysporum, Alternaria alternata and yeast-like fungi. Most often species isolated from the soil was Penicillium citreo-viride. CONCLUSIONS: All the results of the research demonstrate the potential hazard to the health of people working in agriculture. Significant exposure of this professional group is associated with the presence of harmful biological agents present in the grain and soil from its cultivation.","corpus_id":4136302,"score":0},{"doc_id":"24506036","title":"In vitro antifungal activity of three geophytic plant extracts against three post-harvest pathogenic fungi.","abstract":"Plant extracts appear to be one of the most effective alternative methods of plant diseases control which are less harmful to human beings and environment. In vitro antifungal activity of methanolic extracts of three promising wild geophytic plants against three post-harvest pathogenic fungi using radial growth technique was conducted. These extracts included the shoot system (S) and underground parts (R) of Asparagus stipularis, Cyperus capitatus and Stipagrostis lanata. The tested fungi were Alternaria solani, Aspergillus niger and Rhizopus stolonifer. The results exhibited that, all plant extracts had antifungal activity against the tested fungi. The antifungal activity greatly varied depending on plant parts and/or plant species. R. stolonifer was the most susceptible fungus to the tested plant extracts followed by A. niger and then A. solani. On the other hand, the most effective plant extracts against tested fungi were S. lanata (S) and A. stipularis (R). The most effective plant extracts against R. stolonifer were S. lanata (R) and C. capitatus (S). While, the extracts of A. stipularis (R) and S. lanata (S) were the most effective against A. niger. The extracts of C. capitatus (S) and S. lanata (S) exhibited the highest antifungal activity against A. solani. The results demonstrated that, the methanolic extracts of A. stipularis, C. capitatus and S. lanata had potential antifungal activity against A. solani, A. niger and R. stolonifer.","corpus_id":32234282,"score":0},{"doc_id":"24732324","title":"Importance of saprotrophic freshwater fungi for pollen degradation.","abstract":"Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.","corpus_id":4583745,"score":0},{"doc_id":"25134345","title":"The effect of saprotrophic fungi on the development and hatching of Fasciola hepatica eggs.","abstract":"The aim of this study was to determine the effect of 6 common soil fungi species: Alternaria alternata (Fr.) Keissl., Aspergillus candidus Link, Penicillium chrysogenum Thom, P. commune Thom, Trichothecium roseum (Pers.) Link and Ulocladium sp., on the hatching of miracidia, i.e., free living larvae of liver fluke (Fasciola hepatica). To this end, the eggs of F. hepatica were incubated in water in the presence of one of the aforementioned fungi species and in tap water (control) at a temperature of 26 degrees C. At the 15th day of incubation we determined the number of nonembryonated, embryonated and hatched eggs. We observed different degrees of antagonistic influences by the tested fungal strains on the development of F. hepatica eggs. Among the examined fungi, the strongest ovistatic effects were exhibited by Trichothecium roseum, Penicillium chrysogenum (R-3) and P. commune. The study showed no morphological damage to the shells of the F. hepatica eggs which may suggest a biochemical basis of antagonistic interactions by the fungi associated with the activity of fungal enzymes, mycotoxins and antibiotics. Low or no activity of peptide hydrolases in Penicillium chrysogenum and P. commune in the API ZYM test suggests their insignificant role in the degradation of shell proteins ofF. hepatica eggs.","corpus_id":26185059,"score":0},{"doc_id":"25213561","title":"Diversity of soil fungi in North 24 Parganas and their antagonistic potential against Leucinodes orbonalis Guen. (Shoot and fruit borer of brinjal).","abstract":"Soil samples were collected from agricultural fields and gardens in North 24 Parganas, West Bengal, and fungi species were isolated from them. Thirty-one fungal species were isolated with 19 found in agricultural soil and 28 in garden soil. Twenty-eight out of 31 were identified using cultural and microscopic characters, and three were unidentified. The diversity of isolated fungi was calculated by Simpson's diversity index. The garden soil possessed more fungal colonies (750) than agricultural soil (477). In agricultural soil, the dominant fungi were Aspergillus niger, Rhizopus oryzae, and Penicillium expansum, and the dominant fungi of garden soil were A. niger and Fusarium moniliforme. Simpson's diversity index indicated that garden soil had more fungal diversity (0.939) than agricultural soil (0.896). The entomopathogenic capacity of the isolated fungi was tested against the brinjal shoot and fruit borer (Leucinodes orbonalis Guen) which is the major insect pest of brinjal. The isolated fungi were screened against larva of L. orbonalis for their entomopathogenic potential. Beauveria bassiana, A. niger, and P. expansum showed appreciable antagonism to L. orbonalis, and their lethal doses with 50 % mortality (LD50s) were 4.0 × 10(7), 9.06 × 10(7), and 1.50 × 10(8) spore/mL, respectively, and their times taken to reach 50 % mortality (LT50s) were 9.77, 10.56, and 10.60 days, respectively. This work suggests the restriction of chemical pesticide application in agricultural fields to increase fungal diversity. The entomopathogenic efficacy of B. bassiana could be used in agricultural fields to increase fugal diversity and protect the brinjal crop.","corpus_id":27441416,"score":0},{"doc_id":"25414142","title":"Fungi in a changing world: growth rates will be elevated, but spore production may decrease in future climates.","abstract":"Very little is known about the impact of climate change on fungi and especially on spore production. Fungal spores can be allergenic, thus being important for human health. The aim of this study was to investigate how climate change influences the responsive ability of fungi by simulating differing environmental regimes. Fungal species with high spore allergenic potential and atmospheric abundance were grown and experimentally examined under a variety of temperatures and different nutrient availability. Each represented the average decadal air temperature of the 1980s, 1990s and 2000s in the UK, along with an Intergovernmental Panel on Climate Change (IPCC) climate change scenario for 2100. All tests were run on six fungal species: Alternaria alternata, Aspergillus niger, Botrytis cinerea, Cladosporium cladosporioides, Cladosporium oxysporum and Epicoccum purpurascens. Mycelium growth rate and spore production were examined on each single species and competitive capacity among species combinations in pairs. All fungal species grew faster at higher temperatures, and this was more pronounced for the temperature projection in 2100. Most species grew faster when there was lower nutrient availability. Exceptions were the species with the highest growth rate (E. purpurascens) and with the highest competition capacity (A. alternata). Most species (except for E. purpurascens) produced more spores in the richer nutrient medium but fewer as temperature increased. C. cladosporioides was an exception, exponentially increasing its spore production in the temperature of the 2100 scenario. Regarding competitive capacity, no species displayed any significant alterations within the environmental range checked. It is suggested that in future climates, fungi will display dramatic growth responses, with faster mycelium growth and lower spore production, with questions risen on relevant allergen potential.","corpus_id":9698981,"score":0},{"doc_id":"26022406","title":"Targeting allergenic fungi in agricultural environments aids the identification of major sources and potential risks for human health.","abstract":"Fungi are, after pollen, the second most important producers of outdoor airborne allergens. To identify sources of airborne fungal allergens, a workflow for qPCR quantification from environmental samples was developed, thoroughly tested, and finally applied. We concentrated on determining the levels of allergenic fungi belonging to Alternaria, Cladosporium, Fusarium, and Trichoderma in plant and soil samples from agricultural fields in which cereals were grown. Our aims were to identify the major sources of allergenic fungi and factors potentially influencing their occurrence. Plant materials were the main source of the tested fungi at and after harvest. Amounts of A. alternata and C. cladosporioides varied significantly in fields under different management conditions, but absolute levels were very high in all cases. This finding suggests that high numbers of allergenic fungi may be an inevitable side effect of farming in several crops. Applied in large-scale studies, the concept described here may help to explain the high number of sensitization to airborne fungal allergens.","corpus_id":52810782,"score":0},{"doc_id":"26348882","title":"Soil fungi for mycoremediation of arsenic pollution in agriculture soils.","abstract":"AIMS: Soil arsenic (As) contamination of food-chains and public health can be mitigated through fungal bioremediation. To enumerate culturable soil fungi, soils were collected from the As-contaminated paddy fields (3-35 mg kg(-1) ) of the middle Indo-Gangetic Plains. METHODS AND RESULTS: Total 54 fungal strains were obtained and identified at their molecular level. All strains were tested for As tolerance (from 100 to 10,000 mg l(-1) arsenate). Fifteen fungal strains, tolerant to 10,000 mg l(-1) arsenate, were studied for As removal in-vivo for 21 days by cultivating them individually in potato dextrose broth enriched with 10 mg l(-1) As. The bioaccumulation of As in fungal biomass ranged from 0·023 to 0·259 g kg(-1). The biovolatilized As ranged from 0·23 to 6·4 mg kg(-1). CONCLUSIONS: Higher As bioaccumulation and biovolatilization observed in the seven fungal strains, Aspergillus oryzae FNBR_L35; Fusarium sp. FNBR_B7, FNBR_LK5 and FNBR_B3; Aspergillus nidulans FNBR_LK1; Rhizomucor variabilis sp. FNBR_B9; and Emericella sp. FNBR_BA5. These fungal strains were also tested and found suitable for significant plant growth promotion in the calendula, withania and oat plants in a greenhouse based pot experiment. SIGNIFICANCE AND IMPACT OF STUDY: These fungal strains can be used for As remediation in As-contaminated agricultural soils.","corpus_id":25803247,"score":0},{"doc_id":"26843941","title":"Mean reproductive traits of fungal assemblages are correlated with resource availability.","abstract":"Organisms have evolved a fascinating variety of strategies and organs for successful reproduction. Fruit bodies are the reproductive organ of fungi and vary considerably in size and shape among species. Our understanding of the mechanisms underlying the differences in fruit body size among species is still limited. Fruit bodies of saprotrophic fungi are smaller than those of mutualistic ectomycorrhizal fungi. If differences in fruit body size are determined by carbon acquisition, then mean reproductive traits of saprotrophic and ectomycorrhizal fungi assemblages should vary differently along gradients of resource availability as carbon acquisition seems more unpredictable and costly for saprotrophs than for ectomycorrhizal fungi. Here, we used 48 local inventories of fungal fruit bodies (plot size: 0.02 ha each) sampled along a gradient of resource availability (growing stock) across 3 years in the Bavarian Forest National Park in Germany to investigate regional and local factors that might influence the distribution of species with different reproductive traits, particularly fruit body size. As predicted, mean fruit body size of local assemblages of saprotrophic fungi was smaller than expected from the distribution of traits of the regional species pool across central and northern Europe, whereas that of ectomycorrhizal fungi did not differ from random expectation. Furthermore and also as expected, mean fruit body size of assemblages of saprotrophic fungi was significantly smaller than for assemblages of ectomycorrhizal species. However, mean fruit body sizes of not only saprotrophic species but also ectomycorrhizal species increased with resource availability, and the mean number of fruit bodies of both assemblages decreased. Our results indicate that the differences in carbon acquisition between saprotrophs and ectomycorrhizal species lead to differences in basic reproductive strategies, with implications for the breadth of their distribution. However, the differences in resource acquisition cannot explain detailed species distribution patterns at a finer, local scale based on their reproductive traits.","corpus_id":12412792,"score":0},{"doc_id":"27154063","title":"Effect of plant extracts on book deteriorated fungal species.","abstract":"The aim of the study was to evaluate the effect of leaf extracts of four plants against some isolated fungal species from deteriorated books. Aqueous, methanol and chloroform extracts of selected plant species were screened in vitro for their antifungal activity against some book deteriorating fungal species. Fifteen species belonging to 09 genera were isolated and identified from infested books in library. Aqueous and solvent extracts of leaves of Azadiracta indica, Callistemon citrinus, Eucalyptus lanceolatus and Pongamia pinnata were tested against some dominant fungal species viz. Chaetomium spiralis, Alternaria alternata, Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus and Rhizopus stolonifer. Solvent extracts exhibited potent inhibitory activity than aqueous extracts. However, these plant extracts exhibited moderate activity against A. flavus, C. spiralis, R. stolonifer and A. alternata.","corpus_id":5119524,"score":0},{"doc_id":"27255701","title":"Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic.","abstract":"Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was lower, while saprotrophic fungi was higher in increased snow depth plots relative to controls. [ Correction added on 23 September 2016 after first online publication: In the preceding sentence, the richness of ECM and saprotrophic fungi were wrongly interchanged and have been fixed in this current version.] ECM fungal richness was related to soil NO3 -N, NH4 -N, and K; and saprotrophic fungi to NO3 -N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long-term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respiration, and stored permafrost carbon.","corpus_id":6493413,"score":0},{"doc_id":"28353091","title":"Diversity of culturable fungi inhabiting petroleum-contaminated soils in Southern Iran.","abstract":"The present study was aimed at characterising species diversity of fungi inhabiting petroleum-contaminated soils of oil fields in a southern region of Iran. Two different techniques were used for fungal isolation including enrichment on atmospheres of phenolic hydrocarbons and crude oil as substrate. Phylogenetic analysis of the internal transcribed spacer of ribosomal DNA was used for taxonomic identification with additional information from the β-tubulin gene for selected taxa. Overall, 183 strains from 14 genera and five orders were obtained: Pleosporales (Alternaria, Curvularia, Stemphylium, Ulocladium), Chaetothyriales (Exophiala), Eurotiales (Aspergillus), Hypocreales (Acremonium, Emericellopsis, Sarocladium, Stachybotrys, Fusarium, Trichoderma, Beauveria), and Capnodiales (Cladosporium). The most frequently isolated strains belonged to the genera Alternaria, Exophiala and Aspergillus. The crude oil substrate was the most successful isolation method, and among the four hydrocarbon enrichments, toluene substrate yielded the highest number of strains. Enrichment on xylene and benzene also yielded herpotrichiellaceous and other filamentous fungi.","corpus_id":23473311,"score":0},{"doc_id":"28539923","title":"Analysis on Fungal Diversity in Rhizosphere Soil of Continuous Cropping Potato Subjected to Different Furrow-Ridge Mulching Managements.","abstract":"Knowledge about fungi diversity following different planting patterns could improve our understanding of soil processes and thus help us to develop sustainable management strategies. The objective of this study was to determine the impact of different furrow-ridge mulching techniques on fungal diversity in rhizosphere soil under continuous cropping system. The investigated treatments were: flat plot without mulch (CK); flat plot with mulch (T1); on-ridge planting with full mulch (T2); on-furrow planting with full mulch (T3); on-ridge planting with half mulch (T4); and on-furrow planting with half mulch (T5). NGS (Illumina) methods and ITS1 sequences were used in monitoring fungi diversity of the potato rhizosphere soil. The fungi diversity in the rhizosphere soil was ranked in the order T5 > T2 > T4 > T1 > CK at the early growth stage and T2 > T3 > T1 > T4 > CK at the late growth stage of potato. The fungal communities found in the rhizosphere soil were Ascomycota, Zygomycota, Basidiomycota, Chytridiomycota, and other unidentified fungal communities. Among the fungal community in the rhizosphere soil, Ascomycota was found to be dominant fungi population, with the highest percentage (89%) in the T5 soil whereas the T2 soils had the lowest percentage (67%). The Fusarium abundance in fully-mulched treated soils was higher than in half-mulched treated soil. The dominant genus in the T4 soil was Mortierella, whereas lower populations (1-2%) of Scutellinia, Cryphonectria, Acremonium, and Alternaria were found in that treatment. Among the eumycetes, the dominant fungal class in all treated soils was the Sordariomycetes, which ranged from 57 to 85% in T2 and T5 soils, respectively. The Fusarium percentages in half-mulched treated soils (T4 and T5) were 55 and 28% lower than that of complete mulched treated soils (T2 and T3), respectively. The cluster analysis results showed that, CK, T4, and T5 treated soils and T1, T2, and T3 treated soils had similarities in microbial compositions, respectively. Potato tuber yield was greater under the on-ridge planting with full mulch (T2) treated soil, followed by on-ridge planting with half-mulch (T4) treated soil. The rhizosphere soil under the on-ridge planting with full-mulch (T2) soil had the highest fungal diversity, suggesting that this management was the best environment for fungi, whereas the on-ridge planting with half-mulch (T4) soil had the minimum abundance of Fusarium.","corpus_id":33874761,"score":0},{"doc_id":"29100947","title":"Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi.","abstract":"BACKGROUND: In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections. MATERIALS AND METHODS: We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis. RESULTS: The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results. CONCLUSION: Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.","corpus_id":4862784,"score":0},{"doc_id":"29568759","title":"Isolation and Molecular Characterization of a Model Antagonistic Pseudomonas aeruginosa Divulging In Vitro Plant Growth Promoting Characteristics.","abstract":"The use of microbial technologies in agriculture is currently expanding quite rapidly with the identification of new bacterial strains, which are more effective in promoting plant growth. In the present study 18 strains of Pseudomonas were isolated from soil sample of Balochistan coastline. Among isolated Pseudomonas strains four designated as SP19, SP22, PS24, and SP25 exhibited biocontrol activities against phytopathogenic fungi, that is, Rhizopus microsporus, Fusarium oxysporum, Aspergillus niger, Alternaria alternata, and Penicillium digitatum; PS24 identified as Pseudomonas aeruginosa by 16srRNA gene bank accession number EU081518 was selected on the basis of its antifungal activity to explore its potential as plant growth promotion. PS24 showed multiple plant growth promoting attributes such as phosphate solubilization activity, indole acetic acid (IAA), siderophore, and HCN production. In order to determine the basis for antifungal properties, antibiotics were extracted from King B broth of PS24 and analyzed by TLC. Pyrrolnitrin antibiotic was detected in the culture of strain PS24. PS24 exhibited antifungal activities found to be positive for hydrogen cyanide synthase Hcn BC gene. Sequencing of gene of Hcn BC gene of strain PS24 revealed 99% homology with the Pseudomonas aeruginosa strain PA01. The sequence of PS24 had been submitted in gene bank accession number KR605499. Ps. aeruginosa PS24 with its multifunctional biocontrol possessions can be used to bioprotect the crop plants from phytopathogens.","corpus_id":4085716,"score":0},{"doc_id":"29724011","title":"Endophytic Fungi in Species of Artemisia.","abstract":"The genus Artemisia, a collection of ~400 hardy herbaceous plant and shrub species, is an important resource contributing to chemistry, medicine, agriculture, industry, and ecology. Its communities of endophytic fungi have only recently begun to be explored. Summarized from studies conducted on the fungal endophytes in Artemisia species, both fungal phylogenetic diversity and the associated bioactivity was examined. Isolations from 14 species of Artemisia have led to 51 genera of fungal endophytes, 28 families, and 18 orders. Endophytes belonged mainly to Ascomycota, except for two taxa of Cantharellales and Sporidiobolales, one taxon of Mucoromycota, and one species of Oomycota. The mostly common families were Pleosporaceae, Trichocomaceae, Leptosphaeriaceae, and Botryosphaeriaceae (relative abundance = 14.89, 8.51, 7.14 and 6.38, respectively). In the search for bioactive metabolites, 27 novel compounds were characterized and 22 metabolites were isolated between 2006 and 2017. The first study on endophytic fungi isolated from species of Artemisia was published but 18 years ago. This summary of recently acquired data illustrates the considerable diversity of biological purposes addressed by fungal endophytes of Artemisia spp.","corpus_id":13914106,"score":0},{"doc_id":"29777126","title":"Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils.","abstract":"Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon (14C) dating CO2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41-56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350-400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ13C values of CO2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa.","corpus_id":21745349,"score":0}],"string":"[\n {\n \"doc_id\": \"19709342\",\n \"title\": \"Comparing phosphorus mobilization strategies using Aspergillus niger for the mineral dissolution of three phosphate rocks.\",\n \"abstract\": \"Phosphorus deficiencies are limiting crop production in agricultural soils worldwide. Locally available sources of raw phosphate rock (PR) are being recognized for their potential role in soil fertility improvement. Phosphorus bioavailability is essential for the efficiency of PRs and can be increased by acid treatments. The utilization of organic acid producing micro-organisms, notably Aspergillus niger, presents a sustainable alternative to the use of strong inorganic acids, but acid production of A. niger strongly depends on the mineral content of the growth media. This study compared the phosphorus mobilization efficiency of two biological treatments, namely addition of acidic cell-free supernatants from A. niger cultivations to PRs and the direct cultivation of A. niger with PRs. The results show that addition of PR to cultivations leads to significant differences in the profile of organic acids produced by A. niger. Additions of PR, especially igneous rocks containing high amounts of iron and manganese, lead to reduced citric acid concentrations. In spite of these differences, phosphorus mobilization was similar between treatments, suggesting that the simpler direct cultivation method was not inferior. In addition to citric acid, it is suggested that oxalic acid contributes to PR solubilization in direct cultivations with A. niger, which would benefit farmers in developing countries where conventional fertilizers are not adequately accessible.\",\n \"corpus_id\": 9537394,\n \"score\": 2\n },\n {\n \"doc_id\": \"20705386\",\n \"title\": \"The effectiveness of arbuscular-mycorrhizal fungi and Aspergillus niger or Phanerochaete chrysosporium treated organic amendments from olive residues upon plant growth in a semi-arid degraded soil.\",\n \"abstract\": \"Arbuscular mycorrhizal (AM) fungi and a residue from dry olive cake (DOC) supplemented with rock phosphate (RP) and treated with either Aspergillus niger (DOC-A) or Phanerochaete chrysosporium (DOC-P), were assayed in a natural, semi-arid soil using Trifolium repens or Dorycnium pentaphyllum plants. The effects of the AM fungi and/or DOC-A were compared with P-fertilisation (P) over eleven successive harvests to evaluate the persistence of the effectiveness of the treatments. The biomass of dually-treated plants after four successive harvests was greater than that obtained for non-treated plants or those receiving the AM inoculum or DOC-A treatments after eleven yields. The AM inoculation was critical for obtaining plant growth benefit from the application of fermented DOC-A residue. The abilities of the treatments to prevent plant drought stress were also assayed. Drought-alleviating effects were evaluated in terms of plant growth, proline and total sugars concentration under alternative drought and re-watering conditions (8th and 9th harvests). The concentrations of both compounds in plant biomass increased under drought when DOC-A amendment and AM inoculation were employed together: they reinforced the plant drought-avoidance capabilities and anti-oxidative defence. Water stress was less compensated in P-fertilised than in DOC-A-treated plants. DOC-P increased D. pentaphyllum biomass, shoot P content, nodule number and AM colonisation, indicating the greater DOC-transforming ability of P. chrysosporium compared to A. niger. The lack of AM colonisation and nodulation in this soil was compensated by the application of DOC-P, particularly with AM inoculum. The management of natural resources (organic amendments and soil microorganisms) represents an important strategy that assured the growth, nutrition and plant establishment in arid, degraded soils, preventing the damage that arises from limited water and nutrient supply.\",\n \"corpus_id\": 22384618,\n \"score\": 2\n },\n {\n \"doc_id\": \"23025081\",\n \"title\": \"[Filamentous and phosphate solubilizing fungi relationships with some edaphic parameters and coffee plantations management].\",\n \"abstract\": \"Relaciones entre los hongos filamentosos y solubilizadores de fosfatos con algunas variables edáficas y el manejo de cafetales. Soil properties and the environment have multiple outcomes on fungal communities. Although, the interaction effects between management intensity, pH, available phosphorus, organic carbon, soil texture and different fractions of water stable macro-aggregates on the communities of microscopic filamentous fungi (MFF), iron phosphate solubilizing fungi (PSF-Fe), and iron and calcium phosphate solubilizing fungi (PSF-(Fe+Ca)), have been previously evaluated in field conditions, this has never been performed in terms of their combined effects, neither with phosphate solubilizing fungi. To assess this, we collected 40 composite soil samples from eight Mexican and Colombian coffee plantations, with different management intensities and physico-chemical edaphic parameters, during 2008-2009. We isolated different communities of MFF, PSF-Fe and PSF-(Fe+Ca), by wet sieving and soil particles culture in Potato-Dextrose-Agar from soil samples, and we classified isolates in terms of their phosphate solubilizing ability. Following the principal component analysis results, we decided to analyze fungal communities and abiotic factors interactions for each country separately. Structural Equation Models revealed that organic carbon was positively associated to MFF richness and number of isolates (lambda>0.58), but its relationship with PSF-Fe and PSF-(Fe+Ca) were variable; while the available phosphorus, pH and water stable macro-aggregate fractions did not show a clear pattern. Management intensity was negatively related to PSF-Fe (lambda < or = -0.21) morphotype richness and the number of isolates in Colombian coffee plantations. We found that the relationships of clay and organic carbon content, and available phosphorus and soil pH, with the species richness and number of isolates of MFF, PSF-Fe and PSF-(Fe+Ca) were highly variable; this made impossible to generalize the responses between saprotrophic fungal groups and geographic zones. The management intensity was not related to species richness and number of isolates of MFF in any coffee areas, while for PSF the relationship could not be defined. The different water stable macro-aggregates fractions did not show a defined pattern in relation to the species richness and the number of isolates of saprophytic and phosphate solubilizing fungi (PSF). This study highlights the need to take into account edaphic and geographic context in order to reach a better understanding of the intensity management effects on MFF and PSF function in agroecosystems.\",\n \"corpus_id\": 44553089,\n \"score\": 2\n },\n {\n \"doc_id\": \"23100719\",\n \"title\": \"Isolation and characterisation of phosphate solubilising microorganisms from the cold desert habitat of Salix alba Linn. in trans Himalayan region of Himachal Pradesh.\",\n \"abstract\": \"Phosphate solubilising microorganisms (PSM) (bacteria and fungi) associated with Salix alba Linn. from Lahaul and Spiti valleys of Himachal Pradesh were isolated on Pikovskaya (PVK), modified Pikovskaya (MPVK) and National Botanical Research Institute agar (NBRIP) media by spread plating. The viable colony count of P-solubilising bacteria (PSB) and fungi (PSF) was higher in rhizosphere than that of non-rhizosphere. The frequency of PSM was highest on MPVK followed by NBRIP and PVK agar. The maximum proportion of PSM out of total bacterial and fungal count was found in upper Keylong while the least in Rong Tong. The PSB frequently were Gram-positive, endosporeforming, motile rods and belonged to Bacillus sp. The PSF mainly belonged to Penicillium sp., Aspergillus fumigatus, A. niger, A. spp. and non-sporulating sterile. Amongst the isolates with high efficiency for tricalcium phosphate (TCP) solubilisation, seven bacterial and seven fungal isolates dissolved higher amount of P from North Carolina rock phosphate (NCRP) than Mussoorie rock phosphate (MRP) and Udaipur rock phosphate (URP). However, the organisms solubilised higher-P in NBRIP broth than PVK broth. SBC5 (Bacillus sp.) and SBC7 (Bacillus sp.) bacterial isolates exhibited maximun P solubilisation (40 and 33 μg ml(-1) respectively) whereas FC28 (Penicillium sp.) isolate (52.3 μg ml(-1)) amongst fungi while solubilising URP. The amount of P solubilised was positively correlated with the decrease in pH of medium. SBC5 (Bacillus sp.), SBC7 (Bacillus sp.) and SBC4 (Micrococcus) decreased the pH of medium from 6.8 to 6.08 while FC28 (Penicillium sp.) and FC39 (Penicillium sp.) isolates of fungi recorded maximum decrease in pH of medium from 6.8 to 5.96 in NBRIP broth.\",\n \"corpus_id\": 9867654,\n \"score\": 2\n },\n {\n \"doc_id\": \"24560283\",\n \"title\": \"Role of phosphate fertilizers in heavy metal uptake and detoxification of toxic metals.\",\n \"abstract\": \"As a nonrenewable resource, phosphorus (P) is the second most important macronutrient for plant growth and nutrition. Demand of phosphorus application in the agricultural production is increasing fast throughout the globe. The bioavailability of phosphorus is distinctively low due to its slow diffusion and high fixation in soils which make phosphorus a key limiting factor for crop production. Applications of phosphorus-based fertilizers improve the soil fertility and agriculture yield but at the same time concerns over a number of factors that lead to environmental damage need to be addressed properly. Phosphate rock mining leads to reallocation and exposure of several heavy metals and radionuclides in crop fields and water bodies throughout the world. Proper management of phosphorus along with its fertilizers is required that may help the maximum utilization by plants and minimum run-off and wastage. Phosphorus solubilizing bacteria along with the root rhizosphere of plant integrated with root morphological and physiological adaptive strategies need to be explored further for utilization of this extremely valuable nonrenewable resource judiciously. The main objective of this review is to assess the role of phosphorus in fertilizers, their uptake along with other elements and signaling during P starvation.\",\n \"corpus_id\": 41540557,\n \"score\": 2\n },\n {\n \"doc_id\": \"25561059\",\n \"title\": \"Mechanisms for solubilization of various insoluble phosphates and activation of immobilized phosphates in different soils by an efficient and salinity-tolerant Aspergillus niger strain An2.\",\n \"abstract\": \"Mechanisms for solubilization of different types of phosphates and activation of immobilized phosphates in different types of soils by an efficient fungal strain An2 were explored and evaluated in this study. An2 was isolated from a Chinese cabbage rhizosphere soil and identified as Aspergillus niger. It could fast release up to 1722, 2066, and 2356 mg L(-1) of soluble phosphorus (P) from 1 % Ca3(PO4)2, Mg3(PO4)2, and AlPO4 (Ca-P, Mg-P, and Al-P) and 215 and 179 mg L(-1) from 0.5 % FePO4 and rock phosphate (Fe-P and RP), respectively. HPLC assay demonstrated that An2 mainly secreted oxalic acid to solubilize Ca-P, Mg-P, Al-P, and Fe-P whereas secreted tartaric acid to solubilize RP. Furthermore, An2 could tolerate salinity up to 4 % NaCl without impairing its phosphate-solubilizing ability. The simulation experiments validated that An2 was able to effectively activate immobilized phosphates in general calcareous, acidic, as well as saline-alkali soils with high total P content. This study shows new insights into the mechanisms for microbial solubilization of different types of phosphates and supports the future application of strain An2 in different types of soils to effectively activate P for plants.\",\n \"corpus_id\": 34638507,\n \"score\": 2\n },\n {\n \"doc_id\": \"25674415\",\n \"title\": \"Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.\",\n \"abstract\": \"Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05% (w/w) but only 0.1% of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8% of the plant dry weight. To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75-90% of added P is precipitated by metal-cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.\",\n \"corpus_id\": 18845624,\n \"score\": 2\n },\n {\n \"doc_id\": \"26469739\",\n \"title\": \"Phosphate solubilization and promotion of maize growth by Penicillium oxalicum P4 and Aspergillus niger P85 in a calcareous soil.\",\n \"abstract\": \"Alternative tactics for improving phosphorus nutrition in crop production are needed in China and elsewhere, as the overapplication of phosphatic fertilizers can adversely impact agricultural sustainability. Penicillium oxalicum P4 and Aspergillus niger P85 were isolated from a calcareous soil in China that had been exposed to excessive application of phosphatic fertilizer for decades. Each isolate excreted a number of organic acids into, acidified, and solubilized phosphorus in a synthetic broth containing insoluble tricalcium phosphate or rock phosphate. Isolate P4, applied as a seed treatment, increased maize fresh mass per plant when rock phosphate was added to the calcareous soil in greenhouse pot studies. Isolate P85 did not increase maize fresh mass per plant but did significantly increase total phosphorus per plant when rock phosphate was added. Significant increases in 7 and 4 organic acids were detected in soil in association with isolates P4 and P85, respectively, relative to the soil-only control. The quantity and (or) number of organic acids produced by these isolates increased when rock phosphate was added to the soil. Both isolates also significantly increased available phosphorus in soil in the presence of added rock phosphate and effectively colonized the maize rhizosphere. Studies reported here indicate that isolate P4 is adapted to and capable of promoting maize growth in a calcareous soil. Plant-growth promotion by this isolate is likely due, at least in part, to increased phosphorus availability resulting from the excretion of organic acids into, and the resulting acidification of, this soil.\",\n \"corpus_id\": 25397971,\n \"score\": 2\n },\n {\n \"doc_id\": \"26805616\",\n \"title\": \"Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils.\",\n \"abstract\": \"Intensive agricultural practices and cultivation of exhaustive crops has deteriorated soil fertility and its quality in agroecosystems. According to an estimate, such practices will convert 30% of the total world cultivated soil into degraded land by 2020. Soil structure and fertility loss are one of the main causes of soil degradation. They are also considered as a major threat to crop production and food security for future generations. Implementing safe and environmental friendly technology would be viable solution for achieving sustainable restoration of degraded soils. Bacterial and fungal inocula have a potential to reinstate the fertility of degraded land through various processes. These microorganisms increase the nutrient bioavailability through nitrogen fixation and mobilization of key nutrients (phosphorus, potassium and iron) to the crop plants while remediate soil structure by improving its aggregation and stability. Success rate of such inocula under field conditions depends on their antagonistic or synergistic interaction with indigenous microbes or their inoculation with organic fertilizers. Co-inoculation of bacteria and fungi with or without organic fertilizer are more beneficial for reinstating the soil fertility and organic matter content than single inoculum. Such factors are of great importance when considering bacteria and fungi inocula for restoration of degraded soils. The overview of presented mechanisms and interactions will help agriculturists in planning sustainable management strategy for reinstating the fertility of degraded soil and assist them in reducing the negative impact of artificial fertilizers on our environment.\",\n \"corpus_id\": 206936928,\n \"score\": 2\n },\n {\n \"doc_id\": \"26850158\",\n \"title\": \"Mycorrhizal fungal communities respond to experimental elevation of soil pH and P availability in temperate hardwood forests.\",\n \"abstract\": \"Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.\",\n \"corpus_id\": 37898479,\n \"score\": 2\n },\n {\n \"doc_id\": \"27102357\",\n \"title\": \"Arbuscular mycorrhizal fungi in soil and roots respond differently to phosphorus inputs in an intensively managed calcareous agricultural soil.\",\n \"abstract\": \"Understanding the diversity and community structure of arbuscular mycorrhizal fungi (AMF) is important for potentially optimizing their role in mining phosphorus (P) in agricultural ecosystems. Here, we conduct a comprehensive study to investigate the vertical distribution of AMF in a calcareous field and their temporal structure in maize-roots with fertilizer P application over a three-year period. The results showed that soil available-P response to P fertilization but maize yields did not. Phosphorus fertilization had no-significant effect on richness of AMF except at greater soil-depths. High P-supply reduced root colonization while optimum-P tended to increase colonization and fungal richness on all sampling occasions. Crop phenology might override P-supply in determining the community composition of active root inhabiting fungi. Significant differences in the community structure of soil AMF were observed between the controls and P treatments in surface soil and the community shift was attributable mainly to available-P, N/P and pH. Vertical distribution was related mainly to soil electrical conductivity and Na content. Our results indicate that the structure of AMF community assemblages is correlated with P fertilization, soil depth and crop phenology. Importantly, phosphorus management must be integrated with other agricultural-practices to ensure the sustainability of agricultural production in salinized soils.\",\n \"corpus_id\": 14178968,\n \"score\": 2\n },\n {\n \"doc_id\": \"27688771\",\n \"title\": \"Phosphate Solubilization Potential of Rhizosphere Fungi Isolated from Plants in Jimma Zone, Southwest Ethiopia.\",\n \"abstract\": \"Phosphorus (P) is one of the major bioelements limiting agricultural production. Phosphate solubilizing fungi play a noteworthy role in increasing the bioavailability of soil phosphates for plants. The present study was aimed at isolating and characterizing phosphate solubilizing fungi from different rhizospheres using both solid and liquid Pikovskaya (PVK) medium. A total of 359 fungal isolates were obtained from 150 rhizosphere soil samples of haricot bean, faba bean, cabbage, tomato, and sugarcane. Among the isolates, 167 (46.52%) solubilized inorganic phosphate. The isolated phosphate solubilizing fungi belonged to genera of Aspergillus (55.69%), Penicillium spp. ( 23.35%), and Fusarium (9.58%). Solubilization index (SI) ranged from 1.10 to 3.05. Isolates designated as JUHbF95 (Aspergillus sp.) and JUFbF59 (Penicillium sp.) solubilized maximum amount of P 728.77 μg·mL(-1) and 514.44 μg mL(-1), respectively, from TCP (tricalcium phosphate) after 15 days of incubation. The highest (363 μg mL(-1)) soluble-P was released from RP with the inoculation of JUHbF95 in the PVK broth after 10 days of incubation. The present study indicated the presence of diverse plant associated P-solubilizing fungi that may serve as potential biofertilizers.\",\n \"corpus_id\": 9160393,\n \"score\": 2\n },\n {\n \"doc_id\": \"27825490\",\n \"title\": \"Phosphate dissolving fungi: Mechanism and application in alleviation of salt stress in wheat.\",\n \"abstract\": \"The present investigation reveals the solubilization efficiency of tri-calcium phosphate (TCP), Udaipur rock phosphate (URP), aluminium phosphate (AP) and ferric phosphate (FP) by Aspergillus niger (ITCC 6719) and Trichoderma harzianum (ITCC 6721) as function of carbon concentrations. Increasing glucose concentration from 1 to 7% in the growth medium, though improved the phosphorus (P) solubilization significantly but each fungal strain preferred different optimum carbon concentrations for mediating solubilization of different P sources. The two fungi employed different mechanisms to reduce medium pH for release of P from TCP, AP and FP. However, URP was solubilized solely through fungal production of citric, succinic, propionic, malic and acetic acid. A linear increase in citric acid production with increasing carbon concentration was recorded during FP solubilization by T. harzianum. The cell free culture filtrate of A. niger detected high phytase and low acid phosphatase activity titre whereas results were vice versa for T. harzianum. Both the fungal strains possessed plant growth promoting attributes such as auxin and sidreophore production and could solubilize Zn. In hydroponic system (with 60mM of sodium chloride concentration), supplementation with culture filtrate from each fungal strain increased the shoot growth of wheat seedlings significantly compared to non culture filtrate control. Use of A.niger as bio-inoculant could be a sustainable approach to improve soil P availability, promote plant growth and alleviate adverse effect of salt stress.\",\n \"corpus_id\": 35215601,\n \"score\": 2\n },\n {\n \"doc_id\": \"27872635\",\n \"title\": \"Rhizosphere Organic Anions Play a Minor Role in Improving Crop Species' Ability to Take Up Residual Phosphorus (P) in Agricultural Soils Low in P Availability.\",\n \"abstract\": \"Many arable lands have accumulated large reserves of residual phosphorus (P) and a relatively large proportion of soil P is less available for uptake by plants. Root released organic anions are widely documented as a key physiological strategy to enhance P availability, while limited information has been generated on the contribution of rhizosphere organic anions to P utilization by crops grown in agricultural soils that are low in available P and high in extractable Ca, Al, and Fe. We studied the role of rhizosphere organic anions in P uptake from residual P in four common crops Triticum aestivum, Avena sativa, Solanum tuberosum, and Brassica napus in low- and high-P availability agricultural soils from long-term fertilization field trials in a mini-rhizotron experiment with four replications. Malate was generally the dominant organic anion. More rhizosphere citrate was detected in low P soils than in high P soil. B. napus showed 74-103% increase of malate in low P loam, compared with clay loam. A. sativa had the greatest rhizosphere citrate concentration in all soils (5.3-15.2 μmol g(-1) root DW). A. sativa also showed the highest level of root colonization by arbuscular mycorrhizal fungi (AMF; 36 and 40%), the greatest root mass ratio (0.51 and 0.66) in the low-P clay loam and loam respectively, and the greatest total P uptake (5.92 mg P/mini-rhizotron) in the low-P loam. B. napus had 15-44% more rhizosphere acid phosphatase (APase) activity, ~0.1-0.4 units lower rhizosphere pH than other species, the greatest increase in rhizosphere water-soluble P in the low-P soils, and the greatest total P uptake in the low-P clay loam. Shoot P content was mainly explained by rhizosphere APase activity, water-soluble P and pH within low P soils across species. Within species, P uptake was mainly linked to rhizosphere water soluble P, APase, and pH in low P soils. The effects of rhizosphere organic anions varied among species and they appeared to play minor roles in improving P availability and uptake.\",\n \"corpus_id\": 7775478,\n \"score\": 2\n },\n {\n \"doc_id\": \"28626450\",\n \"title\": \"Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture.\",\n \"abstract\": \"The use of excess conventional Phosphorus (P) fertilizers to improve agricultural productivity, in order to meet constantly increasing global food demand, potentially causes surface and ground water pollution, waterway eutrophication, soil fertility depletion, and accumulation of toxic elements such as high concentration of selenium (Se), arsenic (As) in the soil. Quite a number of soil microorganisms are capable of solubilizing/mineralizing insoluble soil phosphate to release soluble P and making it available to plants. These microorganisms improve the growth and yield of a wide variety of crops. Thus, inoculating seeds/crops/soil with Phosphate Solubilizing Microorganisms (PSM) is a promising strategy to improve world food production without causing any environmental hazard. Despite their great significance in soil fertility improvement, phosphorus-solubilizing microorganisms have yet to replace conventional chemical fertilizers in commercial agriculture. A better understanding of recent developments in PSM functional diversity, colonizing ability, mode of actions and judicious application should facilitate their use as reliable components of sustainable agricultural systems. In this review, we discussed various soil microorganisms that have the ability to solubilize phosphorus and hence have the potential to be used as bio fertilizers. The mechanisms of inorganic phosphate solubilization by PSM and the mechanisms of organic phosphorus mineralization are highlighted together with some factors that determine the success of this technology. Finally we provide some indications that the use of PSM will promote sustainable agriculture and conclude that this technology is ready for commercial exploitation in various regions worldwide.\",\n \"corpus_id\": 1167346,\n \"score\": 2\n },\n {\n \"doc_id\": \"28769964\",\n \"title\": \"Application of Mycorrhiza and Soil from a Permaculture System Improved Phosphorus Acquisition in Naranjilla.\",\n \"abstract\": \"Naranjilla (Solanum quitoense) is a perennial shrub plant mainly cultivated in Ecuador, Colombia, and Central America where it represents an important cash crop. Current cultivation practices not only cause deforestation and large-scale soil degradation but also make plants highly susceptible to pests and diseases. The use of arbuscular mycorrhizal fungi (AMF) can offer a possibility to overcome these problems. AMF can act beneficially in various ways, for example by improving plant nutrition and growth, water relations, soil structure and stability and protection against biotic and abiotic stresses. In this study, the impact of AMF inoculation on growth and nutrition parameters of naranjilla has been assessed. For inoculation three European reference AMF strains (Rhizoglomus irregulare, Claroideoglomus claroideum, and Cetraspora helvetica) and soils originating from three differently managed naranjilla plantations in Ecuador (conventional, organic, and permaculture) have been used. This allowed for a comparison of the performance of exotic AMF strains (reference strains) versus native consortia contained in the three soils used as inocula. To study fungal communities present in the three soils, trap cultures have been established using naranjilla as host plant. The community structures of AMF and other fungi inhabiting the roots of trap cultured naranjilla were assessed using next generation sequencing (NGS) methods. The growth response experiment has shown that two of the three reference AMF strains, a mixture of the three and soil from a permaculture site led to significantly better acquisition of phosphorus (up to 104%) compared to uninoculated controls. These results suggest that the use of AMF strains and local soils as inoculants represent a valid approach to improve nutrient uptake efficiency of naranjilla and consequently to reduce inputs of mineral fertilizers in the cultivation process. Improved phosphorus acquisition after inoculation with permaculture soil might have been caused by a higher abundance of AMF and the presence of Piriformospora indica as revealed by NGS. A higher frequency of AMF and enhanced root colonization rates in the trap cultures supplemented with permaculture soil highlight the importance of diverse agricultural systems for soil quality and crop production.\",\n \"corpus_id\": 19367198,\n \"score\": 2\n },\n {\n \"doc_id\": \"28865270\",\n \"title\": \"Phosphorus activators contribute to legacy phosphorus availability in agricultural soils: A review.\",\n \"abstract\": \"Phosphorus (P) is one of the most limiting macronutrients for crop productivity and P deficiency is a common phenomenon in agricultural soils worldwide. Despite long-term application of phosphate fertilizers to increase crop yields, P availability is often low, due to the high affinity of phosphate for the soil solid phase. It has been suggested that the accumulated (surplus) P in agricultural soils is sufficient to sustain crop yields worldwide for about 100years. In this paper, we try to clear up the potential for making use of legacy P in soils for crop growth potentially alleviating the global P resource shortage. Specifically, we try to clear up the potential of soil \\\"P activators\\\" for releasing fixed P. P activators accelerate and strengthen process which transform P into bio-available forms via a range of chemical reactions and biological interactions. They include phosphate solubilizing microorganisms, phosphatase enzymes and enzyme activators, low molecular weight organic acids, humic acids, lignin, crop residues, biochar and zeolites. Although reported performance is variable, there is growing evidence that P activators can promote the release of phosphate from soil and, hence, have potential for mitigating the impending global P crisis. Further basic and applied research is required to better understand the mechanisms of interaction of P activators with natural soils and to maximize activator efficacy.\",\n \"corpus_id\": 205129053,\n \"score\": 2\n },\n {\n \"doc_id\": \"29679179\",\n \"title\": \"Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities.\",\n \"abstract\": \"Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger. High-performance liquid chromatography analysis revealed that the mechanism of phosphorus solubilization by CS-1 involved the synthesis and secretion of organic acids, mainly oxalic, tartaric, and citric acids. Furthermore, strain CS-1 exhibited other growth-promoting abilities, including efficient potassium release and degradation of crop straw cellulose. These properties help to returning crop residues to the soil, thereby increasing nutrient availability and sustaining organic matter concentration therein. A pot experiment revealed that CS-1 apparently increased the assessed biometric parameters of wheat seedlings, implying the potential of this strain to be developed as a commercial microbial agent. We used Illumina MiSeq sequencing to investigate the microbial community composition in the rhizosphere of uninoculated wheat plants and wheat plants inoculated with the CS-1 strain to obtain insight into the effect of the CS-1 strain inoculation. The data clearly demonstrated that CS-1 significantly reduced the content of pathogenic fungi, including Gibberella, Fusarium, Monographella, Bipolaris, and Volutella, which cause soil-borne diseases in various crops. Strain CS-1 may hence be developed into a microbial agent for plant growth improvement.\",\n \"corpus_id\": 4974993,\n \"score\": 2\n },\n {\n \"doc_id\": \"19685081\",\n \"title\": \"Ectomycorrhizal fungi and their enzymes in soils: is there enough evidence for their role as facultative soil saprotrophs?\",\n \"abstract\": \"Although ectomycorrhizal (ECM) fungi are generally regarded as dependent upon the supply of carbon from their plant hosts, some recent papers have postulated a role for these fungi in the saprotrophic acquisition of carbon from soil. This theory was mainly based on the increase in enzymatic activity during periods of low photosynthate supply from tree hosts and emergence of the theory has led to a question about the overall influence of saprotrophy by ECM fungi on soil carbon turnover. However, I argue here that there is still not enough evidence to confirm this proposed function. My argument is based on inference from several lines of observation and concern over several aspects of the past studies. First, ECM fungi mainly inhabit deeper soil horizons, in which the availability of carbon compounds with positive energetic value is low. Second, the ability of ECM fungi to produce ligninolytic enzymes and cellulases is much weaker than that of saprotrophic basidiomycetes. This is most apparent in the low copy abundance of corresponding genes in the sequenced genomes of ECM species Laccaria bicolor and Amanita bisporigenes compared to the saprotrophic species Galerina marginata. I offer alternative hypotheses to explain the past observations of increased enzyme activity during starvation periods. These include, the induction of autolytic processes in ECM fungal mycelia or an attack on the host tissues to support escape from a dying root and to allow for a search for new hosts.\",\n \"corpus_id\": 5806797,\n \"score\": 1\n },\n {\n \"doc_id\": \"22439851\",\n \"title\": \"Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils.\",\n \"abstract\": \"Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here, we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize vs. potato), soil type (sand vs. clay-textured soils) and habitat (plant root vs. bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species-poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive 'loss' from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass-cropping history together explained 32% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a 'bottleneck effect' on AMF communities through increased stochastic effects under environmental stress.\",\n \"corpus_id\": 16670908,\n \"score\": 1\n },\n {\n \"doc_id\": \"23997599\",\n \"title\": \"Ecological and physiological studies on soil fungi at Western region, libya.\",\n \"abstract\": \"Sixty three species and 5 varieties belonging to 30 fungal genera were collected from 75 soil samples. Cultivated (29 genera and 58 species + 5 var.), desert (22 and 35 + 2 var.) and saline soil (21 and 41 + 1 var.) fungi were recovered on glucose-, cellulose- and 50% sucrose-Czapek's agar at 28℃. The most common genera were Alternaria, Aspergillus, Emericella, Fusarium, Mycosphaerella, Nectria and Penicillium. The most prevalent species from the three types of soils on the three types of media were Alternaria alternata, Aspergillus flavus, A. fumigatus, A. niger, A. terreus, Emericella nidulans, Fusarium oxysporum, Mycosphaerella tassiana, Nectria haematococca and Penicillium chrysogenum. Chaetomium globosum was in the top of fungi in producing endo-β-1,4-glucanases among the 42 tested isolates obtained from soils on cellulose-Czapek's agar. Maximum production of this enzyme by C. globosum obtained after 6 days of incubation at 30℃ with culture medium containing maltose as a carbon source and ammonium nitrate as a nitrogen source and pH initially adjusted to 6.\",\n \"corpus_id\": 7982269,\n \"score\": 1\n },\n {\n \"doc_id\": \"24315210\",\n \"title\": \"Does a rhizospheric microorganism enhance K⁺ availability in agricultural soils?\",\n \"abstract\": \"The potassium solubilizing microorganisms (KSMs) are a rhizospheric microorganism which solubilizes the insoluble potassium (K) to soluble forms of K for plant growth and yield. K-solubilization is carried out by a large number of saprophytic bacteria (Bacillus mucilaginosus, Bacillus edaphicus, Bacillus circulans, Acidothiobacillus ferrooxidans, Paenibacillus spp.) and fungal strains (Aspergillus spp. and Aspergillus terreus). Major amounts of K containing minerals (muscovite, orthoclase, biotite, feldspar, illite, mica) are present in the soil as a fixed form which is not directly taken up by the plant. Nowadays most of the farmers use injudicious application of chemical fertilizers for achieving maximum productivity. However, the KSMs are most important microorganisms for solubilizing of fixed form of K in soil system. The KSMs are an indigenous rhizospheric microorganism which shows effective interaction between soil and plant systems. The main mechanism of KSMs is acidolysis, chelation, exchange reactions, complexolysis and production of organic acid. According to literature, currently negligible use of potassium fertilizer as a chemical form has been recorded in agriculture for enhancing crop yield. Most of the farmers use only nitrogen and phosphorus and not use the K fertilizer due to unawareness so that the problem of K deficiency occurs in rhizospheric soils. The K fertilizer is also costly as compared to other chemical fertilizers. Therefore, the efficient KSMs should be applied for solubilization of a fixed form of K to an available form of K in the soils. This available K can be easily taken up by the plant for growth and development. Our aim of this review is to elaborate on the studies of indigenous K-solubilizing microbes to develop efficient microbial consortia for solubilization of K in soil which enhances the plant growth and yield of crops. This review highlights the future need for research on potassium (K) in agriculture.\",\n \"corpus_id\": 206936115,\n \"score\": 1\n },\n {\n \"doc_id\": \"24428372\",\n \"title\": \"Survey of Aspergillus section Flavi presence in agricultural soils and effect of glyphosate on nontoxigenic A. flavus growth on soil-based medium.\",\n \"abstract\": \"AIMS: To evaluate the cultivable mycobiota from agricultural soils exposed to pesticides, the aflatoxigenic capacity of Aspergillus section Flavi strains and the effect of glyphosate on lag phase and growth rates of native nontoxigenic Aspergillus flavus under different water potential (MPa) conditions on soil-based medium. METHODS AND RESULTS: Culturable mycobiota analysis from different agricultural soils was performed by the surface spread method. The effect of glyphosate (0-20 mmol l(-1)) on the growth of A. flavus strains was evaluated on a soil extract solid medium. Mycobiota analysis of crop soils showed the presence of twenty-one genera of filamentous fungi. Aspergillus flavus and Aspergillus niger aggregate strains were isolated from the three soil types. Ninety-two per cent of A. flavus strains were toxigenic. In vitro assay results showed that at -0·70 MPa, a significant increase in growth rate in all strains was recorded at 5 and 20 mmol l(-1) of glyphosate. At -2·78 MPa, this parameter remained constant at all glyphosate concentrations, except in GM4 strain where an increase in growth rate was recorded with increasing pesticide concentrations. At -7·06 MPa, a significant increase in growth rate has also been observed in GM 3 strain with 5 mmol l(-1) and in GM 4 strain with 10 and 20 mmol l(-1). CONCLUSIONS: This study showed that the imperfecti fungi Aspergillus spp., Penicillium spp., Trichoderma spp., Cladosporium spp. and Paecilomyces spp. are isolated as prevalent groups in agricultural soil exposed to pesticides, and the capacity of nontoxigenic A. flavus strains to tolerate different glyphosate concentrations under different water potential (MPa) conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This manuscript makes a contribution to the knowledge of cultivable fungal populations from agricultural soils exposed to pesticides and the glyphosate tolerance of A. flavus strains.\",\n \"corpus_id\": 2270156,\n \"score\": 1\n },\n {\n \"doc_id\": \"26115994\",\n \"title\": \"Arbuscular mycorrhizal fungal diversity, root colonization, and soil alkaline phosphatase activity in response to maize-wheat rotation and no-tillage in North China.\",\n \"abstract\": \"Monitoring the effects of no-tillage (NT) in comparison with conventional tillage (CT) on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to compare the species composition and ecological function of soil arbuscular mycorrhizal (AM) fungi during the growth and rotation of crops under NT and CT. From late June 2009 to early June 2010, 32 topsoil (0-15 cm) samples from four individual plots per treatment (CT and NT) were collected at both the jointing and maturation stages of maize (Zea mays L.) and wheat (Triticum aestivum L.) from a long-term experimental field that was established in an Aquic Inceptisol in North China in June 2006. The AM fungal spores were isolated and identified and then used to calculate species diversity indices, including the Shannon- Wiener index (H'), Evenness (E), and Simpson's index (D). The root mycorrhizal colonization and soil alkaline phosphatase activity were also determined. A total of 34 species of AM fungi within nine genera were recorded. Compared with NT, CT negatively affected the soil AM fungal community at the maize sowing stage, leading to decreases in the average diversity indices (from 2.12, 0.79, and 0.82 to 1.79, 0.72, and 0.74 for H', E, and D, respectively), root mycorrhizal colonization (from 28% to 20%), soil alkaline phosphatase activity (from 0.24 to 0.19 mg/g/24 h) and available phosphorus concentration (from 17.4 to 10.5 mg/kg) at the maize jointing stage. However, reductions in diversity indices of H', E, and D were restored to 2.20, 0.81, and 0.84, respectively, at the maize maturation stage. CT should affect the community again at the wheat sowing stage; however, a similar restoration in the species diversity of AM fungi was completed before the wheat jointing stage, and the highest Jaccard index (0.800) for similarity in the species composition of soil AM fungi between CT and NT was recorded at the wheat maturation stage. Our results also demonstrated that NT resulted in the positive protection of the community structure of AM fungi and played an important role in maintaining their functionality especially for maize seedlings.\",\n \"corpus_id\": 6222288,\n \"score\": 1\n },\n {\n \"doc_id\": \"26527297\",\n \"title\": \"Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.\",\n \"abstract\": \"Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.\",\n \"corpus_id\": 7234128,\n \"score\": 1\n },\n {\n \"doc_id\": \"27429478\",\n \"title\": \"Struvite: a slow-release fertiliser for sustainable phosphorus management?\",\n \"abstract\": \"BACKGROUND AND AIM: Recycled sources of phosphorus (P), such as struvite extracted from wastewater, have potential to substitute for more soluble manufactured fertilisers and help reduce the long-term threat to food security from dwindling finite reserves of phosphate rock (PR). This study aimed to determine whether struvite could be a component of a sustainable P fertiliser management strategy for arable crops. METHODS: A combination of laboratory experiments, pot trials and mathematical modelling of the root system examined the P release properties of commercial fertiliser-grade struvite and patterns of P uptake from a low-P sandy soil by two different crop types, in comparison to more soluble inorganic P fertilisers (di-ammonium phosphate (DAP) and triple super phosphate (TSP)). RESULTS: Struvite had greatly enhanced solubility in the presence of organic acid anions; buckwheat, which exudes a high level of organic acids, was more effective at mobilising struvite P than the low level exuder, spring wheat. Struvite granules placed with the seed did not provide the same rate of P supply as placed DAP granules for early growth of spring wheat, but gave equivalent rates of P uptake, yield and apparent fertiliser recovery at harvest, even though only 26 % of struvite granules completely dissolved. Fertiliser mixes containing struvite and DAP applied to spring wheat have potential to provide both optimal early and late season P uptake and improve overall P use efficiency. CONCLUSIONS: We conclude that the potential resource savings and potential efficiency benefits of utilising a recycled slow release fertiliser like struvite offers a more sustainable alternative to only using conventional, high solubility, PR-based fertilisers.\",\n \"corpus_id\": 10561990,\n \"score\": 1\n },\n {\n \"doc_id\": \"28087930\",\n \"title\": \"Fungal Ecology: Principles and Mechanisms of Colonization and Competition by Saprotrophic Fungi.\",\n \"abstract\": \"Decomposer fungi continually deplete the organic resources they inhabit, so successful colonization of new resources is a crucial part of their ecology. Colonization success can be split into (i) the ability to arrive at, gain entry into, and establish within a resource and (ii) the ability to persist within the resource until reproduction and dissemination. Fungi vary in their life history strategies, the three main drivers of which are stress (S-selected), disturbance (ruderal, or R-selected), and incidence of competitors (C-selected); however, fungi often have combinations of characteristics from different strategies. Arrival at a new resource may occur as spores or mycelium, with successful entry and establishment (primary resource capture) within the resource largely dependent on the enzymatic ability of the fungus. The communities that develop in a newly available resource depend on environmental conditions and, in particular, the levels of abiotic stress present (e.g., high temperature, low water availability). Community change occurs when these initial colonizers are replaced by species that are either more combative (secondary resource capture) or better able to tolerate conditions within the resource, either through changing abiotic conditions or due to modification of the resource by the initial colonizers. Competition for territory may involve highly specialized species-specific interactions such as mycoparasitism or may be more general; in both cases combat involves changes in morphology, metabolism, and reactive oxygen species production, and outcomes of these interactions can be altered under different environmental conditions. In summary, community development is not a simple ordered sequence, but a complex ever-changing mosaic.\",\n \"corpus_id\": 3409003,\n \"score\": 1\n },\n {\n \"doc_id\": \"18365728\",\n \"title\": \"[Diversity of facultatively anaerobic microscopic mycelial fungi in soils].\",\n \"abstract\": \"The numbers of microscopic fungi isolated from soil samples after anaerobic incubation varied from tens to several hundreds of CFU per one gram of soil; a total of 30 species was found. This group is composed primarily of mitotic fungi of the ascomycete affinity belonging to the orders Hypocreales (Fusarium solani, F. oxysporum, Fusarium sp., Clonostachys grammicospora, C. rosea. Acremonium sp., Gliocladium penicilloides, Trichoderma aureoviride, T. harzianum, T. polysporum, T. viride. T. koningii, Lecanicillum lecanii, and Tolypocladium inflatum) and Eurotiales (Aspergillus terreus, A. niger, and Paecilomyces lilacimus), as well as to the phylum Zygomycota, to the order Mucorales (Actinomucor elegans, Absidia glauca, Mucor circinelloides, M. hiemalis, M. racemosus, Mucor sp., Rhizopus oryzae, Zygorrhynchus moelleri, Z. heterogamus, and Umbelopsis isabellina) and the order Mortierellales (Mortierella sp.). As much as 10-30% of the total amount of fungal mycelium remains viable for a long time (one month) under anaerobic conditions.\",\n \"corpus_id\": 19715218,\n \"score\": 0\n },\n {\n \"doc_id\": \"19207833\",\n \"title\": \"Antagonism of Microsporum species by soil fungi.\",\n \"abstract\": \"Eighteen fungi isolated from soil by hair bating method were tested against soil inhabiting Microsporum equinum, Microsporum fulvum, Microsporum gypseum and Microsporum racemosum for their antagonistic interactions. Colony inhibition during dual cultures showed inhibition of all the four Microsporum species. The maximum inhibition of M. equinum, M. fulvum, M. gypseum and M. racemosum was caused by Chrysosporium keratinophilum, Chrysosporium tropicum, Curvularia lunata and Chrysosporium lucknowense in dual cultures. On the other hand, M. fulvum showed maximum inhibition of Macrophomina phaseolina (70.1%) while M. equinum, M. gypseum and M. racemosum showed maximum inhibition of Colletotrichum gloeosporoides. Staling products of C. lucknowense accelerated growth of all Microsporum species, C. keratinophilum 3 and Chrysosporium evolceaunui and M. phaseolina accelerated growth of two species of Microsporum. Staling product of Alternaria alternata was most inhibitory. Culture filtrates of Trichophyton vanbreseughemii accelerated the growth of all the four Microsporum species and C. tropicum, C. lucknowense accelerated growth of two species, while Botryotrichum piluliferum accelerated growth of three species of Microsporum. Volatiles showed inhibition of all the Microsporum species ranging from 0.33 to 57.2% except in case of M. fulvum. Lysis of Microsporum mycelium was the most common feature.\",\n \"corpus_id\": 9016373,\n \"score\": 0\n },\n {\n \"doc_id\": \"19579778\",\n \"title\": \"[Antagonistic interactions between saprotrophic fungi and geohelminths. 1. Saprotrophic fungi in the biological control of phytopathogenic geohelminths].\",\n \"abstract\": \"Antagonistyczne interakcje miedzy grzybami saprotroficz- nymi a geohelmintami. 1. Grzyby saprotroficzne w walce biologicznej z nicieniami fitopatogenicznymi. The state of knowledge on the possible antagonism between soil saprotrophic fungi and phytopathogenic nematodes of the genera Meloidogyne, Heterodera, and Globodera is reviewed basing on the literature and our own research. Mycelial colonisation of various developmental stages of these geohelminths is the most common factor thought to reduce their populations in nature. The following parasitic fungi can be found on the cysts, eggs, as well as the larvae of the nematodes: Paecilomyces lilacinus, Verticillium chlamydosporium, Cylindrocarpon destructans, Pochonia chlamydosporia, Fusarium spp., and Penicillium spp. The fungi invade the nematodes, such as Heterodera, Globodera, or Meloidogyne, \\\"passively\\\" penetrating through the natural orifices of the cysts, eggs, and larvae of the host. Equally frequent, however, is a biochemical action of the fungi prior to colonisation, which is linked with production of mycotoxirls or hydrolytic enzymes. Such an active way of fungal penetration of various stages of the phytopathogenic nematodes has been observed in Pochonia chlamydosporia, Penicillium verrucosum var. cyclopium, P. frequentans, Sclerotinia rolfsii, Rhizoctonia solani, and Fusarium spp. Triacylglycerols (TAG), phenols, as well as trichothecene, T-2, have been found in the metabolites extracted from mycelia of these species. Predation by fungi is also a factor that may reduce a population of phytopathogenic nematodes. This form of antagonism is characteristic for nematicidal fungi of the genera Arthrobotrys and Dactylella. These fungi form shrinking rings and hooks in their mycelia by which the fungus entangles and paralyses a migrating form of nematode. Despite the fact that the antagonism between fungi and nematodes is a commonly occurring phenomenon observed in the soil, the nematicidal and nematotoxic properties of fungi have not a wide application in biological plant protection. Up till now, only the bionematicides based on Arthrobotrys robusta (Royal 300 and Royal 350) as well as Paecilomyces lilacinus (Biocon and PL Plus) have found its commercial application.\",\n \"corpus_id\": 41740188,\n \"score\": 0\n },\n {\n \"doc_id\": \"19579779\",\n \"title\": \"[Antagonistic interactions between saprotrophic fungi and geohelminths. 2. Saprotrophic fungi in biocontrol of parasitic geohelminths of humans and animals].\",\n \"abstract\": \"Antagonistyczne interakcje miedzy grzybami saprotroficznymi a geohelmintami. 2. Grzyby saprotroficzne w bioregulacji pasozytniczych geohelmintów człowieka i zwierzat. The soils ecosystem plays an important role in the epidemiology of geohelminth diseases of humans and animals. Soil contamination with ova of the parasitic geohelminths represents a global public health-hazard issue. Biological agents have been thought to control the infective forms of parasites present in the soil. Biocontrol of geohelminths represents an alternative to pesticides (i.e., nematicides), which are not efficient in killing infective nematode forms and, additionally, result in the environment pollution and long-term disturbances in the soil ecosystem homeostasis. The degree of the inhibiting effect of soil saprotrophic fungi on geohelminth embryonic development varies and depends on the species. A number of fungi cause various morphological disorders in the embryos of developing parasitic nematodes, but also have an ovicidal effect. Although the nature of the antagonism between fungi and other living organisms has not been fully explained, it is certain that mycotoxins and fungal enzymes constitute its important components. Considering the studies carried out so far, the antagonistic effect of mold fungi against the infective stages of geohelminths can be fully recommended as a real control factor, especially as these saprotrophs represent a natural factor within the soil environment, that is of particular biochemical activity.\",\n \"corpus_id\": 24760768,\n \"score\": 0\n },\n {\n \"doc_id\": \"19932506\",\n \"title\": \"Phytoremediation of petroleum-polluted soils: application of Polygonum aviculare and its root-associated (penetrated) fungal strains for bioremediation of petroleum-polluted soils.\",\n \"abstract\": \"Petroleum-polluted soils are a common disaster in many countries. Bioremediation of oil contamination in soils is based on the stimulation of petroleum-hydrocarbon-degrading fungal and microbial communities. A field study was conducted in a petroleum-contaminated site to find petroleum-resistant plants and their root-associated fungal strains for use in bioremediation of petroleum-polluted soils. Results and observations showed that the amounts of petroleum pollution in nonvegetated soils were several times higher than in vegetated soils. Plants collected from petroleum-polluted areas were identified using morphological characters. Results indicated that seven plant species were growing on the contaminated sites: Alhaji cameleron L. (Fabaceae), Amaranthus retroflexus L. var. retroflexus (Amaranthaceae), Convolvulus arvensis L. (Convolvulaceae), Chrozophora hierosolymitana Spreg. ( Euphorbiaceae), Noea mucronata L. (Boraginaceae), Poa sp. (Poaceae), and Polygonum aviculare L. (Polygonaceae). The root-associated fungi of each plant were determined and results showed the presence of 11 species that associated with and also penetrated the roots of plants growing in the polluted areas. Altenaria sp. was common to all of the plants and the others had species-specific distribution within the plants. The largest numbers of fungal species (six) were determined for P. aviculare and Poa sp. in polluted areas. However, the variation of fungal strains in the plants collected from petroleum-polluted areas was greater than for nonpolluted ones. Culture of fungi in oil-contaminated media showed that all the studied fungi were resistant to low petroleum pollution (1% v/v) and a few species, especially Fusarium species, showed resistance to higher petroleum pollution (10% v/v) and may be suitable for bioremediation in highly polluted areas. Bioremediation tests with P. aviculare, with and without fungal strains, showed that application of both the plant and its root-associated fungal strains was more effective than of the plant and fungi separately, and Fusarium species were the most effective. Results indicated that fungal strains had the main role in bioremediation of petroleum-polluted soils, but plant roots enhanced the process.\",\n \"corpus_id\": 35676511,\n \"score\": 0\n },\n {\n \"doc_id\": \"21459413\",\n \"title\": \"Biological removal of arsenic pollution by soil fungi.\",\n \"abstract\": \"Fifteen fungal strains were isolated from arsenic contaminated (range 9.45-15.63 mg kg(-1)) agricultural soils from the state of West Bengal, India. Five fungal strains were belonged to the Aspergillus and Trichoderma group each, however, remaining five were identified as the Neocosmospora, Sordaria, Rhizopus, Penicillium and sterile mycelial strain. All these fungal strains were cultivated on medium supplemented with 100, 500, 1000, 5000 and 10,000 mg l(-1) of sodium arsenate. After 30-day cultivation under laboratory conditions, radial growth of these strains was determined and compared with control. Toxicity and tolerance of these strains to arsenate were evaluated on the basis of tolerance index. Out of fifteen, only five fungal strains were found resistant and survived with tolerance index pattern as 0.956 (sterile mycelial strain)>0.311 (Rhizopus sp.)>0.306 (Neocosmospora sp.)>0.212 (Penicillium sp.)>0.189 (Aspergillus sp.) at 10,000 mg l(-1) of arsenate. The arsenic removal efficacy of ten fungal strains, tolerant to 5000 mg l(-1) arsenate, was also assayed under laboratory conditions for 21 days. All these strains were cultivated individually on mycological broth enriched with 10 mg l(-1) of arsenic. The initial and final pH of cultivating medium, fungal biomass and removal of arsenic by each fungal strain were evaluated. Fungal biomass of ten strains removed arsenic biologically from the medium which were ranged from 10.92 to 65.81% depending on fungal species. The flux of biovolatilized arsenic was determined indirectly by estimating the sum of arsenic content in fungal biomass and medium. The mean percent removal as flux of biovolatilized arsenic ranged from 3.71 to 29.86%. The most effective removal of arsenic was observed in the Trichoderma sp., sterile mycelial strain, Neocosmospora sp. and Rhizopus sp. fungal strains. These fungal strains can be effectively used for the bioremediation of arsenic-contaminated agricultural soils.\",\n \"corpus_id\": 45192270,\n \"score\": 0\n },\n {\n \"doc_id\": \"21470255\",\n \"title\": \"Growth of saprotrophic fungi and bacteria in soil.\",\n \"abstract\": \"Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed.\",\n \"corpus_id\": 19771072,\n \"score\": 0\n },\n {\n \"doc_id\": \"21613136\",\n \"title\": \"The fungi: 1, 2, 3 ... 5.1 million species?\",\n \"abstract\": \"PREMISE OF THE STUDY: Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. METHODS: Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. KEY RESULTS: Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. CONCLUSIONS: Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.\",\n \"corpus_id\": 24817330,\n \"score\": 0\n },\n {\n \"doc_id\": \"22022665\",\n \"title\": \"Isolation and identification of microbes associated with mobile phones in Dammam in eastern Saudi Arabia.\",\n \"abstract\": \"OBJECTIVE: This study was conducted to determine microbial contamination of mobile phones in the city of Dammam, in the eastern region of Saudi Arabia, and identify the most important microbial species associated with these phones in order to take the necessary remedial measures. MATERIALS AND METHODS: The analysis of a total of 202 samples was done to identify fungal and pathogenic bacteria isolates. Sterile swabs were firmly passed on the handset, the buttons and the screens of mobile phones, then inoculated into media of bacteria and fungi. Frequency distribution of isolates were calculated. RESULTS: There were 737 isolated of the following bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, Neisseria sicca, Micrococcus luteus, Proteus mirabilis, Bacillus subtilis, and Enterobacter aerogenes at the rate of 56.58, 13.57, 8.01, 7.73, 6.51, 3.66, 2.85 and 1.09% respectively. There were fungal isolates as follows: Alternaria alternata, Aspergillus niger, Cladosporium sp., Penicillium spp., Aspergillus flavus, Aspergillus fumigatus, Rhizopus stolonifer, Aspergillus ochraceus at the rate of 29.07, 26.74, 20.93, 10.47, 6.98, 2.33, 2.33, 1.16%, respectively. CONCLUSIONS: The study showed that all mobile phones under consideration were infected by several microbes, most of which belonged to the natural flora of the human body as well as airborne fungi and soil. This means that it is necessary to sterilize hands after contact with a phone since it is a source of disease transmission.\",\n \"corpus_id\": 21588945,\n \"score\": 0\n },\n {\n \"doc_id\": \"22808743\",\n \"title\": \"[Anaerobic growth ability and alcohol fermentation activity of microscopic fungi].\",\n \"abstract\": \"The method proposed in this study was used to isolate fungi grown under anaerobic conditions and to reveal distinctions in their abundance and species composition in different habitats. The ability of micromycetes of different taxa to grow under anaerobic conditions and ensure alcohol fermentation was determined for a representative sample (344 strains belonging to more than 60 species). The group of fungi growing under anaerobic conditions included species with high, moderate, and low fermentation activity. The ability for anaerobic growth and fermentation depended on the taxonomic affiliation of fungi. In some cases, the expression of these characteristics depended on the habitat from which the strain was isolated. The maximum level of ethanol accumulation in culture liquid (1.2-4.7%) was detected for Absidia spinosa, Aspergillus sp. of group flavus, Aspergillus terreus, Acremonium sp., Mucor circinelloides, Mucor sp., Fusarium oxysporum, F. solani, F. sambucinum, Rhizopus arrhizus var. Arrhizus, Trichoderma atroviride, and Trichoderma sp.\",\n \"corpus_id\": 19325427,\n \"score\": 0\n },\n {\n \"doc_id\": \"23115506\",\n \"title\": \"Diversity of Culturable Soil Micro-fungi along Altitudinal Gradients of Eastern Himalayas.\",\n \"abstract\": \"Very few studies have addressed the phylogenetic diversity of fungi from Northeast India under the Eastern Himalayan range. In the present study, an attempt has been made to study the phylogenetic diversity of culturable soil fungi along the altitudinal gradients of eastern Himalayas. Soil samples from 24 m above sea level to 2,000 m above sea level altitudes of North-East India were collected to investigate soil micro-fungal community structure and diversity. Molecular characterization of the isolates was done by PCR amplification of 18S rDNA using universal primers. Phylogenetic analysis using BLAST revealed variation in the distribution and richness of different fungal biodiversity over a wide range of altitudes. A total of 107 isolates were characterized belonging to the phyla Ascomycota and Zygomycota, corresponding to seven orders (Eurotiales, Hypocreales, Calosphaeriales, Capnodiales, Pleosporales, Mucorales, and Mortierellales) and Incertae sedis. The characterized isolates were analysed for richness, evenness and diversity indices. Fungal diversity had significant correlation with soil physico-chemical parameters and the altitude. Eurotiales and Hypocreales were most diverse and abundant group of fungi along the entire altitudinal stretch. Species of Penicillium (D = 1.44) and Aspergillus (D = 1.288) were found to have highest diversity index followed by Talaromyces (D = 1.26) and Fusarium (D = 1.26). Fungal distribution showed negative correlation with altitude and soil moisture content. Soil temperature, pH, humidity and ambient temperature showed positive correlation with fungal distribution.\",\n \"corpus_id\": 10422794,\n \"score\": 0\n },\n {\n \"doc_id\": \"23143287\",\n \"title\": \"Filamentous fungi transported by birds during migration across the mediterranean sea.\",\n \"abstract\": \"The potential for the transport and diffusion of some pathogenic microorganisms by migratory birds is of concern. Migratory birds may be involved in the dispersal of microorganisms and may play a role of mechanical and biological vectors. The efficiency of dispersal of pathogenic microorganisms depends on a wide range of biotic and abiotic factors that influence the survival or disappearance of a given agent in a geographical area. In the present study, 349 migratory birds were captured in four sites (Mazara del Vallo, Lampedusa, Ustica and Linosa), representing the main stop-over points during spring and autumnal migration, and analyzed for the presence of filamentous fungi. A total of 2,337 filamentous fungi were isolated from 216 birds and identified by a combined phenotypic-genotypic approach to species level. Twelve species were identified in the study, with Cladosporium cladosporioides, Alternaria alternata, and Aspergillus niger as the most abundant. The transport of these fungal species isolated in this study is of considerable importance because some of these species can create dangers to human health.\",\n \"corpus_id\": 15725008,\n \"score\": 0\n },\n {\n \"doc_id\": \"23410063\",\n \"title\": \"In vitro antifungal activity of silver nanoparticles against ocular pathogenic filamentous fungi.\",\n \"abstract\": \"PURPOSE: Fungal keratitis is emerging as a major cause of vision loss in a developing country such as China because of higher incidence and the unavailability of effective antifungals. It is urgent to explore broad-spectrum antifungals to effectively suppress ocular fungal pathogens, and to develop new antifungal eye drops to combat this vision-threatening infection. The aim of this study is to investigate the antifungal activity of silver nanoparticles (nano-Ag) in comparison with that of natamycin against ocular pathogenic filamentous fungi in vitro. METHODS: Susceptibility tests were performed against 216 strains of fungi isolated from patients with fungal keratitis from the Henan Eye Institute in China by broth dilution antifungal susceptibility test of filamentous fungi approved by the Clinical and Laboratory Standards Institute M38-A document. The isolates included 112 Fusarium isolates (82 Fusarium solani species complex, 20 Fusarium verticillioides species complex, and 10 Fusarium oxysporum species complex), 94 Aspergillus isolates (61 Aspergillus flavus species complex, 11 Aspergillus fumigatus species complex, 12 Aspergillus versicolor species complex, and 10 Aspergillus niger species complex), and 10 Alternaria alternata isolates. The minimum inhibitory concentration (MIC) range and mode, the MIC for 50% of the strains tested (MIC50 value), and the MIC90 value were provided for the isolates with the SPSS statistical package. RESULTS: MIC50 value of nano-Ag were 1, 0.5, and 0.5 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of nano-Ag were 1, 1, and 1 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC50 values of natamycin were 4, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of natamycin were 8, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. CONCLUSIONS: Nano-Ag, relative to natamycin, exhibits potent in vitro activity against ocular pathogenic filamentous fungi.\",\n \"corpus_id\": 37031252,\n \"score\": 0\n },\n {\n \"doc_id\": \"23534981\",\n \"title\": \"Biological interactions between soil saprotrophic fungi and Ascaris suum eggs.\",\n \"abstract\": \"The in vitro effect of saprotrophic soil fungi on the embryonic development of Ascaris suum was evaluated. The fungi tested were Aspergillus fumigatus, Aspergillus terreus, Penicillium citrinum, Penicillium expansum, Fusarium oxysporum and Trichothecium roseum, isolated from children's recreation areas in the city of Lodz (Poland). Each species was co-cultured with A. suum egg suspension (6 × 10(3)eggs/ml) at 25 ± 2°C for 60 days. Each day, 100 eggs were randomly collected and their developmental stage was classified macroscopically. Additionally, at days 4, 7, 14, 28, 42 and 60 of incubation, the viability and the percentage of eggs with morphological altered embryo/larva were determined in each sample. Microscopic examination revealed that exposure of eggs to the mycelium of examined fungi inhibited embryogenesis of A. suum. All control culture eggs reached L2 larval stage after 26 days of incubation, while the experimental cultures did so after 32-51 days, depending on the fungal species. Three species were found to exhibit very high inhibitory activity on A. suum egg development: A. terreus, P. expansum and F. oxysporum. Embryopathies and non-viable embryos/larvae were observed significantly more frequently in the eggs co-cultured with fungal species than in control cultures. The fungus-exposed eggs revealed morphological alternations in the early zygotic cleavage, blastula, gastrula and larval stages. After 60 days of incubation with mycelia of P. expansum, A. terreus and F. oxysporum, the mortality of the larvae reached 55.3-60.3%. P. expansum and F. oxysporum showed hyphal penetration and internal egg colonization of A. suum eggs.\",\n \"corpus_id\": 5744976,\n \"score\": 0\n },\n {\n \"doc_id\": \"23997619\",\n \"title\": \"Effect of some food preservatives on the lipolytic activity of beef luncheon fungi.\",\n \"abstract\": \"Beef luncheon meat is one of the most popular meals in several countries in the world including Egypt. Thirty one fungal species and 3 species varieties were recovered from 30 samples of beef luncheon meat collected from different supermarkets in Qena. Alternaria, Aspergillus, Emericella, Mucor, Mycosphaerella, Penicillium and Rhizopus were the most common genera on the two types of media. From the above genera, the most prevalent species were Alternaria alternate, Aspergillus flavus, A. fumigatus, A. niger, A. terreus, Emericella nidulans, Mucor racemosus, Mycosphaerella tassiana, Penicillium chrysogenum and Rhizopus stolonifer. Screening of fungi for their abilities to produce lipase enzyme showed that, ten isolates represented 32.26% of total isolates appeared high lipase production, while sixteen isolates (51.61%) were moderate and 5 isolates (16.13%) were low producers. Aspergillus niger, Fusarium oxysporum and Nectria haematococca produced the highest amount of lipase enzyme, so these fungi were used in further studies. The incorporation of five food preservatives (Disodium phosphate, sodium benzoate, citric acid, potassium sorbate and sodium citrate) individually in the culture medium of lipase production exhibited an inhibitive effect on the mycelial growth and enzyme production by Aspergillus niger, Fusarium oxysporum and Nectria haematococca.\",\n \"corpus_id\": 7061271,\n \"score\": 0\n },\n {\n \"doc_id\": \"24263850\",\n \"title\": \"Conjugation of deoxynivalenol by Alternaria alternata (54028 NRRL), Rhizopus microsporus var. rhizopodiformis (54029 NRRL) and Aspergillus oryzae (5509 NRRL).\",\n \"abstract\": \"Deoxynivalenol (DON, vomitoxin) is a trichothecene mycotoxin which can be considered to be an indicator of Fusarium mycotoxin contamination in grain, feed and food. Recent studies have described the presence of glucose conjugated DON, which is a product of plant metabolism, but there is a lack of information available on DON conjugation by fungi. The aim of the current study was, therefore, to investigate the ability of fungi to metabolize DON into hydrolysable conjugated DON. Alternaria alternata (54028 NRRL) and Rhizopus microsporus var. rhizopodiformis (54029 NRRL) were found to be capable of metabolizing DON into hydrolysable conjugated DON. This ranged from 13-23 % conjugation of DON in potato dextrose agar media and from 11-36 % in corn-based media. There was, however, considerable variation between fungal strains in the ability to conjugate DON as only a slight increase in hydrolysable conjugated DON (1-6 %) was observed when incubating with A. oryzae (5509 NRRL). A. oryzae (5509 NRRL) was also shown to degrade DON (up to 92 %) over 21 days of incubation on corn-based media. The current study shows that conjugation of DON can be achieved through fungal metabolism in addition to being a product of plant metabolism.\",\n \"corpus_id\": 5877764,\n \"score\": 0\n },\n {\n \"doc_id\": \"24494000\",\n \"title\": \"Rye grains and the soil derived from under the organic and conventional rye crops as a potential source of biological agents causing respiratory diseases in farmers.\",\n \"abstract\": \"INTRODUCTION: INTRODUCTION: Due to the specific work environment, farmers are exposed to various biological occupational hazard. Among these factors significant are fungi present in the grain and also in the soil. The fungi may be the cause of human diseases including skin infections, asthma, allergic rhinitis and many others. AIM: The aim of this study was to quantify and identify species of fungi colonizing rye grain samples and the soil under cultivation. MATERIAL AND METHODS: THE MATERIAL CONSISTED OF GRAIN AND SOIL SAMPLES FROM TWO AGRICULTURAL SYSTEMS: organic and conventional. To determine the concentration and composition of fungi in collected samples, two media: Malt Agar (MA, Becton, Dickinson and Company) and Potato Dextrose Agar (PDA, Becton, Dickinson and Company) were used. The composition of species in fungal flora was determined using macroscopic and microscopic methods. The isolates of fungi were ranked in the appropriate classes of biosafety BSL. RESULTS: THE MOST FREQUENTLY ISOLATED FUNGI FROM ORGANIC RYE GRAIN, REGARDLESS OF THE MEDIA USED, WERE SPECIES: Aureobasidium pullulans and Alternaria alternata. In conventional farms, most species isolated from rye grain were: Aureobasidium pullulans, Cladosporium oxysporum, Alternaria alternata and yeast-like fungi. Most often species isolated from the soil was Penicillium citreo-viride. CONCLUSIONS: All the results of the research demonstrate the potential hazard to the health of people working in agriculture. Significant exposure of this professional group is associated with the presence of harmful biological agents present in the grain and soil from its cultivation.\",\n \"corpus_id\": 4136302,\n \"score\": 0\n },\n {\n \"doc_id\": \"24506036\",\n \"title\": \"In vitro antifungal activity of three geophytic plant extracts against three post-harvest pathogenic fungi.\",\n \"abstract\": \"Plant extracts appear to be one of the most effective alternative methods of plant diseases control which are less harmful to human beings and environment. In vitro antifungal activity of methanolic extracts of three promising wild geophytic plants against three post-harvest pathogenic fungi using radial growth technique was conducted. These extracts included the shoot system (S) and underground parts (R) of Asparagus stipularis, Cyperus capitatus and Stipagrostis lanata. The tested fungi were Alternaria solani, Aspergillus niger and Rhizopus stolonifer. The results exhibited that, all plant extracts had antifungal activity against the tested fungi. The antifungal activity greatly varied depending on plant parts and/or plant species. R. stolonifer was the most susceptible fungus to the tested plant extracts followed by A. niger and then A. solani. On the other hand, the most effective plant extracts against tested fungi were S. lanata (S) and A. stipularis (R). The most effective plant extracts against R. stolonifer were S. lanata (R) and C. capitatus (S). While, the extracts of A. stipularis (R) and S. lanata (S) were the most effective against A. niger. The extracts of C. capitatus (S) and S. lanata (S) exhibited the highest antifungal activity against A. solani. The results demonstrated that, the methanolic extracts of A. stipularis, C. capitatus and S. lanata had potential antifungal activity against A. solani, A. niger and R. stolonifer.\",\n \"corpus_id\": 32234282,\n \"score\": 0\n },\n {\n \"doc_id\": \"24732324\",\n \"title\": \"Importance of saprotrophic freshwater fungi for pollen degradation.\",\n \"abstract\": \"Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.\",\n \"corpus_id\": 4583745,\n \"score\": 0\n },\n {\n \"doc_id\": \"25134345\",\n \"title\": \"The effect of saprotrophic fungi on the development and hatching of Fasciola hepatica eggs.\",\n \"abstract\": \"The aim of this study was to determine the effect of 6 common soil fungi species: Alternaria alternata (Fr.) Keissl., Aspergillus candidus Link, Penicillium chrysogenum Thom, P. commune Thom, Trichothecium roseum (Pers.) Link and Ulocladium sp., on the hatching of miracidia, i.e., free living larvae of liver fluke (Fasciola hepatica). To this end, the eggs of F. hepatica were incubated in water in the presence of one of the aforementioned fungi species and in tap water (control) at a temperature of 26 degrees C. At the 15th day of incubation we determined the number of nonembryonated, embryonated and hatched eggs. We observed different degrees of antagonistic influences by the tested fungal strains on the development of F. hepatica eggs. Among the examined fungi, the strongest ovistatic effects were exhibited by Trichothecium roseum, Penicillium chrysogenum (R-3) and P. commune. The study showed no morphological damage to the shells of the F. hepatica eggs which may suggest a biochemical basis of antagonistic interactions by the fungi associated with the activity of fungal enzymes, mycotoxins and antibiotics. Low or no activity of peptide hydrolases in Penicillium chrysogenum and P. commune in the API ZYM test suggests their insignificant role in the degradation of shell proteins ofF. hepatica eggs.\",\n \"corpus_id\": 26185059,\n \"score\": 0\n },\n {\n \"doc_id\": \"25213561\",\n \"title\": \"Diversity of soil fungi in North 24 Parganas and their antagonistic potential against Leucinodes orbonalis Guen. (Shoot and fruit borer of brinjal).\",\n \"abstract\": \"Soil samples were collected from agricultural fields and gardens in North 24 Parganas, West Bengal, and fungi species were isolated from them. Thirty-one fungal species were isolated with 19 found in agricultural soil and 28 in garden soil. Twenty-eight out of 31 were identified using cultural and microscopic characters, and three were unidentified. The diversity of isolated fungi was calculated by Simpson's diversity index. The garden soil possessed more fungal colonies (750) than agricultural soil (477). In agricultural soil, the dominant fungi were Aspergillus niger, Rhizopus oryzae, and Penicillium expansum, and the dominant fungi of garden soil were A. niger and Fusarium moniliforme. Simpson's diversity index indicated that garden soil had more fungal diversity (0.939) than agricultural soil (0.896). The entomopathogenic capacity of the isolated fungi was tested against the brinjal shoot and fruit borer (Leucinodes orbonalis Guen) which is the major insect pest of brinjal. The isolated fungi were screened against larva of L. orbonalis for their entomopathogenic potential. Beauveria bassiana, A. niger, and P. expansum showed appreciable antagonism to L. orbonalis, and their lethal doses with 50 % mortality (LD50s) were 4.0 × 10(7), 9.06 × 10(7), and 1.50 × 10(8) spore/mL, respectively, and their times taken to reach 50 % mortality (LT50s) were 9.77, 10.56, and 10.60 days, respectively. This work suggests the restriction of chemical pesticide application in agricultural fields to increase fungal diversity. The entomopathogenic efficacy of B. bassiana could be used in agricultural fields to increase fugal diversity and protect the brinjal crop.\",\n \"corpus_id\": 27441416,\n \"score\": 0\n },\n {\n \"doc_id\": \"25414142\",\n \"title\": \"Fungi in a changing world: growth rates will be elevated, but spore production may decrease in future climates.\",\n \"abstract\": \"Very little is known about the impact of climate change on fungi and especially on spore production. Fungal spores can be allergenic, thus being important for human health. The aim of this study was to investigate how climate change influences the responsive ability of fungi by simulating differing environmental regimes. Fungal species with high spore allergenic potential and atmospheric abundance were grown and experimentally examined under a variety of temperatures and different nutrient availability. Each represented the average decadal air temperature of the 1980s, 1990s and 2000s in the UK, along with an Intergovernmental Panel on Climate Change (IPCC) climate change scenario for 2100. All tests were run on six fungal species: Alternaria alternata, Aspergillus niger, Botrytis cinerea, Cladosporium cladosporioides, Cladosporium oxysporum and Epicoccum purpurascens. Mycelium growth rate and spore production were examined on each single species and competitive capacity among species combinations in pairs. All fungal species grew faster at higher temperatures, and this was more pronounced for the temperature projection in 2100. Most species grew faster when there was lower nutrient availability. Exceptions were the species with the highest growth rate (E. purpurascens) and with the highest competition capacity (A. alternata). Most species (except for E. purpurascens) produced more spores in the richer nutrient medium but fewer as temperature increased. C. cladosporioides was an exception, exponentially increasing its spore production in the temperature of the 2100 scenario. Regarding competitive capacity, no species displayed any significant alterations within the environmental range checked. It is suggested that in future climates, fungi will display dramatic growth responses, with faster mycelium growth and lower spore production, with questions risen on relevant allergen potential.\",\n \"corpus_id\": 9698981,\n \"score\": 0\n },\n {\n \"doc_id\": \"26022406\",\n \"title\": \"Targeting allergenic fungi in agricultural environments aids the identification of major sources and potential risks for human health.\",\n \"abstract\": \"Fungi are, after pollen, the second most important producers of outdoor airborne allergens. To identify sources of airborne fungal allergens, a workflow for qPCR quantification from environmental samples was developed, thoroughly tested, and finally applied. We concentrated on determining the levels of allergenic fungi belonging to Alternaria, Cladosporium, Fusarium, and Trichoderma in plant and soil samples from agricultural fields in which cereals were grown. Our aims were to identify the major sources of allergenic fungi and factors potentially influencing their occurrence. Plant materials were the main source of the tested fungi at and after harvest. Amounts of A. alternata and C. cladosporioides varied significantly in fields under different management conditions, but absolute levels were very high in all cases. This finding suggests that high numbers of allergenic fungi may be an inevitable side effect of farming in several crops. Applied in large-scale studies, the concept described here may help to explain the high number of sensitization to airborne fungal allergens.\",\n \"corpus_id\": 52810782,\n \"score\": 0\n },\n {\n \"doc_id\": \"26348882\",\n \"title\": \"Soil fungi for mycoremediation of arsenic pollution in agriculture soils.\",\n \"abstract\": \"AIMS: Soil arsenic (As) contamination of food-chains and public health can be mitigated through fungal bioremediation. To enumerate culturable soil fungi, soils were collected from the As-contaminated paddy fields (3-35 mg kg(-1) ) of the middle Indo-Gangetic Plains. METHODS AND RESULTS: Total 54 fungal strains were obtained and identified at their molecular level. All strains were tested for As tolerance (from 100 to 10,000 mg l(-1) arsenate). Fifteen fungal strains, tolerant to 10,000 mg l(-1) arsenate, were studied for As removal in-vivo for 21 days by cultivating them individually in potato dextrose broth enriched with 10 mg l(-1) As. The bioaccumulation of As in fungal biomass ranged from 0·023 to 0·259 g kg(-1). The biovolatilized As ranged from 0·23 to 6·4 mg kg(-1). CONCLUSIONS: Higher As bioaccumulation and biovolatilization observed in the seven fungal strains, Aspergillus oryzae FNBR_L35; Fusarium sp. FNBR_B7, FNBR_LK5 and FNBR_B3; Aspergillus nidulans FNBR_LK1; Rhizomucor variabilis sp. FNBR_B9; and Emericella sp. FNBR_BA5. These fungal strains were also tested and found suitable for significant plant growth promotion in the calendula, withania and oat plants in a greenhouse based pot experiment. SIGNIFICANCE AND IMPACT OF STUDY: These fungal strains can be used for As remediation in As-contaminated agricultural soils.\",\n \"corpus_id\": 25803247,\n \"score\": 0\n },\n {\n \"doc_id\": \"26843941\",\n \"title\": \"Mean reproductive traits of fungal assemblages are correlated with resource availability.\",\n \"abstract\": \"Organisms have evolved a fascinating variety of strategies and organs for successful reproduction. Fruit bodies are the reproductive organ of fungi and vary considerably in size and shape among species. Our understanding of the mechanisms underlying the differences in fruit body size among species is still limited. Fruit bodies of saprotrophic fungi are smaller than those of mutualistic ectomycorrhizal fungi. If differences in fruit body size are determined by carbon acquisition, then mean reproductive traits of saprotrophic and ectomycorrhizal fungi assemblages should vary differently along gradients of resource availability as carbon acquisition seems more unpredictable and costly for saprotrophs than for ectomycorrhizal fungi. Here, we used 48 local inventories of fungal fruit bodies (plot size: 0.02 ha each) sampled along a gradient of resource availability (growing stock) across 3 years in the Bavarian Forest National Park in Germany to investigate regional and local factors that might influence the distribution of species with different reproductive traits, particularly fruit body size. As predicted, mean fruit body size of local assemblages of saprotrophic fungi was smaller than expected from the distribution of traits of the regional species pool across central and northern Europe, whereas that of ectomycorrhizal fungi did not differ from random expectation. Furthermore and also as expected, mean fruit body size of assemblages of saprotrophic fungi was significantly smaller than for assemblages of ectomycorrhizal species. However, mean fruit body sizes of not only saprotrophic species but also ectomycorrhizal species increased with resource availability, and the mean number of fruit bodies of both assemblages decreased. Our results indicate that the differences in carbon acquisition between saprotrophs and ectomycorrhizal species lead to differences in basic reproductive strategies, with implications for the breadth of their distribution. However, the differences in resource acquisition cannot explain detailed species distribution patterns at a finer, local scale based on their reproductive traits.\",\n \"corpus_id\": 12412792,\n \"score\": 0\n },\n {\n \"doc_id\": \"27154063\",\n \"title\": \"Effect of plant extracts on book deteriorated fungal species.\",\n \"abstract\": \"The aim of the study was to evaluate the effect of leaf extracts of four plants against some isolated fungal species from deteriorated books. Aqueous, methanol and chloroform extracts of selected plant species were screened in vitro for their antifungal activity against some book deteriorating fungal species. Fifteen species belonging to 09 genera were isolated and identified from infested books in library. Aqueous and solvent extracts of leaves of Azadiracta indica, Callistemon citrinus, Eucalyptus lanceolatus and Pongamia pinnata were tested against some dominant fungal species viz. Chaetomium spiralis, Alternaria alternata, Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus and Rhizopus stolonifer. Solvent extracts exhibited potent inhibitory activity than aqueous extracts. However, these plant extracts exhibited moderate activity against A. flavus, C. spiralis, R. stolonifer and A. alternata.\",\n \"corpus_id\": 5119524,\n \"score\": 0\n },\n {\n \"doc_id\": \"27255701\",\n \"title\": \"Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic.\",\n \"abstract\": \"Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was lower, while saprotrophic fungi was higher in increased snow depth plots relative to controls. [ Correction added on 23 September 2016 after first online publication: In the preceding sentence, the richness of ECM and saprotrophic fungi were wrongly interchanged and have been fixed in this current version.] ECM fungal richness was related to soil NO3 -N, NH4 -N, and K; and saprotrophic fungi to NO3 -N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long-term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respiration, and stored permafrost carbon.\",\n \"corpus_id\": 6493413,\n \"score\": 0\n },\n {\n \"doc_id\": \"28353091\",\n \"title\": \"Diversity of culturable fungi inhabiting petroleum-contaminated soils in Southern Iran.\",\n \"abstract\": \"The present study was aimed at characterising species diversity of fungi inhabiting petroleum-contaminated soils of oil fields in a southern region of Iran. Two different techniques were used for fungal isolation including enrichment on atmospheres of phenolic hydrocarbons and crude oil as substrate. Phylogenetic analysis of the internal transcribed spacer of ribosomal DNA was used for taxonomic identification with additional information from the β-tubulin gene for selected taxa. Overall, 183 strains from 14 genera and five orders were obtained: Pleosporales (Alternaria, Curvularia, Stemphylium, Ulocladium), Chaetothyriales (Exophiala), Eurotiales (Aspergillus), Hypocreales (Acremonium, Emericellopsis, Sarocladium, Stachybotrys, Fusarium, Trichoderma, Beauveria), and Capnodiales (Cladosporium). The most frequently isolated strains belonged to the genera Alternaria, Exophiala and Aspergillus. The crude oil substrate was the most successful isolation method, and among the four hydrocarbon enrichments, toluene substrate yielded the highest number of strains. Enrichment on xylene and benzene also yielded herpotrichiellaceous and other filamentous fungi.\",\n \"corpus_id\": 23473311,\n \"score\": 0\n },\n {\n \"doc_id\": \"28539923\",\n \"title\": \"Analysis on Fungal Diversity in Rhizosphere Soil of Continuous Cropping Potato Subjected to Different Furrow-Ridge Mulching Managements.\",\n \"abstract\": \"Knowledge about fungi diversity following different planting patterns could improve our understanding of soil processes and thus help us to develop sustainable management strategies. The objective of this study was to determine the impact of different furrow-ridge mulching techniques on fungal diversity in rhizosphere soil under continuous cropping system. The investigated treatments were: flat plot without mulch (CK); flat plot with mulch (T1); on-ridge planting with full mulch (T2); on-furrow planting with full mulch (T3); on-ridge planting with half mulch (T4); and on-furrow planting with half mulch (T5). NGS (Illumina) methods and ITS1 sequences were used in monitoring fungi diversity of the potato rhizosphere soil. The fungi diversity in the rhizosphere soil was ranked in the order T5 > T2 > T4 > T1 > CK at the early growth stage and T2 > T3 > T1 > T4 > CK at the late growth stage of potato. The fungal communities found in the rhizosphere soil were Ascomycota, Zygomycota, Basidiomycota, Chytridiomycota, and other unidentified fungal communities. Among the fungal community in the rhizosphere soil, Ascomycota was found to be dominant fungi population, with the highest percentage (89%) in the T5 soil whereas the T2 soils had the lowest percentage (67%). The Fusarium abundance in fully-mulched treated soils was higher than in half-mulched treated soil. The dominant genus in the T4 soil was Mortierella, whereas lower populations (1-2%) of Scutellinia, Cryphonectria, Acremonium, and Alternaria were found in that treatment. Among the eumycetes, the dominant fungal class in all treated soils was the Sordariomycetes, which ranged from 57 to 85% in T2 and T5 soils, respectively. The Fusarium percentages in half-mulched treated soils (T4 and T5) were 55 and 28% lower than that of complete mulched treated soils (T2 and T3), respectively. The cluster analysis results showed that, CK, T4, and T5 treated soils and T1, T2, and T3 treated soils had similarities in microbial compositions, respectively. Potato tuber yield was greater under the on-ridge planting with full mulch (T2) treated soil, followed by on-ridge planting with half-mulch (T4) treated soil. The rhizosphere soil under the on-ridge planting with full-mulch (T2) soil had the highest fungal diversity, suggesting that this management was the best environment for fungi, whereas the on-ridge planting with half-mulch (T4) soil had the minimum abundance of Fusarium.\",\n \"corpus_id\": 33874761,\n \"score\": 0\n },\n {\n \"doc_id\": \"29100947\",\n \"title\": \"Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi.\",\n \"abstract\": \"BACKGROUND: In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections. MATERIALS AND METHODS: We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis. RESULTS: The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results. CONCLUSION: Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.\",\n \"corpus_id\": 4862784,\n \"score\": 0\n },\n {\n \"doc_id\": \"29568759\",\n \"title\": \"Isolation and Molecular Characterization of a Model Antagonistic Pseudomonas aeruginosa Divulging In Vitro Plant Growth Promoting Characteristics.\",\n \"abstract\": \"The use of microbial technologies in agriculture is currently expanding quite rapidly with the identification of new bacterial strains, which are more effective in promoting plant growth. In the present study 18 strains of Pseudomonas were isolated from soil sample of Balochistan coastline. Among isolated Pseudomonas strains four designated as SP19, SP22, PS24, and SP25 exhibited biocontrol activities against phytopathogenic fungi, that is, Rhizopus microsporus, Fusarium oxysporum, Aspergillus niger, Alternaria alternata, and Penicillium digitatum; PS24 identified as Pseudomonas aeruginosa by 16srRNA gene bank accession number EU081518 was selected on the basis of its antifungal activity to explore its potential as plant growth promotion. PS24 showed multiple plant growth promoting attributes such as phosphate solubilization activity, indole acetic acid (IAA), siderophore, and HCN production. In order to determine the basis for antifungal properties, antibiotics were extracted from King B broth of PS24 and analyzed by TLC. Pyrrolnitrin antibiotic was detected in the culture of strain PS24. PS24 exhibited antifungal activities found to be positive for hydrogen cyanide synthase Hcn BC gene. Sequencing of gene of Hcn BC gene of strain PS24 revealed 99% homology with the Pseudomonas aeruginosa strain PA01. The sequence of PS24 had been submitted in gene bank accession number KR605499. Ps. aeruginosa PS24 with its multifunctional biocontrol possessions can be used to bioprotect the crop plants from phytopathogens.\",\n \"corpus_id\": 4085716,\n \"score\": 0\n },\n {\n \"doc_id\": \"29724011\",\n \"title\": \"Endophytic Fungi in Species of Artemisia.\",\n \"abstract\": \"The genus Artemisia, a collection of ~400 hardy herbaceous plant and shrub species, is an important resource contributing to chemistry, medicine, agriculture, industry, and ecology. Its communities of endophytic fungi have only recently begun to be explored. Summarized from studies conducted on the fungal endophytes in Artemisia species, both fungal phylogenetic diversity and the associated bioactivity was examined. Isolations from 14 species of Artemisia have led to 51 genera of fungal endophytes, 28 families, and 18 orders. Endophytes belonged mainly to Ascomycota, except for two taxa of Cantharellales and Sporidiobolales, one taxon of Mucoromycota, and one species of Oomycota. The mostly common families were Pleosporaceae, Trichocomaceae, Leptosphaeriaceae, and Botryosphaeriaceae (relative abundance = 14.89, 8.51, 7.14 and 6.38, respectively). In the search for bioactive metabolites, 27 novel compounds were characterized and 22 metabolites were isolated between 2006 and 2017. The first study on endophytic fungi isolated from species of Artemisia was published but 18 years ago. This summary of recently acquired data illustrates the considerable diversity of biological purposes addressed by fungal endophytes of Artemisia spp.\",\n \"corpus_id\": 13914106,\n \"score\": 0\n },\n {\n \"doc_id\": \"29777126\",\n \"title\": \"Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils.\",\n \"abstract\": \"Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon (14C) dating CO2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41-56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350-400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ13C values of CO2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa.\",\n \"corpus_id\": 21745349,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":71,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29925657\",\n \"title\": \"Recurrent Loss of APOBEC3H Activity during Primate Evolution.\",\n \"abstract\": \"Genes in the APOBEC3 family encode cytidine deaminases that provide a barrier against viral infection and retrotransposition. Of all the APOBEC3 genes in humans, APOBEC3H (A3H) is the most polymorphic: some genes encode stable and active A3H proteins, while others are unstable and poorly antiviral. Such variation in human A3H affects interactions with the lentiviral antagonist Vif, which counteracts A3H via proteasomal degradation. In order to broaden our understanding of A3H-Vif interactions, as well as its evolution in Old World monkeys, we characterized A3H variation within four African green monkey (AGM) subspecies. We found that A3H is highly polymorphic in AGMs and has lost antiviral activity in multiple Old World monkeys. This loss of function was partially related to protein expression levels but was also influenced by amino acid mutations in the N terminus. Moreover, we demonstrate that the evolution of A3H in the primate lineages leading to AGMs was not driven by Vif. Our work suggests that the activity of A3H is evolutionarily dynamic and may have a negative effect on host fitness, resulting in its recurrent loss in primates. IMPORTANCE Adaptation of viruses to their hosts is critical for viral transmission between different species. Previous studies had identified changes in a protein from the APOBEC3 family that influenced the species specificity of simian immunodeficiency viruses (SIVs) in African green monkeys. We studied the evolution of a related protein in the same system, APOBEC3H, which has experienced a loss of function in humans. This evolutionary approach revealed that recurrent loss of APOBEC3H activity has taken place during primate evolution, suggesting that APOBEC3H places a fitness cost on hosts. The variability of APOBEC3H activity between different primates highlights the differential selective pressures on the APOBEC3 gene family.\",\n \"corpus_id\": 49335207\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18299330","title":"Human cytidine deaminase APOBEC3H restricts HIV-1 replication.","abstract":"The human genome encodes seven APOBEC3 (A3) cytidine deaminases with potential antiretroviral activity: A3A, A3B, A3C, A3DE, A3F, A3G, and A3H. A3G was the first identified to block replication of human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. A3F, A3B, and A3DE were shown later to have similar activities. HIV-1 produces a protein called Vif that is able to neutralize the antiretroviral activities of A3DE, A3F, and A3G, but not A3B. Only the antiretroviral activity of A3H remains to be defined due to its poor expression in cell culture. Here, we studied the mechanism impairing A3H expression. When primate A3H sequences were compared, a premature termination codon was identified on the fifth exon of the human and chimpanzee A3H genes, which significantly decreased their protein expression. It causes a 29-residue deletion from the C terminus, and this truncation did not reduce human A3H protein stability. However, the mRNA levels of the truncated gene were significantly decreased. Human A3H protein expression could be restored to a normal level either by repairing this truncation or through expression from a vector containing an intron from human cytomegalovirus. Once expression was optimized, human A3H could reduce HIV-1 infectivity up to 150-fold. Importantly, HIV-1 Vif failed to neutralize A3H activity. Nevertheless, extensive sequence analysis could not detect any significant levels of G-to-A mutation in the HIV-1 genome by human A3H. Thus, A3H inhibits HIV-1 replication potently by a cytidine deamination-independent mechanism, and optimizing A3H expression in vivo should represent a novel therapeutic strategy for HIV-1 treatment.","corpus_id":26270875,"score":2},{"doc_id":"18419775","title":"Conserved and non-conserved features of HIV-1 and SIVagm Vif mediated suppression of APOBEC3 cytidine deaminases.","abstract":"Human cytidine deaminase APOBEC3C (A3C) acts as a potent inhibitor of SIVagm and can be regulated by both HIV-1 and SIVagm Vif. The mechanism by which Vif suppresses A3C is unknown. In the present study, we demonstrate that both HIV-1 and SIVagm Vif can act in a proteasome-dependent manner to overcome A3C. SIVagm Vif requires the Cullin5-ElonginB-ElonginC E3 ubiquitin ligase for the degradation of A3C as well as the suppression of its antiviral activity. Mutation of a residue critical for the species-specific recognition of human or monkey A3G by HIV-1 Vif or SIVagm Vif in A3C had little effect on HIV-1 or SIVagm Vif-mediated degradation of A3C. Although the amino-terminal region of A3G was not important for Vif-mediated degradation, the corresponding region in A3C was critical. A3C mutants that were competent for Vif binding but resistant to Vif-mediated degradation were identified. These data suggest that primate lentiviral Vif molecules have evolved to recognize multiple host APOBEC3 proteins through distinct mechanisms. However, Cul5-E3 ubiquitin ligase appears to be a common pathway hijacked by HIV-1 and SIV Vif to defeat APOBEC3 proteins. Furthermore, Vif and APOBEC3 binding is not sufficient for target protein degradation indicating an important but uncharacterized Vif function.","corpus_id":28949526,"score":2},{"doc_id":"18779051","title":"Antiretroelement activity of APOBEC3H was lost twice in recent human evolution.","abstract":"The primate APOBEC3 gene locus encodes a family of proteins (APOBEC3A-H) with various antiviral and antiretroelement activities. Here, we trace the evolution of APOBEC3H activity in hominoids to identify a human-specific loss of APOBEC3H antiviral activity. Reconstruction of the predicted ancestral human APOBEC3H protein shows that human ancestors encoded a stable form of this protein with potent antiviral activity. Subsequently, the antiviral activity of APOBEC3H was lost via two polymorphisms that are each independently sufficient to destabilize the protein. Nonetheless, an APOBEC3H allele that encodes a stably expressed protein is still maintained at high frequency, primarily in African populations. This stable APOBEC3H protein has potent activity against retroviruses and retrotransposons, including HIV and LINE-1 elements. The surprising finding that APOBEC3H antiviral activity has been lost in the majority of humans may have important consequences for our susceptibility to retroviral infections as well as ongoing retroelement proliferation in the human genome.","corpus_id":25645505,"score":2},{"doc_id":"18827027","title":"Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1.","abstract":"Human cytidine deaminase apolipoprotein B mRNA-editing catalytic polypeptide-like 3 (APOBEC3) proteins have been classified as either Z1- or Z2-type cytidine deaminases on the basis of phylogenetic analysis of their catalytic domains. Despite the identification of a number of Z1-type domain-containing cytidine deaminases, only one copy of Z2-type cytidine deaminase has been detected in each of the mammalian species evaluated thus far. Z1-type human APOBEC3 proteins are known to exhibit broad activities against diverse retroelements. However, the potential role of the only human Z2-type cytidine deaminase, APOBEC3H (A3H), in the restriction of retroelements has not yet been fully characterized. Here, we demonstrate that human A3H is a potent inhibitor of non-LTR LINE-1 transposition. Interestingly, it was also as efficient as A3G in inhibiting Alu retrotransposition, despite its poor association with Alu RNA. We have further demonstrated, for the first time, that human APOBEC3DE is also a potent inhibitor of Alu retrotransposition. Variants of A3H have divergent antiviral activities against HIV-1-Vif-deficient viruses. Unlike the anti-HIV-1 cytidine deaminases A3G and A3F, A3H is moderately regulated by interferons. These observations suggest that human Z2-type cytidine deaminase A3H variants have varying intrinsic abilities to restrict retroelements and that various APOBEC3 proteins may have evolved distinct inhibitory mechanisms against retroelements.","corpus_id":7774191,"score":2},{"doc_id":"18945781","title":"Polymorphisms and splice variants influence the antiretroviral activity of human APOBEC3H.","abstract":"Human APOBEC3H belongs to the APOBEC3 family of cytidine deaminases that potently inhibit exogenous and endogenous retroviruses. The impact of single nucleotide polymorphisms (SNP) and alternative splicing on the antiretroviral activity of human APOBEC3H is currently unknown. In this study, we show that APOBEC3H transcripts derived from human peripheral blood mononuclear cells are polymorphic in sequence and subject to alternative splicing. We found that APOBEC3H variants encoding a SNP cluster (G105R, K121D and E178D, hapII-RDD) restricted human immunodeficiency virus type 1 (HIV-1) more efficiently than wild-type APOBEC3H (hapI-GKE). All APOBEC3H variants tested were resistant to HIV-1 Vif, the viral protein that efficiently counteracts APOBEC3G/3F activity. Alternative splicing of APOBEC3H was common and resulted in variants with distinct C-terminal regions and variable antiretroviral activities. Splice variants of hapI-GKE displayed a wide range of antiviral activities, whereas similar splicing events in hapII-RDD resulted in proteins that uniformly and efficiently restricted viral infectivity (>20-fold). Site-directed mutagenesis identified G105R in hapI-GKE and D121K in hapII-RDD as critical substitutions leading to an average additional 10-fold increase in antiviral activity. APOBEC3H variants were catalytically active and, similarly to APOBEC3F, favored a GA dinucleotide context. HIV-1 mutagenesis as a mode of action for APOBEC3H is suggested by the decrease of restriction observed with a cytidine deaminase domain mutant and the inverse correlation between G-to-A mutations and infectivity. Thus, the anti-HIV activity of APOBEC3H seems to be regulated by a combination of genomic variation and alternative splicing. Since prevalence of hapII-RDD is high in populations of African descent, these findings raise the possibility that some individuals may harbor effective as well as HIV-1 Vif-resistant intracellular antiviral defense mechanisms.","corpus_id":1499288,"score":2},{"doc_id":"19828612","title":"The range of human APOBEC3H sensitivity to lentiviral Vif proteins.","abstract":"The APOBEC3H gene is polymorphic in humans, with four major population-dependent haplotypes that encode proteins with different levels of antiviral activity. Haplotype II, present most frequently in African populations, encodes the most stable protein and is most active against human immunodeficiency virus type 1 (HIV-1). In contrast to human APOBEC3G, which can be completely counteracted by HIV-1 Vif, the protein encoded by APOBEC3H haplotype II is only partially sensitive to Vif, while the protein encoded by APOBEC3H haplotype I is completely resistant to HIV-1 Vif. We mapped a residue on APOBEC3H that determines this partial Vif sensitivity. However, it is unclear how HIV-1 can replicate in vivo without the ability to neutralize APOBEC3H antiviral activity. In order to directly address this question, we cloned vif genes from HIV-1-infected individuals with different APOBEC3H genotypes and tested them for their ability to inhibit human APOBEC3H. We found that while the APOBEC3H genotype of infected individuals significantly influences the activity of Vif encoded by their virus, none of the Vif variants tested can completely neutralize APOBEC3H as well as they neutralize APOBEC3G. Consistent with this genetic result, APOBEC3H protein expression in human peripheral blood mononuclear cells was below our limit of detection using newly developed antibodies against the endogenous protein. These results demonstrate that human APOBEC3H is not as strong of a selective force for current HIV-1 infections as human APOBEC3G.","corpus_id":25846940,"score":2},{"doc_id":"19939923","title":"A single amino acid difference in human APOBEC3H variants determines HIV-1 Vif sensitivity.","abstract":"Several variants of APOBEC3H (A3H) have been identified in different human populations. Certain variants of this protein are particularly potent inhibitors of retrotransposons and retroviruses, including HIV-1. However, it is not clear whether HIV-1 Vif can recognize and suppress the antiviral activity of A3H variants, as it does with other APOBEC3 proteins. We now report that A3H_Haplotype II (HapII), a potent inhibitor of HIV-1 in the absence of Vif, can indeed be degraded by HIV-1 Vif. Vif-induced degradation of A3H_HapII was blocked by the proteasome inhibitor MG132 and a Cullin5 (Cul5) dominant negative mutant. In addition, Vif mutants that were incapable of assembly with the host E3 ligase complex factors Cul5, ElonginB, and ElonginC were also defective for A3H_HapII suppression. Although we found that Vif hijacks the same E3 ligase to degrade A3H_HapII as it does to inactivate APOBEC3G (A3G) and APOBEC3F (A3F), more Vif motifs were involved in A3H_HapII inactivation than in either A3G or A3F suppression. In contrast to A3H_HapII, A3H_Haplotype I (HapI), which differs in only three amino acids from A3H_HapII, was resistant to HIV-1 Vif-mediated degradation. We also found that residue 121 was critical for determining A3H sensitivity and binding to HIV-1 Vif.","corpus_id":11246227,"score":2},{"doc_id":"20519393","title":"Lentiviral Vif degrades the APOBEC3Z3/APOBEC3H protein of its mammalian host and is capable of cross-species activity.","abstract":"All lentiviruses except equine infectious anemia virus (EIAV) use the small accessory protein Vif to counteract the restriction activity of the relevant APOBEC3 (A3) proteins of their host species. Prior studies have suggested that the Vif-A3 interaction is species specific. Here, using the APOBEC3H (Z3)-type proteins from five distinct mammals, we report that this is generally not the case: some lentiviral Vif proteins are capable of triggering the degradation of both the A3Z3-type protein of their normal host species and those of several other mammals. For instance, SIV(mac) Vif can mediate the degradation of the human, macaque, and cow A3Z3-type proteins but not of the sheep or cat A3Z3-type proteins. Maedi-visna virus (MVV) Vif is similarly promiscuous, degrading not only sheep A3Z3 but also the A3Z3-type proteins of humans, macaques, cows, and cats. In contrast to the neutralization capacity of these Vif proteins, human immunodeficiency virus (HIV), bovine immunodeficiency virus (BIV), and feline immunodeficiency virus (FIV) Vif appear specific to the A3Z3-type protein of their hosts. We conclude, first, that the Vif-A3Z3 interaction can be promiscuous and, second, despite this tendency, that each lentiviral Vif protein is optimized to degrade the A3Z3 protein of its mammalian host. Our results thereby suggest that the Vif-A3Z3 interaction is relevant to lentivirus biology.","corpus_id":43424582,"score":2},{"doc_id":"20519396","title":"The localization of APOBEC3H variants in HIV-1 virions determines their antiviral activity.","abstract":"Several members of the human APOBEC3 family of cytidine deaminases can potently restrict retroviruses such as HIV-1. The single-domain APOBEC3H (A3H) is encoded by four haplotypes, of which only A3H haplotype II-RDD (hapII-RDD) restricts HIV-1 efficiently. The goal of this study was to elucidate the mechanisms underlying the differences in antiviral activity among A3H haplotypes. The naturally occurring A3H hapI-GKE and hapII-RDD variants differ at three amino acid positions. A panel of six site-directed mutants containing combinations of the three variable residues was used to determine A3H protein expression, requirements of A3H virion incorporation, and A3H-Gag interactions. The catalytic activity of each A3H protein was assessed directly by using an Escherichia coli mutator assay. We found that the incorporation efficiencies of A3H variants into HIV-1 virions were comparable despite major differences in cellular expression. An assessment of the enzymes' catalytic activities showed that the deaminase activity of each A3H variant correlated with protein expression, suggesting similar enzymatic efficiencies. Surprisingly, virion incorporation experiments using Gag deletion mutants demonstrated that A3H haplotypes interacted with different Gag regions. A3H hapII-RDD associated with nucleocapsid in an RNA-dependent manner, whereas A3H hapI-GKE associated with the C-terminal part of matrix and the N-terminal capsid domain. Our results show that the A3H hapII-RDD interaction with nucleocapsid is critical for its antiviral activity and that the inability of A3H hapI-GKE to interact with nucleocapsid underlies its limited antiviral potential. Thus, the antiviral activity of A3H haplotypes is determined by its incorporation into the viral core, in proximity to the reverse transcription complex.","corpus_id":206797331,"score":2},{"doc_id":"21167246","title":"APOBEC3H haplotypes and HIV-1 pro-viral vif DNA sequence diversity in early untreated human immunodeficiency virus-1 infection.","abstract":"We examined single nucleotide polymorphisms (SNP) in the APOBEC3 locus on chromosome 22, paired with population sequences of pro-viral human immunodeficiency virus-1 (HIV-1) vif from peripheral blood mononuclear cells, from 96 recently HIV-1-infected treatment-naive adults. We found evidence for the existence of an APOBEC3H linkage disequilibrium (LD) block associated with variation in GA → AA, or APOBEC3F/H signature, sequence changes in pro-viral HIV-1 vif sequence (top 10 significant SNPs with a significant p = 4.8 × 10(-3)). We identified a common five position risk haplotype distal to APOBEC3H (A3Hrh). These markers were in high LD (D' = 1; r(2) = 0.98) to a previously described A3H \"RED\" haplotype containing a variant (E121) with enhanced susceptibility to HIV-1 Vif. This association was confirmed by a haplotype analysis. Homozygote carriers of the A3Hrh had lower GA->AA (A3F/H) sequence editing upon pro-viral HIV-1 vif sequence (p = 0.01), and lower HIV-1 RNA levels over time during early, untreated HIV-1 infection, (p = 0.015 mixed effects model). This effect may be due to enhanced susceptibility of A3H forms to HIV-1 Vif mediated viral suppression of sequence editing activity, slowing viral diversification and escape from immune responses.","corpus_id":40941683,"score":2},{"doc_id":"21270145","title":"Analysis of human APOBEC3H haplotypes and anti-human immunodeficiency virus type 1 activity.","abstract":"Human APOBEC3H (A3H) has one cytidine deaminase domain (CDD) and inhibits the replication of retrotransposons and human immunodeficiency virus type 1 (HIV-1) in a Vif-resistant manner. Human A3H has five single amino acid polymorphisms (N15Δ, R18L, G105R, K121D, and E178D), and four haplotypes (I to IV) have previously been identified in various human populations. Haplotype II was primarily found in African-derived populations, and it was the only one that could be stably expressed. Here, we identified three new haplotypes from six human population samples, which we have named V, VI, and VII. Haplotypes V and VII are stably expressed and inhibit HIV-1 replication. Notably, haplotype V was identified in samples from all African-, Asian-, and Caucasian-derived populations studied. Using haplotype VII, we investigated the A3H anti-HIV-1 mechanism. We found that A3H virion packaging is independent of its CDD but dependent on a (112)YYXW(115) motif. This motif binds HIV-1 nucleocapsid in an RNA-dependent manner, and a single Y112A mutation completely disrupts A3H virion incorporation. We further studied the mechanism of A3H resistance to Vif. Although the previously identified APOBEC3G Vif-responsive motif (128)DPDY(131) is not conserved in A3H, placement of this motif into A3H does not make it become less resistant to HIV-1 Vif. We conclude that stably expressed A3H haplotypes may be more broadly distributed in humans than previously realized, and A3H protein is resistant to Vif. These results have important implications for the role of A3H in retrotransposon and HIV-1 inhibition.","corpus_id":2045222,"score":2},{"doc_id":"21653666","title":"Polymorphism in human APOBEC3H affects a phenotype dominant for subcellular localization and antiviral activity.","abstract":"The APOBEC3 family of cytidine deaminases is part of the innate host defense targeted toward retroviruses and retroelements. APOBEC3H is the most distantly related member of the family and carries functional polymorphisms in current human populations. Haplotype II of APOBEC3H, which is more commonly found in individuals of African descent, encodes a protein with the highest antiviral activity in cells, whereas the other haplotypes encode proteins with weak or no antiviral activity. Here, we show that the different human APOBEC3H haplotypes exhibit differential subcellular localizations, as the haplotype I protein is mostly found in the nucleus and the haplotype II protein is mostly localized to the cytoplasm. The determinant responsible for this phenotype maps to a single amino acid that is also important for APOBEC3H protein stability. Furthermore, we show that the cytoplasmic localization is dominant over nuclear localization, by using fusion proteins of APOBEC3H. Our data support a model in which the APOBEC3H protein encoded by haplotype II is actively retained in the cytoplasm by interacting with specific host factors, whereas the less active protein encoded by haplotype I is allowed to enter the nucleus by a passive mechanism. Together, cytoplasmic localization and its link with protein stability correlate with the ability of APOBEC3H to inhibit HIV replication, providing a mechanistic basis for the differential antiviral activities of different APOBEC3H haplotypes.","corpus_id":20683746,"score":2},{"doc_id":"22013041","title":"The activity spectrum of Vif from multiple HIV-1 subtypes against APOBEC3G, APOBEC3F, and APOBEC3H.","abstract":"The APOBEC3 family comprises seven cytidine deaminases (APOBEC3A [A3A] to A3H), which are expressed to various degrees in HIV-1 susceptible cells. The HIV-1 Vif protein counteracts APOBEC3 restriction by mediating its degradation by the proteasome. We hypothesized that Vif proteins from various HIV-1 subtypes differ in their abilities to counteract different APOBEC3 proteins. Seventeen Vif alleles from seven HIV-1 subtypes were tested for their abilities to degrade and counteract A3G, A3F, and A3H haplotype II (hapII). We show that most Vif alleles neutralize A3G and A3F efficiently but display differences with respect to the inhibition of A3H hapII. The majority of non-subtype B Vif alleles tested presented some activity against A3H hapII, with two subtype F Vif variants being highly effective in counteracting A3H hapII. The residues required for activity were mapped to two residues in the amino-terminal region of Vif (positions 39F and 48H). Coimmunoprecipitations showed that these two amino acids were necessary for association of Vif with A3H hapII. These findings suggest that the A3H hapII binding site in Vif is distinct from the regions important for A3G and A3F recognition and that it requires specific amino acids at positions 39 and 48. The differential Vif activity spectra, especially against A3H hapII, suggest adaptation to APOBEC3 repertoires representative of different human ancestries. Phenotypic assessment of anti-APOBEC3 activity of Vif variants against several cytidine deaminases will help reveal the requirement for successful replication in vivo and ultimately point to interventions targeting the Vif-APOBEC3 interface.","corpus_id":25772290,"score":2},{"doc_id":"22023594","title":"A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection.","abstract":"APOBEC3 genes encode cytidine deaminases endowed with the ability to inhibit retroviruses and retrotransposons. These genes have been targets of natural selection throughout primate evolutionary history. We analyzed their selection pattern in human populations observing that APOBEC3F and 3G are neutrally evolving. Conversely, nucleotide diversity was extremely high for APOBEC3H, and most tests rejected the hypothesis of selective neutrality in Eurasian populations. Haplotype analysis and the derived intraallelic nucleotide diversity test indicated that positive selection has driven the increase in frequency of one haplotype (Hap I) outside Africa. Consistently, population genetic differentiation between African and non-African populations was higher than expected under neutrality. A case-control association analysis indicated that Hap I is associated with protection from sexually transmitted HIV-1 infection. Hap I carries a protein-destabilizing variant and a residue conferring resistance to Vif-mediated degradation. Data herein suggest that lower protein stability might have been traded-off with a higher ability to circumvent Vif-mediated hijacking. Alternatively, transcription regulatory variants might represent the selection target. Our data represent an example of how the selective pressures exerted by extinct or unknown viral agents can be exploited to provide valuable information on the allelic determinants of susceptibility to modern infections.","corpus_id":25238486,"score":2},{"doc_id":"22264516","title":"The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict.","abstract":"APOBEC3G (A3G) is a host cytidine deaminase that inhibits retroviruses. HIV and related primate lentiviruses encode Vif, which counteracts A3G by inducing its degradation. This Vif-mediated A3G inhibition is species specific, suggesting that the A3G-Vif interaction has evolved as primate lentiviruses have adapted to their hosts. We examined the evolutionary dynamics of the A3G-Vif interaction within four African green monkey (AGM) subspecies, which are each naturally infected with a distinct simian immunodeficiency virus (SIV). We identified single amino acid changes within A3G in two AGM subspecies that render it resistant to Vif proteins, except for Vif from the viruses that naturally infect these subspecies. Moreover, experimental infection of AGMs shows that Vif can rapidly adapt to these arising Vif-resistant A3G genotypes. These data suggest that despite being generally nonpathogenic in its natural host, SIV infection selects for Vif-resistant forms of A3G in AGM populations, driving Vif counterevolution and functional divergence.","corpus_id":206685798,"score":2},{"doc_id":"22859935","title":"Reduced APOBEC3H variant anti-viral activities are associated with altered RNA binding activities.","abstract":"APOBEC3H (A3H) is a member of the APOBEC3 family of proteins with varying activities against retroviruses and retrotransposons. The A3H gene contains several single nucleotide polymorphisms and up to seven haplotypes have been detected in humans. Although variations in anti-viral function among A3H haplotypes are not fully understood, only 15N105R-containing A3H variants are known to have potent activities against Vif-deficient HIV-1. Unique motif RLYY(F/Y)W of APOBEC3G (A3G) and APOBEC3F (A3F) required for 7SL RNA binding and HIV-1 incorporation is also conserved in all A3H variants. Like A3G, A3H HapII also demonstrated high binding affinity to host small RNAs such as 7SL and Y RNAs. Mutation of a critical amino acid, W115A resulted in reduced expression level, decreased affinity for 7SL RNA, impairment of virion packaging and reduced anti-viral activity. By comparison, A3H HapI had lower binding affinities to host small RNAs and reduced efficiency of virion incorporation, resulting in significantly reduced anti-viral activity. The SNP ΔN15 commonly found in A3H HapIII and HapIV abolished their abilities to associate with RNAs, and A3H HapIIΔ15N failed to package into HIV-1 virions or exhibited any anti-viral activity. Finally, we showed that A3H variants had distinct cellular localization patterns, which correlated with their different RNA binding affinities. Thus, Pol-III RNA such as 7SL RNA binding is a conserved feature of potent anti-HIV human APOBEC3 cytidine deaminases.","corpus_id":3028921,"score":2},{"doc_id":"23359341","title":"Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses.","abstract":"Naturally circulating lentiviruses are abundant in African primate species today, yet their origins and history of transmitting between hosts remain obscure. As a means to better understand the age of primate lentiviruses, we analyzed primate genomes for signatures of lentivirus-driven evolution. Specifically, we studied the adaptive evolution of host restriction factor APOBEC3G (A3G) in Old World Monkey (OWM) species. We find recurrent mutation of A3G in multiple primate lineages at sites that determine susceptibility to antagonism by the lentiviral accessory protein Vif. Using a broad panel of SIV Vif isolates, we demonstrate that natural variation in OWM A3G confers resistance to Vif-mediated degradation, suggesting that adaptive variants of the host factor were selected upon exposure to pathogenic lentiviruses at least 5-6 million years ago (MYA). Furthermore, in members of the divergent Colobinae subfamily of OWM, a multi-residue insertion event in A3G that arose at least 12 MYA blocks the activity of Vif, suggesting an even more ancient origin of SIV. Moreover, analysis of the lentiviruses associated with Colobinae monkeys reveal that the interface of the A3G-Vif interaction has shifted and given rise to a second genetic conflict. Our analysis of virus-driven evolution describes an ancient yet ongoing genetic conflict between simian primates and lentiviruses on a million-year time scale.","corpus_id":17533340,"score":2},{"doc_id":"23469063","title":"The resistance of human APOBEC3H to HIV-1 NL4-3 molecular clone is determined by a single amino acid in Vif.","abstract":"Some human APOBEC3 cytidine deaminases have antiviral activity against HIV-1 and other retroviruses. The single deaminase domain APOBEC3H (A3H) enzyme is highly polymorphic and multiple A3H haplotypes have been identified. A3H haplotype II (A3H-hapII) possesses the strongest activity against HIV-1. There remains, however, uncertainty regarding the extent to which A3H-hapII is sensitive to HIV-1 Vif mediated degradation. We tested, therefore, the two different reference Vif proteins widely used in previous studies. We show that A3H-hapII is resistant to NL4-3 Vif while it is efficiently degraded by LAI Vif. Co-immunoprecipitation assays demonstrate that LAI Vif, but not NL4-3 Vif associates with A3H-hapII. Chimeras between NL4-3 and LAI Vif identify the amino acid responsible for the differential degradation activity: A histidine at position 48 in Vif confers activity against A3H-hapII, while an asparagine abolishes its anti-A3H activity. Furthermore, the amino acid identity at position 48 only affects the degradation of A3H-hapII, whereas recognition of and activity against human A3D, A3F and A3G are only minimally affected. NL4-3 encoding 48H replicates better than NL4-3 WT (48N) in T cell-lines stably expressing A3H hapII, whereas there is no fitness difference in the absence of APOBEC3. These studies provide an explanation for the conflicting reports regarding A3H resistance to Vif mediated degradation.","corpus_id":13985345,"score":2},{"doc_id":"23870316","title":"Gene loss and adaptation to hominids underlie the ancient origin of HIV-1.","abstract":"HIV-1 resulted from cross-species transmission of SIVcpz, a simian immunodeficiency virus that naturally infects chimpanzees. SIVcpz, in turn, is a recombinant between two SIV lineages from Old World monkeys. Lentiviral interspecies transmissions are partly driven by the evolution and capacity of viral accessory genes, such as vpx, vpr, and vif, to antagonize host antiviral factors, such as SAMHD1 and the APOBEC3 proteins. We show that vpx, which in other lentiviruses antagonizes SAMHD1, was deleted during the creation of SIVcpz. This genomic deletion resulted in the reconstruction of the overlapping vif gene by \"overprinting,\" creating a unique vif that overlaps in its 3' end with the vpr gene and can antagonize hominid APOBEC3s. Moreover, passage of SIVs through chimpanzees facilitated the subsequent adaptation of HIV-1 to humans. Thus, HIV-1 originated through a series of gene loss and adaptation events that generated its chimpanzee precursor and lowered the species barrier to human infection.","corpus_id":40520788,"score":2},{"doc_id":"23938749","title":"Host gene evolution traces the evolutionary history of ancient primate lentiviruses.","abstract":"Simian immunodeficiency viruses (SIVs) have infected primate species long before human immunodeficiency virus has infected humans. Dozens of species-specific lentiviruses are found in African primate species, including two strains that have repeatedly jumped into human populations within the past century. Traditional phylogenetic approaches have grossly underestimated the age of these primate lentiviruses. Instead, here we review how selective pressures imposed by these viruses have fundamentally altered the evolutionary trajectory of hosts genes and, even in cases where there now remains no trace of the viruses themselves, these evolutionary signatures can reveal the types of viruses that were once present. Examination of selection by ancient viruses on the adaptive evolution of host genes has been used to derive minimum age estimates for modern primate lentiviruses. This type of data suggests that ancestors of modern SIV existed in simian primates more than 10 Ma. Moreover, examples of host resistance and viral adaptation have implications not only for estimating the age and host range of ancient primate lentiviruses, but also the pathogenic potential of their modern counterparts.","corpus_id":21373490,"score":2},{"doc_id":"23986590","title":"Vif proteins from diverse primate lentiviral lineages use the same binding site in APOBEC3G.","abstract":"APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty mangabey monkeys (SIVsmm), suggesting that the A3G binding site for Vif proteins of the SIVsmm/HIV-2 lineage differs from that of HIV-1. To map the SIVsmm Vif binding site of A3G, we performed immunoprecipitations of individual A3G domains, Vif/A3G degradation assays and a detailed mutational analysis of human A3G. We show that A3G residue 129, but not the adjacent position 128, confers susceptibility to degradation by SIVsmm Vif. An artificial A3G mutant, the P129D mutant, was resistant to degradation by diverse Vifs from HIV-1, HIV-2, SIVagm, and chimpanzee SIV (SIVcpz), suggesting a conserved lentiviral Vif binding site. Gorilla A3G naturally contains a glutamine (Q) at position 129, which makes its A3G resistant to Vifs from diverse lineages. We speculate that gorilla A3G serves as a barrier against SIVcpz strains. In summary, we show that Vif proteins from distinct lineages bind to the same A3G loop, which includes positions 128 and 129. The multiple adaptations within this loop among diverse primates underscore the importance of counteracting A3G in lentiviral evolution.","corpus_id":25032756,"score":2},{"doc_id":"24139399","title":"HIV-1 Vif adaptation to human APOBEC3H haplotypes.","abstract":"Several human APOBEC3 deaminases can inhibit HIV-1 replication in vitro. HIV-1 Vif counteracts this restriction by targeting APOBEC3 for proteasomal degradation. Human APOBEC3H (A3H) is highly polymorphic, with natural variants differing considerably in anti-HIV-1 activity in vitro. To examine HIV-1 adaptation to variation in A3H activity in a natural infection context, we determined the A3H haplotypes and Vif sequences from 76 recently infected HIV-1 patients. We detected A3H-specific Vif changes suggesting viral adaptation. The patient-derived Vif sequences were used to engineer viruses that specifically differed in their ability to counteract A3H. Replication of these Vif-variant viruses in primary T cells naturally expressing active or inactive A3H haplotypes showed that endogenously expressed A3H restricts HIV-1 replication. Proviral DNA from A3H-restricted viruses showed high levels of G-to-A mutations in an A3H-specific GA dinucleotide context. Taken together, our data validate A3H expressed at endogenous levels as a bona fide HIV-1 restriction factor.","corpus_id":22905101,"score":2},{"doc_id":"24189052","title":"Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all.","abstract":"Several members of the APOBEC3 family of cellular restriction factors provide intrinsic immunity to the host against viral infection. Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through hypermutation of the viral genome, inhibition of reverse transcription, and inhibition of viral DNA integration into the host genome. HIV-1 counteracts APOBEC3 proteins by encoding the viral protein Vif, which contains distinct domains that specifically interact with these APOBEC3 proteins to ensure their proteasomal degradation, allowing virus replication to proceed. Here, we review our current understanding of APOBEC3 structure, editing and non-editing mechanisms of APOBEC3-mediated restriction, Vif-APOBEC3 interactions that trigger APOBEC3 degradation, and the contribution of APOBEC3 proteins to restriction and control of HIV-1 replication in infected patients.","corpus_id":7844655,"score":2},{"doc_id":"25122780","title":"Core-binding factor subunit beta is not required for non-primate lentiviral Vif-mediated APOBEC3 degradation.","abstract":"Viral infectivity factor (Vif) is required for lentivirus fitness and pathogenicity, except in equine infectious anemia virus (EIAV). Vif enhances viral infectivity by a Cullin5-Elongin B/C E3 complex to inactivate the host restriction factor APOBEC3. Core-binding factor subunit beta (CBF-β) is a cell factor that was recently shown to be important for the primate lentiviral Vif function. Non-primate lentiviral Vif also degrades APOBEC3 through the proteasome pathway. However, it is unclear whether CBF-β is required for the non-primate lentiviral Vif function. In this study, we demonstrated that the Vifs of non-primate lentiviruses, including feline immunodeficiency virus (FIV), bovine immunodeficiency virus (BIV), caprine arthritis encephalitis virus (CAEV), and maedi-visna virus (MVV), do not interact with CBF-β. In addition, CBF-β did not promote the stability of FIV, BIV, CAEV, and MVV Vifs. Furthermore, CBF-β silencing or overexpression did not affect non-primate lentiviral Vif-mediated APOBEC3 degradation. Our results suggest that non-primate lentiviral Vif induces APOBEC3 degradation through a different mechanism than primate lentiviral Vif. Importance: The APOBEC3 protein family members are host restriction factors that block retrovirus replication. Vif, an accessory protein of lentivirus, degrades APOBEC3 to rescue viral infectivity by forming Cullin5-Elongin B/C-based E3 complex. CBF-β was proved to be a novel regulator of primate lentiviral Vif function. In this study, we found that CBF-β knockdown or overexpression did not affect FIV Vif's function, which induced polyubiquitination and degradation of APOBEC3 by recruiting the E3 complex in a manner similar to that of HIV-1 Vif. We also showed that other non-primate lentiviral Vifs did not require CBF-β to degrade APOBEC3. CBF-β did not interact with non-primate lentiviral Vifs or promote their stability. These results suggest that a different mechanism exists for the Vif-APOBEC interaction and that non-primates are not suitable animal models for exploring pharmacological interventions that disrupt Vif-CBF-β interaction.","corpus_id":206808386,"score":2},{"doc_id":"25411794","title":"Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity.","abstract":"The Vif protein of HIV-1 allows virus replication by degrading several members of the host-encoded APOBEC3 family of DNA cytosine deaminases. Polymorphisms in both host APOBEC3 genes and the viral vif gene have the potential to impact the extent of virus replication among individuals. The most genetically diverse of the seven human APOBEC3 genes is APOBEC3H with seven known haplotypes. Overexpression studies have shown that a subset of these variants express stable and active proteins, whereas the others encode proteins with a short half-life and little, if any, antiviral activity. We demonstrate that these stable/unstable phenotypes are an intrinsic property of endogenous APOBEC3H proteins in primary CD4+ T lymphocytes and confer differential resistance to HIV-1 infection in a manner that depends on natural variation in the Vif protein of the infecting virus. HIV-1 with a Vif protein hypo-functional for APOBEC3H degradation, yet fully able to counteract APOBEC3D, APOBEC3F, and APOBEC3G, was susceptible to restriction and hypermutation in stable APOBEC3H expressing lymphocytes, but not in unstable APOBEC3H expressing lymphocytes. In contrast, HIV-1 with hyper-functional Vif counteracted stable APOBEC3H proteins as well as all other endogenous APOBEC3s and replicated to high levels. We also found that APOBEC3H protein levels are induced over 10-fold by infection. Finally, we found that the global distribution of stable/unstable APOBEC3H haplotypes correlates with the distribution a critical hyper/hypo-functional Vif amino acid residue. These data combine to strongly suggest that stable APOBEC3H haplotypes present as in vivo barriers to HIV-1 replication, that Vif is capable of adapting to these restrictive pressures, and that an evolutionary equilibrium has yet to be reached.","corpus_id":12686637,"score":2},{"doc_id":"25590520","title":"Evolutionarily conserved pressure for the existence of distinct G2/M cell cycle arrest and A3H inactivation functions in HIV-1 Vif.","abstract":"HIV-1 Vif assembles the Cul5-EloB/C E3 ubiquitin ligase to induce proteasomal degradation of the cellular antiviral APOBEC3 proteins. Detailed structural studies have confirmed critical functional domains in Vif that we have previously identified as important for the interaction of EloB/C, Cul5, and CBFβ. However, the mechanism by which Vif recognizes substrates remains poorly understood. Specific regions of Vif have been identified as being responsible for binding and depleting APOBEC3G and APOBEC3F. Interestingly, we have now identified distinct yet overlapping domains that are required for HIV-1 Vif-mediated G2/M-phase cell cycle arrest and APOBEC3H degradation, but not for the inactivation of APOBEC3G or APOBEC3F. Surprisingly, Vif molecules from primary HIV-1 variants that caused G2/M arrest were unable to inactivate APOBEC3H; on the other hand, HIV-1 Vif variants that could inactivate APOBEC3H were unable to induce G2/M arrest. All of these Vif variants still maintained the ability to inactivate APOBEC3G/F. Thus, primary HIV-1 variants have evolved to possess distinct functional activities that allow them to suppress APOBEC3H or cause G2 cell cycle arrest, using mutually exclusive interface domains. APOBEC3H depletion and G2 arrest are apparently evolutionary selected features that cannot co-exist on a single Vif molecule. The existence and persistence of both types of HIV-1 Vif variant suggests the importance of APOBEC3H suppression and cell cycle regulation for HIV-1's survival in vivo.","corpus_id":21345503,"score":2},{"doc_id":"25614027","title":"Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities.","abstract":"BACKGROUND: Human APOBEC3H (A3H) belongs to the A3 family of host restriction factors, which are cytidine deaminases that catalyze conversion of deoxycytidine to deoxyuridine in single-stranded DNA. A3 proteins contain either one (A3A, A3C, A3H) or two (A3B, A3D, A3F, A3G) Zn-binding domains. A3H has seven haplotypes (I-VII) that exhibit diverse biological phenotypes and geographical distribution in the human population. Its single Zn-coordinating deaminase domain belongs to a phylogenetic cluster (Z3) that is different from the Z1- and Z2-type domains in other human A3 proteins. A3H HapII, unlike A3A or A3C, has potent activity against HIV-1. Here, we sought to identify the determinants of A3H HapII deaminase and antiviral activities, using site-directed sequence- and structure-guided mutagenesis together with cell-based, biochemical, and HIV-1 infectivity assays. RESULTS: We have constructed a homology model of A3H HapII, which is similar to the known structures of other A3 proteins. The model revealed a large cluster of basic residues (not present in A3A or A3C) that are likely to be involved in nucleic acid binding. Indeed, RNase A pretreatment of 293T cell lysates expressing A3H was shown to be required for detection of deaminase activity, indicating that interaction with cellular RNAs inhibits A3H catalytic function. Similar observations have been made with A3G. Analysis of A3H deaminase substrate specificity demonstrated that a 5' T adjacent to the catalytic C is preferred. Changing the putative nucleic acid binding residues identified by the model resulted in reduction or abrogation of enzymatic activity, while substituting Z3-specific residues in A3H to the corresponding residues in other A3 proteins did not affect enzyme function. As shown for A3G and A3F, some A3H mutants were defective in catalysis, but retained antiviral activity against HIV-1vif (-) virions. Furthermore, endogenous reverse transcription assays demonstrated that the E56A catalytic mutant inhibits HIV-1 DNA synthesis, although not as efficiently as wild type. CONCLUSIONS: The molecular and biological activities of A3H are more similar to those of the double-domain A3 proteins than to those of A3A or A3C. Importantly, A3H appears to use both deaminase-dependent and -independent mechanisms to target reverse transcription and restrict HIV-1 replication.","corpus_id":12923119,"score":2},{"doc_id":"25721876","title":"APOBEC3H polymorphisms associated with the susceptibility to HIV-1 infection and AIDS progression in Japanese.","abstract":"Human APOBEC3H (A3H) is a member of APOBEC3 cytidine deaminase family that potently restricts HIV-1 replication. Because A3H is genetically divergent with different intracellular stability and anti-HIV-1 activity in vitro, we investigated a possible association of A3H with susceptibility to HIV-1 infection and disease progression in Japanese populations. A total of 191 HIV-1-infected individuals (HIV group), 93 long-term non-progressors to AIDS (LTNP group) and 421 healthy controls were genotyped for two functional APOBEC3H polymorphisms, rs139292 and rs139297. As compared with the controls, minor allele frequency (MAF) for rs139292 was high in the HIV group (MAF in cases vs. controls; 0.322 vs. 0.263, odds ratio (OR) = 1.33, 95% confidence interval (95% CI) = 1.02-1.74, p = 0.035) and low in the LTNP group (0.161 vs. 0.263, OR = 0.54, 95% CI = 0.36-0.82, p = 0.004, pc = 0.007), whereas the MAF for rs139297 was high in the HIV group (0.367 vs. 0.298, OR = 1.36, 95% CI = 1.07-1.76, p = 0.017, pc = 0.035). In addition, haplotype analyses revealed that the frequencies of A3H-hapC and -hapA were high (0.322 vs. 0.262, OR = 1.33, 95% CI = 1.02-1.74, p = 0.003) and low (0.634 vs. 0.697, OR = 0.75, 95 % CI = 0.58-0.97, p = 0.002), respectively, in the HIV group, whereas the frequencies of A3H-hapC and -hapB were low (0.161 vs. 0.262, OR = 0.54, 95% CI = 0.36-0.82, p = 0.00003) and high (0.097 vs. 0.040, OR = 2.55, 95% CI = 1.40-4.62, p = 0.000008), respectively, in the LTNP group, as compared with those in the controls. These observations suggest that the A3H with low anti-HIV-1 activity, A3H-hapC, is associated with the susceptibility to HIV-1 infection, whereas the A3H producing a stable protein, A3H-hapB, may confer a low risk of disease progression to AIDS.","corpus_id":1432478,"score":2},{"doc_id":"26491161","title":"A Naturally Occurring Domestic Cat APOBEC3 Variant Confers Resistance to Feline Immunodeficiency Virus Infection.","abstract":"UNLABELLED: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) DNA cytosine deaminases can be incorporated into progeny virions and inhibit lentiviral replication. On the other hand, viral infectivity factor (Vif) of lentiviruses antagonizes A3-mediated antiviral activities by degrading A3 proteins. It is known that domestic cat (Felis catus) APOBEC3Z3 (A3Z3), the ortholog of human APOBEC3H, potently suppresses the infectivity of vif-defective feline immunodeficiency virus (FIV). Although a recent report has shown that domestic cat encodes 7 haplotypes (hap I to hap VII) of A3Z3, the relevance of A3Z3 polymorphism in domestic cats with FIV Vif has not yet been addressed. In this study, we demonstrated that these feline A3Z3 variants suppress vif-defective FIV infectivity. We also revealed that codon 65 of feline A3Z3 is a positively selected site and that A3Z3 hap V is subject to positive selection during evolution. It is particularly noteworthy that feline A3Z3 hap V is resistant to FIV Vif-mediated degradation and still inhibits vif-proficient viral infection. Moreover, the side chain size, but not the hydrophobicity, of the amino acid at position 65 determines the resistance to FIV Vif-mediated degradation. Furthermore, phylogenetic analyses have led to the inference that feline A3Z3 hap V emerged approximately 60,000 years ago. Taken together, these findings suggest that feline A3Z3 hap V may have been selected for escape from an ancestral FIV. This is the first evidence for an evolutionary \"arms race\" between the domestic cat and its cognate lentivirus. IMPORTANCE: Gene diversity and selective pressure are intriguing topics in the field of evolutionary biology. A direct interaction between a cellular protein and a viral protein can precipitate an evolutionary arms race between host and virus. One example is primate APOBEC3G, which potently restricts the replication of primate lentiviruses (e.g., human immunodeficiency virus type 1 [HIV-1] and simian immunodeficiency virus [SIV]) if its activity is not counteracted by the viral Vif protein. Here we investigate the ability of 7 naturally occurring variants of feline APOBEC3, APOBEC3Z3 (A3Z3), to inhibit FIV replication. Interestingly, one feline A3Z3 variant is dominant, restrictive, and naturally resistant to FIV Vif-mediated degradation. Phylogenetic analyses revealed that the ancestral change that generated this variant could have been caused by positive Darwinian selection, presumably due to an ancestral FIV infection. The experimental-phylogenetic investigation sheds light on the evolutionary history of the domestic cat, which was likely influenced by lentiviral infection.","corpus_id":3250632,"score":2},{"doc_id":"26559750","title":"APOBEC3H polymorphisms and susceptibility to HIV-1 infection in an Indian population.","abstract":"Human APOBEC3H (A3H) is a member of APOBEC cytidine deaminase family intensively constraining the HIV-1 replication. A3H is known to be polymorphic with different protein stability and anti-HIV-1 activity in vitro. We recently reported that A3H haplotypes composed of two functional polymorphisms, rs139292 (N15del) and rs139297 (G105R), were associated with the susceptibility to HIV-1 infection in Japanese. To confirm the association of A3H and HIV-1 infection in another ethnic group, a total of 241 HIV-1-infected Indian individuals and ethnic-matched 286 healthy controls were analyzed for the A3H polymorphisms. The frequency of 15del allele was high in the HIV-1-infected subjects as compared with the controls (0.477 vs 0.402, odds ratio (OR)=1.36, P=0.014). Haplotype analysis showed that the frequencies of 15del-105R was high (0.475 vs 0.400, OR=1.36, permutation P=0.037) in the HIV-1-infected subjects, confirming the association of A3H polymorphisms with the susceptibility to HIV-1 infection. Journal of Human Genetics advance online publication, 12 November 2015; doi:10.1038/jhg.2015.136.","corpus_id":306663,"score":2},{"doc_id":"27534815","title":"Biochemical Characterization of APOBEC3H Variants: Implications for Their HIV-1 Restriction Activity and mC Modification.","abstract":"APOBEC3H (A3H) is the most polymorphic member of the APOBEC3 family. Seven haplotypes (hap I-VII) and four mRNA splicing variants (SV) of A3H have been identified. The various haplotypes differ in anti-HIV activity, which is attributed to differences in protein stability, subcellular distribution, and/or RNA binding and virion packaging. Here, we report the first comparative biochemical studies of all the A3H variants using highly purified proteins. We show that all haplotypes were stably expressed and could be purified to homogeneity by Escherichia coli expression. Surprisingly, four out of the seven haplotypes showed high cytosine (C) deaminase activity, with hap V displaying extremely high activity that was comparable to the highly active A3A. Furthermore, all four haplotypes that were active in C deamination were also highly active on methylated C (mC), with hap II displaying almost equal deamination efficiency on both. The deamination activity of these A3H variants correlates well with their reported anti-HIV activity for the different haplotypes, suggesting that deaminase activity may be an important factor in determining their respective anti-HIV activities. Moreover, mC deamination of A3H displayed a strong preference for the sequence motif of T-mCpG-C/G, which may suggest a potential role in genomic mC modification at the characteristic \"CpG\" island motif.","corpus_id":206215841,"score":2},{"doc_id":"28031368","title":"The Structural Interface between HIV-1 Vif and Human APOBEC3H.","abstract":"Human APOBEC3H (A3H) is a cytidine deaminase that inhibits HIV-1 replication. To evade this restriction, the HIV-1 Vif protein binds A3H and mediates its proteasomal degradation. To date, little information on the Vif-A3H interface has been available. To decipher how both proteins interact, we first mapped the Vif-binding site on A3H by functionally testing a large set of A3H mutants in single-cycle infectivity and replication assays. Our data show that the two A3H α-helixes α3 and α4 represent the Vif-binding site of A3H. We next used viral adaptation and a set of Vif mutants to identify novel, reciprocal Vif variants that rescued viral infectivity in the presence of two Vif-resistant A3H mutants. These A3H-Vif interaction points were used to generate the first A3H-Vif structure model, which revealed that the A3H helixes α3 and α4 interact with the Vif β-sheet (β2-β5). This model is in good agreement with previously reported Vif and A3H amino acids important for interaction. Based on the predicted A3H-Vif interface, we tested additional points of contact, which validated our model. Moreover, these experiments showed that the A3H and A3G binding sites on HIV-1 Vif are largely distinct, with both host proteins interacting with Vif β-strand 2. Taken together, this virus-host interface model explains previously reported data and will help to identify novel drug targets to combat HIV-1 infection. IMPORTANCE HIV-1 needs to overcome several intracellular restriction factors in order to replicate efficiently. The human APOBEC3 locus encodes seven proteins, of which A3D, A3F, A3G, and A3H restrict HIV-1. HIV encodes the Vif protein, which binds to the APOBEC3 proteins and leads to their proteasomal degradation. No HIV-1 Vif-APOBEC3 costructure exists to date despite extensive research. We and others previously generated HIV-1 Vif costructure models with A3G and A3F by mapping specific contact points between both proteins. Here, we applied a similar approach to HIV-1 Vif and A3H and successfully generated a Vif-A3H interaction model. Importantly, we find that the HIV-1 Vif-A3H interface is distinct from the Vif-A3G and Vif-A3F interfaces, with a small Vif region being important for recognition of both A3G and A3H. Our Vif-A3H structure model informs on how both proteins interact and could guide toward approaches to block the Vif-A3H interface to target HIV replication.","corpus_id":4623329,"score":2},{"doc_id":"28336404","title":"Mapping Region of Human Restriction Factor APOBEC3H Critical for Interaction with HIV-1 Vif.","abstract":"The APOBEC3 (A3) family of cellular cytidine deaminases comprises seven members (A, B, C, D, F, G, and H) that potently inhibit retroviral replication. Human immunodeficiency virus type 1 (HIV-1) Vif is a small pleiotropic protein that specifically inactivates these enzymes, targeting them for ubiquitin-mediated proteasomal degradation. A3 Vif-interaction sites are presumed to fall into three distinct types: A3C/D/F, A3G, and A3H. To date, two types of A3G and A3C/D/F sites have been well characterized, whereas the A3H Vif-binding site remains poorly defined. Here, we explore the residues critical for the A3H-type Vif interaction. To avoid technical difficulties in performing experiments with human A3H haplotype II (hapII), which is relatively resistant to HIV-1 Vif, we employed its ortholog chimpanzee A3H (cA3H), which displays high Vif sensitivity, for a comparison of sensitivity with that of A3H hapII. The Vif susceptibility of A3H hapII-cA3H chimeras and their substitution mutants revealed a single residue at position 97 as a major determinant for the difference in their Vif sensitivities. We further surveyed critical residues by structure-guided mutagenesis using an A3H structural model and thus identified eight additional residues important for Vif sensitivity, which mapped to the α3 and α4 helices of A3H. Interestingly, this area is located on a surface adjacent to the A3G and A3C/D/F interfaces and is composed of negatively charged and hydrophobic patches. These findings suggest that HIV-1 Vif has evolved to utilize three dispersed surfaces for recognizing three types of interfaces on A3 proteins under certain structural constraints.","corpus_id":26918870,"score":2},{"doc_id":"28475648","title":"HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation.","abstract":"APOBEC3 (A3) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation. Prior studies have demonstrated that A3D, A3F, and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models. Human A3H is polymorphic and can be categorized into three phenotypes: stable, intermediate, and unstable. However, the anti-viral effect of endogenous A3H in vivo has yet to be examined. Here we utilize a hematopoietic stem cell-transplanted humanized mouse model and demonstrate that stable A3H robustly affects HIV-1 fitness in vivo. In contrast, the selection pressure mediated by intermediate A3H is relaxed. Intriguingly, viral genomic RNA sequencing reveled that HIV-1 frequently adapts to better counteract stable A3H during replication in humanized mice. Molecular phylogenetic analyses and mathematical modeling suggest that stable A3H may be a critical factor in human-to-human viral transmission. Taken together, this study provides evidence that stable variants of A3H impose selective pressure on HIV-1.","corpus_id":23069011,"score":2},{"doc_id":"28883657","title":"Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H.","abstract":"The APOBEC3 family of cytosine deaminase enzymes are able to restrict replication of retroelements, such as LINE-1. However, each of the seven APOBEC3 enzymes have been reported to act differentially to prevent LINE-1 retrotransposition and the mechanisms of APOBEC3-mediated LINE-1 inhibition has not been well understood. The prevailing view for many years was that APOBEC3-mediated LINE-1 inhibition was deamination-independent and relied on APOBEC3s blocking the LINE-1 reverse transcriptase DNA polymerization or transport of the LINE-1 RNA into the nucleus. However, recently it was shown that APOBEC3A can deaminate cytosine, to form uracil, on transiently exposed single-stranded LINE-1 cDNA and this leads to LINE-1 cDNA degradation. In this study, we confirmed that APOBEC3A is a potent deamination-dependent inhibitor of LINE-1 retrotransposition, but show that in contrast, A3H haplotype II and haplotype V restrict LINE-1 activity using a deamination-independent mechanism. Our study supports the model that different APOBEC3 proteins have evolved to inhibit LINE-1 retrotransposition through distinct mechanisms.","corpus_id":24572310,"score":2},{"doc_id":"29267382","title":"Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans.","abstract":"APOBEC3s (A3s) are potent restriction factors of human immunodeficiency virus type 1/simian immunodeficiency viruses (HIV-1/SIV), and can repress cross-species transmissions of lentiviruses. HIV-1 originated from a zoonotic infection of SIV of chimpanzee (SIVcpz) to humans. However, the impact of human A3s on the replication of SIVcpz remains unclear. By using novel SIVcpz reporter viruses, we identified that human APOBEC3B (A3B) and APOBEC3H (A3H) haplotype II strongly reduced the infectivity of SIVcpz, because both of them are resistant to SIVcpz Vifs. We further demonstrated that human A3H inhibited SIVcpz by deaminase dependent as well independent mechanisms. In addition, other stably expressed human A3H haplotypes and splice variants showed strong antiviral activity against SIVcpz. Moreover, most SIV and HIV lineage Vif proteins could degrade chimpanzee A3H, but no Vifs from SIVcpz and SIV of gorilla (SIVgor) lineages antagonized human A3H haplotype II. Expression of human A3H hapII in human T cells efficiently blocked the spreading replication of SIVcpz. The spreading replication of SIVcpz was also restricted by stable A3H in human PBMCs. Thus, we speculate that stably expressed human A3H protects humans against the cross-species transmission of SIVcpz and that SIVcpz spillover to humans may have started in individuals that harbor haplotypes of unstable A3H proteins.","corpus_id":230108,"score":2},{"doc_id":"29333092","title":"Role of APOBEC3H in the Viral Control of HIV Elite Controller Patients.","abstract":"Background APOBEC3H (A3H) gene presents variation at 2 positions (rs139297 and rs79323350) leading to a non-functional protein. So far, there is no information on the role played by A3H in spontaneous control of HIV. The aim of this study was to evaluate the A3H polymorphisms distribution in a well-characterized group of Elite Controller (EC) subjects. Methods We analyzed the genotype distribution of two different SNPs (rs139297 and rs79323350) of A3H in 30 EC patients and compared with 11 non-controller (NC) HIV patients. Genotyping was performed by PCR, cloning and Sanger sequencing. Both polymorphisms were analyzed jointly in order to adequately attribute the active or inactive status of A3H protein. Results EC subjects included in this study were able to maintain a long-term sustained spontaneous HIV-viral control and optimal CD4-T-cell counts; however, haplotypes leading to an active protein were very poorly represented in these patients. We found that the majority of EC subjects (23/30; 77%) presented allelic combinations leading to an inactive A3H protein, a frequency slightly lower than that observed for NC studied patients (10/11; 91%). Conclusions The high prevalence of non-functional protein coding-genotypes in EC subjects seems to indicate that other innate restriction factors different from APOBEC3H could be implicated in the replication control exhibited by these subjects.","corpus_id":24178885,"score":2},{"doc_id":"18619467","title":"Characterization of conserved motifs in HIV-1 Vif required for APOBEC3G and APOBEC3F interaction.","abstract":"Apolipoprotein B mRNA-editing catalytic polypeptide-like 3G (APOBEC3G, or A3G) and related cytidine deaminases such as apolipoprotein B mRNA-editing catalytic polypeptide-like 3F (APOBEC3F, or A3F) are potent inhibitors of retroviruses. Formation of infectious human immunodeficiency virus (HIV)-1 requires suppression of multiple cytidine deaminases by Vif. HIV-1 Vif suppresses various APOBEC3 proteins through a common mechanism by recruiting Cullin5, ElonginB, and ElonginC E3 ubiquitin ligase to induce target protein polyubiquitination and proteasome-mediated degradation. Domains in Vif that mediate APOBEC3 recognition have not been fully characterized. In the present study, we identified a VxIPLx(4-5)LxPhix(2)YWxL motif in HIV-1 Vif, which is required for efficient interaction between Vif and A3G, Vif-mediated A3G degradation and virion exclusion, and functional suppression of the A3G antiviral activity. Amino acids 52 to 72 of HIV-1 Vif (including the VxIPLx(4-5)LxPhix(2)YWxL motif) alone could mediate interaction with A3G, and this interaction was abolished by mutations of two hydrophobic amino acids in this region. We have also observed that a Vif mutant was ineffective against A3G, yet it retained the ability to interact with Cullin5-E3 ubiquitin complex and A3G, suggesting that interaction with A3G is necessary but not sufficient to inhibit its antiviral function. Unlike the previously identified motif of HIV-1 Vif amino acids 40 to 44, which is only important for A3G suppression, the VxIPLx(4-5)LxPhix(2)YWxL motif is also required for efficient A3F interaction and suppression. On the other hand, another motif, TGERxW, of HIV-1 Vif amino acids 74 to 79 was found to be mainly important for A3F interaction and inhibition. Both the VxIPLx(4-5)LxPhix(2)YWxL and TGERxW motifs are highly conserved among HIV-1, HIV-2, and various simian immunodeficiency virus Vif proteins. Our data suggest that primate lentiviral Vif molecules recognize their autologous APOBEC3 proteins through conserved structural features that represent attractive targets for the development of novel inhibitors.","corpus_id":41901760,"score":1},{"doc_id":"19109396","title":"Regulation of APOBEC3 proteins by a novel YXXL motif in human immunodeficiency virus type 1 Vif and simian immunodeficiency virus SIVagm Vif.","abstract":"The APOBEC3 cytidine deaminases are potent antiviral factors that restrict the replication of human immunodeficiency virus type 1 (HIV-1). In HIV-1-infected CD4+ T cells, the viral accessory protein Vif binds to APOBEC3G (A3G), APOBEC3F (A3F), and APOBEC3C (A3C) and targets these proteins for polyubiquitination by forming an E3 ubiquitin ligase with cullin 5. Previous studies identified regions of HIV-1 Vif, 40YRHHY44 and 12QVDRMR17, which are important for interaction with A3G and A3F, respectively, and showed that Vif residues 54 to 71 are sufficient for A3G binding. Here, we identify 69YXXL72 as a novel conserved motif in HIV-1 Vif that mediates binding to human A3G and its subsequent degradation. Studies on other APOBEC3 proteins revealed that Tyr69 and Leu72 are important for the degradation of A3F and A3C as well. Similar to A3F, A3C regulation is also mediated by Vif residues 12QVDRMR17. Simian immunodeficiency virus (SIV) Vif was shown to bind and degrade African green monkey A3G (agmA3G) and, unexpectedly, human A3C. The YXXL motif of SIVagm Vif was important for the inactivation of agmA3G and human A3C. Unlike HIV-1 Vif, however, SIVagm Vif does not require Tyr40 and His43 for agmA3G degradation. Tyr69 in the YXXL motif was critical for binding of recombinant glutathione S-transferase-Vif(1-94) to A3G in vitro. These results suggest that the YXXL motif in Vif is a potential target for small-molecule inhibitors to block Vif interaction with A3G, A3F, and A3C, and thereby protect cells against HIV-1 infection.","corpus_id":206808184,"score":1},{"doc_id":"20333195","title":"Evolution of olfactory receptor genes in primates dominated by birth-and-death process.","abstract":"Olfactory receptor (OR) is a large family of G protein-coupled receptors that can detect odorant in order to generate the sense of smell. They constitute one of the largest multiple gene families in animals including primates. To better understand the variation in odor perception and evolution of OR genes among primates, we computationally identified OR gene repertoires in orangutans, marmosets, and mouse lemurs and investigated the birth-and-death process of OR genes in the primate lineage. The results showed that 1) all the primate species studied have no more than 400 intact OR genes, fewer than rodents and canine; 2) Despite the similar number of OR genes in the genome, the makeup of the OR gene repertoires between different primate species is quite different as they had undergone dramatic birth-and-death evolution with extensive gene losses in the lineages leading to current species; 3) Apes and Old World monkey (OWM) have similar fraction of pseudogenes, whereas New World monkey (NWM) have fewer pseudogenes. To measure the selective pressure that had affected the OR gene repertoires in primates, we compared the ratio of nonsynonymous with synonymous substitution rates by using 70 one-to-one orthologous quintets among five primate species. We found that OR genes showed relaxed selective constraints in apes (humans, chimpanzees, and orangutans) than in OWMs (macaques) and NWMs (marmosets). We concluded that OR gene repertoires in primates have evolved in such a way to adapt to their respective living environments. Differential selective constraints might play important role in the primate OR gene evolution in each primate species.","corpus_id":10136681,"score":1},{"doc_id":"20444900","title":"Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses.","abstract":"Tetherin/BST-2 is a host-encoded protein that restricts a wide diversity of viruses at the stage of virion release. However, viruses have evolved antagonists of Tetherin, including the Vpu and Nef proteins of primate lentiviruses. Like other host genes subject to viral antagonism, primate Tetherin genes have evolved under positive selection. We show here that viral antagonists acting at three independent sites of selection have driven the evolution of Tetherin, with the strongest selective pressure on the cytoplasmic tail domain. Human Tetherin is unique among the Tetherins of simian primates in that it has a 5-amino-acid deletion that results in the loss of the residue under the strongest positive selection. We show that this residue at amino acid 17 is the site of the functional interaction of Tetherin with Nef, since single amino acid substitutions at this single position can determine the susceptibility of Tetherin to Nef antagonism. While the simian immunodeficiency viruses SIVcpz and SIVgor are able to antagonize their hosts' Tetherin with Nef, human immunodeficiency virus type 1 (HIV-1) Vpu has evolved to counteract Tetherin in humans. We mapped the adaptations in the N-terminal transmembrane domain of Vpu that allow it to counteract human Tetherin. Our combined evolutionary and functional studies have allowed us to reconstruct the host-pathogen interactions that have shaped Tetherin and its lentivirus-encoded antagonists.","corpus_id":20649863,"score":1},{"doc_id":"20592083","title":"Identification of a critical T(Q/D/E)x5ADx2(I/L) motif from primate lentivirus Vif proteins that regulate APOBEC3G and APOBEC3F neutralizing activity.","abstract":"Primate lentiviruses are unique in that they produce several accessory proteins to help in the establishment of productive viral infection. The major function of these proteins is to clear host resistance factors that inhibit viral replication. Vif is one of these proteins. It functions as an adaptor that binds to the cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) and bridges them to a cullin 5 (Cul5) and elongin (Elo) B/C E3 ubiquitin ligase complex for proteasomal degradation. So far, 11 discontinuous domains in Vif have been identified that regulate this degradation process. Here we report another domain, T(Q/D/E)x(5)ADx(2)(I/L), which is located at residues 96 to 107 in the human immunodeficiency virus type 1 (HIV-1) Vif protein. This domain is conserved not only in all HIV-1 subtypes but also in other primate lentiviruses, including HIV-2 and simian immunodeficiency virus (SIV), which infects rhesus macaques (SIVmac) and African green monkeys (SIVagm). Mutations of the critical residues in this motif seriously disrupted Vif's neutralizing activity toward both A3G and A3F. This motif regulates Vif interaction not only with A3G and A3F but also with Cul5. When this motif was inactivated in the HIV-1 genome, Vif failed to exclude A3G and A3F from virions, resulting in abortive HIV replication in nonpermissive human T cells. Thus, T(Q/D/E)x(5)ADx(2)(I/L) is a critical functional motif that directly supports the adaptor function of Vif and is an attractive target for inhibition of Vif function.","corpus_id":206799359,"score":1},{"doc_id":"23707381","title":"A naturally occurring Vif mutant (I107T) attenuates anti-APOBEC3G activity and HIV-1 replication.","abstract":"The human immunodeficiency virus type 1 (HIV-1) Vif protein counteracts the antiviral activity of the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of proteins by targeting the proteins for degradation through the ubiquitin-proteasome pathway. Previous mutagenic studies have shown that multiple domains of Vif are required for interacting with APOBEC3G proteins and the proteasome pathway. However, very few mutagenesis and functional analyses of patient-derived Vif proteins have been conducted. In this study, we amplified and cloned the HIV-1 vif genes from the peripheral blood mononuclear cells (PBMCs) of five HIV-1-infected individuals in Nairobi and further tested the impact of the genes on anti-A3G activity and HIV-1 replication. The gene sequence analysis revealed high genetic variation of vif genes from different HIV-1-infected individuals. Interestingly, the Vif proteins derived from two of the three long-term survivors (LTSs) displayed a significantly impaired ability to mediate the degradation of A3G. In particular, a single amino acid change (I107T) in one of the non-functional LTS Vif variants, which has not been previously identified in the Los Alamos databases of vif sequences, was found to be responsible for the lack of anti-A3G activity. Further study demonstrated that HIV-1 carrying an I107T Vif mutation displayed significantly reduced fitness in A3G(+) T cells and PBMCs. Moreover, co-infecting A3G(+) T cells with both the wild-type and I107T Vif viruses resulted in decreased viral replication. Overall, the results of this study indicate that the HIV-1 Vif residue I107 is important for its anti-APOBEC3G activity and viral replication, which may have implications for viral fitness in vivo.","corpus_id":5215502,"score":1},{"doc_id":"24324150","title":"Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus.","abstract":"Restriction factors are effectors of the innate immune response to viral pathogens that inhibit viral replication by operating as molecular barriers to steps of the viral life cycle. The restriction factor SAMHD1 blocks lentiviral reverse transcription in myeloid cells and resting CD4+ T cells. Many lineages of lentiviruses, including HIV-2 and other simian immunodeficiency viruses, encode accessory genes that serve to counteract host SAMHD1 restriction by causing degradation of the antiviral factor. The viral accessory protein Vpr is responsible for SAMHD1 degradation in some lineages of lentiviruses, whereas in others the related protein Vpx assumes this task. However, HIV-1 has no SAMHD1 degradation capability, leading to questions about the selective advantage of this activity. We use an evolutionary approach to examine the importance of SAMHD1 antagonism for viral fitness by studying adaptation to host SAMHD1 in natural simian immunodeficiency virus infections of African Green Monkeys. We identified multiple SAMHD1 haplotypes in African Green Monkeys and find that the vpr gene from different strains of Simian Immunodeficiency Virus has adapted to the polymorphisms of the African Green Monkey population in which it is found. Such evidence of viral adaptation to host restriction indicates that SAMHD1 antagonism is actively maintained in natural infections and that this function must be advantageous to viral fitness, despite its absence in HIV-1.","corpus_id":76492,"score":1},{"doc_id":"24942576","title":"HIV-1 and HIV-2 Vif interact with human APOBEC3 proteins using completely different determinants.","abstract":"UNLABELLED: Human APOBEC3 (A3) restriction factors provide intrinsic immunity against zoonotic transmission of pathogenic viruses. A3D, A3F, A3G, and A3H haplotype II (A3H-hapII) can be packaged into virion infectivity factor (Vif)-deficient HIVs to inhibit viral replication. To overcome these restriction factors, Vif binds to the A3 proteins in viral producer cells to target them for ubiquitination and proteasomal degradation, thus preventing their packaging into assembling virions. Therefore, the Vif-A3 interactions are attractive targets for novel drug development. HIV-1 and HIV-2 arose via distinct zoonotic transmission events of simian immunodeficiency viruses from chimpanzees and sooty mangabeys, respectively, and Vifs from these viruses have limited homology. To gain insights into the evolution of virus-host interactions that led to successful cross-species transmission of lentiviruses, we characterized the determinants of the interaction between HIV-2 Vif (Vif2) with human A3 proteins and compared them to the previously identified HIV-1 Vif (Vif1) interactions with the A3 proteins. We found that A3G, A3F, and A3H-hapII, but not A3D, were susceptible to Vif2-induced degradation. Alanine-scanning mutational analysis of the first 62 amino acids of Vif2 indicated that Vif2 determinants important for degradation of A3G and A3F are completely distinct from these regions in Vif1, as are the determinants in A3G and A3F that are critical for Vif2-induced degradation. These observations suggest that distinct Vif-A3 interactions evolved independently in different SIVs and their nonhuman primate hosts and conservation of the A3 determinants targeted by the SIV Vif proteins resulted in successful zoonotic transmission into humans. IMPORTANCE: Primate APOBEC3 proteins provide innate immunity against invading pathogens, and Vif proteins of primate lentiviruses have evolved to overcome these host defenses by interacting with them and inducing their proteasomal degradation. HIV-1 and HIV-2 are two human pathogens that induce AIDS, and elucidating interactions between their Vif proteins and human A3 proteins could facilitate the development of novel antiviral drugs. Furthermore, understanding Vif-A3 interactions can provide novel insights into the cross-species transmission events that led to the HIV-1 and HIV-2 pandemics and evolution of host-virus interactions. We carried out mutational analysis of the N-terminal 62 amino acids of HIV-2 Vif (Vif2) and analyzed A3G/A3F chimeras that retained antiviral activity to identify the determinants of the Vif2 and A3 interaction. Our results show that the Vif2-A3 interactions are completely different from the Vif1-A3 interactions, suggesting that these interactions evolved independently and that conservation of the A3 determinants resulted in successful zoonotic transmission into humans.","corpus_id":7776940,"score":1},{"doc_id":"25142583","title":"Cellular requirements for bovine immunodeficiency virus Vif-mediated inactivation of bovine APOBEC3 proteins.","abstract":"UNLABELLED: Human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) viral infectivity factor (Vif) form a CRL5 E3 ubiquitin ligase complex to suppress virus restriction by host APOBEC3 (A3) proteins. The primate lentiviral Vif complex is composed of the unique cofactor core binding factor β (CBF-β) and canonical ligase components Cullin 5 (CUL5), Elongin B/C (ELOB/C), and RBX2. However, the mechanism by which the Vif protein of the related lentivirus bovine immunodeficiency virus (BIV) overcomes its host A3 proteins is less clear. In this study, we show that BIV Vif interacts with Cullin 2 (CUL2), ELOB/C, and RBX1, but not with CBF-β or CUL5, to form a CRL2 E3 ubiquitin ligase and degrade the restrictive bovine A3 proteins (A3Z2Z3 and A3Z3). RNA interference-mediated knockdown of ELOB or CUL2 inhibited BIV Vif-mediated degradation of these A3 proteins, whereas knockdown of CUL5 or CBF-β did not. BIV Vif with mutations in the BC box (Vif SLQ-AAA) or putative VHL box (Vif YI-AA), which cannot interact with ELOB/C or CUL2, respectively, lost the ability to counteract bovine A3 proteins. Moreover, CUL2 and UBE2M dominant negative mutants competitively inhibited the BIV Vif-mediated degradation mechanism. Thus, although the general strategy for inhibiting A3 proteins is conserved between HIV-1/SIV and BIV, the precise mechanisms can differ substantially, with only the HIV-1/SIV Vif proteins requiring CBF-β as a cofactor, HIV-1/SIV Vif using CUL5-RBX2, and BIV Vif using CUL2-RBX1. IMPORTANCE: Primate lentivirus HIV-1 and SIV Vif proteins form a ubiquitin ligase complex to target host antiviral APOBEC3 proteins for degradation. However, the mechanism by which the nonprimate lentivirus BIV Vif inhibits bovine APOBEC3 proteins is unclear. In the present study, we determined the mechanism for BIV Vif-mediated degradation of bovine APOBEC3 proteins and found that it differs from the mechanism of HIV-1/SIV Vif by being CBF-β independent and requiring different ubiquitin ligase scaffolding proteins (CUL2-RBX1 instead of CUL5-RBX2). BIV Vif is the only known retroviral protein that can interact with CUL2. This information broadens our understanding of the distinct mechanisms by which the Vif proteins of different lentiviruses facilitate viral infection. This novel mechanism for assembly of the BIV Vif-APOBEC3 ubiquitin ligase complex advances our understanding of viral hijacking of host E3 ubiquitin ligases and illustrates the evolutionary flexibility of lentiviruses.","corpus_id":31065884,"score":1},{"doc_id":"25275135","title":"Determinants of efficient degradation of APOBEC3 restriction factors by HIV-1 Vif.","abstract":"UNLABELLED: The APOBEC3 deoxycytidine deaminases can restrict the replication of HIV-1 in cell culture to differing degrees. The effects of APOBEC3 enzymes are largely suppressed by HIV-1 Vif that interacts with host proteins to form a Cullin5-Ring E3 ubiquitin ligase that induces (48)K-linked polyubiquitination (poly-Ub) and proteasomal degradation of APOBEC3 enzymes. Vif variants have differing abilities to induce degradation of APOBEC3 enzymes and the underlying biochemical mechanisms for these differences is not fully understood. We hypothesized that by characterizing the interaction of multiple APOBEC3 enzymes and Vif variants we could identify common features that resulted in Vif-mediated degradation and further define the determinants required for efficient Vif-mediated degradation of APOBEC3 enzymes. We used Vifs from HIV-1 NL4-3 (IIIB) and HXB2 to characterize their induced degradation of and interaction with APOBEC3G, APOBEC3G D128K, APOBEC3H, and APOBEC3B in 293T cells. We quantified the APOBEC3G-Vif and APOBEC3H-Vif interaction strengths in vitro using rotational anisotropy. Our biochemical and cellular analyses of the interactions support a model in which the degradation efficiency of VifIIIB and VifHXB2 correlated with both the binding strength of the APOBEC3-Vif interaction and the APOBEC3-Vif interface, which differs for APOBEC3G and APOBEC3H. Notably, Vif bound to APOBEC3H and APOBEC3B in the natural absence of Vif-induced degradation and the interaction resulted in (63)K-linked poly-Ub of APOBEC3H and APOBEC3B, demonstrating additional functionality of the APOBEC3-Vif interaction apart from induction of proteasomal degradation. IMPORTANCE: APOBEC3 enzymes can potently restrict the replication of HIV-1 in the absence of HIV-1 Vif. Vif suppresses APOBEC3 action by inducing their degradation through a direct interaction with APOBEC3 enzymes and other host proteins. Vif variants from different HIV-1 strains have different effects on APOBEC3 enzymes. We used differing Vif degradation capacities of two Vif variants and various APOBEC3 enzymes with differential sensitivities to Vif to delineate determinants of the APOBEC3-Vif interaction that are required for inducing efficient degradation. Using a combined biochemical and cellular approach we identified that the strength of the APOBEC3-Vif binding interaction and the APOBEC3-Vif interface are determinants for degradation efficiency. Our results highlight the importance of using Vif variants with different degradation potential when delineating mechanisms of Vif-induced APOBEC3 degradation and identify features important for consideration in the development of HIV-1 therapies that disrupt the APOBEC3-Vif interaction.","corpus_id":43017915,"score":1},{"doc_id":"26291613","title":"Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface.","abstract":"The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity.","corpus_id":13293015,"score":1},{"doc_id":"26394054","title":"The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys.","abstract":"Cross-species transmissions of viruses from animals to humans are at the origin of major human pathogenic viruses. While the role of ecological and epidemiological factors in the emergence of new pathogens is well documented, the importance of host factors is often unknown. Chimpanzees are the closest relatives of humans and the animal reservoir at the origin of the human AIDS pandemic. However, despite being regularly exposed to monkey lentiviruses through hunting, chimpanzees are naturally infected by only a single simian immunodeficiency virus, SIVcpz. Here, we asked why chimpanzees appear to be protected against the successful emergence of other SIVs. In particular, we investigated the role of the chimpanzee APOBEC3 genes in providing a barrier to infection by most monkey lentiviruses. We found that most SIV Vifs, including Vif from SIVwrc infecting western-red colobus, the chimpanzee's main monkey prey in West Africa, could not antagonize chimpanzee APOBEC3G. Moreover, chimpanzee APOBEC3D, as well as APOBEC3F and APOBEC3H, provided additional protection against SIV Vif antagonism. Consequently, lentiviral replication in primary chimpanzee CD4(+) T cells was dependent on the presence of a lentiviral vif gene that could antagonize chimpanzee APOBEC3s. Finally, by identifying and functionally characterizing several APOBEC3 gene polymorphisms in both common chimpanzees and bonobos, we found that these ape populations encode APOBEC3 proteins that are uniformly resistant to antagonism by monkey lentiviruses.","corpus_id":13781850,"score":1},{"doc_id":"26601257","title":"Transcriptional regulation of APOBEC3 antiviral immunity through the CBF-β/RUNX axis.","abstract":"A diverse set of innate immune mechanisms protects cells from viral infections. The APOBEC3 family of DNA cytosine deaminases is an integral part of these defenses. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H would have the potential to destroy HIV-1 complementary DNA replication intermediates if not for neutralization by a proteasomal degradation mechanism directed by the viral protein Vif. At the core of this complex, Vif heterodimerizes with the transcription cofactor CBF-β, which results in fewer transcription complexes between CBF-β and its normal RUNX partners. Recent studies have shown that the Vif/CBF-β interaction is specific to the primate lentiviruses HIV-1 and SIV (simian immunodeficiency virus), although related nonprimate lentiviruses still require a Vif-dependent mechanism for protection from host species' APOBEC3 enzymes. We provide a molecular explanation for this evolutionary conundrum by showing that CBF-β is required for expression of the aforementioned HIV-1-restrictive APOBEC3 gene repertoire. Knockdown and knockout studies demonstrate that CBF-β is required for APOBEC3 mRNA expression in the nonpermissive T cell line H9 and in primary CD4(+) T lymphocytes. Complementation experiments using CBF-β separation-of-function alleles show that the interaction with RUNX transcription factors is required for APOBEC3 transcriptional regulation. Accordingly, the infectivity of Vif-deficient HIV-1 increases in cells lacking CBF-β, demonstrating the importance of CBF-β/RUNX-mediated transcription in establishing the APOBEC3 antiviral state. These findings demonstrate a major layer of APOBEC3 gene regulation in lymphocytes and suggest that primate lentiviruses evolved to hijack CBF-β in order to simultaneously suppress this potent antiviral defense system at both transcriptional and posttranslational levels.","corpus_id":13157474,"score":1},{"doc_id":"26912618","title":"APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication.","abstract":"UNLABELLED: The multifunctional HIV-1 accessory protein Vif counters the antiviral activities of APOBEC3G (A3G) and APOBEC3F (A3F), and some Vifs counter stable alleles of APOBEC3H (A3H). Studies in humanized mice have shown that HIV-1 lacking Vif expression is not viable. Here, we look at the relative contributions of the three APOBEC3s to viral extinction. Inoculation of bone marrow/liver/thymus (BLT) mice with CCR5-tropic HIV-1JRCSF(JRCSF) expressing a vif gene inactive for A3G but not A3F degradation activity (JRCSFvifH42/43D) displayed either no or delayed replication. JRCSF expressing a vif gene mutated to inactivate A3F degradation but not A3G degradation (JRCSFvifW79S) always replicated to high viral loads with variable delays. JRCSF with vif mutated to lack both A3G and A3F degradation activities (JRCSFvifH42/43DW79S) failed to replicate, mimicking JRCSF without Vif expression (JRCSFΔvif). JRCSF and JRCSFvifH42/43D, but not JRCSFvifW79S or JRCSFvifH42/43DW79S, degraded APOBEC3D. With one exception, JRCSFs expressing mutant Vifs that replicated acquired enforced vif mutations. These mutations partially restored A3G or A3F degradation activity and fully replaced JRCSFvifH42/43D or JRCSFvifW79S by 10 weeks. Surprisingly, induced mutations temporally lagged behind high levels of virus in blood. In the exceptional case, JRCSFvifH42/43D replicated after a prolonged delay with no mutations in vif but instead a V27I mutation in the RNase H coding sequence. JRCSFvifH42/43D infections exhibited massive GG/AG mutations in pol viral DNA, but in viral RNA, there were no fixed mutations in the Gag or reverse transcriptase coding sequence. A3H did not contribute to viral extinction but, in combination with A3F, could delay JRCSF replication. A3H was also found to hypermutate viral DNA. IMPORTANCE: Vif degradation of A3G and A3F enhances viral fitness, as virus with even a partially restored capacity for degradation outgrows JRCSFvifH42/43D and JRCSFvifW79S. Unexpectedly, fixation of mutations that replaced H42/43D or W79S in viral RNA lagged behind the appearance of high viral loads. In one exceptional JRCSFvifH42/43D infection, vif was unchanged but replication proceeded after a long delay. These results suggest that Vif binds and inhibits the non-cytosine deaminase activities of intact A3G and intact A3F, allowing JRCSFvifH42/43D and JRCSFvifW79S to replicate with reduced fitness. Subsequently, enhanced Vif function is acquired by enforced mutations. In infected cells, JRCSFΔvif and JRCSFvifH42/43DW79S are exposed to active A3F and A3G and fail to replicate. JRCSFvifH42/43D Vif degrades A3F and, in some cases, overcomes A3G mutagenic activity to replicate. Vif may have evolved to inhibit A3F and A3G by stoichiometric binding and subsequently acquired the ability to target these proteins to proteasomes.","corpus_id":4765212,"score":1},{"doc_id":"27189538","title":"Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution.","abstract":"LINE-1 (long interspersed element-1) retroelements are the only active autonomous endogenous retroelements in human genomes. Their retrotransposition activity has created close to 50% of the current human genome. Due to the apparent costs of this proliferation, host genomes have evolved multiple mechanisms to curb LINE-1 retrotransposition. Here, we investigate the evolution and function of the LINE-1 restriction factor APOBEC3A, a member of the APOBEC3 cytidine deaminase gene family. We find that APOBEC3A genes have evolved rapidly under diversifying selection in primates, suggesting changes in APOBEC3A have been recurrently selected in a host-pathogen \"arms race.\" Nonetheless, in contrast to previous reports, we find that the LINE-1 restriction activity of APOBEC3A proteins has been strictly conserved throughout simian primate evolution in spite of its pervasive diversifying selection. Based on these results, we conclude that LINE-1s have not driven the rapid evolution of APOBEC3A in primates. In contrast to this conserved LINE-1 restriction, we find that a subset of primate APOBEC3A genes have enhanced antiviral restriction. We trace this gain of antiviral restriction in APOBEC3A to the common ancestor of a subset of Old World monkeys. Thus, APOBEC3A has not only maintained its LINE-1 restriction ability, but also evolved a gain of antiviral specificity against other pathogens. Our findings suggest that while APOBEC3A has evolved to restrict additional pathogens, only those adaptive amino acid changes that leave LINE-1 restriction unperturbed have been tolerated.","corpus_id":27725439,"score":1},{"doc_id":"27581978","title":"Vif Proteins from Diverse Human Immunodeficiency Virus/Simian Immunodeficiency Virus Lineages Have Distinct Binding Sites in A3C.","abstract":"Lentiviruses have evolved the Vif protein to counteract APOBEC3 (A3) restriction factors by targeting them for proteasomal degradation. Previous studies have identified important residues in the interface of human immunodeficiency virus type 1 (HIV-1) Vif and human APOBEC3C (hA3C) or human APOBEC3F (hA3F). However, the interaction between primate A3C proteins and HIV-1 Vif or natural HIV-1 Vif variants is still poorly understood. Here, we report that HIV-1 Vif is inactive against A3Cs of rhesus macaques (rhA3C), sooty mangabey monkeys (smmA3C), and African green monkeys (agmA3C), while HIV-2, African green monkey simian immunodeficiency virus (SIVagm), and SIVmac Vif proteins efficiently mediate the depletion of all tested A3Cs. We identified that residues N/H130 and Q133 in rhA3C and smmA3C are determinants for this HIV-1 Vif-triggered counteraction. We also found that the HIV-1 Vif interaction sites in helix 4 of hA3C and hA3F differ. Vif alleles from diverse HIV-1 subtypes were tested for degradation activities related to hA3C. The subtype F-1 Vif was identified to be inactive for degradation of hA3C and hA3F. The residues that determined F-1 Vif inactivity in the degradation of A3C/A3F were located in the C-terminal region (K167 and D182). Structural analysis of F-1 Vif revealed that impairing the internal salt bridge of E171-K167 restored reduction capacities to A3C/A3F. Furthermore, we found that D101 could also form an internal interaction with K167. Replacing D101 with glycine and R167 with lysine in NL4-3 Vif impaired its counteractivity to A3F and A3C. This finding indicates that internal interactions outside the A3 binding region in HIV-1 Vif influence the capacity to induce degradation of A3C/A3F. IMPORTANCE: The APOBEC3 restriction factors can serve as potential barriers to lentiviral cross-species transmissions. Vif proteins from lentiviruses counteract APOBEC3 by proteasomal degradation. In this study, we found that monkey-derived A3C, rhA3C and smmA3C, were resistant to HIV-1 Vif. This was determined by A3C residues N/H130 and Q133. However, HIV-2, SIVagm, and SIVmac Vif proteins were found to be able to mediate the depletion of all tested primate A3C proteins. In addition, we identified a natural HIV-1 Vif (F-1 Vif) that was inactive in the degradation of hA3C/hA3F. Here, we provide for the first time a model that explains how an internal salt bridge of E171-K167-D101 influences Vif-mediated degradation of hA3C/hA3F. This finding provides a novel way to develop HIV-1 inhibitors by targeting the internal interactions of the Vif protein.","corpus_id":24908195,"score":1},{"doc_id":"28122978","title":"Conserved Interaction of Lentiviral Vif Molecules with HIV-1 Gag and Differential Effects of Species-Specific Vif on Virus Production.","abstract":"The virion infectivity factor (Vif) open reading frame is conserved among most lentiviruses. Vif molecules contribute to viral replication by inactivating host antiviral factors, the APOBEC3 cytidine deaminases. However, various species of lentiviral Vif proteins have evolved different strategies for overcoming host APOBEC3. Whether different species of lentiviral Vif proteins still preserve certain common features has not been reported. Here, we show for the first time that diverse lentiviral Vif molecules maintain the ability to interact with the human immunodeficiency virus type 1 (HIV-1) Gag precursor (Pr55(Gag)) polyprotein. Surprisingly, bovine immunodeficiency virus (BIV) Vif, but not HIV-1 Vif, interfered with HIV-1 production and viral infectivity even in the absence of APOBEC3. Further analysis revealed that BIV Vif demonstrated an enhanced interaction with Pr55(Gag) compared to that of HIV-1 Vif, and BIV Vif defective for the Pr55(Gag) interaction lost its ability to inhibit HIV-1. The C-terminal region of capsid (CA) and the p2 region of Pr55(Gag), which are important for virus assembly and maturation, were involved in the interaction. Transduction of CD4(+) T cells with BIV Vif blocked HIV-1 replication. Thus, the conserved Vif-Pr55(Gag) interaction provides a potential target for the future development of antiviral strategies. IMPORTANCE The conserved Vif accessory proteins of primate lentiviruses HIV-1, simian immunodeficiency virus (SIV), and BIV all form ubiquitin ligase complexes to target host antiviral APOBEC3 proteins for degradation, with different cellular requirements and using different molecular mechanisms. Here, we demonstrate that BIV Vif can interfere with HIV-1 Gag maturation and suppress HIV-1 replication through interaction with the precursor of the Gag (Pr55(Gag)) of HIV-1 in virus-producing cells. Moreover, the HIV-1 and SIV Vif proteins are conserved in terms of their interactions with HIV-1 Pr55(Gag) although HIV-1 Vif proteins bind Pr55(Gag) less efficiently than those of BIV Vif. Our research not only sheds new light on this feature of these conserved lentiviral Vif proteins but also provides a formerly unrecognized target for the development of antiviral strategies. Since increasing the Vif-Pr55(Gag) interaction could potentially suppress virus proliferation, this approach could offer a new strategy for the development of HIV inhibitors.","corpus_id":4549495,"score":1},{"doc_id":"28331087","title":"Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3.","abstract":"The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated antiviral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway. Although the Vif-APOBEC3 interaction and its evolutionary significance, particularly those of primate lentiviruses (including HIV) and primates (including humans), have been well investigated, those of nonprimate lentiviruses and nonprimates are poorly understood. Moreover, the factors that determine lentiviral pathogenicity remain unclear. Here, we focus on feline immunodeficiency virus (FIV), a pathogenic lentivirus in domestic cats, and the interaction between FIV Vif and feline APOBEC3 in terms of viral virulence and evolution. We reveal the significantly reduced diversity of FIV subtype B compared to that of other subtypes, which may associate with the low pathogenicity of this subtype. We also demonstrate that FIV subtype B Vif is less active with regard to feline APOBEC3 degradation. More intriguingly, we further reveal that FIV protease cleaves feline APOBEC3 in released virions. Taken together, our findings provide evidence that a lentivirus encodes two types of anti-APOBEC3 factors, Vif and viral protease. IMPORTANCE During the history of mammalian evolution, mammals coevolved with retroviruses, including lentiviruses. All pathogenic lentiviruses, excluding equine infectious anemia virus, have acquired the vif gene via evolution to combat APOBEC3 proteins, which are intrinsic restriction factors against exogenous lentiviruses. Here we demonstrate that FIV, a pathogenic lentivirus in domestic cats, antagonizes feline APOBEC3 proteins by both Vif and a viral protease. Furthermore, the Vif proteins of an FIV subtype (subtype B) have attenuated their anti-APOBEC3 activity through evolution. Our findings can be a clue to elucidate the complicated evolutionary processes by which lentiviruses adapt to mammals.","corpus_id":4618713,"score":1},{"doc_id":"29618650","title":"Simian Immunodeficiency Virus Vif and Human APOBEC3B Interactions Resemble Those between HIV-1 Vif and Human APOBEC3G.","abstract":"Several members of the APOBEC3 DNA cytosine deaminase family can potently inhibit Vif-deficient human immunodeficiency virus type 1 (HIV-1) by catalyzing cytosine deamination in viral cDNA and impeding reverse transcription. HIV-1 counteracts restriction with the virally encoded Vif protein, which targets relevant APOBEC3 proteins for proteasomal degradation. HIV-1 Vif is optimized for degrading the restrictive human APOBEC3 repertoire, and, in general, lentiviral Vif proteins specifically target the restricting APOBEC3 enzymes of each host species. However, simian immunodeficiency virus SIVmac239 Vif elicits a curiously wide range of APOBEC3 degradation capabilities that include degradation of several human APOBEC3s and even human APOBEC3B, a non-HIV-1-restricting APOBEC3 enzyme. To better understand the molecular determinants of the interaction between SIVmac239 Vif and human APOBEC3B, we analyzed an extensive series of mutants. We found that SIVmac239 Vif interacts with the N-terminal domain of human APOBEC3B and, interestingly, that this occurs within a structural region homologous to the HIV-1 Vif interaction surface of human APOBEC3G. An alanine scan of SIVmac239 Vif revealed several residues required for human APOBEC3B degradation activity. These residues overlap HIV-1 Vif surface residues that interact with human APOBEC3G and are distinct from those that engage APOBEC3F or APOBEC3H. Overall, these studies indicate that the molecular determinants of the functional interaction between human APOBEC3B and SIVmac239 Vif resemble those between human APOBEC3G and HIV-1 Vif. These studies contribute to the growing knowledge of the APOBEC-Vif interaction and may help guide future efforts to disrupt this interaction as an antiviral therapy or exploit the interaction as a novel strategy to inhibit APOBEC3B-dependent tumor evolution. IMPORTANCE Primate APOBEC3 proteins provide innate immunity against retroviruses such as HIV and SIV. HIV-1, the primary cause of AIDS, utilizes its Vif protein to specifically counteract restrictive human APOBEC3 enzymes. SIVmac239 Vif exhibits a much wider range of anti-APOBEC3 activities that includes several rhesus macaque enzymes and extends to multiple proteins in the human APOBEC3 repertoire, including APOBEC3B. Understanding the molecular determinants of the interaction between SIVmac239 Vif and human APOBEC3B adds to existing knowledge on the APOBEC3-Vif interaction and has potential to shed light on what processes may have shaped Vif functionality over evolutionary time. An intimate understanding of this interaction may also lead to a novel cancer therapy because, for instance, creating a derivative of SIVmac239 Vif that specifically targets human APOBEC3B could be used to suppress tumor genomic DNA mutagenesis by this enzyme, slow ongoing tumor evolution, and help prevent poor clinical outcomes.","corpus_id":4608976,"score":1},{"doc_id":"29636069","title":"New World feline APOBEC3 potently controls inter-genus lentiviral transmission.","abstract":"BACKGROUND: The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) gene family appears only in mammalian genomes. Some A3 proteins can be incorporated into progeny virions and inhibit lentiviral replication. In turn, the lentiviral viral infectivity factor (Vif) counteracts the A3-mediated antiviral effect by degrading A3 proteins. Recent investigations have suggested that lentiviral vif genes evolved to combat mammalian APOBEC3 proteins, and have further proposed that the Vif-A3 interaction may help determine the co-evolutionary history of cross-species lentiviral transmission in mammals. RESULTS: Here we address the co-evolutionary relationship between two New World felids, the puma (Puma concolor) and the bobcat (Lynx rufus), and their lentiviruses, which are designated puma lentiviruses (PLVs). We demonstrate that PLV-A Vif counteracts the antiviral action of APOBEC3Z3 (A3Z3) of both puma and bobcat, whereas PLV-B Vif counteracts only puma A3Z3. The species specificity of PLV-B Vif is irrespective of the phylogenic relationships of feline species in the genera Puma, Lynx and Acinonyx. We reveal that the amino acid at position 178 in the puma and bobcat A3Z3 is exposed on the protein surface and determines the sensitivity to PLV-B Vif-mediated degradation. Moreover, although both the puma and bobcat A3Z3 genes are polymorphic, their sensitivity/resistance to PLV Vif-mediated degradation is conserved. CONCLUSIONS: To the best of our knowledge, this is the first study suggesting that the host A3 protein potently controls inter-genus lentiviral transmission. Our findings provide the first evidence suggesting that the co-evolutionary arms race between lentiviruses and mammals has occurred in the New World.","corpus_id":4697371,"score":1},{"doc_id":"19929170","title":"Antiviral activity of the interferon-induced cellular protein BST-2/tetherin.","abstract":"Pathogenic microorganisms encode proteins that antagonize specific aspects of innate or adaptive immunity. Just as the study of the HIV-1 accessory protein Vif led to the identification of cellular cytidine deaminases as host defense proteins, the study of HIV-1 Vpu recently led to the discovery of the interferon-induced transmembrane protein BST-2 (CD317; tetherin) as a novel component of the innate defense against enveloped viruses. BST-2 is an unusually structured protein that restricts the release of fully formed progeny virions from infected cells, presumably by a direct retention mechanism that is independent of any viral protein target. Its spectrum of activity includes at least four virus families: retroviruses, filoviruses, arenaviruses, and herpesviruses. Viral antagonists of BST-2 include HIV-1 Vpu, HIV-2 and SIV Env, SIV Nef, the Ebola envelope glycoprotein, and the K5 protein of KSHV. The mechanisms of antagonism are diverse and currently include viral cooption of cellular endosomal trafficking and protein degradation pathways, including those mediated by ubiquitination. Orthologs of human BST-2 are present in mammals. Primate BST-2 proteins are differentially sensitive to antagonism by lentiviral Vpu and Nef proteins, suggesting that BST-2 has subjected lentiviruses to evolutionary pressure and presents barriers to cross-species transmission. BST-2 functions not only as an effector of the interferon-induced antiviral response but also as a negative feedback regulator of interferon production by plasmacytoid dendritic cells. Future work will focus on the role and regulation of BST-2 during the innate response to viral infection, on the mechanisms of restriction and of antagonism by viral gene products, and on the role of BST-2 in primate lentiviral evolution. The augmentation of BST-2 activity and the inhibition of virally encoded antagonists, in particular Vpu, represent new approaches to the prevention and treatment of HIV-1 infection.","corpus_id":23130024,"score":0},{"doc_id":"22574228","title":"Co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx gene in HIV-1 ancestor.","abstract":"Cross-species transmission and adaptation of simian immunodeficiency viruses (SIVs) to humans have given rise to human immunodeficiency viruses (HIVs). HIV type 1 (HIV-1) and type 2 (HIV-2) were derived from SIVs that infected chimpanzee (SIVcpz) and sooty mangabey (SIVsm), respectively. The HIV-1 restriction factor SAMHD1 inhibits HIV-1 infection in human myeloid cells and can be counteracted by the Vpx protein of HIV-2 and the SIVsm lineage. However, HIV-1 and its ancestor SIVcpz do not encode a Vpx protein and HIV-1 has not evolved a mechanism to overcome SAMHD1-mediated restriction. Here we show that the co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx gene in SIVcpz and HIV-1. We found evidence for positive selection of SAMHD1 in orangutan, gibbon, rhesus macaque, and marmoset, but not in human, chimpanzee and gorilla that are natural hosts of Vpx-negative HIV-1, SIVcpz and SIVgor, respectively, indicating that vpx drives the evolution of primate SAMHD1. Ancestral host state reconstruction and temporal dynamic analyses suggest that the most recent common ancestor of SIVrcm, SIVmnd, SIVcpz, SIVgor and HIV-1 was a SIV that had a vpx gene; however, the vpx gene of SIVcpz was lost approximately 3643 to 2969 years ago during the infection of chimpanzees. Thus, HIV-1 could not inherit the lost vpx gene from its ancestor SIVcpz. The lack of Vpx in HIV-1 results in restricted infection in myeloid cells that are important for antiviral immunity, which could contribute to the AIDS pandemic by escaping the immune responses.","corpus_id":8217948,"score":0},{"doc_id":"24819937","title":"Molecular evolution of the primate α-/θ-defensin multigene family.","abstract":"The primate α-/θ-defensin multigene family encodes versatile endogenous cationic and amphipathic peptides that have broad-spectrum antibacterial, antifungal and antiviral activity. Although previous studies have reported that α-/θ-defensin (DEFA/DEFT) genes are under birth-and-death evolution with frequent duplication and rapid evolution, the phylogenetic relationships of the primate DEFA/DEFT genes; the genetic bases for the existence of similar antimicrobial spectra among closely related species; and the evolutionary processes involved in the emergence of cyclic θ-defensins in Old World monkeys and their subsequent loss of function in humans, chimpanzees and gorillas require further investigation. In this study, the DEFA/DEFT gene repertoires from primate and treeshrew were collected, followed by detailed phylogenetic, sequence and structure, selection pressure and comparative genomics analyses. All treeshrew, prosimian and simian DEFA/DEFT genes are grouped into two major clades, which are tissue-specific for enteric and myeloid defensins in simians. The simian enteric and myeloid α-defensins are classified into six functional gene clusters with diverged sequences, variable structures, altered functional constraints and different selection pressures, which likely reflect the antimicrobial spectra among closely related species. Species-specific duplication or pseudogenization within each simian cluster implies that the antimicrobial spectrum is ever-shifting, most likely challenged by the ever-changing pathogen environment. The DEFT evolved from the myeloid DEFA8. The prosegment of θ-defensin is detected with adaptive changes coevolving with the new protein fold of mature peptide, coincident with the importance of the prosegment for the correct folding of the mature peptide. Lastly, a less-is-hitchhiking hypothesis was proposed as a possible explanation for the expansion of pseudogene DEFTP and the loss of functional DEFT, where the gain or loss of the hitchhiker is determined by its adjacent driver gene during the birth-and-death evolutionary process.","corpus_id":18525877,"score":0}],"string":"[\n {\n \"doc_id\": \"18299330\",\n \"title\": \"Human cytidine deaminase APOBEC3H restricts HIV-1 replication.\",\n \"abstract\": \"The human genome encodes seven APOBEC3 (A3) cytidine deaminases with potential antiretroviral activity: A3A, A3B, A3C, A3DE, A3F, A3G, and A3H. A3G was the first identified to block replication of human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. A3F, A3B, and A3DE were shown later to have similar activities. HIV-1 produces a protein called Vif that is able to neutralize the antiretroviral activities of A3DE, A3F, and A3G, but not A3B. Only the antiretroviral activity of A3H remains to be defined due to its poor expression in cell culture. Here, we studied the mechanism impairing A3H expression. When primate A3H sequences were compared, a premature termination codon was identified on the fifth exon of the human and chimpanzee A3H genes, which significantly decreased their protein expression. It causes a 29-residue deletion from the C terminus, and this truncation did not reduce human A3H protein stability. However, the mRNA levels of the truncated gene were significantly decreased. Human A3H protein expression could be restored to a normal level either by repairing this truncation or through expression from a vector containing an intron from human cytomegalovirus. Once expression was optimized, human A3H could reduce HIV-1 infectivity up to 150-fold. Importantly, HIV-1 Vif failed to neutralize A3H activity. Nevertheless, extensive sequence analysis could not detect any significant levels of G-to-A mutation in the HIV-1 genome by human A3H. Thus, A3H inhibits HIV-1 replication potently by a cytidine deamination-independent mechanism, and optimizing A3H expression in vivo should represent a novel therapeutic strategy for HIV-1 treatment.\",\n \"corpus_id\": 26270875,\n \"score\": 2\n },\n {\n \"doc_id\": \"18419775\",\n \"title\": \"Conserved and non-conserved features of HIV-1 and SIVagm Vif mediated suppression of APOBEC3 cytidine deaminases.\",\n \"abstract\": \"Human cytidine deaminase APOBEC3C (A3C) acts as a potent inhibitor of SIVagm and can be regulated by both HIV-1 and SIVagm Vif. The mechanism by which Vif suppresses A3C is unknown. In the present study, we demonstrate that both HIV-1 and SIVagm Vif can act in a proteasome-dependent manner to overcome A3C. SIVagm Vif requires the Cullin5-ElonginB-ElonginC E3 ubiquitin ligase for the degradation of A3C as well as the suppression of its antiviral activity. Mutation of a residue critical for the species-specific recognition of human or monkey A3G by HIV-1 Vif or SIVagm Vif in A3C had little effect on HIV-1 or SIVagm Vif-mediated degradation of A3C. Although the amino-terminal region of A3G was not important for Vif-mediated degradation, the corresponding region in A3C was critical. A3C mutants that were competent for Vif binding but resistant to Vif-mediated degradation were identified. These data suggest that primate lentiviral Vif molecules have evolved to recognize multiple host APOBEC3 proteins through distinct mechanisms. However, Cul5-E3 ubiquitin ligase appears to be a common pathway hijacked by HIV-1 and SIV Vif to defeat APOBEC3 proteins. Furthermore, Vif and APOBEC3 binding is not sufficient for target protein degradation indicating an important but uncharacterized Vif function.\",\n \"corpus_id\": 28949526,\n \"score\": 2\n },\n {\n \"doc_id\": \"18779051\",\n \"title\": \"Antiretroelement activity of APOBEC3H was lost twice in recent human evolution.\",\n \"abstract\": \"The primate APOBEC3 gene locus encodes a family of proteins (APOBEC3A-H) with various antiviral and antiretroelement activities. Here, we trace the evolution of APOBEC3H activity in hominoids to identify a human-specific loss of APOBEC3H antiviral activity. Reconstruction of the predicted ancestral human APOBEC3H protein shows that human ancestors encoded a stable form of this protein with potent antiviral activity. Subsequently, the antiviral activity of APOBEC3H was lost via two polymorphisms that are each independently sufficient to destabilize the protein. Nonetheless, an APOBEC3H allele that encodes a stably expressed protein is still maintained at high frequency, primarily in African populations. This stable APOBEC3H protein has potent activity against retroviruses and retrotransposons, including HIV and LINE-1 elements. The surprising finding that APOBEC3H antiviral activity has been lost in the majority of humans may have important consequences for our susceptibility to retroviral infections as well as ongoing retroelement proliferation in the human genome.\",\n \"corpus_id\": 25645505,\n \"score\": 2\n },\n {\n \"doc_id\": \"18827027\",\n \"title\": \"Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1.\",\n \"abstract\": \"Human cytidine deaminase apolipoprotein B mRNA-editing catalytic polypeptide-like 3 (APOBEC3) proteins have been classified as either Z1- or Z2-type cytidine deaminases on the basis of phylogenetic analysis of their catalytic domains. Despite the identification of a number of Z1-type domain-containing cytidine deaminases, only one copy of Z2-type cytidine deaminase has been detected in each of the mammalian species evaluated thus far. Z1-type human APOBEC3 proteins are known to exhibit broad activities against diverse retroelements. However, the potential role of the only human Z2-type cytidine deaminase, APOBEC3H (A3H), in the restriction of retroelements has not yet been fully characterized. Here, we demonstrate that human A3H is a potent inhibitor of non-LTR LINE-1 transposition. Interestingly, it was also as efficient as A3G in inhibiting Alu retrotransposition, despite its poor association with Alu RNA. We have further demonstrated, for the first time, that human APOBEC3DE is also a potent inhibitor of Alu retrotransposition. Variants of A3H have divergent antiviral activities against HIV-1-Vif-deficient viruses. Unlike the anti-HIV-1 cytidine deaminases A3G and A3F, A3H is moderately regulated by interferons. These observations suggest that human Z2-type cytidine deaminase A3H variants have varying intrinsic abilities to restrict retroelements and that various APOBEC3 proteins may have evolved distinct inhibitory mechanisms against retroelements.\",\n \"corpus_id\": 7774191,\n \"score\": 2\n },\n {\n \"doc_id\": \"18945781\",\n \"title\": \"Polymorphisms and splice variants influence the antiretroviral activity of human APOBEC3H.\",\n \"abstract\": \"Human APOBEC3H belongs to the APOBEC3 family of cytidine deaminases that potently inhibit exogenous and endogenous retroviruses. The impact of single nucleotide polymorphisms (SNP) and alternative splicing on the antiretroviral activity of human APOBEC3H is currently unknown. In this study, we show that APOBEC3H transcripts derived from human peripheral blood mononuclear cells are polymorphic in sequence and subject to alternative splicing. We found that APOBEC3H variants encoding a SNP cluster (G105R, K121D and E178D, hapII-RDD) restricted human immunodeficiency virus type 1 (HIV-1) more efficiently than wild-type APOBEC3H (hapI-GKE). All APOBEC3H variants tested were resistant to HIV-1 Vif, the viral protein that efficiently counteracts APOBEC3G/3F activity. Alternative splicing of APOBEC3H was common and resulted in variants with distinct C-terminal regions and variable antiretroviral activities. Splice variants of hapI-GKE displayed a wide range of antiviral activities, whereas similar splicing events in hapII-RDD resulted in proteins that uniformly and efficiently restricted viral infectivity (>20-fold). Site-directed mutagenesis identified G105R in hapI-GKE and D121K in hapII-RDD as critical substitutions leading to an average additional 10-fold increase in antiviral activity. APOBEC3H variants were catalytically active and, similarly to APOBEC3F, favored a GA dinucleotide context. HIV-1 mutagenesis as a mode of action for APOBEC3H is suggested by the decrease of restriction observed with a cytidine deaminase domain mutant and the inverse correlation between G-to-A mutations and infectivity. Thus, the anti-HIV activity of APOBEC3H seems to be regulated by a combination of genomic variation and alternative splicing. Since prevalence of hapII-RDD is high in populations of African descent, these findings raise the possibility that some individuals may harbor effective as well as HIV-1 Vif-resistant intracellular antiviral defense mechanisms.\",\n \"corpus_id\": 1499288,\n \"score\": 2\n },\n {\n \"doc_id\": \"19828612\",\n \"title\": \"The range of human APOBEC3H sensitivity to lentiviral Vif proteins.\",\n \"abstract\": \"The APOBEC3H gene is polymorphic in humans, with four major population-dependent haplotypes that encode proteins with different levels of antiviral activity. Haplotype II, present most frequently in African populations, encodes the most stable protein and is most active against human immunodeficiency virus type 1 (HIV-1). In contrast to human APOBEC3G, which can be completely counteracted by HIV-1 Vif, the protein encoded by APOBEC3H haplotype II is only partially sensitive to Vif, while the protein encoded by APOBEC3H haplotype I is completely resistant to HIV-1 Vif. We mapped a residue on APOBEC3H that determines this partial Vif sensitivity. However, it is unclear how HIV-1 can replicate in vivo without the ability to neutralize APOBEC3H antiviral activity. In order to directly address this question, we cloned vif genes from HIV-1-infected individuals with different APOBEC3H genotypes and tested them for their ability to inhibit human APOBEC3H. We found that while the APOBEC3H genotype of infected individuals significantly influences the activity of Vif encoded by their virus, none of the Vif variants tested can completely neutralize APOBEC3H as well as they neutralize APOBEC3G. Consistent with this genetic result, APOBEC3H protein expression in human peripheral blood mononuclear cells was below our limit of detection using newly developed antibodies against the endogenous protein. These results demonstrate that human APOBEC3H is not as strong of a selective force for current HIV-1 infections as human APOBEC3G.\",\n \"corpus_id\": 25846940,\n \"score\": 2\n },\n {\n \"doc_id\": \"19939923\",\n \"title\": \"A single amino acid difference in human APOBEC3H variants determines HIV-1 Vif sensitivity.\",\n \"abstract\": \"Several variants of APOBEC3H (A3H) have been identified in different human populations. Certain variants of this protein are particularly potent inhibitors of retrotransposons and retroviruses, including HIV-1. However, it is not clear whether HIV-1 Vif can recognize and suppress the antiviral activity of A3H variants, as it does with other APOBEC3 proteins. We now report that A3H_Haplotype II (HapII), a potent inhibitor of HIV-1 in the absence of Vif, can indeed be degraded by HIV-1 Vif. Vif-induced degradation of A3H_HapII was blocked by the proteasome inhibitor MG132 and a Cullin5 (Cul5) dominant negative mutant. In addition, Vif mutants that were incapable of assembly with the host E3 ligase complex factors Cul5, ElonginB, and ElonginC were also defective for A3H_HapII suppression. Although we found that Vif hijacks the same E3 ligase to degrade A3H_HapII as it does to inactivate APOBEC3G (A3G) and APOBEC3F (A3F), more Vif motifs were involved in A3H_HapII inactivation than in either A3G or A3F suppression. In contrast to A3H_HapII, A3H_Haplotype I (HapI), which differs in only three amino acids from A3H_HapII, was resistant to HIV-1 Vif-mediated degradation. We also found that residue 121 was critical for determining A3H sensitivity and binding to HIV-1 Vif.\",\n \"corpus_id\": 11246227,\n \"score\": 2\n },\n {\n \"doc_id\": \"20519393\",\n \"title\": \"Lentiviral Vif degrades the APOBEC3Z3/APOBEC3H protein of its mammalian host and is capable of cross-species activity.\",\n \"abstract\": \"All lentiviruses except equine infectious anemia virus (EIAV) use the small accessory protein Vif to counteract the restriction activity of the relevant APOBEC3 (A3) proteins of their host species. Prior studies have suggested that the Vif-A3 interaction is species specific. Here, using the APOBEC3H (Z3)-type proteins from five distinct mammals, we report that this is generally not the case: some lentiviral Vif proteins are capable of triggering the degradation of both the A3Z3-type protein of their normal host species and those of several other mammals. For instance, SIV(mac) Vif can mediate the degradation of the human, macaque, and cow A3Z3-type proteins but not of the sheep or cat A3Z3-type proteins. Maedi-visna virus (MVV) Vif is similarly promiscuous, degrading not only sheep A3Z3 but also the A3Z3-type proteins of humans, macaques, cows, and cats. In contrast to the neutralization capacity of these Vif proteins, human immunodeficiency virus (HIV), bovine immunodeficiency virus (BIV), and feline immunodeficiency virus (FIV) Vif appear specific to the A3Z3-type protein of their hosts. We conclude, first, that the Vif-A3Z3 interaction can be promiscuous and, second, despite this tendency, that each lentiviral Vif protein is optimized to degrade the A3Z3 protein of its mammalian host. Our results thereby suggest that the Vif-A3Z3 interaction is relevant to lentivirus biology.\",\n \"corpus_id\": 43424582,\n \"score\": 2\n },\n {\n \"doc_id\": \"20519396\",\n \"title\": \"The localization of APOBEC3H variants in HIV-1 virions determines their antiviral activity.\",\n \"abstract\": \"Several members of the human APOBEC3 family of cytidine deaminases can potently restrict retroviruses such as HIV-1. The single-domain APOBEC3H (A3H) is encoded by four haplotypes, of which only A3H haplotype II-RDD (hapII-RDD) restricts HIV-1 efficiently. The goal of this study was to elucidate the mechanisms underlying the differences in antiviral activity among A3H haplotypes. The naturally occurring A3H hapI-GKE and hapII-RDD variants differ at three amino acid positions. A panel of six site-directed mutants containing combinations of the three variable residues was used to determine A3H protein expression, requirements of A3H virion incorporation, and A3H-Gag interactions. The catalytic activity of each A3H protein was assessed directly by using an Escherichia coli mutator assay. We found that the incorporation efficiencies of A3H variants into HIV-1 virions were comparable despite major differences in cellular expression. An assessment of the enzymes' catalytic activities showed that the deaminase activity of each A3H variant correlated with protein expression, suggesting similar enzymatic efficiencies. Surprisingly, virion incorporation experiments using Gag deletion mutants demonstrated that A3H haplotypes interacted with different Gag regions. A3H hapII-RDD associated with nucleocapsid in an RNA-dependent manner, whereas A3H hapI-GKE associated with the C-terminal part of matrix and the N-terminal capsid domain. Our results show that the A3H hapII-RDD interaction with nucleocapsid is critical for its antiviral activity and that the inability of A3H hapI-GKE to interact with nucleocapsid underlies its limited antiviral potential. Thus, the antiviral activity of A3H haplotypes is determined by its incorporation into the viral core, in proximity to the reverse transcription complex.\",\n \"corpus_id\": 206797331,\n \"score\": 2\n },\n {\n \"doc_id\": \"21167246\",\n \"title\": \"APOBEC3H haplotypes and HIV-1 pro-viral vif DNA sequence diversity in early untreated human immunodeficiency virus-1 infection.\",\n \"abstract\": \"We examined single nucleotide polymorphisms (SNP) in the APOBEC3 locus on chromosome 22, paired with population sequences of pro-viral human immunodeficiency virus-1 (HIV-1) vif from peripheral blood mononuclear cells, from 96 recently HIV-1-infected treatment-naive adults. We found evidence for the existence of an APOBEC3H linkage disequilibrium (LD) block associated with variation in GA → AA, or APOBEC3F/H signature, sequence changes in pro-viral HIV-1 vif sequence (top 10 significant SNPs with a significant p = 4.8 × 10(-3)). We identified a common five position risk haplotype distal to APOBEC3H (A3Hrh). These markers were in high LD (D' = 1; r(2) = 0.98) to a previously described A3H \\\"RED\\\" haplotype containing a variant (E121) with enhanced susceptibility to HIV-1 Vif. This association was confirmed by a haplotype analysis. Homozygote carriers of the A3Hrh had lower GA->AA (A3F/H) sequence editing upon pro-viral HIV-1 vif sequence (p = 0.01), and lower HIV-1 RNA levels over time during early, untreated HIV-1 infection, (p = 0.015 mixed effects model). This effect may be due to enhanced susceptibility of A3H forms to HIV-1 Vif mediated viral suppression of sequence editing activity, slowing viral diversification and escape from immune responses.\",\n \"corpus_id\": 40941683,\n \"score\": 2\n },\n {\n \"doc_id\": \"21270145\",\n \"title\": \"Analysis of human APOBEC3H haplotypes and anti-human immunodeficiency virus type 1 activity.\",\n \"abstract\": \"Human APOBEC3H (A3H) has one cytidine deaminase domain (CDD) and inhibits the replication of retrotransposons and human immunodeficiency virus type 1 (HIV-1) in a Vif-resistant manner. Human A3H has five single amino acid polymorphisms (N15Δ, R18L, G105R, K121D, and E178D), and four haplotypes (I to IV) have previously been identified in various human populations. Haplotype II was primarily found in African-derived populations, and it was the only one that could be stably expressed. Here, we identified three new haplotypes from six human population samples, which we have named V, VI, and VII. Haplotypes V and VII are stably expressed and inhibit HIV-1 replication. Notably, haplotype V was identified in samples from all African-, Asian-, and Caucasian-derived populations studied. Using haplotype VII, we investigated the A3H anti-HIV-1 mechanism. We found that A3H virion packaging is independent of its CDD but dependent on a (112)YYXW(115) motif. This motif binds HIV-1 nucleocapsid in an RNA-dependent manner, and a single Y112A mutation completely disrupts A3H virion incorporation. We further studied the mechanism of A3H resistance to Vif. Although the previously identified APOBEC3G Vif-responsive motif (128)DPDY(131) is not conserved in A3H, placement of this motif into A3H does not make it become less resistant to HIV-1 Vif. We conclude that stably expressed A3H haplotypes may be more broadly distributed in humans than previously realized, and A3H protein is resistant to Vif. These results have important implications for the role of A3H in retrotransposon and HIV-1 inhibition.\",\n \"corpus_id\": 2045222,\n \"score\": 2\n },\n {\n \"doc_id\": \"21653666\",\n \"title\": \"Polymorphism in human APOBEC3H affects a phenotype dominant for subcellular localization and antiviral activity.\",\n \"abstract\": \"The APOBEC3 family of cytidine deaminases is part of the innate host defense targeted toward retroviruses and retroelements. APOBEC3H is the most distantly related member of the family and carries functional polymorphisms in current human populations. Haplotype II of APOBEC3H, which is more commonly found in individuals of African descent, encodes a protein with the highest antiviral activity in cells, whereas the other haplotypes encode proteins with weak or no antiviral activity. Here, we show that the different human APOBEC3H haplotypes exhibit differential subcellular localizations, as the haplotype I protein is mostly found in the nucleus and the haplotype II protein is mostly localized to the cytoplasm. The determinant responsible for this phenotype maps to a single amino acid that is also important for APOBEC3H protein stability. Furthermore, we show that the cytoplasmic localization is dominant over nuclear localization, by using fusion proteins of APOBEC3H. Our data support a model in which the APOBEC3H protein encoded by haplotype II is actively retained in the cytoplasm by interacting with specific host factors, whereas the less active protein encoded by haplotype I is allowed to enter the nucleus by a passive mechanism. Together, cytoplasmic localization and its link with protein stability correlate with the ability of APOBEC3H to inhibit HIV replication, providing a mechanistic basis for the differential antiviral activities of different APOBEC3H haplotypes.\",\n \"corpus_id\": 20683746,\n \"score\": 2\n },\n {\n \"doc_id\": \"22013041\",\n \"title\": \"The activity spectrum of Vif from multiple HIV-1 subtypes against APOBEC3G, APOBEC3F, and APOBEC3H.\",\n \"abstract\": \"The APOBEC3 family comprises seven cytidine deaminases (APOBEC3A [A3A] to A3H), which are expressed to various degrees in HIV-1 susceptible cells. The HIV-1 Vif protein counteracts APOBEC3 restriction by mediating its degradation by the proteasome. We hypothesized that Vif proteins from various HIV-1 subtypes differ in their abilities to counteract different APOBEC3 proteins. Seventeen Vif alleles from seven HIV-1 subtypes were tested for their abilities to degrade and counteract A3G, A3F, and A3H haplotype II (hapII). We show that most Vif alleles neutralize A3G and A3F efficiently but display differences with respect to the inhibition of A3H hapII. The majority of non-subtype B Vif alleles tested presented some activity against A3H hapII, with two subtype F Vif variants being highly effective in counteracting A3H hapII. The residues required for activity were mapped to two residues in the amino-terminal region of Vif (positions 39F and 48H). Coimmunoprecipitations showed that these two amino acids were necessary for association of Vif with A3H hapII. These findings suggest that the A3H hapII binding site in Vif is distinct from the regions important for A3G and A3F recognition and that it requires specific amino acids at positions 39 and 48. The differential Vif activity spectra, especially against A3H hapII, suggest adaptation to APOBEC3 repertoires representative of different human ancestries. Phenotypic assessment of anti-APOBEC3 activity of Vif variants against several cytidine deaminases will help reveal the requirement for successful replication in vivo and ultimately point to interventions targeting the Vif-APOBEC3 interface.\",\n \"corpus_id\": 25772290,\n \"score\": 2\n },\n {\n \"doc_id\": \"22023594\",\n \"title\": \"A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection.\",\n \"abstract\": \"APOBEC3 genes encode cytidine deaminases endowed with the ability to inhibit retroviruses and retrotransposons. These genes have been targets of natural selection throughout primate evolutionary history. We analyzed their selection pattern in human populations observing that APOBEC3F and 3G are neutrally evolving. Conversely, nucleotide diversity was extremely high for APOBEC3H, and most tests rejected the hypothesis of selective neutrality in Eurasian populations. Haplotype analysis and the derived intraallelic nucleotide diversity test indicated that positive selection has driven the increase in frequency of one haplotype (Hap I) outside Africa. Consistently, population genetic differentiation between African and non-African populations was higher than expected under neutrality. A case-control association analysis indicated that Hap I is associated with protection from sexually transmitted HIV-1 infection. Hap I carries a protein-destabilizing variant and a residue conferring resistance to Vif-mediated degradation. Data herein suggest that lower protein stability might have been traded-off with a higher ability to circumvent Vif-mediated hijacking. Alternatively, transcription regulatory variants might represent the selection target. Our data represent an example of how the selective pressures exerted by extinct or unknown viral agents can be exploited to provide valuable information on the allelic determinants of susceptibility to modern infections.\",\n \"corpus_id\": 25238486,\n \"score\": 2\n },\n {\n \"doc_id\": \"22264516\",\n \"title\": \"The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict.\",\n \"abstract\": \"APOBEC3G (A3G) is a host cytidine deaminase that inhibits retroviruses. HIV and related primate lentiviruses encode Vif, which counteracts A3G by inducing its degradation. This Vif-mediated A3G inhibition is species specific, suggesting that the A3G-Vif interaction has evolved as primate lentiviruses have adapted to their hosts. We examined the evolutionary dynamics of the A3G-Vif interaction within four African green monkey (AGM) subspecies, which are each naturally infected with a distinct simian immunodeficiency virus (SIV). We identified single amino acid changes within A3G in two AGM subspecies that render it resistant to Vif proteins, except for Vif from the viruses that naturally infect these subspecies. Moreover, experimental infection of AGMs shows that Vif can rapidly adapt to these arising Vif-resistant A3G genotypes. These data suggest that despite being generally nonpathogenic in its natural host, SIV infection selects for Vif-resistant forms of A3G in AGM populations, driving Vif counterevolution and functional divergence.\",\n \"corpus_id\": 206685798,\n \"score\": 2\n },\n {\n \"doc_id\": \"22859935\",\n \"title\": \"Reduced APOBEC3H variant anti-viral activities are associated with altered RNA binding activities.\",\n \"abstract\": \"APOBEC3H (A3H) is a member of the APOBEC3 family of proteins with varying activities against retroviruses and retrotransposons. The A3H gene contains several single nucleotide polymorphisms and up to seven haplotypes have been detected in humans. Although variations in anti-viral function among A3H haplotypes are not fully understood, only 15N105R-containing A3H variants are known to have potent activities against Vif-deficient HIV-1. Unique motif RLYY(F/Y)W of APOBEC3G (A3G) and APOBEC3F (A3F) required for 7SL RNA binding and HIV-1 incorporation is also conserved in all A3H variants. Like A3G, A3H HapII also demonstrated high binding affinity to host small RNAs such as 7SL and Y RNAs. Mutation of a critical amino acid, W115A resulted in reduced expression level, decreased affinity for 7SL RNA, impairment of virion packaging and reduced anti-viral activity. By comparison, A3H HapI had lower binding affinities to host small RNAs and reduced efficiency of virion incorporation, resulting in significantly reduced anti-viral activity. The SNP ΔN15 commonly found in A3H HapIII and HapIV abolished their abilities to associate with RNAs, and A3H HapIIΔ15N failed to package into HIV-1 virions or exhibited any anti-viral activity. Finally, we showed that A3H variants had distinct cellular localization patterns, which correlated with their different RNA binding affinities. Thus, Pol-III RNA such as 7SL RNA binding is a conserved feature of potent anti-HIV human APOBEC3 cytidine deaminases.\",\n \"corpus_id\": 3028921,\n \"score\": 2\n },\n {\n \"doc_id\": \"23359341\",\n \"title\": \"Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses.\",\n \"abstract\": \"Naturally circulating lentiviruses are abundant in African primate species today, yet their origins and history of transmitting between hosts remain obscure. As a means to better understand the age of primate lentiviruses, we analyzed primate genomes for signatures of lentivirus-driven evolution. Specifically, we studied the adaptive evolution of host restriction factor APOBEC3G (A3G) in Old World Monkey (OWM) species. We find recurrent mutation of A3G in multiple primate lineages at sites that determine susceptibility to antagonism by the lentiviral accessory protein Vif. Using a broad panel of SIV Vif isolates, we demonstrate that natural variation in OWM A3G confers resistance to Vif-mediated degradation, suggesting that adaptive variants of the host factor were selected upon exposure to pathogenic lentiviruses at least 5-6 million years ago (MYA). Furthermore, in members of the divergent Colobinae subfamily of OWM, a multi-residue insertion event in A3G that arose at least 12 MYA blocks the activity of Vif, suggesting an even more ancient origin of SIV. Moreover, analysis of the lentiviruses associated with Colobinae monkeys reveal that the interface of the A3G-Vif interaction has shifted and given rise to a second genetic conflict. Our analysis of virus-driven evolution describes an ancient yet ongoing genetic conflict between simian primates and lentiviruses on a million-year time scale.\",\n \"corpus_id\": 17533340,\n \"score\": 2\n },\n {\n \"doc_id\": \"23469063\",\n \"title\": \"The resistance of human APOBEC3H to HIV-1 NL4-3 molecular clone is determined by a single amino acid in Vif.\",\n \"abstract\": \"Some human APOBEC3 cytidine deaminases have antiviral activity against HIV-1 and other retroviruses. The single deaminase domain APOBEC3H (A3H) enzyme is highly polymorphic and multiple A3H haplotypes have been identified. A3H haplotype II (A3H-hapII) possesses the strongest activity against HIV-1. There remains, however, uncertainty regarding the extent to which A3H-hapII is sensitive to HIV-1 Vif mediated degradation. We tested, therefore, the two different reference Vif proteins widely used in previous studies. We show that A3H-hapII is resistant to NL4-3 Vif while it is efficiently degraded by LAI Vif. Co-immunoprecipitation assays demonstrate that LAI Vif, but not NL4-3 Vif associates with A3H-hapII. Chimeras between NL4-3 and LAI Vif identify the amino acid responsible for the differential degradation activity: A histidine at position 48 in Vif confers activity against A3H-hapII, while an asparagine abolishes its anti-A3H activity. Furthermore, the amino acid identity at position 48 only affects the degradation of A3H-hapII, whereas recognition of and activity against human A3D, A3F and A3G are only minimally affected. NL4-3 encoding 48H replicates better than NL4-3 WT (48N) in T cell-lines stably expressing A3H hapII, whereas there is no fitness difference in the absence of APOBEC3. These studies provide an explanation for the conflicting reports regarding A3H resistance to Vif mediated degradation.\",\n \"corpus_id\": 13985345,\n \"score\": 2\n },\n {\n \"doc_id\": \"23870316\",\n \"title\": \"Gene loss and adaptation to hominids underlie the ancient origin of HIV-1.\",\n \"abstract\": \"HIV-1 resulted from cross-species transmission of SIVcpz, a simian immunodeficiency virus that naturally infects chimpanzees. SIVcpz, in turn, is a recombinant between two SIV lineages from Old World monkeys. Lentiviral interspecies transmissions are partly driven by the evolution and capacity of viral accessory genes, such as vpx, vpr, and vif, to antagonize host antiviral factors, such as SAMHD1 and the APOBEC3 proteins. We show that vpx, which in other lentiviruses antagonizes SAMHD1, was deleted during the creation of SIVcpz. This genomic deletion resulted in the reconstruction of the overlapping vif gene by \\\"overprinting,\\\" creating a unique vif that overlaps in its 3' end with the vpr gene and can antagonize hominid APOBEC3s. Moreover, passage of SIVs through chimpanzees facilitated the subsequent adaptation of HIV-1 to humans. Thus, HIV-1 originated through a series of gene loss and adaptation events that generated its chimpanzee precursor and lowered the species barrier to human infection.\",\n \"corpus_id\": 40520788,\n \"score\": 2\n },\n {\n \"doc_id\": \"23938749\",\n \"title\": \"Host gene evolution traces the evolutionary history of ancient primate lentiviruses.\",\n \"abstract\": \"Simian immunodeficiency viruses (SIVs) have infected primate species long before human immunodeficiency virus has infected humans. Dozens of species-specific lentiviruses are found in African primate species, including two strains that have repeatedly jumped into human populations within the past century. Traditional phylogenetic approaches have grossly underestimated the age of these primate lentiviruses. Instead, here we review how selective pressures imposed by these viruses have fundamentally altered the evolutionary trajectory of hosts genes and, even in cases where there now remains no trace of the viruses themselves, these evolutionary signatures can reveal the types of viruses that were once present. Examination of selection by ancient viruses on the adaptive evolution of host genes has been used to derive minimum age estimates for modern primate lentiviruses. This type of data suggests that ancestors of modern SIV existed in simian primates more than 10 Ma. Moreover, examples of host resistance and viral adaptation have implications not only for estimating the age and host range of ancient primate lentiviruses, but also the pathogenic potential of their modern counterparts.\",\n \"corpus_id\": 21373490,\n \"score\": 2\n },\n {\n \"doc_id\": \"23986590\",\n \"title\": \"Vif proteins from diverse primate lentiviral lineages use the same binding site in APOBEC3G.\",\n \"abstract\": \"APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty mangabey monkeys (SIVsmm), suggesting that the A3G binding site for Vif proteins of the SIVsmm/HIV-2 lineage differs from that of HIV-1. To map the SIVsmm Vif binding site of A3G, we performed immunoprecipitations of individual A3G domains, Vif/A3G degradation assays and a detailed mutational analysis of human A3G. We show that A3G residue 129, but not the adjacent position 128, confers susceptibility to degradation by SIVsmm Vif. An artificial A3G mutant, the P129D mutant, was resistant to degradation by diverse Vifs from HIV-1, HIV-2, SIVagm, and chimpanzee SIV (SIVcpz), suggesting a conserved lentiviral Vif binding site. Gorilla A3G naturally contains a glutamine (Q) at position 129, which makes its A3G resistant to Vifs from diverse lineages. We speculate that gorilla A3G serves as a barrier against SIVcpz strains. In summary, we show that Vif proteins from distinct lineages bind to the same A3G loop, which includes positions 128 and 129. The multiple adaptations within this loop among diverse primates underscore the importance of counteracting A3G in lentiviral evolution.\",\n \"corpus_id\": 25032756,\n \"score\": 2\n },\n {\n \"doc_id\": \"24139399\",\n \"title\": \"HIV-1 Vif adaptation to human APOBEC3H haplotypes.\",\n \"abstract\": \"Several human APOBEC3 deaminases can inhibit HIV-1 replication in vitro. HIV-1 Vif counteracts this restriction by targeting APOBEC3 for proteasomal degradation. Human APOBEC3H (A3H) is highly polymorphic, with natural variants differing considerably in anti-HIV-1 activity in vitro. To examine HIV-1 adaptation to variation in A3H activity in a natural infection context, we determined the A3H haplotypes and Vif sequences from 76 recently infected HIV-1 patients. We detected A3H-specific Vif changes suggesting viral adaptation. The patient-derived Vif sequences were used to engineer viruses that specifically differed in their ability to counteract A3H. Replication of these Vif-variant viruses in primary T cells naturally expressing active or inactive A3H haplotypes showed that endogenously expressed A3H restricts HIV-1 replication. Proviral DNA from A3H-restricted viruses showed high levels of G-to-A mutations in an A3H-specific GA dinucleotide context. Taken together, our data validate A3H expressed at endogenous levels as a bona fide HIV-1 restriction factor.\",\n \"corpus_id\": 22905101,\n \"score\": 2\n },\n {\n \"doc_id\": \"24189052\",\n \"title\": \"Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all.\",\n \"abstract\": \"Several members of the APOBEC3 family of cellular restriction factors provide intrinsic immunity to the host against viral infection. Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through hypermutation of the viral genome, inhibition of reverse transcription, and inhibition of viral DNA integration into the host genome. HIV-1 counteracts APOBEC3 proteins by encoding the viral protein Vif, which contains distinct domains that specifically interact with these APOBEC3 proteins to ensure their proteasomal degradation, allowing virus replication to proceed. Here, we review our current understanding of APOBEC3 structure, editing and non-editing mechanisms of APOBEC3-mediated restriction, Vif-APOBEC3 interactions that trigger APOBEC3 degradation, and the contribution of APOBEC3 proteins to restriction and control of HIV-1 replication in infected patients.\",\n \"corpus_id\": 7844655,\n \"score\": 2\n },\n {\n \"doc_id\": \"25122780\",\n \"title\": \"Core-binding factor subunit beta is not required for non-primate lentiviral Vif-mediated APOBEC3 degradation.\",\n \"abstract\": \"Viral infectivity factor (Vif) is required for lentivirus fitness and pathogenicity, except in equine infectious anemia virus (EIAV). Vif enhances viral infectivity by a Cullin5-Elongin B/C E3 complex to inactivate the host restriction factor APOBEC3. Core-binding factor subunit beta (CBF-β) is a cell factor that was recently shown to be important for the primate lentiviral Vif function. Non-primate lentiviral Vif also degrades APOBEC3 through the proteasome pathway. However, it is unclear whether CBF-β is required for the non-primate lentiviral Vif function. In this study, we demonstrated that the Vifs of non-primate lentiviruses, including feline immunodeficiency virus (FIV), bovine immunodeficiency virus (BIV), caprine arthritis encephalitis virus (CAEV), and maedi-visna virus (MVV), do not interact with CBF-β. In addition, CBF-β did not promote the stability of FIV, BIV, CAEV, and MVV Vifs. Furthermore, CBF-β silencing or overexpression did not affect non-primate lentiviral Vif-mediated APOBEC3 degradation. Our results suggest that non-primate lentiviral Vif induces APOBEC3 degradation through a different mechanism than primate lentiviral Vif. Importance: The APOBEC3 protein family members are host restriction factors that block retrovirus replication. Vif, an accessory protein of lentivirus, degrades APOBEC3 to rescue viral infectivity by forming Cullin5-Elongin B/C-based E3 complex. CBF-β was proved to be a novel regulator of primate lentiviral Vif function. In this study, we found that CBF-β knockdown or overexpression did not affect FIV Vif's function, which induced polyubiquitination and degradation of APOBEC3 by recruiting the E3 complex in a manner similar to that of HIV-1 Vif. We also showed that other non-primate lentiviral Vifs did not require CBF-β to degrade APOBEC3. CBF-β did not interact with non-primate lentiviral Vifs or promote their stability. These results suggest that a different mechanism exists for the Vif-APOBEC interaction and that non-primates are not suitable animal models for exploring pharmacological interventions that disrupt Vif-CBF-β interaction.\",\n \"corpus_id\": 206808386,\n \"score\": 2\n },\n {\n \"doc_id\": \"25411794\",\n \"title\": \"Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity.\",\n \"abstract\": \"The Vif protein of HIV-1 allows virus replication by degrading several members of the host-encoded APOBEC3 family of DNA cytosine deaminases. Polymorphisms in both host APOBEC3 genes and the viral vif gene have the potential to impact the extent of virus replication among individuals. The most genetically diverse of the seven human APOBEC3 genes is APOBEC3H with seven known haplotypes. Overexpression studies have shown that a subset of these variants express stable and active proteins, whereas the others encode proteins with a short half-life and little, if any, antiviral activity. We demonstrate that these stable/unstable phenotypes are an intrinsic property of endogenous APOBEC3H proteins in primary CD4+ T lymphocytes and confer differential resistance to HIV-1 infection in a manner that depends on natural variation in the Vif protein of the infecting virus. HIV-1 with a Vif protein hypo-functional for APOBEC3H degradation, yet fully able to counteract APOBEC3D, APOBEC3F, and APOBEC3G, was susceptible to restriction and hypermutation in stable APOBEC3H expressing lymphocytes, but not in unstable APOBEC3H expressing lymphocytes. In contrast, HIV-1 with hyper-functional Vif counteracted stable APOBEC3H proteins as well as all other endogenous APOBEC3s and replicated to high levels. We also found that APOBEC3H protein levels are induced over 10-fold by infection. Finally, we found that the global distribution of stable/unstable APOBEC3H haplotypes correlates with the distribution a critical hyper/hypo-functional Vif amino acid residue. These data combine to strongly suggest that stable APOBEC3H haplotypes present as in vivo barriers to HIV-1 replication, that Vif is capable of adapting to these restrictive pressures, and that an evolutionary equilibrium has yet to be reached.\",\n \"corpus_id\": 12686637,\n \"score\": 2\n },\n {\n \"doc_id\": \"25590520\",\n \"title\": \"Evolutionarily conserved pressure for the existence of distinct G2/M cell cycle arrest and A3H inactivation functions in HIV-1 Vif.\",\n \"abstract\": \"HIV-1 Vif assembles the Cul5-EloB/C E3 ubiquitin ligase to induce proteasomal degradation of the cellular antiviral APOBEC3 proteins. Detailed structural studies have confirmed critical functional domains in Vif that we have previously identified as important for the interaction of EloB/C, Cul5, and CBFβ. However, the mechanism by which Vif recognizes substrates remains poorly understood. Specific regions of Vif have been identified as being responsible for binding and depleting APOBEC3G and APOBEC3F. Interestingly, we have now identified distinct yet overlapping domains that are required for HIV-1 Vif-mediated G2/M-phase cell cycle arrest and APOBEC3H degradation, but not for the inactivation of APOBEC3G or APOBEC3F. Surprisingly, Vif molecules from primary HIV-1 variants that caused G2/M arrest were unable to inactivate APOBEC3H; on the other hand, HIV-1 Vif variants that could inactivate APOBEC3H were unable to induce G2/M arrest. All of these Vif variants still maintained the ability to inactivate APOBEC3G/F. Thus, primary HIV-1 variants have evolved to possess distinct functional activities that allow them to suppress APOBEC3H or cause G2 cell cycle arrest, using mutually exclusive interface domains. APOBEC3H depletion and G2 arrest are apparently evolutionary selected features that cannot co-exist on a single Vif molecule. The existence and persistence of both types of HIV-1 Vif variant suggests the importance of APOBEC3H suppression and cell cycle regulation for HIV-1's survival in vivo.\",\n \"corpus_id\": 21345503,\n \"score\": 2\n },\n {\n \"doc_id\": \"25614027\",\n \"title\": \"Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities.\",\n \"abstract\": \"BACKGROUND: Human APOBEC3H (A3H) belongs to the A3 family of host restriction factors, which are cytidine deaminases that catalyze conversion of deoxycytidine to deoxyuridine in single-stranded DNA. A3 proteins contain either one (A3A, A3C, A3H) or two (A3B, A3D, A3F, A3G) Zn-binding domains. A3H has seven haplotypes (I-VII) that exhibit diverse biological phenotypes and geographical distribution in the human population. Its single Zn-coordinating deaminase domain belongs to a phylogenetic cluster (Z3) that is different from the Z1- and Z2-type domains in other human A3 proteins. A3H HapII, unlike A3A or A3C, has potent activity against HIV-1. Here, we sought to identify the determinants of A3H HapII deaminase and antiviral activities, using site-directed sequence- and structure-guided mutagenesis together with cell-based, biochemical, and HIV-1 infectivity assays. RESULTS: We have constructed a homology model of A3H HapII, which is similar to the known structures of other A3 proteins. The model revealed a large cluster of basic residues (not present in A3A or A3C) that are likely to be involved in nucleic acid binding. Indeed, RNase A pretreatment of 293T cell lysates expressing A3H was shown to be required for detection of deaminase activity, indicating that interaction with cellular RNAs inhibits A3H catalytic function. Similar observations have been made with A3G. Analysis of A3H deaminase substrate specificity demonstrated that a 5' T adjacent to the catalytic C is preferred. Changing the putative nucleic acid binding residues identified by the model resulted in reduction or abrogation of enzymatic activity, while substituting Z3-specific residues in A3H to the corresponding residues in other A3 proteins did not affect enzyme function. As shown for A3G and A3F, some A3H mutants were defective in catalysis, but retained antiviral activity against HIV-1vif (-) virions. Furthermore, endogenous reverse transcription assays demonstrated that the E56A catalytic mutant inhibits HIV-1 DNA synthesis, although not as efficiently as wild type. CONCLUSIONS: The molecular and biological activities of A3H are more similar to those of the double-domain A3 proteins than to those of A3A or A3C. Importantly, A3H appears to use both deaminase-dependent and -independent mechanisms to target reverse transcription and restrict HIV-1 replication.\",\n \"corpus_id\": 12923119,\n \"score\": 2\n },\n {\n \"doc_id\": \"25721876\",\n \"title\": \"APOBEC3H polymorphisms associated with the susceptibility to HIV-1 infection and AIDS progression in Japanese.\",\n \"abstract\": \"Human APOBEC3H (A3H) is a member of APOBEC3 cytidine deaminase family that potently restricts HIV-1 replication. Because A3H is genetically divergent with different intracellular stability and anti-HIV-1 activity in vitro, we investigated a possible association of A3H with susceptibility to HIV-1 infection and disease progression in Japanese populations. A total of 191 HIV-1-infected individuals (HIV group), 93 long-term non-progressors to AIDS (LTNP group) and 421 healthy controls were genotyped for two functional APOBEC3H polymorphisms, rs139292 and rs139297. As compared with the controls, minor allele frequency (MAF) for rs139292 was high in the HIV group (MAF in cases vs. controls; 0.322 vs. 0.263, odds ratio (OR) = 1.33, 95% confidence interval (95% CI) = 1.02-1.74, p = 0.035) and low in the LTNP group (0.161 vs. 0.263, OR = 0.54, 95% CI = 0.36-0.82, p = 0.004, pc = 0.007), whereas the MAF for rs139297 was high in the HIV group (0.367 vs. 0.298, OR = 1.36, 95% CI = 1.07-1.76, p = 0.017, pc = 0.035). In addition, haplotype analyses revealed that the frequencies of A3H-hapC and -hapA were high (0.322 vs. 0.262, OR = 1.33, 95% CI = 1.02-1.74, p = 0.003) and low (0.634 vs. 0.697, OR = 0.75, 95 % CI = 0.58-0.97, p = 0.002), respectively, in the HIV group, whereas the frequencies of A3H-hapC and -hapB were low (0.161 vs. 0.262, OR = 0.54, 95% CI = 0.36-0.82, p = 0.00003) and high (0.097 vs. 0.040, OR = 2.55, 95% CI = 1.40-4.62, p = 0.000008), respectively, in the LTNP group, as compared with those in the controls. These observations suggest that the A3H with low anti-HIV-1 activity, A3H-hapC, is associated with the susceptibility to HIV-1 infection, whereas the A3H producing a stable protein, A3H-hapB, may confer a low risk of disease progression to AIDS.\",\n \"corpus_id\": 1432478,\n \"score\": 2\n },\n {\n \"doc_id\": \"26491161\",\n \"title\": \"A Naturally Occurring Domestic Cat APOBEC3 Variant Confers Resistance to Feline Immunodeficiency Virus Infection.\",\n \"abstract\": \"UNLABELLED: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) DNA cytosine deaminases can be incorporated into progeny virions and inhibit lentiviral replication. On the other hand, viral infectivity factor (Vif) of lentiviruses antagonizes A3-mediated antiviral activities by degrading A3 proteins. It is known that domestic cat (Felis catus) APOBEC3Z3 (A3Z3), the ortholog of human APOBEC3H, potently suppresses the infectivity of vif-defective feline immunodeficiency virus (FIV). Although a recent report has shown that domestic cat encodes 7 haplotypes (hap I to hap VII) of A3Z3, the relevance of A3Z3 polymorphism in domestic cats with FIV Vif has not yet been addressed. In this study, we demonstrated that these feline A3Z3 variants suppress vif-defective FIV infectivity. We also revealed that codon 65 of feline A3Z3 is a positively selected site and that A3Z3 hap V is subject to positive selection during evolution. It is particularly noteworthy that feline A3Z3 hap V is resistant to FIV Vif-mediated degradation and still inhibits vif-proficient viral infection. Moreover, the side chain size, but not the hydrophobicity, of the amino acid at position 65 determines the resistance to FIV Vif-mediated degradation. Furthermore, phylogenetic analyses have led to the inference that feline A3Z3 hap V emerged approximately 60,000 years ago. Taken together, these findings suggest that feline A3Z3 hap V may have been selected for escape from an ancestral FIV. This is the first evidence for an evolutionary \\\"arms race\\\" between the domestic cat and its cognate lentivirus. IMPORTANCE: Gene diversity and selective pressure are intriguing topics in the field of evolutionary biology. A direct interaction between a cellular protein and a viral protein can precipitate an evolutionary arms race between host and virus. One example is primate APOBEC3G, which potently restricts the replication of primate lentiviruses (e.g., human immunodeficiency virus type 1 [HIV-1] and simian immunodeficiency virus [SIV]) if its activity is not counteracted by the viral Vif protein. Here we investigate the ability of 7 naturally occurring variants of feline APOBEC3, APOBEC3Z3 (A3Z3), to inhibit FIV replication. Interestingly, one feline A3Z3 variant is dominant, restrictive, and naturally resistant to FIV Vif-mediated degradation. Phylogenetic analyses revealed that the ancestral change that generated this variant could have been caused by positive Darwinian selection, presumably due to an ancestral FIV infection. The experimental-phylogenetic investigation sheds light on the evolutionary history of the domestic cat, which was likely influenced by lentiviral infection.\",\n \"corpus_id\": 3250632,\n \"score\": 2\n },\n {\n \"doc_id\": \"26559750\",\n \"title\": \"APOBEC3H polymorphisms and susceptibility to HIV-1 infection in an Indian population.\",\n \"abstract\": \"Human APOBEC3H (A3H) is a member of APOBEC cytidine deaminase family intensively constraining the HIV-1 replication. A3H is known to be polymorphic with different protein stability and anti-HIV-1 activity in vitro. We recently reported that A3H haplotypes composed of two functional polymorphisms, rs139292 (N15del) and rs139297 (G105R), were associated with the susceptibility to HIV-1 infection in Japanese. To confirm the association of A3H and HIV-1 infection in another ethnic group, a total of 241 HIV-1-infected Indian individuals and ethnic-matched 286 healthy controls were analyzed for the A3H polymorphisms. The frequency of 15del allele was high in the HIV-1-infected subjects as compared with the controls (0.477 vs 0.402, odds ratio (OR)=1.36, P=0.014). Haplotype analysis showed that the frequencies of 15del-105R was high (0.475 vs 0.400, OR=1.36, permutation P=0.037) in the HIV-1-infected subjects, confirming the association of A3H polymorphisms with the susceptibility to HIV-1 infection. Journal of Human Genetics advance online publication, 12 November 2015; doi:10.1038/jhg.2015.136.\",\n \"corpus_id\": 306663,\n \"score\": 2\n },\n {\n \"doc_id\": \"27534815\",\n \"title\": \"Biochemical Characterization of APOBEC3H Variants: Implications for Their HIV-1 Restriction Activity and mC Modification.\",\n \"abstract\": \"APOBEC3H (A3H) is the most polymorphic member of the APOBEC3 family. Seven haplotypes (hap I-VII) and four mRNA splicing variants (SV) of A3H have been identified. The various haplotypes differ in anti-HIV activity, which is attributed to differences in protein stability, subcellular distribution, and/or RNA binding and virion packaging. Here, we report the first comparative biochemical studies of all the A3H variants using highly purified proteins. We show that all haplotypes were stably expressed and could be purified to homogeneity by Escherichia coli expression. Surprisingly, four out of the seven haplotypes showed high cytosine (C) deaminase activity, with hap V displaying extremely high activity that was comparable to the highly active A3A. Furthermore, all four haplotypes that were active in C deamination were also highly active on methylated C (mC), with hap II displaying almost equal deamination efficiency on both. The deamination activity of these A3H variants correlates well with their reported anti-HIV activity for the different haplotypes, suggesting that deaminase activity may be an important factor in determining their respective anti-HIV activities. Moreover, mC deamination of A3H displayed a strong preference for the sequence motif of T-mCpG-C/G, which may suggest a potential role in genomic mC modification at the characteristic \\\"CpG\\\" island motif.\",\n \"corpus_id\": 206215841,\n \"score\": 2\n },\n {\n \"doc_id\": \"28031368\",\n \"title\": \"The Structural Interface between HIV-1 Vif and Human APOBEC3H.\",\n \"abstract\": \"Human APOBEC3H (A3H) is a cytidine deaminase that inhibits HIV-1 replication. To evade this restriction, the HIV-1 Vif protein binds A3H and mediates its proteasomal degradation. To date, little information on the Vif-A3H interface has been available. To decipher how both proteins interact, we first mapped the Vif-binding site on A3H by functionally testing a large set of A3H mutants in single-cycle infectivity and replication assays. Our data show that the two A3H α-helixes α3 and α4 represent the Vif-binding site of A3H. We next used viral adaptation and a set of Vif mutants to identify novel, reciprocal Vif variants that rescued viral infectivity in the presence of two Vif-resistant A3H mutants. These A3H-Vif interaction points were used to generate the first A3H-Vif structure model, which revealed that the A3H helixes α3 and α4 interact with the Vif β-sheet (β2-β5). This model is in good agreement with previously reported Vif and A3H amino acids important for interaction. Based on the predicted A3H-Vif interface, we tested additional points of contact, which validated our model. Moreover, these experiments showed that the A3H and A3G binding sites on HIV-1 Vif are largely distinct, with both host proteins interacting with Vif β-strand 2. Taken together, this virus-host interface model explains previously reported data and will help to identify novel drug targets to combat HIV-1 infection. IMPORTANCE HIV-1 needs to overcome several intracellular restriction factors in order to replicate efficiently. The human APOBEC3 locus encodes seven proteins, of which A3D, A3F, A3G, and A3H restrict HIV-1. HIV encodes the Vif protein, which binds to the APOBEC3 proteins and leads to their proteasomal degradation. No HIV-1 Vif-APOBEC3 costructure exists to date despite extensive research. We and others previously generated HIV-1 Vif costructure models with A3G and A3F by mapping specific contact points between both proteins. Here, we applied a similar approach to HIV-1 Vif and A3H and successfully generated a Vif-A3H interaction model. Importantly, we find that the HIV-1 Vif-A3H interface is distinct from the Vif-A3G and Vif-A3F interfaces, with a small Vif region being important for recognition of both A3G and A3H. Our Vif-A3H structure model informs on how both proteins interact and could guide toward approaches to block the Vif-A3H interface to target HIV replication.\",\n \"corpus_id\": 4623329,\n \"score\": 2\n },\n {\n \"doc_id\": \"28336404\",\n \"title\": \"Mapping Region of Human Restriction Factor APOBEC3H Critical for Interaction with HIV-1 Vif.\",\n \"abstract\": \"The APOBEC3 (A3) family of cellular cytidine deaminases comprises seven members (A, B, C, D, F, G, and H) that potently inhibit retroviral replication. Human immunodeficiency virus type 1 (HIV-1) Vif is a small pleiotropic protein that specifically inactivates these enzymes, targeting them for ubiquitin-mediated proteasomal degradation. A3 Vif-interaction sites are presumed to fall into three distinct types: A3C/D/F, A3G, and A3H. To date, two types of A3G and A3C/D/F sites have been well characterized, whereas the A3H Vif-binding site remains poorly defined. Here, we explore the residues critical for the A3H-type Vif interaction. To avoid technical difficulties in performing experiments with human A3H haplotype II (hapII), which is relatively resistant to HIV-1 Vif, we employed its ortholog chimpanzee A3H (cA3H), which displays high Vif sensitivity, for a comparison of sensitivity with that of A3H hapII. The Vif susceptibility of A3H hapII-cA3H chimeras and their substitution mutants revealed a single residue at position 97 as a major determinant for the difference in their Vif sensitivities. We further surveyed critical residues by structure-guided mutagenesis using an A3H structural model and thus identified eight additional residues important for Vif sensitivity, which mapped to the α3 and α4 helices of A3H. Interestingly, this area is located on a surface adjacent to the A3G and A3C/D/F interfaces and is composed of negatively charged and hydrophobic patches. These findings suggest that HIV-1 Vif has evolved to utilize three dispersed surfaces for recognizing three types of interfaces on A3 proteins under certain structural constraints.\",\n \"corpus_id\": 26918870,\n \"score\": 2\n },\n {\n \"doc_id\": \"28475648\",\n \"title\": \"HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation.\",\n \"abstract\": \"APOBEC3 (A3) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation. Prior studies have demonstrated that A3D, A3F, and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models. Human A3H is polymorphic and can be categorized into three phenotypes: stable, intermediate, and unstable. However, the anti-viral effect of endogenous A3H in vivo has yet to be examined. Here we utilize a hematopoietic stem cell-transplanted humanized mouse model and demonstrate that stable A3H robustly affects HIV-1 fitness in vivo. In contrast, the selection pressure mediated by intermediate A3H is relaxed. Intriguingly, viral genomic RNA sequencing reveled that HIV-1 frequently adapts to better counteract stable A3H during replication in humanized mice. Molecular phylogenetic analyses and mathematical modeling suggest that stable A3H may be a critical factor in human-to-human viral transmission. Taken together, this study provides evidence that stable variants of A3H impose selective pressure on HIV-1.\",\n \"corpus_id\": 23069011,\n \"score\": 2\n },\n {\n \"doc_id\": \"28883657\",\n \"title\": \"Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H.\",\n \"abstract\": \"The APOBEC3 family of cytosine deaminase enzymes are able to restrict replication of retroelements, such as LINE-1. However, each of the seven APOBEC3 enzymes have been reported to act differentially to prevent LINE-1 retrotransposition and the mechanisms of APOBEC3-mediated LINE-1 inhibition has not been well understood. The prevailing view for many years was that APOBEC3-mediated LINE-1 inhibition was deamination-independent and relied on APOBEC3s blocking the LINE-1 reverse transcriptase DNA polymerization or transport of the LINE-1 RNA into the nucleus. However, recently it was shown that APOBEC3A can deaminate cytosine, to form uracil, on transiently exposed single-stranded LINE-1 cDNA and this leads to LINE-1 cDNA degradation. In this study, we confirmed that APOBEC3A is a potent deamination-dependent inhibitor of LINE-1 retrotransposition, but show that in contrast, A3H haplotype II and haplotype V restrict LINE-1 activity using a deamination-independent mechanism. Our study supports the model that different APOBEC3 proteins have evolved to inhibit LINE-1 retrotransposition through distinct mechanisms.\",\n \"corpus_id\": 24572310,\n \"score\": 2\n },\n {\n \"doc_id\": \"29267382\",\n \"title\": \"Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans.\",\n \"abstract\": \"APOBEC3s (A3s) are potent restriction factors of human immunodeficiency virus type 1/simian immunodeficiency viruses (HIV-1/SIV), and can repress cross-species transmissions of lentiviruses. HIV-1 originated from a zoonotic infection of SIV of chimpanzee (SIVcpz) to humans. However, the impact of human A3s on the replication of SIVcpz remains unclear. By using novel SIVcpz reporter viruses, we identified that human APOBEC3B (A3B) and APOBEC3H (A3H) haplotype II strongly reduced the infectivity of SIVcpz, because both of them are resistant to SIVcpz Vifs. We further demonstrated that human A3H inhibited SIVcpz by deaminase dependent as well independent mechanisms. In addition, other stably expressed human A3H haplotypes and splice variants showed strong antiviral activity against SIVcpz. Moreover, most SIV and HIV lineage Vif proteins could degrade chimpanzee A3H, but no Vifs from SIVcpz and SIV of gorilla (SIVgor) lineages antagonized human A3H haplotype II. Expression of human A3H hapII in human T cells efficiently blocked the spreading replication of SIVcpz. The spreading replication of SIVcpz was also restricted by stable A3H in human PBMCs. Thus, we speculate that stably expressed human A3H protects humans against the cross-species transmission of SIVcpz and that SIVcpz spillover to humans may have started in individuals that harbor haplotypes of unstable A3H proteins.\",\n \"corpus_id\": 230108,\n \"score\": 2\n },\n {\n \"doc_id\": \"29333092\",\n \"title\": \"Role of APOBEC3H in the Viral Control of HIV Elite Controller Patients.\",\n \"abstract\": \"Background APOBEC3H (A3H) gene presents variation at 2 positions (rs139297 and rs79323350) leading to a non-functional protein. So far, there is no information on the role played by A3H in spontaneous control of HIV. The aim of this study was to evaluate the A3H polymorphisms distribution in a well-characterized group of Elite Controller (EC) subjects. Methods We analyzed the genotype distribution of two different SNPs (rs139297 and rs79323350) of A3H in 30 EC patients and compared with 11 non-controller (NC) HIV patients. Genotyping was performed by PCR, cloning and Sanger sequencing. Both polymorphisms were analyzed jointly in order to adequately attribute the active or inactive status of A3H protein. Results EC subjects included in this study were able to maintain a long-term sustained spontaneous HIV-viral control and optimal CD4-T-cell counts; however, haplotypes leading to an active protein were very poorly represented in these patients. We found that the majority of EC subjects (23/30; 77%) presented allelic combinations leading to an inactive A3H protein, a frequency slightly lower than that observed for NC studied patients (10/11; 91%). Conclusions The high prevalence of non-functional protein coding-genotypes in EC subjects seems to indicate that other innate restriction factors different from APOBEC3H could be implicated in the replication control exhibited by these subjects.\",\n \"corpus_id\": 24178885,\n \"score\": 2\n },\n {\n \"doc_id\": \"18619467\",\n \"title\": \"Characterization of conserved motifs in HIV-1 Vif required for APOBEC3G and APOBEC3F interaction.\",\n \"abstract\": \"Apolipoprotein B mRNA-editing catalytic polypeptide-like 3G (APOBEC3G, or A3G) and related cytidine deaminases such as apolipoprotein B mRNA-editing catalytic polypeptide-like 3F (APOBEC3F, or A3F) are potent inhibitors of retroviruses. Formation of infectious human immunodeficiency virus (HIV)-1 requires suppression of multiple cytidine deaminases by Vif. HIV-1 Vif suppresses various APOBEC3 proteins through a common mechanism by recruiting Cullin5, ElonginB, and ElonginC E3 ubiquitin ligase to induce target protein polyubiquitination and proteasome-mediated degradation. Domains in Vif that mediate APOBEC3 recognition have not been fully characterized. In the present study, we identified a VxIPLx(4-5)LxPhix(2)YWxL motif in HIV-1 Vif, which is required for efficient interaction between Vif and A3G, Vif-mediated A3G degradation and virion exclusion, and functional suppression of the A3G antiviral activity. Amino acids 52 to 72 of HIV-1 Vif (including the VxIPLx(4-5)LxPhix(2)YWxL motif) alone could mediate interaction with A3G, and this interaction was abolished by mutations of two hydrophobic amino acids in this region. We have also observed that a Vif mutant was ineffective against A3G, yet it retained the ability to interact with Cullin5-E3 ubiquitin complex and A3G, suggesting that interaction with A3G is necessary but not sufficient to inhibit its antiviral function. Unlike the previously identified motif of HIV-1 Vif amino acids 40 to 44, which is only important for A3G suppression, the VxIPLx(4-5)LxPhix(2)YWxL motif is also required for efficient A3F interaction and suppression. On the other hand, another motif, TGERxW, of HIV-1 Vif amino acids 74 to 79 was found to be mainly important for A3F interaction and inhibition. Both the VxIPLx(4-5)LxPhix(2)YWxL and TGERxW motifs are highly conserved among HIV-1, HIV-2, and various simian immunodeficiency virus Vif proteins. Our data suggest that primate lentiviral Vif molecules recognize their autologous APOBEC3 proteins through conserved structural features that represent attractive targets for the development of novel inhibitors.\",\n \"corpus_id\": 41901760,\n \"score\": 1\n },\n {\n \"doc_id\": \"19109396\",\n \"title\": \"Regulation of APOBEC3 proteins by a novel YXXL motif in human immunodeficiency virus type 1 Vif and simian immunodeficiency virus SIVagm Vif.\",\n \"abstract\": \"The APOBEC3 cytidine deaminases are potent antiviral factors that restrict the replication of human immunodeficiency virus type 1 (HIV-1). In HIV-1-infected CD4+ T cells, the viral accessory protein Vif binds to APOBEC3G (A3G), APOBEC3F (A3F), and APOBEC3C (A3C) and targets these proteins for polyubiquitination by forming an E3 ubiquitin ligase with cullin 5. Previous studies identified regions of HIV-1 Vif, 40YRHHY44 and 12QVDRMR17, which are important for interaction with A3G and A3F, respectively, and showed that Vif residues 54 to 71 are sufficient for A3G binding. Here, we identify 69YXXL72 as a novel conserved motif in HIV-1 Vif that mediates binding to human A3G and its subsequent degradation. Studies on other APOBEC3 proteins revealed that Tyr69 and Leu72 are important for the degradation of A3F and A3C as well. Similar to A3F, A3C regulation is also mediated by Vif residues 12QVDRMR17. Simian immunodeficiency virus (SIV) Vif was shown to bind and degrade African green monkey A3G (agmA3G) and, unexpectedly, human A3C. The YXXL motif of SIVagm Vif was important for the inactivation of agmA3G and human A3C. Unlike HIV-1 Vif, however, SIVagm Vif does not require Tyr40 and His43 for agmA3G degradation. Tyr69 in the YXXL motif was critical for binding of recombinant glutathione S-transferase-Vif(1-94) to A3G in vitro. These results suggest that the YXXL motif in Vif is a potential target for small-molecule inhibitors to block Vif interaction with A3G, A3F, and A3C, and thereby protect cells against HIV-1 infection.\",\n \"corpus_id\": 206808184,\n \"score\": 1\n },\n {\n \"doc_id\": \"20333195\",\n \"title\": \"Evolution of olfactory receptor genes in primates dominated by birth-and-death process.\",\n \"abstract\": \"Olfactory receptor (OR) is a large family of G protein-coupled receptors that can detect odorant in order to generate the sense of smell. They constitute one of the largest multiple gene families in animals including primates. To better understand the variation in odor perception and evolution of OR genes among primates, we computationally identified OR gene repertoires in orangutans, marmosets, and mouse lemurs and investigated the birth-and-death process of OR genes in the primate lineage. The results showed that 1) all the primate species studied have no more than 400 intact OR genes, fewer than rodents and canine; 2) Despite the similar number of OR genes in the genome, the makeup of the OR gene repertoires between different primate species is quite different as they had undergone dramatic birth-and-death evolution with extensive gene losses in the lineages leading to current species; 3) Apes and Old World monkey (OWM) have similar fraction of pseudogenes, whereas New World monkey (NWM) have fewer pseudogenes. To measure the selective pressure that had affected the OR gene repertoires in primates, we compared the ratio of nonsynonymous with synonymous substitution rates by using 70 one-to-one orthologous quintets among five primate species. We found that OR genes showed relaxed selective constraints in apes (humans, chimpanzees, and orangutans) than in OWMs (macaques) and NWMs (marmosets). We concluded that OR gene repertoires in primates have evolved in such a way to adapt to their respective living environments. Differential selective constraints might play important role in the primate OR gene evolution in each primate species.\",\n \"corpus_id\": 10136681,\n \"score\": 1\n },\n {\n \"doc_id\": \"20444900\",\n \"title\": \"Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses.\",\n \"abstract\": \"Tetherin/BST-2 is a host-encoded protein that restricts a wide diversity of viruses at the stage of virion release. However, viruses have evolved antagonists of Tetherin, including the Vpu and Nef proteins of primate lentiviruses. Like other host genes subject to viral antagonism, primate Tetherin genes have evolved under positive selection. We show here that viral antagonists acting at three independent sites of selection have driven the evolution of Tetherin, with the strongest selective pressure on the cytoplasmic tail domain. Human Tetherin is unique among the Tetherins of simian primates in that it has a 5-amino-acid deletion that results in the loss of the residue under the strongest positive selection. We show that this residue at amino acid 17 is the site of the functional interaction of Tetherin with Nef, since single amino acid substitutions at this single position can determine the susceptibility of Tetherin to Nef antagonism. While the simian immunodeficiency viruses SIVcpz and SIVgor are able to antagonize their hosts' Tetherin with Nef, human immunodeficiency virus type 1 (HIV-1) Vpu has evolved to counteract Tetherin in humans. We mapped the adaptations in the N-terminal transmembrane domain of Vpu that allow it to counteract human Tetherin. Our combined evolutionary and functional studies have allowed us to reconstruct the host-pathogen interactions that have shaped Tetherin and its lentivirus-encoded antagonists.\",\n \"corpus_id\": 20649863,\n \"score\": 1\n },\n {\n \"doc_id\": \"20592083\",\n \"title\": \"Identification of a critical T(Q/D/E)x5ADx2(I/L) motif from primate lentivirus Vif proteins that regulate APOBEC3G and APOBEC3F neutralizing activity.\",\n \"abstract\": \"Primate lentiviruses are unique in that they produce several accessory proteins to help in the establishment of productive viral infection. The major function of these proteins is to clear host resistance factors that inhibit viral replication. Vif is one of these proteins. It functions as an adaptor that binds to the cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) and bridges them to a cullin 5 (Cul5) and elongin (Elo) B/C E3 ubiquitin ligase complex for proteasomal degradation. So far, 11 discontinuous domains in Vif have been identified that regulate this degradation process. Here we report another domain, T(Q/D/E)x(5)ADx(2)(I/L), which is located at residues 96 to 107 in the human immunodeficiency virus type 1 (HIV-1) Vif protein. This domain is conserved not only in all HIV-1 subtypes but also in other primate lentiviruses, including HIV-2 and simian immunodeficiency virus (SIV), which infects rhesus macaques (SIVmac) and African green monkeys (SIVagm). Mutations of the critical residues in this motif seriously disrupted Vif's neutralizing activity toward both A3G and A3F. This motif regulates Vif interaction not only with A3G and A3F but also with Cul5. When this motif was inactivated in the HIV-1 genome, Vif failed to exclude A3G and A3F from virions, resulting in abortive HIV replication in nonpermissive human T cells. Thus, T(Q/D/E)x(5)ADx(2)(I/L) is a critical functional motif that directly supports the adaptor function of Vif and is an attractive target for inhibition of Vif function.\",\n \"corpus_id\": 206799359,\n \"score\": 1\n },\n {\n \"doc_id\": \"23707381\",\n \"title\": \"A naturally occurring Vif mutant (I107T) attenuates anti-APOBEC3G activity and HIV-1 replication.\",\n \"abstract\": \"The human immunodeficiency virus type 1 (HIV-1) Vif protein counteracts the antiviral activity of the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of proteins by targeting the proteins for degradation through the ubiquitin-proteasome pathway. Previous mutagenic studies have shown that multiple domains of Vif are required for interacting with APOBEC3G proteins and the proteasome pathway. However, very few mutagenesis and functional analyses of patient-derived Vif proteins have been conducted. In this study, we amplified and cloned the HIV-1 vif genes from the peripheral blood mononuclear cells (PBMCs) of five HIV-1-infected individuals in Nairobi and further tested the impact of the genes on anti-A3G activity and HIV-1 replication. The gene sequence analysis revealed high genetic variation of vif genes from different HIV-1-infected individuals. Interestingly, the Vif proteins derived from two of the three long-term survivors (LTSs) displayed a significantly impaired ability to mediate the degradation of A3G. In particular, a single amino acid change (I107T) in one of the non-functional LTS Vif variants, which has not been previously identified in the Los Alamos databases of vif sequences, was found to be responsible for the lack of anti-A3G activity. Further study demonstrated that HIV-1 carrying an I107T Vif mutation displayed significantly reduced fitness in A3G(+) T cells and PBMCs. Moreover, co-infecting A3G(+) T cells with both the wild-type and I107T Vif viruses resulted in decreased viral replication. Overall, the results of this study indicate that the HIV-1 Vif residue I107 is important for its anti-APOBEC3G activity and viral replication, which may have implications for viral fitness in vivo.\",\n \"corpus_id\": 5215502,\n \"score\": 1\n },\n {\n \"doc_id\": \"24324150\",\n \"title\": \"Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus.\",\n \"abstract\": \"Restriction factors are effectors of the innate immune response to viral pathogens that inhibit viral replication by operating as molecular barriers to steps of the viral life cycle. The restriction factor SAMHD1 blocks lentiviral reverse transcription in myeloid cells and resting CD4+ T cells. Many lineages of lentiviruses, including HIV-2 and other simian immunodeficiency viruses, encode accessory genes that serve to counteract host SAMHD1 restriction by causing degradation of the antiviral factor. The viral accessory protein Vpr is responsible for SAMHD1 degradation in some lineages of lentiviruses, whereas in others the related protein Vpx assumes this task. However, HIV-1 has no SAMHD1 degradation capability, leading to questions about the selective advantage of this activity. We use an evolutionary approach to examine the importance of SAMHD1 antagonism for viral fitness by studying adaptation to host SAMHD1 in natural simian immunodeficiency virus infections of African Green Monkeys. We identified multiple SAMHD1 haplotypes in African Green Monkeys and find that the vpr gene from different strains of Simian Immunodeficiency Virus has adapted to the polymorphisms of the African Green Monkey population in which it is found. Such evidence of viral adaptation to host restriction indicates that SAMHD1 antagonism is actively maintained in natural infections and that this function must be advantageous to viral fitness, despite its absence in HIV-1.\",\n \"corpus_id\": 76492,\n \"score\": 1\n },\n {\n \"doc_id\": \"24942576\",\n \"title\": \"HIV-1 and HIV-2 Vif interact with human APOBEC3 proteins using completely different determinants.\",\n \"abstract\": \"UNLABELLED: Human APOBEC3 (A3) restriction factors provide intrinsic immunity against zoonotic transmission of pathogenic viruses. A3D, A3F, A3G, and A3H haplotype II (A3H-hapII) can be packaged into virion infectivity factor (Vif)-deficient HIVs to inhibit viral replication. To overcome these restriction factors, Vif binds to the A3 proteins in viral producer cells to target them for ubiquitination and proteasomal degradation, thus preventing their packaging into assembling virions. Therefore, the Vif-A3 interactions are attractive targets for novel drug development. HIV-1 and HIV-2 arose via distinct zoonotic transmission events of simian immunodeficiency viruses from chimpanzees and sooty mangabeys, respectively, and Vifs from these viruses have limited homology. To gain insights into the evolution of virus-host interactions that led to successful cross-species transmission of lentiviruses, we characterized the determinants of the interaction between HIV-2 Vif (Vif2) with human A3 proteins and compared them to the previously identified HIV-1 Vif (Vif1) interactions with the A3 proteins. We found that A3G, A3F, and A3H-hapII, but not A3D, were susceptible to Vif2-induced degradation. Alanine-scanning mutational analysis of the first 62 amino acids of Vif2 indicated that Vif2 determinants important for degradation of A3G and A3F are completely distinct from these regions in Vif1, as are the determinants in A3G and A3F that are critical for Vif2-induced degradation. These observations suggest that distinct Vif-A3 interactions evolved independently in different SIVs and their nonhuman primate hosts and conservation of the A3 determinants targeted by the SIV Vif proteins resulted in successful zoonotic transmission into humans. IMPORTANCE: Primate APOBEC3 proteins provide innate immunity against invading pathogens, and Vif proteins of primate lentiviruses have evolved to overcome these host defenses by interacting with them and inducing their proteasomal degradation. HIV-1 and HIV-2 are two human pathogens that induce AIDS, and elucidating interactions between their Vif proteins and human A3 proteins could facilitate the development of novel antiviral drugs. Furthermore, understanding Vif-A3 interactions can provide novel insights into the cross-species transmission events that led to the HIV-1 and HIV-2 pandemics and evolution of host-virus interactions. We carried out mutational analysis of the N-terminal 62 amino acids of HIV-2 Vif (Vif2) and analyzed A3G/A3F chimeras that retained antiviral activity to identify the determinants of the Vif2 and A3 interaction. Our results show that the Vif2-A3 interactions are completely different from the Vif1-A3 interactions, suggesting that these interactions evolved independently and that conservation of the A3 determinants resulted in successful zoonotic transmission into humans.\",\n \"corpus_id\": 7776940,\n \"score\": 1\n },\n {\n \"doc_id\": \"25142583\",\n \"title\": \"Cellular requirements for bovine immunodeficiency virus Vif-mediated inactivation of bovine APOBEC3 proteins.\",\n \"abstract\": \"UNLABELLED: Human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) viral infectivity factor (Vif) form a CRL5 E3 ubiquitin ligase complex to suppress virus restriction by host APOBEC3 (A3) proteins. The primate lentiviral Vif complex is composed of the unique cofactor core binding factor β (CBF-β) and canonical ligase components Cullin 5 (CUL5), Elongin B/C (ELOB/C), and RBX2. However, the mechanism by which the Vif protein of the related lentivirus bovine immunodeficiency virus (BIV) overcomes its host A3 proteins is less clear. In this study, we show that BIV Vif interacts with Cullin 2 (CUL2), ELOB/C, and RBX1, but not with CBF-β or CUL5, to form a CRL2 E3 ubiquitin ligase and degrade the restrictive bovine A3 proteins (A3Z2Z3 and A3Z3). RNA interference-mediated knockdown of ELOB or CUL2 inhibited BIV Vif-mediated degradation of these A3 proteins, whereas knockdown of CUL5 or CBF-β did not. BIV Vif with mutations in the BC box (Vif SLQ-AAA) or putative VHL box (Vif YI-AA), which cannot interact with ELOB/C or CUL2, respectively, lost the ability to counteract bovine A3 proteins. Moreover, CUL2 and UBE2M dominant negative mutants competitively inhibited the BIV Vif-mediated degradation mechanism. Thus, although the general strategy for inhibiting A3 proteins is conserved between HIV-1/SIV and BIV, the precise mechanisms can differ substantially, with only the HIV-1/SIV Vif proteins requiring CBF-β as a cofactor, HIV-1/SIV Vif using CUL5-RBX2, and BIV Vif using CUL2-RBX1. IMPORTANCE: Primate lentivirus HIV-1 and SIV Vif proteins form a ubiquitin ligase complex to target host antiviral APOBEC3 proteins for degradation. However, the mechanism by which the nonprimate lentivirus BIV Vif inhibits bovine APOBEC3 proteins is unclear. In the present study, we determined the mechanism for BIV Vif-mediated degradation of bovine APOBEC3 proteins and found that it differs from the mechanism of HIV-1/SIV Vif by being CBF-β independent and requiring different ubiquitin ligase scaffolding proteins (CUL2-RBX1 instead of CUL5-RBX2). BIV Vif is the only known retroviral protein that can interact with CUL2. This information broadens our understanding of the distinct mechanisms by which the Vif proteins of different lentiviruses facilitate viral infection. This novel mechanism for assembly of the BIV Vif-APOBEC3 ubiquitin ligase complex advances our understanding of viral hijacking of host E3 ubiquitin ligases and illustrates the evolutionary flexibility of lentiviruses.\",\n \"corpus_id\": 31065884,\n \"score\": 1\n },\n {\n \"doc_id\": \"25275135\",\n \"title\": \"Determinants of efficient degradation of APOBEC3 restriction factors by HIV-1 Vif.\",\n \"abstract\": \"UNLABELLED: The APOBEC3 deoxycytidine deaminases can restrict the replication of HIV-1 in cell culture to differing degrees. The effects of APOBEC3 enzymes are largely suppressed by HIV-1 Vif that interacts with host proteins to form a Cullin5-Ring E3 ubiquitin ligase that induces (48)K-linked polyubiquitination (poly-Ub) and proteasomal degradation of APOBEC3 enzymes. Vif variants have differing abilities to induce degradation of APOBEC3 enzymes and the underlying biochemical mechanisms for these differences is not fully understood. We hypothesized that by characterizing the interaction of multiple APOBEC3 enzymes and Vif variants we could identify common features that resulted in Vif-mediated degradation and further define the determinants required for efficient Vif-mediated degradation of APOBEC3 enzymes. We used Vifs from HIV-1 NL4-3 (IIIB) and HXB2 to characterize their induced degradation of and interaction with APOBEC3G, APOBEC3G D128K, APOBEC3H, and APOBEC3B in 293T cells. We quantified the APOBEC3G-Vif and APOBEC3H-Vif interaction strengths in vitro using rotational anisotropy. Our biochemical and cellular analyses of the interactions support a model in which the degradation efficiency of VifIIIB and VifHXB2 correlated with both the binding strength of the APOBEC3-Vif interaction and the APOBEC3-Vif interface, which differs for APOBEC3G and APOBEC3H. Notably, Vif bound to APOBEC3H and APOBEC3B in the natural absence of Vif-induced degradation and the interaction resulted in (63)K-linked poly-Ub of APOBEC3H and APOBEC3B, demonstrating additional functionality of the APOBEC3-Vif interaction apart from induction of proteasomal degradation. IMPORTANCE: APOBEC3 enzymes can potently restrict the replication of HIV-1 in the absence of HIV-1 Vif. Vif suppresses APOBEC3 action by inducing their degradation through a direct interaction with APOBEC3 enzymes and other host proteins. Vif variants from different HIV-1 strains have different effects on APOBEC3 enzymes. We used differing Vif degradation capacities of two Vif variants and various APOBEC3 enzymes with differential sensitivities to Vif to delineate determinants of the APOBEC3-Vif interaction that are required for inducing efficient degradation. Using a combined biochemical and cellular approach we identified that the strength of the APOBEC3-Vif binding interaction and the APOBEC3-Vif interface are determinants for degradation efficiency. Our results highlight the importance of using Vif variants with different degradation potential when delineating mechanisms of Vif-induced APOBEC3 degradation and identify features important for consideration in the development of HIV-1 therapies that disrupt the APOBEC3-Vif interaction.\",\n \"corpus_id\": 43017915,\n \"score\": 1\n },\n {\n \"doc_id\": \"26291613\",\n \"title\": \"Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface.\",\n \"abstract\": \"The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity.\",\n \"corpus_id\": 13293015,\n \"score\": 1\n },\n {\n \"doc_id\": \"26394054\",\n \"title\": \"The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys.\",\n \"abstract\": \"Cross-species transmissions of viruses from animals to humans are at the origin of major human pathogenic viruses. While the role of ecological and epidemiological factors in the emergence of new pathogens is well documented, the importance of host factors is often unknown. Chimpanzees are the closest relatives of humans and the animal reservoir at the origin of the human AIDS pandemic. However, despite being regularly exposed to monkey lentiviruses through hunting, chimpanzees are naturally infected by only a single simian immunodeficiency virus, SIVcpz. Here, we asked why chimpanzees appear to be protected against the successful emergence of other SIVs. In particular, we investigated the role of the chimpanzee APOBEC3 genes in providing a barrier to infection by most monkey lentiviruses. We found that most SIV Vifs, including Vif from SIVwrc infecting western-red colobus, the chimpanzee's main monkey prey in West Africa, could not antagonize chimpanzee APOBEC3G. Moreover, chimpanzee APOBEC3D, as well as APOBEC3F and APOBEC3H, provided additional protection against SIV Vif antagonism. Consequently, lentiviral replication in primary chimpanzee CD4(+) T cells was dependent on the presence of a lentiviral vif gene that could antagonize chimpanzee APOBEC3s. Finally, by identifying and functionally characterizing several APOBEC3 gene polymorphisms in both common chimpanzees and bonobos, we found that these ape populations encode APOBEC3 proteins that are uniformly resistant to antagonism by monkey lentiviruses.\",\n \"corpus_id\": 13781850,\n \"score\": 1\n },\n {\n \"doc_id\": \"26601257\",\n \"title\": \"Transcriptional regulation of APOBEC3 antiviral immunity through the CBF-β/RUNX axis.\",\n \"abstract\": \"A diverse set of innate immune mechanisms protects cells from viral infections. The APOBEC3 family of DNA cytosine deaminases is an integral part of these defenses. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H would have the potential to destroy HIV-1 complementary DNA replication intermediates if not for neutralization by a proteasomal degradation mechanism directed by the viral protein Vif. At the core of this complex, Vif heterodimerizes with the transcription cofactor CBF-β, which results in fewer transcription complexes between CBF-β and its normal RUNX partners. Recent studies have shown that the Vif/CBF-β interaction is specific to the primate lentiviruses HIV-1 and SIV (simian immunodeficiency virus), although related nonprimate lentiviruses still require a Vif-dependent mechanism for protection from host species' APOBEC3 enzymes. We provide a molecular explanation for this evolutionary conundrum by showing that CBF-β is required for expression of the aforementioned HIV-1-restrictive APOBEC3 gene repertoire. Knockdown and knockout studies demonstrate that CBF-β is required for APOBEC3 mRNA expression in the nonpermissive T cell line H9 and in primary CD4(+) T lymphocytes. Complementation experiments using CBF-β separation-of-function alleles show that the interaction with RUNX transcription factors is required for APOBEC3 transcriptional regulation. Accordingly, the infectivity of Vif-deficient HIV-1 increases in cells lacking CBF-β, demonstrating the importance of CBF-β/RUNX-mediated transcription in establishing the APOBEC3 antiviral state. These findings demonstrate a major layer of APOBEC3 gene regulation in lymphocytes and suggest that primate lentiviruses evolved to hijack CBF-β in order to simultaneously suppress this potent antiviral defense system at both transcriptional and posttranslational levels.\",\n \"corpus_id\": 13157474,\n \"score\": 1\n },\n {\n \"doc_id\": \"26912618\",\n \"title\": \"APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication.\",\n \"abstract\": \"UNLABELLED: The multifunctional HIV-1 accessory protein Vif counters the antiviral activities of APOBEC3G (A3G) and APOBEC3F (A3F), and some Vifs counter stable alleles of APOBEC3H (A3H). Studies in humanized mice have shown that HIV-1 lacking Vif expression is not viable. Here, we look at the relative contributions of the three APOBEC3s to viral extinction. Inoculation of bone marrow/liver/thymus (BLT) mice with CCR5-tropic HIV-1JRCSF(JRCSF) expressing a vif gene inactive for A3G but not A3F degradation activity (JRCSFvifH42/43D) displayed either no or delayed replication. JRCSF expressing a vif gene mutated to inactivate A3F degradation but not A3G degradation (JRCSFvifW79S) always replicated to high viral loads with variable delays. JRCSF with vif mutated to lack both A3G and A3F degradation activities (JRCSFvifH42/43DW79S) failed to replicate, mimicking JRCSF without Vif expression (JRCSFΔvif). JRCSF and JRCSFvifH42/43D, but not JRCSFvifW79S or JRCSFvifH42/43DW79S, degraded APOBEC3D. With one exception, JRCSFs expressing mutant Vifs that replicated acquired enforced vif mutations. These mutations partially restored A3G or A3F degradation activity and fully replaced JRCSFvifH42/43D or JRCSFvifW79S by 10 weeks. Surprisingly, induced mutations temporally lagged behind high levels of virus in blood. In the exceptional case, JRCSFvifH42/43D replicated after a prolonged delay with no mutations in vif but instead a V27I mutation in the RNase H coding sequence. JRCSFvifH42/43D infections exhibited massive GG/AG mutations in pol viral DNA, but in viral RNA, there were no fixed mutations in the Gag or reverse transcriptase coding sequence. A3H did not contribute to viral extinction but, in combination with A3F, could delay JRCSF replication. A3H was also found to hypermutate viral DNA. IMPORTANCE: Vif degradation of A3G and A3F enhances viral fitness, as virus with even a partially restored capacity for degradation outgrows JRCSFvifH42/43D and JRCSFvifW79S. Unexpectedly, fixation of mutations that replaced H42/43D or W79S in viral RNA lagged behind the appearance of high viral loads. In one exceptional JRCSFvifH42/43D infection, vif was unchanged but replication proceeded after a long delay. These results suggest that Vif binds and inhibits the non-cytosine deaminase activities of intact A3G and intact A3F, allowing JRCSFvifH42/43D and JRCSFvifW79S to replicate with reduced fitness. Subsequently, enhanced Vif function is acquired by enforced mutations. In infected cells, JRCSFΔvif and JRCSFvifH42/43DW79S are exposed to active A3F and A3G and fail to replicate. JRCSFvifH42/43D Vif degrades A3F and, in some cases, overcomes A3G mutagenic activity to replicate. Vif may have evolved to inhibit A3F and A3G by stoichiometric binding and subsequently acquired the ability to target these proteins to proteasomes.\",\n \"corpus_id\": 4765212,\n \"score\": 1\n },\n {\n \"doc_id\": \"27189538\",\n \"title\": \"Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution.\",\n \"abstract\": \"LINE-1 (long interspersed element-1) retroelements are the only active autonomous endogenous retroelements in human genomes. Their retrotransposition activity has created close to 50% of the current human genome. Due to the apparent costs of this proliferation, host genomes have evolved multiple mechanisms to curb LINE-1 retrotransposition. Here, we investigate the evolution and function of the LINE-1 restriction factor APOBEC3A, a member of the APOBEC3 cytidine deaminase gene family. We find that APOBEC3A genes have evolved rapidly under diversifying selection in primates, suggesting changes in APOBEC3A have been recurrently selected in a host-pathogen \\\"arms race.\\\" Nonetheless, in contrast to previous reports, we find that the LINE-1 restriction activity of APOBEC3A proteins has been strictly conserved throughout simian primate evolution in spite of its pervasive diversifying selection. Based on these results, we conclude that LINE-1s have not driven the rapid evolution of APOBEC3A in primates. In contrast to this conserved LINE-1 restriction, we find that a subset of primate APOBEC3A genes have enhanced antiviral restriction. We trace this gain of antiviral restriction in APOBEC3A to the common ancestor of a subset of Old World monkeys. Thus, APOBEC3A has not only maintained its LINE-1 restriction ability, but also evolved a gain of antiviral specificity against other pathogens. Our findings suggest that while APOBEC3A has evolved to restrict additional pathogens, only those adaptive amino acid changes that leave LINE-1 restriction unperturbed have been tolerated.\",\n \"corpus_id\": 27725439,\n \"score\": 1\n },\n {\n \"doc_id\": \"27581978\",\n \"title\": \"Vif Proteins from Diverse Human Immunodeficiency Virus/Simian Immunodeficiency Virus Lineages Have Distinct Binding Sites in A3C.\",\n \"abstract\": \"Lentiviruses have evolved the Vif protein to counteract APOBEC3 (A3) restriction factors by targeting them for proteasomal degradation. Previous studies have identified important residues in the interface of human immunodeficiency virus type 1 (HIV-1) Vif and human APOBEC3C (hA3C) or human APOBEC3F (hA3F). However, the interaction between primate A3C proteins and HIV-1 Vif or natural HIV-1 Vif variants is still poorly understood. Here, we report that HIV-1 Vif is inactive against A3Cs of rhesus macaques (rhA3C), sooty mangabey monkeys (smmA3C), and African green monkeys (agmA3C), while HIV-2, African green monkey simian immunodeficiency virus (SIVagm), and SIVmac Vif proteins efficiently mediate the depletion of all tested A3Cs. We identified that residues N/H130 and Q133 in rhA3C and smmA3C are determinants for this HIV-1 Vif-triggered counteraction. We also found that the HIV-1 Vif interaction sites in helix 4 of hA3C and hA3F differ. Vif alleles from diverse HIV-1 subtypes were tested for degradation activities related to hA3C. The subtype F-1 Vif was identified to be inactive for degradation of hA3C and hA3F. The residues that determined F-1 Vif inactivity in the degradation of A3C/A3F were located in the C-terminal region (K167 and D182). Structural analysis of F-1 Vif revealed that impairing the internal salt bridge of E171-K167 restored reduction capacities to A3C/A3F. Furthermore, we found that D101 could also form an internal interaction with K167. Replacing D101 with glycine and R167 with lysine in NL4-3 Vif impaired its counteractivity to A3F and A3C. This finding indicates that internal interactions outside the A3 binding region in HIV-1 Vif influence the capacity to induce degradation of A3C/A3F. IMPORTANCE: The APOBEC3 restriction factors can serve as potential barriers to lentiviral cross-species transmissions. Vif proteins from lentiviruses counteract APOBEC3 by proteasomal degradation. In this study, we found that monkey-derived A3C, rhA3C and smmA3C, were resistant to HIV-1 Vif. This was determined by A3C residues N/H130 and Q133. However, HIV-2, SIVagm, and SIVmac Vif proteins were found to be able to mediate the depletion of all tested primate A3C proteins. In addition, we identified a natural HIV-1 Vif (F-1 Vif) that was inactive in the degradation of hA3C/hA3F. Here, we provide for the first time a model that explains how an internal salt bridge of E171-K167-D101 influences Vif-mediated degradation of hA3C/hA3F. This finding provides a novel way to develop HIV-1 inhibitors by targeting the internal interactions of the Vif protein.\",\n \"corpus_id\": 24908195,\n \"score\": 1\n },\n {\n \"doc_id\": \"28122978\",\n \"title\": \"Conserved Interaction of Lentiviral Vif Molecules with HIV-1 Gag and Differential Effects of Species-Specific Vif on Virus Production.\",\n \"abstract\": \"The virion infectivity factor (Vif) open reading frame is conserved among most lentiviruses. Vif molecules contribute to viral replication by inactivating host antiviral factors, the APOBEC3 cytidine deaminases. However, various species of lentiviral Vif proteins have evolved different strategies for overcoming host APOBEC3. Whether different species of lentiviral Vif proteins still preserve certain common features has not been reported. Here, we show for the first time that diverse lentiviral Vif molecules maintain the ability to interact with the human immunodeficiency virus type 1 (HIV-1) Gag precursor (Pr55(Gag)) polyprotein. Surprisingly, bovine immunodeficiency virus (BIV) Vif, but not HIV-1 Vif, interfered with HIV-1 production and viral infectivity even in the absence of APOBEC3. Further analysis revealed that BIV Vif demonstrated an enhanced interaction with Pr55(Gag) compared to that of HIV-1 Vif, and BIV Vif defective for the Pr55(Gag) interaction lost its ability to inhibit HIV-1. The C-terminal region of capsid (CA) and the p2 region of Pr55(Gag), which are important for virus assembly and maturation, were involved in the interaction. Transduction of CD4(+) T cells with BIV Vif blocked HIV-1 replication. Thus, the conserved Vif-Pr55(Gag) interaction provides a potential target for the future development of antiviral strategies. IMPORTANCE The conserved Vif accessory proteins of primate lentiviruses HIV-1, simian immunodeficiency virus (SIV), and BIV all form ubiquitin ligase complexes to target host antiviral APOBEC3 proteins for degradation, with different cellular requirements and using different molecular mechanisms. Here, we demonstrate that BIV Vif can interfere with HIV-1 Gag maturation and suppress HIV-1 replication through interaction with the precursor of the Gag (Pr55(Gag)) of HIV-1 in virus-producing cells. Moreover, the HIV-1 and SIV Vif proteins are conserved in terms of their interactions with HIV-1 Pr55(Gag) although HIV-1 Vif proteins bind Pr55(Gag) less efficiently than those of BIV Vif. Our research not only sheds new light on this feature of these conserved lentiviral Vif proteins but also provides a formerly unrecognized target for the development of antiviral strategies. Since increasing the Vif-Pr55(Gag) interaction could potentially suppress virus proliferation, this approach could offer a new strategy for the development of HIV inhibitors.\",\n \"corpus_id\": 4549495,\n \"score\": 1\n },\n {\n \"doc_id\": \"28331087\",\n \"title\": \"Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3.\",\n \"abstract\": \"The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated antiviral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway. Although the Vif-APOBEC3 interaction and its evolutionary significance, particularly those of primate lentiviruses (including HIV) and primates (including humans), have been well investigated, those of nonprimate lentiviruses and nonprimates are poorly understood. Moreover, the factors that determine lentiviral pathogenicity remain unclear. Here, we focus on feline immunodeficiency virus (FIV), a pathogenic lentivirus in domestic cats, and the interaction between FIV Vif and feline APOBEC3 in terms of viral virulence and evolution. We reveal the significantly reduced diversity of FIV subtype B compared to that of other subtypes, which may associate with the low pathogenicity of this subtype. We also demonstrate that FIV subtype B Vif is less active with regard to feline APOBEC3 degradation. More intriguingly, we further reveal that FIV protease cleaves feline APOBEC3 in released virions. Taken together, our findings provide evidence that a lentivirus encodes two types of anti-APOBEC3 factors, Vif and viral protease. IMPORTANCE During the history of mammalian evolution, mammals coevolved with retroviruses, including lentiviruses. All pathogenic lentiviruses, excluding equine infectious anemia virus, have acquired the vif gene via evolution to combat APOBEC3 proteins, which are intrinsic restriction factors against exogenous lentiviruses. Here we demonstrate that FIV, a pathogenic lentivirus in domestic cats, antagonizes feline APOBEC3 proteins by both Vif and a viral protease. Furthermore, the Vif proteins of an FIV subtype (subtype B) have attenuated their anti-APOBEC3 activity through evolution. Our findings can be a clue to elucidate the complicated evolutionary processes by which lentiviruses adapt to mammals.\",\n \"corpus_id\": 4618713,\n \"score\": 1\n },\n {\n \"doc_id\": \"29618650\",\n \"title\": \"Simian Immunodeficiency Virus Vif and Human APOBEC3B Interactions Resemble Those between HIV-1 Vif and Human APOBEC3G.\",\n \"abstract\": \"Several members of the APOBEC3 DNA cytosine deaminase family can potently inhibit Vif-deficient human immunodeficiency virus type 1 (HIV-1) by catalyzing cytosine deamination in viral cDNA and impeding reverse transcription. HIV-1 counteracts restriction with the virally encoded Vif protein, which targets relevant APOBEC3 proteins for proteasomal degradation. HIV-1 Vif is optimized for degrading the restrictive human APOBEC3 repertoire, and, in general, lentiviral Vif proteins specifically target the restricting APOBEC3 enzymes of each host species. However, simian immunodeficiency virus SIVmac239 Vif elicits a curiously wide range of APOBEC3 degradation capabilities that include degradation of several human APOBEC3s and even human APOBEC3B, a non-HIV-1-restricting APOBEC3 enzyme. To better understand the molecular determinants of the interaction between SIVmac239 Vif and human APOBEC3B, we analyzed an extensive series of mutants. We found that SIVmac239 Vif interacts with the N-terminal domain of human APOBEC3B and, interestingly, that this occurs within a structural region homologous to the HIV-1 Vif interaction surface of human APOBEC3G. An alanine scan of SIVmac239 Vif revealed several residues required for human APOBEC3B degradation activity. These residues overlap HIV-1 Vif surface residues that interact with human APOBEC3G and are distinct from those that engage APOBEC3F or APOBEC3H. Overall, these studies indicate that the molecular determinants of the functional interaction between human APOBEC3B and SIVmac239 Vif resemble those between human APOBEC3G and HIV-1 Vif. These studies contribute to the growing knowledge of the APOBEC-Vif interaction and may help guide future efforts to disrupt this interaction as an antiviral therapy or exploit the interaction as a novel strategy to inhibit APOBEC3B-dependent tumor evolution. IMPORTANCE Primate APOBEC3 proteins provide innate immunity against retroviruses such as HIV and SIV. HIV-1, the primary cause of AIDS, utilizes its Vif protein to specifically counteract restrictive human APOBEC3 enzymes. SIVmac239 Vif exhibits a much wider range of anti-APOBEC3 activities that includes several rhesus macaque enzymes and extends to multiple proteins in the human APOBEC3 repertoire, including APOBEC3B. Understanding the molecular determinants of the interaction between SIVmac239 Vif and human APOBEC3B adds to existing knowledge on the APOBEC3-Vif interaction and has potential to shed light on what processes may have shaped Vif functionality over evolutionary time. An intimate understanding of this interaction may also lead to a novel cancer therapy because, for instance, creating a derivative of SIVmac239 Vif that specifically targets human APOBEC3B could be used to suppress tumor genomic DNA mutagenesis by this enzyme, slow ongoing tumor evolution, and help prevent poor clinical outcomes.\",\n \"corpus_id\": 4608976,\n \"score\": 1\n },\n {\n \"doc_id\": \"29636069\",\n \"title\": \"New World feline APOBEC3 potently controls inter-genus lentiviral transmission.\",\n \"abstract\": \"BACKGROUND: The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) gene family appears only in mammalian genomes. Some A3 proteins can be incorporated into progeny virions and inhibit lentiviral replication. In turn, the lentiviral viral infectivity factor (Vif) counteracts the A3-mediated antiviral effect by degrading A3 proteins. Recent investigations have suggested that lentiviral vif genes evolved to combat mammalian APOBEC3 proteins, and have further proposed that the Vif-A3 interaction may help determine the co-evolutionary history of cross-species lentiviral transmission in mammals. RESULTS: Here we address the co-evolutionary relationship between two New World felids, the puma (Puma concolor) and the bobcat (Lynx rufus), and their lentiviruses, which are designated puma lentiviruses (PLVs). We demonstrate that PLV-A Vif counteracts the antiviral action of APOBEC3Z3 (A3Z3) of both puma and bobcat, whereas PLV-B Vif counteracts only puma A3Z3. The species specificity of PLV-B Vif is irrespective of the phylogenic relationships of feline species in the genera Puma, Lynx and Acinonyx. We reveal that the amino acid at position 178 in the puma and bobcat A3Z3 is exposed on the protein surface and determines the sensitivity to PLV-B Vif-mediated degradation. Moreover, although both the puma and bobcat A3Z3 genes are polymorphic, their sensitivity/resistance to PLV Vif-mediated degradation is conserved. CONCLUSIONS: To the best of our knowledge, this is the first study suggesting that the host A3 protein potently controls inter-genus lentiviral transmission. Our findings provide the first evidence suggesting that the co-evolutionary arms race between lentiviruses and mammals has occurred in the New World.\",\n \"corpus_id\": 4697371,\n \"score\": 1\n },\n {\n \"doc_id\": \"19929170\",\n \"title\": \"Antiviral activity of the interferon-induced cellular protein BST-2/tetherin.\",\n \"abstract\": \"Pathogenic microorganisms encode proteins that antagonize specific aspects of innate or adaptive immunity. Just as the study of the HIV-1 accessory protein Vif led to the identification of cellular cytidine deaminases as host defense proteins, the study of HIV-1 Vpu recently led to the discovery of the interferon-induced transmembrane protein BST-2 (CD317; tetherin) as a novel component of the innate defense against enveloped viruses. BST-2 is an unusually structured protein that restricts the release of fully formed progeny virions from infected cells, presumably by a direct retention mechanism that is independent of any viral protein target. Its spectrum of activity includes at least four virus families: retroviruses, filoviruses, arenaviruses, and herpesviruses. Viral antagonists of BST-2 include HIV-1 Vpu, HIV-2 and SIV Env, SIV Nef, the Ebola envelope glycoprotein, and the K5 protein of KSHV. The mechanisms of antagonism are diverse and currently include viral cooption of cellular endosomal trafficking and protein degradation pathways, including those mediated by ubiquitination. Orthologs of human BST-2 are present in mammals. Primate BST-2 proteins are differentially sensitive to antagonism by lentiviral Vpu and Nef proteins, suggesting that BST-2 has subjected lentiviruses to evolutionary pressure and presents barriers to cross-species transmission. BST-2 functions not only as an effector of the interferon-induced antiviral response but also as a negative feedback regulator of interferon production by plasmacytoid dendritic cells. Future work will focus on the role and regulation of BST-2 during the innate response to viral infection, on the mechanisms of restriction and of antagonism by viral gene products, and on the role of BST-2 in primate lentiviral evolution. The augmentation of BST-2 activity and the inhibition of virally encoded antagonists, in particular Vpu, represent new approaches to the prevention and treatment of HIV-1 infection.\",\n \"corpus_id\": 23130024,\n \"score\": 0\n },\n {\n \"doc_id\": \"22574228\",\n \"title\": \"Co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx gene in HIV-1 ancestor.\",\n \"abstract\": \"Cross-species transmission and adaptation of simian immunodeficiency viruses (SIVs) to humans have given rise to human immunodeficiency viruses (HIVs). HIV type 1 (HIV-1) and type 2 (HIV-2) were derived from SIVs that infected chimpanzee (SIVcpz) and sooty mangabey (SIVsm), respectively. The HIV-1 restriction factor SAMHD1 inhibits HIV-1 infection in human myeloid cells and can be counteracted by the Vpx protein of HIV-2 and the SIVsm lineage. However, HIV-1 and its ancestor SIVcpz do not encode a Vpx protein and HIV-1 has not evolved a mechanism to overcome SAMHD1-mediated restriction. Here we show that the co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx gene in SIVcpz and HIV-1. We found evidence for positive selection of SAMHD1 in orangutan, gibbon, rhesus macaque, and marmoset, but not in human, chimpanzee and gorilla that are natural hosts of Vpx-negative HIV-1, SIVcpz and SIVgor, respectively, indicating that vpx drives the evolution of primate SAMHD1. Ancestral host state reconstruction and temporal dynamic analyses suggest that the most recent common ancestor of SIVrcm, SIVmnd, SIVcpz, SIVgor and HIV-1 was a SIV that had a vpx gene; however, the vpx gene of SIVcpz was lost approximately 3643 to 2969 years ago during the infection of chimpanzees. Thus, HIV-1 could not inherit the lost vpx gene from its ancestor SIVcpz. The lack of Vpx in HIV-1 results in restricted infection in myeloid cells that are important for antiviral immunity, which could contribute to the AIDS pandemic by escaping the immune responses.\",\n \"corpus_id\": 8217948,\n \"score\": 0\n },\n {\n \"doc_id\": \"24819937\",\n \"title\": \"Molecular evolution of the primate α-/θ-defensin multigene family.\",\n \"abstract\": \"The primate α-/θ-defensin multigene family encodes versatile endogenous cationic and amphipathic peptides that have broad-spectrum antibacterial, antifungal and antiviral activity. Although previous studies have reported that α-/θ-defensin (DEFA/DEFT) genes are under birth-and-death evolution with frequent duplication and rapid evolution, the phylogenetic relationships of the primate DEFA/DEFT genes; the genetic bases for the existence of similar antimicrobial spectra among closely related species; and the evolutionary processes involved in the emergence of cyclic θ-defensins in Old World monkeys and their subsequent loss of function in humans, chimpanzees and gorillas require further investigation. In this study, the DEFA/DEFT gene repertoires from primate and treeshrew were collected, followed by detailed phylogenetic, sequence and structure, selection pressure and comparative genomics analyses. All treeshrew, prosimian and simian DEFA/DEFT genes are grouped into two major clades, which are tissue-specific for enteric and myeloid defensins in simians. The simian enteric and myeloid α-defensins are classified into six functional gene clusters with diverged sequences, variable structures, altered functional constraints and different selection pressures, which likely reflect the antimicrobial spectra among closely related species. Species-specific duplication or pseudogenization within each simian cluster implies that the antimicrobial spectrum is ever-shifting, most likely challenged by the ever-changing pathogen environment. The DEFT evolved from the myeloid DEFA8. The prosegment of θ-defensin is detected with adaptive changes coevolving with the new protein fold of mature peptide, coincident with the importance of the prosegment for the correct folding of the mature peptide. Lastly, a less-is-hitchhiking hypothesis was proposed as a possible explanation for the expansion of pseudogene DEFTP and the loss of functional DEFT, where the gain or loss of the hitchhiker is determined by its adjacent driver gene during the birth-and-death evolutionary process.\",\n \"corpus_id\": 18525877,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":72,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28693630\",\n \"title\": \"Developmental competence of Dromedary camel (Camelus dromedarius) oocytes selected using brilliant cresyl blue staining.\",\n \"abstract\": \"The objectives of the present studies were to investigate the developmental capacity of dromedary camel oocytes selected by brilliant cresyl blue (BCB) staining and to investigate the expression of select transcripts in germinal vesicle (GV) stage oocytes. These transcripts included BMP15 and GDF9 as important transcripts for folliculogenesis and oocyte development, Zar1 and Mater as maternal transcripts required for embryonic development, Cyclin B1 and CDK1 as cell cycle regulators and Oct4 and STAT3 as transcription factors. Dromedary camel oocytes were retrieved from ovaries collected at a local slaughterhouse. After exposure to BCB staining, cumulus-oocyte complexes (COCs) from BCB+, BCB- and control (selected based on morphological criteria) groups were subjected to in vitro maturation, in vitro fertilization and in vitro culture. For gene expression studies, after BCB staining cumulus cells were stripped off and the completely denuded GV stage oocytes were used for RT-PCR analysis of selected transcripts. BCB+ oocytes showed higher maturation, and fertilization rates compared with BCB- and control groups. Indices of early embryonic development, namely, cleavage at 48 hours post insemination (hpi), and development to morula at day 5 and day 7 blastocyst rates were also significantly higher in the BCB+ group. RT-PCR revealed a higher expression of BMP15, GDF9, Zar1, Mater, Cyclin B1, CDK1, OCT4 and STAT3 in good quality oocytes that stained positively for BCB (BCB+). Collectively, results provide novel information about the use of BCB screening for selecting good quality oocytes to improve in vitro embryo production in the dromedary camel.\",\n \"corpus_id\": 46825797\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18239049","title":"Molecular and subcellular characterisation of oocytes screened for their developmental competence based on glucose-6-phosphate dehydrogenase activity.","abstract":"Oocyte selection based on glucose-6-phosphate dehydrogenase (G6PDH) activity has been successfully used to differentiate between competent and incompetent bovine oocytes. However, the intrinsic molecular and subcellular characteristics of these oocytes have not yet been investigated. Here, we aim to identify molecular and functional markers associated with oocyte developmental potential when selected based on G6PDH activity. Immature compact cumulus-oocyte complexes were stained with brilliant cresyl blue (BCB) for 90 min. Based on their colouration, oocytes were divided into BCB(-) (colourless cytoplasm, high G6PDH activity) and BCB(+) (coloured cytoplasm, low G6PDH activity). The chromatin configuration of the nucleus and the mitochondrial activity of oocytes were determined by fluorescence labelling and photometric measurement. The abundance and phosphorylation pattern of protein kinases Akt and MAP were estimated by Western blot analysis. A bovine cDNA microarray was used to analyse the gene expression profiles of BCB(+) and BCB(-) oocytes. Consequently, marked differences were found in blastocyst rate at day 8 between BCB(+) (33.1+/-3.1%) and BCB(-) (12.1+/-1.5%) oocytes. Moreover, BCB(+) oocytes were found to show higher phosphorylation levels of Akt and MAP kinases and are enriched with genes regulating transcription (SMARCA5), cell cycle (nuclear autoantigenic sperm protein, NASP) and protein biosynthesis (RPS274A and mRNA for elongation factor 1alpha, EF1A). BCB(-) oocytes, which revealed higher mitochondrial activity and still nucleoli in their germinal vesicles, were enriched with genes involved in ATP synthesis (ATP5A1), mitochondrial electron transport (FL405), calcium ion binding (S100A10) and growth factor activity (bone morphogenetic protein 15, BMP15). This study has evidenced molecular and subcellular organisational differences of oocytes with different G6PDH activity.","corpus_id":207150639,"score":2},{"doc_id":"18789618","title":"In vitro and in vivo developmental competence of dromedary (Camelus dromedarius) oocytes following in vitro fertilization or parthenogenetic activation.","abstract":"Parthenogenetic activation of the oocyte represents an important step in the somatic cloning. The aim of the present study was to evaluate the effectiveness (in term of in vitro development) of different methods of parthenogenetic activation of dromedary oocytes. Selected cumulus-oocytes-complexes (n=1264) collected by follicular aspiration from ovaries obtained postmortem were matured in vitro (IVM) for 30 h then divided randomly into seven groups and submitted to artificial activation. Two groups were preactivated with 25 microM of calcium ionophore (CaI) for 20 min then incubated for 4h with either 2mM 6-dimethylaminopurine (6-DMAP) (group 1, n=202) or with 10 microg/mL cycloheximide (CHX) (group 2, n=194). Group 3 (n=172) and group 4 (n=184), oocytes were pretreated with 5 microM ionomycin (Iono) for 5 min then incubated with either 2mM 6-DMAP or 10 microg/mL cycloheximide for 4h, respectively. Group 5 (n=161) and group 6 (n=155) oocytes were preactivated with electrical stimulation (ES) then activated with either 2mM 6-DMAP or 10 microg/mL cycloheximide for 4h, respectively. Group 7 (n=196) oocytes were submitted to in vitro fertilization (IVF) and served as a control. All groups containing oocytes were cultured in vitro following activation or IVF, at 38.5 degrees C under 5% CO(2) in air with >95% humidity. The in vitro development rates of dromedary oocytes exposed to 6-DMAP after CaI (61%), ES (74%) and the IVF group (71%) were similar and significantly greater (P<0.05) than other treatments (10% for group 2, 47% for group 3, 27% for group 4 and 41% for group 6). The blastocyst developmental rate was better (P<0.05) in parthenotes following activation with Iono/6-DMAP (21%) compared to activation with Iono/CHX (12%). However, all were less than that achieved in the IVF group (35%). We conclude that parthenogenetic activation of camel oocytes with 6-DMAP is more effective than activation with CHX for all pre-treatments tested (CaI, Iono or ES). The viability of activated (n=15) or IVF (n=10) hatched-dromedary embryos was examined by transfer to synchronized recipients. An embryonic vesicle was seen by ultrasonography at 15 days post transfer in four females (CaI/6-DMAP: 1/5; 20%, IVF: 3/10; 30%). The only pseudopregnancy obtained with an activated embryo resorbed at 25 days. One of the females receiving the IVF produced embryos aborted at 2 months and the other two females carried to term and gave birth to healthy calves (one female and one male). This study shows that artificial activation of dromedary oocytes with CaI/6-DMAP or ES/6-DMAP is more effective than other treatments in terms of in vitro embryo development. This provides efficient activation conditions which may lead to the development of the somatic cell nuclear transfer procedure in dromedary.","corpus_id":1601507,"score":2},{"doc_id":"19447485","title":"Developmental competence of porcine oocytes selected by brilliant cresyl blue and matured individually in a chemically defined culture medium.","abstract":"The objective of this study was to investigate the effects of oocyte selection using brilliant cresyl blue (BCB) and culture density during individual in vitro maturation (IVM) on porcine oocyte maturity and subsequent embryo development using a chemically defined medium. Cumulus-oocyte complexes (COCs) were classified as BCB-positive or BCB-negative after exposure to a BCB solution for 90 min. The classified COCs were matured in a group (15 COCs per 100-microL droplet) or individually (1 COC per 1-, 2.5-, 5-, or 10-microL droplet). Meiotic competence, intraoocyte glutathione concentration, and developmental competence after intracytoplasmic sperm injection were monitored. The BCB selected oocytes competent for nuclear and cytoplasmic maturation. Furthermore, meiotic competence for oocytes matured individually in a 5-microL droplet was superior (P<0.05) to that of oocytes matured in a 1-microL droplet. Also, the culture density in a 5-microL droplet during IVM resulted in a higher (P<0.05) rate of cleaved embryos than that in a 1-microL droplet and produced a similar rate of blastocysts compared with that of a group culture system. Conversely, BCB selection did not improve cleavage and blastocyst formation. In conclusion, it was possible to predict porcine oocytes competent for maturation using oocyte selection with BCB. Moreover, a 5-microL droplet during the individual IVM culture was most suitable for oocyte maturation and subsequent embryo development, although every culture density used in this study supported development up to the blastocyst stage.","corpus_id":205361227,"score":2},{"doc_id":"19754581","title":"Preliminary study in immature canine oocytes stained with brilliant cresyl blue and obtained from bitches with low and high progesterone serum profiles.","abstract":"This study was conducted: (i) to observe the features and levels of blue colour impregnation in morphologically selected immature canine cumulus oocyte complexes (COCs) stained with the brilliant cresyl blue (BCB) dye, as indicators of quality, and integrity of nuclear oocyte chromatin configuration before in vitro maturation (IVM); (ii) to observe the relationship between the influence of serum progesterone (SP) concentrations from ovary donors and BCB staining of immature dog oocytes. The results showed that out of 138 canine COCs, germinal vesicle (GV) stage prevailed in BCB+ oocytes at percentages of 67.4% (60/89), which were statistically higher than those observed in BCB+/- (52.2%; 23/44) and BCB- (20%; 1/5) oocytes (p = 0.023). Oocytes BCB+ were interpreted as those having completed their growth and therefore possessing the capacity to mature and develop in vitro. Ooplasm and cumulus cells (CCs) of canine oocytes were BCB staining independent. Ooplasm blue colour staining reaction varied between grown oocytes, revealing different levels of glucose-6-phosphate dehydrogenase activity among and within oocytes. Additionally, SP profile of ovary donors was not a relevant indicator for selection of oocytes screened with the BCB stain. Similar numbers of high quality oocytes were observed to be BCB+, BCB+/- and BCB- between groups of females with SP varying from 0 to 2.5 ng/ml (n = 5), and those with SP varying from 2.6 to 16.7 ng/ml (n = 4) (p = 0.680). It may be inferred that bitches with low and high SP profiles have grown oocytes in their ovaries, as determined by the BCB absorbance in their ooplasms.","corpus_id":31997627,"score":2},{"doc_id":"19939331","title":"Developmental competence and expression of the MATER and ZAR1 genes in immature bovine oocytes selected by brilliant cresyl blue.","abstract":"The objective of this work was to evaluate the selection of immature bovine oocytes by brilliant cresyl blue dye (BCB) and expression of transcripts MATER and ZAR1. Cumulus-oocyte complexes (COCs) from slaughterhouse ovaries were exposed to BCB diluted in mDPBS and incubated for 60 min at 38.5 degrees C in humidified air. After exposure those COCs were distributed in two groups, according to their cytoplasm colour: BCB+ (coloured cytoplasm) or BCB- (colourless cytoplasm). The control group was submitted to in vitro maturation (IVM) immediately after morphological selection and holding control group COCs were exposed to mDPBS without BCB but in the same incubation conditions of BCB+ and BCB- group. The COCs of all groups were submitted to IVM, in vitro fertilization (IVF) and in vitro culture (IVC). Cleavage rate (72 h post-insemination) was similar between control (65.3%) and BCB+ (64.4%) groups, but greater than (p < 0.05) holding control (49.8%) and BCB- (51.3%) groups. Blastocyst rate (192 h post-insemination) was not different between BCB+ (18.5%) and control (16.3%) groups, but greater (p < 0.05) than BCB- (8.4%) group. No difference was found for blastocyst rate between holding control group (14.2%), control and BCB+ groups. The relative expression of MATER and ZAR1 genes was evaluated by real-time PCR in immature oocytes collected from the control, holding control, BCB+ and BCB- groups. Despite the relative expression of MATER in holding control, BCB+ and BCB- were down regulated in comparison to control group there was no statistical difference (p > 0.05) in the relative expression of MATER and ZAR1 transcripts among groups. The results indicate that the BCB dye detects immature oocyte populations with different developmental competence, although no improvement in in vitro embryo production using oocytes exposed or not to BCB was observed. Development competence of immature oocytes exposed to BCB does not seem to be associated with variations in the expression of MATER and ZAR1 transcripts.","corpus_id":23233456,"score":2},{"doc_id":"20198711","title":"Cathepsin B activity is related to the quality of bovine cumulus oocyte complexes and its inhibition can improve their developmental competence.","abstract":"Recently, the quantity of cathepsin transcripts in cumulus cells was found to be associated with low-developmental competence of bovine oocytes. In the present study, we investigated (1) the relation between cathepsin B activity and the quality of in vitro-matured cumulus-oocyte complexes (IVM COCs) and denuded oocytes and (2) the effect of a cathepsin B inhibitor (E-64) on embryo development and quality. The activity of cathepsin B was evaluated in IVM COCs and denuded oocytes. After maturation of COCs with or without E-64, followed by in vitro fertilization, zygotes were cultured for 8 days. Cleavage and blastocyst rates were evaluated on days 2 and 8, respectively. Quality of embryos was evaluated by differential staining of day 8 blastocysts. TUNEL staining was conducted on IVM COCs and blastocysts. Cathepsin B activity was clearly detected in the low-quality oocytes, and in the cumulus cells of both high- and low-quality oocytes. This latter activity was diminished by addition of E-64. The presence of E-64 during IVM also significantly increased both the blastocyst rate and the total cell number, and improved blastocyst quality associated with a significant increase of trophoectoderm cells. TUNEL staining revealed that inhibition of cathepsin B significantly decreased the number of apoptotic nuclei in both the cumulus cell layer of matured oocytes and blastocysts. These results indicate that cathepsin B activity can be a useful marker of oocyte quality. Furthermore, inhibition of cathepsin B greatly improves the developmental competence of bovine oocytes and increases the number of high-quality embryos.","corpus_id":27155545,"score":2},{"doc_id":"21295838","title":"Zona pellucida glycoprotein 3 (pZP3) and integrin β2 (ITGB2) mRNA and protein expression in porcine oocytes after single and double exposure to brilliant cresyl blue test.","abstract":"Brilliant cresyl blues (BCB) staining test is a useful tool in assessing the competence of cumulus-oocyte-complexes (COCs) in several mammalian species. It is mostly used to select gametes after they are recovered from the ovary or before and after IVM to isolate those oocytes that reach developmental competency. However, there is evidence that double exposure to BCB test may lead to impaired fertilization or even have a toxic effect on cells. The aim of the present study was to investigate the expression pattern of sperm-egg interaction molecules in oocytes after single and double exposure to BCB test. Follicles were dissected from porcine ovaries after slaughter and aspirated COCs were cultured in standard porcine IVM culture medium (TCM 199) for 44 h. The BCB test was applied to COCs before and after IVM. In developmentally competent oocytes, assessed by determining the activity of glucose-6-phosphate dehydrogenase (G6PDH; BCB test), real-time quantitative PCR reaction methods, western blot and confocal microscopy analysis were applied to determine the transcript levels of porcine zona pellucida glycoprotein 3 (pZP3), and integrin beta 2 (ITGB2), as well as the levels of pZP3 and ITGB2 proteins. In the control group, assessment of the expression of the investigated genes was performed before and after IVM without BCB test. We observed a significantly higher level of pZP3 mRNA in oocytes after single exposure to BCB test compared to control before and after IVM (P < 0.001), and to double staining (P < 0.05). The level of ITGB2 mRNA was also increased in gametes after single exposure to BCB test as compared to control before and after IVM (P < 0.001, P < 0.01, respectively), and double staining (P < 0.05). Western blot analysis demonstrated a higher level of pZP3 protein in oocytes after single staining with BCB as compared to control both before and after IVM (P < 0.001, P < 0.05, respectively) and double staining (P < 0.05). Confocal microscopic observations have revealed the same pattern of increased level of pZP3 and ITGB2 expression after single exposure to BCB test. In both cases we detected specific cytoplasmic localization of both proteins. The ITGB2 protein has zona pellucida and membrane localization in control oocytes before IVM. After IVM and after single exposure to BCB, ITGB2 was also strongly detected in the cytoplasm. In both cases, after double exposure to BCB both proteins were detected only partially in the cytoplasm. Our results suggest that (i) single exposure to BCB increased the expression of sperm-oocyte interaction genes, (ii) double exposure to BCB leads to only partial expression of pZP3 and ITGB2 in oocyte cytoplasm, (iii) the BCB staining test itself may be a cause of specific pZP3 translocation from the zona pellucida to the cytoplasm, and that (iv) in vitro maturation of oocytes may increase ITGB2 expression and translocation from the zona pellucida to the cytoplasm.","corpus_id":5381751,"score":2},{"doc_id":"21757473","title":"Brilliant Cresyl Blue stain selects largest oocytes with highest mitochondrial activity, maturation-promoting factor activity and embryo developmental competence in prepubertal sheep.","abstract":"The aim of this study was to test the Brilliant Cresyl Blue (BCB) stain to select prepubertal sheep oocytes for in vitro blastocyst production. Oocyte diameter, mitochondrial activity, maturation-promoting factor (MPF) activity and mRNA relative expression (RE) of genes related to metabolism (ATPase Na(+)/K(+) transporting α 1 (ATP1A1) and cytochrome c oxidase subunit 1 (COX1)) and constitutive function of the cell (cytoplasmic polyadenylation-element-binding protein (CPEB) and S100A10) were assessed. Immature oocytes were exposed to different BCB concentrations (13, 26, 39 and 52 μM) and classified according to their cytoplasm colouration as grown BCB+ (blue cytoplasm) and growing BCB- (colourless cytoplasm). Staining oocytes with 13 μM BCB during 60 min allows selection of (BCB+) the largest (123.66 μm) and most competent oocytes to develop to the blastocyst stage (21%) with a higher number of cells (69.71 ± 6.19 s.e.m.) compared with non-stained BCB- oocytes (106.82 μm, 9% and 45.91 ± 3.35 s.e.m. respectively). Mitochondrial activity, assessed by MitoTracker Orange CMTMRos probe, was significantly higher in BCB+ than in BCB- oocytes after in vitro maturation (3369 and 1565 AU respectively). MPF activity was assessed by CDC2 kinase activity assay showing significantly higher activity at metaphase II stage in BCB+ than in BCB- oocytes (1.479 ± 0.09 and 1.184 ± 0.05 optical density respectively). The genes analysed in this work, ATP1A1, COX1, CPEB and S100A 10, did not show significant effect in mRNA RE between BCB selected oocytes. In conclusion, BCB stains larger and more competent oocytes to develop to the blastocyst stage with more active mitochondria and MPF activity and higher blastocyst cell number.","corpus_id":36232551,"score":2},{"doc_id":"21791164","title":"Selection of bovine oocytes by brilliant cresyl blue staining: effect on meiosis progression, organelle distribution and embryo development.","abstract":"The selection of competent oocytes for in vitro maturation is still a major problem during bovine in vitro embryo production. Markers for in vitro cytoplasmic maturation, based on the organization of cortical granule and mitochondria, are lacking. We examined the pre-selection of immature bovine oocytes by brilliant cresyl blue stain (BCB test) based on glucose-6-phosphate dehydrogenase (G6PDH) activity during oocyte development. Oocytes were recovered from ovarian follicles exposed to 26 μM BCB stain and classified according to the aspect of their cytoplasm: BCB(+) (oocytes with blue cytoplasm) and BCB(-) (unstained cytoplasm) and then in vitro matured into a conventional in vitro maturation (IVM) medium and standard procedure. In Experiment 1, nuclear maturation was determined by polar body identification, while cytoplasmic maturation was based on cortical granule (CG) migration (peripheral) and mitochondria distribution (central). Evidence of polar body, cortical granule migration and of centrally located mitochondria was significantly (p < 0.05) higher in BCB(+) oocytes than in BCB(-) (polar body present: 65% vs 20%; peripheral CG: 72% vs. 14%; and central mitochondria: 85% vs. 19%, respectively). In Experiment 2, the efficiency pre-selection of bovine oocytes by BCB on embryo development in vitro was assessed. Cleavage rates were similar (75%) among control, BCB(+) and BCB(-) groups, while blastocyst rates on D7 were (p < 0.05) higher (35%) in BCB(+) vs BCB(-) (10%) or control (28%). We showed that the BCB test is efficient to identify competent immature bovine oocytes to undergo synchronous nuclear and cytoplasmic in vitro maturation thus yielding higher in vitro embryo development to blastocyst stage.","corpus_id":206297573,"score":2},{"doc_id":"21791168","title":"Selection of Rattus norvegicus oocytes for in vitro maturation by brilliant cresyl blue staining.","abstract":"The objective of this work was to evaluate the rate of meiosis resumption and nuclear maturation of rat (Rattus norvegicus) oocytes selected for in vitro maturation (IVM) after staining of cumulus-oocyte complexes (COCs) with blue cresyl brilliant (BCB) using different protocols: exposure for 30, 60 or 90 min at 26 μM BCB (Experiment 1), and exposure for 60 min at 13, 20 or 26 μM BCB (Experiment 2). In Experiment 1, the selection of oocytes exposed to BCB for 60 min was found to be the most suitable, as meiosis resumption rates in the BCB(+) group (n = 35/61; 57.37%) were the closest to the observed in the control (not exposed) group (n = 70/90; 77.77%) and statistically higher than the values observed for the BCB(-) group (n = 3/41; 7.32%). Additionally, the more effective evaluation of diagnostic tests (sensitivity and negative predictive value 100%) was observed in COCs exposed for 60 min. In Experiment 2, the 13 μM BCB(+) group presented rates of meiosis resumption (n = 57/72; 72.22%) similar to the control group (n = 87/105; 82.86%) and higher than other concentration groups. However, this results of the analysis between BCB(-) oocytes was also higher in the 13 μM BCB group (n = 28/91; 30.78%) when compared with BCB(-) COCs exposed to 20 μM (n = 3/62; 4.84%) or 26 μM (n = 3/61; 4.92%) BCB. The nuclear maturation rate in the 13 μM BCB group was similar between BCB(+) or BCB(-) oocytes. The 20 μM BCB group had a lower rate of nuclear maturation of BCB(-) oocytes than other groups. Thus, our best results in the selection of Rattus norvegicus oocytes by staining with BCB were obtained using the concentration of 13 μM and 20 μM, and an incubation period of 60 min.","corpus_id":13698500,"score":2},{"doc_id":"21820165","title":"G6PDH-activity in equine oocytes correlates with morphology, expression of candidate genes for viability, and preimplantative in vitro development.","abstract":"Efficiencies for in vitro production of equine embryos are still low due to highly variable developmental competences of equine immature oocytes. In contrast to the equine, in vitro developmental competence of immature oocytes has been predicted successfully by the activity of glucose-6-phosphate dehydrogenase (G6PDH) indicated by brilliant cresyl blue (BCB) dye in a range of different species. Therefore, the aim of the present study was to test the association between G6PDH activity in equine oocytes with: (1) cumulus morphology and oocyte properties in terms of diameter and volume; (2) maturational competence; (3) gene expression of certain molecular markers; and (4) in vitro embryo development after intracytoplasmic sperm injection. Equine oocytes were exposed to BCB stain and were classified as BCB+ or BCB- according to their ability to convert the dye from blue to colorless. Additionally, BCB+ and BCB- oocytes were subclassified as having a compact (Cp) or expanded (Ex) cumulus complex. As a result, BCB+ oocytes had a greater proportion of expanded cumulus oocyte complexes compared with BCB- oocytes (71.2% vs. 49.5%). Moreover, we observed a significant difference in oocyte diameter and volume between BCB+ and BCB- oocytes irrespective of cumulus morphology. BCB+ oocytes reached a higher maturation rate compared with BCB- oocytes (59.0% vs. 28.7%). Regarding the analyzed candidate genes, relative transcript abundance was significantly different for nine genes. The expression of eight genes was significantly higher (P < 0.05) for BCB+ oocytes, including ATPV6E, IF-3, TFAM, DNMT1, STAT3, Aurora-A, ODC1, and CKS2 whereas BCB- oocytes showed higher in expression of COX1. These results are in line with the observed developmental competence. Cleavage rate (45.9% vs. 29.0%) and percentage of embryos that reached the blastocyst stage (9.2% vs. 1.4%) were significantly higher for embryos derived from BCB+ oocytes compared with BCB- oocytes. In conclusion, the present study provides evidence that G6PDH-activity in immature equine oocytes is a useful predictor for subsequent in vitro developmental competence.","corpus_id":25155668,"score":2},{"doc_id":"21870182","title":"Prediction of oocyte developmental competence in ovine using glucose-6-phosphate dehydrogenase (G6PDH) activity determined at retrieval time.","abstract":"PURPOSE: To determine whether G6PDH-activity measured by Brilliant Cresyl Blue known as BCB dye, predicts developmental competence within cohorts of ovine oocytes. METHODS: Ovine oocytes were exposed to BCB staining and categorized into two groups: BCB+ (blue cytoplasm, low G6PDH-activity) and BCB- (colorless cytoplasm, high G6PDH-activity). After maturation in vitro, oocytes were subjected to fertilization followed by in vitro embryo culture. RESULTS: We observed a significant difference in oocyte diameter considering BCB+ and BCB- oocytes. BCB+ and Control groups showed significantly higher maturation rates compared to BCB- group. There were significantly more cleaved embryos in BCB+ and control groups than in BCB- group. Blastocyst rate was significantly higher for BCB+ group compared to control and BCB- groups with control group being significantly higher than BCB- group. CONCLUSION: G6PDH-activity is a strong predictive marker of oocyte competence and may be useful in identifying oocytes with a good prognosis for further develop.","corpus_id":6158666,"score":2},{"doc_id":"22391295","title":"Gene expression pattern of adiponectin and adiponectin receptors in dominant and atretic follicles and oocytes screened based on brilliant cresyl blue staining.","abstract":"Adiponectin and its receptors (AdipoR1 and AdipoR2) are novel endocrine systems that act at various levels to control male and female fertility. The aim of this study was to determine whether adiponectin and its receptors gene expression levels differ between dominant follicle (DF) and atretic follicle (AF) and also between oocytes which were stained positively and negatively with brilliant cresyl blue (BCB(+) and BCB(-)). Based on estradiol/progesterone ratio, follicles from ovaries were classified as AFs and DFs. The stages of estrous cycle (follicular or luteal phases) were defined by macroscopic observation of the ovaries and the uterus. Oocytes were stained with BCB for 90 min. The relative expression of adiponectin, AdipoR1 and AdipoR2 mRNA in theca and cumulus cells and oocytes of different follicles were determined by quantitative real time PCR. Adiponectin and its receptors genes were clearly expressed higher (P<0.05) in theca and cumulus cells and oocytes of DFs than those of AFs during the follicular and luteal phases. BCB(+) oocytes showed a higher (P<0.05) expression of adiponectin and its receptors compared with their BCB(-) counterparts. Positive correlation (r>0.725, P<0.001) was observed between adiponectin mRNA level in ovarian cells of DFs and follicular fluid E2 concentration in follicular phase. Adiponectin mRNA abundance in ovarian cells of AFs showed a significant negative correlation with follicular fluid progesterone concentration in follicular and luteal phases (r<-0.731, P<0.001). This work has revealed the novel association of adiponectin and its receptors genes with follicular dominance and oocyte competence, thereby opening several new avenues of research into the mechanisms of dominance and competence in animal and human.","corpus_id":42591560,"score":2},{"doc_id":"22558373","title":"Oocytes selected using BCB staining enhance nuclear reprogramming and the in vivo development of SCNT embryos in cattle.","abstract":"The selection of good quality oocytes is crucial for in vitro fertilization and somatic cloning. Brilliant cresyl blue (BCB) staining has been used for selection of oocytes from several mammalian species. However, the effects of differential oocyte selection by BCB staining on nuclear reprogramming and in vivo development of SCNT embryos are not well understood. Immature compact cumulus-oocyte complexes (COCs) were divided into control (not exposed to BCB), BCB+ (blue cytoplasm) and BCB- (colorless cytoplasm) groups. We found that BCB+ oocytes yielded a significantly higher somatic cell nuclear transfer (SCNT) blastocyst rate and full term development rate of bovine SCNT embryos than the BCB- and control oocytes. BCB+ embryos (embryos developed from BCB+ oocytes) showed increased acetylation levels of histone H3 at K9 and K18 (AcH3K9, AcH3K18), and methylation levels of histone H3 at K4 (H3K4me2) than BCB- embryos (embryos developed from BCB- oocytes) at the two-cell stage. Furthermore, BCB+ embryos generated more total cells, trophectoderm (TE) cells, and inner cell mass (ICM) cells, and fewer apoptotic cells than BCB- embryos. The expression of SOX2, CDX2, and anti-apoptotic microRNA-21 were up-regulated in the BCB+ blastocysts compared with BCB- blastocysts, whereas the expression of pro-apoptotic gene Bax was down-regulated in BCB+ blastocysts. These results strongly suggest that BCB+ oocytes have a higher nuclear reprogramming capacity, and that BCB staining can be used to select developmentally competent oocytes for nuclear transfer.","corpus_id":7921528,"score":2},{"doc_id":"22675245","title":"Selection of ovine oocytes by brilliant cresyl blue staining.","abstract":"Sheep oocytes derived from the ovaries collected from the slaughterhouse are often used for research on in vitro embryo production, animal cloning, transgenesis, embryonic stem cells, and other embryo biotechnology aspects. Improving the in vitro culture efficiency of oocytes can provide more materials for similar studies. Generally, determination of oocyte quality is mostly based on the layers of cumulus cells and cytoplasm or cytoplasm uniformity and colors. This requires considerable experience to better identify oocyte quality because of the intense subjectivity involved (Gordon (2003), Madison et al. (1992) and De Loos et al. (1992)). BCB staining is a function of glucose-6-phosphate dehydrogenase (G6PD) activity, an enzyme synthesized in developing oocytes, which decreases in activity with maturation. Therefore, unstained oocytes (BCB-) are high in G6PD activity, while the less mature oocytes stains are deep blue (BCB+) due to insuffcient G6PD activity to decolorize the BCB dye.","corpus_id":17010501,"score":2},{"doc_id":"23199746","title":"Lipid content, active mitochondria and brilliant cresyl blue staining in bovine oocytes.","abstract":"Bovine oocytes that stain with brilliant cresyl blue (BCB) have a relatively higher developmental competence. The aim of the present study was to investigate the relationships among BCB staining, lipid content, and active mitochondria. Bovine oocytes (N = 133) with at least three layers of cumulus cells were segregated as BCB retained (BCB+) or metabolized (BCB-) and then stained for active mitochondria (Mitotracker Red) and lipid (Bodipy), with analysis by confocal microscopy. The BCB+ oocytes (N = 45) contained approximately 26% more cytoplasmic lipid than BCB- oocytes (N = 26-27; P < 0.05). Staining for active mitochondria did not differ between the groups. In BCB- oocytes but not BCB+ oocytes, lipid content correlated with active mitochondrial staining (r = 0.48; P < 0.05). Diameter correlated with lipid content for BCB+ oocytes (r = 0.46; P < 0.05), but not for BCB- oocytes (r = 0.16; P > 0.05). Irrespective of BCB staining, both lipid and active mitochondrial content correlated with diameter. In conclusion, the higher lipid content of BCB+ bovine oocytes might provide a cellular and functional basis for their greater developmental competence.","corpus_id":31772792,"score":2},{"doc_id":"23228698","title":"Combination of oocyte and zygote selection by brilliant cresyl blue (BCB) test enhanced prediction of developmental potential to the blastocyst in cattle.","abstract":"The cumulus oocyte complexes (COCs) were obtained from local abattoir. After aspiration, the COCs were allotted into four treatments to evaluation of brilliant cresyl blue (BCB) test. Control treatment (C): oocytes were cultured directly (without exposure to BCB) after recovery in in vitro production (IVP) process. Oocyte treatment (OBCB): immediately after aspiration, COCs were incubated in modified Dulbecco's phosphate-buffered saline (mDPBS) supplemented with 26μM of BCB for 90min and classified into two classes: oocytes with blue cytoplasm coloration (OBCB+: more competent oocytes) and oocytes without blue cytoplasm coloration (OBCB-: low competent oocytes). Directly after classification, the oocytes were maintained undisrupted in the IVP process. Zygote treatment (ZBCB): After oocyte collection, maturation and fertilization, zygotes were stained with BCB for 10min and categorized into three ways, according to whether they were highly stained (ZBCB++: low competent zygotes), moderately stained (ZBCB+: moderate competent zygotes) and unstained (ZBCB-: more competent zygotes). Directly after classification, the zygotes were maintained undisrupted in the culture process. Oocyte and zygote treatments (OBCB/ZBCB): COCs were stained with BCB after recovery and classified into two classes (OBCB+ and OBCB-). After fertilization, the zygotes produced from OBCB+ and OBCB- oocytes were further stained with BCB for 10min and categorized six ways (OBCB+/ZBCB++, OBCB+/ZBCB+, OBCB+/ZBCB-, OBCB-/ZBCB++, OBCB-/ZBCB+ and OBCB-/ZBCB-). Directly after classification, the zygotes were maintained undisrupted in the culture process. The selection rate produced from OBCB treatment (OBCB+; 54.3%) was greater (P<0.05) than ZBCB treatment (ZBCB-; 44.3%). In addition, the selection rate produced from double application (combination of oocyte and zygote selection) of BCB test (OBCB+/ZBCB-: 28.8%) was less (P<0.01) than single application of BCB test (ZBCB-: 44.3%or OBCB+: 54.3%). The percentage of blastocyst production from OBCB+ oocytes (35.7%) and ZBCB- zygotes (36.6%) were greater (P<0.05) than that from C oocytes (25.7%), OBCB- oocytes (16.5%), ZBCB++ (13.5%) and ZBCB+ zygotes (21.3%). However, there were no significant differences (P>0.05) in the percentages of blastocyst production between OBCB+ oocytes (35.7%) and ZBCB- zygotes (36.6%). The proportion of blastocyst production from double application of BCB test (OBCB+/ZBCB-: 48.0%) was greater (P<0.05) than that from single application of BCB test (OBCB+: 35.7% or ZBCB-: 36.6%). In conclusion, current results confirmed that combination of oocyte and zygote selection by BCB test enhanced the efficiency of selecting for high quality embryos, compared to the single BCB test.","corpus_id":25547903,"score":2},{"doc_id":"23369728","title":"Selection of developmentally competent immature equine oocytes with brilliant cresyl blue stain prior to in vitro maturation with equine growth hormone.","abstract":"Immature oocytes synthesize a variety of proteins that include the enzyme glucose-6-phosphate dehydrogenase (G6PDH). Brilliant cresyl blue (BCB) is a vital blue dye that assesses intracellular activity of G6PDH, an indirect measure of oocyte maturation. The objective was to evaluate the BCB test as a criterion to assess developmental competence of equine oocytes and to determine if equine growth hormone (eGH) enhanced in vitro maturation (IVM) of equine oocyte. Cumulus-oocytes complexes (COCs) were recovered by aspirating follicles <30 mm in diameter from abattoir-derived ovaries and were evaluated morphologically. Thereafter, COCs were exposed to BCB (26 μM) for 90 min at 39°C and selected based on the colour of their cytoplasm (BCB positive/BCB+ or BCB negative/BCB-). The COCs were allocated as follows: (a) IVM medium; (b) eGH group; (c) BCB-/IVM; (d) BCB+/IVM; (e) BCB-/eGH; and (f) BCB+/eGH. Then, COCs were cultured in vitro for 30 h, at 39°C in a 5%CO2 humidified air atmosphere. Cumulus-free oocytes were incubated in 10 μg/ml of bis-benzamide for 20 min at 39°C and nuclear maturation was evaluated with epifluorescence microscopy. Of the 39 COCs selected morphologically and subjected to BCB staining, 18/39 (46.2%) were classified as BCB+ and 21/39 (53.8%) as BCB- (P > 0.05). Maturation was not affected significantly by BCB classification, but the maturation rate was higher for oocytes that had been exposed to exogenous eGH versus controls (16/28, 57.1% versus 8/26, 30.8%, P < 0.05). In the present study, the BCB test was not useful for predicting competent equine oocytes prior to IVM. However, eGH enhanced equine oocyte maturation in vitro.","corpus_id":24479582,"score":2},{"doc_id":"24011188","title":"The utility of Brilliant Cresyl Blue (BCB) staining of mammalian oocytes used for in vitro embryo production (IVP).","abstract":"The present article summarizes the results of experiments investigating the Brilliant Cresyl Blue (BCB) staining for selection of immature oocytes before in vitro embryo production or somatic cell nuclear transfer. Developmental competence of oocytes stained with BCB and quality of blastocysts derived from such oocytes as well as the expression of apoptosis-related genes, mitochondrial DNA (mtDNA) replication-related genes and the transcripts encoded by the mitochondrial genome in BCB stained oocytes are discussed.","corpus_id":46514003,"score":2},{"doc_id":"24070583","title":"Mitochondrial content and gene expression profiles in oocyte-derived embryos of cattle selected on the basis of brilliant cresyl blue staining.","abstract":"The aim of this study was to investigate the developmental rate, lipid and mitochondrial distribution and gene expression in oocyte-derived embryos selected on the basis of brilliant cresyl blue (BCB) staining. Lipid content and mitochondrial distribution in Day 8 blastocysts were evaluated by fluorescence intensity, while gene expression was analyzed by real-time PCR. The proportion of blastocysts (30.9%) was greater (P<0.05) in BCB+ than in BCB- oocytes (13%) but not different (P>0.05) from the control group (28.2%). Total cell number was also greater in BCB+ (155.1 ± 36.2) than in BCB- (116.6 ± 40.5) and control (127.5 ± 35.7) blastocysts. Furthermore, the apoptotic cell number was less in BCB+ (3.7 ± 4.4) than in BCB- blastocysts (8.7 ± 8.7) but not different from the control group (5.9 ± 3.9). BCB+ embryos contained more mitochondria compared to BCB- embryos (P<0.05). There was no significant difference in intercellular lipid accumulation in embryos from all groups. Interferon-τ (IFNτ), transforming growth factor β1 (TGFB1) and secreted seminal-vesicle Ly-6 protein 1 (SSLP1) gene expression was greater in BCB+ than in BCB- blastocysts. By contrast, Bcl2-associated X protein (BAX) and heterogeneous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) gene expression was greater in BCB- than in BCB+ and control embryos. In conclusion, oocyte-derived embryos selected on the basis of BCB staining showed differences in developmental rate, quality, mitochondrial content and target gene expression compared to control embryos.","corpus_id":13540279,"score":2},{"doc_id":"24284835","title":"Differences in cytoplasmic maturation between the BCB+ and control porcine oocytes do not justify application of the BCB test for a standard IVM protocol.","abstract":"The Brilliant Cresyl Blue (BCB) test relies on G6PDH activity and a simple protocol for the selection of higher quality oocytes. Although the BCB+ oocytes of all the species that have been investigated are characterized by superior quality when compared to BCB- counterparts, application of the test for embryo production still remains an open issue. The aim of our study was to compare BCB+ and the control oocytes (not subjected to the BCB test) in terms of selected aspects of cytoplasmic maturation (mtDNA copy number, mitochondria distribution, relative transcript abundance of six marker genes). The results of our study revealed more relevant differences within the BCB+ and the control oocytes (before and after IVM) than between the two categories of oocytes. There was no difference in the transcript abundance of the BCB+ and the control oocytes in 5 out of 6 analyzed genes (BMP15, GDF9, ATP5A1, EEF1A, ZAR1) and in mtDNA content (pre-IVM 179609 vs. 176595 and post-IVM 187243 vs. 246984, respectively). With regard to mitochondria distribution in pre- and post-IVM oocytes, there was nonsignificant tendency for a more frequent occurrence of the expected patterns in the BCB+ group. The results of the present study do not support the application of BCB staining in a routine IVM protocol due to relatively high similarity in selected parameters characterizing cytoplasmic maturation of BCB+ and control oocytes. This high similarity may results from the limited amount of less competent BCB- oocytes (10%) still present among nonselected oocytes of proper morphology.","corpus_id":7695478,"score":2},{"doc_id":"24355610","title":"Brilliant cresyl blue staining negatively affects mitochondrial functions in porcine oocytes.","abstract":"The aim of the present study was to examine the effects of brilliant cresyl blue (BCB) staining on mitochondrial functions in porcine oocytes. Cumulus-oocyte complexes (COCs) collected from slaughterhouse-derived porcine ovaries were cultured with (13 μM) or without (0 μM, control) BCB for 60 min. Mitochondrial functions in oocytes were examined immediately after staining or after in vitro maturation. The BCB-stained oocytes produced reactive oxygen species (ROS) at higher levels than control oocytes immediately after staining (2.2-fold, P < 0.001) and after maturation (1.7-fold, P < 0.001). The adenosine triphosphate (ATP) content and mitochondrial membrane potential (MMP) in oocytes were similar for the two groups immediately after staining. However, ATP and relative MMP levels were significantly (P < 0.05) lower in BCB-treated oocytes than in the control (2.18 versus 2.83 pM and 0.82 versus 1.0, respectively). There was no difference in mitochondrial DNA copy number between the two groups after maturation. The ATP content in early developmental stage embryos (3 days after parthenogenetic activation) was lower in the BCB-stained group than that in the control group but the difference was not significant. In conclusion, BCB staining of oocytes at the immature stage compromises mitochondrial functions throughout oocyte maturation, but function is restored during early embryo development.","corpus_id":36694117,"score":2},{"doc_id":"24381853","title":"The Effect of Melatonin on Maturation, Glutathione Level and Expression of H MGB1 Gene in Brilliant Cresyl Blue (BCB) Stained Immature Oocyte.","abstract":"OBJECTIVE: Nutrients and antioxidants in the medium of immature oocyte have a profound effect on maturation, fertilization and development of resulting embryos. In this study the effects of melatonin as an antioxidant agent on maturation, glutathione level and expression of High mobility group box-1 (HMGB1) gene were evaluated in immature oocytes of mice stained with brilliant cresyl blue (BCB). MATERIALS AND METHODS: In this experimental study, immature oocytes were harvested from ovaries of Naval Medical Research Institute (NMRI) mice. Oocytes were stained with 26 μM BCB for 90 minutes and transferred to in vitro maturation medium containing varying doses of melatonin (10-12, 10-9, 10-6, 10-3 M) and without melatonin, for 22-24 hours. Maturation was monitored using an inverted microscope. Glutathione was assessed by monochlorobimane (MCB) staining and HMGB1 expression in mature oocyte was analyzed using real-time polymerase chain reaction (PCR). RESULTS: Melatonin in the concentration of 10-6 M had the most effect on maturation and HMGB1 expression of BCB+ oocytes (p<0.05). Meanwhile melatonin had no effects on glutathione levels. Additionally in immature BCB- oocytes, compared to the control group, melatonin did not affect cytoplasm maturation (p>0.05). CONCLUSION: In vitro treatment with melatonin increases the maturation and HMGB1 expression in BCB+ immature oocytes and has no significant effect on glutathione levels.","corpus_id":8859649,"score":2},{"doc_id":"24913026","title":"Association of glucose-6-phosphate dehydrogenase activity with oocyte cytoplasmic lipid content, developmental competence, and expression of candidate genes in a sheep model.","abstract":"PURPOSE: To evaluate associations of glucose-6-phosphate dehydrogenase (G6PDH) activity in sheep oocytes with cytoplasmic lipid content, maturational competence, developmental competence to the blastocyst stage, and gene expression of certain molecular markers. METHODS: Before brilliant cresyl blue (BCB) staining test, oocytes were classified as high, middle, and low cytoplasmic lipid content (HCLC, MCLC, and LCLC) and after the test as having low or high G6PDH-activity (BCB(+) and BCB(-), respectively). After maturation in vitro, a group of oocytes were subjected to IVF followed by in vitro embryo culture and another group was used for evaluation of expression of candidate genes. RESULTS: The cleavage and blastosyst rates were lowest (P < 0.05) in LCLC group, intermediate (P < 0.05) in MCLC group and highest (P < 0.05) in HCLC group. More (P < 0.05) oocytes in HCLC group were BCB(+), and higher (P < 0.05) maturation, cleavage, and blastocyst rates were seen for BCB(+) oocytes than the BCB(-) oocytes. Our gene expression data indicated that mRNA transcript abundance of ITGB2, pZP3, BMP15, and GDF9 genes was similar between BCB oocytes groups. However, the expression of ATP1A1 was higher (P < 0.05) for BCB(+) oocytes compared to BCB(-) oocytes. In addition, BAX transcript abundance was similar (P > 0.05) among BCB(+), BCB(-), and control groups, before and after maturation in vitro. CONCLUSION: Activity of G6PDH in sheep oocytes is highly associated with lipid content, and compared with the morphological parameters might be a more precise and objective predictor for subsequent developmental competence in vitro.","corpus_id":22982581,"score":2},{"doc_id":"25141841","title":"Expression profile of developmentally important genes between hand-made cloned buffalo embryos produced from reprogramming of donor cell with oocytes extract and selection of recipient cytoplast through brilliant cresyl blue staining and in vitro fertilized embryos.","abstract":"PURPOSE: To compare the expression profile of developmentally important genes between hand-made cloned buffalo embryos produced from reprogramming of donor cell with oocyte extracts and selection of recipient cytoplast through brilliant cresyl blue staining and in vitro fertilized (IVF) embryos. METHODS: Hand-made cloned embryos were produced using oocyte extracts treated donor cells and brilliant cresyl blue (BCB) stained recipient cytoplasts. IVF embryos were produced by culturing 15-20 COCs in BO capacitated sperms from frozen thawed buffalo semen and the mRNA expression patterns of genes implicated in metabolism (GLUT1), pluripotency (OCT4), DNA methylation (DNMT1), pro- apoptosis (BAX) and anti-apoptosis (BCL2) were evaluated at 8- to16- cell stage embryos. RESULTS: A significantly (P < 0.05) higher number of 8- to16- cell and blastocyst stages (73.9 %, 32.8 %, respectively) were reported in hand-made cloning (HMC) as compared to in vitro fertilization (49.2 %, 24.2 %, respectively). The amount of RNA recovered from 8- to 16- cell embryos of HMC and in vitro fertilization did not appear to be influenced by the method of embryo generation (3.76 ± 0.61 and 3.82 ± 0.62 ng/μl for HMC and in vitro fertilization embryos, respectively). There were no differences in the expression of the mRNA transcripts of genes (GLUT1, OCT4, DNMT1, BAX and BCL2) were analysed by real-time PCR between hand-made cloned and IVF embryos. CONCLUSIONS: Pre-treatment of donor cells with oocyte extracts and selection of developmentally competent oocytes through BCB staining for recipient cytoplast preparations may enhance expression of developmentally important genes GLUT1, OCT4, DNMT1, BAX, and BCL2 in hand-made cloned embryos at levels similar to IVF counterparts. These results also support the notion that if developmental differences observed in HMC and in vitro fertilization produced foetuses and neonates are the results of aberrant gene expression during the pre-implantation stage, those differences in expression are subtle or appear after the maternal to zygotic transition stage of development.","corpus_id":29805217,"score":2},{"doc_id":"25627022","title":"Effect of L-carnitine supplementation on maturation and early embryo development of immature mouse oocytes selected by brilliant cresyle blue staining.","abstract":"PURPOSE: The present study was designed to investigate the effect of L-carnitine treatment during IVM on nuclear and cytoplasmic maturation of immature oocytes selected by Brilliant Cresyle Blue (BCB) staining, and their subsequent developmental competence. MATERIALS & METHODS: Compact cumulus-oocyte complexes (COCs) were collected from NMRI mice ovaries and stained with BCB staining. BCB+ (colored cytoplasm) oocytes were then cultured in tissue culture medium (TCM) 199 with 0.0, 0.3 and 0.6 mg/ml L-carnitine. RESULTS: The both L-carnitine concentrations significantly increased the intracellular glutathione (P<0.001), nuclear maturation (P<0.01) and expression levels of cyclin-dependent kinase1 (CDK1) (P<0.05). Moreover, treated oocytes with 0.6 mg/ml L-carnitine showed increased (P < 0.05) expression of mitogen-activated protein kinase1 (MAPK1) mRNA. Also, adding L-carnitine (0.6 mg/ml) to IVM medium significantly increased the cleavage rate (P<0.05). The blastocyst development rate (BDR) in the both L-carnitine treated groups was significantly higher (P<0.001) than the control group. L-carnitine had no significant effect on total blastocyst cell numbers. CONCLUSIONS: These data indicated that L-carnitine supplementation during IVM of immature BCB+ oocytes improved preimplantation developmental competence of oocytes after IVF, probably by accelerating cytoplasmic and nuclear maturation of oocytes. It may provide a novel approach to improving ART outcomes in infertile couples.","corpus_id":24016141,"score":2},{"doc_id":"25704641","title":"Expression of TGFβ superfamily components and other markers of oocyte quality in oocytes selected by brilliant cresyl blue staining: relevance to early embryonic development.","abstract":"Brilliant cresyl blue (BCB) is a super-vital stain that has been used to select competent oocytes in different species. One objective of the present study was to assess the relationship between BCB staining, which correlates with an oocyte's developmental potential, and the transcript abundance for select TGFβ-superfamily components, SMAD2/3 and SMAD1/5 phosphorylation levels, and oocyte (JY1) and cumulus-cell (CTSB, CTSK, CTSS, and CTSZ) transcript markers in bovine oocytes and/or adjacent cumulus cells. The capacity of exogenous follistatin or JY1 supplementation or cathepsin inhibitor treatment to enhance development of embryos derived from low-quality oocytes, based on BCB staining, was also determined. Cumulus-oocyte complexes (COCs) from abattoir-derived ovaries were subjected to BCB staining, and germinal-vesicle-stage oocytes and cumulus cells were harvested from control, BCB+, and BCB- (low-quality oocyte) groups for real-time PCR or Western-blot analysis. Remaining COCs underwent in vitro maturation, in vitro fertilization, and embryo culture in the presence or absence of the above exogenous supplements. Levels of FST, JY1, BMP15, and SMAD1, 2, 3, and 5 transcripts were higher in BCB+ oocytes whereas CTSB, CTSK, CTSS, and CTSZ mRNA abundance was higher in cumulus cells surrounding BCB- oocytes. Western-blot analysis revealed higher SMAD1/5 and SMAD2/3 phosphorylation in BCB+ than BCB- oocytes. Embryo-culture studies demonstrated that follistatin and cathepsin inhibitor treatment, but not JY-1 treatment, improve the developmental competence of BCB- oocytes. These results contribute to a better understanding of molecular indices of oocyte competence.","corpus_id":31772931,"score":2},{"doc_id":"25709633","title":"Developmental competence of bovine oocytes selected based on follicle size and using the brilliant cresyl blue (BCB) test.","abstract":"BACKGROUND: Many studies reported that follicle size has an essential role in developmental potential of oocytes. Also, the brilliant cresyl blue (BCB) test is one of the most important criteria in selection of more competent oocytes. OBJECTIVE: Selection of developmentally competent bovine oocytes. MATERIALS AND METHODS: A total of 1730 bovine cumulus oocyte complexes (COCs) were recovered from the ovaries by follicles isolation and classified into 3 categories according to the diameters of the follicles (small, <3 mm; medium 3-6 mm and large >6 mm). Oocytes were exposed to the BCB stain, diluted in Dulbecco's phosphate-buffered saline, modified with 0.4% bovine serum albumin (BSA) for 90 min. Oocytes with or without blue coloration of the cytoplasm were designated as BCB(+) and BCB(-), respectively. RESULTS: The BCB(+) and control oocytes originated from large and medium follicles exhibited a higher (p<0.0001) cleavage and blastocyst rate than BCB(-) oocytes. Furthermore, the BCB(+) oocytes from large and medium follicles had the highest (p<0.0001) proportion of blastocyst than other treatment groups. In contrast, the BCB(-) oocytes from small follicles had the lowest (p<0.0001) proportion of blastocyst than other treatment groups. Interestingly, the percentage of the BCB(+) oocytes from the large and medium ovarian follicles was significantly higher (p<0.0001), than the BCB(+) oocytes from the small follicles. CONCLUSION: Current results confirmed that each BCB(+) oocyte could not lead to perfect embryo development and the BCB test is not sufficient enough for the identification of oocytes that are competent for in vitro embryo development.","corpus_id":16009830,"score":2},{"doc_id":"25826727","title":"Buffalo embryos produced by handmade cloning from oocytes selected using brilliant cresyl blue staining have better developmental competence and quality and are closer to embryos produced by in vitro fertilization in terms of their epigenetic status and gene expression pattern.","abstract":"We compared handmade cloned (HMC) buffalo blastocysts produced from oocytes stained with Brilliant Cresyl Blue (BCB) and classified into those with blue (BCB+) or colorless cytoplasm (BCB-). The blastocyst rate was higher (p<0.001) for BCB+ than for BCB- oocytes (43.41 ± 2.54 vs. 22.74 ± 1.76%). BCB+ blastocysts had inner cell mass (ICM) cell number, ICM-to-trophectoderm ratio, global level of H3K18ac, apoptotic index, and expression level of BCL-XL, but not that of CASPASE-3, similar to that of blastocysts produced through in vitro fertilization (IVF), which was higher (p<0.05) than that of BCB- blastocysts. The global level of H3K9me2, which was similar in BCB+ and BCB- blastocysts, was higher (p<0.01) than that in IVF blastocysts. The expression level of OCT4 and SOX2 was higher (p<0.05) and that of GATA2 was lower (p<0.05) in BCB+ than that in BCB- blastocysts, whereas that of DNMT1, DNMT3a, NANOG, and CDX2 was not significantly different between the two groups. The expression level of DNMT1, OCT4, NANOG, and SOX2 was lower (p<0.05) and that of CDX2 was higher (p<0.05) in BCB+ than in IVF blastocysts. In conclusion, because BCB+ blastocysts have better developmental competence and are closer to IVF blastocysts in terms of quality, epigenetic status, and gene expression than BCB- blastocysts, BCB staining can be used effectively for selection of developmentally competent oocytes for HMC.","corpus_id":5580099,"score":2},{"doc_id":"25921213","title":"Safety of brilliant cresyl blue staining protocols on human granulosa and cumulus cells.","abstract":"The selection of human immature oocytes destined for in vitro maturation (IVM) is performed according to their cumulus-oocyte complex (COC) morphology. In animal models, oocyte pre-selection with brilliant cresyl blue (BCB) staining improves fertilization and blastocyst rates and even increases the number of calves born. As the granulosa cells and cumulus cells (GCs and CCs) have a close relationship with the oocyte and are available in in vitro fertilization (IVF) programs, applying BCB staining to these cells may help to elucidate whether BCB shows toxicity to human oocytes and to determine the safest protocol for this dye. GCs and CCs were isolated from 24 patients who underwent controlled ovarian stimulation. After 48 h, cells were exposed to: Dulbecco's Modified Eagle Medium (DMEM) with or without phenol red, DPBS and mDPBS for 60 min; 13, 20 and 26 μM BCB for 60 min; and 60, 90 or 120 min to 13 μM BCB. Cellular viability was tested using 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) and trypan blue assays. The 20 and 26 μM BCB exposures resulted in lower cell viability, similar to when cells were exposed to BCB for 90 or 120 min. GCs and CCs viabilities were equal among control group and 13 μM BCB group after 60 min. BCB staining was not toxic to GCs and CCs when the regime of 13 μM BCB for 60 min was used. Due to the close molecular/biochemical relationship between these cells and the gamete, we propose that it is unlikely that the use of BCB could interfere with the viability/health of human oocytes.","corpus_id":28812526,"score":2},{"doc_id":"25943119","title":"Bovine non-competent oocytes (BCB-) negatively impact the capacity of competent (BCB+) oocytes to undergo in vitro maturation, fertilisation and embryonic development.","abstract":"Competent oocyte selection remains a bottleneck in the in vitro production (IVP) of mammalian embryos. Among the vital assays described for selecting competent oocytes for IVP, the brilliant cresyl blue (BCB) test has shown consistent results. The aim of the first experiment was to observe if oocytes directly submitted to IVM show similar cleavage and blastocyst rates as those obtained with oocytes maintained under the same in vitro conditions as the oocytes that undergo the BCB test. Bovine cumulus-oocyte complexes (COCs) were recovered from slaughterhouse-derived ovaries and, after morphological evaluation, were randomised grouped into three groups: (1) directly submitted to IVM; (2) oocytes submitted to the BCB test without the addition of BCB stain (BCB control group); and (3) submitted to the BCB test. The results showed that oocytes directly submitted to IVM reached similar cleavage (48/80 - 60%) and embryonic development rates to the blastocyst stage (10/48 - 21%) as the results obtained with the BCB control group oocytes (45/77 - 58% and 08/45 - 18%, respectively). The aim of the second experiment was to determine the cleavage and blastocyst rates obtained from BCB+ oocytes undergoing IVM in the presence of BCB- oocytes at a ratio of 10:1. COCs were recovered from slaughterhouse-derived ovaries and, after morphological evaluation, were randomised into two groups that were submitted to IVM either directly (1: control group) or submitted to the BCB test prior to IVM. After the BCB test, the COCs were classified as either BCB+ (blue cytoplasm) or BCB- (colourless cytoplasm) and then divided into four experimental groups: (2) BCB+; (3) BCB-; and (4) BCB+ matured in same IVM medium drop as (5) BCB- at a ratio of 10:1. After IVM (24 h), oocytes from the different experimental groups were submitted to in vitro fertilisation (IVF) and in vitro culture (IVC) under the same culture conditions until they reached the blastocyst stage (D7). With regards to the cleavage rate (48 h after IVF), only group 3 (102/229 - 44%) differed (P < 0.05) from the other groups [1 (145/241 - 60%); 2 (150/225 - 67%); 4 (201/318 - 63%) and 5 (21/33 - 63%)]. On day 7, the embryos from group 2 (BCB+) achieved the highest blastocyst rate (46/150 - 31%) (P < 0.05) when compared with the embryo development capacity of the other experimental groups (1: 31/145 - 21%; group 3: 17/102 - 17%; group 4: 46/201 - 23%; and group 5: 2/21 - 10%). In conclusion, submitting BCB+ oocytes that were separated from BCB- oocytes to IVM increases the rate of embryonic development to the blastocyst stage when compared to the control group, BCB- oocyte group, BCB+ paracrine group and BCB- paracrine group. The presence of non-competent oocytes during IVM, even in low proportion (1:10), reduces the capacity of competent oocytes to undergo embryo development and achieve blastocyst stage during IVC.","corpus_id":45627469,"score":2},{"doc_id":"26280459","title":"Gene Expression of Monocarboxylate Transporters and Oocyte-secreted Factors in Bovine Cumulus-oocyte Complexes Selected by Brilliant Cresyl Blue.","abstract":"Oocyte selection based on the brilliant cresyl blue (BCB) staining test has been successfully used to differentiate between competent and incompetent bovine oocytes. Here, the expression of genes involved in transport of monocarboxylates (Mct1-4) and oogenesis specific genes (Bmp15, Gdf9 and Has2) in BCB+ and BCB- selected immature and mature bovine cumulus-oocyte complexes (COC) was evaluated. In order to find specific molecular markers to characterize successful oocyte maturation, our study was also aimed at identifying the expression of Mcts and oogenesis specific genes in denuded oocytes and cumulus cells. Immature COCs morphological appropriate were (i) stained with 26 mm BCB for 90 min before IVM, (ii) exposed to same incubation conditions as stained COCs, but without BCB (holding group) or (iii) transferred into a maturation medium immediately after morphological selection (control group). mRNA expression was investigated by RT-PCR in COCs before and after IVM. No relationship was observed in the relative expression of Has2, Gdf9, Bmp15 or Mct1, 2 and 4 transcripts between BCB+ and BCB- COCs. Transcripts analysis showed that Gdf9 and Bmp15 in BCB+, BCB- and holding groups were up-regulated (p < 0.05) before IVM, while Has2 was up-regulated (p < 0.01) after IVM in the control group. Other genes remained stable during maturation (Mct1, 2 and 4). Our results showed, for the first time, Mct1, 2 and 4 expression in bovine COCs. Mct1 and Mct4 transcripts were present in denuded oocytes and cumulus cell, while Mct2 was detected only in cumulus cells. These differences between the three isoforms in localization suggest unique roles for each in monocarboxylate transport during maturation.","corpus_id":206289479,"score":2},{"doc_id":"26879998","title":"Effects of cilostamide and/or forskolin on the meiotic resumption and development competence of growing ovine oocytes selected by brilliant cresyl blue staining.","abstract":"The relevance of low developmental competence of in vitro-matured oocyte to the incomplete/delayed cytoplasmic maturation, and the heterogeneity of retrieved oocytes is well established in several species. A short phase of prematuration culture was used to allow better oocyte cytoplasmic maturation. The preselection of growing and fully grown oocytes has been proposed to improve developmental competency. This study investigated the effects of phosphodiesterase type 3-specific inhibitor, cilostamide, and adenylate cyclase activator, forskolin, on the resumption of meiosis and developmental competence of growing ovine oocytes selected by brilliant cresyl blue (BCB) staining. Results indicate that cilostamide, forskolin, and their combination significantly (P < 0.05) increased the percentage of growing (BCB-) oocytes maintained at the germinal vesicle stage. However, only forskolin significantly (P < 0.05) increased the yield and quality of blastocysts derived from BCB- oocytes compared with non-BCB-treated oocytes. We conclude that a short prematuration culture with forskolin may improve the in vitro developmental competency of growing oocytes in ovine.","corpus_id":205368686,"score":2},{"doc_id":"27481813","title":"Effect of milrinone on the developmental competence of growing lamb oocytes identified with brilliant cresyl blue.","abstract":"Juvenile in vitro embryo transfer is a novel technique that can be used to increase the rate of genetic gain in a population and presents an alternative to embryo technologies on the basis of adult animals. However, oocytes from prepubertal animals have a lower viability than those obtained from adult ewe oocyte donors. In this research, we aimed to determine the optimum concentration and time of treatment of oocytes from prepubertal lambs with brilliant cresyl blue (BCB) stain and milrinone during IVM. This would improve the developmental rate of lamb oocytes and embryos after IVF. First, lamb cumulus-oocyte complexes were cultured under different concentrations (13 or 26 μM) of BCB staining. Treated lamb oocytes were then divided into BCB- (colorless cytoplasm) and BCB+ (colored cytoplasm) groups on the basis of their glucose-6-phosphate dehydrogenase activity. The blastocyst efficiency rate of BCB+ oocytes treated with 13 μM BCB (37.03%) was significantly higher than that of BCB+ oocytes treated with 26 μM BCB (23.25%) and that of nontreated BCB control oocytes (15.37%), as well as that of BCB- oocytes (6.28%). Both control oocytes and BCB+ oocytes exhibited significantly higher cleavage rates (60.15% and 73.44%, respectively) than that of BCB- oocytes (36.19%). Moreover, the diameter and glutathione content of BCB+ oocytes were found to be significantly greater than those of BCB- oocytes (163.37 vs. 159.25 μm and 6.39 vs. 0.26 pM, respectively). After culturing BCB- oocytes in different concentrations of milrinone (0, 50, 75, and 100 μM) for 3, 6, or 9 hours, results reported that supplementation of IVM medium with 75 μM milrinone for 6 hours yielded a significantly higher proportion of blastocysts than the other treatments. These results show that the staining of lamb cumulus-oocyte complexes with 13 μM BCB before IVM may be used to select developmentally competent lamb oocytes. Furthermore, they suggest that milrinone can be used to promote lamb developmental competence of lamb embryos produced during IVF.","corpus_id":27285496,"score":2},{"doc_id":"27955714","title":"Selection of porcine oocytes in vitro through brilliant cresyl blue staining in distinct incubation media.","abstract":"Staining with brilliant cresyl blue (BCB) may be used for oocyte selection, but BCB staining itself and the most commonly used selection medium (DMPBS) may compromise the development of porcine oocytes in vitro. This study evaluated DNA fragmentation, nuclear maturation, the area of migration of cortical granules (CG) and embryo development for stained (BCB+) and unstained (BCB-) oocytes incubated in DMPBS and in a modified medium (ReproPel) tested for the first time. Unexposed (UN), BCB+ and BCB- oocytes were incubated composing six groups: DMPBS/UN; DMPBS/BCB+; DMPBS/BCB-; ReproPel/UN; ReproPel/BCB+; and ReproPel/BCB-. There were more BCB+ oocytes in ReproPel than in DMPBS (P < 0.05). The DNA fragmentation was evaluated for oocytes in DMPBS/BCB+, DMPBS/BCB-, ReproPel/BCB+, ReproPel/BCB- and in porcine follicular fluid (control). The frequency of oocytes with no DNA fragmentation was greatest (64.6%) in DMPBS/BCB+ and lowest in ReproPel/BCB+ and ReproPel/BCB- (26.8 and 34.1%, respectively) (P < 0.05). Nuclear maturation rates were greater (P < 0.05) for DMPBS/BCB+ (63.1%), ReproPel/UN (55.1%) and ReproPel/BCB+ (50.2%) than for DMPBS/UN (40.8%) and ReproPel/BCB- (35.5%). The area of CG was greater (P < 0.05) for ReproPel/BCB- (80.7%) and DMPBS/UN (77.6%) than for ReproPel/UN (34.7%). Cleavage rates for DMPBS/BCB+ and ReproPel/BCB+ were greater than for DMPBS/UN (P < 0.05). Blastocyst development rates were greatest (P < 0.05) for ReproPel/UN and ReproPel/BCB+. In both media, BCB staining was apparently unable to select competent oocytes, which likely occurred due to toxicity. Despite the similar nuclear maturation and area of CG compared with DMPBS, oocytes selected in ReproPel presented impaired DNA integrity.","corpus_id":24663336,"score":2},{"doc_id":"28063736","title":"Brilliant cresyl blue staining does not present cytotoxic effects on human luteinized follicular cells, according to gene/protein expression, as well as to cytotoxicity tests.","abstract":"In vitro oocyte maturation presents many advantages and its success is related to the selection of fully grown oocytes. In animal models, staining of cumulus-oocyte complexes (COCs) with Brilliant Cresyl Blue (BCB) is widely used for this selection. However, a lack of information about the safety of BCB makes its applicability in humans questionable. Because granulosa and cumulus cells have a close relationship with the oocyte and taking into account that follicular cells are also exposed to BCB when this pre-selection method is applied, we aimed to evaluate the effects of BCB on human follicular cells exposed to BCB. Cytotoxicity tests (Sulforhodamine B and Neutral Red Uptake) and gene and protein expression of elements related to the cell cycle (BAX, BCL2, TP53 and CDKN1A), as well as to cell death and metabolism (GAPDH), glucose consumption, and estradiol and progesterone secretion, were examined in granulosa and cumulus cells with and without exposure to BCB. Regardless estradiol secretion and glucose consumption, all other evaluations presented similar results between control and treated (BCB) groups, independently of cell type. Therefore, our results demonstrate convincingly that BCB seems to be safe for use in humans and it should encourage future studies to evaluate the development of embryos derived from human oocytes selected by BCB staining.","corpus_id":22571519,"score":2},{"doc_id":"28070808","title":"Combined positive effect of oocyte extracts and brilliant cresyl blue stained recipient cytoplasts on epigenetic reprogramming and gene expression in buffalo nuclear transfer embryos.","abstract":"This study examined the effects of buffalo oocyte extracts (BOE) on donor cells reprogramming and molecular characterisation of oocytes screened via brilliant cresyl blue (BCB) staining and comparison of gene expression profiles of developmentally important genes in blastocysts from IVF and cloned derived from BOE treated donor cells with BCB selected recipient cytoplasts. Relative abundance (RA) of OCT4 and NANOG was increased (P < 0.05) and HDAC-1, DNMT-1, and DNMT-3A decreased (P < 0.05) in extract treated cells (ETCs). This ETCs dedifferentiated into neuron-like lineage under appropriate induction condition. The RA of NASP, EEF1A1, DNMT1, ODC1 and RPS27A was increased (P < 0.05) in BCB+ oocytes, whereas ATP5A1 and S100A10 increased (P < 0.05) in BCB- oocytes. Total cell number and RA of OCT4, NANOG, SOX2, DNMT1, IGF2, IGF2R, MNSOD, GLUT1, BAX and BCL2 in cloned blastocysts derived from BCB+ oocytes with ETC more closely followed that of IVF counterparts compared to BCB+ oocytes with extract untreated cell and BCB- oocytes with ETC derived blastocysts. In conclusion, BOE influenced epigenetic reprogramming of buffalo fibroblasts making them suitable donors for nuclear transfer (NT). BCB staining can be effectively used for selection of developmentally competent oocytes for NT. The combined effects of epigenetic reprogramming of donor nuclei by BOE and higher nuclear reprogramming capacity of BCB+ oocytes improve developmentally important gene expression in cloned blastocysts. Whether these improvements have long-term effects on buffalo calves born following embryo transfer remains unknown.","corpus_id":207112094,"score":2},{"doc_id":"28274148","title":"Selection of developmentally competent human oocytes aspirated during cesarean section.","abstract":"PURPOSE: To evaluate the efficiency/safety of Brilliant Cresyl Blue (BCB) staining as a selection method of developmentally competent immature human oocytes. MATERIALS AND METHODS: Immature oocytes of 32 pregnant women were recovered during cesarean section (CS). After retrieval, 92 oocytes were randomly divided into two groups: control (directly disposed to in vitro maturation - IVM) and treated - exposed to BCB 26 μM during 60 min. After staining, the treated group was classified as cytoplasm coloration, BCB positive (blue) or negative (colorless), and then disposed to IVM. Nuclear status was checked after 24 and 48 h of IVM. Nuclear maturation (polar body extrusion), meiosis resumption (absence of germinal vesicle) and degeneration rates were evaluated among the three groups (control, BCB positive and BCB negative) using Generalized Estimating Equations, followed by Bonferroni's correction for multiple comparisons. RESULTS: Nuclear maturation was higher in BCB positive compared to BCB negative, after 24 and 48 h of IVM (p = .004 and p = .032). The control group was equal to BCB positive. There was no difference among groups analyzing meiosis resumption and degeneration rates. CONCLUSION: The BCB test can be a good marker in pre-selection procedures of developmentally competent human oocytes aspirated during CS.","corpus_id":23208478,"score":2},{"doc_id":"17945442","title":"Survivin protein expression in bovine follicular oocytes and their in vitro developmental competence.","abstract":"This study examined the relationship between survivin expression and the stage of development of in vitro cultured bovine oocytes and embryos; and whether survivin expression is affected by the quality of cumulus-oocyte complexes (COCS) or the quality of pre-implantation embryos. A polyclonal antibody was prepared using recombinant bovine survivin protein. Expression of survivin mRNA and protein was analyzed by real-time quantitative RT-PCR and immunocytochemistry. In the first experiment, survivin mRNA expression was examined at developmental stages from germinal vesicle (GV) oocyte to blastocyst, it was significantly decreased after fertilization of matured oocytes (P<0.05), then increased slightly to the 8-cell stage followed by rapid increases at the morula and blastocyst stages (P<0.05). In the second experiment, the effect of oocyte quality on survivin protein, pro-apoptotic (bax, caspase-3) and anti-apoptotic (survivin, bax inhibitor) mRNA expression was examined. Survivin protein was more strongly expressed in good quality COCS than in poor quality COCS. The expression of the anti-apoptotic genes, survivin and bax inhibitor, was significantly higher (P<0.05) and that of the pro-apoptotic genes, bax and caspase-3, was significantly lower (P<0.05) in good compared to poor quality COCS. The developmental competence of good quality COCS (30.4% blastocysts) was significantly better than that of poor quality COCS. In the last experiment also, we confirmed that significantly higher expression of survivin and bax inhibitor genes and significantly lower expression of bax and caspase-3 genes was resulted in good quality blastocysts than in poor quality blastocysts (P<0.05). It was concluded that the expression of survivin was related to the quality of COCS, their developmental competence and the quality of in vitro produced blastocysts. Consequently, survivin may be a good candidate marker for embryo quality.","corpus_id":33927129,"score":1},{"doc_id":"18242678","title":"Chemical activation of in vitro matured dromedary camel (Camelus dromedarius) oocytes: optimization of protocols.","abstract":"Experiments were conducted to study the efficiency of sequential treatments of ionomycine and ethanol combined with phosphorylation inhibitor (6-dimethylaminopurine) or the specific maturation promoting factor inhibitor (roscovitine) in inducing artificial activation in dromedary M-II oocytes. Cumulus oocyte complexes (COCs), collected from slaughterhouse ovaries were cultured at 38.5 degrees C in an atmosphere of 5% CO2 in air for 24-48 h. In experiment 1, the COCs were either fertilized in vitro or activated with 5 microM ionomycine for 5 min or 7% ethanol for 7 min, both followed by exposure to 6-diethylaminopurine or roscovitine for 4h. After 14-15 h of in vitro culture, the oocytes were fixed and stained with 1% aceto-orcein to evaluate their nuclear status. In experiment 2, the oocytes were activated in the same manner as in experiment 1 but were cultured for 7 days to evaluate their post-parthenogenetic development. In experiment 3, oocytes were exposed to the ionomycine for 2, 3, 4 or 5 min to evaluate the better exposure time while as in experiment 4, the oocytes matured for 28-48 h were activated to see the effect of aging on post-parthenogenetic development. Higher proportion (P<0.01) of oocytes was activated in ionomycine/6-DMAP and ionomycine/roscovitine groups when compared with ethanol/6-DMAP, ethanol/roscovitine and in vitro fertilized groups. However, there was no difference (P>0.05) in the proportion of oocytes activated with ethanol when compared with in vitro fertilized group. No significant difference was seen on the proportion of morula on day 7 of culture, however the development to blastocyst stage was higher (P<0.01) in ionomycine/6-DMAP and ionomycine/roscovitine when compared with ethanol/6-DMAP and ethanol/roscovitine treated oocytes. A higher proportion of oocytes reached blastocyst stage when they were exposed to ionomycine for 3 min but they were not significantly different from the others (P>0.05). The proportion of blastocysts obtained was higher (P<0.05) in oocytes activated after 28 h of maturation when compared with oocytes activated after 32, 36, 40, 44 and 48 h of maturation. In conclusion, a protocol for chemical activation of dromedary camel oocytes with ionomycine/6-DMAP is demonstrated and optimized in the present study for further use in the development of assisted reproductive techniques in this species.","corpus_id":45665573,"score":1},{"doc_id":"20088850","title":"In vitro maturation of dromedary (Camelus dromedarius) oocytes: effect of different protein supplementations and epidermal growth factor*.","abstract":"The present experiment was aimed to compare the effect of different protein supplementation sources, foetal calf serum (FCS), oestrous dromedary serum (EDS) and BSA, in experiment 1, and the effect of different concentrations of epidermal growth factor (EGF), in experiment 2, on in vitro nuclear maturation of the dromedary oocytes. Cumulus oocyte complexes (COCs) were harvested from the ovaries collected from a local slaughterhouse by aspirating the visible follicles in PBS supplemented with 5% FCS. Pooled COCs were randomly distributed to 4-well culture plates containing 500 μl of the maturation medium and cultured at 38.5 °C in an atmosphere of 5% CO(2) in air for 32-36 h. The basic maturation medium consisted of TCM-199 supplemented with 0.1 mg/ml L-glutamine, 0.8 mg/ml sodium bicarbonate, 0.25 mg/ml pyruvate, 50 μg/ml gentamicin, 10 μg/ml bFSH, 10 μg/ml bLH and 1 μg/ml estradiol. In experiment 1, this medium was supplemented with 10% FCS, 10% EDS or 0.4% BSA, whereas in experiment 2, it was supplemented with 0.4% BSA and 0, 10, 20 or 50 ng/ml of EGF. The oocytes were fixed, stained with 1% aceto-orcein stain and their nuclear status was evaluated. Oocytes were classified as germinal vesicle, diakinesis, metaphase-I, anaphase-I (A-I), metaphase-II (M-II) and those with degenerated, fragmented, scattered, activated or without visible chromatin as others. There was no difference (p > 0.05) observed in the proportion of oocytes reaching M-II stage between the media supplemented with FCS (71.5 ± 4.8), EDS (72.8 ± 2.9) and BSA (72.7 ± 6.2). In experiment 2, a higher proportion (p < 0.05) of oocytes reached M-II stage when the medium was supplemented with 20 ng/ml of EGF (81.4 ± 3.2) when compared with the media supplemented with 10 ng/ml (66.9 ± 4.1) and control (67.2 ± 7.1) groups. It may be concluded that the maturation media for dromedary camel oocytes can be supplemented with any of the three protein sources, i.e. FCS, EDS and BSA without any significant differences on the maturation rates. Also, a supplementation of 20 ng/ml of EGF in the maturation medium seems to be optimal and improves the nuclear maturation of dromedary camel oocytes.","corpus_id":25783678,"score":1},{"doc_id":"20451991","title":"Ultrasonographic-guided retrieval of cumulus oocyte complexes after super-stimulation in dromedary camel (Camelus dromedarius).","abstract":"In Experiment 1, studies were conducted to apply the transvaginal ultrasound guided ovum pick-up (OPU) technique in dromedary camels after their ovarian super-stimulation and in vivo oocyte maturation. In Experiment 2, the developmental potential of two commonly used oocyte types, i.e., in vivo matured oocytes collected by OPU and abattoir derived in vitro-matured oocytes was compared after their chemical activation. In Experiment 3, developmental competence of oocytes collected from super-stimulated camels by OPU, matured either in vivo or in vitro, was compared after their chemical activation. Mature female dromedary camels super-stimulated with a combination of eCG and pFSH were given an injection of 20 microg of the GnRH analogue, buserelin 24, 26, or 28 h before the scheduled OPU. For collection of cumulus oocyte complexes (COCs) the transducer was guided through the vulva into the cranial most portion of the vagina and 17-gauge, 55 cm single-lumen needle was placed in the needle guide of the ultrasound probe and advanced through the vaginal fornix and into the follicle. Follicular fluid was aspirated using a regulated vacuum pump into tubes containing embryo-flushing media. Aspirates were searched for COCs using a stereomicroscope, and they were then denuded of cumulus cells by hyaluronidase and repeated pipetting. The oocytes were classified as mature (with a visible polar body), immature (with no visible polar body), activated (with divided or fragmented ooplasm) and others (degenerated and abnormal). Overall an average of 12.12 +/- 7.9 COCs were aspirated per animal with an oocyte recovery rate from the aspirated follicles of about 77%. The majority (> 90%) of the collected COCs by OPU were with loose and expanded cumulus cells. The proportion of matured oocytes obtained at 28-29 h (91.2 +/- 4.1) and 26-27 h (82.1 +/- 3.4) were higher (P < 0.005) when compared with those obtained at 24-25 h (40.4 +/- 16.3) after GnRH administration. In Experiment 2, a higher proportion (P < 0.05) of in vivo matured oocytes cleaved (84.6 +/- 2.1 vs. 60.9 +/- 6.6) and developed to blastocyst stages (52.4 +/- 4.1 vs. 30.5 +/- 3.3) when compared with in vitro matured oocytes collected from slaughterhouse ovaries. In Experiment 3, no difference was observed between the developmental competences of oocytes, collected from super stimulated camels, matured in vitro with those collected after their in vivo maturation. In conclusion, about 80-90% mature oocytes can be collected by ultrasound guided transvaginal ovum pick-up from super-stimulated dromedary camels 26-28 h after GnRH administration. The developmental response, to chemical activation, of in vivo matured oocytes collected by ultrasound guided transvaginal OPU is better than in vitro matured oocytes obtained from slaughterhouse ovaries. However, no difference was observed in the developmental competence of oocytes collected by OPU whether they were matured in vivo or in vitro.","corpus_id":13490405,"score":1},{"doc_id":"21791167","title":"Effect of oocyte-secreted factors on porcine in vitro maturation, cumulus expansion and developmental competence of parthenotes.","abstract":"The oocyte is known from recent studies in the mouse, cow, sheep and human to be a central regulator of follicular cell function. However, in the pig, little information is known about the regulation of cumulus expansion by oocyte-secreted factors and oocyte quality. We investigated the possible effects of oocyte-secreted factors during in vitro maturation on cumulus expansion and on porcine oocytes as judged by subsequent embryonic development after parthenogenetic activation. Cumulus-oocyte complexes (COC) from antral follicles of pig ovaries collected from a local abattoir were divided into control and treatment groups and were cultured in tissue culture medium 199 supplemented with follicle-stimulating hormone. Treatment groups consisted of increasing numbers of denuded oocytes (DO) co-cultured with COC (at ratios of COC to DO of 1:1, 1:2, 1:3, 1:4 and 1:5). After incubation for 44 h, cumulus expansion and maturation rates were assessed and oocytes were activated parthenogenetically. Cumulus expansion in the 1 COC:4 DO and 1 COC:5 DO groups was low and altered because full dispersion of the outer layer did not occur. Cell viability was not affected, as measured by the automated cell counter, but scanning electron microscopy revealed only a scanty extracellular matrix. Blastocyst rate was significantly higher in the 1 COC:4 DO (34.4%) and in the 1 COC:5 DO (34.9%) groups (p < 0.05) when compared with other groups. Maturation rate, cleavage rate and total cell number showed no significant difference between control and treatment groups. Amplification by reverse transcription polymerase chain reaction (RT-PCR) showed up-regulation of growth differentiation factor 9 (GDF9) in the cumulus cells in the 1 COC:4 DO group at 44 h. We conclude that denuded porcine oocytes could improve the maturation of COC as evidenced by increased blastocyst development in the 1 COC:4 DO, even though cumulus expansion was poor. This improvement could be a result of the GDF9 up-regulation.","corpus_id":39926219,"score":1},{"doc_id":"22898494","title":"In vivo vs. in vitro models for studying the effects of elevated temperature on the GV-stage oocyte, subsequent developmental competence and gene expression.","abstract":"The ovarian pool of follicle-enclosed oocytes is highly susceptible to elevated ambient temperature. It is not clear, however, whether the model of using heat shock in vitro simulates the effects of heat stress that animals experience in vivo. The current study examined the reliability of in vitro models, relative to in vivo models, for studying the effects of elevated temperature on the germinal vesicle (GV)-stage oocyte with emphasis on the expression of genes involve in maturation and early embryonic development. Cumulus oocyte complexes (COCs) were aspirated from ovaries arbitrarily collected at the slaughterhouse from multiparous Holstein cows. In the in vivo model, COCs were collected during the hot (May-September) and cold (December-April) seasons and then subjected to in vitro embryo production (IVP) at 38.5°C. In the in vitro model, COCs were collected during the cold season, pre-cultured with 75μM 3-isobutyl-1-methylxanthine (IBMX) for 16h at 38.5 or 41.2°C, and then subjected to IVP. For both models, the relative abundance of C-MOS, GDF9, GAPDH, and POU5F1 transcripts was examined in MII-stage oocytes by real-time PCR. Cleavage and blastocyst developmental rates were higher during the cold vs. hot season. IBMX pre-culture at 38.5°C successfully blocked resumption of meiosis without compromising further embryonic development, and the proportion of cleaved and developed embryos did not differ from the cold season. Exposure of GV-stage oocytes to 41.2°C reduced the proportion of cleaved oocytes developing to blastocysts relative to controls. The most prominent finding was that the relative abundance of the examined genes' transcripts was similarly reduced in heat-stressed oocytes from both models. The in vitro model was reliable and might be relevant for other environmental stressors as well.","corpus_id":46166227,"score":1},{"doc_id":"24374180","title":"A specific inhibitor of CDK1, RO-3306, reversibly arrests meiosis during in vitro maturation of porcine oocytes.","abstract":"CDK1 plays pivotal role in meiotic progression of oocytes from G2 to metaphase II (MII) stage. In this study, we investigated the possibility of utilizing a selective inhibitor of CDK1, RO-3306, as a novel agent for the synchronization of oocyte maturation. Two groups of cumulus-oocyte complexes (COCs) were treated with 10 μM RO-3306. The first group was treated for 44 h, whereas the second group was transferred to drug-free medium after a 20 h treatment. MII-stage oocytes from each group were confirmed by cytoplasmic maturation and embryonic development assays. Treatment of immature porcine oocytes with RO-3306 for 20 h arrested them at the germinal vesicle (GV) stage. The GV-arrest effect of RO-3306 was reversible: when RO-3306-arrested COCs were subsequently cultured for 24h in the absence of RO-3306, 76.19 ± 2.68% of these oocytes reached the MII stage after 44 h of in vitro maturation, a rate similar to that of non-treated control oocytes (79.08 ± 3.23%). Furthermore, RO-3306-treated oocytes transferred to drug-free media did not differ significantly from controls (P>0.05) with respect to cleavage and blastocyst formation upon parthenogenetic activation. To explore the underlying molecular mechanisms, we examined the expression patterns of four representative maternal transcripts, CDK1, Cyclin B1, GDF9, and BMP15, by real-time polymerase chain reaction (PCR) and poly(A)-test PCR (PAT assay). RO-3306 treatment increased expression of CDK1 but had no effect on the expression of the other genes. These data suggest that RO-3306 efficiently blocks and synchronizes the meiotic progression of porcine oocytes at the GV stage without affecting their meiotic and cytoplasmic maturation.","corpus_id":24407130,"score":1},{"doc_id":"24630529","title":"Caffeine supplementation during IVM improves frequencies of nuclear maturation and preimplantation development of dromedary camel oocytes following IVF.","abstract":"Caffeine supplementation during oocyte IVM has been reported to improve preimplantation embryo development and the quality of in vitro-produced blastocysts in a range of species; but no studies have been done in camels. The present study investigated the effect of caffeine supplementation during dromedary camel oocyte IVM on nuclear maturation rates, IVF events, and subsequent preimplantation development. Cumulus-oocyte complexes obtained at slaughter were matured in vitro in caffeine supplemented medium either for 30 hours (caffeine 30 hours) or in the medium without caffeine supplement for 24 hours and then transferred to freshly prepared IVM medium supplemented with 10 mM caffeine for another 6 hours (caffeine 6 hours). Cumulus-oocyte complexes matured for 30 hours in the medium without caffeine supplement were used as a control. Matured oocytes were fertilized in vitro by epididymal spermatozoa of mature male camels collected from a local slaughterhouse. Eighteen hours after insemination, presumptive zygotes were cultured in modified KSOMaa medium for 7 days. Maturation and fertilization rates were significantly higher in the caffeine 6-hour group compared with the control group (P < 0.05), whereas IVM of oocytes in caffeine-supplemented medium for 30 hours did not affect these parameters (P > 0.05). Interestingly, IVM of oocytes in caffeine supplemented medium for 6 hours significantly (P < 0.05) increased the frequencies of blastocyst development by more than two-fold when compared with control (27.78% vs. 11.76%). In conclusion, culturing dromedary camel oocytes in maturation medium without caffeine for 24 hours and then in the medium supplemented with 10 mM caffeine for 6 hours during 30-hour IVM can significantly improve frequencies of nuclear maturation, fertilization rate, and subsequent preimplantation development.","corpus_id":20201120,"score":1},{"doc_id":"24912867","title":"Insulin influences developmental competence of bovine oocytes cultured in α-MEM plus follicle-simulating hormone.","abstract":"The aim of this study was to evaluate the dose-response effect of insulin, plus follicle-simulating hormone (FSH) at a fixed concentration, in a serum-free defined culture medium (DCM) on the in vitro maturation of bovine cumulus-oocyte complexes (COCs). For oocyte nuclear maturation, the expression levels of GDF9, GLUT1, PRDX1 and HSP70.1 transcripts related to oocyte and embryo developmental competence were analysed. For in vitro maturation (IVM), cumulus-oocyte complexes from slaughterhouse ovaries were distributed into four groups based on insulin concentration added to serum-free DCM, which was composed of alpha minimum essential medium (α-MEM), as basal medium: (1) DCM control: 0 ng/ml; (2) DCM1: 1 ng/ml; (3) DCM10: 10 ng/ml; and (4) DCM100: 100 ng/ml. After IVM, the nuclear status of a sample of oocytes was analysed and the other oocytes were submitted for in vitro fertilization (IVF) and in vitro culture (IVC). Different concentrations of insulin did not affect significantly the nuclear maturation and cleavage rate (72 h post-insemination) across all groups. Blastocyst rate (192 h post-insemination) did not differ in DCM control (24.3%), DCM1 (27.0%) and DCM10 (26.3%) groups, but the DCM100 (36.1%) group showed a greater blastocyst rate (P 0.05) was observed at the different insulin concentrations. The results indicated that insulin added to DCM influenced levels of transcripts related to cellular stress (HSP70-1 and PRDX1) and oocyte competence (GDF9) in bovine oocytes and at higher concentrations enhanced blastocyst production.","corpus_id":44394899,"score":1},{"doc_id":"25156970","title":"Seasonal variations in developmental competence and relative abundance of gene transcripts in buffalo (Bubalus bubalis) oocytes.","abstract":"Hot season is a major constraint to production and reproduction in buffaloes. The present work aimed to investigate the effect of season on ovarian function, developmental competence, and the relative abundance of gene expression in buffalo oocytes. Three experiments were conducted. In experiment 1, pairs of buffalo ovaries were collected during cold season (CS, autumn and winter) and hot season (HS, spring and summer), and the number of antral follicles was recorded. Cumulus oocyte complexes (COCs) were aspirated and evaluated according to their morphology into four Grades. In experiment 2, Grade A and B COCs collected during CS and HS were in vitro matured (IVM) for 24 hours under standard conditions at 38.5 °C in a humidified air of 5% CO2. After IVM, cumulus cells were removed and oocytes were fixed, stained with 1% aceto-orcein, and evaluated for nuclear configuration. In vitro matured buffalo oocytes harvested during CS or HS were in vitro fertilized (IVF) using frozen-thawed buffalo semen and cultured in vitro to the blastocyst stage. In experiment 3, buffalo COCs and in vitro matured oocytes were collected during CS and HS, and then snap frozen in liquid nitrogen for gene expression analysis. Total RNA was extracted from COCs and in vitro matured oocytes, and complementary DNA was synthesized; quantitative Reverse Transcription-Polymerase Chain Reaction was performed for eight candidate genes including GAPDH, ACTB, B2M, GDF9, BMP15, HSP70, and SOD2. The results indicated that HS significantly (P < 0.01) decreased the number of antral follicles and the number of COCs recovered per ovary. The number of Grade A, B, and C COCs was lower (P < 0.05) during HS than CS. In vitro maturation of buffalo oocytes during HS significantly (P < 0.01) reduced the number of oocytes reaching the metaphase II stage and increased the percentage of degenerated oocytes compared with CS. Oocytes collected during HS also showed signs of cytoplasmic degeneration. After IVF, cleavage rate was lower (P < 0.01) for oocytes collected during HS, and the percentage of oocytes arrested at the two-cell stage was higher (P < 0.01) than oocytes IVF during CS. Oocytes matured during CS showed a higher (P < 0.01) blastocyst rate than those matured during HS. Also, COCs recovered in HS showed significant (P < 0.05) upregulation of HSP70 mRNA expression compared with those recovered in CS. For in vitro matured oocytes, CS down regulated the transcript abundance of ACTB and upregulated GAPDH and HSP70 mRNA levels compared with HS condition. In conclusion, HS could impair buffalo fertility by reducing the number of antral follicles and oocyte quality. In vitro maturation of buffalo oocytes during HS impairs their nuclear and cytoplasmic maturation, fertilization, and subsequent embryo development to the morula and blastocyst stages. This could be in part because of the altered gene expression found in COCs and in vitro matured oocytes.","corpus_id":205366782,"score":1},{"doc_id":"26165355","title":"Developmental competence of different quality bovine oocytes retrieved through ovum pick-up following in vitro maturation and fertilization.","abstract":"In the present study, oocytes retrieved from cross bred Karan Fries cows by ovum pick-up technique were graded into Group 1 and Group 2, based on the morphological appearance of the individual cumulus-oocyte complexes (COCs). To analyze whether the developmental potential of the COCs bears a relation to morphological appearance, relative expression of a panel of genes associated with; (a) cumulus-oocyte interaction (Cx43, Cx37, GDF9 and BMP15), (b) fertilization (ZP2 and ZP3), (c) embryonic development (HSF1, ZAR1 and bFGF) and (d) apoptosis and survival (BAX, BID and BCL-XL, MCL-1, respectively) was studied at two stages: germinal vesicle (GV) stage and after in vitro maturation. The competence was further corroborated by evaluating the embryonic progression of the presumed zygotes obtained from fertilization of the graded COCs. The gene expression profile and development rate in pooled A and B grade (Group 1) COCs and pooled C and D grade (Group 2) COCs were determined and compared according to the original grades. The results of the study demonstrated that the morphologically characterized Group 2 COCs showed significantly (P<0.05) lower expression for most of the genes related to cumulus-oocyte interplay, fertilization and embryonic development, both at GV stage as well as after maturation. Group 1 COCs also showed greater expression of anti-apoptotic genes (BCL-XL and MCL1) both at GV stage and after maturation, while pro-apoptotic genes (BAX and BID) showed significantly (P<0.05) elevated expression in poor quality COCs at both the stages. The cleavage rate in Group 1 COCs was significantly higher than that of Group 2 (74.46±7.06 v. 31.57±5.32%). The development of the presumed zygotes in Group 2 oocytes proceeded up to 8- to 16-cell stages only, while in Group 1 it progressed up to morulae (35.38±7.11%) and blastocyst stages (9.70±3.15%), indicating their better developmental potential.","corpus_id":31115337,"score":1},{"doc_id":"26952753","title":"The presence of corpus luteum may have a negative impact on in vitro developmental competency of bovine oocytes.","abstract":"The aim of the current study was to investigate the effects of the presence or absence of corpus luteum (CL) on in vitro developmental competence of bovine oocytes. In experiment 1, cumulus oocyte complexes (COCs) were collected from slaughterhouse ovaries and divided according to the presence (CL(+) oocytes) or absence (CL(-) oocytes) of a CL in the ovary. Control oocytes (C group) were obtained from ovaries which were not selected toward the presence or absence of CL. All oocytes were submitted to in vitro maturation, fertilization and culture. In experiment 2, the oocytes from the CL(+) and CL(-) ovaries were divided into grown (BCB(+)) and growing (BCB(-)) categories by means of the brilliant cresyl blue (BCB) test. The oocytes from all groups (CL(+)/BCB(+), CL(-)/BCB(+), CL(+)/BCB(-), CL(-)/BCB(-) and control oocytes) were subjected to in vitro embryo production. In experiment 1, the cleavage and blastocyst rates of CL(-) oocytes were higher than those of CL(+) oocytes (83.9% and 43% vs. 69.3% and 22.5%, respectively). In experiment 2, there was less BCB(+) oocytes (more competent oocytes) in the group of CL(+) oocytes than in the group of CL(-) oocytes. Furthermore, developmental competence of all CL(+) oocytes (CL(+)/BCB(+) and CL(+)/BCB(-)) was lower than that of all CL(-) oocytes (CL(-)/BCB(+) and CL(-)/BCB(-)). Thus, the presence of a corpus luteum in the ovary may have negative effects on developmental competence of ipsilateral oocytes.","corpus_id":28967383,"score":1},{"doc_id":"27448692","title":"GREM1, EGFR, and HAS2; the oocyte competence markers for improved buffalo embryo production in vitro.","abstract":"Selection of competent oocytes is crucial for successful in vitro embryo production and correlating expression profile of oocyte competence markers in cumulus cells with oocyte quality is an important preamble. In the present study, expression profile of oocyte competence markers (GREM1, EGFR, HAS2, and TNFAIP6) was correlated through brilliant cresyl blue (BCB) staining and subsequently with in vitro embryo production. Excellent to good quality buffalo, cumulus oocyte complexes (COCs) were stained with BCB (26 μM) and based on the blue coloration of cytoplasm COCs were divided in two groups as BCB(+ve) and BCB(-ve). Mean percentage of BCB(+ve) oocytes was significantly higher (P < 0.05) than BCB(-ve) oocytes (56.79 ± 1.22 vs. 43.20 ± 1.22), the mean oocyte diameter was also significantly larger (P < 0.05) for the BCB(+ve) group than that of BCB(-ve) group (145.7 ± 1.8 μm vs. 132.7 ± 1.9 μm). The cleavage rate (%), blastocyst rate (%), and total cell number was significantly (P < 0.05) higher in BCB(+ve) than BCB(-ve) group (71.15 ± 2.17 vs. 52.89 ± 2.65; 31.58 ± 1.11 vs. 7.73 ± 0.97, and 93.14 ± 2.42 vs. 71.42 ± 2.09, respectively). Relative mRNA expression of marker genes in cumulus cells increased significantly (P < 0.05) after maturation viz. GREM1 (10.13 folds), EGFR (9.04 folds), HAS2 (27.91 folds), and TNFAIP6 (64.81 folds). Brilliant cresyl blue positive oocytes showed significantly higher (P < 0.05) expression of GREM1, EGFR, and HAS2 transcripts than BCB(-ve) oocytes, however, no significant change in the expression of TNFAIP6 gene was observed. It is concluded from the study that GREM1, EGFR, and HAS2 could be used as molecular markers of oocyte competence for an improved buffalo embryo production in vitro.","corpus_id":34730161,"score":1},{"doc_id":"28224009","title":"Developmental competence of Dromedary camel oocytes fertilized in vitro by frozen-thawed ejaculated and epididymal spermatozoa.","abstract":"The present study aimed to compare the in vitro fertilizing capacity of frozen-thawed ejaculated and epididymal spermatozoa in order to standardize the semen preparation protocol for camel in vitro fertilization (IVF). Semen samples were collected from 7 Dromedary camels by means of artificial vagina (AV). Ten cauda epididymes were obtained from slaughtered adult camels, isolated, incised and rinsed for obtaining the sperm rich fluid. Ejaculated and epididymal spermatozoa were processed for cryopreservation. Fresh and frozen-thawed ejaculated and epididymal spermatozoa were evaluated for motility, livability, membrane and acrosomal integrities. Frozen-thawed ejaculated and epididymal spermatozoa were used to fertilize camel mature oocytes in vitro. The results showed that, the progressive motility of freshly collected epididymal spermatozoa was significantly (P<0.05) higher than ejaculated spermatozoa (49.25 ± 1.75 vs. 38.50 ± 1.50%, respectively). The viability index of epididymal spermatozoa was significantly (P<0.05) higher than that of ejaculated spermatozoa (96.63 ± 2.45 vs. 84.00 ± 4.08, respectively). The post-thaw acrosome and membrane integrities of epididymal spermatozoa were significantly (P<0.05) higher than those of ejaculated spermatozoa. Morula and blastocyst rates of camel oocytes in vitro fertilized by frozen-thawed epididymal spermatozoa (59.4 ± 0.8, 19.12 ± 0.7 and 10.29 ± 0.7%, respectively) were significantly (P<0.05) higher than those fertilized by frozen-thawed ejaculated spermatozoa (48.27 ± 3.1, 11.63 ± 1.1 and 5.43 ± 0.8%, respectively). In conclusion, the Dromedary camel frozen epididymal spermatozoa have the capacity to endure cryopreservation, fertilize oocytes and produce embryos in vitro better than ejaculated sperm.","corpus_id":18355187,"score":1},{"doc_id":"28525345","title":"In vitro production of Sudanese camel (Camelus dromedarius) embryos from epididymal spermatozoa and follicular oocytes of slaughtered animals.","abstract":"Application of assisted reproductive technology in camelidea, such as artificial insemination (AI) and embryo transfer, has been slow in comparison to that for other livestock species. In Egypt, there are few attempts to establish in vitro maturation (IVM) and fertilization (IVF) techniques in dromedary camel. The present study was carried out to produce Sudanese camel embryos using in vitro matured oocytes and epididymal spermatozoa. Dromedary camel ovaries were collected from abattoirs and then, the oocytes were aspirated from all the visible follicles on the ovarian surface (~2-8 mm in a diameter). Meanwhile, Fetal Dromedary Camel Serum (FDCS) was obtained from camel fetuses after slaughtering. Thereafter, only Cumulus Oocyte Complexes (COCs) were matured in vitro in the Tissue Culture Medium (TCM-199) complemented with 10% FDCS. Spermatozoa required for in vitro fertilization were collected from testes (epididymal cauda) of the slaughtered camel bulls. The results clearly showed that the maturation rate of oocytes at metaphase II was about 59.5% while the fertilization rate was around 70.4%. Intriguingly, the embryo rates determined were 13.1%, in 2-cell; 0.0%, in 4-cell; 34.7%, in 8-16% cell; 39.1%, in morula and 13.1% in a blastocyst stage. This study represented a successful in vitro production of Sudanese dromedary camel embryos from epididymal sperm cells and in vitro matured oocytes recovered from slaughtered camels.","corpus_id":19485600,"score":1},{"doc_id":"28586460","title":"A pre-in vitro maturation medium containing cumulus oocyte complex ligand-receptor signaling molecules maintains meiotic arrest, supports the cumulus oocyte complex and improves oocyte developmental competence.","abstract":"STUDY QUESTION: Can a pre in-vitro maturation medium containing signaling molecules rather than chemical/pharmaceutical agents, sustain meiotic arrest and improve developmental competence of in-vitro matured oocytes in CF1 outbred mice?","corpus_id":205213715,"score":1},{"doc_id":"28601148","title":"Leptin supplementation in vitro improved developmental competence of buffalo oocytes and embryos.","abstract":"The aim of the present study was to determine potential role of leptin on in vitro developmental competence of buffalo oocytes and embryos. Slaughterhouse derived culture grade buffalo cumulus oocyte complexes (COCs) were matured in vitro (IVM) with leptin (10 ng/ml) or without leptin (control). In each experiment, a pool of matured COCs was used for further in vitro embryo production and another pool of COCs was used for cumulus cells and mature oocytes isolation to study the relative mRNA expression of developmentally important genes. Presumptive zygotes were cultured in embryo culture (IVC) media supplemented with leptin (10 ng/ml) or without leptin (control). Cleavage rate was higher (p < 0.05) when leptin was supplemented during IVM + IVC, both, as compared to other groups. Higher cleavage rate was observed in leptin-treated groups, though it was non-significant. Blastocyst rate was higher (p < 0.05) in all the leptin treated groups. The relative mRNA expression of LEPR (Ob-Rb), HAS2 and EGFR was significantly (p < 0.05) up-regulated and the expression of CASPASE3 was down-regulated in cumulus cells of leptin-treated groups. The expression of GDF9, BMP15, GLUT1, LEPR and CASPASE3 transcripts in leptin and non-treated oocytes did not differ. The relative mRNA expression of POU5F1and LEPR transcripts in blastocysts was higher (p < 0.05) in leptin-treated groups; the change in expression of GLUT1, INF-τ and CASPASE3 transcripts was not significant (p > 0.05). Thus, it is concluded that leptin promotes developmental competence of bubaline oocytes by modulating cumulus enabling factors and genes regulating pluripotentcy in the blastocysts.","corpus_id":4421939,"score":1},{"doc_id":"28802113","title":"L-carnitine enhances oocyte maturation and improves in vitro development of embryos in dromedary camels (Camelus dromedaries).","abstract":"The aim of the present study was to investigate the effect of L-carnitine (LC) addition during either IVM or IVC on the developmental potential of camel oocytes. In Experiment 1; camel oocytes were matured in the absence (control) or presence of different concentrations of LC (0.25 mg, 0.5 mg, 0.75 mg and 1 mg/ml) for 30 h followed by in vitro fertilization and culture up to blastocyst stage. Our results demonstrated that oocytes treated with 0.5 mg/ml LC showed higher (P < 0.05) rates of maturation (74.7%) and fertilization (62.2%) compared with control group, 0.25 and 1 mg/ml of LC (60.2, 63.9, 59.7; 46.2, 48.7, 47.6%, respectively). Addition of 0.5 mg/ml of LC to IVM medium improved the rates of cleavage and embryo development (morula and blastocyst) than those obtained in the control group, 0.25 and 1 mg/ml of LC. No significant differences were noticed between 0.5 and 0.75 mg/ml of LC supplemented groups in term of maturation, fertilization and culture. In Experiment 2; zygotes resulting from in vitro matured (without LC) and fertilized were cultured in embryo culture medium supplemented with different concentrations of LC (0.25 mg, 0.5 mg, 0.75 mg and 1 mg/ml) or without LC (control). Also, the results showed a higher developmental rates to morula and blastocyst stages while adding L-carnitine at a level of 0.5 or 0.75 mg/ml concentration in the culture medium during IVC when compared with other groups. In conclusion, the results demonstrated the usefulness of L-carnitine supplementation at the level of 0.5 mg/ml during IVM or IVC after on the developmental potential of camel oocytes.","corpus_id":46530001,"score":1},{"doc_id":"18405437","title":"Bovine oocytes and early embryos express Staufen and ELAVL RNA-binding proteins.","abstract":"RNA-binding proteins (RBP) influence RNA editing, localization, stability and translation and may contribute to oocyte developmental competence by regulating the stability and turnover of oogenetic mRNAs. The expression of Staufen 1 and 2 and ELAVL1, ELAVL2 RNA-binding proteins during cow early development was characterized. Cumulus-oocyte complexes were collected from slaughterhouse ovaries, matured, inseminated and subjected to embryo culture in vitro. Oocyte or preimplantation embryo pools were processed for RT-PCR and whole-mount immunofluorescence analysis of mRNA expression and protein distribution. STAU1 and STAU2 and ELAVL1 mRNAs and proteins were detected throughout cow preimplantation development from the germinal vesicle (GV) oocyte to the blastocyst stage. ELAVL2 mRNAs were detectable from the GV to the morula stage, whereas ELAVL2 protein was in all stages examined and localized to both cytoplasm and nuclei. The findings provide a foundation for investigating the role of RBPs during mammalian oocyte maturation and early embryogenesis.","corpus_id":34996021,"score":0},{"doc_id":"24548378","title":"Confocal fluorescence assessment of bioenergy/redox status of dromedary camel (Camelus dromedarius) oocytes before and after in vitro maturation.","abstract":"BACKGROUND: Reproductive biotechnologies in dromedary camel (Camelus dromedarius) are less developed than in other livestock species. The in vitro maturation (IVM) technology is a fundamental step for in vitro embryo production (IVP), and its optimization could represent a way to increase the success rate of IVP. The aim of the present study was to investigate the bioenergy/oxidative status of dromedary camel oocytes before and after IVM by confocal microscopy 3D imaging. METHODS: Oocytes were retrieved by slicing ovaries collected at local slaughterhouses. Recovered oocytes were examined before and after IVM culture for nuclear chromatin configuration and bioenergy/oxidative status, expressed as mitochondria (mt) distribution and activity, intracellular Reactive Oxygen Species (ROS) levels and distribution and mt/ROS colocalization. RESULTS: The mean recovery rate was 6 oocytes/ovary. After IVM, 61% of oocytes resumed meiosis and 36% reached the Metaphase II stage (MII). Oocyte bioenergy/redox confocal characterization revealed changes upon meiosis progression. Immature oocytes at the germinal vesicle (GV) stage were characterised by prevailing homogeneous mt distribution in small aggregates while MI and MII oocytes showed significantly higher rates of pericortical mt distribution organized in tubular networks (P<0.05). Increased mt activity in MI (P<0.001) and MII (P<0.01) oocytes compared to GV stage oocytes was also observed. At any meiotic stage, homogeneous distribution of intracellular ROS was observed. Intracellular ROS levels also increased in MI (P<0.01) and MII (P<0.05) oocytes compared to GV stage oocytes. The mt/ROS colocalization signal increased in MI oocytes (P<0.05). CONCLUSIONS: This study provides indications that qualitative and quantitative indicators of bioenergy and oxidative status in dromedary camel oocytes are modified in relation with oocyte meiotic stage. These data may increase the knowledge of camel oocyte physiology, in order to enhance the efficiency of IVP procedures.","corpus_id":7232816,"score":0},{"doc_id":"26603656","title":"Optimization of a vitrification protocol for hatched blastocysts from the dromedary camel (Camelus dromedarius).","abstract":"The objective of this study was to modify and optimize a vitrification protocol (open pulled straw) that was originally designed for human oocytes and embryos, to make it suitable for the cryopreservation of camel hatched blastocysts. The original open pulled straw protocol was a complex process with 15-minute exposure of oocytes/embryos in 7.5% ethylene glycol (EG) and 7.5% dimethyl sulfoxide (Me2SO) for equilibration, and cooling in 16% EG + 16% Me2SO + 1 M sucrose. Recognizing a need to better control the cryoprotectant (CPA) concentrations, while avoiding toxicity to the embryos, the effects on the survival rate and developmental potential of camel embryos in vitro were investigated using two different methods of loading the CPAs into the embryos (stepwise and semicontinuous increase in concentration), two different loading temperature/time (room temperature ∼24 °C/15 min and body 37 °C/3 min), and the replacement of Me2SO with EG alone or in combination with glycerol (Gly). A total of 145 in vivo-derived embryos were subjected to these processes, and after warming their morphological quality and integrity, and re-expansion was assessed after 0, 2, 24, 48, 72, and 96 hours of culture. Exposure of embryos in a stepwise method was more beneficial to the survival of embryos than was the semicontinuous process, and loading of CPAs at 37 °C with a short exposure time (3 minutes) resulted in an outcome comparable to the original processing at room temperature with a longer exposure time (15 minutes). The replacement of the Me2SO + EG mixture with EG only or a combination of EG + Gly in the vitrification medium significantly improved the outcome of all these evaluation criteria (P < 0.05). The modified protocol of loading EG at 37 °C for 3 minutes has increased the embryo survival of the original protocol from 67% to 91% and the developmental rate from 57% to 83% at 5-day culture. These results were comparable to or better than those reported in human or other species, indicating that this optimized method is well suited to any commercial embryo transfer program in the dromedary camel.","corpus_id":36988289,"score":0},{"doc_id":"29492475","title":"Supplementation of L-carnitine during in vitro maturation of mouse oocytes affects expression of genes involved in oocyte and embryo competence: An experimental study.","abstract":"Background: Oocyte developmental competence is one of the key factors for determining the success rate of assisted reproductive technique. Objective: The aim of the current study was to investigate the effect of L-carnitine (LC) supplementation during in vitro maturation (IVM), on preimplantation embryo development and expression of genes involved in embryo competence derived from oocytes selected with brilliant cresyl blue (BCB) test. Materials and Methods: Cumulus-oocyte complexes (COCs) were obtained from NMRI mice ovaries. COCs were stained with BCB and then BCB+ (colored cytoplasm) oocytes cultured in IVM medium supplemented with 0.3 or 0.6 mg/ml LC. COCs untreated with LC were used as control. Fertilization rate and blastocyst development rate were determined after in vitro fertilization. In addition, quantitative reverse transcriptase polymerase chain reaction was used to measure relative genes expression related with development (Ccnb1, Mos, Ces5, and Dppa2) and apoptosis (Bax and Bcl-xL) in oocytes and embryos. Results: Oocytes treated with both LC concentrations showed higher blastocyst development rate compared with untreated oocytes (p<0.01). Moreover, fertilization rate was increased in oocytes treated with 0.6 mg/ml LC (p<0.01). Treatment of oocytes with both LC concentrations increased (p<0.01) the level of Ccnb1 mRNA in MII oocytes. The two-cell stage embryos and blastocysts derived from LC-treated oocytes (0.6 mg/ml) showed increased the expression levels of Dppa2 and Bcl-xl mRNA, respectively (p<0.01). Conclusion: The results of the present study show that adding of LC to the IVM medium of BCB+ oocytes can ameliorate reproductive success following in vitro fertilization.","corpus_id":3547373,"score":0}],"string":"[\n {\n \"doc_id\": \"18239049\",\n \"title\": \"Molecular and subcellular characterisation of oocytes screened for their developmental competence based on glucose-6-phosphate dehydrogenase activity.\",\n \"abstract\": \"Oocyte selection based on glucose-6-phosphate dehydrogenase (G6PDH) activity has been successfully used to differentiate between competent and incompetent bovine oocytes. However, the intrinsic molecular and subcellular characteristics of these oocytes have not yet been investigated. Here, we aim to identify molecular and functional markers associated with oocyte developmental potential when selected based on G6PDH activity. Immature compact cumulus-oocyte complexes were stained with brilliant cresyl blue (BCB) for 90 min. Based on their colouration, oocytes were divided into BCB(-) (colourless cytoplasm, high G6PDH activity) and BCB(+) (coloured cytoplasm, low G6PDH activity). The chromatin configuration of the nucleus and the mitochondrial activity of oocytes were determined by fluorescence labelling and photometric measurement. The abundance and phosphorylation pattern of protein kinases Akt and MAP were estimated by Western blot analysis. A bovine cDNA microarray was used to analyse the gene expression profiles of BCB(+) and BCB(-) oocytes. Consequently, marked differences were found in blastocyst rate at day 8 between BCB(+) (33.1+/-3.1%) and BCB(-) (12.1+/-1.5%) oocytes. Moreover, BCB(+) oocytes were found to show higher phosphorylation levels of Akt and MAP kinases and are enriched with genes regulating transcription (SMARCA5), cell cycle (nuclear autoantigenic sperm protein, NASP) and protein biosynthesis (RPS274A and mRNA for elongation factor 1alpha, EF1A). BCB(-) oocytes, which revealed higher mitochondrial activity and still nucleoli in their germinal vesicles, were enriched with genes involved in ATP synthesis (ATP5A1), mitochondrial electron transport (FL405), calcium ion binding (S100A10) and growth factor activity (bone morphogenetic protein 15, BMP15). This study has evidenced molecular and subcellular organisational differences of oocytes with different G6PDH activity.\",\n \"corpus_id\": 207150639,\n \"score\": 2\n },\n {\n \"doc_id\": \"18789618\",\n \"title\": \"In vitro and in vivo developmental competence of dromedary (Camelus dromedarius) oocytes following in vitro fertilization or parthenogenetic activation.\",\n \"abstract\": \"Parthenogenetic activation of the oocyte represents an important step in the somatic cloning. The aim of the present study was to evaluate the effectiveness (in term of in vitro development) of different methods of parthenogenetic activation of dromedary oocytes. Selected cumulus-oocytes-complexes (n=1264) collected by follicular aspiration from ovaries obtained postmortem were matured in vitro (IVM) for 30 h then divided randomly into seven groups and submitted to artificial activation. Two groups were preactivated with 25 microM of calcium ionophore (CaI) for 20 min then incubated for 4h with either 2mM 6-dimethylaminopurine (6-DMAP) (group 1, n=202) or with 10 microg/mL cycloheximide (CHX) (group 2, n=194). Group 3 (n=172) and group 4 (n=184), oocytes were pretreated with 5 microM ionomycin (Iono) for 5 min then incubated with either 2mM 6-DMAP or 10 microg/mL cycloheximide for 4h, respectively. Group 5 (n=161) and group 6 (n=155) oocytes were preactivated with electrical stimulation (ES) then activated with either 2mM 6-DMAP or 10 microg/mL cycloheximide for 4h, respectively. Group 7 (n=196) oocytes were submitted to in vitro fertilization (IVF) and served as a control. All groups containing oocytes were cultured in vitro following activation or IVF, at 38.5 degrees C under 5% CO(2) in air with >95% humidity. The in vitro development rates of dromedary oocytes exposed to 6-DMAP after CaI (61%), ES (74%) and the IVF group (71%) were similar and significantly greater (P<0.05) than other treatments (10% for group 2, 47% for group 3, 27% for group 4 and 41% for group 6). The blastocyst developmental rate was better (P<0.05) in parthenotes following activation with Iono/6-DMAP (21%) compared to activation with Iono/CHX (12%). However, all were less than that achieved in the IVF group (35%). We conclude that parthenogenetic activation of camel oocytes with 6-DMAP is more effective than activation with CHX for all pre-treatments tested (CaI, Iono or ES). The viability of activated (n=15) or IVF (n=10) hatched-dromedary embryos was examined by transfer to synchronized recipients. An embryonic vesicle was seen by ultrasonography at 15 days post transfer in four females (CaI/6-DMAP: 1/5; 20%, IVF: 3/10; 30%). The only pseudopregnancy obtained with an activated embryo resorbed at 25 days. One of the females receiving the IVF produced embryos aborted at 2 months and the other two females carried to term and gave birth to healthy calves (one female and one male). This study shows that artificial activation of dromedary oocytes with CaI/6-DMAP or ES/6-DMAP is more effective than other treatments in terms of in vitro embryo development. This provides efficient activation conditions which may lead to the development of the somatic cell nuclear transfer procedure in dromedary.\",\n \"corpus_id\": 1601507,\n \"score\": 2\n },\n {\n \"doc_id\": \"19447485\",\n \"title\": \"Developmental competence of porcine oocytes selected by brilliant cresyl blue and matured individually in a chemically defined culture medium.\",\n \"abstract\": \"The objective of this study was to investigate the effects of oocyte selection using brilliant cresyl blue (BCB) and culture density during individual in vitro maturation (IVM) on porcine oocyte maturity and subsequent embryo development using a chemically defined medium. Cumulus-oocyte complexes (COCs) were classified as BCB-positive or BCB-negative after exposure to a BCB solution for 90 min. The classified COCs were matured in a group (15 COCs per 100-microL droplet) or individually (1 COC per 1-, 2.5-, 5-, or 10-microL droplet). Meiotic competence, intraoocyte glutathione concentration, and developmental competence after intracytoplasmic sperm injection were monitored. The BCB selected oocytes competent for nuclear and cytoplasmic maturation. Furthermore, meiotic competence for oocytes matured individually in a 5-microL droplet was superior (P<0.05) to that of oocytes matured in a 1-microL droplet. Also, the culture density in a 5-microL droplet during IVM resulted in a higher (P<0.05) rate of cleaved embryos than that in a 1-microL droplet and produced a similar rate of blastocysts compared with that of a group culture system. Conversely, BCB selection did not improve cleavage and blastocyst formation. In conclusion, it was possible to predict porcine oocytes competent for maturation using oocyte selection with BCB. Moreover, a 5-microL droplet during the individual IVM culture was most suitable for oocyte maturation and subsequent embryo development, although every culture density used in this study supported development up to the blastocyst stage.\",\n \"corpus_id\": 205361227,\n \"score\": 2\n },\n {\n \"doc_id\": \"19754581\",\n \"title\": \"Preliminary study in immature canine oocytes stained with brilliant cresyl blue and obtained from bitches with low and high progesterone serum profiles.\",\n \"abstract\": \"This study was conducted: (i) to observe the features and levels of blue colour impregnation in morphologically selected immature canine cumulus oocyte complexes (COCs) stained with the brilliant cresyl blue (BCB) dye, as indicators of quality, and integrity of nuclear oocyte chromatin configuration before in vitro maturation (IVM); (ii) to observe the relationship between the influence of serum progesterone (SP) concentrations from ovary donors and BCB staining of immature dog oocytes. The results showed that out of 138 canine COCs, germinal vesicle (GV) stage prevailed in BCB+ oocytes at percentages of 67.4% (60/89), which were statistically higher than those observed in BCB+/- (52.2%; 23/44) and BCB- (20%; 1/5) oocytes (p = 0.023). Oocytes BCB+ were interpreted as those having completed their growth and therefore possessing the capacity to mature and develop in vitro. Ooplasm and cumulus cells (CCs) of canine oocytes were BCB staining independent. Ooplasm blue colour staining reaction varied between grown oocytes, revealing different levels of glucose-6-phosphate dehydrogenase activity among and within oocytes. Additionally, SP profile of ovary donors was not a relevant indicator for selection of oocytes screened with the BCB stain. Similar numbers of high quality oocytes were observed to be BCB+, BCB+/- and BCB- between groups of females with SP varying from 0 to 2.5 ng/ml (n = 5), and those with SP varying from 2.6 to 16.7 ng/ml (n = 4) (p = 0.680). It may be inferred that bitches with low and high SP profiles have grown oocytes in their ovaries, as determined by the BCB absorbance in their ooplasms.\",\n \"corpus_id\": 31997627,\n \"score\": 2\n },\n {\n \"doc_id\": \"19939331\",\n \"title\": \"Developmental competence and expression of the MATER and ZAR1 genes in immature bovine oocytes selected by brilliant cresyl blue.\",\n \"abstract\": \"The objective of this work was to evaluate the selection of immature bovine oocytes by brilliant cresyl blue dye (BCB) and expression of transcripts MATER and ZAR1. Cumulus-oocyte complexes (COCs) from slaughterhouse ovaries were exposed to BCB diluted in mDPBS and incubated for 60 min at 38.5 degrees C in humidified air. After exposure those COCs were distributed in two groups, according to their cytoplasm colour: BCB+ (coloured cytoplasm) or BCB- (colourless cytoplasm). The control group was submitted to in vitro maturation (IVM) immediately after morphological selection and holding control group COCs were exposed to mDPBS without BCB but in the same incubation conditions of BCB+ and BCB- group. The COCs of all groups were submitted to IVM, in vitro fertilization (IVF) and in vitro culture (IVC). Cleavage rate (72 h post-insemination) was similar between control (65.3%) and BCB+ (64.4%) groups, but greater than (p < 0.05) holding control (49.8%) and BCB- (51.3%) groups. Blastocyst rate (192 h post-insemination) was not different between BCB+ (18.5%) and control (16.3%) groups, but greater (p < 0.05) than BCB- (8.4%) group. No difference was found for blastocyst rate between holding control group (14.2%), control and BCB+ groups. The relative expression of MATER and ZAR1 genes was evaluated by real-time PCR in immature oocytes collected from the control, holding control, BCB+ and BCB- groups. Despite the relative expression of MATER in holding control, BCB+ and BCB- were down regulated in comparison to control group there was no statistical difference (p > 0.05) in the relative expression of MATER and ZAR1 transcripts among groups. The results indicate that the BCB dye detects immature oocyte populations with different developmental competence, although no improvement in in vitro embryo production using oocytes exposed or not to BCB was observed. Development competence of immature oocytes exposed to BCB does not seem to be associated with variations in the expression of MATER and ZAR1 transcripts.\",\n \"corpus_id\": 23233456,\n \"score\": 2\n },\n {\n \"doc_id\": \"20198711\",\n \"title\": \"Cathepsin B activity is related to the quality of bovine cumulus oocyte complexes and its inhibition can improve their developmental competence.\",\n \"abstract\": \"Recently, the quantity of cathepsin transcripts in cumulus cells was found to be associated with low-developmental competence of bovine oocytes. In the present study, we investigated (1) the relation between cathepsin B activity and the quality of in vitro-matured cumulus-oocyte complexes (IVM COCs) and denuded oocytes and (2) the effect of a cathepsin B inhibitor (E-64) on embryo development and quality. The activity of cathepsin B was evaluated in IVM COCs and denuded oocytes. After maturation of COCs with or without E-64, followed by in vitro fertilization, zygotes were cultured for 8 days. Cleavage and blastocyst rates were evaluated on days 2 and 8, respectively. Quality of embryos was evaluated by differential staining of day 8 blastocysts. TUNEL staining was conducted on IVM COCs and blastocysts. Cathepsin B activity was clearly detected in the low-quality oocytes, and in the cumulus cells of both high- and low-quality oocytes. This latter activity was diminished by addition of E-64. The presence of E-64 during IVM also significantly increased both the blastocyst rate and the total cell number, and improved blastocyst quality associated with a significant increase of trophoectoderm cells. TUNEL staining revealed that inhibition of cathepsin B significantly decreased the number of apoptotic nuclei in both the cumulus cell layer of matured oocytes and blastocysts. These results indicate that cathepsin B activity can be a useful marker of oocyte quality. Furthermore, inhibition of cathepsin B greatly improves the developmental competence of bovine oocytes and increases the number of high-quality embryos.\",\n \"corpus_id\": 27155545,\n \"score\": 2\n },\n {\n \"doc_id\": \"21295838\",\n \"title\": \"Zona pellucida glycoprotein 3 (pZP3) and integrin β2 (ITGB2) mRNA and protein expression in porcine oocytes after single and double exposure to brilliant cresyl blue test.\",\n \"abstract\": \"Brilliant cresyl blues (BCB) staining test is a useful tool in assessing the competence of cumulus-oocyte-complexes (COCs) in several mammalian species. It is mostly used to select gametes after they are recovered from the ovary or before and after IVM to isolate those oocytes that reach developmental competency. However, there is evidence that double exposure to BCB test may lead to impaired fertilization or even have a toxic effect on cells. The aim of the present study was to investigate the expression pattern of sperm-egg interaction molecules in oocytes after single and double exposure to BCB test. Follicles were dissected from porcine ovaries after slaughter and aspirated COCs were cultured in standard porcine IVM culture medium (TCM 199) for 44 h. The BCB test was applied to COCs before and after IVM. In developmentally competent oocytes, assessed by determining the activity of glucose-6-phosphate dehydrogenase (G6PDH; BCB test), real-time quantitative PCR reaction methods, western blot and confocal microscopy analysis were applied to determine the transcript levels of porcine zona pellucida glycoprotein 3 (pZP3), and integrin beta 2 (ITGB2), as well as the levels of pZP3 and ITGB2 proteins. In the control group, assessment of the expression of the investigated genes was performed before and after IVM without BCB test. We observed a significantly higher level of pZP3 mRNA in oocytes after single exposure to BCB test compared to control before and after IVM (P < 0.001), and to double staining (P < 0.05). The level of ITGB2 mRNA was also increased in gametes after single exposure to BCB test as compared to control before and after IVM (P < 0.001, P < 0.01, respectively), and double staining (P < 0.05). Western blot analysis demonstrated a higher level of pZP3 protein in oocytes after single staining with BCB as compared to control both before and after IVM (P < 0.001, P < 0.05, respectively) and double staining (P < 0.05). Confocal microscopic observations have revealed the same pattern of increased level of pZP3 and ITGB2 expression after single exposure to BCB test. In both cases we detected specific cytoplasmic localization of both proteins. The ITGB2 protein has zona pellucida and membrane localization in control oocytes before IVM. After IVM and after single exposure to BCB, ITGB2 was also strongly detected in the cytoplasm. In both cases, after double exposure to BCB both proteins were detected only partially in the cytoplasm. Our results suggest that (i) single exposure to BCB increased the expression of sperm-oocyte interaction genes, (ii) double exposure to BCB leads to only partial expression of pZP3 and ITGB2 in oocyte cytoplasm, (iii) the BCB staining test itself may be a cause of specific pZP3 translocation from the zona pellucida to the cytoplasm, and that (iv) in vitro maturation of oocytes may increase ITGB2 expression and translocation from the zona pellucida to the cytoplasm.\",\n \"corpus_id\": 5381751,\n \"score\": 2\n },\n {\n \"doc_id\": \"21757473\",\n \"title\": \"Brilliant Cresyl Blue stain selects largest oocytes with highest mitochondrial activity, maturation-promoting factor activity and embryo developmental competence in prepubertal sheep.\",\n \"abstract\": \"The aim of this study was to test the Brilliant Cresyl Blue (BCB) stain to select prepubertal sheep oocytes for in vitro blastocyst production. Oocyte diameter, mitochondrial activity, maturation-promoting factor (MPF) activity and mRNA relative expression (RE) of genes related to metabolism (ATPase Na(+)/K(+) transporting α 1 (ATP1A1) and cytochrome c oxidase subunit 1 (COX1)) and constitutive function of the cell (cytoplasmic polyadenylation-element-binding protein (CPEB) and S100A10) were assessed. Immature oocytes were exposed to different BCB concentrations (13, 26, 39 and 52 μM) and classified according to their cytoplasm colouration as grown BCB+ (blue cytoplasm) and growing BCB- (colourless cytoplasm). Staining oocytes with 13 μM BCB during 60 min allows selection of (BCB+) the largest (123.66 μm) and most competent oocytes to develop to the blastocyst stage (21%) with a higher number of cells (69.71 ± 6.19 s.e.m.) compared with non-stained BCB- oocytes (106.82 μm, 9% and 45.91 ± 3.35 s.e.m. respectively). Mitochondrial activity, assessed by MitoTracker Orange CMTMRos probe, was significantly higher in BCB+ than in BCB- oocytes after in vitro maturation (3369 and 1565 AU respectively). MPF activity was assessed by CDC2 kinase activity assay showing significantly higher activity at metaphase II stage in BCB+ than in BCB- oocytes (1.479 ± 0.09 and 1.184 ± 0.05 optical density respectively). The genes analysed in this work, ATP1A1, COX1, CPEB and S100A 10, did not show significant effect in mRNA RE between BCB selected oocytes. In conclusion, BCB stains larger and more competent oocytes to develop to the blastocyst stage with more active mitochondria and MPF activity and higher blastocyst cell number.\",\n \"corpus_id\": 36232551,\n \"score\": 2\n },\n {\n \"doc_id\": \"21791164\",\n \"title\": \"Selection of bovine oocytes by brilliant cresyl blue staining: effect on meiosis progression, organelle distribution and embryo development.\",\n \"abstract\": \"The selection of competent oocytes for in vitro maturation is still a major problem during bovine in vitro embryo production. Markers for in vitro cytoplasmic maturation, based on the organization of cortical granule and mitochondria, are lacking. We examined the pre-selection of immature bovine oocytes by brilliant cresyl blue stain (BCB test) based on glucose-6-phosphate dehydrogenase (G6PDH) activity during oocyte development. Oocytes were recovered from ovarian follicles exposed to 26 μM BCB stain and classified according to the aspect of their cytoplasm: BCB(+) (oocytes with blue cytoplasm) and BCB(-) (unstained cytoplasm) and then in vitro matured into a conventional in vitro maturation (IVM) medium and standard procedure. In Experiment 1, nuclear maturation was determined by polar body identification, while cytoplasmic maturation was based on cortical granule (CG) migration (peripheral) and mitochondria distribution (central). Evidence of polar body, cortical granule migration and of centrally located mitochondria was significantly (p < 0.05) higher in BCB(+) oocytes than in BCB(-) (polar body present: 65% vs 20%; peripheral CG: 72% vs. 14%; and central mitochondria: 85% vs. 19%, respectively). In Experiment 2, the efficiency pre-selection of bovine oocytes by BCB on embryo development in vitro was assessed. Cleavage rates were similar (75%) among control, BCB(+) and BCB(-) groups, while blastocyst rates on D7 were (p < 0.05) higher (35%) in BCB(+) vs BCB(-) (10%) or control (28%). We showed that the BCB test is efficient to identify competent immature bovine oocytes to undergo synchronous nuclear and cytoplasmic in vitro maturation thus yielding higher in vitro embryo development to blastocyst stage.\",\n \"corpus_id\": 206297573,\n \"score\": 2\n },\n {\n \"doc_id\": \"21791168\",\n \"title\": \"Selection of Rattus norvegicus oocytes for in vitro maturation by brilliant cresyl blue staining.\",\n \"abstract\": \"The objective of this work was to evaluate the rate of meiosis resumption and nuclear maturation of rat (Rattus norvegicus) oocytes selected for in vitro maturation (IVM) after staining of cumulus-oocyte complexes (COCs) with blue cresyl brilliant (BCB) using different protocols: exposure for 30, 60 or 90 min at 26 μM BCB (Experiment 1), and exposure for 60 min at 13, 20 or 26 μM BCB (Experiment 2). In Experiment 1, the selection of oocytes exposed to BCB for 60 min was found to be the most suitable, as meiosis resumption rates in the BCB(+) group (n = 35/61; 57.37%) were the closest to the observed in the control (not exposed) group (n = 70/90; 77.77%) and statistically higher than the values observed for the BCB(-) group (n = 3/41; 7.32%). Additionally, the more effective evaluation of diagnostic tests (sensitivity and negative predictive value 100%) was observed in COCs exposed for 60 min. In Experiment 2, the 13 μM BCB(+) group presented rates of meiosis resumption (n = 57/72; 72.22%) similar to the control group (n = 87/105; 82.86%) and higher than other concentration groups. However, this results of the analysis between BCB(-) oocytes was also higher in the 13 μM BCB group (n = 28/91; 30.78%) when compared with BCB(-) COCs exposed to 20 μM (n = 3/62; 4.84%) or 26 μM (n = 3/61; 4.92%) BCB. The nuclear maturation rate in the 13 μM BCB group was similar between BCB(+) or BCB(-) oocytes. The 20 μM BCB group had a lower rate of nuclear maturation of BCB(-) oocytes than other groups. Thus, our best results in the selection of Rattus norvegicus oocytes by staining with BCB were obtained using the concentration of 13 μM and 20 μM, and an incubation period of 60 min.\",\n \"corpus_id\": 13698500,\n \"score\": 2\n },\n {\n \"doc_id\": \"21820165\",\n \"title\": \"G6PDH-activity in equine oocytes correlates with morphology, expression of candidate genes for viability, and preimplantative in vitro development.\",\n \"abstract\": \"Efficiencies for in vitro production of equine embryos are still low due to highly variable developmental competences of equine immature oocytes. In contrast to the equine, in vitro developmental competence of immature oocytes has been predicted successfully by the activity of glucose-6-phosphate dehydrogenase (G6PDH) indicated by brilliant cresyl blue (BCB) dye in a range of different species. Therefore, the aim of the present study was to test the association between G6PDH activity in equine oocytes with: (1) cumulus morphology and oocyte properties in terms of diameter and volume; (2) maturational competence; (3) gene expression of certain molecular markers; and (4) in vitro embryo development after intracytoplasmic sperm injection. Equine oocytes were exposed to BCB stain and were classified as BCB+ or BCB- according to their ability to convert the dye from blue to colorless. Additionally, BCB+ and BCB- oocytes were subclassified as having a compact (Cp) or expanded (Ex) cumulus complex. As a result, BCB+ oocytes had a greater proportion of expanded cumulus oocyte complexes compared with BCB- oocytes (71.2% vs. 49.5%). Moreover, we observed a significant difference in oocyte diameter and volume between BCB+ and BCB- oocytes irrespective of cumulus morphology. BCB+ oocytes reached a higher maturation rate compared with BCB- oocytes (59.0% vs. 28.7%). Regarding the analyzed candidate genes, relative transcript abundance was significantly different for nine genes. The expression of eight genes was significantly higher (P < 0.05) for BCB+ oocytes, including ATPV6E, IF-3, TFAM, DNMT1, STAT3, Aurora-A, ODC1, and CKS2 whereas BCB- oocytes showed higher in expression of COX1. These results are in line with the observed developmental competence. Cleavage rate (45.9% vs. 29.0%) and percentage of embryos that reached the blastocyst stage (9.2% vs. 1.4%) were significantly higher for embryos derived from BCB+ oocytes compared with BCB- oocytes. In conclusion, the present study provides evidence that G6PDH-activity in immature equine oocytes is a useful predictor for subsequent in vitro developmental competence.\",\n \"corpus_id\": 25155668,\n \"score\": 2\n },\n {\n \"doc_id\": \"21870182\",\n \"title\": \"Prediction of oocyte developmental competence in ovine using glucose-6-phosphate dehydrogenase (G6PDH) activity determined at retrieval time.\",\n \"abstract\": \"PURPOSE: To determine whether G6PDH-activity measured by Brilliant Cresyl Blue known as BCB dye, predicts developmental competence within cohorts of ovine oocytes. METHODS: Ovine oocytes were exposed to BCB staining and categorized into two groups: BCB+ (blue cytoplasm, low G6PDH-activity) and BCB- (colorless cytoplasm, high G6PDH-activity). After maturation in vitro, oocytes were subjected to fertilization followed by in vitro embryo culture. RESULTS: We observed a significant difference in oocyte diameter considering BCB+ and BCB- oocytes. BCB+ and Control groups showed significantly higher maturation rates compared to BCB- group. There were significantly more cleaved embryos in BCB+ and control groups than in BCB- group. Blastocyst rate was significantly higher for BCB+ group compared to control and BCB- groups with control group being significantly higher than BCB- group. CONCLUSION: G6PDH-activity is a strong predictive marker of oocyte competence and may be useful in identifying oocytes with a good prognosis for further develop.\",\n \"corpus_id\": 6158666,\n \"score\": 2\n },\n {\n \"doc_id\": \"22391295\",\n \"title\": \"Gene expression pattern of adiponectin and adiponectin receptors in dominant and atretic follicles and oocytes screened based on brilliant cresyl blue staining.\",\n \"abstract\": \"Adiponectin and its receptors (AdipoR1 and AdipoR2) are novel endocrine systems that act at various levels to control male and female fertility. The aim of this study was to determine whether adiponectin and its receptors gene expression levels differ between dominant follicle (DF) and atretic follicle (AF) and also between oocytes which were stained positively and negatively with brilliant cresyl blue (BCB(+) and BCB(-)). Based on estradiol/progesterone ratio, follicles from ovaries were classified as AFs and DFs. The stages of estrous cycle (follicular or luteal phases) were defined by macroscopic observation of the ovaries and the uterus. Oocytes were stained with BCB for 90 min. The relative expression of adiponectin, AdipoR1 and AdipoR2 mRNA in theca and cumulus cells and oocytes of different follicles were determined by quantitative real time PCR. Adiponectin and its receptors genes were clearly expressed higher (P<0.05) in theca and cumulus cells and oocytes of DFs than those of AFs during the follicular and luteal phases. BCB(+) oocytes showed a higher (P<0.05) expression of adiponectin and its receptors compared with their BCB(-) counterparts. Positive correlation (r>0.725, P<0.001) was observed between adiponectin mRNA level in ovarian cells of DFs and follicular fluid E2 concentration in follicular phase. Adiponectin mRNA abundance in ovarian cells of AFs showed a significant negative correlation with follicular fluid progesterone concentration in follicular and luteal phases (r<-0.731, P<0.001). This work has revealed the novel association of adiponectin and its receptors genes with follicular dominance and oocyte competence, thereby opening several new avenues of research into the mechanisms of dominance and competence in animal and human.\",\n \"corpus_id\": 42591560,\n \"score\": 2\n },\n {\n \"doc_id\": \"22558373\",\n \"title\": \"Oocytes selected using BCB staining enhance nuclear reprogramming and the in vivo development of SCNT embryos in cattle.\",\n \"abstract\": \"The selection of good quality oocytes is crucial for in vitro fertilization and somatic cloning. Brilliant cresyl blue (BCB) staining has been used for selection of oocytes from several mammalian species. However, the effects of differential oocyte selection by BCB staining on nuclear reprogramming and in vivo development of SCNT embryos are not well understood. Immature compact cumulus-oocyte complexes (COCs) were divided into control (not exposed to BCB), BCB+ (blue cytoplasm) and BCB- (colorless cytoplasm) groups. We found that BCB+ oocytes yielded a significantly higher somatic cell nuclear transfer (SCNT) blastocyst rate and full term development rate of bovine SCNT embryos than the BCB- and control oocytes. BCB+ embryos (embryos developed from BCB+ oocytes) showed increased acetylation levels of histone H3 at K9 and K18 (AcH3K9, AcH3K18), and methylation levels of histone H3 at K4 (H3K4me2) than BCB- embryos (embryos developed from BCB- oocytes) at the two-cell stage. Furthermore, BCB+ embryos generated more total cells, trophectoderm (TE) cells, and inner cell mass (ICM) cells, and fewer apoptotic cells than BCB- embryos. The expression of SOX2, CDX2, and anti-apoptotic microRNA-21 were up-regulated in the BCB+ blastocysts compared with BCB- blastocysts, whereas the expression of pro-apoptotic gene Bax was down-regulated in BCB+ blastocysts. These results strongly suggest that BCB+ oocytes have a higher nuclear reprogramming capacity, and that BCB staining can be used to select developmentally competent oocytes for nuclear transfer.\",\n \"corpus_id\": 7921528,\n \"score\": 2\n },\n {\n \"doc_id\": \"22675245\",\n \"title\": \"Selection of ovine oocytes by brilliant cresyl blue staining.\",\n \"abstract\": \"Sheep oocytes derived from the ovaries collected from the slaughterhouse are often used for research on in vitro embryo production, animal cloning, transgenesis, embryonic stem cells, and other embryo biotechnology aspects. Improving the in vitro culture efficiency of oocytes can provide more materials for similar studies. Generally, determination of oocyte quality is mostly based on the layers of cumulus cells and cytoplasm or cytoplasm uniformity and colors. This requires considerable experience to better identify oocyte quality because of the intense subjectivity involved (Gordon (2003), Madison et al. (1992) and De Loos et al. (1992)). BCB staining is a function of glucose-6-phosphate dehydrogenase (G6PD) activity, an enzyme synthesized in developing oocytes, which decreases in activity with maturation. Therefore, unstained oocytes (BCB-) are high in G6PD activity, while the less mature oocytes stains are deep blue (BCB+) due to insuffcient G6PD activity to decolorize the BCB dye.\",\n \"corpus_id\": 17010501,\n \"score\": 2\n },\n {\n \"doc_id\": \"23199746\",\n \"title\": \"Lipid content, active mitochondria and brilliant cresyl blue staining in bovine oocytes.\",\n \"abstract\": \"Bovine oocytes that stain with brilliant cresyl blue (BCB) have a relatively higher developmental competence. The aim of the present study was to investigate the relationships among BCB staining, lipid content, and active mitochondria. Bovine oocytes (N = 133) with at least three layers of cumulus cells were segregated as BCB retained (BCB+) or metabolized (BCB-) and then stained for active mitochondria (Mitotracker Red) and lipid (Bodipy), with analysis by confocal microscopy. The BCB+ oocytes (N = 45) contained approximately 26% more cytoplasmic lipid than BCB- oocytes (N = 26-27; P < 0.05). Staining for active mitochondria did not differ between the groups. In BCB- oocytes but not BCB+ oocytes, lipid content correlated with active mitochondrial staining (r = 0.48; P < 0.05). Diameter correlated with lipid content for BCB+ oocytes (r = 0.46; P < 0.05), but not for BCB- oocytes (r = 0.16; P > 0.05). Irrespective of BCB staining, both lipid and active mitochondrial content correlated with diameter. In conclusion, the higher lipid content of BCB+ bovine oocytes might provide a cellular and functional basis for their greater developmental competence.\",\n \"corpus_id\": 31772792,\n \"score\": 2\n },\n {\n \"doc_id\": \"23228698\",\n \"title\": \"Combination of oocyte and zygote selection by brilliant cresyl blue (BCB) test enhanced prediction of developmental potential to the blastocyst in cattle.\",\n \"abstract\": \"The cumulus oocyte complexes (COCs) were obtained from local abattoir. After aspiration, the COCs were allotted into four treatments to evaluation of brilliant cresyl blue (BCB) test. Control treatment (C): oocytes were cultured directly (without exposure to BCB) after recovery in in vitro production (IVP) process. Oocyte treatment (OBCB): immediately after aspiration, COCs were incubated in modified Dulbecco's phosphate-buffered saline (mDPBS) supplemented with 26μM of BCB for 90min and classified into two classes: oocytes with blue cytoplasm coloration (OBCB+: more competent oocytes) and oocytes without blue cytoplasm coloration (OBCB-: low competent oocytes). Directly after classification, the oocytes were maintained undisrupted in the IVP process. Zygote treatment (ZBCB): After oocyte collection, maturation and fertilization, zygotes were stained with BCB for 10min and categorized into three ways, according to whether they were highly stained (ZBCB++: low competent zygotes), moderately stained (ZBCB+: moderate competent zygotes) and unstained (ZBCB-: more competent zygotes). Directly after classification, the zygotes were maintained undisrupted in the culture process. Oocyte and zygote treatments (OBCB/ZBCB): COCs were stained with BCB after recovery and classified into two classes (OBCB+ and OBCB-). After fertilization, the zygotes produced from OBCB+ and OBCB- oocytes were further stained with BCB for 10min and categorized six ways (OBCB+/ZBCB++, OBCB+/ZBCB+, OBCB+/ZBCB-, OBCB-/ZBCB++, OBCB-/ZBCB+ and OBCB-/ZBCB-). Directly after classification, the zygotes were maintained undisrupted in the culture process. The selection rate produced from OBCB treatment (OBCB+; 54.3%) was greater (P<0.05) than ZBCB treatment (ZBCB-; 44.3%). In addition, the selection rate produced from double application (combination of oocyte and zygote selection) of BCB test (OBCB+/ZBCB-: 28.8%) was less (P<0.01) than single application of BCB test (ZBCB-: 44.3%or OBCB+: 54.3%). The percentage of blastocyst production from OBCB+ oocytes (35.7%) and ZBCB- zygotes (36.6%) were greater (P<0.05) than that from C oocytes (25.7%), OBCB- oocytes (16.5%), ZBCB++ (13.5%) and ZBCB+ zygotes (21.3%). However, there were no significant differences (P>0.05) in the percentages of blastocyst production between OBCB+ oocytes (35.7%) and ZBCB- zygotes (36.6%). The proportion of blastocyst production from double application of BCB test (OBCB+/ZBCB-: 48.0%) was greater (P<0.05) than that from single application of BCB test (OBCB+: 35.7% or ZBCB-: 36.6%). In conclusion, current results confirmed that combination of oocyte and zygote selection by BCB test enhanced the efficiency of selecting for high quality embryos, compared to the single BCB test.\",\n \"corpus_id\": 25547903,\n \"score\": 2\n },\n {\n \"doc_id\": \"23369728\",\n \"title\": \"Selection of developmentally competent immature equine oocytes with brilliant cresyl blue stain prior to in vitro maturation with equine growth hormone.\",\n \"abstract\": \"Immature oocytes synthesize a variety of proteins that include the enzyme glucose-6-phosphate dehydrogenase (G6PDH). Brilliant cresyl blue (BCB) is a vital blue dye that assesses intracellular activity of G6PDH, an indirect measure of oocyte maturation. The objective was to evaluate the BCB test as a criterion to assess developmental competence of equine oocytes and to determine if equine growth hormone (eGH) enhanced in vitro maturation (IVM) of equine oocyte. Cumulus-oocytes complexes (COCs) were recovered by aspirating follicles <30 mm in diameter from abattoir-derived ovaries and were evaluated morphologically. Thereafter, COCs were exposed to BCB (26 μM) for 90 min at 39°C and selected based on the colour of their cytoplasm (BCB positive/BCB+ or BCB negative/BCB-). The COCs were allocated as follows: (a) IVM medium; (b) eGH group; (c) BCB-/IVM; (d) BCB+/IVM; (e) BCB-/eGH; and (f) BCB+/eGH. Then, COCs were cultured in vitro for 30 h, at 39°C in a 5%CO2 humidified air atmosphere. Cumulus-free oocytes were incubated in 10 μg/ml of bis-benzamide for 20 min at 39°C and nuclear maturation was evaluated with epifluorescence microscopy. Of the 39 COCs selected morphologically and subjected to BCB staining, 18/39 (46.2%) were classified as BCB+ and 21/39 (53.8%) as BCB- (P > 0.05). Maturation was not affected significantly by BCB classification, but the maturation rate was higher for oocytes that had been exposed to exogenous eGH versus controls (16/28, 57.1% versus 8/26, 30.8%, P < 0.05). In the present study, the BCB test was not useful for predicting competent equine oocytes prior to IVM. However, eGH enhanced equine oocyte maturation in vitro.\",\n \"corpus_id\": 24479582,\n \"score\": 2\n },\n {\n \"doc_id\": \"24011188\",\n \"title\": \"The utility of Brilliant Cresyl Blue (BCB) staining of mammalian oocytes used for in vitro embryo production (IVP).\",\n \"abstract\": \"The present article summarizes the results of experiments investigating the Brilliant Cresyl Blue (BCB) staining for selection of immature oocytes before in vitro embryo production or somatic cell nuclear transfer. Developmental competence of oocytes stained with BCB and quality of blastocysts derived from such oocytes as well as the expression of apoptosis-related genes, mitochondrial DNA (mtDNA) replication-related genes and the transcripts encoded by the mitochondrial genome in BCB stained oocytes are discussed.\",\n \"corpus_id\": 46514003,\n \"score\": 2\n },\n {\n \"doc_id\": \"24070583\",\n \"title\": \"Mitochondrial content and gene expression profiles in oocyte-derived embryos of cattle selected on the basis of brilliant cresyl blue staining.\",\n \"abstract\": \"The aim of this study was to investigate the developmental rate, lipid and mitochondrial distribution and gene expression in oocyte-derived embryos selected on the basis of brilliant cresyl blue (BCB) staining. Lipid content and mitochondrial distribution in Day 8 blastocysts were evaluated by fluorescence intensity, while gene expression was analyzed by real-time PCR. The proportion of blastocysts (30.9%) was greater (P<0.05) in BCB+ than in BCB- oocytes (13%) but not different (P>0.05) from the control group (28.2%). Total cell number was also greater in BCB+ (155.1 ± 36.2) than in BCB- (116.6 ± 40.5) and control (127.5 ± 35.7) blastocysts. Furthermore, the apoptotic cell number was less in BCB+ (3.7 ± 4.4) than in BCB- blastocysts (8.7 ± 8.7) but not different from the control group (5.9 ± 3.9). BCB+ embryos contained more mitochondria compared to BCB- embryos (P<0.05). There was no significant difference in intercellular lipid accumulation in embryos from all groups. Interferon-τ (IFNτ), transforming growth factor β1 (TGFB1) and secreted seminal-vesicle Ly-6 protein 1 (SSLP1) gene expression was greater in BCB+ than in BCB- blastocysts. By contrast, Bcl2-associated X protein (BAX) and heterogeneous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) gene expression was greater in BCB- than in BCB+ and control embryos. In conclusion, oocyte-derived embryos selected on the basis of BCB staining showed differences in developmental rate, quality, mitochondrial content and target gene expression compared to control embryos.\",\n \"corpus_id\": 13540279,\n \"score\": 2\n },\n {\n \"doc_id\": \"24284835\",\n \"title\": \"Differences in cytoplasmic maturation between the BCB+ and control porcine oocytes do not justify application of the BCB test for a standard IVM protocol.\",\n \"abstract\": \"The Brilliant Cresyl Blue (BCB) test relies on G6PDH activity and a simple protocol for the selection of higher quality oocytes. Although the BCB+ oocytes of all the species that have been investigated are characterized by superior quality when compared to BCB- counterparts, application of the test for embryo production still remains an open issue. The aim of our study was to compare BCB+ and the control oocytes (not subjected to the BCB test) in terms of selected aspects of cytoplasmic maturation (mtDNA copy number, mitochondria distribution, relative transcript abundance of six marker genes). The results of our study revealed more relevant differences within the BCB+ and the control oocytes (before and after IVM) than between the two categories of oocytes. There was no difference in the transcript abundance of the BCB+ and the control oocytes in 5 out of 6 analyzed genes (BMP15, GDF9, ATP5A1, EEF1A, ZAR1) and in mtDNA content (pre-IVM 179609 vs. 176595 and post-IVM 187243 vs. 246984, respectively). With regard to mitochondria distribution in pre- and post-IVM oocytes, there was nonsignificant tendency for a more frequent occurrence of the expected patterns in the BCB+ group. The results of the present study do not support the application of BCB staining in a routine IVM protocol due to relatively high similarity in selected parameters characterizing cytoplasmic maturation of BCB+ and control oocytes. This high similarity may results from the limited amount of less competent BCB- oocytes (10%) still present among nonselected oocytes of proper morphology.\",\n \"corpus_id\": 7695478,\n \"score\": 2\n },\n {\n \"doc_id\": \"24355610\",\n \"title\": \"Brilliant cresyl blue staining negatively affects mitochondrial functions in porcine oocytes.\",\n \"abstract\": \"The aim of the present study was to examine the effects of brilliant cresyl blue (BCB) staining on mitochondrial functions in porcine oocytes. Cumulus-oocyte complexes (COCs) collected from slaughterhouse-derived porcine ovaries were cultured with (13 μM) or without (0 μM, control) BCB for 60 min. Mitochondrial functions in oocytes were examined immediately after staining or after in vitro maturation. The BCB-stained oocytes produced reactive oxygen species (ROS) at higher levels than control oocytes immediately after staining (2.2-fold, P < 0.001) and after maturation (1.7-fold, P < 0.001). The adenosine triphosphate (ATP) content and mitochondrial membrane potential (MMP) in oocytes were similar for the two groups immediately after staining. However, ATP and relative MMP levels were significantly (P < 0.05) lower in BCB-treated oocytes than in the control (2.18 versus 2.83 pM and 0.82 versus 1.0, respectively). There was no difference in mitochondrial DNA copy number between the two groups after maturation. The ATP content in early developmental stage embryos (3 days after parthenogenetic activation) was lower in the BCB-stained group than that in the control group but the difference was not significant. In conclusion, BCB staining of oocytes at the immature stage compromises mitochondrial functions throughout oocyte maturation, but function is restored during early embryo development.\",\n \"corpus_id\": 36694117,\n \"score\": 2\n },\n {\n \"doc_id\": \"24381853\",\n \"title\": \"The Effect of Melatonin on Maturation, Glutathione Level and Expression of H MGB1 Gene in Brilliant Cresyl Blue (BCB) Stained Immature Oocyte.\",\n \"abstract\": \"OBJECTIVE: Nutrients and antioxidants in the medium of immature oocyte have a profound effect on maturation, fertilization and development of resulting embryos. In this study the effects of melatonin as an antioxidant agent on maturation, glutathione level and expression of High mobility group box-1 (HMGB1) gene were evaluated in immature oocytes of mice stained with brilliant cresyl blue (BCB). MATERIALS AND METHODS: In this experimental study, immature oocytes were harvested from ovaries of Naval Medical Research Institute (NMRI) mice. Oocytes were stained with 26 μM BCB for 90 minutes and transferred to in vitro maturation medium containing varying doses of melatonin (10-12, 10-9, 10-6, 10-3 M) and without melatonin, for 22-24 hours. Maturation was monitored using an inverted microscope. Glutathione was assessed by monochlorobimane (MCB) staining and HMGB1 expression in mature oocyte was analyzed using real-time polymerase chain reaction (PCR). RESULTS: Melatonin in the concentration of 10-6 M had the most effect on maturation and HMGB1 expression of BCB+ oocytes (p<0.05). Meanwhile melatonin had no effects on glutathione levels. Additionally in immature BCB- oocytes, compared to the control group, melatonin did not affect cytoplasm maturation (p>0.05). CONCLUSION: In vitro treatment with melatonin increases the maturation and HMGB1 expression in BCB+ immature oocytes and has no significant effect on glutathione levels.\",\n \"corpus_id\": 8859649,\n \"score\": 2\n },\n {\n \"doc_id\": \"24913026\",\n \"title\": \"Association of glucose-6-phosphate dehydrogenase activity with oocyte cytoplasmic lipid content, developmental competence, and expression of candidate genes in a sheep model.\",\n \"abstract\": \"PURPOSE: To evaluate associations of glucose-6-phosphate dehydrogenase (G6PDH) activity in sheep oocytes with cytoplasmic lipid content, maturational competence, developmental competence to the blastocyst stage, and gene expression of certain molecular markers. METHODS: Before brilliant cresyl blue (BCB) staining test, oocytes were classified as high, middle, and low cytoplasmic lipid content (HCLC, MCLC, and LCLC) and after the test as having low or high G6PDH-activity (BCB(+) and BCB(-), respectively). After maturation in vitro, a group of oocytes were subjected to IVF followed by in vitro embryo culture and another group was used for evaluation of expression of candidate genes. RESULTS: The cleavage and blastosyst rates were lowest (P < 0.05) in LCLC group, intermediate (P < 0.05) in MCLC group and highest (P < 0.05) in HCLC group. More (P < 0.05) oocytes in HCLC group were BCB(+), and higher (P < 0.05) maturation, cleavage, and blastocyst rates were seen for BCB(+) oocytes than the BCB(-) oocytes. Our gene expression data indicated that mRNA transcript abundance of ITGB2, pZP3, BMP15, and GDF9 genes was similar between BCB oocytes groups. However, the expression of ATP1A1 was higher (P < 0.05) for BCB(+) oocytes compared to BCB(-) oocytes. In addition, BAX transcript abundance was similar (P > 0.05) among BCB(+), BCB(-), and control groups, before and after maturation in vitro. CONCLUSION: Activity of G6PDH in sheep oocytes is highly associated with lipid content, and compared with the morphological parameters might be a more precise and objective predictor for subsequent developmental competence in vitro.\",\n \"corpus_id\": 22982581,\n \"score\": 2\n },\n {\n \"doc_id\": \"25141841\",\n \"title\": \"Expression profile of developmentally important genes between hand-made cloned buffalo embryos produced from reprogramming of donor cell with oocytes extract and selection of recipient cytoplast through brilliant cresyl blue staining and in vitro fertilized embryos.\",\n \"abstract\": \"PURPOSE: To compare the expression profile of developmentally important genes between hand-made cloned buffalo embryos produced from reprogramming of donor cell with oocyte extracts and selection of recipient cytoplast through brilliant cresyl blue staining and in vitro fertilized (IVF) embryos. METHODS: Hand-made cloned embryos were produced using oocyte extracts treated donor cells and brilliant cresyl blue (BCB) stained recipient cytoplasts. IVF embryos were produced by culturing 15-20 COCs in BO capacitated sperms from frozen thawed buffalo semen and the mRNA expression patterns of genes implicated in metabolism (GLUT1), pluripotency (OCT4), DNA methylation (DNMT1), pro- apoptosis (BAX) and anti-apoptosis (BCL2) were evaluated at 8- to16- cell stage embryos. RESULTS: A significantly (P < 0.05) higher number of 8- to16- cell and blastocyst stages (73.9 %, 32.8 %, respectively) were reported in hand-made cloning (HMC) as compared to in vitro fertilization (49.2 %, 24.2 %, respectively). The amount of RNA recovered from 8- to 16- cell embryos of HMC and in vitro fertilization did not appear to be influenced by the method of embryo generation (3.76 ± 0.61 and 3.82 ± 0.62 ng/μl for HMC and in vitro fertilization embryos, respectively). There were no differences in the expression of the mRNA transcripts of genes (GLUT1, OCT4, DNMT1, BAX and BCL2) were analysed by real-time PCR between hand-made cloned and IVF embryos. CONCLUSIONS: Pre-treatment of donor cells with oocyte extracts and selection of developmentally competent oocytes through BCB staining for recipient cytoplast preparations may enhance expression of developmentally important genes GLUT1, OCT4, DNMT1, BAX, and BCL2 in hand-made cloned embryos at levels similar to IVF counterparts. These results also support the notion that if developmental differences observed in HMC and in vitro fertilization produced foetuses and neonates are the results of aberrant gene expression during the pre-implantation stage, those differences in expression are subtle or appear after the maternal to zygotic transition stage of development.\",\n \"corpus_id\": 29805217,\n \"score\": 2\n },\n {\n \"doc_id\": \"25627022\",\n \"title\": \"Effect of L-carnitine supplementation on maturation and early embryo development of immature mouse oocytes selected by brilliant cresyle blue staining.\",\n \"abstract\": \"PURPOSE: The present study was designed to investigate the effect of L-carnitine treatment during IVM on nuclear and cytoplasmic maturation of immature oocytes selected by Brilliant Cresyle Blue (BCB) staining, and their subsequent developmental competence. MATERIALS & METHODS: Compact cumulus-oocyte complexes (COCs) were collected from NMRI mice ovaries and stained with BCB staining. BCB+ (colored cytoplasm) oocytes were then cultured in tissue culture medium (TCM) 199 with 0.0, 0.3 and 0.6 mg/ml L-carnitine. RESULTS: The both L-carnitine concentrations significantly increased the intracellular glutathione (P<0.001), nuclear maturation (P<0.01) and expression levels of cyclin-dependent kinase1 (CDK1) (P<0.05). Moreover, treated oocytes with 0.6 mg/ml L-carnitine showed increased (P < 0.05) expression of mitogen-activated protein kinase1 (MAPK1) mRNA. Also, adding L-carnitine (0.6 mg/ml) to IVM medium significantly increased the cleavage rate (P<0.05). The blastocyst development rate (BDR) in the both L-carnitine treated groups was significantly higher (P<0.001) than the control group. L-carnitine had no significant effect on total blastocyst cell numbers. CONCLUSIONS: These data indicated that L-carnitine supplementation during IVM of immature BCB+ oocytes improved preimplantation developmental competence of oocytes after IVF, probably by accelerating cytoplasmic and nuclear maturation of oocytes. It may provide a novel approach to improving ART outcomes in infertile couples.\",\n \"corpus_id\": 24016141,\n \"score\": 2\n },\n {\n \"doc_id\": \"25704641\",\n \"title\": \"Expression of TGFβ superfamily components and other markers of oocyte quality in oocytes selected by brilliant cresyl blue staining: relevance to early embryonic development.\",\n \"abstract\": \"Brilliant cresyl blue (BCB) is a super-vital stain that has been used to select competent oocytes in different species. One objective of the present study was to assess the relationship between BCB staining, which correlates with an oocyte's developmental potential, and the transcript abundance for select TGFβ-superfamily components, SMAD2/3 and SMAD1/5 phosphorylation levels, and oocyte (JY1) and cumulus-cell (CTSB, CTSK, CTSS, and CTSZ) transcript markers in bovine oocytes and/or adjacent cumulus cells. The capacity of exogenous follistatin or JY1 supplementation or cathepsin inhibitor treatment to enhance development of embryos derived from low-quality oocytes, based on BCB staining, was also determined. Cumulus-oocyte complexes (COCs) from abattoir-derived ovaries were subjected to BCB staining, and germinal-vesicle-stage oocytes and cumulus cells were harvested from control, BCB+, and BCB- (low-quality oocyte) groups for real-time PCR or Western-blot analysis. Remaining COCs underwent in vitro maturation, in vitro fertilization, and embryo culture in the presence or absence of the above exogenous supplements. Levels of FST, JY1, BMP15, and SMAD1, 2, 3, and 5 transcripts were higher in BCB+ oocytes whereas CTSB, CTSK, CTSS, and CTSZ mRNA abundance was higher in cumulus cells surrounding BCB- oocytes. Western-blot analysis revealed higher SMAD1/5 and SMAD2/3 phosphorylation in BCB+ than BCB- oocytes. Embryo-culture studies demonstrated that follistatin and cathepsin inhibitor treatment, but not JY-1 treatment, improve the developmental competence of BCB- oocytes. These results contribute to a better understanding of molecular indices of oocyte competence.\",\n \"corpus_id\": 31772931,\n \"score\": 2\n },\n {\n \"doc_id\": \"25709633\",\n \"title\": \"Developmental competence of bovine oocytes selected based on follicle size and using the brilliant cresyl blue (BCB) test.\",\n \"abstract\": \"BACKGROUND: Many studies reported that follicle size has an essential role in developmental potential of oocytes. Also, the brilliant cresyl blue (BCB) test is one of the most important criteria in selection of more competent oocytes. OBJECTIVE: Selection of developmentally competent bovine oocytes. MATERIALS AND METHODS: A total of 1730 bovine cumulus oocyte complexes (COCs) were recovered from the ovaries by follicles isolation and classified into 3 categories according to the diameters of the follicles (small, <3 mm; medium 3-6 mm and large >6 mm). Oocytes were exposed to the BCB stain, diluted in Dulbecco's phosphate-buffered saline, modified with 0.4% bovine serum albumin (BSA) for 90 min. Oocytes with or without blue coloration of the cytoplasm were designated as BCB(+) and BCB(-), respectively. RESULTS: The BCB(+) and control oocytes originated from large and medium follicles exhibited a higher (p<0.0001) cleavage and blastocyst rate than BCB(-) oocytes. Furthermore, the BCB(+) oocytes from large and medium follicles had the highest (p<0.0001) proportion of blastocyst than other treatment groups. In contrast, the BCB(-) oocytes from small follicles had the lowest (p<0.0001) proportion of blastocyst than other treatment groups. Interestingly, the percentage of the BCB(+) oocytes from the large and medium ovarian follicles was significantly higher (p<0.0001), than the BCB(+) oocytes from the small follicles. CONCLUSION: Current results confirmed that each BCB(+) oocyte could not lead to perfect embryo development and the BCB test is not sufficient enough for the identification of oocytes that are competent for in vitro embryo development.\",\n \"corpus_id\": 16009830,\n \"score\": 2\n },\n {\n \"doc_id\": \"25826727\",\n \"title\": \"Buffalo embryos produced by handmade cloning from oocytes selected using brilliant cresyl blue staining have better developmental competence and quality and are closer to embryos produced by in vitro fertilization in terms of their epigenetic status and gene expression pattern.\",\n \"abstract\": \"We compared handmade cloned (HMC) buffalo blastocysts produced from oocytes stained with Brilliant Cresyl Blue (BCB) and classified into those with blue (BCB+) or colorless cytoplasm (BCB-). The blastocyst rate was higher (p<0.001) for BCB+ than for BCB- oocytes (43.41 ± 2.54 vs. 22.74 ± 1.76%). BCB+ blastocysts had inner cell mass (ICM) cell number, ICM-to-trophectoderm ratio, global level of H3K18ac, apoptotic index, and expression level of BCL-XL, but not that of CASPASE-3, similar to that of blastocysts produced through in vitro fertilization (IVF), which was higher (p<0.05) than that of BCB- blastocysts. The global level of H3K9me2, which was similar in BCB+ and BCB- blastocysts, was higher (p<0.01) than that in IVF blastocysts. The expression level of OCT4 and SOX2 was higher (p<0.05) and that of GATA2 was lower (p<0.05) in BCB+ than that in BCB- blastocysts, whereas that of DNMT1, DNMT3a, NANOG, and CDX2 was not significantly different between the two groups. The expression level of DNMT1, OCT4, NANOG, and SOX2 was lower (p<0.05) and that of CDX2 was higher (p<0.05) in BCB+ than in IVF blastocysts. In conclusion, because BCB+ blastocysts have better developmental competence and are closer to IVF blastocysts in terms of quality, epigenetic status, and gene expression than BCB- blastocysts, BCB staining can be used effectively for selection of developmentally competent oocytes for HMC.\",\n \"corpus_id\": 5580099,\n \"score\": 2\n },\n {\n \"doc_id\": \"25921213\",\n \"title\": \"Safety of brilliant cresyl blue staining protocols on human granulosa and cumulus cells.\",\n \"abstract\": \"The selection of human immature oocytes destined for in vitro maturation (IVM) is performed according to their cumulus-oocyte complex (COC) morphology. In animal models, oocyte pre-selection with brilliant cresyl blue (BCB) staining improves fertilization and blastocyst rates and even increases the number of calves born. As the granulosa cells and cumulus cells (GCs and CCs) have a close relationship with the oocyte and are available in in vitro fertilization (IVF) programs, applying BCB staining to these cells may help to elucidate whether BCB shows toxicity to human oocytes and to determine the safest protocol for this dye. GCs and CCs were isolated from 24 patients who underwent controlled ovarian stimulation. After 48 h, cells were exposed to: Dulbecco's Modified Eagle Medium (DMEM) with or without phenol red, DPBS and mDPBS for 60 min; 13, 20 and 26 μM BCB for 60 min; and 60, 90 or 120 min to 13 μM BCB. Cellular viability was tested using 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) and trypan blue assays. The 20 and 26 μM BCB exposures resulted in lower cell viability, similar to when cells were exposed to BCB for 90 or 120 min. GCs and CCs viabilities were equal among control group and 13 μM BCB group after 60 min. BCB staining was not toxic to GCs and CCs when the regime of 13 μM BCB for 60 min was used. Due to the close molecular/biochemical relationship between these cells and the gamete, we propose that it is unlikely that the use of BCB could interfere with the viability/health of human oocytes.\",\n \"corpus_id\": 28812526,\n \"score\": 2\n },\n {\n \"doc_id\": \"25943119\",\n \"title\": \"Bovine non-competent oocytes (BCB-) negatively impact the capacity of competent (BCB+) oocytes to undergo in vitro maturation, fertilisation and embryonic development.\",\n \"abstract\": \"Competent oocyte selection remains a bottleneck in the in vitro production (IVP) of mammalian embryos. Among the vital assays described for selecting competent oocytes for IVP, the brilliant cresyl blue (BCB) test has shown consistent results. The aim of the first experiment was to observe if oocytes directly submitted to IVM show similar cleavage and blastocyst rates as those obtained with oocytes maintained under the same in vitro conditions as the oocytes that undergo the BCB test. Bovine cumulus-oocyte complexes (COCs) were recovered from slaughterhouse-derived ovaries and, after morphological evaluation, were randomised grouped into three groups: (1) directly submitted to IVM; (2) oocytes submitted to the BCB test without the addition of BCB stain (BCB control group); and (3) submitted to the BCB test. The results showed that oocytes directly submitted to IVM reached similar cleavage (48/80 - 60%) and embryonic development rates to the blastocyst stage (10/48 - 21%) as the results obtained with the BCB control group oocytes (45/77 - 58% and 08/45 - 18%, respectively). The aim of the second experiment was to determine the cleavage and blastocyst rates obtained from BCB+ oocytes undergoing IVM in the presence of BCB- oocytes at a ratio of 10:1. COCs were recovered from slaughterhouse-derived ovaries and, after morphological evaluation, were randomised into two groups that were submitted to IVM either directly (1: control group) or submitted to the BCB test prior to IVM. After the BCB test, the COCs were classified as either BCB+ (blue cytoplasm) or BCB- (colourless cytoplasm) and then divided into four experimental groups: (2) BCB+; (3) BCB-; and (4) BCB+ matured in same IVM medium drop as (5) BCB- at a ratio of 10:1. After IVM (24 h), oocytes from the different experimental groups were submitted to in vitro fertilisation (IVF) and in vitro culture (IVC) under the same culture conditions until they reached the blastocyst stage (D7). With regards to the cleavage rate (48 h after IVF), only group 3 (102/229 - 44%) differed (P < 0.05) from the other groups [1 (145/241 - 60%); 2 (150/225 - 67%); 4 (201/318 - 63%) and 5 (21/33 - 63%)]. On day 7, the embryos from group 2 (BCB+) achieved the highest blastocyst rate (46/150 - 31%) (P < 0.05) when compared with the embryo development capacity of the other experimental groups (1: 31/145 - 21%; group 3: 17/102 - 17%; group 4: 46/201 - 23%; and group 5: 2/21 - 10%). In conclusion, submitting BCB+ oocytes that were separated from BCB- oocytes to IVM increases the rate of embryonic development to the blastocyst stage when compared to the control group, BCB- oocyte group, BCB+ paracrine group and BCB- paracrine group. The presence of non-competent oocytes during IVM, even in low proportion (1:10), reduces the capacity of competent oocytes to undergo embryo development and achieve blastocyst stage during IVC.\",\n \"corpus_id\": 45627469,\n \"score\": 2\n },\n {\n \"doc_id\": \"26280459\",\n \"title\": \"Gene Expression of Monocarboxylate Transporters and Oocyte-secreted Factors in Bovine Cumulus-oocyte Complexes Selected by Brilliant Cresyl Blue.\",\n \"abstract\": \"Oocyte selection based on the brilliant cresyl blue (BCB) staining test has been successfully used to differentiate between competent and incompetent bovine oocytes. Here, the expression of genes involved in transport of monocarboxylates (Mct1-4) and oogenesis specific genes (Bmp15, Gdf9 and Has2) in BCB+ and BCB- selected immature and mature bovine cumulus-oocyte complexes (COC) was evaluated. In order to find specific molecular markers to characterize successful oocyte maturation, our study was also aimed at identifying the expression of Mcts and oogenesis specific genes in denuded oocytes and cumulus cells. Immature COCs morphological appropriate were (i) stained with 26 mm BCB for 90 min before IVM, (ii) exposed to same incubation conditions as stained COCs, but without BCB (holding group) or (iii) transferred into a maturation medium immediately after morphological selection (control group). mRNA expression was investigated by RT-PCR in COCs before and after IVM. No relationship was observed in the relative expression of Has2, Gdf9, Bmp15 or Mct1, 2 and 4 transcripts between BCB+ and BCB- COCs. Transcripts analysis showed that Gdf9 and Bmp15 in BCB+, BCB- and holding groups were up-regulated (p < 0.05) before IVM, while Has2 was up-regulated (p < 0.01) after IVM in the control group. Other genes remained stable during maturation (Mct1, 2 and 4). Our results showed, for the first time, Mct1, 2 and 4 expression in bovine COCs. Mct1 and Mct4 transcripts were present in denuded oocytes and cumulus cell, while Mct2 was detected only in cumulus cells. These differences between the three isoforms in localization suggest unique roles for each in monocarboxylate transport during maturation.\",\n \"corpus_id\": 206289479,\n \"score\": 2\n },\n {\n \"doc_id\": \"26879998\",\n \"title\": \"Effects of cilostamide and/or forskolin on the meiotic resumption and development competence of growing ovine oocytes selected by brilliant cresyl blue staining.\",\n \"abstract\": \"The relevance of low developmental competence of in vitro-matured oocyte to the incomplete/delayed cytoplasmic maturation, and the heterogeneity of retrieved oocytes is well established in several species. A short phase of prematuration culture was used to allow better oocyte cytoplasmic maturation. The preselection of growing and fully grown oocytes has been proposed to improve developmental competency. This study investigated the effects of phosphodiesterase type 3-specific inhibitor, cilostamide, and adenylate cyclase activator, forskolin, on the resumption of meiosis and developmental competence of growing ovine oocytes selected by brilliant cresyl blue (BCB) staining. Results indicate that cilostamide, forskolin, and their combination significantly (P < 0.05) increased the percentage of growing (BCB-) oocytes maintained at the germinal vesicle stage. However, only forskolin significantly (P < 0.05) increased the yield and quality of blastocysts derived from BCB- oocytes compared with non-BCB-treated oocytes. We conclude that a short prematuration culture with forskolin may improve the in vitro developmental competency of growing oocytes in ovine.\",\n \"corpus_id\": 205368686,\n \"score\": 2\n },\n {\n \"doc_id\": \"27481813\",\n \"title\": \"Effect of milrinone on the developmental competence of growing lamb oocytes identified with brilliant cresyl blue.\",\n \"abstract\": \"Juvenile in vitro embryo transfer is a novel technique that can be used to increase the rate of genetic gain in a population and presents an alternative to embryo technologies on the basis of adult animals. However, oocytes from prepubertal animals have a lower viability than those obtained from adult ewe oocyte donors. In this research, we aimed to determine the optimum concentration and time of treatment of oocytes from prepubertal lambs with brilliant cresyl blue (BCB) stain and milrinone during IVM. This would improve the developmental rate of lamb oocytes and embryos after IVF. First, lamb cumulus-oocyte complexes were cultured under different concentrations (13 or 26 μM) of BCB staining. Treated lamb oocytes were then divided into BCB- (colorless cytoplasm) and BCB+ (colored cytoplasm) groups on the basis of their glucose-6-phosphate dehydrogenase activity. The blastocyst efficiency rate of BCB+ oocytes treated with 13 μM BCB (37.03%) was significantly higher than that of BCB+ oocytes treated with 26 μM BCB (23.25%) and that of nontreated BCB control oocytes (15.37%), as well as that of BCB- oocytes (6.28%). Both control oocytes and BCB+ oocytes exhibited significantly higher cleavage rates (60.15% and 73.44%, respectively) than that of BCB- oocytes (36.19%). Moreover, the diameter and glutathione content of BCB+ oocytes were found to be significantly greater than those of BCB- oocytes (163.37 vs. 159.25 μm and 6.39 vs. 0.26 pM, respectively). After culturing BCB- oocytes in different concentrations of milrinone (0, 50, 75, and 100 μM) for 3, 6, or 9 hours, results reported that supplementation of IVM medium with 75 μM milrinone for 6 hours yielded a significantly higher proportion of blastocysts than the other treatments. These results show that the staining of lamb cumulus-oocyte complexes with 13 μM BCB before IVM may be used to select developmentally competent lamb oocytes. Furthermore, they suggest that milrinone can be used to promote lamb developmental competence of lamb embryos produced during IVF.\",\n \"corpus_id\": 27285496,\n \"score\": 2\n },\n {\n \"doc_id\": \"27955714\",\n \"title\": \"Selection of porcine oocytes in vitro through brilliant cresyl blue staining in distinct incubation media.\",\n \"abstract\": \"Staining with brilliant cresyl blue (BCB) may be used for oocyte selection, but BCB staining itself and the most commonly used selection medium (DMPBS) may compromise the development of porcine oocytes in vitro. This study evaluated DNA fragmentation, nuclear maturation, the area of migration of cortical granules (CG) and embryo development for stained (BCB+) and unstained (BCB-) oocytes incubated in DMPBS and in a modified medium (ReproPel) tested for the first time. Unexposed (UN), BCB+ and BCB- oocytes were incubated composing six groups: DMPBS/UN; DMPBS/BCB+; DMPBS/BCB-; ReproPel/UN; ReproPel/BCB+; and ReproPel/BCB-. There were more BCB+ oocytes in ReproPel than in DMPBS (P < 0.05). The DNA fragmentation was evaluated for oocytes in DMPBS/BCB+, DMPBS/BCB-, ReproPel/BCB+, ReproPel/BCB- and in porcine follicular fluid (control). The frequency of oocytes with no DNA fragmentation was greatest (64.6%) in DMPBS/BCB+ and lowest in ReproPel/BCB+ and ReproPel/BCB- (26.8 and 34.1%, respectively) (P < 0.05). Nuclear maturation rates were greater (P < 0.05) for DMPBS/BCB+ (63.1%), ReproPel/UN (55.1%) and ReproPel/BCB+ (50.2%) than for DMPBS/UN (40.8%) and ReproPel/BCB- (35.5%). The area of CG was greater (P < 0.05) for ReproPel/BCB- (80.7%) and DMPBS/UN (77.6%) than for ReproPel/UN (34.7%). Cleavage rates for DMPBS/BCB+ and ReproPel/BCB+ were greater than for DMPBS/UN (P < 0.05). Blastocyst development rates were greatest (P < 0.05) for ReproPel/UN and ReproPel/BCB+. In both media, BCB staining was apparently unable to select competent oocytes, which likely occurred due to toxicity. Despite the similar nuclear maturation and area of CG compared with DMPBS, oocytes selected in ReproPel presented impaired DNA integrity.\",\n \"corpus_id\": 24663336,\n \"score\": 2\n },\n {\n \"doc_id\": \"28063736\",\n \"title\": \"Brilliant cresyl blue staining does not present cytotoxic effects on human luteinized follicular cells, according to gene/protein expression, as well as to cytotoxicity tests.\",\n \"abstract\": \"In vitro oocyte maturation presents many advantages and its success is related to the selection of fully grown oocytes. In animal models, staining of cumulus-oocyte complexes (COCs) with Brilliant Cresyl Blue (BCB) is widely used for this selection. However, a lack of information about the safety of BCB makes its applicability in humans questionable. Because granulosa and cumulus cells have a close relationship with the oocyte and taking into account that follicular cells are also exposed to BCB when this pre-selection method is applied, we aimed to evaluate the effects of BCB on human follicular cells exposed to BCB. Cytotoxicity tests (Sulforhodamine B and Neutral Red Uptake) and gene and protein expression of elements related to the cell cycle (BAX, BCL2, TP53 and CDKN1A), as well as to cell death and metabolism (GAPDH), glucose consumption, and estradiol and progesterone secretion, were examined in granulosa and cumulus cells with and without exposure to BCB. Regardless estradiol secretion and glucose consumption, all other evaluations presented similar results between control and treated (BCB) groups, independently of cell type. Therefore, our results demonstrate convincingly that BCB seems to be safe for use in humans and it should encourage future studies to evaluate the development of embryos derived from human oocytes selected by BCB staining.\",\n \"corpus_id\": 22571519,\n \"score\": 2\n },\n {\n \"doc_id\": \"28070808\",\n \"title\": \"Combined positive effect of oocyte extracts and brilliant cresyl blue stained recipient cytoplasts on epigenetic reprogramming and gene expression in buffalo nuclear transfer embryos.\",\n \"abstract\": \"This study examined the effects of buffalo oocyte extracts (BOE) on donor cells reprogramming and molecular characterisation of oocytes screened via brilliant cresyl blue (BCB) staining and comparison of gene expression profiles of developmentally important genes in blastocysts from IVF and cloned derived from BOE treated donor cells with BCB selected recipient cytoplasts. Relative abundance (RA) of OCT4 and NANOG was increased (P < 0.05) and HDAC-1, DNMT-1, and DNMT-3A decreased (P < 0.05) in extract treated cells (ETCs). This ETCs dedifferentiated into neuron-like lineage under appropriate induction condition. The RA of NASP, EEF1A1, DNMT1, ODC1 and RPS27A was increased (P < 0.05) in BCB+ oocytes, whereas ATP5A1 and S100A10 increased (P < 0.05) in BCB- oocytes. Total cell number and RA of OCT4, NANOG, SOX2, DNMT1, IGF2, IGF2R, MNSOD, GLUT1, BAX and BCL2 in cloned blastocysts derived from BCB+ oocytes with ETC more closely followed that of IVF counterparts compared to BCB+ oocytes with extract untreated cell and BCB- oocytes with ETC derived blastocysts. In conclusion, BOE influenced epigenetic reprogramming of buffalo fibroblasts making them suitable donors for nuclear transfer (NT). BCB staining can be effectively used for selection of developmentally competent oocytes for NT. The combined effects of epigenetic reprogramming of donor nuclei by BOE and higher nuclear reprogramming capacity of BCB+ oocytes improve developmentally important gene expression in cloned blastocysts. Whether these improvements have long-term effects on buffalo calves born following embryo transfer remains unknown.\",\n \"corpus_id\": 207112094,\n \"score\": 2\n },\n {\n \"doc_id\": \"28274148\",\n \"title\": \"Selection of developmentally competent human oocytes aspirated during cesarean section.\",\n \"abstract\": \"PURPOSE: To evaluate the efficiency/safety of Brilliant Cresyl Blue (BCB) staining as a selection method of developmentally competent immature human oocytes. MATERIALS AND METHODS: Immature oocytes of 32 pregnant women were recovered during cesarean section (CS). After retrieval, 92 oocytes were randomly divided into two groups: control (directly disposed to in vitro maturation - IVM) and treated - exposed to BCB 26 μM during 60 min. After staining, the treated group was classified as cytoplasm coloration, BCB positive (blue) or negative (colorless), and then disposed to IVM. Nuclear status was checked after 24 and 48 h of IVM. Nuclear maturation (polar body extrusion), meiosis resumption (absence of germinal vesicle) and degeneration rates were evaluated among the three groups (control, BCB positive and BCB negative) using Generalized Estimating Equations, followed by Bonferroni's correction for multiple comparisons. RESULTS: Nuclear maturation was higher in BCB positive compared to BCB negative, after 24 and 48 h of IVM (p = .004 and p = .032). The control group was equal to BCB positive. There was no difference among groups analyzing meiosis resumption and degeneration rates. CONCLUSION: The BCB test can be a good marker in pre-selection procedures of developmentally competent human oocytes aspirated during CS.\",\n \"corpus_id\": 23208478,\n \"score\": 2\n },\n {\n \"doc_id\": \"17945442\",\n \"title\": \"Survivin protein expression in bovine follicular oocytes and their in vitro developmental competence.\",\n \"abstract\": \"This study examined the relationship between survivin expression and the stage of development of in vitro cultured bovine oocytes and embryos; and whether survivin expression is affected by the quality of cumulus-oocyte complexes (COCS) or the quality of pre-implantation embryos. A polyclonal antibody was prepared using recombinant bovine survivin protein. Expression of survivin mRNA and protein was analyzed by real-time quantitative RT-PCR and immunocytochemistry. In the first experiment, survivin mRNA expression was examined at developmental stages from germinal vesicle (GV) oocyte to blastocyst, it was significantly decreased after fertilization of matured oocytes (P<0.05), then increased slightly to the 8-cell stage followed by rapid increases at the morula and blastocyst stages (P<0.05). In the second experiment, the effect of oocyte quality on survivin protein, pro-apoptotic (bax, caspase-3) and anti-apoptotic (survivin, bax inhibitor) mRNA expression was examined. Survivin protein was more strongly expressed in good quality COCS than in poor quality COCS. The expression of the anti-apoptotic genes, survivin and bax inhibitor, was significantly higher (P<0.05) and that of the pro-apoptotic genes, bax and caspase-3, was significantly lower (P<0.05) in good compared to poor quality COCS. The developmental competence of good quality COCS (30.4% blastocysts) was significantly better than that of poor quality COCS. In the last experiment also, we confirmed that significantly higher expression of survivin and bax inhibitor genes and significantly lower expression of bax and caspase-3 genes was resulted in good quality blastocysts than in poor quality blastocysts (P<0.05). It was concluded that the expression of survivin was related to the quality of COCS, their developmental competence and the quality of in vitro produced blastocysts. Consequently, survivin may be a good candidate marker for embryo quality.\",\n \"corpus_id\": 33927129,\n \"score\": 1\n },\n {\n \"doc_id\": \"18242678\",\n \"title\": \"Chemical activation of in vitro matured dromedary camel (Camelus dromedarius) oocytes: optimization of protocols.\",\n \"abstract\": \"Experiments were conducted to study the efficiency of sequential treatments of ionomycine and ethanol combined with phosphorylation inhibitor (6-dimethylaminopurine) or the specific maturation promoting factor inhibitor (roscovitine) in inducing artificial activation in dromedary M-II oocytes. Cumulus oocyte complexes (COCs), collected from slaughterhouse ovaries were cultured at 38.5 degrees C in an atmosphere of 5% CO2 in air for 24-48 h. In experiment 1, the COCs were either fertilized in vitro or activated with 5 microM ionomycine for 5 min or 7% ethanol for 7 min, both followed by exposure to 6-diethylaminopurine or roscovitine for 4h. After 14-15 h of in vitro culture, the oocytes were fixed and stained with 1% aceto-orcein to evaluate their nuclear status. In experiment 2, the oocytes were activated in the same manner as in experiment 1 but were cultured for 7 days to evaluate their post-parthenogenetic development. In experiment 3, oocytes were exposed to the ionomycine for 2, 3, 4 or 5 min to evaluate the better exposure time while as in experiment 4, the oocytes matured for 28-48 h were activated to see the effect of aging on post-parthenogenetic development. Higher proportion (P<0.01) of oocytes was activated in ionomycine/6-DMAP and ionomycine/roscovitine groups when compared with ethanol/6-DMAP, ethanol/roscovitine and in vitro fertilized groups. However, there was no difference (P>0.05) in the proportion of oocytes activated with ethanol when compared with in vitro fertilized group. No significant difference was seen on the proportion of morula on day 7 of culture, however the development to blastocyst stage was higher (P<0.01) in ionomycine/6-DMAP and ionomycine/roscovitine when compared with ethanol/6-DMAP and ethanol/roscovitine treated oocytes. A higher proportion of oocytes reached blastocyst stage when they were exposed to ionomycine for 3 min but they were not significantly different from the others (P>0.05). The proportion of blastocysts obtained was higher (P<0.05) in oocytes activated after 28 h of maturation when compared with oocytes activated after 32, 36, 40, 44 and 48 h of maturation. In conclusion, a protocol for chemical activation of dromedary camel oocytes with ionomycine/6-DMAP is demonstrated and optimized in the present study for further use in the development of assisted reproductive techniques in this species.\",\n \"corpus_id\": 45665573,\n \"score\": 1\n },\n {\n \"doc_id\": \"20088850\",\n \"title\": \"In vitro maturation of dromedary (Camelus dromedarius) oocytes: effect of different protein supplementations and epidermal growth factor*.\",\n \"abstract\": \"The present experiment was aimed to compare the effect of different protein supplementation sources, foetal calf serum (FCS), oestrous dromedary serum (EDS) and BSA, in experiment 1, and the effect of different concentrations of epidermal growth factor (EGF), in experiment 2, on in vitro nuclear maturation of the dromedary oocytes. Cumulus oocyte complexes (COCs) were harvested from the ovaries collected from a local slaughterhouse by aspirating the visible follicles in PBS supplemented with 5% FCS. Pooled COCs were randomly distributed to 4-well culture plates containing 500 μl of the maturation medium and cultured at 38.5 °C in an atmosphere of 5% CO(2) in air for 32-36 h. The basic maturation medium consisted of TCM-199 supplemented with 0.1 mg/ml L-glutamine, 0.8 mg/ml sodium bicarbonate, 0.25 mg/ml pyruvate, 50 μg/ml gentamicin, 10 μg/ml bFSH, 10 μg/ml bLH and 1 μg/ml estradiol. In experiment 1, this medium was supplemented with 10% FCS, 10% EDS or 0.4% BSA, whereas in experiment 2, it was supplemented with 0.4% BSA and 0, 10, 20 or 50 ng/ml of EGF. The oocytes were fixed, stained with 1% aceto-orcein stain and their nuclear status was evaluated. Oocytes were classified as germinal vesicle, diakinesis, metaphase-I, anaphase-I (A-I), metaphase-II (M-II) and those with degenerated, fragmented, scattered, activated or without visible chromatin as others. There was no difference (p > 0.05) observed in the proportion of oocytes reaching M-II stage between the media supplemented with FCS (71.5 ± 4.8), EDS (72.8 ± 2.9) and BSA (72.7 ± 6.2). In experiment 2, a higher proportion (p < 0.05) of oocytes reached M-II stage when the medium was supplemented with 20 ng/ml of EGF (81.4 ± 3.2) when compared with the media supplemented with 10 ng/ml (66.9 ± 4.1) and control (67.2 ± 7.1) groups. It may be concluded that the maturation media for dromedary camel oocytes can be supplemented with any of the three protein sources, i.e. FCS, EDS and BSA without any significant differences on the maturation rates. Also, a supplementation of 20 ng/ml of EGF in the maturation medium seems to be optimal and improves the nuclear maturation of dromedary camel oocytes.\",\n \"corpus_id\": 25783678,\n \"score\": 1\n },\n {\n \"doc_id\": \"20451991\",\n \"title\": \"Ultrasonographic-guided retrieval of cumulus oocyte complexes after super-stimulation in dromedary camel (Camelus dromedarius).\",\n \"abstract\": \"In Experiment 1, studies were conducted to apply the transvaginal ultrasound guided ovum pick-up (OPU) technique in dromedary camels after their ovarian super-stimulation and in vivo oocyte maturation. In Experiment 2, the developmental potential of two commonly used oocyte types, i.e., in vivo matured oocytes collected by OPU and abattoir derived in vitro-matured oocytes was compared after their chemical activation. In Experiment 3, developmental competence of oocytes collected from super-stimulated camels by OPU, matured either in vivo or in vitro, was compared after their chemical activation. Mature female dromedary camels super-stimulated with a combination of eCG and pFSH were given an injection of 20 microg of the GnRH analogue, buserelin 24, 26, or 28 h before the scheduled OPU. For collection of cumulus oocyte complexes (COCs) the transducer was guided through the vulva into the cranial most portion of the vagina and 17-gauge, 55 cm single-lumen needle was placed in the needle guide of the ultrasound probe and advanced through the vaginal fornix and into the follicle. Follicular fluid was aspirated using a regulated vacuum pump into tubes containing embryo-flushing media. Aspirates were searched for COCs using a stereomicroscope, and they were then denuded of cumulus cells by hyaluronidase and repeated pipetting. The oocytes were classified as mature (with a visible polar body), immature (with no visible polar body), activated (with divided or fragmented ooplasm) and others (degenerated and abnormal). Overall an average of 12.12 +/- 7.9 COCs were aspirated per animal with an oocyte recovery rate from the aspirated follicles of about 77%. The majority (> 90%) of the collected COCs by OPU were with loose and expanded cumulus cells. The proportion of matured oocytes obtained at 28-29 h (91.2 +/- 4.1) and 26-27 h (82.1 +/- 3.4) were higher (P < 0.005) when compared with those obtained at 24-25 h (40.4 +/- 16.3) after GnRH administration. In Experiment 2, a higher proportion (P < 0.05) of in vivo matured oocytes cleaved (84.6 +/- 2.1 vs. 60.9 +/- 6.6) and developed to blastocyst stages (52.4 +/- 4.1 vs. 30.5 +/- 3.3) when compared with in vitro matured oocytes collected from slaughterhouse ovaries. In Experiment 3, no difference was observed between the developmental competences of oocytes, collected from super stimulated camels, matured in vitro with those collected after their in vivo maturation. In conclusion, about 80-90% mature oocytes can be collected by ultrasound guided transvaginal ovum pick-up from super-stimulated dromedary camels 26-28 h after GnRH administration. The developmental response, to chemical activation, of in vivo matured oocytes collected by ultrasound guided transvaginal OPU is better than in vitro matured oocytes obtained from slaughterhouse ovaries. However, no difference was observed in the developmental competence of oocytes collected by OPU whether they were matured in vivo or in vitro.\",\n \"corpus_id\": 13490405,\n \"score\": 1\n },\n {\n \"doc_id\": \"21791167\",\n \"title\": \"Effect of oocyte-secreted factors on porcine in vitro maturation, cumulus expansion and developmental competence of parthenotes.\",\n \"abstract\": \"The oocyte is known from recent studies in the mouse, cow, sheep and human to be a central regulator of follicular cell function. However, in the pig, little information is known about the regulation of cumulus expansion by oocyte-secreted factors and oocyte quality. We investigated the possible effects of oocyte-secreted factors during in vitro maturation on cumulus expansion and on porcine oocytes as judged by subsequent embryonic development after parthenogenetic activation. Cumulus-oocyte complexes (COC) from antral follicles of pig ovaries collected from a local abattoir were divided into control and treatment groups and were cultured in tissue culture medium 199 supplemented with follicle-stimulating hormone. Treatment groups consisted of increasing numbers of denuded oocytes (DO) co-cultured with COC (at ratios of COC to DO of 1:1, 1:2, 1:3, 1:4 and 1:5). After incubation for 44 h, cumulus expansion and maturation rates were assessed and oocytes were activated parthenogenetically. Cumulus expansion in the 1 COC:4 DO and 1 COC:5 DO groups was low and altered because full dispersion of the outer layer did not occur. Cell viability was not affected, as measured by the automated cell counter, but scanning electron microscopy revealed only a scanty extracellular matrix. Blastocyst rate was significantly higher in the 1 COC:4 DO (34.4%) and in the 1 COC:5 DO (34.9%) groups (p < 0.05) when compared with other groups. Maturation rate, cleavage rate and total cell number showed no significant difference between control and treatment groups. Amplification by reverse transcription polymerase chain reaction (RT-PCR) showed up-regulation of growth differentiation factor 9 (GDF9) in the cumulus cells in the 1 COC:4 DO group at 44 h. We conclude that denuded porcine oocytes could improve the maturation of COC as evidenced by increased blastocyst development in the 1 COC:4 DO, even though cumulus expansion was poor. This improvement could be a result of the GDF9 up-regulation.\",\n \"corpus_id\": 39926219,\n \"score\": 1\n },\n {\n \"doc_id\": \"22898494\",\n \"title\": \"In vivo vs. in vitro models for studying the effects of elevated temperature on the GV-stage oocyte, subsequent developmental competence and gene expression.\",\n \"abstract\": \"The ovarian pool of follicle-enclosed oocytes is highly susceptible to elevated ambient temperature. It is not clear, however, whether the model of using heat shock in vitro simulates the effects of heat stress that animals experience in vivo. The current study examined the reliability of in vitro models, relative to in vivo models, for studying the effects of elevated temperature on the germinal vesicle (GV)-stage oocyte with emphasis on the expression of genes involve in maturation and early embryonic development. Cumulus oocyte complexes (COCs) were aspirated from ovaries arbitrarily collected at the slaughterhouse from multiparous Holstein cows. In the in vivo model, COCs were collected during the hot (May-September) and cold (December-April) seasons and then subjected to in vitro embryo production (IVP) at 38.5°C. In the in vitro model, COCs were collected during the cold season, pre-cultured with 75μM 3-isobutyl-1-methylxanthine (IBMX) for 16h at 38.5 or 41.2°C, and then subjected to IVP. For both models, the relative abundance of C-MOS, GDF9, GAPDH, and POU5F1 transcripts was examined in MII-stage oocytes by real-time PCR. Cleavage and blastocyst developmental rates were higher during the cold vs. hot season. IBMX pre-culture at 38.5°C successfully blocked resumption of meiosis without compromising further embryonic development, and the proportion of cleaved and developed embryos did not differ from the cold season. Exposure of GV-stage oocytes to 41.2°C reduced the proportion of cleaved oocytes developing to blastocysts relative to controls. The most prominent finding was that the relative abundance of the examined genes' transcripts was similarly reduced in heat-stressed oocytes from both models. The in vitro model was reliable and might be relevant for other environmental stressors as well.\",\n \"corpus_id\": 46166227,\n \"score\": 1\n },\n {\n \"doc_id\": \"24374180\",\n \"title\": \"A specific inhibitor of CDK1, RO-3306, reversibly arrests meiosis during in vitro maturation of porcine oocytes.\",\n \"abstract\": \"CDK1 plays pivotal role in meiotic progression of oocytes from G2 to metaphase II (MII) stage. In this study, we investigated the possibility of utilizing a selective inhibitor of CDK1, RO-3306, as a novel agent for the synchronization of oocyte maturation. Two groups of cumulus-oocyte complexes (COCs) were treated with 10 μM RO-3306. The first group was treated for 44 h, whereas the second group was transferred to drug-free medium after a 20 h treatment. MII-stage oocytes from each group were confirmed by cytoplasmic maturation and embryonic development assays. Treatment of immature porcine oocytes with RO-3306 for 20 h arrested them at the germinal vesicle (GV) stage. The GV-arrest effect of RO-3306 was reversible: when RO-3306-arrested COCs were subsequently cultured for 24h in the absence of RO-3306, 76.19 ± 2.68% of these oocytes reached the MII stage after 44 h of in vitro maturation, a rate similar to that of non-treated control oocytes (79.08 ± 3.23%). Furthermore, RO-3306-treated oocytes transferred to drug-free media did not differ significantly from controls (P>0.05) with respect to cleavage and blastocyst formation upon parthenogenetic activation. To explore the underlying molecular mechanisms, we examined the expression patterns of four representative maternal transcripts, CDK1, Cyclin B1, GDF9, and BMP15, by real-time polymerase chain reaction (PCR) and poly(A)-test PCR (PAT assay). RO-3306 treatment increased expression of CDK1 but had no effect on the expression of the other genes. These data suggest that RO-3306 efficiently blocks and synchronizes the meiotic progression of porcine oocytes at the GV stage without affecting their meiotic and cytoplasmic maturation.\",\n \"corpus_id\": 24407130,\n \"score\": 1\n },\n {\n \"doc_id\": \"24630529\",\n \"title\": \"Caffeine supplementation during IVM improves frequencies of nuclear maturation and preimplantation development of dromedary camel oocytes following IVF.\",\n \"abstract\": \"Caffeine supplementation during oocyte IVM has been reported to improve preimplantation embryo development and the quality of in vitro-produced blastocysts in a range of species; but no studies have been done in camels. The present study investigated the effect of caffeine supplementation during dromedary camel oocyte IVM on nuclear maturation rates, IVF events, and subsequent preimplantation development. Cumulus-oocyte complexes obtained at slaughter were matured in vitro in caffeine supplemented medium either for 30 hours (caffeine 30 hours) or in the medium without caffeine supplement for 24 hours and then transferred to freshly prepared IVM medium supplemented with 10 mM caffeine for another 6 hours (caffeine 6 hours). Cumulus-oocyte complexes matured for 30 hours in the medium without caffeine supplement were used as a control. Matured oocytes were fertilized in vitro by epididymal spermatozoa of mature male camels collected from a local slaughterhouse. Eighteen hours after insemination, presumptive zygotes were cultured in modified KSOMaa medium for 7 days. Maturation and fertilization rates were significantly higher in the caffeine 6-hour group compared with the control group (P < 0.05), whereas IVM of oocytes in caffeine-supplemented medium for 30 hours did not affect these parameters (P > 0.05). Interestingly, IVM of oocytes in caffeine supplemented medium for 6 hours significantly (P < 0.05) increased the frequencies of blastocyst development by more than two-fold when compared with control (27.78% vs. 11.76%). In conclusion, culturing dromedary camel oocytes in maturation medium without caffeine for 24 hours and then in the medium supplemented with 10 mM caffeine for 6 hours during 30-hour IVM can significantly improve frequencies of nuclear maturation, fertilization rate, and subsequent preimplantation development.\",\n \"corpus_id\": 20201120,\n \"score\": 1\n },\n {\n \"doc_id\": \"24912867\",\n \"title\": \"Insulin influences developmental competence of bovine oocytes cultured in α-MEM plus follicle-simulating hormone.\",\n \"abstract\": \"The aim of this study was to evaluate the dose-response effect of insulin, plus follicle-simulating hormone (FSH) at a fixed concentration, in a serum-free defined culture medium (DCM) on the in vitro maturation of bovine cumulus-oocyte complexes (COCs). For oocyte nuclear maturation, the expression levels of GDF9, GLUT1, PRDX1 and HSP70.1 transcripts related to oocyte and embryo developmental competence were analysed. For in vitro maturation (IVM), cumulus-oocyte complexes from slaughterhouse ovaries were distributed into four groups based on insulin concentration added to serum-free DCM, which was composed of alpha minimum essential medium (α-MEM), as basal medium: (1) DCM control: 0 ng/ml; (2) DCM1: 1 ng/ml; (3) DCM10: 10 ng/ml; and (4) DCM100: 100 ng/ml. After IVM, the nuclear status of a sample of oocytes was analysed and the other oocytes were submitted for in vitro fertilization (IVF) and in vitro culture (IVC). Different concentrations of insulin did not affect significantly the nuclear maturation and cleavage rate (72 h post-insemination) across all groups. Blastocyst rate (192 h post-insemination) did not differ in DCM control (24.3%), DCM1 (27.0%) and DCM10 (26.3%) groups, but the DCM100 (36.1%) group showed a greater blastocyst rate (P 0.05) was observed at the different insulin concentrations. The results indicated that insulin added to DCM influenced levels of transcripts related to cellular stress (HSP70-1 and PRDX1) and oocyte competence (GDF9) in bovine oocytes and at higher concentrations enhanced blastocyst production.\",\n \"corpus_id\": 44394899,\n \"score\": 1\n },\n {\n \"doc_id\": \"25156970\",\n \"title\": \"Seasonal variations in developmental competence and relative abundance of gene transcripts in buffalo (Bubalus bubalis) oocytes.\",\n \"abstract\": \"Hot season is a major constraint to production and reproduction in buffaloes. The present work aimed to investigate the effect of season on ovarian function, developmental competence, and the relative abundance of gene expression in buffalo oocytes. Three experiments were conducted. In experiment 1, pairs of buffalo ovaries were collected during cold season (CS, autumn and winter) and hot season (HS, spring and summer), and the number of antral follicles was recorded. Cumulus oocyte complexes (COCs) were aspirated and evaluated according to their morphology into four Grades. In experiment 2, Grade A and B COCs collected during CS and HS were in vitro matured (IVM) for 24 hours under standard conditions at 38.5 °C in a humidified air of 5% CO2. After IVM, cumulus cells were removed and oocytes were fixed, stained with 1% aceto-orcein, and evaluated for nuclear configuration. In vitro matured buffalo oocytes harvested during CS or HS were in vitro fertilized (IVF) using frozen-thawed buffalo semen and cultured in vitro to the blastocyst stage. In experiment 3, buffalo COCs and in vitro matured oocytes were collected during CS and HS, and then snap frozen in liquid nitrogen for gene expression analysis. Total RNA was extracted from COCs and in vitro matured oocytes, and complementary DNA was synthesized; quantitative Reverse Transcription-Polymerase Chain Reaction was performed for eight candidate genes including GAPDH, ACTB, B2M, GDF9, BMP15, HSP70, and SOD2. The results indicated that HS significantly (P < 0.01) decreased the number of antral follicles and the number of COCs recovered per ovary. The number of Grade A, B, and C COCs was lower (P < 0.05) during HS than CS. In vitro maturation of buffalo oocytes during HS significantly (P < 0.01) reduced the number of oocytes reaching the metaphase II stage and increased the percentage of degenerated oocytes compared with CS. Oocytes collected during HS also showed signs of cytoplasmic degeneration. After IVF, cleavage rate was lower (P < 0.01) for oocytes collected during HS, and the percentage of oocytes arrested at the two-cell stage was higher (P < 0.01) than oocytes IVF during CS. Oocytes matured during CS showed a higher (P < 0.01) blastocyst rate than those matured during HS. Also, COCs recovered in HS showed significant (P < 0.05) upregulation of HSP70 mRNA expression compared with those recovered in CS. For in vitro matured oocytes, CS down regulated the transcript abundance of ACTB and upregulated GAPDH and HSP70 mRNA levels compared with HS condition. In conclusion, HS could impair buffalo fertility by reducing the number of antral follicles and oocyte quality. In vitro maturation of buffalo oocytes during HS impairs their nuclear and cytoplasmic maturation, fertilization, and subsequent embryo development to the morula and blastocyst stages. This could be in part because of the altered gene expression found in COCs and in vitro matured oocytes.\",\n \"corpus_id\": 205366782,\n \"score\": 1\n },\n {\n \"doc_id\": \"26165355\",\n \"title\": \"Developmental competence of different quality bovine oocytes retrieved through ovum pick-up following in vitro maturation and fertilization.\",\n \"abstract\": \"In the present study, oocytes retrieved from cross bred Karan Fries cows by ovum pick-up technique were graded into Group 1 and Group 2, based on the morphological appearance of the individual cumulus-oocyte complexes (COCs). To analyze whether the developmental potential of the COCs bears a relation to morphological appearance, relative expression of a panel of genes associated with; (a) cumulus-oocyte interaction (Cx43, Cx37, GDF9 and BMP15), (b) fertilization (ZP2 and ZP3), (c) embryonic development (HSF1, ZAR1 and bFGF) and (d) apoptosis and survival (BAX, BID and BCL-XL, MCL-1, respectively) was studied at two stages: germinal vesicle (GV) stage and after in vitro maturation. The competence was further corroborated by evaluating the embryonic progression of the presumed zygotes obtained from fertilization of the graded COCs. The gene expression profile and development rate in pooled A and B grade (Group 1) COCs and pooled C and D grade (Group 2) COCs were determined and compared according to the original grades. The results of the study demonstrated that the morphologically characterized Group 2 COCs showed significantly (P<0.05) lower expression for most of the genes related to cumulus-oocyte interplay, fertilization and embryonic development, both at GV stage as well as after maturation. Group 1 COCs also showed greater expression of anti-apoptotic genes (BCL-XL and MCL1) both at GV stage and after maturation, while pro-apoptotic genes (BAX and BID) showed significantly (P<0.05) elevated expression in poor quality COCs at both the stages. The cleavage rate in Group 1 COCs was significantly higher than that of Group 2 (74.46±7.06 v. 31.57±5.32%). The development of the presumed zygotes in Group 2 oocytes proceeded up to 8- to 16-cell stages only, while in Group 1 it progressed up to morulae (35.38±7.11%) and blastocyst stages (9.70±3.15%), indicating their better developmental potential.\",\n \"corpus_id\": 31115337,\n \"score\": 1\n },\n {\n \"doc_id\": \"26952753\",\n \"title\": \"The presence of corpus luteum may have a negative impact on in vitro developmental competency of bovine oocytes.\",\n \"abstract\": \"The aim of the current study was to investigate the effects of the presence or absence of corpus luteum (CL) on in vitro developmental competence of bovine oocytes. In experiment 1, cumulus oocyte complexes (COCs) were collected from slaughterhouse ovaries and divided according to the presence (CL(+) oocytes) or absence (CL(-) oocytes) of a CL in the ovary. Control oocytes (C group) were obtained from ovaries which were not selected toward the presence or absence of CL. All oocytes were submitted to in vitro maturation, fertilization and culture. In experiment 2, the oocytes from the CL(+) and CL(-) ovaries were divided into grown (BCB(+)) and growing (BCB(-)) categories by means of the brilliant cresyl blue (BCB) test. The oocytes from all groups (CL(+)/BCB(+), CL(-)/BCB(+), CL(+)/BCB(-), CL(-)/BCB(-) and control oocytes) were subjected to in vitro embryo production. In experiment 1, the cleavage and blastocyst rates of CL(-) oocytes were higher than those of CL(+) oocytes (83.9% and 43% vs. 69.3% and 22.5%, respectively). In experiment 2, there was less BCB(+) oocytes (more competent oocytes) in the group of CL(+) oocytes than in the group of CL(-) oocytes. Furthermore, developmental competence of all CL(+) oocytes (CL(+)/BCB(+) and CL(+)/BCB(-)) was lower than that of all CL(-) oocytes (CL(-)/BCB(+) and CL(-)/BCB(-)). Thus, the presence of a corpus luteum in the ovary may have negative effects on developmental competence of ipsilateral oocytes.\",\n \"corpus_id\": 28967383,\n \"score\": 1\n },\n {\n \"doc_id\": \"27448692\",\n \"title\": \"GREM1, EGFR, and HAS2; the oocyte competence markers for improved buffalo embryo production in vitro.\",\n \"abstract\": \"Selection of competent oocytes is crucial for successful in vitro embryo production and correlating expression profile of oocyte competence markers in cumulus cells with oocyte quality is an important preamble. In the present study, expression profile of oocyte competence markers (GREM1, EGFR, HAS2, and TNFAIP6) was correlated through brilliant cresyl blue (BCB) staining and subsequently with in vitro embryo production. Excellent to good quality buffalo, cumulus oocyte complexes (COCs) were stained with BCB (26 μM) and based on the blue coloration of cytoplasm COCs were divided in two groups as BCB(+ve) and BCB(-ve). Mean percentage of BCB(+ve) oocytes was significantly higher (P < 0.05) than BCB(-ve) oocytes (56.79 ± 1.22 vs. 43.20 ± 1.22), the mean oocyte diameter was also significantly larger (P < 0.05) for the BCB(+ve) group than that of BCB(-ve) group (145.7 ± 1.8 μm vs. 132.7 ± 1.9 μm). The cleavage rate (%), blastocyst rate (%), and total cell number was significantly (P < 0.05) higher in BCB(+ve) than BCB(-ve) group (71.15 ± 2.17 vs. 52.89 ± 2.65; 31.58 ± 1.11 vs. 7.73 ± 0.97, and 93.14 ± 2.42 vs. 71.42 ± 2.09, respectively). Relative mRNA expression of marker genes in cumulus cells increased significantly (P < 0.05) after maturation viz. GREM1 (10.13 folds), EGFR (9.04 folds), HAS2 (27.91 folds), and TNFAIP6 (64.81 folds). Brilliant cresyl blue positive oocytes showed significantly higher (P < 0.05) expression of GREM1, EGFR, and HAS2 transcripts than BCB(-ve) oocytes, however, no significant change in the expression of TNFAIP6 gene was observed. It is concluded from the study that GREM1, EGFR, and HAS2 could be used as molecular markers of oocyte competence for an improved buffalo embryo production in vitro.\",\n \"corpus_id\": 34730161,\n \"score\": 1\n },\n {\n \"doc_id\": \"28224009\",\n \"title\": \"Developmental competence of Dromedary camel oocytes fertilized in vitro by frozen-thawed ejaculated and epididymal spermatozoa.\",\n \"abstract\": \"The present study aimed to compare the in vitro fertilizing capacity of frozen-thawed ejaculated and epididymal spermatozoa in order to standardize the semen preparation protocol for camel in vitro fertilization (IVF). Semen samples were collected from 7 Dromedary camels by means of artificial vagina (AV). Ten cauda epididymes were obtained from slaughtered adult camels, isolated, incised and rinsed for obtaining the sperm rich fluid. Ejaculated and epididymal spermatozoa were processed for cryopreservation. Fresh and frozen-thawed ejaculated and epididymal spermatozoa were evaluated for motility, livability, membrane and acrosomal integrities. Frozen-thawed ejaculated and epididymal spermatozoa were used to fertilize camel mature oocytes in vitro. The results showed that, the progressive motility of freshly collected epididymal spermatozoa was significantly (P<0.05) higher than ejaculated spermatozoa (49.25 ± 1.75 vs. 38.50 ± 1.50%, respectively). The viability index of epididymal spermatozoa was significantly (P<0.05) higher than that of ejaculated spermatozoa (96.63 ± 2.45 vs. 84.00 ± 4.08, respectively). The post-thaw acrosome and membrane integrities of epididymal spermatozoa were significantly (P<0.05) higher than those of ejaculated spermatozoa. Morula and blastocyst rates of camel oocytes in vitro fertilized by frozen-thawed epididymal spermatozoa (59.4 ± 0.8, 19.12 ± 0.7 and 10.29 ± 0.7%, respectively) were significantly (P<0.05) higher than those fertilized by frozen-thawed ejaculated spermatozoa (48.27 ± 3.1, 11.63 ± 1.1 and 5.43 ± 0.8%, respectively). In conclusion, the Dromedary camel frozen epididymal spermatozoa have the capacity to endure cryopreservation, fertilize oocytes and produce embryos in vitro better than ejaculated sperm.\",\n \"corpus_id\": 18355187,\n \"score\": 1\n },\n {\n \"doc_id\": \"28525345\",\n \"title\": \"In vitro production of Sudanese camel (Camelus dromedarius) embryos from epididymal spermatozoa and follicular oocytes of slaughtered animals.\",\n \"abstract\": \"Application of assisted reproductive technology in camelidea, such as artificial insemination (AI) and embryo transfer, has been slow in comparison to that for other livestock species. In Egypt, there are few attempts to establish in vitro maturation (IVM) and fertilization (IVF) techniques in dromedary camel. The present study was carried out to produce Sudanese camel embryos using in vitro matured oocytes and epididymal spermatozoa. Dromedary camel ovaries were collected from abattoirs and then, the oocytes were aspirated from all the visible follicles on the ovarian surface (~2-8 mm in a diameter). Meanwhile, Fetal Dromedary Camel Serum (FDCS) was obtained from camel fetuses after slaughtering. Thereafter, only Cumulus Oocyte Complexes (COCs) were matured in vitro in the Tissue Culture Medium (TCM-199) complemented with 10% FDCS. Spermatozoa required for in vitro fertilization were collected from testes (epididymal cauda) of the slaughtered camel bulls. The results clearly showed that the maturation rate of oocytes at metaphase II was about 59.5% while the fertilization rate was around 70.4%. Intriguingly, the embryo rates determined were 13.1%, in 2-cell; 0.0%, in 4-cell; 34.7%, in 8-16% cell; 39.1%, in morula and 13.1% in a blastocyst stage. This study represented a successful in vitro production of Sudanese dromedary camel embryos from epididymal sperm cells and in vitro matured oocytes recovered from slaughtered camels.\",\n \"corpus_id\": 19485600,\n \"score\": 1\n },\n {\n \"doc_id\": \"28586460\",\n \"title\": \"A pre-in vitro maturation medium containing cumulus oocyte complex ligand-receptor signaling molecules maintains meiotic arrest, supports the cumulus oocyte complex and improves oocyte developmental competence.\",\n \"abstract\": \"STUDY QUESTION: Can a pre in-vitro maturation medium containing signaling molecules rather than chemical/pharmaceutical agents, sustain meiotic arrest and improve developmental competence of in-vitro matured oocytes in CF1 outbred mice?\",\n \"corpus_id\": 205213715,\n \"score\": 1\n },\n {\n \"doc_id\": \"28601148\",\n \"title\": \"Leptin supplementation in vitro improved developmental competence of buffalo oocytes and embryos.\",\n \"abstract\": \"The aim of the present study was to determine potential role of leptin on in vitro developmental competence of buffalo oocytes and embryos. Slaughterhouse derived culture grade buffalo cumulus oocyte complexes (COCs) were matured in vitro (IVM) with leptin (10 ng/ml) or without leptin (control). In each experiment, a pool of matured COCs was used for further in vitro embryo production and another pool of COCs was used for cumulus cells and mature oocytes isolation to study the relative mRNA expression of developmentally important genes. Presumptive zygotes were cultured in embryo culture (IVC) media supplemented with leptin (10 ng/ml) or without leptin (control). Cleavage rate was higher (p < 0.05) when leptin was supplemented during IVM + IVC, both, as compared to other groups. Higher cleavage rate was observed in leptin-treated groups, though it was non-significant. Blastocyst rate was higher (p < 0.05) in all the leptin treated groups. The relative mRNA expression of LEPR (Ob-Rb), HAS2 and EGFR was significantly (p < 0.05) up-regulated and the expression of CASPASE3 was down-regulated in cumulus cells of leptin-treated groups. The expression of GDF9, BMP15, GLUT1, LEPR and CASPASE3 transcripts in leptin and non-treated oocytes did not differ. The relative mRNA expression of POU5F1and LEPR transcripts in blastocysts was higher (p < 0.05) in leptin-treated groups; the change in expression of GLUT1, INF-τ and CASPASE3 transcripts was not significant (p > 0.05). Thus, it is concluded that leptin promotes developmental competence of bubaline oocytes by modulating cumulus enabling factors and genes regulating pluripotentcy in the blastocysts.\",\n \"corpus_id\": 4421939,\n \"score\": 1\n },\n {\n \"doc_id\": \"28802113\",\n \"title\": \"L-carnitine enhances oocyte maturation and improves in vitro development of embryos in dromedary camels (Camelus dromedaries).\",\n \"abstract\": \"The aim of the present study was to investigate the effect of L-carnitine (LC) addition during either IVM or IVC on the developmental potential of camel oocytes. In Experiment 1; camel oocytes were matured in the absence (control) or presence of different concentrations of LC (0.25 mg, 0.5 mg, 0.75 mg and 1 mg/ml) for 30 h followed by in vitro fertilization and culture up to blastocyst stage. Our results demonstrated that oocytes treated with 0.5 mg/ml LC showed higher (P < 0.05) rates of maturation (74.7%) and fertilization (62.2%) compared with control group, 0.25 and 1 mg/ml of LC (60.2, 63.9, 59.7; 46.2, 48.7, 47.6%, respectively). Addition of 0.5 mg/ml of LC to IVM medium improved the rates of cleavage and embryo development (morula and blastocyst) than those obtained in the control group, 0.25 and 1 mg/ml of LC. No significant differences were noticed between 0.5 and 0.75 mg/ml of LC supplemented groups in term of maturation, fertilization and culture. In Experiment 2; zygotes resulting from in vitro matured (without LC) and fertilized were cultured in embryo culture medium supplemented with different concentrations of LC (0.25 mg, 0.5 mg, 0.75 mg and 1 mg/ml) or without LC (control). Also, the results showed a higher developmental rates to morula and blastocyst stages while adding L-carnitine at a level of 0.5 or 0.75 mg/ml concentration in the culture medium during IVC when compared with other groups. In conclusion, the results demonstrated the usefulness of L-carnitine supplementation at the level of 0.5 mg/ml during IVM or IVC after on the developmental potential of camel oocytes.\",\n \"corpus_id\": 46530001,\n \"score\": 1\n },\n {\n \"doc_id\": \"18405437\",\n \"title\": \"Bovine oocytes and early embryos express Staufen and ELAVL RNA-binding proteins.\",\n \"abstract\": \"RNA-binding proteins (RBP) influence RNA editing, localization, stability and translation and may contribute to oocyte developmental competence by regulating the stability and turnover of oogenetic mRNAs. The expression of Staufen 1 and 2 and ELAVL1, ELAVL2 RNA-binding proteins during cow early development was characterized. Cumulus-oocyte complexes were collected from slaughterhouse ovaries, matured, inseminated and subjected to embryo culture in vitro. Oocyte or preimplantation embryo pools were processed for RT-PCR and whole-mount immunofluorescence analysis of mRNA expression and protein distribution. STAU1 and STAU2 and ELAVL1 mRNAs and proteins were detected throughout cow preimplantation development from the germinal vesicle (GV) oocyte to the blastocyst stage. ELAVL2 mRNAs were detectable from the GV to the morula stage, whereas ELAVL2 protein was in all stages examined and localized to both cytoplasm and nuclei. The findings provide a foundation for investigating the role of RBPs during mammalian oocyte maturation and early embryogenesis.\",\n \"corpus_id\": 34996021,\n \"score\": 0\n },\n {\n \"doc_id\": \"24548378\",\n \"title\": \"Confocal fluorescence assessment of bioenergy/redox status of dromedary camel (Camelus dromedarius) oocytes before and after in vitro maturation.\",\n \"abstract\": \"BACKGROUND: Reproductive biotechnologies in dromedary camel (Camelus dromedarius) are less developed than in other livestock species. The in vitro maturation (IVM) technology is a fundamental step for in vitro embryo production (IVP), and its optimization could represent a way to increase the success rate of IVP. The aim of the present study was to investigate the bioenergy/oxidative status of dromedary camel oocytes before and after IVM by confocal microscopy 3D imaging. METHODS: Oocytes were retrieved by slicing ovaries collected at local slaughterhouses. Recovered oocytes were examined before and after IVM culture for nuclear chromatin configuration and bioenergy/oxidative status, expressed as mitochondria (mt) distribution and activity, intracellular Reactive Oxygen Species (ROS) levels and distribution and mt/ROS colocalization. RESULTS: The mean recovery rate was 6 oocytes/ovary. After IVM, 61% of oocytes resumed meiosis and 36% reached the Metaphase II stage (MII). Oocyte bioenergy/redox confocal characterization revealed changes upon meiosis progression. Immature oocytes at the germinal vesicle (GV) stage were characterised by prevailing homogeneous mt distribution in small aggregates while MI and MII oocytes showed significantly higher rates of pericortical mt distribution organized in tubular networks (P<0.05). Increased mt activity in MI (P<0.001) and MII (P<0.01) oocytes compared to GV stage oocytes was also observed. At any meiotic stage, homogeneous distribution of intracellular ROS was observed. Intracellular ROS levels also increased in MI (P<0.01) and MII (P<0.05) oocytes compared to GV stage oocytes. The mt/ROS colocalization signal increased in MI oocytes (P<0.05). CONCLUSIONS: This study provides indications that qualitative and quantitative indicators of bioenergy and oxidative status in dromedary camel oocytes are modified in relation with oocyte meiotic stage. These data may increase the knowledge of camel oocyte physiology, in order to enhance the efficiency of IVP procedures.\",\n \"corpus_id\": 7232816,\n \"score\": 0\n },\n {\n \"doc_id\": \"26603656\",\n \"title\": \"Optimization of a vitrification protocol for hatched blastocysts from the dromedary camel (Camelus dromedarius).\",\n \"abstract\": \"The objective of this study was to modify and optimize a vitrification protocol (open pulled straw) that was originally designed for human oocytes and embryos, to make it suitable for the cryopreservation of camel hatched blastocysts. The original open pulled straw protocol was a complex process with 15-minute exposure of oocytes/embryos in 7.5% ethylene glycol (EG) and 7.5% dimethyl sulfoxide (Me2SO) for equilibration, and cooling in 16% EG + 16% Me2SO + 1 M sucrose. Recognizing a need to better control the cryoprotectant (CPA) concentrations, while avoiding toxicity to the embryos, the effects on the survival rate and developmental potential of camel embryos in vitro were investigated using two different methods of loading the CPAs into the embryos (stepwise and semicontinuous increase in concentration), two different loading temperature/time (room temperature ∼24 °C/15 min and body 37 °C/3 min), and the replacement of Me2SO with EG alone or in combination with glycerol (Gly). A total of 145 in vivo-derived embryos were subjected to these processes, and after warming their morphological quality and integrity, and re-expansion was assessed after 0, 2, 24, 48, 72, and 96 hours of culture. Exposure of embryos in a stepwise method was more beneficial to the survival of embryos than was the semicontinuous process, and loading of CPAs at 37 °C with a short exposure time (3 minutes) resulted in an outcome comparable to the original processing at room temperature with a longer exposure time (15 minutes). The replacement of the Me2SO + EG mixture with EG only or a combination of EG + Gly in the vitrification medium significantly improved the outcome of all these evaluation criteria (P < 0.05). The modified protocol of loading EG at 37 °C for 3 minutes has increased the embryo survival of the original protocol from 67% to 91% and the developmental rate from 57% to 83% at 5-day culture. These results were comparable to or better than those reported in human or other species, indicating that this optimized method is well suited to any commercial embryo transfer program in the dromedary camel.\",\n \"corpus_id\": 36988289,\n \"score\": 0\n },\n {\n \"doc_id\": \"29492475\",\n \"title\": \"Supplementation of L-carnitine during in vitro maturation of mouse oocytes affects expression of genes involved in oocyte and embryo competence: An experimental study.\",\n \"abstract\": \"Background: Oocyte developmental competence is one of the key factors for determining the success rate of assisted reproductive technique. Objective: The aim of the current study was to investigate the effect of L-carnitine (LC) supplementation during in vitro maturation (IVM), on preimplantation embryo development and expression of genes involved in embryo competence derived from oocytes selected with brilliant cresyl blue (BCB) test. Materials and Methods: Cumulus-oocyte complexes (COCs) were obtained from NMRI mice ovaries. COCs were stained with BCB and then BCB+ (colored cytoplasm) oocytes cultured in IVM medium supplemented with 0.3 or 0.6 mg/ml LC. COCs untreated with LC were used as control. Fertilization rate and blastocyst development rate were determined after in vitro fertilization. In addition, quantitative reverse transcriptase polymerase chain reaction was used to measure relative genes expression related with development (Ccnb1, Mos, Ces5, and Dppa2) and apoptosis (Bax and Bcl-xL) in oocytes and embryos. Results: Oocytes treated with both LC concentrations showed higher blastocyst development rate compared with untreated oocytes (p<0.01). Moreover, fertilization rate was increased in oocytes treated with 0.6 mg/ml LC (p<0.01). Treatment of oocytes with both LC concentrations increased (p<0.01) the level of Ccnb1 mRNA in MII oocytes. The two-cell stage embryos and blastocysts derived from LC-treated oocytes (0.6 mg/ml) showed increased the expression levels of Dppa2 and Bcl-xl mRNA, respectively (p<0.01). Conclusion: The results of the present study show that adding of LC to the IVM medium of BCB+ oocytes can ameliorate reproductive success following in vitro fertilization.\",\n \"corpus_id\": 3547373,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":73,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29264603\",\n \"title\": \"Contiguous hydrophobic and charged surface patches in short helix-constrained peptides drive cell permeability.\",\n \"abstract\": \"Most protein-protein interactions occur inside cells. Peptides can inhibit protein-protein interactions but tend not to enter cells. We systematically compare cell permeability for 8-12 residue model peptides with helix-inducing lactam/hydrocarbon linkers between amino acid sidechains. Cell uptake increases when hydrophobic residues and lactam linkers (i, i + 4) form a contiguous hydrophobic surface patch. Uptake increases further when both hydrophobic and positively charged (but not neutral or negative) residues are clustered into like surface patches. Amphipathicity alone is however insufficient for cell uptake of acyclic sequences. Changing the linker from lactam to hydrocarbon further increases uptake, but also promotes cell lysis. Helicity, positive charge and amphipathicity together promote cell permeability. Most known bioactive helical peptides do not optimally cluster residues for amphipathicity and so are likely unoptimised for cell uptake.\",\n \"corpus_id\": 30349725\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18098173","title":"Effects of net charge and the number of positively charged residues on the biological activity of amphipathic alpha-helical cationic antimicrobial peptides.","abstract":"In our previous study, we utilized a 26-residue amphipathic alpha-helical antimicrobial peptide L-V13K (Chen et al., Antimicrob Agents Chemother 2007, 51, 1398-1406) as the framework to study the effects of peptide hydrophobicity on the mechanism of its antimicrobial action. In this study, we explored the effects of net charge and the number of positively charged residues on the hydrophilic/polar face of L-V13K on its biological activity (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity, helicity, and peptide self-association). The net charge of V13K analogs at pH 7 varied between -5 and +10 and the number of positively charged residues varied from 1 to 10. The minimal inhibitory concentrations (MIC) against six strains of Pseudomonas aeruginosa as well as other gram-negative and gram-positive bacteria were determined along with the maximal peptide concentration that produces no hemolysis of human red blood cells (MHC). Our results show that the number of positively charged residues on the polar face and net charge are both important for both antimicrobial activity and hemolytic activity. The most dramatic observation is the sharp transition of hemolytic activity on increasing one positive charge on the polar face of V13K i.e., the change from +8 to +9 resulted in greater than 32-fold increase in hemolytic activity (250 microg/ml to <7.8 microg/ml, respectively).","corpus_id":11073670,"score":2},{"doc_id":"18186474","title":"On defining the dynamics of hydrophobic patches on protein surfaces.","abstract":"We present a simple and efficient method called PATCHTRACK, for studying the dynamics of hydrophobic surface patches. It tracks the patches on snapshot structures taken from a Molecular Dynamics simulation. They are connected into so-called patch runs, which are subsequently clustered into so-called recurrent patches. The method is applied to simulations of three different proteins. Protein motion causes addition and removal of one or more atoms to a patch, resulting in size fluctuations of around 25%. The fluctuations eventually lead to the break-up of a patch, and their average life span is therefore remarkably short at around 4 ps. However, some patch runs are much more stable, lasting hundreds of picoseconds. One such case is the largest patch in amicyanin that is known to be biologically relevant. Another case, previously not reported, is found in phospholipase A(2), where the functional significance of a large recurrent patch formed by Leu58 and Phe94 seems likely. This patch appears to have been overlooked as it is relatively small in the X-ray structure, demonstrating the utility of the current method. The most frequently occurring patch size is 40-60 A(2), but sizes of up to 500 A(2) are also observed. There is no clear relation between patch run durations and their average size. However, long-lasting patch runs tend not to have large fluctuations. The recurrent patches have alternating periods of \"liveness\" and \"dormancy\"; around 25% of them is predominantly in the live state.","corpus_id":25759192,"score":2},{"doc_id":"18434320","title":"Origin of low mammalian cell toxicity in a class of highly active antimicrobial amphipathic helical peptides.","abstract":"We recently described a novel antimicrobial peptide, RTA3, derived from the commensal organism Streptococcus mitis, with strong anti-Gram-negative activity, low salt sensitivity, and minimal mammalian cell toxicity in vitro and in vivo. This peptide conforms to the positively charged, amphipathic helical peptide motif, but has a positively charged amino acid (Arg-5) on the nonpolar face of the helical structure that is induced upon membrane binding. We surmised that disruption of the hydrophobic face with a positively charged residue plays a role in minimizing eukaryotic cell toxicity, and we tested this using a mutant with an R5L substitution. The greatly enhanced toxicity in the mutant peptide correlated with its ability to bind and adopt helical conformations upon interacting with neutral membranes; the wild type peptide RTA3 did not bind to neutral membranes (binding constant reduced by at least 1000-fold). Spectroscopic analysis indicates that disruption of the hydrophobic face of the parent peptide is accommodated in negatively charged membranes without partial peptide unfolding. These observations apply generally to amphipathic helical peptides of this class as we obtained similar results with a peptide and mutant pair (Chen, Y., Mant, C. T., Farmer, S. W., Hancock, R. E., Vasil, M. L., and Hodges, R. S. (2005) J. Biol. Chem. 280, 12316-12329) having similar structural properties. In contrast to previous interpretations, we demonstrate that these peptides simply do not bind well to membranes (like those of eukaryotes) with exclusively neutral lipids in their external bilayer leaflet. We highlight a significant role for tryptophan in promoting binding of amphipathic helical peptides to neutral bilayers, augmenting the arsenal of strategies to reduce mammalian toxicity in antimicrobial peptides.","corpus_id":22700884,"score":2},{"doc_id":"18658220","title":"Structure and dynamics of helix-0 of the N-BAR domain in lipid micelles and bilayers.","abstract":"Bin/Amphiphysin/Rvs-homology (BAR) domains generate and sense membrane curvature by binding the negatively charged membrane to their positively charged concave surfaces. N-BAR domains contain an N-terminal extension (helix-0) predicted to form an amphipathic helix upon membrane binding. We determined the NMR structure and nano-to-picosecond dynamics of helix-0 of the human Bin1/Amphiphysin II BAR domain in sodium dodecyl sulfate and dodecylphosphocholine micelles. Molecular dynamics simulations of this 34-amino acid peptide revealed electrostatic and hydrophobic interactions with the detergent molecules that induce helical structure formation from residues 8-10 toward the C-terminus. The orientation in the micelles was experimentally confirmed by backbone amide proton exchange. The simulation and the experiment indicated that the N-terminal region is disordered, and the peptide curves to adopted the micelle shape. Deletion of helix-0 reduced tubulation of liposomes by the BAR domain, whereas the helix-0 peptide itself was fusogenic. These findings support models for membrane curving by BAR domains in which helix-0 increases the binding affinity to the membrane and enhances curvature generation.","corpus_id":42380634,"score":2},{"doc_id":"19045429","title":"Model simulations of the adsorption of statherin to solid surfaces: Effects of surface charge and hydrophobicity.","abstract":"The structural properties of the salivary protein statherin upon adsorption have been examined using a coarse-grained model and Monte Carlo simulation. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. To mimic hydrophobically modified surfaces, an extra short-ranged interaction was implemented between the amino acids and the surface. It has been shown that the adsorption and the thickness of the adsorbed layer are determined by (i) the affinity for the surface, i.e., denser layer with an extrashort-ranged potential, and (ii) the distribution of the charges along the chain. If all the amino acids have a high affinity for the surface, the protein adsorbs in a train conformation, if the surface is negatively charged the protein adsorbs in a tail-train conformation, whereas if the surface is positively charged the protein adsorbs in a loop conformation. The latter gives rise to a more confined adsorbed layer.","corpus_id":1697069,"score":2},{"doc_id":"19550040","title":"Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes.","abstract":"We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from -1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide-membrane interactions.","corpus_id":20559171,"score":2},{"doc_id":"19885920","title":"Importance of the spatial display of charged residues in heparin-peptide interactions.","abstract":"Many studies have examined consensus sequences required for protein-glycosaminoglycan interactions. Through the synthesis of helical heparin binding peptides, this study probes the relationship between spatial arrangement of positive charge and heparin binding affinity. Peptides with a linear distribution of positive charge along one face of the alpha-helix had the highest affinity for heparin. Moving the basic residues away from a single face resulted in drastic changes in heparin binding affinity of up to three orders of magnitude. These findings demonstrate that amino acid sequences, different from the known heparin binding consensus sequences, will form high affinity protein-heparin binding interactions when the charged residues are aligned linearly.","corpus_id":5149095,"score":2},{"doc_id":"20158215","title":"Bridged beta(3)-peptide inhibitors of p53-hDM2 complexation: correlation between affinity and cell permeability.","abstract":"Beta-peptides possess several features that are desirable in peptidomimetics; they are easily synthesized, fold into stable secondary structures in physiologic buffers, and resist proteolysis. They can also bind to a diverse array of proteins to inhibit their interactions with alpha-helical ligands. beta-peptides are usually not cell-permeable, however, and this feature limits their utility as research tools and potential therapeutics. Appending an Arg(8) sequence to a beta-peptide improves uptake but adds considerable mass. We previously reported that embedding a small cationic patch within a PPII, alpha-, or beta-peptide helix improves uptake without the addition of significant mass. In another mass-neutral strategy, Verdine, Walensky, and others have reported that insertion of a hydrocarbon bridge between the i and i + 4 positions of an alpha-helix also increases cell uptake. Here we describe a series of beta-peptides containing diether and hydrocarbon bridges and compare them on the basis of cell uptake and localization, affinities for hDM2, and 14-helix structure. Our results highlight the relative merits of the cationic-patch and hydrophobic-bridge strategies for improving beta-peptide uptake and identify a surprising correlation between uptake efficiency and hDM2 affinity.","corpus_id":207152437,"score":2},{"doc_id":"20346912","title":"Thermodynamics of RTA3 peptide binding to membranes and consequences for antimicrobial activity.","abstract":"RTA3 is an alpha-helical, amphipathic peptide with broad-spectrum activity against Gram-negative bacteria and low mammalian cell toxicity. RTA3 contains a cysteine residue, replacement of which with an alanine or serine (RTA3-C15S) virtually abolishes antimicrobial activity. Much of the activity of RTA3 can be recovered in RTA3-C15L, indicating that the C15 residue functions largely as a bulky hydrophobic side chain promoting target cell membrane interactions. The poorly active RTA3-C15S is a useful variant for assessing the mechanistic aspects of RTA3 activity. Binding and membrane perturbation in vesicles containing different proportions of negative surface charge are analyzed in terms of amino acid-specific free energy contributions to interfacial binding, which likely underlie variations in antimicrobial activity amongst RTA3 variants. Comparison with published free energy scales indicates that the reduced electrostatic contribution to binding to membranes having reduced negative surface charge can be compensated in RTA3 (but not RTA3-C15S) by a slightly deeper insertion of the C-terminus of the peptide to maximize hydrophobic contributions to binding. Analysis of inner membrane (IM)- and outer membrane (OM)-selective permeabilization of Escherichiacoli demonstrates a broad similarity between peptide effects on vesicles with low negative surface charge (20% negatively charged lipids), E.coli membrane perturbation, and antimicrobial activity, supporting a role for membrane perturbation in the killing mechanism of RTA3. The results demonstrate that large variations in antimicrobial activity on subtle changes in amino acid sequence in helical amphipathic peptides can be rationalized in terms of the thermodynamics of peptide binding to membranes, allowing a more systematic understanding of antimicrobial activity in these peptides.","corpus_id":28918133,"score":2},{"doc_id":"20572020","title":"Interaction of an ionic complementary peptide with a hydrophobic graphite surface.","abstract":"Protein adsorption on a surface plays an important role in biomaterial science and medicine. It is strongly related to the interaction between the protein residues and the surface. Here we report all-atom molecular dynamics simulations of the adsorption of an ionic complementary peptide, EAK16-II, to the hydrophobic highly ordered pyrolytic graphite surface. We find that, the hydrophobic interaction is the main force to govern the adsorption, and the peptide interchain electrostatic interaction affects the adsorption rate. Under neutral pH condition, the interchain electrostatic attraction facilitates the adsorption, whereas under acidic and basic conditions, because of the protonation and deprotonation of glutamic acid and lysine residues, respectively, the resulting electrostatic repulsion slows down the adsorption. We also found that under basic condition, during the adsorption peptide Chain II will be up against a choice to adsorb to the surface through the hydrophobic interaction or to form a temporary hydrophobic core with the deposited peptide Chain I. These results provide a basis for understanding some of the fundamental interactions governing peptide adsorption on the surface, which can shed new light on novel applications, such as the design of implant devices and drug delivery materials.","corpus_id":21034771,"score":2},{"doc_id":"20673228","title":"Amphipathic antimicrobial peptides--from biophysics to therapeutics?","abstract":"Amphipathic peptides are accommodated within the diffuse gradient of polarity that characterizes the interfacial regions of phospholipid bilayer membranes. Interfacial membrane interactions are key to the diverse biological functions and activities of these peptides, which encompass a large class of antimicrobial peptides, including the helical peptides magainin, melittin, and RTA3 derived from the commensal bacterium Streptococcus mitis. For these peptides in vitro efficacy (high antimicrobial activity with minimal mammalian cell toxicity, equivalent to high potential therapeutic index; PTI), can be broadly understood in relation to the thermodynamics of interfacial binding and membrane disruption in membranes having surface charges that correspond to bacterial and mammalian cell membranes, respectively. Peptides with disrupted amphipathicity resulting from a positively charged amino acid residue on the non-polar helix face, can have greatly enhanced PTI, although a balance of amphipathicity, hydrophobicity and positive charge is required for retention of high antimicrobial activity. These observations are illustrated with recent examples from the literature, and studies on RTA3 and magainin analogues from our laboratories. Despite the identification and optimisation of peptides with very good PTI, a focus on addressing toxicity upon systemic administration and poor in vivo efficacy is likely to be required to translate growing understanding of the relationships between peptide interfacial activity and effects on cells, into novel systemic therapeutics.","corpus_id":22813147,"score":2},{"doc_id":"21257813","title":"Mutational analysis of residues in the helical region of the class IIa bacteriocin pediocin PA-1.","abstract":"A 15-mer fragment that is derived from the helical region in the C-terminal half of pediocin PA-1 inhibited the activity of pediocin PA-1. Of 13 other pediocin-like (hybrid) bacteriocins, only the hybrid bacteriocin Sak/Ped was markedly inhibited by the 15-mer fragment. Sak/Ped was the only one of these bacteriocins that had a sequence (in the C-terminal helix-containing half) identical to that of the 15-mer fragment, indicating that the fragment inhibits pediocin-like bacteriocins in a sequence-dependent manner. By replacing (one at a time) all 15 residues in the fragment with Ala or Leu, five residues (K1, A2, T4, N8, and A15) were identified as being especially important for the inhibitory action of the fragment. The results suggest that the corresponding residues (K20, A21, T23, N27, and A34, respectively) in pediocin PA-1 might be involved in interactions between pediocin PA-1 and its receptor. To characterize the environment surrounding these five residues when pediocin PA-1 interacts with target cells, these residues were replaced (one at a time) with a hydrophobic large (Leu) residue, a hydrophilic charged (Asp or Arg) residue, and a small (Ala or Gly) residue. The results revealed that residues A21 and A34 are in a spatially constrained environment, since the replacement with a small (Gly) residue was the only substitution that did not markedly reduce the bacteriocin activity. The positive charge in K20 and the polar amide group in N27 appeared to interact with electronegative groups, since the replacement of these two residues with a positive (Arg) residue was well tolerated, while replacement with a negative (Asp) residue was detrimental to the bacteriocin activity. K20 was in a less constrained environment than N27, since the replacement of K20 with a large hydrophobic (Leu) residue was tolerated fairly well and to a greater extent than N27. T23 seemed to be in an environment that was not restricted with respect to size, polarity, and charge, since replacements with large (Leu) and small (Ala) hydrophobic residues and a hydrophilic negative (Asp) residue were tolerated fairly well (2- to 6-fold reduction in activity). Moreover, the replacement of T23 with a large positive (Arg) residue resulted in wild-type or better-than-wild-type activity.","corpus_id":3079556,"score":2},{"doc_id":"21409455","title":"Hydrophobicity drives the cellular uptake of short cationic peptide ligands.","abstract":"Short cationic linear peptide analogs (LPAs, prepared as Arg-C( n )-Arg-C( n )-Lys, where C( n ) represents an alkyl linkage with n = 4, 7 or 11) were synthesized and tested in human breast carcinoma BT-20 and CCRF-CEM leukemia cells for their application as targeting ligands. With constant LPA charge (+4), increasing the alkyl linkage increases the hydrophobic/hydrophilic balance and provides a systematic means of examining combined electrostatic and hydrophobic peptide-membrane interactions. Fluorescently conjugated LPA-C(11) (F-LPA-C(11)) demonstrated significant uptake, whereas there was negligible uptake of the shorter LPAs. By varying temperature (4°C and 37°C) and cell type, the results suggest that LPA-C(11) internalization is nonendocytic and nonspecific. The effect of LPA binding on the phase behavior, structure, and permeability of model membranes composed of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine (DPPC/DPPS, 85/15) was studied using differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and fluorescence leakage studies to gain insight into the LPA uptake mechanism. While all LPAs led to phase separation, LPA-C(11), possessing the longest alkyl linkage, was able to penetrate into the bilayer and caused holes to form, which led to membrane disintegration. This was confirmed by rapid and complete dye release by LPA-C(11). We propose that LPA-C(11) achieves uptake by anchoring to the membrane via hydrophobicity and forming transient membrane voids. LPAs may be advantageous as drug transporter ligands because they are small, water soluble, and easy to prepare.","corpus_id":22780672,"score":2},{"doc_id":"21523491","title":"Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X(L).","abstract":"The B-cell lymphoma 2 (Bcl-2) family of proteins regulates the intrinsic pathway of apoptosis. Interactions between specific anti- and pro-apoptotic Bcl-2 proteins determine the fate of a cell. Anti-apoptotic Bcl-2 proteins have been shown to be over-expressed in certain cancers and they are attractive targets for developing anti-cancer drugs. Peptides from the BH3 region of pro-apoptotic proteins have been shown to interact with anti-apoptotic Bcl-2 proteins and induce biological activity similar to that observed in parent proteins. However, the specificity of BH3 peptides derived from different pro-apoptotic proteins differ for different anti-apoptotic Bcl-2 proteins. In this study, we have investigated the relationship between the stable helical nature of BH3 peptides and their affinities to Bcl-X(L), an anti-apoptotic Bcl-2 protein. We have carried out molecular dynamics simulations of six BH3 peptides derived from Bak, Bad and Bim pro-apoptotic proteins for a period of 50 ns each in aqueous medium. Due to the amphipathic nature of BH3 peptides, the hydrophobic residues on the hydrophobic face tend to cluster together in all BH3 peptides. While this process resulted in a complete loss of helical structure in 16-mer Bak and 16-mer Bad wild type peptides, stabilizing interactions in the hydrophilic face of the BH3 peptides and capping interactions helped to maintain partial helical character in 16-mer Bad mutant and 16-mer Bim peptides. The latter two 16-mer peptides exhibit higher affinity for Bcl-X(L). Similarly the longer BH3 peptides, 25-mer Bad and 33-mer Bim, also resulted in smaller and stable helical fragments and their helical conformation is stabilized by interactions between residues in the solvent-exposed hydrophilic half of the peptide. The stable nature of helical segment in a BH3 peptide can be directly correlated to its binding affinity and the helical region encompassed the highly conserved Leu residue. We propose that upon approaching the hydrophobic groove of anti-apoptotic proteins, a longer helix will be induced in high affinity BH3 peptides by extending the smaller stable helical segments around the conserved Leu residue in both N- and C-terminal regions. The results reported in this study will have implications in developing peptide-based inhibitors for anti-apoptotic Bcl-2 proteins.","corpus_id":685198,"score":2},{"doc_id":"21875799","title":"Cellular uptake of Aib-containing amphipathic helix peptide.","abstract":"Cell-penetrating peptides (CPPs) are useful tools for the delivery of hydrophilic bioactive molecules, such as peptides, proteins, and oligonucleotides, across the cell membrane. To realize the delivery of therapeutic macromolecules by CPPs, the CPPs are required to show resistance to protease and no cytotoxicity. In order to produce potent non-toxic and protease-resistant CPPs with high cellular uptake, we designed an amphipathic helix peptide using α-aminoisobutyric acid (Aib, U) and named it MAP(Aib). In the MAP(Aib) molecule, five Aib residues are aligned on the hydrophobic face of the helix and five lysine (K) residues are aligned on the hydrophilic face. MAP(Aib) showed potent resistance to trypsin and pronase compared with MAP, an amphipathic helix peptide formed by usual amino acids. Fluorescein-labeled MAP(Aib) efficiently traversed the A549 cell membrane, diffusing into the cytoplasm and slightly into the nucleus without exerting any cytotoxicity. In contrast, MAP was poorly taken up by the cell. These results indicate that the incorporation of Aib residues into CPPs markedly improves cellular uptake and MAP(Aib) may be a useful tool for the delivery of hydrophilic macromolecules.","corpus_id":13361019,"score":2},{"doc_id":"22290189","title":"Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides.","abstract":"Antimicrobial peptides often permeabilize biological membranes via a pore mechanism. Two pore types have been proposed: toroidal, where the pore is partly lined by lipid, and barrel-stave, where a cylindrical pore is completely lined by peptides. What drives the preference of antimicrobial peptides for a certain pore type is not yet fully understood. According to neutron scattering and oriented circular dichroism, melittin and MG-H2 induce toroidal pores whereas alamethicin forms barrel-stave pores. In previous work we found that indeed melittin seems to favor toroidal pores whereas alamethicin favors cylindrical pores. Here we designed mutants of these two peptides and the magainin analog MG-H2, aimed to probe how the distribution of charges along the helix and its imperfectly amphipathic structure influence pore formation. Molecular dynamics (MD) simulations of the peptides in a pre-formed cylindrical pore have been performed. The duration of the simulations was 136ns to 216ns. We found that a melittin mutant with lysine 7 neutralized favors cylindrical pores whereas a MG-H2 mutant with lysines in the N-terminal half of these peptides neutralized and an alamethicin mutant with a positive charge at the position 7 form semitoroidal pores. These results suggest that charged residues within the N-terminal half are important for toroidal pore formation. Toroidal pores produced by MG-H2 are more disordered than the melittin pores, likely because of the charged residues located in the middle of the MG-H2 helix (K11 and K14). Imperfect amphipathicity of melittin seems to play a role in its preference for toroidal pores since the substitutions of charged residues located within the nonpolar face by hydrophobic residues suppress evolution of a toroidal pore. The mutations change the position of lysine 7 near the N-terminus, relative to the lower leaflet headgroups. The MD simulations also show that the melittin P14A mutant forms a toroidal pore, but its configuration diverges from that of melittin and it is probably metastable.","corpus_id":33098301,"score":2},{"doc_id":"22783871","title":"Adsorption of unstructured protein β-casein to hydrophobic and charged surfaces.","abstract":"In this Monte Carlo simulation study we use mesoscopic modeling to show that β-casein, an unstructured milk protein, adsorbs to surfaces not only due to direct electrostatic and hydrophobic interactions but also due to structural rearrangement and charge regulation due to proton uptake and release. β-casein acts as an amphiphilic chameleon, changing properties according to the chemical environment, and binding is observed to both positively and negatively charged surfaces. The binding mechanisms, however, are fundamentally different. A detailed, per-residue-level analysis shows that the adsorption process is controlled by a few very specific regions of the protein and that these change dramatically with pH. Caseins, being the most abundant proteins in milk, are crucial for the properties of fermented dairy products, such as nutrition, texture, and viscosity, but may also influence adhesion to packaging materials. The latter leads to product losses of about 10%, leading to economical and environmental problems.","corpus_id":41458963,"score":2},{"doc_id":"22837667","title":"Role of helicity on the anticancer mechanism of action of cationic-helical peptides.","abstract":"In the present study, the 26-residue amphipathic α-helical peptide A12L/A20L (Ac-KWKSFLKTFKSLKKTVLHTLLKAISS-amide) with strong anticancer activity and specificity was used as the framework to study the effects of helicity of α-helical anticancer peptides on biological activities. Helicity was systematically modulated by introducing d-amino acids to replace the original l-amino acids on the non-polar face or the polar face of the helix. Peptide helicity was measured by circular dichroism spectroscopy and was demonstrated to correlate with peptide hydrophobicity and the number of d-amino acid substitutions. Biological studies showed that strong hemolytic activity of peptides generally correlated with high hydrophobicity and helicity. Lower helicity caused the decrease of anti-HeLa activity of peptides. By introducing d-amino acids to replace the original l-amino acids on the non-polar face or the polar face of the helix, we improved the therapeutic index of A12L/A20L against HeLa cells by 9-fold and 22-fold, respectively. These results show that the helicity of anticancer peptides plays a crucial role for biological activities. This specific rational approach of peptide design could be a powerful method to improve the specificity of anticancer peptides as promising therapeutics in clinical practices.","corpus_id":395634,"score":2},{"doc_id":"24021230","title":"Design of imperfectly amphipathic α-helical antimicrobial peptides with enhanced cell selectivity.","abstract":"Antimicrobial peptides (AMPs), which are produced by multicellular organisms as a defense mechanism against competing pathogenic microbes, appear to be excellent candidates for the development of novel antimicrobial agents. Amphipathicity is traditionally believed to be crucial to the de novo design or systematic optimization of AMPs. In this study, we designed a series of short α-helical AMPs with imperfect amphipathicity to augment the arsenal of strategies and to gain further insights into their antimicrobial and hemolytic activity. These imperfectly amphipathic α-helical AMPs were designed by replacing the paired charged amino acid residues on the polar face of an amphipathic peptide with tryptophan residues on the basis of α-helical protein folding principles. PRW4, an imperfectly amphipathic α-helical AMP with hydrogen bonds formed by paired tryptophan residues, was observed to be more selective towards bacterial cells than toward human red blood cells. PRW4 was also effective against Gram-negative and Gram-positive bacteria, and fluorescence spectroscopy, flow cytometry, scanning electron microscopy and transmission electron microscopy indicated that PRW4 killed microbial cells by permeabilizing the cell membrane and damaging their membrane integrity. Therefore, disruptive amphipathicity has excellent potential for the rational design and optimization of AMPs with promising antimicrobial activities.","corpus_id":205247649,"score":2},{"doc_id":"24743023","title":"Peptide:lipid ratio and membrane surface charge determine the mechanism of action of the antimicrobial peptide BP100. Conformational and functional studies.","abstract":"The cecropin-melittin hybrid antimicrobial peptide BP100 (H-KKLFKKILKYL-NH2) is selective for Gram-negative bacteria, negatively charged membranes, and weakly hemolytic. We studied BP100 conformational and functional properties upon interaction with large unilamellar vesicles, LUVs, and giant unilamellar vesicles, GUVs, containing variable proportions of phosphatidylcholine (PC) and negatively charged phosphatidylglycerol (PG). CD and NMR spectra showed that upon binding to PG-containing LUVs BP100 acquires α-helical conformation, the helix spanning residues 3-11. Theoretical analyses indicated that the helix is amphipathic and surface-seeking. CD and dynamic light scattering data evinced peptide and/or vesicle aggregation, modulated by peptide:lipid ratio and PG content. BP100 decreased the absolute value of the zeta potential (ζ) of LUVs with low PG contents; for higher PG, binding was analyzed as an ion-exchange process. At high salt, BP100-induced LUVS leakage requires higher peptide concentration, indicating that both electrostatic and hydrophobic interactions contribute to peptide binding. While a gradual release took place at low peptide:lipid ratios, instantaneous loss occurred at high ratios, suggesting vesicle disruption. Optical microscopy of GUVs confirmed BP100-promoted disruption of negatively charged membranes. The mechanism of action of BP100 is determined by both peptide:lipid ratio and negatively charged lipid content. While gradual release results from membrane perturbation by a small number of peptide molecules giving rise to changes in acyl chain packing, lipid clustering (leading to membrane defects), and/or membrane thinning, membrane disruption results from a sequence of events - large-scale peptide and lipid clustering, giving rise to peptide-lipid patches that eventually would leave the membrane in a carpet-like mechanism.","corpus_id":205845550,"score":2},{"doc_id":"24828311","title":"Comparative α-helicity of cyclic pentapeptides in water.","abstract":"Helix-constrained polypeptides have attracted great interest for modulating protein-protein interactions (PPI). It is not known which are the most effective helix-inducing strategies for designing PPI agonists/antagonists. Cyclization linkers (X1-X5) were compared here, using circular dichroism and 2D NMR spectroscopy, for α-helix induction in simple model pentapeptides, Ac-cyclo(1,5)-[X1-Ala-Ala-Ala-X5]-NH2, in water. In this very stringent test of helix induction, a Lys1→Asp5 lactam linker conferred greatest α-helicity, hydrocarbon and triazole linkers induced a mix of α- and 3₁₀-helicity, while thio- and dithioether linkers produced less helicity. The lactam-linked cyclic pentapeptide was also the most effective α-helix nucleator attached to a 13-residue model peptide.","corpus_id":205379007,"score":2},{"doc_id":"24842084","title":"Effects of residue 5-point mutation and N-terminus hydrophobic residues on temporin-SHc physicochemical and biological properties.","abstract":"Temporin-SHc (FLSHIAGFLSNLFamide) first isolated from skin extraction of the Tunisian frog Pelophylax saharica, which shows potent antimicrobial activity against Gram-positive bacteria and is highly active against yeasts and fungi without hemolytic activity at antimicrobial concentrations. The peptide adopts well-defined α-helical conformation when bound to SDS micelles. In this study, we explored the effects of residue at position 5 and the N-terminus hydrophobic character on the hydrophilic/polar face of temp-SHc, on its biological activities (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity and helicity). Antibacterial and hemolytic properties of temporin-SHc derivatives depend strongly on physicochemical properties. Therefore, slight decreasing amphipathicity together with hydrophobicity and helicity by the substitution Ile(5) → Leu decreased antimicrobial potency approximately twofold without changing of hemolytic activity. It is noteworthy that a conservative amino acid substitution decreases the antimicrobial activity, underlining the differences between Leu/Ile side chains insertion into the lipid bilayer. While the modification of N-terminal hydrophobic character by four residue inversion decreased amphipathicity (twofold) of (4-1)L5temp-SHc and resulted in an increase in antibacterial activity against E. coli, E. faecalis and C. parapsilosis of at least fourfold, its therapeutic potential is limited by its drastic increase of hemolysis (LC₅₀ = 2 μM). We found that the percentage of helicity of temp-SHc analog is directly correlated to its hemolytic activity. Last, the hydrophobic N-terminal character is an important determinant of antimicrobial activity.","corpus_id":6453777,"score":2},{"doc_id":"24857611","title":"Terminal residue hydrophobicity modulates transmembrane helix-helix interactions.","abstract":"Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as \"small-XXX-small\" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰). Using gel electrophoresis, circular dichroism, and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate (SDS), we found that mutation of F90 to residues such as A, I, L, or V maintains the onset of TM2-TM2 dimerization, whereas mutation to E, G, Q, N, S, or T abrogates dimer formation. We attribute this sensitivity to changes in local hydrophobicity, viz., a decrease in hydrophobicity reduces local lipid-peptide interactions, which in turn disrupts peptide α-helicity and hence the effectiveness of an incipient interaction-compatible surface. Our results show that the secondary structure and oligomeric state of PLP TM2 Lys-tagged peptides are significantly modulated by the specific nature of their C-terminal boundary residue, thus providing insight as to how point mutations, particularly where they produce disease states, can compromise the folding process.","corpus_id":35569279,"score":2},{"doc_id":"25329983","title":"Peptides with the same composition, hydrophobicity, and hydrophobic moment bind to phospholipid bilayers with different affinities.","abstract":"We investigated the dependence of membrane binding on amino acid sequence for a series of amphipathic peptides derived from δ-lysin. δ-Lysin is a 26 amino acid, N-terminally formylated, hemolytic peptide that forms an amphipathic α-helix bound at membrane-water interfaces. A shortened peptide, lysette, was derived from δ-lysin by deletion of the four N-terminal amino acid residues. Five variants of lysette were synthesized by altering the amino acid sequence such that the overall hydrophobic moment remained essentially the same for all peptides. Peptide-lipid equilibrium dissociation constants and helicities of peptides bound to zwitterionic lipid vesicles were determined by stopped-flow fluorescence and circular dichroism. We found that binding to phosphatidylcholine bilayers was a function of the helicity of the bound peptide alone and independent of the a priori hydrophobic moment or the ability to form intramolecular salt bridges. Molecular dynamics (MD) simulations on two of the peptides suggest that sequence determines the insertion depth into the bilayer. The location of the two aspartate residues at the C-terminus of lysette-2 leads to a loss of helical content in the simulations, which correlates with faster desorption from the bilayer as compared to lysette. We also found a systematic deviation of the experimentally determined dissociation constant and that predicted by the Wimley-White interfacial hydrophobicity scale. The reason for the discrepancy remains unresolved but appears to correlate with a predominance of isoleucine over leucine residues in the lysette family of peptides.","corpus_id":14200083,"score":2},{"doc_id":"25372782","title":"N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids.","abstract":"Capping rules, which govern interactions of helical peptides with hydrophobic surfaces, were never established before due to lack of methods for the direct measurement of polypeptide structure on the interphase boundary. We employed proteomic techniques and peptide retention modeling in reversed-phase chromatography to generate a data set sufficient for amino acid population analysis at helix ends. We found that interactions of amphipathic helical peptides with a hydrophobic C18 phase are induced by a unique motif featuring hydrophobic residues in the N1 and N2 positions adjacent to the N-cap (Asn, Asp, Ser, Thr, Gly), followed by Glu, Gln, or Asp in position N3 to complete a capping box. A favorable N-capping arrangement prior to amphipathic helix may result in the highest hydrophobicity (retention on C18 columns) of Asp/Asn (or Glu/Gln) peptide analogues among all naturally occurring amino acids when placed in N-cap or N3 position, respectively. These results contradict all previously reported hydrophobicity scales and provide new insights into our understanding of the phenomenon of hydrophobic interactions.","corpus_id":46321652,"score":2},{"doc_id":"25735802","title":"Characterization of antimicrobial activity and mechanisms of low amphipathic peptides with different α-helical propensity.","abstract":"Antimicrobial peptides (AMPs) serve as a defense mechanism within multicellular organisms and are attracting increasing attention because of their potential application in the treatment of multidrug-resistant infections. Amphipathicity has long been believed to be the most important consideration for the structural modification and design of both naturally occurring and synthetic AMPs. Previous studies indicated that disruptive amphipathicity formed by replacing the paired charged amino acid residues on the polar face of an amphipathic helix with tryptophan residues linked with hydrogen bonds on the basis of α-helical protein folding principles endowed the AMPs with increased cell selectivity. In an attempt to augment and hone this strategy further, we designed a series of imperfect amphipathic peptides by placing different types of amino acid residues at the hydrogen bond linked positions of α-helix structures to characterize their antimicrobial properties and mechanism of action. The d-Trp-substituted sequence (PRW4-d) showed greater antimicrobial potency than Cys-(C4), Asp-(D4), Ile-(I4), and Pro-(P4) substituted sequences, comparable to the l-Trp-substituted parent sequence (PRW4). Furthermore, the total replacement of Lys residues with Arg residues along the peptide sequence (PRW4-R) exhibited enhanced antimicrobial activity and cell selectivity. In addition, no cytotoxicity was observed among these synthetic peptides. PRW4-d and PRW4-R maintained their activities in the presence of physiological salts and human serum. The fluorescence spectroscopy, flow cytometry, and electron microscopy observations indicated that the optimized sequences exhibited excellent antimicrobial potency by inducing cytoplasmic membrane potential loss, membrane permeabilization and disruption. Collectively, the results could be useful for designing short AMPs with great antimicrobial activity and cell selectivity.","corpus_id":205249881,"score":2},{"doc_id":"27195657","title":"Amphipathicity Determines Different Cytotoxic Mechanisms of Lysine- or Arginine-Rich Cationic Hydrophobic Peptides in Cancer Cells.","abstract":"Cationic amphipathic peptides (CAPs) are known to be able to cause membrane destabilization and induce cell death, yet how the hydrophobicity, amphipathicity, and lysine (K)/arginine (R) composition synergistically affect the peptide activity remains incompletely understood. Here, we designed a panel of peptides based on the well-known anticancer peptide KLA. Increasing hydrophobicity enhanced the cytotoxicities of both the K- and R-rich peptides. Peptides with an intact amphipathic helical interface can cause instant cell death through a membrane lysis mechanism. Interestingly, rearranging the residue positions to minimize amphipathicity caused a great decrease of cytotoxicity to the K-rich peptides but not to the R-rich peptides. The amphipathicity-minimized R-rich peptide 6 (RL2) (RLLRLLRLRRLLRL-NH2) penetrated the cell membrane and induced caspase-3-dependent apoptotic cell death. We found that the modulation of hydrophobicity, amphipathicity, and K/R residues leads to distinct mechanisms of action of cationic hydrophobic peptides. Amphipathicity-reduced, arginine-rich cationic hydrophobic peptides (CHPs) may represent a new class of peptide therapeutics.","corpus_id":206617830,"score":2},{"doc_id":"27547919","title":"Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices.","abstract":"Hydrocarbon-stapled peptides are a class of bioactive alpha-helical ligands developed to dissect and target protein interactions. While there is consensus that stapled peptides can be effective chemical tools for investigating protein regulation, their broader utility for therapeutic modulation of intracellular interactions remains an active area of study. In particular, the design principles for generating cell-permeable stapled peptides are empiric, yet consistent intracellular access is essential to in vivo application. Here, we used an unbiased statistical approach to determine which biophysical parameters dictate the uptake of stapled-peptide libraries. We found that staple placement at the amphipathic boundary combined with optimal hydrophobic and helical content are the key drivers of cellular uptake, whereas excess hydrophobicity and positive charge at isolated amino acid positions can trigger membrane lysis at elevated peptide dosing. Our results provide a design roadmap for maximizing the potential to generate cell-permeable stapled peptides with on-mechanism cellular activity.","corpus_id":7877088,"score":2},{"doc_id":"27966361","title":"Identification of Short Hydrophobic Cell-Penetrating Peptides for Cytosolic Peptide Delivery by Rational Design.","abstract":"Cell-penetrating peptides (CPPs) enhance the cellular uptake of membrane-impermeable molecules. Most CPPs are highly cationic, potentially increasing the risk of toxic side effects and leading to accumulation in organs such as the liver. As a consequence, there is an unmet need for less cationic CPPs. However, design principles for effective CPPs are still missing. Here, we demonstrate a design principle based on a classification of peptides according to accumulated side-chain polarity and hydrophobicity. We show that in comparison to randomly selected peptides, CPPs cover a distinct parameter space. We designed peptides of only six to nine amino acids with a maximum of three positive charges covering this property space. All peptides were tested for cellular uptake and subcellular distribution. Following an initial round of screening we enriched the collection with short and hydrophobic peptides and introduced d-amino acid substitutions and lactam bridges which increased cell uptake, in particular for long-term incubation. Using a GFP complementation assay, for the most active peptides we demonstrate cytosolic delivery of a biologically active cargo peptide.","corpus_id":206520365,"score":2},{"doc_id":"28636317","title":"Downsizing Proto-oncogene cFos to Short Helix-Constrained Peptides That Bind Jun.","abstract":"The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components. Structural integrity in the presence and absence of Jun was assessed by circular dichroism spectroscopy, while the thermodynamics of binding to cFos was measured by isothermal titration calorimetry. A 25-residue constrained peptide, one-third shorter yet 25% more helical than the structurally characterized 37-residue Fos-derived peptide, retained 80% of the binding free energy as a result of preorganization in a Jun-binding helix conformation, with the entropy gain (TΔS = +3.2 kcal/mol) compensating for the enthalpy loss. Attaching a cell-penetrating peptide (TAT48-57) and a nuclear localization signal (SV40) promoted cell uptake, localization to the nucleus, and inhibition of the proliferation of two breast cancer cell lines.","corpus_id":206527543,"score":2},{"doc_id":"28741867","title":"Targeting of a helix-loop-helix transcriptional regulator by a short helical peptide.","abstract":"The Id proteins (Id1-4) are cell cycle regulators that play a key role during development, in cancer and vascular disorders. They contain a conserved helix-loop-helix (HLH) domain that folds into a parallel four-helix bundle upon self- or heteroassociation with basic-HLH transcription factors. By using such protein-protein interactions, the Id proteins inhibit cell differentiation and promote cell cycle progression. Accordingly, their supporting role in cancer has been convincingly demonstrated, which makes these proteins interesting therapeutic targets. Here we present a short peptide containing a (i,i+4)-lactam bridge and a hydrophobic (Φ) three-residue motif Φ(i)-Φ(i+3)-Φ(i+6), which adopted a helical conformation in water, showed Id-protein binding in the low-micromolar range, penetrated into breast (MCF7 and T47D) and bladder (T24) cancer cells, accumulated in the nucleus, and reduced cell viability to about 50%. Thus, this cyclopeptide is a promising scaffold to develop Id-protein binders impairing cancer cell viability.","corpus_id":5013620,"score":2},{"doc_id":"29420899","title":"Importance of Net Hydrophobicity in the Cellular Uptake of All-Hydrocarbon Stapled Peptides.","abstract":"All-hydrocarbon stapled peptides make up a promising class of protein-protein interaction regulators; their potential therapeutic benefit arises because they have a high binding affinity and specificity for intracellular molecules. The cell permeation efficacy of these peptides is a critical determinant of their bioactivity. However, the factors that determine their cellular uptake remain an active area of research. In this study, we evaluated the effect of stapled (or cross-linked) formation on the cellular uptake of six known all-hydrocarbon stapled peptides. We found that the rate of cellular uptake of unstapled peptides (i.e., those bearing olefinic non-natural amino acids that are not subjected to olefin metathesis) was higher than that for the corresponding stapled peptides. Additionally, the insertion of these olefinic non-natural amino acids into peptide sequences significantly increased their rate of cellular uptake. According to the high-performance liquid chromatography retention times, the overall hydrophobicity of unstapled peptides was greater than that of stapled peptides, followed by that of the original peptides without olefinic non-natural amino acids. There was not a close correlation between helical content and the rate of cellular uptake of these peptides. Therefore, the increase in overall hydrophobicity resulting from the introduction of non-natural amino acids, rather than the structural stabilization resulting from staple formation, is the key driver promoting cellular uptake. Macropinocytosis, a form of fluid-phase endocytosis, was involved in the cellular uptake of all six peptides.","corpus_id":3709285,"score":2},{"doc_id":"29431766","title":"Glucuronic acid as a helix-inducing linker in short peptides.","abstract":"A new strategy is demonstrated for making peptides helical, using a carbohydrate to bridge between sidechains at each end of a pentapeptide. CD and NMR spectra establish that both an α-helix and a 310-helix structure can form depending upon the bridge.","corpus_id":206076160,"score":2},{"doc_id":"29461066","title":"Chemically Diverse Helix-Constrained Peptides Using Selenocysteine Crosslinking.","abstract":"The use of selenocysteines and various cross-linkers to induce helicity in a bioactive peptide is described. The higher reactivity of selenocysteine, relative to cysteine, facilitates rapid cross-linking within unprotected linear peptides under mild aqueous conditions. Alkylating agents of variable topology and electrophilicity were used to link pairs of selenocysteines within a p53 peptide. Facile selenoether formation enables diverse tailoring of the helical peptide structure.","corpus_id":3643745,"score":2},{"doc_id":"29568420","title":"Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning.","abstract":"Due to their enhanced stability and cell permeability, cyclic cell-penetrating peptides have been widely used as delivery vectors for transporting cell-impermeable cargos into cells. In this study, we synthesized a panel of conformationally constrained peptides with either α-helix or β-hairpin conformations. We tuned the amphiphilicity of these constrained peptides with different distributions of charged or hydrophobic residues and compared their cellular uptake efficiencies in different cell lines. We found that the amphipathicity of these conformationally constrained peptides correlates well with their cellular uptake efficiency. We proposed that peptides with larger hydrophobic moments (HMs) have stronger binding affinities with the cell membrane which further accelerates the endocytosis process. This finding should provide an approach towards the design of more potent conformationally constrained cell-penetrating peptides for biomedical applications.","corpus_id":2617023,"score":2},{"doc_id":"18540660","title":"Fundamental design principles that guide induction of helix upon formation of stable peptide-nanoparticle complexes.","abstract":"We have shown that it is possible to design a peptide that has a very low helical content when free in solution but that adopts a well-defined helix when interacting with silica nanoparticles. From a systematic variation of the amino acid composition and distribution in designed peptides, it has been shown that the ability to form helical structure upon binding to the silica surface is dominated by two factors. First, the helical content is strongly correlated with the net positive charge on the side of the helix that interacts with the silica, and arginine residues are strongly favored over lysine residues in these positions. The second important factor is to have a high net negative charge on the side of the helix that faces the solution. Apparently, both attractive and repulsive electrostatic forces dominate the induction and stabilization of a bound helix. It is also evident that using amino acids that have high propensity to form helix in solution are also advantageous for the formation of helix on surfaces.","corpus_id":5281363,"score":1},{"doc_id":"18630933","title":"A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation.","abstract":"Alpha-helices constitute the largest class of protein secondary structures and play a major role in mediating protein-protein interactions. Development of stable mimics of short alpha-helices would be invaluable for inhibition of protein-protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in alpha-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS alpha-helices feature a carbon-carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix-coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short alpha-helices. The HBS method affords preorganized alpha-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an attractive strategy for generation of ligands for protein receptors because placement of the cross-link on the inside of the helix does not block solvent-exposed molecular recognition surfaces of the molecule. Our metathesis-based synthetic strategy utilizes standard Fmoc solid phase peptide synthesis methodology, resins, and reagents and provides HBS helices in sufficient amounts for subsequent biophysical and biological analyses. Extensive conformational analysis of HBS alpha-helices with 2D NMR, circular dichroism spectroscopies and X-ray crystallography confirms the alpha-helical structure in these compounds. The crystal structure indicates that all i and i + 4 C=O and NH hydrogen-bonding partners fall within distances and angles expected for a fully hydrogen-bonded alpha-helix. The backbone conformation of HBS alpha-helix in the crystal structure superimposes with an rms difference of 0.75 A onto the backbone conformation of a model alpha-helix. Significantly, the backbone torsion angles for the HBS helix residues fall within the range expected for a canonical alpha-helix. Thermal and chemical denaturation studies suggest that the HBS approach provides exceptionally stable alpha-helices from a variety of short sequences, which retain their helical conformation in aqueous buffers at exceptionally high temperatures. The high degree of thermal stability observed for HBS helices is consistent with the theoretical predictions for a nucleated helix. The HBS approach was devised to afford internally constrained helices so that the molecular recognition surface of the helix and its protein binding properties are not compromised by the constraining moiety. Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity.","corpus_id":206827831,"score":1},{"doc_id":"19074438","title":"GroEL Recognizes an Amphipathic Helix and Binds to the Hydrophobic Side.","abstract":"GroEL is an essential Escherichia coli molecular chaperon that uses ATP to facilitate correct folding of a range of proteins in a cell. Central to the GroEL substrate diversity is how GroEL recognizes the substrates. The interaction between GroEL and substrate has been proposed to be largely hydrophobic because GroEL interacts with proteins in non-native conformations but not in native forms. Analysis of GroEL substrate proteins reveals that one of its main substrates are proteins with alphabeta folding domains, suggesting that GroEL may stabilize the collapsed alphabeta core by binding to hydrophobic surfaces that are usually buried between the alpha and beta elements. In this study, we characterize the interaction between GroEL and a peptide derived from our previous selection via a phage display method. NMR studies map the peptide-binding site to the region containing Helices H and I, which is consistent with evidence that this region comprises the primary substrate-binding site. The peptide is largely unstructured in solution but adopts a helical conformation when bound to the GroEL apical domain with a moderate affinity (K(d) = 17.1 +/- 2.5 microm). The helical conformation aligns residues to form an amphipathic structure, and the hydrophobic side of this amphipathic helix interacts with GroEL as suggested by fluorescence quenching studies. Together with previous structural studies on the GroEL-peptide complexes, our work supports the notion that the amphipathic secondary elements in the substrate proteins may be the structural motif recognized by GroEL.","corpus_id":24924344,"score":1},{"doc_id":"20025243","title":"Hydrophobic residues in helix 8 of cannabinoid receptor 1 are critical for structural and functional properties.","abstract":"In addition to the heptahelical transmembrane domain shared by all G protein-coupled receptors (GPCRs), many class A GPCRs adopt a helical domain, termed helix 8, in the membrane-proximal region of the C terminus. We investigated the role of residues in the hydrophobic and hydrophilic faces of amphiphilic helix 8 of human cannabinoid receptor 1 (CB1). To differentiate between a role for specific residues and global features, we made two key mutants: one involving replacement of the highly hydrophobic groups, Leu404, Phe408, and Phe412, all with alanine and the second involving substitution of the basic residues, Lys402, Arg405, and Arg409, all with the neutral glutamine. The former showed a very low B(max) based on binding isotherms, a minimal E(max) based on GTPgammaS binding analysis, and defective localization relative to the wild-type CB1 receptor as revealed by confocal microscopy. However, the latter mutant and the wild-type receptors were indistinguishable. Circular dichroism spectroscopy of purified peptides with corresponding sequences indicated that the highly hydrophobic residues are critical for maintaining a strong helical structure in detergent, whereas the positively charged residues are not. Further investigation of mutant receptors revealed that CB1 localization requires a threshold level of hydrophobicity but not specific amino acids. Moreover, mutant receptors carrying two- to six-residue insertions amino-terminal to helix 8 revealed a graded decrease in B(max) values. Our results identify the key helix 8 components (including hydrophobicity of specific residues, structure, and location relative to TM7) determinant for receptor localization leading to robust ligand binding and G protein activation.","corpus_id":9073135,"score":1},{"doc_id":"20669185","title":"Helicity of short E-R/K peptides.","abstract":"Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide-based drug design. Previous studies of synthetic Ala-based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E-R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E-R/K-based peptides show significant helix content. Peptides containing one or more E-R interactions display greater helicity than those with similar E-K interactions. Significant helicity is achieved in Arg-based E-R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E-R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.","corpus_id":27477206,"score":1},{"doc_id":"21949789","title":"Exposed hydrophobic residues in human immunodeficiency virus type 1 Vpr helix-1 are important for cell cycle arrest and cell death.","abstract":"The human immunodeficiency virus type 1 (HIV-1) accessory protein viral protein R (Vpr) is a major determinant for virus-induced G2/M cell cycle arrest and cytopathicity. Vpr is thought to perform these functions through the interaction with partner proteins. The NMR structure of Vpr revealed solvent exposed hydrophobic amino acids along helices 1 and 3 of Vpr, which could be putative protein binding domains. We previously showed that the hydrophobic patch along helix-3 was important for G2/M blockade and cytopathicity. Mutations of the exposed hydrophobic residues along helix-1 were found to reduce Vpr-induced cell cycle arrest and cell death as well. The levels of toxicity during virion delivery of Vpr correlated with G2/M arrest. Thus, the exposed hydrophobic amino acids in the amino-terminal helix-1 are important for the cell cycle arrest and cytopathicity functions of Vpr.","corpus_id":9171446,"score":1},{"doc_id":"22052825","title":"Effect of introducing a short amyloidogenic sequence from the Aβ peptide at the N-terminus of 18-residue amphipathic helical peptides.","abstract":"Fibril formation is the hallmark of pathogenesis in Alzheimer's disease and other amyloid disorders caused by conformational alterations leading to the aggregation of soluble monomers. Aβ40 self-associates to form amyloid fibrils. Its central seven-residue segment KLVFFAE (Aβ16-22), which is thought to be crucial for fibril formation of the full-length peptide, forms fibrils even in isolation. Context-dependent induction of amyloid formation by such sequences in peptides, which otherwise do not have that propensity, is of considerable interest. We have examined the effect of introducing the Aβ16-22 sequence at the N-terminus of two amphipathic helical 18-residue peptides Ac-WYSEMKRNVQRLERAIEE-am and Ac-KQLIRFLKRLDRNLWGLA-am, which have high average hydrophobic moment <μH> values but have net charges of 0 and +4, respectively, at neutral pH. Upon incubation in aqueous buffer, fibril-like aggregates were discernible by transmission electron microscopy for the peptide with only 0 net charge, which also displayed ThT binding and β-structure. Although both the sequences have been derived from amphipathic helical segments in globular proteins and possess high average hydrophobic moments, the +4 charge peptide lacks the ability to form fibrils, while the peptide with 0 charge has the tendency to form fibrillar structures. Variation in the net charge and the presence of several glutamic acids in the sequence of the peptide with net charge 0 appear to favor the formation of fibrils when the Aβ16-22 sequence is attached at the N-terminus.","corpus_id":44873240,"score":1},{"doc_id":"22223219","title":"Computational protein design with explicit consideration of surface hydrophobic patches.","abstract":"De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studies with Rosetta have shown that this limits surface hydrophobics to the naturally occurring frequency (∼28%), but that it does not prevent the formation of hydrophobic patches that are considerably larger than those observed in naturally occurring proteins. Here, we describe a new score term that explicitly detects and penalizes the formation of hydrophobic patches during computational protein design. With the new term, we are able to design protein surfaces that include hydrophobic amino acids at naturally occurring frequencies, but do not have large hydrophobic patches. By adjusting the strength of the new score term, the emphasis of surface redesigns can be switched between maintaining solubility and maximizing folding free energy.","corpus_id":21986052,"score":1},{"doc_id":"22720789","title":"Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization.","abstract":"BACKGROUND: The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. RESULTS: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don't. While the nature of transitions of LCC's sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues' cliques. CONCLUSIONS: The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. The thermophiles do not only have the higher number of long-range interactions; they also have larger cluster of connected residues at higher interaction strengths among amino acids, than their mesophilic counterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding and stabilization; at the same time, it shed light on the higher communication ability of hydrophobic subnetworks over the others. The results give an indication of the controlling role of hydrophobic subclusters in determining protein's folding rate. The occurrences of higher perimeters of hydrophobic and charged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distant part of primary structure of a protein through London van der Waals interaction.","corpus_id":5485673,"score":1},{"doc_id":"22803956","title":"Relationship between helix stability and binding affinities: molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent.","abstract":"The anti-apoptotic protein Bfl-1, also known as A1, belongs to the Bcl-2 family of proteins and interacts with pro-apoptotic Bcl-2 counterparts to regulate programmed cell death. As demonstrated for other anti-apoptotic Bcl-2 proteins, Bfl-1/A1 has also been shown to be overexpressed in various human cancers and hence they are attractive targets for anticancer drugs. Peptides derived from the BH3 region of pro-apoptotic Bcl-2 proteins have been shown to elicit similar biological response as that of parent proteins. BH3 peptides from different pro-apoptotic proteins have wide range of affinities for Bfl-1/A1. Experimentally determined complex structures show that the hydrophobic side of amphipathic BH3 peptides binds to the hydrophobic groove formed by the α-helical bundle of Bfl-1/A1 protein. Apart from the length and amino acid composition, a BH3 peptide's ability to form a stable helical structure has been suggested to be important for its high binding affinity. Molecular dynamics simulations of three BH3 peptides derived from the pro-apoptotic proteins Bak, Bid, and Bmf were carried out each for a period of at least 100 ns after 2 ns equilibration run. The length of simulated BH3 peptides varied from 22 to 24 residues and their binding affinities for Bfl-1/A1 varied from 1 to 180 nM. Our results show that the hydrophobic residues from the hydrophobic face of BH3 peptides tend to cluster together quickly to avoid being exposed to the solvent. This resulted in either reduction of helix length or complete loss of helical character. Bak and Bid BH3 peptides with high affinities for Bf1-1/A1 have stable helical segments in the N-terminal region. The highly conserved Leu residue lies just outside the helical region at the C-terminal end. Capping interactions arising out of N-cap residues seem to be extremely important to maintain the helical stability. Favorable hydrophilic interactions between residues also give further stability to the helix fragment and at least one of the interacting residues resides within the helical region. Bmf BH3 peptide with a weaker binding affinity for Bmf-1/A1 completely lost its helical character at the end of 100 ns production run and a further 50 ns simulation showed that the Bmf peptide continues to remain in random conformation. The present study clearly establishes a link between a BH3 peptide's ability to form a stable helical segment and its high binding affinity for an anti-apoptotic protein. To further test this hypothesis, we simulated a mutant Bmf peptide for 100 ns in which two residues R129 and H146 were substituted by Asn in silico in the wild-type peptide. Introduction of N-terminal Asn clearly enabled the formation of capping interactions at the N-terminus and resulted in a stable N-terminal helical segment. This demonstrates that the knowledge of interactions that help to maintain stable helical segments in a high-affinity BH3 peptide will help in designing highly specific peptide-based drugs/inhibitors. Such molecules will have the ability to bind a particular anti-apoptotic protein with high affinity.","corpus_id":19171537,"score":1},{"doc_id":"23510797","title":"Peptides that form β-sheets on hydrophobic surfaces accelerate surface-induced insulin amyloidal aggregation.","abstract":"Interactions between proteins and material or cellular surfaces are able to trigger protein aggregation in vitro and in vivo. The human insulin peptide segment LVEALYL is able to accelerate insulin aggregation in the presence of hydrophobic surfaces. We show that this peptide needs to be previously adsorbed on a hydrophobic surface to induce insulin aggregation. Moreover, the study of different mutant peptides proves that its sequence is less important than the secondary structure of the adsorbed peptide on the surface. Indeed, these pro-aggregative peptides act by providing stable β-sheets to incoming insulin molecules, thereby accelerating insulin adsorption locally and facilitating the conformational changes required for insulin aggregation. Conversely, a peptide known to form α-helices on hydrophobic surfaces delays insulin aggregation.","corpus_id":207661978,"score":1},{"doc_id":"24220211","title":"Mutational analysis of the rotavirus NSP4 enterotoxic domain that binds to caveolin-1.","abstract":"BACKGROUND: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction. METHODS: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed to alanine (NSP446-175-ala6); and three residues in the hydrophobic face were altered to charged amino acids (NSP4(46-175)-HydroMut). In total, twelve mutants of NSP4 were generated to define the cav-1 binding site. Synthetic peptides corresponding to the hydrophobic and charged faces of NSP4 were examined for structural changes by circular dichroism (CD) and diarrhea induction by a neonatal mouse study. RESULTS: Mutations of the hydrophilic face (NSP4(46-175)-Ala6) bound cav-1 akin to wild type NSP4. In contrast, disruption of the hydrophobic face (NSP4(46-175)-HydroMut) failed to bind cav-1. These data suggest NSP4 and cav-1 associate via a hydrophobic interaction. Analyses of mutant synthetic peptides in which the hydrophobic residues in the enterotoxic domain of NSP4 were altered suggested a critical hydrophobic residue. Both NSP4HydroMut112-140, that contains three charged amino acids (aa113, 124, 131) changed from the original hydrophobic residues and NSP4AlaAcidic112-140 that contained three alanine residues substituted for negatively charged (aa114, 125, 132) amino acids failed to induce diarrhea. Whereas peptides NSP4wild type 112-140 and NSP4AlaBasic112-140 that contained three alanine substituted for positively charged (aa115, 119, 133) amino acids, induced diarrhea. CONCLUSIONS: These data show that the cav-1 binding domain is within the hydrophobic face of the NSP4 amphipathic helix. The integrity of the helical structure is important for both cav-1 binding and diarrhea induction implying a connection between NSP4 functional and binding activities.","corpus_id":2198979,"score":1},{"doc_id":"24664416","title":"Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element.","abstract":"Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.","corpus_id":23566537,"score":1},{"doc_id":"24744084","title":"Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids.","abstract":"The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb-Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb-Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ 1 dihedral combinations (g+, g+) and (g-, g+), respectively. These low energy conformations were also observed in intrahelical Asp-Arg and Glu-Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.","corpus_id":17137775,"score":1},{"doc_id":"25083348","title":"Surfactant protein C peptides with salt-bridges (\"ion-locks\") promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein.","abstract":"Background. Surfactant protein C (SP-C; 35 residues) in lungs has a cationic N-terminal domain with two cysteines covalently linked to palmitoyls and a C-terminal region enriched in Val, Leu and Ile. Native SP-C shows high surface activity, due to SP-C inserting in the bilayer with its cationic N-terminus binding to the polar headgroup and its hydrophobic C-terminus embedded as a tilted, transmembrane α-helix. The palmitoylcysteines in SP-C act as 'helical adjuvants' to maintain activity by overriding the β-sheet propensities of the native sequences. Objective. We studied SP-C peptides lacking palmitoyls, but containing glutamate and lysine at 4-residue intervals, to assess whether SP-C peptides with salt-bridges (\"ion-locks\") promote surface activity by mimicking the α-helix and membrane topography of native SP-C. Methods. SP-C mimics were synthesized that reproduce native sequences, but without palmitoyls (i.e., SP-Css or SP-Cff, with serines or phenylalanines replacing the two cysteines). Ion-lock SP-C molecules were prepared by incorporating single or double Glu(-)-Lys(+) into the parent SP-C's. The secondary structures of SP-C mimics were studied with Fourier transform infrared (FTIR) spectroscopy and PASTA, an algorithm that predicts β-sheet propensities based on the energies of the various β-sheet pairings. The membrane topography of SP-C mimics was investigated with orientated and hydrogen/deuterium (H/D) exchange FTIR, and also Membrane Protein Explorer (MPEx) hydropathy analysis. In vitro surface activity was determined using adsorption surface pressure isotherms and captive bubble surfactometry, and in vivo surface activity from lung function measures in a rabbit model of surfactant deficiency. Results. PASTA calculations predicted that the SP-Css and SP-Cff peptides should each form parallel β-sheet aggregates, with FTIR spectroscopy confirming high parallel β-sheet with 'amyloid-like' properties. The enhanced β-sheet properties for SP-Css and SP-Cff are likely responsible for their low surfactant activities in the in vitro and in vivo assays. Although standard (12)C-FTIR study showed that the α-helicity of these SP-C sequences in lipids was uniformly increased with Glu(-)-Lys(+) insertions, elevated surfactant activity was only selectively observed. Additional results from oriented and H/D exchange FTIR experiments indicated that the high surfactant activities depend on the SP-C ion-locks recapitulating both the α-helicity and the membrane topography of native SP-C. SP-Css ion-lock 1, an SP-Css with a salt-bridge for a Glu(-)-Lys(+) ion-pair predicted from MPEx hydropathy calculations, demonstrated enhanced surfactant activity and a transmembrane helix simulating those of native SP-C. Conclusion. Highly active SP-C mimics were developed that replace the palmitoyls of SP-C with intrapeptide salt-bridges and represent a new class of synthetic surfactants with therapeutic interest.","corpus_id":15067387,"score":1},{"doc_id":"25418176","title":"Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein.","abstract":"The inner membrane of Gram-negative bacteria is negatively charged, rendering positively charged cytoplasmic proteins in close proximity likely candidates for protein-membrane interactions. YscU is a Yersinia pseudotuberculosis type III secretion system protein crucial for bacterial pathogenesis. The protein contains a highly conserved positively charged linker sequence that separates membrane-spanning and cytoplasmic (YscUC) domains. Although disordered in solution, inspection of the primary sequence of the linker reveals that positively charged residues are separated with a typical helical periodicity. Here, we demonstrate that the linker sequence of YscU undergoes a largely electrostatically driven coil-to-helix transition upon binding to negatively charged membrane interfaces. Using membrane-mimicking sodium dodecyl sulfate micelles, an NMR derived structural model reveals the induction of three helical segments in the linker. The overall linker placement in sodium dodecyl sulfate micelles was identified by NMR experiments including paramagnetic relaxation enhancements. Partitioning of individual residues agrees with their hydrophobicity and supports an interfacial positioning of the helices. Replacement of positively charged linker residues with alanine resulted in YscUC variants displaying attenuated membrane-binding affinities, suggesting that the membrane interaction depends on positive charges within the linker. In vivo experiments with bacteria expressing these YscU replacements resulted in phenotypes displaying significantly reduced effector protein secretion levels. Taken together, our data identify a previously unknown membrane-interacting surface of YscUC that, when perturbed by mutations, disrupts the function of the pathogenic machinery in Yersinia.","corpus_id":13757736,"score":1},{"doc_id":"26054932","title":"Design and characterization of a new peptide vector for short interfering RNA delivery.","abstract":"RNA interference holds tremendous potential as one of the most powerful therapeutic strategies. However, the properties of short interfering RNA (siRNA), such as hydrophilicity, negative charge, and instability in serum have limited its applications; therefore, significant efforts have been undertaken to improve its cellular uptake. Cell penetrating peptides have been utilized to deliver various biologically active molecules, such as proteins, liposomes, nanoparticles, peptide nucleic acids, and recently small interfering RNAs. Here, we introduce a new cell penetrating peptide GL1(Ac-GLWRAWLWKAFLASNWRRLLRLLR-NH2) to improve the intracellular uptake of siRNA. This peptide consists of four tryptophan residues that facilitated its binding with the cell membrane, five arginine residues and one lysine residue which are positively charged at physiological pH, which induced the formation of peptide-siRNA complexes and enhanced the affinity of the peptide and cell membrane. Moreover, GL1 adopted helical secondary structure due to the altered distribution of polar and nonpolar residues in the sequence. In this study, we investigated the effect of peptide/siRNA molar ratio on the particle size, surface charge, secondary structure, and uptake efficiency. The results showed that GL1 formed stable complexes with siRNA mainly through electrostatic interaction and hydrophobic interaction, and the complexes displayed a spherical shape with the size of ~100 nm and positive surface charge. Utilizing the techniques of fluorescence microscopy and flow cytometry, the intracellular localization of Cy3-labeled GAPDH siRNA was visualized and the cellular uptake was quantified. It is worth noting that in the serum free environment, compared to Lipofectamine 2000, GL1 achieved higher cellular uptake of siRNA (~95%); in the presence of serum, GL1 retained the same level of siRNA cellular uptake (~84%) as Lipofectamine 2000. In addition, the viability of cells treated by GL1 in all studied molar ratios was >85%, which was significantly higher than that treated by Lipofectamine 2000 (~70%). Taken together, the peptide GL1 demonstrated promise as a siRNA delivery system.","corpus_id":6360345,"score":1},{"doc_id":"27237727","title":"SAP(E) - A cell-penetrating polyproline helix at lipid interfaces.","abstract":"Cell-penetrating peptides (CPPs) are short membrane-permeating amino acid sequences that can be used to deliver cargoes, e.g. drugs, into cells. The mechanism for CPP internalization is still subject of ongoing research. An interesting family of CPPs is the sweet arrow peptides - SAP(E) - which are known to adopt a polyproline II helical secondary structure. SAP(E) peptides stand out among CPPs because they carry a net negative charge while most CPPs are positively charged, the latter being conducive to electrostatic interaction with generally negatively charged membranes. For SAP(E)s, an internalization mechanism has been proposed, based on polypeptide aggregation on the cell surface, followed by an endocytic uptake. However, this process has not yet been observed directly - since peptide-membrane interactions are inherently difficult to monitor on a molecular scale. Here, we use sum frequency generation (SFG) vibrational spectroscopy to investigate molecular interactions of SAP(E) with differently charged model membranes, in both mono- and bi-layer configurations. The data suggest that the initial binding mechanism is accompanied by structural changes of the peptide. Also, the peptide-model membrane interaction depends on the charge of the lipid headgroup with phosphocholine being a favorable binding site. Moreover, while direct penetration has also been observed for some CPPs, the spectroscopy reveals that for SAP(E), its interaction with model membranes remains limited to the headgroup region, and insertion into the hydrophobic core of the lipid layer does not occur.","corpus_id":8117127,"score":1},{"doc_id":"29074350","title":"Effects of charge and hydrophobicity on the oligomerization of peptides derived from IAPP.","abstract":"Changes in pH resulting in modifications of charge can dramatically alter the folding and interaction of proteins. This article probes the effects of charge and hydrophobicity on the oligomerization of macrocyclic β-sheet peptides derived from residues 11-17 of IAPP (RLANFLV). Previous studies have shown that a macrocyclic β-sheet peptide containing this IAPP sequence (peptide 1Arg) does not form oligomers in aqueous solution at low millimolar concentrations. Replacing arginine with the uncharged isostere citrulline generates a homologue (peptide 1Cit) that forms a tetramer consisting of a sandwich of hydrogen-bonded dimers. The current study probes the role of charge and hydrophobicity by changing residue 11 to glutamic acid (peptide 1Glu) and leucine (peptide 1Leu). Diffusion-ordered spectroscopy (DOSY) studies show that peptides 1Glu and 1Leu form tetramers in solution. NOESY studies confirm that both peptides form the same sandwich-like tetramer as peptide 1Cit. 1H NMR spectroscopy at various concentrations reveals that peptide 1Leu has the highest propensity to form tetramers. The effects of pH and charge on oligomerization are further probed by incorporating histidine at position 11 (peptide 1His). DOSY studies show that peptide 1His forms a tetramer at high pH. At low pH, peptide 1His forms a new species that has not been previously observed by our research group-a dimer. These studies demonstrate the importance of charge and hydrophobicity in the oligomerization of IAPP-derived peptides.","corpus_id":3821190,"score":1},{"doc_id":"19782154","title":"The role of hydrophobic and negatively charged surface patches of lipid-free apolipoprotein A-I in lipid binding and ABCA1-mediated cholesterol efflux.","abstract":"Recent models of lipid-free apolipoprotein A-I, including a cross-link/homology model and an X-ray crystal structure have identified two potential functionally relevant \"patches\" on the protein surface. The first is a hydrophobic surface patch composed of leucine residues 42, 44, 46, and 47 and the second a negatively charged patch composed of glutamic acid residues 179, 191, and 198. To determine if these domains play a functional role, these surface patches were disrupted by site-directed mutagenesis and the bacterially expressed mutants were compared with respect to their ability to bind lipid and stimulate ABCA1-mediated cholesterol efflux. It was found that neither patch plays a significant functional role in the ability of apoA-I to accept cholesterol in an ABCA1-dependent manner, but that the hydrophobic patch did affect the ability of apoA-I to clear DMPC liposomes. Interestingly, contrary to previous predictions, disruption of the hydrophobic surface patch enhanced the lipid binding ability of apoA-I. The hydrophobic surface patch may be important to the structural stability of lipid-free apoA-I or may be a necessary permissive structural element for lipid binding.","corpus_id":38785163,"score":0},{"doc_id":"20798341","title":"Charges in the hydrophobic interior of proteins.","abstract":"Charges are inherently incompatible with hydrophobic environments. Presumably for this reason, ionizable residues are usually excluded from the hydrophobic interior of proteins and are found instead at the surface, where they can interact with bulk water. Paradoxically, ionizable groups buried in the hydrophobic interior of proteins play essential roles, especially in biological energy transduction. To examine the unusual properties of internal ionizable groups we measured the pK(a) of glutamic acid residues at 25 internal positions in a stable form of staphylococcal nuclease. Two of 25 Glu residues titrated with normal pK(a) near 4.5; the other 23 titrated with elevated pK(a) values ranging from 5.2-9.4, with an average value of 7.7. Trp fluorescence and far-UV circular dichroism were used to monitor the effects of internal charges on conformation. These data demonstrate that although charges buried in proteins are indeed destabilizing, charged side chains can be buried readily in the hydrophobic core of stable proteins without the need for specialized structural adaptations to stabilize them, and without inducing any major conformational reorganization. The apparent dielectric effect experienced by the internal charges is considerably higher than the low dielectric constants of hydrophobic matter used to represent the protein interior in electrostatic continuum models of proteins. The high thermodynamic stability required for proteins to withstand the presence of buried charges suggests a pathway for the evolution of enzymes, and it underscores the need to mind thermodynamic stability in any strategy for engineering novel or altered enzymatic active sites in proteins.","corpus_id":25040424,"score":0},{"doc_id":"23422441","title":"α-Helix mimicry with α/β-peptides.","abstract":"We describe a general strategy for creating peptidic oligomers that have unnatural backbones but nevertheless adopt a conformation very similar to the α-helix. These oligomers contain both α- and β-amino acid residues (α/β-peptides). If the β content reaches 25-30% of the residue total, and the β residues are evenly distributed along the backbone, then substantial resistance to proteolytic degradation is often observed. These α/β-peptides can mimic the informational properties of α-helices involved in protein-protein recognition events, as documented in numerous crystal structures. Thus, these unnatural oligomers can be a source of antagonists of undesirable protein-protein interactions that are mediated by natural α-helices, or agonists of receptors for which the natural polypeptide ligands are α-helical. Successes include mimicry of BH3 domains found in proapoptotic proteins, which leads to ligands for antiapoptotic Bcl-2 family proteins, and mimicry of the gp41 CHR domain, which leads to inhibition of HIV infection in cell-based assays.","corpus_id":31267715,"score":0},{"doc_id":"23496521","title":"Interaction between heterogeneously charged surfaces: surface patches and charge modulation.","abstract":"When solid surfaces are immersed in aqueous solutions, some of their charges can dissociate and leave behind charged patches on the surface. Although the charges are distributed heterogeneously on the surface, most of the theoretical models treat them as homogeneous. For overall non-neutral surfaces, the assumption of surface charge homogeneity is rather reasonable since the leading terms of two such interacting surfaces depend on the nonzero average charge. However, for overall neutral surfaces the nature of the surface charge distribution is crucial in determining the intersurface interaction. In the present work we study the interaction between two charged surfaces across an aqueous solution for several charge distributions. The analysis is preformed within the framework of the linearized Poisson-Boltzmann theory. For periodic charge distributions the interaction is found to be repulsive at small separations, unless the two surface distributions are completely out-of-phase with respect to each other. For quenched random charge distributions we find that due to the presence of the ionic solution in between the surfaces, the intersurface repulsion dominates over the attraction in the linear regime of the Poisson-Boltzmann theory. The effect of quenched charge heterogeneity is found to be particularly substantial in the case of large charged domains.","corpus_id":10181505,"score":0},{"doc_id":"24829339","title":"Glutamic acid at residue 125 of the prM helix domain interacts with positively charged amino acids in E protein domain II for Japanese encephalitis virus-like-particle production.","abstract":"UNLABELLED: Interaction between E and prM proteins in flavivirus-infected cells is a major factor for virus-like particle (VLP) production. The prM helical (prM-H) domain is topologically close to and may interact with domain II of the E protein (EDII). In this study, we investigated prM-H domain amino acid residues facing Japanese encephalitis virus EDII using site-directed mutagenesis to determine their roles in prM-E interaction and VLP production. Our results indicate that negatively charged prM-E125 residue at the prM-H domain affected VLP production via one or more interactions with positively charged E-K93 and E-H246 residues at EDII. Exchanges of oppositely charged residue side chains at prM-E125/E-K93 and prM-E125/E-H246 are recoverable for VLP production. The prM-E125 and E-H246 residues are conserved and that the positive charge of the E-K93 residue is preserved in different flavivirus groups. These findings suggest that the electrostatic attractions of prM-E125, E-K93, and E-H246 residues are important to flavivirus VLP production and that inhibiting these interactions is a potential strategy for blocking flavivirus infections. IMPORTANCE: Molecular interaction between E and prM proteins of Japanese encephalitis virus is a major driving force for virus-like particle (VLP) production. The current high-resolution structures available for prM-E complexes do not include the membrane proximal stem region of prM. The prM stem region contains an N-terminal loop and a helix domain (prM-H). Since the prM-H domain is topologically close to domain II of the E protein (EDII), this study was to determine molecular interactions between the prM-H domain and EDII. We found that the molecular interactions between prM-E125 residue and positively charged E-K93 and E-H246 residues at EDII are critical for VLP production. More importantly, the prM-E125 and E-H246 residues are conserved and the positive charge of the E-K93 residue is preserved in different flavivirus groups. Our findings help refine the structure and molecular interactions on the flavivirus surface and reveal a potential strategy for blocking flavivirus infections by inhibiting these electrostatic interactions.","corpus_id":35256885,"score":0},{"doc_id":"25257385","title":"Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.","abstract":"α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins.","corpus_id":19661758,"score":0}],"string":"[\n {\n \"doc_id\": \"18098173\",\n \"title\": \"Effects of net charge and the number of positively charged residues on the biological activity of amphipathic alpha-helical cationic antimicrobial peptides.\",\n \"abstract\": \"In our previous study, we utilized a 26-residue amphipathic alpha-helical antimicrobial peptide L-V13K (Chen et al., Antimicrob Agents Chemother 2007, 51, 1398-1406) as the framework to study the effects of peptide hydrophobicity on the mechanism of its antimicrobial action. In this study, we explored the effects of net charge and the number of positively charged residues on the hydrophilic/polar face of L-V13K on its biological activity (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity, helicity, and peptide self-association). The net charge of V13K analogs at pH 7 varied between -5 and +10 and the number of positively charged residues varied from 1 to 10. The minimal inhibitory concentrations (MIC) against six strains of Pseudomonas aeruginosa as well as other gram-negative and gram-positive bacteria were determined along with the maximal peptide concentration that produces no hemolysis of human red blood cells (MHC). Our results show that the number of positively charged residues on the polar face and net charge are both important for both antimicrobial activity and hemolytic activity. The most dramatic observation is the sharp transition of hemolytic activity on increasing one positive charge on the polar face of V13K i.e., the change from +8 to +9 resulted in greater than 32-fold increase in hemolytic activity (250 microg/ml to <7.8 microg/ml, respectively).\",\n \"corpus_id\": 11073670,\n \"score\": 2\n },\n {\n \"doc_id\": \"18186474\",\n \"title\": \"On defining the dynamics of hydrophobic patches on protein surfaces.\",\n \"abstract\": \"We present a simple and efficient method called PATCHTRACK, for studying the dynamics of hydrophobic surface patches. It tracks the patches on snapshot structures taken from a Molecular Dynamics simulation. They are connected into so-called patch runs, which are subsequently clustered into so-called recurrent patches. The method is applied to simulations of three different proteins. Protein motion causes addition and removal of one or more atoms to a patch, resulting in size fluctuations of around 25%. The fluctuations eventually lead to the break-up of a patch, and their average life span is therefore remarkably short at around 4 ps. However, some patch runs are much more stable, lasting hundreds of picoseconds. One such case is the largest patch in amicyanin that is known to be biologically relevant. Another case, previously not reported, is found in phospholipase A(2), where the functional significance of a large recurrent patch formed by Leu58 and Phe94 seems likely. This patch appears to have been overlooked as it is relatively small in the X-ray structure, demonstrating the utility of the current method. The most frequently occurring patch size is 40-60 A(2), but sizes of up to 500 A(2) are also observed. There is no clear relation between patch run durations and their average size. However, long-lasting patch runs tend not to have large fluctuations. The recurrent patches have alternating periods of \\\"liveness\\\" and \\\"dormancy\\\"; around 25% of them is predominantly in the live state.\",\n \"corpus_id\": 25759192,\n \"score\": 2\n },\n {\n \"doc_id\": \"18434320\",\n \"title\": \"Origin of low mammalian cell toxicity in a class of highly active antimicrobial amphipathic helical peptides.\",\n \"abstract\": \"We recently described a novel antimicrobial peptide, RTA3, derived from the commensal organism Streptococcus mitis, with strong anti-Gram-negative activity, low salt sensitivity, and minimal mammalian cell toxicity in vitro and in vivo. This peptide conforms to the positively charged, amphipathic helical peptide motif, but has a positively charged amino acid (Arg-5) on the nonpolar face of the helical structure that is induced upon membrane binding. We surmised that disruption of the hydrophobic face with a positively charged residue plays a role in minimizing eukaryotic cell toxicity, and we tested this using a mutant with an R5L substitution. The greatly enhanced toxicity in the mutant peptide correlated with its ability to bind and adopt helical conformations upon interacting with neutral membranes; the wild type peptide RTA3 did not bind to neutral membranes (binding constant reduced by at least 1000-fold). Spectroscopic analysis indicates that disruption of the hydrophobic face of the parent peptide is accommodated in negatively charged membranes without partial peptide unfolding. These observations apply generally to amphipathic helical peptides of this class as we obtained similar results with a peptide and mutant pair (Chen, Y., Mant, C. T., Farmer, S. W., Hancock, R. E., Vasil, M. L., and Hodges, R. S. (2005) J. Biol. Chem. 280, 12316-12329) having similar structural properties. In contrast to previous interpretations, we demonstrate that these peptides simply do not bind well to membranes (like those of eukaryotes) with exclusively neutral lipids in their external bilayer leaflet. We highlight a significant role for tryptophan in promoting binding of amphipathic helical peptides to neutral bilayers, augmenting the arsenal of strategies to reduce mammalian toxicity in antimicrobial peptides.\",\n \"corpus_id\": 22700884,\n \"score\": 2\n },\n {\n \"doc_id\": \"18658220\",\n \"title\": \"Structure and dynamics of helix-0 of the N-BAR domain in lipid micelles and bilayers.\",\n \"abstract\": \"Bin/Amphiphysin/Rvs-homology (BAR) domains generate and sense membrane curvature by binding the negatively charged membrane to their positively charged concave surfaces. N-BAR domains contain an N-terminal extension (helix-0) predicted to form an amphipathic helix upon membrane binding. We determined the NMR structure and nano-to-picosecond dynamics of helix-0 of the human Bin1/Amphiphysin II BAR domain in sodium dodecyl sulfate and dodecylphosphocholine micelles. Molecular dynamics simulations of this 34-amino acid peptide revealed electrostatic and hydrophobic interactions with the detergent molecules that induce helical structure formation from residues 8-10 toward the C-terminus. The orientation in the micelles was experimentally confirmed by backbone amide proton exchange. The simulation and the experiment indicated that the N-terminal region is disordered, and the peptide curves to adopted the micelle shape. Deletion of helix-0 reduced tubulation of liposomes by the BAR domain, whereas the helix-0 peptide itself was fusogenic. These findings support models for membrane curving by BAR domains in which helix-0 increases the binding affinity to the membrane and enhances curvature generation.\",\n \"corpus_id\": 42380634,\n \"score\": 2\n },\n {\n \"doc_id\": \"19045429\",\n \"title\": \"Model simulations of the adsorption of statherin to solid surfaces: Effects of surface charge and hydrophobicity.\",\n \"abstract\": \"The structural properties of the salivary protein statherin upon adsorption have been examined using a coarse-grained model and Monte Carlo simulation. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. To mimic hydrophobically modified surfaces, an extra short-ranged interaction was implemented between the amino acids and the surface. It has been shown that the adsorption and the thickness of the adsorbed layer are determined by (i) the affinity for the surface, i.e., denser layer with an extrashort-ranged potential, and (ii) the distribution of the charges along the chain. If all the amino acids have a high affinity for the surface, the protein adsorbs in a train conformation, if the surface is negatively charged the protein adsorbs in a tail-train conformation, whereas if the surface is positively charged the protein adsorbs in a loop conformation. The latter gives rise to a more confined adsorbed layer.\",\n \"corpus_id\": 1697069,\n \"score\": 2\n },\n {\n \"doc_id\": \"19550040\",\n \"title\": \"Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes.\",\n \"abstract\": \"We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from -1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide-membrane interactions.\",\n \"corpus_id\": 20559171,\n \"score\": 2\n },\n {\n \"doc_id\": \"19885920\",\n \"title\": \"Importance of the spatial display of charged residues in heparin-peptide interactions.\",\n \"abstract\": \"Many studies have examined consensus sequences required for protein-glycosaminoglycan interactions. Through the synthesis of helical heparin binding peptides, this study probes the relationship between spatial arrangement of positive charge and heparin binding affinity. Peptides with a linear distribution of positive charge along one face of the alpha-helix had the highest affinity for heparin. Moving the basic residues away from a single face resulted in drastic changes in heparin binding affinity of up to three orders of magnitude. These findings demonstrate that amino acid sequences, different from the known heparin binding consensus sequences, will form high affinity protein-heparin binding interactions when the charged residues are aligned linearly.\",\n \"corpus_id\": 5149095,\n \"score\": 2\n },\n {\n \"doc_id\": \"20158215\",\n \"title\": \"Bridged beta(3)-peptide inhibitors of p53-hDM2 complexation: correlation between affinity and cell permeability.\",\n \"abstract\": \"Beta-peptides possess several features that are desirable in peptidomimetics; they are easily synthesized, fold into stable secondary structures in physiologic buffers, and resist proteolysis. They can also bind to a diverse array of proteins to inhibit their interactions with alpha-helical ligands. beta-peptides are usually not cell-permeable, however, and this feature limits their utility as research tools and potential therapeutics. Appending an Arg(8) sequence to a beta-peptide improves uptake but adds considerable mass. We previously reported that embedding a small cationic patch within a PPII, alpha-, or beta-peptide helix improves uptake without the addition of significant mass. In another mass-neutral strategy, Verdine, Walensky, and others have reported that insertion of a hydrocarbon bridge between the i and i + 4 positions of an alpha-helix also increases cell uptake. Here we describe a series of beta-peptides containing diether and hydrocarbon bridges and compare them on the basis of cell uptake and localization, affinities for hDM2, and 14-helix structure. Our results highlight the relative merits of the cationic-patch and hydrophobic-bridge strategies for improving beta-peptide uptake and identify a surprising correlation between uptake efficiency and hDM2 affinity.\",\n \"corpus_id\": 207152437,\n \"score\": 2\n },\n {\n \"doc_id\": \"20346912\",\n \"title\": \"Thermodynamics of RTA3 peptide binding to membranes and consequences for antimicrobial activity.\",\n \"abstract\": \"RTA3 is an alpha-helical, amphipathic peptide with broad-spectrum activity against Gram-negative bacteria and low mammalian cell toxicity. RTA3 contains a cysteine residue, replacement of which with an alanine or serine (RTA3-C15S) virtually abolishes antimicrobial activity. Much of the activity of RTA3 can be recovered in RTA3-C15L, indicating that the C15 residue functions largely as a bulky hydrophobic side chain promoting target cell membrane interactions. The poorly active RTA3-C15S is a useful variant for assessing the mechanistic aspects of RTA3 activity. Binding and membrane perturbation in vesicles containing different proportions of negative surface charge are analyzed in terms of amino acid-specific free energy contributions to interfacial binding, which likely underlie variations in antimicrobial activity amongst RTA3 variants. Comparison with published free energy scales indicates that the reduced electrostatic contribution to binding to membranes having reduced negative surface charge can be compensated in RTA3 (but not RTA3-C15S) by a slightly deeper insertion of the C-terminus of the peptide to maximize hydrophobic contributions to binding. Analysis of inner membrane (IM)- and outer membrane (OM)-selective permeabilization of Escherichiacoli demonstrates a broad similarity between peptide effects on vesicles with low negative surface charge (20% negatively charged lipids), E.coli membrane perturbation, and antimicrobial activity, supporting a role for membrane perturbation in the killing mechanism of RTA3. The results demonstrate that large variations in antimicrobial activity on subtle changes in amino acid sequence in helical amphipathic peptides can be rationalized in terms of the thermodynamics of peptide binding to membranes, allowing a more systematic understanding of antimicrobial activity in these peptides.\",\n \"corpus_id\": 28918133,\n \"score\": 2\n },\n {\n \"doc_id\": \"20572020\",\n \"title\": \"Interaction of an ionic complementary peptide with a hydrophobic graphite surface.\",\n \"abstract\": \"Protein adsorption on a surface plays an important role in biomaterial science and medicine. It is strongly related to the interaction between the protein residues and the surface. Here we report all-atom molecular dynamics simulations of the adsorption of an ionic complementary peptide, EAK16-II, to the hydrophobic highly ordered pyrolytic graphite surface. We find that, the hydrophobic interaction is the main force to govern the adsorption, and the peptide interchain electrostatic interaction affects the adsorption rate. Under neutral pH condition, the interchain electrostatic attraction facilitates the adsorption, whereas under acidic and basic conditions, because of the protonation and deprotonation of glutamic acid and lysine residues, respectively, the resulting electrostatic repulsion slows down the adsorption. We also found that under basic condition, during the adsorption peptide Chain II will be up against a choice to adsorb to the surface through the hydrophobic interaction or to form a temporary hydrophobic core with the deposited peptide Chain I. These results provide a basis for understanding some of the fundamental interactions governing peptide adsorption on the surface, which can shed new light on novel applications, such as the design of implant devices and drug delivery materials.\",\n \"corpus_id\": 21034771,\n \"score\": 2\n },\n {\n \"doc_id\": \"20673228\",\n \"title\": \"Amphipathic antimicrobial peptides--from biophysics to therapeutics?\",\n \"abstract\": \"Amphipathic peptides are accommodated within the diffuse gradient of polarity that characterizes the interfacial regions of phospholipid bilayer membranes. Interfacial membrane interactions are key to the diverse biological functions and activities of these peptides, which encompass a large class of antimicrobial peptides, including the helical peptides magainin, melittin, and RTA3 derived from the commensal bacterium Streptococcus mitis. For these peptides in vitro efficacy (high antimicrobial activity with minimal mammalian cell toxicity, equivalent to high potential therapeutic index; PTI), can be broadly understood in relation to the thermodynamics of interfacial binding and membrane disruption in membranes having surface charges that correspond to bacterial and mammalian cell membranes, respectively. Peptides with disrupted amphipathicity resulting from a positively charged amino acid residue on the non-polar helix face, can have greatly enhanced PTI, although a balance of amphipathicity, hydrophobicity and positive charge is required for retention of high antimicrobial activity. These observations are illustrated with recent examples from the literature, and studies on RTA3 and magainin analogues from our laboratories. Despite the identification and optimisation of peptides with very good PTI, a focus on addressing toxicity upon systemic administration and poor in vivo efficacy is likely to be required to translate growing understanding of the relationships between peptide interfacial activity and effects on cells, into novel systemic therapeutics.\",\n \"corpus_id\": 22813147,\n \"score\": 2\n },\n {\n \"doc_id\": \"21257813\",\n \"title\": \"Mutational analysis of residues in the helical region of the class IIa bacteriocin pediocin PA-1.\",\n \"abstract\": \"A 15-mer fragment that is derived from the helical region in the C-terminal half of pediocin PA-1 inhibited the activity of pediocin PA-1. Of 13 other pediocin-like (hybrid) bacteriocins, only the hybrid bacteriocin Sak/Ped was markedly inhibited by the 15-mer fragment. Sak/Ped was the only one of these bacteriocins that had a sequence (in the C-terminal helix-containing half) identical to that of the 15-mer fragment, indicating that the fragment inhibits pediocin-like bacteriocins in a sequence-dependent manner. By replacing (one at a time) all 15 residues in the fragment with Ala or Leu, five residues (K1, A2, T4, N8, and A15) were identified as being especially important for the inhibitory action of the fragment. The results suggest that the corresponding residues (K20, A21, T23, N27, and A34, respectively) in pediocin PA-1 might be involved in interactions between pediocin PA-1 and its receptor. To characterize the environment surrounding these five residues when pediocin PA-1 interacts with target cells, these residues were replaced (one at a time) with a hydrophobic large (Leu) residue, a hydrophilic charged (Asp or Arg) residue, and a small (Ala or Gly) residue. The results revealed that residues A21 and A34 are in a spatially constrained environment, since the replacement with a small (Gly) residue was the only substitution that did not markedly reduce the bacteriocin activity. The positive charge in K20 and the polar amide group in N27 appeared to interact with electronegative groups, since the replacement of these two residues with a positive (Arg) residue was well tolerated, while replacement with a negative (Asp) residue was detrimental to the bacteriocin activity. K20 was in a less constrained environment than N27, since the replacement of K20 with a large hydrophobic (Leu) residue was tolerated fairly well and to a greater extent than N27. T23 seemed to be in an environment that was not restricted with respect to size, polarity, and charge, since replacements with large (Leu) and small (Ala) hydrophobic residues and a hydrophilic negative (Asp) residue were tolerated fairly well (2- to 6-fold reduction in activity). Moreover, the replacement of T23 with a large positive (Arg) residue resulted in wild-type or better-than-wild-type activity.\",\n \"corpus_id\": 3079556,\n \"score\": 2\n },\n {\n \"doc_id\": \"21409455\",\n \"title\": \"Hydrophobicity drives the cellular uptake of short cationic peptide ligands.\",\n \"abstract\": \"Short cationic linear peptide analogs (LPAs, prepared as Arg-C( n )-Arg-C( n )-Lys, where C( n ) represents an alkyl linkage with n = 4, 7 or 11) were synthesized and tested in human breast carcinoma BT-20 and CCRF-CEM leukemia cells for their application as targeting ligands. With constant LPA charge (+4), increasing the alkyl linkage increases the hydrophobic/hydrophilic balance and provides a systematic means of examining combined electrostatic and hydrophobic peptide-membrane interactions. Fluorescently conjugated LPA-C(11) (F-LPA-C(11)) demonstrated significant uptake, whereas there was negligible uptake of the shorter LPAs. By varying temperature (4°C and 37°C) and cell type, the results suggest that LPA-C(11) internalization is nonendocytic and nonspecific. The effect of LPA binding on the phase behavior, structure, and permeability of model membranes composed of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine (DPPC/DPPS, 85/15) was studied using differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and fluorescence leakage studies to gain insight into the LPA uptake mechanism. While all LPAs led to phase separation, LPA-C(11), possessing the longest alkyl linkage, was able to penetrate into the bilayer and caused holes to form, which led to membrane disintegration. This was confirmed by rapid and complete dye release by LPA-C(11). We propose that LPA-C(11) achieves uptake by anchoring to the membrane via hydrophobicity and forming transient membrane voids. LPAs may be advantageous as drug transporter ligands because they are small, water soluble, and easy to prepare.\",\n \"corpus_id\": 22780672,\n \"score\": 2\n },\n {\n \"doc_id\": \"21523491\",\n \"title\": \"Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X(L).\",\n \"abstract\": \"The B-cell lymphoma 2 (Bcl-2) family of proteins regulates the intrinsic pathway of apoptosis. Interactions between specific anti- and pro-apoptotic Bcl-2 proteins determine the fate of a cell. Anti-apoptotic Bcl-2 proteins have been shown to be over-expressed in certain cancers and they are attractive targets for developing anti-cancer drugs. Peptides from the BH3 region of pro-apoptotic proteins have been shown to interact with anti-apoptotic Bcl-2 proteins and induce biological activity similar to that observed in parent proteins. However, the specificity of BH3 peptides derived from different pro-apoptotic proteins differ for different anti-apoptotic Bcl-2 proteins. In this study, we have investigated the relationship between the stable helical nature of BH3 peptides and their affinities to Bcl-X(L), an anti-apoptotic Bcl-2 protein. We have carried out molecular dynamics simulations of six BH3 peptides derived from Bak, Bad and Bim pro-apoptotic proteins for a period of 50 ns each in aqueous medium. Due to the amphipathic nature of BH3 peptides, the hydrophobic residues on the hydrophobic face tend to cluster together in all BH3 peptides. While this process resulted in a complete loss of helical structure in 16-mer Bak and 16-mer Bad wild type peptides, stabilizing interactions in the hydrophilic face of the BH3 peptides and capping interactions helped to maintain partial helical character in 16-mer Bad mutant and 16-mer Bim peptides. The latter two 16-mer peptides exhibit higher affinity for Bcl-X(L). Similarly the longer BH3 peptides, 25-mer Bad and 33-mer Bim, also resulted in smaller and stable helical fragments and their helical conformation is stabilized by interactions between residues in the solvent-exposed hydrophilic half of the peptide. The stable nature of helical segment in a BH3 peptide can be directly correlated to its binding affinity and the helical region encompassed the highly conserved Leu residue. We propose that upon approaching the hydrophobic groove of anti-apoptotic proteins, a longer helix will be induced in high affinity BH3 peptides by extending the smaller stable helical segments around the conserved Leu residue in both N- and C-terminal regions. The results reported in this study will have implications in developing peptide-based inhibitors for anti-apoptotic Bcl-2 proteins.\",\n \"corpus_id\": 685198,\n \"score\": 2\n },\n {\n \"doc_id\": \"21875799\",\n \"title\": \"Cellular uptake of Aib-containing amphipathic helix peptide.\",\n \"abstract\": \"Cell-penetrating peptides (CPPs) are useful tools for the delivery of hydrophilic bioactive molecules, such as peptides, proteins, and oligonucleotides, across the cell membrane. To realize the delivery of therapeutic macromolecules by CPPs, the CPPs are required to show resistance to protease and no cytotoxicity. In order to produce potent non-toxic and protease-resistant CPPs with high cellular uptake, we designed an amphipathic helix peptide using α-aminoisobutyric acid (Aib, U) and named it MAP(Aib). In the MAP(Aib) molecule, five Aib residues are aligned on the hydrophobic face of the helix and five lysine (K) residues are aligned on the hydrophilic face. MAP(Aib) showed potent resistance to trypsin and pronase compared with MAP, an amphipathic helix peptide formed by usual amino acids. Fluorescein-labeled MAP(Aib) efficiently traversed the A549 cell membrane, diffusing into the cytoplasm and slightly into the nucleus without exerting any cytotoxicity. In contrast, MAP was poorly taken up by the cell. These results indicate that the incorporation of Aib residues into CPPs markedly improves cellular uptake and MAP(Aib) may be a useful tool for the delivery of hydrophilic macromolecules.\",\n \"corpus_id\": 13361019,\n \"score\": 2\n },\n {\n \"doc_id\": \"22290189\",\n \"title\": \"Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides.\",\n \"abstract\": \"Antimicrobial peptides often permeabilize biological membranes via a pore mechanism. Two pore types have been proposed: toroidal, where the pore is partly lined by lipid, and barrel-stave, where a cylindrical pore is completely lined by peptides. What drives the preference of antimicrobial peptides for a certain pore type is not yet fully understood. According to neutron scattering and oriented circular dichroism, melittin and MG-H2 induce toroidal pores whereas alamethicin forms barrel-stave pores. In previous work we found that indeed melittin seems to favor toroidal pores whereas alamethicin favors cylindrical pores. Here we designed mutants of these two peptides and the magainin analog MG-H2, aimed to probe how the distribution of charges along the helix and its imperfectly amphipathic structure influence pore formation. Molecular dynamics (MD) simulations of the peptides in a pre-formed cylindrical pore have been performed. The duration of the simulations was 136ns to 216ns. We found that a melittin mutant with lysine 7 neutralized favors cylindrical pores whereas a MG-H2 mutant with lysines in the N-terminal half of these peptides neutralized and an alamethicin mutant with a positive charge at the position 7 form semitoroidal pores. These results suggest that charged residues within the N-terminal half are important for toroidal pore formation. Toroidal pores produced by MG-H2 are more disordered than the melittin pores, likely because of the charged residues located in the middle of the MG-H2 helix (K11 and K14). Imperfect amphipathicity of melittin seems to play a role in its preference for toroidal pores since the substitutions of charged residues located within the nonpolar face by hydrophobic residues suppress evolution of a toroidal pore. The mutations change the position of lysine 7 near the N-terminus, relative to the lower leaflet headgroups. The MD simulations also show that the melittin P14A mutant forms a toroidal pore, but its configuration diverges from that of melittin and it is probably metastable.\",\n \"corpus_id\": 33098301,\n \"score\": 2\n },\n {\n \"doc_id\": \"22783871\",\n \"title\": \"Adsorption of unstructured protein β-casein to hydrophobic and charged surfaces.\",\n \"abstract\": \"In this Monte Carlo simulation study we use mesoscopic modeling to show that β-casein, an unstructured milk protein, adsorbs to surfaces not only due to direct electrostatic and hydrophobic interactions but also due to structural rearrangement and charge regulation due to proton uptake and release. β-casein acts as an amphiphilic chameleon, changing properties according to the chemical environment, and binding is observed to both positively and negatively charged surfaces. The binding mechanisms, however, are fundamentally different. A detailed, per-residue-level analysis shows that the adsorption process is controlled by a few very specific regions of the protein and that these change dramatically with pH. Caseins, being the most abundant proteins in milk, are crucial for the properties of fermented dairy products, such as nutrition, texture, and viscosity, but may also influence adhesion to packaging materials. The latter leads to product losses of about 10%, leading to economical and environmental problems.\",\n \"corpus_id\": 41458963,\n \"score\": 2\n },\n {\n \"doc_id\": \"22837667\",\n \"title\": \"Role of helicity on the anticancer mechanism of action of cationic-helical peptides.\",\n \"abstract\": \"In the present study, the 26-residue amphipathic α-helical peptide A12L/A20L (Ac-KWKSFLKTFKSLKKTVLHTLLKAISS-amide) with strong anticancer activity and specificity was used as the framework to study the effects of helicity of α-helical anticancer peptides on biological activities. Helicity was systematically modulated by introducing d-amino acids to replace the original l-amino acids on the non-polar face or the polar face of the helix. Peptide helicity was measured by circular dichroism spectroscopy and was demonstrated to correlate with peptide hydrophobicity and the number of d-amino acid substitutions. Biological studies showed that strong hemolytic activity of peptides generally correlated with high hydrophobicity and helicity. Lower helicity caused the decrease of anti-HeLa activity of peptides. By introducing d-amino acids to replace the original l-amino acids on the non-polar face or the polar face of the helix, we improved the therapeutic index of A12L/A20L against HeLa cells by 9-fold and 22-fold, respectively. These results show that the helicity of anticancer peptides plays a crucial role for biological activities. This specific rational approach of peptide design could be a powerful method to improve the specificity of anticancer peptides as promising therapeutics in clinical practices.\",\n \"corpus_id\": 395634,\n \"score\": 2\n },\n {\n \"doc_id\": \"24021230\",\n \"title\": \"Design of imperfectly amphipathic α-helical antimicrobial peptides with enhanced cell selectivity.\",\n \"abstract\": \"Antimicrobial peptides (AMPs), which are produced by multicellular organisms as a defense mechanism against competing pathogenic microbes, appear to be excellent candidates for the development of novel antimicrobial agents. Amphipathicity is traditionally believed to be crucial to the de novo design or systematic optimization of AMPs. In this study, we designed a series of short α-helical AMPs with imperfect amphipathicity to augment the arsenal of strategies and to gain further insights into their antimicrobial and hemolytic activity. These imperfectly amphipathic α-helical AMPs were designed by replacing the paired charged amino acid residues on the polar face of an amphipathic peptide with tryptophan residues on the basis of α-helical protein folding principles. PRW4, an imperfectly amphipathic α-helical AMP with hydrogen bonds formed by paired tryptophan residues, was observed to be more selective towards bacterial cells than toward human red blood cells. PRW4 was also effective against Gram-negative and Gram-positive bacteria, and fluorescence spectroscopy, flow cytometry, scanning electron microscopy and transmission electron microscopy indicated that PRW4 killed microbial cells by permeabilizing the cell membrane and damaging their membrane integrity. Therefore, disruptive amphipathicity has excellent potential for the rational design and optimization of AMPs with promising antimicrobial activities.\",\n \"corpus_id\": 205247649,\n \"score\": 2\n },\n {\n \"doc_id\": \"24743023\",\n \"title\": \"Peptide:lipid ratio and membrane surface charge determine the mechanism of action of the antimicrobial peptide BP100. Conformational and functional studies.\",\n \"abstract\": \"The cecropin-melittin hybrid antimicrobial peptide BP100 (H-KKLFKKILKYL-NH2) is selective for Gram-negative bacteria, negatively charged membranes, and weakly hemolytic. We studied BP100 conformational and functional properties upon interaction with large unilamellar vesicles, LUVs, and giant unilamellar vesicles, GUVs, containing variable proportions of phosphatidylcholine (PC) and negatively charged phosphatidylglycerol (PG). CD and NMR spectra showed that upon binding to PG-containing LUVs BP100 acquires α-helical conformation, the helix spanning residues 3-11. Theoretical analyses indicated that the helix is amphipathic and surface-seeking. CD and dynamic light scattering data evinced peptide and/or vesicle aggregation, modulated by peptide:lipid ratio and PG content. BP100 decreased the absolute value of the zeta potential (ζ) of LUVs with low PG contents; for higher PG, binding was analyzed as an ion-exchange process. At high salt, BP100-induced LUVS leakage requires higher peptide concentration, indicating that both electrostatic and hydrophobic interactions contribute to peptide binding. While a gradual release took place at low peptide:lipid ratios, instantaneous loss occurred at high ratios, suggesting vesicle disruption. Optical microscopy of GUVs confirmed BP100-promoted disruption of negatively charged membranes. The mechanism of action of BP100 is determined by both peptide:lipid ratio and negatively charged lipid content. While gradual release results from membrane perturbation by a small number of peptide molecules giving rise to changes in acyl chain packing, lipid clustering (leading to membrane defects), and/or membrane thinning, membrane disruption results from a sequence of events - large-scale peptide and lipid clustering, giving rise to peptide-lipid patches that eventually would leave the membrane in a carpet-like mechanism.\",\n \"corpus_id\": 205845550,\n \"score\": 2\n },\n {\n \"doc_id\": \"24828311\",\n \"title\": \"Comparative α-helicity of cyclic pentapeptides in water.\",\n \"abstract\": \"Helix-constrained polypeptides have attracted great interest for modulating protein-protein interactions (PPI). It is not known which are the most effective helix-inducing strategies for designing PPI agonists/antagonists. Cyclization linkers (X1-X5) were compared here, using circular dichroism and 2D NMR spectroscopy, for α-helix induction in simple model pentapeptides, Ac-cyclo(1,5)-[X1-Ala-Ala-Ala-X5]-NH2, in water. In this very stringent test of helix induction, a Lys1→Asp5 lactam linker conferred greatest α-helicity, hydrocarbon and triazole linkers induced a mix of α- and 3₁₀-helicity, while thio- and dithioether linkers produced less helicity. The lactam-linked cyclic pentapeptide was also the most effective α-helix nucleator attached to a 13-residue model peptide.\",\n \"corpus_id\": 205379007,\n \"score\": 2\n },\n {\n \"doc_id\": \"24842084\",\n \"title\": \"Effects of residue 5-point mutation and N-terminus hydrophobic residues on temporin-SHc physicochemical and biological properties.\",\n \"abstract\": \"Temporin-SHc (FLSHIAGFLSNLFamide) first isolated from skin extraction of the Tunisian frog Pelophylax saharica, which shows potent antimicrobial activity against Gram-positive bacteria and is highly active against yeasts and fungi without hemolytic activity at antimicrobial concentrations. The peptide adopts well-defined α-helical conformation when bound to SDS micelles. In this study, we explored the effects of residue at position 5 and the N-terminus hydrophobic character on the hydrophilic/polar face of temp-SHc, on its biological activities (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity and helicity). Antibacterial and hemolytic properties of temporin-SHc derivatives depend strongly on physicochemical properties. Therefore, slight decreasing amphipathicity together with hydrophobicity and helicity by the substitution Ile(5) → Leu decreased antimicrobial potency approximately twofold without changing of hemolytic activity. It is noteworthy that a conservative amino acid substitution decreases the antimicrobial activity, underlining the differences between Leu/Ile side chains insertion into the lipid bilayer. While the modification of N-terminal hydrophobic character by four residue inversion decreased amphipathicity (twofold) of (4-1)L5temp-SHc and resulted in an increase in antibacterial activity against E. coli, E. faecalis and C. parapsilosis of at least fourfold, its therapeutic potential is limited by its drastic increase of hemolysis (LC₅₀ = 2 μM). We found that the percentage of helicity of temp-SHc analog is directly correlated to its hemolytic activity. Last, the hydrophobic N-terminal character is an important determinant of antimicrobial activity.\",\n \"corpus_id\": 6453777,\n \"score\": 2\n },\n {\n \"doc_id\": \"24857611\",\n \"title\": \"Terminal residue hydrophobicity modulates transmembrane helix-helix interactions.\",\n \"abstract\": \"Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as \\\"small-XXX-small\\\" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰). Using gel electrophoresis, circular dichroism, and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate (SDS), we found that mutation of F90 to residues such as A, I, L, or V maintains the onset of TM2-TM2 dimerization, whereas mutation to E, G, Q, N, S, or T abrogates dimer formation. We attribute this sensitivity to changes in local hydrophobicity, viz., a decrease in hydrophobicity reduces local lipid-peptide interactions, which in turn disrupts peptide α-helicity and hence the effectiveness of an incipient interaction-compatible surface. Our results show that the secondary structure and oligomeric state of PLP TM2 Lys-tagged peptides are significantly modulated by the specific nature of their C-terminal boundary residue, thus providing insight as to how point mutations, particularly where they produce disease states, can compromise the folding process.\",\n \"corpus_id\": 35569279,\n \"score\": 2\n },\n {\n \"doc_id\": \"25329983\",\n \"title\": \"Peptides with the same composition, hydrophobicity, and hydrophobic moment bind to phospholipid bilayers with different affinities.\",\n \"abstract\": \"We investigated the dependence of membrane binding on amino acid sequence for a series of amphipathic peptides derived from δ-lysin. δ-Lysin is a 26 amino acid, N-terminally formylated, hemolytic peptide that forms an amphipathic α-helix bound at membrane-water interfaces. A shortened peptide, lysette, was derived from δ-lysin by deletion of the four N-terminal amino acid residues. Five variants of lysette were synthesized by altering the amino acid sequence such that the overall hydrophobic moment remained essentially the same for all peptides. Peptide-lipid equilibrium dissociation constants and helicities of peptides bound to zwitterionic lipid vesicles were determined by stopped-flow fluorescence and circular dichroism. We found that binding to phosphatidylcholine bilayers was a function of the helicity of the bound peptide alone and independent of the a priori hydrophobic moment or the ability to form intramolecular salt bridges. Molecular dynamics (MD) simulations on two of the peptides suggest that sequence determines the insertion depth into the bilayer. The location of the two aspartate residues at the C-terminus of lysette-2 leads to a loss of helical content in the simulations, which correlates with faster desorption from the bilayer as compared to lysette. We also found a systematic deviation of the experimentally determined dissociation constant and that predicted by the Wimley-White interfacial hydrophobicity scale. The reason for the discrepancy remains unresolved but appears to correlate with a predominance of isoleucine over leucine residues in the lysette family of peptides.\",\n \"corpus_id\": 14200083,\n \"score\": 2\n },\n {\n \"doc_id\": \"25372782\",\n \"title\": \"N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids.\",\n \"abstract\": \"Capping rules, which govern interactions of helical peptides with hydrophobic surfaces, were never established before due to lack of methods for the direct measurement of polypeptide structure on the interphase boundary. We employed proteomic techniques and peptide retention modeling in reversed-phase chromatography to generate a data set sufficient for amino acid population analysis at helix ends. We found that interactions of amphipathic helical peptides with a hydrophobic C18 phase are induced by a unique motif featuring hydrophobic residues in the N1 and N2 positions adjacent to the N-cap (Asn, Asp, Ser, Thr, Gly), followed by Glu, Gln, or Asp in position N3 to complete a capping box. A favorable N-capping arrangement prior to amphipathic helix may result in the highest hydrophobicity (retention on C18 columns) of Asp/Asn (or Glu/Gln) peptide analogues among all naturally occurring amino acids when placed in N-cap or N3 position, respectively. These results contradict all previously reported hydrophobicity scales and provide new insights into our understanding of the phenomenon of hydrophobic interactions.\",\n \"corpus_id\": 46321652,\n \"score\": 2\n },\n {\n \"doc_id\": \"25735802\",\n \"title\": \"Characterization of antimicrobial activity and mechanisms of low amphipathic peptides with different α-helical propensity.\",\n \"abstract\": \"Antimicrobial peptides (AMPs) serve as a defense mechanism within multicellular organisms and are attracting increasing attention because of their potential application in the treatment of multidrug-resistant infections. Amphipathicity has long been believed to be the most important consideration for the structural modification and design of both naturally occurring and synthetic AMPs. Previous studies indicated that disruptive amphipathicity formed by replacing the paired charged amino acid residues on the polar face of an amphipathic helix with tryptophan residues linked with hydrogen bonds on the basis of α-helical protein folding principles endowed the AMPs with increased cell selectivity. In an attempt to augment and hone this strategy further, we designed a series of imperfect amphipathic peptides by placing different types of amino acid residues at the hydrogen bond linked positions of α-helix structures to characterize their antimicrobial properties and mechanism of action. The d-Trp-substituted sequence (PRW4-d) showed greater antimicrobial potency than Cys-(C4), Asp-(D4), Ile-(I4), and Pro-(P4) substituted sequences, comparable to the l-Trp-substituted parent sequence (PRW4). Furthermore, the total replacement of Lys residues with Arg residues along the peptide sequence (PRW4-R) exhibited enhanced antimicrobial activity and cell selectivity. In addition, no cytotoxicity was observed among these synthetic peptides. PRW4-d and PRW4-R maintained their activities in the presence of physiological salts and human serum. The fluorescence spectroscopy, flow cytometry, and electron microscopy observations indicated that the optimized sequences exhibited excellent antimicrobial potency by inducing cytoplasmic membrane potential loss, membrane permeabilization and disruption. Collectively, the results could be useful for designing short AMPs with great antimicrobial activity and cell selectivity.\",\n \"corpus_id\": 205249881,\n \"score\": 2\n },\n {\n \"doc_id\": \"27195657\",\n \"title\": \"Amphipathicity Determines Different Cytotoxic Mechanisms of Lysine- or Arginine-Rich Cationic Hydrophobic Peptides in Cancer Cells.\",\n \"abstract\": \"Cationic amphipathic peptides (CAPs) are known to be able to cause membrane destabilization and induce cell death, yet how the hydrophobicity, amphipathicity, and lysine (K)/arginine (R) composition synergistically affect the peptide activity remains incompletely understood. Here, we designed a panel of peptides based on the well-known anticancer peptide KLA. Increasing hydrophobicity enhanced the cytotoxicities of both the K- and R-rich peptides. Peptides with an intact amphipathic helical interface can cause instant cell death through a membrane lysis mechanism. Interestingly, rearranging the residue positions to minimize amphipathicity caused a great decrease of cytotoxicity to the K-rich peptides but not to the R-rich peptides. The amphipathicity-minimized R-rich peptide 6 (RL2) (RLLRLLRLRRLLRL-NH2) penetrated the cell membrane and induced caspase-3-dependent apoptotic cell death. We found that the modulation of hydrophobicity, amphipathicity, and K/R residues leads to distinct mechanisms of action of cationic hydrophobic peptides. Amphipathicity-reduced, arginine-rich cationic hydrophobic peptides (CHPs) may represent a new class of peptide therapeutics.\",\n \"corpus_id\": 206617830,\n \"score\": 2\n },\n {\n \"doc_id\": \"27547919\",\n \"title\": \"Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices.\",\n \"abstract\": \"Hydrocarbon-stapled peptides are a class of bioactive alpha-helical ligands developed to dissect and target protein interactions. While there is consensus that stapled peptides can be effective chemical tools for investigating protein regulation, their broader utility for therapeutic modulation of intracellular interactions remains an active area of study. In particular, the design principles for generating cell-permeable stapled peptides are empiric, yet consistent intracellular access is essential to in vivo application. Here, we used an unbiased statistical approach to determine which biophysical parameters dictate the uptake of stapled-peptide libraries. We found that staple placement at the amphipathic boundary combined with optimal hydrophobic and helical content are the key drivers of cellular uptake, whereas excess hydrophobicity and positive charge at isolated amino acid positions can trigger membrane lysis at elevated peptide dosing. Our results provide a design roadmap for maximizing the potential to generate cell-permeable stapled peptides with on-mechanism cellular activity.\",\n \"corpus_id\": 7877088,\n \"score\": 2\n },\n {\n \"doc_id\": \"27966361\",\n \"title\": \"Identification of Short Hydrophobic Cell-Penetrating Peptides for Cytosolic Peptide Delivery by Rational Design.\",\n \"abstract\": \"Cell-penetrating peptides (CPPs) enhance the cellular uptake of membrane-impermeable molecules. Most CPPs are highly cationic, potentially increasing the risk of toxic side effects and leading to accumulation in organs such as the liver. As a consequence, there is an unmet need for less cationic CPPs. However, design principles for effective CPPs are still missing. Here, we demonstrate a design principle based on a classification of peptides according to accumulated side-chain polarity and hydrophobicity. We show that in comparison to randomly selected peptides, CPPs cover a distinct parameter space. We designed peptides of only six to nine amino acids with a maximum of three positive charges covering this property space. All peptides were tested for cellular uptake and subcellular distribution. Following an initial round of screening we enriched the collection with short and hydrophobic peptides and introduced d-amino acid substitutions and lactam bridges which increased cell uptake, in particular for long-term incubation. Using a GFP complementation assay, for the most active peptides we demonstrate cytosolic delivery of a biologically active cargo peptide.\",\n \"corpus_id\": 206520365,\n \"score\": 2\n },\n {\n \"doc_id\": \"28636317\",\n \"title\": \"Downsizing Proto-oncogene cFos to Short Helix-Constrained Peptides That Bind Jun.\",\n \"abstract\": \"The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components. Structural integrity in the presence and absence of Jun was assessed by circular dichroism spectroscopy, while the thermodynamics of binding to cFos was measured by isothermal titration calorimetry. A 25-residue constrained peptide, one-third shorter yet 25% more helical than the structurally characterized 37-residue Fos-derived peptide, retained 80% of the binding free energy as a result of preorganization in a Jun-binding helix conformation, with the entropy gain (TΔS = +3.2 kcal/mol) compensating for the enthalpy loss. Attaching a cell-penetrating peptide (TAT48-57) and a nuclear localization signal (SV40) promoted cell uptake, localization to the nucleus, and inhibition of the proliferation of two breast cancer cell lines.\",\n \"corpus_id\": 206527543,\n \"score\": 2\n },\n {\n \"doc_id\": \"28741867\",\n \"title\": \"Targeting of a helix-loop-helix transcriptional regulator by a short helical peptide.\",\n \"abstract\": \"The Id proteins (Id1-4) are cell cycle regulators that play a key role during development, in cancer and vascular disorders. They contain a conserved helix-loop-helix (HLH) domain that folds into a parallel four-helix bundle upon self- or heteroassociation with basic-HLH transcription factors. By using such protein-protein interactions, the Id proteins inhibit cell differentiation and promote cell cycle progression. Accordingly, their supporting role in cancer has been convincingly demonstrated, which makes these proteins interesting therapeutic targets. Here we present a short peptide containing a (i,i+4)-lactam bridge and a hydrophobic (Φ) three-residue motif Φ(i)-Φ(i+3)-Φ(i+6), which adopted a helical conformation in water, showed Id-protein binding in the low-micromolar range, penetrated into breast (MCF7 and T47D) and bladder (T24) cancer cells, accumulated in the nucleus, and reduced cell viability to about 50%. Thus, this cyclopeptide is a promising scaffold to develop Id-protein binders impairing cancer cell viability.\",\n \"corpus_id\": 5013620,\n \"score\": 2\n },\n {\n \"doc_id\": \"29420899\",\n \"title\": \"Importance of Net Hydrophobicity in the Cellular Uptake of All-Hydrocarbon Stapled Peptides.\",\n \"abstract\": \"All-hydrocarbon stapled peptides make up a promising class of protein-protein interaction regulators; their potential therapeutic benefit arises because they have a high binding affinity and specificity for intracellular molecules. The cell permeation efficacy of these peptides is a critical determinant of their bioactivity. However, the factors that determine their cellular uptake remain an active area of research. In this study, we evaluated the effect of stapled (or cross-linked) formation on the cellular uptake of six known all-hydrocarbon stapled peptides. We found that the rate of cellular uptake of unstapled peptides (i.e., those bearing olefinic non-natural amino acids that are not subjected to olefin metathesis) was higher than that for the corresponding stapled peptides. Additionally, the insertion of these olefinic non-natural amino acids into peptide sequences significantly increased their rate of cellular uptake. According to the high-performance liquid chromatography retention times, the overall hydrophobicity of unstapled peptides was greater than that of stapled peptides, followed by that of the original peptides without olefinic non-natural amino acids. There was not a close correlation between helical content and the rate of cellular uptake of these peptides. Therefore, the increase in overall hydrophobicity resulting from the introduction of non-natural amino acids, rather than the structural stabilization resulting from staple formation, is the key driver promoting cellular uptake. Macropinocytosis, a form of fluid-phase endocytosis, was involved in the cellular uptake of all six peptides.\",\n \"corpus_id\": 3709285,\n \"score\": 2\n },\n {\n \"doc_id\": \"29431766\",\n \"title\": \"Glucuronic acid as a helix-inducing linker in short peptides.\",\n \"abstract\": \"A new strategy is demonstrated for making peptides helical, using a carbohydrate to bridge between sidechains at each end of a pentapeptide. CD and NMR spectra establish that both an α-helix and a 310-helix structure can form depending upon the bridge.\",\n \"corpus_id\": 206076160,\n \"score\": 2\n },\n {\n \"doc_id\": \"29461066\",\n \"title\": \"Chemically Diverse Helix-Constrained Peptides Using Selenocysteine Crosslinking.\",\n \"abstract\": \"The use of selenocysteines and various cross-linkers to induce helicity in a bioactive peptide is described. The higher reactivity of selenocysteine, relative to cysteine, facilitates rapid cross-linking within unprotected linear peptides under mild aqueous conditions. Alkylating agents of variable topology and electrophilicity were used to link pairs of selenocysteines within a p53 peptide. Facile selenoether formation enables diverse tailoring of the helical peptide structure.\",\n \"corpus_id\": 3643745,\n \"score\": 2\n },\n {\n \"doc_id\": \"29568420\",\n \"title\": \"Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning.\",\n \"abstract\": \"Due to their enhanced stability and cell permeability, cyclic cell-penetrating peptides have been widely used as delivery vectors for transporting cell-impermeable cargos into cells. In this study, we synthesized a panel of conformationally constrained peptides with either α-helix or β-hairpin conformations. We tuned the amphiphilicity of these constrained peptides with different distributions of charged or hydrophobic residues and compared their cellular uptake efficiencies in different cell lines. We found that the amphipathicity of these conformationally constrained peptides correlates well with their cellular uptake efficiency. We proposed that peptides with larger hydrophobic moments (HMs) have stronger binding affinities with the cell membrane which further accelerates the endocytosis process. This finding should provide an approach towards the design of more potent conformationally constrained cell-penetrating peptides for biomedical applications.\",\n \"corpus_id\": 2617023,\n \"score\": 2\n },\n {\n \"doc_id\": \"18540660\",\n \"title\": \"Fundamental design principles that guide induction of helix upon formation of stable peptide-nanoparticle complexes.\",\n \"abstract\": \"We have shown that it is possible to design a peptide that has a very low helical content when free in solution but that adopts a well-defined helix when interacting with silica nanoparticles. From a systematic variation of the amino acid composition and distribution in designed peptides, it has been shown that the ability to form helical structure upon binding to the silica surface is dominated by two factors. First, the helical content is strongly correlated with the net positive charge on the side of the helix that interacts with the silica, and arginine residues are strongly favored over lysine residues in these positions. The second important factor is to have a high net negative charge on the side of the helix that faces the solution. Apparently, both attractive and repulsive electrostatic forces dominate the induction and stabilization of a bound helix. It is also evident that using amino acids that have high propensity to form helix in solution are also advantageous for the formation of helix on surfaces.\",\n \"corpus_id\": 5281363,\n \"score\": 1\n },\n {\n \"doc_id\": \"18630933\",\n \"title\": \"A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation.\",\n \"abstract\": \"Alpha-helices constitute the largest class of protein secondary structures and play a major role in mediating protein-protein interactions. Development of stable mimics of short alpha-helices would be invaluable for inhibition of protein-protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in alpha-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS alpha-helices feature a carbon-carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix-coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short alpha-helices. The HBS method affords preorganized alpha-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an attractive strategy for generation of ligands for protein receptors because placement of the cross-link on the inside of the helix does not block solvent-exposed molecular recognition surfaces of the molecule. Our metathesis-based synthetic strategy utilizes standard Fmoc solid phase peptide synthesis methodology, resins, and reagents and provides HBS helices in sufficient amounts for subsequent biophysical and biological analyses. Extensive conformational analysis of HBS alpha-helices with 2D NMR, circular dichroism spectroscopies and X-ray crystallography confirms the alpha-helical structure in these compounds. The crystal structure indicates that all i and i + 4 C=O and NH hydrogen-bonding partners fall within distances and angles expected for a fully hydrogen-bonded alpha-helix. The backbone conformation of HBS alpha-helix in the crystal structure superimposes with an rms difference of 0.75 A onto the backbone conformation of a model alpha-helix. Significantly, the backbone torsion angles for the HBS helix residues fall within the range expected for a canonical alpha-helix. Thermal and chemical denaturation studies suggest that the HBS approach provides exceptionally stable alpha-helices from a variety of short sequences, which retain their helical conformation in aqueous buffers at exceptionally high temperatures. The high degree of thermal stability observed for HBS helices is consistent with the theoretical predictions for a nucleated helix. The HBS approach was devised to afford internally constrained helices so that the molecular recognition surface of the helix and its protein binding properties are not compromised by the constraining moiety. Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity.\",\n \"corpus_id\": 206827831,\n \"score\": 1\n },\n {\n \"doc_id\": \"19074438\",\n \"title\": \"GroEL Recognizes an Amphipathic Helix and Binds to the Hydrophobic Side.\",\n \"abstract\": \"GroEL is an essential Escherichia coli molecular chaperon that uses ATP to facilitate correct folding of a range of proteins in a cell. Central to the GroEL substrate diversity is how GroEL recognizes the substrates. The interaction between GroEL and substrate has been proposed to be largely hydrophobic because GroEL interacts with proteins in non-native conformations but not in native forms. Analysis of GroEL substrate proteins reveals that one of its main substrates are proteins with alphabeta folding domains, suggesting that GroEL may stabilize the collapsed alphabeta core by binding to hydrophobic surfaces that are usually buried between the alpha and beta elements. In this study, we characterize the interaction between GroEL and a peptide derived from our previous selection via a phage display method. NMR studies map the peptide-binding site to the region containing Helices H and I, which is consistent with evidence that this region comprises the primary substrate-binding site. The peptide is largely unstructured in solution but adopts a helical conformation when bound to the GroEL apical domain with a moderate affinity (K(d) = 17.1 +/- 2.5 microm). The helical conformation aligns residues to form an amphipathic structure, and the hydrophobic side of this amphipathic helix interacts with GroEL as suggested by fluorescence quenching studies. Together with previous structural studies on the GroEL-peptide complexes, our work supports the notion that the amphipathic secondary elements in the substrate proteins may be the structural motif recognized by GroEL.\",\n \"corpus_id\": 24924344,\n \"score\": 1\n },\n {\n \"doc_id\": \"20025243\",\n \"title\": \"Hydrophobic residues in helix 8 of cannabinoid receptor 1 are critical for structural and functional properties.\",\n \"abstract\": \"In addition to the heptahelical transmembrane domain shared by all G protein-coupled receptors (GPCRs), many class A GPCRs adopt a helical domain, termed helix 8, in the membrane-proximal region of the C terminus. We investigated the role of residues in the hydrophobic and hydrophilic faces of amphiphilic helix 8 of human cannabinoid receptor 1 (CB1). To differentiate between a role for specific residues and global features, we made two key mutants: one involving replacement of the highly hydrophobic groups, Leu404, Phe408, and Phe412, all with alanine and the second involving substitution of the basic residues, Lys402, Arg405, and Arg409, all with the neutral glutamine. The former showed a very low B(max) based on binding isotherms, a minimal E(max) based on GTPgammaS binding analysis, and defective localization relative to the wild-type CB1 receptor as revealed by confocal microscopy. However, the latter mutant and the wild-type receptors were indistinguishable. Circular dichroism spectroscopy of purified peptides with corresponding sequences indicated that the highly hydrophobic residues are critical for maintaining a strong helical structure in detergent, whereas the positively charged residues are not. Further investigation of mutant receptors revealed that CB1 localization requires a threshold level of hydrophobicity but not specific amino acids. Moreover, mutant receptors carrying two- to six-residue insertions amino-terminal to helix 8 revealed a graded decrease in B(max) values. Our results identify the key helix 8 components (including hydrophobicity of specific residues, structure, and location relative to TM7) determinant for receptor localization leading to robust ligand binding and G protein activation.\",\n \"corpus_id\": 9073135,\n \"score\": 1\n },\n {\n \"doc_id\": \"20669185\",\n \"title\": \"Helicity of short E-R/K peptides.\",\n \"abstract\": \"Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide-based drug design. Previous studies of synthetic Ala-based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E-R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E-R/K-based peptides show significant helix content. Peptides containing one or more E-R interactions display greater helicity than those with similar E-K interactions. Significant helicity is achieved in Arg-based E-R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E-R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.\",\n \"corpus_id\": 27477206,\n \"score\": 1\n },\n {\n \"doc_id\": \"21949789\",\n \"title\": \"Exposed hydrophobic residues in human immunodeficiency virus type 1 Vpr helix-1 are important for cell cycle arrest and cell death.\",\n \"abstract\": \"The human immunodeficiency virus type 1 (HIV-1) accessory protein viral protein R (Vpr) is a major determinant for virus-induced G2/M cell cycle arrest and cytopathicity. Vpr is thought to perform these functions through the interaction with partner proteins. The NMR structure of Vpr revealed solvent exposed hydrophobic amino acids along helices 1 and 3 of Vpr, which could be putative protein binding domains. We previously showed that the hydrophobic patch along helix-3 was important for G2/M blockade and cytopathicity. Mutations of the exposed hydrophobic residues along helix-1 were found to reduce Vpr-induced cell cycle arrest and cell death as well. The levels of toxicity during virion delivery of Vpr correlated with G2/M arrest. Thus, the exposed hydrophobic amino acids in the amino-terminal helix-1 are important for the cell cycle arrest and cytopathicity functions of Vpr.\",\n \"corpus_id\": 9171446,\n \"score\": 1\n },\n {\n \"doc_id\": \"22052825\",\n \"title\": \"Effect of introducing a short amyloidogenic sequence from the Aβ peptide at the N-terminus of 18-residue amphipathic helical peptides.\",\n \"abstract\": \"Fibril formation is the hallmark of pathogenesis in Alzheimer's disease and other amyloid disorders caused by conformational alterations leading to the aggregation of soluble monomers. Aβ40 self-associates to form amyloid fibrils. Its central seven-residue segment KLVFFAE (Aβ16-22), which is thought to be crucial for fibril formation of the full-length peptide, forms fibrils even in isolation. Context-dependent induction of amyloid formation by such sequences in peptides, which otherwise do not have that propensity, is of considerable interest. We have examined the effect of introducing the Aβ16-22 sequence at the N-terminus of two amphipathic helical 18-residue peptides Ac-WYSEMKRNVQRLERAIEE-am and Ac-KQLIRFLKRLDRNLWGLA-am, which have high average hydrophobic moment <μH> values but have net charges of 0 and +4, respectively, at neutral pH. Upon incubation in aqueous buffer, fibril-like aggregates were discernible by transmission electron microscopy for the peptide with only 0 net charge, which also displayed ThT binding and β-structure. Although both the sequences have been derived from amphipathic helical segments in globular proteins and possess high average hydrophobic moments, the +4 charge peptide lacks the ability to form fibrils, while the peptide with 0 charge has the tendency to form fibrillar structures. Variation in the net charge and the presence of several glutamic acids in the sequence of the peptide with net charge 0 appear to favor the formation of fibrils when the Aβ16-22 sequence is attached at the N-terminus.\",\n \"corpus_id\": 44873240,\n \"score\": 1\n },\n {\n \"doc_id\": \"22223219\",\n \"title\": \"Computational protein design with explicit consideration of surface hydrophobic patches.\",\n \"abstract\": \"De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studies with Rosetta have shown that this limits surface hydrophobics to the naturally occurring frequency (∼28%), but that it does not prevent the formation of hydrophobic patches that are considerably larger than those observed in naturally occurring proteins. Here, we describe a new score term that explicitly detects and penalizes the formation of hydrophobic patches during computational protein design. With the new term, we are able to design protein surfaces that include hydrophobic amino acids at naturally occurring frequencies, but do not have large hydrophobic patches. By adjusting the strength of the new score term, the emphasis of surface redesigns can be switched between maintaining solubility and maximizing folding free energy.\",\n \"corpus_id\": 21986052,\n \"score\": 1\n },\n {\n \"doc_id\": \"22720789\",\n \"title\": \"Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization.\",\n \"abstract\": \"BACKGROUND: The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. RESULTS: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don't. While the nature of transitions of LCC's sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues' cliques. CONCLUSIONS: The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. The thermophiles do not only have the higher number of long-range interactions; they also have larger cluster of connected residues at higher interaction strengths among amino acids, than their mesophilic counterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding and stabilization; at the same time, it shed light on the higher communication ability of hydrophobic subnetworks over the others. The results give an indication of the controlling role of hydrophobic subclusters in determining protein's folding rate. The occurrences of higher perimeters of hydrophobic and charged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distant part of primary structure of a protein through London van der Waals interaction.\",\n \"corpus_id\": 5485673,\n \"score\": 1\n },\n {\n \"doc_id\": \"22803956\",\n \"title\": \"Relationship between helix stability and binding affinities: molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent.\",\n \"abstract\": \"The anti-apoptotic protein Bfl-1, also known as A1, belongs to the Bcl-2 family of proteins and interacts with pro-apoptotic Bcl-2 counterparts to regulate programmed cell death. As demonstrated for other anti-apoptotic Bcl-2 proteins, Bfl-1/A1 has also been shown to be overexpressed in various human cancers and hence they are attractive targets for anticancer drugs. Peptides derived from the BH3 region of pro-apoptotic Bcl-2 proteins have been shown to elicit similar biological response as that of parent proteins. BH3 peptides from different pro-apoptotic proteins have wide range of affinities for Bfl-1/A1. Experimentally determined complex structures show that the hydrophobic side of amphipathic BH3 peptides binds to the hydrophobic groove formed by the α-helical bundle of Bfl-1/A1 protein. Apart from the length and amino acid composition, a BH3 peptide's ability to form a stable helical structure has been suggested to be important for its high binding affinity. Molecular dynamics simulations of three BH3 peptides derived from the pro-apoptotic proteins Bak, Bid, and Bmf were carried out each for a period of at least 100 ns after 2 ns equilibration run. The length of simulated BH3 peptides varied from 22 to 24 residues and their binding affinities for Bfl-1/A1 varied from 1 to 180 nM. Our results show that the hydrophobic residues from the hydrophobic face of BH3 peptides tend to cluster together quickly to avoid being exposed to the solvent. This resulted in either reduction of helix length or complete loss of helical character. Bak and Bid BH3 peptides with high affinities for Bf1-1/A1 have stable helical segments in the N-terminal region. The highly conserved Leu residue lies just outside the helical region at the C-terminal end. Capping interactions arising out of N-cap residues seem to be extremely important to maintain the helical stability. Favorable hydrophilic interactions between residues also give further stability to the helix fragment and at least one of the interacting residues resides within the helical region. Bmf BH3 peptide with a weaker binding affinity for Bmf-1/A1 completely lost its helical character at the end of 100 ns production run and a further 50 ns simulation showed that the Bmf peptide continues to remain in random conformation. The present study clearly establishes a link between a BH3 peptide's ability to form a stable helical segment and its high binding affinity for an anti-apoptotic protein. To further test this hypothesis, we simulated a mutant Bmf peptide for 100 ns in which two residues R129 and H146 were substituted by Asn in silico in the wild-type peptide. Introduction of N-terminal Asn clearly enabled the formation of capping interactions at the N-terminus and resulted in a stable N-terminal helical segment. This demonstrates that the knowledge of interactions that help to maintain stable helical segments in a high-affinity BH3 peptide will help in designing highly specific peptide-based drugs/inhibitors. Such molecules will have the ability to bind a particular anti-apoptotic protein with high affinity.\",\n \"corpus_id\": 19171537,\n \"score\": 1\n },\n {\n \"doc_id\": \"23510797\",\n \"title\": \"Peptides that form β-sheets on hydrophobic surfaces accelerate surface-induced insulin amyloidal aggregation.\",\n \"abstract\": \"Interactions between proteins and material or cellular surfaces are able to trigger protein aggregation in vitro and in vivo. The human insulin peptide segment LVEALYL is able to accelerate insulin aggregation in the presence of hydrophobic surfaces. We show that this peptide needs to be previously adsorbed on a hydrophobic surface to induce insulin aggregation. Moreover, the study of different mutant peptides proves that its sequence is less important than the secondary structure of the adsorbed peptide on the surface. Indeed, these pro-aggregative peptides act by providing stable β-sheets to incoming insulin molecules, thereby accelerating insulin adsorption locally and facilitating the conformational changes required for insulin aggregation. Conversely, a peptide known to form α-helices on hydrophobic surfaces delays insulin aggregation.\",\n \"corpus_id\": 207661978,\n \"score\": 1\n },\n {\n \"doc_id\": \"24220211\",\n \"title\": \"Mutational analysis of the rotavirus NSP4 enterotoxic domain that binds to caveolin-1.\",\n \"abstract\": \"BACKGROUND: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction. METHODS: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed to alanine (NSP446-175-ala6); and three residues in the hydrophobic face were altered to charged amino acids (NSP4(46-175)-HydroMut). In total, twelve mutants of NSP4 were generated to define the cav-1 binding site. Synthetic peptides corresponding to the hydrophobic and charged faces of NSP4 were examined for structural changes by circular dichroism (CD) and diarrhea induction by a neonatal mouse study. RESULTS: Mutations of the hydrophilic face (NSP4(46-175)-Ala6) bound cav-1 akin to wild type NSP4. In contrast, disruption of the hydrophobic face (NSP4(46-175)-HydroMut) failed to bind cav-1. These data suggest NSP4 and cav-1 associate via a hydrophobic interaction. Analyses of mutant synthetic peptides in which the hydrophobic residues in the enterotoxic domain of NSP4 were altered suggested a critical hydrophobic residue. Both NSP4HydroMut112-140, that contains three charged amino acids (aa113, 124, 131) changed from the original hydrophobic residues and NSP4AlaAcidic112-140 that contained three alanine residues substituted for negatively charged (aa114, 125, 132) amino acids failed to induce diarrhea. Whereas peptides NSP4wild type 112-140 and NSP4AlaBasic112-140 that contained three alanine substituted for positively charged (aa115, 119, 133) amino acids, induced diarrhea. CONCLUSIONS: These data show that the cav-1 binding domain is within the hydrophobic face of the NSP4 amphipathic helix. The integrity of the helical structure is important for both cav-1 binding and diarrhea induction implying a connection between NSP4 functional and binding activities.\",\n \"corpus_id\": 2198979,\n \"score\": 1\n },\n {\n \"doc_id\": \"24664416\",\n \"title\": \"Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element.\",\n \"abstract\": \"Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.\",\n \"corpus_id\": 23566537,\n \"score\": 1\n },\n {\n \"doc_id\": \"24744084\",\n \"title\": \"Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids.\",\n \"abstract\": \"The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb-Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb-Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ 1 dihedral combinations (g+, g+) and (g-, g+), respectively. These low energy conformations were also observed in intrahelical Asp-Arg and Glu-Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.\",\n \"corpus_id\": 17137775,\n \"score\": 1\n },\n {\n \"doc_id\": \"25083348\",\n \"title\": \"Surfactant protein C peptides with salt-bridges (\\\"ion-locks\\\") promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein.\",\n \"abstract\": \"Background. Surfactant protein C (SP-C; 35 residues) in lungs has a cationic N-terminal domain with two cysteines covalently linked to palmitoyls and a C-terminal region enriched in Val, Leu and Ile. Native SP-C shows high surface activity, due to SP-C inserting in the bilayer with its cationic N-terminus binding to the polar headgroup and its hydrophobic C-terminus embedded as a tilted, transmembrane α-helix. The palmitoylcysteines in SP-C act as 'helical adjuvants' to maintain activity by overriding the β-sheet propensities of the native sequences. Objective. We studied SP-C peptides lacking palmitoyls, but containing glutamate and lysine at 4-residue intervals, to assess whether SP-C peptides with salt-bridges (\\\"ion-locks\\\") promote surface activity by mimicking the α-helix and membrane topography of native SP-C. Methods. SP-C mimics were synthesized that reproduce native sequences, but without palmitoyls (i.e., SP-Css or SP-Cff, with serines or phenylalanines replacing the two cysteines). Ion-lock SP-C molecules were prepared by incorporating single or double Glu(-)-Lys(+) into the parent SP-C's. The secondary structures of SP-C mimics were studied with Fourier transform infrared (FTIR) spectroscopy and PASTA, an algorithm that predicts β-sheet propensities based on the energies of the various β-sheet pairings. The membrane topography of SP-C mimics was investigated with orientated and hydrogen/deuterium (H/D) exchange FTIR, and also Membrane Protein Explorer (MPEx) hydropathy analysis. In vitro surface activity was determined using adsorption surface pressure isotherms and captive bubble surfactometry, and in vivo surface activity from lung function measures in a rabbit model of surfactant deficiency. Results. PASTA calculations predicted that the SP-Css and SP-Cff peptides should each form parallel β-sheet aggregates, with FTIR spectroscopy confirming high parallel β-sheet with 'amyloid-like' properties. The enhanced β-sheet properties for SP-Css and SP-Cff are likely responsible for their low surfactant activities in the in vitro and in vivo assays. Although standard (12)C-FTIR study showed that the α-helicity of these SP-C sequences in lipids was uniformly increased with Glu(-)-Lys(+) insertions, elevated surfactant activity was only selectively observed. Additional results from oriented and H/D exchange FTIR experiments indicated that the high surfactant activities depend on the SP-C ion-locks recapitulating both the α-helicity and the membrane topography of native SP-C. SP-Css ion-lock 1, an SP-Css with a salt-bridge for a Glu(-)-Lys(+) ion-pair predicted from MPEx hydropathy calculations, demonstrated enhanced surfactant activity and a transmembrane helix simulating those of native SP-C. Conclusion. Highly active SP-C mimics were developed that replace the palmitoyls of SP-C with intrapeptide salt-bridges and represent a new class of synthetic surfactants with therapeutic interest.\",\n \"corpus_id\": 15067387,\n \"score\": 1\n },\n {\n \"doc_id\": \"25418176\",\n \"title\": \"Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein.\",\n \"abstract\": \"The inner membrane of Gram-negative bacteria is negatively charged, rendering positively charged cytoplasmic proteins in close proximity likely candidates for protein-membrane interactions. YscU is a Yersinia pseudotuberculosis type III secretion system protein crucial for bacterial pathogenesis. The protein contains a highly conserved positively charged linker sequence that separates membrane-spanning and cytoplasmic (YscUC) domains. Although disordered in solution, inspection of the primary sequence of the linker reveals that positively charged residues are separated with a typical helical periodicity. Here, we demonstrate that the linker sequence of YscU undergoes a largely electrostatically driven coil-to-helix transition upon binding to negatively charged membrane interfaces. Using membrane-mimicking sodium dodecyl sulfate micelles, an NMR derived structural model reveals the induction of three helical segments in the linker. The overall linker placement in sodium dodecyl sulfate micelles was identified by NMR experiments including paramagnetic relaxation enhancements. Partitioning of individual residues agrees with their hydrophobicity and supports an interfacial positioning of the helices. Replacement of positively charged linker residues with alanine resulted in YscUC variants displaying attenuated membrane-binding affinities, suggesting that the membrane interaction depends on positive charges within the linker. In vivo experiments with bacteria expressing these YscU replacements resulted in phenotypes displaying significantly reduced effector protein secretion levels. Taken together, our data identify a previously unknown membrane-interacting surface of YscUC that, when perturbed by mutations, disrupts the function of the pathogenic machinery in Yersinia.\",\n \"corpus_id\": 13757736,\n \"score\": 1\n },\n {\n \"doc_id\": \"26054932\",\n \"title\": \"Design and characterization of a new peptide vector for short interfering RNA delivery.\",\n \"abstract\": \"RNA interference holds tremendous potential as one of the most powerful therapeutic strategies. However, the properties of short interfering RNA (siRNA), such as hydrophilicity, negative charge, and instability in serum have limited its applications; therefore, significant efforts have been undertaken to improve its cellular uptake. Cell penetrating peptides have been utilized to deliver various biologically active molecules, such as proteins, liposomes, nanoparticles, peptide nucleic acids, and recently small interfering RNAs. Here, we introduce a new cell penetrating peptide GL1(Ac-GLWRAWLWKAFLASNWRRLLRLLR-NH2) to improve the intracellular uptake of siRNA. This peptide consists of four tryptophan residues that facilitated its binding with the cell membrane, five arginine residues and one lysine residue which are positively charged at physiological pH, which induced the formation of peptide-siRNA complexes and enhanced the affinity of the peptide and cell membrane. Moreover, GL1 adopted helical secondary structure due to the altered distribution of polar and nonpolar residues in the sequence. In this study, we investigated the effect of peptide/siRNA molar ratio on the particle size, surface charge, secondary structure, and uptake efficiency. The results showed that GL1 formed stable complexes with siRNA mainly through electrostatic interaction and hydrophobic interaction, and the complexes displayed a spherical shape with the size of ~100 nm and positive surface charge. Utilizing the techniques of fluorescence microscopy and flow cytometry, the intracellular localization of Cy3-labeled GAPDH siRNA was visualized and the cellular uptake was quantified. It is worth noting that in the serum free environment, compared to Lipofectamine 2000, GL1 achieved higher cellular uptake of siRNA (~95%); in the presence of serum, GL1 retained the same level of siRNA cellular uptake (~84%) as Lipofectamine 2000. In addition, the viability of cells treated by GL1 in all studied molar ratios was >85%, which was significantly higher than that treated by Lipofectamine 2000 (~70%). Taken together, the peptide GL1 demonstrated promise as a siRNA delivery system.\",\n \"corpus_id\": 6360345,\n \"score\": 1\n },\n {\n \"doc_id\": \"27237727\",\n \"title\": \"SAP(E) - A cell-penetrating polyproline helix at lipid interfaces.\",\n \"abstract\": \"Cell-penetrating peptides (CPPs) are short membrane-permeating amino acid sequences that can be used to deliver cargoes, e.g. drugs, into cells. The mechanism for CPP internalization is still subject of ongoing research. An interesting family of CPPs is the sweet arrow peptides - SAP(E) - which are known to adopt a polyproline II helical secondary structure. SAP(E) peptides stand out among CPPs because they carry a net negative charge while most CPPs are positively charged, the latter being conducive to electrostatic interaction with generally negatively charged membranes. For SAP(E)s, an internalization mechanism has been proposed, based on polypeptide aggregation on the cell surface, followed by an endocytic uptake. However, this process has not yet been observed directly - since peptide-membrane interactions are inherently difficult to monitor on a molecular scale. Here, we use sum frequency generation (SFG) vibrational spectroscopy to investigate molecular interactions of SAP(E) with differently charged model membranes, in both mono- and bi-layer configurations. The data suggest that the initial binding mechanism is accompanied by structural changes of the peptide. Also, the peptide-model membrane interaction depends on the charge of the lipid headgroup with phosphocholine being a favorable binding site. Moreover, while direct penetration has also been observed for some CPPs, the spectroscopy reveals that for SAP(E), its interaction with model membranes remains limited to the headgroup region, and insertion into the hydrophobic core of the lipid layer does not occur.\",\n \"corpus_id\": 8117127,\n \"score\": 1\n },\n {\n \"doc_id\": \"29074350\",\n \"title\": \"Effects of charge and hydrophobicity on the oligomerization of peptides derived from IAPP.\",\n \"abstract\": \"Changes in pH resulting in modifications of charge can dramatically alter the folding and interaction of proteins. This article probes the effects of charge and hydrophobicity on the oligomerization of macrocyclic β-sheet peptides derived from residues 11-17 of IAPP (RLANFLV). Previous studies have shown that a macrocyclic β-sheet peptide containing this IAPP sequence (peptide 1Arg) does not form oligomers in aqueous solution at low millimolar concentrations. Replacing arginine with the uncharged isostere citrulline generates a homologue (peptide 1Cit) that forms a tetramer consisting of a sandwich of hydrogen-bonded dimers. The current study probes the role of charge and hydrophobicity by changing residue 11 to glutamic acid (peptide 1Glu) and leucine (peptide 1Leu). Diffusion-ordered spectroscopy (DOSY) studies show that peptides 1Glu and 1Leu form tetramers in solution. NOESY studies confirm that both peptides form the same sandwich-like tetramer as peptide 1Cit. 1H NMR spectroscopy at various concentrations reveals that peptide 1Leu has the highest propensity to form tetramers. The effects of pH and charge on oligomerization are further probed by incorporating histidine at position 11 (peptide 1His). DOSY studies show that peptide 1His forms a tetramer at high pH. At low pH, peptide 1His forms a new species that has not been previously observed by our research group-a dimer. These studies demonstrate the importance of charge and hydrophobicity in the oligomerization of IAPP-derived peptides.\",\n \"corpus_id\": 3821190,\n \"score\": 1\n },\n {\n \"doc_id\": \"19782154\",\n \"title\": \"The role of hydrophobic and negatively charged surface patches of lipid-free apolipoprotein A-I in lipid binding and ABCA1-mediated cholesterol efflux.\",\n \"abstract\": \"Recent models of lipid-free apolipoprotein A-I, including a cross-link/homology model and an X-ray crystal structure have identified two potential functionally relevant \\\"patches\\\" on the protein surface. The first is a hydrophobic surface patch composed of leucine residues 42, 44, 46, and 47 and the second a negatively charged patch composed of glutamic acid residues 179, 191, and 198. To determine if these domains play a functional role, these surface patches were disrupted by site-directed mutagenesis and the bacterially expressed mutants were compared with respect to their ability to bind lipid and stimulate ABCA1-mediated cholesterol efflux. It was found that neither patch plays a significant functional role in the ability of apoA-I to accept cholesterol in an ABCA1-dependent manner, but that the hydrophobic patch did affect the ability of apoA-I to clear DMPC liposomes. Interestingly, contrary to previous predictions, disruption of the hydrophobic surface patch enhanced the lipid binding ability of apoA-I. The hydrophobic surface patch may be important to the structural stability of lipid-free apoA-I or may be a necessary permissive structural element for lipid binding.\",\n \"corpus_id\": 38785163,\n \"score\": 0\n },\n {\n \"doc_id\": \"20798341\",\n \"title\": \"Charges in the hydrophobic interior of proteins.\",\n \"abstract\": \"Charges are inherently incompatible with hydrophobic environments. Presumably for this reason, ionizable residues are usually excluded from the hydrophobic interior of proteins and are found instead at the surface, where they can interact with bulk water. Paradoxically, ionizable groups buried in the hydrophobic interior of proteins play essential roles, especially in biological energy transduction. To examine the unusual properties of internal ionizable groups we measured the pK(a) of glutamic acid residues at 25 internal positions in a stable form of staphylococcal nuclease. Two of 25 Glu residues titrated with normal pK(a) near 4.5; the other 23 titrated with elevated pK(a) values ranging from 5.2-9.4, with an average value of 7.7. Trp fluorescence and far-UV circular dichroism were used to monitor the effects of internal charges on conformation. These data demonstrate that although charges buried in proteins are indeed destabilizing, charged side chains can be buried readily in the hydrophobic core of stable proteins without the need for specialized structural adaptations to stabilize them, and without inducing any major conformational reorganization. The apparent dielectric effect experienced by the internal charges is considerably higher than the low dielectric constants of hydrophobic matter used to represent the protein interior in electrostatic continuum models of proteins. The high thermodynamic stability required for proteins to withstand the presence of buried charges suggests a pathway for the evolution of enzymes, and it underscores the need to mind thermodynamic stability in any strategy for engineering novel or altered enzymatic active sites in proteins.\",\n \"corpus_id\": 25040424,\n \"score\": 0\n },\n {\n \"doc_id\": \"23422441\",\n \"title\": \"α-Helix mimicry with α/β-peptides.\",\n \"abstract\": \"We describe a general strategy for creating peptidic oligomers that have unnatural backbones but nevertheless adopt a conformation very similar to the α-helix. These oligomers contain both α- and β-amino acid residues (α/β-peptides). If the β content reaches 25-30% of the residue total, and the β residues are evenly distributed along the backbone, then substantial resistance to proteolytic degradation is often observed. These α/β-peptides can mimic the informational properties of α-helices involved in protein-protein recognition events, as documented in numerous crystal structures. Thus, these unnatural oligomers can be a source of antagonists of undesirable protein-protein interactions that are mediated by natural α-helices, or agonists of receptors for which the natural polypeptide ligands are α-helical. Successes include mimicry of BH3 domains found in proapoptotic proteins, which leads to ligands for antiapoptotic Bcl-2 family proteins, and mimicry of the gp41 CHR domain, which leads to inhibition of HIV infection in cell-based assays.\",\n \"corpus_id\": 31267715,\n \"score\": 0\n },\n {\n \"doc_id\": \"23496521\",\n \"title\": \"Interaction between heterogeneously charged surfaces: surface patches and charge modulation.\",\n \"abstract\": \"When solid surfaces are immersed in aqueous solutions, some of their charges can dissociate and leave behind charged patches on the surface. Although the charges are distributed heterogeneously on the surface, most of the theoretical models treat them as homogeneous. For overall non-neutral surfaces, the assumption of surface charge homogeneity is rather reasonable since the leading terms of two such interacting surfaces depend on the nonzero average charge. However, for overall neutral surfaces the nature of the surface charge distribution is crucial in determining the intersurface interaction. In the present work we study the interaction between two charged surfaces across an aqueous solution for several charge distributions. The analysis is preformed within the framework of the linearized Poisson-Boltzmann theory. For periodic charge distributions the interaction is found to be repulsive at small separations, unless the two surface distributions are completely out-of-phase with respect to each other. For quenched random charge distributions we find that due to the presence of the ionic solution in between the surfaces, the intersurface repulsion dominates over the attraction in the linear regime of the Poisson-Boltzmann theory. The effect of quenched charge heterogeneity is found to be particularly substantial in the case of large charged domains.\",\n \"corpus_id\": 10181505,\n \"score\": 0\n },\n {\n \"doc_id\": \"24829339\",\n \"title\": \"Glutamic acid at residue 125 of the prM helix domain interacts with positively charged amino acids in E protein domain II for Japanese encephalitis virus-like-particle production.\",\n \"abstract\": \"UNLABELLED: Interaction between E and prM proteins in flavivirus-infected cells is a major factor for virus-like particle (VLP) production. The prM helical (prM-H) domain is topologically close to and may interact with domain II of the E protein (EDII). In this study, we investigated prM-H domain amino acid residues facing Japanese encephalitis virus EDII using site-directed mutagenesis to determine their roles in prM-E interaction and VLP production. Our results indicate that negatively charged prM-E125 residue at the prM-H domain affected VLP production via one or more interactions with positively charged E-K93 and E-H246 residues at EDII. Exchanges of oppositely charged residue side chains at prM-E125/E-K93 and prM-E125/E-H246 are recoverable for VLP production. The prM-E125 and E-H246 residues are conserved and that the positive charge of the E-K93 residue is preserved in different flavivirus groups. These findings suggest that the electrostatic attractions of prM-E125, E-K93, and E-H246 residues are important to flavivirus VLP production and that inhibiting these interactions is a potential strategy for blocking flavivirus infections. IMPORTANCE: Molecular interaction between E and prM proteins of Japanese encephalitis virus is a major driving force for virus-like particle (VLP) production. The current high-resolution structures available for prM-E complexes do not include the membrane proximal stem region of prM. The prM stem region contains an N-terminal loop and a helix domain (prM-H). Since the prM-H domain is topologically close to domain II of the E protein (EDII), this study was to determine molecular interactions between the prM-H domain and EDII. We found that the molecular interactions between prM-E125 residue and positively charged E-K93 and E-H246 residues at EDII are critical for VLP production. More importantly, the prM-E125 and E-H246 residues are conserved and the positive charge of the E-K93 residue is preserved in different flavivirus groups. Our findings help refine the structure and molecular interactions on the flavivirus surface and reveal a potential strategy for blocking flavivirus infections by inhibiting these electrostatic interactions.\",\n \"corpus_id\": 35256885,\n \"score\": 0\n },\n {\n \"doc_id\": \"25257385\",\n \"title\": \"Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.\",\n \"abstract\": \"α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins.\",\n \"corpus_id\": 19661758,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":74,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29028926\",\n \"title\": \"Structure-based prediction of protein- peptide binding regions using Random Forest.\",\n \"abstract\": \"Motivation: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein-peptide interactions can be analyzed by studying the structures of protein-peptide complexes. However, only a small portion has known complex structures and experimental determination of protein-peptide interaction is costly and inefficient. Thus, predicting peptide-binding sites computationally will be useful to improve efficiency and cost effectiveness of experimental studies. Here, we established a machine learning method called SPRINT-Str (Structure-based prediction of protein-Peptide Residue-level Interaction) to use structural information for predicting protein-peptide binding residues. These predicted binding residues are then employed to infer the peptide-binding site by a clustering algorithm. Results: SPRINT-Str achieves robust and consistent results for prediction of protein-peptide binding regions in terms of residues and sites. Matthews' Correlation Coefficient (MCC) for 10-fold cross validation and independent test set are 0.27 and 0.293, respectively, as well as 0.775 and 0.782, respectively for area under the curve. The prediction outperforms other state-of-the-art methods, including our previously developed sequence-based method. A further spatial neighbor clustering of predicted binding residues leads to prediction of binding sites at 20-116% higher coverage than the next best method at all precision levels in the test set. The application of SPRINT-Str to protein binding with DNA, RNA and carbohydrate confirms the method's capability of separating peptide-binding sites from other functional sites. More importantly, similar performance in prediction of binding residues and sites is obtained when experimentally determined structures are replaced by unbound structures or quality model structures built from homologs, indicating its wide applicability. Availability and implementation: http://sparks-lab.org/server/SPRINT-Str. Contact: yangyd25@mail.sysu.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3767544\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19508202","title":"Improve the prediction of RNA-binding residues using structural neighbours.","abstract":"The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the predictions over existing methods. Using a multiple linear regression approach and 6-fold cross validation, our best model can achieve an overall correct rate of 87.8% and MCC of 0.47, with a specificity of 93.4%, correctly predict 52.4% of the RNA-binding residues for a dataset containing 107 non-homologous RNA-binding proteins. Compared with existing methods, including the amino acid compositions of structure neighbors lead to clearly improvement. A web server was developed for predicting RNA binding residues in a protein sequence (or structure),which is available at http://mcgill.3322.org/RNA/.","corpus_id":32567641,"score":2},{"doc_id":"20483814","title":"Prediction of protein-RNA binding sites by a random forest method with combined features.","abstract":"MOTIVATION: Protein-RNA interactions play a key role in a number of biological processes, such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and eukaryotic spliceosomes. As a result, a reliable identification of RNA binding site of a protein is important for functional annotation and site-directed mutagenesis. Accumulated data of experimental protein-RNA interactions reveal that a RNA binding residue with different neighbor amino acids often exhibits different preferences for its RNA partners, which in turn can be assessed by the interacting interdependence of the amino acid fragment and RNA nucleotide. RESULTS: In this work, we propose a novel classification method to identify the RNA binding sites in proteins by combining a new interacting feature (interaction propensity) with other sequence- and structure-based features. Specifically, the interaction propensity represents a binding specificity of a protein residue to the interacting RNA nucleotide by considering its two-side neighborhood in a protein residue triplet. The sequence as well as the structure-based features of the residues are combined together to discriminate the interaction propensity of amino acids with RNA. We predict RNA interacting residues in proteins by implementing a well-built random forest classifier. The experiments show that our method is able to detect the annotated protein-RNA interaction sites in a high accuracy. Our method achieves an accuracy of 84.5%, F-measure of 0.85 and AUC of 0.92 prediction of the RNA binding residues for a dataset containing 205 non-homologous RNA binding proteins, and also outperforms several existing RNA binding residue predictors, such as RNABindR, BindN, RNAProB and PPRint, and some alternative machine learning methods, such as support vector machine, naive Bayes and neural network in the comparison study. Furthermore, we provide some biological insights into the roles of sequences and structures in protein-RNA interactions by both evaluating the importance of features for their contributions in predictive accuracy and analyzing the binding patterns of interacting residues. AVAILABILITY: All the source data and code are available at http://www.aporc.org/doc/wiki/PRNA or http://www.sysbio.ac.cn/datatools.asp CONTACT: lnchen@sibs.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":15065218,"score":2},{"doc_id":"22258275","title":"Prediction of hot spots in protein interfaces using a random forest model with hybrid features.","abstract":"Prediction of hot spots in protein interfaces provides crucial information for the research on protein-protein interaction and drug design. Existing machine learning methods generally judge whether a given residue is likely to be a hot spot by extracting features only from the target residue. However, hot spots usually form a small cluster of residues which are tightly packed together at the center of protein interface. With this in mind, we present a novel method to extract hybrid features which incorporate a wide range of information of the target residue and its spatially neighboring residues, i.e. the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). We provide a novel random forest (RF) model to effectively integrate these hybrid features for predicting hot spots in protein interfaces. Our method can achieve accuracy (ACC) of 82.4% and Matthew's correlation coefficient (MCC) of 0.482 in Alanine Scanning Energetics Database, and ACC of 77.6% and MCC of 0.429 in Binding Interface Database. In a comparison study, performance of our RF model exceeds other existing methods, such as Robetta, FOLDEF, KFC, KFC2, MINERVA and HotPoint. Of our hybrid features, three physicochemical features of target residues (mass, polarizability and isoelectric point), the relative side-chain accessible surface area and the average depth index of mirror-contact residues are found to be the main discriminative features in hot spots prediction. We also confirm that hot spots tend to form large contact surface areas between two interacting proteins. Source data and code are available at: http://www.aporc.org/doc/wiki/HotSpot.","corpus_id":6263515,"score":2},{"doc_id":"22574904","title":"Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.","abstract":"BACKGROUND: RNA molecules play diverse functional and structural roles in cells. They function as messengers for transferring genetic information from DNA to proteins, as the primary genetic material in many viruses, as catalysts (ribozymes) important for protein synthesis and RNA processing, and as essential and ubiquitous regulators of gene expression in living organisms. Many of these functions depend on precisely orchestrated interactions between RNA molecules and specific proteins in cells. Understanding the molecular mechanisms by which proteins recognize and bind RNA is essential for comprehending the functional implications of these interactions, but the recognition 'code' that mediates interactions between proteins and RNA is not yet understood. Success in deciphering this code would dramatically impact the development of new therapeutic strategies for intervening in devastating diseases such as AIDS and cancer. Because of the high cost of experimental determination of protein-RNA interfaces, there is an increasing reliance on statistical machine learning methods for training predictors of RNA-binding residues in proteins. However, because of differences in the choice of datasets, performance measures, and data representations used, it has been difficult to obtain an accurate assessment of the current state of the art in protein-RNA interface prediction. RESULTS: We provide a review of published approaches for predicting RNA-binding residues in proteins and a systematic comparison and critical assessment of protein-RNA interface residue predictors trained using these approaches on three carefully curated non-redundant datasets. We directly compare two widely used machine learning algorithms (Naïve Bayes (NB) and Support Vector Machine (SVM)) using three different data representations in which features are encoded using either sequence- or structure-based windows. Our results show that (i) Sequence-based classifiers that use a position-specific scoring matrix (PSSM)-based representation (PSSMSeq) outperform those that use an amino acid identity based representation (IDSeq) or a smoothed PSSM (SmoPSSMSeq); (ii) Structure-based classifiers that use smoothed PSSM representation (SmoPSSMStr) outperform those that use PSSM (PSSMStr) as well as sequence identity based representation (IDStr). PSSMSeq classifiers, when tested on an independent test set of 44 proteins, achieve performance that is comparable to that of three state-of-the-art structure-based predictors (including those that exploit geometric features) in terms of Matthews Correlation Coefficient (MCC), although the structure-based methods achieve substantially higher Specificity (albeit at the expense of Sensitivity) compared to sequence-based methods. We also find that the expected performance of the classifiers on a residue level can be markedly different from that on a protein level. Our experiments show that the classifiers trained on three different non-redundant protein-RNA interface datasets achieve comparable cross-validation performance. However, we find that the results are significantly affected by differences in the distance threshold used to define interface residues. CONCLUSIONS: Our results demonstrate that protein-RNA interface residue predictors that use a PSSM-based encoding of sequence windows outperform classifiers that use other encodings of sequence windows. While structure-based methods that exploit geometric features can yield significant increases in the Specificity of protein-RNA interface residue predictions, such increases are offset by decreases in Sensitivity. These results underscore the importance of comparing alternative methods using rigorous statistical procedures, multiple performance measures, and datasets that are constructed based on several alternative definitions of interface residues and redundancy cutoffs as well as including evaluations on independent test sets into the comparisons.","corpus_id":15531335,"score":2},{"doc_id":"22848404","title":"Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.","abstract":"Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date.","corpus_id":7507823,"score":2},{"doc_id":"23737141","title":"DNABind: a hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.","abstract":"Accurate prediction of DNA-binding residues has become a problem of increasing importance in structural bioinformatics. Here, we presented DNABind, a novel hybrid algorithm for identifying these crucial residues by exploiting the complementarity between machine learning- and template-based methods. Our machine learning-based method was based on the probabilistic combination of a structure-based and a sequence-based predictor, both of which were implemented using support vector machines algorithms. The former included our well-designed structural features, such as solvent accessibility, local geometry, topological features, and relative positions, which can effectively quantify the difference between DNA-binding and nonbinding residues. The latter combined evolutionary conservation features with three other sequence attributes. Our template-based method depended on structural alignment and utilized the template structure from known protein-DNA complexes to infer DNA-binding residues. We showed that the template method had excellent performance when reliable templates were found for the query proteins but tended to be strongly influenced by the template quality as well as the conformational changes upon DNA binding. In contrast, the machine learning approach yielded better performance when high-quality templates were not available (about 1/3 cases in our dataset) or the query protein was subject to intensive transformation changes upon DNA binding. Our extensive experiments indicated that the hybrid approach can distinctly improve the performance of the individual methods for both bound and unbound structures. DNABind also significantly outperformed the state-of-art algorithms by around 10% in terms of Matthews's correlation coefficient. The proposed methodology could also have wide application in various protein functional site annotations. DNABind is freely available at http://mleg.cse.sc.edu/DNABind/.","corpus_id":206407482,"score":2},{"doc_id":"24854765","title":"RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies.","abstract":"Computational prediction of RNA-binding residues is helpful in uncovering the mechanisms underlying protein-RNA interactions. Traditional algorithms individually applied feature- or template-based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA-binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA-Binding Residue Detector) by combining these two strategies. We developed a feature-based approach that is an ensemble learning predictor comprising multiple structure-based classifiers, in which well-defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template-based predictor to recognize the putative RNA-binding regions by structurally aligning the query protein to the RNA-binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature- and template-based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state-of-the-art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA-binding proteins and thus incorrectly predicted the DNA-binding regions as RNA-binding interfaces. Finally, we implemented the RBRDetector algorithm as a user-friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector.","corpus_id":36833308,"score":2},{"doc_id":"25075532","title":"Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues.","abstract":"The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming increasingly important for the research on protein-protein interaction and drug design. For each interface residue or target residue to be predicted, the authors extract hybrid features which incorporate a wide range of information of the target residue and its spatial neighbor residues, that is, the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). Here, feature selection is performed using random forests to avoid over-fitting. Thereafter, the extreme learning machine is employed to effectively integrate these hybrid features for predicting hot spots in protein interfaces. By the 5-fold cross validation in the training set, their method can achieve accuracy (ACC) of 82.1% and Matthew's correlation coefficient (MCC) of 0.459, and outperforms some alternative machine learning methods in the comparison study. Furthermore, their method achieves ACC of 76.8% and MCC of 0.401 in the independent test set, and is more effective than the major existing hot spot predictors. Their prediction method offers a powerful tool for uncovering candidate residues in the studies of alanine scanning mutagenesis for functional protein interaction sites.","corpus_id":206191106,"score":2},{"doc_id":"26833816","title":"Sequence-based prediction of protein-peptide binding sites using support vector machine.","abstract":"Protein-peptide interactions are essential for all cellular processes including DNA repair, replication, gene-expression, and metabolism. As most protein-peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein-peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine-learning method called SPRINT to make Sequence-based prediction of Protein-peptide Residue-level Interactions. SPRINT yields a robust and consistent performance for 10-fold cross validations and independent test. The most important feature is evolution-generated sequence profiles. For the test set (1056 binding and non-binding residues), it yields a Matthews' Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence-based technique shows comparable or more accurate than structure-based methods for peptide-binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/. © 2016 Wiley Periodicals, Inc.","corpus_id":5071902,"score":2},{"doc_id":"27623166","title":"Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.","abstract":"Carbohydrate-binding proteins play significant roles in many diseases including cancer. Here, we established a machine-learning-based method (called sequence-based prediction of residue-level interaction sites of carbohydrates, SPRINT-CBH) to predict carbohydrate-binding sites in proteins using support vector machines (SVMs). We found that integrating evolution-derived sequence profiles with additional information on sequence and predicted solvent accessible surface area leads to a reasonably accurate, robust, and predictive method, with area under receiver operating characteristic curve (AUC) of 0.78 and 0.77 and Matthew's correlation coefficient of 0.34 and 0.29, respectively for 10-fold cross validation and independent test without balancing binding and nonbinding residues. The quality of the method is further demonstrated by having statistically significantly more binding residues predicted for carbohydrate-binding proteins than presumptive nonbinding proteins in the human proteome, and by the bias of rare alleles toward predicted carbohydrate-binding sites for nonsynonymous mutations from the 1000 genome project. SPRINT-CBH is available as an online server at http://sparks-lab.org/server/SPRINT-CBH .","corpus_id":99187577,"score":2},{"doc_id":"27993780","title":"RBPPred: predicting RNA-binding proteins from sequence using SVM.","abstract":"Motivation: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computational prediction is much more efficient than experimental methods and may have guiding significance on the experiment design. Results: In this study, we present the RBPPred (an RNA-binding protein predictor), a new method based on the support vector machine, to predict whether a protein binds RNAs, based on a comprehensive feature representation. By integrating the physicochemical properties with the evolutionary information of protein sequences, the new approach RBPPred performed much better than state-of-the-art methods. The results show that RBPPred correctly predicted 83% of 2780 RBPs and 96% out of 7093 non-RBPs with MCC of 0.808 using the 10-fold cross validation. Furthermore, we achieved a sensitivity of 84%, specificity of 97% and MCC of 0.788 on the testing set of human proteome. In addition we tested the capability of RBPPred to identify new RBPs, which further confirmed the practicability and predictability of the method. Availability and Implementation: RBPPred program can be accessed at: http://rnabinding.com/RBPPred.html . Contact: liushiyong@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3818271,"score":2},{"doc_id":"28073761","title":"Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.","abstract":"Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in protein-protein interactions. Such predictions are typically based on machine learning methods that take advantage of the properties and sequence positions of amino acids that are known to be involved in interaction. In this paper, we evaluate the importance of various features using Random Forest (RF), and include as a novel feature backbone flexibility predicted from sequences to further optimise protein interface prediction. Results: We observe that there is no single sequence feature that enables pinpointing interacting sites in our Random Forest models. However, combining different properties does increase the performance of interface prediction. Our homomeric-trained RF interface predictor is able to distinguish interface from non-interface residues with an area under the ROC curve of 0.72 in a homomeric test-set. The heteromeric-trained RF interface predictor performs better than existing predictors on a independent heteromeric test-set. We trained a more general predictor on the combined homomeric and heteromeric dataset, and show that in addition to predicting homomeric interfaces, it is also able to pinpoint interface residues in heterodimers. This suggests that our random forest model and the features included capture common properties of both homodimer and heterodimer interfaces. Availability and Implementation: The predictors and test datasets used in our analyses are freely available ( http://www.ibi.vu.nl/downloads/RF_PPI/ ). Contact: k.a.feenstra@vu.nl. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3740647,"score":2},{"doc_id":"29281004","title":"Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.","abstract":"Motivation: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Results: Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. Availability and implementation: The PrabHot webserver is freely available at http://denglab.org/PrabHot/. Contact: leideng@csu.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3820508,"score":2},{"doc_id":"18235992","title":"PRINTR: prediction of RNA binding sites in proteins using SVM and profiles.","abstract":"Protein-RNA interactions play a key role in a number of biological processes such as protein synthesis, mRNA processing, assembly and function of ribosomes and eukaryotic spliceosomes. A reliable identification of RNA-binding sites in RNA-binding proteins is important for functional annotation and site-directed mutagenesis. We developed a novel method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the prediction of protein residues at RNA-binding surfaces. One is given the sequence information of a protein chain that is known to interact with RNA; the other is given the structural information. Thus, five different inputs have been tested. Coupled with PSI-BLAST profiles and predicted secondary structure, the present approach yields a Matthews correlation coefficient (MCC) of 0.432 by a 7-fold cross-validation, which is the best among all previous reported RNA-binding sites prediction methods. When given the structural information, we have obtained the MCC value of 0.457, with PSSMs, observed secondary structure and solvent accessibility information assigned by DSSP as input. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/printr/ .","corpus_id":1035800,"score":1},{"doc_id":"18940825","title":"Predicting small ligand binding sites in proteins using backbone structure.","abstract":"MOTIVATION: Specific non-covalent binding of metal ions and ligands, such as nucleotides and cofactors, is essential for the function of many proteins. Computational methods are useful for predicting the location of such binding sites when experimental information is lacking. Methods that use structural information, when available, are particularly promising since they can potentially identify non-contiguous binding motifs that cannot be found using only the amino acid sequence. Furthermore, a prediction method that can utilize low-resolution models is advantageous because high-resolution structures are available for only a relatively small fraction of proteins. RESULTS: SitePredict is a machine learning-based method for predicting binding sites in protein structures for specific metal ions or small molecules. The method uses Random Forest classifiers trained on diverse residue-based site properties including spatial clustering of residue types and evolutionary conservation. SitePredict was tested by cross-validation on a set of known binding sites for six different metal ions and five different small molecules in a non-redundant set of protein-ligand complex structures. The prediction performance was good for all ligands considered, as reflected by AUC values of at least 0.8. Furthermore, a more realistic test on unbound structures showed only a slight decrease in the accuracy. The properties that contribute the most to the prediction accuracy of each ligand were also examined. Finally, examples of predicted binding sites in homology models and uncharacterized proteins are discussed. AVAILABILITY: Binding site prediction results for all PDB protein structures and human protein homology models are available at http://sitepredict.org/.","corpus_id":2258881,"score":1},{"doc_id":"19008251","title":"Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.","abstract":"MOTIVATION: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical-chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class. RESULTS: The results show that the RF model achieves 91.41% overall accuracy with Matthew's correlation coefficient of 0.70 and an area under the receiver operating characteristic curve (AUC) of 0.913. To our knowledge, the RF method using the hybrid feature is currently the computationally optimal approach for predicting DNA-binding sites in proteins from amino acid sequences without using three-dimensional (3D) structural information. We have demonstrated that the prediction results are useful for understanding protein-DNA interactions. AVAILABILITY: DBindR web server implementation is freely available at http://www.cbi.seu.edu.cn/DBindR/DBindR.htm.","corpus_id":3616970,"score":1},{"doc_id":"19128505","title":"Large-scale prediction of long disordered regions in proteins using random forests.","abstract":"BACKGROUND: Many proteins contain disordered regions that lack fixed three-dimensional (3D) structure under physiological conditions but have important biological functions. Prediction of disordered regions in protein sequences is important for understanding protein function and in high-throughput determination of protein structures. Machine learning techniques, including neural networks and support vector machines have been widely used in such predictions. Predictors designed for long disordered regions are usually less successful in predicting short disordered regions. Combining prediction of short and long disordered regions will dramatically increase the complexity of the prediction algorithm and make the predictor unsuitable for large-scale applications. Efficient batch prediction of long disordered regions alone is of greater interest in large-scale proteome studies. RESULTS: A new algorithm, IUPforest-L, for predicting long disordered regions using the random forest learning model is proposed in this paper. IUPforest-L is based on the Moreau-Broto auto-correlation function of amino acid indices (AAIs) and other physicochemical features of the primary sequences. In 10-fold cross validation tests, IUPforest-L can achieve an area of 89.5% under the receiver operating characteristic (ROC) curve. Compared with existing disorder predictors, IUPforest-L has high prediction accuracy and is efficient for predicting long disordered regions in large-scale proteomes. CONCLUSION: The random forest model based on the auto-correlation functions of the AAIs within a protein fragment and other physicochemical features could effectively detect long disordered regions in proteins. A new predictor, IUPforest-L, was developed to batch predict long disordered regions in proteins, and the server can be accessed from http://dmg.cs.rmit.edu.au/IUPforest/IUPforest-L.php.","corpus_id":400254,"score":1},{"doc_id":"19389733","title":"Protein function annotation from sequence: prediction of residues interacting with RNA.","abstract":"MOTIVATION: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein. RESULTS: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at www.bioinformatics.sussex.ac.uk/PIRANHA or http://piranha.protein.osaka-u.ac.jp. SUPPLEMENTARY INFORMATION: Supplementary data are available at the Bioinformatics online.","corpus_id":6695218,"score":1},{"doc_id":"19594868","title":"Prediction of DNA-binding residues from protein sequence information using random forests.","abstract":"BACKGROUND: Protein-DNA interactions are involved in many biological processes essential for cellular function. To understand the molecular mechanism of protein-DNA recognition, it is necessary to identify the DNA-binding residues in DNA-binding proteins. However, structural data are available for only a few hundreds of protein-DNA complexes. With the rapid accumulation of sequence data, it becomes an important but challenging task to accurately predict DNA-binding residues directly from amino acid sequence data. RESULTS: A new machine learning approach has been developed in this study for predicting DNA-binding residues from amino acid sequence data. The approach used both the labelled data instances collected from the available structures of protein-DNA complexes and the abundant unlabeled data found in protein sequence databases. The evolutionary information contained in the unlabeled sequence data was represented as position-specific scoring matrices (PSSMs) and several new descriptors. The sequence-derived features were then used to train random forests (RFs), which could handle a large number of input variables and avoid model overfitting. The use of evolutionary information was found to significantly improve classifier performance. The RF classifier was further evaluated using a separate test dataset, and the predicted DNA-binding residues were examined in the context of three-dimensional structures. CONCLUSION: The results suggest that the RF-based approach gives rise to more accurate prediction of DNA-binding residues than previous studies. A new web server called BindN-RF http://bioinfo.ggc.org/bindn-rf/ has thus been developed to make the RF classifier accessible to the biological research community.","corpus_id":10367995,"score":1},{"doc_id":"21268114","title":"Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature.","abstract":"The identification of RNA-binding residues in proteins is important in several areas such as protein function, posttranscriptional regulation and drug design. We have developed PRBR (Prediction of RNA Binding Residues), a novel method for identifying RNA-binding residues from amino acid sequences. Our method combines a hybrid feature with the enriched random forest (ERF) algorithm. The hybrid feature is composed of predicted secondary structure information and three novel features: evolutionary information combined with conservation information of the physicochemical properties of amino acids and the information about dependency of amino acids with regards to polarity-charge and hydrophobicity in the protein sequences. Our results demonstrate that the PRBR model achieves 0.5637 Matthew's correlation coefficient (MCC) and 88.63% overall accuracy (ACC) with 53.70% sensitivity (SE) and 96.97% specificity (SP). By comparing the performance of each feature we found that all three novel features contribute to the improved predictions. Area under the curve (AUC) statistics from receiver operating characteristic curve analysis was compared between PRBR model and other models. The results show that PRBR achieves the highest AUC value (0.8675) which represents that PRBR attains excellent performance on predicting the RNA-binding residues in proteins. The PRBR web-server implementation is freely available at http://www.cbi.seu.edu.cn/PRBR/.","corpus_id":23950803,"score":1},{"doc_id":"22016406","title":"Predicting residue-residue contacts using random forest models.","abstract":"MOTIVATION: Protein residue-residue contact prediction can be useful in predicting protein 3D structures. Current algorithms for such a purpose leave room for improvement. RESULTS: We develop ProC_S3, a set of Random Forest algorithm-based models, for predicting residue-residue contact maps. The models are constructed based on a collection of 1490 non-redundant, high-resolution protein structures using >1280 sequence-based features. A new amino acid residue contact propensity matrix and a new set of seven amino acid groups based on contact preference are developed and used in ProC_S3. ProC_S3 delivers a 3-fold cross-validated accuracy of 26.9% with coverage of 4.7% for top L/5 predictions (L is the number of residues in a protein) of long-range contacts (sequence separation ≥24). Further benchmark tests deliver an accuracy of 29.7% and coverage of 5.6% for an independent set of 329 proteins. In the recently completed Ninth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), ProC_S3 is ranked as No. 1, No. 3, and No. 2 accuracies in the top L/5, L/10 and best 5 predictions of long-range contacts, respectively, among 18 automatic prediction servers. AVAILABILITY: http://www.abl.ku.edu/proc/proc_s3.html. CONTACT: jwfang@ku.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":28117970,"score":1},{"doc_id":"23166753","title":"An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins.","abstract":"Zinc-binding proteins are the most abundant metalloproteins in the Protein Data Bank where the zinc ions usually have catalytic, regulatory or structural roles critical for the function of the protein. Accurate prediction of zinc-binding sites is not only useful for the inference of protein function but also important for the prediction of 3D structure. Here, we present a new integrative framework that combines multiple sequence and structural properties and graph-theoretic network features, followed by an efficient feature selection to improve prediction of zinc-binding sites. We investigate what information can be retrieved from the sequence, structure and network levels that is relevant to zinc-binding site prediction. We perform a two-step feature selection using random forest to remove redundant features and quantify the relative importance of the retrieved features. Benchmarking on a high-quality structural dataset containing 1,103 protein chains and 484 zinc-binding residues, our method achieved >80% recall at a precision of 75% for the zinc-binding residues Cys, His, Glu and Asp on 5-fold cross-validation tests, which is a 10%-28% higher recall at the 75% equal precision compared to SitePredict and zincfinder at residue level using the same dataset. The independent test also indicates that our method has achieved recall of 0.790 and 0.759 at residue and protein levels, respectively, which is a performance better than the other two methods. Moreover, AUC (the Area Under the Curve) and AURPC (the Area Under the Recall-Precision Curve) by our method are also respectively better than those of the other two methods. Our method can not only be applied to large-scale identification of zinc-binding sites when structural information of the target is available, but also give valuable insights into important features arising from different levels that collectively characterize the zinc-binding sites. The scripts and datasets are available at http://protein.cau.edu.cn/zincidentifier/.","corpus_id":8625079,"score":1},{"doc_id":"23514235","title":"Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration.","abstract":"BACKGROUND: Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions. RESULTS: Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time. CONCLUSIONS: In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance for protein-ligand binding region prediction. Based on the same approach and rationale, this method can also be applied to predict carbohydrate-antibody interactions for further design and development of carbohydrate-based vaccines. PLB-SAVE is available at http://save.cs.ntou.edu.tw.","corpus_id":2498808,"score":1},{"doc_id":"24211525","title":"Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces.","abstract":"Flavin mono-nucleotide (FMN) is a cofactor which is involved in many biological reactions. The insights on protein-FMN interactions aid the protein functional annotation and also facilitate in drug design. In this study, we have established a new method, making use of an encoding scheme of the three-dimensional probability density maps that describe the distributions of 40 non-covalent interacting atom types around protein surfaces, to predict FMN-binding sites on protein surfaces. One machine learning model was trained for each of the 30 protein atom types to predict tentative FMN-binding sites on protein structures. The method's capability was evaluated by five-fold cross-validation on a dataset containing 81 non-redundant FMN-binding protein structures and further tested on independent datasets of 30 and 15 non-redundant protein structures respectively. These predictions achieved an accuracy of 0.94, 0.94 and 0.96 with the Matthews correlation coefficient (MCC) of 0.53, 0.53 and 0.65 respectively for the three protein structure sets. The prediction capability is superior to the existing method. This is the first structure-based approach that does not rely on evolutionary information for predicting FMN-interacting residues. The webserver for the prediction is available at http://ismblab.genomics.sinica.edu.tw/.","corpus_id":23986112,"score":1},{"doc_id":"24475169","title":"Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.","abstract":"Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred can be an alternative perspective predictor for large-scale determination of DNA-binding proteins.","corpus_id":8320048,"score":1},{"doc_id":"24846307","title":"RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.","abstract":"Protein-RNA interactions are central to essential cellular processes such as protein synthesis and regulation of gene expression and play roles in human infectious and genetic diseases. Reliable identification of protein-RNA interfaces is critical for understanding the structural bases and functional implications of such interactions and for developing effective approaches to rational drug design. Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins. Here we report two novel approaches: (i) HomPRIP, a sequence homology-based method for predicting RNA-binding sites in proteins; (ii) RNABindRPlus, a new method that combines predictions from HomPRIP with those from an optimized Support Vector Machine (SVM) classifier trained on a benchmark dataset of 198 RNA-binding proteins. Although highly reliable, HomPRIP cannot make predictions for the unaligned parts of query proteins and its coverage is limited by the availability of close sequence homologs of the query protein with experimentally determined RNA-binding sites. RNABindRPlus overcomes these limitations. We compared the performance of HomPRIP and RNABindRPlus with that of several state-of-the-art predictors on two test sets, RB44 and RB111. On a subset of proteins for which homologs with experimentally determined interfaces could be reliably identified, HomPRIP outperformed all other methods achieving an MCC of 0.63 on RB44 and 0.83 on RB111. RNABindRPlus was able to predict RNA-binding residues of all proteins in both test sets, achieving an MCC of 0.55 and 0.37, respectively, and outperforming all other methods, including those that make use of structure-derived features of proteins. More importantly, RNABindRPlus outperforms all other methods for any choice of tradeoff between precision and recall. An important advantage of both HomPRIP and RNABindRPlus is that they rely on readily available sequence and sequence-derived features of RNA-binding proteins. A webserver implementation of both methods is freely available at http://einstein.cs.iastate.edu/RNABindRPlus/.","corpus_id":13527970,"score":1},{"doc_id":"25113160","title":"Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.","abstract":"As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of our knowledge, this is the first attempt to predict protein-binding nucleotides in a given DNA sequence from the sequence data alone.","corpus_id":1554684,"score":1},{"doc_id":"25907142","title":"Predicting protein-binding RNA nucleotides with consideration of binding partners.","abstract":"In recent years several computational methods have been developed to predict RNA-binding sites in protein. Most of these methods do not consider interacting partners of a protein, so they predict the same RNA-binding sites for a given protein sequence even if the protein binds to different RNAs. Unlike the problem of predicting RNA-binding sites in protein, the problem of predicting protein-binding sites in RNA has received little attention mainly because it is much more difficult and shows a lower accuracy on average. In our previous study, we developed a method that predicts protein-binding nucleotides from an RNA sequence. In an effort to improve the prediction accuracy and usefulness of the previous method, we developed a new method that uses both RNA and protein sequence data. In this study, we identified effective features of RNA and protein molecules and developed a new support vector machine (SVM) model to predict protein-binding nucleotides from RNA and protein sequence data. The new model that used both protein and RNA sequence data achieved a sensitivity of 86.5%, a specificity of 86.2%, a positive predictive value (PPV) of 72.6%, a negative predictive value (NPV) of 93.8% and Matthews correlation coefficient (MCC) of 0.69 in a 10-fold cross validation; it achieved a sensitivity of 58.8%, a specificity of 87.4%, a PPV of 65.1%, a NPV of 84.2% and MCC of 0.48 in independent testing. For comparative purpose, we built another prediction model that used RNA sequence data alone and ran it on the same dataset. In a 10 fold-cross validation it achieved a sensitivity of 85.7%, a specificity of 80.5%, a PPV of 67.7%, a NPV of 92.2% and MCC of 0.63; in independent testing it achieved a sensitivity of 67.7%, a specificity of 78.8%, a PPV of 57.6%, a NPV of 85.2% and MCC of 0.45. In both cross-validations and independent testing, the new model that used both RNA and protein sequences showed a better performance than the model that used RNA sequence data alone in most performance measures. To the best of our knowledge, this is the first sequence-based prediction of protein-binding nucleotides in RNA which considers the binding partner of RNA. The new model will provide valuable information for designing biochemical experiments to find putative protein-binding sites in RNA with unknown structure.","corpus_id":25976649,"score":1},{"doc_id":"26405960","title":"Predicting a DNA-binding protein using random forest with multiple mathematical features.","abstract":"DNA-binding proteins are involved and play a crucial role in a lot of important biological processes. Hence, the identification of the DNA-binding proteins is a challenging and significant problem. In order to reveal the intrinsic information correlated to DNA-binding, nine classes of candidate features based on different mathematical fields are applied to construct the prediction model with random forest. They are fractal dimension, conjoint triad feature, Hilbert-Huang Transformation, amino acid composition, dipeptide composition, chaos game representation, and the corresponding information entropies. These mathematical expressions are evaluated with 5-fold cross validation test. The results of numerical simulations show that the mathematical features consisted of amino acid composition, fractal dimension and information entropies of amino acid and chaos game representation achieve the best performance. Its accuracy is 0.8157, and Matthew's correlation coefficient (MCC) achieves 0.5968 on the benchmark dataset from DNA-Prot. By analyzing the components of top combination of the nine candidate features, the concepts of fractal dimension and information entropy are the effective and vital features, which can provide complementary sequence-order information on the basis of amino acid composition.","corpus_id":16047378,"score":1},{"doc_id":"26568622","title":"Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.","abstract":"MOTIVATION: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. RESULTS: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":22034498,"score":1},{"doc_id":"27259543","title":"DBSI server: DNA binding site identifier.","abstract":"UNLABELLED: : Protein-nucleic acid interactions are among the most important intermolecular interactions in the regulation of cellular events. Identifying residues involved in these interactions from protein structure alone is an important challenge. Here we introduce the webserver interface to DNA Binding Site Identifier (DBSI), a powerful structure-based SVM model for the prediction and visualization of DNA binding sites on protein structures. DBSI has been shown to be a top-performing model to predict DNA binding sites on the surface of a protein or peptide and shows promise in predicting RNA binding sites. AVAILABILITY AND IMPLEMENTATION: Server is available at http://dbsi.mitchell-lab.org CONTACT: jcmitchell@wisc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":13178732,"score":1},{"doc_id":"27266516","title":"Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors.","abstract":"BACKGROUND: RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins. Newly developed discriminative descriptors will help to improve the prediction accuracy of these prediction methods and provide further meaningful information for researchers. RESULTS: In this work, we designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the two features were powerful for identifying RNA-binding protein residues. Using these two features and other excellent structure- and sequence-based features, a random forest classifier was constructed to predict RNA-binding residues. The area under the receiver operating characteristic curve (AUC) of five-fold cross-validation for our method on training set RBP195 was 0.900, and when applied to the test set RBP68, the prediction accuracy (ACC) was 0.868, and the F-score was 0.631. CONCLUSIONS: The good prediction performance of our method revealed that the two newly designed descriptors could be discriminative for inferring protein residues interacting with RNAs. To facilitate the use of our method, a web-server called RNAProSite, which implements the proposed method, was constructed and is freely available at http://lilab.ecust.edu.cn/NABind .","corpus_id":1265451,"score":1},{"doc_id":"27403208","title":"bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.","abstract":"MOTIVATION: Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. RESULTS: By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset. For 210 bound dataset, bSiteFinder achieved high accuracies up to 94.8 % (MCC 0.95). For another 48 bound/unbound dataset, bSiteFinder achieved high accuracies up to 93.8 % for bound proteins (MCC 0.95) and 85.4 % for unbound proteins (MCC 0.72). Our bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/, and the source code is provided at the methods page. CONCLUSION: An online bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/. Our work lays a foundation for functional annotation of protein and structure-based drug design. With ever increasing numbers of three-dimensional protein-ligand complex structures, our server should be more accurate and less time-consuming. Graphical Abstract bSiteFinder (http://binfo.shmtu.edu.cn/bsitefinder/) as a protein-binding sites prediction server was developed based on the largest database of bound templates so far with stringent quality control. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server have been significantly improved. What's more, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset.","corpus_id":16103515,"score":1},{"doc_id":"28056090","title":"Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.","abstract":"MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. RESULTS: Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. AVAILABILITY: http://raptorx.uchicago.edu/ContactMap/.","corpus_id":605957,"score":1},{"doc_id":"28130235","title":"ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.","abstract":"Motivation: The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge. Results: We present ISPRED4, an improved structure-based predictor of PPI sites on unbound monomer surfaces. ISPRED4 relies on machine-learning methods and it incorporates features extracted from protein sequence and structure. Cross-validation experiments are carried out on a new dataset that includes 151 high-resolution protein complexes and indicate that ISPRED4 achieves a per-residue Matthew Correlation Coefficient of 0.48 and an overall accuracy of 0.85. Benchmarking results show that ISPRED4 is one of the top-performing PPI site predictors developed so far. Contact: gigi@biocomp.unibo.it. Availability and Implementation: ISPRED4 and datasets used in this study are available at http://ispred4.biocomp.unibo.it .","corpus_id":2850711,"score":1},{"doc_id":"28334224","title":"Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.","abstract":"Motivation: The study of transcriptional regulation is still difficult yet fundamental in molecular biology research. While the development of both in vivo and in vitro profiling techniques have significantly enhanced our knowledge of transcription factor (TF)-DNA interactions, computational models of TF-DNA interactions are relatively simple and may not reveal sufficient biological insight. In particular, supervised learning based models for TF-DNA interactions attempt to map sequence-level features ( k -mers) to binding event but usually ignore the location of k -mers, which can cause data fragmentation and consequently inferior model performance. Results: Here, we propose a novel algorithm based on the so-called multiple-instance learning (MIL) paradigm. MIL breaks each DNA sequence into multiple overlapping subsequences and models each subsequence separately, therefore implicitly takes into consideration binding site locations, resulting in both higher accuracy and better interpretability of the models. The result from both in vivo and in vitro TFDNA interaction data show that our approach significantly outperformconventional single-instance learning based algorithms. Importantly, the models learned from in vitro data using our approach can predict in vivo binding with very good accuracy. In addition, the location information obtained by our method provides additional insight for motif finding results from ChIP-Seq data. Finally, our approach can be easily combined with other state-of-the-art TF-DNA interaction modeling methods. Availability: http://www.cs.utsa.edu/∼jruan/MIL /. Contact: jianhua.ruan@utsa.edu. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4447497,"score":1},{"doc_id":"28361677","title":"Predicting protein-binding regions in RNA using nucleotide profiles and compositions.","abstract":"BACKGROUND: Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding sites in protein-RNA interactions. However, most computational methods are limited to finding RNA-binding sites in proteins instead of protein-binding sites in RNAs. Predicting protein-binding sites in RNA is more challenging than predicting RNA-binding sites in proteins. Recent computational methods for finding protein-binding sites in RNAs have several drawbacks for practical use. RESULTS: We developed a new support vector machine (SVM) model for predicting protein-binding regions in mRNA sequences. The model uses sequence profiles constructed from log-odds scores of mono- and di-nucleotides and nucleotide compositions. The model was evaluated by standard 10-fold cross validation, leave-one-protein-out (LOPO) cross validation and independent testing. Since actual mRNA sequences have more non-binding regions than protein-binding regions, we tested the model on several datasets with different ratios of protein-binding regions to non-binding regions. The best performance of the model was obtained in a balanced dataset of positive and negative instances. 10-fold cross validation with a balanced dataset achieved a sensitivity of 91.6%, a specificity of 92.4%, an accuracy of 92.0%, a positive predictive value (PPV) of 91.7%, a negative predictive value (NPV) of 92.3% and a Matthews correlation coefficient (MCC) of 0.840. LOPO cross validation showed a lower performance than the 10-fold cross validation, but the performance remains high (87.6% accuracy and 0.752 MCC). In testing the model on independent datasets, it achieved an accuracy of 82.2% and an MCC of 0.656. Testing of our model and other state-of-the-art methods on a same dataset showed that our model is better than the others. CONCLUSIONS: Sequence profiles of log-odds scores of mono- and di-nucleotides were much more powerful features than nucleotide compositions in finding protein-binding regions in RNA sequences. But, a slight performance gain was obtained when using the sequence profiles along with nucleotide compositions. These are preliminary results of ongoing research, but demonstrate the potential of our approach as a powerful predictor of protein-binding regions in RNA. The program and supporting data are available at http://bclab.inha.ac.kr/RBPbinding .","corpus_id":11927189,"score":1},{"doc_id":"28851273","title":"EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.","abstract":"BACKGROUND: Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues. RESULTS: In this paper, we first propose a novel residue encoding method, referred to as the Position Specific Score Matrix (PSSM) Relation Transformation (PSSM-RT), to encode residues by utilizing the relationships of evolutionary information between residues. PDNA-62 and PDNA-224 are used to evaluate PSSM-RT and two existing PSSM encoding methods by five-fold cross-validation. Performance evaluations indicate that PSSM-RT is more effective than previous methods. This validates the point that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction. An ensemble learning classifier (EL_PSSM-RT) is also proposed by combining ensemble learning model and PSSM-RT to better handle the imbalance between binding and non-binding residues in datasets. EL_PSSM-RT is evaluated by five-fold cross-validation using PDNA-62 and PDNA-224 as well as two independent datasets TS-72 and TS-61. Performance comparisons with existing predictors on the four datasets demonstrate that EL_PSSM-RT is the best-performing method among all the predicting methods with improvement between 0.02-0.07 for MCC, 4.18-21.47% for ST and 0.013-0.131 for AUC. Furthermore, we analyze the importance of the pair-relationships extracted by PSSM-RT and the results validates the usefulness of PSSM-RT for encoding DNA-binding residues. CONCLUSIONS: We propose a novel prediction method for the prediction of DNA-binding residue with the inclusion of relationship of evolutionary information and ensemble learning. Performance evaluation shows that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction and ensemble learning can be used to address the data imbalance issue between binding and non-binding residues. A web service of EL_PSSM-RT ( http://hlt.hitsz.edu.cn:8080/PSSM-RT_SVM/ ) is provided for free access to the biological research community.","corpus_id":21146302,"score":1},{"doc_id":"29219069","title":"A boosting approach for prediction of protein-RNA binding residues.","abstract":"BACKGROUND: RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex. RESULTS: We propose PredRBR, an effectively computational approach to predict RNA-binding residues. PredRBR is built with gradient tree boosting and an optimal feature set selected from a large number of sequence and structure characteristics and two categories of structural neighborhood properties. In cross-validation experiments on the RBP170 data set show that PredRBR achieves an overall accuracy of 0.84, a sensitivity of 0.85, MCC of 0.55 and AUC of 0.92, which are significantly better than that of other widely used machine learning algorithms such as Support Vector Machine, Random Forest, and Adaboost. We further calculate the feature importance of different feature categories and find that structural neighborhood characteristics are critical in the recognization of RNA binding residues. Also, PredRBR yields significantly better prediction accuracy on an independent test set (RBP101) in comparison with other state-of-the-art methods. CONCLUSIONS: The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree boosting algorithm combined with the optimal selected features.","corpus_id":25996800,"score":1},{"doc_id":"29390084","title":"Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.","abstract":"Motivation: Protein-protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontology (GO) being one of the most successful projects. Several PPI evaluation algorithms have been based on the application of probabilistic frameworks or machine learning algorithms to GO properties. Here, we introduce a new training set design and machine learning based approach that combines dependent heterogeneous protein annotations from the entire ontology to evaluate putative co-complex protein interactions determined by empirical studies. Results: PPI annotations are built combinatorically using corresponding GO terms and InterPro annotation. We use a S.cerevisiae high-confidence complex dataset as a positive training set. A series of classifiers based on Maximum Entropy and support vector machines (SVMs), each with a composite counterpart algorithm, are trained on a series of training sets. These achieve a high performance area under the ROC curve of ≤0.97, outperforming go2ppi-a previously established prediction tool for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations. Availability and implementation: https://github.com/ima23/maxent-ppi. Contact: sbh11@cl.cam.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3795861,"score":1},{"doc_id":"29547921","title":"CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.","abstract":"Motivation: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction. Results: We developed three methods for the prediction of CoA- and CoA derivatives-binding residues, including an ab initio method SVMpred, a template-based method TemPred and a consensus-based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility. The engine for classification in SVMpred is selected as the support vector machine. For TemPred, the prediction is transferred from homologous templates in the training set, which are detected by the program HHsearch. The assessment on an independent test set consisting of 73 proteins shows that SVMpred and TemPred achieve Matthews correlation coefficient (MCC) of 0.438 and 0.481, respectively. Analysis on the predictions by SVMpred and TemPred shows that these two methods are complementary to each other. Therefore, we combined them together, forming the third method CoABind, which further improves the MCC to 0.489 on the same set. Experiments demonstrate that the proposed methods significantly outperform the state-of-the-art general-purpose ligand-binding residues prediction algorithm COACH. As the first-of-its-kind method, we anticipate CoABind to be helpful for studying CoA-protein interaction. Availability and implementation: http://yanglab.nankai.edu.cn/CoABind. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3941562,"score":1},{"doc_id":"19087303","title":"Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.","abstract":"BACKGROUND: The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task. RESULTS: In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes), Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation coefficient (MCC), sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be superior to that of other similar programs. Furthermore, a set of test cases with different lengths of sequences was constructed to examine Pep-3D-Search's capability in searching sequences on a 3D structure. The experimental results demonstrated the excellent search capability of Pep-3D-Search, especially when the length of the query sequence becomes longer; the iteration numbers of Pep-3D-Search to precisely localize the target paths did not obviously increase. This means that Pep-3D-Search has the potential to quickly localize the epitope regions mimicked by longer mimotopes. CONCLUSION: Our Pep-3D-Search provides a powerful approach for localizing the surface region mimicked by the mimotopes. As a publicly available tool, Pep-3D-Search can be utilized and conveniently evaluated, and it can also be used to complement other existing tools. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material. More detailed materials may be accessed at (http://kyc.nenu.edu.cn/Pep3DSearch/).","corpus_id":6458253,"score":0},{"doc_id":"19696878","title":"Accurate prediction of DnaK-peptide binding via homology modelling and experimental data.","abstract":"Molecular chaperones are essential elements of the protein quality control machinery that governs translocation and folding of nascent polypeptides, refolding and degradation of misfolded proteins, and activation of a wide range of client proteins. The prokaryotic heat-shock protein DnaK is the E. coli representative of the ubiquitous Hsp70 family, which specializes in the binding of exposed hydrophobic regions in unfolded polypeptides. Accurate prediction of DnaK binding sites in E. coli proteins is an essential prerequisite to understand the precise function of this chaperone and the properties of its substrate proteins. In order to map DnaK binding sites in protein sequences, we have developed an algorithm that combines sequence information from peptide binding experiments and structural parameters from homology modelling. We show that this combination significantly outperforms either single approach. The final predictor had a Matthews correlation coefficient (MCC) of 0.819 when assessed over the 144 tested peptide sequences to detect true positives and true negatives. To test the robustness of the learning set, we have conducted a simulated cross-validation, where we omit sequences from the learning sets and calculate the rate of repredicting them. This resulted in a surprisingly good MCC of 0.703. The algorithm was also able to perform equally well on a blind test set of binders and non-binders, of which there was no prior knowledge in the learning sets. The algorithm is freely available at http://limbo.vib.be.","corpus_id":12981835,"score":0},{"doc_id":"20954182","title":"Structure-based prediction of protein-peptide specificity in Rosetta.","abstract":"Protein-peptide interactions mediate many of the connections in intracellular signaling networks. A generalized computational framework for atomically precise modeling of protein-peptide specificity may allow for predicting molecular interactions, anticipating the effects of drugs and genetic mutations, and redesigning molecules for new interactions. We have developed an extensible, general algorithm for structure-based prediction of protein-peptide specificity as part of the Rosetta molecular modeling package. The algorithm is not restricted to any one peptide-binding domain family and, at minimum, does not require an experimentally characterized structure of the target protein nor any information about sequence specificity; although known structural data can be incorporated when available to improve performance. We demonstrate substantial success in specificity prediction across a diverse set of peptide-binding proteins, and show how performance is affected when incorporating varying degrees of input structural data. We also illustrate how structure-based approaches can provide atomic-level insight into mechanisms of peptide recognition and can predict the effects of point mutations on peptide specificity. Shortcomings and artifacts of our benchmark predictions are explained and limits on the generality of the method are explored. This work provides a promising foundation upon which further development of completely generalized, de novo prediction of peptide specificity may progress.","corpus_id":1166838,"score":0},{"doc_id":"21903632","title":"Protein-protein binding affinity prediction on a diverse set of structures.","abstract":"MOTIVATION: Accurate binding free energy functions for protein-protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes. RESULTS: We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein-protein binding. AVAILABILITY: The molecular descriptor set and descriptor values for all complexes are available in the Supplementary Material. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/~Affinity. CONTACT: paul.bates@cancer.org.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":24470510,"score":0},{"doc_id":"21955494","title":"Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction.","abstract":"A full understanding of the mechanism of post- transcriptional regulation requires more than simple two- state prediction (binding or not binding) for RNA binding proteins. Here we report a sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly accurate complex structure prediction (77% of residues are within 4°A RMSD from native in average for the independent test set) but also achieves the best performing two-state binding or non-binding prediction with an accuracy of 98%, precision of 84%, and Mathews correlation coefficient (MCC) of 0.62. Moreover, it predicts binding residues with an accuracy of 84%, precision of 66% and MCC value of 0.51. In addition, it has a success rate of 77% in predicting RNA binding types (mRNA, tRNA or rRNA). We further demonstrate that it makes more than 10% improvement either in precision or sensitivity than PSI- BLAST, HHPRED and our previously developed structure- based technique. This method expects to be useful for highly accurate genome-scale, high-resolution prediction of RNA-binding proteins and their complex structures. A web server (SPOT) is freely available for academic users at http://sparks.informatics.iupui.edu.","corpus_id":207520490,"score":0},{"doc_id":"22046350","title":"Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach.","abstract":"Integral membrane proteins constitute 25-30% of genomes and play crucial roles in many biological processes. However, less than 1% of membrane protein structures are in the Protein Data Bank. In this context, it is important to develop reliable computational methods for predicting the structures of membrane proteins. Here, we present the first application of random forest (RF) for residue-residue contact prediction in transmembrane proteins, which we term as TMhhcp. Rigorous cross-validation tests indicate that the built RF models provide a more favorable prediction performance compared with two state-of-the-art methods, i.e., TMHcon and MEMPACK. Using a strict leave-one-protein-out jackknifing procedure, they were capable of reaching the top L/5 prediction accuracies of 49.5% and 48.8% for two different residue contact definitions, respectively. The predicted residue contacts were further employed to predict interacting helical pairs and achieved the Matthew's correlation coefficients of 0.430 and 0.424, according to two different residue contact definitions, respectively. To facilitate the academic community, the TMhhcp server has been made freely accessible at http://protein.cau.edu.cn/tmhhcp.","corpus_id":2242921,"score":0},{"doc_id":"23193223","title":"Defining and predicting structurally conserved regions in protein superfamilies.","abstract":"MOTIVATION: The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. Accurate SCR predictions can benefit homology modelling and sequence alignment. RESULTS: Using pairwise DaliLite alignments among a set of homologous structures, we devised a simple measure of structural conservation, termed structural conservation index (SCI). SCI was used to distinguish SCRs from non-SCRs. A database of SCRs was compiled from 386 SCOP superfamilies containing 6489 protein domains. Artificial neural networks were then trained to predict SCRs with various features deduced from a single structure and homologous sequences. Assessment of the predictions via a 5-fold cross-validation method revealed that predictions based on features derived from a single structure perform similarly to ones based on homologous sequences, while combining sequence and structural features was optimal in terms of accuracy (0.755) and Matthews correlation coefficient (0.476). These results suggest that even without information from multiple structures, it is still possible to effectively predict SCRs for a protein. Finally, inspection of the structures with the worst predictions pinpoints difficulties in SCR definitions. AVAILABILITY: The SCR database and the prediction server can be found at http://prodata.swmed.edu/SCR. CONTACT: 91huangi@gmail.com or grishin@chop.swmed.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.","corpus_id":13920055,"score":0},{"doc_id":"23912807","title":"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).","abstract":"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/","corpus_id":3008401,"score":0},{"doc_id":"24573478","title":"SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.","abstract":"RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.","corpus_id":25754262,"score":0},{"doc_id":"24792350","title":"Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.","abstract":"As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions). A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC) of 0.77 with high precision (94%) and high sensitivity (65%). We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA)] is available as an on-line server at http://sparks-lab.org.","corpus_id":4633868,"score":0},{"doc_id":"27307637","title":"RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.","abstract":"MOTIVATION: Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. RESULTS: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein-RNA structure-based models on an unprecedented scale. AVAILABILITY AND IMPLEMENTATION: Software and models are freely available at http://rck.csail.mit.edu/ CONTACT: bab@mit.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":13847721,"score":0},{"doc_id":"27318206","title":"STRUM: structure-based prediction of protein stability changes upon single-point mutation.","abstract":"MOTIVATION: Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling. RESULTS: We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations. AVAILABILITY AND IMPLEMENTATION: http://zhanglab.ccmb.med.umich.edu/STRUM/ CONTACT: qiang@suda.edu.cn and zhng@umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":23067707,"score":0},{"doc_id":"27587688","title":"AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.","abstract":"MOTIVATION: Protein intrinsically disordered regions (IDRs) play an important role in many biological processes. Two key properties of IDRs are (i) the occurrence is proteome-wide and (ii) the ratio of disordered residues is about 6%, which makes it challenging to accurately predict IDRs. Most IDR prediction methods use sequence profile to improve accuracy, which prevents its application to proteome-wide prediction since it is time-consuming to generate sequence profiles. On the other hand, the methods without using sequence profile fare much worse than using sequence profile. METHOD: This article formulates IDR prediction as a sequence labeling problem and employs a new machine learning method called Deep Convolutional Neural Fields (DeepCNF) to solve it. DeepCNF is an integration of deep convolutional neural networks (DCNN) and conditional random fields (CRF); it can model not only complex sequence-structure relationship in a hierarchical manner, but also correlation among adjacent residues. To deal with highly imbalanced order/disorder ratio, instead of training DeepCNF by widely used maximum-likelihood, we develop a novel approach to train it by maximizing area under the ROC curve (AUC), which is an unbiased measure for class-imbalanced data. RESULTS: Our experimental results show that our IDR prediction method AUCpreD outperforms existing popular disorder predictors. More importantly, AUCpreD works very well even without sequence profile, comparing favorably to or even outperforming many methods using sequence profile. Therefore, our method works for proteome-wide disorder prediction while yielding similar or better accuracy than the others. AVAILABILITY AND IMPLEMENTATION: http://raptorx2.uchicago.edu/StructurePropertyPred/predict/ CONTACT: wangsheng@uchicago.edu, jinboxu@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":6346206,"score":0},{"doc_id":"27797773","title":"LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction.","abstract":"Motivation: The quality of fragment library determines the efficiency of fragment assembly, an approach that is widely used in most de novo protein-structure prediction algorithms. Conventional fragment libraries are constructed mainly based on the identities of amino acids, sometimes facilitated by predicted information including dihedral angles and secondary structures. However, it remains challenging to identify near-native fragment structures with low sequence homology. Results: We introduce a novel fragment-library-construction algorithm, LRFragLib, to improve the detection of near-native low-homology fragments of 7-10 residues, using a multi-stage, flexible selection protocol. Based on logistic regression scoring models, LRFragLib outperforms existing techniques by achieving a significantly higher precision and a comparable coverage on recent CASP protein sets in sampling near-native structures. The method also has a comparable computational efficiency to the fastest existing techniques with substantially reduced memory usage. Availability and Implementation: The source code is available for download at http://166.111.152.91/Downloads.html. Contact: hgong@tsinghua.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3740469,"score":0},{"doc_id":"28430949","title":"Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility.","abstract":"Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some \"short to intermediate\" non-local interactions. Here, we employed Long Short Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. Results: We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j|>19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5%, and 10% in the mean absolute error for backbone ϕ ,Ψ, θ , and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted Cα atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and Ψ angles. We expect the method to be useful for assisting protein structure and function prediction. Availability: The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . Contact: yaoqi.zhou@griffith.edu.au , yuedong.yang@griffith.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3764023,"score":0},{"doc_id":"29028891","title":"On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.","abstract":"Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other. Predicting the binding free energy of proteins provides new opportunities to modulate and control protein-protein interactions. However, existing methods require the 3D structure of the complex to predict its affinity, severely limiting their application to interactions with known structures. Results: We present a new approach that relies on the unbound protein structures and protein docking to predict protein-protein binding affinities. Through the study of the docking space (i.e. decoys), the method predicts the binding affinity of the query proteins when the actual structure of the complex itself is unknown. We tested our approach on a set of globular and soluble proteins of the newest affinity benchmark, obtaining accuracy values comparable to other state-of-art methods: a 0.4 correlation coefficient between the experimental and predicted values of ΔG and an error < 3 Kcal/mol. Availability and implementation: The binding affinity predictor is implemented and available at http://sbi.upf.edu/BADock and https://github.com/badocksbi/BADock. Contact: j.planas-iglesias@warwick.ac.uk or baldo.oliva@upf.edu. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3297556,"score":0},{"doc_id":"29069295","title":"PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine.","abstract":"Motivation: Protein solubility can be a decisive factor in both research and production efficiency, and in silico sequence-based predictors that can accurately estimate solubility outcomes are highly sought. Results: In this study, we present a novel approach termed PRotein SolubIlity Predictor (PaRSnIP), which uses a gradient boosting machine algorithm as well as an approximation of sequence and structural features of the protein of interest. Based on an independent test set, PaRSnIP outperformed other state-of-the-art sequence-based methods by more than 9% in accuracy and 0.17 in Matthew's correlation coefficient, with an overall accuracy of 74% and Matthew's correlation coefficient of 0.48. Additionally, PaRSnIP provides importance scores for all features used in training. We observed higher fractions of exposed residues to associate positively with protein solubility and tripeptide stretches with multiple histidines to associate negatively with solubility. The improved prediction accuracy of PaRSnIP should enable it to predict protein solubility with greater reliability and to screen for sequence variants with enhanced manufacturability. Availability and implementation: PaRSnIP software is available for download under GitHub (https://github.com/RedaRawi/PaRSnIP). Contact: gwo-yu.chuang@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4576871,"score":0},{"doc_id":"29416743","title":"DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest.","abstract":"DNase I hypersensitive sites (DHSs) are genomic regions that provide important information regarding the presence of transcriptional regulatory elements and the state of chromatin. Therefore, identifying DHSs in uncharacterized DNA sequences is crucial for understanding their biological functions and mechanisms. Although many experimental methods have been proposed to identify DHSs, they have proven to be expensive for genome-wide application. Therefore, it is necessary to develop computational methods for DHS prediction. In this study, we proposed a support vector machine (SVM)-based method for predicting DHSs, called DHSpred (DNase I Hypersensitive Site predictor in human DNA sequences), which was trained with 174 optimal features. The optimal combination of features was identified from a large set that included nucleotide composition and di- and trinucleotide physicochemical properties, using a random forest algorithm. DHSpred achieved a Matthews correlation coefficient and accuracy of 0.660 and 0.871, respectively, which were 3% higher than those of control SVM predictors trained with non-optimized features, indicating the efficiency of the feature selection method. Furthermore, the performance of DHSpred was superior to that of state-of-the-art predictors. An online prediction server has been developed to assist the scientific community, and is freely available at: http://www.thegleelab.org/DHSpred.html.","corpus_id":46789543,"score":0},{"doc_id":"29554211","title":"DeepSol: a deep learning framework for sequence-based protein solubility prediction.","abstract":"Motivation: Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors. In this work we propose, DeepSol, a novel Deep Learning-based protein solubility predictor. The backbone of our framework is a convolutional neural network that exploits k-mer structure and additional sequence and structural features extracted from the protein sequence. Results: DeepSol outperformed all known sequence-based state-of-the-art solubility prediction methods and attained an accuracy of 0.77 and Matthew's correlation coefficient of 0.55. The superior prediction accuracy of DeepSol allows to screen for sequences with enhanced production capacity and can more reliably predict solubility of novel proteins. Availability and implementation: DeepSol's best performing models and results are publicly deposited at https://doi.org/10.5281/zenodo.1162886 (Khurana and Mall, 2018). Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4042479,"score":0}],"string":"[\n {\n \"doc_id\": \"19508202\",\n \"title\": \"Improve the prediction of RNA-binding residues using structural neighbours.\",\n \"abstract\": \"The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the predictions over existing methods. Using a multiple linear regression approach and 6-fold cross validation, our best model can achieve an overall correct rate of 87.8% and MCC of 0.47, with a specificity of 93.4%, correctly predict 52.4% of the RNA-binding residues for a dataset containing 107 non-homologous RNA-binding proteins. Compared with existing methods, including the amino acid compositions of structure neighbors lead to clearly improvement. A web server was developed for predicting RNA binding residues in a protein sequence (or structure),which is available at http://mcgill.3322.org/RNA/.\",\n \"corpus_id\": 32567641,\n \"score\": 2\n },\n {\n \"doc_id\": \"20483814\",\n \"title\": \"Prediction of protein-RNA binding sites by a random forest method with combined features.\",\n \"abstract\": \"MOTIVATION: Protein-RNA interactions play a key role in a number of biological processes, such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and eukaryotic spliceosomes. As a result, a reliable identification of RNA binding site of a protein is important for functional annotation and site-directed mutagenesis. Accumulated data of experimental protein-RNA interactions reveal that a RNA binding residue with different neighbor amino acids often exhibits different preferences for its RNA partners, which in turn can be assessed by the interacting interdependence of the amino acid fragment and RNA nucleotide. RESULTS: In this work, we propose a novel classification method to identify the RNA binding sites in proteins by combining a new interacting feature (interaction propensity) with other sequence- and structure-based features. Specifically, the interaction propensity represents a binding specificity of a protein residue to the interacting RNA nucleotide by considering its two-side neighborhood in a protein residue triplet. The sequence as well as the structure-based features of the residues are combined together to discriminate the interaction propensity of amino acids with RNA. We predict RNA interacting residues in proteins by implementing a well-built random forest classifier. The experiments show that our method is able to detect the annotated protein-RNA interaction sites in a high accuracy. Our method achieves an accuracy of 84.5%, F-measure of 0.85 and AUC of 0.92 prediction of the RNA binding residues for a dataset containing 205 non-homologous RNA binding proteins, and also outperforms several existing RNA binding residue predictors, such as RNABindR, BindN, RNAProB and PPRint, and some alternative machine learning methods, such as support vector machine, naive Bayes and neural network in the comparison study. Furthermore, we provide some biological insights into the roles of sequences and structures in protein-RNA interactions by both evaluating the importance of features for their contributions in predictive accuracy and analyzing the binding patterns of interacting residues. AVAILABILITY: All the source data and code are available at http://www.aporc.org/doc/wiki/PRNA or http://www.sysbio.ac.cn/datatools.asp CONTACT: lnchen@sibs.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 15065218,\n \"score\": 2\n },\n {\n \"doc_id\": \"22258275\",\n \"title\": \"Prediction of hot spots in protein interfaces using a random forest model with hybrid features.\",\n \"abstract\": \"Prediction of hot spots in protein interfaces provides crucial information for the research on protein-protein interaction and drug design. Existing machine learning methods generally judge whether a given residue is likely to be a hot spot by extracting features only from the target residue. However, hot spots usually form a small cluster of residues which are tightly packed together at the center of protein interface. With this in mind, we present a novel method to extract hybrid features which incorporate a wide range of information of the target residue and its spatially neighboring residues, i.e. the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). We provide a novel random forest (RF) model to effectively integrate these hybrid features for predicting hot spots in protein interfaces. Our method can achieve accuracy (ACC) of 82.4% and Matthew's correlation coefficient (MCC) of 0.482 in Alanine Scanning Energetics Database, and ACC of 77.6% and MCC of 0.429 in Binding Interface Database. In a comparison study, performance of our RF model exceeds other existing methods, such as Robetta, FOLDEF, KFC, KFC2, MINERVA and HotPoint. Of our hybrid features, three physicochemical features of target residues (mass, polarizability and isoelectric point), the relative side-chain accessible surface area and the average depth index of mirror-contact residues are found to be the main discriminative features in hot spots prediction. We also confirm that hot spots tend to form large contact surface areas between two interacting proteins. Source data and code are available at: http://www.aporc.org/doc/wiki/HotSpot.\",\n \"corpus_id\": 6263515,\n \"score\": 2\n },\n {\n \"doc_id\": \"22574904\",\n \"title\": \"Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.\",\n \"abstract\": \"BACKGROUND: RNA molecules play diverse functional and structural roles in cells. They function as messengers for transferring genetic information from DNA to proteins, as the primary genetic material in many viruses, as catalysts (ribozymes) important for protein synthesis and RNA processing, and as essential and ubiquitous regulators of gene expression in living organisms. Many of these functions depend on precisely orchestrated interactions between RNA molecules and specific proteins in cells. Understanding the molecular mechanisms by which proteins recognize and bind RNA is essential for comprehending the functional implications of these interactions, but the recognition 'code' that mediates interactions between proteins and RNA is not yet understood. Success in deciphering this code would dramatically impact the development of new therapeutic strategies for intervening in devastating diseases such as AIDS and cancer. Because of the high cost of experimental determination of protein-RNA interfaces, there is an increasing reliance on statistical machine learning methods for training predictors of RNA-binding residues in proteins. However, because of differences in the choice of datasets, performance measures, and data representations used, it has been difficult to obtain an accurate assessment of the current state of the art in protein-RNA interface prediction. RESULTS: We provide a review of published approaches for predicting RNA-binding residues in proteins and a systematic comparison and critical assessment of protein-RNA interface residue predictors trained using these approaches on three carefully curated non-redundant datasets. We directly compare two widely used machine learning algorithms (Naïve Bayes (NB) and Support Vector Machine (SVM)) using three different data representations in which features are encoded using either sequence- or structure-based windows. Our results show that (i) Sequence-based classifiers that use a position-specific scoring matrix (PSSM)-based representation (PSSMSeq) outperform those that use an amino acid identity based representation (IDSeq) or a smoothed PSSM (SmoPSSMSeq); (ii) Structure-based classifiers that use smoothed PSSM representation (SmoPSSMStr) outperform those that use PSSM (PSSMStr) as well as sequence identity based representation (IDStr). PSSMSeq classifiers, when tested on an independent test set of 44 proteins, achieve performance that is comparable to that of three state-of-the-art structure-based predictors (including those that exploit geometric features) in terms of Matthews Correlation Coefficient (MCC), although the structure-based methods achieve substantially higher Specificity (albeit at the expense of Sensitivity) compared to sequence-based methods. We also find that the expected performance of the classifiers on a residue level can be markedly different from that on a protein level. Our experiments show that the classifiers trained on three different non-redundant protein-RNA interface datasets achieve comparable cross-validation performance. However, we find that the results are significantly affected by differences in the distance threshold used to define interface residues. CONCLUSIONS: Our results demonstrate that protein-RNA interface residue predictors that use a PSSM-based encoding of sequence windows outperform classifiers that use other encodings of sequence windows. While structure-based methods that exploit geometric features can yield significant increases in the Specificity of protein-RNA interface residue predictions, such increases are offset by decreases in Sensitivity. These results underscore the importance of comparing alternative methods using rigorous statistical procedures, multiple performance measures, and datasets that are constructed based on several alternative definitions of interface residues and redundancy cutoffs as well as including evaluations on independent test sets into the comparisons.\",\n \"corpus_id\": 15531335,\n \"score\": 2\n },\n {\n \"doc_id\": \"22848404\",\n \"title\": \"Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.\",\n \"abstract\": \"Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date.\",\n \"corpus_id\": 7507823,\n \"score\": 2\n },\n {\n \"doc_id\": \"23737141\",\n \"title\": \"DNABind: a hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.\",\n \"abstract\": \"Accurate prediction of DNA-binding residues has become a problem of increasing importance in structural bioinformatics. Here, we presented DNABind, a novel hybrid algorithm for identifying these crucial residues by exploiting the complementarity between machine learning- and template-based methods. Our machine learning-based method was based on the probabilistic combination of a structure-based and a sequence-based predictor, both of which were implemented using support vector machines algorithms. The former included our well-designed structural features, such as solvent accessibility, local geometry, topological features, and relative positions, which can effectively quantify the difference between DNA-binding and nonbinding residues. The latter combined evolutionary conservation features with three other sequence attributes. Our template-based method depended on structural alignment and utilized the template structure from known protein-DNA complexes to infer DNA-binding residues. We showed that the template method had excellent performance when reliable templates were found for the query proteins but tended to be strongly influenced by the template quality as well as the conformational changes upon DNA binding. In contrast, the machine learning approach yielded better performance when high-quality templates were not available (about 1/3 cases in our dataset) or the query protein was subject to intensive transformation changes upon DNA binding. Our extensive experiments indicated that the hybrid approach can distinctly improve the performance of the individual methods for both bound and unbound structures. DNABind also significantly outperformed the state-of-art algorithms by around 10% in terms of Matthews's correlation coefficient. The proposed methodology could also have wide application in various protein functional site annotations. DNABind is freely available at http://mleg.cse.sc.edu/DNABind/.\",\n \"corpus_id\": 206407482,\n \"score\": 2\n },\n {\n \"doc_id\": \"24854765\",\n \"title\": \"RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies.\",\n \"abstract\": \"Computational prediction of RNA-binding residues is helpful in uncovering the mechanisms underlying protein-RNA interactions. Traditional algorithms individually applied feature- or template-based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA-binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA-Binding Residue Detector) by combining these two strategies. We developed a feature-based approach that is an ensemble learning predictor comprising multiple structure-based classifiers, in which well-defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template-based predictor to recognize the putative RNA-binding regions by structurally aligning the query protein to the RNA-binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature- and template-based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state-of-the-art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA-binding proteins and thus incorrectly predicted the DNA-binding regions as RNA-binding interfaces. Finally, we implemented the RBRDetector algorithm as a user-friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector.\",\n \"corpus_id\": 36833308,\n \"score\": 2\n },\n {\n \"doc_id\": \"25075532\",\n \"title\": \"Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues.\",\n \"abstract\": \"The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming increasingly important for the research on protein-protein interaction and drug design. For each interface residue or target residue to be predicted, the authors extract hybrid features which incorporate a wide range of information of the target residue and its spatial neighbor residues, that is, the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). Here, feature selection is performed using random forests to avoid over-fitting. Thereafter, the extreme learning machine is employed to effectively integrate these hybrid features for predicting hot spots in protein interfaces. By the 5-fold cross validation in the training set, their method can achieve accuracy (ACC) of 82.1% and Matthew's correlation coefficient (MCC) of 0.459, and outperforms some alternative machine learning methods in the comparison study. Furthermore, their method achieves ACC of 76.8% and MCC of 0.401 in the independent test set, and is more effective than the major existing hot spot predictors. Their prediction method offers a powerful tool for uncovering candidate residues in the studies of alanine scanning mutagenesis for functional protein interaction sites.\",\n \"corpus_id\": 206191106,\n \"score\": 2\n },\n {\n \"doc_id\": \"26833816\",\n \"title\": \"Sequence-based prediction of protein-peptide binding sites using support vector machine.\",\n \"abstract\": \"Protein-peptide interactions are essential for all cellular processes including DNA repair, replication, gene-expression, and metabolism. As most protein-peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein-peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine-learning method called SPRINT to make Sequence-based prediction of Protein-peptide Residue-level Interactions. SPRINT yields a robust and consistent performance for 10-fold cross validations and independent test. The most important feature is evolution-generated sequence profiles. For the test set (1056 binding and non-binding residues), it yields a Matthews' Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence-based technique shows comparable or more accurate than structure-based methods for peptide-binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/. © 2016 Wiley Periodicals, Inc.\",\n \"corpus_id\": 5071902,\n \"score\": 2\n },\n {\n \"doc_id\": \"27623166\",\n \"title\": \"Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.\",\n \"abstract\": \"Carbohydrate-binding proteins play significant roles in many diseases including cancer. Here, we established a machine-learning-based method (called sequence-based prediction of residue-level interaction sites of carbohydrates, SPRINT-CBH) to predict carbohydrate-binding sites in proteins using support vector machines (SVMs). We found that integrating evolution-derived sequence profiles with additional information on sequence and predicted solvent accessible surface area leads to a reasonably accurate, robust, and predictive method, with area under receiver operating characteristic curve (AUC) of 0.78 and 0.77 and Matthew's correlation coefficient of 0.34 and 0.29, respectively for 10-fold cross validation and independent test without balancing binding and nonbinding residues. The quality of the method is further demonstrated by having statistically significantly more binding residues predicted for carbohydrate-binding proteins than presumptive nonbinding proteins in the human proteome, and by the bias of rare alleles toward predicted carbohydrate-binding sites for nonsynonymous mutations from the 1000 genome project. SPRINT-CBH is available as an online server at http://sparks-lab.org/server/SPRINT-CBH .\",\n \"corpus_id\": 99187577,\n \"score\": 2\n },\n {\n \"doc_id\": \"27993780\",\n \"title\": \"RBPPred: predicting RNA-binding proteins from sequence using SVM.\",\n \"abstract\": \"Motivation: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computational prediction is much more efficient than experimental methods and may have guiding significance on the experiment design. Results: In this study, we present the RBPPred (an RNA-binding protein predictor), a new method based on the support vector machine, to predict whether a protein binds RNAs, based on a comprehensive feature representation. By integrating the physicochemical properties with the evolutionary information of protein sequences, the new approach RBPPred performed much better than state-of-the-art methods. The results show that RBPPred correctly predicted 83% of 2780 RBPs and 96% out of 7093 non-RBPs with MCC of 0.808 using the 10-fold cross validation. Furthermore, we achieved a sensitivity of 84%, specificity of 97% and MCC of 0.788 on the testing set of human proteome. In addition we tested the capability of RBPPred to identify new RBPs, which further confirmed the practicability and predictability of the method. Availability and Implementation: RBPPred program can be accessed at: http://rnabinding.com/RBPPred.html . Contact: liushiyong@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3818271,\n \"score\": 2\n },\n {\n \"doc_id\": \"28073761\",\n \"title\": \"Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.\",\n \"abstract\": \"Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in protein-protein interactions. Such predictions are typically based on machine learning methods that take advantage of the properties and sequence positions of amino acids that are known to be involved in interaction. In this paper, we evaluate the importance of various features using Random Forest (RF), and include as a novel feature backbone flexibility predicted from sequences to further optimise protein interface prediction. Results: We observe that there is no single sequence feature that enables pinpointing interacting sites in our Random Forest models. However, combining different properties does increase the performance of interface prediction. Our homomeric-trained RF interface predictor is able to distinguish interface from non-interface residues with an area under the ROC curve of 0.72 in a homomeric test-set. The heteromeric-trained RF interface predictor performs better than existing predictors on a independent heteromeric test-set. We trained a more general predictor on the combined homomeric and heteromeric dataset, and show that in addition to predicting homomeric interfaces, it is also able to pinpoint interface residues in heterodimers. This suggests that our random forest model and the features included capture common properties of both homodimer and heterodimer interfaces. Availability and Implementation: The predictors and test datasets used in our analyses are freely available ( http://www.ibi.vu.nl/downloads/RF_PPI/ ). Contact: k.a.feenstra@vu.nl. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3740647,\n \"score\": 2\n },\n {\n \"doc_id\": \"29281004\",\n \"title\": \"Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.\",\n \"abstract\": \"Motivation: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Results: Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. Availability and implementation: The PrabHot webserver is freely available at http://denglab.org/PrabHot/. Contact: leideng@csu.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3820508,\n \"score\": 2\n },\n {\n \"doc_id\": \"18235992\",\n \"title\": \"PRINTR: prediction of RNA binding sites in proteins using SVM and profiles.\",\n \"abstract\": \"Protein-RNA interactions play a key role in a number of biological processes such as protein synthesis, mRNA processing, assembly and function of ribosomes and eukaryotic spliceosomes. A reliable identification of RNA-binding sites in RNA-binding proteins is important for functional annotation and site-directed mutagenesis. We developed a novel method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the prediction of protein residues at RNA-binding surfaces. One is given the sequence information of a protein chain that is known to interact with RNA; the other is given the structural information. Thus, five different inputs have been tested. Coupled with PSI-BLAST profiles and predicted secondary structure, the present approach yields a Matthews correlation coefficient (MCC) of 0.432 by a 7-fold cross-validation, which is the best among all previous reported RNA-binding sites prediction methods. When given the structural information, we have obtained the MCC value of 0.457, with PSSMs, observed secondary structure and solvent accessibility information assigned by DSSP as input. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/printr/ .\",\n \"corpus_id\": 1035800,\n \"score\": 1\n },\n {\n \"doc_id\": \"18940825\",\n \"title\": \"Predicting small ligand binding sites in proteins using backbone structure.\",\n \"abstract\": \"MOTIVATION: Specific non-covalent binding of metal ions and ligands, such as nucleotides and cofactors, is essential for the function of many proteins. Computational methods are useful for predicting the location of such binding sites when experimental information is lacking. Methods that use structural information, when available, are particularly promising since they can potentially identify non-contiguous binding motifs that cannot be found using only the amino acid sequence. Furthermore, a prediction method that can utilize low-resolution models is advantageous because high-resolution structures are available for only a relatively small fraction of proteins. RESULTS: SitePredict is a machine learning-based method for predicting binding sites in protein structures for specific metal ions or small molecules. The method uses Random Forest classifiers trained on diverse residue-based site properties including spatial clustering of residue types and evolutionary conservation. SitePredict was tested by cross-validation on a set of known binding sites for six different metal ions and five different small molecules in a non-redundant set of protein-ligand complex structures. The prediction performance was good for all ligands considered, as reflected by AUC values of at least 0.8. Furthermore, a more realistic test on unbound structures showed only a slight decrease in the accuracy. The properties that contribute the most to the prediction accuracy of each ligand were also examined. Finally, examples of predicted binding sites in homology models and uncharacterized proteins are discussed. AVAILABILITY: Binding site prediction results for all PDB protein structures and human protein homology models are available at http://sitepredict.org/.\",\n \"corpus_id\": 2258881,\n \"score\": 1\n },\n {\n \"doc_id\": \"19008251\",\n \"title\": \"Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.\",\n \"abstract\": \"MOTIVATION: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical-chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class. RESULTS: The results show that the RF model achieves 91.41% overall accuracy with Matthew's correlation coefficient of 0.70 and an area under the receiver operating characteristic curve (AUC) of 0.913. To our knowledge, the RF method using the hybrid feature is currently the computationally optimal approach for predicting DNA-binding sites in proteins from amino acid sequences without using three-dimensional (3D) structural information. We have demonstrated that the prediction results are useful for understanding protein-DNA interactions. AVAILABILITY: DBindR web server implementation is freely available at http://www.cbi.seu.edu.cn/DBindR/DBindR.htm.\",\n \"corpus_id\": 3616970,\n \"score\": 1\n },\n {\n \"doc_id\": \"19128505\",\n \"title\": \"Large-scale prediction of long disordered regions in proteins using random forests.\",\n \"abstract\": \"BACKGROUND: Many proteins contain disordered regions that lack fixed three-dimensional (3D) structure under physiological conditions but have important biological functions. Prediction of disordered regions in protein sequences is important for understanding protein function and in high-throughput determination of protein structures. Machine learning techniques, including neural networks and support vector machines have been widely used in such predictions. Predictors designed for long disordered regions are usually less successful in predicting short disordered regions. Combining prediction of short and long disordered regions will dramatically increase the complexity of the prediction algorithm and make the predictor unsuitable for large-scale applications. Efficient batch prediction of long disordered regions alone is of greater interest in large-scale proteome studies. RESULTS: A new algorithm, IUPforest-L, for predicting long disordered regions using the random forest learning model is proposed in this paper. IUPforest-L is based on the Moreau-Broto auto-correlation function of amino acid indices (AAIs) and other physicochemical features of the primary sequences. In 10-fold cross validation tests, IUPforest-L can achieve an area of 89.5% under the receiver operating characteristic (ROC) curve. Compared with existing disorder predictors, IUPforest-L has high prediction accuracy and is efficient for predicting long disordered regions in large-scale proteomes. CONCLUSION: The random forest model based on the auto-correlation functions of the AAIs within a protein fragment and other physicochemical features could effectively detect long disordered regions in proteins. A new predictor, IUPforest-L, was developed to batch predict long disordered regions in proteins, and the server can be accessed from http://dmg.cs.rmit.edu.au/IUPforest/IUPforest-L.php.\",\n \"corpus_id\": 400254,\n \"score\": 1\n },\n {\n \"doc_id\": \"19389733\",\n \"title\": \"Protein function annotation from sequence: prediction of residues interacting with RNA.\",\n \"abstract\": \"MOTIVATION: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein. RESULTS: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at www.bioinformatics.sussex.ac.uk/PIRANHA or http://piranha.protein.osaka-u.ac.jp. SUPPLEMENTARY INFORMATION: Supplementary data are available at the Bioinformatics online.\",\n \"corpus_id\": 6695218,\n \"score\": 1\n },\n {\n \"doc_id\": \"19594868\",\n \"title\": \"Prediction of DNA-binding residues from protein sequence information using random forests.\",\n \"abstract\": \"BACKGROUND: Protein-DNA interactions are involved in many biological processes essential for cellular function. To understand the molecular mechanism of protein-DNA recognition, it is necessary to identify the DNA-binding residues in DNA-binding proteins. However, structural data are available for only a few hundreds of protein-DNA complexes. With the rapid accumulation of sequence data, it becomes an important but challenging task to accurately predict DNA-binding residues directly from amino acid sequence data. RESULTS: A new machine learning approach has been developed in this study for predicting DNA-binding residues from amino acid sequence data. The approach used both the labelled data instances collected from the available structures of protein-DNA complexes and the abundant unlabeled data found in protein sequence databases. The evolutionary information contained in the unlabeled sequence data was represented as position-specific scoring matrices (PSSMs) and several new descriptors. The sequence-derived features were then used to train random forests (RFs), which could handle a large number of input variables and avoid model overfitting. The use of evolutionary information was found to significantly improve classifier performance. The RF classifier was further evaluated using a separate test dataset, and the predicted DNA-binding residues were examined in the context of three-dimensional structures. CONCLUSION: The results suggest that the RF-based approach gives rise to more accurate prediction of DNA-binding residues than previous studies. A new web server called BindN-RF http://bioinfo.ggc.org/bindn-rf/ has thus been developed to make the RF classifier accessible to the biological research community.\",\n \"corpus_id\": 10367995,\n \"score\": 1\n },\n {\n \"doc_id\": \"21268114\",\n \"title\": \"Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature.\",\n \"abstract\": \"The identification of RNA-binding residues in proteins is important in several areas such as protein function, posttranscriptional regulation and drug design. We have developed PRBR (Prediction of RNA Binding Residues), a novel method for identifying RNA-binding residues from amino acid sequences. Our method combines a hybrid feature with the enriched random forest (ERF) algorithm. The hybrid feature is composed of predicted secondary structure information and three novel features: evolutionary information combined with conservation information of the physicochemical properties of amino acids and the information about dependency of amino acids with regards to polarity-charge and hydrophobicity in the protein sequences. Our results demonstrate that the PRBR model achieves 0.5637 Matthew's correlation coefficient (MCC) and 88.63% overall accuracy (ACC) with 53.70% sensitivity (SE) and 96.97% specificity (SP). By comparing the performance of each feature we found that all three novel features contribute to the improved predictions. Area under the curve (AUC) statistics from receiver operating characteristic curve analysis was compared between PRBR model and other models. The results show that PRBR achieves the highest AUC value (0.8675) which represents that PRBR attains excellent performance on predicting the RNA-binding residues in proteins. The PRBR web-server implementation is freely available at http://www.cbi.seu.edu.cn/PRBR/.\",\n \"corpus_id\": 23950803,\n \"score\": 1\n },\n {\n \"doc_id\": \"22016406\",\n \"title\": \"Predicting residue-residue contacts using random forest models.\",\n \"abstract\": \"MOTIVATION: Protein residue-residue contact prediction can be useful in predicting protein 3D structures. Current algorithms for such a purpose leave room for improvement. RESULTS: We develop ProC_S3, a set of Random Forest algorithm-based models, for predicting residue-residue contact maps. The models are constructed based on a collection of 1490 non-redundant, high-resolution protein structures using >1280 sequence-based features. A new amino acid residue contact propensity matrix and a new set of seven amino acid groups based on contact preference are developed and used in ProC_S3. ProC_S3 delivers a 3-fold cross-validated accuracy of 26.9% with coverage of 4.7% for top L/5 predictions (L is the number of residues in a protein) of long-range contacts (sequence separation ≥24). Further benchmark tests deliver an accuracy of 29.7% and coverage of 5.6% for an independent set of 329 proteins. In the recently completed Ninth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), ProC_S3 is ranked as No. 1, No. 3, and No. 2 accuracies in the top L/5, L/10 and best 5 predictions of long-range contacts, respectively, among 18 automatic prediction servers. AVAILABILITY: http://www.abl.ku.edu/proc/proc_s3.html. CONTACT: jwfang@ku.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 28117970,\n \"score\": 1\n },\n {\n \"doc_id\": \"23166753\",\n \"title\": \"An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins.\",\n \"abstract\": \"Zinc-binding proteins are the most abundant metalloproteins in the Protein Data Bank where the zinc ions usually have catalytic, regulatory or structural roles critical for the function of the protein. Accurate prediction of zinc-binding sites is not only useful for the inference of protein function but also important for the prediction of 3D structure. Here, we present a new integrative framework that combines multiple sequence and structural properties and graph-theoretic network features, followed by an efficient feature selection to improve prediction of zinc-binding sites. We investigate what information can be retrieved from the sequence, structure and network levels that is relevant to zinc-binding site prediction. We perform a two-step feature selection using random forest to remove redundant features and quantify the relative importance of the retrieved features. Benchmarking on a high-quality structural dataset containing 1,103 protein chains and 484 zinc-binding residues, our method achieved >80% recall at a precision of 75% for the zinc-binding residues Cys, His, Glu and Asp on 5-fold cross-validation tests, which is a 10%-28% higher recall at the 75% equal precision compared to SitePredict and zincfinder at residue level using the same dataset. The independent test also indicates that our method has achieved recall of 0.790 and 0.759 at residue and protein levels, respectively, which is a performance better than the other two methods. Moreover, AUC (the Area Under the Curve) and AURPC (the Area Under the Recall-Precision Curve) by our method are also respectively better than those of the other two methods. Our method can not only be applied to large-scale identification of zinc-binding sites when structural information of the target is available, but also give valuable insights into important features arising from different levels that collectively characterize the zinc-binding sites. The scripts and datasets are available at http://protein.cau.edu.cn/zincidentifier/.\",\n \"corpus_id\": 8625079,\n \"score\": 1\n },\n {\n \"doc_id\": \"23514235\",\n \"title\": \"Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration.\",\n \"abstract\": \"BACKGROUND: Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions. RESULTS: Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time. CONCLUSIONS: In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance for protein-ligand binding region prediction. Based on the same approach and rationale, this method can also be applied to predict carbohydrate-antibody interactions for further design and development of carbohydrate-based vaccines. PLB-SAVE is available at http://save.cs.ntou.edu.tw.\",\n \"corpus_id\": 2498808,\n \"score\": 1\n },\n {\n \"doc_id\": \"24211525\",\n \"title\": \"Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces.\",\n \"abstract\": \"Flavin mono-nucleotide (FMN) is a cofactor which is involved in many biological reactions. The insights on protein-FMN interactions aid the protein functional annotation and also facilitate in drug design. In this study, we have established a new method, making use of an encoding scheme of the three-dimensional probability density maps that describe the distributions of 40 non-covalent interacting atom types around protein surfaces, to predict FMN-binding sites on protein surfaces. One machine learning model was trained for each of the 30 protein atom types to predict tentative FMN-binding sites on protein structures. The method's capability was evaluated by five-fold cross-validation on a dataset containing 81 non-redundant FMN-binding protein structures and further tested on independent datasets of 30 and 15 non-redundant protein structures respectively. These predictions achieved an accuracy of 0.94, 0.94 and 0.96 with the Matthews correlation coefficient (MCC) of 0.53, 0.53 and 0.65 respectively for the three protein structure sets. The prediction capability is superior to the existing method. This is the first structure-based approach that does not rely on evolutionary information for predicting FMN-interacting residues. The webserver for the prediction is available at http://ismblab.genomics.sinica.edu.tw/.\",\n \"corpus_id\": 23986112,\n \"score\": 1\n },\n {\n \"doc_id\": \"24475169\",\n \"title\": \"Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.\",\n \"abstract\": \"Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred can be an alternative perspective predictor for large-scale determination of DNA-binding proteins.\",\n \"corpus_id\": 8320048,\n \"score\": 1\n },\n {\n \"doc_id\": \"24846307\",\n \"title\": \"RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.\",\n \"abstract\": \"Protein-RNA interactions are central to essential cellular processes such as protein synthesis and regulation of gene expression and play roles in human infectious and genetic diseases. Reliable identification of protein-RNA interfaces is critical for understanding the structural bases and functional implications of such interactions and for developing effective approaches to rational drug design. Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins. Here we report two novel approaches: (i) HomPRIP, a sequence homology-based method for predicting RNA-binding sites in proteins; (ii) RNABindRPlus, a new method that combines predictions from HomPRIP with those from an optimized Support Vector Machine (SVM) classifier trained on a benchmark dataset of 198 RNA-binding proteins. Although highly reliable, HomPRIP cannot make predictions for the unaligned parts of query proteins and its coverage is limited by the availability of close sequence homologs of the query protein with experimentally determined RNA-binding sites. RNABindRPlus overcomes these limitations. We compared the performance of HomPRIP and RNABindRPlus with that of several state-of-the-art predictors on two test sets, RB44 and RB111. On a subset of proteins for which homologs with experimentally determined interfaces could be reliably identified, HomPRIP outperformed all other methods achieving an MCC of 0.63 on RB44 and 0.83 on RB111. RNABindRPlus was able to predict RNA-binding residues of all proteins in both test sets, achieving an MCC of 0.55 and 0.37, respectively, and outperforming all other methods, including those that make use of structure-derived features of proteins. More importantly, RNABindRPlus outperforms all other methods for any choice of tradeoff between precision and recall. An important advantage of both HomPRIP and RNABindRPlus is that they rely on readily available sequence and sequence-derived features of RNA-binding proteins. A webserver implementation of both methods is freely available at http://einstein.cs.iastate.edu/RNABindRPlus/.\",\n \"corpus_id\": 13527970,\n \"score\": 1\n },\n {\n \"doc_id\": \"25113160\",\n \"title\": \"Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.\",\n \"abstract\": \"As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of our knowledge, this is the first attempt to predict protein-binding nucleotides in a given DNA sequence from the sequence data alone.\",\n \"corpus_id\": 1554684,\n \"score\": 1\n },\n {\n \"doc_id\": \"25907142\",\n \"title\": \"Predicting protein-binding RNA nucleotides with consideration of binding partners.\",\n \"abstract\": \"In recent years several computational methods have been developed to predict RNA-binding sites in protein. Most of these methods do not consider interacting partners of a protein, so they predict the same RNA-binding sites for a given protein sequence even if the protein binds to different RNAs. Unlike the problem of predicting RNA-binding sites in protein, the problem of predicting protein-binding sites in RNA has received little attention mainly because it is much more difficult and shows a lower accuracy on average. In our previous study, we developed a method that predicts protein-binding nucleotides from an RNA sequence. In an effort to improve the prediction accuracy and usefulness of the previous method, we developed a new method that uses both RNA and protein sequence data. In this study, we identified effective features of RNA and protein molecules and developed a new support vector machine (SVM) model to predict protein-binding nucleotides from RNA and protein sequence data. The new model that used both protein and RNA sequence data achieved a sensitivity of 86.5%, a specificity of 86.2%, a positive predictive value (PPV) of 72.6%, a negative predictive value (NPV) of 93.8% and Matthews correlation coefficient (MCC) of 0.69 in a 10-fold cross validation; it achieved a sensitivity of 58.8%, a specificity of 87.4%, a PPV of 65.1%, a NPV of 84.2% and MCC of 0.48 in independent testing. For comparative purpose, we built another prediction model that used RNA sequence data alone and ran it on the same dataset. In a 10 fold-cross validation it achieved a sensitivity of 85.7%, a specificity of 80.5%, a PPV of 67.7%, a NPV of 92.2% and MCC of 0.63; in independent testing it achieved a sensitivity of 67.7%, a specificity of 78.8%, a PPV of 57.6%, a NPV of 85.2% and MCC of 0.45. In both cross-validations and independent testing, the new model that used both RNA and protein sequences showed a better performance than the model that used RNA sequence data alone in most performance measures. To the best of our knowledge, this is the first sequence-based prediction of protein-binding nucleotides in RNA which considers the binding partner of RNA. The new model will provide valuable information for designing biochemical experiments to find putative protein-binding sites in RNA with unknown structure.\",\n \"corpus_id\": 25976649,\n \"score\": 1\n },\n {\n \"doc_id\": \"26405960\",\n \"title\": \"Predicting a DNA-binding protein using random forest with multiple mathematical features.\",\n \"abstract\": \"DNA-binding proteins are involved and play a crucial role in a lot of important biological processes. Hence, the identification of the DNA-binding proteins is a challenging and significant problem. In order to reveal the intrinsic information correlated to DNA-binding, nine classes of candidate features based on different mathematical fields are applied to construct the prediction model with random forest. They are fractal dimension, conjoint triad feature, Hilbert-Huang Transformation, amino acid composition, dipeptide composition, chaos game representation, and the corresponding information entropies. These mathematical expressions are evaluated with 5-fold cross validation test. The results of numerical simulations show that the mathematical features consisted of amino acid composition, fractal dimension and information entropies of amino acid and chaos game representation achieve the best performance. Its accuracy is 0.8157, and Matthew's correlation coefficient (MCC) achieves 0.5968 on the benchmark dataset from DNA-Prot. By analyzing the components of top combination of the nine candidate features, the concepts of fractal dimension and information entropy are the effective and vital features, which can provide complementary sequence-order information on the basis of amino acid composition.\",\n \"corpus_id\": 16047378,\n \"score\": 1\n },\n {\n \"doc_id\": \"26568622\",\n \"title\": \"Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.\",\n \"abstract\": \"MOTIVATION: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. RESULTS: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 22034498,\n \"score\": 1\n },\n {\n \"doc_id\": \"27259543\",\n \"title\": \"DBSI server: DNA binding site identifier.\",\n \"abstract\": \"UNLABELLED: : Protein-nucleic acid interactions are among the most important intermolecular interactions in the regulation of cellular events. Identifying residues involved in these interactions from protein structure alone is an important challenge. Here we introduce the webserver interface to DNA Binding Site Identifier (DBSI), a powerful structure-based SVM model for the prediction and visualization of DNA binding sites on protein structures. DBSI has been shown to be a top-performing model to predict DNA binding sites on the surface of a protein or peptide and shows promise in predicting RNA binding sites. AVAILABILITY AND IMPLEMENTATION: Server is available at http://dbsi.mitchell-lab.org CONTACT: jcmitchell@wisc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 13178732,\n \"score\": 1\n },\n {\n \"doc_id\": \"27266516\",\n \"title\": \"Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors.\",\n \"abstract\": \"BACKGROUND: RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins. Newly developed discriminative descriptors will help to improve the prediction accuracy of these prediction methods and provide further meaningful information for researchers. RESULTS: In this work, we designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the two features were powerful for identifying RNA-binding protein residues. Using these two features and other excellent structure- and sequence-based features, a random forest classifier was constructed to predict RNA-binding residues. The area under the receiver operating characteristic curve (AUC) of five-fold cross-validation for our method on training set RBP195 was 0.900, and when applied to the test set RBP68, the prediction accuracy (ACC) was 0.868, and the F-score was 0.631. CONCLUSIONS: The good prediction performance of our method revealed that the two newly designed descriptors could be discriminative for inferring protein residues interacting with RNAs. To facilitate the use of our method, a web-server called RNAProSite, which implements the proposed method, was constructed and is freely available at http://lilab.ecust.edu.cn/NABind .\",\n \"corpus_id\": 1265451,\n \"score\": 1\n },\n {\n \"doc_id\": \"27403208\",\n \"title\": \"bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.\",\n \"abstract\": \"MOTIVATION: Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. RESULTS: By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset. For 210 bound dataset, bSiteFinder achieved high accuracies up to 94.8 % (MCC 0.95). For another 48 bound/unbound dataset, bSiteFinder achieved high accuracies up to 93.8 % for bound proteins (MCC 0.95) and 85.4 % for unbound proteins (MCC 0.72). Our bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/, and the source code is provided at the methods page. CONCLUSION: An online bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/. Our work lays a foundation for functional annotation of protein and structure-based drug design. With ever increasing numbers of three-dimensional protein-ligand complex structures, our server should be more accurate and less time-consuming. Graphical Abstract bSiteFinder (http://binfo.shmtu.edu.cn/bsitefinder/) as a protein-binding sites prediction server was developed based on the largest database of bound templates so far with stringent quality control. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server have been significantly improved. What's more, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset.\",\n \"corpus_id\": 16103515,\n \"score\": 1\n },\n {\n \"doc_id\": \"28056090\",\n \"title\": \"Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.\",\n \"abstract\": \"MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. RESULTS: Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. AVAILABILITY: http://raptorx.uchicago.edu/ContactMap/.\",\n \"corpus_id\": 605957,\n \"score\": 1\n },\n {\n \"doc_id\": \"28130235\",\n \"title\": \"ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.\",\n \"abstract\": \"Motivation: The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge. Results: We present ISPRED4, an improved structure-based predictor of PPI sites on unbound monomer surfaces. ISPRED4 relies on machine-learning methods and it incorporates features extracted from protein sequence and structure. Cross-validation experiments are carried out on a new dataset that includes 151 high-resolution protein complexes and indicate that ISPRED4 achieves a per-residue Matthew Correlation Coefficient of 0.48 and an overall accuracy of 0.85. Benchmarking results show that ISPRED4 is one of the top-performing PPI site predictors developed so far. Contact: gigi@biocomp.unibo.it. Availability and Implementation: ISPRED4 and datasets used in this study are available at http://ispred4.biocomp.unibo.it .\",\n \"corpus_id\": 2850711,\n \"score\": 1\n },\n {\n \"doc_id\": \"28334224\",\n \"title\": \"Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.\",\n \"abstract\": \"Motivation: The study of transcriptional regulation is still difficult yet fundamental in molecular biology research. While the development of both in vivo and in vitro profiling techniques have significantly enhanced our knowledge of transcription factor (TF)-DNA interactions, computational models of TF-DNA interactions are relatively simple and may not reveal sufficient biological insight. In particular, supervised learning based models for TF-DNA interactions attempt to map sequence-level features ( k -mers) to binding event but usually ignore the location of k -mers, which can cause data fragmentation and consequently inferior model performance. Results: Here, we propose a novel algorithm based on the so-called multiple-instance learning (MIL) paradigm. MIL breaks each DNA sequence into multiple overlapping subsequences and models each subsequence separately, therefore implicitly takes into consideration binding site locations, resulting in both higher accuracy and better interpretability of the models. The result from both in vivo and in vitro TFDNA interaction data show that our approach significantly outperformconventional single-instance learning based algorithms. Importantly, the models learned from in vitro data using our approach can predict in vivo binding with very good accuracy. In addition, the location information obtained by our method provides additional insight for motif finding results from ChIP-Seq data. Finally, our approach can be easily combined with other state-of-the-art TF-DNA interaction modeling methods. Availability: http://www.cs.utsa.edu/∼jruan/MIL /. Contact: jianhua.ruan@utsa.edu. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4447497,\n \"score\": 1\n },\n {\n \"doc_id\": \"28361677\",\n \"title\": \"Predicting protein-binding regions in RNA using nucleotide profiles and compositions.\",\n \"abstract\": \"BACKGROUND: Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding sites in protein-RNA interactions. However, most computational methods are limited to finding RNA-binding sites in proteins instead of protein-binding sites in RNAs. Predicting protein-binding sites in RNA is more challenging than predicting RNA-binding sites in proteins. Recent computational methods for finding protein-binding sites in RNAs have several drawbacks for practical use. RESULTS: We developed a new support vector machine (SVM) model for predicting protein-binding regions in mRNA sequences. The model uses sequence profiles constructed from log-odds scores of mono- and di-nucleotides and nucleotide compositions. The model was evaluated by standard 10-fold cross validation, leave-one-protein-out (LOPO) cross validation and independent testing. Since actual mRNA sequences have more non-binding regions than protein-binding regions, we tested the model on several datasets with different ratios of protein-binding regions to non-binding regions. The best performance of the model was obtained in a balanced dataset of positive and negative instances. 10-fold cross validation with a balanced dataset achieved a sensitivity of 91.6%, a specificity of 92.4%, an accuracy of 92.0%, a positive predictive value (PPV) of 91.7%, a negative predictive value (NPV) of 92.3% and a Matthews correlation coefficient (MCC) of 0.840. LOPO cross validation showed a lower performance than the 10-fold cross validation, but the performance remains high (87.6% accuracy and 0.752 MCC). In testing the model on independent datasets, it achieved an accuracy of 82.2% and an MCC of 0.656. Testing of our model and other state-of-the-art methods on a same dataset showed that our model is better than the others. CONCLUSIONS: Sequence profiles of log-odds scores of mono- and di-nucleotides were much more powerful features than nucleotide compositions in finding protein-binding regions in RNA sequences. But, a slight performance gain was obtained when using the sequence profiles along with nucleotide compositions. These are preliminary results of ongoing research, but demonstrate the potential of our approach as a powerful predictor of protein-binding regions in RNA. The program and supporting data are available at http://bclab.inha.ac.kr/RBPbinding .\",\n \"corpus_id\": 11927189,\n \"score\": 1\n },\n {\n \"doc_id\": \"28851273\",\n \"title\": \"EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.\",\n \"abstract\": \"BACKGROUND: Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues. RESULTS: In this paper, we first propose a novel residue encoding method, referred to as the Position Specific Score Matrix (PSSM) Relation Transformation (PSSM-RT), to encode residues by utilizing the relationships of evolutionary information between residues. PDNA-62 and PDNA-224 are used to evaluate PSSM-RT and two existing PSSM encoding methods by five-fold cross-validation. Performance evaluations indicate that PSSM-RT is more effective than previous methods. This validates the point that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction. An ensemble learning classifier (EL_PSSM-RT) is also proposed by combining ensemble learning model and PSSM-RT to better handle the imbalance between binding and non-binding residues in datasets. EL_PSSM-RT is evaluated by five-fold cross-validation using PDNA-62 and PDNA-224 as well as two independent datasets TS-72 and TS-61. Performance comparisons with existing predictors on the four datasets demonstrate that EL_PSSM-RT is the best-performing method among all the predicting methods with improvement between 0.02-0.07 for MCC, 4.18-21.47% for ST and 0.013-0.131 for AUC. Furthermore, we analyze the importance of the pair-relationships extracted by PSSM-RT and the results validates the usefulness of PSSM-RT for encoding DNA-binding residues. CONCLUSIONS: We propose a novel prediction method for the prediction of DNA-binding residue with the inclusion of relationship of evolutionary information and ensemble learning. Performance evaluation shows that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction and ensemble learning can be used to address the data imbalance issue between binding and non-binding residues. A web service of EL_PSSM-RT ( http://hlt.hitsz.edu.cn:8080/PSSM-RT_SVM/ ) is provided for free access to the biological research community.\",\n \"corpus_id\": 21146302,\n \"score\": 1\n },\n {\n \"doc_id\": \"29219069\",\n \"title\": \"A boosting approach for prediction of protein-RNA binding residues.\",\n \"abstract\": \"BACKGROUND: RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex. RESULTS: We propose PredRBR, an effectively computational approach to predict RNA-binding residues. PredRBR is built with gradient tree boosting and an optimal feature set selected from a large number of sequence and structure characteristics and two categories of structural neighborhood properties. In cross-validation experiments on the RBP170 data set show that PredRBR achieves an overall accuracy of 0.84, a sensitivity of 0.85, MCC of 0.55 and AUC of 0.92, which are significantly better than that of other widely used machine learning algorithms such as Support Vector Machine, Random Forest, and Adaboost. We further calculate the feature importance of different feature categories and find that structural neighborhood characteristics are critical in the recognization of RNA binding residues. Also, PredRBR yields significantly better prediction accuracy on an independent test set (RBP101) in comparison with other state-of-the-art methods. CONCLUSIONS: The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree boosting algorithm combined with the optimal selected features.\",\n \"corpus_id\": 25996800,\n \"score\": 1\n },\n {\n \"doc_id\": \"29390084\",\n \"title\": \"Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.\",\n \"abstract\": \"Motivation: Protein-protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontology (GO) being one of the most successful projects. Several PPI evaluation algorithms have been based on the application of probabilistic frameworks or machine learning algorithms to GO properties. Here, we introduce a new training set design and machine learning based approach that combines dependent heterogeneous protein annotations from the entire ontology to evaluate putative co-complex protein interactions determined by empirical studies. Results: PPI annotations are built combinatorically using corresponding GO terms and InterPro annotation. We use a S.cerevisiae high-confidence complex dataset as a positive training set. A series of classifiers based on Maximum Entropy and support vector machines (SVMs), each with a composite counterpart algorithm, are trained on a series of training sets. These achieve a high performance area under the ROC curve of ≤0.97, outperforming go2ppi-a previously established prediction tool for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations. Availability and implementation: https://github.com/ima23/maxent-ppi. Contact: sbh11@cl.cam.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3795861,\n \"score\": 1\n },\n {\n \"doc_id\": \"29547921\",\n \"title\": \"CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.\",\n \"abstract\": \"Motivation: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction. Results: We developed three methods for the prediction of CoA- and CoA derivatives-binding residues, including an ab initio method SVMpred, a template-based method TemPred and a consensus-based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility. The engine for classification in SVMpred is selected as the support vector machine. For TemPred, the prediction is transferred from homologous templates in the training set, which are detected by the program HHsearch. The assessment on an independent test set consisting of 73 proteins shows that SVMpred and TemPred achieve Matthews correlation coefficient (MCC) of 0.438 and 0.481, respectively. Analysis on the predictions by SVMpred and TemPred shows that these two methods are complementary to each other. Therefore, we combined them together, forming the third method CoABind, which further improves the MCC to 0.489 on the same set. Experiments demonstrate that the proposed methods significantly outperform the state-of-the-art general-purpose ligand-binding residues prediction algorithm COACH. As the first-of-its-kind method, we anticipate CoABind to be helpful for studying CoA-protein interaction. Availability and implementation: http://yanglab.nankai.edu.cn/CoABind. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3941562,\n \"score\": 1\n },\n {\n \"doc_id\": \"19087303\",\n \"title\": \"Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.\",\n \"abstract\": \"BACKGROUND: The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task. RESULTS: In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes), Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation coefficient (MCC), sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be superior to that of other similar programs. Furthermore, a set of test cases with different lengths of sequences was constructed to examine Pep-3D-Search's capability in searching sequences on a 3D structure. The experimental results demonstrated the excellent search capability of Pep-3D-Search, especially when the length of the query sequence becomes longer; the iteration numbers of Pep-3D-Search to precisely localize the target paths did not obviously increase. This means that Pep-3D-Search has the potential to quickly localize the epitope regions mimicked by longer mimotopes. CONCLUSION: Our Pep-3D-Search provides a powerful approach for localizing the surface region mimicked by the mimotopes. As a publicly available tool, Pep-3D-Search can be utilized and conveniently evaluated, and it can also be used to complement other existing tools. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material. More detailed materials may be accessed at (http://kyc.nenu.edu.cn/Pep3DSearch/).\",\n \"corpus_id\": 6458253,\n \"score\": 0\n },\n {\n \"doc_id\": \"19696878\",\n \"title\": \"Accurate prediction of DnaK-peptide binding via homology modelling and experimental data.\",\n \"abstract\": \"Molecular chaperones are essential elements of the protein quality control machinery that governs translocation and folding of nascent polypeptides, refolding and degradation of misfolded proteins, and activation of a wide range of client proteins. The prokaryotic heat-shock protein DnaK is the E. coli representative of the ubiquitous Hsp70 family, which specializes in the binding of exposed hydrophobic regions in unfolded polypeptides. Accurate prediction of DnaK binding sites in E. coli proteins is an essential prerequisite to understand the precise function of this chaperone and the properties of its substrate proteins. In order to map DnaK binding sites in protein sequences, we have developed an algorithm that combines sequence information from peptide binding experiments and structural parameters from homology modelling. We show that this combination significantly outperforms either single approach. The final predictor had a Matthews correlation coefficient (MCC) of 0.819 when assessed over the 144 tested peptide sequences to detect true positives and true negatives. To test the robustness of the learning set, we have conducted a simulated cross-validation, where we omit sequences from the learning sets and calculate the rate of repredicting them. This resulted in a surprisingly good MCC of 0.703. The algorithm was also able to perform equally well on a blind test set of binders and non-binders, of which there was no prior knowledge in the learning sets. The algorithm is freely available at http://limbo.vib.be.\",\n \"corpus_id\": 12981835,\n \"score\": 0\n },\n {\n \"doc_id\": \"20954182\",\n \"title\": \"Structure-based prediction of protein-peptide specificity in Rosetta.\",\n \"abstract\": \"Protein-peptide interactions mediate many of the connections in intracellular signaling networks. A generalized computational framework for atomically precise modeling of protein-peptide specificity may allow for predicting molecular interactions, anticipating the effects of drugs and genetic mutations, and redesigning molecules for new interactions. We have developed an extensible, general algorithm for structure-based prediction of protein-peptide specificity as part of the Rosetta molecular modeling package. The algorithm is not restricted to any one peptide-binding domain family and, at minimum, does not require an experimentally characterized structure of the target protein nor any information about sequence specificity; although known structural data can be incorporated when available to improve performance. We demonstrate substantial success in specificity prediction across a diverse set of peptide-binding proteins, and show how performance is affected when incorporating varying degrees of input structural data. We also illustrate how structure-based approaches can provide atomic-level insight into mechanisms of peptide recognition and can predict the effects of point mutations on peptide specificity. Shortcomings and artifacts of our benchmark predictions are explained and limits on the generality of the method are explored. This work provides a promising foundation upon which further development of completely generalized, de novo prediction of peptide specificity may progress.\",\n \"corpus_id\": 1166838,\n \"score\": 0\n },\n {\n \"doc_id\": \"21903632\",\n \"title\": \"Protein-protein binding affinity prediction on a diverse set of structures.\",\n \"abstract\": \"MOTIVATION: Accurate binding free energy functions for protein-protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes. RESULTS: We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein-protein binding. AVAILABILITY: The molecular descriptor set and descriptor values for all complexes are available in the Supplementary Material. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/~Affinity. CONTACT: paul.bates@cancer.org.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 24470510,\n \"score\": 0\n },\n {\n \"doc_id\": \"21955494\",\n \"title\": \"Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction.\",\n \"abstract\": \"A full understanding of the mechanism of post- transcriptional regulation requires more than simple two- state prediction (binding or not binding) for RNA binding proteins. Here we report a sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly accurate complex structure prediction (77% of residues are within 4°A RMSD from native in average for the independent test set) but also achieves the best performing two-state binding or non-binding prediction with an accuracy of 98%, precision of 84%, and Mathews correlation coefficient (MCC) of 0.62. Moreover, it predicts binding residues with an accuracy of 84%, precision of 66% and MCC value of 0.51. In addition, it has a success rate of 77% in predicting RNA binding types (mRNA, tRNA or rRNA). We further demonstrate that it makes more than 10% improvement either in precision or sensitivity than PSI- BLAST, HHPRED and our previously developed structure- based technique. This method expects to be useful for highly accurate genome-scale, high-resolution prediction of RNA-binding proteins and their complex structures. A web server (SPOT) is freely available for academic users at http://sparks.informatics.iupui.edu.\",\n \"corpus_id\": 207520490,\n \"score\": 0\n },\n {\n \"doc_id\": \"22046350\",\n \"title\": \"Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach.\",\n \"abstract\": \"Integral membrane proteins constitute 25-30% of genomes and play crucial roles in many biological processes. However, less than 1% of membrane protein structures are in the Protein Data Bank. In this context, it is important to develop reliable computational methods for predicting the structures of membrane proteins. Here, we present the first application of random forest (RF) for residue-residue contact prediction in transmembrane proteins, which we term as TMhhcp. Rigorous cross-validation tests indicate that the built RF models provide a more favorable prediction performance compared with two state-of-the-art methods, i.e., TMHcon and MEMPACK. Using a strict leave-one-protein-out jackknifing procedure, they were capable of reaching the top L/5 prediction accuracies of 49.5% and 48.8% for two different residue contact definitions, respectively. The predicted residue contacts were further employed to predict interacting helical pairs and achieved the Matthew's correlation coefficients of 0.430 and 0.424, according to two different residue contact definitions, respectively. To facilitate the academic community, the TMhhcp server has been made freely accessible at http://protein.cau.edu.cn/tmhhcp.\",\n \"corpus_id\": 2242921,\n \"score\": 0\n },\n {\n \"doc_id\": \"23193223\",\n \"title\": \"Defining and predicting structurally conserved regions in protein superfamilies.\",\n \"abstract\": \"MOTIVATION: The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. Accurate SCR predictions can benefit homology modelling and sequence alignment. RESULTS: Using pairwise DaliLite alignments among a set of homologous structures, we devised a simple measure of structural conservation, termed structural conservation index (SCI). SCI was used to distinguish SCRs from non-SCRs. A database of SCRs was compiled from 386 SCOP superfamilies containing 6489 protein domains. Artificial neural networks were then trained to predict SCRs with various features deduced from a single structure and homologous sequences. Assessment of the predictions via a 5-fold cross-validation method revealed that predictions based on features derived from a single structure perform similarly to ones based on homologous sequences, while combining sequence and structural features was optimal in terms of accuracy (0.755) and Matthews correlation coefficient (0.476). These results suggest that even without information from multiple structures, it is still possible to effectively predict SCRs for a protein. Finally, inspection of the structures with the worst predictions pinpoints difficulties in SCR definitions. AVAILABILITY: The SCR database and the prediction server can be found at http://prodata.swmed.edu/SCR. CONTACT: 91huangi@gmail.com or grishin@chop.swmed.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.\",\n \"corpus_id\": 13920055,\n \"score\": 0\n },\n {\n \"doc_id\": \"23912807\",\n \"title\": \"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).\",\n \"abstract\": \"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/\",\n \"corpus_id\": 3008401,\n \"score\": 0\n },\n {\n \"doc_id\": \"24573478\",\n \"title\": \"SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.\",\n \"abstract\": \"RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.\",\n \"corpus_id\": 25754262,\n \"score\": 0\n },\n {\n \"doc_id\": \"24792350\",\n \"title\": \"Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.\",\n \"abstract\": \"As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions). A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC) of 0.77 with high precision (94%) and high sensitivity (65%). We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA)] is available as an on-line server at http://sparks-lab.org.\",\n \"corpus_id\": 4633868,\n \"score\": 0\n },\n {\n \"doc_id\": \"27307637\",\n \"title\": \"RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.\",\n \"abstract\": \"MOTIVATION: Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. RESULTS: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein-RNA structure-based models on an unprecedented scale. AVAILABILITY AND IMPLEMENTATION: Software and models are freely available at http://rck.csail.mit.edu/ CONTACT: bab@mit.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 13847721,\n \"score\": 0\n },\n {\n \"doc_id\": \"27318206\",\n \"title\": \"STRUM: structure-based prediction of protein stability changes upon single-point mutation.\",\n \"abstract\": \"MOTIVATION: Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling. RESULTS: We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations. AVAILABILITY AND IMPLEMENTATION: http://zhanglab.ccmb.med.umich.edu/STRUM/ CONTACT: qiang@suda.edu.cn and zhng@umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 23067707,\n \"score\": 0\n },\n {\n \"doc_id\": \"27587688\",\n \"title\": \"AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.\",\n \"abstract\": \"MOTIVATION: Protein intrinsically disordered regions (IDRs) play an important role in many biological processes. Two key properties of IDRs are (i) the occurrence is proteome-wide and (ii) the ratio of disordered residues is about 6%, which makes it challenging to accurately predict IDRs. Most IDR prediction methods use sequence profile to improve accuracy, which prevents its application to proteome-wide prediction since it is time-consuming to generate sequence profiles. On the other hand, the methods without using sequence profile fare much worse than using sequence profile. METHOD: This article formulates IDR prediction as a sequence labeling problem and employs a new machine learning method called Deep Convolutional Neural Fields (DeepCNF) to solve it. DeepCNF is an integration of deep convolutional neural networks (DCNN) and conditional random fields (CRF); it can model not only complex sequence-structure relationship in a hierarchical manner, but also correlation among adjacent residues. To deal with highly imbalanced order/disorder ratio, instead of training DeepCNF by widely used maximum-likelihood, we develop a novel approach to train it by maximizing area under the ROC curve (AUC), which is an unbiased measure for class-imbalanced data. RESULTS: Our experimental results show that our IDR prediction method AUCpreD outperforms existing popular disorder predictors. More importantly, AUCpreD works very well even without sequence profile, comparing favorably to or even outperforming many methods using sequence profile. Therefore, our method works for proteome-wide disorder prediction while yielding similar or better accuracy than the others. AVAILABILITY AND IMPLEMENTATION: http://raptorx2.uchicago.edu/StructurePropertyPred/predict/ CONTACT: wangsheng@uchicago.edu, jinboxu@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 6346206,\n \"score\": 0\n },\n {\n \"doc_id\": \"27797773\",\n \"title\": \"LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction.\",\n \"abstract\": \"Motivation: The quality of fragment library determines the efficiency of fragment assembly, an approach that is widely used in most de novo protein-structure prediction algorithms. Conventional fragment libraries are constructed mainly based on the identities of amino acids, sometimes facilitated by predicted information including dihedral angles and secondary structures. However, it remains challenging to identify near-native fragment structures with low sequence homology. Results: We introduce a novel fragment-library-construction algorithm, LRFragLib, to improve the detection of near-native low-homology fragments of 7-10 residues, using a multi-stage, flexible selection protocol. Based on logistic regression scoring models, LRFragLib outperforms existing techniques by achieving a significantly higher precision and a comparable coverage on recent CASP protein sets in sampling near-native structures. The method also has a comparable computational efficiency to the fastest existing techniques with substantially reduced memory usage. Availability and Implementation: The source code is available for download at http://166.111.152.91/Downloads.html. Contact: hgong@tsinghua.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3740469,\n \"score\": 0\n },\n {\n \"doc_id\": \"28430949\",\n \"title\": \"Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility.\",\n \"abstract\": \"Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some \\\"short to intermediate\\\" non-local interactions. Here, we employed Long Short Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. Results: We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j|>19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5%, and 10% in the mean absolute error for backbone ϕ ,Ψ, θ , and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted Cα atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and Ψ angles. We expect the method to be useful for assisting protein structure and function prediction. Availability: The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . Contact: yaoqi.zhou@griffith.edu.au , yuedong.yang@griffith.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3764023,\n \"score\": 0\n },\n {\n \"doc_id\": \"29028891\",\n \"title\": \"On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.\",\n \"abstract\": \"Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other. Predicting the binding free energy of proteins provides new opportunities to modulate and control protein-protein interactions. However, existing methods require the 3D structure of the complex to predict its affinity, severely limiting their application to interactions with known structures. Results: We present a new approach that relies on the unbound protein structures and protein docking to predict protein-protein binding affinities. Through the study of the docking space (i.e. decoys), the method predicts the binding affinity of the query proteins when the actual structure of the complex itself is unknown. We tested our approach on a set of globular and soluble proteins of the newest affinity benchmark, obtaining accuracy values comparable to other state-of-art methods: a 0.4 correlation coefficient between the experimental and predicted values of ΔG and an error < 3 Kcal/mol. Availability and implementation: The binding affinity predictor is implemented and available at http://sbi.upf.edu/BADock and https://github.com/badocksbi/BADock. Contact: j.planas-iglesias@warwick.ac.uk or baldo.oliva@upf.edu. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3297556,\n \"score\": 0\n },\n {\n \"doc_id\": \"29069295\",\n \"title\": \"PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine.\",\n \"abstract\": \"Motivation: Protein solubility can be a decisive factor in both research and production efficiency, and in silico sequence-based predictors that can accurately estimate solubility outcomes are highly sought. Results: In this study, we present a novel approach termed PRotein SolubIlity Predictor (PaRSnIP), which uses a gradient boosting machine algorithm as well as an approximation of sequence and structural features of the protein of interest. Based on an independent test set, PaRSnIP outperformed other state-of-the-art sequence-based methods by more than 9% in accuracy and 0.17 in Matthew's correlation coefficient, with an overall accuracy of 74% and Matthew's correlation coefficient of 0.48. Additionally, PaRSnIP provides importance scores for all features used in training. We observed higher fractions of exposed residues to associate positively with protein solubility and tripeptide stretches with multiple histidines to associate negatively with solubility. The improved prediction accuracy of PaRSnIP should enable it to predict protein solubility with greater reliability and to screen for sequence variants with enhanced manufacturability. Availability and implementation: PaRSnIP software is available for download under GitHub (https://github.com/RedaRawi/PaRSnIP). Contact: gwo-yu.chuang@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4576871,\n \"score\": 0\n },\n {\n \"doc_id\": \"29416743\",\n \"title\": \"DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest.\",\n \"abstract\": \"DNase I hypersensitive sites (DHSs) are genomic regions that provide important information regarding the presence of transcriptional regulatory elements and the state of chromatin. Therefore, identifying DHSs in uncharacterized DNA sequences is crucial for understanding their biological functions and mechanisms. Although many experimental methods have been proposed to identify DHSs, they have proven to be expensive for genome-wide application. Therefore, it is necessary to develop computational methods for DHS prediction. In this study, we proposed a support vector machine (SVM)-based method for predicting DHSs, called DHSpred (DNase I Hypersensitive Site predictor in human DNA sequences), which was trained with 174 optimal features. The optimal combination of features was identified from a large set that included nucleotide composition and di- and trinucleotide physicochemical properties, using a random forest algorithm. DHSpred achieved a Matthews correlation coefficient and accuracy of 0.660 and 0.871, respectively, which were 3% higher than those of control SVM predictors trained with non-optimized features, indicating the efficiency of the feature selection method. Furthermore, the performance of DHSpred was superior to that of state-of-the-art predictors. An online prediction server has been developed to assist the scientific community, and is freely available at: http://www.thegleelab.org/DHSpred.html.\",\n \"corpus_id\": 46789543,\n \"score\": 0\n },\n {\n \"doc_id\": \"29554211\",\n \"title\": \"DeepSol: a deep learning framework for sequence-based protein solubility prediction.\",\n \"abstract\": \"Motivation: Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors. In this work we propose, DeepSol, a novel Deep Learning-based protein solubility predictor. The backbone of our framework is a convolutional neural network that exploits k-mer structure and additional sequence and structural features extracted from the protein sequence. Results: DeepSol outperformed all known sequence-based state-of-the-art solubility prediction methods and attained an accuracy of 0.77 and Matthew's correlation coefficient of 0.55. The superior prediction accuracy of DeepSol allows to screen for sequences with enhanced production capacity and can more reliably predict solubility of novel proteins. Availability and implementation: DeepSol's best performing models and results are publicly deposited at https://doi.org/10.5281/zenodo.1162886 (Khurana and Mall, 2018). Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4042479,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":75,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28057679\",\n \"title\": \"SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.\",\n \"abstract\": \"Motivation: The high cost of drug discovery motivates the development of accurate virtual screening tools. Binding-homology, which takes advantage of known protein-ligand binding pairs, has emerged as a powerful discrimination technique. In order to exploit all available binding data, modelled structures of ligand-binding sequences may be used to create an expanded structural binding template library. Results: SPOT-Ligand 2 has demonstrated significantly improved screening performance over its previous version by expanding the template library 15 times over the previous one. It also performed better than or similar to other binding-homology approaches on the DUD and DUD-E benchmarks. Availability and Implementation: The server is available online at http://sparks-lab.org . Contacts: yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3752403\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19503616","title":"FINDSITE: a threading-based approach to ligand homology modeling.","abstract":"Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required. Previously, we showed that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Here, we demonstrate that across an evolutionarily related, but distant family of proteins, the ligands that bind to the common binding site contain a set of strongly conserved anchor functional groups as well as a variable region that accounts for their binding specificity. Furthermore, the sequence and structure conservation of residues contacting the anchor functional groups is significantly higher than those contacting ligand variable regions. Exploiting these insights, we developed FINDSITE(LHM) that employs structural information extracted from weakly related proteins to perform rapid ligand docking by homology modeling. In large scale benchmarking, using the predicted anchor-binding mode and the crystal structure of the receptor, FINDSITE(LHM) outperforms classical docking approaches with an average ligand RMSD from native of approximately 2.5 A. For weakly homologous receptor protein models, using FINDSITE(LHM), the fraction of recovered binding residues and specific contacts is 0.66 (0.55) and 0.49 (0.38) for highly confident (all) targets, respectively. Finally, in virtual screening for HIV-1 protease inhibitors, using similarity to the ligand anchor region yields significantly improved enrichment factors. Thus, the rather accurate, computationally inexpensive FINDSITE(LHM) algorithm should be a useful approach to assist in the discovery of novel biopharmaceuticals.","corpus_id":761758,"score":2},{"doc_id":"19685924","title":"LigMatch: a multiple structure-based ligand matching method for 3D virtual screening.","abstract":"We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive 'template' conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping.","corpus_id":25859947,"score":2},{"doc_id":"22574683","title":"FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.","abstract":"We have developed FINDSITE(X), an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSER(VMT), TASSER(VMT)-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITE(X) is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSER(VMT)-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 nonredundant (TC < 0.7) ligand set combined with ligands from the GLIDA database (a total of 88,949 compounds). Testing (excluding GPCRs whose sequence identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF(0.01)) is 22.7, whereas EF(0.01) by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, the average EF(0.01) reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html .","corpus_id":10440631,"score":2},{"doc_id":"22978550","title":"Identification of ligand templates using local structure alignment for structure-based drug design.","abstract":"With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.","corpus_id":12778406,"score":2},{"doc_id":"23240691","title":"FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.","abstract":"Virtual ligand screening is an integral part of the modern drug discovery process. Traditional ligand-based, virtual screening approaches are fast but require a set of structurally diverse ligands known to bind to the target. Traditional structure-based approaches require high-resolution target protein structures and are computationally demanding. In contrast, the recently developed threading/structure-based FINDSITE-based approaches have the advantage that they are as fast as traditional ligand-based approaches and yet overcome the limitations of traditional ligand- or structure-based approaches. These new methods can use predicted low-resolution structures and infer the likelihood of a ligand binding to a target by utilizing ligand information excised from the target's remote or close homologous proteins and/or libraries of ligand binding databases. Here, we develop an improved version of FINDSITE, FINDSITE(filt), that filters out false positive ligands in threading identified templates by a better binding site detection procedure that includes information about the binding site amino acid similarity. We then combine FINDSITE(filt) with FINDSITE(X) that uses publicly available binding databases ChEMBL and DrugBank for virtual ligand screening. The combined approach, FINDSITE(comb), is compared to two traditional docking methods, AUTODOCK Vina and DOCK 6, on the DUD benchmark set. It is shown to be significantly better in terms of enrichment factor, dependence on target structure quality, and speed. FINDSITE(comb) is then tested for virtual ligand screening on a large set of 3576 generic targets from the DrugBank database as well as a set of 168 Human GPCRs. Excluding close homologues, FINDSITE(comb) gives an average enrichment factor of 52.1 for generic targets and 22.3 for GPCRs within the top 1% of the screened compound library. Around 65% of the targets have better than random enrichment factors. The performance is insensitive to target structure quality, as long as it has a TM-score ≥ 0.4 to native. Thus, FINDSITE(comb) makes the screening of millions of compounds across entire proteomes feasible. The FINDSITE(comb) web service is freely available for academic users at http://cssb.biology.gatech.edu/skolnick/webservice/FINDSITE-COMB/index.html.","corpus_id":17644770,"score":2},{"doc_id":"23396123","title":"MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.","abstract":"SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":6954469,"score":2},{"doc_id":"23415854","title":"Are predicted protein structures of any value for binding site prediction and virtual ligand screening?","abstract":"The recently developed field of ligand homology modeling (LHM) that extends the ideas of protein homology modeling to the prediction of ligand binding sites and for use in virtual ligand screening has emerged as a powerful new approach. Unlike traditional docking methodologies, LHM can be applied to low-to-moderate resolution predicted as well as experimental structures with little if any diminution in performance; thereby enabling ≈ 75% of an average proteome to have potentially significant virtual screening predictions. In large scale benchmarking, LHM is able to predict off-target ligand binding. Thus, despite the widespread belief to the contrary, low-to-moderate resolution predicted structures have considerable utility for biochemical function prediction.","corpus_id":7385589,"score":2},{"doc_id":"24328054","title":"SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.","abstract":"We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.","corpus_id":1270662,"score":2},{"doc_id":"24341870","title":"Improving structural similarity based virtual screening using background knowledge.","abstract":"BACKGROUND: Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structural similarity measures. However, their general nature can lead to insufficient performance in some application cases. In this paper, we provide a link between ranking-based virtual screening and fragment-based data mining methods. The inclusion of binding-relevant background knowledge into a structural similarity measure improves the quality of the similarity rankings. This background knowledge in the form of binding relevant substructures can either be derived by hand selection or by automated fragment-based data mining methods. RESULTS: In virtual screening experiments we show that our approach clearly improves enrichment factors with both applied variants of our approach: the extension of the structural similarity measure with background knowledge in the form of a hand-selected relevant substructure or the extension of the similarity measure with background knowledge derived with data mining methods. CONCLUSION: Our study shows that adding binding relevant background knowledge can lead to significantly improved similarity rankings in virtual screening and that even basic data mining approaches can lead to competitive results making hand-selection of the background knowledge less crucial. This is especially important in drug discovery and development projects where no receptor structure is available or more frequently no verified binding mode is known and mostly ligand based approaches can be applied to generate hit compounds.","corpus_id":935114,"score":2},{"doc_id":"24877883","title":"Best of both worlds: on the complementarity of ligand-based and structure-based virtual screening.","abstract":"Virtual screening with docking is an integral component of drug design, particularly during hit finding phases. While successful prospective studies of virtual screening exist, it remains a significant challenge to identify best practices a priori due to the many factors that influence the final outcome, including targets, data sets, software, metrics, and expert knowledge of the users. This study investigates the extent to which ligand-based methods can be applied to improve structure-based methods. The use of ligand-based methods to modulate the number of hits identified using the protein-ligand complex and also the diversity of these hits from the crystallographic ligand is discussed. In this study, 40 CDK2 ligand complexes were used together with two external data sets containing both actives and inactives from GlaxoSmithKline (GSK) and actives and decoys from the Directory of Useful Decoys (DUD). Results show how ligand-based modeling can be used to select a more appropriate protein conformation for docking, as well as to assess the reliability of the docking experiment. The time gained by reducing the pool of virtual screening candidates via ligand-based similarity can be invested in more accurate docking procedures, as well as in downstream labor-intensive approaches (e.g., visual inspection) maximizing the use of the chemical and biological information available. This provides a framework for molecular modeling scientists that are involved in initiating virtual screening campaigns with practical advice to make best use of the information available to them.","corpus_id":5998530,"score":2},{"doc_id":"25336501","title":"LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.","abstract":"MOTIVATION: Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. RESULTS: We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. AVAILABILITY AND IMPLEMENTATION: LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: skolnick@gatech.edu.","corpus_id":12839538,"score":2},{"doc_id":"25350693","title":"Extended template-based modeling and evaluation method using consensus of binding mode of GPCRs for virtual screening.","abstract":"G-protein-coupled receptors (GPCRs) are a pharmaceutically important protein family because they mediate numerous physiological functions. The crystal structures of several GPCR subtypes have been determined recently, encouraging efforts to apply structure-based virtual screening (SBVS) along with ligand-based virtual screening (LBVS) to improve the hit rate of active ligands from large chemical libraries. Three-dimensional models are also necessary for GPCR targets whose structures are unknown. Current challenges include the selection of structural templates from available structurally known GPCRs to use for accurate modeling and understanding the diversity of sites recognizing distinct ligands. We have developed and validated an extended template-based modeling and evaluation method for SBVS. Models were generated using a fragmental template procedure in addition to typical template-based modeling methods. The reliability of the models was evaluated using a virtual screening test with known active ligands and decoys and the consensus of the binding mode using the protein-ligand interaction fingerprint (PLIF) derived from the results of docking simulations. This novel workflow was applied to three targets with known structures (human dopamine receptor 3, human histamine H1 receptor, and human delta opioid receptor) and to a target with an unknown structure (human serotonin 2A receptor). In each case, model structures having high ligand selectivity with consensus binding mode were generated.","corpus_id":12747975,"score":2},{"doc_id":"25359888","title":"Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.","abstract":"MOTIVATION: Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects. RESULTS: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods. AVAILABILITY AND IMPLEMENTATION: http://kiharalab.org/patchsurfer2.0/ CONTACT: dkihara@purdue.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":2581408,"score":2},{"doc_id":"25709030","title":"Generating \"fragment-based virtual library\" using pocket similarity search of ligand-receptor complexes.","abstract":"As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.","corpus_id":36180208,"score":2},{"doc_id":"26225536","title":"PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.","abstract":"Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand-binding pockets in proteins is small. PoLi identifies similar ligand-binding pockets in a holo template protein library, selectively copies relevant parts of template ligands, and uses them for VS. In practice, PoLi is a hybrid structure and ligand-based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6, respectively, in the top 1% of the screened library. In contrast, traditional docking-based VS using AutoDock Vina and homology-based VS using FINDSITE(filt) have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets, respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods.","corpus_id":1362559,"score":2},{"doc_id":"26330079","title":"Performance evaluation of structure based and ligand based virtual screening methods on ten selected anti-cancer targets.","abstract":"Virtual screening has become an important tool in drug discovery process. Structure based and ligand based approaches are generally used in virtual screening process. To date, several benchmark sets for evaluating the performance of the virtual screening tool are available. In this study, our aim is to compare the performance of both structure based and ligand based virtual screening methods. Ten anti-cancer targets and their corresponding benchmark sets from 'Demanding Evaluation Kits for Objective In silico Screening' (DEKOIS) library were selected. X-ray crystal structures of protein-ligand complexes were selected based on their resolution. Openeye tools such as FRED, vROCS were used and the results were carefully analyzed. At EF1%, vROCS produced better results but at EF5% and EF10%, both FRED and ROCS produced almost similar results. It was noticed that the enrichment factor values were decreased while going from EF1% to EF5% and EF10% in many cases.","corpus_id":8368775,"score":2},{"doc_id":"27074979","title":"SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.","abstract":"Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this \"ab initio\" approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. © 2016 Wiley Periodicals, Inc.","corpus_id":20462287,"score":2},{"doc_id":"27500657","title":"PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.","abstract":"Virtual screening has become an indispensable procedure in drug discovery. Virtual screening methods can be classified into two categories: ligand-based and structure-based. While the former have advantages, including being quick to compute, in general they are relatively weak at discovering novel active compounds because they use known actives as references. On the other hand, structure-based methods have higher potential to find novel compounds because they directly predict the binding affinity of a ligand in a target binding pocket, albeit with substantially lower speed than ligand-based methods. Here we report a novel structure-based virtual screening method, PL-PatchSurfer2. In PL-PatchSurfer2, protein and ligand surfaces are represented by a set of overlapping local patches, each of which is represented by three-dimensional Zernike descriptors (3DZDs). By means of 3DZDs, the shapes and physicochemical complementarities of local surface regions of a pocket surface and a ligand molecule can be concisely and effectively computed. Compared with the previous version of the program, the performance of PL-PatchSurfer2 is substantially improved by the addition of two more features, atom-based hydrophobicity and hydrogen-bond acceptors and donors. Benchmark studies showed that PL-PatchSurfer2 performed better than or comparable to popular existing methods. Particularly, PL-PatchSurfer2 significantly outperformed existing methods when apo-form or template-based protein models were used for queries. The computational time of PL-PatchSurfer2 is about 20 times shorter than those of conventional structure-based methods. The PL-PatchSurfer2 program is available at http://www.kiharalab.org/plps2/ .","corpus_id":2395995,"score":2},{"doc_id":"27565795","title":"mRAISE: an alternative algorithmic approach to ligand-based virtual screening.","abstract":"Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at http://www.zbh.uni-hamburg.de/mraise-dataset.html . The table of all PDB codes contained in the ensembles can be found in the supplementary material. The software tool mRAISE is freely available for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).","corpus_id":29225191,"score":2},{"doc_id":"28315995","title":"Ligand-based virtual screening under partial shape constraints.","abstract":"Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).","corpus_id":24800457,"score":2},{"doc_id":"29036579","title":"HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques.","abstract":"Summary: Molecular-similarity searches based on two-dimensional (2D) fingerprint and three-dimensional (3D) shape represent two widely used ligand-based virtual screening (VS) methods in computer-aided drug design. 2D fingerprint-based VS utilizes the binary fragment information on a known ligand, whereas 3D shape-based VS takes advantage of geometric information for predefined features from a 3D conformation. Given their different advantages, it would be desirable to hybridize 2D fingerprint and 3D shape molecular-similarity approaches in drug discovery. Here, we presented a general hybrid molecular-similarity protocol, referred to as HybridSim, obtained by combining the 2D fingerprint- and 3D shape-based similarity search methods and evaluated its performance on 595,036 actives and decoys for 40 pharmaceutically relevant targets available in the Directory of Useful Decoys Enhanced (DUD-E). Our results showed that HybridSim significantly improved the overall performance in 40 VS projects as compared with using only 2D fingerprint and 3D shape methods. Furthermore, HybridSim-VS, the first online platform using the proposed HybridSim method coupled with 17,839,945 screenable and purchasable compounds, was developed to provide large-scale and proficient VS capabilities to experts and nonexperts in the field. Availability and implementation: HybridSim-VS web server is freely available at http://www.rcidm.org/HybridSim-VS/. Contact: lingwang@scut.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":2855344,"score":2},{"doc_id":"29462237","title":"LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.","abstract":"Motivation: Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. Results: We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1 415 871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. Availability and implementation: http://zhanglab.ccmb.med.umich.edu/LS-align/. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3445717,"score":2},{"doc_id":"18442221","title":"Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring.","abstract":"The current study investigates the combination of two recently reported techniques for the improvement of homology model-based virtual screening for G-protein coupled receptor (GPCR) ligands. First, ligand-supported homology modeling was used to generate receptor models that were in agreement with mutagenesis data and structure-activity relationship information of the ligands. Second, interaction patterns from known ligands to the receptor were applied for scoring and rank ordering compounds from a virtual library using ligand-receptor interaction fingerprint-based similarity (IFS). Our approach was evaluated in retrospective virtual screening experiments for antagonists of the metabotropic glutamate receptor (mGluR) subtype 5. The results of our approach were compared to the results obtained by conventional scoring functions (Dock-Score, PMF-Score, Gold-Score, ChemScore, and FlexX-Score). The IFS lead to significantly higher enrichment rates, relative to the competing scoring functions. Though using a target-biased scoring approach, the results were not biased toward the chemical classes of the reference structures. Our results indicate that the presented approach has the potential to serve as a general setup for successful structure-based GPCR virtual screening.","corpus_id":27403518,"score":1},{"doc_id":"19642282","title":"Improving homology models for protein-ligand binding sites.","abstract":"In order to improve the prediction of protein-ligand binding sites through homology modeling, we incorporate knowledge of the binding residues into the modeling framework. Residues are identified as binding or nonbinding based on their true labels as well as labels predicted from structure and sequence. The sequence predictions were made using a support vector machine framework which employs a sophisticated window-based kernel. Binding labels are used with a very sensitive sequence alignment method to align the target and template. Relevant parameters governing the alignment process are searched for optimal values. Based on our results, homology models of the binding site can be improved if a priori knowledge of the binding residues is available. For target-template pairs with low sequence identity and high structural diversity our sequence-based prediction method provided sufficient information to realize this improvement.","corpus_id":14118805,"score":1},{"doc_id":"20025561","title":"Protein structure prediction in structure-based ligand design and virtual screening.","abstract":"Advances in protein modeling algorithms and state-of-the-art sequence similarity comparison and fold recognition methods, in combination with growing protein structure information, are facilitating \"genome-to-drug lead\" approaches in which chemicals are virtually screened against computationally-predicted protein targets. Although the quality of predicted protein structures by homology modeling methods, and thus their applicability to drug discovery initiatives, predominantly depends on the sequence similarity between the protein of known structure and the protein target to be modeled, recent research underscores that this approach can be used to significant advantage in the identification and optimization of lead compounds, as well as for the identification and validation of drug targets. Rational structure-based drug design cycles begin with an iterative procedure that is dependent on the initial determination of the structure of the target protein, followed by the prediction of ligands for the target protein from molecular modeling computation. The structure determination of all proteins encoded by vast genome sequencing efforts appears to be an unrealistic goal with current technologies. Therefore, other approaches based on the development of technology useful for accurately predicting and modeling the structures of proteins have become exceedingly important in certain structure-based drug design efforts. This review provides an overview of the recent method advancements in protein structure prediction by homology modeling and includes an assessment of the application of homology modeling to pharmaceutically relevant questions. In addition, examples of successful applications of homology modeling approaches to genome-to-drug lead investigations are described.","corpus_id":40532349,"score":1},{"doc_id":"20434455","title":"Homology-modelling protein-ligand interactions: allowing for ligand-induced conformational change.","abstract":"Current homology-modelling methods do not consider small molecules in their automated processes. Therefore, the development of a reliable tool for protein-ligand homology modelling is an important next step in generating plausible models for molecular interactions. Two automated protein-ligand homology-modelling strategies, requiring no expert knowledge from the user, are investigated here. Both employ the \"induced fit\" concept with flexibility in side chains and ligand. The most successful strategy superimposes the new ligand over the original ligand before homology modelling, allowing the new ligand to be taken into consideration during protein modelling (rather than after), facilitating conformational change in the local backbone if necessary. We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult target complexes are also successfully modelled, reproducing native protein-ligand contacts with significantly different biological substrates and different binding-site conformations. These include the modelling of Cdk5 (cyclin-dependent kinase 5) from Cdk2, thymidine phosphorylase from a bacterial homologue, and dihydrofolate reductase from a recombinant variant with a markedly different inhibitor. In terms of average modelling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 A (and 2.0 A for the protein binding site) for \"easy\" cases and 2.9 A for the ligand (and 2.7 A for the protein binding site) in \"hard\" cases. This demonstrates the importance of selecting an optimal template. Ligand-modelling accuracy is strongly dependent on target-template ligand structural similarity, rather than target-template sequence identity. However, protein-modelling accuracy is dependent on both. Our automated protein-ligand homology-modelling strategy generates a higher degree of accuracy than homology modelling followed by docking, generating an average ligand RMSD that is 1-2 A better than docking with homology models.","corpus_id":40968760,"score":1},{"doc_id":"22183538","title":"How to benchmark methods for structure-based virtual screening of large compound libraries.","abstract":"Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.","corpus_id":206678021,"score":1},{"doc_id":"22569590","title":"Surflex-Dock: Docking benchmarks and real-world application.","abstract":"Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.","corpus_id":27281484,"score":1},{"doc_id":"23398329","title":"Ligand-optimized homology models of D₁ and D₂ dopamine receptors: application for virtual screening.","abstract":"Recent breakthroughs in crystallographic studies of G protein-coupled receptors (GPCRs), together with continuous progress in molecular modeling methods, have opened new perspectives for structure-based drug discovery. A crucial enhancement in this area was development of induced fit docking procedures that allow optimization of binding pocket conformation guided by the features of its active ligands. In the course of our research program aimed at discovery of novel antipsychotic agents, our attention focused on dopaminergic D2 and D1 receptors (D2R and D1R). Thus, we decided to investigate whether the availability of a novel structure of the closely related D3 receptor and application of induced fit docking procedures for binding pocket refinement would permit the building of models of D2R and D1R that facilitate a successful virtual screening (VS). Here, we provide an in-depth description of the modeling procedure and the discussion of the results of a VS benchmark we performed to compare efficiency of the ligand-optimized receptors in comparison with the regular homology models. We observed that application of the ligand-optimized models significantly improved the VS performance both in terms of BEDROC (0.325 vs 0.182 for D1R and 0.383 vs 0.301 for D2R) as well as EF1% (20 vs 11 for D1R and 18 vs 10 for D2R). In contrast, no improvement was observed for the performance of a D2R model built on the D3R template, when compared with that derived from the structure of the previously published and more evolutionary distant β2 adrenergic receptor. The comparison of results for receptors built according to various protocols and templates revealed that the most significant factor for the receptor performance was a proper selection of \"tool ligand\" used in induced fit docking procedure. Taken together, our results suggest that the described homology modeling procedure could be a viable tool for structure-based GPCR ligand design, even for the targets for which only a relatively distant structural template is available.","corpus_id":33336236,"score":1},{"doc_id":"23541165","title":"Structure-based virtual screening of MT2 melatonin receptor: influence of template choice and structural refinement.","abstract":"Developing GPCR homology models for structure-based virtual screening requires the choice of a suitable template and refinement of binding site residues. We explored this systematically for the MT2 melatonin receptor, with the aim to build a receptor homology model that is optimized for the enrichment of active melatoninergic ligands. A set of 12 MT2 melatonin receptor models was built using different GPCR X-ray structural templates and submitted to a virtual screening campaign on a set of compounds composed of 29 known melatonin receptor ligands and 2560 drug-like decoys. To evaluate the effect of including a priori information in receptor models, 12 representative melatonin receptor ligands were placed into the MT2 receptor models in poses consistent with known mutagenesis data and with assessed pharmacophore models. The receptor structures were then adapted to the ligands by induced-fit docking. Most of the 144 ligand-adapted MT2 receptor models showed significant improvements in screening enrichments compared to the unrefined homology models, with some template/refinement combinations giving excellent enrichment factors. The discriminating ability of the models was further tested on the 29 active ligands plus a set of 21 inactive or low-affinity compounds from the same chemical classes. Rotameric states of side chains for some residues, presumed to be involved in the binding process, were correlated with screening effectiveness, suggesting the existence of specific receptor conformations able to recognize active compounds. The top MT2 receptor model was able to identify 24 of 29 active ligands among the first 2% of the screened database. This work provides insights into the use of refined GPCR homology models for virtual screening.","corpus_id":22493493,"score":1},{"doc_id":"24318891","title":"Structure-based virtual screening for the identification of RNA-binding ligands.","abstract":"Structure-based virtual screening exploits the 3D structure of the target as a template for the discovery of new ligands. It is a key method for hit discovery and was originally developed for protein targets. Recently, this method has also been applied to RNA targets. This chapter gives an overview of this method and its application in the context of ligand discovery for RNA. In addition, it describes in detail how to conduct virtual screening for RNA targets, making use of software that is free for noncommercial use. Some advice on how to avoid common pitfalls in virtual screening is also given.","corpus_id":37480232,"score":1},{"doc_id":"24573478","title":"SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.","abstract":"RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.","corpus_id":25754262,"score":1},{"doc_id":"24813470","title":"Impact of template choice on homology model efficiency in virtual screening.","abstract":"Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, only the closest ones are chosen for homology modeling purposes. To validate the aforementioned approach, we performed homology modeling of four serotonin receptors (5-HT1AR, 5-HT2AR, 5-HT6R, 5-HT7R) for virtual screening purposes, using 10 available G-Protein Coupled Receptors (GPCR) templates with diverse evolutionary distances to the targets, with various approaches to alignment construction and model building. The resulting models were further validated in two steps by means of ligand docking and enrichment calculation, using Glide software. The final quality of the models was determined in virtual screening-like experiments by the AUROC score of the resulting ROC curves. The outcome of this research showed that no correlation between sequence identity and model quality was found, leading to the conclusion that the closest phylogenetic relative is not always the best template for homology modeling.","corpus_id":22066070,"score":1},{"doc_id":"24900272","title":"Homology Model and Docking-Based Virtual Screening for Ligands of the σ1 Receptor.","abstract":"This study presents for the first time the 3D model of the σ1 receptor protein as obtained from homology modeling techniques, shows the applicability of this structure to docking-based virtual screening, defines a computational strategy to optimize the results based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring, and provides evidence that these in silico models and recipes are powerful tools on which virtual screening of new σ1 ligands can be based. In particular, the validation of the applicability of docking-based virtual screening to homology models is of utmost importance, since no crystal structure is available to date for the σ1 receptor, and this missing information still constitutes a major hurdle for a rational ligand design for this important protein target.","corpus_id":22380771,"score":1},{"doc_id":"25116840","title":"Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study.","abstract":"Accurate and affordable assessment of ligand-protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure-activity information may prove useful. Here, we introduce one such filter based upon three-dimensional structural protein-ligand interaction fingerprints (SPLIF). SPLIF permits quantitative assessment of whether a docking pose interacts with the protein target similarly to a known ligand and rescues active compounds penalized by poor initial docking scores. An extensive benchmark study on 10 diverse data sets selected from the DUD-E database has been performed in order to evaluate the absolute and relative efficiency of this method. SPLIF demonstrated an overall better performance than relevant standard methods.","corpus_id":17006573,"score":1},{"doc_id":"25220914","title":"Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.","abstract":"Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.","corpus_id":15918793,"score":1},{"doc_id":"25232727","title":"eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.","abstract":"Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.","corpus_id":6379524,"score":1},{"doc_id":"26454279","title":"Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.","abstract":"MOTIVATION: The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. RESULTS: The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. AVAILABILITY AND IMPLEMENTATION: SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org CONTACT: : yaoqi.zhou@griffith.edu.au.","corpus_id":-1,"score":1},{"doc_id":"26803160","title":"Alloscore: a method for predicting allosteric ligand-protein interactions.","abstract":"UNLABELLED: Allosteric ligands have increasingly gained attention as potential therapeutic agents due to their higher target selectivity and lower toxicity compared with classic orthosteric ligands. Despite the great interest in the development of allosteric drugs as a new tactic in drug discovery, the understanding of the ligand-protein interactions underlying allosteric binding represents a key challenge. Herein, we introduce Alloscore, a web server that predicts the binding affinities of allosteric ligand-protein interactions. This method exhibits prominent performance in describing allosteric binding and could be useful in allosteric virtual screening and the structural optimization of allosteric agonists/antagonists. AVAILABILITY AND IMPLEMENTATION: The Alloscore server and tutorials are freely available at http://mdl.shsmu.edu.cn/alloscore CONTACT: jian.zhang@sjtu.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":27137471,"score":1},{"doc_id":"28011765","title":"RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening.","abstract":"Summary: Evaluation of the capacity for separating actives from challenging decoys is a crucial metric of performance related to molecular docking or a virtual screening workflow. The Directory of Useful Decoys (DUD) and its enhanced version (DUD-E) provide a benchmark for molecular docking, although they only contain a limited set of decoys for limited targets. DecoyFinder was released to compensate the limitations of DUD or DUD-E for building target-specific decoy sets. However, desirable query template design, generation of multiple decoy sets of similar quality, and computational speed remain bottlenecks, particularly when the numbers of queried actives and retrieved decoys increases to hundreds or more. Here, we developed a program suite called RApid DEcoy Retriever (RADER) to facilitate the decoy-based assessment of virtual screening. This program adopts a novel database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. RADER provides two operational modes: as a command-line tool and on a web server. Validation of the performance and efficiency of RADER was also conducted and is described. Availability and Implementation: RADER web server and a local version are freely available at http://rcidm.org/rader/ . Contact: lingwang@scut.edu.cn or went@scut.edu.cn . Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3770961,"score":1},{"doc_id":"28150235","title":"Structure-Based Virtual Screening.","abstract":"Structure-based virtual screening (SBVS) is a computational approach used in the early-stage drug discovery campaign to search a chemical compound library for novel bioactive molecules against a certain drug target. It utilizes the three-dimensional (3D) structure of the biological target, obtained from X-ray, NMR, or computational modeling, to dock a collection of chemical compounds into the binding site and select a subset of these compounds based on the predicted binding scores for further biological evaluation. In the present work, we illustrate the basic process of conducting a SBVS with examples using freely accessible tools and resources.","corpus_id":3555685,"score":1},{"doc_id":"19627087","title":"Modern homology modeling of G-protein coupled receptors: which structural template to use?","abstract":"The recent availability in the literature of new crystal structures of inactive G-protein coupled receptors (GPCRs) prompted us to study the extent to which these crystal structures constitute an advantage over the former prototypic rhodopsin template for homology modeling of the transmembrane (TM) region of human class A GPCRs. Our results suggest that better templates than those currently available are required by the majority of these GPCRs to generate homology models that are accurate enough for simple virtual screening aimed at computer-aided drug discovery. Thus, we investigated: (1) which class A GPCRs would have the highest impact as potential templates for homology modeling of other GPCRs, if their structures were solved, and (2) the extent to which multiple-template homology modeling (using all currently available GPCR crystal structures) provides an improvement over single-template homology modeling, as evaluated by the accuracy of rigid protein-flexible ligand docking on these models.","corpus_id":39145087,"score":0},{"doc_id":"21873637","title":"Spatial clustering of protein binding sites for template based protein docking.","abstract":"MOTIVATION: In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes. RESULTS: This article presents KBDOCK, a 3D database approach for spatially clustering protein binding sites and for performing template-based (knowledge-based) protein docking. KBDOCK combines residue contact information from the 3DID database with the Pfam protein domain family classification together with coordinate data from the Protein Data Bank. This allows the 3D configurations of all known hetero domain-domain interactions to be superposed and clustered for each Pfam family. We find that most Pfam domain families have up to four hetero binding sites, and over 60% of all domain families have just one hetero binding site. The utility of this approach for template-based docking is demonstrated using 73 complexes from the Protein Docking Benchmark. Overall, up to 45 out of 73 complexes may be modelled by direct homology to existing domain interfaces, and key binding site information is found for 24 of the 28 remaining complexes. These results show that KBDOCK can often provide useful information for predicting the structures of unknown protein complexes. AVAILABILITY: http://kbdock.loria.fr/ CONTACT: Dave. Ritchie@inria.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":10132360,"score":0},{"doc_id":"23413437","title":"GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity.","abstract":"SUMMARY: A large number of proteins function as homo-oligomers; therefore, predicting homo-oligomeric structure of proteins is of primary importance for understanding protein function at the molecular level. Here, we introduce a web server for prediction of protein homo-oligomer structure. The server takes a protein monomer structure as input and predicts its homo-oligomer structure from oligomer templates selected based on sequence and tertiary/quaternary structure similarity. Using protein model structures as input, the server shows clear improvement over the best methods of CASP9 in predicting oligomeric structures from amino acid sequences. AVAILABILITY: http://galaxy.seoklab.org/gemini. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":15094536,"score":0},{"doc_id":"24328076","title":"Homology modeling of human muscarinic acetylcholine receptors.","abstract":"We have developed homology models of the acetylcholine muscarinic receptors M₁R-M₅R, based on the β₂-adrenergic receptor crystal as the template. This is the first report of homology modeling of all five subtypes of acetylcholine muscarinic receptors with binding sites optimized for ligand binding. The models were evaluated for their ability to discriminate between muscarinic antagonists and decoy compounds using virtual screening using enrichment factors, area under the ROC curve (AUC), and an early enrichment measure, LogAUC. The models produce rational binding modes of docked ligands as well as good enrichment capacity when tested against property-matched decoy libraries, which demonstrates their unbiased predictive ability. To test the relative effects of homology model template selection and the binding site optimization procedure, we generated and evaluated a naïve M₂R model, using the M₃R crystal structure as a template. Our results confirm previous findings that binding site optimization using ligand(s) active at a particular receptor, i.e. including functional knowledge into the model building process, has a more pronounced effect on model quality than target-template sequence similarity. The optimized M₁R-M₅R homology models are made available as part of the Supporting Information to allow researchers to use these structures, compare them to their own results, and thus advance the development of better modeling approaches.","corpus_id":30897753,"score":0},{"doc_id":"25492406","title":"Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements.","abstract":"MOTIVATION: Cysteine residues have particular structural and functional relevance in proteins because of their ability to form covalent disulfide bonds. Bioinformatics tools that can accurately predict cysteine bonding states are already available, whereas it remains challenging to infer the disulfide connectivity pattern of unknown protein sequences. Improving accuracy in this area is highly relevant for the structural and functional annotation of proteins. RESULTS: We predict the intra-chain disulfide bond connectivity patterns starting from known cysteine bonding states with an evolutionary-based unsupervised approach called Sephiroth that relies on high-quality alignments obtained with HHblits and is based on a coarse-grained cluster-based modelization of tandem cysteine mutations within a protein family. We compared our method with state-of-the-art unsupervised predictors and achieve a performance improvement of 25-27% while requiring an order of magnitude less of aligned homologous sequences (∼10(3) instead of ∼10(4)). AVAILABILITY AND IMPLEMENTATION: The software described in this article and the datasets used are available at http://ibsquare.be/sephiroth. CONTACT: wvranken@vub.ac.be SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.","corpus_id":43913726,"score":0},{"doc_id":"25701568","title":"AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.","abstract":"MOTIVATION: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. RESULTS: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with 'inserted' domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. AVAILABILITY AND IMPLEMENTATION: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. CONTACT: adam@sanfordburnham.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":1552318,"score":0},{"doc_id":"26254434","title":"Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.","abstract":"MOTIVATION: Template-based modeling, the most successful approach for predicting protein 3D structure, often requires detecting distant evolutionary relationships between the target sequence and proteins of known structure. Developed for this purpose, fold recognition methods use elaborate strategies to exploit evolutionary information, mainly by encoding amino acid sequence into profiles. Since protein structure is more conserved than sequence, the inclusion of structural information can improve the detection of remote homology. RESULTS: Here, we present ORION, a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure. Our method uses the 16-state structural alphabet Protein Blocks, which provides an accurate 1D description of protein structure local conformations. ORION systematically outperforms PSI-BLAST and HHsearch on several benchmarks, including target sequences from the modeling competitions CASP8, 9 and 10, and detects ∼10% more templates at fold and superfamily SCOP levels. AVAILABILITY: Software freely available for download at http://www.dsimb.inserm.fr/orion/. CONTACT: jean-christophe.gelly@univ-paris-diderot.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":11919129,"score":0},{"doc_id":"26454278","title":"FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.","abstract":"The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors. AVAILABILITY AND IMPLEMENTATION: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/. CONTACT: shuaicli@cityu.edu.hk, dbu@ict.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":12915055,"score":0},{"doc_id":"26545824","title":"Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.","abstract":"MOTIVATION: Predictive tools that model protein-ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein-ligand binding predictive tools would be useful. RESULTS: We developed a system for automatically generating protein-ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5-1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands. AVAILABILITY AND IMPLEMENTATION: The source code and web application are freely available for download at http://utprot.net. They are implemented in Python and supported on Linux. CONTACT: shimizu@bi.a.u-tokyo.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":16676373,"score":0},{"doc_id":"26568622","title":"Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.","abstract":"MOTIVATION: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. RESULTS: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":22034498,"score":0},{"doc_id":"26704597","title":"Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.","abstract":"MOTIVATION: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus the need for tools which in particular can make local structural alignments of RNAs is only increasing. RESULTS: To meet the demand for both large scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2,000-6,000 nucleotides improve execution up to a factor of five. AVAILABILITY AND IMPLEMENTATION: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign CONTACT: gorodkin@rth.dk SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.","corpus_id":18683999,"score":0},{"doc_id":"27354702","title":"AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms.","abstract":"MOTIVATION: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. RESULTS: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. AVAILABILITY AND IMPLEMENTATION: http://adfr.scripps.edu/AutoDockFR/autosite.html CONTACT: sanner@scripps.eduSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":206344707,"score":0},{"doc_id":"27378301","title":"Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals.","abstract":"MOTIVATION: More than half of proteins require binding of metal and acid radical ions for their structure and function. Identification of the ion-binding locations is important for understanding the biological functions of proteins. Due to the small size and high versatility of the metal and acid radical ions, however, computational prediction of their binding sites remains difficult. RESULTS: We proposed a new ligand-specific approach devoted to the binding site prediction of 13 metal ions (Zn(2+), Cu(2+), Fe(2+), Fe(3+), Ca(2+), Mg(2+), Mn(2+), Na(+), K(+)) and acid radical ion ligands (CO3(2-), NO2(-), SO4(2-), PO4(3-)) that are most frequently seen in protein databases. A sequence-based ab initio model is first trained on sequence profiles, where a modified AdaBoost algorithm is extended to balance binding and non-binding residue samples. A composite method IonCom is then developed to combine the ab initio model with multiple threading alignments for further improving the robustness of the binding site predictions. The pipeline was tested using 5-fold cross validations on a comprehensive set of 2,100 non-redundant proteins bound with 3,075 small ion ligands. Significant advantage was demonstrated compared with the state of the art ligand-binding methods including COACH and TargetS for high-accuracy ion-binding site identification. Detailed data analyses show that the major advantage of IonCom lies at the integration of complementary ab initio and template-based components. Ion-specific feature design and binding library selection also contribute to the improvement of small ion ligand binding predictions. AVAILABILITY AND IMPLEMENTATION: http://zhanglab.ccmb.med.umich.edu/IonCom CONTACT: hxz@imut.edu.cn or zhng@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":1105667,"score":0},{"doc_id":"27551104","title":"Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks.","abstract":"MOTIVATION: Backbone structures and solvent accessible surface area of proteins are benefited from continuous real value prediction because it removes the arbitrariness of defining boundary between different secondary-structure and solvent-accessibility states. However, lacking the confidence score for predicted values has limited their applications. Here we investigated whether or not we can make a reasonable prediction of absolute errors for predicted backbone torsion angles, Cα-atom-based angles and torsion angles, solvent accessibility, contact numbers and half-sphere exposures by employing deep neural networks. RESULTS: We found that angle-based errors can be predicted most accurately with Spearman correlation coefficient (SPC) between predicted and actual errors at about 0.6. This is followed by solvent accessibility (SPC∼0.5). The errors on contact-based structural properties are most difficult to predict (SPC between 0.2 and 0.3). We showed that predicted errors are significantly better error indicators than the average errors based on secondary-structure and amino-acid residue types. We further demonstrated the usefulness of predicted errors in model quality assessment. These error or confidence indictors are expected to be useful for prediction, assessment, and refinement of protein structures. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org as a part of SPIDER2 package. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3666040,"score":0},{"doc_id":"28011771","title":"Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.","abstract":"Motivation: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction. Results: The new method, named SPOT-Disorder, has steadily improved over a similar method using a traditional, window-based neural network (SPINE-D) in all datasets tested without separate training on short and long disordered regions. Independent tests on four other datasets including the datasets from critical assessment of structure prediction (CASP) techniques and >10 000 annotated proteins from MobiDB, confirmed SPOT-Disorder as one of the best methods in disorder prediction. Moreover, initial studies indicate that the method is more accurate in predicting functional sites in disordered regions. These results highlight the usefulness combining LSTM with deep bidirectional recurrent neural networks in capturing non-local, long-range interactions for bioinformatics applications. Availability and Implementation: SPOT-disorder is available as a web server and as a standalone program at: http://sparks-lab.org/server/SPOT-disorder/index.php . Contact: j.hanson@griffith.edu.au or yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au. Supplementary information: Supplementary data is available at Bioinformatics online.","corpus_id":3703781,"score":0},{"doc_id":"28398502","title":"PyGOLD: a python based API for docking based virtual screening workflow generation.","abstract":"Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD. However, within an automated virtual screening workflow it is not feasible to use the GUI in between every step to change the GOLD configuration file. Thus, a python module called PyGOLD was developed, to parse, edit and write the GOLD configuration file and to automate docking based virtual screening workflows. Availability and Implementation: The latest version of PyGOLD, its documentation and example scripts are available at: http://www.ccb.tu-dortmund.de/koch or http://www.agkoch.de. PyGOLD is implemented in Python and can be imported as a standard python module without any further dependencies. Contact: oliver.koch@agkoch.de, oliver.koch@tu-dortmund.de. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4448498,"score":0},{"doc_id":"28430949","title":"Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility.","abstract":"Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some \"short to intermediate\" non-local interactions. Here, we employed Long Short Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. Results: We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j|>19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5%, and 10% in the mean absolute error for backbone ϕ ,Ψ, θ , and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted Cα atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and Ψ angles. We expect the method to be useful for assisting protein structure and function prediction. Availability: The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . Contact: yaoqi.zhou@griffith.edu.au , yuedong.yang@griffith.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3764023,"score":0},{"doc_id":"29040432","title":"Machine learning accelerates MD-based binding pose prediction between ligands and proteins.","abstract":"Motivation: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short Molecular Dynamics (MD) simulations, such as MM-PBSA and MM-GBSA, among generated docking poses have been used. Since molecular structures obtained from MD simulation depend on the initial condition, taking the average over different initial conditions leads to better accuracy. Prediction accuracy of protein-ligand binding poses can be improved with multiple runs at different initial velocity. Results: This paper shows that a machine learning method, called Best Arm Identification, can optimally control the number of MD runs for each binding pose. It allows us to identify a correct binding pose with a minimum number of total runs. Our experiment using three proteins and eight inhibitors showed that the computational cost can be reduced substantially without sacrificing accuracy. This method can be applied for controlling all kinds of molecular simulations to obtain best results under restricted computational resources. Availability and implementation: Code and data are available on GitHub at https://github.com/tsudalab/bpbi. Contact: terayama@cbms.k.u-tokyo.ac.jp or tsuda@k.u-tokyo.ac.jp. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3764446,"score":0},{"doc_id":"29462243","title":"Combining co-evolution and secondary structure prediction to improve fragment library generation.","abstract":"Motivation: Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction. Results: We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results. Availability and implementation: Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3414290,"score":0}],"string":"[\n {\n \"doc_id\": \"19503616\",\n \"title\": \"FINDSITE: a threading-based approach to ligand homology modeling.\",\n \"abstract\": \"Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required. Previously, we showed that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Here, we demonstrate that across an evolutionarily related, but distant family of proteins, the ligands that bind to the common binding site contain a set of strongly conserved anchor functional groups as well as a variable region that accounts for their binding specificity. Furthermore, the sequence and structure conservation of residues contacting the anchor functional groups is significantly higher than those contacting ligand variable regions. Exploiting these insights, we developed FINDSITE(LHM) that employs structural information extracted from weakly related proteins to perform rapid ligand docking by homology modeling. In large scale benchmarking, using the predicted anchor-binding mode and the crystal structure of the receptor, FINDSITE(LHM) outperforms classical docking approaches with an average ligand RMSD from native of approximately 2.5 A. For weakly homologous receptor protein models, using FINDSITE(LHM), the fraction of recovered binding residues and specific contacts is 0.66 (0.55) and 0.49 (0.38) for highly confident (all) targets, respectively. Finally, in virtual screening for HIV-1 protease inhibitors, using similarity to the ligand anchor region yields significantly improved enrichment factors. Thus, the rather accurate, computationally inexpensive FINDSITE(LHM) algorithm should be a useful approach to assist in the discovery of novel biopharmaceuticals.\",\n \"corpus_id\": 761758,\n \"score\": 2\n },\n {\n \"doc_id\": \"19685924\",\n \"title\": \"LigMatch: a multiple structure-based ligand matching method for 3D virtual screening.\",\n \"abstract\": \"We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive 'template' conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping.\",\n \"corpus_id\": 25859947,\n \"score\": 2\n },\n {\n \"doc_id\": \"22574683\",\n \"title\": \"FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.\",\n \"abstract\": \"We have developed FINDSITE(X), an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSER(VMT), TASSER(VMT)-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITE(X) is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSER(VMT)-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 nonredundant (TC < 0.7) ligand set combined with ligands from the GLIDA database (a total of 88,949 compounds). Testing (excluding GPCRs whose sequence identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF(0.01)) is 22.7, whereas EF(0.01) by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, the average EF(0.01) reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html .\",\n \"corpus_id\": 10440631,\n \"score\": 2\n },\n {\n \"doc_id\": \"22978550\",\n \"title\": \"Identification of ligand templates using local structure alignment for structure-based drug design.\",\n \"abstract\": \"With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.\",\n \"corpus_id\": 12778406,\n \"score\": 2\n },\n {\n \"doc_id\": \"23240691\",\n \"title\": \"FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.\",\n \"abstract\": \"Virtual ligand screening is an integral part of the modern drug discovery process. Traditional ligand-based, virtual screening approaches are fast but require a set of structurally diverse ligands known to bind to the target. Traditional structure-based approaches require high-resolution target protein structures and are computationally demanding. In contrast, the recently developed threading/structure-based FINDSITE-based approaches have the advantage that they are as fast as traditional ligand-based approaches and yet overcome the limitations of traditional ligand- or structure-based approaches. These new methods can use predicted low-resolution structures and infer the likelihood of a ligand binding to a target by utilizing ligand information excised from the target's remote or close homologous proteins and/or libraries of ligand binding databases. Here, we develop an improved version of FINDSITE, FINDSITE(filt), that filters out false positive ligands in threading identified templates by a better binding site detection procedure that includes information about the binding site amino acid similarity. We then combine FINDSITE(filt) with FINDSITE(X) that uses publicly available binding databases ChEMBL and DrugBank for virtual ligand screening. The combined approach, FINDSITE(comb), is compared to two traditional docking methods, AUTODOCK Vina and DOCK 6, on the DUD benchmark set. It is shown to be significantly better in terms of enrichment factor, dependence on target structure quality, and speed. FINDSITE(comb) is then tested for virtual ligand screening on a large set of 3576 generic targets from the DrugBank database as well as a set of 168 Human GPCRs. Excluding close homologues, FINDSITE(comb) gives an average enrichment factor of 52.1 for generic targets and 22.3 for GPCRs within the top 1% of the screened compound library. Around 65% of the targets have better than random enrichment factors. The performance is insensitive to target structure quality, as long as it has a TM-score ≥ 0.4 to native. Thus, FINDSITE(comb) makes the screening of millions of compounds across entire proteomes feasible. The FINDSITE(comb) web service is freely available for academic users at http://cssb.biology.gatech.edu/skolnick/webservice/FINDSITE-COMB/index.html.\",\n \"corpus_id\": 17644770,\n \"score\": 2\n },\n {\n \"doc_id\": \"23396123\",\n \"title\": \"MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.\",\n \"abstract\": \"SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 6954469,\n \"score\": 2\n },\n {\n \"doc_id\": \"23415854\",\n \"title\": \"Are predicted protein structures of any value for binding site prediction and virtual ligand screening?\",\n \"abstract\": \"The recently developed field of ligand homology modeling (LHM) that extends the ideas of protein homology modeling to the prediction of ligand binding sites and for use in virtual ligand screening has emerged as a powerful new approach. Unlike traditional docking methodologies, LHM can be applied to low-to-moderate resolution predicted as well as experimental structures with little if any diminution in performance; thereby enabling ≈ 75% of an average proteome to have potentially significant virtual screening predictions. In large scale benchmarking, LHM is able to predict off-target ligand binding. Thus, despite the widespread belief to the contrary, low-to-moderate resolution predicted structures have considerable utility for biochemical function prediction.\",\n \"corpus_id\": 7385589,\n \"score\": 2\n },\n {\n \"doc_id\": \"24328054\",\n \"title\": \"SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.\",\n \"abstract\": \"We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.\",\n \"corpus_id\": 1270662,\n \"score\": 2\n },\n {\n \"doc_id\": \"24341870\",\n \"title\": \"Improving structural similarity based virtual screening using background knowledge.\",\n \"abstract\": \"BACKGROUND: Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structural similarity measures. However, their general nature can lead to insufficient performance in some application cases. In this paper, we provide a link between ranking-based virtual screening and fragment-based data mining methods. The inclusion of binding-relevant background knowledge into a structural similarity measure improves the quality of the similarity rankings. This background knowledge in the form of binding relevant substructures can either be derived by hand selection or by automated fragment-based data mining methods. RESULTS: In virtual screening experiments we show that our approach clearly improves enrichment factors with both applied variants of our approach: the extension of the structural similarity measure with background knowledge in the form of a hand-selected relevant substructure or the extension of the similarity measure with background knowledge derived with data mining methods. CONCLUSION: Our study shows that adding binding relevant background knowledge can lead to significantly improved similarity rankings in virtual screening and that even basic data mining approaches can lead to competitive results making hand-selection of the background knowledge less crucial. This is especially important in drug discovery and development projects where no receptor structure is available or more frequently no verified binding mode is known and mostly ligand based approaches can be applied to generate hit compounds.\",\n \"corpus_id\": 935114,\n \"score\": 2\n },\n {\n \"doc_id\": \"24877883\",\n \"title\": \"Best of both worlds: on the complementarity of ligand-based and structure-based virtual screening.\",\n \"abstract\": \"Virtual screening with docking is an integral component of drug design, particularly during hit finding phases. While successful prospective studies of virtual screening exist, it remains a significant challenge to identify best practices a priori due to the many factors that influence the final outcome, including targets, data sets, software, metrics, and expert knowledge of the users. This study investigates the extent to which ligand-based methods can be applied to improve structure-based methods. The use of ligand-based methods to modulate the number of hits identified using the protein-ligand complex and also the diversity of these hits from the crystallographic ligand is discussed. In this study, 40 CDK2 ligand complexes were used together with two external data sets containing both actives and inactives from GlaxoSmithKline (GSK) and actives and decoys from the Directory of Useful Decoys (DUD). Results show how ligand-based modeling can be used to select a more appropriate protein conformation for docking, as well as to assess the reliability of the docking experiment. The time gained by reducing the pool of virtual screening candidates via ligand-based similarity can be invested in more accurate docking procedures, as well as in downstream labor-intensive approaches (e.g., visual inspection) maximizing the use of the chemical and biological information available. This provides a framework for molecular modeling scientists that are involved in initiating virtual screening campaigns with practical advice to make best use of the information available to them.\",\n \"corpus_id\": 5998530,\n \"score\": 2\n },\n {\n \"doc_id\": \"25336501\",\n \"title\": \"LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.\",\n \"abstract\": \"MOTIVATION: Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. RESULTS: We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. AVAILABILITY AND IMPLEMENTATION: LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: skolnick@gatech.edu.\",\n \"corpus_id\": 12839538,\n \"score\": 2\n },\n {\n \"doc_id\": \"25350693\",\n \"title\": \"Extended template-based modeling and evaluation method using consensus of binding mode of GPCRs for virtual screening.\",\n \"abstract\": \"G-protein-coupled receptors (GPCRs) are a pharmaceutically important protein family because they mediate numerous physiological functions. The crystal structures of several GPCR subtypes have been determined recently, encouraging efforts to apply structure-based virtual screening (SBVS) along with ligand-based virtual screening (LBVS) to improve the hit rate of active ligands from large chemical libraries. Three-dimensional models are also necessary for GPCR targets whose structures are unknown. Current challenges include the selection of structural templates from available structurally known GPCRs to use for accurate modeling and understanding the diversity of sites recognizing distinct ligands. We have developed and validated an extended template-based modeling and evaluation method for SBVS. Models were generated using a fragmental template procedure in addition to typical template-based modeling methods. The reliability of the models was evaluated using a virtual screening test with known active ligands and decoys and the consensus of the binding mode using the protein-ligand interaction fingerprint (PLIF) derived from the results of docking simulations. This novel workflow was applied to three targets with known structures (human dopamine receptor 3, human histamine H1 receptor, and human delta opioid receptor) and to a target with an unknown structure (human serotonin 2A receptor). In each case, model structures having high ligand selectivity with consensus binding mode were generated.\",\n \"corpus_id\": 12747975,\n \"score\": 2\n },\n {\n \"doc_id\": \"25359888\",\n \"title\": \"Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.\",\n \"abstract\": \"MOTIVATION: Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects. RESULTS: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods. AVAILABILITY AND IMPLEMENTATION: http://kiharalab.org/patchsurfer2.0/ CONTACT: dkihara@purdue.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 2581408,\n \"score\": 2\n },\n {\n \"doc_id\": \"25709030\",\n \"title\": \"Generating \\\"fragment-based virtual library\\\" using pocket similarity search of ligand-receptor complexes.\",\n \"abstract\": \"As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.\",\n \"corpus_id\": 36180208,\n \"score\": 2\n },\n {\n \"doc_id\": \"26225536\",\n \"title\": \"PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.\",\n \"abstract\": \"Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand-binding pockets in proteins is small. PoLi identifies similar ligand-binding pockets in a holo template protein library, selectively copies relevant parts of template ligands, and uses them for VS. In practice, PoLi is a hybrid structure and ligand-based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6, respectively, in the top 1% of the screened library. In contrast, traditional docking-based VS using AutoDock Vina and homology-based VS using FINDSITE(filt) have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets, respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods.\",\n \"corpus_id\": 1362559,\n \"score\": 2\n },\n {\n \"doc_id\": \"26330079\",\n \"title\": \"Performance evaluation of structure based and ligand based virtual screening methods on ten selected anti-cancer targets.\",\n \"abstract\": \"Virtual screening has become an important tool in drug discovery process. Structure based and ligand based approaches are generally used in virtual screening process. To date, several benchmark sets for evaluating the performance of the virtual screening tool are available. In this study, our aim is to compare the performance of both structure based and ligand based virtual screening methods. Ten anti-cancer targets and their corresponding benchmark sets from 'Demanding Evaluation Kits for Objective In silico Screening' (DEKOIS) library were selected. X-ray crystal structures of protein-ligand complexes were selected based on their resolution. Openeye tools such as FRED, vROCS were used and the results were carefully analyzed. At EF1%, vROCS produced better results but at EF5% and EF10%, both FRED and ROCS produced almost similar results. It was noticed that the enrichment factor values were decreased while going from EF1% to EF5% and EF10% in many cases.\",\n \"corpus_id\": 8368775,\n \"score\": 2\n },\n {\n \"doc_id\": \"27074979\",\n \"title\": \"SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.\",\n \"abstract\": \"Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this \\\"ab initio\\\" approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. © 2016 Wiley Periodicals, Inc.\",\n \"corpus_id\": 20462287,\n \"score\": 2\n },\n {\n \"doc_id\": \"27500657\",\n \"title\": \"PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.\",\n \"abstract\": \"Virtual screening has become an indispensable procedure in drug discovery. Virtual screening methods can be classified into two categories: ligand-based and structure-based. While the former have advantages, including being quick to compute, in general they are relatively weak at discovering novel active compounds because they use known actives as references. On the other hand, structure-based methods have higher potential to find novel compounds because they directly predict the binding affinity of a ligand in a target binding pocket, albeit with substantially lower speed than ligand-based methods. Here we report a novel structure-based virtual screening method, PL-PatchSurfer2. In PL-PatchSurfer2, protein and ligand surfaces are represented by a set of overlapping local patches, each of which is represented by three-dimensional Zernike descriptors (3DZDs). By means of 3DZDs, the shapes and physicochemical complementarities of local surface regions of a pocket surface and a ligand molecule can be concisely and effectively computed. Compared with the previous version of the program, the performance of PL-PatchSurfer2 is substantially improved by the addition of two more features, atom-based hydrophobicity and hydrogen-bond acceptors and donors. Benchmark studies showed that PL-PatchSurfer2 performed better than or comparable to popular existing methods. Particularly, PL-PatchSurfer2 significantly outperformed existing methods when apo-form or template-based protein models were used for queries. The computational time of PL-PatchSurfer2 is about 20 times shorter than those of conventional structure-based methods. The PL-PatchSurfer2 program is available at http://www.kiharalab.org/plps2/ .\",\n \"corpus_id\": 2395995,\n \"score\": 2\n },\n {\n \"doc_id\": \"27565795\",\n \"title\": \"mRAISE: an alternative algorithmic approach to ligand-based virtual screening.\",\n \"abstract\": \"Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at http://www.zbh.uni-hamburg.de/mraise-dataset.html . The table of all PDB codes contained in the ensembles can be found in the supplementary material. The software tool mRAISE is freely available for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).\",\n \"corpus_id\": 29225191,\n \"score\": 2\n },\n {\n \"doc_id\": \"28315995\",\n \"title\": \"Ligand-based virtual screening under partial shape constraints.\",\n \"abstract\": \"Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).\",\n \"corpus_id\": 24800457,\n \"score\": 2\n },\n {\n \"doc_id\": \"29036579\",\n \"title\": \"HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques.\",\n \"abstract\": \"Summary: Molecular-similarity searches based on two-dimensional (2D) fingerprint and three-dimensional (3D) shape represent two widely used ligand-based virtual screening (VS) methods in computer-aided drug design. 2D fingerprint-based VS utilizes the binary fragment information on a known ligand, whereas 3D shape-based VS takes advantage of geometric information for predefined features from a 3D conformation. Given their different advantages, it would be desirable to hybridize 2D fingerprint and 3D shape molecular-similarity approaches in drug discovery. Here, we presented a general hybrid molecular-similarity protocol, referred to as HybridSim, obtained by combining the 2D fingerprint- and 3D shape-based similarity search methods and evaluated its performance on 595,036 actives and decoys for 40 pharmaceutically relevant targets available in the Directory of Useful Decoys Enhanced (DUD-E). Our results showed that HybridSim significantly improved the overall performance in 40 VS projects as compared with using only 2D fingerprint and 3D shape methods. Furthermore, HybridSim-VS, the first online platform using the proposed HybridSim method coupled with 17,839,945 screenable and purchasable compounds, was developed to provide large-scale and proficient VS capabilities to experts and nonexperts in the field. Availability and implementation: HybridSim-VS web server is freely available at http://www.rcidm.org/HybridSim-VS/. Contact: lingwang@scut.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 2855344,\n \"score\": 2\n },\n {\n \"doc_id\": \"29462237\",\n \"title\": \"LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.\",\n \"abstract\": \"Motivation: Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. Results: We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1 415 871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. Availability and implementation: http://zhanglab.ccmb.med.umich.edu/LS-align/. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3445717,\n \"score\": 2\n },\n {\n \"doc_id\": \"18442221\",\n \"title\": \"Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring.\",\n \"abstract\": \"The current study investigates the combination of two recently reported techniques for the improvement of homology model-based virtual screening for G-protein coupled receptor (GPCR) ligands. First, ligand-supported homology modeling was used to generate receptor models that were in agreement with mutagenesis data and structure-activity relationship information of the ligands. Second, interaction patterns from known ligands to the receptor were applied for scoring and rank ordering compounds from a virtual library using ligand-receptor interaction fingerprint-based similarity (IFS). Our approach was evaluated in retrospective virtual screening experiments for antagonists of the metabotropic glutamate receptor (mGluR) subtype 5. The results of our approach were compared to the results obtained by conventional scoring functions (Dock-Score, PMF-Score, Gold-Score, ChemScore, and FlexX-Score). The IFS lead to significantly higher enrichment rates, relative to the competing scoring functions. Though using a target-biased scoring approach, the results were not biased toward the chemical classes of the reference structures. Our results indicate that the presented approach has the potential to serve as a general setup for successful structure-based GPCR virtual screening.\",\n \"corpus_id\": 27403518,\n \"score\": 1\n },\n {\n \"doc_id\": \"19642282\",\n \"title\": \"Improving homology models for protein-ligand binding sites.\",\n \"abstract\": \"In order to improve the prediction of protein-ligand binding sites through homology modeling, we incorporate knowledge of the binding residues into the modeling framework. Residues are identified as binding or nonbinding based on their true labels as well as labels predicted from structure and sequence. The sequence predictions were made using a support vector machine framework which employs a sophisticated window-based kernel. Binding labels are used with a very sensitive sequence alignment method to align the target and template. Relevant parameters governing the alignment process are searched for optimal values. Based on our results, homology models of the binding site can be improved if a priori knowledge of the binding residues is available. For target-template pairs with low sequence identity and high structural diversity our sequence-based prediction method provided sufficient information to realize this improvement.\",\n \"corpus_id\": 14118805,\n \"score\": 1\n },\n {\n \"doc_id\": \"20025561\",\n \"title\": \"Protein structure prediction in structure-based ligand design and virtual screening.\",\n \"abstract\": \"Advances in protein modeling algorithms and state-of-the-art sequence similarity comparison and fold recognition methods, in combination with growing protein structure information, are facilitating \\\"genome-to-drug lead\\\" approaches in which chemicals are virtually screened against computationally-predicted protein targets. Although the quality of predicted protein structures by homology modeling methods, and thus their applicability to drug discovery initiatives, predominantly depends on the sequence similarity between the protein of known structure and the protein target to be modeled, recent research underscores that this approach can be used to significant advantage in the identification and optimization of lead compounds, as well as for the identification and validation of drug targets. Rational structure-based drug design cycles begin with an iterative procedure that is dependent on the initial determination of the structure of the target protein, followed by the prediction of ligands for the target protein from molecular modeling computation. The structure determination of all proteins encoded by vast genome sequencing efforts appears to be an unrealistic goal with current technologies. Therefore, other approaches based on the development of technology useful for accurately predicting and modeling the structures of proteins have become exceedingly important in certain structure-based drug design efforts. This review provides an overview of the recent method advancements in protein structure prediction by homology modeling and includes an assessment of the application of homology modeling to pharmaceutically relevant questions. In addition, examples of successful applications of homology modeling approaches to genome-to-drug lead investigations are described.\",\n \"corpus_id\": 40532349,\n \"score\": 1\n },\n {\n \"doc_id\": \"20434455\",\n \"title\": \"Homology-modelling protein-ligand interactions: allowing for ligand-induced conformational change.\",\n \"abstract\": \"Current homology-modelling methods do not consider small molecules in their automated processes. Therefore, the development of a reliable tool for protein-ligand homology modelling is an important next step in generating plausible models for molecular interactions. Two automated protein-ligand homology-modelling strategies, requiring no expert knowledge from the user, are investigated here. Both employ the \\\"induced fit\\\" concept with flexibility in side chains and ligand. The most successful strategy superimposes the new ligand over the original ligand before homology modelling, allowing the new ligand to be taken into consideration during protein modelling (rather than after), facilitating conformational change in the local backbone if necessary. We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult target complexes are also successfully modelled, reproducing native protein-ligand contacts with significantly different biological substrates and different binding-site conformations. These include the modelling of Cdk5 (cyclin-dependent kinase 5) from Cdk2, thymidine phosphorylase from a bacterial homologue, and dihydrofolate reductase from a recombinant variant with a markedly different inhibitor. In terms of average modelling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 A (and 2.0 A for the protein binding site) for \\\"easy\\\" cases and 2.9 A for the ligand (and 2.7 A for the protein binding site) in \\\"hard\\\" cases. This demonstrates the importance of selecting an optimal template. Ligand-modelling accuracy is strongly dependent on target-template ligand structural similarity, rather than target-template sequence identity. However, protein-modelling accuracy is dependent on both. Our automated protein-ligand homology-modelling strategy generates a higher degree of accuracy than homology modelling followed by docking, generating an average ligand RMSD that is 1-2 A better than docking with homology models.\",\n \"corpus_id\": 40968760,\n \"score\": 1\n },\n {\n \"doc_id\": \"22183538\",\n \"title\": \"How to benchmark methods for structure-based virtual screening of large compound libraries.\",\n \"abstract\": \"Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.\",\n \"corpus_id\": 206678021,\n \"score\": 1\n },\n {\n \"doc_id\": \"22569590\",\n \"title\": \"Surflex-Dock: Docking benchmarks and real-world application.\",\n \"abstract\": \"Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.\",\n \"corpus_id\": 27281484,\n \"score\": 1\n },\n {\n \"doc_id\": \"23398329\",\n \"title\": \"Ligand-optimized homology models of D₁ and D₂ dopamine receptors: application for virtual screening.\",\n \"abstract\": \"Recent breakthroughs in crystallographic studies of G protein-coupled receptors (GPCRs), together with continuous progress in molecular modeling methods, have opened new perspectives for structure-based drug discovery. A crucial enhancement in this area was development of induced fit docking procedures that allow optimization of binding pocket conformation guided by the features of its active ligands. In the course of our research program aimed at discovery of novel antipsychotic agents, our attention focused on dopaminergic D2 and D1 receptors (D2R and D1R). Thus, we decided to investigate whether the availability of a novel structure of the closely related D3 receptor and application of induced fit docking procedures for binding pocket refinement would permit the building of models of D2R and D1R that facilitate a successful virtual screening (VS). Here, we provide an in-depth description of the modeling procedure and the discussion of the results of a VS benchmark we performed to compare efficiency of the ligand-optimized receptors in comparison with the regular homology models. We observed that application of the ligand-optimized models significantly improved the VS performance both in terms of BEDROC (0.325 vs 0.182 for D1R and 0.383 vs 0.301 for D2R) as well as EF1% (20 vs 11 for D1R and 18 vs 10 for D2R). In contrast, no improvement was observed for the performance of a D2R model built on the D3R template, when compared with that derived from the structure of the previously published and more evolutionary distant β2 adrenergic receptor. The comparison of results for receptors built according to various protocols and templates revealed that the most significant factor for the receptor performance was a proper selection of \\\"tool ligand\\\" used in induced fit docking procedure. Taken together, our results suggest that the described homology modeling procedure could be a viable tool for structure-based GPCR ligand design, even for the targets for which only a relatively distant structural template is available.\",\n \"corpus_id\": 33336236,\n \"score\": 1\n },\n {\n \"doc_id\": \"23541165\",\n \"title\": \"Structure-based virtual screening of MT2 melatonin receptor: influence of template choice and structural refinement.\",\n \"abstract\": \"Developing GPCR homology models for structure-based virtual screening requires the choice of a suitable template and refinement of binding site residues. We explored this systematically for the MT2 melatonin receptor, with the aim to build a receptor homology model that is optimized for the enrichment of active melatoninergic ligands. A set of 12 MT2 melatonin receptor models was built using different GPCR X-ray structural templates and submitted to a virtual screening campaign on a set of compounds composed of 29 known melatonin receptor ligands and 2560 drug-like decoys. To evaluate the effect of including a priori information in receptor models, 12 representative melatonin receptor ligands were placed into the MT2 receptor models in poses consistent with known mutagenesis data and with assessed pharmacophore models. The receptor structures were then adapted to the ligands by induced-fit docking. Most of the 144 ligand-adapted MT2 receptor models showed significant improvements in screening enrichments compared to the unrefined homology models, with some template/refinement combinations giving excellent enrichment factors. The discriminating ability of the models was further tested on the 29 active ligands plus a set of 21 inactive or low-affinity compounds from the same chemical classes. Rotameric states of side chains for some residues, presumed to be involved in the binding process, were correlated with screening effectiveness, suggesting the existence of specific receptor conformations able to recognize active compounds. The top MT2 receptor model was able to identify 24 of 29 active ligands among the first 2% of the screened database. This work provides insights into the use of refined GPCR homology models for virtual screening.\",\n \"corpus_id\": 22493493,\n \"score\": 1\n },\n {\n \"doc_id\": \"24318891\",\n \"title\": \"Structure-based virtual screening for the identification of RNA-binding ligands.\",\n \"abstract\": \"Structure-based virtual screening exploits the 3D structure of the target as a template for the discovery of new ligands. It is a key method for hit discovery and was originally developed for protein targets. Recently, this method has also been applied to RNA targets. This chapter gives an overview of this method and its application in the context of ligand discovery for RNA. In addition, it describes in detail how to conduct virtual screening for RNA targets, making use of software that is free for noncommercial use. Some advice on how to avoid common pitfalls in virtual screening is also given.\",\n \"corpus_id\": 37480232,\n \"score\": 1\n },\n {\n \"doc_id\": \"24573478\",\n \"title\": \"SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.\",\n \"abstract\": \"RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.\",\n \"corpus_id\": 25754262,\n \"score\": 1\n },\n {\n \"doc_id\": \"24813470\",\n \"title\": \"Impact of template choice on homology model efficiency in virtual screening.\",\n \"abstract\": \"Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, only the closest ones are chosen for homology modeling purposes. To validate the aforementioned approach, we performed homology modeling of four serotonin receptors (5-HT1AR, 5-HT2AR, 5-HT6R, 5-HT7R) for virtual screening purposes, using 10 available G-Protein Coupled Receptors (GPCR) templates with diverse evolutionary distances to the targets, with various approaches to alignment construction and model building. The resulting models were further validated in two steps by means of ligand docking and enrichment calculation, using Glide software. The final quality of the models was determined in virtual screening-like experiments by the AUROC score of the resulting ROC curves. The outcome of this research showed that no correlation between sequence identity and model quality was found, leading to the conclusion that the closest phylogenetic relative is not always the best template for homology modeling.\",\n \"corpus_id\": 22066070,\n \"score\": 1\n },\n {\n \"doc_id\": \"24900272\",\n \"title\": \"Homology Model and Docking-Based Virtual Screening for Ligands of the σ1 Receptor.\",\n \"abstract\": \"This study presents for the first time the 3D model of the σ1 receptor protein as obtained from homology modeling techniques, shows the applicability of this structure to docking-based virtual screening, defines a computational strategy to optimize the results based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring, and provides evidence that these in silico models and recipes are powerful tools on which virtual screening of new σ1 ligands can be based. In particular, the validation of the applicability of docking-based virtual screening to homology models is of utmost importance, since no crystal structure is available to date for the σ1 receptor, and this missing information still constitutes a major hurdle for a rational ligand design for this important protein target.\",\n \"corpus_id\": 22380771,\n \"score\": 1\n },\n {\n \"doc_id\": \"25116840\",\n \"title\": \"Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study.\",\n \"abstract\": \"Accurate and affordable assessment of ligand-protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure-activity information may prove useful. Here, we introduce one such filter based upon three-dimensional structural protein-ligand interaction fingerprints (SPLIF). SPLIF permits quantitative assessment of whether a docking pose interacts with the protein target similarly to a known ligand and rescues active compounds penalized by poor initial docking scores. An extensive benchmark study on 10 diverse data sets selected from the DUD-E database has been performed in order to evaluate the absolute and relative efficiency of this method. SPLIF demonstrated an overall better performance than relevant standard methods.\",\n \"corpus_id\": 17006573,\n \"score\": 1\n },\n {\n \"doc_id\": \"25220914\",\n \"title\": \"Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.\",\n \"abstract\": \"Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.\",\n \"corpus_id\": 15918793,\n \"score\": 1\n },\n {\n \"doc_id\": \"25232727\",\n \"title\": \"eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.\",\n \"abstract\": \"Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.\",\n \"corpus_id\": 6379524,\n \"score\": 1\n },\n {\n \"doc_id\": \"26454279\",\n \"title\": \"Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.\",\n \"abstract\": \"MOTIVATION: The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. RESULTS: The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. AVAILABILITY AND IMPLEMENTATION: SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org CONTACT: : yaoqi.zhou@griffith.edu.au.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26803160\",\n \"title\": \"Alloscore: a method for predicting allosteric ligand-protein interactions.\",\n \"abstract\": \"UNLABELLED: Allosteric ligands have increasingly gained attention as potential therapeutic agents due to their higher target selectivity and lower toxicity compared with classic orthosteric ligands. Despite the great interest in the development of allosteric drugs as a new tactic in drug discovery, the understanding of the ligand-protein interactions underlying allosteric binding represents a key challenge. Herein, we introduce Alloscore, a web server that predicts the binding affinities of allosteric ligand-protein interactions. This method exhibits prominent performance in describing allosteric binding and could be useful in allosteric virtual screening and the structural optimization of allosteric agonists/antagonists. AVAILABILITY AND IMPLEMENTATION: The Alloscore server and tutorials are freely available at http://mdl.shsmu.edu.cn/alloscore CONTACT: jian.zhang@sjtu.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 27137471,\n \"score\": 1\n },\n {\n \"doc_id\": \"28011765\",\n \"title\": \"RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening.\",\n \"abstract\": \"Summary: Evaluation of the capacity for separating actives from challenging decoys is a crucial metric of performance related to molecular docking or a virtual screening workflow. The Directory of Useful Decoys (DUD) and its enhanced version (DUD-E) provide a benchmark for molecular docking, although they only contain a limited set of decoys for limited targets. DecoyFinder was released to compensate the limitations of DUD or DUD-E for building target-specific decoy sets. However, desirable query template design, generation of multiple decoy sets of similar quality, and computational speed remain bottlenecks, particularly when the numbers of queried actives and retrieved decoys increases to hundreds or more. Here, we developed a program suite called RApid DEcoy Retriever (RADER) to facilitate the decoy-based assessment of virtual screening. This program adopts a novel database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. RADER provides two operational modes: as a command-line tool and on a web server. Validation of the performance and efficiency of RADER was also conducted and is described. Availability and Implementation: RADER web server and a local version are freely available at http://rcidm.org/rader/ . Contact: lingwang@scut.edu.cn or went@scut.edu.cn . Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3770961,\n \"score\": 1\n },\n {\n \"doc_id\": \"28150235\",\n \"title\": \"Structure-Based Virtual Screening.\",\n \"abstract\": \"Structure-based virtual screening (SBVS) is a computational approach used in the early-stage drug discovery campaign to search a chemical compound library for novel bioactive molecules against a certain drug target. It utilizes the three-dimensional (3D) structure of the biological target, obtained from X-ray, NMR, or computational modeling, to dock a collection of chemical compounds into the binding site and select a subset of these compounds based on the predicted binding scores for further biological evaluation. In the present work, we illustrate the basic process of conducting a SBVS with examples using freely accessible tools and resources.\",\n \"corpus_id\": 3555685,\n \"score\": 1\n },\n {\n \"doc_id\": \"19627087\",\n \"title\": \"Modern homology modeling of G-protein coupled receptors: which structural template to use?\",\n \"abstract\": \"The recent availability in the literature of new crystal structures of inactive G-protein coupled receptors (GPCRs) prompted us to study the extent to which these crystal structures constitute an advantage over the former prototypic rhodopsin template for homology modeling of the transmembrane (TM) region of human class A GPCRs. Our results suggest that better templates than those currently available are required by the majority of these GPCRs to generate homology models that are accurate enough for simple virtual screening aimed at computer-aided drug discovery. Thus, we investigated: (1) which class A GPCRs would have the highest impact as potential templates for homology modeling of other GPCRs, if their structures were solved, and (2) the extent to which multiple-template homology modeling (using all currently available GPCR crystal structures) provides an improvement over single-template homology modeling, as evaluated by the accuracy of rigid protein-flexible ligand docking on these models.\",\n \"corpus_id\": 39145087,\n \"score\": 0\n },\n {\n \"doc_id\": \"21873637\",\n \"title\": \"Spatial clustering of protein binding sites for template based protein docking.\",\n \"abstract\": \"MOTIVATION: In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes. RESULTS: This article presents KBDOCK, a 3D database approach for spatially clustering protein binding sites and for performing template-based (knowledge-based) protein docking. KBDOCK combines residue contact information from the 3DID database with the Pfam protein domain family classification together with coordinate data from the Protein Data Bank. This allows the 3D configurations of all known hetero domain-domain interactions to be superposed and clustered for each Pfam family. We find that most Pfam domain families have up to four hetero binding sites, and over 60% of all domain families have just one hetero binding site. The utility of this approach for template-based docking is demonstrated using 73 complexes from the Protein Docking Benchmark. Overall, up to 45 out of 73 complexes may be modelled by direct homology to existing domain interfaces, and key binding site information is found for 24 of the 28 remaining complexes. These results show that KBDOCK can often provide useful information for predicting the structures of unknown protein complexes. AVAILABILITY: http://kbdock.loria.fr/ CONTACT: Dave. Ritchie@inria.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 10132360,\n \"score\": 0\n },\n {\n \"doc_id\": \"23413437\",\n \"title\": \"GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity.\",\n \"abstract\": \"SUMMARY: A large number of proteins function as homo-oligomers; therefore, predicting homo-oligomeric structure of proteins is of primary importance for understanding protein function at the molecular level. Here, we introduce a web server for prediction of protein homo-oligomer structure. The server takes a protein monomer structure as input and predicts its homo-oligomer structure from oligomer templates selected based on sequence and tertiary/quaternary structure similarity. Using protein model structures as input, the server shows clear improvement over the best methods of CASP9 in predicting oligomeric structures from amino acid sequences. AVAILABILITY: http://galaxy.seoklab.org/gemini. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 15094536,\n \"score\": 0\n },\n {\n \"doc_id\": \"24328076\",\n \"title\": \"Homology modeling of human muscarinic acetylcholine receptors.\",\n \"abstract\": \"We have developed homology models of the acetylcholine muscarinic receptors M₁R-M₅R, based on the β₂-adrenergic receptor crystal as the template. This is the first report of homology modeling of all five subtypes of acetylcholine muscarinic receptors with binding sites optimized for ligand binding. The models were evaluated for their ability to discriminate between muscarinic antagonists and decoy compounds using virtual screening using enrichment factors, area under the ROC curve (AUC), and an early enrichment measure, LogAUC. The models produce rational binding modes of docked ligands as well as good enrichment capacity when tested against property-matched decoy libraries, which demonstrates their unbiased predictive ability. To test the relative effects of homology model template selection and the binding site optimization procedure, we generated and evaluated a naïve M₂R model, using the M₃R crystal structure as a template. Our results confirm previous findings that binding site optimization using ligand(s) active at a particular receptor, i.e. including functional knowledge into the model building process, has a more pronounced effect on model quality than target-template sequence similarity. The optimized M₁R-M₅R homology models are made available as part of the Supporting Information to allow researchers to use these structures, compare them to their own results, and thus advance the development of better modeling approaches.\",\n \"corpus_id\": 30897753,\n \"score\": 0\n },\n {\n \"doc_id\": \"25492406\",\n \"title\": \"Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements.\",\n \"abstract\": \"MOTIVATION: Cysteine residues have particular structural and functional relevance in proteins because of their ability to form covalent disulfide bonds. Bioinformatics tools that can accurately predict cysteine bonding states are already available, whereas it remains challenging to infer the disulfide connectivity pattern of unknown protein sequences. Improving accuracy in this area is highly relevant for the structural and functional annotation of proteins. RESULTS: We predict the intra-chain disulfide bond connectivity patterns starting from known cysteine bonding states with an evolutionary-based unsupervised approach called Sephiroth that relies on high-quality alignments obtained with HHblits and is based on a coarse-grained cluster-based modelization of tandem cysteine mutations within a protein family. We compared our method with state-of-the-art unsupervised predictors and achieve a performance improvement of 25-27% while requiring an order of magnitude less of aligned homologous sequences (∼10(3) instead of ∼10(4)). AVAILABILITY AND IMPLEMENTATION: The software described in this article and the datasets used are available at http://ibsquare.be/sephiroth. CONTACT: wvranken@vub.ac.be SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.\",\n \"corpus_id\": 43913726,\n \"score\": 0\n },\n {\n \"doc_id\": \"25701568\",\n \"title\": \"AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.\",\n \"abstract\": \"MOTIVATION: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. RESULTS: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with 'inserted' domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. AVAILABILITY AND IMPLEMENTATION: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. CONTACT: adam@sanfordburnham.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 1552318,\n \"score\": 0\n },\n {\n \"doc_id\": \"26254434\",\n \"title\": \"Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.\",\n \"abstract\": \"MOTIVATION: Template-based modeling, the most successful approach for predicting protein 3D structure, often requires detecting distant evolutionary relationships between the target sequence and proteins of known structure. Developed for this purpose, fold recognition methods use elaborate strategies to exploit evolutionary information, mainly by encoding amino acid sequence into profiles. Since protein structure is more conserved than sequence, the inclusion of structural information can improve the detection of remote homology. RESULTS: Here, we present ORION, a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure. Our method uses the 16-state structural alphabet Protein Blocks, which provides an accurate 1D description of protein structure local conformations. ORION systematically outperforms PSI-BLAST and HHsearch on several benchmarks, including target sequences from the modeling competitions CASP8, 9 and 10, and detects ∼10% more templates at fold and superfamily SCOP levels. AVAILABILITY: Software freely available for download at http://www.dsimb.inserm.fr/orion/. CONTACT: jean-christophe.gelly@univ-paris-diderot.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 11919129,\n \"score\": 0\n },\n {\n \"doc_id\": \"26454278\",\n \"title\": \"FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.\",\n \"abstract\": \"The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors. AVAILABILITY AND IMPLEMENTATION: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/. CONTACT: shuaicli@cityu.edu.hk, dbu@ict.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 12915055,\n \"score\": 0\n },\n {\n \"doc_id\": \"26545824\",\n \"title\": \"Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.\",\n \"abstract\": \"MOTIVATION: Predictive tools that model protein-ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein-ligand binding predictive tools would be useful. RESULTS: We developed a system for automatically generating protein-ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5-1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands. AVAILABILITY AND IMPLEMENTATION: The source code and web application are freely available for download at http://utprot.net. They are implemented in Python and supported on Linux. CONTACT: shimizu@bi.a.u-tokyo.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 16676373,\n \"score\": 0\n },\n {\n \"doc_id\": \"26568622\",\n \"title\": \"Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.\",\n \"abstract\": \"MOTIVATION: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. RESULTS: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 22034498,\n \"score\": 0\n },\n {\n \"doc_id\": \"26704597\",\n \"title\": \"Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.\",\n \"abstract\": \"MOTIVATION: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus the need for tools which in particular can make local structural alignments of RNAs is only increasing. RESULTS: To meet the demand for both large scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2,000-6,000 nucleotides improve execution up to a factor of five. AVAILABILITY AND IMPLEMENTATION: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign CONTACT: gorodkin@rth.dk SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.\",\n \"corpus_id\": 18683999,\n \"score\": 0\n },\n {\n \"doc_id\": \"27354702\",\n \"title\": \"AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms.\",\n \"abstract\": \"MOTIVATION: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. RESULTS: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. AVAILABILITY AND IMPLEMENTATION: http://adfr.scripps.edu/AutoDockFR/autosite.html CONTACT: sanner@scripps.eduSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 206344707,\n \"score\": 0\n },\n {\n \"doc_id\": \"27378301\",\n \"title\": \"Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals.\",\n \"abstract\": \"MOTIVATION: More than half of proteins require binding of metal and acid radical ions for their structure and function. Identification of the ion-binding locations is important for understanding the biological functions of proteins. Due to the small size and high versatility of the metal and acid radical ions, however, computational prediction of their binding sites remains difficult. RESULTS: We proposed a new ligand-specific approach devoted to the binding site prediction of 13 metal ions (Zn(2+), Cu(2+), Fe(2+), Fe(3+), Ca(2+), Mg(2+), Mn(2+), Na(+), K(+)) and acid radical ion ligands (CO3(2-), NO2(-), SO4(2-), PO4(3-)) that are most frequently seen in protein databases. A sequence-based ab initio model is first trained on sequence profiles, where a modified AdaBoost algorithm is extended to balance binding and non-binding residue samples. A composite method IonCom is then developed to combine the ab initio model with multiple threading alignments for further improving the robustness of the binding site predictions. The pipeline was tested using 5-fold cross validations on a comprehensive set of 2,100 non-redundant proteins bound with 3,075 small ion ligands. Significant advantage was demonstrated compared with the state of the art ligand-binding methods including COACH and TargetS for high-accuracy ion-binding site identification. Detailed data analyses show that the major advantage of IonCom lies at the integration of complementary ab initio and template-based components. Ion-specific feature design and binding library selection also contribute to the improvement of small ion ligand binding predictions. AVAILABILITY AND IMPLEMENTATION: http://zhanglab.ccmb.med.umich.edu/IonCom CONTACT: hxz@imut.edu.cn or zhng@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 1105667,\n \"score\": 0\n },\n {\n \"doc_id\": \"27551104\",\n \"title\": \"Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks.\",\n \"abstract\": \"MOTIVATION: Backbone structures and solvent accessible surface area of proteins are benefited from continuous real value prediction because it removes the arbitrariness of defining boundary between different secondary-structure and solvent-accessibility states. However, lacking the confidence score for predicted values has limited their applications. Here we investigated whether or not we can make a reasonable prediction of absolute errors for predicted backbone torsion angles, Cα-atom-based angles and torsion angles, solvent accessibility, contact numbers and half-sphere exposures by employing deep neural networks. RESULTS: We found that angle-based errors can be predicted most accurately with Spearman correlation coefficient (SPC) between predicted and actual errors at about 0.6. This is followed by solvent accessibility (SPC∼0.5). The errors on contact-based structural properties are most difficult to predict (SPC between 0.2 and 0.3). We showed that predicted errors are significantly better error indicators than the average errors based on secondary-structure and amino-acid residue types. We further demonstrated the usefulness of predicted errors in model quality assessment. These error or confidence indictors are expected to be useful for prediction, assessment, and refinement of protein structures. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org as a part of SPIDER2 package. CONTACT: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3666040,\n \"score\": 0\n },\n {\n \"doc_id\": \"28011771\",\n \"title\": \"Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.\",\n \"abstract\": \"Motivation: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction. Results: The new method, named SPOT-Disorder, has steadily improved over a similar method using a traditional, window-based neural network (SPINE-D) in all datasets tested without separate training on short and long disordered regions. Independent tests on four other datasets including the datasets from critical assessment of structure prediction (CASP) techniques and >10 000 annotated proteins from MobiDB, confirmed SPOT-Disorder as one of the best methods in disorder prediction. Moreover, initial studies indicate that the method is more accurate in predicting functional sites in disordered regions. These results highlight the usefulness combining LSTM with deep bidirectional recurrent neural networks in capturing non-local, long-range interactions for bioinformatics applications. Availability and Implementation: SPOT-disorder is available as a web server and as a standalone program at: http://sparks-lab.org/server/SPOT-disorder/index.php . Contact: j.hanson@griffith.edu.au or yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au. Supplementary information: Supplementary data is available at Bioinformatics online.\",\n \"corpus_id\": 3703781,\n \"score\": 0\n },\n {\n \"doc_id\": \"28398502\",\n \"title\": \"PyGOLD: a python based API for docking based virtual screening workflow generation.\",\n \"abstract\": \"Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD. However, within an automated virtual screening workflow it is not feasible to use the GUI in between every step to change the GOLD configuration file. Thus, a python module called PyGOLD was developed, to parse, edit and write the GOLD configuration file and to automate docking based virtual screening workflows. Availability and Implementation: The latest version of PyGOLD, its documentation and example scripts are available at: http://www.ccb.tu-dortmund.de/koch or http://www.agkoch.de. PyGOLD is implemented in Python and can be imported as a standard python module without any further dependencies. Contact: oliver.koch@agkoch.de, oliver.koch@tu-dortmund.de. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4448498,\n \"score\": 0\n },\n {\n \"doc_id\": \"28430949\",\n \"title\": \"Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility.\",\n \"abstract\": \"Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some \\\"short to intermediate\\\" non-local interactions. Here, we employed Long Short Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. Results: We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j|>19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5%, and 10% in the mean absolute error for backbone ϕ ,Ψ, θ , and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted Cα atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and Ψ angles. We expect the method to be useful for assisting protein structure and function prediction. Availability: The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . Contact: yaoqi.zhou@griffith.edu.au , yuedong.yang@griffith.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3764023,\n \"score\": 0\n },\n {\n \"doc_id\": \"29040432\",\n \"title\": \"Machine learning accelerates MD-based binding pose prediction between ligands and proteins.\",\n \"abstract\": \"Motivation: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short Molecular Dynamics (MD) simulations, such as MM-PBSA and MM-GBSA, among generated docking poses have been used. Since molecular structures obtained from MD simulation depend on the initial condition, taking the average over different initial conditions leads to better accuracy. Prediction accuracy of protein-ligand binding poses can be improved with multiple runs at different initial velocity. Results: This paper shows that a machine learning method, called Best Arm Identification, can optimally control the number of MD runs for each binding pose. It allows us to identify a correct binding pose with a minimum number of total runs. Our experiment using three proteins and eight inhibitors showed that the computational cost can be reduced substantially without sacrificing accuracy. This method can be applied for controlling all kinds of molecular simulations to obtain best results under restricted computational resources. Availability and implementation: Code and data are available on GitHub at https://github.com/tsudalab/bpbi. Contact: terayama@cbms.k.u-tokyo.ac.jp or tsuda@k.u-tokyo.ac.jp. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3764446,\n \"score\": 0\n },\n {\n \"doc_id\": \"29462243\",\n \"title\": \"Combining co-evolution and secondary structure prediction to improve fragment library generation.\",\n \"abstract\": \"Motivation: Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction. Results: We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results. Availability and implementation: Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3414290,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":76,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27147026\",\n \"title\": \"Direct detection of the (229)Th nuclear clock transition.\",\n \"abstract\": \"Today's most precise time and frequency measurements are performed with optical atomic clocks. However, it has been proposed that they could potentially be outperformed by a nuclear clock, which employs a nuclear transition instead of an atomic shell transition. There is only one known nuclear state that could serve as a nuclear clock using currently available technology, namely, the isomeric first excited state of (229)Th (denoted (229m)Th). Here we report the direct detection of this nuclear state, which is further confirmation of the existence of the isomer and lays the foundation for precise studies of its decay parameters. On the basis of this direct detection, the isomeric energy is constrained to between 6.3 and 18.3 electronvolts, and the half-life is found to be longer than 60 seconds for (229m)Th(2+). More precise determinations appear to be within reach, and would pave the way to the development of a nuclear frequency standard.\",\n \"corpus_id\": 205248786\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19519091","title":"Proposed experimental method to determine alpha sensitivity of splitting between ground and 7.6 eV isomeric states in 229Th.","abstract":"The 7.6 eV electromagnetic transition between the nearly degenerate ground state and first excited state in the 229Th nucleus may be very sensitive to potential changes in the fine-structure constant, alpha=e2/variant Planck's over 2pic. However, the sensitivity is not known, and nuclear calculations are currently unable to determine it. We propose measurements of the differences of atomic transition frequencies between thorium atoms (or ions) with the nucleus in the ground state and in the first excited (isomeric) state. This will enable extraction of the change in nuclear charge radius and electric-quadrupole moment between the isomers, and hence the alpha dependence of the isomeric transition frequency with reasonable accuracy.","corpus_id":32016190,"score":2},{"doc_id":"20867093","title":"Exponential increase of energy level density in atoms: Th and Th II.","abstract":"We present analytical estimates and numerical calculations showing that the energy level density in open-shell atoms increases exponentially with the increase of excitation energy. As an example, we use the relativistic Hartree-Fock and configuration interaction methods to calculate the density of states of Th and Th II. The result is used to estimate the effect of electrons on the nuclear transition which is considered for the nuclear clock.","corpus_id":9116791,"score":2},{"doc_id":"21231100","title":"Excitation of the isomeric 229mTh nuclear state via an electronic bridge process in 229Th+.","abstract":"We consider the excitation of the nuclear transition 229gTh-229mTh near 7.6 eV in singly ionized thorium via an electronic bridge process. The process relies on the excitation of the electron shell by two laser photons whose sum frequency is equal to the nuclear transition frequency. This scheme allows us to determine the nuclear transition frequency with high accuracy. Based on calculations of the electronic level structure of Th+ which combine the configuration-interaction method and many-body perturbation theory, we estimate that a nuclear excitation rate in the range of 10 s⁻¹ can be obtained using conventional laser sources.","corpus_id":26691210,"score":2},{"doc_id":"21599361","title":"Proposal for a nuclear gamma-ray laser of optical range.","abstract":"A possibility of the amplification of the 7.6 eV γ radiation by the stimulated γ emission of the ensemble of the (229m)Th isomeric nuclei in a host dielectric crystal is proved theoretically. This amplification is a result of (1) the excitation of a large number of (229m)Th isomers by laser radiation, (2) the creation of the inverse population of nuclear levels in a cooled sample owing to the interaction of thorium nuclei with the crystal electric field or with an external magnetic field, (3) the emission or absorption of the optical photons by thorium nuclei in the crystal without recoil, and (4) the nuclear spin relaxation through the conduction electrons of the metallic covering.","corpus_id":40173588,"score":2},{"doc_id":"22540568","title":"Single-ion nuclear clock for metrology at the 19th decimal place.","abstract":"The 7.6(5) eV nuclear magnetic-dipole transition in a single 229Th3+ ion may provide the foundation for an optical clock of superb accuracy. A virtual clock transition composed of stretched states within the 5F(5/2) electronic ground level of both nuclear ground and isomeric manifolds is proposed. It is shown to offer unprecedented systematic shift suppression, allowing for clock performance with a total fractional inaccuracy approaching 1×10(-19).","corpus_id":40863227,"score":2},{"doc_id":"23215066","title":"Observation of the deexcitation of the (229m)Th nuclear isomer.","abstract":"The (229)Th nucleus possesses the lowest-energy nuclear isomeric state. Two widely accepted indirect measurements of the transition energy place it within reach of existing laser capabilities. Direct searches for the isomer deexcitation have proven elusive despite extensive effort over the past couple of decades. There is now a growing interest in finding this unique transition because of its potential applications in nuclear, atomic, condensed matter, and optical physics, quantum information, metrology, and cosmology, including the development of a new type of clock based on this nuclear transition. In this Letter we report the first direct observation of the deexcitation of the lowest-lying isomeric state in (229)Th. By collecting (229)Th recoils following the alpha decay of (233)U into MgF(2) plates and measuring the subsequent light emission, we have isolated the isomer deexcitation and measured the transition's half-life to be 6±1 h. Through comparison measurements with (235m)U isomer, we found that the observed (229m)Th deexcitation signal originates from photon emission rather than internal conversion electron emission. This discovery lays the groundwork for optical and laser spectroscopy of (229m)Th nuclear isomer and the development of a (229)Th nuclear clock.","corpus_id":23528635,"score":2},{"doc_id":"23368553","title":"Coherence-enhanced optical determination of the 229Th isomeric transition.","abstract":"The impact of coherent light propagation on the excitation and fluorescence of thorium nuclei in a crystal lattice environment is investigated theoretically. We find that in the forward direction, the fluorescence signal exhibits characteristic intensity modulations dominated by a sped-up initial decay signal that is orders of magnitude faster. This feature can be exploited for the optical determination of the isomeric transition energy. In order to obtain a unmistakable signature of the isomeric nuclear fluorescence, we put forward a novel scheme for the direct measurement of the transition energy via electromagnetically modified nuclear forward scattering involving two fields that couple to three nuclear states.","corpus_id":9119621,"score":2},{"doc_id":"24580690","title":"Hyperfine structure in 229gTh3+ as a probe of the 229gTh→ 229mTh nuclear excitation energy.","abstract":"We identify a potential means to extract the 229gTh→ 229mTh nuclear excitation energy from precision microwave spectroscopy of the 5F(5/2,7/2) hyperfine manifolds in the ion 229gTh3+. The hyperfine interaction mixes this ground fine structure doublet with states of the nuclear isomer, introducing small but observable shifts to the hyperfine sublevels. We demonstrate how accurate atomic structure calculations may be combined with the measurement of the hyperfine intervals to quantify the effects of this mixing. Further knowledge of the magnetic dipole decay rate of the isomer, as recently reported, allows an indirect determination of the nuclear excitation energy.","corpus_id":46019966,"score":2},{"doc_id":"24937606","title":"Investigation of thorium salts as candidate materials for direct observation of the (229m)Th nuclear transition.","abstract":"Recent efforts to measure the (229m)Th → (229g)Th nuclear transition sparked interest in understanding the electronic structure of wide-gap thorium salts. Such materials could be used to measure this nuclear transition using optical spectroscopy in solid-state devices. Here, we present screened hybrid density functional theory and many-body G0W0 calculations of two candidate materials, namely, Na2ThF6 and ThF4, for such a measurement. Our results show an electronic gap larger than 10 eV for both materials, suggesting that the internal conversion nuclear de-excitation channel would be suppressed in these materials. We also present results for ThX4 (X = Cl, Br, I), materials with smaller gaps significantly easier to access experimentally.","corpus_id":20810437,"score":2},{"doc_id":"25844000","title":"Prospects for measuring the 229Th isomer energy using a metallic magnetic microcalorimeter.","abstract":"The Thorium-229 isotope features a nuclear isomer state with an extremely low energy. The currently most accepted energy value, 7.8±0.5 eV, was obtained from an indirect measurement using a NASA x-ray microcalorimeter with an instrumental resolution 26 eV. We study, how state-of-the-art magnetic metallic microcalorimeters with an energy resolution down to a few eV can be used to measure the isomer energy. In particular, resolving the 29.18 keV doublet in the γ-spectrum following the α-decay of Uranium-233, corresponding to the decay into the ground and isomer state, allows to measure the isomer transition energy without additional theoretical input parameters, and increase the energy accuracy. We study the possibility of resolving the 29.18 keV line as a doublet and the dependence of the attainable precision of the energy measurement on the signal and background count rates and the instrumental resolution.","corpus_id":5241191,"score":2},{"doc_id":"25906029","title":"Multisectional linear ion trap and novel loading method for optical spectroscopy of electron and nuclear transitions.","abstract":"There is a growing need for the development of atomic and nuclear frequency standards because of the important contribution of methods for precision time and frequency measurements to the development of fundamental science, technology, and the economy. It is also conditioned by their potential use in optical clocks and quantum logic applications. It is especially important to develop a universal method that could allow one to use ions of most elements effectively (including ones that are not easily evaporated) proposed for the above-mentioned applications. A linear quadrupole ion trap for the optical spectroscopy of electron and nuclear transitions has been developed and evaluated experimentally. An ion source construction is based on an ultra-high vacuum evaporator in which a metal sample is subjected to an electron beam of energy up to 1 keV, resulting in the appearance of gaseous atoms and ions of various charge state. The linear ion trap consists of five successive quadrupole sections including an entrance quadrupole section, quadrupole mass filter, quadrupole ion guide, ion-trap section, and exit quadrupole section. The same radiofrequency but a different direct current voltage feeds the quadrupole sections. The instrument allows the mass and energy selected trapping of ions from ion beams of various intensities and their localization in the area of laser irradiation. The preliminary results presented show that the proposed instrument and methods allow one to produce effectively up to triply charged thorium ions as well as to trap ions for future spectroscopic study. The instrument is proposed for future use in optical clocks and quantum logic application development.","corpus_id":22584427,"score":2},{"doc_id":"26197124","title":"Results of a Direct Search Using Synchrotron Radiation for the Low-Energy (229)Th Nuclear Isomeric Transition.","abstract":"We report the results of a direct search for the (229)Th (I(π)=3/2(+)←5/2(+)) nuclear isomeric transition, performed by exposing (229)Th-doped LiSrAlF(6) crystals to tunable vacuum-ultraviolet synchrotron radiation and observing any resulting fluorescence. We also use existing nuclear physics data to establish a range of possible transition strengths for the isomeric transition. We find no evidence for the thorium nuclear transition between 7.3 eV and 8.8 eV with transition lifetime (1-2) s≲τ≲(2000-5600) s. This measurement excludes roughly half of the favored transition search area and can be used to direct future searches.","corpus_id":1322253,"score":2},{"doc_id":"26502749","title":"Radioluminescence and photoluminescence of Th:CaF2 crystals.","abstract":"We study thorium-doped CaF2 crystals as a possible platform for optical spectroscopy of the (229)Th nuclear isomer transition. We anticipate two major sources of background signal that might cover the nuclear spectroscopy signal: VUV-photoluminescence, caused by the probe light, and radioluminescence, caused by the radioactive decay of (229)Th and its daughters. We find a rich photoluminescence spectrum at wavelengths above 260 nm, and radioluminescence emission above 220 nm. This is very promising, as fluorescence originating from the isomer transition, predicted at a wavelength shorter than 200 nm, could be filtered spectrally from the crystal luminescence. Furthermore, we investigate the temperature-dependent decay time of the luminescence, as well as thermoluminescence properties. Our findings allow for an immediate optimization of spectroscopy protocols for both the initial search for the nuclear transition using synchrotron radiation, as well as future optical clock operation with narrow-linewidth lasers.","corpus_id":15417434,"score":2},{"doc_id":"28186791","title":"Lifetime Measurement of the ^{229}Th Nuclear Isomer.","abstract":"The first excited isomeric state of ^{229}Th possesses the lowest energy among all known excited nuclear states. The expected energy is accessible with today's laser technology and in principle allows for a direct optical laser excitation of the nucleus. The isomer decays via three channels to its ground state (internal conversion, γ decay, and bound internal conversion), whose strengths depend on the charge state of ^{229m}Th. We report on the measurement of the internal-conversion decay half-life of neutral ^{229m}Th. A half-life of 7±1 μs has been measured, which is in the range of theoretical predictions and, based on the theoretically expected lifetime of ≈10^{4} s of the photonic decay channel, gives further support for an internal conversion coefficient of ≈10^{9}, thus constraining the strength of a radiative branch in the presence of internal conversion.","corpus_id":37518294,"score":2},{"doc_id":"28598657","title":"Reduced Transition Probabilities for the Gamma Decay of the 7.8 eV Isomer in ^{229}Th.","abstract":"The reduced magnetic dipole and electric quadrupole transition probabilities for the radiative decay of the ^{229}Th 7.8 eV isomer to the ground state are predicted within a detailed nuclear-structure model approach. We show that the presence and decay of this isomer can only be accounted for by the Coriolis mixing emerging from a remarkably fine interplay between the coherent quadrupole-octupole motion of the nuclear core and the single-nucleon motion within a reflection-asymmetric deformed potential. We find that the magnetic dipole transition probability which determines the radiative lifetime of the isomer is considerably smaller than presently estimated. The so-far disregarded electric quadrupole component may have non-negligible contributions to the internal conversion channel. These findings support new directions in the experimental search of the ^{229}Th transition frequency for the development of a future nuclear frequency standard.","corpus_id":40694257,"score":2},{"doc_id":"29341722","title":"A Laser Excitation Scheme for ^{229m}Th.","abstract":"Direct laser excitation of the lowest known nuclear excited state in ^{229}Th has been a long-standing objective. It is generally assumed that reaching this goal would require a considerably reduced uncertainty of the isomer's excitation energy compared to the presently adopted value of (7.8±0.5) eV. Here we present a direct laser excitation scheme for ^{229m}Th, which circumvents this requirement. The proposed excitation scheme makes use of already existing laser technology and therefore paves the way for nuclear laser spectroscopy. In this concept, the recently experimentally observed internal-conversion decay channel of the isomeric state is used for probing the isomeric population. A signal-to-background ratio of better than 10^{4} and a total measurement time of less than three days for laser scanning appear to be achievable.","corpus_id":42216312,"score":2},{"doc_id":"29670266","title":"Laser spectroscopic characterization of the nuclear-clock isomer 229mTh.","abstract":"The isotope 229Th is the only nucleus known to possess an excited state 229mTh in the energy range of a few electronvolts-a transition energy typical for electrons in the valence shell of atoms, but about four orders of magnitude lower than typical nuclear excitation energies. Of the many applications that have been proposed for this nuclear system, which is accessible by optical methods, the most promising is a highly precise nuclear clock that outperforms existing atomic timekeepers. Here we present the laser spectroscopic investigation of the hyperfine structure of the doubly charged 229mTh ion and the determination of the fundamental nuclear properties of the isomer, namely, its magnetic dipole and electric quadrupole moments, as well as its nuclear charge radius. Following the recent direct detection of this long-sought isomer, we provide detailed insight into its nuclear structure and present a method for its non-destructive optical detection.","corpus_id":4990345,"score":2},{"doc_id":"29694057","title":"Decay Rate of the Nuclear Isomer ^{229}Th(3/2^{+},7.8 eV) in a Dielectric Sphere, Thin Film, and Metal Cavity.","abstract":"The main decay channels of the anomalous low-energy 3/2^{+}(7.8±0.5 eV) isomeric level of the ^{229}Th nucleus, namely the γ emission and internal conversion, inside a dielectric sphere, dielectric thin film, and conducting spherical microcavity are investigated theoretically, taking into account the effect of media interfaces. It is shown that (1) the γ decay rate of the nuclear isomer inside a dielectric thin film and dielectric microsphere placed in a vacuum or in a metal cavity can decrease (increase) in dozen of times, (2) the γ activity of the distributed source as a function of time can be nonexponential, and (3) the metal cavity, whose size is of the order of the radiation wavelength, does not affect the probability of the internal conversion in ^{229}Th, because the virtual photon attenuates at much shorter distances and the reflected wave is very weak.","corpus_id":13857642,"score":2},{"doc_id":"19792559","title":"Spin-1/2 optical lattice clock.","abstract":"We experimentally investigate an optical clock based on ;{171}Yb (I = 1/2) atoms confined in an optical lattice. We have evaluated all known frequency shifts to the clock transition, including a density-dependent collision shift, with a fractional uncertainty of 3.4 x 10;{-16}, limited principally by uncertainty in the blackbody radiation Stark shift. We measured the absolute clock transition frequency relative to the NIST-F1 Cs fountain clock and find the frequency to be 518 295 836 590 865.2(0.7) Hz.","corpus_id":7416845,"score":1},{"doc_id":"22481777","title":"Blackbody radiation shifts in optical atomic clocks.","abstract":"A review of recent theoretical calculations of blackbody radiation (BBR) shifts in optical atomic clocks is presented. We summarize previous results for monovalent ions that were obtained by a relativistic all-order single-double method, where all single and double excitations of the Dirac- Fock wave function are included to all orders of perturbation theory. A recently developed method for accurate calculations of BBR shifts in divalent atoms is then presented. This approach combines the relativistic all-order method and the configuration interaction method, which provides for accurate treatment of correlation corrections in atoms with two valence electrons. Calculations of the BBR shifts in B+, Al+, and In+ have enabled us to reduce the present fractional uncertainties in the frequencies of their clock transitions as measured at room temperature: to 4 × 10-19 for Al+ and 10-18 for B+ and In+. These uncertainties approach recent estimates of the limits of precision of currently proposed optical atomic clocks. We discuss directions of future theoretical developments for reducing clock uncertainties resulting from blackbody radiation shifts.","corpus_id":16838058,"score":1},{"doc_id":"22539714","title":"A 920-kilometer optical fiber link for frequency metrology at the 19th decimal place.","abstract":"Optical clocks show unprecedented accuracy, surpassing that of previously available clock systems by more than one order of magnitude. Precise intercomparisons will enable a variety of experiments, including tests of fundamental quantum physics and cosmology and applications in geodesy and navigation. Well-established, satellite-based techniques for microwave dissemination are not adequate to compare optical clocks. Here, we present phase-stabilized distribution of an optical frequency over 920 kilometers of telecommunication fiber. We used two antiparallel fiber links to determine their fractional frequency instability (modified Allan deviation) to 5 × 10(-15) in a 1-second integration time, reaching 10(-18) in less than 1000 seconds. For long integration times τ, the deviation from the expected frequency value has been constrained to within 4 × 10(-19). The link may serve as part of a Europe-wide optical frequency dissemination network.","corpus_id":19895554,"score":1},{"doc_id":"23037353","title":"Direct comparison of a Ca+ single-ion clock against a Sr lattice clock to verify the absolute frequency measurement.","abstract":"Optical frequency comparison of the (40)Ca(+) clock transition ν(Ca)((2)S(1/2-)(2D(5/2), 729 nm) against the (87)Sr optical lattice clock transition ν(Sr) ((1)S(0)-(3)P(0), 698 nm) has resulted in a frequency ratio ν(Ca) / ν(Sr) = 0.957 631 202 358 049 9(2 3). The rapid nature of optical comparison allowed the statistical uncertainty of frequency ratio ν(Ca) / ν(Sr) to reach 1 × 10(-15) in 1000s and yielded a value consistent with that calculated from separate absolute frequency measurements of ν(Ca) using the International Atomic Time (TAI) link. The total uncertainty of the frequency ratio using optical comparison (free from microwave link uncertainties) is smaller than that obtained using absolute frequency measurement, demonstrating the advantage of optical frequency evaluation. We note that the absolute frequency of (40)Ca(+) we measure deviates from other published values by more than three times our measurement uncertainty.","corpus_id":10441002,"score":1},{"doc_id":"23679589","title":"s-Wave collisional frequency shift of a fermion clock.","abstract":"We report an s-wave collisional frequency shift of an atomic clock based on fermions. In contrast to bosons, the fermion clock shift is insensitive to the population difference of the clock states, set by the first pulse area in Ramsey spectroscopy, θ(1). The fermion shift instead depends strongly on the second pulse area θ(2). It allows the shift to be canceled, nominally at θ(2)=π/2, but correlations perturb the null to slightly larger θ(2). The frequency shift is relevant for optical lattice clocks and increases with the spatial inhomogeneity of the clock excitation field, naturally larger at optical frequencies.","corpus_id":13315531,"score":1},{"doc_id":"23970562","title":"An atomic clock with 10(-18) instability.","abstract":"Atomic clocks have been instrumental in science and technology, leading to innovations such as global positioning, advanced communications, and tests of fundamental constant variation. Timekeeping precision at 1 part in 10(18) enables new timing applications in relativistic geodesy, enhanced Earth- and space-based navigation and telescopy, and new tests of physics beyond the standard model. Here, we describe the development and operation of two optical lattice clocks, both using spin-polarized, ultracold atomic ytterbium. A measurement comparing these systems demonstrates an unprecedented atomic clock instability of 1.6 × 10(-18) after only 7 hours of averaging.","corpus_id":206549862,"score":1},{"doc_id":"24463513","title":"An optical lattice clock with accuracy and stability at the 10(-18) level.","abstract":"Progress in atomic, optical and quantum science has led to rapid improvements in atomic clocks. At the same time, atomic clock research has helped to advance the frontiers of science, affecting both fundamental and applied research. The ability to control quantum states of individual atoms and photons is central to quantum information science and precision measurement, and optical clocks based on single ions have achieved the lowest systematic uncertainty of any frequency standard. Although many-atom lattice clocks have shown advantages in measurement precision over trapped-ion clocks, their accuracy has remained 16 times worse. Here we demonstrate a many-atom system that achieves an accuracy of 6.4 × 10(-18), which is not only better than a single-ion-based clock, but also reduces the required measurement time by two orders of magnitude. By systematically evaluating all known sources of uncertainty, including in situ monitoring of the blackbody radiation environment, we improve the accuracy of optical lattice clocks by a factor of 22. This single clock has simultaneously achieved the best known performance in the key characteristics necessary for consideration as a primary standard-stability and accuracy. More stable and accurate atomic clocks will benefit a wide range of fields, such as the realization and distribution of SI units, the search for time variation of fundamental constants, clock-based geodesy and other precision tests of the fundamental laws of nature. This work also connects to the development of quantum sensors and many-body quantum state engineering (such as spin squeezing) to advance measurement precision beyond the standard quantum limit.","corpus_id":4461081,"score":1},{"doc_id":"24718165","title":"Frequency ratio measurement of 171Yb and 87Sr optical lattice clocks.","abstract":"The frequency ratio of the (1)S(0)(F = 1/2)-(3)P(0)(F = 1/2) clock transition in (171)Yb and the (1)S(0)(F = 9/2)-(3)P(0)(F = 9/2) clock transition in (87)Sr is measured by an optical-optical direct frequency link between two optical lattice clocks. We determined the ratio (ν(Yb)/ν(Sr)) to be 1.207 507 039 343 341 2(17) fractional standard uncertainty of 1.4 × 10(-15) [corrected]. The measurement uncertainty of the frequency ratio is smaller than that obtained from absolute frequency measurements using the International Atomic Time (TAI) link. The measured ratio agrees well with that derived from the absolute frequency measurement results obtained at NIST and JILA, Boulder, CO using their Cs-fountain clock. Our measurement enables the first international comparison of the frequency ratios of optical clocks. The measured frequency ratio will be reported to the International Committee for Weights and Measures for a discussion related to the redefinition of the second.","corpus_id":207329094,"score":1},{"doc_id":"25083643","title":"Measurement of the hyperfine quenching rate of the clock transition in 171YB.","abstract":"We report the first experimental determination of the hyperfine quenching rate of the 6s(2) (1)S(0)(F = 1/2) - 6s6p (3)P(0)(F = 1/2) transition in (171)Yb with nuclear spin I = 1/2. This rate determines the natural linewidth and the Rabi frequency of the clock transition of a Yb optical frequency standard. Our technique involves spectrally resolved fluorescence decay measurements of the lowest lying (3)P(0,1) levels of neutral Yb atoms embedded in a solid Ne matrix. The solid Ne provides a simple way to trap a large number of atoms as well as an efficient mechanism for populating (3)P(0). The decay rates in solid Ne are modified by medium effects including the index-of-refraction dependence. We find the (3)P(0) hyperfine quenching rate to be (4.42 ± 0.35) × 10(-2) s(-1) for free (171)Yb, which agrees with recent ab initio calculations.","corpus_id":45636356,"score":1},{"doc_id":"25121654","title":"Direct comparison of optical lattice clocks with an intercontinental baseline of 9000 km.","abstract":"We have demonstrated a direct frequency comparison between two ⁸⁷Sr lattice clocks operated in intercontinentally separated laboratories in real time. Two-way satellite time and frequency transfer technique, based on the carrier-phase, was employed for a direct comparison, with a baseline of 9000 km between Japan and Germany. A frequency comparison was achieved for 83,640 s, resulting in a fractional difference of (1.1±1.6)×10⁻¹⁵, where the statistical part is the largest contributor to the uncertainty. This measurement directly confirms the agreement of the two optical frequency standards on an intercontinental scale.","corpus_id":7835779,"score":1},{"doc_id":"25479482","title":"Frequency ratio of two optical clock transitions in 171Yb+ and constraints on the time variation of fundamental constants.","abstract":"Singly ionized ytterbium, with ultranarrow optical clock transitions at 467 and 436 nm, is a convenient system for the realization of optical atomic clocks and tests of present-day variation of fundamental constants. We present the first direct measurement of the frequency ratio of these two clock transitions, without reference to a cesium primary standard, and using the same single ion of 171Yb+. The absolute frequencies of both transitions are also presented, each with a relative standard uncertainty of 6×10(-16). Combining our results with those from other experiments, we report a threefold improvement in the constraint on the time variation of the proton-to-electron mass ratio, μ/μ=0.2(1.1)×10(-16) yr(-1), along with an improved constraint on time variation of the fine structure constant, α/α=-0.7(2.1)×10(-17) yr(-1).","corpus_id":30505674,"score":1},{"doc_id":"26459877","title":"Direct frequency comb optical frequency standard based on two-photon transitions of thermal atoms.","abstract":"Optical clocks have been the focus of science and technology research areas due to their capability to provide highest frequency accuracy and stability to date. Their superior frequency performance promises significant advances in the fields of fundamental research as well as practical applications including satellite-based navigation and ranging. In traditional optical clocks, ultrastable optical cavities, laser cooling and particle (atoms or a single ion) trapping techniques are employed to guarantee high stability and accuracy. However, on the other hand, they make optical clocks an entire optical tableful of equipment, and cannot work continuously for a long time; as a result, they restrict optical clocks used as very convenient and compact time-keeping clocks. In this article, we proposed, and experimentally demonstrated, a novel scheme of optical frequency standard based on comb-directly-excited atomic two-photon transitions. By taking advantage of the natural properties of the comb and two-photon transitions, this frequency standard achieves a simplified structure, high robustness as well as decent frequency stability, which promise widespread applications in various scenarios.","corpus_id":16134761,"score":1},{"doc_id":"26705620","title":"Towards a Mg Lattice Clock: Observation of the ^{1}S_{0}-^{3}P_{0} Transition and Determination of the Magic Wavelength.","abstract":"We optically excite the electronic state 3s3p ^{3}P_{0} in ^{24}Mg atoms, laser cooled and trapped in a magic-wavelength lattice. An applied magnetic field enhances the coupling of the light to the otherwise strictly forbidden transition. We determine the magic wavelength, the quadratic magnetic Zeeman shift, and the transition frequency to be 468.46(21) nm, -206.6(2.0) MHz/T^{2}, and 655 058 646 691(101) kHz, respectively. These are compared with theoretical predictions and results from complementary experiments. We also develop a high-precision relativistic structure model for magnesium, give an improved theoretical value for the blackbody radiation shift, and discuss a clock based on bosonic magnesium.","corpus_id":206265528,"score":1},{"doc_id":"27503795","title":"A clock network for geodesy and fundamental science.","abstract":"Leveraging the unrivalled performance of optical clocks as key tools for geo-science, for astronomy and for fundamental physics beyond the standard model requires comparing the frequency of distant optical clocks faithfully. Here, we report on the comparison and agreement of two strontium optical clocks at an uncertainty of 5 × 10(-17) via a newly established phase-coherent frequency link connecting Paris and Braunschweig using 1,415 km of telecom fibre. The remote comparison is limited only by the instability and uncertainty of the strontium lattice clocks themselves, with negligible contributions from the optical frequency transfer. A fractional precision of 3 × 10(-17) is reached after only 1,000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than any previous long-distance clock comparison. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optical dissemination of the SI-second.","corpus_id":14769489,"score":1},{"doc_id":"27740781","title":"Improvement of an Atomic Clock using Squeezed Vacuum.","abstract":"Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case, the vacuum noise restricts the precision of the interferometer to the standard quantum limit (SQL). Here, we propose and experimentally demonstrate a novel clock configuration that surpasses the SQL by squeezing the vacuum in the empty input state. We create a squeezed vacuum state containing an average of 0.75 atoms to improve the clock sensitivity of 10000 atoms by 2.05_{-0.37}^{+0.34} dB. The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based on atomic squeezed vacuum.","corpus_id":36182186,"score":1},{"doc_id":"27757423","title":"Superradiance on the millihertz linewidth strontium clock transition.","abstract":"Laser frequency noise contributes a significant limitation to today's best atomic clocks. A proposed solution to this problem is to create a superradiant laser using an optical clock transition as its gain medium. This laser would act as an active atomic clock and would be highly immune to the fluctuations in reference cavity length that limit today's best lasers. We demonstrate and characterize superradiant emission from the millihertz linewidth clock transition in an ensemble of laser-cooled (87)Sr atoms trapped within a high-finesse optical cavity. We measure a collective enhancement of the emission rate into the cavity mode by a factor of more than 10,000 compared to independently radiating atoms. We also demonstrate a method for seeding superradiant emission and observe interference between two independent transitions lasing simultaneously. We use this interference to characterize the relative spectral properties of the two lasing subensembles.","corpus_id":15533256,"score":1},{"doc_id":"29328726","title":"Atom Interferometry with the Sr Optical Clock Transition.","abstract":"We report on the realization of a matter-wave interferometer based on single-photon interaction on the ultranarrow optical clock transition of strontium atoms. We experimentally demonstrate its operation as a gravimeter and as a gravity gradiometer. No reduction of interferometric contrast was observed for a total interferometer time up to ∼10 ms, limited by geometric constraints of the apparatus. Single-photon interferometers represent a new class of high-precision sensors that could be used for the detection of gravitational waves in so far unexplored frequency ranges and to enlighten the boundary between quantum mechanics and general relativity.","corpus_id":206305543,"score":1},{"doc_id":"29420479","title":"Isomer depletion as experimental evidence of nuclear excitation by electron capture.","abstract":"The atomic nucleus and its electrons are often thought of as independent systems that are held together in the atom by their mutual attraction. Their interaction, however, leads to other important effects, such as providing an additional decay mode for excited nuclear states, whereby the nucleus releases energy by ejecting an atomic electron instead of by emitting a γ-ray. This 'internal conversion' has been known for about a hundred years and can be used to study nuclei and their interaction with their electrons. In the inverse process-nuclear excitation by electron capture (NEEC)-a free electron is captured into an atomic vacancy and can excite the nucleus to a higher-energy state, provided that the kinetic energy of the free electron plus the magnitude of its binding energy once captured matches the nuclear energy difference between the two states. NEEC was predicted in 1976 and has not hitherto been observed. Here we report evidence of NEEC in molybdenum-93 and determine the probability and cross-section for the process in a beam-based experimental scenario. Our results provide a standard for the assessment of theoretical models relevant to NEEC, which predict cross-sections that span many orders of magnitude. The greatest practical effect of the NEEC process may be on the survival of nuclei in stellar environments, in which it could excite isomers (that is, long-lived nuclear states) to shorter-lived states. Such excitations may reduce the abundance of the isotope after its production. This is an example of 'isomer depletion', which has been investigated previously through other reactions, but is used here to obtain evidence for NEEC.","corpus_id":3297033,"score":1},{"doc_id":"29542992","title":"Optical Lattice Clocks with Weakly Bound Molecules.","abstract":"Optical molecular clocks promise unparalleled sensitivity to the temporal variation of the electron-to-proton mass ratio and insight into possible new physics beyond the standard model. We propose to realize a molecular clock with bosonic ^{174}Yb_{2} molecules, where the forbidden ^{1}S_{0}→^{3}P_{0} clock transition would be induced magnetically. The use of a bosonic species avoids possible complications due to the hyperfine structure present in fermionic species. While direct clock line photoassociation would be challenging, weakly bound ground state molecules could be produced by stimulated Raman adiabatic passage and used instead. The recent scattering measurements [L. Franchi, et al. New J. Phys. 19, 103037 (2017)NJOPFM1367-263010.1088/1367-2630/aa8fb4] enable us to determine the positions of target ^{1}S_{0}+^{3}P_{0} vibrational levels and calculate the Franck-Condon factors for clock transitions between ground and excited molecular states. The resulting magnetically induced Rabi frequencies are similar to those for atoms hinting that an experimental realization is feasible. A successful observation could pave the way towards Hz-level molecular spectroscopy.","corpus_id":3892512,"score":1},{"doc_id":"29667603","title":"Atomic clocks for geodesy.","abstract":"We review experimental progress on optical atomic clocks and frequency transfer, and consider the prospects of using these technologies for geodetic measurements. Today, optical atomic frequency standards have reached relative frequency inaccuracies below 10-17, opening new fields of fundamental and applied research. The dependence of atomic frequencies on the gravitational potential makes atomic clocks ideal candidates for the search for deviations in the predictions of Einstein's general relativity, tests of modern unifying theories and the development of new gravity field sensors. In this review, we introduce the concepts of optical atomic clocks and present the status of international clock development and comparison. Besides further improvement in stability and accuracy of today's best clocks, a large effort is put into increasing the reliability and technological readiness for applications outside of specialized laboratories with compact, portable devices. With relative frequency uncertainties of 10-18, comparisons of optical frequency standards are foreseen to contribute together with satellite and terrestrial data to the precise determination of fundamental height reference systems in geodesy with a resolution at the cm-level. The long-term stability of atomic standards will deliver excellent long-term height references for geodetic measurements and for the modelling and understanding of our Earth.","corpus_id":4939307,"score":1},{"doc_id":"18636527","title":"Mass and lifetime measurements of exotic nuclei in storage rings.","abstract":"Mass and lifetime measurements lead to the discovery and understanding of basic properties of matter. The isotopic nature of the chemical elements, nuclear binding, and the location and strength of nuclear shells are the most outstanding examples leading to the development of the first nuclear models. More recent are the discoveries of new structures of nuclides far from the valley of stability. A new generation of direct mass measurements which allows the exploration of extended areas of the nuclear mass surface with high accuracy has been opened up with the combination of the Experimental Storage Ring ESR and the FRragment Separator FRS at GSI Darmstadt. In-flight separated nuclei are stored in the ring. Their masses are directly determined from the revolution frequency. Dependent on the half-life two complementary methods are applied. Schottky Mass Spectrometry SMS relies on the measurement of the revolution frequency of electron cooled stored ions. The cooling time determines the lower half-life limit to the order of seconds. For Isochronous Mass Spectrometry IMS the ring is operated in an isochronous ion-optical mode. The revolution frequency of the individual ions coasting in the ring is measured using a time-of-flight method. Nuclides with lifetimes down to microseconds become accessible. With SMS masses of several hundreds nuclides have been measured simultaneously with an accuracy in the 2 x 10(-7)-range. This high accuracy and the ability to study large areas of the mass surface are ideal tools to discover new nuclear structure properties and to guide improvements for theoretical mass models. In addition, nuclear half-lives of stored bare and highly charged ions have been measured. This new experimental development is a significant progress since nuclear decay characteristics are mostly known for neutral atoms. For bare and highly charged ions new nuclear decay modes become possible, such as bound-state beta decay. Dramatic changes in the nuclear lifetime have been observed in highly charged ions compared to neutral atoms due to blocking of nuclear decay channels caused by the modified atomic interaction. High ionization degrees prevail in hot stellar matter and thus these experiments have great relevance for the understanding of the synthesis of elements in the universe and astrophysical scenarios in general.","corpus_id":16812701,"score":0},{"doc_id":"19113267","title":"Frequency shifts in an optical lattice clock due to magnetic-dipole and electric-quadrupole transitions.","abstract":"We report a hitherto undiscovered frequency shift for forbidden J = 0-->J = 0 clock transitions excited in atoms confined to an optical lattice. These shifts result from magnetic-dipole and electric-quadrupole transitions, which have a spatial dependence in an optical lattice that differs from that of the stronger electric-dipole transitions. In combination with the residual translational motion of atoms in an optical lattice, this spatial mismatch leads to a frequency shift via differential energy level spacing in the lattice wells for ground state and excited state atoms. We estimate that this effect could lead to fractional frequency shifts as large as 10(-16), which might prevent lattice-based optical clocks from reaching their predicted performance levels. Moreover, these effects could shift the magic wavelength in lattice clocks in three dimensions by as much as 100 MHz, depending on the lattice configuration.","corpus_id":6473324,"score":0},{"doc_id":"19792426","title":"Smallest known Q value of any nuclear decay: the rare beta;{-} decay of ;{115}In(9/2;{+}) --> ;{115}Sn(3/2;{+}).","abstract":"The ground-state-to-ground-state Q_{beta;{-}} value of ;{115}In was determined to 497.68(17) keV using a high-precision Penning trap facility at the University of Jyväskylä, Finland. From this, a Q_{beta;{-}} value of 0.35(17) keV was obtained for the rare beta;{-} decay to the first excited state of ;{115}Sn at 497.334(22) keV. The partial half-life was determined to 4.1(6) x 10;{20} yr using ultra low-background gamma-ray spectrometry in an underground laboratory. Theoretical modeling of this 2nd-forbidden unique beta;{-} transition was also undertaken and resulted in Q_{beta;{-}} = 57_{-12};{+19} eV using the measured half-life. The discrepancy between theory and experiment could be attributed to atomic effects enhanced by the low Q value. The present study implies that this transition has the lowest Q value of any known nuclear beta decay.","corpus_id":1890942,"score":0},{"doc_id":"21365108","title":"Photon induced isomerization in the first excited state of the 7-azaindole-(H2O)3 cluster.","abstract":"A picosecond pump and probe experiment has been applied to study the excited state dynamics of 7-azaindole-water 1 ∶ 2 and 1 ∶ 3 clusters [7AI(H(2)O)(2,3)] in the gas phase. The vibrational-mode selective Excited-State-Triple-Proton Transfer (ESTPT) in 7AI(H(2)O)(2) proposed from the frequency-resolved study has been confirmed by picosecond decays. The decay times for the vibronic states involving the ESTPT promoting mode σ(1) (850-1000 ps) are much shorter than those for the other vibronic states (2100-4600 ps). In the (1 + 1) REMPI spectrum of 7AI(H(2)O)(3) measured by nanosecond laser pulses, the vibronic bands with an energy higher than 200 cm(-1) above the origin of the S(1) state become very weak. In contrast, the vibronic bands in the same region emerge in the (1 + 1') REMPI spectrum of 7AI(H(2)O)(3) with picosecond pulses. The decay times drastically decrease when increasing the vibrational energy above 200 cm(-1). Ab initio calculations show that a second stable \"cyclic-nonplanar isomer\" exists in addition to a \"bridged-planar isomer\", and that an isomerization from a bridged-planar isomer to a cyclic-nonplanar isomer is most probably responsible for the short lifetimes of the vibronic states of 7AI(H(2)O)(3).","corpus_id":24793284,"score":0},{"doc_id":"21770559","title":"Extended coherence time on the clock transition of optically trapped rubidium.","abstract":"Optically trapped ensembles are of crucial importance for frequency measurements and quantum memories but generally suffer from strong dephasing due to inhomogeneous density and light shifts. We demonstrate a drastic increase of the coherence time to 21 s on the magnetic field insensitive clock transition of (87)Rb by applying the recently discovered spin self-rephasing [C. Deutsch et al., Phys. Rev. Lett. 105, 020401 (2010)]. This result confirms the general nature of this new mechanism and thus shows its applicability in atom clocks and quantum memories. A systematic investigation of all relevant frequency shifts and noise contributions yields a stability of 2.4×10(-11)τ(-1/2), where τ is the integration time in seconds. Based on a set of technical improvements, the presented frequency standard is predicted to rival the stability of microwave fountain clocks in a potentially much more compact setup.","corpus_id":36865779,"score":0},{"doc_id":"21935014","title":"All-optical link for direct comparison of distant optical clocks.","abstract":"We developed an all-optical link system for making remote comparisons of two distant ultra-stable optical clocks. An optical carrier transfer system based on a fiber interferometer was employed to compensate the phase noise accumulated during the propagation through a fiber link. Transfer stabilities of 2 × 10(-15) at 1 second and 4 × 10(-18) at 1000 seconds were achieved in a 90-km link. An active polarization control system was additionally introduced to maintain the transmitted light in an adequate polarization, and consequently, a stable and reliable comparison was accomplished. The instabilities of the all-optical link system, including those of the erbium doped fiber amplifiers (EDFAs) which are free from phase-noise compensation, were below 2 × 10(-15) at 1 second and 7 × 10(-17) at 1000 seconds. The system was available for the direct comparison of two distant (87)Sr lattice clocks via an urban fiber link of 60 km. This technique will be essential for the measuring the reproducibility of optical frequency standards.","corpus_id":11991552,"score":0},{"doc_id":"23002828","title":"Unveiling the intruder deformed 02(+) state in 34Si.","abstract":"The 02(+) state in 34Si has been populated at the GANIL-LISE3 facility through the β decay of a newly discovered 1(+) isomer in 34Al of 26(1) ms half-life. The simultaneous detection of e(+)e(-) pairs allowed the determination of the excitation energy E(02(+))=2719(3) keV and the half-life T(1/2)=19.4(7) ns, from which an electric monopole strength of ρ(2)(E0)=13.0(0.9)×10(-3) was deduced. The 2(1)(+) state is observed to decay both to the 0(1)(+) ground state and to the newly observed 0(2)(+) state [via a 607(2) keV transition] with a ratio R(2(1)(+)→0(1)(+)/2(1)(+)→0(2)(+))=1380(717). Gathering all information, a weak mixing with the 0(1)(+) and a large deformation parameter of β=0.29(4) are found for the 0(2)(+) state, in good agreement with shell model calculations using a new SDPF-U-MIX interaction allowing np-nh excitations across the N=20 shell gap.","corpus_id":8144365,"score":0},{"doc_id":"24802723","title":"Detection of weak frequency jumps for GNSS onboard clocks.","abstract":"In this paper, a weak frequency jump detection method is developed for onboard clocks in global navigation satellite systems (GNSS). A Kalman filter is employed to facilitate the onboard real-time processing of atomic clock measurements, whose N-step prediction residuals are used to construct the weak frequency jump detector. Numerical simulations show that the method can successfully detect weak frequency jumps. The detection method proposed in this paper is helpful for autonomous integrity monitoring of GNSS satellite clocks, and can also be applied to other frequency anomalies with an appropriately modified detector.","corpus_id":21821249,"score":0},{"doc_id":"25166798","title":"Direct observation of long-lived isomers in 212Bi.","abstract":"Long-lived isomers in (212)Bi have been studied following (238)U projectile fragmentation at 670 MeV per nucleon. The fragmentation products were injected as highly charged ions into a storage ring, giving access to masses and half-lives. While the excitation energy of the first isomer of (212)Bi was confirmed, the second isomer was observed at 1478(30) keV, in contrast to the previously accepted value of >1910 keV. It was also found to have an extended Lorentz-corrected in-ring half-life >30 min, compared to 7.0(3) min for the neutral atom. Both the energy and half-life differences can be understood as being due a substantial, though previously unrecognized, internal decay branch for neutral atoms. Earlier shell-model calculations are now found to give good agreement with the isomer excitation energy. Furthermore, these and new calculations predict the existence of states at slightly higher energy that could facilitate isomer deexcitation studies.","corpus_id":15763004,"score":0},{"doc_id":"25615314","title":"Isomer decay spectroscopy of 164Sm and 166Gd: midshell collectivity around N=100.","abstract":"Excited states in the N=102 isotones 166Gd and 164Sm have been observed following isomeric decay for the first time at RIBF, RIKEN. The half-lives of the isomeric states have been measured to be 950(60) and 600(140) ns for 166Gd and 164Sm, respectively. Based on the decay patterns and potential energy surface calculations, including β6 deformation, a spin and parity of 6- has been assigned to the isomeric states in both nuclei. Collective observables are discussed in light of the systematics of the region, giving insight into nuclear shape evolution. The decrease in the ground-band energies of 166Gd and 164Sm (N=102) compared to 164Gd and 162Sm (N=100), respectively, presents evidence for the predicted deformed shell closure at N=100.","corpus_id":19214937,"score":0},{"doc_id":"25734183","title":"Hanle detection for optical clocks.","abstract":"Considering the strong inhomogeneous spatial polarization and intensity distribution of spontaneous decay fluorescence due to the Hanle effect, we propose and demonstrate a universe Hanle detection configuration of electron-shelving method for optical clocks. Experimental results from Ca atomic beam optical frequency standard with electron-shelving method show that a designed Hanle detection geometry with optimized magnetic field direction, detection laser beam propagation and polarization direction, and detector position can improve the fluorescence collection rate by more than one order of magnitude comparing with that of inefficient geometry. With the fixed 423 nm fluorescence, the improved 657 nm optical frequency standard signal intensity is presented. The potential application of the Hanle detection geometry designed for facilitating the fluorescence collection for optical lattice clock with a limited solid angle of the fluorescence collection has been discussed. The Hanle detection geometry is also effective for ion detection in ion optical clock and quantum information experiments. Besides, a cylinder fluorescence collection structure is designed to increase the solid angle of the fluorescence collection in Ca atomic beam optical frequency standard.","corpus_id":16808075,"score":0},{"doc_id":"25855457","title":"Measurement of the first ionization potential of lawrencium, element 103.","abstract":"The chemical properties of an element are primarily governed by the configuration of electrons in the valence shell. Relativistic effects influence the electronic structure of heavy elements in the sixth row of the periodic table, and these effects increase dramatically in the seventh row--including the actinides--even affecting ground-state configurations. Atomic s and p1/2 orbitals are stabilized by relativistic effects, whereas p3/2, d and f orbitals are destabilized, so that ground-state configurations of heavy elements may differ from those of lighter elements in the same group. The first ionization potential (IP1) is a measure of the energy required to remove one valence electron from a neutral atom, and is an atomic property that reflects the outermost electronic configuration. Precise and accurate experimental determination of IP1 gives information on the binding energy of valence electrons, and also, therefore, on the degree of relativistic stabilization. However, such measurements are hampered by the difficulty in obtaining the heaviest elements on scales of more than one atom at a time. Here we report that the experimentally obtained IP1 of the heaviest actinide, lawrencium (Lr, atomic number 103), is 4.96(+0.08)(-0.07) electronvolts. The IP1 of Lr was measured with (256)Lr (half-life 27 seconds) using an efficient surface ion-source and a radioisotope detection system coupled to a mass separator. The measured IP1 is in excellent agreement with the value of 4.963(15) electronvolts predicted here by state-of-the-art relativistic calculations. The present work provides a reliable benchmark for theoretical calculations and also opens the way for IP1 measurements of superheavy elements (that is, transactinides) on an atom-at-a-time scale.","corpus_id":4384213,"score":0},{"doc_id":"26196619","title":"Measurement of Magic Wavelengths for the ^{40}Ca^{+} Clock Transition.","abstract":"We demonstrate experimentally the existence of magic wavelengths and determine the ratio of oscillator strengths for a single trapped ion. For the first time, two magic wavelengths near 396 nm for the ^{40}Ca^{+} clock transition are measured simultaneously with high precision. By tuning the applied laser to an intermediate wavelength between transitions 4s_{1/2}→4p_{1/2} and 4s_{1/2}→4p_{3/2}, the sensitivity of the clock transition Stark shift to the oscillator strengths is greatly enhanced. Furthermore, with the measured magic wavelengths, we determine the ratio of the oscillator strengths with a deviation of less than 0.5%. Our experimental method may be applied to measure magic wavelengths for other ion clock transitions. Promisingly, the measurement of these magic wavelengths paves the way to building all-optical trapped ion clocks.","corpus_id":8619206,"score":0},{"doc_id":"26197020","title":"The half-life of ²²⁷Th by direct and indirect measurements.","abstract":"Utilising a chemically purified solution the radioactive half-life of (227)Th has been determined indirectly by observation of the ingrowth of (223)Ra using an ionisation chamber (IC) and for the first time by direct observation of the change in activity with time using a high-purity germanium (HPGe) γ-ray spectrometer. The radioactive decay was observed for ~104 days (~5.6 half-lives) by γ-ray spectrometry and approximately 63 days and 72 days (~3.4 and ~3.9 half-lives) using an ionisation chamber (IC). The resulting half-life values - 18.695 (4) days (IC) and 18.683 (20) days (HPGe) - are consistent and detailed uncertainty budgets are presented for the two measurement techniques. A weighted mean of our results of 18.695 (4) days is inconsistent with the most precise published half-life value of 18.7176 (52) days (Jordan and Blanke, 1967). A critical evaluation of literature data has been performed, indicating a paucity of reliable and independent measurements. Selected independent published values have been used to determine a recommended half-life of 18.697 (7) days. A method has been introduced in the course of this work so that the recommended half-life of (227)Th as determined by ingrowth can be modified if a different (223)Ra half-life has been determined, evaluated and adopted.","corpus_id":26095962,"score":0},{"doc_id":"26469051","title":"Observation of the competitive double-gamma nuclear decay.","abstract":"The double-gamma (γγ)-decay of a quantum system in an excited state is a fundamental second-order process of quantum electrodynamics. In contrast to the well-known single-gamma (γ)-decay, the γγ-decay is characterized by the simultaneous emission of two γ quanta, each with a continuous energy spectrum. In nuclear physics, this exotic decay mode has only been observed for transitions between states with spin-parity quantum numbers J(π) = 0(+) (refs 1-3). Single-gamma decays-the main experimental obstacle to observing the γγ-decay-are strictly forbidden for these 0(+) → 0(+) transitions. Here we report the observation of the γγ-decay of an excited nuclear state (J(π) = 11/2(-)) that is directly competing with an allowed γ-decay (to ground state J(π) = 3/2(+)). The branching ratio of the competitive γγ-decay of the 11/2(-) isomer of (137)Ba to the ground state relative to its single γ-decay was determined to be (2.05 ± 0.37) × 10(-6). From the measured angular correlation and the shape of the energy spectra of the individual γ-rays, the contributing combinations of multipolarities of the γ radiation were determined. Transition matrix elements calculated using the quasiparticle-phonon model reproduce our measurements well. The γγ-decay rate gives access to so far unexplored important nuclear structure information, such as the generalized (off-diagonal) nuclear electric polarizabilities and magnetic susceptibilities.","corpus_id":4450701,"score":0},{"doc_id":"26849600","title":"Synthetic Spin-Orbit Coupling in an Optical Lattice Clock.","abstract":"We propose the use of optical lattice clocks operated with fermionic alkaline-earth atoms to study spin-orbit coupling (SOC) in interacting many-body systems. The SOC emerges naturally during the clock interrogation, when atoms are allowed to tunnel and accumulate a phase set by the ratio of the \"magic\" lattice wavelength to the clock transition wavelength. We demonstrate how standard protocols such as Rabi and Ramsey spectroscopy that take advantage of the sub-Hertz resolution of state-of-the-art clock lasers can perform momentum-resolved band tomography and determine SOC-induced s-wave collisions in nuclear-spin-polarized fermions. With the use of a second counterpropagating clock beam, we propose a method for engineering controlled atomic transport and study how it is modified by p- and s-wave interactions. The proposed spectroscopic probes provide clean and well-resolved signatures at current clock operating temperatures.","corpus_id":31942577,"score":0},{"doc_id":"27203317","title":"Isomer Shift and Magnetic Moment of the Long-Lived 1/2^{+} Isomer in _{30}^{79}Zn_{49}: Signature of Shape Coexistence near ^{78}Ni.","abstract":"Collinear laser spectroscopy is performed on the _{30}^{79}Zn_{49} isotope at ISOLDE-CERN. The existence of a long-lived isomer with a few hundred milliseconds half-life is confirmed, and the nuclear spins and moments of the ground and isomeric states in ^{79}Zn as well as the isomer shift are measured. From the observed hyperfine structures, spins I=9/2 and I=1/2 are firmly assigned to the ground and isomeric states. The magnetic moment μ (^{79}Zn)=-1.1866(10)μ_{N}, confirms the spin-parity 9/2^{+} with a νg_{9/2}^{-1} shell-model configuration, in excellent agreement with the prediction from large scale shell-model theories. The magnetic moment μ (^{79m}Zn)=-1.0180(12)μ_{N} supports a positive parity for the isomer, with a wave function dominated by a 2h-1p neutron excitation across the N=50 shell gap. The large isomer shift reveals an increase of the intruder isomer mean square charge radius with respect to that of the ground state, δ⟨r_{c}^{2}⟩^{79,79m}=+0.204(6) fm^{2}, providing first evidence of shape coexistence.","corpus_id":7925243,"score":0},{"doc_id":"27432734","title":"An exacting transition probability measurement - a direct test of atomic many-body theories.","abstract":"A new protocol for measuring the branching fraction of hydrogenic atoms with only statistically limited uncertainty is proposed and demonstrated for the decay of the P3/2 level of the barium ion, with precision below 0.5%. Heavy hydrogenic atoms like the barium ion are test beds for fundamental physics such as atomic parity violation and they also hold the key to understanding nucleo-synthesis in stars. To draw definitive conclusion about possible physics beyond the standard model by measuring atomic parity violation in the barium ion it is necessary to measure the dipole transition probabilities of low-lying excited states with a precision better than 1%. Furthermore, enhancing our understanding of the barium puzzle in barium stars requires branching fraction data for proper modelling of nucleo-synthesis. Our measurements are the first to provide a direct test of quantum many-body calculations on the barium ion with a precision below one percent and more importantly with no known systematic uncertainties. The unique measurement protocol proposed here can be easily extended to any decay with more than two channels and hence paves the way for measuring the branching fractions of other hydrogenic atoms with no significant systematic uncertainties.","corpus_id":17464158,"score":0},{"doc_id":"27680707","title":"Atom-at-a-time laser resonance ionization spectroscopy of nobelium.","abstract":"Optical spectroscopy of a primordial isotope has traditionally formed the basis for understanding the atomic structure of an element. Such studies have been conducted for most elements and theoretical modelling can be performed to high precision, taking into account relativistic effects that scale approximately as the square of the atomic number. However, for the transfermium elements (those with atomic numbers greater than 100), the atomic structure is experimentally unknown. These radioactive elements are produced in nuclear fusion reactions at rates of only a few atoms per second at most and must be studied immediately following their production, which has so far precluded their optical spectroscopy. Here we report laser resonance ionization spectroscopy of nobelium (No; atomic number 102) in single-atom-at-a-time quantities, in which we identify the ground-state transition (1)S0(1)P1. By combining this result with data from an observed Rydberg series, we obtain an upper limit for the ionization potential of nobelium. These accurate results from direct laser excitations of outer-shell electrons cannot be achieved using state-of-the-art relativistic many-body calculations that include quantum electrodynamic effects, owing to large uncertainties in the modelled transition energies of the complex systems under consideration. Our work opens the door to high-precision measurements of various atomic and nuclear properties of elements heavier than nobelium, and motivates future theoretical work.","corpus_id":205250445,"score":0},{"doc_id":"28009197","title":"Nuclear Excitation by Two-Photon Electron Transition.","abstract":"A new mechanism of nuclear excitation via two-photon electron transitions (NETP) is proposed and studied theoretically. As a generic example, detailed calculations are performed for the E1E1 1s2s^{1}S_{0}→1s^{2}^{1}S_{0} two-photon decay of a He-like ^{225}Ac^{87+} ion with a resonant excitation of the 3/2+ nuclear state with an energy of 40.09(5) keV. The probability for such a two-photon decay via the nuclear excitation is found to be P_{NETP}=3.5×10^{-9} and, thus, is comparable with other mechanisms, such as nuclear excitation by electron transition and by electron capture. The possibility for the experimental observation of the proposed mechanism is thoroughly discussed.","corpus_id":34868512,"score":0},{"doc_id":"29053333","title":"Spin Resonance Clock Transition of the Endohedral Fullerene ^{15}N@C_{60}.","abstract":"The endohedral fullerene ^{15}N@C_{60} has narrow electron paramagnetic resonance lines which have been proposed as the basis for a condensed-matter portable atomic clock. We measure the low-frequency spectrum of this molecule, identifying and characterizing a clock transition at which the frequency becomes insensitive to magnetic field. We infer a linewidth at the clock field of 100 kHz. Using experimental data, we are able to place a bound on the clock's projected frequency stability. We discuss ways to improve the frequency stability to be competitive with existing miniature clocks.","corpus_id":13826533,"score":0},{"doc_id":"29481161","title":"Tailoring Laser-Generated Plasmas for Efficient Nuclear Excitation by Electron Capture.","abstract":"The optimal parameters for nuclear excitation by electron capture in plasma environments generated by the interaction of ultrastrong optical lasers with solid matter are investigated theoretically. As a case study we consider a 4.85 keV nuclear transition starting from the long-lived ^{93m}Mo isomer that can lead to the release of the stored 2.4 MeV excitation energy. We find that due to the complex plasma dynamics, the nuclear excitation rate and the actual number of excited nuclei do not reach their maximum at the same laser parameters. The nuclear excitation achievable with a high-power optical laser is up to twelve and up to six orders of magnitude larger than the values predicted for direct resonant and secondary plasma-mediated excitation at the x-ray free electron laser, respectively. Our results show that the experimental observation of the nuclear excitation of ^{93m}Mo and the subsequent release of stored energy should be possible at laser facilities available today.","corpus_id":3703860,"score":0}],"string":"[\n {\n \"doc_id\": \"19519091\",\n \"title\": \"Proposed experimental method to determine alpha sensitivity of splitting between ground and 7.6 eV isomeric states in 229Th.\",\n \"abstract\": \"The 7.6 eV electromagnetic transition between the nearly degenerate ground state and first excited state in the 229Th nucleus may be very sensitive to potential changes in the fine-structure constant, alpha=e2/variant Planck's over 2pic. However, the sensitivity is not known, and nuclear calculations are currently unable to determine it. We propose measurements of the differences of atomic transition frequencies between thorium atoms (or ions) with the nucleus in the ground state and in the first excited (isomeric) state. This will enable extraction of the change in nuclear charge radius and electric-quadrupole moment between the isomers, and hence the alpha dependence of the isomeric transition frequency with reasonable accuracy.\",\n \"corpus_id\": 32016190,\n \"score\": 2\n },\n {\n \"doc_id\": \"20867093\",\n \"title\": \"Exponential increase of energy level density in atoms: Th and Th II.\",\n \"abstract\": \"We present analytical estimates and numerical calculations showing that the energy level density in open-shell atoms increases exponentially with the increase of excitation energy. As an example, we use the relativistic Hartree-Fock and configuration interaction methods to calculate the density of states of Th and Th II. The result is used to estimate the effect of electrons on the nuclear transition which is considered for the nuclear clock.\",\n \"corpus_id\": 9116791,\n \"score\": 2\n },\n {\n \"doc_id\": \"21231100\",\n \"title\": \"Excitation of the isomeric 229mTh nuclear state via an electronic bridge process in 229Th+.\",\n \"abstract\": \"We consider the excitation of the nuclear transition 229gTh-229mTh near 7.6 eV in singly ionized thorium via an electronic bridge process. The process relies on the excitation of the electron shell by two laser photons whose sum frequency is equal to the nuclear transition frequency. This scheme allows us to determine the nuclear transition frequency with high accuracy. Based on calculations of the electronic level structure of Th+ which combine the configuration-interaction method and many-body perturbation theory, we estimate that a nuclear excitation rate in the range of 10 s⁻¹ can be obtained using conventional laser sources.\",\n \"corpus_id\": 26691210,\n \"score\": 2\n },\n {\n \"doc_id\": \"21599361\",\n \"title\": \"Proposal for a nuclear gamma-ray laser of optical range.\",\n \"abstract\": \"A possibility of the amplification of the 7.6 eV γ radiation by the stimulated γ emission of the ensemble of the (229m)Th isomeric nuclei in a host dielectric crystal is proved theoretically. This amplification is a result of (1) the excitation of a large number of (229m)Th isomers by laser radiation, (2) the creation of the inverse population of nuclear levels in a cooled sample owing to the interaction of thorium nuclei with the crystal electric field or with an external magnetic field, (3) the emission or absorption of the optical photons by thorium nuclei in the crystal without recoil, and (4) the nuclear spin relaxation through the conduction electrons of the metallic covering.\",\n \"corpus_id\": 40173588,\n \"score\": 2\n },\n {\n \"doc_id\": \"22540568\",\n \"title\": \"Single-ion nuclear clock for metrology at the 19th decimal place.\",\n \"abstract\": \"The 7.6(5) eV nuclear magnetic-dipole transition in a single 229Th3+ ion may provide the foundation for an optical clock of superb accuracy. A virtual clock transition composed of stretched states within the 5F(5/2) electronic ground level of both nuclear ground and isomeric manifolds is proposed. It is shown to offer unprecedented systematic shift suppression, allowing for clock performance with a total fractional inaccuracy approaching 1×10(-19).\",\n \"corpus_id\": 40863227,\n \"score\": 2\n },\n {\n \"doc_id\": \"23215066\",\n \"title\": \"Observation of the deexcitation of the (229m)Th nuclear isomer.\",\n \"abstract\": \"The (229)Th nucleus possesses the lowest-energy nuclear isomeric state. Two widely accepted indirect measurements of the transition energy place it within reach of existing laser capabilities. Direct searches for the isomer deexcitation have proven elusive despite extensive effort over the past couple of decades. There is now a growing interest in finding this unique transition because of its potential applications in nuclear, atomic, condensed matter, and optical physics, quantum information, metrology, and cosmology, including the development of a new type of clock based on this nuclear transition. In this Letter we report the first direct observation of the deexcitation of the lowest-lying isomeric state in (229)Th. By collecting (229)Th recoils following the alpha decay of (233)U into MgF(2) plates and measuring the subsequent light emission, we have isolated the isomer deexcitation and measured the transition's half-life to be 6±1 h. Through comparison measurements with (235m)U isomer, we found that the observed (229m)Th deexcitation signal originates from photon emission rather than internal conversion electron emission. This discovery lays the groundwork for optical and laser spectroscopy of (229m)Th nuclear isomer and the development of a (229)Th nuclear clock.\",\n \"corpus_id\": 23528635,\n \"score\": 2\n },\n {\n \"doc_id\": \"23368553\",\n \"title\": \"Coherence-enhanced optical determination of the 229Th isomeric transition.\",\n \"abstract\": \"The impact of coherent light propagation on the excitation and fluorescence of thorium nuclei in a crystal lattice environment is investigated theoretically. We find that in the forward direction, the fluorescence signal exhibits characteristic intensity modulations dominated by a sped-up initial decay signal that is orders of magnitude faster. This feature can be exploited for the optical determination of the isomeric transition energy. In order to obtain a unmistakable signature of the isomeric nuclear fluorescence, we put forward a novel scheme for the direct measurement of the transition energy via electromagnetically modified nuclear forward scattering involving two fields that couple to three nuclear states.\",\n \"corpus_id\": 9119621,\n \"score\": 2\n },\n {\n \"doc_id\": \"24580690\",\n \"title\": \"Hyperfine structure in 229gTh3+ as a probe of the 229gTh→ 229mTh nuclear excitation energy.\",\n \"abstract\": \"We identify a potential means to extract the 229gTh→ 229mTh nuclear excitation energy from precision microwave spectroscopy of the 5F(5/2,7/2) hyperfine manifolds in the ion 229gTh3+. The hyperfine interaction mixes this ground fine structure doublet with states of the nuclear isomer, introducing small but observable shifts to the hyperfine sublevels. We demonstrate how accurate atomic structure calculations may be combined with the measurement of the hyperfine intervals to quantify the effects of this mixing. Further knowledge of the magnetic dipole decay rate of the isomer, as recently reported, allows an indirect determination of the nuclear excitation energy.\",\n \"corpus_id\": 46019966,\n \"score\": 2\n },\n {\n \"doc_id\": \"24937606\",\n \"title\": \"Investigation of thorium salts as candidate materials for direct observation of the (229m)Th nuclear transition.\",\n \"abstract\": \"Recent efforts to measure the (229m)Th → (229g)Th nuclear transition sparked interest in understanding the electronic structure of wide-gap thorium salts. Such materials could be used to measure this nuclear transition using optical spectroscopy in solid-state devices. Here, we present screened hybrid density functional theory and many-body G0W0 calculations of two candidate materials, namely, Na2ThF6 and ThF4, for such a measurement. Our results show an electronic gap larger than 10 eV for both materials, suggesting that the internal conversion nuclear de-excitation channel would be suppressed in these materials. We also present results for ThX4 (X = Cl, Br, I), materials with smaller gaps significantly easier to access experimentally.\",\n \"corpus_id\": 20810437,\n \"score\": 2\n },\n {\n \"doc_id\": \"25844000\",\n \"title\": \"Prospects for measuring the 229Th isomer energy using a metallic magnetic microcalorimeter.\",\n \"abstract\": \"The Thorium-229 isotope features a nuclear isomer state with an extremely low energy. The currently most accepted energy value, 7.8±0.5 eV, was obtained from an indirect measurement using a NASA x-ray microcalorimeter with an instrumental resolution 26 eV. We study, how state-of-the-art magnetic metallic microcalorimeters with an energy resolution down to a few eV can be used to measure the isomer energy. In particular, resolving the 29.18 keV doublet in the γ-spectrum following the α-decay of Uranium-233, corresponding to the decay into the ground and isomer state, allows to measure the isomer transition energy without additional theoretical input parameters, and increase the energy accuracy. We study the possibility of resolving the 29.18 keV line as a doublet and the dependence of the attainable precision of the energy measurement on the signal and background count rates and the instrumental resolution.\",\n \"corpus_id\": 5241191,\n \"score\": 2\n },\n {\n \"doc_id\": \"25906029\",\n \"title\": \"Multisectional linear ion trap and novel loading method for optical spectroscopy of electron and nuclear transitions.\",\n \"abstract\": \"There is a growing need for the development of atomic and nuclear frequency standards because of the important contribution of methods for precision time and frequency measurements to the development of fundamental science, technology, and the economy. It is also conditioned by their potential use in optical clocks and quantum logic applications. It is especially important to develop a universal method that could allow one to use ions of most elements effectively (including ones that are not easily evaporated) proposed for the above-mentioned applications. A linear quadrupole ion trap for the optical spectroscopy of electron and nuclear transitions has been developed and evaluated experimentally. An ion source construction is based on an ultra-high vacuum evaporator in which a metal sample is subjected to an electron beam of energy up to 1 keV, resulting in the appearance of gaseous atoms and ions of various charge state. The linear ion trap consists of five successive quadrupole sections including an entrance quadrupole section, quadrupole mass filter, quadrupole ion guide, ion-trap section, and exit quadrupole section. The same radiofrequency but a different direct current voltage feeds the quadrupole sections. The instrument allows the mass and energy selected trapping of ions from ion beams of various intensities and their localization in the area of laser irradiation. The preliminary results presented show that the proposed instrument and methods allow one to produce effectively up to triply charged thorium ions as well as to trap ions for future spectroscopic study. The instrument is proposed for future use in optical clocks and quantum logic application development.\",\n \"corpus_id\": 22584427,\n \"score\": 2\n },\n {\n \"doc_id\": \"26197124\",\n \"title\": \"Results of a Direct Search Using Synchrotron Radiation for the Low-Energy (229)Th Nuclear Isomeric Transition.\",\n \"abstract\": \"We report the results of a direct search for the (229)Th (I(π)=3/2(+)←5/2(+)) nuclear isomeric transition, performed by exposing (229)Th-doped LiSrAlF(6) crystals to tunable vacuum-ultraviolet synchrotron radiation and observing any resulting fluorescence. We also use existing nuclear physics data to establish a range of possible transition strengths for the isomeric transition. We find no evidence for the thorium nuclear transition between 7.3 eV and 8.8 eV with transition lifetime (1-2) s≲τ≲(2000-5600) s. This measurement excludes roughly half of the favored transition search area and can be used to direct future searches.\",\n \"corpus_id\": 1322253,\n \"score\": 2\n },\n {\n \"doc_id\": \"26502749\",\n \"title\": \"Radioluminescence and photoluminescence of Th:CaF2 crystals.\",\n \"abstract\": \"We study thorium-doped CaF2 crystals as a possible platform for optical spectroscopy of the (229)Th nuclear isomer transition. We anticipate two major sources of background signal that might cover the nuclear spectroscopy signal: VUV-photoluminescence, caused by the probe light, and radioluminescence, caused by the radioactive decay of (229)Th and its daughters. We find a rich photoluminescence spectrum at wavelengths above 260 nm, and radioluminescence emission above 220 nm. This is very promising, as fluorescence originating from the isomer transition, predicted at a wavelength shorter than 200 nm, could be filtered spectrally from the crystal luminescence. Furthermore, we investigate the temperature-dependent decay time of the luminescence, as well as thermoluminescence properties. Our findings allow for an immediate optimization of spectroscopy protocols for both the initial search for the nuclear transition using synchrotron radiation, as well as future optical clock operation with narrow-linewidth lasers.\",\n \"corpus_id\": 15417434,\n \"score\": 2\n },\n {\n \"doc_id\": \"28186791\",\n \"title\": \"Lifetime Measurement of the ^{229}Th Nuclear Isomer.\",\n \"abstract\": \"The first excited isomeric state of ^{229}Th possesses the lowest energy among all known excited nuclear states. The expected energy is accessible with today's laser technology and in principle allows for a direct optical laser excitation of the nucleus. The isomer decays via three channels to its ground state (internal conversion, γ decay, and bound internal conversion), whose strengths depend on the charge state of ^{229m}Th. We report on the measurement of the internal-conversion decay half-life of neutral ^{229m}Th. A half-life of 7±1 μs has been measured, which is in the range of theoretical predictions and, based on the theoretically expected lifetime of ≈10^{4} s of the photonic decay channel, gives further support for an internal conversion coefficient of ≈10^{9}, thus constraining the strength of a radiative branch in the presence of internal conversion.\",\n \"corpus_id\": 37518294,\n \"score\": 2\n },\n {\n \"doc_id\": \"28598657\",\n \"title\": \"Reduced Transition Probabilities for the Gamma Decay of the 7.8 eV Isomer in ^{229}Th.\",\n \"abstract\": \"The reduced magnetic dipole and electric quadrupole transition probabilities for the radiative decay of the ^{229}Th 7.8 eV isomer to the ground state are predicted within a detailed nuclear-structure model approach. We show that the presence and decay of this isomer can only be accounted for by the Coriolis mixing emerging from a remarkably fine interplay between the coherent quadrupole-octupole motion of the nuclear core and the single-nucleon motion within a reflection-asymmetric deformed potential. We find that the magnetic dipole transition probability which determines the radiative lifetime of the isomer is considerably smaller than presently estimated. The so-far disregarded electric quadrupole component may have non-negligible contributions to the internal conversion channel. These findings support new directions in the experimental search of the ^{229}Th transition frequency for the development of a future nuclear frequency standard.\",\n \"corpus_id\": 40694257,\n \"score\": 2\n },\n {\n \"doc_id\": \"29341722\",\n \"title\": \"A Laser Excitation Scheme for ^{229m}Th.\",\n \"abstract\": \"Direct laser excitation of the lowest known nuclear excited state in ^{229}Th has been a long-standing objective. It is generally assumed that reaching this goal would require a considerably reduced uncertainty of the isomer's excitation energy compared to the presently adopted value of (7.8±0.5) eV. Here we present a direct laser excitation scheme for ^{229m}Th, which circumvents this requirement. The proposed excitation scheme makes use of already existing laser technology and therefore paves the way for nuclear laser spectroscopy. In this concept, the recently experimentally observed internal-conversion decay channel of the isomeric state is used for probing the isomeric population. A signal-to-background ratio of better than 10^{4} and a total measurement time of less than three days for laser scanning appear to be achievable.\",\n \"corpus_id\": 42216312,\n \"score\": 2\n },\n {\n \"doc_id\": \"29670266\",\n \"title\": \"Laser spectroscopic characterization of the nuclear-clock isomer 229mTh.\",\n \"abstract\": \"The isotope 229Th is the only nucleus known to possess an excited state 229mTh in the energy range of a few electronvolts-a transition energy typical for electrons in the valence shell of atoms, but about four orders of magnitude lower than typical nuclear excitation energies. Of the many applications that have been proposed for this nuclear system, which is accessible by optical methods, the most promising is a highly precise nuclear clock that outperforms existing atomic timekeepers. Here we present the laser spectroscopic investigation of the hyperfine structure of the doubly charged 229mTh ion and the determination of the fundamental nuclear properties of the isomer, namely, its magnetic dipole and electric quadrupole moments, as well as its nuclear charge radius. Following the recent direct detection of this long-sought isomer, we provide detailed insight into its nuclear structure and present a method for its non-destructive optical detection.\",\n \"corpus_id\": 4990345,\n \"score\": 2\n },\n {\n \"doc_id\": \"29694057\",\n \"title\": \"Decay Rate of the Nuclear Isomer ^{229}Th(3/2^{+},7.8 eV) in a Dielectric Sphere, Thin Film, and Metal Cavity.\",\n \"abstract\": \"The main decay channels of the anomalous low-energy 3/2^{+}(7.8±0.5 eV) isomeric level of the ^{229}Th nucleus, namely the γ emission and internal conversion, inside a dielectric sphere, dielectric thin film, and conducting spherical microcavity are investigated theoretically, taking into account the effect of media interfaces. It is shown that (1) the γ decay rate of the nuclear isomer inside a dielectric thin film and dielectric microsphere placed in a vacuum or in a metal cavity can decrease (increase) in dozen of times, (2) the γ activity of the distributed source as a function of time can be nonexponential, and (3) the metal cavity, whose size is of the order of the radiation wavelength, does not affect the probability of the internal conversion in ^{229}Th, because the virtual photon attenuates at much shorter distances and the reflected wave is very weak.\",\n \"corpus_id\": 13857642,\n \"score\": 2\n },\n {\n \"doc_id\": \"19792559\",\n \"title\": \"Spin-1/2 optical lattice clock.\",\n \"abstract\": \"We experimentally investigate an optical clock based on ;{171}Yb (I = 1/2) atoms confined in an optical lattice. We have evaluated all known frequency shifts to the clock transition, including a density-dependent collision shift, with a fractional uncertainty of 3.4 x 10;{-16}, limited principally by uncertainty in the blackbody radiation Stark shift. We measured the absolute clock transition frequency relative to the NIST-F1 Cs fountain clock and find the frequency to be 518 295 836 590 865.2(0.7) Hz.\",\n \"corpus_id\": 7416845,\n \"score\": 1\n },\n {\n \"doc_id\": \"22481777\",\n \"title\": \"Blackbody radiation shifts in optical atomic clocks.\",\n \"abstract\": \"A review of recent theoretical calculations of blackbody radiation (BBR) shifts in optical atomic clocks is presented. We summarize previous results for monovalent ions that were obtained by a relativistic all-order single-double method, where all single and double excitations of the Dirac- Fock wave function are included to all orders of perturbation theory. A recently developed method for accurate calculations of BBR shifts in divalent atoms is then presented. This approach combines the relativistic all-order method and the configuration interaction method, which provides for accurate treatment of correlation corrections in atoms with two valence electrons. Calculations of the BBR shifts in B+, Al+, and In+ have enabled us to reduce the present fractional uncertainties in the frequencies of their clock transitions as measured at room temperature: to 4 × 10-19 for Al+ and 10-18 for B+ and In+. These uncertainties approach recent estimates of the limits of precision of currently proposed optical atomic clocks. We discuss directions of future theoretical developments for reducing clock uncertainties resulting from blackbody radiation shifts.\",\n \"corpus_id\": 16838058,\n \"score\": 1\n },\n {\n \"doc_id\": \"22539714\",\n \"title\": \"A 920-kilometer optical fiber link for frequency metrology at the 19th decimal place.\",\n \"abstract\": \"Optical clocks show unprecedented accuracy, surpassing that of previously available clock systems by more than one order of magnitude. Precise intercomparisons will enable a variety of experiments, including tests of fundamental quantum physics and cosmology and applications in geodesy and navigation. Well-established, satellite-based techniques for microwave dissemination are not adequate to compare optical clocks. Here, we present phase-stabilized distribution of an optical frequency over 920 kilometers of telecommunication fiber. We used two antiparallel fiber links to determine their fractional frequency instability (modified Allan deviation) to 5 × 10(-15) in a 1-second integration time, reaching 10(-18) in less than 1000 seconds. For long integration times τ, the deviation from the expected frequency value has been constrained to within 4 × 10(-19). The link may serve as part of a Europe-wide optical frequency dissemination network.\",\n \"corpus_id\": 19895554,\n \"score\": 1\n },\n {\n \"doc_id\": \"23037353\",\n \"title\": \"Direct comparison of a Ca+ single-ion clock against a Sr lattice clock to verify the absolute frequency measurement.\",\n \"abstract\": \"Optical frequency comparison of the (40)Ca(+) clock transition ν(Ca)((2)S(1/2-)(2D(5/2), 729 nm) against the (87)Sr optical lattice clock transition ν(Sr) ((1)S(0)-(3)P(0), 698 nm) has resulted in a frequency ratio ν(Ca) / ν(Sr) = 0.957 631 202 358 049 9(2 3). The rapid nature of optical comparison allowed the statistical uncertainty of frequency ratio ν(Ca) / ν(Sr) to reach 1 × 10(-15) in 1000s and yielded a value consistent with that calculated from separate absolute frequency measurements of ν(Ca) using the International Atomic Time (TAI) link. The total uncertainty of the frequency ratio using optical comparison (free from microwave link uncertainties) is smaller than that obtained using absolute frequency measurement, demonstrating the advantage of optical frequency evaluation. We note that the absolute frequency of (40)Ca(+) we measure deviates from other published values by more than three times our measurement uncertainty.\",\n \"corpus_id\": 10441002,\n \"score\": 1\n },\n {\n \"doc_id\": \"23679589\",\n \"title\": \"s-Wave collisional frequency shift of a fermion clock.\",\n \"abstract\": \"We report an s-wave collisional frequency shift of an atomic clock based on fermions. In contrast to bosons, the fermion clock shift is insensitive to the population difference of the clock states, set by the first pulse area in Ramsey spectroscopy, θ(1). The fermion shift instead depends strongly on the second pulse area θ(2). It allows the shift to be canceled, nominally at θ(2)=π/2, but correlations perturb the null to slightly larger θ(2). The frequency shift is relevant for optical lattice clocks and increases with the spatial inhomogeneity of the clock excitation field, naturally larger at optical frequencies.\",\n \"corpus_id\": 13315531,\n \"score\": 1\n },\n {\n \"doc_id\": \"23970562\",\n \"title\": \"An atomic clock with 10(-18) instability.\",\n \"abstract\": \"Atomic clocks have been instrumental in science and technology, leading to innovations such as global positioning, advanced communications, and tests of fundamental constant variation. Timekeeping precision at 1 part in 10(18) enables new timing applications in relativistic geodesy, enhanced Earth- and space-based navigation and telescopy, and new tests of physics beyond the standard model. Here, we describe the development and operation of two optical lattice clocks, both using spin-polarized, ultracold atomic ytterbium. A measurement comparing these systems demonstrates an unprecedented atomic clock instability of 1.6 × 10(-18) after only 7 hours of averaging.\",\n \"corpus_id\": 206549862,\n \"score\": 1\n },\n {\n \"doc_id\": \"24463513\",\n \"title\": \"An optical lattice clock with accuracy and stability at the 10(-18) level.\",\n \"abstract\": \"Progress in atomic, optical and quantum science has led to rapid improvements in atomic clocks. At the same time, atomic clock research has helped to advance the frontiers of science, affecting both fundamental and applied research. The ability to control quantum states of individual atoms and photons is central to quantum information science and precision measurement, and optical clocks based on single ions have achieved the lowest systematic uncertainty of any frequency standard. Although many-atom lattice clocks have shown advantages in measurement precision over trapped-ion clocks, their accuracy has remained 16 times worse. Here we demonstrate a many-atom system that achieves an accuracy of 6.4 × 10(-18), which is not only better than a single-ion-based clock, but also reduces the required measurement time by two orders of magnitude. By systematically evaluating all known sources of uncertainty, including in situ monitoring of the blackbody radiation environment, we improve the accuracy of optical lattice clocks by a factor of 22. This single clock has simultaneously achieved the best known performance in the key characteristics necessary for consideration as a primary standard-stability and accuracy. More stable and accurate atomic clocks will benefit a wide range of fields, such as the realization and distribution of SI units, the search for time variation of fundamental constants, clock-based geodesy and other precision tests of the fundamental laws of nature. This work also connects to the development of quantum sensors and many-body quantum state engineering (such as spin squeezing) to advance measurement precision beyond the standard quantum limit.\",\n \"corpus_id\": 4461081,\n \"score\": 1\n },\n {\n \"doc_id\": \"24718165\",\n \"title\": \"Frequency ratio measurement of 171Yb and 87Sr optical lattice clocks.\",\n \"abstract\": \"The frequency ratio of the (1)S(0)(F = 1/2)-(3)P(0)(F = 1/2) clock transition in (171)Yb and the (1)S(0)(F = 9/2)-(3)P(0)(F = 9/2) clock transition in (87)Sr is measured by an optical-optical direct frequency link between two optical lattice clocks. We determined the ratio (ν(Yb)/ν(Sr)) to be 1.207 507 039 343 341 2(17) fractional standard uncertainty of 1.4 × 10(-15) [corrected]. The measurement uncertainty of the frequency ratio is smaller than that obtained from absolute frequency measurements using the International Atomic Time (TAI) link. The measured ratio agrees well with that derived from the absolute frequency measurement results obtained at NIST and JILA, Boulder, CO using their Cs-fountain clock. Our measurement enables the first international comparison of the frequency ratios of optical clocks. The measured frequency ratio will be reported to the International Committee for Weights and Measures for a discussion related to the redefinition of the second.\",\n \"corpus_id\": 207329094,\n \"score\": 1\n },\n {\n \"doc_id\": \"25083643\",\n \"title\": \"Measurement of the hyperfine quenching rate of the clock transition in 171YB.\",\n \"abstract\": \"We report the first experimental determination of the hyperfine quenching rate of the 6s(2) (1)S(0)(F = 1/2) - 6s6p (3)P(0)(F = 1/2) transition in (171)Yb with nuclear spin I = 1/2. This rate determines the natural linewidth and the Rabi frequency of the clock transition of a Yb optical frequency standard. Our technique involves spectrally resolved fluorescence decay measurements of the lowest lying (3)P(0,1) levels of neutral Yb atoms embedded in a solid Ne matrix. The solid Ne provides a simple way to trap a large number of atoms as well as an efficient mechanism for populating (3)P(0). The decay rates in solid Ne are modified by medium effects including the index-of-refraction dependence. We find the (3)P(0) hyperfine quenching rate to be (4.42 ± 0.35) × 10(-2) s(-1) for free (171)Yb, which agrees with recent ab initio calculations.\",\n \"corpus_id\": 45636356,\n \"score\": 1\n },\n {\n \"doc_id\": \"25121654\",\n \"title\": \"Direct comparison of optical lattice clocks with an intercontinental baseline of 9000 km.\",\n \"abstract\": \"We have demonstrated a direct frequency comparison between two ⁸⁷Sr lattice clocks operated in intercontinentally separated laboratories in real time. Two-way satellite time and frequency transfer technique, based on the carrier-phase, was employed for a direct comparison, with a baseline of 9000 km between Japan and Germany. A frequency comparison was achieved for 83,640 s, resulting in a fractional difference of (1.1±1.6)×10⁻¹⁵, where the statistical part is the largest contributor to the uncertainty. This measurement directly confirms the agreement of the two optical frequency standards on an intercontinental scale.\",\n \"corpus_id\": 7835779,\n \"score\": 1\n },\n {\n \"doc_id\": \"25479482\",\n \"title\": \"Frequency ratio of two optical clock transitions in 171Yb+ and constraints on the time variation of fundamental constants.\",\n \"abstract\": \"Singly ionized ytterbium, with ultranarrow optical clock transitions at 467 and 436 nm, is a convenient system for the realization of optical atomic clocks and tests of present-day variation of fundamental constants. We present the first direct measurement of the frequency ratio of these two clock transitions, without reference to a cesium primary standard, and using the same single ion of 171Yb+. The absolute frequencies of both transitions are also presented, each with a relative standard uncertainty of 6×10(-16). Combining our results with those from other experiments, we report a threefold improvement in the constraint on the time variation of the proton-to-electron mass ratio, μ/μ=0.2(1.1)×10(-16) yr(-1), along with an improved constraint on time variation of the fine structure constant, α/α=-0.7(2.1)×10(-17) yr(-1).\",\n \"corpus_id\": 30505674,\n \"score\": 1\n },\n {\n \"doc_id\": \"26459877\",\n \"title\": \"Direct frequency comb optical frequency standard based on two-photon transitions of thermal atoms.\",\n \"abstract\": \"Optical clocks have been the focus of science and technology research areas due to their capability to provide highest frequency accuracy and stability to date. Their superior frequency performance promises significant advances in the fields of fundamental research as well as practical applications including satellite-based navigation and ranging. In traditional optical clocks, ultrastable optical cavities, laser cooling and particle (atoms or a single ion) trapping techniques are employed to guarantee high stability and accuracy. However, on the other hand, they make optical clocks an entire optical tableful of equipment, and cannot work continuously for a long time; as a result, they restrict optical clocks used as very convenient and compact time-keeping clocks. In this article, we proposed, and experimentally demonstrated, a novel scheme of optical frequency standard based on comb-directly-excited atomic two-photon transitions. By taking advantage of the natural properties of the comb and two-photon transitions, this frequency standard achieves a simplified structure, high robustness as well as decent frequency stability, which promise widespread applications in various scenarios.\",\n \"corpus_id\": 16134761,\n \"score\": 1\n },\n {\n \"doc_id\": \"26705620\",\n \"title\": \"Towards a Mg Lattice Clock: Observation of the ^{1}S_{0}-^{3}P_{0} Transition and Determination of the Magic Wavelength.\",\n \"abstract\": \"We optically excite the electronic state 3s3p ^{3}P_{0} in ^{24}Mg atoms, laser cooled and trapped in a magic-wavelength lattice. An applied magnetic field enhances the coupling of the light to the otherwise strictly forbidden transition. We determine the magic wavelength, the quadratic magnetic Zeeman shift, and the transition frequency to be 468.46(21) nm, -206.6(2.0) MHz/T^{2}, and 655 058 646 691(101) kHz, respectively. These are compared with theoretical predictions and results from complementary experiments. We also develop a high-precision relativistic structure model for magnesium, give an improved theoretical value for the blackbody radiation shift, and discuss a clock based on bosonic magnesium.\",\n \"corpus_id\": 206265528,\n \"score\": 1\n },\n {\n \"doc_id\": \"27503795\",\n \"title\": \"A clock network for geodesy and fundamental science.\",\n \"abstract\": \"Leveraging the unrivalled performance of optical clocks as key tools for geo-science, for astronomy and for fundamental physics beyond the standard model requires comparing the frequency of distant optical clocks faithfully. Here, we report on the comparison and agreement of two strontium optical clocks at an uncertainty of 5 × 10(-17) via a newly established phase-coherent frequency link connecting Paris and Braunschweig using 1,415 km of telecom fibre. The remote comparison is limited only by the instability and uncertainty of the strontium lattice clocks themselves, with negligible contributions from the optical frequency transfer. A fractional precision of 3 × 10(-17) is reached after only 1,000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than any previous long-distance clock comparison. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optical dissemination of the SI-second.\",\n \"corpus_id\": 14769489,\n \"score\": 1\n },\n {\n \"doc_id\": \"27740781\",\n \"title\": \"Improvement of an Atomic Clock using Squeezed Vacuum.\",\n \"abstract\": \"Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case, the vacuum noise restricts the precision of the interferometer to the standard quantum limit (SQL). Here, we propose and experimentally demonstrate a novel clock configuration that surpasses the SQL by squeezing the vacuum in the empty input state. We create a squeezed vacuum state containing an average of 0.75 atoms to improve the clock sensitivity of 10000 atoms by 2.05_{-0.37}^{+0.34} dB. The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based on atomic squeezed vacuum.\",\n \"corpus_id\": 36182186,\n \"score\": 1\n },\n {\n \"doc_id\": \"27757423\",\n \"title\": \"Superradiance on the millihertz linewidth strontium clock transition.\",\n \"abstract\": \"Laser frequency noise contributes a significant limitation to today's best atomic clocks. A proposed solution to this problem is to create a superradiant laser using an optical clock transition as its gain medium. This laser would act as an active atomic clock and would be highly immune to the fluctuations in reference cavity length that limit today's best lasers. We demonstrate and characterize superradiant emission from the millihertz linewidth clock transition in an ensemble of laser-cooled (87)Sr atoms trapped within a high-finesse optical cavity. We measure a collective enhancement of the emission rate into the cavity mode by a factor of more than 10,000 compared to independently radiating atoms. We also demonstrate a method for seeding superradiant emission and observe interference between two independent transitions lasing simultaneously. We use this interference to characterize the relative spectral properties of the two lasing subensembles.\",\n \"corpus_id\": 15533256,\n \"score\": 1\n },\n {\n \"doc_id\": \"29328726\",\n \"title\": \"Atom Interferometry with the Sr Optical Clock Transition.\",\n \"abstract\": \"We report on the realization of a matter-wave interferometer based on single-photon interaction on the ultranarrow optical clock transition of strontium atoms. We experimentally demonstrate its operation as a gravimeter and as a gravity gradiometer. No reduction of interferometric contrast was observed for a total interferometer time up to ∼10 ms, limited by geometric constraints of the apparatus. Single-photon interferometers represent a new class of high-precision sensors that could be used for the detection of gravitational waves in so far unexplored frequency ranges and to enlighten the boundary between quantum mechanics and general relativity.\",\n \"corpus_id\": 206305543,\n \"score\": 1\n },\n {\n \"doc_id\": \"29420479\",\n \"title\": \"Isomer depletion as experimental evidence of nuclear excitation by electron capture.\",\n \"abstract\": \"The atomic nucleus and its electrons are often thought of as independent systems that are held together in the atom by their mutual attraction. Their interaction, however, leads to other important effects, such as providing an additional decay mode for excited nuclear states, whereby the nucleus releases energy by ejecting an atomic electron instead of by emitting a γ-ray. This 'internal conversion' has been known for about a hundred years and can be used to study nuclei and their interaction with their electrons. In the inverse process-nuclear excitation by electron capture (NEEC)-a free electron is captured into an atomic vacancy and can excite the nucleus to a higher-energy state, provided that the kinetic energy of the free electron plus the magnitude of its binding energy once captured matches the nuclear energy difference between the two states. NEEC was predicted in 1976 and has not hitherto been observed. Here we report evidence of NEEC in molybdenum-93 and determine the probability and cross-section for the process in a beam-based experimental scenario. Our results provide a standard for the assessment of theoretical models relevant to NEEC, which predict cross-sections that span many orders of magnitude. The greatest practical effect of the NEEC process may be on the survival of nuclei in stellar environments, in which it could excite isomers (that is, long-lived nuclear states) to shorter-lived states. Such excitations may reduce the abundance of the isotope after its production. This is an example of 'isomer depletion', which has been investigated previously through other reactions, but is used here to obtain evidence for NEEC.\",\n \"corpus_id\": 3297033,\n \"score\": 1\n },\n {\n \"doc_id\": \"29542992\",\n \"title\": \"Optical Lattice Clocks with Weakly Bound Molecules.\",\n \"abstract\": \"Optical molecular clocks promise unparalleled sensitivity to the temporal variation of the electron-to-proton mass ratio and insight into possible new physics beyond the standard model. We propose to realize a molecular clock with bosonic ^{174}Yb_{2} molecules, where the forbidden ^{1}S_{0}→^{3}P_{0} clock transition would be induced magnetically. The use of a bosonic species avoids possible complications due to the hyperfine structure present in fermionic species. While direct clock line photoassociation would be challenging, weakly bound ground state molecules could be produced by stimulated Raman adiabatic passage and used instead. The recent scattering measurements [L. Franchi, et al. New J. Phys. 19, 103037 (2017)NJOPFM1367-263010.1088/1367-2630/aa8fb4] enable us to determine the positions of target ^{1}S_{0}+^{3}P_{0} vibrational levels and calculate the Franck-Condon factors for clock transitions between ground and excited molecular states. The resulting magnetically induced Rabi frequencies are similar to those for atoms hinting that an experimental realization is feasible. A successful observation could pave the way towards Hz-level molecular spectroscopy.\",\n \"corpus_id\": 3892512,\n \"score\": 1\n },\n {\n \"doc_id\": \"29667603\",\n \"title\": \"Atomic clocks for geodesy.\",\n \"abstract\": \"We review experimental progress on optical atomic clocks and frequency transfer, and consider the prospects of using these technologies for geodetic measurements. Today, optical atomic frequency standards have reached relative frequency inaccuracies below 10-17, opening new fields of fundamental and applied research. The dependence of atomic frequencies on the gravitational potential makes atomic clocks ideal candidates for the search for deviations in the predictions of Einstein's general relativity, tests of modern unifying theories and the development of new gravity field sensors. In this review, we introduce the concepts of optical atomic clocks and present the status of international clock development and comparison. Besides further improvement in stability and accuracy of today's best clocks, a large effort is put into increasing the reliability and technological readiness for applications outside of specialized laboratories with compact, portable devices. With relative frequency uncertainties of 10-18, comparisons of optical frequency standards are foreseen to contribute together with satellite and terrestrial data to the precise determination of fundamental height reference systems in geodesy with a resolution at the cm-level. The long-term stability of atomic standards will deliver excellent long-term height references for geodetic measurements and for the modelling and understanding of our Earth.\",\n \"corpus_id\": 4939307,\n \"score\": 1\n },\n {\n \"doc_id\": \"18636527\",\n \"title\": \"Mass and lifetime measurements of exotic nuclei in storage rings.\",\n \"abstract\": \"Mass and lifetime measurements lead to the discovery and understanding of basic properties of matter. The isotopic nature of the chemical elements, nuclear binding, and the location and strength of nuclear shells are the most outstanding examples leading to the development of the first nuclear models. More recent are the discoveries of new structures of nuclides far from the valley of stability. A new generation of direct mass measurements which allows the exploration of extended areas of the nuclear mass surface with high accuracy has been opened up with the combination of the Experimental Storage Ring ESR and the FRragment Separator FRS at GSI Darmstadt. In-flight separated nuclei are stored in the ring. Their masses are directly determined from the revolution frequency. Dependent on the half-life two complementary methods are applied. Schottky Mass Spectrometry SMS relies on the measurement of the revolution frequency of electron cooled stored ions. The cooling time determines the lower half-life limit to the order of seconds. For Isochronous Mass Spectrometry IMS the ring is operated in an isochronous ion-optical mode. The revolution frequency of the individual ions coasting in the ring is measured using a time-of-flight method. Nuclides with lifetimes down to microseconds become accessible. With SMS masses of several hundreds nuclides have been measured simultaneously with an accuracy in the 2 x 10(-7)-range. This high accuracy and the ability to study large areas of the mass surface are ideal tools to discover new nuclear structure properties and to guide improvements for theoretical mass models. In addition, nuclear half-lives of stored bare and highly charged ions have been measured. This new experimental development is a significant progress since nuclear decay characteristics are mostly known for neutral atoms. For bare and highly charged ions new nuclear decay modes become possible, such as bound-state beta decay. Dramatic changes in the nuclear lifetime have been observed in highly charged ions compared to neutral atoms due to blocking of nuclear decay channels caused by the modified atomic interaction. High ionization degrees prevail in hot stellar matter and thus these experiments have great relevance for the understanding of the synthesis of elements in the universe and astrophysical scenarios in general.\",\n \"corpus_id\": 16812701,\n \"score\": 0\n },\n {\n \"doc_id\": \"19113267\",\n \"title\": \"Frequency shifts in an optical lattice clock due to magnetic-dipole and electric-quadrupole transitions.\",\n \"abstract\": \"We report a hitherto undiscovered frequency shift for forbidden J = 0-->J = 0 clock transitions excited in atoms confined to an optical lattice. These shifts result from magnetic-dipole and electric-quadrupole transitions, which have a spatial dependence in an optical lattice that differs from that of the stronger electric-dipole transitions. In combination with the residual translational motion of atoms in an optical lattice, this spatial mismatch leads to a frequency shift via differential energy level spacing in the lattice wells for ground state and excited state atoms. We estimate that this effect could lead to fractional frequency shifts as large as 10(-16), which might prevent lattice-based optical clocks from reaching their predicted performance levels. Moreover, these effects could shift the magic wavelength in lattice clocks in three dimensions by as much as 100 MHz, depending on the lattice configuration.\",\n \"corpus_id\": 6473324,\n \"score\": 0\n },\n {\n \"doc_id\": \"19792426\",\n \"title\": \"Smallest known Q value of any nuclear decay: the rare beta;{-} decay of ;{115}In(9/2;{+}) --> ;{115}Sn(3/2;{+}).\",\n \"abstract\": \"The ground-state-to-ground-state Q_{beta;{-}} value of ;{115}In was determined to 497.68(17) keV using a high-precision Penning trap facility at the University of Jyväskylä, Finland. From this, a Q_{beta;{-}} value of 0.35(17) keV was obtained for the rare beta;{-} decay to the first excited state of ;{115}Sn at 497.334(22) keV. The partial half-life was determined to 4.1(6) x 10;{20} yr using ultra low-background gamma-ray spectrometry in an underground laboratory. Theoretical modeling of this 2nd-forbidden unique beta;{-} transition was also undertaken and resulted in Q_{beta;{-}} = 57_{-12};{+19} eV using the measured half-life. The discrepancy between theory and experiment could be attributed to atomic effects enhanced by the low Q value. The present study implies that this transition has the lowest Q value of any known nuclear beta decay.\",\n \"corpus_id\": 1890942,\n \"score\": 0\n },\n {\n \"doc_id\": \"21365108\",\n \"title\": \"Photon induced isomerization in the first excited state of the 7-azaindole-(H2O)3 cluster.\",\n \"abstract\": \"A picosecond pump and probe experiment has been applied to study the excited state dynamics of 7-azaindole-water 1 ∶ 2 and 1 ∶ 3 clusters [7AI(H(2)O)(2,3)] in the gas phase. The vibrational-mode selective Excited-State-Triple-Proton Transfer (ESTPT) in 7AI(H(2)O)(2) proposed from the frequency-resolved study has been confirmed by picosecond decays. The decay times for the vibronic states involving the ESTPT promoting mode σ(1) (850-1000 ps) are much shorter than those for the other vibronic states (2100-4600 ps). In the (1 + 1) REMPI spectrum of 7AI(H(2)O)(3) measured by nanosecond laser pulses, the vibronic bands with an energy higher than 200 cm(-1) above the origin of the S(1) state become very weak. In contrast, the vibronic bands in the same region emerge in the (1 + 1') REMPI spectrum of 7AI(H(2)O)(3) with picosecond pulses. The decay times drastically decrease when increasing the vibrational energy above 200 cm(-1). Ab initio calculations show that a second stable \\\"cyclic-nonplanar isomer\\\" exists in addition to a \\\"bridged-planar isomer\\\", and that an isomerization from a bridged-planar isomer to a cyclic-nonplanar isomer is most probably responsible for the short lifetimes of the vibronic states of 7AI(H(2)O)(3).\",\n \"corpus_id\": 24793284,\n \"score\": 0\n },\n {\n \"doc_id\": \"21770559\",\n \"title\": \"Extended coherence time on the clock transition of optically trapped rubidium.\",\n \"abstract\": \"Optically trapped ensembles are of crucial importance for frequency measurements and quantum memories but generally suffer from strong dephasing due to inhomogeneous density and light shifts. We demonstrate a drastic increase of the coherence time to 21 s on the magnetic field insensitive clock transition of (87)Rb by applying the recently discovered spin self-rephasing [C. Deutsch et al., Phys. Rev. Lett. 105, 020401 (2010)]. This result confirms the general nature of this new mechanism and thus shows its applicability in atom clocks and quantum memories. A systematic investigation of all relevant frequency shifts and noise contributions yields a stability of 2.4×10(-11)τ(-1/2), where τ is the integration time in seconds. Based on a set of technical improvements, the presented frequency standard is predicted to rival the stability of microwave fountain clocks in a potentially much more compact setup.\",\n \"corpus_id\": 36865779,\n \"score\": 0\n },\n {\n \"doc_id\": \"21935014\",\n \"title\": \"All-optical link for direct comparison of distant optical clocks.\",\n \"abstract\": \"We developed an all-optical link system for making remote comparisons of two distant ultra-stable optical clocks. An optical carrier transfer system based on a fiber interferometer was employed to compensate the phase noise accumulated during the propagation through a fiber link. Transfer stabilities of 2 × 10(-15) at 1 second and 4 × 10(-18) at 1000 seconds were achieved in a 90-km link. An active polarization control system was additionally introduced to maintain the transmitted light in an adequate polarization, and consequently, a stable and reliable comparison was accomplished. The instabilities of the all-optical link system, including those of the erbium doped fiber amplifiers (EDFAs) which are free from phase-noise compensation, were below 2 × 10(-15) at 1 second and 7 × 10(-17) at 1000 seconds. The system was available for the direct comparison of two distant (87)Sr lattice clocks via an urban fiber link of 60 km. This technique will be essential for the measuring the reproducibility of optical frequency standards.\",\n \"corpus_id\": 11991552,\n \"score\": 0\n },\n {\n \"doc_id\": \"23002828\",\n \"title\": \"Unveiling the intruder deformed 02(+) state in 34Si.\",\n \"abstract\": \"The 02(+) state in 34Si has been populated at the GANIL-LISE3 facility through the β decay of a newly discovered 1(+) isomer in 34Al of 26(1) ms half-life. The simultaneous detection of e(+)e(-) pairs allowed the determination of the excitation energy E(02(+))=2719(3) keV and the half-life T(1/2)=19.4(7) ns, from which an electric monopole strength of ρ(2)(E0)=13.0(0.9)×10(-3) was deduced. The 2(1)(+) state is observed to decay both to the 0(1)(+) ground state and to the newly observed 0(2)(+) state [via a 607(2) keV transition] with a ratio R(2(1)(+)→0(1)(+)/2(1)(+)→0(2)(+))=1380(717). Gathering all information, a weak mixing with the 0(1)(+) and a large deformation parameter of β=0.29(4) are found for the 0(2)(+) state, in good agreement with shell model calculations using a new SDPF-U-MIX interaction allowing np-nh excitations across the N=20 shell gap.\",\n \"corpus_id\": 8144365,\n \"score\": 0\n },\n {\n \"doc_id\": \"24802723\",\n \"title\": \"Detection of weak frequency jumps for GNSS onboard clocks.\",\n \"abstract\": \"In this paper, a weak frequency jump detection method is developed for onboard clocks in global navigation satellite systems (GNSS). A Kalman filter is employed to facilitate the onboard real-time processing of atomic clock measurements, whose N-step prediction residuals are used to construct the weak frequency jump detector. Numerical simulations show that the method can successfully detect weak frequency jumps. The detection method proposed in this paper is helpful for autonomous integrity monitoring of GNSS satellite clocks, and can also be applied to other frequency anomalies with an appropriately modified detector.\",\n \"corpus_id\": 21821249,\n \"score\": 0\n },\n {\n \"doc_id\": \"25166798\",\n \"title\": \"Direct observation of long-lived isomers in 212Bi.\",\n \"abstract\": \"Long-lived isomers in (212)Bi have been studied following (238)U projectile fragmentation at 670 MeV per nucleon. The fragmentation products were injected as highly charged ions into a storage ring, giving access to masses and half-lives. While the excitation energy of the first isomer of (212)Bi was confirmed, the second isomer was observed at 1478(30) keV, in contrast to the previously accepted value of >1910 keV. It was also found to have an extended Lorentz-corrected in-ring half-life >30 min, compared to 7.0(3) min for the neutral atom. Both the energy and half-life differences can be understood as being due a substantial, though previously unrecognized, internal decay branch for neutral atoms. Earlier shell-model calculations are now found to give good agreement with the isomer excitation energy. Furthermore, these and new calculations predict the existence of states at slightly higher energy that could facilitate isomer deexcitation studies.\",\n \"corpus_id\": 15763004,\n \"score\": 0\n },\n {\n \"doc_id\": \"25615314\",\n \"title\": \"Isomer decay spectroscopy of 164Sm and 166Gd: midshell collectivity around N=100.\",\n \"abstract\": \"Excited states in the N=102 isotones 166Gd and 164Sm have been observed following isomeric decay for the first time at RIBF, RIKEN. The half-lives of the isomeric states have been measured to be 950(60) and 600(140) ns for 166Gd and 164Sm, respectively. Based on the decay patterns and potential energy surface calculations, including β6 deformation, a spin and parity of 6- has been assigned to the isomeric states in both nuclei. Collective observables are discussed in light of the systematics of the region, giving insight into nuclear shape evolution. The decrease in the ground-band energies of 166Gd and 164Sm (N=102) compared to 164Gd and 162Sm (N=100), respectively, presents evidence for the predicted deformed shell closure at N=100.\",\n \"corpus_id\": 19214937,\n \"score\": 0\n },\n {\n \"doc_id\": \"25734183\",\n \"title\": \"Hanle detection for optical clocks.\",\n \"abstract\": \"Considering the strong inhomogeneous spatial polarization and intensity distribution of spontaneous decay fluorescence due to the Hanle effect, we propose and demonstrate a universe Hanle detection configuration of electron-shelving method for optical clocks. Experimental results from Ca atomic beam optical frequency standard with electron-shelving method show that a designed Hanle detection geometry with optimized magnetic field direction, detection laser beam propagation and polarization direction, and detector position can improve the fluorescence collection rate by more than one order of magnitude comparing with that of inefficient geometry. With the fixed 423 nm fluorescence, the improved 657 nm optical frequency standard signal intensity is presented. The potential application of the Hanle detection geometry designed for facilitating the fluorescence collection for optical lattice clock with a limited solid angle of the fluorescence collection has been discussed. The Hanle detection geometry is also effective for ion detection in ion optical clock and quantum information experiments. Besides, a cylinder fluorescence collection structure is designed to increase the solid angle of the fluorescence collection in Ca atomic beam optical frequency standard.\",\n \"corpus_id\": 16808075,\n \"score\": 0\n },\n {\n \"doc_id\": \"25855457\",\n \"title\": \"Measurement of the first ionization potential of lawrencium, element 103.\",\n \"abstract\": \"The chemical properties of an element are primarily governed by the configuration of electrons in the valence shell. Relativistic effects influence the electronic structure of heavy elements in the sixth row of the periodic table, and these effects increase dramatically in the seventh row--including the actinides--even affecting ground-state configurations. Atomic s and p1/2 orbitals are stabilized by relativistic effects, whereas p3/2, d and f orbitals are destabilized, so that ground-state configurations of heavy elements may differ from those of lighter elements in the same group. The first ionization potential (IP1) is a measure of the energy required to remove one valence electron from a neutral atom, and is an atomic property that reflects the outermost electronic configuration. Precise and accurate experimental determination of IP1 gives information on the binding energy of valence electrons, and also, therefore, on the degree of relativistic stabilization. However, such measurements are hampered by the difficulty in obtaining the heaviest elements on scales of more than one atom at a time. Here we report that the experimentally obtained IP1 of the heaviest actinide, lawrencium (Lr, atomic number 103), is 4.96(+0.08)(-0.07) electronvolts. The IP1 of Lr was measured with (256)Lr (half-life 27 seconds) using an efficient surface ion-source and a radioisotope detection system coupled to a mass separator. The measured IP1 is in excellent agreement with the value of 4.963(15) electronvolts predicted here by state-of-the-art relativistic calculations. The present work provides a reliable benchmark for theoretical calculations and also opens the way for IP1 measurements of superheavy elements (that is, transactinides) on an atom-at-a-time scale.\",\n \"corpus_id\": 4384213,\n \"score\": 0\n },\n {\n \"doc_id\": \"26196619\",\n \"title\": \"Measurement of Magic Wavelengths for the ^{40}Ca^{+} Clock Transition.\",\n \"abstract\": \"We demonstrate experimentally the existence of magic wavelengths and determine the ratio of oscillator strengths for a single trapped ion. For the first time, two magic wavelengths near 396 nm for the ^{40}Ca^{+} clock transition are measured simultaneously with high precision. By tuning the applied laser to an intermediate wavelength between transitions 4s_{1/2}→4p_{1/2} and 4s_{1/2}→4p_{3/2}, the sensitivity of the clock transition Stark shift to the oscillator strengths is greatly enhanced. Furthermore, with the measured magic wavelengths, we determine the ratio of the oscillator strengths with a deviation of less than 0.5%. Our experimental method may be applied to measure magic wavelengths for other ion clock transitions. Promisingly, the measurement of these magic wavelengths paves the way to building all-optical trapped ion clocks.\",\n \"corpus_id\": 8619206,\n \"score\": 0\n },\n {\n \"doc_id\": \"26197020\",\n \"title\": \"The half-life of ²²⁷Th by direct and indirect measurements.\",\n \"abstract\": \"Utilising a chemically purified solution the radioactive half-life of (227)Th has been determined indirectly by observation of the ingrowth of (223)Ra using an ionisation chamber (IC) and for the first time by direct observation of the change in activity with time using a high-purity germanium (HPGe) γ-ray spectrometer. The radioactive decay was observed for ~104 days (~5.6 half-lives) by γ-ray spectrometry and approximately 63 days and 72 days (~3.4 and ~3.9 half-lives) using an ionisation chamber (IC). The resulting half-life values - 18.695 (4) days (IC) and 18.683 (20) days (HPGe) - are consistent and detailed uncertainty budgets are presented for the two measurement techniques. A weighted mean of our results of 18.695 (4) days is inconsistent with the most precise published half-life value of 18.7176 (52) days (Jordan and Blanke, 1967). A critical evaluation of literature data has been performed, indicating a paucity of reliable and independent measurements. Selected independent published values have been used to determine a recommended half-life of 18.697 (7) days. A method has been introduced in the course of this work so that the recommended half-life of (227)Th as determined by ingrowth can be modified if a different (223)Ra half-life has been determined, evaluated and adopted.\",\n \"corpus_id\": 26095962,\n \"score\": 0\n },\n {\n \"doc_id\": \"26469051\",\n \"title\": \"Observation of the competitive double-gamma nuclear decay.\",\n \"abstract\": \"The double-gamma (γγ)-decay of a quantum system in an excited state is a fundamental second-order process of quantum electrodynamics. In contrast to the well-known single-gamma (γ)-decay, the γγ-decay is characterized by the simultaneous emission of two γ quanta, each with a continuous energy spectrum. In nuclear physics, this exotic decay mode has only been observed for transitions between states with spin-parity quantum numbers J(π) = 0(+) (refs 1-3). Single-gamma decays-the main experimental obstacle to observing the γγ-decay-are strictly forbidden for these 0(+) → 0(+) transitions. Here we report the observation of the γγ-decay of an excited nuclear state (J(π) = 11/2(-)) that is directly competing with an allowed γ-decay (to ground state J(π) = 3/2(+)). The branching ratio of the competitive γγ-decay of the 11/2(-) isomer of (137)Ba to the ground state relative to its single γ-decay was determined to be (2.05 ± 0.37) × 10(-6). From the measured angular correlation and the shape of the energy spectra of the individual γ-rays, the contributing combinations of multipolarities of the γ radiation were determined. Transition matrix elements calculated using the quasiparticle-phonon model reproduce our measurements well. The γγ-decay rate gives access to so far unexplored important nuclear structure information, such as the generalized (off-diagonal) nuclear electric polarizabilities and magnetic susceptibilities.\",\n \"corpus_id\": 4450701,\n \"score\": 0\n },\n {\n \"doc_id\": \"26849600\",\n \"title\": \"Synthetic Spin-Orbit Coupling in an Optical Lattice Clock.\",\n \"abstract\": \"We propose the use of optical lattice clocks operated with fermionic alkaline-earth atoms to study spin-orbit coupling (SOC) in interacting many-body systems. The SOC emerges naturally during the clock interrogation, when atoms are allowed to tunnel and accumulate a phase set by the ratio of the \\\"magic\\\" lattice wavelength to the clock transition wavelength. We demonstrate how standard protocols such as Rabi and Ramsey spectroscopy that take advantage of the sub-Hertz resolution of state-of-the-art clock lasers can perform momentum-resolved band tomography and determine SOC-induced s-wave collisions in nuclear-spin-polarized fermions. With the use of a second counterpropagating clock beam, we propose a method for engineering controlled atomic transport and study how it is modified by p- and s-wave interactions. The proposed spectroscopic probes provide clean and well-resolved signatures at current clock operating temperatures.\",\n \"corpus_id\": 31942577,\n \"score\": 0\n },\n {\n \"doc_id\": \"27203317\",\n \"title\": \"Isomer Shift and Magnetic Moment of the Long-Lived 1/2^{+} Isomer in _{30}^{79}Zn_{49}: Signature of Shape Coexistence near ^{78}Ni.\",\n \"abstract\": \"Collinear laser spectroscopy is performed on the _{30}^{79}Zn_{49} isotope at ISOLDE-CERN. The existence of a long-lived isomer with a few hundred milliseconds half-life is confirmed, and the nuclear spins and moments of the ground and isomeric states in ^{79}Zn as well as the isomer shift are measured. From the observed hyperfine structures, spins I=9/2 and I=1/2 are firmly assigned to the ground and isomeric states. The magnetic moment μ (^{79}Zn)=-1.1866(10)μ_{N}, confirms the spin-parity 9/2^{+} with a νg_{9/2}^{-1} shell-model configuration, in excellent agreement with the prediction from large scale shell-model theories. The magnetic moment μ (^{79m}Zn)=-1.0180(12)μ_{N} supports a positive parity for the isomer, with a wave function dominated by a 2h-1p neutron excitation across the N=50 shell gap. The large isomer shift reveals an increase of the intruder isomer mean square charge radius with respect to that of the ground state, δ⟨r_{c}^{2}⟩^{79,79m}=+0.204(6) fm^{2}, providing first evidence of shape coexistence.\",\n \"corpus_id\": 7925243,\n \"score\": 0\n },\n {\n \"doc_id\": \"27432734\",\n \"title\": \"An exacting transition probability measurement - a direct test of atomic many-body theories.\",\n \"abstract\": \"A new protocol for measuring the branching fraction of hydrogenic atoms with only statistically limited uncertainty is proposed and demonstrated for the decay of the P3/2 level of the barium ion, with precision below 0.5%. Heavy hydrogenic atoms like the barium ion are test beds for fundamental physics such as atomic parity violation and they also hold the key to understanding nucleo-synthesis in stars. To draw definitive conclusion about possible physics beyond the standard model by measuring atomic parity violation in the barium ion it is necessary to measure the dipole transition probabilities of low-lying excited states with a precision better than 1%. Furthermore, enhancing our understanding of the barium puzzle in barium stars requires branching fraction data for proper modelling of nucleo-synthesis. Our measurements are the first to provide a direct test of quantum many-body calculations on the barium ion with a precision below one percent and more importantly with no known systematic uncertainties. The unique measurement protocol proposed here can be easily extended to any decay with more than two channels and hence paves the way for measuring the branching fractions of other hydrogenic atoms with no significant systematic uncertainties.\",\n \"corpus_id\": 17464158,\n \"score\": 0\n },\n {\n \"doc_id\": \"27680707\",\n \"title\": \"Atom-at-a-time laser resonance ionization spectroscopy of nobelium.\",\n \"abstract\": \"Optical spectroscopy of a primordial isotope has traditionally formed the basis for understanding the atomic structure of an element. Such studies have been conducted for most elements and theoretical modelling can be performed to high precision, taking into account relativistic effects that scale approximately as the square of the atomic number. However, for the transfermium elements (those with atomic numbers greater than 100), the atomic structure is experimentally unknown. These radioactive elements are produced in nuclear fusion reactions at rates of only a few atoms per second at most and must be studied immediately following their production, which has so far precluded their optical spectroscopy. Here we report laser resonance ionization spectroscopy of nobelium (No; atomic number 102) in single-atom-at-a-time quantities, in which we identify the ground-state transition (1)S0(1)P1. By combining this result with data from an observed Rydberg series, we obtain an upper limit for the ionization potential of nobelium. These accurate results from direct laser excitations of outer-shell electrons cannot be achieved using state-of-the-art relativistic many-body calculations that include quantum electrodynamic effects, owing to large uncertainties in the modelled transition energies of the complex systems under consideration. Our work opens the door to high-precision measurements of various atomic and nuclear properties of elements heavier than nobelium, and motivates future theoretical work.\",\n \"corpus_id\": 205250445,\n \"score\": 0\n },\n {\n \"doc_id\": \"28009197\",\n \"title\": \"Nuclear Excitation by Two-Photon Electron Transition.\",\n \"abstract\": \"A new mechanism of nuclear excitation via two-photon electron transitions (NETP) is proposed and studied theoretically. As a generic example, detailed calculations are performed for the E1E1 1s2s^{1}S_{0}→1s^{2}^{1}S_{0} two-photon decay of a He-like ^{225}Ac^{87+} ion with a resonant excitation of the 3/2+ nuclear state with an energy of 40.09(5) keV. The probability for such a two-photon decay via the nuclear excitation is found to be P_{NETP}=3.5×10^{-9} and, thus, is comparable with other mechanisms, such as nuclear excitation by electron transition and by electron capture. The possibility for the experimental observation of the proposed mechanism is thoroughly discussed.\",\n \"corpus_id\": 34868512,\n \"score\": 0\n },\n {\n \"doc_id\": \"29053333\",\n \"title\": \"Spin Resonance Clock Transition of the Endohedral Fullerene ^{15}N@C_{60}.\",\n \"abstract\": \"The endohedral fullerene ^{15}N@C_{60} has narrow electron paramagnetic resonance lines which have been proposed as the basis for a condensed-matter portable atomic clock. We measure the low-frequency spectrum of this molecule, identifying and characterizing a clock transition at which the frequency becomes insensitive to magnetic field. We infer a linewidth at the clock field of 100 kHz. Using experimental data, we are able to place a bound on the clock's projected frequency stability. We discuss ways to improve the frequency stability to be competitive with existing miniature clocks.\",\n \"corpus_id\": 13826533,\n \"score\": 0\n },\n {\n \"doc_id\": \"29481161\",\n \"title\": \"Tailoring Laser-Generated Plasmas for Efficient Nuclear Excitation by Electron Capture.\",\n \"abstract\": \"The optimal parameters for nuclear excitation by electron capture in plasma environments generated by the interaction of ultrastrong optical lasers with solid matter are investigated theoretically. As a case study we consider a 4.85 keV nuclear transition starting from the long-lived ^{93m}Mo isomer that can lead to the release of the stored 2.4 MeV excitation energy. We find that due to the complex plasma dynamics, the nuclear excitation rate and the actual number of excited nuclei do not reach their maximum at the same laser parameters. The nuclear excitation achievable with a high-power optical laser is up to twelve and up to six orders of magnitude larger than the values predicted for direct resonant and secondary plasma-mediated excitation at the x-ray free electron laser, respectively. Our results show that the experimental observation of the nuclear excitation of ^{93m}Mo and the subsequent release of stored energy should be possible at laser facilities available today.\",\n \"corpus_id\": 3703860,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":77,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29740598\",\n \"title\": \"A single-atom 3D sub-attonewton force sensor.\",\n \"abstract\": \"Forces drive all physical interactions. High-sensitivity measurement of the effect of forces enables the quantitative investigation of physical phenomena. Laser-cooled trapped atomic ions are a well-controlled quantum system whose low mass, strong Coulomb interaction, and readily detectable fluorescence signal make them a favorable platform for precision metrology. We demonstrate a three-dimensional sub-attonewton sensitivity force sensor based on a super-resolution imaging of a single trapped ion. The force is detected by measuring the ion's displacement in three dimensions with nanometer precision. Observed sensitivities were 372 ± 9, 347 ± 18, and 808 ± 51 zN/[Formula: see text], corresponding to 24×, 87×, and 21× above the quantum limit. We verified this technique by measuring a 95-zN light pressure force, an important systematic effect in optically based sensors.\",\n \"corpus_id\": 13665106\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20729835","title":"Ultrasensitive detection of force and displacement using trapped ions.","abstract":"The ability to detect extremely small forces and nanoscale displacements is vital for disciplines such as precision spin-resonance imaging, microscopy, and tests of fundamental physical phenomena. Current force-detection sensitivity limits have surpassed 1 aN Hz(-1/2) (refs 6,7) through coupling of nanomechanical resonators to a variety of physical readout systems. Here, we demonstrate that crystals of trapped atomic ions behave as nanoscale mechanical oscillators and may form the core of exquisitely sensitive force and displacement detectors. We report the detection of forces with a sensitivity of 390 +/- 150 yN Hz(-1/2), which is more than three orders of magnitude better than existing reports using nanofabricated devices(7), and discriminate ion displacements of approximately 18 nm. Our technique is based on the excitation of tunable normal motional modes in an ion trap and detection through phase-coherent Doppler velocimetry, and should ultimately allow force detection with a sensitivity better than 1 yN Hz(-1/2) (ref. 16). Trapped-ion-based sensors could enable scientists to explore new regimes in materials science where augmented force, field and displacement sensitivity may be traded against reduced spatial resolution.","corpus_id":21558623,"score":2},{"doc_id":"21544142","title":"Single-ion quantum lock-in amplifier.","abstract":"Quantum metrology uses tools from quantum information science to improve measurement signal-to-noise ratios. The challenge is to increase sensitivity while reducing susceptibility to noise, tasks that are often in conflict. Lock-in measurement is a detection scheme designed to overcome this difficulty by spectrally separating signal from noise. Here we report on the implementation of a quantum analogue to the classical lock-in amplifier. All the lock-in operations--modulation, detection and mixing--are performed through the application of non-commuting quantum operators to the electronic spin state of a single, trapped Sr(+) ion. We significantly increase its sensitivity to external fields while extending phase coherence by three orders of magnitude, to more than one second. Using this technique, we measure frequency shifts with a sensitivity of 0.42 Hz Hz(-1/2) (corresponding to a magnetic field measurement sensitivity of 15 pT Hz(-1/2)), obtaining an uncertainty of less than 10 mHz (350 fT) after 3,720 seconds of averaging. These sensitivities are limited by quantum projection noise and improve on other single-spin probe technologies by two orders of magnitude. Our reported sensitivity is sufficient for the measurement of parity non-conservation, as well as the detection of the magnetic field of a single electronic spin one micrometre from an ion detector with nanometre resolution. As a first application, we perform light shift spectroscopy of a narrow optical quadrupole transition. Finally, we emphasize that the quantum lock-in technique is generic and can potentially enhance the sensitivity of any quantum sensor.","corpus_id":3208184,"score":2},{"doc_id":"22760632","title":"Absorption imaging of a single atom.","abstract":"Absorption imaging has played a key role in the advancement of science from van Leeuwenhoek's discovery of red blood cells to modern observations of dust clouds in stellar nebulas and Bose-Einstein condensates. Here we show the first absorption imaging of a single atom isolated in a vacuum. The optical properties of atoms are thoroughly understood, so a single atom is an ideal system for testing the limits of absorption imaging. A single atomic ion was confined in an RF Paul trap and the absorption imaged at near wavelength resolution with a phase Fresnel lens. The observed image contrast of 3.1 (3)% is the maximum theoretically allowed for the imaging resolution of our set-up. The absorption of photons by single atoms is of immediate interest for quantum information processing. Our results also point out new opportunities in imaging of light-sensitive samples both in the optical and X-ray regimes.","corpus_id":5616535,"score":2},{"doc_id":"24970079","title":"Quantum metrology. Optically measuring force near the standard quantum limit.","abstract":"The Heisenberg uncertainty principle sets a lower bound on the noise in a force measurement based on continuously detecting a mechanical oscillator's position. This bound, the standard quantum limit, can be reached when the oscillator subjected to the force is unperturbed by its environment and when measurement imprecision from photon shot noise is balanced against disturbance from measurement back-action. We applied an external force to the center-of-mass motion of an ultracold atom cloud in a high-finesse optical cavity and measured the resulting motion optically. When the driving force is resonant with the cloud's oscillation frequency, we achieve a sensitivity that is a factor of 4 above the standard quantum limit and consistent with theoretical predictions given the atoms' residual thermal disturbance and the photodetection quantum efficiency.","corpus_id":206554506,"score":2},{"doc_id":"27306426","title":"High-precision force sensing using a single trapped ion.","abstract":"We introduce quantum sensing schemes for measuring very weak forces with a single trapped ion. They use the spin-motional coupling induced by the laser-ion interaction to transfer the relevant force information to the spin-degree of freedom. Therefore, the force estimation is carried out simply by observing the Ramsey-type oscillations of the ion spin states. Three quantum probes are considered, which are represented by systems obeying the Jaynes-Cummings, quantum Rabi (in 1D) and Jahn-Teller (in 2D) models. By using dynamical decoupling schemes in the Jaynes-Cummings and Jahn-Teller models, our force sensing protocols can be made robust to the spin dephasing caused by the thermal and magnetic field fluctuations. In the quantum-Rabi probe, the residual spin-phonon coupling vanishes, which makes this sensing protocol naturally robust to thermally-induced spin dephasing. We show that the proposed techniques can be used to sense the axial and transverse components of the force with a sensitivity beyond the range, i.e. in the (xennonewton, 10(-27)). The Jahn-Teller protocol, in particular, can be used to implement a two-channel vector spectrum analyzer for measuring ultra-low voltages.","corpus_id":4866453,"score":2},{"doc_id":"27367376","title":"Ultrasensitive Magnetometer using a Single Atom.","abstract":"Precision sensing, and in particular high precision magnetometry, is a central goal of research into quantum technologies. For magnetometers, often trade-offs exist between sensitivity, spatial resolution, and frequency range. The precision, and thus the sensitivity of magnetometry, scales as 1/sqrt[T_{2}] with the phase coherence time T_{2} of the sensing system playing the role of a key determinant. Adapting a dynamical decoupling scheme that allows for extending T_{2} by orders of magnitude and merging it with a magnetic sensing protocol, we achieve a measurement sensitivity even for high frequency fields close to the standard quantum limit. Using a single atomic ion as a sensor, we experimentally attain a sensitivity of 4.6 pT/sqrt[Hz] for an alternating-current magnetic field near 14 MHz. Based on the principle demonstrated here, this unprecedented sensitivity combined with spatial resolution in the nanometer range and tunability from direct current to the gigahertz range could be used for magnetic imaging in as of yet inaccessible parameter regimes.","corpus_id":31926600,"score":2},{"doc_id":"27749835","title":"A universal and ultrasensitive vectorial nanomechanical sensor for imaging 2D force fields.","abstract":"The miniaturization of force probes into nanomechanical oscillators enables ultrasensitive investigations of forces on dimensions smaller than their characteristic length scales. It also unravels the vectorial character of the force field and how its topology impacts the measurement. Here we present an ultrasensitive method for imaging two-dimensional vectorial force fields by optomechanically following the bidimensional Brownian motion of a singly clamped nanowire. This approach relies on angular and spectral tomography of its quasi-frequency-degenerated transverse mechanical polarizations: immersing the nanoresonator in a vectorial force field not only shifts its eigenfrequencies but also rotates the orientation of the eigenmodes, as a nanocompass. This universal method is employed to map a tunable electrostatic force field whose spatial gradients can even dominate the intrinsic nanowire properties. Enabling vectorial force field imaging with demonstrated sensitivities of attonewton variations over the nanoprobe Brownian trajectory will have a strong impact on scientific exploration at the nanoscale.","corpus_id":29463120,"score":2},{"doc_id":"28186103","title":"Quantum lock-in force sensing using optical clock Doppler velocimetry.","abstract":"Force sensors are at the heart of different technologies such as atomic force microscopy or inertial sensing. These sensors often rely on the measurement of the displacement amplitude of mechanical oscillators under applied force. The best sensitivity is typically achieved when the force is alternating at the mechanical resonance frequency of the oscillator, thus increasing its response by the mechanical quality factor. The measurement of low-frequency forces, that are below resonance, is a more difficult task as the resulting oscillation amplitudes are significantly lower. Here we use a single-trapped (88)Sr(+) ion as a force sensor. The ion is electrically driven at a frequency much lower than the trap resonance frequency. We measure small amplitude of motion by measuring the periodic Doppler shift of an atomic optical clock transition, enhanced using the quantum lock-in technique. We report frequency force detection sensitivity as low as 2.8 × 10(-20) NHz(-1/2).","corpus_id":11123313,"score":2},{"doc_id":"18583603","title":"Quantum state engineering and precision metrology using state-insensitive light traps.","abstract":"Precision metrology and quantum measurement often demand that matter be prepared in well-defined quantum states for both internal and external degrees of freedom. Laser-cooled neutral atoms localized in a deeply confining optical potential satisfy this requirement. With an appropriate choice of wavelength and polarization for the optical trap, two electronic states of an atom can experience the same trapping potential, permitting coherent control of electronic transitions independent of the atomic center-of-mass motion. Here, we review a number of recent experiments that use this approach to investigate precision quantum metrology for optical atomic clocks and coherent control of optical interactions of single atoms and photons within the context of cavity quantum electrodynamics. We also provide a brief survey of promising prospects for future work.","corpus_id":27388210,"score":1},{"doc_id":"20016597","title":"Photon-by-photon feedback control of a single-atom trajectory.","abstract":"Feedback is one of the most powerful techniques for the control of classical systems. An extension into the quantum domain is desirable as it could allow the production of non-trivial quantum states and protection against decoherence. The difficulties associated with quantum, as opposed to classical, feedback arise from the quantum measurement process-in particular the quantum projection noise and the limited measurement rate-as well as from quantum fluctuations perturbing the evolution in a driven open system. Here we demonstrate real-time feedback control of the motion of a single atom trapped in an optical cavity. Individual probe photons carrying information about the atomic position activate a dipole laser that steers the atom on timescales 70 times shorter than the atom's oscillation period in the trap. Depending on the specific implementation, the trapping time is increased by a factor of more than four owing to feedback cooling, which can remove almost all the kinetic energy of the atom in a quarter of an oscillation period. Our results show that the detected photon flux reflects the atomic motion, and thus mark a step towards the exploration of the quantum trajectory of a single atom at the standard quantum limit.","corpus_id":4432136,"score":1},{"doc_id":"20066528","title":"Single-photon atomic force microscopy.","abstract":"In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed \"single-photon atomic force microscopy\" (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.","corpus_id":39410037,"score":1},{"doc_id":"20113129","title":"Microdisplacement sensor using an optically trapped microprobe based on the interference scale.","abstract":"Positioning technology is one of the most important technologies for developing microsystems. In particular, displacement sensors are necessary for positioning devices with nanoscale accuracy. In this study, we propose a new displacement sensor that uses an interference scale as a linear scale and a laser-trapped microsphere as a sensing probe. This sensor has a wide measuring range, high resolution, and accessibility for narrow target areas. A glass microsphere was optically trapped by means of the laser trapping technique. Between the target surface and the probe, an interference scale was generated along the optical axis. The scale origin was fixed on the target surface. The distance between the probe and the target surface could be measured in terms of the shift in the interference scale. This study investigated the fundamental performance of the sensor. The resolution and accuracy of the sensor were 10 and +/-50 nm, respectively; these values could be improved by using trapping lasers having shorter wavelengths. The measurable range was 250 microm. This sensor can provide useful displacement information from a target area having dimensions smaller than 15 microm. In addition, the displacement sensor can measure the distance even for surfaces inclined at angles less than 15 degrees; thus, a flexible arrangement can be used to carry out measurements. In addition, the direction of displacement can be identified.","corpus_id":21951749,"score":1},{"doc_id":"20150495","title":"Resonance fluorescence of a single artificial atom.","abstract":"An atom in open space can be detected by means of resonant absorption and reemission of electromagnetic waves, known as resonance fluorescence, which is a fundamental phenomenon of quantum optics. We report on the observation of scattering of propagating waves by a single artificial atom. The behavior of the artificial atom, a superconducting macroscopic two-level system, is in a quantitative agreement with the predictions of quantum optics for a pointlike scatterer interacting with the electromagnetic field in one-dimensional open space. The strong atom-field interaction as revealed in a high degree of extinction of propagating waves will allow applications of controllable artificial atoms in quantum optics and photonics.","corpus_id":206523434,"score":1},{"doc_id":"20366407","title":"Realization of a quantum walk with one and two trapped ions.","abstract":"We experimentally demonstrate a quantum walk on a line in phase space using one and two trapped ions. A walk with up to 23 steps is realized by subjecting an ion to state-dependent displacement operations interleaved with quantum coin tossing operations. To analyze the ion's motional state after each step we apply a technique that directly maps the probability density distribution onto the ion's internal state. The measured probability distributions and the position's second moment clearly show the nonclassical character of the quantum walk. To further highlight the difference between the classical (random) and the quantum walk, we demonstrate the reversibility of the latter. Finally, we extend the quantum walk by using two ions, giving the walker the additional possibility to stay instead of taking a step.","corpus_id":19177982,"score":1},{"doc_id":"21230903","title":"Electromagnetically induced transparency from a single atom in free space.","abstract":"In this Letter, we report an absorption spectroscopy experiment and the observation of electromagnetically induced transparency from a single trapped atom. We focus a weak and narrow band Gaussian light beam onto an optically cooled 138Ba+ ion using a high numerical aperture lens. Extinction of this beam is observed with measured values of up to 1.35%. We demonstrate electromagnetically induced transparency of the ion by tuning a strong control beam over a two-photon resonance in a three-level Λ-type system. The probe beam extinction is inhibited by more than 75% due to population trapping.","corpus_id":21605616,"score":1},{"doc_id":"21430776","title":"Interaction-based quantum metrology showing scaling beyond the Heisenberg limit.","abstract":"Quantum metrology aims to use entanglement and other quantum resources to improve precision measurement. An interferometer using N independent particles to measure a parameter χ can achieve at best the standard quantum limit of sensitivity, δχ ∝ N(-1/2). However, using N entangled particles and exotic states, such an interferometer can in principle achieve the Heisenberg limit, δχ ∝ N(-1). Recent theoretical work has argued that interactions among particles may be a valuable resource for quantum metrology, allowing scaling beyond the Heisenberg limit. Specifically, a k-particle interaction will produce sensitivity δχ ∝ N(-k) with appropriate entangled states and δχ ∝ N(-(k-1/2)) even without entanglement. Here we demonstrate 'super-Heisenberg' scaling of δχ ∝ N(-3/2) in a nonlinear, non-destructive measurement of the magnetization of an atomic ensemble. We use fast optical nonlinearities to generate a pairwise photon-photon interaction (corresponding to k = 2) while preserving quantum-noise-limited performance. We observe super-Heisenberg scaling over two orders of magnitude in N, limited at large numbers by higher-order nonlinear effects, in good agreement with theory. For a measurement of limited duration, super-Heisenberg scaling allows the nonlinear measurement to overtake in sensitivity a comparable linear measurement with the same number of photons. In other situations, however, higher-order nonlinearities prevent this crossover from occurring, reflecting the subtle relationship between scaling and sensitivity in nonlinear systems. Our work shows that interparticle interactions can improve sensitivity in a quantum-limited measurement, and experimentally demonstrates a new resource for quantum metrology.","corpus_id":199679770,"score":1},{"doc_id":"21660745","title":"Atomic force microscopy as nanorobot.","abstract":"Atomic force microscopy (AFM) is a powerful and widely used imaging technique that can visualize single molecules under physiological condition at the nanometer scale. In this chapter, an AFM-based nanorobot for biological studies is introduced. Using the AFM tip as an end effector, the AFM can be modified into a nanorobot that can manipulate biological objects at the single-molecule level. By functionalizing the AFM tip with specific antibodies, the nanorobot is able to identify specific types of receptors on the cell membrane. It is similar to the fluorescent optical microscopy but with higher resolution. By locally updating the AFM image based on interaction force information and objects' model during nanomanipulation, real-time visual feedback is obtained through the augmented reality interface. The development of the AFM-based nanorobotic system enables us to conduct in situ imaging, sensing, and manipulation simultaneously at the nanometer scale (e.g., protein and DNA levels). The AFM-based nanorobotic system offers several advantages and capabilities for studying structure-function relationships of biological specimens. As a result, many biomedical applications can be achieved by the AFM-based nanorobotic system.","corpus_id":11238900,"score":1},{"doc_id":"22368463","title":"Development of a hybrid atomic force microscopic measurement system combined with white light scanning interferometry.","abstract":"A hybrid atomic force microscopic (AFM) measurement system combined with white light scanning interferometry for micro/nanometer dimensional measurement is developed. The system is based on a high precision large-range positioning platform with nanometer accuracy on which a white light scanning interferometric module and an AFM head are built. A compact AFM head is developed using a self-sensing tuning fork probe. The head need no external optical sensors to detect the deflection of the cantilever, which saves room on the head, and it can be directly fixed under an optical microscopic interferometric system. To enhance the system's dynamic response, the frequency modulation (FM) mode is adopted for the AFM head. The measuring data can be traceable through three laser interferometers in the system. The lateral scanning range can reach 25 mm × 25 mm by using a large-range positioning platform. A hybrid method combining AFM and white light scanning interferometry is proposed to improve the AFM measurement efficiency. In this method, the sample is measured firstly by white light scanning interferometry to get an overall coarse morphology, and then, further measured with higher resolution by AFM. Several measuring experiments on standard samples demonstrate the system's good measurement performance and feasibility of the hybrid measurement method.","corpus_id":14693933,"score":1},{"doc_id":"22380080","title":"Measurement of probe displacement to the thermal resolution limit in photonic force microscopy using a miniature quadrant photodetector.","abstract":"A photonic force microscope comprises of an optically trapped micro-probe and a position detection system to track the motion of the probe. Signal collection for motion detection is often carried out using the backscattered light off the probe-however, this mode has problems of low S/N due to the small backscattering cross sections of the micro-probes typically used. The position sensors often used in these cases are quadrant photodetectors. To ensure maximum sensitivity of such detectors, it would help if the detector size matched with the detection beam radius after the condenser lens (which for backscattered detection would be the trapping objective itself). To suit this condition, we have used a miniature displacement sensor whose dimensions makes it ideal to work with 1:1 images of micrometer-sized trapped probes in the backscattering detection mode. The detector is based on the quadrant photo-integrated chip in the optical pick-up head of a compact disc player. Using this detector, we measured absolute displacements of an optically trapped 1.1 μm probe with a resolution of ∼10 nm for a bandwidth of 10 Hz at 95% significance without any sample or laser stabilization. We characterized our optical trap for different sized probes by measuring the power spectrum for each probe to 1% accuracy, and found that for 1.1 μm diameter probes, the noise in our position measurement matched the thermal resolution limit for averaging times up to 10 ms. We also achieved a linear response range of around 385 nm with cross talk between axes ≃4% for 1.1 μm diameter probes. The detector has extremely high bandwidth (few MHz) and low optical power threshold-other factors that can lead to its widespread use in photonic force microscopy.","corpus_id":5882313,"score":1},{"doc_id":"22790343","title":"Experimental quantum simulations of many-body physics with trapped ions.","abstract":"Direct experimental access to some of the most intriguing quantum phenomena is not granted due to the lack of precise control of the relevant parameters in their naturally intricate environment. Their simulation on conventional computers is impossible, since quantum behaviour arising with superposition states or entanglement is not efficiently translatable into the classical language. However, one could gain deeper insight into complex quantum dynamics by experimentally simulating the quantum behaviour of interest in another quantum system, where the relevant parameters and interactions can be controlled and robust effects detected sufficiently well. Systems of trapped ions provide unique control of both the internal (electronic) and external (motional) degrees of freedom. The mutual Coulomb interaction between the ions allows for large interaction strengths at comparatively large mutual ion distances enabling individual control and readout. Systems of trapped ions therefore exhibit a prominent system in several physical disciplines, for example, quantum information processing or metrology. Here, we will give an overview of different trapping techniques of ions as well as implementations for coherent manipulation of their quantum states and discuss the related theoretical basics. We then report on the experimental and theoretical progress in simulating quantum many-body physics with trapped ions and present current approaches for scaling up to more ions and more-dimensional systems.","corpus_id":30689533,"score":1},{"doc_id":"23473144","title":"Atom-atom entanglement by single-photon detection.","abstract":"A scheme for entangling distant atoms is realized, as proposed in the seminal paper by [C. Cabrillo et al., Phys. Rev. A 59, 1025 (1999)]. The protocol is based on quantum interference and detection of a single photon scattered from two effectively one meter distant laser cooled and trapped atomic ions. The detection of a single photon heralds entanglement of two internal states of the trapped ions with high rate and with a fidelity limited mostly by atomic motion. Control of the entangled state phase is demonstrated by changing the path length of the single-photon interferometer.","corpus_id":2063579,"score":1},{"doc_id":"23618764","title":"Coupling a single trapped atom to a nanoscale optical cavity.","abstract":"Hybrid quantum devices, in which dissimilar quantum systems are combined in order to attain qualities not available with either system alone, may enable far-reaching control in quantum measurement, sensing, and information processing. A paradigmatic example is trapped ultracold atoms, which offer excellent quantum coherent properties, coupled to nanoscale solid-state systems, which allow for strong interactions. We demonstrate a deterministic interface between a single trapped rubidium atom and a nanoscale photonic crystal cavity. Precise control over the atom's position allows us to probe the cavity near-field with a resolution below the diffraction limit and to observe large atom-photon coupling. This approach may enable the realization of integrated, strongly coupled quantum nano-optical circuits.","corpus_id":9924385,"score":1},{"doc_id":"23767719","title":"Ground-state cooling of a single atom at the center of an optical cavity.","abstract":"A single neutral atom is trapped in a three-dimensional optical lattice at the center of a high-finesse optical resonator. Using fluorescence imaging and a shiftable standing-wave trap, the atom is deterministically loaded into the maximum of the intracavity field where the atom-cavity coupling is strong. After 5 ms of Raman sideband cooling, the three-dimensional motional ground state is populated with a probability of (89±2)%. Our system is the first to simultaneously achieve quantum control over all degrees of freedom of a single atom: its position and momentum, its internal state, and its coupling to light.","corpus_id":21176284,"score":1},{"doc_id":"24717513","title":"Nanophotonic quantum phase switch with a single atom.","abstract":"By analogy to transistors in classical electronic circuits, quantum optical switches are important elements of quantum circuits and quantum networks. Operated at the fundamental limit where a single quantum of light or matter controls another field or material system, such a switch may enable applications such as long-distance quantum communication, distributed quantum information processing and metrology, and the exploration of novel quantum states of matter. Here, by strongly coupling a photon to a single atom trapped in the near field of a nanoscale photonic crystal cavity, we realize a system in which a single atom switches the phase of a photon and a single photon modifies the atom's phase. We experimentally demonstrate an atom-induced optical phase shift that is nonlinear at the two-photon level, a photon number router that separates individual photons and photon pairs into different output modes, and a single-photon switch in which a single 'gate' photon controls the propagation of a subsequent probe field. These techniques pave the way to integrated quantum nanophotonic networks involving multiple atomic nodes connected by guided light.","corpus_id":2393975,"score":1},{"doc_id":"25401537","title":"Coupled optical resonance laser locking.","abstract":"We have demonstrated simultaneous laser frequency stabilization of a UV and IR laser, to coupled transitions of ions in the same spectroscopic sample, by detecting only the absorption of the UV laser. Separate signals for locking the different lasers are obtained by modulating each laser at a different frequency and using lock-in detection of a single photodiode signal. Experimentally, we simultaneously lock a 369 nm and a 935 nm laser to the (2)S(1/2) → (2)(P(1/2) and (2)D(3/2) → (3)D([3/2]1/2) transitions, respectively, of Yb(+) ions generated in a hollow cathode discharge lamp. Stabilized lasers at these frequencies are required for cooling and trapping Yb(+) ions, used in quantum information and in high precision metrology experiments. This technique should be readily applicable to other ion and neutral atom systems requiring multiple stabilized lasers.","corpus_id":10028409,"score":1},{"doc_id":"25723099","title":"Ultrasensitive room-temperature piezoresistive transduction in graphene-based nanoelectromechanical systems.","abstract":"The low mass and high quality factors that nanomechanical resonators exhibit lead to exceptional sensitivity in the frequency domain. This is especially appealing for the design of ultrasensitive force and mass sensors. The sensitivity of a nanomechanical mass and force sensor depends on its mass and quality factor; a low resonator mass and a higher quality factor reduce both the minimum resolvable mass and force. Graphene, a single atomic layer thick membrane is an ideal candidate for nanoelectromechanical resonators due to its extremely low mass and high stiffness. Here, we show that by employing the intrinsic piezoresistivity of graphene to transduce its motion in nanoelectromechanical systems, we approach a force resolution of 16.3 ± 0.8 aN/Hz(1/2) and a minimum detectable mass of 1.41 ± 0.02 zeptograms (10(-21) g) at ambient temperature. Quality factors of the driven response of the order of 10(3) at pressures ∼10(-6) Torr on several devices are also observed. Moreover, we demonstrate this at ambient temperature on chemical-vapor-deposition-grown graphene to allow for scale-up, thus demonstrating its potential for applications requiring exquisite force and mass resolution such as mass spectroscopy and magnetic resonance force microscopy.","corpus_id":26891628,"score":1},{"doc_id":"26672553","title":"Multi-element logic gates for trapped-ion qubits.","abstract":"Precision control over hybrid physical systems at the quantum level is important for the realization of many quantum-based technologies. In the field of quantum information processing (QIP) and quantum networking, various proposals discuss the possibility of hybrid architectures where specific tasks are delegated to the most suitable subsystem. For example, in quantum networks, it may be advantageous to transfer information from a subsystem that has good memory properties to another subsystem that is more efficient at transporting information between nodes in the network. For trapped ions, a hybrid system formed of different species introduces extra degrees of freedom that can be exploited to expand and refine the control of the system. Ions of different elements have previously been used in QIP experiments for sympathetic cooling, creation of entanglement through dissipation, and quantum non-demolition measurement of one species with another. Here we demonstrate an entangling quantum gate between ions of different elements which can serve as an important building block of QIP, quantum networking, precision spectroscopy, metrology, and quantum simulation. A geometric phase gate between a (9)Be(+) ion and a (25)Mg(+) ion is realized through an effective spin-spin interaction generated by state-dependent forces induced with laser beams. Combined with single-qubit gates and same-species entangling gates, this mixed-element entangling gate provides a complete set of gates over such a hybrid system for universal QIP. Using a sequence of such gates, we demonstrate a CNOT (controlled-NOT) gate and a SWAP gate. We further demonstrate the robustness of these gates against thermal excitation and show improved detection in quantum logic spectroscopy. We also observe a strong violation of a CHSH (Clauser-Horne-Shimony-Holt)-type Bell inequality on entangled states composed of different ion species.","corpus_id":4450528,"score":1},{"doc_id":"26855427","title":"Non-destructive state detection for quantum logic spectroscopy of molecular ions.","abstract":"Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds.","corpus_id":205247267,"score":1},{"doc_id":"27582467","title":"Atom-atom interactions around the band edge of a photonic crystal waveguide.","abstract":"Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.","corpus_id":20885649,"score":1},{"doc_id":"27587128","title":"Robust atomic force microscopy using multiple sensors.","abstract":"Atomic force microscopy typically relies on high-resolution high-bandwidth cantilever deflection measurements based control for imaging and estimating sample topography and properties. More precisely, in amplitude-modulation atomic force microscopy (AM-AFM), the control effort that regulates deflection amplitude is used as an estimate of sample topography; similarly, contact-mode AFM uses regulation of deflection signal to generate sample topography. In this article, a control design scheme based on an additional feedback mechanism that uses vertical z-piezo motion sensor, which augments the deflection based control scheme, is proposed and evaluated. The proposed scheme exploits the fact that the piezo motion sensor, though inferior to the cantilever deflection signal in terms of resolution and bandwidth, provides information on piezo actuator dynamics that is not easily retrievable from the deflection signal. The augmented design results in significant improvements in imaging bandwidth and robustness, especially in AM-AFM, where the complicated underlying nonlinear dynamics inhibits estimating piezo motions from deflection signals. In AM-AFM experiments, the two-sensor based design demonstrates a substantial improvement in robustness to modeling uncertainties by practically eliminating the peak in the sensitivity plot without affecting the closed-loop bandwidth when compared to a design that does not use the piezo-position sensor based feedback. The contact-mode imaging results, which use proportional-integral controllers for cantilever-deflection regulation, demonstrate improvements in bandwidth and robustness to modeling uncertainties, respectively, by over 30% and 20%. The piezo-sensor based feedback is developed using H∞ control framework.","corpus_id":6156688,"score":1},{"doc_id":"27782583","title":"Development of low temperature atomic force microscopy with an optical beam deflection system capable of simultaneously detecting the lateral and vertical forces.","abstract":"The atomic force microscopy (AFM) is a very important tool for imaging and investigating the complex force interactions on sample surfaces with high spatial resolution. In the AFM, two types of detection systems of the tip-sample interaction forces have been used: an optical detection system and an electrical detection system. In optical detection systems, such as optical beam deflection system or optical fiber interferometer system, both the lateral and the vertical tip-sample forces can be measured simultaneously. In electrical detection systems, such as qPlus or Kolibri sensors, either the lateral or vertical forces can be measured. Simultaneous measurement of the lateral and vertical interaction forces effectively allows investigation of force interactions because the force is a vector with magnitude and direction. In this study, we developed a low-temperature, frequency-modulation AFM using an optical beam deflection system to simultaneously measure the vertical and lateral forces. In this system, the heat sources, such as a laser diode and a current-to-voltage converter, for measuring the photocurrent of the four-segmented photodiode are located outside the observation chamber to avoid a temperature increase of the AFM unit. The focused optical beam is three-dimensionally adjustable on the back side of the cantilever. We demonstrate low-noise displacement measurement of the cantilever and successful atomic resolution imaging using the vertical and lateral forces at low temperatures.","corpus_id":43606018,"score":1},{"doc_id":"27999246","title":"Design and Sensitivity Analysis Simulation of a Novel 3D Force Sensor Based on a Parallel Mechanism.","abstract":"Automated force measurement is one of the most important technologies in realizing intelligent automation systems. However, while many methods are available for micro-force sensing, measuring large three-dimensional (3D) forces and loads remains a significant challenge. Accordingly, the present study proposes a novel 3D force sensor based on a parallel mechanism. The transformation function and sensitivity index of the proposed sensor are analytically derived. The simulation results show that the sensor has a larger effective measuring capability than traditional force sensors. Moreover, the sensor has a greater measurement sensitivity for horizontal forces than for vertical forces over most of the measurable force region. In other words, compared to traditional force sensors, the proposed sensor is more sensitive to shear forces than normal forces.","corpus_id":3197355,"score":1},{"doc_id":"28492258","title":"Preparation and coherent manipulation of pure quantum states of a single molecular ion.","abstract":"Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH(+)) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.","corpus_id":205255882,"score":1},{"doc_id":"28663571","title":"Single ion fluorescence excited with a single mode of an UV frequency comb.","abstract":"Optical frequency combs have revolutionized the measurement of optical frequencies and improved the precision of spectroscopic experiments. Besides their importance as a frequency-measuring ruler, the frequency combs themselves can excite target transitions (direct frequency comb spectroscopy). The direct frequency comb spectroscopy may extend the optical frequency metrology into spectral regions unreachable by continuous wave lasers. In high precision spectroscopy, atoms/ions/molecules trapped in place have been often used as a target to minimize systematic effects. Here, we demonstrate direct frequency comb spectroscopy of single (25)Mg ions confined in a Paul trap, at deep-UV wavelengths. Only one mode out of about 20,000 can be resonant at a time. Even then we can detect the induced fluorescence with a spatially resolving single photon camera, allowing us to determine the absolute transition frequency. The demonstration shows that the direct frequency comb spectroscopy is an important tool for frequency metrology for shorter wavelengths where continuous wave lasers are unavailable. Frequency combs are useful tools in high precision measurement including atomic transitions and atomic clocks. Here the authors demonstrate direct frequency comb spectroscopy to shorter wavelengths by probing a transition frequency in a trapped Mg+ ion using a single mode of a UV frequency comb.","corpus_id":24331103,"score":1},{"doc_id":"28707930","title":"Trapped Ions in Rydberg-Dressed Atomic Gases.","abstract":"We theoretically study trapped ions that are immersed in an ultracold gas of Rydberg-dressed atoms. By off-resonant coupling on a dipole-forbidden transition, the adiabatic atom-ion potential can be made repulsive. We study the energy exchange between the atoms and a single trapped ion and find that Langevin collisions are inhibited in the ultracold regime for these repulsive interactions. Therefore, the proposed system avoids recently observed ion heating in hybrid atom-ion systems caused by coupling to the ion's radio frequency trapping field and retains ultracold temperatures even in the presence of excess micromotion.","corpus_id":206293324,"score":1},{"doc_id":"29084886","title":"Non-thermalization in trapped atomic ion spin chains.","abstract":"Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.","corpus_id":19588325,"score":1},{"doc_id":"29269423","title":"Coherent single-atom superradiance.","abstract":"Superradiance is a quantum phenomenon emerging in macroscopic systems whereby correlated single atoms cooperatively emit photons. Demonstration of controlled collective atom-field interactions has resulted from the ability to directly imprint correlations with an atomic ensemble. Here we report cavity-mediated coherent single-atom superradiance: Single atoms with predefined correlation traverse a high-quality factor cavity one by one, emitting photons cooperatively with the N atoms that have already gone through the cavity (N represents the number of atoms). Enhanced collective photoemission of N-squared dependence was observed even when the intracavity atom number was less than unity. The correlation among single atoms was achieved by nanometer-precision position control and phase-aligned state manipulation of atoms by using a nanohole-array aperture. Our results demonstrate a platform for phase-controlled atom-field interactions.","corpus_id":206665366,"score":1},{"doc_id":"29350951","title":"High-Fidelity Preservation of Quantum Information During Trapped-Ion Transport.","abstract":"A promising scheme for building scalable quantum simulators and computers is the synthesis of a scalable system using interconnected subsystems. A prerequisite for this approach is the ability to faithfully transfer quantum information between subsystems. With trapped atomic ions, this can be realized by transporting ions with quantum information encoded into their internal states. Here, we measure with high precision the fidelity of quantum information encoded into hyperfine states of a ^{171}Yb^{+} ion during ion transport in a microstructured Paul trap. Ramsey spectroscopy of the ion's internal state is interleaved with up to 4000 transport operations over a distance of 280 μm each taking 12.8 μs. We obtain a state fidelity of 99.9994( _{-7}^{+6})% per ion transport.","corpus_id":206305845,"score":1},{"doc_id":"18377016","title":"Calibration of lateral force measurements in atomic force microscopy with a piezoresistive force sensor.","abstract":"We present here a method to calibrate the lateral force in the atomic force microscope. This method makes use of an accurately calibrated force sensor composed of a tipless piezoresistive cantilever and corresponding signal amplifying and processing electronics. Two ways of force loading with different loading points were compared by scanning the top and side edges of the piezoresistive cantilever. Conversion factors between the lateral force and photodiode signal using three types of atomic force microscope cantilevers with rectangular geometries (normal spring constants from 0.092 to 1.24 N/m and lateral stiffness from 10.34 to 101.06 N/m) were measured in experiments using the proposed method. When used properly, this method calibrates the conversion factors that are accurate to +/-12.4% or better. This standard has less error than the commonly used method based on the cantilever's beam mechanics. Methods such of this allow accurate and direct conversion between lateral forces and photodiode signals without any knowledge of the cantilevers and the laser measuring system.","corpus_id":12888966,"score":0},{"doc_id":"19158918","title":"Interferometric 3D tracking of several particles in a scanning laser focus.","abstract":"High-Speed tracking of several particles allows measuring dynamic long-range interactions relevant to biotechnology and colloidal physics. In this paper we extend the successful technique of 3D back-focal plane interferometry to oscillating laser beams and show that two or more particles can be trapped and tracked with a precision of a few nanometers in all three dimensions. The tracking rate of several kHz is only limited by the scan speed of the beam steering device. Several tests proof the linearity and orthogonality of our detection scheme, which is of interest to optical tweezing applications and various metrologies. As an example we show the position cross-correlations of three diffusing particles in a scanning line optical trap.","corpus_id":44591136,"score":0},{"doc_id":"19509448","title":"QPlus: atomic force microscopy on single-crystal insulators with small oscillation amplitudes at 5 K.","abstract":"Based on a proven low temperature scanning tunneling microscope (STM) platform, we have integrated a QPlus sensor, which employs a quartz tuning fork for force detection in non-contact atomic force microscopy (AFM). For combined STM operation, this sensor has key advantages over conventional sensors. For quantitative force spectroscopy on insulating thin films or semiconductors, decoupling of the tunneling current and the piezo-electrically induced AFM signal is important. In addition, extremely low signals require the first amplification stage to be very close to the sensor, i.e. to be compatible with low temperatures. We present atomic resolution imaging on single-crystal NaCl(100) with oscillation amplitudes below 100 pm (peak-to-peak) and operation at higher flexural modes in constant frequency shift (df) imaging feedback. We also present atomic resolution measurements on MgO(100) and Au(111), and first evaluation measurements of the QPlus sensor in Kelvin probe microscopy on Si(111) 7 x 7.","corpus_id":12910021,"score":0},{"doc_id":"21412333","title":"Single-spin addressing in an atomic Mott insulator.","abstract":"Ultracold atoms in optical lattices provide a versatile tool with which to investigate fundamental properties of quantum many-body systems. In particular, the high degree of control of experimental parameters has allowed the study of many interesting phenomena, such as quantum phase transitions and quantum spin dynamics. Here we demonstrate how such control can be implemented at the most fundamental level of a single spin at a specific site of an optical lattice. Using a tightly focused laser beam together with a microwave field, we were able to flip the spin of individual atoms in a Mott insulator with sub-diffraction-limited resolution, well below the lattice spacing. The Mott insulator provided us with a large two-dimensional array of perfectly arranged atoms, in which we created arbitrary spin patterns by sequentially addressing selected lattice sites after freezing out the atom distribution. We directly monitored the tunnelling quantum dynamics of single atoms in the lattice prepared along a single line, and observed that our addressing scheme leaves the atoms in the motional ground state. The results should enable studies of entropy transport and the quantum dynamics of spin impurities, the implementation of novel cooling schemes, and the engineering of quantum many-body phases and various quantum information processing applications.","corpus_id":4352129,"score":0},{"doc_id":"21529015","title":"A high-pressure atomic force microscope for imaging in supercritical carbon dioxide.","abstract":"A high-pressure atomic force microscope (AFM) that enables in situ, atomic scale measurements of topography of solid surfaces in contact with supercritical CO(2) (scCO(2)) fluids has been developed. This apparatus overcomes the pressure limitations of the hydrothermal AFM and is designed to handle pressures up to 100 atm at temperatures up to ∼350 K. A standard optically-based cantilever deflection detection system was chosen. When imaging in compressible supercritical fluids such as scCO(2), precise control of pressure and temperature in the fluid cell is the primary technical challenge. Noise levels and imaging resolution depend on minimization of fluid density fluctuations that change the fluid refractive index and hence the laser path. We demonstrate with our apparatus in situ atomic scale imaging of a calcite (CaCO(3)) mineral surface in scCO(2); both single, monatomic steps and dynamic processes occurring on the (1014) surface are presented. This new AFM provides unprecedented in situ access to interfacial phenomena at solid-fluid interfaces under pressure.","corpus_id":19207228,"score":0},{"doc_id":"21930566","title":"Ultracold atoms and precise time standards.","abstract":"Experimental techniques of laser cooling and trapping, along with other cooling techniques, have produced gaseous samples of atoms so cold that they are, for many practical purposes, in the quantum ground state of their centre-of-mass motion. Such low velocities have virtually eliminated effects such as Doppler shifts, relativistic time dilation and observation-time broadening that previously limited the performance of atomic frequency standards. Today, the best laser-cooled, caesium atomic fountain, microwave frequency standards realize the International System of Units (SI) definition of the second to a relative accuracy of ≈3×10(-16). Optical frequency standards, which do not realize the SI second, have even better performance: cold neutral atoms trapped in optical lattices now yield relative systematic uncertainties of ≈1×10(-16), whereas cold-trapped ions have systematic uncertainties of 9×10(-18). We will discuss the current limitations in the performance of neutral atom atomic frequency standards and prospects for the future.","corpus_id":21394623,"score":0},{"doc_id":"23563845","title":"A surface-patterned chip as a strong source of ultracold atoms for quantum technologies.","abstract":"Laser-cooled atoms are central to modern precision measurements. They are also increasingly important as an enabling technology for experimental cavity quantum electrodynamics, quantum information processing and matter-wave interferometry. Although significant progress has been made in miniaturizing atomic metrological devices, these are limited in accuracy by their use of hot atomic ensembles and buffer gases. Advances have also been made in producing portable apparatus that benefits from the advantages of atoms in the microkelvin regime. However, simplifying atomic cooling and loading using microfabrication technology has proved difficult. In this Letter we address this problem, realizing an atom chip that enables the integration of laser cooling and trapping into a compact apparatus. Our source delivers ten thousand times more atoms than previous magneto-optical traps with microfabricated optics and, for the first time, can reach sub-Doppler temperatures. Moreover, the same chip design offers a simple way to form stable optical lattices. These features, combined with simplicity of fabrication and ease of operation, make these new traps a key advance in the development of cold-atom technology for high-accuracy, portable measurement devices.","corpus_id":205450448,"score":0},{"doc_id":"24483741","title":"Accurate atom counting in mesoscopic ensembles.","abstract":"Many cold atom experiments rely on precise atom number detection, especially in the context of quantum-enhanced metrology where effects at the single particle level are important. Here, we investigate the limits of atom number counting via resonant fluorescence detection for mesoscopic samples of trapped atoms. We characterize the precision of these fluorescence measurements beginning from the single-atom level up to more than one thousand. By investigating the primary noise sources, we obtain single-atom resolution for atom numbers as high as 1200. This capability is an essential prerequisite for future experiments with highly entangled states of mesoscopic atomic ensembles.","corpus_id":3025216,"score":0},{"doc_id":"24720757","title":"Hyphenating atomic force microscopy.","abstract":"Atomic force microscopy can be readily combined with complementary instrumental techniques ranging from optical to mass-sensitive methods. This Feature highlights recent advances on hyphenated AFM technology, which enables localized studies and mapping of complementary information at surfaces and interfaces.","corpus_id":31174177,"score":0},{"doc_id":"24758916","title":"High-coherence electron and ion bunches from laser-cooled atoms.","abstract":"Cold atom electron and ion sources produce electron bunches and ion beams by photoionization of laser-cooled atoms. They offer high coherence and the potential for high brightness, with applications including ultra-fast electron-diffractive imaging of dynamic processes at the nanoscale. The effective brightness of electron sources has been limited by nonlinear divergence caused by repulsive interactions between the electrons, known as the Coulomb explosion. It has been shown that electron bunches with ellipsoidal shape and uniform density distribution have linear internal Coulomb fields, such that the Coulomb explosion can be reversed using conventional optics. Our source can create bunches shaped in three dimensions and hence in principle achieve the transverse spatial coherence and brightness needed for picosecond-diffractive imaging with nanometer resolution. Here we present results showing how the shaping capability can be used to measure the spatial coherence properties of the cold electron source. We also investigate space-charge effects with ions and generate electron bunches with durations of a few hundred picoseconds. Future development of the cold atom electron and ion source will increase the bunch charge and charge density, demonstrate reversal of Coulomb explosion, and ultimately, ultra-fast coherent electron-diffractive imaging.","corpus_id":649723,"score":0},{"doc_id":"25267655","title":"Single-spin stochastic optical reconstruction microscopy.","abstract":"We experimentally demonstrate precision addressing of single-quantum emitters by combined optical microscopy and spin resonance techniques. To this end, we use nitrogen vacancy (NV) color centers in diamond confined within a few ten nanometers as individually resolvable quantum systems. By developing a stochastic optical reconstruction microscopy (STORM) technique for NV centers, we are able to simultaneously perform sub-diffraction-limit imaging and optically detected spin resonance (ODMR) measurements on NV spins. This allows the assignment of spin resonance spectra to individual NV center locations with nanometer-scale resolution and thus further improves spatial discrimination. For example, we resolved formerly indistinguishable emitters by their spectra. Furthermore, ODMR spectra contain metrology information allowing for sub-diffraction-limit sensing of, for instance, magnetic or electric fields with inherently parallel data acquisition. As an example, we have detected nuclear spins with nanometer-scale precision. Finally, we give prospects of how this technique can evolve into a fully parallel quantum sensor for nanometer resolution imaging of delocalized quantum correlations.","corpus_id":226408,"score":0},{"doc_id":"25766230","title":"Coulomb crystallization of highly charged ions.","abstract":"Control over the motional degrees of freedom of atoms, ions, and molecules in a field-free environment enables unrivalled measurement accuracies but has yet to be applied to highly charged ions (HCIs), which are of particular interest to future atomic clock designs and searches for physics beyond the Standard Model. Here, we report on the Coulomb crystallization of HCIs (specifically (40)Ar(13+)) produced in an electron beam ion trap and retrapped in a cryogenic linear radiofrequency trap by means of sympathetic motional cooling through Coulomb interaction with a directly laser-cooled ensemble of Be(+) ions. We also demonstrate cooling of a single Ar(13+) ion by a single Be(+) ion-the prerequisite for quantum logic spectroscopy with a potential 10(-19) accuracy level. Achieving a seven-orders-of-magnitude decrease in HCI temperature starting at megakelvin down to the millikelvin range removes the major obstacle for HCI investigation with high-precision laser spectroscopy.","corpus_id":20711393,"score":0},{"doc_id":"26191667","title":"Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature.","abstract":"Advanced optical traps can probe single molecules with Ångstrom-scale precision, but drift limits the utility of these instruments. To achieve Å-scale stability, a differential measurement scheme between a pair of laser foci was introduced that substantially exceeds the inherent mechanical stability of various types of microscopes at room temperature. By using lock-in detection to measure both lasers with a single quadrant photodiode, we enhanced the differential stability of this optical reference frame and thereby stabilized an optical-trapping microscope to 0.2 Å laterally over 100 s based on the Allan deviation. In three dimensions, we achieved stabilities of 1 Å over 1,000 s and 1 nm over 15 h. This stability was complemented by high measurement bandwidth (100 kHz). Overall, our compact back-scattered detection enables an ultrastable measurement platform compatible with optical traps, atomic force microscopy, and optical microscopy, including super-resolution techniques.","corpus_id":36983769,"score":0},{"doc_id":"26787887","title":"Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction.","abstract":"The large plasma glycoprotein von Willebrand factor (VWF) senses hydrodynamic forces in the bloodstream and responds to elevated forces with abrupt elongation, thereby increasing its adhesiveness to platelets and collagen. Remarkably, forces on VWF are elevated at sites of vascular injury, where VWF's hemostatic potential is important to mediate platelet aggregation and to recruit platelets to the subendothelial layer. Adversely, elevated forces in stenosed vessels lead to an increased risk of VWF-mediated thrombosis. To dissect the remarkable force-sensing ability of VWF, we have performed atomic force microscopy (AFM)-based single-molecule force measurements on dimers, the smallest repeating subunits of VWF multimers. We have identified a strong intermonomer interaction that involves the D4 domain and critically depends on the presence of divalent ions, consistent with results from small-angle X-ray scattering (SAXS). Dissociation of this strong interaction occurred at forces above [Formula: see text]50 pN and provided [Formula: see text]80 nm of additional length to the elongation of dimers. Corroborated by the static conformation of VWF, visualized by AFM imaging, we estimate that in VWF multimers approximately one-half of the constituent dimers are firmly closed via the strong intermonomer interaction. As firmly closed dimers markedly shorten VWF's effective length contributing to force sensing, they can be expected to tune VWF's sensitivity to hydrodynamic flow in the blood and to thereby significantly affect VWF's function in hemostasis and thrombosis.","corpus_id":1143652,"score":0},{"doc_id":"27474417","title":"Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.","abstract":"Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc.","corpus_id":4475129,"score":0},{"doc_id":"27852983","title":"Ultracold neutral plasmas.","abstract":"By photoionizing samples of laser-cooled atoms with laser light tuned just above the ionization limit, plasmas can be created with electron and ion temperatures below 10 K. These ultracold neutral plasmas have extended the temperature bounds of plasma physics by two orders of magnitude. Table-top experiments, using many of the tools from atomic physics, allow for the study of plasma phenomena in this new regime with independent control over the density and temperature of the plasma through the excitation process. Characteristic of these systems is an inhomogeneous density profile, inherited from the density distribution of the laser-cooled neutral atom sample. Most work has dealt with unconfined plasmas in vacuum, which expand outward at velocities of order 100 m/s, governed by electron pressure, and with lifetimes of order 100 μs, limited by stray electric fields. Using detection of charged particles and optical detection techniques, a wide variety of properties and phenomena have been observed, including expansion dynamics, collective excitations in both the electrons and ions, and collisional properties. Through three-body recombination collisions, the plasmas rapidly form Rydberg atoms, and clouds of cold Rydberg atoms have been observed to spontaneously avalanche ionize to form plasmas. Of particular interest is the possibility of the formation of strongly coupled plasmas, where Coulomb forces dominate thermal motion and correlations become important. The strongest impediment to strong coupling is disorder-induced heating, a process in which Coulomb energy from an initially disordered sample is converted into thermal energy. This restricts electrons to a weakly coupled regime and leaves the ions barely within the strongly coupled regime. This review will give an overview of the field of ultracold neutral plasmas, from its inception in 1999 to current work, including efforts to increase strong coupling and effects on plasma properties due to strong coupling.","corpus_id":1272219,"score":0},{"doc_id":"28009205","title":"Dynamics of a Ground-State Cooled Ion Colliding with Ultracold Atoms.","abstract":"Ultracold atom-ion mixtures are gaining increasing interest due to their potential applications in ultracold and state-controlled chemistry, quantum computing, and many-body physics. Here, we studied the dynamics of a single ground-state cooled ion during few, to many, Langevin (spiraling) collisions with ultracold atoms. We measured the ion's energy distribution and observed a clear deviation from the Maxwell-Boltzmann distribution, characterized by an exponential tail, to a power-law distribution best described by a Tsallis function. Unlike previous experiments, the energy scale of atom-ion interactions is not determined by either the atomic cloud temperature or the ion's trap residual excess-micromotion energy. Instead, it is determined by the force the atom exerts on the ion during a collision which is then amplified by the trap dynamics. This effect is intrinsic to ion Paul traps and sets the lower bound of atom-ion steady-state interaction energy in these systems. Despite the fact that our system is eventually driven out of the ultracold regime, we are capable of studying quantum effects by limiting the interaction to the first collision when the ion is initialized in the ground state of the trap.","corpus_id":6154237,"score":0},{"doc_id":"28120826","title":"Super-Coulombic atom-atom interactions in hyperbolic media.","abstract":"Dipole-dipole interactions, which govern phenomena such as cooperative Lamb shifts, superradiant decay rates, Van der Waals forces and resonance energy transfer rates, are conventionally limited to the Coulombic near-field. Here we reveal a class of real-photon and virtual-photon long-range quantum electrodynamic interactions that have a singularity in media with hyperbolic dispersion. The singularity in the dipole-dipole coupling, referred to as a super-Coulombic interaction, is a result of an effective interaction distance that goes to zero in the ideal limit irrespective of the physical distance. We investigate the entire landscape of atom-atom interactions in hyperbolic media confirming the giant long-range enhancement. We also propose multiple experimental platforms to verify our predicted effect with phonon-polaritonic hexagonal boron nitride, plasmonic super-lattices and hyperbolic meta-surfaces as well. Our work paves the way for the control of cold atoms above hyperbolic meta-surfaces and the study of many-body physics with hyperbolic media.","corpus_id":16386934,"score":0},{"doc_id":"28710414","title":"Resonant driving of a single photon emitter embedded in a mechanical oscillator.","abstract":"Coupling a microscopic mechanical resonator to a nanoscale quantum system enables control of the mechanical resonator via the quantum system and vice-versa. The coupling is usually achieved through functionalization of the mechanical resonator, but this results in additional mass and dissipation channels. An alternative is an intrinsic coupling based on strain. Here we employ a monolithic semiconductor system: the nanoscale quantum system is a semiconductor quantum dot (QD) located inside a nanowire. We demonstrate the resonant optical driving of the QD transition in such a structure. The noise spectrum of the resonance fluorescence signal, recorded in the single-photon counting regime, reveals a coupling to mechanical modes of different types. We measure a sensitivity to displacement of 65 fm/[Formula: see text] limited by charge noise in the device. Finally, we use thermal excitation of the different modes to determine the location of the QD within the trumpet, and calculate the contribution of the Brownian motion to the dephasing of the emitter. Resonant driving of a nanoscale quantum system coupled to a microscopic mechanical resonator may have uses in precision sensing and quantum information. The authors realize this by tailoring the geometry of a semiconductor nanowire embedding a quantum dot, detecting sub-picometre displacements.","corpus_id":28722859,"score":0},{"doc_id":"29109531","title":"A robust single-beam optical trap for a gram-scale mechanical oscillator.","abstract":"Precise optical control of microscopic particles has been mastered over the past three decades, with atoms, molecules and nano-particles now routinely trapped and cooled with extraordinary precision, enabling rapid progress in the study of quantum phenomena. Achieving the same level of control over macroscopic objects is expected to bring further advances in precision measurement, quantum information processing and fundamental tests of quantum mechanics. However, cavity optomechanical systems dominated by radiation pressure - so-called 'optical springs' - are inherently unstable due to the delayed dynamical response of the cavity. Here we demonstrate a fully stable, single-beam optical trap for a gram-scale mechanical oscillator. The interaction of radiation pressure with thermo-optic feedback generates damping that exceeds the mechanical loss by four orders of magnitude. The stability of the resultant spring is robust to changes in laser power and detuning, and allows purely passive self-locking of the cavity. Our results open up a new way of trapping and cooling macroscopic objects for optomechanical experiments.","corpus_id":5825484,"score":0},{"doc_id":"29301265","title":"Atomic Force Microscopy Sidewall Imaging with a Quartz Tuning Fork Force Sensor.","abstract":"Sidewall roughness measurement is becoming increasingly important in the micro-electromechanical systems and nanoelectronics devices. Atomic force microscopy (AFM) is an emerging technique for sidewall scanning and roughness measurement due to its high resolution, three-dimensional imaging capability and high accuracy. We report an AFM sidewall imaging method with a quartz tuning fork (QTF) force sensor. A self sensing and actuating force sensor is fabricated by microassembling a commercial AFM cantilever (tip apex radius ≤10 nm) to a QTF. The attached lightweight cantilever allows high-sensitivity force detection (7.4% Q factor reduction) and sidewall imaging with high lateral resolution. Owing to its unique configuration, the tip of the sensor can detect sidewall surface orthogonally during imaging, which reduces lateral friction. In experiments, sidewalls of a micro-electro-mechanical system (MEMS) structure fabricated by deep reactive ion etching process and a standard step grating are scanned and the sidewall roughness, line edge roughness and sidewall angles are measured.","corpus_id":3491865,"score":0},{"doc_id":"29459410","title":"Recent progress of laser spectroscopy experiments on antiprotonic helium.","abstract":"The Atomic Spectroscopy and Collisions Using Slow Antiprotons (ASACUSA) collaboration is currently carrying out laser spectroscopy experiments on antiprotonic helium [Formula: see text] atoms at CERN's Antiproton Decelerator facility. Two-photon spectroscopic techniques have been employed to reduce the Doppler width of the measured [Formula: see text] resonance lines, and determine the atomic transition frequencies to a fractional precision of 2.3-5 parts in 109 More recently, single-photon spectroscopy of buffer-gas cooled [Formula: see text] has reached a similar precision. By comparing the results with three-body quantum electrodynamics calculations, the antiproton-to-electron mass ratio was determined as [Formula: see text], which agrees with the known proton-to-electron mass ratio with a precision of 8×10-10 The high-quality antiproton beam provided by the future Extra Low Energy Antiproton Ring (ELENA) facility should enable further improvements in the experimental precision. This article is part of the Theo Murphy meeting issue 'Antiproton physics in the ELENA era'.","corpus_id":3443665,"score":0}],"string":"[\n {\n \"doc_id\": \"20729835\",\n \"title\": \"Ultrasensitive detection of force and displacement using trapped ions.\",\n \"abstract\": \"The ability to detect extremely small forces and nanoscale displacements is vital for disciplines such as precision spin-resonance imaging, microscopy, and tests of fundamental physical phenomena. Current force-detection sensitivity limits have surpassed 1 aN Hz(-1/2) (refs 6,7) through coupling of nanomechanical resonators to a variety of physical readout systems. Here, we demonstrate that crystals of trapped atomic ions behave as nanoscale mechanical oscillators and may form the core of exquisitely sensitive force and displacement detectors. We report the detection of forces with a sensitivity of 390 +/- 150 yN Hz(-1/2), which is more than three orders of magnitude better than existing reports using nanofabricated devices(7), and discriminate ion displacements of approximately 18 nm. Our technique is based on the excitation of tunable normal motional modes in an ion trap and detection through phase-coherent Doppler velocimetry, and should ultimately allow force detection with a sensitivity better than 1 yN Hz(-1/2) (ref. 16). Trapped-ion-based sensors could enable scientists to explore new regimes in materials science where augmented force, field and displacement sensitivity may be traded against reduced spatial resolution.\",\n \"corpus_id\": 21558623,\n \"score\": 2\n },\n {\n \"doc_id\": \"21544142\",\n \"title\": \"Single-ion quantum lock-in amplifier.\",\n \"abstract\": \"Quantum metrology uses tools from quantum information science to improve measurement signal-to-noise ratios. The challenge is to increase sensitivity while reducing susceptibility to noise, tasks that are often in conflict. Lock-in measurement is a detection scheme designed to overcome this difficulty by spectrally separating signal from noise. Here we report on the implementation of a quantum analogue to the classical lock-in amplifier. All the lock-in operations--modulation, detection and mixing--are performed through the application of non-commuting quantum operators to the electronic spin state of a single, trapped Sr(+) ion. We significantly increase its sensitivity to external fields while extending phase coherence by three orders of magnitude, to more than one second. Using this technique, we measure frequency shifts with a sensitivity of 0.42 Hz Hz(-1/2) (corresponding to a magnetic field measurement sensitivity of 15 pT Hz(-1/2)), obtaining an uncertainty of less than 10 mHz (350 fT) after 3,720 seconds of averaging. These sensitivities are limited by quantum projection noise and improve on other single-spin probe technologies by two orders of magnitude. Our reported sensitivity is sufficient for the measurement of parity non-conservation, as well as the detection of the magnetic field of a single electronic spin one micrometre from an ion detector with nanometre resolution. As a first application, we perform light shift spectroscopy of a narrow optical quadrupole transition. Finally, we emphasize that the quantum lock-in technique is generic and can potentially enhance the sensitivity of any quantum sensor.\",\n \"corpus_id\": 3208184,\n \"score\": 2\n },\n {\n \"doc_id\": \"22760632\",\n \"title\": \"Absorption imaging of a single atom.\",\n \"abstract\": \"Absorption imaging has played a key role in the advancement of science from van Leeuwenhoek's discovery of red blood cells to modern observations of dust clouds in stellar nebulas and Bose-Einstein condensates. Here we show the first absorption imaging of a single atom isolated in a vacuum. The optical properties of atoms are thoroughly understood, so a single atom is an ideal system for testing the limits of absorption imaging. A single atomic ion was confined in an RF Paul trap and the absorption imaged at near wavelength resolution with a phase Fresnel lens. The observed image contrast of 3.1 (3)% is the maximum theoretically allowed for the imaging resolution of our set-up. The absorption of photons by single atoms is of immediate interest for quantum information processing. Our results also point out new opportunities in imaging of light-sensitive samples both in the optical and X-ray regimes.\",\n \"corpus_id\": 5616535,\n \"score\": 2\n },\n {\n \"doc_id\": \"24970079\",\n \"title\": \"Quantum metrology. Optically measuring force near the standard quantum limit.\",\n \"abstract\": \"The Heisenberg uncertainty principle sets a lower bound on the noise in a force measurement based on continuously detecting a mechanical oscillator's position. This bound, the standard quantum limit, can be reached when the oscillator subjected to the force is unperturbed by its environment and when measurement imprecision from photon shot noise is balanced against disturbance from measurement back-action. We applied an external force to the center-of-mass motion of an ultracold atom cloud in a high-finesse optical cavity and measured the resulting motion optically. When the driving force is resonant with the cloud's oscillation frequency, we achieve a sensitivity that is a factor of 4 above the standard quantum limit and consistent with theoretical predictions given the atoms' residual thermal disturbance and the photodetection quantum efficiency.\",\n \"corpus_id\": 206554506,\n \"score\": 2\n },\n {\n \"doc_id\": \"27306426\",\n \"title\": \"High-precision force sensing using a single trapped ion.\",\n \"abstract\": \"We introduce quantum sensing schemes for measuring very weak forces with a single trapped ion. They use the spin-motional coupling induced by the laser-ion interaction to transfer the relevant force information to the spin-degree of freedom. Therefore, the force estimation is carried out simply by observing the Ramsey-type oscillations of the ion spin states. Three quantum probes are considered, which are represented by systems obeying the Jaynes-Cummings, quantum Rabi (in 1D) and Jahn-Teller (in 2D) models. By using dynamical decoupling schemes in the Jaynes-Cummings and Jahn-Teller models, our force sensing protocols can be made robust to the spin dephasing caused by the thermal and magnetic field fluctuations. In the quantum-Rabi probe, the residual spin-phonon coupling vanishes, which makes this sensing protocol naturally robust to thermally-induced spin dephasing. We show that the proposed techniques can be used to sense the axial and transverse components of the force with a sensitivity beyond the range, i.e. in the (xennonewton, 10(-27)). The Jahn-Teller protocol, in particular, can be used to implement a two-channel vector spectrum analyzer for measuring ultra-low voltages.\",\n \"corpus_id\": 4866453,\n \"score\": 2\n },\n {\n \"doc_id\": \"27367376\",\n \"title\": \"Ultrasensitive Magnetometer using a Single Atom.\",\n \"abstract\": \"Precision sensing, and in particular high precision magnetometry, is a central goal of research into quantum technologies. For magnetometers, often trade-offs exist between sensitivity, spatial resolution, and frequency range. The precision, and thus the sensitivity of magnetometry, scales as 1/sqrt[T_{2}] with the phase coherence time T_{2} of the sensing system playing the role of a key determinant. Adapting a dynamical decoupling scheme that allows for extending T_{2} by orders of magnitude and merging it with a magnetic sensing protocol, we achieve a measurement sensitivity even for high frequency fields close to the standard quantum limit. Using a single atomic ion as a sensor, we experimentally attain a sensitivity of 4.6 pT/sqrt[Hz] for an alternating-current magnetic field near 14 MHz. Based on the principle demonstrated here, this unprecedented sensitivity combined with spatial resolution in the nanometer range and tunability from direct current to the gigahertz range could be used for magnetic imaging in as of yet inaccessible parameter regimes.\",\n \"corpus_id\": 31926600,\n \"score\": 2\n },\n {\n \"doc_id\": \"27749835\",\n \"title\": \"A universal and ultrasensitive vectorial nanomechanical sensor for imaging 2D force fields.\",\n \"abstract\": \"The miniaturization of force probes into nanomechanical oscillators enables ultrasensitive investigations of forces on dimensions smaller than their characteristic length scales. It also unravels the vectorial character of the force field and how its topology impacts the measurement. Here we present an ultrasensitive method for imaging two-dimensional vectorial force fields by optomechanically following the bidimensional Brownian motion of a singly clamped nanowire. This approach relies on angular and spectral tomography of its quasi-frequency-degenerated transverse mechanical polarizations: immersing the nanoresonator in a vectorial force field not only shifts its eigenfrequencies but also rotates the orientation of the eigenmodes, as a nanocompass. This universal method is employed to map a tunable electrostatic force field whose spatial gradients can even dominate the intrinsic nanowire properties. Enabling vectorial force field imaging with demonstrated sensitivities of attonewton variations over the nanoprobe Brownian trajectory will have a strong impact on scientific exploration at the nanoscale.\",\n \"corpus_id\": 29463120,\n \"score\": 2\n },\n {\n \"doc_id\": \"28186103\",\n \"title\": \"Quantum lock-in force sensing using optical clock Doppler velocimetry.\",\n \"abstract\": \"Force sensors are at the heart of different technologies such as atomic force microscopy or inertial sensing. These sensors often rely on the measurement of the displacement amplitude of mechanical oscillators under applied force. The best sensitivity is typically achieved when the force is alternating at the mechanical resonance frequency of the oscillator, thus increasing its response by the mechanical quality factor. The measurement of low-frequency forces, that are below resonance, is a more difficult task as the resulting oscillation amplitudes are significantly lower. Here we use a single-trapped (88)Sr(+) ion as a force sensor. The ion is electrically driven at a frequency much lower than the trap resonance frequency. We measure small amplitude of motion by measuring the periodic Doppler shift of an atomic optical clock transition, enhanced using the quantum lock-in technique. We report frequency force detection sensitivity as low as 2.8 × 10(-20) NHz(-1/2).\",\n \"corpus_id\": 11123313,\n \"score\": 2\n },\n {\n \"doc_id\": \"18583603\",\n \"title\": \"Quantum state engineering and precision metrology using state-insensitive light traps.\",\n \"abstract\": \"Precision metrology and quantum measurement often demand that matter be prepared in well-defined quantum states for both internal and external degrees of freedom. Laser-cooled neutral atoms localized in a deeply confining optical potential satisfy this requirement. With an appropriate choice of wavelength and polarization for the optical trap, two electronic states of an atom can experience the same trapping potential, permitting coherent control of electronic transitions independent of the atomic center-of-mass motion. Here, we review a number of recent experiments that use this approach to investigate precision quantum metrology for optical atomic clocks and coherent control of optical interactions of single atoms and photons within the context of cavity quantum electrodynamics. We also provide a brief survey of promising prospects for future work.\",\n \"corpus_id\": 27388210,\n \"score\": 1\n },\n {\n \"doc_id\": \"20016597\",\n \"title\": \"Photon-by-photon feedback control of a single-atom trajectory.\",\n \"abstract\": \"Feedback is one of the most powerful techniques for the control of classical systems. An extension into the quantum domain is desirable as it could allow the production of non-trivial quantum states and protection against decoherence. The difficulties associated with quantum, as opposed to classical, feedback arise from the quantum measurement process-in particular the quantum projection noise and the limited measurement rate-as well as from quantum fluctuations perturbing the evolution in a driven open system. Here we demonstrate real-time feedback control of the motion of a single atom trapped in an optical cavity. Individual probe photons carrying information about the atomic position activate a dipole laser that steers the atom on timescales 70 times shorter than the atom's oscillation period in the trap. Depending on the specific implementation, the trapping time is increased by a factor of more than four owing to feedback cooling, which can remove almost all the kinetic energy of the atom in a quarter of an oscillation period. Our results show that the detected photon flux reflects the atomic motion, and thus mark a step towards the exploration of the quantum trajectory of a single atom at the standard quantum limit.\",\n \"corpus_id\": 4432136,\n \"score\": 1\n },\n {\n \"doc_id\": \"20066528\",\n \"title\": \"Single-photon atomic force microscopy.\",\n \"abstract\": \"In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed \\\"single-photon atomic force microscopy\\\" (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.\",\n \"corpus_id\": 39410037,\n \"score\": 1\n },\n {\n \"doc_id\": \"20113129\",\n \"title\": \"Microdisplacement sensor using an optically trapped microprobe based on the interference scale.\",\n \"abstract\": \"Positioning technology is one of the most important technologies for developing microsystems. In particular, displacement sensors are necessary for positioning devices with nanoscale accuracy. In this study, we propose a new displacement sensor that uses an interference scale as a linear scale and a laser-trapped microsphere as a sensing probe. This sensor has a wide measuring range, high resolution, and accessibility for narrow target areas. A glass microsphere was optically trapped by means of the laser trapping technique. Between the target surface and the probe, an interference scale was generated along the optical axis. The scale origin was fixed on the target surface. The distance between the probe and the target surface could be measured in terms of the shift in the interference scale. This study investigated the fundamental performance of the sensor. The resolution and accuracy of the sensor were 10 and +/-50 nm, respectively; these values could be improved by using trapping lasers having shorter wavelengths. The measurable range was 250 microm. This sensor can provide useful displacement information from a target area having dimensions smaller than 15 microm. In addition, the displacement sensor can measure the distance even for surfaces inclined at angles less than 15 degrees; thus, a flexible arrangement can be used to carry out measurements. In addition, the direction of displacement can be identified.\",\n \"corpus_id\": 21951749,\n \"score\": 1\n },\n {\n \"doc_id\": \"20150495\",\n \"title\": \"Resonance fluorescence of a single artificial atom.\",\n \"abstract\": \"An atom in open space can be detected by means of resonant absorption and reemission of electromagnetic waves, known as resonance fluorescence, which is a fundamental phenomenon of quantum optics. We report on the observation of scattering of propagating waves by a single artificial atom. The behavior of the artificial atom, a superconducting macroscopic two-level system, is in a quantitative agreement with the predictions of quantum optics for a pointlike scatterer interacting with the electromagnetic field in one-dimensional open space. The strong atom-field interaction as revealed in a high degree of extinction of propagating waves will allow applications of controllable artificial atoms in quantum optics and photonics.\",\n \"corpus_id\": 206523434,\n \"score\": 1\n },\n {\n \"doc_id\": \"20366407\",\n \"title\": \"Realization of a quantum walk with one and two trapped ions.\",\n \"abstract\": \"We experimentally demonstrate a quantum walk on a line in phase space using one and two trapped ions. A walk with up to 23 steps is realized by subjecting an ion to state-dependent displacement operations interleaved with quantum coin tossing operations. To analyze the ion's motional state after each step we apply a technique that directly maps the probability density distribution onto the ion's internal state. The measured probability distributions and the position's second moment clearly show the nonclassical character of the quantum walk. To further highlight the difference between the classical (random) and the quantum walk, we demonstrate the reversibility of the latter. Finally, we extend the quantum walk by using two ions, giving the walker the additional possibility to stay instead of taking a step.\",\n \"corpus_id\": 19177982,\n \"score\": 1\n },\n {\n \"doc_id\": \"21230903\",\n \"title\": \"Electromagnetically induced transparency from a single atom in free space.\",\n \"abstract\": \"In this Letter, we report an absorption spectroscopy experiment and the observation of electromagnetically induced transparency from a single trapped atom. We focus a weak and narrow band Gaussian light beam onto an optically cooled 138Ba+ ion using a high numerical aperture lens. Extinction of this beam is observed with measured values of up to 1.35%. We demonstrate electromagnetically induced transparency of the ion by tuning a strong control beam over a two-photon resonance in a three-level Λ-type system. The probe beam extinction is inhibited by more than 75% due to population trapping.\",\n \"corpus_id\": 21605616,\n \"score\": 1\n },\n {\n \"doc_id\": \"21430776\",\n \"title\": \"Interaction-based quantum metrology showing scaling beyond the Heisenberg limit.\",\n \"abstract\": \"Quantum metrology aims to use entanglement and other quantum resources to improve precision measurement. An interferometer using N independent particles to measure a parameter χ can achieve at best the standard quantum limit of sensitivity, δχ ∝ N(-1/2). However, using N entangled particles and exotic states, such an interferometer can in principle achieve the Heisenberg limit, δχ ∝ N(-1). Recent theoretical work has argued that interactions among particles may be a valuable resource for quantum metrology, allowing scaling beyond the Heisenberg limit. Specifically, a k-particle interaction will produce sensitivity δχ ∝ N(-k) with appropriate entangled states and δχ ∝ N(-(k-1/2)) even without entanglement. Here we demonstrate 'super-Heisenberg' scaling of δχ ∝ N(-3/2) in a nonlinear, non-destructive measurement of the magnetization of an atomic ensemble. We use fast optical nonlinearities to generate a pairwise photon-photon interaction (corresponding to k = 2) while preserving quantum-noise-limited performance. We observe super-Heisenberg scaling over two orders of magnitude in N, limited at large numbers by higher-order nonlinear effects, in good agreement with theory. For a measurement of limited duration, super-Heisenberg scaling allows the nonlinear measurement to overtake in sensitivity a comparable linear measurement with the same number of photons. In other situations, however, higher-order nonlinearities prevent this crossover from occurring, reflecting the subtle relationship between scaling and sensitivity in nonlinear systems. Our work shows that interparticle interactions can improve sensitivity in a quantum-limited measurement, and experimentally demonstrates a new resource for quantum metrology.\",\n \"corpus_id\": 199679770,\n \"score\": 1\n },\n {\n \"doc_id\": \"21660745\",\n \"title\": \"Atomic force microscopy as nanorobot.\",\n \"abstract\": \"Atomic force microscopy (AFM) is a powerful and widely used imaging technique that can visualize single molecules under physiological condition at the nanometer scale. In this chapter, an AFM-based nanorobot for biological studies is introduced. Using the AFM tip as an end effector, the AFM can be modified into a nanorobot that can manipulate biological objects at the single-molecule level. By functionalizing the AFM tip with specific antibodies, the nanorobot is able to identify specific types of receptors on the cell membrane. It is similar to the fluorescent optical microscopy but with higher resolution. By locally updating the AFM image based on interaction force information and objects' model during nanomanipulation, real-time visual feedback is obtained through the augmented reality interface. The development of the AFM-based nanorobotic system enables us to conduct in situ imaging, sensing, and manipulation simultaneously at the nanometer scale (e.g., protein and DNA levels). The AFM-based nanorobotic system offers several advantages and capabilities for studying structure-function relationships of biological specimens. As a result, many biomedical applications can be achieved by the AFM-based nanorobotic system.\",\n \"corpus_id\": 11238900,\n \"score\": 1\n },\n {\n \"doc_id\": \"22368463\",\n \"title\": \"Development of a hybrid atomic force microscopic measurement system combined with white light scanning interferometry.\",\n \"abstract\": \"A hybrid atomic force microscopic (AFM) measurement system combined with white light scanning interferometry for micro/nanometer dimensional measurement is developed. The system is based on a high precision large-range positioning platform with nanometer accuracy on which a white light scanning interferometric module and an AFM head are built. A compact AFM head is developed using a self-sensing tuning fork probe. The head need no external optical sensors to detect the deflection of the cantilever, which saves room on the head, and it can be directly fixed under an optical microscopic interferometric system. To enhance the system's dynamic response, the frequency modulation (FM) mode is adopted for the AFM head. The measuring data can be traceable through three laser interferometers in the system. The lateral scanning range can reach 25 mm × 25 mm by using a large-range positioning platform. A hybrid method combining AFM and white light scanning interferometry is proposed to improve the AFM measurement efficiency. In this method, the sample is measured firstly by white light scanning interferometry to get an overall coarse morphology, and then, further measured with higher resolution by AFM. Several measuring experiments on standard samples demonstrate the system's good measurement performance and feasibility of the hybrid measurement method.\",\n \"corpus_id\": 14693933,\n \"score\": 1\n },\n {\n \"doc_id\": \"22380080\",\n \"title\": \"Measurement of probe displacement to the thermal resolution limit in photonic force microscopy using a miniature quadrant photodetector.\",\n \"abstract\": \"A photonic force microscope comprises of an optically trapped micro-probe and a position detection system to track the motion of the probe. Signal collection for motion detection is often carried out using the backscattered light off the probe-however, this mode has problems of low S/N due to the small backscattering cross sections of the micro-probes typically used. The position sensors often used in these cases are quadrant photodetectors. To ensure maximum sensitivity of such detectors, it would help if the detector size matched with the detection beam radius after the condenser lens (which for backscattered detection would be the trapping objective itself). To suit this condition, we have used a miniature displacement sensor whose dimensions makes it ideal to work with 1:1 images of micrometer-sized trapped probes in the backscattering detection mode. The detector is based on the quadrant photo-integrated chip in the optical pick-up head of a compact disc player. Using this detector, we measured absolute displacements of an optically trapped 1.1 μm probe with a resolution of ∼10 nm for a bandwidth of 10 Hz at 95% significance without any sample or laser stabilization. We characterized our optical trap for different sized probes by measuring the power spectrum for each probe to 1% accuracy, and found that for 1.1 μm diameter probes, the noise in our position measurement matched the thermal resolution limit for averaging times up to 10 ms. We also achieved a linear response range of around 385 nm with cross talk between axes ≃4% for 1.1 μm diameter probes. The detector has extremely high bandwidth (few MHz) and low optical power threshold-other factors that can lead to its widespread use in photonic force microscopy.\",\n \"corpus_id\": 5882313,\n \"score\": 1\n },\n {\n \"doc_id\": \"22790343\",\n \"title\": \"Experimental quantum simulations of many-body physics with trapped ions.\",\n \"abstract\": \"Direct experimental access to some of the most intriguing quantum phenomena is not granted due to the lack of precise control of the relevant parameters in their naturally intricate environment. Their simulation on conventional computers is impossible, since quantum behaviour arising with superposition states or entanglement is not efficiently translatable into the classical language. However, one could gain deeper insight into complex quantum dynamics by experimentally simulating the quantum behaviour of interest in another quantum system, where the relevant parameters and interactions can be controlled and robust effects detected sufficiently well. Systems of trapped ions provide unique control of both the internal (electronic) and external (motional) degrees of freedom. The mutual Coulomb interaction between the ions allows for large interaction strengths at comparatively large mutual ion distances enabling individual control and readout. Systems of trapped ions therefore exhibit a prominent system in several physical disciplines, for example, quantum information processing or metrology. Here, we will give an overview of different trapping techniques of ions as well as implementations for coherent manipulation of their quantum states and discuss the related theoretical basics. We then report on the experimental and theoretical progress in simulating quantum many-body physics with trapped ions and present current approaches for scaling up to more ions and more-dimensional systems.\",\n \"corpus_id\": 30689533,\n \"score\": 1\n },\n {\n \"doc_id\": \"23473144\",\n \"title\": \"Atom-atom entanglement by single-photon detection.\",\n \"abstract\": \"A scheme for entangling distant atoms is realized, as proposed in the seminal paper by [C. Cabrillo et al., Phys. Rev. A 59, 1025 (1999)]. The protocol is based on quantum interference and detection of a single photon scattered from two effectively one meter distant laser cooled and trapped atomic ions. The detection of a single photon heralds entanglement of two internal states of the trapped ions with high rate and with a fidelity limited mostly by atomic motion. Control of the entangled state phase is demonstrated by changing the path length of the single-photon interferometer.\",\n \"corpus_id\": 2063579,\n \"score\": 1\n },\n {\n \"doc_id\": \"23618764\",\n \"title\": \"Coupling a single trapped atom to a nanoscale optical cavity.\",\n \"abstract\": \"Hybrid quantum devices, in which dissimilar quantum systems are combined in order to attain qualities not available with either system alone, may enable far-reaching control in quantum measurement, sensing, and information processing. A paradigmatic example is trapped ultracold atoms, which offer excellent quantum coherent properties, coupled to nanoscale solid-state systems, which allow for strong interactions. We demonstrate a deterministic interface between a single trapped rubidium atom and a nanoscale photonic crystal cavity. Precise control over the atom's position allows us to probe the cavity near-field with a resolution below the diffraction limit and to observe large atom-photon coupling. This approach may enable the realization of integrated, strongly coupled quantum nano-optical circuits.\",\n \"corpus_id\": 9924385,\n \"score\": 1\n },\n {\n \"doc_id\": \"23767719\",\n \"title\": \"Ground-state cooling of a single atom at the center of an optical cavity.\",\n \"abstract\": \"A single neutral atom is trapped in a three-dimensional optical lattice at the center of a high-finesse optical resonator. Using fluorescence imaging and a shiftable standing-wave trap, the atom is deterministically loaded into the maximum of the intracavity field where the atom-cavity coupling is strong. After 5 ms of Raman sideband cooling, the three-dimensional motional ground state is populated with a probability of (89±2)%. Our system is the first to simultaneously achieve quantum control over all degrees of freedom of a single atom: its position and momentum, its internal state, and its coupling to light.\",\n \"corpus_id\": 21176284,\n \"score\": 1\n },\n {\n \"doc_id\": \"24717513\",\n \"title\": \"Nanophotonic quantum phase switch with a single atom.\",\n \"abstract\": \"By analogy to transistors in classical electronic circuits, quantum optical switches are important elements of quantum circuits and quantum networks. Operated at the fundamental limit where a single quantum of light or matter controls another field or material system, such a switch may enable applications such as long-distance quantum communication, distributed quantum information processing and metrology, and the exploration of novel quantum states of matter. Here, by strongly coupling a photon to a single atom trapped in the near field of a nanoscale photonic crystal cavity, we realize a system in which a single atom switches the phase of a photon and a single photon modifies the atom's phase. We experimentally demonstrate an atom-induced optical phase shift that is nonlinear at the two-photon level, a photon number router that separates individual photons and photon pairs into different output modes, and a single-photon switch in which a single 'gate' photon controls the propagation of a subsequent probe field. These techniques pave the way to integrated quantum nanophotonic networks involving multiple atomic nodes connected by guided light.\",\n \"corpus_id\": 2393975,\n \"score\": 1\n },\n {\n \"doc_id\": \"25401537\",\n \"title\": \"Coupled optical resonance laser locking.\",\n \"abstract\": \"We have demonstrated simultaneous laser frequency stabilization of a UV and IR laser, to coupled transitions of ions in the same spectroscopic sample, by detecting only the absorption of the UV laser. Separate signals for locking the different lasers are obtained by modulating each laser at a different frequency and using lock-in detection of a single photodiode signal. Experimentally, we simultaneously lock a 369 nm and a 935 nm laser to the (2)S(1/2) → (2)(P(1/2) and (2)D(3/2) → (3)D([3/2]1/2) transitions, respectively, of Yb(+) ions generated in a hollow cathode discharge lamp. Stabilized lasers at these frequencies are required for cooling and trapping Yb(+) ions, used in quantum information and in high precision metrology experiments. This technique should be readily applicable to other ion and neutral atom systems requiring multiple stabilized lasers.\",\n \"corpus_id\": 10028409,\n \"score\": 1\n },\n {\n \"doc_id\": \"25723099\",\n \"title\": \"Ultrasensitive room-temperature piezoresistive transduction in graphene-based nanoelectromechanical systems.\",\n \"abstract\": \"The low mass and high quality factors that nanomechanical resonators exhibit lead to exceptional sensitivity in the frequency domain. This is especially appealing for the design of ultrasensitive force and mass sensors. The sensitivity of a nanomechanical mass and force sensor depends on its mass and quality factor; a low resonator mass and a higher quality factor reduce both the minimum resolvable mass and force. Graphene, a single atomic layer thick membrane is an ideal candidate for nanoelectromechanical resonators due to its extremely low mass and high stiffness. Here, we show that by employing the intrinsic piezoresistivity of graphene to transduce its motion in nanoelectromechanical systems, we approach a force resolution of 16.3 ± 0.8 aN/Hz(1/2) and a minimum detectable mass of 1.41 ± 0.02 zeptograms (10(-21) g) at ambient temperature. Quality factors of the driven response of the order of 10(3) at pressures ∼10(-6) Torr on several devices are also observed. Moreover, we demonstrate this at ambient temperature on chemical-vapor-deposition-grown graphene to allow for scale-up, thus demonstrating its potential for applications requiring exquisite force and mass resolution such as mass spectroscopy and magnetic resonance force microscopy.\",\n \"corpus_id\": 26891628,\n \"score\": 1\n },\n {\n \"doc_id\": \"26672553\",\n \"title\": \"Multi-element logic gates for trapped-ion qubits.\",\n \"abstract\": \"Precision control over hybrid physical systems at the quantum level is important for the realization of many quantum-based technologies. In the field of quantum information processing (QIP) and quantum networking, various proposals discuss the possibility of hybrid architectures where specific tasks are delegated to the most suitable subsystem. For example, in quantum networks, it may be advantageous to transfer information from a subsystem that has good memory properties to another subsystem that is more efficient at transporting information between nodes in the network. For trapped ions, a hybrid system formed of different species introduces extra degrees of freedom that can be exploited to expand and refine the control of the system. Ions of different elements have previously been used in QIP experiments for sympathetic cooling, creation of entanglement through dissipation, and quantum non-demolition measurement of one species with another. Here we demonstrate an entangling quantum gate between ions of different elements which can serve as an important building block of QIP, quantum networking, precision spectroscopy, metrology, and quantum simulation. A geometric phase gate between a (9)Be(+) ion and a (25)Mg(+) ion is realized through an effective spin-spin interaction generated by state-dependent forces induced with laser beams. Combined with single-qubit gates and same-species entangling gates, this mixed-element entangling gate provides a complete set of gates over such a hybrid system for universal QIP. Using a sequence of such gates, we demonstrate a CNOT (controlled-NOT) gate and a SWAP gate. We further demonstrate the robustness of these gates against thermal excitation and show improved detection in quantum logic spectroscopy. We also observe a strong violation of a CHSH (Clauser-Horne-Shimony-Holt)-type Bell inequality on entangled states composed of different ion species.\",\n \"corpus_id\": 4450528,\n \"score\": 1\n },\n {\n \"doc_id\": \"26855427\",\n \"title\": \"Non-destructive state detection for quantum logic spectroscopy of molecular ions.\",\n \"abstract\": \"Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds.\",\n \"corpus_id\": 205247267,\n \"score\": 1\n },\n {\n \"doc_id\": \"27582467\",\n \"title\": \"Atom-atom interactions around the band edge of a photonic crystal waveguide.\",\n \"abstract\": \"Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.\",\n \"corpus_id\": 20885649,\n \"score\": 1\n },\n {\n \"doc_id\": \"27587128\",\n \"title\": \"Robust atomic force microscopy using multiple sensors.\",\n \"abstract\": \"Atomic force microscopy typically relies on high-resolution high-bandwidth cantilever deflection measurements based control for imaging and estimating sample topography and properties. More precisely, in amplitude-modulation atomic force microscopy (AM-AFM), the control effort that regulates deflection amplitude is used as an estimate of sample topography; similarly, contact-mode AFM uses regulation of deflection signal to generate sample topography. In this article, a control design scheme based on an additional feedback mechanism that uses vertical z-piezo motion sensor, which augments the deflection based control scheme, is proposed and evaluated. The proposed scheme exploits the fact that the piezo motion sensor, though inferior to the cantilever deflection signal in terms of resolution and bandwidth, provides information on piezo actuator dynamics that is not easily retrievable from the deflection signal. The augmented design results in significant improvements in imaging bandwidth and robustness, especially in AM-AFM, where the complicated underlying nonlinear dynamics inhibits estimating piezo motions from deflection signals. In AM-AFM experiments, the two-sensor based design demonstrates a substantial improvement in robustness to modeling uncertainties by practically eliminating the peak in the sensitivity plot without affecting the closed-loop bandwidth when compared to a design that does not use the piezo-position sensor based feedback. The contact-mode imaging results, which use proportional-integral controllers for cantilever-deflection regulation, demonstrate improvements in bandwidth and robustness to modeling uncertainties, respectively, by over 30% and 20%. The piezo-sensor based feedback is developed using H∞ control framework.\",\n \"corpus_id\": 6156688,\n \"score\": 1\n },\n {\n \"doc_id\": \"27782583\",\n \"title\": \"Development of low temperature atomic force microscopy with an optical beam deflection system capable of simultaneously detecting the lateral and vertical forces.\",\n \"abstract\": \"The atomic force microscopy (AFM) is a very important tool for imaging and investigating the complex force interactions on sample surfaces with high spatial resolution. In the AFM, two types of detection systems of the tip-sample interaction forces have been used: an optical detection system and an electrical detection system. In optical detection systems, such as optical beam deflection system or optical fiber interferometer system, both the lateral and the vertical tip-sample forces can be measured simultaneously. In electrical detection systems, such as qPlus or Kolibri sensors, either the lateral or vertical forces can be measured. Simultaneous measurement of the lateral and vertical interaction forces effectively allows investigation of force interactions because the force is a vector with magnitude and direction. In this study, we developed a low-temperature, frequency-modulation AFM using an optical beam deflection system to simultaneously measure the vertical and lateral forces. In this system, the heat sources, such as a laser diode and a current-to-voltage converter, for measuring the photocurrent of the four-segmented photodiode are located outside the observation chamber to avoid a temperature increase of the AFM unit. The focused optical beam is three-dimensionally adjustable on the back side of the cantilever. We demonstrate low-noise displacement measurement of the cantilever and successful atomic resolution imaging using the vertical and lateral forces at low temperatures.\",\n \"corpus_id\": 43606018,\n \"score\": 1\n },\n {\n \"doc_id\": \"27999246\",\n \"title\": \"Design and Sensitivity Analysis Simulation of a Novel 3D Force Sensor Based on a Parallel Mechanism.\",\n \"abstract\": \"Automated force measurement is one of the most important technologies in realizing intelligent automation systems. However, while many methods are available for micro-force sensing, measuring large three-dimensional (3D) forces and loads remains a significant challenge. Accordingly, the present study proposes a novel 3D force sensor based on a parallel mechanism. The transformation function and sensitivity index of the proposed sensor are analytically derived. The simulation results show that the sensor has a larger effective measuring capability than traditional force sensors. Moreover, the sensor has a greater measurement sensitivity for horizontal forces than for vertical forces over most of the measurable force region. In other words, compared to traditional force sensors, the proposed sensor is more sensitive to shear forces than normal forces.\",\n \"corpus_id\": 3197355,\n \"score\": 1\n },\n {\n \"doc_id\": \"28492258\",\n \"title\": \"Preparation and coherent manipulation of pure quantum states of a single molecular ion.\",\n \"abstract\": \"Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH(+)) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.\",\n \"corpus_id\": 205255882,\n \"score\": 1\n },\n {\n \"doc_id\": \"28663571\",\n \"title\": \"Single ion fluorescence excited with a single mode of an UV frequency comb.\",\n \"abstract\": \"Optical frequency combs have revolutionized the measurement of optical frequencies and improved the precision of spectroscopic experiments. Besides their importance as a frequency-measuring ruler, the frequency combs themselves can excite target transitions (direct frequency comb spectroscopy). The direct frequency comb spectroscopy may extend the optical frequency metrology into spectral regions unreachable by continuous wave lasers. In high precision spectroscopy, atoms/ions/molecules trapped in place have been often used as a target to minimize systematic effects. Here, we demonstrate direct frequency comb spectroscopy of single (25)Mg ions confined in a Paul trap, at deep-UV wavelengths. Only one mode out of about 20,000 can be resonant at a time. Even then we can detect the induced fluorescence with a spatially resolving single photon camera, allowing us to determine the absolute transition frequency. The demonstration shows that the direct frequency comb spectroscopy is an important tool for frequency metrology for shorter wavelengths where continuous wave lasers are unavailable. Frequency combs are useful tools in high precision measurement including atomic transitions and atomic clocks. Here the authors demonstrate direct frequency comb spectroscopy to shorter wavelengths by probing a transition frequency in a trapped Mg+ ion using a single mode of a UV frequency comb.\",\n \"corpus_id\": 24331103,\n \"score\": 1\n },\n {\n \"doc_id\": \"28707930\",\n \"title\": \"Trapped Ions in Rydberg-Dressed Atomic Gases.\",\n \"abstract\": \"We theoretically study trapped ions that are immersed in an ultracold gas of Rydberg-dressed atoms. By off-resonant coupling on a dipole-forbidden transition, the adiabatic atom-ion potential can be made repulsive. We study the energy exchange between the atoms and a single trapped ion and find that Langevin collisions are inhibited in the ultracold regime for these repulsive interactions. Therefore, the proposed system avoids recently observed ion heating in hybrid atom-ion systems caused by coupling to the ion's radio frequency trapping field and retains ultracold temperatures even in the presence of excess micromotion.\",\n \"corpus_id\": 206293324,\n \"score\": 1\n },\n {\n \"doc_id\": \"29084886\",\n \"title\": \"Non-thermalization in trapped atomic ion spin chains.\",\n \"abstract\": \"Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.\",\n \"corpus_id\": 19588325,\n \"score\": 1\n },\n {\n \"doc_id\": \"29269423\",\n \"title\": \"Coherent single-atom superradiance.\",\n \"abstract\": \"Superradiance is a quantum phenomenon emerging in macroscopic systems whereby correlated single atoms cooperatively emit photons. Demonstration of controlled collective atom-field interactions has resulted from the ability to directly imprint correlations with an atomic ensemble. Here we report cavity-mediated coherent single-atom superradiance: Single atoms with predefined correlation traverse a high-quality factor cavity one by one, emitting photons cooperatively with the N atoms that have already gone through the cavity (N represents the number of atoms). Enhanced collective photoemission of N-squared dependence was observed even when the intracavity atom number was less than unity. The correlation among single atoms was achieved by nanometer-precision position control and phase-aligned state manipulation of atoms by using a nanohole-array aperture. Our results demonstrate a platform for phase-controlled atom-field interactions.\",\n \"corpus_id\": 206665366,\n \"score\": 1\n },\n {\n \"doc_id\": \"29350951\",\n \"title\": \"High-Fidelity Preservation of Quantum Information During Trapped-Ion Transport.\",\n \"abstract\": \"A promising scheme for building scalable quantum simulators and computers is the synthesis of a scalable system using interconnected subsystems. A prerequisite for this approach is the ability to faithfully transfer quantum information between subsystems. With trapped atomic ions, this can be realized by transporting ions with quantum information encoded into their internal states. Here, we measure with high precision the fidelity of quantum information encoded into hyperfine states of a ^{171}Yb^{+} ion during ion transport in a microstructured Paul trap. Ramsey spectroscopy of the ion's internal state is interleaved with up to 4000 transport operations over a distance of 280 μm each taking 12.8 μs. We obtain a state fidelity of 99.9994( _{-7}^{+6})% per ion transport.\",\n \"corpus_id\": 206305845,\n \"score\": 1\n },\n {\n \"doc_id\": \"18377016\",\n \"title\": \"Calibration of lateral force measurements in atomic force microscopy with a piezoresistive force sensor.\",\n \"abstract\": \"We present here a method to calibrate the lateral force in the atomic force microscope. This method makes use of an accurately calibrated force sensor composed of a tipless piezoresistive cantilever and corresponding signal amplifying and processing electronics. Two ways of force loading with different loading points were compared by scanning the top and side edges of the piezoresistive cantilever. Conversion factors between the lateral force and photodiode signal using three types of atomic force microscope cantilevers with rectangular geometries (normal spring constants from 0.092 to 1.24 N/m and lateral stiffness from 10.34 to 101.06 N/m) were measured in experiments using the proposed method. When used properly, this method calibrates the conversion factors that are accurate to +/-12.4% or better. This standard has less error than the commonly used method based on the cantilever's beam mechanics. Methods such of this allow accurate and direct conversion between lateral forces and photodiode signals without any knowledge of the cantilevers and the laser measuring system.\",\n \"corpus_id\": 12888966,\n \"score\": 0\n },\n {\n \"doc_id\": \"19158918\",\n \"title\": \"Interferometric 3D tracking of several particles in a scanning laser focus.\",\n \"abstract\": \"High-Speed tracking of several particles allows measuring dynamic long-range interactions relevant to biotechnology and colloidal physics. In this paper we extend the successful technique of 3D back-focal plane interferometry to oscillating laser beams and show that two or more particles can be trapped and tracked with a precision of a few nanometers in all three dimensions. The tracking rate of several kHz is only limited by the scan speed of the beam steering device. Several tests proof the linearity and orthogonality of our detection scheme, which is of interest to optical tweezing applications and various metrologies. As an example we show the position cross-correlations of three diffusing particles in a scanning line optical trap.\",\n \"corpus_id\": 44591136,\n \"score\": 0\n },\n {\n \"doc_id\": \"19509448\",\n \"title\": \"QPlus: atomic force microscopy on single-crystal insulators with small oscillation amplitudes at 5 K.\",\n \"abstract\": \"Based on a proven low temperature scanning tunneling microscope (STM) platform, we have integrated a QPlus sensor, which employs a quartz tuning fork for force detection in non-contact atomic force microscopy (AFM). For combined STM operation, this sensor has key advantages over conventional sensors. For quantitative force spectroscopy on insulating thin films or semiconductors, decoupling of the tunneling current and the piezo-electrically induced AFM signal is important. In addition, extremely low signals require the first amplification stage to be very close to the sensor, i.e. to be compatible with low temperatures. We present atomic resolution imaging on single-crystal NaCl(100) with oscillation amplitudes below 100 pm (peak-to-peak) and operation at higher flexural modes in constant frequency shift (df) imaging feedback. We also present atomic resolution measurements on MgO(100) and Au(111), and first evaluation measurements of the QPlus sensor in Kelvin probe microscopy on Si(111) 7 x 7.\",\n \"corpus_id\": 12910021,\n \"score\": 0\n },\n {\n \"doc_id\": \"21412333\",\n \"title\": \"Single-spin addressing in an atomic Mott insulator.\",\n \"abstract\": \"Ultracold atoms in optical lattices provide a versatile tool with which to investigate fundamental properties of quantum many-body systems. In particular, the high degree of control of experimental parameters has allowed the study of many interesting phenomena, such as quantum phase transitions and quantum spin dynamics. Here we demonstrate how such control can be implemented at the most fundamental level of a single spin at a specific site of an optical lattice. Using a tightly focused laser beam together with a microwave field, we were able to flip the spin of individual atoms in a Mott insulator with sub-diffraction-limited resolution, well below the lattice spacing. The Mott insulator provided us with a large two-dimensional array of perfectly arranged atoms, in which we created arbitrary spin patterns by sequentially addressing selected lattice sites after freezing out the atom distribution. We directly monitored the tunnelling quantum dynamics of single atoms in the lattice prepared along a single line, and observed that our addressing scheme leaves the atoms in the motional ground state. The results should enable studies of entropy transport and the quantum dynamics of spin impurities, the implementation of novel cooling schemes, and the engineering of quantum many-body phases and various quantum information processing applications.\",\n \"corpus_id\": 4352129,\n \"score\": 0\n },\n {\n \"doc_id\": \"21529015\",\n \"title\": \"A high-pressure atomic force microscope for imaging in supercritical carbon dioxide.\",\n \"abstract\": \"A high-pressure atomic force microscope (AFM) that enables in situ, atomic scale measurements of topography of solid surfaces in contact with supercritical CO(2) (scCO(2)) fluids has been developed. This apparatus overcomes the pressure limitations of the hydrothermal AFM and is designed to handle pressures up to 100 atm at temperatures up to ∼350 K. A standard optically-based cantilever deflection detection system was chosen. When imaging in compressible supercritical fluids such as scCO(2), precise control of pressure and temperature in the fluid cell is the primary technical challenge. Noise levels and imaging resolution depend on minimization of fluid density fluctuations that change the fluid refractive index and hence the laser path. We demonstrate with our apparatus in situ atomic scale imaging of a calcite (CaCO(3)) mineral surface in scCO(2); both single, monatomic steps and dynamic processes occurring on the (1014) surface are presented. This new AFM provides unprecedented in situ access to interfacial phenomena at solid-fluid interfaces under pressure.\",\n \"corpus_id\": 19207228,\n \"score\": 0\n },\n {\n \"doc_id\": \"21930566\",\n \"title\": \"Ultracold atoms and precise time standards.\",\n \"abstract\": \"Experimental techniques of laser cooling and trapping, along with other cooling techniques, have produced gaseous samples of atoms so cold that they are, for many practical purposes, in the quantum ground state of their centre-of-mass motion. Such low velocities have virtually eliminated effects such as Doppler shifts, relativistic time dilation and observation-time broadening that previously limited the performance of atomic frequency standards. Today, the best laser-cooled, caesium atomic fountain, microwave frequency standards realize the International System of Units (SI) definition of the second to a relative accuracy of ≈3×10(-16). Optical frequency standards, which do not realize the SI second, have even better performance: cold neutral atoms trapped in optical lattices now yield relative systematic uncertainties of ≈1×10(-16), whereas cold-trapped ions have systematic uncertainties of 9×10(-18). We will discuss the current limitations in the performance of neutral atom atomic frequency standards and prospects for the future.\",\n \"corpus_id\": 21394623,\n \"score\": 0\n },\n {\n \"doc_id\": \"23563845\",\n \"title\": \"A surface-patterned chip as a strong source of ultracold atoms for quantum technologies.\",\n \"abstract\": \"Laser-cooled atoms are central to modern precision measurements. They are also increasingly important as an enabling technology for experimental cavity quantum electrodynamics, quantum information processing and matter-wave interferometry. Although significant progress has been made in miniaturizing atomic metrological devices, these are limited in accuracy by their use of hot atomic ensembles and buffer gases. Advances have also been made in producing portable apparatus that benefits from the advantages of atoms in the microkelvin regime. However, simplifying atomic cooling and loading using microfabrication technology has proved difficult. In this Letter we address this problem, realizing an atom chip that enables the integration of laser cooling and trapping into a compact apparatus. Our source delivers ten thousand times more atoms than previous magneto-optical traps with microfabricated optics and, for the first time, can reach sub-Doppler temperatures. Moreover, the same chip design offers a simple way to form stable optical lattices. These features, combined with simplicity of fabrication and ease of operation, make these new traps a key advance in the development of cold-atom technology for high-accuracy, portable measurement devices.\",\n \"corpus_id\": 205450448,\n \"score\": 0\n },\n {\n \"doc_id\": \"24483741\",\n \"title\": \"Accurate atom counting in mesoscopic ensembles.\",\n \"abstract\": \"Many cold atom experiments rely on precise atom number detection, especially in the context of quantum-enhanced metrology where effects at the single particle level are important. Here, we investigate the limits of atom number counting via resonant fluorescence detection for mesoscopic samples of trapped atoms. We characterize the precision of these fluorescence measurements beginning from the single-atom level up to more than one thousand. By investigating the primary noise sources, we obtain single-atom resolution for atom numbers as high as 1200. This capability is an essential prerequisite for future experiments with highly entangled states of mesoscopic atomic ensembles.\",\n \"corpus_id\": 3025216,\n \"score\": 0\n },\n {\n \"doc_id\": \"24720757\",\n \"title\": \"Hyphenating atomic force microscopy.\",\n \"abstract\": \"Atomic force microscopy can be readily combined with complementary instrumental techniques ranging from optical to mass-sensitive methods. This Feature highlights recent advances on hyphenated AFM technology, which enables localized studies and mapping of complementary information at surfaces and interfaces.\",\n \"corpus_id\": 31174177,\n \"score\": 0\n },\n {\n \"doc_id\": \"24758916\",\n \"title\": \"High-coherence electron and ion bunches from laser-cooled atoms.\",\n \"abstract\": \"Cold atom electron and ion sources produce electron bunches and ion beams by photoionization of laser-cooled atoms. They offer high coherence and the potential for high brightness, with applications including ultra-fast electron-diffractive imaging of dynamic processes at the nanoscale. The effective brightness of electron sources has been limited by nonlinear divergence caused by repulsive interactions between the electrons, known as the Coulomb explosion. It has been shown that electron bunches with ellipsoidal shape and uniform density distribution have linear internal Coulomb fields, such that the Coulomb explosion can be reversed using conventional optics. Our source can create bunches shaped in three dimensions and hence in principle achieve the transverse spatial coherence and brightness needed for picosecond-diffractive imaging with nanometer resolution. Here we present results showing how the shaping capability can be used to measure the spatial coherence properties of the cold electron source. We also investigate space-charge effects with ions and generate electron bunches with durations of a few hundred picoseconds. Future development of the cold atom electron and ion source will increase the bunch charge and charge density, demonstrate reversal of Coulomb explosion, and ultimately, ultra-fast coherent electron-diffractive imaging.\",\n \"corpus_id\": 649723,\n \"score\": 0\n },\n {\n \"doc_id\": \"25267655\",\n \"title\": \"Single-spin stochastic optical reconstruction microscopy.\",\n \"abstract\": \"We experimentally demonstrate precision addressing of single-quantum emitters by combined optical microscopy and spin resonance techniques. To this end, we use nitrogen vacancy (NV) color centers in diamond confined within a few ten nanometers as individually resolvable quantum systems. By developing a stochastic optical reconstruction microscopy (STORM) technique for NV centers, we are able to simultaneously perform sub-diffraction-limit imaging and optically detected spin resonance (ODMR) measurements on NV spins. This allows the assignment of spin resonance spectra to individual NV center locations with nanometer-scale resolution and thus further improves spatial discrimination. For example, we resolved formerly indistinguishable emitters by their spectra. Furthermore, ODMR spectra contain metrology information allowing for sub-diffraction-limit sensing of, for instance, magnetic or electric fields with inherently parallel data acquisition. As an example, we have detected nuclear spins with nanometer-scale precision. Finally, we give prospects of how this technique can evolve into a fully parallel quantum sensor for nanometer resolution imaging of delocalized quantum correlations.\",\n \"corpus_id\": 226408,\n \"score\": 0\n },\n {\n \"doc_id\": \"25766230\",\n \"title\": \"Coulomb crystallization of highly charged ions.\",\n \"abstract\": \"Control over the motional degrees of freedom of atoms, ions, and molecules in a field-free environment enables unrivalled measurement accuracies but has yet to be applied to highly charged ions (HCIs), which are of particular interest to future atomic clock designs and searches for physics beyond the Standard Model. Here, we report on the Coulomb crystallization of HCIs (specifically (40)Ar(13+)) produced in an electron beam ion trap and retrapped in a cryogenic linear radiofrequency trap by means of sympathetic motional cooling through Coulomb interaction with a directly laser-cooled ensemble of Be(+) ions. We also demonstrate cooling of a single Ar(13+) ion by a single Be(+) ion-the prerequisite for quantum logic spectroscopy with a potential 10(-19) accuracy level. Achieving a seven-orders-of-magnitude decrease in HCI temperature starting at megakelvin down to the millikelvin range removes the major obstacle for HCI investigation with high-precision laser spectroscopy.\",\n \"corpus_id\": 20711393,\n \"score\": 0\n },\n {\n \"doc_id\": \"26191667\",\n \"title\": \"Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature.\",\n \"abstract\": \"Advanced optical traps can probe single molecules with Ångstrom-scale precision, but drift limits the utility of these instruments. To achieve Å-scale stability, a differential measurement scheme between a pair of laser foci was introduced that substantially exceeds the inherent mechanical stability of various types of microscopes at room temperature. By using lock-in detection to measure both lasers with a single quadrant photodiode, we enhanced the differential stability of this optical reference frame and thereby stabilized an optical-trapping microscope to 0.2 Å laterally over 100 s based on the Allan deviation. In three dimensions, we achieved stabilities of 1 Å over 1,000 s and 1 nm over 15 h. This stability was complemented by high measurement bandwidth (100 kHz). Overall, our compact back-scattered detection enables an ultrastable measurement platform compatible with optical traps, atomic force microscopy, and optical microscopy, including super-resolution techniques.\",\n \"corpus_id\": 36983769,\n \"score\": 0\n },\n {\n \"doc_id\": \"26787887\",\n \"title\": \"Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction.\",\n \"abstract\": \"The large plasma glycoprotein von Willebrand factor (VWF) senses hydrodynamic forces in the bloodstream and responds to elevated forces with abrupt elongation, thereby increasing its adhesiveness to platelets and collagen. Remarkably, forces on VWF are elevated at sites of vascular injury, where VWF's hemostatic potential is important to mediate platelet aggregation and to recruit platelets to the subendothelial layer. Adversely, elevated forces in stenosed vessels lead to an increased risk of VWF-mediated thrombosis. To dissect the remarkable force-sensing ability of VWF, we have performed atomic force microscopy (AFM)-based single-molecule force measurements on dimers, the smallest repeating subunits of VWF multimers. We have identified a strong intermonomer interaction that involves the D4 domain and critically depends on the presence of divalent ions, consistent with results from small-angle X-ray scattering (SAXS). Dissociation of this strong interaction occurred at forces above [Formula: see text]50 pN and provided [Formula: see text]80 nm of additional length to the elongation of dimers. Corroborated by the static conformation of VWF, visualized by AFM imaging, we estimate that in VWF multimers approximately one-half of the constituent dimers are firmly closed via the strong intermonomer interaction. As firmly closed dimers markedly shorten VWF's effective length contributing to force sensing, they can be expected to tune VWF's sensitivity to hydrodynamic flow in the blood and to thereby significantly affect VWF's function in hemostasis and thrombosis.\",\n \"corpus_id\": 1143652,\n \"score\": 0\n },\n {\n \"doc_id\": \"27474417\",\n \"title\": \"Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.\",\n \"abstract\": \"Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc.\",\n \"corpus_id\": 4475129,\n \"score\": 0\n },\n {\n \"doc_id\": \"27852983\",\n \"title\": \"Ultracold neutral plasmas.\",\n \"abstract\": \"By photoionizing samples of laser-cooled atoms with laser light tuned just above the ionization limit, plasmas can be created with electron and ion temperatures below 10 K. These ultracold neutral plasmas have extended the temperature bounds of plasma physics by two orders of magnitude. Table-top experiments, using many of the tools from atomic physics, allow for the study of plasma phenomena in this new regime with independent control over the density and temperature of the plasma through the excitation process. Characteristic of these systems is an inhomogeneous density profile, inherited from the density distribution of the laser-cooled neutral atom sample. Most work has dealt with unconfined plasmas in vacuum, which expand outward at velocities of order 100 m/s, governed by electron pressure, and with lifetimes of order 100 μs, limited by stray electric fields. Using detection of charged particles and optical detection techniques, a wide variety of properties and phenomena have been observed, including expansion dynamics, collective excitations in both the electrons and ions, and collisional properties. Through three-body recombination collisions, the plasmas rapidly form Rydberg atoms, and clouds of cold Rydberg atoms have been observed to spontaneously avalanche ionize to form plasmas. Of particular interest is the possibility of the formation of strongly coupled plasmas, where Coulomb forces dominate thermal motion and correlations become important. The strongest impediment to strong coupling is disorder-induced heating, a process in which Coulomb energy from an initially disordered sample is converted into thermal energy. This restricts electrons to a weakly coupled regime and leaves the ions barely within the strongly coupled regime. This review will give an overview of the field of ultracold neutral plasmas, from its inception in 1999 to current work, including efforts to increase strong coupling and effects on plasma properties due to strong coupling.\",\n \"corpus_id\": 1272219,\n \"score\": 0\n },\n {\n \"doc_id\": \"28009205\",\n \"title\": \"Dynamics of a Ground-State Cooled Ion Colliding with Ultracold Atoms.\",\n \"abstract\": \"Ultracold atom-ion mixtures are gaining increasing interest due to their potential applications in ultracold and state-controlled chemistry, quantum computing, and many-body physics. Here, we studied the dynamics of a single ground-state cooled ion during few, to many, Langevin (spiraling) collisions with ultracold atoms. We measured the ion's energy distribution and observed a clear deviation from the Maxwell-Boltzmann distribution, characterized by an exponential tail, to a power-law distribution best described by a Tsallis function. Unlike previous experiments, the energy scale of atom-ion interactions is not determined by either the atomic cloud temperature or the ion's trap residual excess-micromotion energy. Instead, it is determined by the force the atom exerts on the ion during a collision which is then amplified by the trap dynamics. This effect is intrinsic to ion Paul traps and sets the lower bound of atom-ion steady-state interaction energy in these systems. Despite the fact that our system is eventually driven out of the ultracold regime, we are capable of studying quantum effects by limiting the interaction to the first collision when the ion is initialized in the ground state of the trap.\",\n \"corpus_id\": 6154237,\n \"score\": 0\n },\n {\n \"doc_id\": \"28120826\",\n \"title\": \"Super-Coulombic atom-atom interactions in hyperbolic media.\",\n \"abstract\": \"Dipole-dipole interactions, which govern phenomena such as cooperative Lamb shifts, superradiant decay rates, Van der Waals forces and resonance energy transfer rates, are conventionally limited to the Coulombic near-field. Here we reveal a class of real-photon and virtual-photon long-range quantum electrodynamic interactions that have a singularity in media with hyperbolic dispersion. The singularity in the dipole-dipole coupling, referred to as a super-Coulombic interaction, is a result of an effective interaction distance that goes to zero in the ideal limit irrespective of the physical distance. We investigate the entire landscape of atom-atom interactions in hyperbolic media confirming the giant long-range enhancement. We also propose multiple experimental platforms to verify our predicted effect with phonon-polaritonic hexagonal boron nitride, plasmonic super-lattices and hyperbolic meta-surfaces as well. Our work paves the way for the control of cold atoms above hyperbolic meta-surfaces and the study of many-body physics with hyperbolic media.\",\n \"corpus_id\": 16386934,\n \"score\": 0\n },\n {\n \"doc_id\": \"28710414\",\n \"title\": \"Resonant driving of a single photon emitter embedded in a mechanical oscillator.\",\n \"abstract\": \"Coupling a microscopic mechanical resonator to a nanoscale quantum system enables control of the mechanical resonator via the quantum system and vice-versa. The coupling is usually achieved through functionalization of the mechanical resonator, but this results in additional mass and dissipation channels. An alternative is an intrinsic coupling based on strain. Here we employ a monolithic semiconductor system: the nanoscale quantum system is a semiconductor quantum dot (QD) located inside a nanowire. We demonstrate the resonant optical driving of the QD transition in such a structure. The noise spectrum of the resonance fluorescence signal, recorded in the single-photon counting regime, reveals a coupling to mechanical modes of different types. We measure a sensitivity to displacement of 65 fm/[Formula: see text] limited by charge noise in the device. Finally, we use thermal excitation of the different modes to determine the location of the QD within the trumpet, and calculate the contribution of the Brownian motion to the dephasing of the emitter. Resonant driving of a nanoscale quantum system coupled to a microscopic mechanical resonator may have uses in precision sensing and quantum information. The authors realize this by tailoring the geometry of a semiconductor nanowire embedding a quantum dot, detecting sub-picometre displacements.\",\n \"corpus_id\": 28722859,\n \"score\": 0\n },\n {\n \"doc_id\": \"29109531\",\n \"title\": \"A robust single-beam optical trap for a gram-scale mechanical oscillator.\",\n \"abstract\": \"Precise optical control of microscopic particles has been mastered over the past three decades, with atoms, molecules and nano-particles now routinely trapped and cooled with extraordinary precision, enabling rapid progress in the study of quantum phenomena. Achieving the same level of control over macroscopic objects is expected to bring further advances in precision measurement, quantum information processing and fundamental tests of quantum mechanics. However, cavity optomechanical systems dominated by radiation pressure - so-called 'optical springs' - are inherently unstable due to the delayed dynamical response of the cavity. Here we demonstrate a fully stable, single-beam optical trap for a gram-scale mechanical oscillator. The interaction of radiation pressure with thermo-optic feedback generates damping that exceeds the mechanical loss by four orders of magnitude. The stability of the resultant spring is robust to changes in laser power and detuning, and allows purely passive self-locking of the cavity. Our results open up a new way of trapping and cooling macroscopic objects for optomechanical experiments.\",\n \"corpus_id\": 5825484,\n \"score\": 0\n },\n {\n \"doc_id\": \"29301265\",\n \"title\": \"Atomic Force Microscopy Sidewall Imaging with a Quartz Tuning Fork Force Sensor.\",\n \"abstract\": \"Sidewall roughness measurement is becoming increasingly important in the micro-electromechanical systems and nanoelectronics devices. Atomic force microscopy (AFM) is an emerging technique for sidewall scanning and roughness measurement due to its high resolution, three-dimensional imaging capability and high accuracy. We report an AFM sidewall imaging method with a quartz tuning fork (QTF) force sensor. A self sensing and actuating force sensor is fabricated by microassembling a commercial AFM cantilever (tip apex radius ≤10 nm) to a QTF. The attached lightweight cantilever allows high-sensitivity force detection (7.4% Q factor reduction) and sidewall imaging with high lateral resolution. Owing to its unique configuration, the tip of the sensor can detect sidewall surface orthogonally during imaging, which reduces lateral friction. In experiments, sidewalls of a micro-electro-mechanical system (MEMS) structure fabricated by deep reactive ion etching process and a standard step grating are scanned and the sidewall roughness, line edge roughness and sidewall angles are measured.\",\n \"corpus_id\": 3491865,\n \"score\": 0\n },\n {\n \"doc_id\": \"29459410\",\n \"title\": \"Recent progress of laser spectroscopy experiments on antiprotonic helium.\",\n \"abstract\": \"The Atomic Spectroscopy and Collisions Using Slow Antiprotons (ASACUSA) collaboration is currently carrying out laser spectroscopy experiments on antiprotonic helium [Formula: see text] atoms at CERN's Antiproton Decelerator facility. Two-photon spectroscopic techniques have been employed to reduce the Doppler width of the measured [Formula: see text] resonance lines, and determine the atomic transition frequencies to a fractional precision of 2.3-5 parts in 109 More recently, single-photon spectroscopy of buffer-gas cooled [Formula: see text] has reached a similar precision. By comparing the results with three-body quantum electrodynamics calculations, the antiproton-to-electron mass ratio was determined as [Formula: see text], which agrees with the known proton-to-electron mass ratio with a precision of 8×10-10 The high-quality antiproton beam provided by the future Extra Low Energy Antiproton Ring (ELENA) facility should enable further improvements in the experimental precision. This article is part of the Theo Murphy meeting issue 'Antiproton physics in the ELENA era'.\",\n \"corpus_id\": 3443665,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":78,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28322227\",\n \"title\": \"Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor.\",\n \"abstract\": \"Reliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge. Here, we demonstrate that a graphene single-crystal domain patterned into multiple channels can measure time- and concentration-dependent DNA hybridization kinetics and affinity reliably and sensitively, with a detection limit of 10 pM for DNA. It can distinguish single-base mutations quantitatively in real time. An analytical model is developed to estimate probe density, efficiency of hybridization and the maximum sensor response. The results suggest a promising future for cost-effective, high-throughput screening of drug candidates, genetic variations and disease biomarkers by using an integrated, miniaturized, all-electrical multiplexed, graphene-based DNA array.\",\n \"corpus_id\": 18219381\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18207730","title":"A novel fluorescence-based array biosensor: principle and application to DNA hybridization assays.","abstract":"A novel fluorescence-based array biosensor targeted for field applications, such as environmental monitoring, has been developed, and successfully applied to DNA hybridization assays. The purpose was to meet the demand for automated, portable but easy-to-maintain systems allowing continuous flow monitoring of surface reactions. The biosensor presented here can be distinguished from the existing systems by the optical method used, which provides an enhanced simplicity and robustness, and enables a simple maintenance by potentially unskilled personnel. The system is based on a conventional microscope slide which acts both as transducer and biological array sensor. The excited fluorescence is guided by total internal reflection into the slide to the detector which is directly interfaced to the slide. Each region of the sensor array is successively optically interrogated, and the detection of the corresponding fluorescent emission synchronized. A real-time three-analyte analysis is thus feasible without any mechanical scanning movement or optical imaging systems as generally used in the existing instruments. The ability of the biosensor to operate in continuous flow for several tens of hours has been demonstrated. The biosensor has been assessed in terms of stability, and slide-to-slide reproducibility, which is found to be less than 3.7%, thus far below the standard biological reproducibility. DNA hybridization assays were performed to estimate a limit of detection, which was found to be 16 mol/microm(2), and to determine the reaction kinetics associated to the DNA model used. The developed biosensor is thus shown to be able to predict reaction kinetics, and to monitor in real time surface reactions between targets and probes.","corpus_id":34857259,"score":2},{"doc_id":"18405656","title":"Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet.","abstract":"ForteBio's Octet optical biosensor harnesses biolayer interferometry to detect and quantify molecular interactions using disposable fiber-optic biosensors that address samples from an open shaking microplate without any microfluidics. We recruited a monoclonal antibody against a panel of peptides to compare the Octet directly with Biacore's well-established 3000 platform and Bio-Rad's recently launched ProteOn XPR36 array system, which use surface plasmon resonance (SPR) to detect the binding of one analyte over four surfaces and six analytes over six surfaces, respectively. A sink method was used to prevent analyte from rebinding the ligand-coated Octet tips and enabled us to extract accurate kinetic rate constants, as judged by their close agreement with those determined by SPR. Although the Octet is not sensitive enough to detect the binding of small molecules directly, it can access their affinities indirectly via solution competition experiments. We conducted similar experiments on the SPR instruments to validate these measurements. The Octet is emerging as a versatile complement to other more sophisticated biosensors, and the ProteOn provides high-quality data near the sensitivity of Biacore but in a more multiplexed format. Our results provide a benchmark for assessing the performance of the above-mentioned sensors.","corpus_id":9018161,"score":2},{"doc_id":"18644712","title":"Real-time protein biosensor arrays based on surface plasmon resonance differential phase imaging.","abstract":"This paper reports the application of differential phase surface plasmon resonance (SPR) imaging in two-dimensional (2D) protein biosensor arrays. Our phase imaging approach offers a distinct advantage over the conventional angular SPR technique in terms of utilization efficiency of optical sensor elements in the imaging device. In the angular approach, each biosensor site in the biosensor array requires a linear array of optical detector elements to locate the SPR angular dip. The maximum biosensor density that a two-dimensional imaging device can offer is a one-dimensional SPR biosensor array. On the other hand, the phase-sensitive SPR approach captures data in the time domain instead of the spatial domain. It is possible that each pixel in the captured interferogram represents one sensor site, thus offering high-density two-dimensional biosensor arrays. In addition, our differential phase approach improves detection resolution through removing common-mode disturbances. Experimental results demonstrate a system resolution of 8.8 x 10(-7)RIU (refractive index unit). Real-time monitoring of bovine serum albumin (BSA)/anti-BSA binding interactions at various concentration levels was achieved using a biosensor array. The detection limit was 0.77 microg/ml. The reported two-dimensional SPR biosensor array offers a real-time and non-labeling detection tool for high-throughput protein array analysis. It may find promising applications in protein therapeutics, drug screening and clinical diagnostics.","corpus_id":19399551,"score":2},{"doc_id":"19054661","title":"Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.","abstract":"Optical biosensing based on fluorescence detection has arguably become the standard technique for quantifying extents of hybridization between surface-immobilized probes and fluorophore-labeled analyte targets in DNA microarrays. However, electrochemical detection techniques are emerging which could eliminate the need for physically bulky optical instrumentation, enabling the design of portable devices for point-of-care applications. Unlike fluorescence detection, which can function well using a passive substrate (one without integrated electronics), multiplexed electrochemical detection requires an electronically active substrate to analyze each array site and benefits from the addition of integrated electronic instrumentation to further reduce platform size and eliminate the electromagnetic interference that can result from bringing non-amplified signals off chip. We report on an active electrochemical biosensor array, constructed with a standard complementary metal-oxide-semiconductor (CMOS) technology, to perform quantitative DNA hybridization detection on chip using targets conjugated with ferrocene redox labels. A 4 x 4 array of gold working electrodes and integrated potentiostat electronics, consisting of control amplifiers and current-input analog-to-digital converters, on a custom-designed 5 mm x 3 mm CMOS chip drive redox reactions using cyclic voltammetry, sense DNA binding, and transmit digital data off chip for analysis. We demonstrate multiplexed and specific detection of DNA targets as well as real-time monitoring of hybridization, a task that is difficult, if not impossible, with traditional fluorescence-based microarrays.","corpus_id":9192371,"score":2},{"doc_id":"19723688","title":"Real-time DNA microarray analysis.","abstract":"We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays.","corpus_id":5234752,"score":2},{"doc_id":"19781931","title":"Label-free low-cost disposable DNA hybridization detection systems using organic TFTs.","abstract":"Organic thin film transistors (OTFT) are potentially very attractive for making portable and disposable DNA hybridization detection toolkits because of their ultra-low-cost manufacturing and potentially high sensitivity. To make a self-supported DNA sensor, we herein report an OTFT-based label-free DNA hybridization detection system integrating electrically read DNA hybridization sensors and microfluidic delivery channels. We previously reported DNA-doped OTFTs acting as electrically read DNA sensors. In this article, we first study physics of DNA sensitivity of OTFTs, clarifying the doping mechanism. The article also presents a method of verification of the immobilization and presence of DNA on the surface using TOF-SIMS analysis. As a further step, sources of variation of measured data and methods of minimization are discussed using a novel photolithography-based microfluidics fabrication method, directly enabling on-chip hybridization and self-supported DNA detection. By integrating the sensors with microfluidics, for the first time, we demonstrate necessary technologies required to realize disposable, rapid turn-around tools for field-deployable genetic diagnosis.","corpus_id":110488112,"score":2},{"doc_id":"19802851","title":"Integrated electrochemical DNA biosensors for lab-on-a-chip devices.","abstract":"Analytical devices able to perform accurate and fast automatic DNA detection or sequencing procedures have many potential benefits in the biomedical and environmental fields. The conversion of biological or biochemical responses into quantifiable optical, mechanical or electronic signals is achieved by means of biosensors. Most of these transducing elements can be miniaturized and incorporated into lab-on-a-chip devices, also known as Micro Total Analysis Systems. The use of multiple DNA biosensors integrated in these miniaturized laboratories, which perform several analytical operations at the microscale, has many cost and efficiency advantages. Tiny amounts of reagents and samples are needed and highly sensitive, fast and parallel assays can be done at low cost. A particular type of DNA biosensors are the ones used based on electrochemical principles. These sensors offer several advantages over the popular fluorescence-based detection schemes. The resulting signal is electrical and can be processed by conventional electronics in a very cheap and fast manner. Furthermore, the integration and miniaturization of electrochemical transducers in a microsystem makes easier its fabrication in front of the most common currently used detection method. In this review, different electrochemical DNA biosensors integrated in analytical microfluidic devices are discussed and some early stage commercial products based on this strategy are presented.","corpus_id":21925845,"score":2},{"doc_id":"20093001","title":"Direct label-free electrical immunodetection in human serum using a flow-through-apparatus approach with integrated field-effect transistors.","abstract":"In order to identify changes in the levels of key proteins in response to the onset or development of a disease, the research fields of proteomics and genomics seek to develop new biomarkers. Specifically, simple and fast biomarker screens have a central role in many areas of healthcare, including disease diagnosis and drug discovery. Biologically modified field-effect transistor (BioFET) is one of the most attractive approaches because of the on-chip integration of the sensor array, fast response, high reliability and low-cost mass production. However, the BioFETs used to detect macromolecules have been operated only in buffer solution with low salt concentrations because of the Debye screening length of blood or serum. Here we report a novel detection technique for direct label-free immunodetection of cancer markers in human serum using a Si-FET that was fabricated by conventional photolithographic processes. The proposed sensing method shows no dissociation of antigen-antibody binding as in general immunoassays, unlike the previous reports on Si-FET sensors. This method therefore overcomes the Debye length problem of immunodetection in human fluids, such as serum, that are generally encountered by FET-based biosensors. Our results demonstrate specific label-free and real-time immunodetection of a cancer marker at a concentration of 0.2 ng/mL in human serum, quantitative detection of the marker from 0.2 to 114 ng/mL, and successful multiplexed sensing of three different cancer markers. We believe that connecting our simple electrical detection method, which does not require pretreatment of serum, with well-established whole blood filter technology will contribute to the development of new point-of-care testing (POCT) sensors.","corpus_id":21319540,"score":2},{"doc_id":"20486666","title":"Real-time biomolecular binding detection using a sensitive photonic crystal biosensor.","abstract":"Real-time measurement of specific biomolecular interactions is critical to many areas of biological research. A number of label-free techniques for directly monitoring biomolecular binding have been developed, but it is still challenging to measure the binding kinetics of very small molecules, to detect low concentrations of analyte molecules, or to detect low affinity interactions. In this study, we report the development of a highly sensitive photonic crystal biosensor for label-free, real-time biomolecular binding analysis. We characterize the performance of this biosensor using a standard streptavidin-biotin binding system. Optimization of the surface functionalization methods for streptavidin immobilization on the silica sensing surface is presented, and the specific binding of biotinylated analyte molecules ranging over 3 orders of magnitude in molecular weight, including very small molecules (<250 Da), DNA oligonucleotides, proteins, and antibodies (>150 000 Da), are detected in real time with a high signal-to-noise ratio. Finally, we document the sensor efficiency for low mass adsorption, as well as multilayered molecular interactions. By all important metrics for sensitivity, we anticipate this photonic crystal biosensor will provide new capabilities for highly sensitive measurements of biomolecular binding.","corpus_id":24366550,"score":2},{"doc_id":"20820739","title":"Nanoelectronic biosensors based on CVD grown graphene.","abstract":"Graphene, a single-atom-thick and two-dimensional carbon material, has attracted great attention recently. Because of its unique electrical, physical, and optical properties, graphene has great potential to be a novel alternative to carbon nanotubes in biosensing. We demonstrate the use of large-sized CVD grown graphene films configured as field-effect transistors for real-time biomolecular sensing. Glucose or glutamate molecules were detected by the conductance change of the graphene transistor as the molecules are oxidized by the specific redox enzyme (glucose oxidase or glutamic dehydrogenase) functionalized onto the graphene film. This study indicates that graphene is a promising candidate for the development of real-time nanoelectronic biosensors.","corpus_id":3836668,"score":2},{"doc_id":"20976351","title":"Microwave-assisted synthesis of highly water-soluble graphene towards electrical DNA sensor.","abstract":"Graphene sheets have the potential for practical applications in electrochemical devices, but their development has been impeded by critical problems with aggregation of graphene sheets. Here, we demonstrated a facile and bottom-up approach for fabrication of DNA sensor device using water-soluble sulfonated reduced graphene oxide (SRGO) sheets via microwave-assisted sulfonation (MAS), showing enhanced sensitivity, reliability, and low detection limit. Key to achieving these performances is the fabrication of the SRGOs, where the MAS method enabled SRGOs to be highly dispersed in water (10 mg mL(-1)) due to the acidic sulfonated groups generated within 3 min of the functionalization reaction. The water-soluble SRGO-DNA (SRGOD) hybrids prepared by electrostatic interactions between a flat single layer of graphene sheets and DNAs are suitable for fabrication of electrical DNA sensor devices because of the unique electrical characteristics of SRGODs. The high sensing performance of SRGOD sensors was demonstrated with detection of DNA hybridization using complementary DNAs, single base mismatched DNAs, and noncomplementary DNAs, with results showing higher sensitivity and lower detection limit than those of reduced graphene oxide-based DNA sensors. Simple and easy fabrication of DNA sensor devices using SRGODs is expected to provide an effective way for electrical detection of DNA hybridization using miniature sensors without the labor-intensive labeling of the sensor and complex measurement equipment.","corpus_id":39700712,"score":2},{"doc_id":"21948419","title":"Nanowire biosensors for label-free, real-time, ultrasensitive protein detection.","abstract":"Sensitive and quantitative analysis of proteins is central to disease diagnosis, drug screening, and proteomic studies. Among recent research advances exploiting new nanomaterials for biomolecule analysis, silicon nanowires (SiNWs), which are configured as field-effect transistors (FETs), have emerged as one of the most promising and powerful platforms for label-free, real-time, and highly sensitive electrical detection of proteins as well as many other biological species. Here, we describe a detailed protocol for realizing SiNW biosensors for protein detection that includes SiNW synthesis, FET device fabrication, surface receptor functionalization, and electrical sensing measurements. Moreover, incorporating both p-type and n-type SiNWs in the same sensor array provides a unique means of internal control for sensing signal verification.","corpus_id":7711328,"score":2},{"doc_id":"22089471","title":"Real-time DNA detection using Pt nanoparticle-decorated reduced graphene oxide field-effect transistors.","abstract":"A large-area, continuous, few-layer reduced graphene oxide (rGO) thin film has been fabricated on a Si/SiO(2) wafer using the Langmuir-Blodgett (LB) method followed by thermal reduction. After photochemical reduction of Pt nanoparticles (PtNPs) on rGO, the obtained PtNPs/rGO composite is employed as the conductive channel in a solution-gated field effect transistor (FET), which is then used for real-time detection of hybridization of single-stranded DNA (ssDNA) with high sensitivity (2.4 nM). Such a simple, but effective method for fabrication of rGO-based transistors shows great potential for mass-production of graphene-based electronic biosensors.","corpus_id":5208897,"score":2},{"doc_id":"22110861","title":"Label-free electrical detection of DNA hybridization using carbon nanotubes and graphene.","abstract":"The interface between biosystems and nanomaterials is emerging for detection of various biomolecules and subtle cellular activities. In particular, the development of cost-effective and sequence-selective DNA detection is urgent for the diagnosis of genetic or pathogenic diseases. Graphene-based nanocarbon materials, such as carbon nanotubes and thin graphene layers, have been employed as biosensors because they are biocompatible, extraordinarily sensitive, and promising for large-area detection. Electrical and label-free detection of DNA can be achieved by monitoring the conductance change of devices fabricated from these carbon materials. Here, the recent advances in this research area are briefly reviewed. The key issues and perspectives of future development are also discussed.","corpus_id":9516434,"score":2},{"doc_id":"22252647","title":"Increasing the detection speed of an all-electronic real-time biosensor.","abstract":"Biosensor response time, which depends sensitively on the transport of biomolecules to the sensor surface, is a critical concern for future biosensor applications. We have fabricated carbon nanotube field-effect transistor biosensors and quantified protein binding rates onto these nanoelectronic sensors. Using this experimental platform we test the effectiveness of a protein repellent coating designed to enhance protein flux to the all-electronic real-time biosensor. We observe a 2.5-fold increase in the initial protein flux to the sensor when upstream binding sites are blocked. Mass transport modelling is used to calculate the maximal flux enhancement that is possible with this strategy. Our results demonstrate a new methodology for characterizing nanoelectronic biosensor performance, and demonstrate a mass transport optimization strategy that is applicable to a wide range of microfluidic based biosensors.","corpus_id":5141243,"score":2},{"doc_id":"22635097","title":"Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors.","abstract":"Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein-ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein-ligand binding pairs. The rate constant of the association and dissociation of the protein-ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions.","corpus_id":16109660,"score":2},{"doc_id":"22841443","title":"Step-gate polysilicon nanowires field effect transistor compatible with CMOS technology for label-free DNA biosensor.","abstract":"Currently, detection of DNA hybridization using fluorescence-based detection technique requires expensive optical systems and complex bioinformatics tools. Hence, the development of new low cost devices that enable direct and highly sensitive detection stimulates a lot of research efforts. Particularly, devices based on silicon nanowires are emerging as ultrasensitive electrical sensors for the direct detection of biological species thanks to their high surface to volume ratio. In this study, we propose innovative devices using step-gate polycrystalline silicon nanowire FET (poly-Si NW FETs), achieved with simple and low cost fabrication process, and used as ultrasensitive electronic sensor for DNA hybridization. The poly-SiNWs are synthesized using the sidewall spacer formation technique. The detailed fabrication procedure for a step-gate NWFET sensor is described in this paper. No-complementary and complementary DNA sequences were clearly discriminated and detection limit to 1 fM range is observed. This first result using this nano-device is promising for the development of low cost and ultrasensitive polysilicon nanowires based DNA sensors compatible with the CMOS technology.","corpus_id":16598849,"score":2},{"doc_id":"22985088","title":"Enhanced sensing of nucleic acids with silicon nanowire field effect transistor biosensors.","abstract":"Silicon nanowire (SiNW) field effect transistors (FETs) have emerged as powerful sensors for ultrasensitive, direct electrical readout, and label-free biological/chemical detection. The sensing mechanism of SiNW-FET can be understood in terms of the change in charge density at the SiNW surface after hybridization. So far, there have been limited systematic studies on fundamental factors related to device sensitivity to further make clear the overall effect on sensing sensitivity. Here, we present an analytical result for our triangle cross-section wire for predicting the sensitivity of nanowire surface-charge sensors. It was confirmed through sensing experiments that the back-gated SiNW-FET sensor had the highest percentage current response in the subthreshold regime and the sensor performance could be optimized in low buffer ionic strength and at moderate probe concentration. The optimized SiNW-FET nanosensor revealed ultrahigh sensitivity for rapid and reliable detection of target DNA with a detection limit of 0.1 fM and high specificity for single-nucleotide polymorphism discrimination. In our work, enhanced sensing of biological species by optimization of operating parameters and fundamental understanding for SiNW FET detection limit was obtained.","corpus_id":207564561,"score":2},{"doc_id":"23084065","title":"Droplet-based microscale colorimetric biosensor for multiplexed DNA analysis via a graphene nanoprobe.","abstract":"The development of simple and inexpensive DNA detection strategy is very significant for droplet-based microfluidic system. Here, a droplet-based biosensor for multiplexed DNA analysis is developed with a common imaging device by using fluorescence-based colorimetric method and a graphene nanoprobe. With the aid of droplet manipulation technique, droplet size adjustment, droplet fusion and droplet trap are realized accurately and precisely. Due to the high quenching efficiency of graphene oxide (GO), in the absence of target DNAs, the droplet containing two single-stranded DNA probes and GO shows dark color, in which the DNA probes are labeled carboxy fluorescein (FAM) and 6-carboxy-X-rhodamine (ROX), respectively. The droplet changes from dark to bright color when the DNA probes form double helix with the specific target DNAs leading to the dyes far away from GO. This colorimetric droplet biosensor exhibits a quantitative capability for simultaneous detection of two different target DNAs with the detection limits of 9.46 and 9.67×10(-8)M, respectively. It is also demonstrated that this biosensor platform can become a promising detection tool in high throughput applications with low consumption of reagents. Moreover, the incorporation of graphene nanoprobe and droplet technique can drive the biosensor field one more step to some extent.","corpus_id":24607677,"score":2},{"doc_id":"23355762","title":"Microneedle Biosensor: A Method for Direct Label-free Real Time Protein Detection.","abstract":"Here we present the development of an array of electrical micro-biosensors in a microfluidic channel, called microneedle biosensors. A microneedle biosensor is a real-time, label-free, direct electrical detection platform, which is capable of high sensitivity detection, measuring the change in ionic current and impedance modulation, due to the presence or reaction of biomolecules such as proteins and nucleic acids. In this study, we successfully fabricated and electrically characterized the sensors and demonstrated successful detection of target protein. In this study, we used biotinylated bovine serum albumin as the receptor and streptavidin as the target analyte.","corpus_id":42253383,"score":2},{"doc_id":"23685314","title":"A novel graphene-DNA biosensor for selective detection of mercury ions.","abstract":"A novel electrochemical biosensor for sensitive and selective detection of mercury (II) ions (Hg²⁺) based on a DNA grafted graphene is proposed. Graphene oxide (GO) was reduced by dopamine, and then the single-strand probe DNA modified at the 5'-end with an alkylamino modifier (NH₂-ssDNA) was grafted on the reduced graphene oxide (RGO) surface via Michael addition reaction. In the presence of Hg²⁺, the target DNA with four thymine-thymine (T-T) mismatches would hybridize with the probe DNA on the glassy carbon electrode (GCE) through T-Hg²⁺-T coordination chemistry. The hybridization of the two oligonucleotides leads to the increase in the peak currents of [Ru(NH₃)₆]³⁺, which could be used for electrochemical sensing of Hg²⁺. The difference in the value of the peak currents of [Ru(NH₃)₆]³⁺ before and after DNA hybridization was linear with the concentration of Hg²⁺ in the range from 8.0×10⁻⁹ to 1.0×10⁻⁷ M with a linear coefficiency of 0.996. The detection limit was 5.0×10⁻⁹ M (S/N=3). The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of Hg²⁺. Particularly, the proposed method was applied successfully to the determination of Hg²⁺ in real environmental samples.","corpus_id":206164843,"score":2},{"doc_id":"24517158","title":"Development of solution-gated graphene transistor model for biosensors.","abstract":": The distinctive properties of graphene, characterized by its high carrier mobility and biocompatibility, have stimulated extreme scientific interest as a promising nanomaterial for future nanoelectronic applications. In particular, graphene-based transistors have been developed rapidly and are considered as an option for DNA sensing applications. Recent findings in the field of DNA biosensors have led to a renewed interest in the identification of genetic risk factors associated with complex human diseases for diagnosis of cancers or hereditary diseases. In this paper, an analytical model of graphene-based solution gated field effect transistors (SGFET) is proposed to constitute an important step towards development of DNA biosensors with high sensitivity and selectivity. Inspired by this fact, a novel strategy for a DNA sensor model with capability of single-nucleotide polymorphism detection is proposed and extensively explained. First of all, graphene-based DNA sensor model is optimized using particle swarm optimization algorithm. Based on the sensing mechanism of DNA sensors, detective parameters (Ids and Vgmin) are suggested to facilitate the decision making process. Finally, the behaviour of graphene-based SGFET is predicted in the presence of single-nucleotide polymorphism with an accuracy of more than 98% which guarantees the reliability of the optimized model for any application of the graphene-based DNA sensor. It is expected to achieve the rapid, quick and economical detection of DNA hybridization which could speed up the realization of the next generation of the homecare sensor system.","corpus_id":15653532,"score":2},{"doc_id":"24528470","title":"Ultrasensitive label-free detection of PNA-DNA hybridization by reduced graphene oxide field-effect transistor biosensor.","abstract":"A reduced graphene oxide (R-GO)-based field-effect transistor (FET) biosensor used for ultrasensitive label-free detection of DNA via peptide nucleic acid (PNA)-DNA hybridization is reported. In this work, R-GO was prepared by reduction of GO with hydrazine, and the FET biosensor was fabricated by drop-casting the R-GO suspension onto the sensor surface. PNA instead of DNA as the capture probe was employed, and DNA detection was performed through PNA-DNA hybridization by the R-GO FET biosensor. The detection limit as low as 100 fM was achieved, which is 1 order of magnitude lower than that of the previously reported graphene FET DNA biosensor based on DNA-DNA hybridization. Moreover, the R-GO FET biosensor was able to distinguish the complementary DNA from one-base mismatched DNA and noncomplementary DNA. Interestingly, the fabricated DNA biosensor was found to have a regeneration capability. The developed R-GO FET DNA biosensor shows ultrasensitivity and high specificity, indicating its potential applications in disease diagnostics as a point-of-care tool.","corpus_id":24090334,"score":2},{"doc_id":"24588742","title":"MoS₂ field-effect transistor for next-generation label-free biosensors.","abstract":"Biosensors based on field-effect transistors (FETs) have attracted much attention, as they offer rapid, inexpensive, and label-free detection. While the low sensitivity of FET biosensors based on bulk 3D structures has been overcome by using 1D structures (nanotubes/nanowires), the latter face severe fabrication challenges, impairing their practical applications. In this paper, we introduce and demonstrate FET biosensors based on molybdenum disulfide (MoS2), which provides extremely high sensitivity and at the same time offers easy patternability and device fabrication, due to its 2D atomically layered structure. A MoS2-based pH sensor achieving sensitivity as high as 713 for a pH change by 1 unit along with efficient operation over a wide pH range (3-9) is demonstrated. Ultrasensitive and specific protein sensing is also achieved with a sensitivity of 196 even at 100 femtomolar concentration. While graphene is also a 2D material, we show here that it cannot compete with a MoS2-based FET biosensor, which surpasses the sensitivity of that based on graphene by more than 74-fold. Moreover, we establish through theoretical analysis that MoS2 is greatly advantageous for biosensor device scaling without compromising its sensitivity, which is beneficial for single molecular detection. Furthermore, MoS2, with its highly flexible and transparent nature, can offer new opportunities in advanced diagnostics and medical prostheses. This unique fusion of desirable properties makes MoS2 a highly potential candidate for next-generation low-cost biosensors.","corpus_id":11444878,"score":2},{"doc_id":"24632459","title":"Simple and label-free electrochemical impedance Amelogenin gene hybridization biosensing based on reduced graphene oxide.","abstract":"The increasing desire for sensitive, easy, low-cost, and label free methods for the detection of DNA sequences has become a vital matter in biomedical research. For the first time a novel label-free biosensor for sensitive detection of Amelogenin gene (AMEL) using reduced graphene oxide modified glassy carbon electrode (GCE/RGO) has been developed. In this work, detection of DNA hybridization of the target and probe DNA was investigated by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). The optimum conditions were found for the immobilization of probe on RGO surface and its hybridization with the target DNA. CV and EIS carried out in an aqueous solution containing [Fe(CN)6](3-/4-) redox pair have been used for the biosensor characterization. The biosensor has a wide linear range from 1.0×10(-20) to 1.0×10(-14)M with the lower detection limit of 3.2×10(-21)M. Moreover, the present electrochemical detection offers some unique advantages such as ultrahigh sensitivity, simplicity, and feasibility for apparatus miniaturization in analytical tests. The excellent performance of the biosensor is attributed to large surface-to-volume ratio and high conductivity of RGO, which enhances the probe absorption and promotes direct electron transfer between probe and the electrode surface. This electrochemical DNA sensor could be used for the detection of specific ssDNA sequence in real biological samples.","corpus_id":7405942,"score":2},{"doc_id":"25189574","title":"Electrophoretic and field-effect graphene for all-electrical DNA array technology.","abstract":"Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.","corpus_id":1043741,"score":2},{"doc_id":"25285529","title":"A microfluidic-based electrochemical biochip for label-free DNA hybridization analysis.","abstract":"Miniaturization of analytical benchtop procedures into the micro-scale provides significant advantages in regards to reaction time, cost, and integration of pre-processing steps. Utilizing these devices towards the analysis of DNA hybridization events is important because it offers a technology for real time assessment of biomarkers at the point-of-care for various diseases. However, when the device footprint decreases the dominance of various physical phenomena increases. These phenomena influence the fabrication precision and operation reliability of the device. Therefore, there is a great need to accurately fabricate and operate these devices in a reproducible manner in order to improve the overall performance. Here, we describe the protocols and the methods used for the fabrication and the operation of a microfluidic-based electrochemical biochip for accurate analysis of DNA hybridization events. The biochip is composed of two parts: a microfluidic chip with three parallel micro-channels made of polydimethylsiloxane (PDMS), and a 3 x 3 arrayed electrochemical micro-chip. The DNA hybridization events are detected using electrochemical impedance spectroscopy (EIS) analysis. The EIS analysis enables monitoring variations of the properties of the electrochemical system that are dominant at these length scales. With the ability to monitor changes of both charge transfer and diffusional resistance with the biosensor, we demonstrate the selectivity to complementary ssDNA targets, a calculated detection limit of 3.8 nM, and a 13% cross-reactivity with other non-complementary ssDNA following 20 min of incubation. This methodology can improve the performance of miniaturized devices by elucidating on the behavior of diffusion at the micro-scale regime and by enabling the study of DNA hybridization events.","corpus_id":41450238,"score":2},{"doc_id":"25741743","title":"Detection of DNA and poly-l-lysine using CVD graphene-channel FET biosensors.","abstract":"A graphene channel field-effect biosensor is demonstrated for detecting the binding of double-stranded DNA and poly-l-lysine. Sensors consist of chemical vapor deposition graphene transferred using a clean, etchant-free transfer method. The presence of DNA and poly-l-lysine are detected by the conductance change of the graphene transistor. A readily measured shift in the Dirac voltage (the voltage at which the graphene's resistance peaks) is observed after the graphene channel is exposed to solutions containing DNA or poly-l-lysine. The 'Dirac voltage shift' is attributed to the binding/unbinding of charged molecules on the graphene surface. The polarity of the response changes to positive direction with poly-l-lysine and negative direction with DNA. This response results in detection limits of 8 pM for 48.5 kbp DNA and 11 pM for poly-l-lysine. The biosensors are easy to fabricate, reusable and are promising as sensors of a wide variety of charged biomolecules.","corpus_id":23184478,"score":2},{"doc_id":"25770609","title":"Simple and label-free detection of DNA hybridization on a modified graphene nanosheets electrode.","abstract":"In this study, an effective method was devised to synthesize amelogenin genes in solution and to amplify electrical detection of DNA hybridization based on graphene nanosheets (GNs) modified glassy carbon electrode (GCE). GNs are well known as effective biocompatible and conductive materials that can provide large surface area and a sufficient numbers of binding points for DNA immobilization. The biosensor fabrication processes and the electrochemical responses of probe immobilization and hybridization with target DNA were investigated by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) using [Fe(CN)6](3-/4-) as an electrochemical redox. Due to minimum nonspecific DNA adsorption, a very high specificity of DNA hybridization was achieved, and the hybridization rate of the target DNA in optimum conditions was increased significantly. With this approach, the target DNA could be quantified in a linear range from 1.0×10(-20) to 1.0×10(-14) mol L(-1) for the first segment and from 1.0×10(-13) to 1.0×10(-6) mol L(-1) for the second segment, with a detection limit of 7.1×10(-21) mol L(-1) by 3s(b). In addition, the biosensor exhibited a high level of stability and repeatability, even for the determination of DNA sequences in real samples without amplification.","corpus_id":43789026,"score":2},{"doc_id":"25853238","title":"A monocrystal graphene domain biosensor array with differential output for real-time monitoring of glucose and normal saline.","abstract":"A biosensor array with differential output based on a monocrystal graphene domain is proposed to realize high resolution measurements. The differential output structure can eliminate the noise that comes from graphene crystal orientation and grain boundary, as well as the fluctuation that comes from the contact resistance and experiment process, so as to improve resolution in the lower concentration. We have fabricated a high quality monocrystal graphene domain that has millimeter size by the chemical vapor deposition method. Two identical graphene ribbons that are cut from the same domain are used as field effect transistor source-to-drain channels for the reference and the test of differential output, respectively. The experimental results show that the source-to-drain current has a fast response shorter than 0.5 second in glucose, normal saline and pH buffer solutions of different concentrations. Sensitivity increases exponentially with the increase of concentration of the tested liquid and the high resolution range is 0.01-2 wt% in glucose and 0.0009-0.018 wt% in saline, and the highest resolutions of glucose and saline are 0.01 wt% and 0.0009 wt%, respectively. We have fabricated a 1 × 4 array structure with differential outputs that pave the way for rapidly detecting ultra-low concentration of analytes.","corpus_id":23145180,"score":2},{"doc_id":"25965056","title":"Ultrarapid and ultrasensitive electrical detection of proteins in a three-dimensional biosensor with high capture efficiency.","abstract":"The realization of a high-throughput biosensor platform with ultrarapid detection of biomolecular interactions and an ultralow limit of detection in the femtomolar (fM) range or below has been retarded due to sluggish binding kinetics caused by the scarcity of probe molecules on the nanostructures and/or limited mass transport. Here, as a new method for the highly efficient capture of biomolecules at extremely low concentration, we tested a three-dimensional (3D) platform of a bioelectronic field-effect transistor (bio-FET) with vertically aligned and highly dense one-dimensional (1D) ZnO nanorods (NRs) as a sensing surface capped by an ultrathin TiO2 layer for improved electrolytic stability on a chemical-vapor-deposited graphene (Gr) channel. The ultrarapid detection capability with a very fast response time (∼1 min) at the fM level of proteins in the proposed 3D bio-FET is primarily attributed to the fast binding kinetics of the probe-target proteins due to the small diffusion length of the target molecules to reach the sensor surface and the substantial number of probe molecules available on the largely increased surface area of the vertical ZnO NRs. This new 3D electrical biosensor platform can be easily extended to other electrochemical nanobiosensors and has great potential for practical applications in miniaturized biosensor integrated systems.","corpus_id":19841648,"score":2},{"doc_id":"26197105","title":"A Highly Responsive Silicon Nanowire/Amplifier MOSFET Hybrid Biosensor.","abstract":"This study demonstrates a hybrid biosensor comprised of a silicon nanowire (SiNW) integrated with an amplifier MOSFET to improve the current response of field-effect-transistor (FET)-based biosensors. The hybrid biosensor is fabricated using conventional CMOS technology, which has the potential advantage of high density and low noise performance. The biosensor shows a current response of 5.74 decades per pH for pH detection, which is 2.5 × 10(5) times larger than that of a single SiNW sensor. In addition, we demonstrate charged polymer detection using the biosensor, with a high current change of 4.5 × 10(5) with a 500 nM concentration of poly(allylamine hydrochloride). In addition, we demonstrate a wide dynamic range can be obtained by adjusting the liquid gate voltage. We expect that this biosensor will be advantageous and practical for biosensor applications which requires lower noise, high speed, and high density.","corpus_id":509707,"score":2},{"doc_id":"26203889","title":"Fabrication of Ultrasensitive Field-Effect Transistor DNA Biosensors by a Directional Transfer Technique Based on CVD-Grown Graphene.","abstract":"Most graphene field-effect transistor (G-FET) biosensors are fabricated through a routine process, in which graphene is transferred onto a Si/SiO2 substrate and then devices are subsequently produced by micromanufacture processes. However, such a fabrication approach can introduce contamination onto the graphene surface during the lithographic process, resulting in interference for the subsequent biosensing. In this work, we have developed a novel directional transfer technique to fabricate G-FET biosensors based on chemical-vapor-deposition- (CVD-) grown single-layer graphene (SLG) and applied this biosensor for the sensitive detection of DNA. A FET device with six individual array sensors was first fabricated, and SLG obtained by the CVD-growth method was transferred onto the sensor surface in a directional manner. Afterward, peptide nucleic acid (PNA) was covalently immobilized on the graphene surface, and DNA detection was realized by applying specific target DNA to the PNA-functionalized G-FET biosensor. The developed G-FET biosensor was able to detect target DNA at concentrations as low as 10 fM, which is 1 order of magnitude lower than those reported in a previous work. In addition, the biosensor was capable of distinguishing the complementary DNA from one-base-mismatched DNA and noncomplementary DNA. The directional transfer technique for the fabrication of G-FET biosensors is simple, and the as-constructed G-FET DNA biosensor shows ultrasensitivity and high specificity, indicating its potential application in disease diagnostics as a point-of-care tool.","corpus_id":206394876,"score":2},{"doc_id":"26237346","title":"Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays.","abstract":"Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.","corpus_id":19463367,"score":2},{"doc_id":"26367906","title":"Compact multi-channel surface plasmon resonance sensor for real-time multi-analyte biosensing.","abstract":"A compact multi-channel surface plasmon resonance (SPR) biosensor is demonstrated based on a tablet as the measurement platform. The SPR biosensor employs a bundle of fiber-optic SPR sensors as the multiplexed sensing elements that are illuminated by a light-emitting diode (LED) plane light source and detected by a cordless camera. The multi-channel SPR biosensor was based on optical fiber components for precise, label-free and high-throughput detection without the use of complex, specialized or fragile instrumentation that would require optical calibration. The reference and control channels compensated for the fluctuation of the LED light source and the bulk refractive index, increasing the accuracy and reliability of the biosensor. The multi-channel SPR biosensor was applied for multi-analyte biosensing of immunoglobulin G (IgG) and concanavalin A (Con A). The channels functionalized with staphylococcal protein A (SPA) and ribonuclease B (RNase B) only showed relative intensity responses to their corresponding analytes. Moreover, the multi-channel SPR sensors responded to the specific detection of IgG and Con A with an approximately linear relative intensity response to the analyte concentration. Hence, multiple analytes were simultaneously and quantitatively detected with the multi-channel SPR biosensor. This compact, cost-effective multi-channel SPR biosensor is adapted for point-of-care tests, which are important in healthcare and environmental monitoring and for biomolecular interaction analysis.","corpus_id":28490512,"score":2},{"doc_id":"26367921","title":"Micro-capillary-based evanescent field biosensor for sensitive, label-free DNA detection.","abstract":"We proposed and demonstrated a micro-capillary-based, high-sensitivity evanescent field biosensor for the cost-effective, rapid, and sensitive analysis and detection of specific DNA sequences. By functionalizing the surface of the tubing wall with ssDNA probe sequences, label-free DNA detection is achieved. The wavelength shift response of the surface-functionalized biosensors to DNA hybridization is monitored in real time. Our experiments show that the biosensor can operate at room temperature and is capable of performing label-free hybridization detection, analyte concentration measurement and nucleotide mismatch detection through a single sensing device. The sensor has many advantages, such as a simple manufacturing process, standardized production control, reliable quality, low cost and an economic demodulator. The compact nature and miniature size of the biosensing detection system makes it a good candidate for the rapid and highly sensitive detection of low-concentration analytes in micro-samples for cost-effective, real-time, and on-site analysis in the fields of life science, pharmaceutical chemistry, medical science and criminal investigation.","corpus_id":34813363,"score":2},{"doc_id":"26387446","title":"Electrochemical DNA biosensor based on a glassy carbon electrode modified with gold nanoparticles and graphene for sensitive determination of Klebsiella pneumoniae carbapenemase.","abstract":"We describe the fabrication of a sensitive electrochemical DNA biosensor for determination of Klebsiella pneumoniae carbapenemase (KPC). The highly sensitive and selective electrochemical biosensor for DNA detection was constructed based on a glassy carbon electrode (GCE) modified with gold nanoparticles (Au-NPs) and graphene (Gr). Then Au-NPs/Gr/GCE was characterized by scanning electro miroscope (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The hybridization detection was measured by diffierential pulse voltammetry (DPV) using methylene blue (MB) as the hybridization indicator. The dynamic range of detection of the sensor for the target DNA sequences was from 1×10(-12) to 1×10(-7)mol/L, with a detection limit of 2×10(-13)mol/L. The DNA biosensor had excellent specificity for distinguishing complementary DNA sequence in the presence of non-complementary and mismatched DNA sequence. The results demonstrated that the Au-NPs/Gr nanocomposite was a promising substrate for the development of high-performance electrocatalysts for determination of KPC.","corpus_id":205745928,"score":2},{"doc_id":"26445172","title":"Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.","abstract":"Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.","corpus_id":6886645,"score":2},{"doc_id":"26709827","title":"Label-Free Direct Detection of miRNAs with Poly-Silicon Nanowire Biosensors.","abstract":"BACKGROUND: The diagnostic and prognostic value of microRNAs (miRNAs) in a variety of diseases is promising. The novel silicon nanowire (SiNW) biosensors have advantages in molecular detection because of their high sensitivity and fast response. In this study, poly-crystalline silicon nanowire field-effect transistor (poly-SiNW FET) device was developed to achieve specific and ultrasensitive detection of miRNAs without labeling and amplification. METHODS: The poly-SiNW FET was fabricated by a top-down Complementary Metal Oxide Semiconductor (CMOS) wafer fabrication based technique. Single strand DNA (ssDNA) probe was bind to the surface of the poly-SiNW device which was silanated and aldehyde-modified. By comparing the difference of resistance value before and after ssDNA and miRNA hybridization, poly-SiNW device can be used to detect standard and real miRNA samples. RESULTS: Poly-SiNW device with different structures (different line width and different pitch) was applied to detect standard Let-7b sample with a detection limitation of 1 fM. One-base mismatched sequence could be distinguished meanwhile. Furthermore, these poly-SiNW arrays can detect snRNA U6 in total RNA samples extracted from HepG2 cells with a detection limitation of 0.2 μg/mL. In general, structures with pitch showed better results than those without pitch in detection of both Let-7b and snRNA U6. Moreover, structures with smaller pitch showed better detection efficacy. CONCLUSION: Our findings suggest that poly-SiNW arrays could detect standard and real miRNA sample without labeling or amplification. Poly-SiNW biosensor device is promising for miRNA detection.","corpus_id":6525566,"score":2},{"doc_id":"26780442","title":"Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids.","abstract":"The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.","corpus_id":24914461,"score":2},{"doc_id":"26945181","title":"Label-free in-situ real-time DNA hybridization kinetics detection employing microfiber-assisted Mach-Zehnder interferometer.","abstract":"A label-free DNA biosensor based on microfiber-assisted Mach-Zehnder interferometer (MAMZI) for in-situ real-time DNA hybridization kinetics detection has been proposed and experimentally demonstrated. A microfiber of hundreds of microns in length is fabricated by tapering a segment of standard single-mode fiber (SMF) to construct the U-shaped microcavity between the lead-in and lead-out SMFs. Thanks to the mode field mismatching between the SMF and microfiber, the incident guided mode light would separate into two beams that respectively propagate in the air microcavity and the microfiber. Consequently, interference between different light modes would occur at the joint between the microfiber and the lead-out SMF. Experimental results indicate that owing to the participation of opening cavity modes in the modal interference process, the interferometric spectrum of our proposed microcavity sensor is highly sensitive to the variation of environmental refractive index (RI), especially for the RI range around 1.34 which is useful for most biological applications. The microfiber functionalization is achieved by stepwise modifying the microfiber with monolayer Poly-l-lysine (PLL) and single-stranded DNA (ssDNA) probes to produce the sensitive surface that could uniquely attach specific target ssDNAs. The fiber surface functionalization as well as DNA hybridization processes have been experimentally investigated for different target ssDNA solutions in real time. The interferometric transmission spectrum shows large wavelength shift for different biological phases, and a detection limit conservatively down to 0.0001pmol/μL has been acquired by employing the U-shaped microcavity of 176.88μm in length. Our proposed DNA biosensor possesses several advantages such as compact size, ease of fabrication, and strong response for DNA hybridization, which make it a promising candidate for potential applications in such rapidly expanding areas as medical diagnosis, cancer screenings, medicine examination and environmental engineering, etc.","corpus_id":6467190,"score":2},{"doc_id":"27298347","title":"Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.","abstract":"Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.","corpus_id":24235375,"score":2},{"doc_id":"27532480","title":"Scalable Production of High-Sensitivity, Label-Free DNA Biosensors Based on Back-Gated Graphene Field Effect Transistors.","abstract":"Scalable production of all-electronic DNA biosensors with high sensitivity and selectivity is a critical enabling step for research and applications associated with detection of DNA hybridization. We have developed a scalable and very reproducible (>90% yield) fabrication process for label-free DNA biosensors based upon graphene field effect transistors (GFETs) functionalized with single-stranded probe DNA. The shift of the GFET sensor Dirac point voltage varied systematically with the concentration of target DNA. The biosensors demonstrated a broad analytical range and limit of detection of 1 fM for 60-mer DNA oligonucleotide. In control experiments with mismatched DNA oligomers, the impact of the mismatch position on the DNA hybridization strength was confirmed. This class of highly sensitive DNA biosensors offers the prospect of detection of DNA hybridization and sequencing in a rapid, inexpensive, and accurate way.","corpus_id":13186445,"score":2},{"doc_id":"27534818","title":"Precise and selective sensing of DNA-DNA hybridization by graphene/Si-nanowires diode-type biosensors.","abstract":"Single-Si-nanowire (NW)-based DNA sensors have been recently developed, but their sensitivity is very limited because of high noise signals, originating from small source-drain current of the single Si NW. Here, we demonstrate that chemical-vapor-deposition-grown large-scale graphene/surface-modified vertical-Si-NW-arrays junctions can be utilized as diode-type biosensors for highly-sensitive and -selective detection of specific oligonucleotides. For this, a twenty-seven-base-long synthetic oligonucleotide, which is a fragment of human DENND2D promoter sequence, is first decorated as a probe on the surface of vertical Si-NW arrays, and then the complementary oligonucleotide is hybridized to the probe. This hybridization gives rise to a doping effect on the surface of Si NWs, resulting in the increase of the current in the biosensor. The current of the biosensor increases from 19 to 120% as the concentration of the target DNA varies from 0.1 to 500 nM. In contrast, such biosensing does not come into play by the use of the oligonucleotide with incompatible or mismatched sequences. Similar results are observed from photoluminescence microscopic images and spectra. The biosensors show very-uniform current changes with standard deviations ranging ~1 to ~10% by ten-times endurance tests. These results are very promising for their applications in accurate, selective, and stable biosensing.","corpus_id":13766674,"score":2},{"doc_id":"27676459","title":"Scalable Production of Sensor Arrays Based on High-Mobility Hybrid Graphene Field Effect Transistors.","abstract":"We have developed a scalable fabrication process for the production of DNA biosensors based on gold nanoparticle-decorated graphene field effect transistors (AuNP-Gr-FETs), where monodisperse AuNPs are created through physical vapor deposition followed by thermal annealing. The FETs are created in a four-probe configuration, using an optimized bilayer photolithography process that yields chemically clean devices, as confirmed by XPS and AFM, with high carrier mobility (3590 ± 710 cm(2)/V·s) and low unintended doping (Dirac voltages of 9.4 ± 2.7 V). The AuNP-Gr-FETs were readily functionalized with thiolated probe DNA to yield DNA biosensors with a detection limit of 1 nM and high specificity against noncomplementary DNA. Our work provides a pathway toward the scalable fabrication of high-performance AuNP-Gr-FET devices for label-free nucleic acid testing in a realistic clinical setting.","corpus_id":23441045,"score":2},{"doc_id":"27779853","title":"Real-Time Monitoring of Nitric Oxide at Single-Cell Level with Porphyrin-Functionalized Graphene Field-Effect Transistor Biosensor.","abstract":"An ultrasensitive and highly efficient assay for real-time monitoring of nitric oxide (NO) at single-cell level based on a reduced graphene oxide (RGO) and iron-porphyrin-functionalized graphene (FGPCs) field-effect transistor (FET) biosensor is reported. A layer-to-layer assembly of RGO and FGPCs on a prefabricated FET sensor surface through π-π stacking interaction allowed superior electrical conductivity caused by RGO, and highly catalytic specificity induced by metalloporphyrin, ensuring the ultrasensitive and highly specific detection of NO. The results demonstrated that the RGO/FGPCs FET biosensor was capable of real-time monitoring of NO in the range from 1 pM to 100 nM with the limit of detection as low as 1 pM in phosphate-buffered saline (PBS) and 10 pM in the cell medium, respectively. Moreover, the developed biosensor could be used for real-time monitoring of NO released from human umbilical vein endothelial cells (HUVECs) at single-cell level. Along with its miniaturized sizes, ultrasensitive characteristics, and fast response, the FET biosensor is promising as a new platform for potential biological and diagnostic applications.","corpus_id":13574816,"score":2},{"doc_id":"27930344","title":"Specific detection of biomolecules in physiological solutions using graphene transistor biosensors.","abstract":"Nanomaterial-based field-effect transistor (FET) sensors are capable of label-free real-time chemical and biological detection with high sensitivity and spatial resolution, although direct measurements in high-ionic-strength physiological solutions remain challenging due to the Debye screening effect. Recently, we demonstrated a general strategy to overcome this challenge by incorporating a biomolecule-permeable polymer layer on the surface of silicon nanowire FET sensors. The permeable polymer layer can increase the effective screening length immediately adjacent to the device surface and thereby enable real-time detection of biomolecules in high-ionic-strength solutions. Here, we describe studies demonstrating both the generality of this concept and application to specific protein detection using graphene FET sensors. Concentration-dependent measurements made with polyethylene glycol (PEG)-modified graphene devices exhibited real-time reversible detection of prostate specific antigen (PSA) from 1 to 1,000 nM in 100 mM phosphate buffer. In addition, comodification of graphene devices with PEG and DNA aptamers yielded specific irreversible binding and detection of PSA in pH 7.4 1x PBS solutions, whereas control experiments with proteins that do not bind to the aptamer showed smaller reversible signals. In addition, the active aptamer receptor of the modified graphene devices could be regenerated to yield multiuse selective PSA sensing under physiological conditions. The current work presents an important concept toward the application of nanomaterial-based FET sensors for biochemical sensing in physiological environments and thus could lead to powerful tools for basic research and healthcare.","corpus_id":4873583,"score":2},{"doc_id":"28299688","title":"All-Electrical Graphene DNA Sensor Array.","abstract":"Electrical sensing of biomolecules has been an important pursuit due to the label-free operation and chip-scale construct such sensing modality can enable. In particular, electrical biomolecular sensors based on nanomaterials such as semiconductor nanowires, carbon nanotubes, and graphene have demonstrated high sensitivity, which in the case of nanowires and carbon nanotubes can surpass typical optical detection sensitivity. Among these nanomaterials, graphene is well suited for a practical candidate for implementing a large-scale array of biomolecular sensors, as its two-dimensional morphology is readily compatible with industry standard top-down fabrication techniques. In our recent work published in 2014 Nature Communications, we demonstrated these benefits by creating DNA sensor arrays from chemical vapor deposition (CVD) graphene. The present chapter, which is a review of this recent work, outlines procedures demonstrating the use of individual graphene sites of the array in dual roles--electrophoretic electrodes for site specific probe DNA immobilization and field effect transistor (FET) sensors for detection of target DNA hybridization. The 100 fM detection sensitivity achieved in 7 out of 8 graphene FET sensors in the array combined with the alternative use of the graphene channels as electrophoretic electrodes for probe deposition represent steps toward creating an all-electrical multiplexed DNA array.","corpus_id":3596254,"score":2},{"doc_id":"28448040","title":"Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms.","abstract":"Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.","corpus_id":3792820,"score":2},{"doc_id":"28604366","title":"Flexible electrochemical biosensors based on graphene nanowalls for the real-time measurement of lactate.","abstract":"We demonstrate a flexible biosensor for lactate detection based on l-lactate oxidase immobilized by chitosan film cross-linked with glutaraldehyde on the surface of a graphene nanowall (GNW) electrode. The oxygen-plasma technique was developed to enhance the wettability of the GNWs, and the strength of the sensor's oxidation response depended on the concentration of lactate. First, in order to eliminate interference from other substances, biosensors were primarily tested in deionized water and displayed good electrochemical reversibility at different scan rates (20-100 mV s(-1)), a large index range (1.0 μM to 10.0 mM) and a low detection limit (1.0 μM) for lactate. Next, these sensors were further examined in phosphate buffer solution (to mimick human body fluids), and still exhibited high sensitivity, stability and flexibility. These results show that the GNW-based lactate biosensors possess important potential for application in clinical analysis, sports medicine and the food industry.","corpus_id":3699349,"score":2},{"doc_id":"29039202","title":"Nanoelectronic Platform for Ultrasensitive Detection of Protein Biomarkers in Serum using DNA Amplification.","abstract":"Silicon nanowire field effect transistors (NWFETs) are low noise, low power, ultrasensitive biosensors that are highly amenable to integration. However, using NWFETs to achieve direct protein detection in physiological buffers such as blood serum remains difficult due to Debye screening, nonspecific binding, and stringent functionalization requirements. In this work, we performed an indirect sandwich immunoassay in serum combined with exponential DNA amplification and pH measurement by ultrasensitive NWFET sensors. Measurements of model cytokine interleukin-2 concentrations from <20 fM to >200 pM were demonstrated, surpassing the conventional NWFET urease-based readout. Our approach paves way for future development of universal, highly sensitive, miniaturized, and integrated nanoelectronic devices that can be applied to a wide variety of analytes.","corpus_id":31825364,"score":2},{"doc_id":"29147003","title":"Real-time wash-free detection of unlabeled PNA-DNA hybridization using discrete FET sensor.","abstract":"We demonstrate an electrochemical sensor for detection of unlabeled single-stranded DNA using peptide nucleic acid (PNA) probes coupled to the field-effect transistor (FET) gate. The label-free detection relies on the intrinsic charge of the DNA backbone. Similar detection schemes have mainly concentrated on sensitivity improvement with an emphasis on new sensor structures. Our approach focuses on using an extended-gate that separates the FET and the sensing electrode yielding a simple and mass fabricable device. We used PNA probes for efficient hybridization in low salt conditions that is required to avoid the counter ion screening. As a result, significant part of the target DNA lies within the screening length of the sensor. With this, we achieved a wash-free detection where typical gate potential shifts are more than 70 mV with 1 µM target DNA. We routinely obtained a real-time, label- and wash-free specific detection of target DNA in nanomolar concentration with low-cost electronics and the responses were achieved within minutes after introducing targets to the solution. Furthermore, the results suggest that the sensor performance is limited by specificity rather than by sensitivity and using low-cost electronics does not limit the sensor performance in the presented sensor configuration.","corpus_id":20288207,"score":2},{"doc_id":"29308810","title":"Real-time subcellular imaging based on graphene biosensors.","abstract":"Non-invasive living cell microscopy in real time is essential for a wide variety of biomedical research. Here, we present a subcellular refractive index imaging technique for living cells based on a graphene biosensor system. Owing to the optical reflectivity differences of graphene to s- and p-polarizations, a 45° generalized-cylindrical-vector-polarized laser beam is employed to demodulate the reflected cylindrical vector beam for differential detecting. Benefitting from the vector beam-enabled common-path graphene biosensor, the imaging spatial resolution and refractive index sensitivity are noticeably improved. Subcellular refractive index mapping of live human colonic cancer cells is perfectly achieved without inducing any cell damage. Furthermore, real-time monitoring of an individual cell is also performed with the disassembly of the cell nucleolus clearly observed. This technique would be a promising tool for the study of living cell morphology, kinetics, and pathology, and for other biomedical research.","corpus_id":206109960,"score":2},{"doc_id":"29355779","title":"The field effect transistor DNA biosensor based on ITO nanowires in label-free hepatitis B virus detecting compatible with CMOS technology.","abstract":"In this paper the field-effect transistor DNA biosensor for detecting hepatitis B virus (HBV) based on indium tin oxide nanowires (ITO NWs) in label free approach has been fabricated. Because of ITO nanowires intensive conductance and functional modified surface, the probe immobilization and target hybridization were increased strongly. The high resolution transmission electron microscopy (HRTEM) measurement showed that ITO nanowires were crystalline and less than 50nm in diameter. The single-stranded hepatitis B virus DNA (SS-DNA) was immobilized as probe on the Au-modified nanowires. The DNA targets were measured in a linear concentration range from 1fM to 10µM. The detection limit of the DNA biosensor was about 1fM. The time of the hybridization process for defined single strand was 90min. The switching ratio of the biosensor between \"on\" and \"off\" state was ~ 1.1 × 105. For sensing the specificity of the biosensor, non-complementary, mismatch and complementary DNA oligonucleotide sequences were clearly discriminated. The HBV biosensor confirmed the highly satisfied specificity for differentiating complementary sequences from non-complementary and the mismatch oligonucleotides. The response time of the DNA sensor was 37s with a high reproducibility. The stability and repeatability of the DNA biosensor showed that the peak current of the biosensor retained 98% and 96% of its initial response for measurements after three and five weeks, respectively.","corpus_id":46844411,"score":2},{"doc_id":"29696084","title":"Graphene-based biosensors.","abstract":"Reliable data obtained from analysis of DNA, proteins, bacteria and other disease-related molecules or organisms in biological samples have become a fundamental and crucial part of human health diagnostics and therapy. The development of non-invasive tests that are rapid, sensitive, specific and simple would allow patient discomfort to be prevented, delays in diagnosis to be avoided and the status of a disease to be followed up. Bioanalysis is thus a progressive discipline for which the future holds many exciting opportunities. The use of biosensors for the early diagnosis of diseases has become widely accepted as a point-of-care diagnosis with appropriate specificity in a short time. To allow a reliable diagnosis of a disease at an early stage, highly sensitive biosensors are required as the corresponding biomarkers are generally expressed at very low concentrations. In the past 50 years, various biosensors have been researched and developed encompassing a wide range of applications. This contrasts the limited number of commercially available biosensors. When it comes to sensing of biomarkers with the required picomolar (pM) sensitivity for real-time sensing of biological samples, only a handful of sensing systems have been proposed, and these are often rather complex and costly. Lately, graphene-based materials have been considered as superior over other nanomaterials for the development of sensitive biosensors. The advantages of graphene-based sensor interfaces are numerous, including enhanced surface loading of the desired ligand due to the high surface-to-volume ratio, excellent conductivity and a small band gap that is beneficial for sensitive electrical and electrochemical read-outs, as well as tunable optical properties for optical read-outs such as fluorescence and plasmonics. In this paper, we review the advances made in recent years on graphene-based biosensors in the field of medical diagnosis.","corpus_id":13962344,"score":2},{"doc_id":"24528665","title":"Graphene nano-ink biosensor arrays on a microfluidic paper for multiplexed detection of metabolites.","abstract":"The development of a miniaturized and low-cost platform for the highly sensitive, selective and rapid detection of multiplexed metabolites is of great interest for healthcare, pharmaceuticals, food science, and environmental monitoring. Graphene is a delicate single-layer, two-dimensional network of carbon atoms with extraordinary electrical sensing capability. Microfluidic paper with printing technique is a low cost matrix. Here, we demonstrated the development of graphene-ink based biosensor arrays on a microfluidic paper for the multiplexed detection of different metabolites, such as glucose, lactate, xanthine and cholesterol. Our results show that the graphene biosensor arrays can detect multiple metabolites on a microfluidic paper sensitively, rapidly and simultaneously. The device exhibits a fast measuring time of less than 2 min, a low detection limit of 0.3 μM, and a dynamic detection range of 0.3-15 μM. The process is simple and inexpensive to operate and requires a low consumption of sample volume. We anticipate that these results could open exciting opportunities for a variety of applications.","corpus_id":21897140,"score":1},{"doc_id":"25248104","title":"Direct ultrasensitive electrical detection of prostate cancer biomarkers with CMOS-compatible n- and p-type silicon nanowire sensor arrays.","abstract":"Sensitive and quantitative analysis of proteins is central to disease diagnosis, drug screening, and proteomic studies. Here, a label-free, real-time, simultaneous and ultrasensitive prostate-specific antigen (PSA) sensor was developed using CMOS-compatible silicon nanowire field effect transistors (SiNW FET). Highly responsive n- and p-type SiNW arrays were fabricated and integrated on a single chip with a complementary metal oxide semiconductor (CMOS) compatible anisotropic self-stop etching technique which eliminated the need for a hybrid method. The incorporated n- and p-type nanowires revealed complementary electrical response upon PSA binding, providing a unique means of internal control for sensing signal verification. The highly selective, simultaneous and multiplexed detection of PSA marker at attomolar concentrations, a level useful for clinical diagnosis of prostate cancer, was demonstrated. The detection ability was corroborated to be effective by comparing the detection results at different pH values. Furthermore, the real-time measurement was also carried out in a clinically relevant sample of blood serum, indicating the practicable development of rapid, robust, high-performance, and low-cost diagnostic systems.","corpus_id":12743382,"score":1},{"doc_id":"25790830","title":"Multiplex serum cytokine immunoassay using nanoplasmonic biosensor microarrays.","abstract":"Precise monitoring of the rapidly changing immune status during the course of a disease requires multiplex analysis of cytokines from frequently sampled human blood. However, the current lack of rapid, multiplex, and low volume assays makes immune monitoring for clinical decision-making (e.g., critically ill patients) impractical. Without such assays, immune monitoring is even virtually impossible for infants and neonates with infectious diseases and/or immune mediated disorders as access to their blood in large quantities is prohibited. Localized surface plasmon resonance (LSPR)-based microfluidic optical biosensing is a promising approach to fill this technical gap as it could potentially permit real-time refractometric detection of biomolecular binding on a metallic nanoparticle surface and sensor miniaturization, both leading to rapid and sample-sparing analyte analysis. Despite this promise, practical implementation of such a microfluidic assay for cytokine biomarker detection in serum samples has not been established primarily due to the limited sensitivity of LSPR biosensing. Here, we developed a high-throughput, label-free, multiarrayed LSPR optical biosensor device with 480 nanoplasmonic sensing spots in microfluidic channel arrays and demonstrated parallel multiplex immunoassays of six cytokines in a complex serum matrix on a single device chip while overcoming technical limitations. The device was fabricated using easy-to-implement, one-step microfluidic patterning and antibody conjugation of gold nanorods (AuNRs). When scanning the scattering light intensity across the microarrays of AuNR ensembles with dark-field imaging optics, our LSPR biosensing technique allowed for high-sensitivity quantitative cytokine measurements at concentrations down to 5-20 pg/mL from a 1 μL serum sample. Using the nanoplasmonic biosensor microarray device, we demonstrated the ability to monitor the inflammatory responses of infants following cardiopulmonary bypass (CPB) surgery through tracking the time-course variations of their serum cytokines. The whole parallel on-chip assays, which involved the loading, incubation, and washing of samples and reagents, and 10-fold replicated multianalyte detection for each sample using the entire biosensor arrays, were completed within 40 min.","corpus_id":-1,"score":1},{"doc_id":"26435280","title":"Escherichia coli bacteria detection by using graphene-based biosensor.","abstract":"Graphene is an allotrope of carbon with two-dimensional (2D) monolayer honeycombs. A larger detection area and higher sensitivity can be provided by graphene-based nanosenor because of its 2D structure. In addition, owing to its special characteristics, including electrical, optical and physical properties, graphene is known as a more suitable candidate compared to other materials used in the sensor application. A novel model employing a field-effect transistor structure using graphene is proposed and the current-voltage (I-V) characteristics of graphene are employed to model the sensing mechanism. This biosensor can detect Escherichia coli (E. coli) bacteria, providing high levels of sensitivity. It is observed that the graphene device experiences a drastic increase in conductance when exposed to E. coli bacteria at 0-10(5) cfu/ml concentration. The simple, fast response and high sensitivity of this nanoelectronic biosensor make it a suitable device in screening and functional studies of antibacterial drugs and an ideal high-throughput platform which can detect any pathogenic bacteria. Artificial neural network and support vector regression algorithms have also been used to provide other models for the I-V characteristic. A satisfactory agreement has been presented by comparison between the proposed models with the experimental data.","corpus_id":20825513,"score":1},{"doc_id":"29630304","title":"Graphene Based Biosensor Model for Escherichia Coli Bacteria Detection.","abstract":"As a new nanomaterial, graphene demonstrates great potential as an electrode for biomedical applications in sensing molecules and cells. Thus, development of biosensors based on graphene is gaining much interest due to its exceptional properties such as, large surface-to-volume ratio, high conductivity and high flexibility. In this work a liquid gated graphene field effect transistor based biosensor model is analytically developed for electrical detection of Escherichia Coli O157:H7 bacteria. The effect of graphene functionalization on the graphene conductance in the presence of E. coli is investigated. E. coli absorption effects on the graphene surface in the form of conductance variation are considered. Therefore the graphene conductance as a function of E. coli concentration which controls the current–voltage characteristics of biosensors is presented. According to the simulated results, the proposed sensor model can be applied as a powerful tool to predict the biosensor performance.","corpus_id":4804887,"score":1}],"string":"[\n {\n \"doc_id\": \"18207730\",\n \"title\": \"A novel fluorescence-based array biosensor: principle and application to DNA hybridization assays.\",\n \"abstract\": \"A novel fluorescence-based array biosensor targeted for field applications, such as environmental monitoring, has been developed, and successfully applied to DNA hybridization assays. The purpose was to meet the demand for automated, portable but easy-to-maintain systems allowing continuous flow monitoring of surface reactions. The biosensor presented here can be distinguished from the existing systems by the optical method used, which provides an enhanced simplicity and robustness, and enables a simple maintenance by potentially unskilled personnel. The system is based on a conventional microscope slide which acts both as transducer and biological array sensor. The excited fluorescence is guided by total internal reflection into the slide to the detector which is directly interfaced to the slide. Each region of the sensor array is successively optically interrogated, and the detection of the corresponding fluorescent emission synchronized. A real-time three-analyte analysis is thus feasible without any mechanical scanning movement or optical imaging systems as generally used in the existing instruments. The ability of the biosensor to operate in continuous flow for several tens of hours has been demonstrated. The biosensor has been assessed in terms of stability, and slide-to-slide reproducibility, which is found to be less than 3.7%, thus far below the standard biological reproducibility. DNA hybridization assays were performed to estimate a limit of detection, which was found to be 16 mol/microm(2), and to determine the reaction kinetics associated to the DNA model used. The developed biosensor is thus shown to be able to predict reaction kinetics, and to monitor in real time surface reactions between targets and probes.\",\n \"corpus_id\": 34857259,\n \"score\": 2\n },\n {\n \"doc_id\": \"18405656\",\n \"title\": \"Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet.\",\n \"abstract\": \"ForteBio's Octet optical biosensor harnesses biolayer interferometry to detect and quantify molecular interactions using disposable fiber-optic biosensors that address samples from an open shaking microplate without any microfluidics. We recruited a monoclonal antibody against a panel of peptides to compare the Octet directly with Biacore's well-established 3000 platform and Bio-Rad's recently launched ProteOn XPR36 array system, which use surface plasmon resonance (SPR) to detect the binding of one analyte over four surfaces and six analytes over six surfaces, respectively. A sink method was used to prevent analyte from rebinding the ligand-coated Octet tips and enabled us to extract accurate kinetic rate constants, as judged by their close agreement with those determined by SPR. Although the Octet is not sensitive enough to detect the binding of small molecules directly, it can access their affinities indirectly via solution competition experiments. We conducted similar experiments on the SPR instruments to validate these measurements. The Octet is emerging as a versatile complement to other more sophisticated biosensors, and the ProteOn provides high-quality data near the sensitivity of Biacore but in a more multiplexed format. Our results provide a benchmark for assessing the performance of the above-mentioned sensors.\",\n \"corpus_id\": 9018161,\n \"score\": 2\n },\n {\n \"doc_id\": \"18644712\",\n \"title\": \"Real-time protein biosensor arrays based on surface plasmon resonance differential phase imaging.\",\n \"abstract\": \"This paper reports the application of differential phase surface plasmon resonance (SPR) imaging in two-dimensional (2D) protein biosensor arrays. Our phase imaging approach offers a distinct advantage over the conventional angular SPR technique in terms of utilization efficiency of optical sensor elements in the imaging device. In the angular approach, each biosensor site in the biosensor array requires a linear array of optical detector elements to locate the SPR angular dip. The maximum biosensor density that a two-dimensional imaging device can offer is a one-dimensional SPR biosensor array. On the other hand, the phase-sensitive SPR approach captures data in the time domain instead of the spatial domain. It is possible that each pixel in the captured interferogram represents one sensor site, thus offering high-density two-dimensional biosensor arrays. In addition, our differential phase approach improves detection resolution through removing common-mode disturbances. Experimental results demonstrate a system resolution of 8.8 x 10(-7)RIU (refractive index unit). Real-time monitoring of bovine serum albumin (BSA)/anti-BSA binding interactions at various concentration levels was achieved using a biosensor array. The detection limit was 0.77 microg/ml. The reported two-dimensional SPR biosensor array offers a real-time and non-labeling detection tool for high-throughput protein array analysis. It may find promising applications in protein therapeutics, drug screening and clinical diagnostics.\",\n \"corpus_id\": 19399551,\n \"score\": 2\n },\n {\n \"doc_id\": \"19054661\",\n \"title\": \"Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.\",\n \"abstract\": \"Optical biosensing based on fluorescence detection has arguably become the standard technique for quantifying extents of hybridization between surface-immobilized probes and fluorophore-labeled analyte targets in DNA microarrays. However, electrochemical detection techniques are emerging which could eliminate the need for physically bulky optical instrumentation, enabling the design of portable devices for point-of-care applications. Unlike fluorescence detection, which can function well using a passive substrate (one without integrated electronics), multiplexed electrochemical detection requires an electronically active substrate to analyze each array site and benefits from the addition of integrated electronic instrumentation to further reduce platform size and eliminate the electromagnetic interference that can result from bringing non-amplified signals off chip. We report on an active electrochemical biosensor array, constructed with a standard complementary metal-oxide-semiconductor (CMOS) technology, to perform quantitative DNA hybridization detection on chip using targets conjugated with ferrocene redox labels. A 4 x 4 array of gold working electrodes and integrated potentiostat electronics, consisting of control amplifiers and current-input analog-to-digital converters, on a custom-designed 5 mm x 3 mm CMOS chip drive redox reactions using cyclic voltammetry, sense DNA binding, and transmit digital data off chip for analysis. We demonstrate multiplexed and specific detection of DNA targets as well as real-time monitoring of hybridization, a task that is difficult, if not impossible, with traditional fluorescence-based microarrays.\",\n \"corpus_id\": 9192371,\n \"score\": 2\n },\n {\n \"doc_id\": \"19723688\",\n \"title\": \"Real-time DNA microarray analysis.\",\n \"abstract\": \"We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays.\",\n \"corpus_id\": 5234752,\n \"score\": 2\n },\n {\n \"doc_id\": \"19781931\",\n \"title\": \"Label-free low-cost disposable DNA hybridization detection systems using organic TFTs.\",\n \"abstract\": \"Organic thin film transistors (OTFT) are potentially very attractive for making portable and disposable DNA hybridization detection toolkits because of their ultra-low-cost manufacturing and potentially high sensitivity. To make a self-supported DNA sensor, we herein report an OTFT-based label-free DNA hybridization detection system integrating electrically read DNA hybridization sensors and microfluidic delivery channels. We previously reported DNA-doped OTFTs acting as electrically read DNA sensors. In this article, we first study physics of DNA sensitivity of OTFTs, clarifying the doping mechanism. The article also presents a method of verification of the immobilization and presence of DNA on the surface using TOF-SIMS analysis. As a further step, sources of variation of measured data and methods of minimization are discussed using a novel photolithography-based microfluidics fabrication method, directly enabling on-chip hybridization and self-supported DNA detection. By integrating the sensors with microfluidics, for the first time, we demonstrate necessary technologies required to realize disposable, rapid turn-around tools for field-deployable genetic diagnosis.\",\n \"corpus_id\": 110488112,\n \"score\": 2\n },\n {\n \"doc_id\": \"19802851\",\n \"title\": \"Integrated electrochemical DNA biosensors for lab-on-a-chip devices.\",\n \"abstract\": \"Analytical devices able to perform accurate and fast automatic DNA detection or sequencing procedures have many potential benefits in the biomedical and environmental fields. The conversion of biological or biochemical responses into quantifiable optical, mechanical or electronic signals is achieved by means of biosensors. Most of these transducing elements can be miniaturized and incorporated into lab-on-a-chip devices, also known as Micro Total Analysis Systems. The use of multiple DNA biosensors integrated in these miniaturized laboratories, which perform several analytical operations at the microscale, has many cost and efficiency advantages. Tiny amounts of reagents and samples are needed and highly sensitive, fast and parallel assays can be done at low cost. A particular type of DNA biosensors are the ones used based on electrochemical principles. These sensors offer several advantages over the popular fluorescence-based detection schemes. The resulting signal is electrical and can be processed by conventional electronics in a very cheap and fast manner. Furthermore, the integration and miniaturization of electrochemical transducers in a microsystem makes easier its fabrication in front of the most common currently used detection method. In this review, different electrochemical DNA biosensors integrated in analytical microfluidic devices are discussed and some early stage commercial products based on this strategy are presented.\",\n \"corpus_id\": 21925845,\n \"score\": 2\n },\n {\n \"doc_id\": \"20093001\",\n \"title\": \"Direct label-free electrical immunodetection in human serum using a flow-through-apparatus approach with integrated field-effect transistors.\",\n \"abstract\": \"In order to identify changes in the levels of key proteins in response to the onset or development of a disease, the research fields of proteomics and genomics seek to develop new biomarkers. Specifically, simple and fast biomarker screens have a central role in many areas of healthcare, including disease diagnosis and drug discovery. Biologically modified field-effect transistor (BioFET) is one of the most attractive approaches because of the on-chip integration of the sensor array, fast response, high reliability and low-cost mass production. However, the BioFETs used to detect macromolecules have been operated only in buffer solution with low salt concentrations because of the Debye screening length of blood or serum. Here we report a novel detection technique for direct label-free immunodetection of cancer markers in human serum using a Si-FET that was fabricated by conventional photolithographic processes. The proposed sensing method shows no dissociation of antigen-antibody binding as in general immunoassays, unlike the previous reports on Si-FET sensors. This method therefore overcomes the Debye length problem of immunodetection in human fluids, such as serum, that are generally encountered by FET-based biosensors. Our results demonstrate specific label-free and real-time immunodetection of a cancer marker at a concentration of 0.2 ng/mL in human serum, quantitative detection of the marker from 0.2 to 114 ng/mL, and successful multiplexed sensing of three different cancer markers. We believe that connecting our simple electrical detection method, which does not require pretreatment of serum, with well-established whole blood filter technology will contribute to the development of new point-of-care testing (POCT) sensors.\",\n \"corpus_id\": 21319540,\n \"score\": 2\n },\n {\n \"doc_id\": \"20486666\",\n \"title\": \"Real-time biomolecular binding detection using a sensitive photonic crystal biosensor.\",\n \"abstract\": \"Real-time measurement of specific biomolecular interactions is critical to many areas of biological research. A number of label-free techniques for directly monitoring biomolecular binding have been developed, but it is still challenging to measure the binding kinetics of very small molecules, to detect low concentrations of analyte molecules, or to detect low affinity interactions. In this study, we report the development of a highly sensitive photonic crystal biosensor for label-free, real-time biomolecular binding analysis. We characterize the performance of this biosensor using a standard streptavidin-biotin binding system. Optimization of the surface functionalization methods for streptavidin immobilization on the silica sensing surface is presented, and the specific binding of biotinylated analyte molecules ranging over 3 orders of magnitude in molecular weight, including very small molecules (<250 Da), DNA oligonucleotides, proteins, and antibodies (>150 000 Da), are detected in real time with a high signal-to-noise ratio. Finally, we document the sensor efficiency for low mass adsorption, as well as multilayered molecular interactions. By all important metrics for sensitivity, we anticipate this photonic crystal biosensor will provide new capabilities for highly sensitive measurements of biomolecular binding.\",\n \"corpus_id\": 24366550,\n \"score\": 2\n },\n {\n \"doc_id\": \"20820739\",\n \"title\": \"Nanoelectronic biosensors based on CVD grown graphene.\",\n \"abstract\": \"Graphene, a single-atom-thick and two-dimensional carbon material, has attracted great attention recently. Because of its unique electrical, physical, and optical properties, graphene has great potential to be a novel alternative to carbon nanotubes in biosensing. We demonstrate the use of large-sized CVD grown graphene films configured as field-effect transistors for real-time biomolecular sensing. Glucose or glutamate molecules were detected by the conductance change of the graphene transistor as the molecules are oxidized by the specific redox enzyme (glucose oxidase or glutamic dehydrogenase) functionalized onto the graphene film. This study indicates that graphene is a promising candidate for the development of real-time nanoelectronic biosensors.\",\n \"corpus_id\": 3836668,\n \"score\": 2\n },\n {\n \"doc_id\": \"20976351\",\n \"title\": \"Microwave-assisted synthesis of highly water-soluble graphene towards electrical DNA sensor.\",\n \"abstract\": \"Graphene sheets have the potential for practical applications in electrochemical devices, but their development has been impeded by critical problems with aggregation of graphene sheets. Here, we demonstrated a facile and bottom-up approach for fabrication of DNA sensor device using water-soluble sulfonated reduced graphene oxide (SRGO) sheets via microwave-assisted sulfonation (MAS), showing enhanced sensitivity, reliability, and low detection limit. Key to achieving these performances is the fabrication of the SRGOs, where the MAS method enabled SRGOs to be highly dispersed in water (10 mg mL(-1)) due to the acidic sulfonated groups generated within 3 min of the functionalization reaction. The water-soluble SRGO-DNA (SRGOD) hybrids prepared by electrostatic interactions between a flat single layer of graphene sheets and DNAs are suitable for fabrication of electrical DNA sensor devices because of the unique electrical characteristics of SRGODs. The high sensing performance of SRGOD sensors was demonstrated with detection of DNA hybridization using complementary DNAs, single base mismatched DNAs, and noncomplementary DNAs, with results showing higher sensitivity and lower detection limit than those of reduced graphene oxide-based DNA sensors. Simple and easy fabrication of DNA sensor devices using SRGODs is expected to provide an effective way for electrical detection of DNA hybridization using miniature sensors without the labor-intensive labeling of the sensor and complex measurement equipment.\",\n \"corpus_id\": 39700712,\n \"score\": 2\n },\n {\n \"doc_id\": \"21948419\",\n \"title\": \"Nanowire biosensors for label-free, real-time, ultrasensitive protein detection.\",\n \"abstract\": \"Sensitive and quantitative analysis of proteins is central to disease diagnosis, drug screening, and proteomic studies. Among recent research advances exploiting new nanomaterials for biomolecule analysis, silicon nanowires (SiNWs), which are configured as field-effect transistors (FETs), have emerged as one of the most promising and powerful platforms for label-free, real-time, and highly sensitive electrical detection of proteins as well as many other biological species. Here, we describe a detailed protocol for realizing SiNW biosensors for protein detection that includes SiNW synthesis, FET device fabrication, surface receptor functionalization, and electrical sensing measurements. Moreover, incorporating both p-type and n-type SiNWs in the same sensor array provides a unique means of internal control for sensing signal verification.\",\n \"corpus_id\": 7711328,\n \"score\": 2\n },\n {\n \"doc_id\": \"22089471\",\n \"title\": \"Real-time DNA detection using Pt nanoparticle-decorated reduced graphene oxide field-effect transistors.\",\n \"abstract\": \"A large-area, continuous, few-layer reduced graphene oxide (rGO) thin film has been fabricated on a Si/SiO(2) wafer using the Langmuir-Blodgett (LB) method followed by thermal reduction. After photochemical reduction of Pt nanoparticles (PtNPs) on rGO, the obtained PtNPs/rGO composite is employed as the conductive channel in a solution-gated field effect transistor (FET), which is then used for real-time detection of hybridization of single-stranded DNA (ssDNA) with high sensitivity (2.4 nM). Such a simple, but effective method for fabrication of rGO-based transistors shows great potential for mass-production of graphene-based electronic biosensors.\",\n \"corpus_id\": 5208897,\n \"score\": 2\n },\n {\n \"doc_id\": \"22110861\",\n \"title\": \"Label-free electrical detection of DNA hybridization using carbon nanotubes and graphene.\",\n \"abstract\": \"The interface between biosystems and nanomaterials is emerging for detection of various biomolecules and subtle cellular activities. In particular, the development of cost-effective and sequence-selective DNA detection is urgent for the diagnosis of genetic or pathogenic diseases. Graphene-based nanocarbon materials, such as carbon nanotubes and thin graphene layers, have been employed as biosensors because they are biocompatible, extraordinarily sensitive, and promising for large-area detection. Electrical and label-free detection of DNA can be achieved by monitoring the conductance change of devices fabricated from these carbon materials. Here, the recent advances in this research area are briefly reviewed. The key issues and perspectives of future development are also discussed.\",\n \"corpus_id\": 9516434,\n \"score\": 2\n },\n {\n \"doc_id\": \"22252647\",\n \"title\": \"Increasing the detection speed of an all-electronic real-time biosensor.\",\n \"abstract\": \"Biosensor response time, which depends sensitively on the transport of biomolecules to the sensor surface, is a critical concern for future biosensor applications. We have fabricated carbon nanotube field-effect transistor biosensors and quantified protein binding rates onto these nanoelectronic sensors. Using this experimental platform we test the effectiveness of a protein repellent coating designed to enhance protein flux to the all-electronic real-time biosensor. We observe a 2.5-fold increase in the initial protein flux to the sensor when upstream binding sites are blocked. Mass transport modelling is used to calculate the maximal flux enhancement that is possible with this strategy. Our results demonstrate a new methodology for characterizing nanoelectronic biosensor performance, and demonstrate a mass transport optimization strategy that is applicable to a wide range of microfluidic based biosensors.\",\n \"corpus_id\": 5141243,\n \"score\": 2\n },\n {\n \"doc_id\": \"22635097\",\n \"title\": \"Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors.\",\n \"abstract\": \"Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein-ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein-ligand binding pairs. The rate constant of the association and dissociation of the protein-ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions.\",\n \"corpus_id\": 16109660,\n \"score\": 2\n },\n {\n \"doc_id\": \"22841443\",\n \"title\": \"Step-gate polysilicon nanowires field effect transistor compatible with CMOS technology for label-free DNA biosensor.\",\n \"abstract\": \"Currently, detection of DNA hybridization using fluorescence-based detection technique requires expensive optical systems and complex bioinformatics tools. Hence, the development of new low cost devices that enable direct and highly sensitive detection stimulates a lot of research efforts. Particularly, devices based on silicon nanowires are emerging as ultrasensitive electrical sensors for the direct detection of biological species thanks to their high surface to volume ratio. In this study, we propose innovative devices using step-gate polycrystalline silicon nanowire FET (poly-Si NW FETs), achieved with simple and low cost fabrication process, and used as ultrasensitive electronic sensor for DNA hybridization. The poly-SiNWs are synthesized using the sidewall spacer formation technique. The detailed fabrication procedure for a step-gate NWFET sensor is described in this paper. No-complementary and complementary DNA sequences were clearly discriminated and detection limit to 1 fM range is observed. This first result using this nano-device is promising for the development of low cost and ultrasensitive polysilicon nanowires based DNA sensors compatible with the CMOS technology.\",\n \"corpus_id\": 16598849,\n \"score\": 2\n },\n {\n \"doc_id\": \"22985088\",\n \"title\": \"Enhanced sensing of nucleic acids with silicon nanowire field effect transistor biosensors.\",\n \"abstract\": \"Silicon nanowire (SiNW) field effect transistors (FETs) have emerged as powerful sensors for ultrasensitive, direct electrical readout, and label-free biological/chemical detection. The sensing mechanism of SiNW-FET can be understood in terms of the change in charge density at the SiNW surface after hybridization. So far, there have been limited systematic studies on fundamental factors related to device sensitivity to further make clear the overall effect on sensing sensitivity. Here, we present an analytical result for our triangle cross-section wire for predicting the sensitivity of nanowire surface-charge sensors. It was confirmed through sensing experiments that the back-gated SiNW-FET sensor had the highest percentage current response in the subthreshold regime and the sensor performance could be optimized in low buffer ionic strength and at moderate probe concentration. The optimized SiNW-FET nanosensor revealed ultrahigh sensitivity for rapid and reliable detection of target DNA with a detection limit of 0.1 fM and high specificity for single-nucleotide polymorphism discrimination. In our work, enhanced sensing of biological species by optimization of operating parameters and fundamental understanding for SiNW FET detection limit was obtained.\",\n \"corpus_id\": 207564561,\n \"score\": 2\n },\n {\n \"doc_id\": \"23084065\",\n \"title\": \"Droplet-based microscale colorimetric biosensor for multiplexed DNA analysis via a graphene nanoprobe.\",\n \"abstract\": \"The development of simple and inexpensive DNA detection strategy is very significant for droplet-based microfluidic system. Here, a droplet-based biosensor for multiplexed DNA analysis is developed with a common imaging device by using fluorescence-based colorimetric method and a graphene nanoprobe. With the aid of droplet manipulation technique, droplet size adjustment, droplet fusion and droplet trap are realized accurately and precisely. Due to the high quenching efficiency of graphene oxide (GO), in the absence of target DNAs, the droplet containing two single-stranded DNA probes and GO shows dark color, in which the DNA probes are labeled carboxy fluorescein (FAM) and 6-carboxy-X-rhodamine (ROX), respectively. The droplet changes from dark to bright color when the DNA probes form double helix with the specific target DNAs leading to the dyes far away from GO. This colorimetric droplet biosensor exhibits a quantitative capability for simultaneous detection of two different target DNAs with the detection limits of 9.46 and 9.67×10(-8)M, respectively. It is also demonstrated that this biosensor platform can become a promising detection tool in high throughput applications with low consumption of reagents. Moreover, the incorporation of graphene nanoprobe and droplet technique can drive the biosensor field one more step to some extent.\",\n \"corpus_id\": 24607677,\n \"score\": 2\n },\n {\n \"doc_id\": \"23355762\",\n \"title\": \"Microneedle Biosensor: A Method for Direct Label-free Real Time Protein Detection.\",\n \"abstract\": \"Here we present the development of an array of electrical micro-biosensors in a microfluidic channel, called microneedle biosensors. A microneedle biosensor is a real-time, label-free, direct electrical detection platform, which is capable of high sensitivity detection, measuring the change in ionic current and impedance modulation, due to the presence or reaction of biomolecules such as proteins and nucleic acids. In this study, we successfully fabricated and electrically characterized the sensors and demonstrated successful detection of target protein. In this study, we used biotinylated bovine serum albumin as the receptor and streptavidin as the target analyte.\",\n \"corpus_id\": 42253383,\n \"score\": 2\n },\n {\n \"doc_id\": \"23685314\",\n \"title\": \"A novel graphene-DNA biosensor for selective detection of mercury ions.\",\n \"abstract\": \"A novel electrochemical biosensor for sensitive and selective detection of mercury (II) ions (Hg²⁺) based on a DNA grafted graphene is proposed. Graphene oxide (GO) was reduced by dopamine, and then the single-strand probe DNA modified at the 5'-end with an alkylamino modifier (NH₂-ssDNA) was grafted on the reduced graphene oxide (RGO) surface via Michael addition reaction. In the presence of Hg²⁺, the target DNA with four thymine-thymine (T-T) mismatches would hybridize with the probe DNA on the glassy carbon electrode (GCE) through T-Hg²⁺-T coordination chemistry. The hybridization of the two oligonucleotides leads to the increase in the peak currents of [Ru(NH₃)₆]³⁺, which could be used for electrochemical sensing of Hg²⁺. The difference in the value of the peak currents of [Ru(NH₃)₆]³⁺ before and after DNA hybridization was linear with the concentration of Hg²⁺ in the range from 8.0×10⁻⁹ to 1.0×10⁻⁷ M with a linear coefficiency of 0.996. The detection limit was 5.0×10⁻⁹ M (S/N=3). The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of Hg²⁺. Particularly, the proposed method was applied successfully to the determination of Hg²⁺ in real environmental samples.\",\n \"corpus_id\": 206164843,\n \"score\": 2\n },\n {\n \"doc_id\": \"24517158\",\n \"title\": \"Development of solution-gated graphene transistor model for biosensors.\",\n \"abstract\": \": The distinctive properties of graphene, characterized by its high carrier mobility and biocompatibility, have stimulated extreme scientific interest as a promising nanomaterial for future nanoelectronic applications. In particular, graphene-based transistors have been developed rapidly and are considered as an option for DNA sensing applications. Recent findings in the field of DNA biosensors have led to a renewed interest in the identification of genetic risk factors associated with complex human diseases for diagnosis of cancers or hereditary diseases. In this paper, an analytical model of graphene-based solution gated field effect transistors (SGFET) is proposed to constitute an important step towards development of DNA biosensors with high sensitivity and selectivity. Inspired by this fact, a novel strategy for a DNA sensor model with capability of single-nucleotide polymorphism detection is proposed and extensively explained. First of all, graphene-based DNA sensor model is optimized using particle swarm optimization algorithm. Based on the sensing mechanism of DNA sensors, detective parameters (Ids and Vgmin) are suggested to facilitate the decision making process. Finally, the behaviour of graphene-based SGFET is predicted in the presence of single-nucleotide polymorphism with an accuracy of more than 98% which guarantees the reliability of the optimized model for any application of the graphene-based DNA sensor. It is expected to achieve the rapid, quick and economical detection of DNA hybridization which could speed up the realization of the next generation of the homecare sensor system.\",\n \"corpus_id\": 15653532,\n \"score\": 2\n },\n {\n \"doc_id\": \"24528470\",\n \"title\": \"Ultrasensitive label-free detection of PNA-DNA hybridization by reduced graphene oxide field-effect transistor biosensor.\",\n \"abstract\": \"A reduced graphene oxide (R-GO)-based field-effect transistor (FET) biosensor used for ultrasensitive label-free detection of DNA via peptide nucleic acid (PNA)-DNA hybridization is reported. In this work, R-GO was prepared by reduction of GO with hydrazine, and the FET biosensor was fabricated by drop-casting the R-GO suspension onto the sensor surface. PNA instead of DNA as the capture probe was employed, and DNA detection was performed through PNA-DNA hybridization by the R-GO FET biosensor. The detection limit as low as 100 fM was achieved, which is 1 order of magnitude lower than that of the previously reported graphene FET DNA biosensor based on DNA-DNA hybridization. Moreover, the R-GO FET biosensor was able to distinguish the complementary DNA from one-base mismatched DNA and noncomplementary DNA. Interestingly, the fabricated DNA biosensor was found to have a regeneration capability. The developed R-GO FET DNA biosensor shows ultrasensitivity and high specificity, indicating its potential applications in disease diagnostics as a point-of-care tool.\",\n \"corpus_id\": 24090334,\n \"score\": 2\n },\n {\n \"doc_id\": \"24588742\",\n \"title\": \"MoS₂ field-effect transistor for next-generation label-free biosensors.\",\n \"abstract\": \"Biosensors based on field-effect transistors (FETs) have attracted much attention, as they offer rapid, inexpensive, and label-free detection. While the low sensitivity of FET biosensors based on bulk 3D structures has been overcome by using 1D structures (nanotubes/nanowires), the latter face severe fabrication challenges, impairing their practical applications. In this paper, we introduce and demonstrate FET biosensors based on molybdenum disulfide (MoS2), which provides extremely high sensitivity and at the same time offers easy patternability and device fabrication, due to its 2D atomically layered structure. A MoS2-based pH sensor achieving sensitivity as high as 713 for a pH change by 1 unit along with efficient operation over a wide pH range (3-9) is demonstrated. Ultrasensitive and specific protein sensing is also achieved with a sensitivity of 196 even at 100 femtomolar concentration. While graphene is also a 2D material, we show here that it cannot compete with a MoS2-based FET biosensor, which surpasses the sensitivity of that based on graphene by more than 74-fold. Moreover, we establish through theoretical analysis that MoS2 is greatly advantageous for biosensor device scaling without compromising its sensitivity, which is beneficial for single molecular detection. Furthermore, MoS2, with its highly flexible and transparent nature, can offer new opportunities in advanced diagnostics and medical prostheses. This unique fusion of desirable properties makes MoS2 a highly potential candidate for next-generation low-cost biosensors.\",\n \"corpus_id\": 11444878,\n \"score\": 2\n },\n {\n \"doc_id\": \"24632459\",\n \"title\": \"Simple and label-free electrochemical impedance Amelogenin gene hybridization biosensing based on reduced graphene oxide.\",\n \"abstract\": \"The increasing desire for sensitive, easy, low-cost, and label free methods for the detection of DNA sequences has become a vital matter in biomedical research. For the first time a novel label-free biosensor for sensitive detection of Amelogenin gene (AMEL) using reduced graphene oxide modified glassy carbon electrode (GCE/RGO) has been developed. In this work, detection of DNA hybridization of the target and probe DNA was investigated by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). The optimum conditions were found for the immobilization of probe on RGO surface and its hybridization with the target DNA. CV and EIS carried out in an aqueous solution containing [Fe(CN)6](3-/4-) redox pair have been used for the biosensor characterization. The biosensor has a wide linear range from 1.0×10(-20) to 1.0×10(-14)M with the lower detection limit of 3.2×10(-21)M. Moreover, the present electrochemical detection offers some unique advantages such as ultrahigh sensitivity, simplicity, and feasibility for apparatus miniaturization in analytical tests. The excellent performance of the biosensor is attributed to large surface-to-volume ratio and high conductivity of RGO, which enhances the probe absorption and promotes direct electron transfer between probe and the electrode surface. This electrochemical DNA sensor could be used for the detection of specific ssDNA sequence in real biological samples.\",\n \"corpus_id\": 7405942,\n \"score\": 2\n },\n {\n \"doc_id\": \"25189574\",\n \"title\": \"Electrophoretic and field-effect graphene for all-electrical DNA array technology.\",\n \"abstract\": \"Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.\",\n \"corpus_id\": 1043741,\n \"score\": 2\n },\n {\n \"doc_id\": \"25285529\",\n \"title\": \"A microfluidic-based electrochemical biochip for label-free DNA hybridization analysis.\",\n \"abstract\": \"Miniaturization of analytical benchtop procedures into the micro-scale provides significant advantages in regards to reaction time, cost, and integration of pre-processing steps. Utilizing these devices towards the analysis of DNA hybridization events is important because it offers a technology for real time assessment of biomarkers at the point-of-care for various diseases. However, when the device footprint decreases the dominance of various physical phenomena increases. These phenomena influence the fabrication precision and operation reliability of the device. Therefore, there is a great need to accurately fabricate and operate these devices in a reproducible manner in order to improve the overall performance. Here, we describe the protocols and the methods used for the fabrication and the operation of a microfluidic-based electrochemical biochip for accurate analysis of DNA hybridization events. The biochip is composed of two parts: a microfluidic chip with three parallel micro-channels made of polydimethylsiloxane (PDMS), and a 3 x 3 arrayed electrochemical micro-chip. The DNA hybridization events are detected using electrochemical impedance spectroscopy (EIS) analysis. The EIS analysis enables monitoring variations of the properties of the electrochemical system that are dominant at these length scales. With the ability to monitor changes of both charge transfer and diffusional resistance with the biosensor, we demonstrate the selectivity to complementary ssDNA targets, a calculated detection limit of 3.8 nM, and a 13% cross-reactivity with other non-complementary ssDNA following 20 min of incubation. This methodology can improve the performance of miniaturized devices by elucidating on the behavior of diffusion at the micro-scale regime and by enabling the study of DNA hybridization events.\",\n \"corpus_id\": 41450238,\n \"score\": 2\n },\n {\n \"doc_id\": \"25741743\",\n \"title\": \"Detection of DNA and poly-l-lysine using CVD graphene-channel FET biosensors.\",\n \"abstract\": \"A graphene channel field-effect biosensor is demonstrated for detecting the binding of double-stranded DNA and poly-l-lysine. Sensors consist of chemical vapor deposition graphene transferred using a clean, etchant-free transfer method. The presence of DNA and poly-l-lysine are detected by the conductance change of the graphene transistor. A readily measured shift in the Dirac voltage (the voltage at which the graphene's resistance peaks) is observed after the graphene channel is exposed to solutions containing DNA or poly-l-lysine. The 'Dirac voltage shift' is attributed to the binding/unbinding of charged molecules on the graphene surface. The polarity of the response changes to positive direction with poly-l-lysine and negative direction with DNA. This response results in detection limits of 8 pM for 48.5 kbp DNA and 11 pM for poly-l-lysine. The biosensors are easy to fabricate, reusable and are promising as sensors of a wide variety of charged biomolecules.\",\n \"corpus_id\": 23184478,\n \"score\": 2\n },\n {\n \"doc_id\": \"25770609\",\n \"title\": \"Simple and label-free detection of DNA hybridization on a modified graphene nanosheets electrode.\",\n \"abstract\": \"In this study, an effective method was devised to synthesize amelogenin genes in solution and to amplify electrical detection of DNA hybridization based on graphene nanosheets (GNs) modified glassy carbon electrode (GCE). GNs are well known as effective biocompatible and conductive materials that can provide large surface area and a sufficient numbers of binding points for DNA immobilization. The biosensor fabrication processes and the electrochemical responses of probe immobilization and hybridization with target DNA were investigated by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) using [Fe(CN)6](3-/4-) as an electrochemical redox. Due to minimum nonspecific DNA adsorption, a very high specificity of DNA hybridization was achieved, and the hybridization rate of the target DNA in optimum conditions was increased significantly. With this approach, the target DNA could be quantified in a linear range from 1.0×10(-20) to 1.0×10(-14) mol L(-1) for the first segment and from 1.0×10(-13) to 1.0×10(-6) mol L(-1) for the second segment, with a detection limit of 7.1×10(-21) mol L(-1) by 3s(b). In addition, the biosensor exhibited a high level of stability and repeatability, even for the determination of DNA sequences in real samples without amplification.\",\n \"corpus_id\": 43789026,\n \"score\": 2\n },\n {\n \"doc_id\": \"25853238\",\n \"title\": \"A monocrystal graphene domain biosensor array with differential output for real-time monitoring of glucose and normal saline.\",\n \"abstract\": \"A biosensor array with differential output based on a monocrystal graphene domain is proposed to realize high resolution measurements. The differential output structure can eliminate the noise that comes from graphene crystal orientation and grain boundary, as well as the fluctuation that comes from the contact resistance and experiment process, so as to improve resolution in the lower concentration. We have fabricated a high quality monocrystal graphene domain that has millimeter size by the chemical vapor deposition method. Two identical graphene ribbons that are cut from the same domain are used as field effect transistor source-to-drain channels for the reference and the test of differential output, respectively. The experimental results show that the source-to-drain current has a fast response shorter than 0.5 second in glucose, normal saline and pH buffer solutions of different concentrations. Sensitivity increases exponentially with the increase of concentration of the tested liquid and the high resolution range is 0.01-2 wt% in glucose and 0.0009-0.018 wt% in saline, and the highest resolutions of glucose and saline are 0.01 wt% and 0.0009 wt%, respectively. We have fabricated a 1 × 4 array structure with differential outputs that pave the way for rapidly detecting ultra-low concentration of analytes.\",\n \"corpus_id\": 23145180,\n \"score\": 2\n },\n {\n \"doc_id\": \"25965056\",\n \"title\": \"Ultrarapid and ultrasensitive electrical detection of proteins in a three-dimensional biosensor with high capture efficiency.\",\n \"abstract\": \"The realization of a high-throughput biosensor platform with ultrarapid detection of biomolecular interactions and an ultralow limit of detection in the femtomolar (fM) range or below has been retarded due to sluggish binding kinetics caused by the scarcity of probe molecules on the nanostructures and/or limited mass transport. Here, as a new method for the highly efficient capture of biomolecules at extremely low concentration, we tested a three-dimensional (3D) platform of a bioelectronic field-effect transistor (bio-FET) with vertically aligned and highly dense one-dimensional (1D) ZnO nanorods (NRs) as a sensing surface capped by an ultrathin TiO2 layer for improved electrolytic stability on a chemical-vapor-deposited graphene (Gr) channel. The ultrarapid detection capability with a very fast response time (∼1 min) at the fM level of proteins in the proposed 3D bio-FET is primarily attributed to the fast binding kinetics of the probe-target proteins due to the small diffusion length of the target molecules to reach the sensor surface and the substantial number of probe molecules available on the largely increased surface area of the vertical ZnO NRs. This new 3D electrical biosensor platform can be easily extended to other electrochemical nanobiosensors and has great potential for practical applications in miniaturized biosensor integrated systems.\",\n \"corpus_id\": 19841648,\n \"score\": 2\n },\n {\n \"doc_id\": \"26197105\",\n \"title\": \"A Highly Responsive Silicon Nanowire/Amplifier MOSFET Hybrid Biosensor.\",\n \"abstract\": \"This study demonstrates a hybrid biosensor comprised of a silicon nanowire (SiNW) integrated with an amplifier MOSFET to improve the current response of field-effect-transistor (FET)-based biosensors. The hybrid biosensor is fabricated using conventional CMOS technology, which has the potential advantage of high density and low noise performance. The biosensor shows a current response of 5.74 decades per pH for pH detection, which is 2.5 × 10(5) times larger than that of a single SiNW sensor. In addition, we demonstrate charged polymer detection using the biosensor, with a high current change of 4.5 × 10(5) with a 500 nM concentration of poly(allylamine hydrochloride). In addition, we demonstrate a wide dynamic range can be obtained by adjusting the liquid gate voltage. We expect that this biosensor will be advantageous and practical for biosensor applications which requires lower noise, high speed, and high density.\",\n \"corpus_id\": 509707,\n \"score\": 2\n },\n {\n \"doc_id\": \"26203889\",\n \"title\": \"Fabrication of Ultrasensitive Field-Effect Transistor DNA Biosensors by a Directional Transfer Technique Based on CVD-Grown Graphene.\",\n \"abstract\": \"Most graphene field-effect transistor (G-FET) biosensors are fabricated through a routine process, in which graphene is transferred onto a Si/SiO2 substrate and then devices are subsequently produced by micromanufacture processes. However, such a fabrication approach can introduce contamination onto the graphene surface during the lithographic process, resulting in interference for the subsequent biosensing. In this work, we have developed a novel directional transfer technique to fabricate G-FET biosensors based on chemical-vapor-deposition- (CVD-) grown single-layer graphene (SLG) and applied this biosensor for the sensitive detection of DNA. A FET device with six individual array sensors was first fabricated, and SLG obtained by the CVD-growth method was transferred onto the sensor surface in a directional manner. Afterward, peptide nucleic acid (PNA) was covalently immobilized on the graphene surface, and DNA detection was realized by applying specific target DNA to the PNA-functionalized G-FET biosensor. The developed G-FET biosensor was able to detect target DNA at concentrations as low as 10 fM, which is 1 order of magnitude lower than those reported in a previous work. In addition, the biosensor was capable of distinguishing the complementary DNA from one-base-mismatched DNA and noncomplementary DNA. The directional transfer technique for the fabrication of G-FET biosensors is simple, and the as-constructed G-FET DNA biosensor shows ultrasensitivity and high specificity, indicating its potential application in disease diagnostics as a point-of-care tool.\",\n \"corpus_id\": 206394876,\n \"score\": 2\n },\n {\n \"doc_id\": \"26237346\",\n \"title\": \"Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays.\",\n \"abstract\": \"Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.\",\n \"corpus_id\": 19463367,\n \"score\": 2\n },\n {\n \"doc_id\": \"26367906\",\n \"title\": \"Compact multi-channel surface plasmon resonance sensor for real-time multi-analyte biosensing.\",\n \"abstract\": \"A compact multi-channel surface plasmon resonance (SPR) biosensor is demonstrated based on a tablet as the measurement platform. The SPR biosensor employs a bundle of fiber-optic SPR sensors as the multiplexed sensing elements that are illuminated by a light-emitting diode (LED) plane light source and detected by a cordless camera. The multi-channel SPR biosensor was based on optical fiber components for precise, label-free and high-throughput detection without the use of complex, specialized or fragile instrumentation that would require optical calibration. The reference and control channels compensated for the fluctuation of the LED light source and the bulk refractive index, increasing the accuracy and reliability of the biosensor. The multi-channel SPR biosensor was applied for multi-analyte biosensing of immunoglobulin G (IgG) and concanavalin A (Con A). The channels functionalized with staphylococcal protein A (SPA) and ribonuclease B (RNase B) only showed relative intensity responses to their corresponding analytes. Moreover, the multi-channel SPR sensors responded to the specific detection of IgG and Con A with an approximately linear relative intensity response to the analyte concentration. Hence, multiple analytes were simultaneously and quantitatively detected with the multi-channel SPR biosensor. This compact, cost-effective multi-channel SPR biosensor is adapted for point-of-care tests, which are important in healthcare and environmental monitoring and for biomolecular interaction analysis.\",\n \"corpus_id\": 28490512,\n \"score\": 2\n },\n {\n \"doc_id\": \"26367921\",\n \"title\": \"Micro-capillary-based evanescent field biosensor for sensitive, label-free DNA detection.\",\n \"abstract\": \"We proposed and demonstrated a micro-capillary-based, high-sensitivity evanescent field biosensor for the cost-effective, rapid, and sensitive analysis and detection of specific DNA sequences. By functionalizing the surface of the tubing wall with ssDNA probe sequences, label-free DNA detection is achieved. The wavelength shift response of the surface-functionalized biosensors to DNA hybridization is monitored in real time. Our experiments show that the biosensor can operate at room temperature and is capable of performing label-free hybridization detection, analyte concentration measurement and nucleotide mismatch detection through a single sensing device. The sensor has many advantages, such as a simple manufacturing process, standardized production control, reliable quality, low cost and an economic demodulator. The compact nature and miniature size of the biosensing detection system makes it a good candidate for the rapid and highly sensitive detection of low-concentration analytes in micro-samples for cost-effective, real-time, and on-site analysis in the fields of life science, pharmaceutical chemistry, medical science and criminal investigation.\",\n \"corpus_id\": 34813363,\n \"score\": 2\n },\n {\n \"doc_id\": \"26387446\",\n \"title\": \"Electrochemical DNA biosensor based on a glassy carbon electrode modified with gold nanoparticles and graphene for sensitive determination of Klebsiella pneumoniae carbapenemase.\",\n \"abstract\": \"We describe the fabrication of a sensitive electrochemical DNA biosensor for determination of Klebsiella pneumoniae carbapenemase (KPC). The highly sensitive and selective electrochemical biosensor for DNA detection was constructed based on a glassy carbon electrode (GCE) modified with gold nanoparticles (Au-NPs) and graphene (Gr). Then Au-NPs/Gr/GCE was characterized by scanning electro miroscope (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The hybridization detection was measured by diffierential pulse voltammetry (DPV) using methylene blue (MB) as the hybridization indicator. The dynamic range of detection of the sensor for the target DNA sequences was from 1×10(-12) to 1×10(-7)mol/L, with a detection limit of 2×10(-13)mol/L. The DNA biosensor had excellent specificity for distinguishing complementary DNA sequence in the presence of non-complementary and mismatched DNA sequence. The results demonstrated that the Au-NPs/Gr nanocomposite was a promising substrate for the development of high-performance electrocatalysts for determination of KPC.\",\n \"corpus_id\": 205745928,\n \"score\": 2\n },\n {\n \"doc_id\": \"26445172\",\n \"title\": \"Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.\",\n \"abstract\": \"Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.\",\n \"corpus_id\": 6886645,\n \"score\": 2\n },\n {\n \"doc_id\": \"26709827\",\n \"title\": \"Label-Free Direct Detection of miRNAs with Poly-Silicon Nanowire Biosensors.\",\n \"abstract\": \"BACKGROUND: The diagnostic and prognostic value of microRNAs (miRNAs) in a variety of diseases is promising. The novel silicon nanowire (SiNW) biosensors have advantages in molecular detection because of their high sensitivity and fast response. In this study, poly-crystalline silicon nanowire field-effect transistor (poly-SiNW FET) device was developed to achieve specific and ultrasensitive detection of miRNAs without labeling and amplification. METHODS: The poly-SiNW FET was fabricated by a top-down Complementary Metal Oxide Semiconductor (CMOS) wafer fabrication based technique. Single strand DNA (ssDNA) probe was bind to the surface of the poly-SiNW device which was silanated and aldehyde-modified. By comparing the difference of resistance value before and after ssDNA and miRNA hybridization, poly-SiNW device can be used to detect standard and real miRNA samples. RESULTS: Poly-SiNW device with different structures (different line width and different pitch) was applied to detect standard Let-7b sample with a detection limitation of 1 fM. One-base mismatched sequence could be distinguished meanwhile. Furthermore, these poly-SiNW arrays can detect snRNA U6 in total RNA samples extracted from HepG2 cells with a detection limitation of 0.2 μg/mL. In general, structures with pitch showed better results than those without pitch in detection of both Let-7b and snRNA U6. Moreover, structures with smaller pitch showed better detection efficacy. CONCLUSION: Our findings suggest that poly-SiNW arrays could detect standard and real miRNA sample without labeling or amplification. Poly-SiNW biosensor device is promising for miRNA detection.\",\n \"corpus_id\": 6525566,\n \"score\": 2\n },\n {\n \"doc_id\": \"26780442\",\n \"title\": \"Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids.\",\n \"abstract\": \"The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.\",\n \"corpus_id\": 24914461,\n \"score\": 2\n },\n {\n \"doc_id\": \"26945181\",\n \"title\": \"Label-free in-situ real-time DNA hybridization kinetics detection employing microfiber-assisted Mach-Zehnder interferometer.\",\n \"abstract\": \"A label-free DNA biosensor based on microfiber-assisted Mach-Zehnder interferometer (MAMZI) for in-situ real-time DNA hybridization kinetics detection has been proposed and experimentally demonstrated. A microfiber of hundreds of microns in length is fabricated by tapering a segment of standard single-mode fiber (SMF) to construct the U-shaped microcavity between the lead-in and lead-out SMFs. Thanks to the mode field mismatching between the SMF and microfiber, the incident guided mode light would separate into two beams that respectively propagate in the air microcavity and the microfiber. Consequently, interference between different light modes would occur at the joint between the microfiber and the lead-out SMF. Experimental results indicate that owing to the participation of opening cavity modes in the modal interference process, the interferometric spectrum of our proposed microcavity sensor is highly sensitive to the variation of environmental refractive index (RI), especially for the RI range around 1.34 which is useful for most biological applications. The microfiber functionalization is achieved by stepwise modifying the microfiber with monolayer Poly-l-lysine (PLL) and single-stranded DNA (ssDNA) probes to produce the sensitive surface that could uniquely attach specific target ssDNAs. The fiber surface functionalization as well as DNA hybridization processes have been experimentally investigated for different target ssDNA solutions in real time. The interferometric transmission spectrum shows large wavelength shift for different biological phases, and a detection limit conservatively down to 0.0001pmol/μL has been acquired by employing the U-shaped microcavity of 176.88μm in length. Our proposed DNA biosensor possesses several advantages such as compact size, ease of fabrication, and strong response for DNA hybridization, which make it a promising candidate for potential applications in such rapidly expanding areas as medical diagnosis, cancer screenings, medicine examination and environmental engineering, etc.\",\n \"corpus_id\": 6467190,\n \"score\": 2\n },\n {\n \"doc_id\": \"27298347\",\n \"title\": \"Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.\",\n \"abstract\": \"Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.\",\n \"corpus_id\": 24235375,\n \"score\": 2\n },\n {\n \"doc_id\": \"27532480\",\n \"title\": \"Scalable Production of High-Sensitivity, Label-Free DNA Biosensors Based on Back-Gated Graphene Field Effect Transistors.\",\n \"abstract\": \"Scalable production of all-electronic DNA biosensors with high sensitivity and selectivity is a critical enabling step for research and applications associated with detection of DNA hybridization. We have developed a scalable and very reproducible (>90% yield) fabrication process for label-free DNA biosensors based upon graphene field effect transistors (GFETs) functionalized with single-stranded probe DNA. The shift of the GFET sensor Dirac point voltage varied systematically with the concentration of target DNA. The biosensors demonstrated a broad analytical range and limit of detection of 1 fM for 60-mer DNA oligonucleotide. In control experiments with mismatched DNA oligomers, the impact of the mismatch position on the DNA hybridization strength was confirmed. This class of highly sensitive DNA biosensors offers the prospect of detection of DNA hybridization and sequencing in a rapid, inexpensive, and accurate way.\",\n \"corpus_id\": 13186445,\n \"score\": 2\n },\n {\n \"doc_id\": \"27534818\",\n \"title\": \"Precise and selective sensing of DNA-DNA hybridization by graphene/Si-nanowires diode-type biosensors.\",\n \"abstract\": \"Single-Si-nanowire (NW)-based DNA sensors have been recently developed, but their sensitivity is very limited because of high noise signals, originating from small source-drain current of the single Si NW. Here, we demonstrate that chemical-vapor-deposition-grown large-scale graphene/surface-modified vertical-Si-NW-arrays junctions can be utilized as diode-type biosensors for highly-sensitive and -selective detection of specific oligonucleotides. For this, a twenty-seven-base-long synthetic oligonucleotide, which is a fragment of human DENND2D promoter sequence, is first decorated as a probe on the surface of vertical Si-NW arrays, and then the complementary oligonucleotide is hybridized to the probe. This hybridization gives rise to a doping effect on the surface of Si NWs, resulting in the increase of the current in the biosensor. The current of the biosensor increases from 19 to 120% as the concentration of the target DNA varies from 0.1 to 500 nM. In contrast, such biosensing does not come into play by the use of the oligonucleotide with incompatible or mismatched sequences. Similar results are observed from photoluminescence microscopic images and spectra. The biosensors show very-uniform current changes with standard deviations ranging ~1 to ~10% by ten-times endurance tests. These results are very promising for their applications in accurate, selective, and stable biosensing.\",\n \"corpus_id\": 13766674,\n \"score\": 2\n },\n {\n \"doc_id\": \"27676459\",\n \"title\": \"Scalable Production of Sensor Arrays Based on High-Mobility Hybrid Graphene Field Effect Transistors.\",\n \"abstract\": \"We have developed a scalable fabrication process for the production of DNA biosensors based on gold nanoparticle-decorated graphene field effect transistors (AuNP-Gr-FETs), where monodisperse AuNPs are created through physical vapor deposition followed by thermal annealing. The FETs are created in a four-probe configuration, using an optimized bilayer photolithography process that yields chemically clean devices, as confirmed by XPS and AFM, with high carrier mobility (3590 ± 710 cm(2)/V·s) and low unintended doping (Dirac voltages of 9.4 ± 2.7 V). The AuNP-Gr-FETs were readily functionalized with thiolated probe DNA to yield DNA biosensors with a detection limit of 1 nM and high specificity against noncomplementary DNA. Our work provides a pathway toward the scalable fabrication of high-performance AuNP-Gr-FET devices for label-free nucleic acid testing in a realistic clinical setting.\",\n \"corpus_id\": 23441045,\n \"score\": 2\n },\n {\n \"doc_id\": \"27779853\",\n \"title\": \"Real-Time Monitoring of Nitric Oxide at Single-Cell Level with Porphyrin-Functionalized Graphene Field-Effect Transistor Biosensor.\",\n \"abstract\": \"An ultrasensitive and highly efficient assay for real-time monitoring of nitric oxide (NO) at single-cell level based on a reduced graphene oxide (RGO) and iron-porphyrin-functionalized graphene (FGPCs) field-effect transistor (FET) biosensor is reported. A layer-to-layer assembly of RGO and FGPCs on a prefabricated FET sensor surface through π-π stacking interaction allowed superior electrical conductivity caused by RGO, and highly catalytic specificity induced by metalloporphyrin, ensuring the ultrasensitive and highly specific detection of NO. The results demonstrated that the RGO/FGPCs FET biosensor was capable of real-time monitoring of NO in the range from 1 pM to 100 nM with the limit of detection as low as 1 pM in phosphate-buffered saline (PBS) and 10 pM in the cell medium, respectively. Moreover, the developed biosensor could be used for real-time monitoring of NO released from human umbilical vein endothelial cells (HUVECs) at single-cell level. Along with its miniaturized sizes, ultrasensitive characteristics, and fast response, the FET biosensor is promising as a new platform for potential biological and diagnostic applications.\",\n \"corpus_id\": 13574816,\n \"score\": 2\n },\n {\n \"doc_id\": \"27930344\",\n \"title\": \"Specific detection of biomolecules in physiological solutions using graphene transistor biosensors.\",\n \"abstract\": \"Nanomaterial-based field-effect transistor (FET) sensors are capable of label-free real-time chemical and biological detection with high sensitivity and spatial resolution, although direct measurements in high-ionic-strength physiological solutions remain challenging due to the Debye screening effect. Recently, we demonstrated a general strategy to overcome this challenge by incorporating a biomolecule-permeable polymer layer on the surface of silicon nanowire FET sensors. The permeable polymer layer can increase the effective screening length immediately adjacent to the device surface and thereby enable real-time detection of biomolecules in high-ionic-strength solutions. Here, we describe studies demonstrating both the generality of this concept and application to specific protein detection using graphene FET sensors. Concentration-dependent measurements made with polyethylene glycol (PEG)-modified graphene devices exhibited real-time reversible detection of prostate specific antigen (PSA) from 1 to 1,000 nM in 100 mM phosphate buffer. In addition, comodification of graphene devices with PEG and DNA aptamers yielded specific irreversible binding and detection of PSA in pH 7.4 1x PBS solutions, whereas control experiments with proteins that do not bind to the aptamer showed smaller reversible signals. In addition, the active aptamer receptor of the modified graphene devices could be regenerated to yield multiuse selective PSA sensing under physiological conditions. The current work presents an important concept toward the application of nanomaterial-based FET sensors for biochemical sensing in physiological environments and thus could lead to powerful tools for basic research and healthcare.\",\n \"corpus_id\": 4873583,\n \"score\": 2\n },\n {\n \"doc_id\": \"28299688\",\n \"title\": \"All-Electrical Graphene DNA Sensor Array.\",\n \"abstract\": \"Electrical sensing of biomolecules has been an important pursuit due to the label-free operation and chip-scale construct such sensing modality can enable. In particular, electrical biomolecular sensors based on nanomaterials such as semiconductor nanowires, carbon nanotubes, and graphene have demonstrated high sensitivity, which in the case of nanowires and carbon nanotubes can surpass typical optical detection sensitivity. Among these nanomaterials, graphene is well suited for a practical candidate for implementing a large-scale array of biomolecular sensors, as its two-dimensional morphology is readily compatible with industry standard top-down fabrication techniques. In our recent work published in 2014 Nature Communications, we demonstrated these benefits by creating DNA sensor arrays from chemical vapor deposition (CVD) graphene. The present chapter, which is a review of this recent work, outlines procedures demonstrating the use of individual graphene sites of the array in dual roles--electrophoretic electrodes for site specific probe DNA immobilization and field effect transistor (FET) sensors for detection of target DNA hybridization. The 100 fM detection sensitivity achieved in 7 out of 8 graphene FET sensors in the array combined with the alternative use of the graphene channels as electrophoretic electrodes for probe deposition represent steps toward creating an all-electrical multiplexed DNA array.\",\n \"corpus_id\": 3596254,\n \"score\": 2\n },\n {\n \"doc_id\": \"28448040\",\n \"title\": \"Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms.\",\n \"abstract\": \"Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.\",\n \"corpus_id\": 3792820,\n \"score\": 2\n },\n {\n \"doc_id\": \"28604366\",\n \"title\": \"Flexible electrochemical biosensors based on graphene nanowalls for the real-time measurement of lactate.\",\n \"abstract\": \"We demonstrate a flexible biosensor for lactate detection based on l-lactate oxidase immobilized by chitosan film cross-linked with glutaraldehyde on the surface of a graphene nanowall (GNW) electrode. The oxygen-plasma technique was developed to enhance the wettability of the GNWs, and the strength of the sensor's oxidation response depended on the concentration of lactate. First, in order to eliminate interference from other substances, biosensors were primarily tested in deionized water and displayed good electrochemical reversibility at different scan rates (20-100 mV s(-1)), a large index range (1.0 μM to 10.0 mM) and a low detection limit (1.0 μM) for lactate. Next, these sensors were further examined in phosphate buffer solution (to mimick human body fluids), and still exhibited high sensitivity, stability and flexibility. These results show that the GNW-based lactate biosensors possess important potential for application in clinical analysis, sports medicine and the food industry.\",\n \"corpus_id\": 3699349,\n \"score\": 2\n },\n {\n \"doc_id\": \"29039202\",\n \"title\": \"Nanoelectronic Platform for Ultrasensitive Detection of Protein Biomarkers in Serum using DNA Amplification.\",\n \"abstract\": \"Silicon nanowire field effect transistors (NWFETs) are low noise, low power, ultrasensitive biosensors that are highly amenable to integration. However, using NWFETs to achieve direct protein detection in physiological buffers such as blood serum remains difficult due to Debye screening, nonspecific binding, and stringent functionalization requirements. In this work, we performed an indirect sandwich immunoassay in serum combined with exponential DNA amplification and pH measurement by ultrasensitive NWFET sensors. Measurements of model cytokine interleukin-2 concentrations from <20 fM to >200 pM were demonstrated, surpassing the conventional NWFET urease-based readout. Our approach paves way for future development of universal, highly sensitive, miniaturized, and integrated nanoelectronic devices that can be applied to a wide variety of analytes.\",\n \"corpus_id\": 31825364,\n \"score\": 2\n },\n {\n \"doc_id\": \"29147003\",\n \"title\": \"Real-time wash-free detection of unlabeled PNA-DNA hybridization using discrete FET sensor.\",\n \"abstract\": \"We demonstrate an electrochemical sensor for detection of unlabeled single-stranded DNA using peptide nucleic acid (PNA) probes coupled to the field-effect transistor (FET) gate. The label-free detection relies on the intrinsic charge of the DNA backbone. Similar detection schemes have mainly concentrated on sensitivity improvement with an emphasis on new sensor structures. Our approach focuses on using an extended-gate that separates the FET and the sensing electrode yielding a simple and mass fabricable device. We used PNA probes for efficient hybridization in low salt conditions that is required to avoid the counter ion screening. As a result, significant part of the target DNA lies within the screening length of the sensor. With this, we achieved a wash-free detection where typical gate potential shifts are more than 70 mV with 1 µM target DNA. We routinely obtained a real-time, label- and wash-free specific detection of target DNA in nanomolar concentration with low-cost electronics and the responses were achieved within minutes after introducing targets to the solution. Furthermore, the results suggest that the sensor performance is limited by specificity rather than by sensitivity and using low-cost electronics does not limit the sensor performance in the presented sensor configuration.\",\n \"corpus_id\": 20288207,\n \"score\": 2\n },\n {\n \"doc_id\": \"29308810\",\n \"title\": \"Real-time subcellular imaging based on graphene biosensors.\",\n \"abstract\": \"Non-invasive living cell microscopy in real time is essential for a wide variety of biomedical research. Here, we present a subcellular refractive index imaging technique for living cells based on a graphene biosensor system. Owing to the optical reflectivity differences of graphene to s- and p-polarizations, a 45° generalized-cylindrical-vector-polarized laser beam is employed to demodulate the reflected cylindrical vector beam for differential detecting. Benefitting from the vector beam-enabled common-path graphene biosensor, the imaging spatial resolution and refractive index sensitivity are noticeably improved. Subcellular refractive index mapping of live human colonic cancer cells is perfectly achieved without inducing any cell damage. Furthermore, real-time monitoring of an individual cell is also performed with the disassembly of the cell nucleolus clearly observed. This technique would be a promising tool for the study of living cell morphology, kinetics, and pathology, and for other biomedical research.\",\n \"corpus_id\": 206109960,\n \"score\": 2\n },\n {\n \"doc_id\": \"29355779\",\n \"title\": \"The field effect transistor DNA biosensor based on ITO nanowires in label-free hepatitis B virus detecting compatible with CMOS technology.\",\n \"abstract\": \"In this paper the field-effect transistor DNA biosensor for detecting hepatitis B virus (HBV) based on indium tin oxide nanowires (ITO NWs) in label free approach has been fabricated. Because of ITO nanowires intensive conductance and functional modified surface, the probe immobilization and target hybridization were increased strongly. The high resolution transmission electron microscopy (HRTEM) measurement showed that ITO nanowires were crystalline and less than 50nm in diameter. The single-stranded hepatitis B virus DNA (SS-DNA) was immobilized as probe on the Au-modified nanowires. The DNA targets were measured in a linear concentration range from 1fM to 10µM. The detection limit of the DNA biosensor was about 1fM. The time of the hybridization process for defined single strand was 90min. The switching ratio of the biosensor between \\\"on\\\" and \\\"off\\\" state was ~ 1.1 × 105. For sensing the specificity of the biosensor, non-complementary, mismatch and complementary DNA oligonucleotide sequences were clearly discriminated. The HBV biosensor confirmed the highly satisfied specificity for differentiating complementary sequences from non-complementary and the mismatch oligonucleotides. The response time of the DNA sensor was 37s with a high reproducibility. The stability and repeatability of the DNA biosensor showed that the peak current of the biosensor retained 98% and 96% of its initial response for measurements after three and five weeks, respectively.\",\n \"corpus_id\": 46844411,\n \"score\": 2\n },\n {\n \"doc_id\": \"29696084\",\n \"title\": \"Graphene-based biosensors.\",\n \"abstract\": \"Reliable data obtained from analysis of DNA, proteins, bacteria and other disease-related molecules or organisms in biological samples have become a fundamental and crucial part of human health diagnostics and therapy. The development of non-invasive tests that are rapid, sensitive, specific and simple would allow patient discomfort to be prevented, delays in diagnosis to be avoided and the status of a disease to be followed up. Bioanalysis is thus a progressive discipline for which the future holds many exciting opportunities. The use of biosensors for the early diagnosis of diseases has become widely accepted as a point-of-care diagnosis with appropriate specificity in a short time. To allow a reliable diagnosis of a disease at an early stage, highly sensitive biosensors are required as the corresponding biomarkers are generally expressed at very low concentrations. In the past 50 years, various biosensors have been researched and developed encompassing a wide range of applications. This contrasts the limited number of commercially available biosensors. When it comes to sensing of biomarkers with the required picomolar (pM) sensitivity for real-time sensing of biological samples, only a handful of sensing systems have been proposed, and these are often rather complex and costly. Lately, graphene-based materials have been considered as superior over other nanomaterials for the development of sensitive biosensors. The advantages of graphene-based sensor interfaces are numerous, including enhanced surface loading of the desired ligand due to the high surface-to-volume ratio, excellent conductivity and a small band gap that is beneficial for sensitive electrical and electrochemical read-outs, as well as tunable optical properties for optical read-outs such as fluorescence and plasmonics. In this paper, we review the advances made in recent years on graphene-based biosensors in the field of medical diagnosis.\",\n \"corpus_id\": 13962344,\n \"score\": 2\n },\n {\n \"doc_id\": \"24528665\",\n \"title\": \"Graphene nano-ink biosensor arrays on a microfluidic paper for multiplexed detection of metabolites.\",\n \"abstract\": \"The development of a miniaturized and low-cost platform for the highly sensitive, selective and rapid detection of multiplexed metabolites is of great interest for healthcare, pharmaceuticals, food science, and environmental monitoring. Graphene is a delicate single-layer, two-dimensional network of carbon atoms with extraordinary electrical sensing capability. Microfluidic paper with printing technique is a low cost matrix. Here, we demonstrated the development of graphene-ink based biosensor arrays on a microfluidic paper for the multiplexed detection of different metabolites, such as glucose, lactate, xanthine and cholesterol. Our results show that the graphene biosensor arrays can detect multiple metabolites on a microfluidic paper sensitively, rapidly and simultaneously. The device exhibits a fast measuring time of less than 2 min, a low detection limit of 0.3 μM, and a dynamic detection range of 0.3-15 μM. The process is simple and inexpensive to operate and requires a low consumption of sample volume. We anticipate that these results could open exciting opportunities for a variety of applications.\",\n \"corpus_id\": 21897140,\n \"score\": 1\n },\n {\n \"doc_id\": \"25248104\",\n \"title\": \"Direct ultrasensitive electrical detection of prostate cancer biomarkers with CMOS-compatible n- and p-type silicon nanowire sensor arrays.\",\n \"abstract\": \"Sensitive and quantitative analysis of proteins is central to disease diagnosis, drug screening, and proteomic studies. Here, a label-free, real-time, simultaneous and ultrasensitive prostate-specific antigen (PSA) sensor was developed using CMOS-compatible silicon nanowire field effect transistors (SiNW FET). Highly responsive n- and p-type SiNW arrays were fabricated and integrated on a single chip with a complementary metal oxide semiconductor (CMOS) compatible anisotropic self-stop etching technique which eliminated the need for a hybrid method. The incorporated n- and p-type nanowires revealed complementary electrical response upon PSA binding, providing a unique means of internal control for sensing signal verification. The highly selective, simultaneous and multiplexed detection of PSA marker at attomolar concentrations, a level useful for clinical diagnosis of prostate cancer, was demonstrated. The detection ability was corroborated to be effective by comparing the detection results at different pH values. Furthermore, the real-time measurement was also carried out in a clinically relevant sample of blood serum, indicating the practicable development of rapid, robust, high-performance, and low-cost diagnostic systems.\",\n \"corpus_id\": 12743382,\n \"score\": 1\n },\n {\n \"doc_id\": \"25790830\",\n \"title\": \"Multiplex serum cytokine immunoassay using nanoplasmonic biosensor microarrays.\",\n \"abstract\": \"Precise monitoring of the rapidly changing immune status during the course of a disease requires multiplex analysis of cytokines from frequently sampled human blood. However, the current lack of rapid, multiplex, and low volume assays makes immune monitoring for clinical decision-making (e.g., critically ill patients) impractical. Without such assays, immune monitoring is even virtually impossible for infants and neonates with infectious diseases and/or immune mediated disorders as access to their blood in large quantities is prohibited. Localized surface plasmon resonance (LSPR)-based microfluidic optical biosensing is a promising approach to fill this technical gap as it could potentially permit real-time refractometric detection of biomolecular binding on a metallic nanoparticle surface and sensor miniaturization, both leading to rapid and sample-sparing analyte analysis. Despite this promise, practical implementation of such a microfluidic assay for cytokine biomarker detection in serum samples has not been established primarily due to the limited sensitivity of LSPR biosensing. Here, we developed a high-throughput, label-free, multiarrayed LSPR optical biosensor device with 480 nanoplasmonic sensing spots in microfluidic channel arrays and demonstrated parallel multiplex immunoassays of six cytokines in a complex serum matrix on a single device chip while overcoming technical limitations. The device was fabricated using easy-to-implement, one-step microfluidic patterning and antibody conjugation of gold nanorods (AuNRs). When scanning the scattering light intensity across the microarrays of AuNR ensembles with dark-field imaging optics, our LSPR biosensing technique allowed for high-sensitivity quantitative cytokine measurements at concentrations down to 5-20 pg/mL from a 1 μL serum sample. Using the nanoplasmonic biosensor microarray device, we demonstrated the ability to monitor the inflammatory responses of infants following cardiopulmonary bypass (CPB) surgery through tracking the time-course variations of their serum cytokines. The whole parallel on-chip assays, which involved the loading, incubation, and washing of samples and reagents, and 10-fold replicated multianalyte detection for each sample using the entire biosensor arrays, were completed within 40 min.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26435280\",\n \"title\": \"Escherichia coli bacteria detection by using graphene-based biosensor.\",\n \"abstract\": \"Graphene is an allotrope of carbon with two-dimensional (2D) monolayer honeycombs. A larger detection area and higher sensitivity can be provided by graphene-based nanosenor because of its 2D structure. In addition, owing to its special characteristics, including electrical, optical and physical properties, graphene is known as a more suitable candidate compared to other materials used in the sensor application. A novel model employing a field-effect transistor structure using graphene is proposed and the current-voltage (I-V) characteristics of graphene are employed to model the sensing mechanism. This biosensor can detect Escherichia coli (E. coli) bacteria, providing high levels of sensitivity. It is observed that the graphene device experiences a drastic increase in conductance when exposed to E. coli bacteria at 0-10(5) cfu/ml concentration. The simple, fast response and high sensitivity of this nanoelectronic biosensor make it a suitable device in screening and functional studies of antibacterial drugs and an ideal high-throughput platform which can detect any pathogenic bacteria. Artificial neural network and support vector regression algorithms have also been used to provide other models for the I-V characteristic. A satisfactory agreement has been presented by comparison between the proposed models with the experimental data.\",\n \"corpus_id\": 20825513,\n \"score\": 1\n },\n {\n \"doc_id\": \"29630304\",\n \"title\": \"Graphene Based Biosensor Model for Escherichia Coli Bacteria Detection.\",\n \"abstract\": \"As a new nanomaterial, graphene demonstrates great potential as an electrode for biomedical applications in sensing molecules and cells. Thus, development of biosensors based on graphene is gaining much interest due to its exceptional properties such as, large surface-to-volume ratio, high conductivity and high flexibility. In this work a liquid gated graphene field effect transistor based biosensor model is analytically developed for electrical detection of Escherichia Coli O157:H7 bacteria. The effect of graphene functionalization on the graphene conductance in the presence of E. coli is investigated. E. coli absorption effects on the graphene surface in the form of conductance variation are considered. Therefore the graphene conductance as a function of E. coli concentration which controls the current–voltage characteristics of biosensors is presented. According to the simulated results, the proposed sensor model can be applied as a powerful tool to predict the biosensor performance.\",\n \"corpus_id\": 4804887,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":79,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24905476\",\n \"title\": \"Quantifying ligand-receptor interactions for gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer's disease.\",\n \"abstract\": \"There is a need for continued development of acetylcholinesterase (AChE) inhibitors that could prolong the life of acetylcholine in the synaptic cleft and also prevent the aggregation of amyloid peptides associated with Alzheimer's disease. The lack of a 3D-QSAR model which specifically deconvulates the type of interactions and quantifies them in terms of energies has motivated us to report a CoRIA model vis-à-vis the standard 3D-QSAR methods, CoMFA and CoMSIA. The CoRIA model was found to be statistically superior to the CoMFA and CoMSIA models and it could efficiently extract key residues involved in ligand recognition and binding to AChE. These interactions were quantified to gauge the magnitude of their contribution to the biological activity. In order to validate the CoRIA model, a pharmacophore map was first constructed and then used to virtually screen public databases, from which novel scaffolds were cherry picked that were not present in the training set. The biological activities of these novel molecules were then predicted by the CoRIA, CoMFA, and CoMSIA models. The hits identified were purchased and their biological activities were measured by the Ellman's method for AChE inhibition. The predicted activities are in unison with the experimentally measured biological activities.\",\n \"corpus_id\": 22408188\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18219446","title":"A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants.","abstract":"Quantitative Structure-Activity Relationships (QSAR) are being used since decades for prediction of biological activity, lead optimization, classification, identification and explanation of the mechanisms of drug action, and prediction of novel structural leads in drug discovery. Though the technique has lived up to its expectations in many aspects, much work still needs to be done in relation to problems related to the rational design of peptides. Peptides are the drugs of choice in many situations, however, designing them rationally is a complicated task and the complexity increases with the length of their sequence. In order to deal with the problem of peptide optimization, one of our recently developed QSAR formalisms CoRIA (Comparative Residue Interaction Analysis) is being expanded and modified as: reverse-CoRIA (rCoRIA) and mixed-CoRIA (mCoRIA) approaches. In these methodologies, the peptide is fragmented into individual units and the interaction energies (van der Waals, Coulombic and hydrophobic) of each amino acid in the peptide with the receptor as a whole (rCoRIA) and with individual active site residues in the receptor (mCoRIA) are calculated, which along with other thermodynamic descriptors, are used as independent variables that are correlated to the biological activity by chemometric methods. As a test case, the three CoRIA methodologies have been validated on a dataset of diverse nonamer peptides that bind to the Class I major histocompatibility complex molecule HLA-A*0201, and for which some structure activity relationships have already been reported. The different models developed, and validated both internally as well as externally, were found to be robust with statistically significant values of r(2) (correlation coefficient) and r(2)(pred) (predictive r(2)). These models were able to identify all the structure activity relationships known for this class of peptides, as well uncover some new relationships. This means that these methodologies will perform well for other peptide datasets too. The major advantage of these approaches is that they explicitly utilize the 3D structures of small molecules or peptides as well as their macromolecular targets, to extract position-specific information about important interactions between the ligand and receptor, which can assist the medicinal and computational chemists in designing new molecules, and biologists in studying the influence of mutations in the target receptor on ligand binding.","corpus_id":11465528,"score":2},{"doc_id":"18515163","title":"An investigation of structurally diverse carbamates for acetylcholinesterase (AChE) inhibition using 3D-QSAR analysis.","abstract":"In order to identify the essential structural features and physicochemical properties for acetylcholinesterase (AChE) inhibitory activity in some carbamate derivatives, the systematic QSAR (Quantitative Structure Activity Relationship) studies (CoMFA, advance CoMFA and CoMSIA) have been carried out on a series of (total 78 molecules) taking 52 and 26 molecules in training and test set, respectively. Statistically significant 3D-QSAR (three-dimensional Quantitative Structure Activity Relationship) models were developed on training set molecules using CoMFA and CoMSIA and validated against test set compounds. The highly predictive models (CoMFA q(2)=0.733, r(2)=0.967, predictive r(2)=0.732, CoMSIA q(2)=0.641, r(2)=0.936, predictive r(2)=0.812) well explained the variance in binding affinities both for the training and the test set compounds. The generated models suggest that steric, electrostatic and hydrophobic interactions play an important role in describing the variation in binding affinity. In particular the carbamoyl nitrogen should be more electropositive; substitutions on this nitrogen should have high steric bulk and hydrophobicity while the amino nitrogen should be electronegative in order to have better activity. These studies may provide important insights into structural variations leading to the development of novel AChE inhibitors which may be useful in the development of novel molecules for the treatment of Alzheimer's disease.","corpus_id":5354346,"score":2},{"doc_id":"18630262","title":"Construction of the pharmacophore model of acetylcholinesterase inhibitor.","abstract":"Based on ninety three acetylcholinesterase inhibitors (AChEIs) which have the same mechanism of action but are different in structural characteristics, the pharmacophore model for acetylcholinesterase inhibitor was constructed by the CATALYST system. The optimal pharmacophore model with three hydrophobic units, a ring aromatic unit and a hydrogen-bond acceptor unit were confirmed (Weight = 3.29, RMS = 0.53, total cost-null cost = 62.75, Correl = 0.93, Config = 19.05). This pharmacophore model will act on the double active site of acetylcholinesterase and is able to predict the activity of known acetylcholinesterase inhibitors that are used for clinical treatment of Alzheimer's disease (AD), and can be further used to identify structurally diverse compounds that have higher activity treating with Alzheimer's disease (AD) by virtual screening.","corpus_id":28648492,"score":2},{"doc_id":"18855672","title":"Acetylcholinesterase inhibitors as disease-modifying therapies for Alzheimer's disease.","abstract":"The therapeutic arsenal for the treatment of Alzheimer's disease (AD) remains confined to a group of four inhibitors of AChE and one NMDA receptor antagonist, which are used to provide a relief of the very late symptoms of the dementia, i.e. the cognitive and functional decline. In line with the growing body of evidence of the pivotal role of the beta-amyloid peptide (Abeta) in the pathogenesis of AD, alternative classes of drugs targeting mainly the formation or the aggregation of Abeta are actively pursued by the pharmaceutical industry, as they could positively modify the course of AD, stopping or slowing down disease progression. While the first amyloid-directed disease-modifying drugs go ahead with their clinical development and could reach the market as soon as 2009, mounting preclinical and clinical evidences is pointing towards a disease-modifying role also for currently marketed anti-Alzheimer AChE inhibitors (AChEIs), particularly for donepezil. In this review, the neuroprotective effects exhibited by currently commercialized AChEIs will be briefly discussed, together with the secondary mechanisms through which they could exert such effects. This review will focus also on particular classes of AChEIs, namely dual binding site AChEIs, which are being purposely designed to target Abeta aggregation and / or other biological targets that contribute to AD pathogenesis, thus constituting very promising disease-modifying anti-Alzheimer drug candidates.","corpus_id":12235312,"score":2},{"doc_id":"19048312","title":"Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA).","abstract":"Since the recognition of HIV-1 integrase as a novel and rational target for HIV therapeutics, remarkable progress has been made in the development of integrase inhibitors. Computational techniques have played a critical role in accelerating research in this area. However, most previous computational studies were based solely on ligand information. In the present work, we describe the application of one of our recently developed receptor-based 3D-quantitative structure activity relationships (QSAR) methods, i.e. comparative residue interaction analysis (CoRIA), in exploring the events involved in ligand-integrase binding. In this methodology, the non-bonded interaction energies (van der Waals and Coulombic) of the inhibitors with individual active site residues of the integrase enzyme are calculated and, along with other thermodynamic descriptors, are correlated with biological activity using chemometric methods. Different combinations of descriptors were used to develop three types of QSAR models, all of which were found to be statistically significant by internal and external validation. This is the first report of such a dedicated receptor-based 3D-QSAR approach being applied to comprehend the integrase-inhibitor recognition process. In addition, the study was performed on 13-different series of inhibitors, thereby exploring the most structurally diverse data set ever used in understanding the inhibition of HIV-1 integrase. The major advantage of this technique is that it can quantitatively extract crucial residues and identify the nature of interactions between the ligand and receptor that modulate activity. The models suggest that Asp64, Thr66, Val77, Asp116, Glu152 and Lys159 are the key residues influencing the binding of ligands with the integrase enzyme, and the majority of these results are in line with earlier studies. The approach facilitates easy lead-to-hit conversion and design of novel inhibitors by optimisation of the interaction of ligands with these specific residues of the integrase enzyme.","corpus_id":21343788,"score":2},{"doc_id":"19441865","title":"Consensus superiority of the pharmacophore-based alignment, over maximum common substructure (MCS): 3D-QSAR studies on carbamates as acetylcholinesterase inhibitors.","abstract":"In view of the nonavailability of complete X-ray structure of carbamates cocrystallized with AChE enzyme, the 3D-QSAR model development based on cocrystallized conformer (CCBA) as well as docked conformer-based alignment (DCBA) is not feasible. Therefore, the only two alternatives viz. pharmacophore and maximum common substructure-based alignments are left for the 3D-QSAR comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) model development. So, in the present study, the 3D-QSAR models have been developed using both alignment methods, where CoMFA and CoMSIA models based on pharmacophore-based alignment were in good agreement with each other and demonstrated significant superiority over MCS-based alignment in terms of leave-one-out (LOO) cross-validated q(2) values of 0.573 and 0.723 and the r(2) values of 0.972 and 0.950, respectively. The validation of the best CoMFA and CoMSIA models based on pharmacophore (Hip-Hop)-based alignment on a test set of 17 compounds provided significant predictive r(2) [r(2)(pred(test))] of 0.614 and 0.788, respectively. The contour map analyses revealed the relative importance of steric, electrostatic, and hydrophobicity for AChE inhibition activity. However, hydrophobic factor plays a major contribution to the AChE inhibitory activity modulation which is in strong agreement with the fact that the AChE is having a wide active site gorge (approximately 20 A) occupied by a large number of hydrophobic amino acid residues.","corpus_id":18436858,"score":2},{"doc_id":"20580236","title":"Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors.","abstract":"Following indications from pharmacophore-based virtual screening of natural product databases, morphinan and isoquinoline compounds were tested in vitro for acetylcholinesterase (AChE) inhibition. After the first screen, active and inactive compounds were used to build a ligand-based pharmacophore model in order to prioritize compounds for biological testing. Among the virtual hits tested, the enrichment of actives was significantly higher than in a random selection of test compounds. The most active compounds were biochemically tested for their activity on mu, delta, and kappa opioid receptors.","corpus_id":43105539,"score":2},{"doc_id":"21074294","title":"Receptor-dependent (RD) 3D-QSAR approach of a series of benzylpiperidine inhibitors of human acetylcholinesterase (HuAChE).","abstract":"Acetylcholine inhibitors (AChEIs) are currently considered as potential drugs for treating Alzheimer disease. In this work, we developed a receptor-dependent 3D-QSAR (RD-3D-QSAR) models based on a series of 60 benzylpiperidine inhibitors of human acetylcholinesterase to support the design of new AChEIs. The best two models, A-F (N = 47, q(2) = 0.736, r(2) = 0.860) and C-F (N = 47, q(2) = 0.753, r(2) = =0.900) were developed and validated by a combined GA-PLS approach, available in WOLF. Residues of the aromatic gorge (Tyr341 and Trp439) and catalytic triad (His447) are related to both equations showing the consistency of these models with the SAR. Based on those models we have proposed four new benzylpiperidine derivatives and predicted the pIC(50) for each molecule. The good predicted potency of benzylpiperidine derivative, IIa, indicates that it is a potential candidate as a new HuAChE inhibitor.","corpus_id":2351356,"score":2},{"doc_id":"21251245","title":"The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies.","abstract":"BACKGROUND: Alzheimer's disease (AD) is the most common cause of dementia characterized by progressive cognitive impairment in the elderly people. The most dramatic abnormalities are those of the cholinergic system. Acetylcholinesterase (AChE) plays a key role in the regulation of the cholinergic system, and hence, inhibition of AChE has emerged as one of the most promising strategies for the treatment of AD. METHODS: In this study, we suggest a workflow for the identification and prioritization of potential compounds targeted against AChE. In order to elucidate the essential structural features for AChE, three-dimensional pharmacophore models were constructed using Discovery Studio 2.5.5 (DS 2.5.5) program based on a set of known AChE inhibitors. RESULTS: The best five-features pharmacophore model, which includes one hydrogen bond donor and four hydrophobic features, was generated from a training set of 62 compounds that yielded a correlation coefficient of R = 0.851 and a high prediction of fit values for a set of 26 test molecules with a correlation of R² = 0.830. Our pharmacophore model also has a high Güner-Henry score and enrichment factor. Virtual screening performed on the NCI database obtained new inhibitors which have the potential to inhibit AChE and to protect neurons from Aβ toxicity. The hit compounds were subsequently subjected to molecular docking and evaluated by consensus scoring function, which resulted in 9 compounds with high pharmacophore fit values and predicted biological activity scores. These compounds showed interactions with important residues at the active site. CONCLUSIONS: The information gained from this study may assist in the discovery of potential AChE inhibitors that are highly selective for its dual binding sites.","corpus_id":9421995,"score":2},{"doc_id":"21516778","title":"[Molecular modeling of acetylcholinesterase interaction with irreversible and reversible organophosphorous inhibitors].","abstract":"Three-dimensional Quantitative Structure-Activity Relationship models were designed for irreversible and reversible acetylcholinesterase inhibitors by molecular modeling methods. In case of irreversible inhibitors CoMFA (the comparative analysis of molecular fields) or CoMSIA (the comparative analysis of indexes of molecular similarity) descriptors together with HYBOT 3D fields provide more statistically valid 3D-QSAR models. This indicates importance of donor-acceptor interactions for irreversible acetylcholinesterase inhibition. In case of reversible organophosphorous inhibitors good quality model for structure-activity relationships was developed using CoMFA fields. The obtained models have good predictive power and can be used for estimation of new organophosphorous compounds inhibitor activity that in turn correlates with toxicity of these compounds.","corpus_id":32203629,"score":2},{"doc_id":"21707398","title":"In silico design and search for acetylcholinesterase inhibitors in Alzheimer's disease with a suitable pharmacokinetic profile and low toxicity.","abstract":"Alzheimer's disease is a complex neurodegenerative disorder of the central nervous system, characterized by amyloid-β deposits, τ-protein aggregation, oxidative stress and reduced levels of acetylcholine in the brain. One pharmacological approach is to restore acetylcholine level by inhibiting acetylcholinesterase (AChE) with reversible inhibitors, such as galanthamine, thus helping to improve the cognitive symptoms of the disease. In order to design new galanthamine derivatives and search for novel, potential inhibitors with improved interactions, as well as a suitable pharmacokinetic profile and low toxicity, several molecular modeling techniques were applied. These techniques included the investigation of AChE-drug complexes (1QT1 and 1ACJ Protein Data Bank codes), ligand-binding sites calculation within the active site of the enzyme, pharmacophore perception of galanthamine derivatives, virtual screening, toxicophorical analysis and estimation of pharmacokinetics properties. A total of four galanthamine derivatives having a N-alkyl-phenyl chain were designed, since the tertiary amine substituents could reach the peripheral anionic site that is not occupied by galanthamine. In addition, 12 drug-like compounds from the Ilibdiverse database were selected by virtual screening as novel, hypothetical AChE inhibitors. The toxicophorical analysis revealed that only four proposed inhibitors have chemical groups able to develop mutagenicity and chromosome damage. The remaining compounds showed only mild or none toxicophorical alerts. At least three screened compounds presented theoric parameters consistent with good oral bioavailability. The designed molecules have the potential to become new lead compounds that might guide the design of drugs with optimized pharmacodynamic and pharmacokinetic properties in order to improve the treatment of Alzheimer's disease by creating new pharmacotherapeutic options.","corpus_id":34580333,"score":2},{"doc_id":"22257528","title":"A review on coumarins as acetylcholinesterase inhibitors for Alzheimer's disease.","abstract":"Acetylcholinesterase (AChE) enzyme inhibition is an important target for the management of Alzheimer disease (AD) and AChE inhibitors are the main stay drugs for its management. Coumarins are the phytochemicals with wide range of biological activities including AChE inhibition. The scientists have attempted to explore the coumarin template for synthesizing novel AChE inhibitors with additional pharmacological activities including decrease in beta-amyloid (Aβ) deposition and beta-secretase inhibition that are also important for AD management. Most of the designed schemes have involved incorporation of a catalytic site interacting moiety at 3- and 4-positions of the coumarin ring. The present review describes these differently synthesized coumarin derivatives as AChE inhibitors for management of AD.","corpus_id":35709216,"score":2},{"doc_id":"22303974","title":"QSAR applications during last decade on inhibitors of acetylcholinesterase in Alzheimer's disease.","abstract":"This article reviews multi-criteria QSAR applications on Acetylcholinesterase inhibitors as palliative drugs for Alzheimer's Disease, published in the period 2001-2011. It includes QSAR models for different series of compounds, comparative studies, and advances in methodologies. This period is marked by a shift in focus from palliative treatment to pathogenesis. However, we believe that research into palliative treatment should continue. More comparative studies are desirable. In order to facilitate comparative and general studies on Acetylcholinesterase inhibitors, a standard experimental protocol for measuring an inhibitor's potency is needed. Finally, we recommend chemists to work closely with system and molecular biologists.","corpus_id":9649185,"score":2},{"doc_id":"22996404","title":"Molecular docking and receptor-specific 3D-QSAR studies of acetylcholinesterase inhibitors.","abstract":"The reversible inhibition of acetylcholinesterase (AChE) has become a promising target for the treatment of Alzheimer's disease (AD) which is mainly associated with low in vivo levels of acetylcholine (ACh). The availability of AChE crystal structures with and without a ligand triggered the effort to find a structure-based design of acetylcholinesterase inhibitors (AChEIs) for AD. The major problem observed with the structure-based design was the feeble robustness of the scoring functions toward the correlation of docking scores with inhibitory potencies of known ligands. This prompted us to develop new prediction models using the stepwise regression analysis based on consensus of different docking and their scoring methods (GOLD, LigandFit, and GLIDE). In the present investigation, a dataset of 91 molecules belonging to 9 different structural classes of heterocyclic compounds with an activity range of 0.008 to 281,000 nM was considered for docking studies and development of AChE-specific 3D-QSAR models. The model (M1) developed using consensus of docking scores of scoring functions viz. Glide score, Gold score, Chem score, ASP score, PMF score, and DOCK score was found to be the best (R(2) = 0.938, Q(2) = 0.925, R(pred)(2) = 0.919, R(2)m((overall)) = 0.936) compared to other consensus models. Docking studies revealed that the molecules with proper alignment in the active site gorge and the ability to interact with all the crucial amino acid residues, in particular by forming π-π stacking interactions with Trp84 at the catalytic anionic site (CAS) and Trp279 at peripheral anionic site (PAS), showed augmented potencies with consequent improvement in patient cognition and reduced the formation of senile plaques associated with AD. Further, the descriptors that signify the association of the ligands with the receptor as well as ADME properties of the ligands were also analyzed by means of the set of ligands that have been pre-positioned with respect to a receptor after docking analysis and considered as independent variables to generate a linear model (M3 and M4) using a stepwise multiple linear regression method to get additional insight into the physicochemical requirements for effective binding of ligands with AChE as well as for prediction of AChE inhibition. The developed AChE-specific prediction models (M1-M4) satisfactorily reflect the structure-activity relationship of the existing AChEIs and have all the potential to facilitate the process of design and development of new potent AChEIs.","corpus_id":16282405,"score":2},{"doc_id":"23073222","title":"The 3D-QSAR study of 110 diverse, dual binding, acetylcholinesterase inhibitors based on alignment independent descriptors (GRIND-2). The effects of conformation on predictive power and interpretability of the models.","abstract":"The 3D-QSAR analysis based on alignment independent descriptors (GRIND-2) was performed on the set of 110 structurally diverse, dual binding AChE reversible inhibitors. Three separate models were built, based on different conformations, generated following next criteria: (i) minimum energy conformations, (ii) conformation most similar to the co-crystalized ligand conformation, and (iii) docked conformation. We found that regardless on conformation used, all the three models had good statistic and predictivity. The models revealed the importance of protonated pyridine nitrogen of tacrine moiety for anti AChE activity, and recognized HBA and HBD interactions as highly important for the potency. This was revealed by the variables associated with protonated pyridinium nitrogen, and the two amino groups of the linker. MIFs calculated with the N1 (pyridinium nitrogen) and the DRY GRID probes in the AChE active site enabled us to establish the relationship between amino acid residues within AChE active site and the variables having high impact on models. External predictive power of the models was tested on the set of 40 AChE reversible inhibitors, most of them structurally different from the training set. Some of those compounds were tested on the different enzyme source. We found that external predictivity was highly sensitive on conformations used. Model based on docked conformations had superior predictive ability, emphasizing the need for the employment of conformations built by taking into account geometrical restrictions of AChE active site gorge.","corpus_id":6729282,"score":2},{"doc_id":"23353586","title":"Identification of potential bivalent inhibitors from natural compounds for acetylcholinesterase through in silico screening using multiple pharmacophores.","abstract":"The symptomatic cure observed in the treatment of Alzheimer's disease (AD) by FDA approved drugs could possibly be due to their specificity against the active site of acetylcholinesterase (AChE) and not by targeting its pathogenicity. The AD pathogenicity involved in AChE protein is mainly due to amyloid beta peptide aggregation, which is triggered specifically by peripheral anionic site (PAS) of AChE. In the present study, a workflow has been developed for the identification and prioritization of potential compounds that could interact not only with the catalytic site but also with the PAS of AChE. To elucidate the essential structural elements of such inhibitors, pharmacophore models were constructed using PHASE, based on a set of fifteen best known AChE inhibitors. All these models on validation were further restricted to the best seven. These were transferred to PHASE database screening platform for screening 89,425 molecules deposited at the \"ZINC natural product database\". Novel lead molecules retrieved were subsequently subjected to molecular docking and ADME profiling. A set of 12 compounds were identified with high pharmacophore fit values and good predicted biological activity scores. These compounds not only showed higher affinity for catalytic residues, but also for Trp86 and Trp286, which are important, at PAS of AChE. The knowledge gained from this study, could lead to the discovery of potential AChE inhibitors that are highly specific for AD treatment as they are bivalent lead molecules endowed with dual binding ability for both catalytic site and PAS of AChE.","corpus_id":24103449,"score":2},{"doc_id":"23777291","title":"Acetylcholinesterase inhibitors: structure based design, synthesis, pharmacophore modeling, and virtual screening.","abstract":"Acetylcholinesterase (AChE) is a main drug target, and its inhibitors have demonstrated functionality in the symptomatic treatment of Alzheimer's disease (AD). In this study, a series of novel AChE inhibitors were designed and their inhibitory activity was evaluated with 2D quantitative structure-activity relationship (QSAR) studies using a training set of 20 known compounds for which IC₅₀ values had previously been determined. The QSAR model was calculated based on seven unique descriptors. Model validation was determined by predicting IC₅₀ values for a test set of 20 independent compounds with measured IC₅₀ values. A correlation analysis was carried out comparing the statistics of the measured IC₅₀ values with predicted ones. These selectivity-determining descriptors were interpreted graphically in terms of principal component analyses (PCA). A 3D pharmacophore model was also created based on the activity of the training set. In addition, absorption, distribution, metabolism, and excretion (ADME) descriptors were also determined to evaluate their pharmacokinetic properties. Finally, molecular docking of these novel molecules into the AChE binding domain indicated that three molecules (6c, 7c, and 7h) should have significantly higher affinities and solvation energies than the known standard drug donepezil. The docking studies of 2H-thiazolo[3,2-a]pyrimidines (6a-6j) and 5H-thiazolo[3,2-a] pyrimidines (7a-7j) with human AChE have demonstrated that these ligands bind to the dual sites of the enzyme. Simple and ecofriendly syntheses and diastereomeric crystallizations of 2H-thiazolo [3,2-a]pyrimidines and 5H-thiazolo[3,2-a] pyrimidines are described. The solid-state structures for the HBr salts of compounds 6a, 6e, 7a, and 7i have been determined using single-crystal X-ray diffraction techniques, and X-ray powder patterns were measured for the bulk solid remaining after solvent was removed from solutions containing 6a and 7a. These studies provide valuable insight for designing more potent and selective inhibitors for the treatment of AD.","corpus_id":11205381,"score":2},{"doc_id":"24010934","title":"CoMFA, CoMSIA and HQSAR studies of acetylcholinesterase inhibitors.","abstract":"A quantitative structure-activity relationship (QSAR) study has been carried out on acetylcholinesterase (AChE) inhibitors with comparative field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram quantitative structure-activity relationship (HQSAR). In order to investigate the effect of alignment on modeling and find out the best alignment strategy, three different alignment rules were applied to generate CoMFA and CoMSIA models. Statistical results of the highly significant models (CoMFA q² = 0.748, r² =0.996, predicted r² =0.789; CoMSIA q² =0.755, r² =0.973, predicted r² = 0.706; HQSAR q² = 0.884, r² = 0.973, predicted r² = 0.734) reveal considerable predictive ability. Analysis of the contour maps of CoMFA and CoMSIA models and the atomic contribution maps of HQSAR model may contribute to develop novel and potential AChE inhibitors.","corpus_id":39548895,"score":2},{"doc_id":"24325852","title":"Pharmacophore mapping-based virtual screening followed by molecular docking studies in search of potential acetylcholinesterase inhibitors as anti-Alzheimer's agents.","abstract":"Alzheimer's disease (AD) is turning out to be one of the lethal diseases in older people. Acetylcholinesterase (AChE) is a crucial target in designing of drugs against AD. The present in silico study was carried out to explore natural compounds as potential AChE inhibitors. Virtual screening, via drug-like ADMET filter, best pharmacophore model and molecular docking analyses, has been utilized to identify putative novel AChE inhibitors. The InterBioScreen's Natural Compound (NC) database was first filtered by applying drug-like ADMET properties and then with the pharmacophore-based virtual screening followed by molecular docking analyses. Based on docking score, interaction patterns and calculated activity, the final hits were selected and these consist of coumarin and non-coumarin classes of compounds. Few hits were found to have been already reported for their AChE inhibitory activity in different literatures confirming reliability of our pharmacophore model. The remaining hits are suggested to be potential AChE inhibitors for AD.","corpus_id":2421305,"score":2},{"doc_id":"24657052","title":"Quinolone-benzylpiperidine derivatives as novel acetylcholinesterase inhibitor and antioxidant hybrids for Alzheimer disease.","abstract":"Design, synthesis and evaluation of new acetylcholinesterase inhibitors by combining quinolinecarboxamide to a benzylpiperidine moiety are described. Then, a series of hybrids have been developed by introducing radical scavengers. Molecular modeling was performed and structure activity relationships are discussed. Among the series, most potent compounds show effective AchE inhibitions, high selectivities over butyrylcholinesterase and high radical scavenging activities. On the basis of this work, the ability of quinolone derivatives to serve in the design of N-benzylpiperidine linked multipotent molecules for the treatment of Alzheimer Disease has been established.","corpus_id":6497774,"score":2},{"doc_id":"25378907","title":"Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer's disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids.","abstract":"The design, synthesis, and biochemical evaluation of donepezil-pyridyl hybrids (DPHs) as multipotent cholinesterase (ChE) and monoamine oxidase (MAO) inhibitors for the potential treatment of Alzheimer's disease (AD) is reported. The 3D-quantitative structure-activity relationship study was used to define 3D-pharmacophores for inhibition of MAO A/B, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes and to design DPHs as novel multi-target drug candidates with potential impact in the therapy of AD. DPH14 (Electrophorus electricus AChE [EeAChE]: half maximal inhibitory concentration [IC50] =1.1±0.3 nM; equine butyrylcholinesterase [eqBuChE]: IC50 =600±80 nM) was 318-fold more potent for the inhibition of AChE, and 1.3-fold less potent for the inhibition of BuChE than the reference compound ASS234. DPH14 is a potent human recombinant BuChE (hBuChE) inhibitor, in the same range as DPH12 or DPH16, but 13.1-fold less potent than DPH15 for the inhibition of human recombinant AChE (hAChE). Compared with donepezil, DPH14 is almost equipotent for the inhibition of hAChE, and 8.8-fold more potent for hBuChE. Concerning human monoamine oxidase (hMAO) A inhibition, only DPH9 and 5 proved active, compound DPH9 being the most potent (IC50 [MAO A] =5,700±2,100 nM). For hMAO B, only DPHs 13 and 14 were moderate inhibitors, and compound DPH14 was the most potent (IC50 [MAO B] =3,950±940 nM). Molecular modeling of inhibitor DPH14 within EeAChE showed a binding mode with an extended conformation, interacting simultaneously with both catalytic and peripheral sites of EeAChE thanks to a linker of appropriate length. Absortion, distribution, metabolism, excretion and toxicity analysis showed that structures lacking phenyl-substituent show better druglikeness profiles; in particular, DPHs13-15 showed the most suitable absortion, distribution, metabolism, excretion and toxicity properties. Novel donepezil-pyridyl hybrid DPH14 is a potent, moderately selective hAChE and selective irreversible hMAO B inhibitor which might be considered as a promising compound for further development for the treatment of AD.","corpus_id":4508492,"score":2},{"doc_id":"25960230","title":"Use of ligand-based pharmacophore modeling and docking approach to find novel acetylcholinesterase inhibitors for treating Alzheimer's.","abstract":"Alzheimer's disease is a neurological disorder in which the patient suffers from memory loss and impaired cognitive abilities. Though the main cause of the disease is not yet known, depletion of neurotransmitter at synaptic junctions, accumulation of insoluble beta amyloid plaques and neurofibrillary tangles are the main pathologies associated with it. The FDA approved drugs for alzheimer's belong to the category of acetylcholinesterase inhibitors. But most of the drugs have been observed to be associated with adverse side effects. In this study, we have developed a pharmacophore (responsible for interaction with acetylcholinesterase active site) based on the already existing drugs and drug candidates. This pharmacophore was used to search for novel AChE inhibitors with altogether different chemical scaffold using high throughput virtual screening and docking studies. Finally, we have reported two compounds, OPA and OMT, which possess high affinity for catalytic site of AChE enzyme and thus, can be considered as potential AChE inhibitors for the symptomatic treatment of Alzheimer's.","corpus_id":8243356,"score":2},{"doc_id":"26202430","title":"Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.","abstract":"Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs.","corpus_id":205331473,"score":2},{"doc_id":"26412714","title":"6-Methyluracil Derivatives as Bifunctional Acetylcholinesterase Inhibitors for the Treatment of Alzheimer's Disease.","abstract":"Novel 6-methyluracil derivatives with ω-(substituted benzylethylamino)alkyl chains at the nitrogen atoms of the pyrimidine ring were designed and synthesized. The numbers of methylene groups in the alkyl chains were varied along with the electron-withdrawing substituents on the benzyl rings. The compounds are mixed-type reversible inhibitors of cholinesterases, and some of them show remarkable selectivity for human acetylcholinesterase (hAChE), with inhibitory potency in the nanomolar range, more than 10 000-fold higher than that for human butyrylcholinesterase (hBuChE). Molecular modeling studies indicate that these compounds are bifunctional AChE inhibitors, spanning the enzyme active site gorge and binding to its peripheral anionic site (PAS). In vivo experiments show that the 6-methyluracil derivatives are able to penetrate the blood-brain barrier (BBB), inhibiting brain-tissue AChE. The most potent AChE inhibitor, 3 d (1,3-bis[5-(o-nitrobenzylethylamino)pentyl]-6-methyluracil), was found to improve working memory in scopolamine and transgenic APP/PS1 murine models of Alzheimer's disease, and to significantly decrease the number and area of β-amyloid peptide plaques in the brain.","corpus_id":42848004,"score":2},{"doc_id":"26438408","title":"Combined 3D-QSAR, molecular docking, and molecular dynamics study of tacrine derivatives as potential acetylcholinesterase (AChE) inhibitors of Alzheimer's disease.","abstract":"Acetylcholinesterase (AChE) is one of the key targets of drugs for treating Alzheimer's disease (AD). Tacrine is an approved drug with AChE-inhibitory activity. In this paper, 3D-QSAR, molecular docking, and molecular dynamics were carried out in order to study 60 tacrine derivatives and their AChE-inhibitory activities. 3D-QSAR modeling resulted in an optimal CoMFA model with q(2) = 0.552 and r(2) = 0.983 and an optimal CoMSIA model with q(2) = 0.581 and r(2) = 0.989. These QSAR models also showed that the steric and H-bond fields of these compounds are important influences on their activities. The interactions between these inhibitors and AChE were further explored through molecular docking and molecular dynamics simulation. A few key residues (Tyr70, Trp84, Tyr121, Trp279, and Phe330) at the binding site of AChE were identified. The results of this study improve our understanding of the mechanisms of AChE inhibitors and afford valuable information that should aid the design of novel potential AChE inhibitors. Graphical Abstract Superposition of backbone atoms of the lowest-energy structure obtained from MD simulation (magenta) onto those of the structure of the initial molecular docking model (green).","corpus_id":397898,"score":2},{"doc_id":"26832327","title":"Design and prediction of new acetylcholinesterase inhibitor via quantitative structure activity relationship of huprines derivatives.","abstract":"Acetylcholinesterase (AChE) is an important enzyme in the pathogenesis of Alzheimer's disease (AD). Comparative quantitative structure-activity relationship (QSAR) analyses on some huprines inhibitors against AChE were carried out using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and hologram QSAR (HQSAR) methods. Three highly predictive QSAR models were constructed successfully based on the training set. The CoMFA, CoMSIA, and HQSAR models have values of r (2) = 0.988, q (2) = 0.757, ONC = 6; r (2) = 0.966, q (2) = 0.645, ONC = 5; and r (2) = 0.957, q (2) = 0.736, ONC = 6. The predictabilities were validated using an external test sets, and the predictive r (2) values obtained by the three models were 0.984, 0.973, and 0.783, respectively. The analysis was performed by combining the CoMFA and CoMSIA field distributions with the active sites of the AChE to further understand the vital interactions between huprines and the protease. On the basis of the QSAR study, 14 new potent molecules have been designed and six of them are predicted to be more active than the best active compound 24 described in the literature. The final QSAR models could be helpful in design and development of novel active AChE inhibitors.","corpus_id":23383808,"score":2},{"doc_id":"27410776","title":"Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease.","abstract":"In Alzheimer's disease (AD), the level of Acetylcholine (ACh) neurotransmitter is reduced. Since Acetylcholinesterase (AChE) cleaves ACh, inhibitors of AChE are very much sought after for AD treatment. The side effects of current inhibitors necessitate development of newer AChE inhibitors. Isoalloxazine derivatives have proved to be promising (AChE) inhibitors. However, their structure-activity relationship studies have not been reported till date. In the present work, various quantitative structure-activity relationship (QSAR) building methods such as multiple linear regression (MLR), partial least squares ,and principal component regression were employed to derive 3D-QSAR models using steric and electrostatic field descriptors. Statistically significant model was obtained using MLR coupled with stepwise selection method having r(2) = .9405, cross validated r(2) (q(2)) = .6683, and a high predictability (pred_r(2) = .6206 and standard error, pred_r(2)se = .2491). Steric and electrostatic contribution plot revealed three electrostatic fields E_496, E_386 and E_577 and one steric field S_60 contributing towards biological activity. A ligand-based 3D-pharmacophore model was generated consisting of eight pharmacophore features. Isoalloxazine derivatives were docked against human AChE, which revealed critical residues implicated in hydrogen bonds as well as hydrophobic interactions. The binding modes of docked complexes (AChE_IA1 and AChE_IA14) were validated by molecular dynamics simulation which showed their stable trajectories in terms of root mean square deviation and molecular mechanics/Poisson-Boltzmann surface area binding free energy analysis revealed key residues contributing significantly to overall binding energy. The present study may be useful in the design of more potent Isoalloxazine derivatives as AChE inhibitors.","corpus_id":3525286,"score":2},{"doc_id":"27801451","title":"The discovery of new acetylcholinesterase inhibitors derived from pharmacophore modeling, virtual screening, docking simulation and bioassays.","abstract":"Hyperactivity of acetylcholinesterase (AChE) in the brain is the immediate cause of Alzheimer's disease (AD), which is one of the most prevalent fatal diseases afflicting numerous older people. In this research, an in silico study was carried out to find potential AChE inhibitors from a large chemical library. With clustering and lots of comprehensive analysis, some molecules were screened using in vitro bioassays. The IC50 values against AChE ranged from 33.620 to 101.570 μM, while the inhibition ratios at 50 μM ranged from 11.37% to 77.35%. The binding mode between the inhibitor and the binding sites of AChE was studied. Four residues (Tyr133, Tyr124, Ser203 and Trp86) were suggested to be crucial because they can form hydrogen bonds with the ligand. Therefore, ZYQ1 and its derivatives might represent a promising starting point for the development of highly potent lead compounds for the treatment of AD.","corpus_id":3870340,"score":2},{"doc_id":"28275924","title":"2D-SAR and 3D-QSAR analyses for acetylcholinesterase inhibitors.","abstract":"Alzheimer's disease (AD) accounts for almost three quarters of dementia patients and interferes people's normal life. Great progress has been made recently in the study of Acetylcholinesterase (AChE), known as one of AD's biomarkers. In this study, acetylcholinesterase inhibitors (AChEI) were collected to build a two-dimensional structure-activity relationship (2D-SAR) model and three-dimensional quantitative structure-activity relationship (3D-QSAR) model based on feature selection method combined with random forest. After calculation, the prediction accuracy of the 2D-SAR model was 89.63% by using the tenfold cross-validation test and 87.27% for the independent test set. Three cutting ways were employed to build 3D-QSAR models. A model with the highest [Formula: see text] (cross-validated correlation coefficient) and [Formula: see text](non-cross-validated correlation coefficient) was obtained to predict AChEI activity. The mean absolute error (MAE) of the training set and the test set was 0.0689 and 0.5273, respectively. In addition, molecular docking was also employed to reveal that the ionization state of the compounds had an impact upon their interaction with AChE. Molecular docking results indicate that Ser124 might be one of the active site residues.","corpus_id":2412109,"score":2},{"doc_id":"28417668","title":"Exploring molecular structural requirement for AChE inhibition through multi-chemometric and dynamics simulation analyses.","abstract":"The acetylcholinesterase enzyme (AChE) plays an important role in central and peripheral nervous systems. Acetylcholine (ACh) acts through the regulation of AChE activity, which can play a key role in accelerating senile amyloid β-peptide (Aβ) plaque deposition. Therefore, inhibition of the AChE enzyme can be used as a key principle to prevent ACh depletion. The present study has been emphasized to explore both ligand- and structure-based 3D QSAR, HQSAR, pharmacophore, molecular docking and simulation studies on a set of structurally diverse inhibitors to optimize prime structural features responsible for selective binding to AChE, and vis-à-vis inhibiting enzyme activity. The pharmacophore model showed the importance of HB acceptor and donor, positive ionization and hydrophobic features of the molecule for effective binding. Structure-based docking and simulation studies adjudged the significance of features obtained from ligand-based 3D QSAR, CoMFA (Q(2) = .608, [Formula: see text] = .700), CoMSIA (Q(2) = .632, [Formula: see text] = .734), HQSAR (Q(2) = .850, [Formula: see text] = .693) and pharmacophore (Q(2) = .839, ROCscore = .769) models. The aim of the present study is to identify the essential structural and physicochemical profiles of molecules that can provide therapeutic benefits with less toxicity. Structurally diverse compounds have been used for the study, and the generated models showed the large applicability domain.","corpus_id":3807493,"score":2},{"doc_id":"29198175","title":"New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer's disease: Synthesis, molecular modeling, NMR, and biological evaluation.","abstract":"Two new compounds (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dihydroacridin-1(2H)-ylidene)hydrazinecarbothiomide (3) and (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dhihydroacridin-1(2H)-ylidene)hydrazinecarboxamide (4) were synthesized and evaluated for their anticholinesterase activities. In vitro tests performed by NMR and Ellman's tests, pointed to a mixed kinetic mechanism for the inhibition of acetylcholinesterase (AChE). This result was corroborated through further docking and molecular dynamics studies, suggesting that the new compounds can work as gorge-spanning ligands by interacting with two different binding sites inside AChE. Also, in silico toxicity evaluation suggested that these new compounds can be less toxic than tacrine.","corpus_id":196635597,"score":2},{"doc_id":"29336270","title":"In silico Structure-based Identification of Novel Acetylcholinesterase Inhibitors Against Alzheimer's Disease.","abstract":"OBJECTIVE AND BACKGROUND: Inhibition of acetylcholinesterase (AChE) has gained much importance since the discovery of the involvement of peripheral anionic site as an allosteric regulator of AChE. Characterized by the formation of β-amyloid plaques, Alzheimer's disease (AD) is currently one of the leading causes of death across the world. Progression in this neurodegenerative disorder causes deficit in the cholinergic activity that leads towards cognitive decline. Therapeutic interventions in AD are largely focused upon AChE inhibitors designed essentially to prevent the loss of cholinergic function. The multifactorial AD pathology calls for Multitarget-directed ligands (MTDLs) to follow up on various components of the disease. Considering this approach, other related AD targets were also selected. Structure-based virtual screening was relied upon for the identification of lead compounds with anti-AD effect. METHOD: Several chemoinformatics approaches were used in this study, reporting four multi-target inhibitors: MCULE-7149246649-0-1, MCULE-6730554226-0-4, MCULE-1176268617-0-6 and MCULE-8592892575-0-1 with high binding energies that indicate better AChE inhibitory activity. Additional in-silico analysis hypothesized the abundant presence of aromatic interactions to be pivotal for interaction of selected compounds to the acetyl-cholinesterase. Additionally, we presented an alternative approach to determine protein-ligand stability by calculating the Gibbs-free energy change over time. Furthermore, this allows to rank potential hits for further in-vitro testing. RESULTS AND CONCLUSION: With no predicted indication of adverse effects on humans, this study unravels four active multi-target inhibitors against AChE with promising affinities and good ADMET profile for the potential use in AD treatment.","corpus_id":11982852,"score":2},{"doc_id":"18444627","title":"Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.","abstract":"Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of structurally related steroidal alkaloids as butyrylcholinesterase (BuChE) inhibitors. Docking studies were employed to position the inhibitors into the BuChE active site to determine the most probable binding mode. The strategy was to explore multiple inhibitor conformations in producing a more reliable 3D-QSAR model. These multiple conformations were derived using the FlexS program. The conformation selection step for CoMFA was done by genetic algorithm. The genetic algorithm based CoMFA approach was found to be the best. Both CoMFA and CoMSIA yielded significant cross-validated q(2) values of 0.701 and 0.627 and the r(2) values of 0.979 and 0.982, respectively. These statistically significant models were validated by a test set of five compounds. Comparison of CoMFA and CoMSIA contour maps helped to identify structural requirements for the inhibitors and serves as a basis for the design of the next generation of the inhibitor analogues. The results demonstrate that the combination of ligand-based and receptor-based modeling with use of a genetic algorithm is a powerful approach to build 3D-QSAR models. These data can be used for the lead optimization process with respect to inhibition enhancement which is important for the drug discovery and development for Alzheimer's disease.","corpus_id":16170684,"score":1},{"doc_id":"21094069","title":"Binding research on flavones as ligands of β-amyloid aggregates by fluorescence and their 3D-QSAR, docking studies.","abstract":"The K(d)s (dissociation constants) of 21 flavone derivatives have been obtained by fluorescence in vitro when binding with Aβ(1-40) (β-amyloid(1-40)) aggregates protein. Extensive 3D-QSAR (quantitative structure-activity relationship) studies were performed on the fluorescent flavones, which are excellent ligands of Aβ(1-40) aggregates protein. Comparative molecular similarity indices analysis (CoMSIA) technique was used to relate the binding affinities with the ligand structures, and the QSAR model was obtained using the CoMFA technique. The QSAR model was proved to statistically significant and have high predictive power: the CoMSIA model yielded the cross-validated q2 = 0.512 and the non-cross-validated r2 = 0.911. This model showed that electrostatic (22.5%) and H-bond interaction (acceptor 15.3%; donor 45.1%) properties played major roles in ligand binding process. The QSAR model was further graphically interpreted in terms of field contribution maps. In order to further investigate the specific binding site of the flavones in the Aβ(1-40) aggregates, preliminary docking studies were performed. According to the 3D-QSAR results, the possible binding site in the protein was proposed in order to direct the molecular docking studies. A good correlation (R2: 0.846) between the calculated binding energies and the experimental binding affinities (pK(d)s) suggests that the identified binding site is reliable. The 3D-QSAR model and the information of the ligand-protein interaction will be helpful in the selection of flavones to be structurally modified and labeled by a radio nuclide for imaging Aβ(1-40) aggregates in the AD (Alzheimer's disease) brain.","corpus_id":10016563,"score":1},{"doc_id":"22039875","title":"Hybrid-based multi-target ligands for the treatment of Alzheimer's disease.","abstract":"Progresses in medicinal chemistry over the last few years have focused on the design and synthesis of hybrid compounds, molecules encompassing in a single scaffold two pharmacophores from known entities endowed with well established biological activities. The interest in this topic is related to the increasing emphasis on the identification of the different factors involved in a number of disorders, such as the complex multifactorial Alzheimer's disease (AD), and hybrid- based strategy has become a focal point in this medicinal chemistry field since it could lead to derivatives with an improved biological profile. Using this strategy, acetylcholinesterase inhibitors (AChEIs) have been extensively coupled with properly selected bioactive molecules to obtain homo- and heterodimers endowed with increased potency together with supplementary actions. In the past decade the inhibition of the AChE induced aggregation of the -amyloid peptide into the senile plaques, which is a key event in the neurotoxic cascade of AD, has been considered a relevant approach leading to several dual binding site inhibitors, able to contact both the peripheral anionic site of AChE and the active site. In recent years, pioneering efforts have been performed to obtain novel AChEIs that, beyond the capability to inhibit AChE, were able to hit a number of specific AD targets. In particular, these compounds proved to possess antioxidant, anti-inflammatory, or neuroprotective activities, useful to block or revert the progression of the disease. This review summarizes the progresses that have been made in the design of hybrid molecules for the treatment of AD.","corpus_id":12094936,"score":1},{"doc_id":"22216416","title":"New acetylcholinesterase inhibitors for Alzheimer's disease.","abstract":"Acetylcholinesterase (AChE) remains a highly viable target for the symptomatic improvement in Alzheimer's disease (AD) because cholinergic deficit is a consistent and early finding in AD. The treatment approach of inhibiting peripheral AchE for myasthenia gravis had effectively proven that AchE inhibition was a reachable therapeutic target. Subsequently tacrine, donepezil, rivastigmine, and galantamine were developed and approved for the symptomatic treatment of AD. Since then, multiple cholinesterase inhibitors (ChEI) continue to be developed. These include newer ChEIs, naturally derived ChEIs, hybrids, and synthetic analogues. In this paper, we summarize the different types of ChEIs in development and their respective mechanisms of actions. This pharmacological approach continues to be active with many promising compounds.","corpus_id":1887212,"score":1},{"doc_id":"23039767","title":"Structure-based design and synthesis of benzothiazole phosphonate analogues with inhibitors of human ABAD-Aβ for treatment of Alzheimer's disease.","abstract":"Amyloid binding alcohol dehydrogenase, a mitochondrial protein, is a cofactor facilitating amyloid-β peptide (Aβ) induced cell stress. Antagonizing Aβ-ABAD interaction protects against aberrant mitochondrial and neuronal function and improves learning memory in the Alzheimer's disease mouse model. Therefore, it offers a potential target for Alzheimer's drug design, by identifying potential inhibitors of Aβ-ABAD interaction. 2D QSAR methods were applied to novel compounds with known IC(50) values, which formed a training set. A correlation analysis was carried out comparing the statistics of the measured IC(50) with predicted values. These selectivity-determining descriptors were interpreted graphically in terms of principle component analyses, which are highly informative for the lead optimization process with respect to activity enhancement. A 3D pharmacophore model also was created. The 2D QSAR and 3D pharmacophore models will assist in high-throughput screening. In addition, ADME descriptors were also determined to study their pharmacokinetic properties. Finally, amyloid binding alcohol dehydrogenase molecular docking study of these novel molecules was undertaken to determine whether these compounds exhibit significant binding affinity with the binding site. We have synthesized only the compounds that have shown the best drug-like properties as candidates for further studies.","corpus_id":207104675,"score":1},{"doc_id":"23408593","title":"Interaction of metal chelators with different molecular forms of acetylcholinesterase and its significance in Alzheimer's disease treatment.","abstract":"The peripheral anionic site (PAS) of acetylcholinesterase (AChE) is involved in amyloid beta (Aβ) peptides aggregation of Alzheimer's disease (AD). AChE exhibits an aryl acylamidase (AAA) activity along with the well known esterase activity. Numerous studies have reported the beneficiary effect of metal chelators in AD treatment. Hence, a comparative study on the effect of metal chelators on both the esterase and AAA activity of AChE globular (G4 and G1) molecular forms was performed. The inhibitory effect of 1,10-phenanthroline was high towards AChE esterase activity. The corresponding IC50 values for esterase activity of G4 and G1-form was 190 µM and 770 µM and for AAA activity it was 270 µM and 2.74 mM, respectively. Kinetic studies on both forms of AChE show that 1,10-phenanthroline inhibits esterase in competitive and AAA activity in non-competitive manner. Protection studies further revealed that the nature of 1,10-phenanthroline inhibition on AChE is through its direct binding to protein rather than its metal chelation property. Molecular docking studies shows orientation of 1,10-phenathroline in the PAS through hydrophobic interactions with the PAS residues (Trp286, Tyr124 and Tyr341) and hydrogen bonding with Phe295. Further molecular dynamics simulation of \"hAChE-1,10-phenanthroline\" complex revealed that both hydrogen and hydrophobic interaction contribute equally for 1,10-phenanthroline binding to hAChE. Such an interaction of 1,10-phenanthroline on PAS may hinder \"AChE-Aβ peptide\" complex formation. Hence, 1,10-phenanthroline can act as a lead molecule for developing drug(s) against AD ailment with dual functions namely, anti-cholinesterase and anti-amyloid aggregation potency in a single chemical entity.","corpus_id":6964800,"score":1},{"doc_id":"24805972","title":"Oxime-dipeptides as anticholinesterase, reactivator of phosphonylated-serine of AChE catalytic triad: probing the mechanistic insight by MM-GBSA, dynamics simulations and DFT analysis.","abstract":"Neuropathological cascades leading to reduced cholinergic transmission in Alzheimer's disease led to development of AChE-inhibitors. Although lethal dose of some inhibitors cause interruption with AChE mediated mechanism but reversible AChE inhibitors can assist in protection from inhibition of AChE and hence in an aim to probe potential molecules as anticholinesterase and as reactivators, computationally structure-based approach has been exploited in this work for designing new 2-amino-3-pyridoixime-dipeptides conjugates. We have combined MD simulations with flexible ligand docking approach to determine binding specificity of 2-amino-3-pyridoixime dipeptides towards AChE (PDB 2WHP). PAS residues are found to be responsible for oxime-dipeptides binding along with π-π interactions with Trp86 and Tyr286, hydrogen bonding with side chains of Asp74 and Tyr341 (Gscore -10.801 and MM-GBSA free energy -34.89 kcal/mol). The docking results depicted complementary multivalent interactions along with good binding affinity as predicted from MM-GBSA analysis. The 2-amino-3-pyridoxime-(Arg-Asn) AChE systems subjected to MD simulations under explicit solvent systems with NPT and NVT ensemble. MD simulations uncovered dynamic behavior of 2-amino-3-pyridoxime-(Arg-Asn) and exposed its mobile nature and competence to form strong long range-order contacts towards active site residues to approach inhibited serine residue and facilitated via large contribution from hydrogen bonding and water bridges along with slow and large movements of adjacent important residues. In an effort to evaluate the complete potential surface profile, 2-amino-3-pyridoxime induced reactivation pathway of sarin-serine adduct has been investigated by the DFT approach at the vacuum MO6/6-311G (d, p) level along with the Poisson-Boltzmann solvation model and found to be of relatively low energy barrier. The pKa evaluation has revealed the major deprotonated 2-amino-3-pyridoixime species having pKa of 6.47 and hence making 2-amino-3-pyridoxime-(Arg-Asn) potential anticholinesterase and reactivator for AChE under the physiological pH.","corpus_id":6385396,"score":1},{"doc_id":"25435329","title":"Chemometric design to explore pharmacophore features of BACE inhibitors for controlling Alzheimer's disease.","abstract":"The β-amyloid precursor protein cleavage enzyme (BACE) has been conceived to be an attractive therapeutic target to control Alzheimer's disease (AD). Validated ligand-based pharmacophore mapping was combined with 3D QSAR modeling approaches that include CoMFA, CoMSIA and HQSAR techniques to identify structural and physico-chemical requirements for a potential BACE inhibitor using a database containing 980 structurally diverse compounds, assembled from different reports. A structure-based docking technique was also used to validate the features obtained from the ligand-based models, which were further used to screen the database of compounds designed by a de novo approach. Contour maps of 3D QSAR models, CoMFA (R(2) = 0.880, se = 0.402, Q(2) = 0.596, Rpred(2) = 0.713,) and CoMSIA (R(2) = 0.903, se = 0.362, Q(2) = 0.578, Rpred(2) = 0.715), and a pharmacophore space model (R(2) = 0.833, rmsd = 1.578, Q(2) = 0.845, Rpred(2) = 0. 764) depict that the models are robust and provide an explanation of the important features such as steric, electrostatic, hydrophobic, positive ionization, hydrogen bond acceptor and donor properties, which play important roles for interaction with the receptor site cavity. The HQSAR study (R(2) = 0.823, se = 0.488, Q(2) = 0.823, Rpred(2) = 0.768) and de novo design, which generate new fragments, illustrated the important molecular fingerprints for inhibition. The docking study elucidated the important interactions between the amino acid residues (Gly11, Thr72, Asp228, Gly230, Thr231, Arg235) at the catalytic site of the receptor and the ligand, indicating the structural requirements of the inhibitors. The de novo designed molecules were further screened for ADMET properties, and ligand-receptor interactions of the top hits were analysed by molecular docking to explore pharmacophore features of BACE inhibitors.","corpus_id":4717888,"score":1},{"doc_id":"25537270","title":"Sulfonamides as multifunctional agents for Alzheimer's disease.","abstract":"Sulfonamide linker-based inhibitors with extended linear structure were designed and synthesized with the aim of producing multifunctional agents against several processes involved in the pathology of Alzheimer's disease (AD). The potency of the compounds were assessed in the inhibition of Aβ self-assembly (fibril and oligomer formation), in modulating cholinesterase (AChE, BuChE) activity, and scavenging free radicals. Several compounds exhibited promising Aβ self-assembly and cholinesterase inhibition and in parallel, showed good free radical scavenging properties. The investigation of the scaffold described in this study resulted in the identification of three compounds (14, 19 and 26) as promising leads for the further design of multifunctional drug candidates for AD.","corpus_id":8665497,"score":1},{"doc_id":"25588616","title":"Ligand-based 3D QSAR analysis of reactivation potency of mono- and bis-pyridinium aldoximes toward VX-inhibited rat acetylcholinesterase.","abstract":"To predict unknown reactivation potencies of 12 mono- and bis-pyridinium aldoximes for VX-inhibited rat acetylcholinesterase (rAChE), three-dimensional quantitative structure-activity relationship (3D QSAR) analysis has been carried out. Utilizing molecular interaction fields (MIFs) calculated by molecular mechanical (MMFF94) and quantum chemical (B3LYP/6-31G*) methods, two satisfactory ligand-based CoMFA models have been developed: 1. R(2)=0.9989, Q(LOO)(2)=0.9090, Q(LTO)(2)=0.8921, Q(LMO(20%))(2)=0.8853, R(ext)(2)=0.9259, SDEP(ext)=6.8938; 2. R(2)=0.9962, Q(LOO)(2)=0.9368, Q(LTO)(2)=0.9298, Q(LMO(20%))(2)=0.9248, R(ext)(2)=0.8905, SDEP(ext)=6.6756. High statistical significance of the 3D QSAR models has been achieved through the application of several data noise reduction techniques (i.e. smart region definition SRD, fractional factor design FFD, uninformative/iterative variable elimination UVE/IVE) on the original MIFs. Besides the ligand-based CoMFA models, an alignment molecular set constructed by flexible molecular docking has been also studied. The contour maps as well as the predicted reactivation potencies resulting from 3D QSAR analyses help better understand which structural features are associated with increased reactivation potency of studied compounds.","corpus_id":24958403,"score":1},{"doc_id":"25747777","title":"In silico analysis of binding of neurotoxic venom ligands with acetylcholinesterase for therapeutic use in treatment of Alzheimer's disease.","abstract":"Acetylcholinesterases (AChE) are enzymes that function in hydrolyzing the neurotransmitter acetylcholine. Diminished levels of acetylcholine have been reported for various neurodegenerative diseases, especially Alzheimer's. Therefore, acetylcholinesterase inhibitors are being considered quite effective in treating these diseases. Fasciculin 2 is a toxin isolated from Eastern green mamba that had been reported as a reversible acetylcholinesterase inhibitor. In this study, we have reported the in silico analysis of venom toxins via various computational tools used for drug designing, to find out the protein-protein interaction of these toxins in complex with acetylcholinesterase enzyme. In total 15 toxins have been selected from the venoms of various species as ligand dataset, to study their binding interactions with the acetylcholinesterase enzyme.","corpus_id":2244207,"score":1},{"doc_id":"25794302","title":"Pharmacophore based 3DQSAR of phenothiazines as specific human butyrylcholinesterase inhibitors for treatment of Alzheimer's disease.","abstract":"Quantitative three dimensional structure activity relationship (3D-QSAR) studies were performed on phenothiazine derivatives as Butyrylcholinesterase (BuChE) inhibitors. Pharmacophore Alignment and Scoring Engine (PHASE) was used to develop predictive Common Pharmacophore Hypotheses (CPHs). The alignment thus obtained was used for Comparative Molecular Field Analysis (CoMFA)/Comparative Molecular Similarity Indices Analysis (CoMSIA) model development. A fourpoint common pharmacophore hypothesis, comprising of one acceptor, one hydrophobic region and two aromatic ring centres was generated. A structurally diverse set of 80 molecules was used of which 56 were grouped into training set to develop the model and the rest 24 molecules into test set to validate the CoMFA/CoMSIA models. The models so developed showed a good r(2)predictive of 0.7587 for CoMFA and 0.7737 for CoMSIA. CoMFA and CoMSIA models had excellent Q(2) (cross-validated coefficient) of 0.7125 and 0.7093, respectively which showed high correlative and predictive abilities of the models. The 3-D contour maps of CoMFA/CoMSIA provided interpretable explanation of SAR for the compounds and also permitted interesting conclusions about the substituent effects on the phenothiazine derivatives. The outcomes of the study would help in the rational design of novel and potent therapeutic agents as specific BuChE inhibitors for symptomatic or disease modifying treatment of AD.","corpus_id":23332125,"score":1},{"doc_id":"26003339","title":"From AChE to BACE1 inhibitors: The role of the amine on the indanone scaffold.","abstract":"In recent years, a progressive increase in age-related disorders could be observed in most western countries, among which Alzheimer's disease (AD) is one of the most challenging. BACE1 could be seen as an attractive target to develop disease-modifying compounds, and in this context, a new series of hybrid molecules was designed and synthesized, based on a previously identified multitarget lead compound. In particular, the amino side chain was appropriately modified to fit BACE1 as additional target. In vitro testing results pointed out compound 8 (IC50=2.49±0.08 μM), bearing the bulky bis(4-fluorophenyl)methyl)piperazine substituent, as the most potent BACE1 inhibitor of the series.","corpus_id":19907161,"score":1},{"doc_id":"26032855","title":"Multiple Ligands Targeting Cholinesterases and β-Amyloid: Synthesis, Biological Evaluation of Heterodimeric Compounds with Benzylamine Pharmacophore.","abstract":"Alzheimer's disease (AD) is a fatal and complex neurodegenerative disorder for which effective treatment remains the unmet challenge. Using donepezil as a starting point, we aimed to develop novel potential anti-AD agents with a multidirectional biological profile. We designed the target compounds as dual binding site acetylcholinesterase inhibitors, where the N-benzylamine pharmacophore is responsible for interactions with the catalytic anionic site of the enzyme. The heteroaromatic fragment responsible for interactions with the peripheral anionic site was modified and three different heterocycles were introduced: isoindoline, isoindolin-1-one, and saccharine. Based on the results of the pharmacological evaluation, we identified compound 8b with a saccharine moiety as the most potent and selective human acetylcholinesterase inhibitor (IC50 = 33 nM) and beta amyloid aggregation inhibitor. It acts as a non-competitive acetylcholinesterase inhibitor and is able to cross the blood-brain barrier in vitro. We believe that compound 8b represents an important lead compound for further development as potential anti-AD agent.","corpus_id":205417841,"score":1},{"doc_id":"26639718","title":"6-Methyluracil derivatives as acetylcholinesterase inhibitors for treatment of Alzheimer's disease.","abstract":"BACKGROUND: Alzheimer's disease (AD) is the major age-related progressive neurodegenerative disorder. The brain of AD patients suffers from loss of cholinergic neurons and decreased number of synapses [1]. AD is caused by an imbalance between Aβ production and clearance, resulting in increased amount of Aβ in various forms [2]. Reduction of Aβ production and increasing clearance of Aβ pathogenic forms are key targets in the development of potential therapeutic agents for AD treatment. Unfortunately, only nosotropic approaches for treatment of AD are currently effective in humans. These approaches mainly focus on the inhibition of brain acetyl-cholinesterase (AChE) to increase lifetime of cerebral acetylcholine [3]. It is important to emphasize that AChE itself promotes the formation of Aβ fibrils in vitro and Aβ plaques in the cerebral cortex of transgenic mouse models of AD [4]. This property of AChE results from interaction between Aβ and the peripheral anionic site of the enzyme (PAS) [5]. Dual binding site inhibitors of both catalytic active site (CAS) and PAS can simultaneously improve cognition and slow down the rate of Aβ-induced neural degeneration. Unfortunately, the assortment of AChE PAS ligands is still extremely limited. OBJECTIVE: To study putative advantages of AChE non-charged PAS inhibitors based on 6-methyluracil derivatives for the treatment of Alzheimer's disease. METHODS: In vitro studies. Concentration of drug producing 50% of AChE/BuChE activity inhibition (IC50) was measured using the method of Ellman et al. [6]. Toxicological experiments were performed using IP injection of the different compounds in mice. LD50, dose (in mg/kg) causing lethal effects in 50% of animals was taken as a criterion of toxicity [7]. The ability of compound to block in vitro AChE-induced Aβ1-40 aggregation was studied using a thioflavin T (ThT) fluorescent probe [8].In vivo biological assays. For in vivo blood-brain barrier permeation assay brains were removed 30 min after IP injection of LD50 dose of tested compound injection. The inhibitory potency was measured using the method of Ellman. Scopolamine and transgenic models of AD were used to evaluate the influence of compound 35 on spatial memory performance. Water solution of scopolamine was injected to mice (ip) 20 minutes before starting memory test during 14 days [9]. Mice were assigned to 7 groups, including 4 groups receiving injection (ip) of compound in different dosages, donepezil-treated mice (donepezil is conventionally used to treat Alzheimer's disease), positive and negative control groups. Double transgenic (APP/PS1) mice expressing a chimeric mouse/human amyloid precursor protein and a mutant of human presenilin-1 [10] were assigned to 4 groups, including transgenic animals injected (ip) with compound 35 or donepezil solution, positive (transgenes injected with water) and negative (wild-type mice) controls. To evaluate spatial memory performance, mice were trained on a reward alternation task using a conventional T-maze [11]. The criterion for a mouse having learned the rewarded alternation task was 3 consecutive days of at least 5 correct responses out of the 6 free trials. For β-amyloid peptide load was evaluated quantitatively as a number and summary area of Thioflavine S fluorescent spots in cerebral cortex and hippocampal images using Image J program. Statistical analyses were performed using the Mann-Whitney test. RESULTS: We evaluated the acute toxicity of the most active compounds. The most potent AChE inhibitor compound 35 (IC50 (AChE) = 5 ± 0.5 nM) exhibited the lowest LD50 values (51 mg/kg) and inhibited brain AChE by more than 71 ± 1%. Compound 35 at 10 nM, exhibited a significant (35 ± 9%) inhibitory activity toward human AChE-induced Aβ aggregation. Scopolamine injection induced significant decrease in correct choice percentage in T-maze, as well as decrease in percentage of mice reaching criterion for learning the task by day 14. This memory deficit was relieved to some extent either by compound 35 (5 mg/kg) or donepezil (reference compound) treatment (0.75 mg/kg). Interestingly, higher doses of compound 35 (10 and 15 mg/kg) produced less therapeutic effect on spatial memory deficit. Group of APP/PS1 mice showed 3 times lower percentage of reaching behavioral criterion and lower percentage of correct choice in T-maze alternation task comparing to WT mice, whereas compound 35 (5 mg/kg) or Donepezil treatment effectively improved these parameters in APP/PS1 mice. Compound 35 treatment (5 mg/kg) during 14 days significantly reduced percentage of summary area and number of β-amyloid peptide (βAP) deposits visualized in sections of cerebral cortex, dentate gyrus, and hippocampal CA3 area in APP/PS1 mice. The most prominent reduction of βAP load by compound 35 treatment was found in CA3 area and cerebral cortex. Meanwhile, Donepezil treatment (1 mg/kg) during 14 days significantly reduced βAP load in cerebral cortex but not in dentate gyrus and CA3 area. CONCLUSIONS: Experiments showed that the most potent AChE inhibitor compound 35 (6-methyluracil derivative) permeated the blood-brain barrier, improved working memory in the APP/PS1 transgenic mice and significantly reduced the number and area of Aβ plaques in the brain. Thus, compound 35 is a promising candidate as a bi-functional inhibitor of AChE for treatment of AD.","corpus_id":4531190,"score":1},{"doc_id":"27823887","title":"Targeting Alzheimer's disease by investigating previously unexplored chemical space surrounding the cholinesterase inhibitor donepezil.","abstract":"A series of twenty seven acetylcholinesterase inhibitors, as potential agents for the treatment of Alzheimer's disease, were designed and synthesised based upon previously unexplored chemical space surrounding the molecular skeleton of the drug donepezil, which is currently used for the management of mild to severe Alzheimer's disease. Two series of analogues were prepared, the first looking at the replacement of the piperidine ring in donepezil with different sized saturated N-containing ring systems and the second looking at the introduction of different linkers between the indanone and piperidine rings in donepezil. The most active analogue 5,6-dimethoxy-1-oxo-2,3-dihydro-1H-inden-2-yl 1-benzylpiperidine-4-carboxylate (67) afforded an in vitro IC50 value of 0.03 ± 0.07 μM against acetylcholinesterase with no cytotoxicity observed (IC50 of >100 μM, SH-SY5Y cell line). In comparison donepezil had an IC50 of 0.05 ± 0.06 μM and an observed cytotoxicity IC50 of 15.54 ± 1.12 μM. Molecular modelling showed a strong correlation between activity and in silico binding in the active site of acetylcholinesterase.","corpus_id":36967057,"score":1},{"doc_id":"29676170","title":"Discovery of novel dual acetylcholinesterase inhibitors with antifibrillogenic activity related to Alzheimer's disease.","abstract":"AIM: Alzheimer's disease is a progressive and neurodegenerative disorder of the CNS, affecting elderly people. The current pharmacological approach is based on the improvement of cholinergic neurotransmission by inhibiting acetylcholinesterase (AChE) with AChE inhibitors. The disease is also characterized by the accelerated accumulation of β-amyloid plaques around neurons. Furthermore, in vitro studies revealed that AChE can induce β-amyloid peptide (Aβ) aggregation. METHODOLOGY: Computer-aided molecular design by virtual screening was here employed to discover novel potential AChE inhibitors, with antifibrillogenic properties, in other words, inhibiting Aβ aggregation. RESULTS: Compounds 1, 4 and 6 showed interesting AChE inhibition. In addition, they particularly inhibit Aβ aggregation in vitro, indicating to be promising novel anti-Alzheimer agents.","corpus_id":4973994,"score":1},{"doc_id":"18076152","title":"3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors.","abstract":"The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B polymerase inhibitory activity of structurally diverse test set compounds and to yield reliable clues for further optimization of the benzimidazole derivatives in the data set.","corpus_id":21651552,"score":0},{"doc_id":"18771818","title":"3D-QSAR studies of boron-containing dipeptides as proteasome inhibitors with CoMFA and CoMSIA methods.","abstract":"Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed for a series of dipeptide boronate proteasome inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. A training set containing 46 molecules served to establish the models. The optimum CoMFA and CoMSIA models obtained for the training set were all statistically significant with cross-validated coefficients (q(2)) of 0.676 and 0.630 and conventional coefficients (r(2)) of 0.989 and 0.956, respectively. The predictive capacities of both models were successfully validated by calculating a test set of 13 molecules that were not included in the training set. The predicted correlation coefficients (r(2)(pred)) of CoMFA and CoMSIA are 0.963 and 0.919, respectively. The CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of beta5 subunit of 20S proteasome, which suggests that the 3D-QSAR models constructed in this paper can be used to guide the development of novel dipeptide boronate inhibitors of 20S proteasome.","corpus_id":30412104,"score":0},{"doc_id":"19779936","title":"Receptor based 3D-QSAR to identify putative binders of Mycobacterium tuberculosis Enoyl acyl carrier protein reductase.","abstract":"In the current study, the applicability and scope of 3D-QSAR models (CoMFA and CoMSIA) to complement virtual screening using 3D pharmacophore and molecular docking is examined and applied to identify potential hits against Mycobacterium tuberculosis Enoyl acyl carrier protein reductase (MtENR). Initially CoMFA and CoMSIA models were developed using series of structurally related arylamides as MtENR inhibitors. Docking studies were employed to position the inhibitors into MtENR active site to derive receptor based 3D-QSAR models. Both CoMFA and CoMSIA yielded significant cross validated q(2) values of 0.663 and 0.639 and r(2) values of 0.989 and 0.963, respectively. The statistically significant models were validated by a test set of eight compounds with predictive r(2) value of 0.882 and 0.875 for CoMFA and CoMSIA. The contour maps from 3D-QSAR models in combination with docked binding structures help to better interpret the structure activity relationship. Integrated with CoMFA and CoMSIA predictive models structure based (3D-pharmacophore and molecular docking) virtual screening have been employed to explore potential hits against MtENR. A representative set of 20 compounds with high predicted IC(50) values were sorted out in the present study.","corpus_id":11563646,"score":0},{"doc_id":"20179991","title":"Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors.","abstract":"A chemical feature-based pharmacophore model was developed for Tumor Necrosis Factor-alpha converting enzyme (TACE) inhibitors. A five point pharmacophore model having two hydrogen bond acceptors (A), one hydrogen bond donor (D) and two aromatic rings (R) with discrete geometries as pharmacophoric features was developed. The pharmacophore model so generated was then utilized for in silico screening of a database. The pharmacophore model so developed was validated by using four compounds having proven TACE inhibitory activity which were grafted into the database. These compounds mapped well onto the five listed pharmacophoric features. This validated pharmacophore model was also used for alignment of molecules in CoMFA and CoMSIA analysis. The contour maps of the CoMFA/CoMSIA models were utilized to provide structural insight for activity improvement of potential novel TACE inhibitors. The pharmacophore model so developed could be used for in silico screening of any commercial/in house database for identification of TACE inhibiting lead compounds, and the leads so identified could be optimized using the developed CoMSIA model. The present work highlights the tremendous potential of the two mutually complementary ligand-based drug designing techniques (i.e. pharmacophore mapping and 3D-QSAR analysis) using TACE inhibitors as prototype biologically active molecules.","corpus_id":31910353,"score":0},{"doc_id":"21615159","title":"A new protocol for predicting novel GSK-3β ATP competitive inhibitors.","abstract":"Glycogen synthase kinase 3β (GSK-3β) is a potential therapeutic target for cancer, type-2 diabetes, and Alzheimer's disease. This paper proposes a new lead identification protocol that predicts new GSK-3β ATP competitive inhibitors with topologically diverse scaffolds. First, three-dimensional quantitative structure-activity relationship (3D QSAR) models were built and validated. These models are based upon known GSK-3β inhibitors, benzofuran-3-yl-(indol-3-yl) maleimides, by means of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Second, 28 826 maleimide derivatives were selected from the PubChem database. After filtration via Lipinski's rules, 10 429 maleimide derivatives were left. Third, the FlexX-dock program was employed to virtually screen the 10 429 compounds against GSK-3β. This resulted in 617 virtual hits. Fourth, the 3D QSAR models predicted that from the 617 virtual hits, 93 compounds would have GSK-3β inhibition values of less than 15 nM. Finally, from the 93 predicted active hits, 23 compounds were confirmed as GSK-3β inhibitors from literatures; their GSK-3β inhibition ranged from 1.3 to 480 nM. Therefore, the hits rate of our virtual screening protocol is greater than 25%. The protocol combines ligand- and structure-based approaches and therefore validates both approaches and is capable of identifying new hits with topologically diverse scaffolds.","corpus_id":8008681,"score":0},{"doc_id":"21798778","title":"Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors.","abstract":"Cathepsin B has been found being responsible for many human diseases. Inhibitors of cathepsin B, a ubiquitous lysosomal cysteine protease, have been developed as a promising treatment for human diseases resulting from malfunction and over-expression of this enzyme. Through a high throughput screening assay, a set of compounds were found able to inhibit the enzymatic activity of cathepsin B. The binding structures of these active compounds were modeled through docking simulation. Three-dimensional (3D) quantitative structure-activity relationship (QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on the docked structures of the compounds. Strong correlations were obtained for both CoMFA and CoMSIA models with cross-validated correlation coefficients (q²) of 0.605 and 0.605 and the regression correlation coefficients (r²) of 0.999 and 0.997, respectively. The robustness of these models was further validated using leave-one-out (LOO) method and training-test set method. The activities of eight (8) randomly selected compounds were predicted using models built from training set of compounds with prediction errors of less than 1 unit for most compounds in CoMFA and CoMSIA models. Structural features for compounds with improved activity are suggested based on the analysis of the CoMFA and CoMSIA contour maps and the property map of the protein ligand binding site. These results may help to provide better understanding of the structure-activity relationship of cathepsin B inhibitors and to facilitate lead optimization and novel inhibitor design. The multi-conformation method to build 3D QSAR is very effective approach to obtain satisfactory models with high correlation with experimental results and high prediction power for unknown compounds.","corpus_id":13195120,"score":0},{"doc_id":"25405729","title":"3D QSAR studies, pharmacophore modeling and virtual screening on a series of steroidal aromatase inhibitors.","abstract":"Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of SAIs to build 3D QSAR models. The reliable and predictive CoMFA and CoMSIA models were obtained with statistical results (CoMFA: q² = 0.636, r²(ncv) = 0.988, r²(pred) = 0.658; CoMSIA: q² = 0.843, r²(ncv) = 0.989, r²(pred) = 0.601). This 3D QSAR approach provides significant insights that can be used to develop novel and potent SAIs. In addition, Genetic algorithm with linear assignment of hypermolecular alignment of database (GALAHAD) was used to derive 3D pharmacophore models. The selected pharmacophore model contains two acceptor atoms and four hydrophobic centers, which was used as a 3D query for virtual screening against NCI2000 database. Six hit compounds were obtained and their biological activities were further predicted by the CoMFA and CoMSIA models, which are expected to design potent and novel SAIs.","corpus_id":31041745,"score":0},{"doc_id":"26416560","title":"In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening.","abstract":"c-KIT is a component of the platelet-derived growth factor receptor family, classified as type-III receptor tyrosine kinase. c-KIT has been reported to be involved in, small cell lung cancer, other malignant human cancers, and inflammatory and autoimmune diseases associated with mast cells. Available c-KIT inhibitors suffer from tribulations of growing resistance or cardiac toxicity. A combined in silico pharmacophore and structure-based virtual screening was performed to identify novel potential c-KIT inhibitors. In the present study, five molecules from the ZINC database were retrieved as new potential c-KIT inhibitors, using Schrödinger's Maestro 9.0 molecular modeling suite. An atom-featured 3D QSAR model was built using previously reported c-KIT inhibitors containing the indolin-2-one scaffold. The developed 3D QSAR model ADHRR.24 was found to be significant ([Formula: see text]) and instituted to be sufficiently robust with good predictive accuracy, as confirmed through external validation approaches, Y-randomization and GH approach [GH score 0.84 and Enrichment factor (E) 4.964]. The present QSAR model was further validated for the OECD principle 3, in that the applicability domain was calculated using a \"standardization approach.\" Molecular docking of the QSAR dataset molecules and final ZINC hits were performed on the c-KIT receptor (PDB ID: 3G0E). Docking interactions were in agreement with the developed 3D QSAR model. Model ADHRR.24 was explored for ligand-based virtual screening followed by in silico ADME prediction studies. Five molecules from the ZINC database were obtained as potential c-KIT inhibitors with high in -silico predicted activity and strong key binding interactions with the c-KIT receptor.","corpus_id":1963586,"score":0},{"doc_id":"27064095","title":"Exploring Structural and Physicochemical Profiles of Potential GSK-3β Inhibitors Using Structure- and Ligand-Based Modeling Studies.","abstract":"Glycogen synthase kinase-3β (GSK-3β) is a promising target for therapeutic invasion of Alzheimer's disease (AD). The kinase enzyme plays major role in pathological process for the formation of β-amyloid plaques and neurofibrillary tangles in AD. In the present study, structure-based pharmacophore and ligand-based 3D QSAR, HQSAR and pharmacophore mapping studies have been emphasized to explore the possible structural requirement of this potential kinase inhibitors using a structurally diverse set of compounds. The developed models were validated with the interaction study at the catalytic cleft. The 3D QSAR studies yield robust models of CoMFA R(2) = 0.965, se = 0.212, Q(2) = 0.525, R(2)pred = 0.709, r(2)m = 0.579 and CoMSIA: R(2) = 0.935, se = 0.289, Q(2) = 0.581, R(2)pred = 0.723, r(2)m = 0.935, that explain the importance of steric, electrostatic, hydrogen bond (HB) acceptor of the molecule for inhibition of GSK-3β. The HQSAR study (R(2) = 0.871, se = 0.400, Q(2) = 0.639, R(2)pred = 0.721, r(2)m = 0.664) indicated the fragments of the molecular fingerprints that might be important for inhibition. Both structure- and ligand-based pharmacophore mapping proposed that acceptor and donor features of the molecule are essential for receptor-ligand interactions. Molecular diversity provides an opportunity on wide range of applicability for the GSK-3β inhibitors, and depicts information on the structural and properties requirement for effective binding at the active site selectivity that minimize the side effects with therapeutic benefits.","corpus_id":22232142,"score":0},{"doc_id":"28714799","title":"In silico approaches to identify novel myeloid cell leukemia-1 (Mcl-1) inhibitors for treatment of cancer.","abstract":"Myeloid cell leukemia-1 (Mcl-1) has been a validated and attractive target for cancer therapy. Over-expression of Mcl-1 in many cancers allows cancer cells to evade apoptosis and contributes to the resistance to current chemotherapeutics. Here, we identified new Mcl-1 inhibitors using a multi-step virtual screening approach. First, based on two different ligand-receptor complexes, 20 pharmacophore models were established by simultaneously using 'Receptor-Ligand Pharmacophore Generation' method and manual build feature method, and then carefully validated by a test database. Then, pharmacophore-based virtual screening (PB-VS) could be performed by using the 20 pharmacophore models. In addition, docking study was used to predict the possible binding poses of compounds, and the docking parameters were optimized before performing docking-based virtual screening (DB-VS). Moreover, a 3D QSAR model was established by applying the 55 aligned Mcl-1 inhibitors. The 55 inhibitors sharing the same scaffold were docked into the Mcl-1 active site before alignment, then the inhibitors with possible binding conformations were aligned. For the training set, the 3D QSAR model gave a correlation coefficient r(2) of 0.996; for the test set, the correlation coefficient r(2) was 0.812. Therefore, the developed 3D QSAR model was a good model, which could be applied for carrying out 3D QSAR-based virtual screening (QSARD-VS). After the above three virtual screening methods orderly filtering, 23 potential inhibitors with novel scaffolds were identified. Furthermore, we have discussed in detail the mapping results of two potent compounds onto pharmacophore models, 3D QSAR model, and the interactions between the compounds and active site residues.","corpus_id":27820782,"score":0},{"doc_id":"29085766","title":"Exploration of 3,6-dihydroimidazo(4,5-d)pyrrolo(2,3-b)pyridin-2(1H)-one derivatives as JAK inhibitors using various in silico techniques.","abstract":"This study focuses on understanding the structural features of 3,6-dihydroimidazo(4,5-d)pyrrolo(2,3-b)pyridin-2(1H)-one (dpp) derivatives to computationally identify new JAK inhibiting compounds. For the purpose, a novel virtual screening strategy, with 2D and 3D-QSAR (CoMFA and CoMSIA), data mining, pharmacophore modeling, ADMET prediction, multi-targeted protein-based docking and inverse QSAR, was employed. The 2D-QSAR equations developed for the JAK3, JAK2 and JAK1 involved five physicochemical descriptors. These descriptors correlate with the anti-RA activity with R2 values for JAK3, JAK2 and JAK1 are 0.9811, 0.8620 and 0.9740, respectively. The 3D-QSAR studies such as CoMFA and CoMSIA carried out through PLS analysis of the training set of JAK3, JAK2 and JAK1, gave Q2 values as 0.369, 0.476 and 0.490; [Formula: see text] values as 0.863, 0.684 and 0.724 and, F values as 23.098, 28.139 and 31.438, respectively. The contour maps produced by the CoMFA and CoMSIA models were used to understand the importance of hydrogen bond donor, acceptor, hydrophobic, steric and electrostatic interactions. The molecular docking studies of these selected compounds with various JAK proteins were carried out and the protein-ligand interactions were also studied. The study concluded that dpp15(s) is a highly potent JAK inhibitor with a very good predicted IC50 value.","corpus_id":31580777,"score":0}],"string":"[\n {\n \"doc_id\": \"18219446\",\n \"title\": \"A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants.\",\n \"abstract\": \"Quantitative Structure-Activity Relationships (QSAR) are being used since decades for prediction of biological activity, lead optimization, classification, identification and explanation of the mechanisms of drug action, and prediction of novel structural leads in drug discovery. Though the technique has lived up to its expectations in many aspects, much work still needs to be done in relation to problems related to the rational design of peptides. Peptides are the drugs of choice in many situations, however, designing them rationally is a complicated task and the complexity increases with the length of their sequence. In order to deal with the problem of peptide optimization, one of our recently developed QSAR formalisms CoRIA (Comparative Residue Interaction Analysis) is being expanded and modified as: reverse-CoRIA (rCoRIA) and mixed-CoRIA (mCoRIA) approaches. In these methodologies, the peptide is fragmented into individual units and the interaction energies (van der Waals, Coulombic and hydrophobic) of each amino acid in the peptide with the receptor as a whole (rCoRIA) and with individual active site residues in the receptor (mCoRIA) are calculated, which along with other thermodynamic descriptors, are used as independent variables that are correlated to the biological activity by chemometric methods. As a test case, the three CoRIA methodologies have been validated on a dataset of diverse nonamer peptides that bind to the Class I major histocompatibility complex molecule HLA-A*0201, and for which some structure activity relationships have already been reported. The different models developed, and validated both internally as well as externally, were found to be robust with statistically significant values of r(2) (correlation coefficient) and r(2)(pred) (predictive r(2)). These models were able to identify all the structure activity relationships known for this class of peptides, as well uncover some new relationships. This means that these methodologies will perform well for other peptide datasets too. The major advantage of these approaches is that they explicitly utilize the 3D structures of small molecules or peptides as well as their macromolecular targets, to extract position-specific information about important interactions between the ligand and receptor, which can assist the medicinal and computational chemists in designing new molecules, and biologists in studying the influence of mutations in the target receptor on ligand binding.\",\n \"corpus_id\": 11465528,\n \"score\": 2\n },\n {\n \"doc_id\": \"18515163\",\n \"title\": \"An investigation of structurally diverse carbamates for acetylcholinesterase (AChE) inhibition using 3D-QSAR analysis.\",\n \"abstract\": \"In order to identify the essential structural features and physicochemical properties for acetylcholinesterase (AChE) inhibitory activity in some carbamate derivatives, the systematic QSAR (Quantitative Structure Activity Relationship) studies (CoMFA, advance CoMFA and CoMSIA) have been carried out on a series of (total 78 molecules) taking 52 and 26 molecules in training and test set, respectively. Statistically significant 3D-QSAR (three-dimensional Quantitative Structure Activity Relationship) models were developed on training set molecules using CoMFA and CoMSIA and validated against test set compounds. The highly predictive models (CoMFA q(2)=0.733, r(2)=0.967, predictive r(2)=0.732, CoMSIA q(2)=0.641, r(2)=0.936, predictive r(2)=0.812) well explained the variance in binding affinities both for the training and the test set compounds. The generated models suggest that steric, electrostatic and hydrophobic interactions play an important role in describing the variation in binding affinity. In particular the carbamoyl nitrogen should be more electropositive; substitutions on this nitrogen should have high steric bulk and hydrophobicity while the amino nitrogen should be electronegative in order to have better activity. These studies may provide important insights into structural variations leading to the development of novel AChE inhibitors which may be useful in the development of novel molecules for the treatment of Alzheimer's disease.\",\n \"corpus_id\": 5354346,\n \"score\": 2\n },\n {\n \"doc_id\": \"18630262\",\n \"title\": \"Construction of the pharmacophore model of acetylcholinesterase inhibitor.\",\n \"abstract\": \"Based on ninety three acetylcholinesterase inhibitors (AChEIs) which have the same mechanism of action but are different in structural characteristics, the pharmacophore model for acetylcholinesterase inhibitor was constructed by the CATALYST system. The optimal pharmacophore model with three hydrophobic units, a ring aromatic unit and a hydrogen-bond acceptor unit were confirmed (Weight = 3.29, RMS = 0.53, total cost-null cost = 62.75, Correl = 0.93, Config = 19.05). This pharmacophore model will act on the double active site of acetylcholinesterase and is able to predict the activity of known acetylcholinesterase inhibitors that are used for clinical treatment of Alzheimer's disease (AD), and can be further used to identify structurally diverse compounds that have higher activity treating with Alzheimer's disease (AD) by virtual screening.\",\n \"corpus_id\": 28648492,\n \"score\": 2\n },\n {\n \"doc_id\": \"18855672\",\n \"title\": \"Acetylcholinesterase inhibitors as disease-modifying therapies for Alzheimer's disease.\",\n \"abstract\": \"The therapeutic arsenal for the treatment of Alzheimer's disease (AD) remains confined to a group of four inhibitors of AChE and one NMDA receptor antagonist, which are used to provide a relief of the very late symptoms of the dementia, i.e. the cognitive and functional decline. In line with the growing body of evidence of the pivotal role of the beta-amyloid peptide (Abeta) in the pathogenesis of AD, alternative classes of drugs targeting mainly the formation or the aggregation of Abeta are actively pursued by the pharmaceutical industry, as they could positively modify the course of AD, stopping or slowing down disease progression. While the first amyloid-directed disease-modifying drugs go ahead with their clinical development and could reach the market as soon as 2009, mounting preclinical and clinical evidences is pointing towards a disease-modifying role also for currently marketed anti-Alzheimer AChE inhibitors (AChEIs), particularly for donepezil. In this review, the neuroprotective effects exhibited by currently commercialized AChEIs will be briefly discussed, together with the secondary mechanisms through which they could exert such effects. This review will focus also on particular classes of AChEIs, namely dual binding site AChEIs, which are being purposely designed to target Abeta aggregation and / or other biological targets that contribute to AD pathogenesis, thus constituting very promising disease-modifying anti-Alzheimer drug candidates.\",\n \"corpus_id\": 12235312,\n \"score\": 2\n },\n {\n \"doc_id\": \"19048312\",\n \"title\": \"Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA).\",\n \"abstract\": \"Since the recognition of HIV-1 integrase as a novel and rational target for HIV therapeutics, remarkable progress has been made in the development of integrase inhibitors. Computational techniques have played a critical role in accelerating research in this area. However, most previous computational studies were based solely on ligand information. In the present work, we describe the application of one of our recently developed receptor-based 3D-quantitative structure activity relationships (QSAR) methods, i.e. comparative residue interaction analysis (CoRIA), in exploring the events involved in ligand-integrase binding. In this methodology, the non-bonded interaction energies (van der Waals and Coulombic) of the inhibitors with individual active site residues of the integrase enzyme are calculated and, along with other thermodynamic descriptors, are correlated with biological activity using chemometric methods. Different combinations of descriptors were used to develop three types of QSAR models, all of which were found to be statistically significant by internal and external validation. This is the first report of such a dedicated receptor-based 3D-QSAR approach being applied to comprehend the integrase-inhibitor recognition process. In addition, the study was performed on 13-different series of inhibitors, thereby exploring the most structurally diverse data set ever used in understanding the inhibition of HIV-1 integrase. The major advantage of this technique is that it can quantitatively extract crucial residues and identify the nature of interactions between the ligand and receptor that modulate activity. The models suggest that Asp64, Thr66, Val77, Asp116, Glu152 and Lys159 are the key residues influencing the binding of ligands with the integrase enzyme, and the majority of these results are in line with earlier studies. The approach facilitates easy lead-to-hit conversion and design of novel inhibitors by optimisation of the interaction of ligands with these specific residues of the integrase enzyme.\",\n \"corpus_id\": 21343788,\n \"score\": 2\n },\n {\n \"doc_id\": \"19441865\",\n \"title\": \"Consensus superiority of the pharmacophore-based alignment, over maximum common substructure (MCS): 3D-QSAR studies on carbamates as acetylcholinesterase inhibitors.\",\n \"abstract\": \"In view of the nonavailability of complete X-ray structure of carbamates cocrystallized with AChE enzyme, the 3D-QSAR model development based on cocrystallized conformer (CCBA) as well as docked conformer-based alignment (DCBA) is not feasible. Therefore, the only two alternatives viz. pharmacophore and maximum common substructure-based alignments are left for the 3D-QSAR comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) model development. So, in the present study, the 3D-QSAR models have been developed using both alignment methods, where CoMFA and CoMSIA models based on pharmacophore-based alignment were in good agreement with each other and demonstrated significant superiority over MCS-based alignment in terms of leave-one-out (LOO) cross-validated q(2) values of 0.573 and 0.723 and the r(2) values of 0.972 and 0.950, respectively. The validation of the best CoMFA and CoMSIA models based on pharmacophore (Hip-Hop)-based alignment on a test set of 17 compounds provided significant predictive r(2) [r(2)(pred(test))] of 0.614 and 0.788, respectively. The contour map analyses revealed the relative importance of steric, electrostatic, and hydrophobicity for AChE inhibition activity. However, hydrophobic factor plays a major contribution to the AChE inhibitory activity modulation which is in strong agreement with the fact that the AChE is having a wide active site gorge (approximately 20 A) occupied by a large number of hydrophobic amino acid residues.\",\n \"corpus_id\": 18436858,\n \"score\": 2\n },\n {\n \"doc_id\": \"20580236\",\n \"title\": \"Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors.\",\n \"abstract\": \"Following indications from pharmacophore-based virtual screening of natural product databases, morphinan and isoquinoline compounds were tested in vitro for acetylcholinesterase (AChE) inhibition. After the first screen, active and inactive compounds were used to build a ligand-based pharmacophore model in order to prioritize compounds for biological testing. Among the virtual hits tested, the enrichment of actives was significantly higher than in a random selection of test compounds. The most active compounds were biochemically tested for their activity on mu, delta, and kappa opioid receptors.\",\n \"corpus_id\": 43105539,\n \"score\": 2\n },\n {\n \"doc_id\": \"21074294\",\n \"title\": \"Receptor-dependent (RD) 3D-QSAR approach of a series of benzylpiperidine inhibitors of human acetylcholinesterase (HuAChE).\",\n \"abstract\": \"Acetylcholine inhibitors (AChEIs) are currently considered as potential drugs for treating Alzheimer disease. In this work, we developed a receptor-dependent 3D-QSAR (RD-3D-QSAR) models based on a series of 60 benzylpiperidine inhibitors of human acetylcholinesterase to support the design of new AChEIs. The best two models, A-F (N = 47, q(2) = 0.736, r(2) = 0.860) and C-F (N = 47, q(2) = 0.753, r(2) = =0.900) were developed and validated by a combined GA-PLS approach, available in WOLF. Residues of the aromatic gorge (Tyr341 and Trp439) and catalytic triad (His447) are related to both equations showing the consistency of these models with the SAR. Based on those models we have proposed four new benzylpiperidine derivatives and predicted the pIC(50) for each molecule. The good predicted potency of benzylpiperidine derivative, IIa, indicates that it is a potential candidate as a new HuAChE inhibitor.\",\n \"corpus_id\": 2351356,\n \"score\": 2\n },\n {\n \"doc_id\": \"21251245\",\n \"title\": \"The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies.\",\n \"abstract\": \"BACKGROUND: Alzheimer's disease (AD) is the most common cause of dementia characterized by progressive cognitive impairment in the elderly people. The most dramatic abnormalities are those of the cholinergic system. Acetylcholinesterase (AChE) plays a key role in the regulation of the cholinergic system, and hence, inhibition of AChE has emerged as one of the most promising strategies for the treatment of AD. METHODS: In this study, we suggest a workflow for the identification and prioritization of potential compounds targeted against AChE. In order to elucidate the essential structural features for AChE, three-dimensional pharmacophore models were constructed using Discovery Studio 2.5.5 (DS 2.5.5) program based on a set of known AChE inhibitors. RESULTS: The best five-features pharmacophore model, which includes one hydrogen bond donor and four hydrophobic features, was generated from a training set of 62 compounds that yielded a correlation coefficient of R = 0.851 and a high prediction of fit values for a set of 26 test molecules with a correlation of R² = 0.830. Our pharmacophore model also has a high Güner-Henry score and enrichment factor. Virtual screening performed on the NCI database obtained new inhibitors which have the potential to inhibit AChE and to protect neurons from Aβ toxicity. The hit compounds were subsequently subjected to molecular docking and evaluated by consensus scoring function, which resulted in 9 compounds with high pharmacophore fit values and predicted biological activity scores. These compounds showed interactions with important residues at the active site. CONCLUSIONS: The information gained from this study may assist in the discovery of potential AChE inhibitors that are highly selective for its dual binding sites.\",\n \"corpus_id\": 9421995,\n \"score\": 2\n },\n {\n \"doc_id\": \"21516778\",\n \"title\": \"[Molecular modeling of acetylcholinesterase interaction with irreversible and reversible organophosphorous inhibitors].\",\n \"abstract\": \"Three-dimensional Quantitative Structure-Activity Relationship models were designed for irreversible and reversible acetylcholinesterase inhibitors by molecular modeling methods. In case of irreversible inhibitors CoMFA (the comparative analysis of molecular fields) or CoMSIA (the comparative analysis of indexes of molecular similarity) descriptors together with HYBOT 3D fields provide more statistically valid 3D-QSAR models. This indicates importance of donor-acceptor interactions for irreversible acetylcholinesterase inhibition. In case of reversible organophosphorous inhibitors good quality model for structure-activity relationships was developed using CoMFA fields. The obtained models have good predictive power and can be used for estimation of new organophosphorous compounds inhibitor activity that in turn correlates with toxicity of these compounds.\",\n \"corpus_id\": 32203629,\n \"score\": 2\n },\n {\n \"doc_id\": \"21707398\",\n \"title\": \"In silico design and search for acetylcholinesterase inhibitors in Alzheimer's disease with a suitable pharmacokinetic profile and low toxicity.\",\n \"abstract\": \"Alzheimer's disease is a complex neurodegenerative disorder of the central nervous system, characterized by amyloid-β deposits, τ-protein aggregation, oxidative stress and reduced levels of acetylcholine in the brain. One pharmacological approach is to restore acetylcholine level by inhibiting acetylcholinesterase (AChE) with reversible inhibitors, such as galanthamine, thus helping to improve the cognitive symptoms of the disease. In order to design new galanthamine derivatives and search for novel, potential inhibitors with improved interactions, as well as a suitable pharmacokinetic profile and low toxicity, several molecular modeling techniques were applied. These techniques included the investigation of AChE-drug complexes (1QT1 and 1ACJ Protein Data Bank codes), ligand-binding sites calculation within the active site of the enzyme, pharmacophore perception of galanthamine derivatives, virtual screening, toxicophorical analysis and estimation of pharmacokinetics properties. A total of four galanthamine derivatives having a N-alkyl-phenyl chain were designed, since the tertiary amine substituents could reach the peripheral anionic site that is not occupied by galanthamine. In addition, 12 drug-like compounds from the Ilibdiverse database were selected by virtual screening as novel, hypothetical AChE inhibitors. The toxicophorical analysis revealed that only four proposed inhibitors have chemical groups able to develop mutagenicity and chromosome damage. The remaining compounds showed only mild or none toxicophorical alerts. At least three screened compounds presented theoric parameters consistent with good oral bioavailability. The designed molecules have the potential to become new lead compounds that might guide the design of drugs with optimized pharmacodynamic and pharmacokinetic properties in order to improve the treatment of Alzheimer's disease by creating new pharmacotherapeutic options.\",\n \"corpus_id\": 34580333,\n \"score\": 2\n },\n {\n \"doc_id\": \"22257528\",\n \"title\": \"A review on coumarins as acetylcholinesterase inhibitors for Alzheimer's disease.\",\n \"abstract\": \"Acetylcholinesterase (AChE) enzyme inhibition is an important target for the management of Alzheimer disease (AD) and AChE inhibitors are the main stay drugs for its management. Coumarins are the phytochemicals with wide range of biological activities including AChE inhibition. The scientists have attempted to explore the coumarin template for synthesizing novel AChE inhibitors with additional pharmacological activities including decrease in beta-amyloid (Aβ) deposition and beta-secretase inhibition that are also important for AD management. Most of the designed schemes have involved incorporation of a catalytic site interacting moiety at 3- and 4-positions of the coumarin ring. The present review describes these differently synthesized coumarin derivatives as AChE inhibitors for management of AD.\",\n \"corpus_id\": 35709216,\n \"score\": 2\n },\n {\n \"doc_id\": \"22303974\",\n \"title\": \"QSAR applications during last decade on inhibitors of acetylcholinesterase in Alzheimer's disease.\",\n \"abstract\": \"This article reviews multi-criteria QSAR applications on Acetylcholinesterase inhibitors as palliative drugs for Alzheimer's Disease, published in the period 2001-2011. It includes QSAR models for different series of compounds, comparative studies, and advances in methodologies. This period is marked by a shift in focus from palliative treatment to pathogenesis. However, we believe that research into palliative treatment should continue. More comparative studies are desirable. In order to facilitate comparative and general studies on Acetylcholinesterase inhibitors, a standard experimental protocol for measuring an inhibitor's potency is needed. Finally, we recommend chemists to work closely with system and molecular biologists.\",\n \"corpus_id\": 9649185,\n \"score\": 2\n },\n {\n \"doc_id\": \"22996404\",\n \"title\": \"Molecular docking and receptor-specific 3D-QSAR studies of acetylcholinesterase inhibitors.\",\n \"abstract\": \"The reversible inhibition of acetylcholinesterase (AChE) has become a promising target for the treatment of Alzheimer's disease (AD) which is mainly associated with low in vivo levels of acetylcholine (ACh). The availability of AChE crystal structures with and without a ligand triggered the effort to find a structure-based design of acetylcholinesterase inhibitors (AChEIs) for AD. The major problem observed with the structure-based design was the feeble robustness of the scoring functions toward the correlation of docking scores with inhibitory potencies of known ligands. This prompted us to develop new prediction models using the stepwise regression analysis based on consensus of different docking and their scoring methods (GOLD, LigandFit, and GLIDE). In the present investigation, a dataset of 91 molecules belonging to 9 different structural classes of heterocyclic compounds with an activity range of 0.008 to 281,000 nM was considered for docking studies and development of AChE-specific 3D-QSAR models. The model (M1) developed using consensus of docking scores of scoring functions viz. Glide score, Gold score, Chem score, ASP score, PMF score, and DOCK score was found to be the best (R(2) = 0.938, Q(2) = 0.925, R(pred)(2) = 0.919, R(2)m((overall)) = 0.936) compared to other consensus models. Docking studies revealed that the molecules with proper alignment in the active site gorge and the ability to interact with all the crucial amino acid residues, in particular by forming π-π stacking interactions with Trp84 at the catalytic anionic site (CAS) and Trp279 at peripheral anionic site (PAS), showed augmented potencies with consequent improvement in patient cognition and reduced the formation of senile plaques associated with AD. Further, the descriptors that signify the association of the ligands with the receptor as well as ADME properties of the ligands were also analyzed by means of the set of ligands that have been pre-positioned with respect to a receptor after docking analysis and considered as independent variables to generate a linear model (M3 and M4) using a stepwise multiple linear regression method to get additional insight into the physicochemical requirements for effective binding of ligands with AChE as well as for prediction of AChE inhibition. The developed AChE-specific prediction models (M1-M4) satisfactorily reflect the structure-activity relationship of the existing AChEIs and have all the potential to facilitate the process of design and development of new potent AChEIs.\",\n \"corpus_id\": 16282405,\n \"score\": 2\n },\n {\n \"doc_id\": \"23073222\",\n \"title\": \"The 3D-QSAR study of 110 diverse, dual binding, acetylcholinesterase inhibitors based on alignment independent descriptors (GRIND-2). The effects of conformation on predictive power and interpretability of the models.\",\n \"abstract\": \"The 3D-QSAR analysis based on alignment independent descriptors (GRIND-2) was performed on the set of 110 structurally diverse, dual binding AChE reversible inhibitors. Three separate models were built, based on different conformations, generated following next criteria: (i) minimum energy conformations, (ii) conformation most similar to the co-crystalized ligand conformation, and (iii) docked conformation. We found that regardless on conformation used, all the three models had good statistic and predictivity. The models revealed the importance of protonated pyridine nitrogen of tacrine moiety for anti AChE activity, and recognized HBA and HBD interactions as highly important for the potency. This was revealed by the variables associated with protonated pyridinium nitrogen, and the two amino groups of the linker. MIFs calculated with the N1 (pyridinium nitrogen) and the DRY GRID probes in the AChE active site enabled us to establish the relationship between amino acid residues within AChE active site and the variables having high impact on models. External predictive power of the models was tested on the set of 40 AChE reversible inhibitors, most of them structurally different from the training set. Some of those compounds were tested on the different enzyme source. We found that external predictivity was highly sensitive on conformations used. Model based on docked conformations had superior predictive ability, emphasizing the need for the employment of conformations built by taking into account geometrical restrictions of AChE active site gorge.\",\n \"corpus_id\": 6729282,\n \"score\": 2\n },\n {\n \"doc_id\": \"23353586\",\n \"title\": \"Identification of potential bivalent inhibitors from natural compounds for acetylcholinesterase through in silico screening using multiple pharmacophores.\",\n \"abstract\": \"The symptomatic cure observed in the treatment of Alzheimer's disease (AD) by FDA approved drugs could possibly be due to their specificity against the active site of acetylcholinesterase (AChE) and not by targeting its pathogenicity. The AD pathogenicity involved in AChE protein is mainly due to amyloid beta peptide aggregation, which is triggered specifically by peripheral anionic site (PAS) of AChE. In the present study, a workflow has been developed for the identification and prioritization of potential compounds that could interact not only with the catalytic site but also with the PAS of AChE. To elucidate the essential structural elements of such inhibitors, pharmacophore models were constructed using PHASE, based on a set of fifteen best known AChE inhibitors. All these models on validation were further restricted to the best seven. These were transferred to PHASE database screening platform for screening 89,425 molecules deposited at the \\\"ZINC natural product database\\\". Novel lead molecules retrieved were subsequently subjected to molecular docking and ADME profiling. A set of 12 compounds were identified with high pharmacophore fit values and good predicted biological activity scores. These compounds not only showed higher affinity for catalytic residues, but also for Trp86 and Trp286, which are important, at PAS of AChE. The knowledge gained from this study, could lead to the discovery of potential AChE inhibitors that are highly specific for AD treatment as they are bivalent lead molecules endowed with dual binding ability for both catalytic site and PAS of AChE.\",\n \"corpus_id\": 24103449,\n \"score\": 2\n },\n {\n \"doc_id\": \"23777291\",\n \"title\": \"Acetylcholinesterase inhibitors: structure based design, synthesis, pharmacophore modeling, and virtual screening.\",\n \"abstract\": \"Acetylcholinesterase (AChE) is a main drug target, and its inhibitors have demonstrated functionality in the symptomatic treatment of Alzheimer's disease (AD). In this study, a series of novel AChE inhibitors were designed and their inhibitory activity was evaluated with 2D quantitative structure-activity relationship (QSAR) studies using a training set of 20 known compounds for which IC₅₀ values had previously been determined. The QSAR model was calculated based on seven unique descriptors. Model validation was determined by predicting IC₅₀ values for a test set of 20 independent compounds with measured IC₅₀ values. A correlation analysis was carried out comparing the statistics of the measured IC₅₀ values with predicted ones. These selectivity-determining descriptors were interpreted graphically in terms of principal component analyses (PCA). A 3D pharmacophore model was also created based on the activity of the training set. In addition, absorption, distribution, metabolism, and excretion (ADME) descriptors were also determined to evaluate their pharmacokinetic properties. Finally, molecular docking of these novel molecules into the AChE binding domain indicated that three molecules (6c, 7c, and 7h) should have significantly higher affinities and solvation energies than the known standard drug donepezil. The docking studies of 2H-thiazolo[3,2-a]pyrimidines (6a-6j) and 5H-thiazolo[3,2-a] pyrimidines (7a-7j) with human AChE have demonstrated that these ligands bind to the dual sites of the enzyme. Simple and ecofriendly syntheses and diastereomeric crystallizations of 2H-thiazolo [3,2-a]pyrimidines and 5H-thiazolo[3,2-a] pyrimidines are described. The solid-state structures for the HBr salts of compounds 6a, 6e, 7a, and 7i have been determined using single-crystal X-ray diffraction techniques, and X-ray powder patterns were measured for the bulk solid remaining after solvent was removed from solutions containing 6a and 7a. These studies provide valuable insight for designing more potent and selective inhibitors for the treatment of AD.\",\n \"corpus_id\": 11205381,\n \"score\": 2\n },\n {\n \"doc_id\": \"24010934\",\n \"title\": \"CoMFA, CoMSIA and HQSAR studies of acetylcholinesterase inhibitors.\",\n \"abstract\": \"A quantitative structure-activity relationship (QSAR) study has been carried out on acetylcholinesterase (AChE) inhibitors with comparative field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram quantitative structure-activity relationship (HQSAR). In order to investigate the effect of alignment on modeling and find out the best alignment strategy, three different alignment rules were applied to generate CoMFA and CoMSIA models. Statistical results of the highly significant models (CoMFA q² = 0.748, r² =0.996, predicted r² =0.789; CoMSIA q² =0.755, r² =0.973, predicted r² = 0.706; HQSAR q² = 0.884, r² = 0.973, predicted r² = 0.734) reveal considerable predictive ability. Analysis of the contour maps of CoMFA and CoMSIA models and the atomic contribution maps of HQSAR model may contribute to develop novel and potential AChE inhibitors.\",\n \"corpus_id\": 39548895,\n \"score\": 2\n },\n {\n \"doc_id\": \"24325852\",\n \"title\": \"Pharmacophore mapping-based virtual screening followed by molecular docking studies in search of potential acetylcholinesterase inhibitors as anti-Alzheimer's agents.\",\n \"abstract\": \"Alzheimer's disease (AD) is turning out to be one of the lethal diseases in older people. Acetylcholinesterase (AChE) is a crucial target in designing of drugs against AD. The present in silico study was carried out to explore natural compounds as potential AChE inhibitors. Virtual screening, via drug-like ADMET filter, best pharmacophore model and molecular docking analyses, has been utilized to identify putative novel AChE inhibitors. The InterBioScreen's Natural Compound (NC) database was first filtered by applying drug-like ADMET properties and then with the pharmacophore-based virtual screening followed by molecular docking analyses. Based on docking score, interaction patterns and calculated activity, the final hits were selected and these consist of coumarin and non-coumarin classes of compounds. Few hits were found to have been already reported for their AChE inhibitory activity in different literatures confirming reliability of our pharmacophore model. The remaining hits are suggested to be potential AChE inhibitors for AD.\",\n \"corpus_id\": 2421305,\n \"score\": 2\n },\n {\n \"doc_id\": \"24657052\",\n \"title\": \"Quinolone-benzylpiperidine derivatives as novel acetylcholinesterase inhibitor and antioxidant hybrids for Alzheimer disease.\",\n \"abstract\": \"Design, synthesis and evaluation of new acetylcholinesterase inhibitors by combining quinolinecarboxamide to a benzylpiperidine moiety are described. Then, a series of hybrids have been developed by introducing radical scavengers. Molecular modeling was performed and structure activity relationships are discussed. Among the series, most potent compounds show effective AchE inhibitions, high selectivities over butyrylcholinesterase and high radical scavenging activities. On the basis of this work, the ability of quinolone derivatives to serve in the design of N-benzylpiperidine linked multipotent molecules for the treatment of Alzheimer Disease has been established.\",\n \"corpus_id\": 6497774,\n \"score\": 2\n },\n {\n \"doc_id\": \"25378907\",\n \"title\": \"Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer's disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids.\",\n \"abstract\": \"The design, synthesis, and biochemical evaluation of donepezil-pyridyl hybrids (DPHs) as multipotent cholinesterase (ChE) and monoamine oxidase (MAO) inhibitors for the potential treatment of Alzheimer's disease (AD) is reported. The 3D-quantitative structure-activity relationship study was used to define 3D-pharmacophores for inhibition of MAO A/B, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes and to design DPHs as novel multi-target drug candidates with potential impact in the therapy of AD. DPH14 (Electrophorus electricus AChE [EeAChE]: half maximal inhibitory concentration [IC50] =1.1±0.3 nM; equine butyrylcholinesterase [eqBuChE]: IC50 =600±80 nM) was 318-fold more potent for the inhibition of AChE, and 1.3-fold less potent for the inhibition of BuChE than the reference compound ASS234. DPH14 is a potent human recombinant BuChE (hBuChE) inhibitor, in the same range as DPH12 or DPH16, but 13.1-fold less potent than DPH15 for the inhibition of human recombinant AChE (hAChE). Compared with donepezil, DPH14 is almost equipotent for the inhibition of hAChE, and 8.8-fold more potent for hBuChE. Concerning human monoamine oxidase (hMAO) A inhibition, only DPH9 and 5 proved active, compound DPH9 being the most potent (IC50 [MAO A] =5,700±2,100 nM). For hMAO B, only DPHs 13 and 14 were moderate inhibitors, and compound DPH14 was the most potent (IC50 [MAO B] =3,950±940 nM). Molecular modeling of inhibitor DPH14 within EeAChE showed a binding mode with an extended conformation, interacting simultaneously with both catalytic and peripheral sites of EeAChE thanks to a linker of appropriate length. Absortion, distribution, metabolism, excretion and toxicity analysis showed that structures lacking phenyl-substituent show better druglikeness profiles; in particular, DPHs13-15 showed the most suitable absortion, distribution, metabolism, excretion and toxicity properties. Novel donepezil-pyridyl hybrid DPH14 is a potent, moderately selective hAChE and selective irreversible hMAO B inhibitor which might be considered as a promising compound for further development for the treatment of AD.\",\n \"corpus_id\": 4508492,\n \"score\": 2\n },\n {\n \"doc_id\": \"25960230\",\n \"title\": \"Use of ligand-based pharmacophore modeling and docking approach to find novel acetylcholinesterase inhibitors for treating Alzheimer's.\",\n \"abstract\": \"Alzheimer's disease is a neurological disorder in which the patient suffers from memory loss and impaired cognitive abilities. Though the main cause of the disease is not yet known, depletion of neurotransmitter at synaptic junctions, accumulation of insoluble beta amyloid plaques and neurofibrillary tangles are the main pathologies associated with it. The FDA approved drugs for alzheimer's belong to the category of acetylcholinesterase inhibitors. But most of the drugs have been observed to be associated with adverse side effects. In this study, we have developed a pharmacophore (responsible for interaction with acetylcholinesterase active site) based on the already existing drugs and drug candidates. This pharmacophore was used to search for novel AChE inhibitors with altogether different chemical scaffold using high throughput virtual screening and docking studies. Finally, we have reported two compounds, OPA and OMT, which possess high affinity for catalytic site of AChE enzyme and thus, can be considered as potential AChE inhibitors for the symptomatic treatment of Alzheimer's.\",\n \"corpus_id\": 8243356,\n \"score\": 2\n },\n {\n \"doc_id\": \"26202430\",\n \"title\": \"Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.\",\n \"abstract\": \"Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs.\",\n \"corpus_id\": 205331473,\n \"score\": 2\n },\n {\n \"doc_id\": \"26412714\",\n \"title\": \"6-Methyluracil Derivatives as Bifunctional Acetylcholinesterase Inhibitors for the Treatment of Alzheimer's Disease.\",\n \"abstract\": \"Novel 6-methyluracil derivatives with ω-(substituted benzylethylamino)alkyl chains at the nitrogen atoms of the pyrimidine ring were designed and synthesized. The numbers of methylene groups in the alkyl chains were varied along with the electron-withdrawing substituents on the benzyl rings. The compounds are mixed-type reversible inhibitors of cholinesterases, and some of them show remarkable selectivity for human acetylcholinesterase (hAChE), with inhibitory potency in the nanomolar range, more than 10 000-fold higher than that for human butyrylcholinesterase (hBuChE). Molecular modeling studies indicate that these compounds are bifunctional AChE inhibitors, spanning the enzyme active site gorge and binding to its peripheral anionic site (PAS). In vivo experiments show that the 6-methyluracil derivatives are able to penetrate the blood-brain barrier (BBB), inhibiting brain-tissue AChE. The most potent AChE inhibitor, 3 d (1,3-bis[5-(o-nitrobenzylethylamino)pentyl]-6-methyluracil), was found to improve working memory in scopolamine and transgenic APP/PS1 murine models of Alzheimer's disease, and to significantly decrease the number and area of β-amyloid peptide plaques in the brain.\",\n \"corpus_id\": 42848004,\n \"score\": 2\n },\n {\n \"doc_id\": \"26438408\",\n \"title\": \"Combined 3D-QSAR, molecular docking, and molecular dynamics study of tacrine derivatives as potential acetylcholinesterase (AChE) inhibitors of Alzheimer's disease.\",\n \"abstract\": \"Acetylcholinesterase (AChE) is one of the key targets of drugs for treating Alzheimer's disease (AD). Tacrine is an approved drug with AChE-inhibitory activity. In this paper, 3D-QSAR, molecular docking, and molecular dynamics were carried out in order to study 60 tacrine derivatives and their AChE-inhibitory activities. 3D-QSAR modeling resulted in an optimal CoMFA model with q(2) = 0.552 and r(2) = 0.983 and an optimal CoMSIA model with q(2) = 0.581 and r(2) = 0.989. These QSAR models also showed that the steric and H-bond fields of these compounds are important influences on their activities. The interactions between these inhibitors and AChE were further explored through molecular docking and molecular dynamics simulation. A few key residues (Tyr70, Trp84, Tyr121, Trp279, and Phe330) at the binding site of AChE were identified. The results of this study improve our understanding of the mechanisms of AChE inhibitors and afford valuable information that should aid the design of novel potential AChE inhibitors. Graphical Abstract Superposition of backbone atoms of the lowest-energy structure obtained from MD simulation (magenta) onto those of the structure of the initial molecular docking model (green).\",\n \"corpus_id\": 397898,\n \"score\": 2\n },\n {\n \"doc_id\": \"26832327\",\n \"title\": \"Design and prediction of new acetylcholinesterase inhibitor via quantitative structure activity relationship of huprines derivatives.\",\n \"abstract\": \"Acetylcholinesterase (AChE) is an important enzyme in the pathogenesis of Alzheimer's disease (AD). Comparative quantitative structure-activity relationship (QSAR) analyses on some huprines inhibitors against AChE were carried out using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and hologram QSAR (HQSAR) methods. Three highly predictive QSAR models were constructed successfully based on the training set. The CoMFA, CoMSIA, and HQSAR models have values of r (2) = 0.988, q (2) = 0.757, ONC = 6; r (2) = 0.966, q (2) = 0.645, ONC = 5; and r (2) = 0.957, q (2) = 0.736, ONC = 6. The predictabilities were validated using an external test sets, and the predictive r (2) values obtained by the three models were 0.984, 0.973, and 0.783, respectively. The analysis was performed by combining the CoMFA and CoMSIA field distributions with the active sites of the AChE to further understand the vital interactions between huprines and the protease. On the basis of the QSAR study, 14 new potent molecules have been designed and six of them are predicted to be more active than the best active compound 24 described in the literature. The final QSAR models could be helpful in design and development of novel active AChE inhibitors.\",\n \"corpus_id\": 23383808,\n \"score\": 2\n },\n {\n \"doc_id\": \"27410776\",\n \"title\": \"Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease.\",\n \"abstract\": \"In Alzheimer's disease (AD), the level of Acetylcholine (ACh) neurotransmitter is reduced. Since Acetylcholinesterase (AChE) cleaves ACh, inhibitors of AChE are very much sought after for AD treatment. The side effects of current inhibitors necessitate development of newer AChE inhibitors. Isoalloxazine derivatives have proved to be promising (AChE) inhibitors. However, their structure-activity relationship studies have not been reported till date. In the present work, various quantitative structure-activity relationship (QSAR) building methods such as multiple linear regression (MLR), partial least squares ,and principal component regression were employed to derive 3D-QSAR models using steric and electrostatic field descriptors. Statistically significant model was obtained using MLR coupled with stepwise selection method having r(2) = .9405, cross validated r(2) (q(2)) = .6683, and a high predictability (pred_r(2) = .6206 and standard error, pred_r(2)se = .2491). Steric and electrostatic contribution plot revealed three electrostatic fields E_496, E_386 and E_577 and one steric field S_60 contributing towards biological activity. A ligand-based 3D-pharmacophore model was generated consisting of eight pharmacophore features. Isoalloxazine derivatives were docked against human AChE, which revealed critical residues implicated in hydrogen bonds as well as hydrophobic interactions. The binding modes of docked complexes (AChE_IA1 and AChE_IA14) were validated by molecular dynamics simulation which showed their stable trajectories in terms of root mean square deviation and molecular mechanics/Poisson-Boltzmann surface area binding free energy analysis revealed key residues contributing significantly to overall binding energy. The present study may be useful in the design of more potent Isoalloxazine derivatives as AChE inhibitors.\",\n \"corpus_id\": 3525286,\n \"score\": 2\n },\n {\n \"doc_id\": \"27801451\",\n \"title\": \"The discovery of new acetylcholinesterase inhibitors derived from pharmacophore modeling, virtual screening, docking simulation and bioassays.\",\n \"abstract\": \"Hyperactivity of acetylcholinesterase (AChE) in the brain is the immediate cause of Alzheimer's disease (AD), which is one of the most prevalent fatal diseases afflicting numerous older people. In this research, an in silico study was carried out to find potential AChE inhibitors from a large chemical library. With clustering and lots of comprehensive analysis, some molecules were screened using in vitro bioassays. The IC50 values against AChE ranged from 33.620 to 101.570 μM, while the inhibition ratios at 50 μM ranged from 11.37% to 77.35%. The binding mode between the inhibitor and the binding sites of AChE was studied. Four residues (Tyr133, Tyr124, Ser203 and Trp86) were suggested to be crucial because they can form hydrogen bonds with the ligand. Therefore, ZYQ1 and its derivatives might represent a promising starting point for the development of highly potent lead compounds for the treatment of AD.\",\n \"corpus_id\": 3870340,\n \"score\": 2\n },\n {\n \"doc_id\": \"28275924\",\n \"title\": \"2D-SAR and 3D-QSAR analyses for acetylcholinesterase inhibitors.\",\n \"abstract\": \"Alzheimer's disease (AD) accounts for almost three quarters of dementia patients and interferes people's normal life. Great progress has been made recently in the study of Acetylcholinesterase (AChE), known as one of AD's biomarkers. In this study, acetylcholinesterase inhibitors (AChEI) were collected to build a two-dimensional structure-activity relationship (2D-SAR) model and three-dimensional quantitative structure-activity relationship (3D-QSAR) model based on feature selection method combined with random forest. After calculation, the prediction accuracy of the 2D-SAR model was 89.63% by using the tenfold cross-validation test and 87.27% for the independent test set. Three cutting ways were employed to build 3D-QSAR models. A model with the highest [Formula: see text] (cross-validated correlation coefficient) and [Formula: see text](non-cross-validated correlation coefficient) was obtained to predict AChEI activity. The mean absolute error (MAE) of the training set and the test set was 0.0689 and 0.5273, respectively. In addition, molecular docking was also employed to reveal that the ionization state of the compounds had an impact upon their interaction with AChE. Molecular docking results indicate that Ser124 might be one of the active site residues.\",\n \"corpus_id\": 2412109,\n \"score\": 2\n },\n {\n \"doc_id\": \"28417668\",\n \"title\": \"Exploring molecular structural requirement for AChE inhibition through multi-chemometric and dynamics simulation analyses.\",\n \"abstract\": \"The acetylcholinesterase enzyme (AChE) plays an important role in central and peripheral nervous systems. Acetylcholine (ACh) acts through the regulation of AChE activity, which can play a key role in accelerating senile amyloid β-peptide (Aβ) plaque deposition. Therefore, inhibition of the AChE enzyme can be used as a key principle to prevent ACh depletion. The present study has been emphasized to explore both ligand- and structure-based 3D QSAR, HQSAR, pharmacophore, molecular docking and simulation studies on a set of structurally diverse inhibitors to optimize prime structural features responsible for selective binding to AChE, and vis-à-vis inhibiting enzyme activity. The pharmacophore model showed the importance of HB acceptor and donor, positive ionization and hydrophobic features of the molecule for effective binding. Structure-based docking and simulation studies adjudged the significance of features obtained from ligand-based 3D QSAR, CoMFA (Q(2) = .608, [Formula: see text] = .700), CoMSIA (Q(2) = .632, [Formula: see text] = .734), HQSAR (Q(2) = .850, [Formula: see text] = .693) and pharmacophore (Q(2) = .839, ROCscore = .769) models. The aim of the present study is to identify the essential structural and physicochemical profiles of molecules that can provide therapeutic benefits with less toxicity. Structurally diverse compounds have been used for the study, and the generated models showed the large applicability domain.\",\n \"corpus_id\": 3807493,\n \"score\": 2\n },\n {\n \"doc_id\": \"29198175\",\n \"title\": \"New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer's disease: Synthesis, molecular modeling, NMR, and biological evaluation.\",\n \"abstract\": \"Two new compounds (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dihydroacridin-1(2H)-ylidene)hydrazinecarbothiomide (3) and (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dhihydroacridin-1(2H)-ylidene)hydrazinecarboxamide (4) were synthesized and evaluated for their anticholinesterase activities. In vitro tests performed by NMR and Ellman's tests, pointed to a mixed kinetic mechanism for the inhibition of acetylcholinesterase (AChE). This result was corroborated through further docking and molecular dynamics studies, suggesting that the new compounds can work as gorge-spanning ligands by interacting with two different binding sites inside AChE. Also, in silico toxicity evaluation suggested that these new compounds can be less toxic than tacrine.\",\n \"corpus_id\": 196635597,\n \"score\": 2\n },\n {\n \"doc_id\": \"29336270\",\n \"title\": \"In silico Structure-based Identification of Novel Acetylcholinesterase Inhibitors Against Alzheimer's Disease.\",\n \"abstract\": \"OBJECTIVE AND BACKGROUND: Inhibition of acetylcholinesterase (AChE) has gained much importance since the discovery of the involvement of peripheral anionic site as an allosteric regulator of AChE. Characterized by the formation of β-amyloid plaques, Alzheimer's disease (AD) is currently one of the leading causes of death across the world. Progression in this neurodegenerative disorder causes deficit in the cholinergic activity that leads towards cognitive decline. Therapeutic interventions in AD are largely focused upon AChE inhibitors designed essentially to prevent the loss of cholinergic function. The multifactorial AD pathology calls for Multitarget-directed ligands (MTDLs) to follow up on various components of the disease. Considering this approach, other related AD targets were also selected. Structure-based virtual screening was relied upon for the identification of lead compounds with anti-AD effect. METHOD: Several chemoinformatics approaches were used in this study, reporting four multi-target inhibitors: MCULE-7149246649-0-1, MCULE-6730554226-0-4, MCULE-1176268617-0-6 and MCULE-8592892575-0-1 with high binding energies that indicate better AChE inhibitory activity. Additional in-silico analysis hypothesized the abundant presence of aromatic interactions to be pivotal for interaction of selected compounds to the acetyl-cholinesterase. Additionally, we presented an alternative approach to determine protein-ligand stability by calculating the Gibbs-free energy change over time. Furthermore, this allows to rank potential hits for further in-vitro testing. RESULTS AND CONCLUSION: With no predicted indication of adverse effects on humans, this study unravels four active multi-target inhibitors against AChE with promising affinities and good ADMET profile for the potential use in AD treatment.\",\n \"corpus_id\": 11982852,\n \"score\": 2\n },\n {\n \"doc_id\": \"18444627\",\n \"title\": \"Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.\",\n \"abstract\": \"Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of structurally related steroidal alkaloids as butyrylcholinesterase (BuChE) inhibitors. Docking studies were employed to position the inhibitors into the BuChE active site to determine the most probable binding mode. The strategy was to explore multiple inhibitor conformations in producing a more reliable 3D-QSAR model. These multiple conformations were derived using the FlexS program. The conformation selection step for CoMFA was done by genetic algorithm. The genetic algorithm based CoMFA approach was found to be the best. Both CoMFA and CoMSIA yielded significant cross-validated q(2) values of 0.701 and 0.627 and the r(2) values of 0.979 and 0.982, respectively. These statistically significant models were validated by a test set of five compounds. Comparison of CoMFA and CoMSIA contour maps helped to identify structural requirements for the inhibitors and serves as a basis for the design of the next generation of the inhibitor analogues. The results demonstrate that the combination of ligand-based and receptor-based modeling with use of a genetic algorithm is a powerful approach to build 3D-QSAR models. These data can be used for the lead optimization process with respect to inhibition enhancement which is important for the drug discovery and development for Alzheimer's disease.\",\n \"corpus_id\": 16170684,\n \"score\": 1\n },\n {\n \"doc_id\": \"21094069\",\n \"title\": \"Binding research on flavones as ligands of β-amyloid aggregates by fluorescence and their 3D-QSAR, docking studies.\",\n \"abstract\": \"The K(d)s (dissociation constants) of 21 flavone derivatives have been obtained by fluorescence in vitro when binding with Aβ(1-40) (β-amyloid(1-40)) aggregates protein. Extensive 3D-QSAR (quantitative structure-activity relationship) studies were performed on the fluorescent flavones, which are excellent ligands of Aβ(1-40) aggregates protein. Comparative molecular similarity indices analysis (CoMSIA) technique was used to relate the binding affinities with the ligand structures, and the QSAR model was obtained using the CoMFA technique. The QSAR model was proved to statistically significant and have high predictive power: the CoMSIA model yielded the cross-validated q2 = 0.512 and the non-cross-validated r2 = 0.911. This model showed that electrostatic (22.5%) and H-bond interaction (acceptor 15.3%; donor 45.1%) properties played major roles in ligand binding process. The QSAR model was further graphically interpreted in terms of field contribution maps. In order to further investigate the specific binding site of the flavones in the Aβ(1-40) aggregates, preliminary docking studies were performed. According to the 3D-QSAR results, the possible binding site in the protein was proposed in order to direct the molecular docking studies. A good correlation (R2: 0.846) between the calculated binding energies and the experimental binding affinities (pK(d)s) suggests that the identified binding site is reliable. The 3D-QSAR model and the information of the ligand-protein interaction will be helpful in the selection of flavones to be structurally modified and labeled by a radio nuclide for imaging Aβ(1-40) aggregates in the AD (Alzheimer's disease) brain.\",\n \"corpus_id\": 10016563,\n \"score\": 1\n },\n {\n \"doc_id\": \"22039875\",\n \"title\": \"Hybrid-based multi-target ligands for the treatment of Alzheimer's disease.\",\n \"abstract\": \"Progresses in medicinal chemistry over the last few years have focused on the design and synthesis of hybrid compounds, molecules encompassing in a single scaffold two pharmacophores from known entities endowed with well established biological activities. The interest in this topic is related to the increasing emphasis on the identification of the different factors involved in a number of disorders, such as the complex multifactorial Alzheimer's disease (AD), and hybrid- based strategy has become a focal point in this medicinal chemistry field since it could lead to derivatives with an improved biological profile. Using this strategy, acetylcholinesterase inhibitors (AChEIs) have been extensively coupled with properly selected bioactive molecules to obtain homo- and heterodimers endowed with increased potency together with supplementary actions. In the past decade the inhibition of the AChE induced aggregation of the -amyloid peptide into the senile plaques, which is a key event in the neurotoxic cascade of AD, has been considered a relevant approach leading to several dual binding site inhibitors, able to contact both the peripheral anionic site of AChE and the active site. In recent years, pioneering efforts have been performed to obtain novel AChEIs that, beyond the capability to inhibit AChE, were able to hit a number of specific AD targets. In particular, these compounds proved to possess antioxidant, anti-inflammatory, or neuroprotective activities, useful to block or revert the progression of the disease. This review summarizes the progresses that have been made in the design of hybrid molecules for the treatment of AD.\",\n \"corpus_id\": 12094936,\n \"score\": 1\n },\n {\n \"doc_id\": \"22216416\",\n \"title\": \"New acetylcholinesterase inhibitors for Alzheimer's disease.\",\n \"abstract\": \"Acetylcholinesterase (AChE) remains a highly viable target for the symptomatic improvement in Alzheimer's disease (AD) because cholinergic deficit is a consistent and early finding in AD. The treatment approach of inhibiting peripheral AchE for myasthenia gravis had effectively proven that AchE inhibition was a reachable therapeutic target. Subsequently tacrine, donepezil, rivastigmine, and galantamine were developed and approved for the symptomatic treatment of AD. Since then, multiple cholinesterase inhibitors (ChEI) continue to be developed. These include newer ChEIs, naturally derived ChEIs, hybrids, and synthetic analogues. In this paper, we summarize the different types of ChEIs in development and their respective mechanisms of actions. This pharmacological approach continues to be active with many promising compounds.\",\n \"corpus_id\": 1887212,\n \"score\": 1\n },\n {\n \"doc_id\": \"23039767\",\n \"title\": \"Structure-based design and synthesis of benzothiazole phosphonate analogues with inhibitors of human ABAD-Aβ for treatment of Alzheimer's disease.\",\n \"abstract\": \"Amyloid binding alcohol dehydrogenase, a mitochondrial protein, is a cofactor facilitating amyloid-β peptide (Aβ) induced cell stress. Antagonizing Aβ-ABAD interaction protects against aberrant mitochondrial and neuronal function and improves learning memory in the Alzheimer's disease mouse model. Therefore, it offers a potential target for Alzheimer's drug design, by identifying potential inhibitors of Aβ-ABAD interaction. 2D QSAR methods were applied to novel compounds with known IC(50) values, which formed a training set. A correlation analysis was carried out comparing the statistics of the measured IC(50) with predicted values. These selectivity-determining descriptors were interpreted graphically in terms of principle component analyses, which are highly informative for the lead optimization process with respect to activity enhancement. A 3D pharmacophore model also was created. The 2D QSAR and 3D pharmacophore models will assist in high-throughput screening. In addition, ADME descriptors were also determined to study their pharmacokinetic properties. Finally, amyloid binding alcohol dehydrogenase molecular docking study of these novel molecules was undertaken to determine whether these compounds exhibit significant binding affinity with the binding site. We have synthesized only the compounds that have shown the best drug-like properties as candidates for further studies.\",\n \"corpus_id\": 207104675,\n \"score\": 1\n },\n {\n \"doc_id\": \"23408593\",\n \"title\": \"Interaction of metal chelators with different molecular forms of acetylcholinesterase and its significance in Alzheimer's disease treatment.\",\n \"abstract\": \"The peripheral anionic site (PAS) of acetylcholinesterase (AChE) is involved in amyloid beta (Aβ) peptides aggregation of Alzheimer's disease (AD). AChE exhibits an aryl acylamidase (AAA) activity along with the well known esterase activity. Numerous studies have reported the beneficiary effect of metal chelators in AD treatment. Hence, a comparative study on the effect of metal chelators on both the esterase and AAA activity of AChE globular (G4 and G1) molecular forms was performed. The inhibitory effect of 1,10-phenanthroline was high towards AChE esterase activity. The corresponding IC50 values for esterase activity of G4 and G1-form was 190 µM and 770 µM and for AAA activity it was 270 µM and 2.74 mM, respectively. Kinetic studies on both forms of AChE show that 1,10-phenanthroline inhibits esterase in competitive and AAA activity in non-competitive manner. Protection studies further revealed that the nature of 1,10-phenanthroline inhibition on AChE is through its direct binding to protein rather than its metal chelation property. Molecular docking studies shows orientation of 1,10-phenathroline in the PAS through hydrophobic interactions with the PAS residues (Trp286, Tyr124 and Tyr341) and hydrogen bonding with Phe295. Further molecular dynamics simulation of \\\"hAChE-1,10-phenanthroline\\\" complex revealed that both hydrogen and hydrophobic interaction contribute equally for 1,10-phenanthroline binding to hAChE. Such an interaction of 1,10-phenanthroline on PAS may hinder \\\"AChE-Aβ peptide\\\" complex formation. Hence, 1,10-phenanthroline can act as a lead molecule for developing drug(s) against AD ailment with dual functions namely, anti-cholinesterase and anti-amyloid aggregation potency in a single chemical entity.\",\n \"corpus_id\": 6964800,\n \"score\": 1\n },\n {\n \"doc_id\": \"24805972\",\n \"title\": \"Oxime-dipeptides as anticholinesterase, reactivator of phosphonylated-serine of AChE catalytic triad: probing the mechanistic insight by MM-GBSA, dynamics simulations and DFT analysis.\",\n \"abstract\": \"Neuropathological cascades leading to reduced cholinergic transmission in Alzheimer's disease led to development of AChE-inhibitors. Although lethal dose of some inhibitors cause interruption with AChE mediated mechanism but reversible AChE inhibitors can assist in protection from inhibition of AChE and hence in an aim to probe potential molecules as anticholinesterase and as reactivators, computationally structure-based approach has been exploited in this work for designing new 2-amino-3-pyridoixime-dipeptides conjugates. We have combined MD simulations with flexible ligand docking approach to determine binding specificity of 2-amino-3-pyridoixime dipeptides towards AChE (PDB 2WHP). PAS residues are found to be responsible for oxime-dipeptides binding along with π-π interactions with Trp86 and Tyr286, hydrogen bonding with side chains of Asp74 and Tyr341 (Gscore -10.801 and MM-GBSA free energy -34.89 kcal/mol). The docking results depicted complementary multivalent interactions along with good binding affinity as predicted from MM-GBSA analysis. The 2-amino-3-pyridoxime-(Arg-Asn) AChE systems subjected to MD simulations under explicit solvent systems with NPT and NVT ensemble. MD simulations uncovered dynamic behavior of 2-amino-3-pyridoxime-(Arg-Asn) and exposed its mobile nature and competence to form strong long range-order contacts towards active site residues to approach inhibited serine residue and facilitated via large contribution from hydrogen bonding and water bridges along with slow and large movements of adjacent important residues. In an effort to evaluate the complete potential surface profile, 2-amino-3-pyridoxime induced reactivation pathway of sarin-serine adduct has been investigated by the DFT approach at the vacuum MO6/6-311G (d, p) level along with the Poisson-Boltzmann solvation model and found to be of relatively low energy barrier. The pKa evaluation has revealed the major deprotonated 2-amino-3-pyridoixime species having pKa of 6.47 and hence making 2-amino-3-pyridoxime-(Arg-Asn) potential anticholinesterase and reactivator for AChE under the physiological pH.\",\n \"corpus_id\": 6385396,\n \"score\": 1\n },\n {\n \"doc_id\": \"25435329\",\n \"title\": \"Chemometric design to explore pharmacophore features of BACE inhibitors for controlling Alzheimer's disease.\",\n \"abstract\": \"The β-amyloid precursor protein cleavage enzyme (BACE) has been conceived to be an attractive therapeutic target to control Alzheimer's disease (AD). Validated ligand-based pharmacophore mapping was combined with 3D QSAR modeling approaches that include CoMFA, CoMSIA and HQSAR techniques to identify structural and physico-chemical requirements for a potential BACE inhibitor using a database containing 980 structurally diverse compounds, assembled from different reports. A structure-based docking technique was also used to validate the features obtained from the ligand-based models, which were further used to screen the database of compounds designed by a de novo approach. Contour maps of 3D QSAR models, CoMFA (R(2) = 0.880, se = 0.402, Q(2) = 0.596, Rpred(2) = 0.713,) and CoMSIA (R(2) = 0.903, se = 0.362, Q(2) = 0.578, Rpred(2) = 0.715), and a pharmacophore space model (R(2) = 0.833, rmsd = 1.578, Q(2) = 0.845, Rpred(2) = 0. 764) depict that the models are robust and provide an explanation of the important features such as steric, electrostatic, hydrophobic, positive ionization, hydrogen bond acceptor and donor properties, which play important roles for interaction with the receptor site cavity. The HQSAR study (R(2) = 0.823, se = 0.488, Q(2) = 0.823, Rpred(2) = 0.768) and de novo design, which generate new fragments, illustrated the important molecular fingerprints for inhibition. The docking study elucidated the important interactions between the amino acid residues (Gly11, Thr72, Asp228, Gly230, Thr231, Arg235) at the catalytic site of the receptor and the ligand, indicating the structural requirements of the inhibitors. The de novo designed molecules were further screened for ADMET properties, and ligand-receptor interactions of the top hits were analysed by molecular docking to explore pharmacophore features of BACE inhibitors.\",\n \"corpus_id\": 4717888,\n \"score\": 1\n },\n {\n \"doc_id\": \"25537270\",\n \"title\": \"Sulfonamides as multifunctional agents for Alzheimer's disease.\",\n \"abstract\": \"Sulfonamide linker-based inhibitors with extended linear structure were designed and synthesized with the aim of producing multifunctional agents against several processes involved in the pathology of Alzheimer's disease (AD). The potency of the compounds were assessed in the inhibition of Aβ self-assembly (fibril and oligomer formation), in modulating cholinesterase (AChE, BuChE) activity, and scavenging free radicals. Several compounds exhibited promising Aβ self-assembly and cholinesterase inhibition and in parallel, showed good free radical scavenging properties. The investigation of the scaffold described in this study resulted in the identification of three compounds (14, 19 and 26) as promising leads for the further design of multifunctional drug candidates for AD.\",\n \"corpus_id\": 8665497,\n \"score\": 1\n },\n {\n \"doc_id\": \"25588616\",\n \"title\": \"Ligand-based 3D QSAR analysis of reactivation potency of mono- and bis-pyridinium aldoximes toward VX-inhibited rat acetylcholinesterase.\",\n \"abstract\": \"To predict unknown reactivation potencies of 12 mono- and bis-pyridinium aldoximes for VX-inhibited rat acetylcholinesterase (rAChE), three-dimensional quantitative structure-activity relationship (3D QSAR) analysis has been carried out. Utilizing molecular interaction fields (MIFs) calculated by molecular mechanical (MMFF94) and quantum chemical (B3LYP/6-31G*) methods, two satisfactory ligand-based CoMFA models have been developed: 1. R(2)=0.9989, Q(LOO)(2)=0.9090, Q(LTO)(2)=0.8921, Q(LMO(20%))(2)=0.8853, R(ext)(2)=0.9259, SDEP(ext)=6.8938; 2. R(2)=0.9962, Q(LOO)(2)=0.9368, Q(LTO)(2)=0.9298, Q(LMO(20%))(2)=0.9248, R(ext)(2)=0.8905, SDEP(ext)=6.6756. High statistical significance of the 3D QSAR models has been achieved through the application of several data noise reduction techniques (i.e. smart region definition SRD, fractional factor design FFD, uninformative/iterative variable elimination UVE/IVE) on the original MIFs. Besides the ligand-based CoMFA models, an alignment molecular set constructed by flexible molecular docking has been also studied. The contour maps as well as the predicted reactivation potencies resulting from 3D QSAR analyses help better understand which structural features are associated with increased reactivation potency of studied compounds.\",\n \"corpus_id\": 24958403,\n \"score\": 1\n },\n {\n \"doc_id\": \"25747777\",\n \"title\": \"In silico analysis of binding of neurotoxic venom ligands with acetylcholinesterase for therapeutic use in treatment of Alzheimer's disease.\",\n \"abstract\": \"Acetylcholinesterases (AChE) are enzymes that function in hydrolyzing the neurotransmitter acetylcholine. Diminished levels of acetylcholine have been reported for various neurodegenerative diseases, especially Alzheimer's. Therefore, acetylcholinesterase inhibitors are being considered quite effective in treating these diseases. Fasciculin 2 is a toxin isolated from Eastern green mamba that had been reported as a reversible acetylcholinesterase inhibitor. In this study, we have reported the in silico analysis of venom toxins via various computational tools used for drug designing, to find out the protein-protein interaction of these toxins in complex with acetylcholinesterase enzyme. In total 15 toxins have been selected from the venoms of various species as ligand dataset, to study their binding interactions with the acetylcholinesterase enzyme.\",\n \"corpus_id\": 2244207,\n \"score\": 1\n },\n {\n \"doc_id\": \"25794302\",\n \"title\": \"Pharmacophore based 3DQSAR of phenothiazines as specific human butyrylcholinesterase inhibitors for treatment of Alzheimer's disease.\",\n \"abstract\": \"Quantitative three dimensional structure activity relationship (3D-QSAR) studies were performed on phenothiazine derivatives as Butyrylcholinesterase (BuChE) inhibitors. Pharmacophore Alignment and Scoring Engine (PHASE) was used to develop predictive Common Pharmacophore Hypotheses (CPHs). The alignment thus obtained was used for Comparative Molecular Field Analysis (CoMFA)/Comparative Molecular Similarity Indices Analysis (CoMSIA) model development. A fourpoint common pharmacophore hypothesis, comprising of one acceptor, one hydrophobic region and two aromatic ring centres was generated. A structurally diverse set of 80 molecules was used of which 56 were grouped into training set to develop the model and the rest 24 molecules into test set to validate the CoMFA/CoMSIA models. The models so developed showed a good r(2)predictive of 0.7587 for CoMFA and 0.7737 for CoMSIA. CoMFA and CoMSIA models had excellent Q(2) (cross-validated coefficient) of 0.7125 and 0.7093, respectively which showed high correlative and predictive abilities of the models. The 3-D contour maps of CoMFA/CoMSIA provided interpretable explanation of SAR for the compounds and also permitted interesting conclusions about the substituent effects on the phenothiazine derivatives. The outcomes of the study would help in the rational design of novel and potent therapeutic agents as specific BuChE inhibitors for symptomatic or disease modifying treatment of AD.\",\n \"corpus_id\": 23332125,\n \"score\": 1\n },\n {\n \"doc_id\": \"26003339\",\n \"title\": \"From AChE to BACE1 inhibitors: The role of the amine on the indanone scaffold.\",\n \"abstract\": \"In recent years, a progressive increase in age-related disorders could be observed in most western countries, among which Alzheimer's disease (AD) is one of the most challenging. BACE1 could be seen as an attractive target to develop disease-modifying compounds, and in this context, a new series of hybrid molecules was designed and synthesized, based on a previously identified multitarget lead compound. In particular, the amino side chain was appropriately modified to fit BACE1 as additional target. In vitro testing results pointed out compound 8 (IC50=2.49±0.08 μM), bearing the bulky bis(4-fluorophenyl)methyl)piperazine substituent, as the most potent BACE1 inhibitor of the series.\",\n \"corpus_id\": 19907161,\n \"score\": 1\n },\n {\n \"doc_id\": \"26032855\",\n \"title\": \"Multiple Ligands Targeting Cholinesterases and β-Amyloid: Synthesis, Biological Evaluation of Heterodimeric Compounds with Benzylamine Pharmacophore.\",\n \"abstract\": \"Alzheimer's disease (AD) is a fatal and complex neurodegenerative disorder for which effective treatment remains the unmet challenge. Using donepezil as a starting point, we aimed to develop novel potential anti-AD agents with a multidirectional biological profile. We designed the target compounds as dual binding site acetylcholinesterase inhibitors, where the N-benzylamine pharmacophore is responsible for interactions with the catalytic anionic site of the enzyme. The heteroaromatic fragment responsible for interactions with the peripheral anionic site was modified and three different heterocycles were introduced: isoindoline, isoindolin-1-one, and saccharine. Based on the results of the pharmacological evaluation, we identified compound 8b with a saccharine moiety as the most potent and selective human acetylcholinesterase inhibitor (IC50 = 33 nM) and beta amyloid aggregation inhibitor. It acts as a non-competitive acetylcholinesterase inhibitor and is able to cross the blood-brain barrier in vitro. We believe that compound 8b represents an important lead compound for further development as potential anti-AD agent.\",\n \"corpus_id\": 205417841,\n \"score\": 1\n },\n {\n \"doc_id\": \"26639718\",\n \"title\": \"6-Methyluracil derivatives as acetylcholinesterase inhibitors for treatment of Alzheimer's disease.\",\n \"abstract\": \"BACKGROUND: Alzheimer's disease (AD) is the major age-related progressive neurodegenerative disorder. The brain of AD patients suffers from loss of cholinergic neurons and decreased number of synapses [1]. AD is caused by an imbalance between Aβ production and clearance, resulting in increased amount of Aβ in various forms [2]. Reduction of Aβ production and increasing clearance of Aβ pathogenic forms are key targets in the development of potential therapeutic agents for AD treatment. Unfortunately, only nosotropic approaches for treatment of AD are currently effective in humans. These approaches mainly focus on the inhibition of brain acetyl-cholinesterase (AChE) to increase lifetime of cerebral acetylcholine [3]. It is important to emphasize that AChE itself promotes the formation of Aβ fibrils in vitro and Aβ plaques in the cerebral cortex of transgenic mouse models of AD [4]. This property of AChE results from interaction between Aβ and the peripheral anionic site of the enzyme (PAS) [5]. Dual binding site inhibitors of both catalytic active site (CAS) and PAS can simultaneously improve cognition and slow down the rate of Aβ-induced neural degeneration. Unfortunately, the assortment of AChE PAS ligands is still extremely limited. OBJECTIVE: To study putative advantages of AChE non-charged PAS inhibitors based on 6-methyluracil derivatives for the treatment of Alzheimer's disease. METHODS: In vitro studies. Concentration of drug producing 50% of AChE/BuChE activity inhibition (IC50) was measured using the method of Ellman et al. [6]. Toxicological experiments were performed using IP injection of the different compounds in mice. LD50, dose (in mg/kg) causing lethal effects in 50% of animals was taken as a criterion of toxicity [7]. The ability of compound to block in vitro AChE-induced Aβ1-40 aggregation was studied using a thioflavin T (ThT) fluorescent probe [8].In vivo biological assays. For in vivo blood-brain barrier permeation assay brains were removed 30 min after IP injection of LD50 dose of tested compound injection. The inhibitory potency was measured using the method of Ellman. Scopolamine and transgenic models of AD were used to evaluate the influence of compound 35 on spatial memory performance. Water solution of scopolamine was injected to mice (ip) 20 minutes before starting memory test during 14 days [9]. Mice were assigned to 7 groups, including 4 groups receiving injection (ip) of compound in different dosages, donepezil-treated mice (donepezil is conventionally used to treat Alzheimer's disease), positive and negative control groups. Double transgenic (APP/PS1) mice expressing a chimeric mouse/human amyloid precursor protein and a mutant of human presenilin-1 [10] were assigned to 4 groups, including transgenic animals injected (ip) with compound 35 or donepezil solution, positive (transgenes injected with water) and negative (wild-type mice) controls. To evaluate spatial memory performance, mice were trained on a reward alternation task using a conventional T-maze [11]. The criterion for a mouse having learned the rewarded alternation task was 3 consecutive days of at least 5 correct responses out of the 6 free trials. For β-amyloid peptide load was evaluated quantitatively as a number and summary area of Thioflavine S fluorescent spots in cerebral cortex and hippocampal images using Image J program. Statistical analyses were performed using the Mann-Whitney test. RESULTS: We evaluated the acute toxicity of the most active compounds. The most potent AChE inhibitor compound 35 (IC50 (AChE) = 5 ± 0.5 nM) exhibited the lowest LD50 values (51 mg/kg) and inhibited brain AChE by more than 71 ± 1%. Compound 35 at 10 nM, exhibited a significant (35 ± 9%) inhibitory activity toward human AChE-induced Aβ aggregation. Scopolamine injection induced significant decrease in correct choice percentage in T-maze, as well as decrease in percentage of mice reaching criterion for learning the task by day 14. This memory deficit was relieved to some extent either by compound 35 (5 mg/kg) or donepezil (reference compound) treatment (0.75 mg/kg). Interestingly, higher doses of compound 35 (10 and 15 mg/kg) produced less therapeutic effect on spatial memory deficit. Group of APP/PS1 mice showed 3 times lower percentage of reaching behavioral criterion and lower percentage of correct choice in T-maze alternation task comparing to WT mice, whereas compound 35 (5 mg/kg) or Donepezil treatment effectively improved these parameters in APP/PS1 mice. Compound 35 treatment (5 mg/kg) during 14 days significantly reduced percentage of summary area and number of β-amyloid peptide (βAP) deposits visualized in sections of cerebral cortex, dentate gyrus, and hippocampal CA3 area in APP/PS1 mice. The most prominent reduction of βAP load by compound 35 treatment was found in CA3 area and cerebral cortex. Meanwhile, Donepezil treatment (1 mg/kg) during 14 days significantly reduced βAP load in cerebral cortex but not in dentate gyrus and CA3 area. CONCLUSIONS: Experiments showed that the most potent AChE inhibitor compound 35 (6-methyluracil derivative) permeated the blood-brain barrier, improved working memory in the APP/PS1 transgenic mice and significantly reduced the number and area of Aβ plaques in the brain. Thus, compound 35 is a promising candidate as a bi-functional inhibitor of AChE for treatment of AD.\",\n \"corpus_id\": 4531190,\n \"score\": 1\n },\n {\n \"doc_id\": \"27823887\",\n \"title\": \"Targeting Alzheimer's disease by investigating previously unexplored chemical space surrounding the cholinesterase inhibitor donepezil.\",\n \"abstract\": \"A series of twenty seven acetylcholinesterase inhibitors, as potential agents for the treatment of Alzheimer's disease, were designed and synthesised based upon previously unexplored chemical space surrounding the molecular skeleton of the drug donepezil, which is currently used for the management of mild to severe Alzheimer's disease. Two series of analogues were prepared, the first looking at the replacement of the piperidine ring in donepezil with different sized saturated N-containing ring systems and the second looking at the introduction of different linkers between the indanone and piperidine rings in donepezil. The most active analogue 5,6-dimethoxy-1-oxo-2,3-dihydro-1H-inden-2-yl 1-benzylpiperidine-4-carboxylate (67) afforded an in vitro IC50 value of 0.03 ± 0.07 μM against acetylcholinesterase with no cytotoxicity observed (IC50 of >100 μM, SH-SY5Y cell line). In comparison donepezil had an IC50 of 0.05 ± 0.06 μM and an observed cytotoxicity IC50 of 15.54 ± 1.12 μM. Molecular modelling showed a strong correlation between activity and in silico binding in the active site of acetylcholinesterase.\",\n \"corpus_id\": 36967057,\n \"score\": 1\n },\n {\n \"doc_id\": \"29676170\",\n \"title\": \"Discovery of novel dual acetylcholinesterase inhibitors with antifibrillogenic activity related to Alzheimer's disease.\",\n \"abstract\": \"AIM: Alzheimer's disease is a progressive and neurodegenerative disorder of the CNS, affecting elderly people. The current pharmacological approach is based on the improvement of cholinergic neurotransmission by inhibiting acetylcholinesterase (AChE) with AChE inhibitors. The disease is also characterized by the accelerated accumulation of β-amyloid plaques around neurons. Furthermore, in vitro studies revealed that AChE can induce β-amyloid peptide (Aβ) aggregation. METHODOLOGY: Computer-aided molecular design by virtual screening was here employed to discover novel potential AChE inhibitors, with antifibrillogenic properties, in other words, inhibiting Aβ aggregation. RESULTS: Compounds 1, 4 and 6 showed interesting AChE inhibition. In addition, they particularly inhibit Aβ aggregation in vitro, indicating to be promising novel anti-Alzheimer agents.\",\n \"corpus_id\": 4973994,\n \"score\": 1\n },\n {\n \"doc_id\": \"18076152\",\n \"title\": \"3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors.\",\n \"abstract\": \"The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B polymerase inhibitory activity of structurally diverse test set compounds and to yield reliable clues for further optimization of the benzimidazole derivatives in the data set.\",\n \"corpus_id\": 21651552,\n \"score\": 0\n },\n {\n \"doc_id\": \"18771818\",\n \"title\": \"3D-QSAR studies of boron-containing dipeptides as proteasome inhibitors with CoMFA and CoMSIA methods.\",\n \"abstract\": \"Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed for a series of dipeptide boronate proteasome inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. A training set containing 46 molecules served to establish the models. The optimum CoMFA and CoMSIA models obtained for the training set were all statistically significant with cross-validated coefficients (q(2)) of 0.676 and 0.630 and conventional coefficients (r(2)) of 0.989 and 0.956, respectively. The predictive capacities of both models were successfully validated by calculating a test set of 13 molecules that were not included in the training set. The predicted correlation coefficients (r(2)(pred)) of CoMFA and CoMSIA are 0.963 and 0.919, respectively. The CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of beta5 subunit of 20S proteasome, which suggests that the 3D-QSAR models constructed in this paper can be used to guide the development of novel dipeptide boronate inhibitors of 20S proteasome.\",\n \"corpus_id\": 30412104,\n \"score\": 0\n },\n {\n \"doc_id\": \"19779936\",\n \"title\": \"Receptor based 3D-QSAR to identify putative binders of Mycobacterium tuberculosis Enoyl acyl carrier protein reductase.\",\n \"abstract\": \"In the current study, the applicability and scope of 3D-QSAR models (CoMFA and CoMSIA) to complement virtual screening using 3D pharmacophore and molecular docking is examined and applied to identify potential hits against Mycobacterium tuberculosis Enoyl acyl carrier protein reductase (MtENR). Initially CoMFA and CoMSIA models were developed using series of structurally related arylamides as MtENR inhibitors. Docking studies were employed to position the inhibitors into MtENR active site to derive receptor based 3D-QSAR models. Both CoMFA and CoMSIA yielded significant cross validated q(2) values of 0.663 and 0.639 and r(2) values of 0.989 and 0.963, respectively. The statistically significant models were validated by a test set of eight compounds with predictive r(2) value of 0.882 and 0.875 for CoMFA and CoMSIA. The contour maps from 3D-QSAR models in combination with docked binding structures help to better interpret the structure activity relationship. Integrated with CoMFA and CoMSIA predictive models structure based (3D-pharmacophore and molecular docking) virtual screening have been employed to explore potential hits against MtENR. A representative set of 20 compounds with high predicted IC(50) values were sorted out in the present study.\",\n \"corpus_id\": 11563646,\n \"score\": 0\n },\n {\n \"doc_id\": \"20179991\",\n \"title\": \"Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors.\",\n \"abstract\": \"A chemical feature-based pharmacophore model was developed for Tumor Necrosis Factor-alpha converting enzyme (TACE) inhibitors. A five point pharmacophore model having two hydrogen bond acceptors (A), one hydrogen bond donor (D) and two aromatic rings (R) with discrete geometries as pharmacophoric features was developed. The pharmacophore model so generated was then utilized for in silico screening of a database. The pharmacophore model so developed was validated by using four compounds having proven TACE inhibitory activity which were grafted into the database. These compounds mapped well onto the five listed pharmacophoric features. This validated pharmacophore model was also used for alignment of molecules in CoMFA and CoMSIA analysis. The contour maps of the CoMFA/CoMSIA models were utilized to provide structural insight for activity improvement of potential novel TACE inhibitors. The pharmacophore model so developed could be used for in silico screening of any commercial/in house database for identification of TACE inhibiting lead compounds, and the leads so identified could be optimized using the developed CoMSIA model. The present work highlights the tremendous potential of the two mutually complementary ligand-based drug designing techniques (i.e. pharmacophore mapping and 3D-QSAR analysis) using TACE inhibitors as prototype biologically active molecules.\",\n \"corpus_id\": 31910353,\n \"score\": 0\n },\n {\n \"doc_id\": \"21615159\",\n \"title\": \"A new protocol for predicting novel GSK-3β ATP competitive inhibitors.\",\n \"abstract\": \"Glycogen synthase kinase 3β (GSK-3β) is a potential therapeutic target for cancer, type-2 diabetes, and Alzheimer's disease. This paper proposes a new lead identification protocol that predicts new GSK-3β ATP competitive inhibitors with topologically diverse scaffolds. First, three-dimensional quantitative structure-activity relationship (3D QSAR) models were built and validated. These models are based upon known GSK-3β inhibitors, benzofuran-3-yl-(indol-3-yl) maleimides, by means of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Second, 28 826 maleimide derivatives were selected from the PubChem database. After filtration via Lipinski's rules, 10 429 maleimide derivatives were left. Third, the FlexX-dock program was employed to virtually screen the 10 429 compounds against GSK-3β. This resulted in 617 virtual hits. Fourth, the 3D QSAR models predicted that from the 617 virtual hits, 93 compounds would have GSK-3β inhibition values of less than 15 nM. Finally, from the 93 predicted active hits, 23 compounds were confirmed as GSK-3β inhibitors from literatures; their GSK-3β inhibition ranged from 1.3 to 480 nM. Therefore, the hits rate of our virtual screening protocol is greater than 25%. The protocol combines ligand- and structure-based approaches and therefore validates both approaches and is capable of identifying new hits with topologically diverse scaffolds.\",\n \"corpus_id\": 8008681,\n \"score\": 0\n },\n {\n \"doc_id\": \"21798778\",\n \"title\": \"Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors.\",\n \"abstract\": \"Cathepsin B has been found being responsible for many human diseases. Inhibitors of cathepsin B, a ubiquitous lysosomal cysteine protease, have been developed as a promising treatment for human diseases resulting from malfunction and over-expression of this enzyme. Through a high throughput screening assay, a set of compounds were found able to inhibit the enzymatic activity of cathepsin B. The binding structures of these active compounds were modeled through docking simulation. Three-dimensional (3D) quantitative structure-activity relationship (QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on the docked structures of the compounds. Strong correlations were obtained for both CoMFA and CoMSIA models with cross-validated correlation coefficients (q²) of 0.605 and 0.605 and the regression correlation coefficients (r²) of 0.999 and 0.997, respectively. The robustness of these models was further validated using leave-one-out (LOO) method and training-test set method. The activities of eight (8) randomly selected compounds were predicted using models built from training set of compounds with prediction errors of less than 1 unit for most compounds in CoMFA and CoMSIA models. Structural features for compounds with improved activity are suggested based on the analysis of the CoMFA and CoMSIA contour maps and the property map of the protein ligand binding site. These results may help to provide better understanding of the structure-activity relationship of cathepsin B inhibitors and to facilitate lead optimization and novel inhibitor design. The multi-conformation method to build 3D QSAR is very effective approach to obtain satisfactory models with high correlation with experimental results and high prediction power for unknown compounds.\",\n \"corpus_id\": 13195120,\n \"score\": 0\n },\n {\n \"doc_id\": \"25405729\",\n \"title\": \"3D QSAR studies, pharmacophore modeling and virtual screening on a series of steroidal aromatase inhibitors.\",\n \"abstract\": \"Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of SAIs to build 3D QSAR models. The reliable and predictive CoMFA and CoMSIA models were obtained with statistical results (CoMFA: q² = 0.636, r²(ncv) = 0.988, r²(pred) = 0.658; CoMSIA: q² = 0.843, r²(ncv) = 0.989, r²(pred) = 0.601). This 3D QSAR approach provides significant insights that can be used to develop novel and potent SAIs. In addition, Genetic algorithm with linear assignment of hypermolecular alignment of database (GALAHAD) was used to derive 3D pharmacophore models. The selected pharmacophore model contains two acceptor atoms and four hydrophobic centers, which was used as a 3D query for virtual screening against NCI2000 database. Six hit compounds were obtained and their biological activities were further predicted by the CoMFA and CoMSIA models, which are expected to design potent and novel SAIs.\",\n \"corpus_id\": 31041745,\n \"score\": 0\n },\n {\n \"doc_id\": \"26416560\",\n \"title\": \"In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening.\",\n \"abstract\": \"c-KIT is a component of the platelet-derived growth factor receptor family, classified as type-III receptor tyrosine kinase. c-KIT has been reported to be involved in, small cell lung cancer, other malignant human cancers, and inflammatory and autoimmune diseases associated with mast cells. Available c-KIT inhibitors suffer from tribulations of growing resistance or cardiac toxicity. A combined in silico pharmacophore and structure-based virtual screening was performed to identify novel potential c-KIT inhibitors. In the present study, five molecules from the ZINC database were retrieved as new potential c-KIT inhibitors, using Schrödinger's Maestro 9.0 molecular modeling suite. An atom-featured 3D QSAR model was built using previously reported c-KIT inhibitors containing the indolin-2-one scaffold. The developed 3D QSAR model ADHRR.24 was found to be significant ([Formula: see text]) and instituted to be sufficiently robust with good predictive accuracy, as confirmed through external validation approaches, Y-randomization and GH approach [GH score 0.84 and Enrichment factor (E) 4.964]. The present QSAR model was further validated for the OECD principle 3, in that the applicability domain was calculated using a \\\"standardization approach.\\\" Molecular docking of the QSAR dataset molecules and final ZINC hits were performed on the c-KIT receptor (PDB ID: 3G0E). Docking interactions were in agreement with the developed 3D QSAR model. Model ADHRR.24 was explored for ligand-based virtual screening followed by in silico ADME prediction studies. Five molecules from the ZINC database were obtained as potential c-KIT inhibitors with high in -silico predicted activity and strong key binding interactions with the c-KIT receptor.\",\n \"corpus_id\": 1963586,\n \"score\": 0\n },\n {\n \"doc_id\": \"27064095\",\n \"title\": \"Exploring Structural and Physicochemical Profiles of Potential GSK-3β Inhibitors Using Structure- and Ligand-Based Modeling Studies.\",\n \"abstract\": \"Glycogen synthase kinase-3β (GSK-3β) is a promising target for therapeutic invasion of Alzheimer's disease (AD). The kinase enzyme plays major role in pathological process for the formation of β-amyloid plaques and neurofibrillary tangles in AD. In the present study, structure-based pharmacophore and ligand-based 3D QSAR, HQSAR and pharmacophore mapping studies have been emphasized to explore the possible structural requirement of this potential kinase inhibitors using a structurally diverse set of compounds. The developed models were validated with the interaction study at the catalytic cleft. The 3D QSAR studies yield robust models of CoMFA R(2) = 0.965, se = 0.212, Q(2) = 0.525, R(2)pred = 0.709, r(2)m = 0.579 and CoMSIA: R(2) = 0.935, se = 0.289, Q(2) = 0.581, R(2)pred = 0.723, r(2)m = 0.935, that explain the importance of steric, electrostatic, hydrogen bond (HB) acceptor of the molecule for inhibition of GSK-3β. The HQSAR study (R(2) = 0.871, se = 0.400, Q(2) = 0.639, R(2)pred = 0.721, r(2)m = 0.664) indicated the fragments of the molecular fingerprints that might be important for inhibition. Both structure- and ligand-based pharmacophore mapping proposed that acceptor and donor features of the molecule are essential for receptor-ligand interactions. Molecular diversity provides an opportunity on wide range of applicability for the GSK-3β inhibitors, and depicts information on the structural and properties requirement for effective binding at the active site selectivity that minimize the side effects with therapeutic benefits.\",\n \"corpus_id\": 22232142,\n \"score\": 0\n },\n {\n \"doc_id\": \"28714799\",\n \"title\": \"In silico approaches to identify novel myeloid cell leukemia-1 (Mcl-1) inhibitors for treatment of cancer.\",\n \"abstract\": \"Myeloid cell leukemia-1 (Mcl-1) has been a validated and attractive target for cancer therapy. Over-expression of Mcl-1 in many cancers allows cancer cells to evade apoptosis and contributes to the resistance to current chemotherapeutics. Here, we identified new Mcl-1 inhibitors using a multi-step virtual screening approach. First, based on two different ligand-receptor complexes, 20 pharmacophore models were established by simultaneously using 'Receptor-Ligand Pharmacophore Generation' method and manual build feature method, and then carefully validated by a test database. Then, pharmacophore-based virtual screening (PB-VS) could be performed by using the 20 pharmacophore models. In addition, docking study was used to predict the possible binding poses of compounds, and the docking parameters were optimized before performing docking-based virtual screening (DB-VS). Moreover, a 3D QSAR model was established by applying the 55 aligned Mcl-1 inhibitors. The 55 inhibitors sharing the same scaffold were docked into the Mcl-1 active site before alignment, then the inhibitors with possible binding conformations were aligned. For the training set, the 3D QSAR model gave a correlation coefficient r(2) of 0.996; for the test set, the correlation coefficient r(2) was 0.812. Therefore, the developed 3D QSAR model was a good model, which could be applied for carrying out 3D QSAR-based virtual screening (QSARD-VS). After the above three virtual screening methods orderly filtering, 23 potential inhibitors with novel scaffolds were identified. Furthermore, we have discussed in detail the mapping results of two potent compounds onto pharmacophore models, 3D QSAR model, and the interactions between the compounds and active site residues.\",\n \"corpus_id\": 27820782,\n \"score\": 0\n },\n {\n \"doc_id\": \"29085766\",\n \"title\": \"Exploration of 3,6-dihydroimidazo(4,5-d)pyrrolo(2,3-b)pyridin-2(1H)-one derivatives as JAK inhibitors using various in silico techniques.\",\n \"abstract\": \"This study focuses on understanding the structural features of 3,6-dihydroimidazo(4,5-d)pyrrolo(2,3-b)pyridin-2(1H)-one (dpp) derivatives to computationally identify new JAK inhibiting compounds. For the purpose, a novel virtual screening strategy, with 2D and 3D-QSAR (CoMFA and CoMSIA), data mining, pharmacophore modeling, ADMET prediction, multi-targeted protein-based docking and inverse QSAR, was employed. The 2D-QSAR equations developed for the JAK3, JAK2 and JAK1 involved five physicochemical descriptors. These descriptors correlate with the anti-RA activity with R2 values for JAK3, JAK2 and JAK1 are 0.9811, 0.8620 and 0.9740, respectively. The 3D-QSAR studies such as CoMFA and CoMSIA carried out through PLS analysis of the training set of JAK3, JAK2 and JAK1, gave Q2 values as 0.369, 0.476 and 0.490; [Formula: see text] values as 0.863, 0.684 and 0.724 and, F values as 23.098, 28.139 and 31.438, respectively. The contour maps produced by the CoMFA and CoMSIA models were used to understand the importance of hydrogen bond donor, acceptor, hydrophobic, steric and electrostatic interactions. The molecular docking studies of these selected compounds with various JAK proteins were carried out and the protein-ligand interactions were also studied. The study concluded that dpp15(s) is a highly potent JAK inhibitor with a very good predicted IC50 value.\",\n \"corpus_id\": 31580777,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":80,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27707790\",\n \"title\": \"Landscape of Genomic Alterations in Pituitary Adenomas.\",\n \"abstract\": \"Purpose: Pituitary adenomas are the second most common primary brain tumor, yet their genetic profiles are incompletely understood. Experimental Design: We performed whole-exome sequencing of 42 pituitary macroadenomas and matched normal DNA. These adenomas included hormonally active and inactive tumors, ones with typical or atypical histology, and ones that were primary or recurrent. Results: We identified mutations, insertions/deletions, and copy-number alterations. Nearly one-third of samples (29%) had chromosome arm-level copy-number alterations across large fractions of the genome. Despite such widespread genomic disruption, these tumors had few focal events, which is unusual among highly disrupted cancers. The other 71% of tumors formed a distinct molecular class, with somatic copy number alterations involving less than 6% of the genome. Among the highly disrupted group, 75% were functional adenomas or atypical null-cell adenomas, whereas 87% of the less-disrupted group were nonfunctional adenomas. We confirmed this association between functional subtype and disruption in a validation dataset of 87 pituitary adenomas. Analysis of previously published expression data from an additional 50 adenomas showed that arm-level alterations significantly impacted transcript levels, and that the disrupted samples were characterized by expression changes associated with poor outcome in other cancers. Arm-level losses of chromosomes 1, 2, 11, and 18 were significantly recurrent. No significantly recurrent mutations were identified, suggesting no genes are altered by exonic mutations across large fractions of pituitary macroadenomas. Conclusions: These data indicate that sporadic pituitary adenomas have distinct copy-number profiles that associate with hormonal and histologic subtypes and influence gene expression. Clin Cancer Res; 23(7); 1841-51. ©2016 AACR.\",\n \"corpus_id\": 207730077\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18300794","title":"Pituitary tumors and hyperplasia in multiple endocrine neoplasia type 1 syndrome (MEN1): a case-control study in a series of 77 patients versus 2509 non-MEN1 patients.","abstract":"Patients affected by the multiple endocrine neoplasia type I syndrome (MEN1) display a high incidence of pituitary adenomas, though it is still unknown whether these pituitary tumors have specific pathologic features that would distinguish them from sporadic pituitary adenomas. Pituitary tissue specimens of 77 MEN1 patients from the GTE (Groupe d'étude des Tumeurs Endocrines) register were compared with unselected 2509 non-MEN1 sporadic pituitary tumors and also to a control subgroup of 296 cases, where 1 MEN1 tumor was matched with 4 sporadic tumors of the same hormonal immunoprofile. Sex, age, size, and invasiveness of tumors, and menin gene mutations were documented. Histologic analysis took into account 33 items, including immunocytochemical data, the proliferative marker Ki-67, and an examination of the juxtatumoral pituitary. MEN1 tumors were significantly larger and more often invasive by histology. MEN1 patients with large pituitary tumors (grade IV) were younger than non-MEN1 patients. MEN1 tumors had no other characteristic histologic features and no predominance of any one hormone producing subtype. However, plurihormonal adenomas versus monohormonal and nonimmunoreactive adenomas were more frequent in MEN1 tumors (39%) than in the control non-MEN1 group (P = 0.001). Especially, the growth hormone and prolactin plurihormonality with unusual association with follicle-stimulating hormone, luteinizing hormone, or adrenocorticotropic hormone was more frequent in MEN1 tumors. In addition, multiple adenomas were significantly more frequent (4% vs. 0.1%; P < 0.0001), especially prolactin-adrenocorticotropic hormone. Somatotroph hyperplasia, with or without a microadenoma was found in only 3 MEN1 patients, with growth hormone-releasing hormone hypersecretion by a pancreatic tumor in 2 of them. All types of mutation were observed, including frameshifts, nonsenses, missenses, and 1 case of germline MEN1 encompassing large deletion, strongly suggesting the absence of any phenotype-genotype correlation.","corpus_id":25209721,"score":2},{"doc_id":"18381572","title":"The role of the aryl hydrocarbon receptor-interacting protein gene in familial and sporadic pituitary adenomas.","abstract":"CONTEXT: Mutations have been identified in the aryl hydrocarbon receptor-interacting protein (AIP) gene in familial isolated pituitary adenomas (FIPA). It is not clear, however, how this molecular chaperone is involved in tumorigenesis. OBJECTIVE: AIP sequence changes and expression were studied in FIPA and sporadic adenomas. The function of normal and mutated AIP molecules was studied on cell proliferation and protein-protein interaction. Cellular and ultrastructural AIP localization was determined in pituitary cells. PATIENTS: Twenty-six FIPA kindreds and 85 sporadic pituitary adenoma patients were included in the study. RESULTS: Nine families harbored AIP mutations. Overexpression of wild-type AIP in TIG3 and HEK293 human fibroblast and GH3 pituitary cell lines dramatically reduced cell proliferation, whereas mutant AIP lost this ability. All the mutations led to a disruption of the protein-protein interaction between AIP and phosphodiesterase-4A5. In normal pituitary, AIP colocalizes exclusively with GH and prolactin, and it is found in association with the secretory vesicle, as shown by double-immunofluorescence and electron microscopy staining. In sporadic pituitary adenomas, however, AIP is expressed in all tumor types. In addition, whereas AIP is expressed in the secretory vesicle in GH-secreting tumors, similar to normal GH-secreting cells, in lactotroph, corticotroph, and nonfunctioning adenomas, it is localized to the cytoplasm and not in the secretory vesicles. CONCLUSIONS: Our functional evaluation of AIP mutations is consistent with a tumor-suppressor role for AIP and its involvement in familial acromegaly. The abnormal expression and subcellular localization of AIP in sporadic pituitary adenomas indicate deranged regulation of this protein during tumorigenesis.","corpus_id":28488929,"score":2},{"doc_id":"18628514","title":"Large genomic deletions in AIP in pituitary adenoma predisposition.","abstract":"CONTEXT: Germline mutations in AIP have been recently shown to cause pituitary adenoma predisposition (PAP). Subsequently, many intragenic germline mutations have been reported, both in familial and in sporadic settings. OBJECTIVE: Our objective was to evaluate the possible contribution of large genomic germline AIP deletions, an important mutation type in tumor predisposition syndromes, in PAP. DESIGN: Here, we applied the multiplex ligation-dependent probe amplification assay to examine whether large genomic AIP or MEN1 alterations account for a subset of PAP cases. PATIENTS: The study was performed on familial and sporadic pituitary adenoma cases of European origin, which had previously tested negative for germline AIP and MEN1 mutations by sequencing. RESULTS: Two of 21 pituitary adenoma families (9.5%) were found to harbor an AIP deletion. No copy number changes were detected among 67 sporadic pituitary adenoma patients. No MEN1 deletions were found. CONCLUSIONS: The present study shows that large genomic AIP deletions account for a subset of PAP. Therefore, in suspected PAP cases undergoing counseling and AIP genetic testing, multiplex ligation-dependent probe amplification could be considered if direct sequencing does not identify a mutation.","corpus_id":24578909,"score":2},{"doc_id":"18973139","title":"Frequent loss of the CDKN2C (p18INK4c) gene product in pituitary adenomas.","abstract":"Genomic alterations of cyclin-dependent kinase inhibitors have been demonstrated in a variety of tumor types including brain tumors. Among them, the cyclin-dependent kinase inhibitor 2A (CDKN2A or p16(INK4a)) gene has been shown to be frequently deleted or inactivated in astrocytic tumors. The CDKN2C (p18(INK4c)) gene is functionally related to CDKN2A. Moreover, mice with targeted disruption of CDKN2C alone or combined CDKN2C and cyclin-dependent kinase inhibitor 1B (CDKN1B or p27(Kip1)), or CDKN2C and TP53 gene disruption develop pituitary adenomas (PA) at high frequencies. The purpose of our study was to investigate genetic alterations of the CDKN2C gene by analysis of loss of heterozygosity (LOH), screening for mutations, analysis of promoter methylation, and protein expression in 38 PAs. In addition, genomic alterations and protein expression of the cell cycle genes CDKN2A and its alternatively spliced form, p14(ARF), as well as the retinoblastoma RB1 gene were investigated. LOH at the CDKN2C gene locus was detected in 25% of pituitary adenomas, whereas the RB1 and CDKN2A loci were altered in only 10%. No mutations were detected within the coding regions of the CDKN2C gene. However, 39.5% of adenomas displayed CDKN2C promoter methylation. The absence of CDKN2C protein was correlated with LOH of the CDKN2C locus on chromosome 1 and with methylation of the CDKN2C promoter. This is the first report to describe that the tumor suppressor gene CDKN2C is frequently targeted by genomic alterations in pituitary adenoma. The most common genetic alteration was promoter methylation suggesting that inactivation of CDKN2C by this mechanism may play an important role in pituitary adenoma development. Additional Supporting Information may be found in the online version of this article.","corpus_id":28486628,"score":2},{"doc_id":"20833337","title":"The genetics of pituitary adenomas.","abstract":"Pituitary adenomas are one of the most frequent intracranial tumors with a prevalence of clinically-apparent tumors close to 1:1000 of the general population. They are clinically significant because of hormone overproduction and/or tumor mass effects in addition to the need for neurosurgery, medical therapies and radiotherapy. The majority of pituitary adenomas have a sporadic origin with recognized genetic mutations seldom being found; somatotropinomas are an exception, presenting frequent somatic GNAS mutations. In this and other phenotypes, tumorigenesis could possibly be explained by altered function of genes implicated in cell cycle regulation, growth factors or their receptors, cell-signaling pathways, specific hormonal factors or other molecules with still unclear mechanisms of action. Genetic changes, such as allelic loss or gene amplification, and epigenetic changes, usually by promoter methylation, have been implicated in abnormal gene expression, but alternative mechanisms may be present. Familial cases of pituitary adenomas represent 5% of all pituitary tumors. MEN1 mutations cause multiple endocrine neoplasia type 1 (MEN1), while the Carney complex (CNC) is characterized by mutations in the protein kinase A regulatory subunit-1alpha (PRKAR1A) gene or changes in a locus at 2p16. Recently, a MEN1-like condition, MEN4, was found to be related to mutations in the CDKN1B gene. The clinical entity of familial isolated pituitary adenomas (FIPA) is characterized by genetic defects in the aryl hydrocarbon receptor interacting protein (AIP) gene in about 15% of all kindreds and 50% of homogenous somatotropinoma families. Identification of familial cases of pituitary adenomas is important as these tumors may be more aggressive than their sporadic counterparts.","corpus_id":261272358,"score":2},{"doc_id":"20868211","title":"Atypical pituitary adenomas: incidence, clinical characteristics, and implications.","abstract":"OBJECT: The 2004 WHO classification of pituitary adenomas now includes an \"atypical\" variant, defined as follows: MIB-1 proliferative index greater than 3%, excessive p53 immunoreactivity, and increased mitotic activity. The authors review the incidence of this atypical histopathological subtype and its correlation with tumor subtype, invasion, and surgical features. METHODS: The records of 121 consecutive patients who underwent transsphenoidal surgery for pituitary adenomas during an 18-month period were retrospectively reviewed for evidence of atypical adenomas. RESULTS: Eighteen adenomas (15%) met the criteria for atypical lesions; 17 (94%) of the 18 were macroadenomas. On imaging, 15 (83%) demonstrated imaging evidence of surrounding invasion, compared with 45% of typical adenomas (p = 0.004). Atypical tumors occurred in 12 female (67%) and 6 male (33%) patients. Patient age ranged from 16 to 70 years (mean 48 years). Nine patients (50%) had hormonally active tumors, and 9 had nonfunctional lesions. Four (22%) of the 18 patients presented to us with recurrent tumors. Immunohistochemical analysis demonstrated the following tumor subtypes: GH-secreting adenoma with plurihormonal staining (5 patients [28%]); null-cell adenoma (5 patients [28%]); silent ACTH tumor (3 patients [17%]), ACTH-staining tumor with Cushing's disease (2 patients [11%]), prolactinoma (2 patients [11%]), and silent FSH-staining tumor (1 patient [6%]). The MIB-1 labeling index ranged from 3% to 20% (mean 7%). CONCLUSIONS: Atypical tumors were identified in 15% of resected pituitary adenomas, and they tended to be aggressive, invasive macroadenomas. More longitudinal follow-up is required to determine whether surgical outcomes, potential for recurrence, or metastasis of atypical adenomas vary significantly from their typical counterparts.","corpus_id":6934129,"score":2},{"doc_id":"22772969","title":"Examination of the relationship between chromosome abnormality in pituitary adenomas and tumor invasiveness by normal karyotype analysis and interphase fluorescence staining.","abstract":"To study the potential relationship between chromosome abnormality and tumor invasiveness in pituitary adenomas. To use conventional R-band cytogenetic karyotype analysis and interphase fluorescence in situ hybridization using centromeric probe of chromosomes 8, 9, and 11 to detect chromosome abnormality in 30 cases of pituitary adenoma. All chromosomes except chromosomes 4, 16, and Y show significant variation between invasive and noninvasive pituitary adenomas. Chromosomes 8 and 12 display some type of numeric alteration in all endocrine subtypes of pituitary adenoma. Numeric alterations in chromosomes 9, 11, and 19 are more frequently detected in invasive pituitary adenomas compared with noninvasive tumors. Numeric alterations in chromosomes are common in all endocrine subtype pituitary adenomas. Furthermore, chromosome numbers are significantly different in invasive and noninvasive pituitary adenomas. On the basis of our study and literature review, we conclude that while chromosomes 8 and 12 may play important roles in the occurrence of pituitary adenomas, chromosomes 9, 11, and 19 may be specifically associated with invasiveness.","corpus_id":22049462,"score":2},{"doc_id":"22782554","title":"Mutation and genomic amplification of the PIK3CA proto-oncogene in pituitary adenomas.","abstract":"The tumorigenesis of pituitary adenomas is poorly understood. Mutations of the PIK3CA proto-oncogene, which encodes the p110-α catalytic subunit of PI3K, have been reported in various types of human cancers regarding the role of the gene in cell proliferation and survival through activation of the PI3K/Akt signaling pathway. Only one Chinese study described somatic mutations and amplification of the PIK3CA gene in a large series of pituitary adenomas. The aim of the present study was to determine genetic alterations of PIK3CA in a second series that consisted of 33 pituitary adenomas of different subtypes diagnosed by immunohistochemistry: 6 adrenocorticotropic hormone-secreting microadenomas, 5 growth hormone-secreting macroadenomas, 7 prolactin-secreting macroadenomas, and 15 nonfunctioning macroadenomas. Direct sequencing of exons 9 and 20 assessed by qPCR was employed to investigate the presence of mutations and genomic amplification defined as a copy number ≥4. Previously identified PIK3CA mutations (exon 20) were detected in four cases (12.1%). Interestingly, the Chinese study reported mutations only in invasive tumors, while we found a PIK3CA mutation in one noninvasive corticotroph microadenoma. PIK3CA amplification was observed in 21.2% (7/33) of the cases. This study demonstrates the presence of somatic mutations and amplifications of the PIK3CA gene in a second series of pituitary adenomas, corroborating the previously described involvement of the PI3K/Akt signaling pathway in the tumorigenic process of this gland.","corpus_id":2154202,"score":2},{"doc_id":"22855342","title":"Whole-exome sequencing studies of nonhereditary (sporadic) parathyroid adenomas.","abstract":"CONTEXT: Genetic abnormalities, such as those of multiple endocrine neoplasia type 1 (MEN1) and Cyclin D1 (CCND1) genes, occur in <50% of nonhereditary (sporadic) parathyroid adenomas. OBJECTIVE: To identify genetic abnormalities in nonhereditary parathyroid adenomas by whole-exome sequence analysis. DESIGN: Whole-exome sequence analysis was performed on parathyroid adenomas and leukocyte DNA samples from 16 postmenopausal women without a family history of parathyroid tumors or MEN1 and in whom primary hyperparathyroidism due to single-gland disease was cured by surgery. Somatic variants confirmed in this discovery set were assessed in 24 other parathyroid adenomas. RESULTS: Over 90% of targeted exons were captured and represented by more than 10 base reads. Analysis identified 212 somatic variants (median eight per tumor; range, 2-110), with the majority being heterozygous nonsynonymous single-nucleotide variants that predicted missense amino acid substitutions. Somatic MEN1 mutations occurred in six of 16 (∼35%) parathyroid adenomas, in association with loss of heterozygosity on chromosome 11. However, no other gene was mutated in more than one tumor. Mutations in several genes that may represent low-frequency driver mutations were identified, including a protection of telomeres 1 (POT1) mutation that resulted in exon skipping and disruption to the single-stranded DNA-binding domain, which may contribute to increased genomic instability and the observed high mutation rate in one tumor. CONCLUSIONS: Parathyroid adenomas typically harbor few somatic variants, consistent with their low proliferation rates. MEN1 mutation represents the major driver in sporadic parathyroid tumorigenesis although multiple low-frequency driver mutations likely account for tumors not harboring somatic MEN1 mutations.","corpus_id":25412306,"score":2},{"doc_id":"23049073","title":"Somatic complex I disruptive mitochondrial DNA mutations are modifiers of tumorigenesis that correlate with low genomic instability in pituitary adenomas.","abstract":"Mitochondrial DNA (mtDNA) mutations leading to the disruption of respiratory complex I (CI) have been shown to exhibit anti-tumorigenic effects, at variance with those impairing only the function but not the assembly of the complex, which appear to contribute positively to cancer development. Owing to the challenges in the analysis of the multi-copy mitochondrial genome, it is yet to be determined whether tumour-associated mtDNA lesions occur as somatic modifying factors or as germ-line predisposing elements. Here we investigated the whole mitochondrial genome sequence of 20 pituitary adenomas with oncocytic phenotype and identified pathogenic and/or novel mtDNA mutations in 60% of the cases. Using highly sensitive techniques, namely fluorescent PCR and allele-specific locked nucleic acid quantitative PCR, we identified the most likely somatic nature of these mutations in our sample set, since none of the mutations was detected in the corresponding blood tissue of the patients analysed. Furthermore, we have subjected a series of 48 pituitary adenomas to a high-resolution array comparative genomic hybridization analysis, which revealed that CI disruptive mutations, and the oncocytic phenotype, significantly correlate with low number of chromosomal aberrations in the nuclear genome. We conclude that CI disruptive mutations in pituitary adenomas are somatic modifiers of tumorigenesis most likely contributing not only to the development of oncocytic change, but also to a less aggressive tumour phenotype, as indicated by a stable karyotype.","corpus_id":12026300,"score":2},{"doc_id":"23450047","title":"Whole-exome sequencing studies of nonfunctioning pituitary adenomas.","abstract":"CONTEXT: The tumorigenic role of genetic abnormalities in sporadic pituitary nonfunctioning adenomas (NFAs), which usually originate from gonadotroph cells, is unknown. OBJECTIVE: The objective of the study was to identify somatic genetic abnormalities in sporadic pituitary NFAs. DESIGN: Whole-exome sequencing was performed using DNA from 7 pituitary NFAs and leukocyte samples obtained from the same patients. Somatic variants were confirmed by dideoxynucleotide sequencing, and candidate driver genes were assessed in an additional 24 pituitary NFAs. RESULTS: Whole-exome sequencing achieved a high degree of coverage such that approximately 97% of targeted bases were represented by more than 10 base reads; 24 somatic variants were identified and confirmed in the discovery set of 7 pituitary NFAs (mean 3.5 variants/tumor; range 1-7). Approximately 80% of variants occurred as missense single nucleotide variants and the remainder were synonymous changes or small frameshift deletions. Each of the 24 mutations occurred in independent genes with no recurrent mutations. Mutations were not observed in genes previously associated with pituitary tumorigenesis, although somatic variants in putative driver genes including platelet-derived growth factor D (PDGFD), N-myc down-regulated gene family member 4 (NDRG4), and Zipper sterile-α-motif kinase (ZAK) were identified; however, DNA sequence analysis of these in the validation set of 24 pituitary NFAs did not reveal any mutations indicating that these genes are unlikely to contribute significantly in the etiology of sporadic pituitary NFAs. CONCLUSIONS: Pituitary NFAs harbor few somatic mutations consistent with their low proliferation rates and benign nature, but mechanisms other than somatic mutation are likely involved in the etiology of sporadic pituitary NFAs.","corpus_id":13898977,"score":2},{"doc_id":"24781529","title":"A pilot genome-scale profiling of DNA methylation in sporadic pituitary macroadenomas: association with tumor invasion and histopathological subtype.","abstract":"Pituitary adenomas (PAs) are neoplasms that may cause a variety of neurological and endocrine effects. Although known causal contributors include heredity, hormonal influence and somatic mutations, the pathophysiologic mechanisms driving tumorigenesis and invasion of sporadic PAs remain unknown. We hypothesized that alterations in DNA methylation are associated with PA invasion and histopathology subtype, and that genome-scale methylation analysis may complement current classification methods for sporadic PAs. Twenty-four surgically-resected sporadic PAs with varying histopathological subtypes were assigned dichotomized Knosp invasion scores and examined using genome-wide DNA methylation profiling and RNA sequencing. PA samples clustered into subgroups according to functional status. Compared with hormonally-active PAs, nonfunctional PAs exhibited global DNA hypermethylation (mean beta-value 0.47 versus 0.42, P = 0.005); the most significant site of differential DNA methylation was within the promoter region of the potassium voltage-gated channel KCNAB2 (FDR = 5.11×10-10). Pathway analysis of promoter-associated CpGs showed that nonfunctional PAs are potentially associated with the ion-channel activity signal pathway. DNA hypermethylation tended to be negatively correlated with gene expression. DNA methylation analysis may be used to identify candidate genes involved in PA function and may potentially complement current standard immunostaining classification in sporadic PAs. DNA hypermethylation of KCNAB2 and downstream ion-channel activity signal pathways may contribute to the endocrine-inactive status of nonfunctional PAs.","corpus_id":16148820,"score":2},{"doc_id":"25490274","title":"Whole-exome sequencing characterizes the landscape of somatic mutations and copy number alterations in adrenocortical carcinoma.","abstract":"CONTEXT: Adrenocortical carcinoma (ACC) is a rare and lethal malignancy with a poorly defined etiology, and the molecular genetics of ACC are incompletely understood. OBJECTIVE: To utilize whole-exome sequencing for genetic characterization of the underlying somatic mutations and copy number alterations present in ACC. DESIGN: Screening for somatic mutation events and copy number alterations (CNAs) was performed by comparative analysis of tumors and matched normal samples from 41 patients with ACC. RESULTS: In total, 966 nonsynonymous somatic mutations were detected, including 40 tumors with a mean of 16 mutations per sample and one tumor with 314 mutations. Somatic mutations in ACC-associated genes included TP53 (8/41 tumors, 19.5%) and CTNNB1 (4/41, 9.8%). Genes with potential disease-causing mutations included GNAS, NF2, and RB1, and recurrently mutated genes with unknown roles in tumorigenesis comprised CDC27, SCN7A, and SDK1. Recurrent CNAs included amplification at 5p15.33 including TERT (6/41, 14.6%) and homozygous deletion at 22q12.1 including the Wnt repressors ZNRF3 and KREMEN1 (4/41 9.8% and 3/41, 7.3%, respectively). Somatic mutations in ACC-established genes and recurrent ZNRF3 and TERT loci CNAs were mutually exclusive in the majority of cases. Moreover, gene ontology identified Wnt signaling as the most frequently mutated pathway in ACCs. CONCLUSIONS: These findings highlight the importance of Wnt pathway dysregulation in ACC and corroborate the finding of homozygous deletion of Wnt repressors ZNRF3 and KREMEN1. Overall, mutations in either TP53 or CTNNB1 as well as focal CNAs at the ZNRF3 or TERT loci denote mutually exclusive events, suggesting separate mechanisms underlying the development of these tumors.","corpus_id":8510815,"score":2},{"doc_id":"26280510","title":"Whole-Genome Sequencing of Growth Hormone (GH)-Secreting Pituitary Adenomas.","abstract":"CONTEXT: The somatic landscape of pituitary adenomas is largely unknown. Identification of somatic alterations aims at better understanding of tumor pathology. OBJECTIVE: The objective of the study was a genome-wide characterization of somatic single-nucleotide variants, structural variants, and copy-number aberrations in somatotropinomas. DESIGN AND SETTING: Whole-genome sequencing and single-nucleotide polymorphism array analyses were performed on 12 fresh-frozen somatotropinomas and their corresponding blood samples. All the coding somatic variants were confirmed by Sanger sequencing. PATIENTS: Studied tumors were somatotropinomas. Apart from one AIP mutation-positive patient, all cases were mutation negative for the established germline mutations associated with pituitary adenomas. INTERVENTION(S): There were no interventions. MAIN OUTCOME MEASURES: Somatic variants were identified with an established computational pipeline and filtered against germline data. Somatic copy number alteration analyses were performed using segmentation-based approaches. RESULTS: A genome-wide analysis revealed on average 129 somatic single-nucleotide variants per tumor. Further analysis of coding regions showed on average 2.3 single-nucleotide variants per tumor. The only recurrent somatic events were the oncogenic GNAS mutation (p.Arg201Cys) and shared chromosome losses (chromosomes 1, 6, 13, 14, 15, 16, 18, 22). Analysis of somatic structural variants revealed one tumor with a complex chromosomal rearrangement. CONCLUSIONS: Somatotropinomas showed a low number of somatic genetic alterations. Whereas no novel recurrently mutated genes could be identified, the somatic landscape has potential to affect the Ca(2+) and ATP pathways known to be involved in the pituitary tumorigenesis. Further studies, eg, methylome and transcriptome analyses, are needed to investigate possible interplay between the recurrent chromosome losses and epigenetic factors.","corpus_id":34982199,"score":2},{"doc_id":"26701869","title":"Landscape of somatic mutations in sporadic GH-secreting pituitary adenomas.","abstract":"CONTEXT: Alterations in the cAMP signaling pathway are common in hormonally active endocrine tumors. Somatic mutations at GNAS are causative in 30-40% of GH-secreting adenomas. Recently, mutations affecting the USP8 and PRKACA gene have been reported in ACTH-secreting pituitary adenomas and cortisol-secreting adrenocortical adenomas respectively. However, the pathogenesis of many GH-secreting adenomas remains unclear. AIM: Comprehensive genetic characterization of sporadic GH-secreting adenomas and identification of new driver mutations. DESIGN: Screening for somatic mutations was performed in 67 GH-secreting adenomas by targeted sequencing for GNAS, PRKACA, and USP8 mutations (n=31) and next-generation exome sequencing (n=36). RESULTS: By targeted sequencing, known activating mutations in GNAS were detected in five cases (16.1%), while no somatic mutations were observed in both PRKACA and USP8. Whole-exome sequencing identified 132 protein-altering somatic mutations in 31/36 tumors with a median of three mutations per sample (range: 1-13). The only recurrent mutations have been observed in GNAS (31.4% of cases). However, seven genes involved in cAMP signaling pathway were affected in 14 of 36 samples and eight samples harbored variants in genes involved in the calcium signaling or metabolism. At the enrichment analysis, several altered genes resulted to be associated with developmental processes. No significant correlation between genetic alterations and the clinical data was observed. CONCLUSION: This study provides a comprehensive analysis of somatic mutations in a large series of GH-secreting adenomas. No novel recurrent genetic alterations have been observed, but the data suggest that beside cAMP pathway, calcium signaling might be involved in the pathogenesis of these tumors.","corpus_id":-1,"score":2},{"doc_id":"26792934","title":"Very low frequency of germline GPR101 genetic variation and no biallelic defects with AIP in a large cohort of patients with sporadic pituitary adenomas.","abstract":"CONTEXT: Recently, germline and somatic GPR101 p.(E308D) mutation was found in patients with isolated acromegaly. It is not known whether GPR101 point mutations are associated with other histological types of pituitary adenoma. OBJECTIVE: We sought germline GPR101 mutations in patients with sporadic pituitary adenomas, and compared the phenotypes of GPR101 mutation carriers and AIP mutation carriers. DESIGN: An observational cohort study performed between 2007 and 2014 in a single referral center. PARTICIPANTS: This prospective study involved 766 unselected patients (413 women) with sporadic pituitary adenomas of all histotypes. METHODS: Entire GPR101 and AIP coding sequence were screened for germline mutations. RESULTS: Twelve patients (1.6%) were found to carry the GPR101 p.(E308D) mutation or rare GPR101 variants. The minor allele frequency of the GPR101 mutation and variants was higher in patients with pituitary adenomas than in unaffected individuals included in the Exome Aggregation Consortium database. Three of the six patients with the GPR101 p.(E308D) mutation had adult-onset acromegaly, two had adrenocorticotropin-secreting adenomas, and one had a nonfunctioning macroadenoma. Six patients carried rare GPR101 variants. Germline AIP mutations or rare AIP variants were identified in 32 patients (4.2%). AIP mutation carriers were younger at diagnosis than GPR101 mutation carriers and non carriers. None of the patients harbored mutations in both the GPR101 and AIP genes. CONCLUSION: Germline GPR101 mutations are very rare in patients with sporadic pituitary adenomas of various histotypes. No digenism with AIP was identified. Further studies are required to establish whether and how genetic variation in GPR101 gene contributes to pituitary tumorigenesis.","corpus_id":31892731,"score":2},{"doc_id":"27854551","title":"Whole-Exome Sequencing Study of Thyrotropin-Secreting Pituitary Adenomas.","abstract":"Context: Thyrotropin (TSH)-secreting pituitary adenomas (TSHomas) are a rare cause of hyperthyroidism, and the genetic aberrations responsible remain unknown. Objective: To identify somatic genetic abnormalities in TSHomas. Design and Setting: A single-nucleotide polymorphism (SNP) array analysis was performed on 8 TSHomas. Four tumors with no allelic losses or limited loss of heterozygosity were selected, and whole-exome sequencing was performed, including their corresponding blood samples. Somatic variants were confirmed by Sanger sequencing. A set of 8 tumors was also assessed to validate candidate genes. Patients: Twelve patients with sporadic TSHomas were examined. Results: The overall performance of whole-exome sequencing was good, with an average coverage of each base in the targeted region of 97.6%. Six DNA variants were confirmed as candidate driver mutations, with an average of 1.5 somatic mutations per tumor. No mutations were recurrent. Two of these mutations were found in genes with an established role in malignant tumorigenesis (SMOX and SYTL3), and 4 had unknown roles (ZSCAN23, ASTN2, R3HDM2, and CWH43). Similarly, an SNP array analysis revealed frequent chromosomal regions of copy number gains, including recurrent gains at loci harboring 4 of these 6 genes. Conclusions: Several candidate somatic mutations and changes in copy numbers for TSHomas were identified. The results showed no recurrence of mutations in the tumors studied but a low number of mutations, thereby highlighting their benign nature. Further studies on a larger cohort of TSHomas, along with the use of epigenetic and transcriptomic approaches, may reveal the underlying genetic lesions.","corpus_id":3724032,"score":2},{"doc_id":"28486603","title":"Clinical identification of oncogenic drivers and copy number alterations in pituitary tumors.","abstract":"Pituitary tumors are the second most common adult primary brain tumor, with a variable clinical course. Recent work has identified a number of genetic determinants of pituitary tumor subtypes, which may augment classic histopathologic classification schemes. We sought to determine whether pituitary tumors could be stratified based on objective molecular characteristics using a clinical genomics assay. We profiled pituitary tumors using OncoPanel, a clinical multiplexed next-generation sequencing assay and retrospectively collected the clinical information and sequencing results for 127 patients from 2012-2016 at the Brigham and Women's Hospital. We analyzed 127 pituitary tumors, including 114 adenomas, 5 craniopharyngiomas, and 8 tumors of other histologies. We observed recurrent BRAFV600E mutations in papillary craniopharyngiomas, CTNNB1 mutations in adamantinomatous craniopharyngiomas, and activating GNAS mutations in GH-secreting adenomas. Furthermore, we validated the presence of two distinct genomic subclasses in adenomas, those with disrupted or quiet copy-number profiles, and the significant association of disruption with functional hormone status (p < 0.05). We report the first clinical implementation of next-generation sequencing of pituitary tumors. We confirmed previously identified molecular subclasses for these tumors, and show that routine screening as part of clinical practice is both feasible and informative. This large-scale proof of principle study may help to guide future institutional efforts for pituitary tumor classification, as well as incorporation into prospective analysis as part of clinical trials.","corpus_id":22578844,"score":2},{"doc_id":"28790112","title":"Burden and profile of somatic mutation in duodenal adenomas from patients with familial adenomatous- and MUTYH-associated polyposis.","abstract":"PURPOSE: Duodenal polyposis and cancer are important causes of morbidity and mortality in familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP). This study aimed to comprehensively characterize somatic genetic changes in FAP and MAP duodenal adenomas to better understand duodenal tumorigenesis in these disorders.<br /><br />Experimental Design: Sixty-nine adenomas were biopsied during endoscopy in 16 FAP and 10 MAP patients with duodenal polyposis. Ten FAP and 10 MAP adenomas and matched blood DNA samples were exome sequenced, 42 further adenomas underwent targeted sequencing and 47 were studied by array comparative genomic hybridization. Findings in FAP and MAP duodenal adenomas were compared to each other and to the reported mutational landscape in FAP and MAP colorectal adenomas.<br /><br />Results: MAP duodenal adenomas had significantly more protein-changing somatic mutations (P = 0.018), truncating mutations (P = 0.006) and copy number variants (P = 0.005) than FAP duodenal adenomas, even though MAP patients had lower Spigelman stage duodenal polyposis. Fifteen genes were significantly recurrently mutated. Targeted sequencing of APC, KRAS, PTCHD2 and PLCL1 identified further mutations in each of these genes in additional duodenal adenomas. In contrast to MAP and FAP colorectal adenomas, neither exome nor targeted sequencing identified WTX mutations (P=0.0017).<br /><br />Conclusions: The mutational landscapes in FAP and MAP duodenal adenomas overlapped with, but had significant differences to those reported in colorectal adenomas. The significantly higher burden of somatic mutations in MAP than FAP duodenal adenomas despite lower Spigelman stage disease could increase cancer risk in the context of apparently less severe benign disease.","corpus_id":263568241,"score":2},{"doc_id":"29396598","title":"Genomic Alterations in Sporadic Pituitary Tumors.","abstract":"PURPOSE OF REVIEW: Pituitary tumors are undergoing a transformation in histopathologic and molecular classification, coincident with the continued refinement of increasingly powerful methods of genomic annotation and discovery. We highlight novel genomic alterations identified in pituitary adenomas and craniopharyngiomas and discuss their clinical implications. RECENT FINDINGS: Sporadic pituitary adenomas are associated with relatively few recurrent somatic mutations. Recurrent mutations occur largely in subsets of hormone-producing tumors, including GNAS and GPR101 in somatotroph adenomas and USP8 in corticotroph adenomas. Additionally, they manifest with a dichotomous signature of copy number alterations, ranging from almost none to widespread genome instability, while microduplication of chromosome Xq26.3, containing the GNAS gene, defines X-linked acrogigantism. Papillary craniopharyngiomas are defined by BRAF V600E mutations while β-catenin alterations characterize adamantinomatous craniopharyngiomas. Genomic annotation of pituitary tumors is defining increasing subsets of neuroendocrine adenohypophyseal tumors and craniopharyngiomas, offering rationale-based pharmacologic targets and potential biomarkers for clinical outcome.","corpus_id":25114185,"score":2},{"doc_id":"29410024","title":"DNA methylation profiling in nonfunctioning pituitary adenomas.","abstract":"Nonfunctioning pituitary adenomas (NFPAs) are among the most frequent intracranial tumors but their molecular background, including changes in epigenetic regulation, remains poorly understood. We performed genome-wide DNA methylation profiling of 34 NFPAs and normal pituitary samples. Methylation status of the selected genomic regions and expression level of corresponding genes were assessed in a group of 75 patients. NFPAs exhibited distinct global methylation profile as compared to normal pituitary. Aberrant DNA methylation appears to contribute to deregulation of the cancer-related pathways as shown by preliminary functional analysis. Promoter hypermethylation and decreased expression level of SFN, STAT5A, DUSP1, PTPRE and FGFR2 was confirmed in the enlarged group of NFPAs. Difference in the methylation profiles between invasive and non-invasive NFPAs is very slight. Nevertheless, invasiveness-related aberrant epigenetic deregulation of the particular genes was found including upregulation of ITPKB and downregulation CNKSR1 in invasive tumors.","corpus_id":46750106,"score":2},{"doc_id":"29474559","title":"Genomic Alterations and Complex Subclonal Architecture in Sporadic GH-Secreting Pituitary Adenomas.","abstract":"Purpose: The molecular pathogenesis of growth hormone-secreting pituitary adenomas is not fully understood. Cytogenetic alterations might serve as alternative driver events in GNAS mutation-negative somatotroph tumors. Experimental Design: We performed cytogenetic profiling of pituitary adenomas obtained from 39 patients with acromegaly and four patients with sporadic gigantism by using array comparative genomic hybridization analysis. We explored intratumor DNA copy-number heterogeneity in two tumor samples by using DNA fluorescence in situ hybridization (FISH). Results: Based on copy-number profiles, we found two groups of adenomas: a low-copy-number alteration (CNA) group (<12% of genomic disruption, 63% of tumors) and a high-CNA group (24% to 45% of genomic disruption, 37% of tumors). Arm-level CNAs were the most common abnormalities. GNAS mutation-positive adenomas belonged exclusively to the low-CNA group, whereas a subgroup of GNAS mutation-negative adenomas had a high degree of genomic disruption. We detected chromothripsis-related CNA profiles in two adenoma samples from an AIP mutation-positive patient with acromegaly and a patient with sporadic gigantism. RNA sequencing of these two samples identified 17 fusion transcripts, most of which resulted from chromothripsis-related chromosomal rearrangements. DNA FISH analysis of these samples demonstrated a subclonal architecture with up to six distinct cell populations in each tumor. Conclusion: Somatotroph pituitary adenomas display substantial intertumor and intratumor DNA copy-number heterogeneity, as revealed by variable CNA profiles and complex subclonal architecture. The extensive cytogenetic burden in a subgroup of GNAS mutation-negative somatotroph adenomas points to an alternative tumorigenic pathway linked to genomic instability.","corpus_id":3518794,"score":2},{"doc_id":"19401813","title":"Expression of p18(INK4C) is down-regulated in human pituitary adenomas.","abstract":"Cyclin-dependent kinase inhibitors represented by the INK4 family comprising p16(INK4A), p15(INK4B), p18(INK4C), and p19(INK4D) are regulators of the cell cycle shown to be aberrant in many types of cancer. Mice lacking p18(Ink4c) exhibit a series of phenotypes including the development of widespread organomegaly and pituitary adenomas. The objective of our study is to examine the role of p18(INK4C) in the pathogenesis of human pituitary tumors. The protein and mRNA levels of p18(INK4C) were examined by immunohistochemistry and real-time reverse transcription-polymerase chain reaction, respectively. The methylation status of the p18(INK4C) gene promoter and somatic mutations of the p18(INK4C) gene were also investigated. p18(INK4C) protein expression was lost or significantly reduced in 64% of pituitary adenomas compared with levels in normal pituitary glands. p18(INK4C) mRNA levels were low in all ACTH adenomas and non-functioning (NF)-FSH and in 42%, 70% and 66% of GH, PRL, and subtype 3 adenomas, respectively. p18(INK4C) mRNA levels were significantly associated with p18(INK4C) protein levels. Neither methylated promoters in pituitary adenomas, except in one NF-FSH adenoma, nor somatic mutations of the p18(INK4C) gene in any pituitary adenomas were detected. The down-regulation of p18(INK4C) expression may contribute to the tumorigenesis of pituitary adenomas.","corpus_id":38658573,"score":1},{"doc_id":"20015288","title":"Genomic landscape of meningiomas.","abstract":"Meningiomas are one of the most common adult brain tumors. For most patients, surgical excision is curative. However, up to 20% recur. Currently, the molecular determinants predicting recurrence and malignant transformation are lacking. We performed retrospective global genetic and genomic analysis of 85 meningioma samples of various grades. Copy number alterations were assessed by 100K single-nucleotide polymorphism arrays and correlated with gene expression, proliferation indices and clinical outcome. In addition to chromosome 22q loss, which was detected in the majority of clinical samples, chromosome 6q and 14q loss was significantly more common in recurrent tumors and was associated with anaplastic histology. Five \"classes\" of meningiomas were detected by gene expression analysis that correlated with copy number alterations, recurrent status and malignant histology. These classes more accurately identified recurrent tumors relative to Ki-67 index and extent of surgical resection, and highlight substantial expression heterogeneity between meningiomas. These data offer the most complete description of the genomic landscape of meningiomas, and provide broad genomic information that may be used to further stratify meningioma patients into prognostic risk groups.","corpus_id":24557277,"score":1},{"doc_id":"25545346","title":"The genomic landscape of phaeochromocytoma.","abstract":"Phaeochromocytomas (PCCs) and paragangliomas (PGLs) are rare neural crest-derived tumours originating from adrenal chromaffin cells or extra-adrenal sympathetic and parasympathetic tissues. More than a third of PCC/PGL cases are associated with heritable syndromes involving 13 or more known genes. These genes have been broadly partitioned into two groups based on pseudo-hypoxic and receptor tyrosine kinase (RTK) signalling pathways. Many of these genes can also become somatically mutated, although up to one third of sporadic cases have no known genetic driver. Furthermore, little is known of the genes that co-operate with known driver genes to initiate and drive tumourigenesis. To explore the genomic landscape of PCC/PGL, we applied exome sequencing, high-density SNP-array analysis, and RNA sequencing to 36 PCCs and four functional PGL tumours. All tumours displayed low mutation frequency, in contrast to frequent large segmental copy-number alterations, aneuploidy, and evidence for chromothripsis in one case. Multi-region sampling of one benign familial PCC tumour provided evidence for the timing of mutations during tumourigenesis and ongoing clonal evolution. Thirty-one of 40 (77.5%) cases could be explained by germline or somatic mutations or structural alterations affecting known PCC/PGL genes. Deleterious somatic mutations were also identified in known tumour-suppressor genes associated with genome maintenance and epigenetic modulation. A multitude of other genes were also found mutated that are likely important for normal neuroendocrine cell function. We revisited the gene-expression subtyping of PCC/PGL by integrating published microarray data with our RNA-seq data, enabling the identification of six robust gene-expression subtypes. The majority of cases in our cohort with no identifiable driver mutation were classified into a gene-expression subtype bearing similarity to MAX mutant PCC/PGL. Our data suggest there are yet unknown PCC/PGL cancer genes that can phenocopy MAX mutant PCC/PGL tumours. This study provides new insight into the molecular diversity and genetic origins of PCC/PGL tumours.","corpus_id":20412293,"score":1},{"doc_id":"26643872","title":"Genomic landscape of liposarcoma.","abstract":"Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.","corpus_id":3742639,"score":1},{"doc_id":"27221540","title":"Genomic Landscape of Colorectal Mucosa and Adenomas.","abstract":"The molecular basis of the adenoma-to-carcinoma transition has been deduced using comparative analysis of genetic alterations observed through the sequential steps of intestinal carcinogenesis. However, comprehensive genomic analyses of adenomas and at-risk mucosa are still lacking. Therefore, our aim was to characterize the genomic landscape of colonic at-risk mucosa and adenomas. We analyzed the mutation profile and copy number changes of 25 adenomas and adjacent mucosa from 12 familial adenomatous polyposis patients using whole-exome sequencing and validated allelic imbalances (AI) in 37 adenomas using SNP arrays. We assessed for evidence of clonality and performed estimations on the proportions of driver and passenger mutations using a systems biology approach. Adenomas had lower mutational rates than did colorectal cancers and showed recurrent alterations in known cancer driver genes (APC, KRAS, FBXW7, TCF7L2) and AIs in chromosomes 5, 7, and 13. Moreover, 80% of adenomas had somatic alterations in WNT pathway genes. Adenomas displayed evidence of multiclonality similar to stage I carcinomas. Strong correlations between mutational rate and patient age were observed in at-risk mucosa and adenomas. Our data indicate that at least 23% of somatic mutations are present in at-risk mucosa prior to adenoma initiation. The genomic profiles of at-risk mucosa and adenomas illustrate the evolution from normal tissue to carcinoma via greater resolution of molecular changes at the inflection point of premalignant lesions. Furthermore, substantial genomic variation exists in at-risk mucosa before adenoma formation, and deregulation of the WNT pathway is required to foster carcinogenesis. Cancer Prev Res; 9(6); 417-27. ©2016 AACR.","corpus_id":25118462,"score":1},{"doc_id":"27340278","title":"Whole-Exome Sequencing of Salivary Gland Mucoepidermoid Carcinoma.","abstract":"PURPOSE: Mucoepidermoid carcinoma (MEC) is the most common salivary gland malignancy. To explore the genetic origins of MEC, we performed systematic genomic analyses of these tumors. EXPERIMENTAL DESIGN: Whole-exome sequencing and gene copy-number analyses were performed for 18 primary cancers with matched normal tissue. FISH was used to determine the presence or absence of the MECT1-MAML2 translocation in 17 tumors. RESULTS: TP53 was the most commonly mutated gene in MEC (28%), and mutations were found only in intermediate- and high-grade tumors. Tumors with TP53 mutations had more mutations overall than tumors without TP53 mutations (P = 0.006). POU6F2 was the second most frequently mutated gene, found in three low-grade MECs with the same in-frame deletion. Somatic alterations in IRAK1, MAP3K9, ITGAL, ERBB4, OTOGL, KMT2C, and OBSCN were identified in at least two of the 18 tumors sequenced. FISH analysis confirmed the presence of the MECT1-MAML2 translocation in 15 of 17 tumors (88%). CONCLUSIONS: Through these integrated genomic analyses, MECT1-MAML2 translocation and somatic TP53 and POU6F2 mutations appear to be the main drivers of MEC. Clin Cancer Res; 23(1); 283-8. ©2016 AACR.","corpus_id":24241276,"score":1},{"doc_id":"27723760","title":"The genomic landscape of schwannoma.","abstract":"Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q. The fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma. Methylation profiling identified distinct molecular subgroups of schwannomas that were associated with anatomical location. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated ERK, increased proliferation, increased invasion and in vivo tumorigenesis. Targeting of the MEK-ERK pathway was effective in fusion-positive Schwann cells, suggesting a possible therapeutic approach for this subset of tumors.","corpus_id":3687140,"score":1},{"doc_id":"27742789","title":"Novel Genetic Causes of Pituitary Adenomas.","abstract":"Recently, a number of novel genetic alterations have been identified that predispose individuals to pituitary adenomas. Clinically relevant pituitary adenomas are relatively common, present in 0.1% of the general population. They are mostly benign monoclonal neoplasms that arise from any of the five hormone-secreting cell types of the anterior lobe of the pituitary gland, and cause disease due to hormonal alterations and local space-occupying effects. The pathomechanism of pituitary adenomas includes alterations in cell-cycle regulation and growth factor signaling, which are mostly due to epigenetic changes; somatic and especially germline mutations occur more rarely. A significant proportion of growth hormone- and adrenocorticotrophin-secreting adenomas have activating somatic mutations in the GNAS and USP8 genes, respectively. Rarely, germline mutations predispose to pituitary tumorigenesis, often in a familial setting. Classical tumor predisposition syndromes include multiple endocrine neoplasia type 1 (MEN1) and type 4 (MEN4) syndromes, Carney complex, and McCune-Albright syndrome. Pituitary tumors have also been described in association with neurofibromatosis type 1, DICER1 syndrome, and SDHx mutations. Pituitary adenomas with no other associated tumors have been described as familial isolated pituitary adenomas. Patients with AIP or GPR101 mutations often present with pituitary gigantism either in a familial or simplex setting. GNAS and GPR101 mutations that arise in early embryonic age can lead to somatic mosaicism involving the pituitary gland and resulting in growth hormone excess. Senescence has been suggested as the key mechanism protecting pituitary adenomas turning malignant in the overwhelming majority of cases. Here we briefly summarize the genetic background of pituitary adenomas, with an emphasis on the recent developments in this field. Clin Cancer Res; 22(20); 5030-42. ©2016 AACR SEE ALL ARTICLES IN THIS CCR FOCUS SECTION, \"ENDOCRINE CANCERS REVISING PARADIGMS\".","corpus_id":29036761,"score":1},{"doc_id":"28348108","title":"Comprehensive somatic genome alterations of urachal carcinoma.","abstract":"BACKGROUND: Urachal cancer is a rare cancer that develops in the urachus. Because of its rarity, standard treatment therapies for urachal cancer are not established, and chemotherapeutic regimens for bladder cancer have been unsuccessful for patients with urachal cancer. Hence, we aim to understand a systematic molecular characterisation of urachal cancer. METHODS: We identified somatic single-nucleotide variations (SNVs)/indels and somatic copy number aberrations (SCNAs) in the 17 patients by using whole-exome sequencing (WES) and OncoScan platform (Affymetrix) as follows: tumour-normal paired sequencing (WES, n=10), tumour-only sequencing (WES, n=1; targeted deep sequencing, n=16), and OncoScan (n=17). RESULTS: Our analyses identified 27 genes with somatic SNVs and indels, as well as six genes (APC, COL5A1, KIF26B, LRP1B, SMAD4 and TP53) that were recurrent in at least two patients. By analysing the SCNAs, we found that the extent of chromosomal amplification was highly associated with the patient's cancer stage. Interestingly, 35% (6/17) of the patients had focal DNA amplifications in fibroblast growth factor receptor family genes. The integration of somatic SNVs, indels and SCNAs revealed significant alterations in the mitogen-activated protein kinase signalling pathways. CONCLUSIONS: Our genome-wide analysis of urachal cancer suggests that molecular characteristics may be important for the treatment of urachal cancer.","corpus_id":206998389,"score":1},{"doc_id":"29489754","title":"The landscape of genomic alterations across childhood cancers.","abstract":"Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.","corpus_id":3807522,"score":1},{"doc_id":"19918804","title":"Our changing view of the genomic landscape of cancer.","abstract":"Sporadic tumours, which account for the majority of all human cancers, arise from the acquisition of somatic, genetic and epigenetic alterations leading to changes in gene sequence, structure, copy number and expression. Within the last decade, the availability of a complete sequence-based map of the human genome, coupled with significant technological advances, has revolutionized the search for somatic alterations in tumour genomes. Recent landmark studies, which resequenced all coding exons within breast, colorectal, brain and pancreatic cancers, have shed new light on the genomic landscape of cancer. Within a given tumour type there are many infrequently mutated genes and a few frequently mutated genes, resulting in incredible genetic heterogeneity. However, when the altered genes are placed into biological processes and biochemical pathways, this complexity is significantly reduced and shared pathways that are affected in significant numbers of tumours can be discerned. The advent of next-generation sequencing technologies has opened up the potential to resequence entire tumour genomes to interrogate protein-encoding genes, non-coding RNA genes, non-genic regions and the mitochondrial genome. During the next decade it is anticipated that the most common forms of human cancer will be systematically surveyed to identify the underlying somatic changes in gene copy number, sequence and expression. The resulting catalogues of somatic alterations will point to candidate cancer genes requiring further validation to determine whether they have a causal role in tumourigenesis. The hope is that this knowledge will fuel improvements in cancer diagnosis, prognosis and therapy, based on the specific molecular alterations that drive individual tumours. In this review, I will provide a historical perspective on the identification of somatic alterations in the pre- and post-genomic eras, with a particular emphasis on recent pioneering studies that have provided unprecedented insights into the genomic landscape of human cancer.","corpus_id":42897873,"score":0},{"doc_id":"20802469","title":"Detection of chromosome copy number alterations in metanephric adenomas by array comparative genomic hybridization.","abstract":"Metanephric adenoma is a rare benign renal tumor typically found in adults. Previous cytogenetic analyses, including karyotyping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization, have yielded conflicting results regarding the somatic genetic aberrations of these tumors. In this study, we investigated the genomic profile of nine cases of metanephric adenoma using array comparative genomic hybridization. Two cases revealed multiple chromosomal gains and losses. Three cases showed sporadic chromosomal imbalances involving no more than three chromosomes. Four cases showed normal chromosome copy numbers. The gain of chromosome 19 was the most common finding (five cases), and FISH using 19p and 19q telomeric probes further confirmed this finding. We did not observe consistent gains of chromosomes 7 and 17, which are common in papillary renal cell carcinoma, neither did we find chromosomal alterations frequently present in Wilms' tumors, including chromosome gains of 1q, 7q, and 12, and losses of 11p and 16q. Our series demonstrates that the genetic profile of metanephric adenoma is fundamentally distinct from those of papillary renal cell carcinoma and Wilms' tumor.","corpus_id":7515498,"score":0},{"doc_id":"22156295","title":"Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency.","abstract":"Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they showed a 10.5-fold increase in the rate of somatic indels, e.g., truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in the correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas and confirmed MLH1 haploinsufficiency. We observed a much higher rate of indel mutations in the affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1, and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers.","corpus_id":33383320,"score":0},{"doc_id":"22300766","title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.","abstract":"Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of tumors. Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor-normal pairs. Unlike most current approaches, our algorithm reads data from both samples simultaneously; a heuristic and statistical algorithm detects sequence variants and classifies them by somatic status (germline, somatic, or LOH); while a comparison of normalized read depth delineates relative copy number changes. We apply these methods to the analysis of exome sequence data from 151 high-grade ovarian tumors characterized as part of the Cancer Genome Atlas (TCGA). We validated some 7790 somatic coding mutations, achieving 93% sensitivity and 85% precision for single nucleotide variant (SNV) detection. Exome-based CNA analysis identified 29 large-scale alterations and 619 focal events per tumor on average. As in our previous analysis of these data, we observed frequent amplification of oncogenes (e.g., CCNE1, MYC) and deletion of tumor suppressors (NF1, PTEN, and CDKN2A). We searched for additional recurrent focal CNAs using the correlation matrix diagonal segmentation (CMDS) algorithm, which identified 424 significant events affecting 582 genes. Taken together, our results demonstrate the robust performance of VarScan 2 for somatic mutation and CNA detection and shed new light on the landscape of genetic alterations in ovarian cancer.","corpus_id":18280129,"score":0},{"doc_id":"23029479","title":"Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.","abstract":"Mutations in the hyperparathyroidism type 2 (HRPT2/CDC73) gene and alterations in the parafibromin protein have been established in the majority of parathyroid carcinomas and in subsets of parathyroid adenomas. While it is known that CDC73-mutated parathyroid tumors display specific gene expression changes compared to CDC73 wild-type cases, the molecular cytogenetic profile in CDC73-mutated cases compared to unselected adenomas (with an expected very low frequency of CDC73 mutations) remains unknown. For this purpose, nine parathyroid tumors with established CDC73 gene inactivating mutations (three carcinomas, one atypical adenoma and five adenomas) were analyzed for copy number alterations and loss of heterozygosity using array-comparative genomic hybridization (a-CGH) and single nucleotide polymorphism (SNP) microarrays, respectively. Furthermore, CDC73 gene promoter methylation levels were assessed using bisulfite Pyrosequencing. The panel included seven tumors with single mutation and three with double mutations of the CDC73 gene. The carcinomas displayed copy number alterations in agreement with previous studies, whereas the CDC73-mutated adenomas did not display the same pattern of alterations at loci frequently deleted in unselected parathyroid tumors. Furthermore, gross losses of chromosomal material at 1p and 13 were significantly (p = 0.012) associated with parathyroid carcinomas as opposed to adenomas. Quantitative PCR-based copy number loss regarding CDC73 was observed in three adenomas, while all the carcinomas were diploid or showed copy number gain for CDC73 gene. Hypermethylation of the CDC73 gene promoter was not observed. Our data could suggest that CDC73-mutated parathyroid adenomas exhibit a partly unique cytogenetic profile in addition to that of carcinomas and unselected adenomas. Furthermore, CDC73-mutated carcinomas displayed losses at 1p and 13 which are not seen in CDC73-mutated adenomas, making these regions of interest for further studies regarding malignant properties in tumors from CDC73-mutated cases. However, due to the small sample size, validation of the results in a larger cohort is warranted.","corpus_id":11325195,"score":0},{"doc_id":"23074045","title":"High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.","abstract":"Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT.","corpus_id":21832127,"score":0},{"doc_id":"23531283","title":"MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.","abstract":"BACKGROUND: Most tumors are the result of accumulated genomic alterations in somatic cells. The emerging spectrum of alterations in tumors is complex and the identification of relevant genes and pathways remains a challenge. Furthermore, key cancer genes are usually found amplified or deleted in chromosomal regions containing many other genes. Point mutations, on the other hand, provide exquisite information about amino acid changes that could be implicated in the oncogenic process. Current large-scale genomic projects provide high throughput genomic data in a large number of well-characterized tumor samples. METHODS: We define a Bayesian approach designed to identify candidate cancer genes by integrating copy number and point mutation information. Our method exploits the concept that small and recurrent alterations in tumors are more informative in the search for cancer genes. Thus, the algorithm (Mutations with Common Focal Alterations, or MutComFocal) seeks focal copy number alterations and recurrent point mutations within high throughput data from large panels of tumor samples. RESULTS: We apply MutComFocal to Diffuse Large B-cell Lymphoma (DLBCL) data from four different high throughput studies, totaling 78 samples assessed for copy number alterations by single nucleotide polymorphism (SNP) array analysis and 65 samples assayed for protein changing point mutations by whole exome/whole transcriptome sequencing. In addition to recapitulating known alterations, MutComFocal identifies ARID1B, ROBO2 and MRS1 as candidate tumor suppressors and KLHL6, IL31 and LRP1 as putative oncogenes in DLBCL. CONCLUSIONS: We present a Bayesian approach for the identification of candidate cancer genes by integrating data collected in large number of cancer patients, across different studies. When trained on a well-studied dataset, MutComFocal is able to identify most of the reported characterized alterations. The application of MutComFocal to large-scale cancer data provides the opportunity to pinpoint the key functional genomic alterations in tumors.","corpus_id":11925257,"score":0},{"doc_id":"24308032","title":"The genomic landscape of oesophagogastric junctional adenocarcinoma.","abstract":"The incidence of oesophagogastric junctional (OGJ) adenocarcinoma is rising rapidly in western countries, in contrast to the declining frequency of distal gastric carcinoma. Treatment options for adenocarcinomas involving the oesophagogastric junction are limited and the overall prognosis is extremely poor. To determine the genomic landscape of OGJ adenocarcinoma, exomes of eight tumours and matched germline DNA were subjected to massively parallel DNA sequencing. Microsatellite instability was observed in three tumours which coincided with an elevated number of somatic mutations. In total, 117 genes were identified that had predicted coding alterations in more than one tumour. Potentially actionable coding mutations were identified in 67 of these genes, including those in CR2, HGF , FGFR4, and ESRRB. Twenty-nine genes harbouring somatic coding mutations and copy number changes in the MSS OGJ dataset are also known to be altered with similar predicted functional consequence in other tumour types. Compared with the published mutational profile of gastric cancers, 49% (57/117) of recurrently mutated genes were unique to OGJ tumours. TP53, SYNE1, and ARID1A were amongst the most frequently mutated genes in a larger OGJ cohort. Our study provides an insight into the mutational landscape of OGJ adenocarcinomas and confirms that this is a highly mutated and heterogeneous disease. Furthermore, we have uncovered somatic mutations in therapeutically relevant genes which may represent candidate drug targets.","corpus_id":24219275,"score":0},{"doc_id":"24390348","title":"Landscape of genomic alterations in cervical carcinomas.","abstract":"Cervical cancer is responsible for 10-15% of cancer-related deaths in women worldwide. The aetiological role of infection with high-risk human papilloma viruses (HPVs) in cervical carcinomas is well established. Previous studies have also implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical carcinomas. Here we report whole-exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole-genome sequencing of 14 tumour-normal pairs. Previously unknown somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%), TP53 (5%) and ERBB2 (6%). We also observe somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas have higher frequencies of somatic nucleotide substitutions occurring at cytosines preceded by thymines (Tp*C sites) than adenocarcinomas. Gene expression levels at HPV integration sites were statistically significantly higher in tumours with HPV integration compared with expression of the same genes in tumours without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest new strategies to combat this disease.","corpus_id":205236942,"score":0},{"doc_id":"24943349","title":"Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.","abstract":"BACKGROUND: The outcome of patients with metastatic colorectal carcinoma (mCRC) following first line therapy is poor, with median survival of less than one year. The purpose of this study was to identify candidate therapeutically targetable somatic events in mCRC patient samples by whole genome sequencing (WGS), so as to obtain targeted treatment strategies for individual patients. METHODS: Four patients were recruited, all of whom had received > 2 prior therapy regimens. Percutaneous needle biopsies of metastases were performed with whole blood collection for the extraction of constitutional DNA. One tumor was not included in this study as the quality of tumor tissue was not sufficient for further analysis. WGS was performed using Illumina paired end chemistry on HiSeq2000 sequencing systems, which yielded coverage of greater than 30X for all samples. NGS data were processed and analyzed to detect somatic genomic alterations including point mutations, indels, copy number alterations, translocations and rearrangements. RESULTS: All 3 tumor samples had KRAS mutations, while 2 tumors contained mutations in the APC gene and the PIK3CA gene. Although we did not identify a TCF7L2-VTI1A translocation, we did detect a TCF7L2 mutation in one tumor. Among the other interesting mutated genes was INPPL1, an important gene involved in PI3 kinase signaling. Functional studies demonstrated that inhibition of INPPL1 reduced growth of CRC cells, suggesting that INPPL1 may promote growth in CRC. CONCLUSIONS: Our study further supports potential molecularly defined therapeutic contexts that might provide insights into treatment strategies for refractory mCRC. New insights into the role of INPPL1 in colon tumor cell growth have also been identified. Continued development of appropriate targeted agents towards specific events may be warranted to help improve outcomes in CRC.","corpus_id":580286,"score":0},{"doc_id":"25597018","title":"Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated Genes in Seminomas.","abstract":"BACKGROUND: Testicular germ cell tumors are the most common cancer diagnosed in young men, and seminomas are the most common type of these cancers. There have been no exome-wide examinations of genes mutated in seminomas or of overall rates of nonsilent somatic mutations in these tumors. OBJECTIVE: The objective was to analyze somatic mutations in seminomas to determine which genes are affected and to determine rates of nonsilent mutations. DESIGN, SETTING, AND PARTICIPANTS: Eight seminomas and matched normal samples were surgically obtained from eight patients. INTERVENTION: DNA was extracted from tissue samples and exome sequenced on massively parallel Illumina DNA sequencers. Single-nucleotide polymorphism chip-based copy number analysis was also performed to assess copy number alterations. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The DNA sequencing read data were analyzed to detect somatic mutations including single-nucleotide substitutions and short insertions and deletions. The detected mutations were validated by independent sequencing and further checked for subclonality. RESULTS AND LIMITATIONS: The rate of nonsynonymous somatic mutations averaged 0.31 mutations/Mb. We detected nonsilent somatic mutations in 96 genes that were not previously known to be mutated in seminomas, of which some may be driver mutations. Many of the mutations appear to have been present in subclonal populations. In addition, two genes, KIT and KRAS, were affected in two tumors each with mutations that were previously observed in other cancers and are presumably oncogenic. CONCLUSIONS: Our study, the first report on exome sequencing of seminomas, detected somatic mutations in 96 new genes, several of which may be targetable drivers. Furthermore, our results show that seminoma mutation rates are five times higher than previously thought, but are nevertheless low compared to other common cancers. Similar low rates are seen in other cancers that also have excellent rates of remission achieved with chemotherapy. PATIENT SUMMARY: We examined the DNA sequences of seminomas, the most common type of testicular germ cell cancer. Our study identified 96 new genes in which mutations occurred during seminoma development, some of which might contribute to cancer development or progression. The study also showed that the rates of DNA mutations during seminoma development are higher than previously thought, but still lower than for other common solid-organ cancers. Such low rates are also observed among other cancers that, like seminomas, show excellent rates of disease remission after chemotherapy.","corpus_id":10255493,"score":0},{"doc_id":"25600428","title":"Genomic copy number alterations of primary and secondary metastasizing pleomorphic adenomas.","abstract":"AIMS: Metastasizing pleomorphic adenoma (MPA) is a rare tumour, and its mechanism of metastasis still is unknown. To date, there has been no study on MPA genomics. We analysed primary and secondary MPAs with array comparative genomic hybridization to identify somatic copy number alterations and affected genes. METHODS AND RESULTS: Tumour DNA samples from primary (parotid salivary gland) and secondary (scalp skin) MPAs were subjected to array comparative genomic hybridization investigation, and the data were analysed with NEXUS COPY NUMBER DISCOVERY. The primary MPA showed copy number losses affecting 3p22.2p14.3 and 19p13.3p123, and a complex pattern of four different deletions at chromosome 6. The 3p deletion encompassed several genes: CTNNB1, SETD2, BAP1, and PBRM1, among others. The secondary MPA showed a genomic profile similar to that of the primary MPA, with acquisition of additional copy number changes affecting 9p24.3p13.1 (loss), 19q11q13.43 (gain), and 22q11.1q13.33 (gain). CONCLUSION: Our findings indicated a clonal origin of the secondary MPA, as both tumours shared a common profile of genomic copy number alterations. Furthermore, we were able to detect in the primary tumour a specific pattern of copy number alterations that could explain the metastasizing characteristic, whereas the secondary MPA showed a more unbalanced genome.","corpus_id":36907353,"score":0},{"doc_id":"26386145","title":"An Old Story Retold: Loss of G1 Control Defines A Distinct Genomic Subtype of Esophageal Squamous Cell Carcinoma.","abstract":"Esophageal squamous cell carcinoma (ESCC) has a high mortality rate. To determine the molecular basis of ESCC development, this study sought to identify characteristic genome-wide alterations in ESCC, including exonic mutations and structural alterations. The clinical implications of these genetic alterations were also analyzed. Exome sequencing and verification were performed for nine pairs of ESCC and the matched blood samples, followed by validation with additional samples using Sanger sequencing. Whole-genome SNP arrays were employed to detect copy number alteration (CNA) and loss of heterozygosity (LOH) in 55 cases, including the nine ESCC samples subjected to exome sequencing. A total of 108 non-synonymous somatic mutations (NSSMs) in 102 genes were verified in nine patients. The chromatin modification process was found to be enriched in our gene ontology (GO) analysis. Tumor genomes with TP53 mutations were significantly more unstable than those without TP53 mutations. In terms of the landscape of genomic alterations, deletion of 9p21.3 covering CDKN2A/2B (30.9%), amplification of 11q13.3 covering CCND1 (30.9%), and TP53 point mutation (50.9%) occurred in two-thirds of the cases. These results suggest that the deregulation of the G1 phase during the cell cycle is a key event in ESCC. Furthermore, six minimal common regions were found to be significantly altered in ESCC samples and three of them, 9p21.3, 7p11.2, and 3p12.1, were associated with lymph node metastasis. With the high correlation of TP53 mutation and genomic instability in ESCC, the amplification of CCND1, the deletion of CDKN2A/2B, and the somatic mutation of TP53 appear to play pivotal roles via G1 deregulation and therefore helps to classify this cancer into different genomic subtypes. These findings provide clinical significance that could be useful in future molecular diagnoses and therapeutic targeting.","corpus_id":9582461,"score":0},{"doc_id":"26857264","title":"Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer.","abstract":"Gastric cancer and esophageal cancer are the second and sixth leading causes of cancer-related death worldwide. Multiple genomic alterations underlying gastric cancer and esophageal squamous cell carcinoma (ESCC) have been identified, but the full spectrum of genomic structural variations and mutations have yet to be uncovered. Here, we report the results of whole-genome sequencing of 30 samples comprising tumor and blood from 15 patients, four of whom presented with ESCC, seven with gastric cardia adenocarcinoma (GCA), and four with gastric noncardia adenocarcinoma. Analyses revealed that an A>C mutation was common in GCA, and in addition to the preferential nucleotide sequence of A located 5 prime to the mutation as noted in previous studies, we found enrichment of T in the 5 prime base. The A>C mutations in GCA suggested that oxidation of guanine may be a potential mechanism underlying cancer mutagenesis. Furthermore, we identified genes with mutations in gastric cancer and ESCC, including well-known cancer genes, TP53, JAK3, BRCA2, FGF2, FBXW7, MSH3, PTCH, NF1, ERBB2, and CHEK2, and potentially novel cancer-associated genes, KISS1R, AMH, MNX1, WNK2, and PRKRIR Finally, we identified recurrent chromosome alterations in at least 30% of tumors in genes, including MACROD2, FHIT, and PARK2 that were often intragenic deletions. These structural alterations were validated using the The Cancer Genome Atlas dataset. Our studies provide new insights into understanding the genomic landscape, genome instability, and mutation profile underlying gastric cancer and ESCC development. Cancer Res; 76(7); 1714-23. ©2016 AACR.","corpus_id":3230797,"score":0},{"doc_id":"26960396","title":"The Genomic Landscape of Male Breast Cancers.","abstract":"PURPOSE: Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers. EXPERIMENTAL DESIGN: All male breast cancers were estrogen receptor-positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor-normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers. RESULTS: Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A-like or luminal B-like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair-related genes. CONCLUSIONS: Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045-56. ©2016 AACR.","corpus_id":5761563,"score":0},{"doc_id":"27091409","title":"Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures.","abstract":"PURPOSE: There is substantial heterogeneity within human papillomavirus (HPV)-associated head and neck cancer (HNC) tumors that predispose them to different outcomes; however, the molecular heterogeneity in this subgroup is poorly characterized due to various historical reasons. EXPERIMENTAL DESIGN: We performed unsupervised gene expression clustering on deeply annotated (transcriptome and genome) HPV(+) HNC samples from two cohorts (84 total primary tumors), including 18 HPV(-) HNC samples, to discover subtypes and characterize the differences between subgroups in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number alterations, and mutation frequencies. RESULTS: We identified two distinct HPV(+) subtypes (namely HPV-KRT and HPV-IMU). HPV-KRT is characterized by elevated expression of genes in keratinocyte differentiation and oxidation-reduction process, whereas HPV-IMU has strong immune response and mesenchymal differentiation. The differences in expression are likely connected to the differences in HPV characteristics and genomic changes. HPV-KRT has more genic viral integration, lower E2/E4/E5 expression levels, and higher ratio of spliced to full-length HPV oncogene E6 than HPV-IMU; the subgroups also show differences in copy number alterations and mutations, in particular the loss of chr16q in HPV-IMU and gain of chr3q and PIK3CA mutation in HPV-KRT. CONCLUSIONS: Our characterization of two subtypes of HPV(+) HNC tumors provides valuable molecular level information that point to two main carcinogenic paths. Together, these results shed light on stratifications of the HPV(+) HNCs and will help to guide personalized care for HPV(+) HNC patients. Clin Cancer Res; 22(18); 4735-45. ©2016 AACR.","corpus_id":207676242,"score":0},{"doc_id":"27126562","title":"Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes.","abstract":"Retinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited. To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses. Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors. Targeted therapy based on these subclonal events might be insufficient for complete tumor control.","corpus_id":5404337,"score":0},{"doc_id":"27685995","title":"Genome Analysis of Osteosarcoma Progression Samples Identifies FGFR1 Overexpression as a Potential Treatment Target and CHM as a Candidate Tumor Suppressor Gene.","abstract":"Osteosarcoma (OS) is the most common primary malignant tumor of bone, showing complex chromosomal rearrangements but with few known consistent changes. Deeper biological understanding is crucial to find new therapies to improve patient survival. We have sequenced the whole exome of two primary tumors (before and after chemotherapy), one metastatic tumor and a matched normal sample from two OS patients, to identify mutations involved in cancer biology. The metastatic samples were also RNA sequenced. By RNA sequencing we identified dysregulated expression levels of drug resistance- and apoptosis-related genes. Two fusion transcripts were identified in one patient (OS111); the first resulted in p53 inactivation by fusing the first exon of TP53 to the fifth exon of FAM45A. The second fusion joined the two first exons of FGFR1 to the second exon of ZNF343. Furthermore, FGFR1 was amplified and highly expressed, representing a potential treatment target in this patient. Whole exome sequencing revealed large intertumor heterogeneity, with surprisingly few shared mutations. Careful evaluation and validation of the data sets revealed a number of artefacts, but one recurrent mutation was validated, a nonsense mutation in CHM (patient OS106), which also was the mutation with the highest expression frequency (53%). The second patient (OS111) had wild-type CHM, but a downregulated expression level. In a panel of 71 clinical samples, we confirmed significant low expression of CHM compared to the controls (p = 0.003). Furthermore, by analyzing public datasets, we identified a significant association between low expression and poor survival in two other cancer types. Together, these results suggest CHM as a candidate tumor suppressor gene that warrants further investigation.","corpus_id":1272783,"score":0},{"doc_id":"27709558","title":"DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.","abstract":"BACKGROUND: DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study. METHODS: Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up. RESULTS: DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and TGF-β and apoptosis signaling, were found to be most significantly affected. CONCLUSIONS: Our results suggest that CNAs in CRC tumor tissues are associated with concomitant changes in the expression of cancer-related genes. In other genes epigenetic mechanism may be at work. Up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, appear to be associated with a poor survival. These alterations may, in addition to Dukes' staging, be employed as new prognostic biomarkers for the prediction of clinical outcome in CRC patients.","corpus_id":7894803,"score":0},{"doc_id":"27745836","title":"Comprehensive Genetic Landscape of Uveal Melanoma by Whole-Genome Sequencing.","abstract":"Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified. Recurrent coding mutations were found in the known UM drivers GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. Other genes, i.e., TP53BP1, CSMD1, TTC28, DLK2, and KTN1, were also found to harbor somatic mutations in more than one individual, possibly indicating a previously undescribed association with UM pathogenesis. De novo assembly of unmatched reads from non-coding DNA revealed peculiar copy-number variations defining specific UM subtypes, which in turn could be associated with metastatic transformation. Mutational-driven comparison with other tumor types showed that UM is very similar to pediatric tumors, characterized by very few somatic insults and, possibly, important epigenetic changes. Through the analysis of whole-genome sequencing data, our findings shed new light on the molecular genetics of uveal melanoma, delineating it as an atypical tumor of the adult for which somatic events other than mutations in exonic DNA shape its genetic landscape and define its metastatic potential.","corpus_id":11562597,"score":0},{"doc_id":"27923066","title":"Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study.","abstract":"BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. We detected driver genes by testing whether the nonsynonymous mutation rate was significantly higher than the background mutation rate and replicated our findings in public datasets with 724 samples. We performed subclonality analysis for mutations based on mutant allele data and copy number alteration data. We also tested the association between mutation signatures and clinical outcomes, including distant metastasis, survival, and tumor grade. We identified and replicated two novel candidate driver genes, POU class 4 homeobox 2 (POU4F2) (mutated in 9 [8.9%] samples) and ZKSCAN1 (mutated in 6 [5.9%] samples), and characterized their major deleterious mutations. ZKSCAN1 was part of a mutually exclusive gene set that included the RTK/RAS/RAF pathway genes BRAF, EGFR, KRAS, MET, and NF1, indicating an important driver role for this gene. Moreover, we observed strong associations between methylation in specific genomic regions and somatic mutation patterns. In the tumor evolution analysis, four driver genes had a significantly lower fraction of subclonal mutations (FSM), including TP53 (p = 0.007), KEAP1 (p = 0.012), STK11 (p = 0.0076), and EGFR (p = 0.0078), suggesting a tumor initiation role for these genes. Subclonal mutations were significantly enriched in APOBEC-related signatures (p < 2.5×10-50). The total number of somatic mutations (p = 0.0039) and the fraction of transitions (p = 5.5×10-4) were associated with increased risk of distant metastasis. Our study's limitations include a small number of LUAD patients for subgroup analyses and a single-sample design for investigation of subclonality. CONCLUSIONS: These data provide a genomic characterization of LUAD pathogenesis and progression. The distinct clonal and subclonal mutation signatures suggest possible diverse carcinogenesis pathways for endogenous and exogenous exposures, and may serve as a foundation for more effective treatments for this lethal disease. LUAD's high heterogeneity emphasizes the need to further study this tumor type and to associate genomic findings with clinical outcomes.","corpus_id":8765709,"score":0},{"doc_id":"28181325","title":"Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation.","abstract":"Pleomorphic xanthoastrocytoma (PXA) is a rare localized glioma characterized by frequent BRAF V600E mutation and CDKN2A/B deletion. We explored the association of copy-number variants (CNVs) with BRAF mutations, tumor grade, and patient survival in a cohort of 41 PXA patients using OncoScan chromosomal microarray. Primary resection specimens were available in 38 cases, including 24 PXA and 14 anaplastic PXA (A-PXA), 23 BRAF V600E mutant tumors (61%). CNVs were identified in all cases and most frequently involved chromosome 9 with homozygous CDKN2A/B deletion (n = 33, 87%), a higher proportion than previously detected by comparative genomic hybridization (50%-60%) (37). CDKN2A/B deletion was present in similar proportion of PXA (83%), A-PXA (93%), BRAF V600E (87%), and wild-type (87%) tumors. Whole chromosome gains/losses were frequent, including gains +7 (n = 15), +2 (n = 11), +5 (n = 10), +21 (n = 10), +20 (n = 9), +12 (n = 8), +15 (n = 8), and losses -22 (n = 11), -14 (n = 7), -13 (n = 5). Losses and copy-neutral loss of heterozygosity were significantly more common in A-PXA, involving chromosomes 22 (P = 0.009) and 14 (P = 0.03). Amplification of 8p and 12q was identified in a single tumor. Histologic grade was a robust predictor of overall survival (P = 0.003), while other copy-number changes, including CDKN2A/B deletion, did not show significant association with survival. Distinct histologic patterns of anaplasia included increased mitotic activity in an otherwise classic PXA or associated with small cell, fibrillary, or epithelioid morphology, with loss of SMARCB1 expression in one case. In 10 cases, matched specimens were compared, including A-PXA with areas of distinct low- and high-grade morphology (n = 2), matched primary/tumor recurrence (n = 7), or both (n = 1). Copy-number changes on recurrence/anaplastic transformation were complex and highly variable, from nearly identical profiles to numerous copy-number changes. Overall, we confirm CDKN2A/B deletion as key a feature of PXA not associated with tumor grade or BRAF mutation, but central to the underlying genetics of PXA.","corpus_id":3942062,"score":0},{"doc_id":"28607096","title":"The somatic mutation landscape of premalignant colorectal adenoma.","abstract":"OBJECTIVE: There are few studies which characterised the molecular alterations in premalignant colorectal adenomas. Our major goal was to establish colorectal adenoma genome atlas and identify molecular markers of progression from colorectal adenoma to adenocarcinoma. DESIGN: Whole-exome sequencing and targeted sequencing were carried out in 149 adenoma samples and paired blood from patients with conventional adenoma or sessile serrated adenoma to characterise the somatic mutation landscape for premalignant colorectal lesions. The identified somatic mutations were compared with those in colorectal cancer (CRC) samples from The Cancer Genome Atlas. A supervised random forest model was employed to identify gene panels differentiating adenoma from CRC. RESULTS: Similar somatic mutation frequencies, but distinctive driver mutations, were observed in sessile serrated adenomas and conventional adenomas. The final model included 20 genes and was able to separate the somatic mutation profile of colorectal adenoma and adenocarcinoma with an area under the curve of 0.941. CONCLUSION: The findings of this project hold potential to better identify patients with adenoma who may be candidates for targeted surveillance programmes and preventive interventions to reduce the incidence of CRC.","corpus_id":5167455,"score":0},{"doc_id":"28710315","title":"Shallow whole genome sequencing on circulating cell-free DNA allows reliable non-invasive copy number profiling in neuroblastoma patients.","abstract":"PURPOSE: <p>Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of NB patients could offer a valuable alternative to primary tumor DNA for CNA profiling.</p> <br /><br />Experimental Design: <p>In 37 NB patients cfDNA analysis using shallow whole genome sequencing (sWGS) was compared to arrayCGH analysis of primary tumor tissue.</p> <br /><br />Results: <p>Comparison of CNA profiles on cfDNA showed highly concordant patterns, particularly in high-stage patients. Numerical chromosome imbalances as well as large and focal structural aberrations including MYCN and LIN28B amplification and ATRX deletion could be readily detected with sWGS using a low input of cfDNA.</p> <br /><br />Conclusions: <p>In conclusion, sWGS analysis on cfDNA offers a cost-effective, non-invasive, rapid, robust and sensitive alternative for tumor DNA copy number profiling in most NB patients.","corpus_id":19774549,"score":0},{"doc_id":"28789476","title":"Molecular Transition of an Adult Low-Grade Brain Tumor to an Atypical Teratoid/Rhabdoid Tumor Over a Time-Course of 14 Years.","abstract":"Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system is a highly malignant, pediatric brain tumor typically arising de novo. Inactivation of SMARCB1 is a defining molecular event. We present here a rare case of an adult (35 years) low-grade SMARCB1-deleted brain tumor with transition into prototypical AT/RT over 14 years. Molecular analysis was performed for 3 tumor presentations including copy number analysis, DNA methylation analysis (450k), and whole exome sequencing. We detected the identical somatic SMARCB1 deletion at all 3 time-points. In an unsupervised hierarchical clustering of methylation data together with 127 reference cases comprising 9 brain tumor classes all 3 manifestations clustered with AT/RT. Exome sequencing revealed an increase of mutational burden over time. The acquired mutations and additional copy number changes did not affect known cancer genes. In conclusion, we demonstrate molecular changes associated with histological and clinical transition of a low-grade brain tumor to an adult AT/RT. Our observation of a stable disease course for nearly 10 years in a tumor with SMARCB1 loss and an AT/RT-like DNA methylation profile indicates that caution may be required in the diagnostic interpretation of such findings in adult patients.","corpus_id":42816748,"score":0},{"doc_id":"29030356","title":"Cell-Cycle and DNA-Damage Response Pathway Is Involved in Leptomeningeal Metastasis of Non-Small Cell Lung Cancer.","abstract":"Purpose: Leptomeningeal metastasis (LM) is a detrimental complication of non-small cell lung cancer (NSCLC) and associated with poor prognosis. However, the underlying mechanisms of the metastasis process are still poorly understood. Experimental Design: We performed next-generation panel sequencing of primary tumor tissue, cerebrospinal fluid (CSF), and matched normal controls from epidermal growth factor receptor (EGFR) mutation-positive NSCLC patients with LM.Results: The status of EGFR-activating mutations was highly concordant between primary tumor and CSF. PIK3CA aberrations were high in these patients, implicating an association with LM risk. Intriguingly, low overlapping of somatic protein-changing variants was observed between paired CSF and primary lesions, exhibiting tumor heterogeneity and genetic divergence. Moreover, genes with CSF-recurrent genomic alterations were predominantly involved in cell-cycle regulation and DNA-damage response (DDR), suggesting a role of the pathway in LM development. Conclusions: Our study has shed light on the genomic variations of NSCLC-LM, demonstrated genetic heterogeneity and divergence, uncovered involvement of cell-cycle and DDR pathway, and paved the way for potential therapeutic approaches to this unmet medical need. Clin Cancer Res; 24(1); 209-16. ©2017 AACR.","corpus_id":11055603,"score":0},{"doc_id":"29351916","title":"Pathways Impacted by Genomic Alterations in Pulmonary Carcinoid Tumors.","abstract":"Purpose: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors. Experimental Design: We performed integrated genomic analysis of carcinoid tumors comprising whole genome and exome sequencing, mRNA expression profiling and SNP genotyping of specimens from normal lung, TC and AC, and small cell lung carcinoma (SCLC) to fully represent the lung neuroendocrine tumor spectrum. Results: Analysis of sequencing data found recurrent mutations in cancer genes including ATP1A2, CNNM1, MACF1, RAB38, NF1, RAD51C, TAF1L, EPHB2, POLR3B, and AGFG1 The mutated genes are involved in biological processes including cellular metabolism, cell division cycle, cell death, apoptosis, and immune regulation. The top most significantly mutated genes were TMEM41B, DEFB127, WDYHV1, and TBPL1 Pathway analysis of significantly mutated and cancer driver genes implicated MAPK/ERK and amyloid beta precursor protein (APP) pathways whereas analysis of CNV and gene expression data suggested deregulation of the NF-κB and MAPK/ERK pathways. The mutation signature was predominantly C>T and T>C transitions with a minor contribution of T>G transversions. Conclusions: This study identified mutated genes affecting cancer relevant pathways and biological processes that could provide opportunities for developing targeted therapies for pulmonary carcinoid tumors. Clin Cancer Res; 24(7); 1691-704. ©2018 AACR.","corpus_id":4584205,"score":0}],"string":"[\n {\n \"doc_id\": \"18300794\",\n \"title\": \"Pituitary tumors and hyperplasia in multiple endocrine neoplasia type 1 syndrome (MEN1): a case-control study in a series of 77 patients versus 2509 non-MEN1 patients.\",\n \"abstract\": \"Patients affected by the multiple endocrine neoplasia type I syndrome (MEN1) display a high incidence of pituitary adenomas, though it is still unknown whether these pituitary tumors have specific pathologic features that would distinguish them from sporadic pituitary adenomas. Pituitary tissue specimens of 77 MEN1 patients from the GTE (Groupe d'étude des Tumeurs Endocrines) register were compared with unselected 2509 non-MEN1 sporadic pituitary tumors and also to a control subgroup of 296 cases, where 1 MEN1 tumor was matched with 4 sporadic tumors of the same hormonal immunoprofile. Sex, age, size, and invasiveness of tumors, and menin gene mutations were documented. Histologic analysis took into account 33 items, including immunocytochemical data, the proliferative marker Ki-67, and an examination of the juxtatumoral pituitary. MEN1 tumors were significantly larger and more often invasive by histology. MEN1 patients with large pituitary tumors (grade IV) were younger than non-MEN1 patients. MEN1 tumors had no other characteristic histologic features and no predominance of any one hormone producing subtype. However, plurihormonal adenomas versus monohormonal and nonimmunoreactive adenomas were more frequent in MEN1 tumors (39%) than in the control non-MEN1 group (P = 0.001). Especially, the growth hormone and prolactin plurihormonality with unusual association with follicle-stimulating hormone, luteinizing hormone, or adrenocorticotropic hormone was more frequent in MEN1 tumors. In addition, multiple adenomas were significantly more frequent (4% vs. 0.1%; P < 0.0001), especially prolactin-adrenocorticotropic hormone. Somatotroph hyperplasia, with or without a microadenoma was found in only 3 MEN1 patients, with growth hormone-releasing hormone hypersecretion by a pancreatic tumor in 2 of them. All types of mutation were observed, including frameshifts, nonsenses, missenses, and 1 case of germline MEN1 encompassing large deletion, strongly suggesting the absence of any phenotype-genotype correlation.\",\n \"corpus_id\": 25209721,\n \"score\": 2\n },\n {\n \"doc_id\": \"18381572\",\n \"title\": \"The role of the aryl hydrocarbon receptor-interacting protein gene in familial and sporadic pituitary adenomas.\",\n \"abstract\": \"CONTEXT: Mutations have been identified in the aryl hydrocarbon receptor-interacting protein (AIP) gene in familial isolated pituitary adenomas (FIPA). It is not clear, however, how this molecular chaperone is involved in tumorigenesis. OBJECTIVE: AIP sequence changes and expression were studied in FIPA and sporadic adenomas. The function of normal and mutated AIP molecules was studied on cell proliferation and protein-protein interaction. Cellular and ultrastructural AIP localization was determined in pituitary cells. PATIENTS: Twenty-six FIPA kindreds and 85 sporadic pituitary adenoma patients were included in the study. RESULTS: Nine families harbored AIP mutations. Overexpression of wild-type AIP in TIG3 and HEK293 human fibroblast and GH3 pituitary cell lines dramatically reduced cell proliferation, whereas mutant AIP lost this ability. All the mutations led to a disruption of the protein-protein interaction between AIP and phosphodiesterase-4A5. In normal pituitary, AIP colocalizes exclusively with GH and prolactin, and it is found in association with the secretory vesicle, as shown by double-immunofluorescence and electron microscopy staining. In sporadic pituitary adenomas, however, AIP is expressed in all tumor types. In addition, whereas AIP is expressed in the secretory vesicle in GH-secreting tumors, similar to normal GH-secreting cells, in lactotroph, corticotroph, and nonfunctioning adenomas, it is localized to the cytoplasm and not in the secretory vesicles. CONCLUSIONS: Our functional evaluation of AIP mutations is consistent with a tumor-suppressor role for AIP and its involvement in familial acromegaly. The abnormal expression and subcellular localization of AIP in sporadic pituitary adenomas indicate deranged regulation of this protein during tumorigenesis.\",\n \"corpus_id\": 28488929,\n \"score\": 2\n },\n {\n \"doc_id\": \"18628514\",\n \"title\": \"Large genomic deletions in AIP in pituitary adenoma predisposition.\",\n \"abstract\": \"CONTEXT: Germline mutations in AIP have been recently shown to cause pituitary adenoma predisposition (PAP). Subsequently, many intragenic germline mutations have been reported, both in familial and in sporadic settings. OBJECTIVE: Our objective was to evaluate the possible contribution of large genomic germline AIP deletions, an important mutation type in tumor predisposition syndromes, in PAP. DESIGN: Here, we applied the multiplex ligation-dependent probe amplification assay to examine whether large genomic AIP or MEN1 alterations account for a subset of PAP cases. PATIENTS: The study was performed on familial and sporadic pituitary adenoma cases of European origin, which had previously tested negative for germline AIP and MEN1 mutations by sequencing. RESULTS: Two of 21 pituitary adenoma families (9.5%) were found to harbor an AIP deletion. No copy number changes were detected among 67 sporadic pituitary adenoma patients. No MEN1 deletions were found. CONCLUSIONS: The present study shows that large genomic AIP deletions account for a subset of PAP. Therefore, in suspected PAP cases undergoing counseling and AIP genetic testing, multiplex ligation-dependent probe amplification could be considered if direct sequencing does not identify a mutation.\",\n \"corpus_id\": 24578909,\n \"score\": 2\n },\n {\n \"doc_id\": \"18973139\",\n \"title\": \"Frequent loss of the CDKN2C (p18INK4c) gene product in pituitary adenomas.\",\n \"abstract\": \"Genomic alterations of cyclin-dependent kinase inhibitors have been demonstrated in a variety of tumor types including brain tumors. Among them, the cyclin-dependent kinase inhibitor 2A (CDKN2A or p16(INK4a)) gene has been shown to be frequently deleted or inactivated in astrocytic tumors. The CDKN2C (p18(INK4c)) gene is functionally related to CDKN2A. Moreover, mice with targeted disruption of CDKN2C alone or combined CDKN2C and cyclin-dependent kinase inhibitor 1B (CDKN1B or p27(Kip1)), or CDKN2C and TP53 gene disruption develop pituitary adenomas (PA) at high frequencies. The purpose of our study was to investigate genetic alterations of the CDKN2C gene by analysis of loss of heterozygosity (LOH), screening for mutations, analysis of promoter methylation, and protein expression in 38 PAs. In addition, genomic alterations and protein expression of the cell cycle genes CDKN2A and its alternatively spliced form, p14(ARF), as well as the retinoblastoma RB1 gene were investigated. LOH at the CDKN2C gene locus was detected in 25% of pituitary adenomas, whereas the RB1 and CDKN2A loci were altered in only 10%. No mutations were detected within the coding regions of the CDKN2C gene. However, 39.5% of adenomas displayed CDKN2C promoter methylation. The absence of CDKN2C protein was correlated with LOH of the CDKN2C locus on chromosome 1 and with methylation of the CDKN2C promoter. This is the first report to describe that the tumor suppressor gene CDKN2C is frequently targeted by genomic alterations in pituitary adenoma. The most common genetic alteration was promoter methylation suggesting that inactivation of CDKN2C by this mechanism may play an important role in pituitary adenoma development. Additional Supporting Information may be found in the online version of this article.\",\n \"corpus_id\": 28486628,\n \"score\": 2\n },\n {\n \"doc_id\": \"20833337\",\n \"title\": \"The genetics of pituitary adenomas.\",\n \"abstract\": \"Pituitary adenomas are one of the most frequent intracranial tumors with a prevalence of clinically-apparent tumors close to 1:1000 of the general population. They are clinically significant because of hormone overproduction and/or tumor mass effects in addition to the need for neurosurgery, medical therapies and radiotherapy. The majority of pituitary adenomas have a sporadic origin with recognized genetic mutations seldom being found; somatotropinomas are an exception, presenting frequent somatic GNAS mutations. In this and other phenotypes, tumorigenesis could possibly be explained by altered function of genes implicated in cell cycle regulation, growth factors or their receptors, cell-signaling pathways, specific hormonal factors or other molecules with still unclear mechanisms of action. Genetic changes, such as allelic loss or gene amplification, and epigenetic changes, usually by promoter methylation, have been implicated in abnormal gene expression, but alternative mechanisms may be present. Familial cases of pituitary adenomas represent 5% of all pituitary tumors. MEN1 mutations cause multiple endocrine neoplasia type 1 (MEN1), while the Carney complex (CNC) is characterized by mutations in the protein kinase A regulatory subunit-1alpha (PRKAR1A) gene or changes in a locus at 2p16. Recently, a MEN1-like condition, MEN4, was found to be related to mutations in the CDKN1B gene. The clinical entity of familial isolated pituitary adenomas (FIPA) is characterized by genetic defects in the aryl hydrocarbon receptor interacting protein (AIP) gene in about 15% of all kindreds and 50% of homogenous somatotropinoma families. Identification of familial cases of pituitary adenomas is important as these tumors may be more aggressive than their sporadic counterparts.\",\n \"corpus_id\": 261272358,\n \"score\": 2\n },\n {\n \"doc_id\": \"20868211\",\n \"title\": \"Atypical pituitary adenomas: incidence, clinical characteristics, and implications.\",\n \"abstract\": \"OBJECT: The 2004 WHO classification of pituitary adenomas now includes an \\\"atypical\\\" variant, defined as follows: MIB-1 proliferative index greater than 3%, excessive p53 immunoreactivity, and increased mitotic activity. The authors review the incidence of this atypical histopathological subtype and its correlation with tumor subtype, invasion, and surgical features. METHODS: The records of 121 consecutive patients who underwent transsphenoidal surgery for pituitary adenomas during an 18-month period were retrospectively reviewed for evidence of atypical adenomas. RESULTS: Eighteen adenomas (15%) met the criteria for atypical lesions; 17 (94%) of the 18 were macroadenomas. On imaging, 15 (83%) demonstrated imaging evidence of surrounding invasion, compared with 45% of typical adenomas (p = 0.004). Atypical tumors occurred in 12 female (67%) and 6 male (33%) patients. Patient age ranged from 16 to 70 years (mean 48 years). Nine patients (50%) had hormonally active tumors, and 9 had nonfunctional lesions. Four (22%) of the 18 patients presented to us with recurrent tumors. Immunohistochemical analysis demonstrated the following tumor subtypes: GH-secreting adenoma with plurihormonal staining (5 patients [28%]); null-cell adenoma (5 patients [28%]); silent ACTH tumor (3 patients [17%]), ACTH-staining tumor with Cushing's disease (2 patients [11%]), prolactinoma (2 patients [11%]), and silent FSH-staining tumor (1 patient [6%]). The MIB-1 labeling index ranged from 3% to 20% (mean 7%). CONCLUSIONS: Atypical tumors were identified in 15% of resected pituitary adenomas, and they tended to be aggressive, invasive macroadenomas. More longitudinal follow-up is required to determine whether surgical outcomes, potential for recurrence, or metastasis of atypical adenomas vary significantly from their typical counterparts.\",\n \"corpus_id\": 6934129,\n \"score\": 2\n },\n {\n \"doc_id\": \"22772969\",\n \"title\": \"Examination of the relationship between chromosome abnormality in pituitary adenomas and tumor invasiveness by normal karyotype analysis and interphase fluorescence staining.\",\n \"abstract\": \"To study the potential relationship between chromosome abnormality and tumor invasiveness in pituitary adenomas. To use conventional R-band cytogenetic karyotype analysis and interphase fluorescence in situ hybridization using centromeric probe of chromosomes 8, 9, and 11 to detect chromosome abnormality in 30 cases of pituitary adenoma. All chromosomes except chromosomes 4, 16, and Y show significant variation between invasive and noninvasive pituitary adenomas. Chromosomes 8 and 12 display some type of numeric alteration in all endocrine subtypes of pituitary adenoma. Numeric alterations in chromosomes 9, 11, and 19 are more frequently detected in invasive pituitary adenomas compared with noninvasive tumors. Numeric alterations in chromosomes are common in all endocrine subtype pituitary adenomas. Furthermore, chromosome numbers are significantly different in invasive and noninvasive pituitary adenomas. On the basis of our study and literature review, we conclude that while chromosomes 8 and 12 may play important roles in the occurrence of pituitary adenomas, chromosomes 9, 11, and 19 may be specifically associated with invasiveness.\",\n \"corpus_id\": 22049462,\n \"score\": 2\n },\n {\n \"doc_id\": \"22782554\",\n \"title\": \"Mutation and genomic amplification of the PIK3CA proto-oncogene in pituitary adenomas.\",\n \"abstract\": \"The tumorigenesis of pituitary adenomas is poorly understood. Mutations of the PIK3CA proto-oncogene, which encodes the p110-α catalytic subunit of PI3K, have been reported in various types of human cancers regarding the role of the gene in cell proliferation and survival through activation of the PI3K/Akt signaling pathway. Only one Chinese study described somatic mutations and amplification of the PIK3CA gene in a large series of pituitary adenomas. The aim of the present study was to determine genetic alterations of PIK3CA in a second series that consisted of 33 pituitary adenomas of different subtypes diagnosed by immunohistochemistry: 6 adrenocorticotropic hormone-secreting microadenomas, 5 growth hormone-secreting macroadenomas, 7 prolactin-secreting macroadenomas, and 15 nonfunctioning macroadenomas. Direct sequencing of exons 9 and 20 assessed by qPCR was employed to investigate the presence of mutations and genomic amplification defined as a copy number ≥4. Previously identified PIK3CA mutations (exon 20) were detected in four cases (12.1%). Interestingly, the Chinese study reported mutations only in invasive tumors, while we found a PIK3CA mutation in one noninvasive corticotroph microadenoma. PIK3CA amplification was observed in 21.2% (7/33) of the cases. This study demonstrates the presence of somatic mutations and amplifications of the PIK3CA gene in a second series of pituitary adenomas, corroborating the previously described involvement of the PI3K/Akt signaling pathway in the tumorigenic process of this gland.\",\n \"corpus_id\": 2154202,\n \"score\": 2\n },\n {\n \"doc_id\": \"22855342\",\n \"title\": \"Whole-exome sequencing studies of nonhereditary (sporadic) parathyroid adenomas.\",\n \"abstract\": \"CONTEXT: Genetic abnormalities, such as those of multiple endocrine neoplasia type 1 (MEN1) and Cyclin D1 (CCND1) genes, occur in <50% of nonhereditary (sporadic) parathyroid adenomas. OBJECTIVE: To identify genetic abnormalities in nonhereditary parathyroid adenomas by whole-exome sequence analysis. DESIGN: Whole-exome sequence analysis was performed on parathyroid adenomas and leukocyte DNA samples from 16 postmenopausal women without a family history of parathyroid tumors or MEN1 and in whom primary hyperparathyroidism due to single-gland disease was cured by surgery. Somatic variants confirmed in this discovery set were assessed in 24 other parathyroid adenomas. RESULTS: Over 90% of targeted exons were captured and represented by more than 10 base reads. Analysis identified 212 somatic variants (median eight per tumor; range, 2-110), with the majority being heterozygous nonsynonymous single-nucleotide variants that predicted missense amino acid substitutions. Somatic MEN1 mutations occurred in six of 16 (∼35%) parathyroid adenomas, in association with loss of heterozygosity on chromosome 11. However, no other gene was mutated in more than one tumor. Mutations in several genes that may represent low-frequency driver mutations were identified, including a protection of telomeres 1 (POT1) mutation that resulted in exon skipping and disruption to the single-stranded DNA-binding domain, which may contribute to increased genomic instability and the observed high mutation rate in one tumor. CONCLUSIONS: Parathyroid adenomas typically harbor few somatic variants, consistent with their low proliferation rates. MEN1 mutation represents the major driver in sporadic parathyroid tumorigenesis although multiple low-frequency driver mutations likely account for tumors not harboring somatic MEN1 mutations.\",\n \"corpus_id\": 25412306,\n \"score\": 2\n },\n {\n \"doc_id\": \"23049073\",\n \"title\": \"Somatic complex I disruptive mitochondrial DNA mutations are modifiers of tumorigenesis that correlate with low genomic instability in pituitary adenomas.\",\n \"abstract\": \"Mitochondrial DNA (mtDNA) mutations leading to the disruption of respiratory complex I (CI) have been shown to exhibit anti-tumorigenic effects, at variance with those impairing only the function but not the assembly of the complex, which appear to contribute positively to cancer development. Owing to the challenges in the analysis of the multi-copy mitochondrial genome, it is yet to be determined whether tumour-associated mtDNA lesions occur as somatic modifying factors or as germ-line predisposing elements. Here we investigated the whole mitochondrial genome sequence of 20 pituitary adenomas with oncocytic phenotype and identified pathogenic and/or novel mtDNA mutations in 60% of the cases. Using highly sensitive techniques, namely fluorescent PCR and allele-specific locked nucleic acid quantitative PCR, we identified the most likely somatic nature of these mutations in our sample set, since none of the mutations was detected in the corresponding blood tissue of the patients analysed. Furthermore, we have subjected a series of 48 pituitary adenomas to a high-resolution array comparative genomic hybridization analysis, which revealed that CI disruptive mutations, and the oncocytic phenotype, significantly correlate with low number of chromosomal aberrations in the nuclear genome. We conclude that CI disruptive mutations in pituitary adenomas are somatic modifiers of tumorigenesis most likely contributing not only to the development of oncocytic change, but also to a less aggressive tumour phenotype, as indicated by a stable karyotype.\",\n \"corpus_id\": 12026300,\n \"score\": 2\n },\n {\n \"doc_id\": \"23450047\",\n \"title\": \"Whole-exome sequencing studies of nonfunctioning pituitary adenomas.\",\n \"abstract\": \"CONTEXT: The tumorigenic role of genetic abnormalities in sporadic pituitary nonfunctioning adenomas (NFAs), which usually originate from gonadotroph cells, is unknown. OBJECTIVE: The objective of the study was to identify somatic genetic abnormalities in sporadic pituitary NFAs. DESIGN: Whole-exome sequencing was performed using DNA from 7 pituitary NFAs and leukocyte samples obtained from the same patients. Somatic variants were confirmed by dideoxynucleotide sequencing, and candidate driver genes were assessed in an additional 24 pituitary NFAs. RESULTS: Whole-exome sequencing achieved a high degree of coverage such that approximately 97% of targeted bases were represented by more than 10 base reads; 24 somatic variants were identified and confirmed in the discovery set of 7 pituitary NFAs (mean 3.5 variants/tumor; range 1-7). Approximately 80% of variants occurred as missense single nucleotide variants and the remainder were synonymous changes or small frameshift deletions. Each of the 24 mutations occurred in independent genes with no recurrent mutations. Mutations were not observed in genes previously associated with pituitary tumorigenesis, although somatic variants in putative driver genes including platelet-derived growth factor D (PDGFD), N-myc down-regulated gene family member 4 (NDRG4), and Zipper sterile-α-motif kinase (ZAK) were identified; however, DNA sequence analysis of these in the validation set of 24 pituitary NFAs did not reveal any mutations indicating that these genes are unlikely to contribute significantly in the etiology of sporadic pituitary NFAs. CONCLUSIONS: Pituitary NFAs harbor few somatic mutations consistent with their low proliferation rates and benign nature, but mechanisms other than somatic mutation are likely involved in the etiology of sporadic pituitary NFAs.\",\n \"corpus_id\": 13898977,\n \"score\": 2\n },\n {\n \"doc_id\": \"24781529\",\n \"title\": \"A pilot genome-scale profiling of DNA methylation in sporadic pituitary macroadenomas: association with tumor invasion and histopathological subtype.\",\n \"abstract\": \"Pituitary adenomas (PAs) are neoplasms that may cause a variety of neurological and endocrine effects. Although known causal contributors include heredity, hormonal influence and somatic mutations, the pathophysiologic mechanisms driving tumorigenesis and invasion of sporadic PAs remain unknown. We hypothesized that alterations in DNA methylation are associated with PA invasion and histopathology subtype, and that genome-scale methylation analysis may complement current classification methods for sporadic PAs. Twenty-four surgically-resected sporadic PAs with varying histopathological subtypes were assigned dichotomized Knosp invasion scores and examined using genome-wide DNA methylation profiling and RNA sequencing. PA samples clustered into subgroups according to functional status. Compared with hormonally-active PAs, nonfunctional PAs exhibited global DNA hypermethylation (mean beta-value 0.47 versus 0.42, P = 0.005); the most significant site of differential DNA methylation was within the promoter region of the potassium voltage-gated channel KCNAB2 (FDR = 5.11×10-10). Pathway analysis of promoter-associated CpGs showed that nonfunctional PAs are potentially associated with the ion-channel activity signal pathway. DNA hypermethylation tended to be negatively correlated with gene expression. DNA methylation analysis may be used to identify candidate genes involved in PA function and may potentially complement current standard immunostaining classification in sporadic PAs. DNA hypermethylation of KCNAB2 and downstream ion-channel activity signal pathways may contribute to the endocrine-inactive status of nonfunctional PAs.\",\n \"corpus_id\": 16148820,\n \"score\": 2\n },\n {\n \"doc_id\": \"25490274\",\n \"title\": \"Whole-exome sequencing characterizes the landscape of somatic mutations and copy number alterations in adrenocortical carcinoma.\",\n \"abstract\": \"CONTEXT: Adrenocortical carcinoma (ACC) is a rare and lethal malignancy with a poorly defined etiology, and the molecular genetics of ACC are incompletely understood. OBJECTIVE: To utilize whole-exome sequencing for genetic characterization of the underlying somatic mutations and copy number alterations present in ACC. DESIGN: Screening for somatic mutation events and copy number alterations (CNAs) was performed by comparative analysis of tumors and matched normal samples from 41 patients with ACC. RESULTS: In total, 966 nonsynonymous somatic mutations were detected, including 40 tumors with a mean of 16 mutations per sample and one tumor with 314 mutations. Somatic mutations in ACC-associated genes included TP53 (8/41 tumors, 19.5%) and CTNNB1 (4/41, 9.8%). Genes with potential disease-causing mutations included GNAS, NF2, and RB1, and recurrently mutated genes with unknown roles in tumorigenesis comprised CDC27, SCN7A, and SDK1. Recurrent CNAs included amplification at 5p15.33 including TERT (6/41, 14.6%) and homozygous deletion at 22q12.1 including the Wnt repressors ZNRF3 and KREMEN1 (4/41 9.8% and 3/41, 7.3%, respectively). Somatic mutations in ACC-established genes and recurrent ZNRF3 and TERT loci CNAs were mutually exclusive in the majority of cases. Moreover, gene ontology identified Wnt signaling as the most frequently mutated pathway in ACCs. CONCLUSIONS: These findings highlight the importance of Wnt pathway dysregulation in ACC and corroborate the finding of homozygous deletion of Wnt repressors ZNRF3 and KREMEN1. Overall, mutations in either TP53 or CTNNB1 as well as focal CNAs at the ZNRF3 or TERT loci denote mutually exclusive events, suggesting separate mechanisms underlying the development of these tumors.\",\n \"corpus_id\": 8510815,\n \"score\": 2\n },\n {\n \"doc_id\": \"26280510\",\n \"title\": \"Whole-Genome Sequencing of Growth Hormone (GH)-Secreting Pituitary Adenomas.\",\n \"abstract\": \"CONTEXT: The somatic landscape of pituitary adenomas is largely unknown. Identification of somatic alterations aims at better understanding of tumor pathology. OBJECTIVE: The objective of the study was a genome-wide characterization of somatic single-nucleotide variants, structural variants, and copy-number aberrations in somatotropinomas. DESIGN AND SETTING: Whole-genome sequencing and single-nucleotide polymorphism array analyses were performed on 12 fresh-frozen somatotropinomas and their corresponding blood samples. All the coding somatic variants were confirmed by Sanger sequencing. PATIENTS: Studied tumors were somatotropinomas. Apart from one AIP mutation-positive patient, all cases were mutation negative for the established germline mutations associated with pituitary adenomas. INTERVENTION(S): There were no interventions. MAIN OUTCOME MEASURES: Somatic variants were identified with an established computational pipeline and filtered against germline data. Somatic copy number alteration analyses were performed using segmentation-based approaches. RESULTS: A genome-wide analysis revealed on average 129 somatic single-nucleotide variants per tumor. Further analysis of coding regions showed on average 2.3 single-nucleotide variants per tumor. The only recurrent somatic events were the oncogenic GNAS mutation (p.Arg201Cys) and shared chromosome losses (chromosomes 1, 6, 13, 14, 15, 16, 18, 22). Analysis of somatic structural variants revealed one tumor with a complex chromosomal rearrangement. CONCLUSIONS: Somatotropinomas showed a low number of somatic genetic alterations. Whereas no novel recurrently mutated genes could be identified, the somatic landscape has potential to affect the Ca(2+) and ATP pathways known to be involved in the pituitary tumorigenesis. Further studies, eg, methylome and transcriptome analyses, are needed to investigate possible interplay between the recurrent chromosome losses and epigenetic factors.\",\n \"corpus_id\": 34982199,\n \"score\": 2\n },\n {\n \"doc_id\": \"26701869\",\n \"title\": \"Landscape of somatic mutations in sporadic GH-secreting pituitary adenomas.\",\n \"abstract\": \"CONTEXT: Alterations in the cAMP signaling pathway are common in hormonally active endocrine tumors. Somatic mutations at GNAS are causative in 30-40% of GH-secreting adenomas. Recently, mutations affecting the USP8 and PRKACA gene have been reported in ACTH-secreting pituitary adenomas and cortisol-secreting adrenocortical adenomas respectively. However, the pathogenesis of many GH-secreting adenomas remains unclear. AIM: Comprehensive genetic characterization of sporadic GH-secreting adenomas and identification of new driver mutations. DESIGN: Screening for somatic mutations was performed in 67 GH-secreting adenomas by targeted sequencing for GNAS, PRKACA, and USP8 mutations (n=31) and next-generation exome sequencing (n=36). RESULTS: By targeted sequencing, known activating mutations in GNAS were detected in five cases (16.1%), while no somatic mutations were observed in both PRKACA and USP8. Whole-exome sequencing identified 132 protein-altering somatic mutations in 31/36 tumors with a median of three mutations per sample (range: 1-13). The only recurrent mutations have been observed in GNAS (31.4% of cases). However, seven genes involved in cAMP signaling pathway were affected in 14 of 36 samples and eight samples harbored variants in genes involved in the calcium signaling or metabolism. At the enrichment analysis, several altered genes resulted to be associated with developmental processes. No significant correlation between genetic alterations and the clinical data was observed. CONCLUSION: This study provides a comprehensive analysis of somatic mutations in a large series of GH-secreting adenomas. No novel recurrent genetic alterations have been observed, but the data suggest that beside cAMP pathway, calcium signaling might be involved in the pathogenesis of these tumors.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"26792934\",\n \"title\": \"Very low frequency of germline GPR101 genetic variation and no biallelic defects with AIP in a large cohort of patients with sporadic pituitary adenomas.\",\n \"abstract\": \"CONTEXT: Recently, germline and somatic GPR101 p.(E308D) mutation was found in patients with isolated acromegaly. It is not known whether GPR101 point mutations are associated with other histological types of pituitary adenoma. OBJECTIVE: We sought germline GPR101 mutations in patients with sporadic pituitary adenomas, and compared the phenotypes of GPR101 mutation carriers and AIP mutation carriers. DESIGN: An observational cohort study performed between 2007 and 2014 in a single referral center. PARTICIPANTS: This prospective study involved 766 unselected patients (413 women) with sporadic pituitary adenomas of all histotypes. METHODS: Entire GPR101 and AIP coding sequence were screened for germline mutations. RESULTS: Twelve patients (1.6%) were found to carry the GPR101 p.(E308D) mutation or rare GPR101 variants. The minor allele frequency of the GPR101 mutation and variants was higher in patients with pituitary adenomas than in unaffected individuals included in the Exome Aggregation Consortium database. Three of the six patients with the GPR101 p.(E308D) mutation had adult-onset acromegaly, two had adrenocorticotropin-secreting adenomas, and one had a nonfunctioning macroadenoma. Six patients carried rare GPR101 variants. Germline AIP mutations or rare AIP variants were identified in 32 patients (4.2%). AIP mutation carriers were younger at diagnosis than GPR101 mutation carriers and non carriers. None of the patients harbored mutations in both the GPR101 and AIP genes. CONCLUSION: Germline GPR101 mutations are very rare in patients with sporadic pituitary adenomas of various histotypes. No digenism with AIP was identified. Further studies are required to establish whether and how genetic variation in GPR101 gene contributes to pituitary tumorigenesis.\",\n \"corpus_id\": 31892731,\n \"score\": 2\n },\n {\n \"doc_id\": \"27854551\",\n \"title\": \"Whole-Exome Sequencing Study of Thyrotropin-Secreting Pituitary Adenomas.\",\n \"abstract\": \"Context: Thyrotropin (TSH)-secreting pituitary adenomas (TSHomas) are a rare cause of hyperthyroidism, and the genetic aberrations responsible remain unknown. Objective: To identify somatic genetic abnormalities in TSHomas. Design and Setting: A single-nucleotide polymorphism (SNP) array analysis was performed on 8 TSHomas. Four tumors with no allelic losses or limited loss of heterozygosity were selected, and whole-exome sequencing was performed, including their corresponding blood samples. Somatic variants were confirmed by Sanger sequencing. A set of 8 tumors was also assessed to validate candidate genes. Patients: Twelve patients with sporadic TSHomas were examined. Results: The overall performance of whole-exome sequencing was good, with an average coverage of each base in the targeted region of 97.6%. Six DNA variants were confirmed as candidate driver mutations, with an average of 1.5 somatic mutations per tumor. No mutations were recurrent. Two of these mutations were found in genes with an established role in malignant tumorigenesis (SMOX and SYTL3), and 4 had unknown roles (ZSCAN23, ASTN2, R3HDM2, and CWH43). Similarly, an SNP array analysis revealed frequent chromosomal regions of copy number gains, including recurrent gains at loci harboring 4 of these 6 genes. Conclusions: Several candidate somatic mutations and changes in copy numbers for TSHomas were identified. The results showed no recurrence of mutations in the tumors studied but a low number of mutations, thereby highlighting their benign nature. Further studies on a larger cohort of TSHomas, along with the use of epigenetic and transcriptomic approaches, may reveal the underlying genetic lesions.\",\n \"corpus_id\": 3724032,\n \"score\": 2\n },\n {\n \"doc_id\": \"28486603\",\n \"title\": \"Clinical identification of oncogenic drivers and copy number alterations in pituitary tumors.\",\n \"abstract\": \"Pituitary tumors are the second most common adult primary brain tumor, with a variable clinical course. Recent work has identified a number of genetic determinants of pituitary tumor subtypes, which may augment classic histopathologic classification schemes. We sought to determine whether pituitary tumors could be stratified based on objective molecular characteristics using a clinical genomics assay. We profiled pituitary tumors using OncoPanel, a clinical multiplexed next-generation sequencing assay and retrospectively collected the clinical information and sequencing results for 127 patients from 2012-2016 at the Brigham and Women's Hospital. We analyzed 127 pituitary tumors, including 114 adenomas, 5 craniopharyngiomas, and 8 tumors of other histologies. We observed recurrent BRAFV600E mutations in papillary craniopharyngiomas, CTNNB1 mutations in adamantinomatous craniopharyngiomas, and activating GNAS mutations in GH-secreting adenomas. Furthermore, we validated the presence of two distinct genomic subclasses in adenomas, those with disrupted or quiet copy-number profiles, and the significant association of disruption with functional hormone status (p < 0.05). We report the first clinical implementation of next-generation sequencing of pituitary tumors. We confirmed previously identified molecular subclasses for these tumors, and show that routine screening as part of clinical practice is both feasible and informative. This large-scale proof of principle study may help to guide future institutional efforts for pituitary tumor classification, as well as incorporation into prospective analysis as part of clinical trials.\",\n \"corpus_id\": 22578844,\n \"score\": 2\n },\n {\n \"doc_id\": \"28790112\",\n \"title\": \"Burden and profile of somatic mutation in duodenal adenomas from patients with familial adenomatous- and MUTYH-associated polyposis.\",\n \"abstract\": \"PURPOSE: Duodenal polyposis and cancer are important causes of morbidity and mortality in familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP). This study aimed to comprehensively characterize somatic genetic changes in FAP and MAP duodenal adenomas to better understand duodenal tumorigenesis in these disorders.<br /><br />Experimental Design: Sixty-nine adenomas were biopsied during endoscopy in 16 FAP and 10 MAP patients with duodenal polyposis. Ten FAP and 10 MAP adenomas and matched blood DNA samples were exome sequenced, 42 further adenomas underwent targeted sequencing and 47 were studied by array comparative genomic hybridization. Findings in FAP and MAP duodenal adenomas were compared to each other and to the reported mutational landscape in FAP and MAP colorectal adenomas.<br /><br />Results: MAP duodenal adenomas had significantly more protein-changing somatic mutations (P = 0.018), truncating mutations (P = 0.006) and copy number variants (P = 0.005) than FAP duodenal adenomas, even though MAP patients had lower Spigelman stage duodenal polyposis. Fifteen genes were significantly recurrently mutated. Targeted sequencing of APC, KRAS, PTCHD2 and PLCL1 identified further mutations in each of these genes in additional duodenal adenomas. In contrast to MAP and FAP colorectal adenomas, neither exome nor targeted sequencing identified WTX mutations (P=0.0017).<br /><br />Conclusions: The mutational landscapes in FAP and MAP duodenal adenomas overlapped with, but had significant differences to those reported in colorectal adenomas. The significantly higher burden of somatic mutations in MAP than FAP duodenal adenomas despite lower Spigelman stage disease could increase cancer risk in the context of apparently less severe benign disease.\",\n \"corpus_id\": 263568241,\n \"score\": 2\n },\n {\n \"doc_id\": \"29396598\",\n \"title\": \"Genomic Alterations in Sporadic Pituitary Tumors.\",\n \"abstract\": \"PURPOSE OF REVIEW: Pituitary tumors are undergoing a transformation in histopathologic and molecular classification, coincident with the continued refinement of increasingly powerful methods of genomic annotation and discovery. We highlight novel genomic alterations identified in pituitary adenomas and craniopharyngiomas and discuss their clinical implications. RECENT FINDINGS: Sporadic pituitary adenomas are associated with relatively few recurrent somatic mutations. Recurrent mutations occur largely in subsets of hormone-producing tumors, including GNAS and GPR101 in somatotroph adenomas and USP8 in corticotroph adenomas. Additionally, they manifest with a dichotomous signature of copy number alterations, ranging from almost none to widespread genome instability, while microduplication of chromosome Xq26.3, containing the GNAS gene, defines X-linked acrogigantism. Papillary craniopharyngiomas are defined by BRAF V600E mutations while β-catenin alterations characterize adamantinomatous craniopharyngiomas. Genomic annotation of pituitary tumors is defining increasing subsets of neuroendocrine adenohypophyseal tumors and craniopharyngiomas, offering rationale-based pharmacologic targets and potential biomarkers for clinical outcome.\",\n \"corpus_id\": 25114185,\n \"score\": 2\n },\n {\n \"doc_id\": \"29410024\",\n \"title\": \"DNA methylation profiling in nonfunctioning pituitary adenomas.\",\n \"abstract\": \"Nonfunctioning pituitary adenomas (NFPAs) are among the most frequent intracranial tumors but their molecular background, including changes in epigenetic regulation, remains poorly understood. We performed genome-wide DNA methylation profiling of 34 NFPAs and normal pituitary samples. Methylation status of the selected genomic regions and expression level of corresponding genes were assessed in a group of 75 patients. NFPAs exhibited distinct global methylation profile as compared to normal pituitary. Aberrant DNA methylation appears to contribute to deregulation of the cancer-related pathways as shown by preliminary functional analysis. Promoter hypermethylation and decreased expression level of SFN, STAT5A, DUSP1, PTPRE and FGFR2 was confirmed in the enlarged group of NFPAs. Difference in the methylation profiles between invasive and non-invasive NFPAs is very slight. Nevertheless, invasiveness-related aberrant epigenetic deregulation of the particular genes was found including upregulation of ITPKB and downregulation CNKSR1 in invasive tumors.\",\n \"corpus_id\": 46750106,\n \"score\": 2\n },\n {\n \"doc_id\": \"29474559\",\n \"title\": \"Genomic Alterations and Complex Subclonal Architecture in Sporadic GH-Secreting Pituitary Adenomas.\",\n \"abstract\": \"Purpose: The molecular pathogenesis of growth hormone-secreting pituitary adenomas is not fully understood. Cytogenetic alterations might serve as alternative driver events in GNAS mutation-negative somatotroph tumors. Experimental Design: We performed cytogenetic profiling of pituitary adenomas obtained from 39 patients with acromegaly and four patients with sporadic gigantism by using array comparative genomic hybridization analysis. We explored intratumor DNA copy-number heterogeneity in two tumor samples by using DNA fluorescence in situ hybridization (FISH). Results: Based on copy-number profiles, we found two groups of adenomas: a low-copy-number alteration (CNA) group (<12% of genomic disruption, 63% of tumors) and a high-CNA group (24% to 45% of genomic disruption, 37% of tumors). Arm-level CNAs were the most common abnormalities. GNAS mutation-positive adenomas belonged exclusively to the low-CNA group, whereas a subgroup of GNAS mutation-negative adenomas had a high degree of genomic disruption. We detected chromothripsis-related CNA profiles in two adenoma samples from an AIP mutation-positive patient with acromegaly and a patient with sporadic gigantism. RNA sequencing of these two samples identified 17 fusion transcripts, most of which resulted from chromothripsis-related chromosomal rearrangements. DNA FISH analysis of these samples demonstrated a subclonal architecture with up to six distinct cell populations in each tumor. Conclusion: Somatotroph pituitary adenomas display substantial intertumor and intratumor DNA copy-number heterogeneity, as revealed by variable CNA profiles and complex subclonal architecture. The extensive cytogenetic burden in a subgroup of GNAS mutation-negative somatotroph adenomas points to an alternative tumorigenic pathway linked to genomic instability.\",\n \"corpus_id\": 3518794,\n \"score\": 2\n },\n {\n \"doc_id\": \"19401813\",\n \"title\": \"Expression of p18(INK4C) is down-regulated in human pituitary adenomas.\",\n \"abstract\": \"Cyclin-dependent kinase inhibitors represented by the INK4 family comprising p16(INK4A), p15(INK4B), p18(INK4C), and p19(INK4D) are regulators of the cell cycle shown to be aberrant in many types of cancer. Mice lacking p18(Ink4c) exhibit a series of phenotypes including the development of widespread organomegaly and pituitary adenomas. The objective of our study is to examine the role of p18(INK4C) in the pathogenesis of human pituitary tumors. The protein and mRNA levels of p18(INK4C) were examined by immunohistochemistry and real-time reverse transcription-polymerase chain reaction, respectively. The methylation status of the p18(INK4C) gene promoter and somatic mutations of the p18(INK4C) gene were also investigated. p18(INK4C) protein expression was lost or significantly reduced in 64% of pituitary adenomas compared with levels in normal pituitary glands. p18(INK4C) mRNA levels were low in all ACTH adenomas and non-functioning (NF)-FSH and in 42%, 70% and 66% of GH, PRL, and subtype 3 adenomas, respectively. p18(INK4C) mRNA levels were significantly associated with p18(INK4C) protein levels. Neither methylated promoters in pituitary adenomas, except in one NF-FSH adenoma, nor somatic mutations of the p18(INK4C) gene in any pituitary adenomas were detected. The down-regulation of p18(INK4C) expression may contribute to the tumorigenesis of pituitary adenomas.\",\n \"corpus_id\": 38658573,\n \"score\": 1\n },\n {\n \"doc_id\": \"20015288\",\n \"title\": \"Genomic landscape of meningiomas.\",\n \"abstract\": \"Meningiomas are one of the most common adult brain tumors. For most patients, surgical excision is curative. However, up to 20% recur. Currently, the molecular determinants predicting recurrence and malignant transformation are lacking. We performed retrospective global genetic and genomic analysis of 85 meningioma samples of various grades. Copy number alterations were assessed by 100K single-nucleotide polymorphism arrays and correlated with gene expression, proliferation indices and clinical outcome. In addition to chromosome 22q loss, which was detected in the majority of clinical samples, chromosome 6q and 14q loss was significantly more common in recurrent tumors and was associated with anaplastic histology. Five \\\"classes\\\" of meningiomas were detected by gene expression analysis that correlated with copy number alterations, recurrent status and malignant histology. These classes more accurately identified recurrent tumors relative to Ki-67 index and extent of surgical resection, and highlight substantial expression heterogeneity between meningiomas. These data offer the most complete description of the genomic landscape of meningiomas, and provide broad genomic information that may be used to further stratify meningioma patients into prognostic risk groups.\",\n \"corpus_id\": 24557277,\n \"score\": 1\n },\n {\n \"doc_id\": \"25545346\",\n \"title\": \"The genomic landscape of phaeochromocytoma.\",\n \"abstract\": \"Phaeochromocytomas (PCCs) and paragangliomas (PGLs) are rare neural crest-derived tumours originating from adrenal chromaffin cells or extra-adrenal sympathetic and parasympathetic tissues. More than a third of PCC/PGL cases are associated with heritable syndromes involving 13 or more known genes. These genes have been broadly partitioned into two groups based on pseudo-hypoxic and receptor tyrosine kinase (RTK) signalling pathways. Many of these genes can also become somatically mutated, although up to one third of sporadic cases have no known genetic driver. Furthermore, little is known of the genes that co-operate with known driver genes to initiate and drive tumourigenesis. To explore the genomic landscape of PCC/PGL, we applied exome sequencing, high-density SNP-array analysis, and RNA sequencing to 36 PCCs and four functional PGL tumours. All tumours displayed low mutation frequency, in contrast to frequent large segmental copy-number alterations, aneuploidy, and evidence for chromothripsis in one case. Multi-region sampling of one benign familial PCC tumour provided evidence for the timing of mutations during tumourigenesis and ongoing clonal evolution. Thirty-one of 40 (77.5%) cases could be explained by germline or somatic mutations or structural alterations affecting known PCC/PGL genes. Deleterious somatic mutations were also identified in known tumour-suppressor genes associated with genome maintenance and epigenetic modulation. A multitude of other genes were also found mutated that are likely important for normal neuroendocrine cell function. We revisited the gene-expression subtyping of PCC/PGL by integrating published microarray data with our RNA-seq data, enabling the identification of six robust gene-expression subtypes. The majority of cases in our cohort with no identifiable driver mutation were classified into a gene-expression subtype bearing similarity to MAX mutant PCC/PGL. Our data suggest there are yet unknown PCC/PGL cancer genes that can phenocopy MAX mutant PCC/PGL tumours. This study provides new insight into the molecular diversity and genetic origins of PCC/PGL tumours.\",\n \"corpus_id\": 20412293,\n \"score\": 1\n },\n {\n \"doc_id\": \"26643872\",\n \"title\": \"Genomic landscape of liposarcoma.\",\n \"abstract\": \"Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.\",\n \"corpus_id\": 3742639,\n \"score\": 1\n },\n {\n \"doc_id\": \"27221540\",\n \"title\": \"Genomic Landscape of Colorectal Mucosa and Adenomas.\",\n \"abstract\": \"The molecular basis of the adenoma-to-carcinoma transition has been deduced using comparative analysis of genetic alterations observed through the sequential steps of intestinal carcinogenesis. However, comprehensive genomic analyses of adenomas and at-risk mucosa are still lacking. Therefore, our aim was to characterize the genomic landscape of colonic at-risk mucosa and adenomas. We analyzed the mutation profile and copy number changes of 25 adenomas and adjacent mucosa from 12 familial adenomatous polyposis patients using whole-exome sequencing and validated allelic imbalances (AI) in 37 adenomas using SNP arrays. We assessed for evidence of clonality and performed estimations on the proportions of driver and passenger mutations using a systems biology approach. Adenomas had lower mutational rates than did colorectal cancers and showed recurrent alterations in known cancer driver genes (APC, KRAS, FBXW7, TCF7L2) and AIs in chromosomes 5, 7, and 13. Moreover, 80% of adenomas had somatic alterations in WNT pathway genes. Adenomas displayed evidence of multiclonality similar to stage I carcinomas. Strong correlations between mutational rate and patient age were observed in at-risk mucosa and adenomas. Our data indicate that at least 23% of somatic mutations are present in at-risk mucosa prior to adenoma initiation. The genomic profiles of at-risk mucosa and adenomas illustrate the evolution from normal tissue to carcinoma via greater resolution of molecular changes at the inflection point of premalignant lesions. Furthermore, substantial genomic variation exists in at-risk mucosa before adenoma formation, and deregulation of the WNT pathway is required to foster carcinogenesis. Cancer Prev Res; 9(6); 417-27. ©2016 AACR.\",\n \"corpus_id\": 25118462,\n \"score\": 1\n },\n {\n \"doc_id\": \"27340278\",\n \"title\": \"Whole-Exome Sequencing of Salivary Gland Mucoepidermoid Carcinoma.\",\n \"abstract\": \"PURPOSE: Mucoepidermoid carcinoma (MEC) is the most common salivary gland malignancy. To explore the genetic origins of MEC, we performed systematic genomic analyses of these tumors. EXPERIMENTAL DESIGN: Whole-exome sequencing and gene copy-number analyses were performed for 18 primary cancers with matched normal tissue. FISH was used to determine the presence or absence of the MECT1-MAML2 translocation in 17 tumors. RESULTS: TP53 was the most commonly mutated gene in MEC (28%), and mutations were found only in intermediate- and high-grade tumors. Tumors with TP53 mutations had more mutations overall than tumors without TP53 mutations (P = 0.006). POU6F2 was the second most frequently mutated gene, found in three low-grade MECs with the same in-frame deletion. Somatic alterations in IRAK1, MAP3K9, ITGAL, ERBB4, OTOGL, KMT2C, and OBSCN were identified in at least two of the 18 tumors sequenced. FISH analysis confirmed the presence of the MECT1-MAML2 translocation in 15 of 17 tumors (88%). CONCLUSIONS: Through these integrated genomic analyses, MECT1-MAML2 translocation and somatic TP53 and POU6F2 mutations appear to be the main drivers of MEC. Clin Cancer Res; 23(1); 283-8. ©2016 AACR.\",\n \"corpus_id\": 24241276,\n \"score\": 1\n },\n {\n \"doc_id\": \"27723760\",\n \"title\": \"The genomic landscape of schwannoma.\",\n \"abstract\": \"Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q. The fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma. Methylation profiling identified distinct molecular subgroups of schwannomas that were associated with anatomical location. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated ERK, increased proliferation, increased invasion and in vivo tumorigenesis. Targeting of the MEK-ERK pathway was effective in fusion-positive Schwann cells, suggesting a possible therapeutic approach for this subset of tumors.\",\n \"corpus_id\": 3687140,\n \"score\": 1\n },\n {\n \"doc_id\": \"27742789\",\n \"title\": \"Novel Genetic Causes of Pituitary Adenomas.\",\n \"abstract\": \"Recently, a number of novel genetic alterations have been identified that predispose individuals to pituitary adenomas. Clinically relevant pituitary adenomas are relatively common, present in 0.1% of the general population. They are mostly benign monoclonal neoplasms that arise from any of the five hormone-secreting cell types of the anterior lobe of the pituitary gland, and cause disease due to hormonal alterations and local space-occupying effects. The pathomechanism of pituitary adenomas includes alterations in cell-cycle regulation and growth factor signaling, which are mostly due to epigenetic changes; somatic and especially germline mutations occur more rarely. A significant proportion of growth hormone- and adrenocorticotrophin-secreting adenomas have activating somatic mutations in the GNAS and USP8 genes, respectively. Rarely, germline mutations predispose to pituitary tumorigenesis, often in a familial setting. Classical tumor predisposition syndromes include multiple endocrine neoplasia type 1 (MEN1) and type 4 (MEN4) syndromes, Carney complex, and McCune-Albright syndrome. Pituitary tumors have also been described in association with neurofibromatosis type 1, DICER1 syndrome, and SDHx mutations. Pituitary adenomas with no other associated tumors have been described as familial isolated pituitary adenomas. Patients with AIP or GPR101 mutations often present with pituitary gigantism either in a familial or simplex setting. GNAS and GPR101 mutations that arise in early embryonic age can lead to somatic mosaicism involving the pituitary gland and resulting in growth hormone excess. Senescence has been suggested as the key mechanism protecting pituitary adenomas turning malignant in the overwhelming majority of cases. Here we briefly summarize the genetic background of pituitary adenomas, with an emphasis on the recent developments in this field. Clin Cancer Res; 22(20); 5030-42. ©2016 AACR SEE ALL ARTICLES IN THIS CCR FOCUS SECTION, \\\"ENDOCRINE CANCERS REVISING PARADIGMS\\\".\",\n \"corpus_id\": 29036761,\n \"score\": 1\n },\n {\n \"doc_id\": \"28348108\",\n \"title\": \"Comprehensive somatic genome alterations of urachal carcinoma.\",\n \"abstract\": \"BACKGROUND: Urachal cancer is a rare cancer that develops in the urachus. Because of its rarity, standard treatment therapies for urachal cancer are not established, and chemotherapeutic regimens for bladder cancer have been unsuccessful for patients with urachal cancer. Hence, we aim to understand a systematic molecular characterisation of urachal cancer. METHODS: We identified somatic single-nucleotide variations (SNVs)/indels and somatic copy number aberrations (SCNAs) in the 17 patients by using whole-exome sequencing (WES) and OncoScan platform (Affymetrix) as follows: tumour-normal paired sequencing (WES, n=10), tumour-only sequencing (WES, n=1; targeted deep sequencing, n=16), and OncoScan (n=17). RESULTS: Our analyses identified 27 genes with somatic SNVs and indels, as well as six genes (APC, COL5A1, KIF26B, LRP1B, SMAD4 and TP53) that were recurrent in at least two patients. By analysing the SCNAs, we found that the extent of chromosomal amplification was highly associated with the patient's cancer stage. Interestingly, 35% (6/17) of the patients had focal DNA amplifications in fibroblast growth factor receptor family genes. The integration of somatic SNVs, indels and SCNAs revealed significant alterations in the mitogen-activated protein kinase signalling pathways. CONCLUSIONS: Our genome-wide analysis of urachal cancer suggests that molecular characteristics may be important for the treatment of urachal cancer.\",\n \"corpus_id\": 206998389,\n \"score\": 1\n },\n {\n \"doc_id\": \"29489754\",\n \"title\": \"The landscape of genomic alterations across childhood cancers.\",\n \"abstract\": \"Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.\",\n \"corpus_id\": 3807522,\n \"score\": 1\n },\n {\n \"doc_id\": \"19918804\",\n \"title\": \"Our changing view of the genomic landscape of cancer.\",\n \"abstract\": \"Sporadic tumours, which account for the majority of all human cancers, arise from the acquisition of somatic, genetic and epigenetic alterations leading to changes in gene sequence, structure, copy number and expression. Within the last decade, the availability of a complete sequence-based map of the human genome, coupled with significant technological advances, has revolutionized the search for somatic alterations in tumour genomes. Recent landmark studies, which resequenced all coding exons within breast, colorectal, brain and pancreatic cancers, have shed new light on the genomic landscape of cancer. Within a given tumour type there are many infrequently mutated genes and a few frequently mutated genes, resulting in incredible genetic heterogeneity. However, when the altered genes are placed into biological processes and biochemical pathways, this complexity is significantly reduced and shared pathways that are affected in significant numbers of tumours can be discerned. The advent of next-generation sequencing technologies has opened up the potential to resequence entire tumour genomes to interrogate protein-encoding genes, non-coding RNA genes, non-genic regions and the mitochondrial genome. During the next decade it is anticipated that the most common forms of human cancer will be systematically surveyed to identify the underlying somatic changes in gene copy number, sequence and expression. The resulting catalogues of somatic alterations will point to candidate cancer genes requiring further validation to determine whether they have a causal role in tumourigenesis. The hope is that this knowledge will fuel improvements in cancer diagnosis, prognosis and therapy, based on the specific molecular alterations that drive individual tumours. In this review, I will provide a historical perspective on the identification of somatic alterations in the pre- and post-genomic eras, with a particular emphasis on recent pioneering studies that have provided unprecedented insights into the genomic landscape of human cancer.\",\n \"corpus_id\": 42897873,\n \"score\": 0\n },\n {\n \"doc_id\": \"20802469\",\n \"title\": \"Detection of chromosome copy number alterations in metanephric adenomas by array comparative genomic hybridization.\",\n \"abstract\": \"Metanephric adenoma is a rare benign renal tumor typically found in adults. Previous cytogenetic analyses, including karyotyping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization, have yielded conflicting results regarding the somatic genetic aberrations of these tumors. In this study, we investigated the genomic profile of nine cases of metanephric adenoma using array comparative genomic hybridization. Two cases revealed multiple chromosomal gains and losses. Three cases showed sporadic chromosomal imbalances involving no more than three chromosomes. Four cases showed normal chromosome copy numbers. The gain of chromosome 19 was the most common finding (five cases), and FISH using 19p and 19q telomeric probes further confirmed this finding. We did not observe consistent gains of chromosomes 7 and 17, which are common in papillary renal cell carcinoma, neither did we find chromosomal alterations frequently present in Wilms' tumors, including chromosome gains of 1q, 7q, and 12, and losses of 11p and 16q. Our series demonstrates that the genetic profile of metanephric adenoma is fundamentally distinct from those of papillary renal cell carcinoma and Wilms' tumor.\",\n \"corpus_id\": 7515498,\n \"score\": 0\n },\n {\n \"doc_id\": \"22156295\",\n \"title\": \"Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency.\",\n \"abstract\": \"Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they showed a 10.5-fold increase in the rate of somatic indels, e.g., truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in the correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas and confirmed MLH1 haploinsufficiency. We observed a much higher rate of indel mutations in the affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1, and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers.\",\n \"corpus_id\": 33383320,\n \"score\": 0\n },\n {\n \"doc_id\": \"22300766\",\n \"title\": \"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.\",\n \"abstract\": \"Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of tumors. Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor-normal pairs. Unlike most current approaches, our algorithm reads data from both samples simultaneously; a heuristic and statistical algorithm detects sequence variants and classifies them by somatic status (germline, somatic, or LOH); while a comparison of normalized read depth delineates relative copy number changes. We apply these methods to the analysis of exome sequence data from 151 high-grade ovarian tumors characterized as part of the Cancer Genome Atlas (TCGA). We validated some 7790 somatic coding mutations, achieving 93% sensitivity and 85% precision for single nucleotide variant (SNV) detection. Exome-based CNA analysis identified 29 large-scale alterations and 619 focal events per tumor on average. As in our previous analysis of these data, we observed frequent amplification of oncogenes (e.g., CCNE1, MYC) and deletion of tumor suppressors (NF1, PTEN, and CDKN2A). We searched for additional recurrent focal CNAs using the correlation matrix diagonal segmentation (CMDS) algorithm, which identified 424 significant events affecting 582 genes. Taken together, our results demonstrate the robust performance of VarScan 2 for somatic mutation and CNA detection and shed new light on the landscape of genetic alterations in ovarian cancer.\",\n \"corpus_id\": 18280129,\n \"score\": 0\n },\n {\n \"doc_id\": \"23029479\",\n \"title\": \"Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.\",\n \"abstract\": \"Mutations in the hyperparathyroidism type 2 (HRPT2/CDC73) gene and alterations in the parafibromin protein have been established in the majority of parathyroid carcinomas and in subsets of parathyroid adenomas. While it is known that CDC73-mutated parathyroid tumors display specific gene expression changes compared to CDC73 wild-type cases, the molecular cytogenetic profile in CDC73-mutated cases compared to unselected adenomas (with an expected very low frequency of CDC73 mutations) remains unknown. For this purpose, nine parathyroid tumors with established CDC73 gene inactivating mutations (three carcinomas, one atypical adenoma and five adenomas) were analyzed for copy number alterations and loss of heterozygosity using array-comparative genomic hybridization (a-CGH) and single nucleotide polymorphism (SNP) microarrays, respectively. Furthermore, CDC73 gene promoter methylation levels were assessed using bisulfite Pyrosequencing. The panel included seven tumors with single mutation and three with double mutations of the CDC73 gene. The carcinomas displayed copy number alterations in agreement with previous studies, whereas the CDC73-mutated adenomas did not display the same pattern of alterations at loci frequently deleted in unselected parathyroid tumors. Furthermore, gross losses of chromosomal material at 1p and 13 were significantly (p = 0.012) associated with parathyroid carcinomas as opposed to adenomas. Quantitative PCR-based copy number loss regarding CDC73 was observed in three adenomas, while all the carcinomas were diploid or showed copy number gain for CDC73 gene. Hypermethylation of the CDC73 gene promoter was not observed. Our data could suggest that CDC73-mutated parathyroid adenomas exhibit a partly unique cytogenetic profile in addition to that of carcinomas and unselected adenomas. Furthermore, CDC73-mutated carcinomas displayed losses at 1p and 13 which are not seen in CDC73-mutated adenomas, making these regions of interest for further studies regarding malignant properties in tumors from CDC73-mutated cases. However, due to the small sample size, validation of the results in a larger cohort is warranted.\",\n \"corpus_id\": 11325195,\n \"score\": 0\n },\n {\n \"doc_id\": \"23074045\",\n \"title\": \"High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.\",\n \"abstract\": \"Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT.\",\n \"corpus_id\": 21832127,\n \"score\": 0\n },\n {\n \"doc_id\": \"23531283\",\n \"title\": \"MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.\",\n \"abstract\": \"BACKGROUND: Most tumors are the result of accumulated genomic alterations in somatic cells. The emerging spectrum of alterations in tumors is complex and the identification of relevant genes and pathways remains a challenge. Furthermore, key cancer genes are usually found amplified or deleted in chromosomal regions containing many other genes. Point mutations, on the other hand, provide exquisite information about amino acid changes that could be implicated in the oncogenic process. Current large-scale genomic projects provide high throughput genomic data in a large number of well-characterized tumor samples. METHODS: We define a Bayesian approach designed to identify candidate cancer genes by integrating copy number and point mutation information. Our method exploits the concept that small and recurrent alterations in tumors are more informative in the search for cancer genes. Thus, the algorithm (Mutations with Common Focal Alterations, or MutComFocal) seeks focal copy number alterations and recurrent point mutations within high throughput data from large panels of tumor samples. RESULTS: We apply MutComFocal to Diffuse Large B-cell Lymphoma (DLBCL) data from four different high throughput studies, totaling 78 samples assessed for copy number alterations by single nucleotide polymorphism (SNP) array analysis and 65 samples assayed for protein changing point mutations by whole exome/whole transcriptome sequencing. In addition to recapitulating known alterations, MutComFocal identifies ARID1B, ROBO2 and MRS1 as candidate tumor suppressors and KLHL6, IL31 and LRP1 as putative oncogenes in DLBCL. CONCLUSIONS: We present a Bayesian approach for the identification of candidate cancer genes by integrating data collected in large number of cancer patients, across different studies. When trained on a well-studied dataset, MutComFocal is able to identify most of the reported characterized alterations. The application of MutComFocal to large-scale cancer data provides the opportunity to pinpoint the key functional genomic alterations in tumors.\",\n \"corpus_id\": 11925257,\n \"score\": 0\n },\n {\n \"doc_id\": \"24308032\",\n \"title\": \"The genomic landscape of oesophagogastric junctional adenocarcinoma.\",\n \"abstract\": \"The incidence of oesophagogastric junctional (OGJ) adenocarcinoma is rising rapidly in western countries, in contrast to the declining frequency of distal gastric carcinoma. Treatment options for adenocarcinomas involving the oesophagogastric junction are limited and the overall prognosis is extremely poor. To determine the genomic landscape of OGJ adenocarcinoma, exomes of eight tumours and matched germline DNA were subjected to massively parallel DNA sequencing. Microsatellite instability was observed in three tumours which coincided with an elevated number of somatic mutations. In total, 117 genes were identified that had predicted coding alterations in more than one tumour. Potentially actionable coding mutations were identified in 67 of these genes, including those in CR2, HGF , FGFR4, and ESRRB. Twenty-nine genes harbouring somatic coding mutations and copy number changes in the MSS OGJ dataset are also known to be altered with similar predicted functional consequence in other tumour types. Compared with the published mutational profile of gastric cancers, 49% (57/117) of recurrently mutated genes were unique to OGJ tumours. TP53, SYNE1, and ARID1A were amongst the most frequently mutated genes in a larger OGJ cohort. Our study provides an insight into the mutational landscape of OGJ adenocarcinomas and confirms that this is a highly mutated and heterogeneous disease. Furthermore, we have uncovered somatic mutations in therapeutically relevant genes which may represent candidate drug targets.\",\n \"corpus_id\": 24219275,\n \"score\": 0\n },\n {\n \"doc_id\": \"24390348\",\n \"title\": \"Landscape of genomic alterations in cervical carcinomas.\",\n \"abstract\": \"Cervical cancer is responsible for 10-15% of cancer-related deaths in women worldwide. The aetiological role of infection with high-risk human papilloma viruses (HPVs) in cervical carcinomas is well established. Previous studies have also implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical carcinomas. Here we report whole-exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole-genome sequencing of 14 tumour-normal pairs. Previously unknown somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%), TP53 (5%) and ERBB2 (6%). We also observe somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas have higher frequencies of somatic nucleotide substitutions occurring at cytosines preceded by thymines (Tp*C sites) than adenocarcinomas. Gene expression levels at HPV integration sites were statistically significantly higher in tumours with HPV integration compared with expression of the same genes in tumours without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest new strategies to combat this disease.\",\n \"corpus_id\": 205236942,\n \"score\": 0\n },\n {\n \"doc_id\": \"24943349\",\n \"title\": \"Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.\",\n \"abstract\": \"BACKGROUND: The outcome of patients with metastatic colorectal carcinoma (mCRC) following first line therapy is poor, with median survival of less than one year. The purpose of this study was to identify candidate therapeutically targetable somatic events in mCRC patient samples by whole genome sequencing (WGS), so as to obtain targeted treatment strategies for individual patients. METHODS: Four patients were recruited, all of whom had received > 2 prior therapy regimens. Percutaneous needle biopsies of metastases were performed with whole blood collection for the extraction of constitutional DNA. One tumor was not included in this study as the quality of tumor tissue was not sufficient for further analysis. WGS was performed using Illumina paired end chemistry on HiSeq2000 sequencing systems, which yielded coverage of greater than 30X for all samples. NGS data were processed and analyzed to detect somatic genomic alterations including point mutations, indels, copy number alterations, translocations and rearrangements. RESULTS: All 3 tumor samples had KRAS mutations, while 2 tumors contained mutations in the APC gene and the PIK3CA gene. Although we did not identify a TCF7L2-VTI1A translocation, we did detect a TCF7L2 mutation in one tumor. Among the other interesting mutated genes was INPPL1, an important gene involved in PI3 kinase signaling. Functional studies demonstrated that inhibition of INPPL1 reduced growth of CRC cells, suggesting that INPPL1 may promote growth in CRC. CONCLUSIONS: Our study further supports potential molecularly defined therapeutic contexts that might provide insights into treatment strategies for refractory mCRC. New insights into the role of INPPL1 in colon tumor cell growth have also been identified. Continued development of appropriate targeted agents towards specific events may be warranted to help improve outcomes in CRC.\",\n \"corpus_id\": 580286,\n \"score\": 0\n },\n {\n \"doc_id\": \"25597018\",\n \"title\": \"Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated Genes in Seminomas.\",\n \"abstract\": \"BACKGROUND: Testicular germ cell tumors are the most common cancer diagnosed in young men, and seminomas are the most common type of these cancers. There have been no exome-wide examinations of genes mutated in seminomas or of overall rates of nonsilent somatic mutations in these tumors. OBJECTIVE: The objective was to analyze somatic mutations in seminomas to determine which genes are affected and to determine rates of nonsilent mutations. DESIGN, SETTING, AND PARTICIPANTS: Eight seminomas and matched normal samples were surgically obtained from eight patients. INTERVENTION: DNA was extracted from tissue samples and exome sequenced on massively parallel Illumina DNA sequencers. Single-nucleotide polymorphism chip-based copy number analysis was also performed to assess copy number alterations. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The DNA sequencing read data were analyzed to detect somatic mutations including single-nucleotide substitutions and short insertions and deletions. The detected mutations were validated by independent sequencing and further checked for subclonality. RESULTS AND LIMITATIONS: The rate of nonsynonymous somatic mutations averaged 0.31 mutations/Mb. We detected nonsilent somatic mutations in 96 genes that were not previously known to be mutated in seminomas, of which some may be driver mutations. Many of the mutations appear to have been present in subclonal populations. In addition, two genes, KIT and KRAS, were affected in two tumors each with mutations that were previously observed in other cancers and are presumably oncogenic. CONCLUSIONS: Our study, the first report on exome sequencing of seminomas, detected somatic mutations in 96 new genes, several of which may be targetable drivers. Furthermore, our results show that seminoma mutation rates are five times higher than previously thought, but are nevertheless low compared to other common cancers. Similar low rates are seen in other cancers that also have excellent rates of remission achieved with chemotherapy. PATIENT SUMMARY: We examined the DNA sequences of seminomas, the most common type of testicular germ cell cancer. Our study identified 96 new genes in which mutations occurred during seminoma development, some of which might contribute to cancer development or progression. The study also showed that the rates of DNA mutations during seminoma development are higher than previously thought, but still lower than for other common solid-organ cancers. Such low rates are also observed among other cancers that, like seminomas, show excellent rates of disease remission after chemotherapy.\",\n \"corpus_id\": 10255493,\n \"score\": 0\n },\n {\n \"doc_id\": \"25600428\",\n \"title\": \"Genomic copy number alterations of primary and secondary metastasizing pleomorphic adenomas.\",\n \"abstract\": \"AIMS: Metastasizing pleomorphic adenoma (MPA) is a rare tumour, and its mechanism of metastasis still is unknown. To date, there has been no study on MPA genomics. We analysed primary and secondary MPAs with array comparative genomic hybridization to identify somatic copy number alterations and affected genes. METHODS AND RESULTS: Tumour DNA samples from primary (parotid salivary gland) and secondary (scalp skin) MPAs were subjected to array comparative genomic hybridization investigation, and the data were analysed with NEXUS COPY NUMBER DISCOVERY. The primary MPA showed copy number losses affecting 3p22.2p14.3 and 19p13.3p123, and a complex pattern of four different deletions at chromosome 6. The 3p deletion encompassed several genes: CTNNB1, SETD2, BAP1, and PBRM1, among others. The secondary MPA showed a genomic profile similar to that of the primary MPA, with acquisition of additional copy number changes affecting 9p24.3p13.1 (loss), 19q11q13.43 (gain), and 22q11.1q13.33 (gain). CONCLUSION: Our findings indicated a clonal origin of the secondary MPA, as both tumours shared a common profile of genomic copy number alterations. Furthermore, we were able to detect in the primary tumour a specific pattern of copy number alterations that could explain the metastasizing characteristic, whereas the secondary MPA showed a more unbalanced genome.\",\n \"corpus_id\": 36907353,\n \"score\": 0\n },\n {\n \"doc_id\": \"26386145\",\n \"title\": \"An Old Story Retold: Loss of G1 Control Defines A Distinct Genomic Subtype of Esophageal Squamous Cell Carcinoma.\",\n \"abstract\": \"Esophageal squamous cell carcinoma (ESCC) has a high mortality rate. To determine the molecular basis of ESCC development, this study sought to identify characteristic genome-wide alterations in ESCC, including exonic mutations and structural alterations. The clinical implications of these genetic alterations were also analyzed. Exome sequencing and verification were performed for nine pairs of ESCC and the matched blood samples, followed by validation with additional samples using Sanger sequencing. Whole-genome SNP arrays were employed to detect copy number alteration (CNA) and loss of heterozygosity (LOH) in 55 cases, including the nine ESCC samples subjected to exome sequencing. A total of 108 non-synonymous somatic mutations (NSSMs) in 102 genes were verified in nine patients. The chromatin modification process was found to be enriched in our gene ontology (GO) analysis. Tumor genomes with TP53 mutations were significantly more unstable than those without TP53 mutations. In terms of the landscape of genomic alterations, deletion of 9p21.3 covering CDKN2A/2B (30.9%), amplification of 11q13.3 covering CCND1 (30.9%), and TP53 point mutation (50.9%) occurred in two-thirds of the cases. These results suggest that the deregulation of the G1 phase during the cell cycle is a key event in ESCC. Furthermore, six minimal common regions were found to be significantly altered in ESCC samples and three of them, 9p21.3, 7p11.2, and 3p12.1, were associated with lymph node metastasis. With the high correlation of TP53 mutation and genomic instability in ESCC, the amplification of CCND1, the deletion of CDKN2A/2B, and the somatic mutation of TP53 appear to play pivotal roles via G1 deregulation and therefore helps to classify this cancer into different genomic subtypes. These findings provide clinical significance that could be useful in future molecular diagnoses and therapeutic targeting.\",\n \"corpus_id\": 9582461,\n \"score\": 0\n },\n {\n \"doc_id\": \"26857264\",\n \"title\": \"Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer.\",\n \"abstract\": \"Gastric cancer and esophageal cancer are the second and sixth leading causes of cancer-related death worldwide. Multiple genomic alterations underlying gastric cancer and esophageal squamous cell carcinoma (ESCC) have been identified, but the full spectrum of genomic structural variations and mutations have yet to be uncovered. Here, we report the results of whole-genome sequencing of 30 samples comprising tumor and blood from 15 patients, four of whom presented with ESCC, seven with gastric cardia adenocarcinoma (GCA), and four with gastric noncardia adenocarcinoma. Analyses revealed that an A>C mutation was common in GCA, and in addition to the preferential nucleotide sequence of A located 5 prime to the mutation as noted in previous studies, we found enrichment of T in the 5 prime base. The A>C mutations in GCA suggested that oxidation of guanine may be a potential mechanism underlying cancer mutagenesis. Furthermore, we identified genes with mutations in gastric cancer and ESCC, including well-known cancer genes, TP53, JAK3, BRCA2, FGF2, FBXW7, MSH3, PTCH, NF1, ERBB2, and CHEK2, and potentially novel cancer-associated genes, KISS1R, AMH, MNX1, WNK2, and PRKRIR Finally, we identified recurrent chromosome alterations in at least 30% of tumors in genes, including MACROD2, FHIT, and PARK2 that were often intragenic deletions. These structural alterations were validated using the The Cancer Genome Atlas dataset. Our studies provide new insights into understanding the genomic landscape, genome instability, and mutation profile underlying gastric cancer and ESCC development. Cancer Res; 76(7); 1714-23. ©2016 AACR.\",\n \"corpus_id\": 3230797,\n \"score\": 0\n },\n {\n \"doc_id\": \"26960396\",\n \"title\": \"The Genomic Landscape of Male Breast Cancers.\",\n \"abstract\": \"PURPOSE: Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers. EXPERIMENTAL DESIGN: All male breast cancers were estrogen receptor-positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor-normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers. RESULTS: Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A-like or luminal B-like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair-related genes. CONCLUSIONS: Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045-56. ©2016 AACR.\",\n \"corpus_id\": 5761563,\n \"score\": 0\n },\n {\n \"doc_id\": \"27091409\",\n \"title\": \"Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures.\",\n \"abstract\": \"PURPOSE: There is substantial heterogeneity within human papillomavirus (HPV)-associated head and neck cancer (HNC) tumors that predispose them to different outcomes; however, the molecular heterogeneity in this subgroup is poorly characterized due to various historical reasons. EXPERIMENTAL DESIGN: We performed unsupervised gene expression clustering on deeply annotated (transcriptome and genome) HPV(+) HNC samples from two cohorts (84 total primary tumors), including 18 HPV(-) HNC samples, to discover subtypes and characterize the differences between subgroups in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number alterations, and mutation frequencies. RESULTS: We identified two distinct HPV(+) subtypes (namely HPV-KRT and HPV-IMU). HPV-KRT is characterized by elevated expression of genes in keratinocyte differentiation and oxidation-reduction process, whereas HPV-IMU has strong immune response and mesenchymal differentiation. The differences in expression are likely connected to the differences in HPV characteristics and genomic changes. HPV-KRT has more genic viral integration, lower E2/E4/E5 expression levels, and higher ratio of spliced to full-length HPV oncogene E6 than HPV-IMU; the subgroups also show differences in copy number alterations and mutations, in particular the loss of chr16q in HPV-IMU and gain of chr3q and PIK3CA mutation in HPV-KRT. CONCLUSIONS: Our characterization of two subtypes of HPV(+) HNC tumors provides valuable molecular level information that point to two main carcinogenic paths. Together, these results shed light on stratifications of the HPV(+) HNCs and will help to guide personalized care for HPV(+) HNC patients. Clin Cancer Res; 22(18); 4735-45. ©2016 AACR.\",\n \"corpus_id\": 207676242,\n \"score\": 0\n },\n {\n \"doc_id\": \"27126562\",\n \"title\": \"Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes.\",\n \"abstract\": \"Retinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited. To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses. Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors. Targeted therapy based on these subclonal events might be insufficient for complete tumor control.\",\n \"corpus_id\": 5404337,\n \"score\": 0\n },\n {\n \"doc_id\": \"27685995\",\n \"title\": \"Genome Analysis of Osteosarcoma Progression Samples Identifies FGFR1 Overexpression as a Potential Treatment Target and CHM as a Candidate Tumor Suppressor Gene.\",\n \"abstract\": \"Osteosarcoma (OS) is the most common primary malignant tumor of bone, showing complex chromosomal rearrangements but with few known consistent changes. Deeper biological understanding is crucial to find new therapies to improve patient survival. We have sequenced the whole exome of two primary tumors (before and after chemotherapy), one metastatic tumor and a matched normal sample from two OS patients, to identify mutations involved in cancer biology. The metastatic samples were also RNA sequenced. By RNA sequencing we identified dysregulated expression levels of drug resistance- and apoptosis-related genes. Two fusion transcripts were identified in one patient (OS111); the first resulted in p53 inactivation by fusing the first exon of TP53 to the fifth exon of FAM45A. The second fusion joined the two first exons of FGFR1 to the second exon of ZNF343. Furthermore, FGFR1 was amplified and highly expressed, representing a potential treatment target in this patient. Whole exome sequencing revealed large intertumor heterogeneity, with surprisingly few shared mutations. Careful evaluation and validation of the data sets revealed a number of artefacts, but one recurrent mutation was validated, a nonsense mutation in CHM (patient OS106), which also was the mutation with the highest expression frequency (53%). The second patient (OS111) had wild-type CHM, but a downregulated expression level. In a panel of 71 clinical samples, we confirmed significant low expression of CHM compared to the controls (p = 0.003). Furthermore, by analyzing public datasets, we identified a significant association between low expression and poor survival in two other cancer types. Together, these results suggest CHM as a candidate tumor suppressor gene that warrants further investigation.\",\n \"corpus_id\": 1272783,\n \"score\": 0\n },\n {\n \"doc_id\": \"27709558\",\n \"title\": \"DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.\",\n \"abstract\": \"BACKGROUND: DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study. METHODS: Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up. RESULTS: DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and TGF-β and apoptosis signaling, were found to be most significantly affected. CONCLUSIONS: Our results suggest that CNAs in CRC tumor tissues are associated with concomitant changes in the expression of cancer-related genes. In other genes epigenetic mechanism may be at work. Up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, appear to be associated with a poor survival. These alterations may, in addition to Dukes' staging, be employed as new prognostic biomarkers for the prediction of clinical outcome in CRC patients.\",\n \"corpus_id\": 7894803,\n \"score\": 0\n },\n {\n \"doc_id\": \"27745836\",\n \"title\": \"Comprehensive Genetic Landscape of Uveal Melanoma by Whole-Genome Sequencing.\",\n \"abstract\": \"Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified. Recurrent coding mutations were found in the known UM drivers GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. Other genes, i.e., TP53BP1, CSMD1, TTC28, DLK2, and KTN1, were also found to harbor somatic mutations in more than one individual, possibly indicating a previously undescribed association with UM pathogenesis. De novo assembly of unmatched reads from non-coding DNA revealed peculiar copy-number variations defining specific UM subtypes, which in turn could be associated with metastatic transformation. Mutational-driven comparison with other tumor types showed that UM is very similar to pediatric tumors, characterized by very few somatic insults and, possibly, important epigenetic changes. Through the analysis of whole-genome sequencing data, our findings shed new light on the molecular genetics of uveal melanoma, delineating it as an atypical tumor of the adult for which somatic events other than mutations in exonic DNA shape its genetic landscape and define its metastatic potential.\",\n \"corpus_id\": 11562597,\n \"score\": 0\n },\n {\n \"doc_id\": \"27923066\",\n \"title\": \"Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study.\",\n \"abstract\": \"BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. We detected driver genes by testing whether the nonsynonymous mutation rate was significantly higher than the background mutation rate and replicated our findings in public datasets with 724 samples. We performed subclonality analysis for mutations based on mutant allele data and copy number alteration data. We also tested the association between mutation signatures and clinical outcomes, including distant metastasis, survival, and tumor grade. We identified and replicated two novel candidate driver genes, POU class 4 homeobox 2 (POU4F2) (mutated in 9 [8.9%] samples) and ZKSCAN1 (mutated in 6 [5.9%] samples), and characterized their major deleterious mutations. ZKSCAN1 was part of a mutually exclusive gene set that included the RTK/RAS/RAF pathway genes BRAF, EGFR, KRAS, MET, and NF1, indicating an important driver role for this gene. Moreover, we observed strong associations between methylation in specific genomic regions and somatic mutation patterns. In the tumor evolution analysis, four driver genes had a significantly lower fraction of subclonal mutations (FSM), including TP53 (p = 0.007), KEAP1 (p = 0.012), STK11 (p = 0.0076), and EGFR (p = 0.0078), suggesting a tumor initiation role for these genes. Subclonal mutations were significantly enriched in APOBEC-related signatures (p < 2.5×10-50). The total number of somatic mutations (p = 0.0039) and the fraction of transitions (p = 5.5×10-4) were associated with increased risk of distant metastasis. Our study's limitations include a small number of LUAD patients for subgroup analyses and a single-sample design for investigation of subclonality. CONCLUSIONS: These data provide a genomic characterization of LUAD pathogenesis and progression. The distinct clonal and subclonal mutation signatures suggest possible diverse carcinogenesis pathways for endogenous and exogenous exposures, and may serve as a foundation for more effective treatments for this lethal disease. LUAD's high heterogeneity emphasizes the need to further study this tumor type and to associate genomic findings with clinical outcomes.\",\n \"corpus_id\": 8765709,\n \"score\": 0\n },\n {\n \"doc_id\": \"28181325\",\n \"title\": \"Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation.\",\n \"abstract\": \"Pleomorphic xanthoastrocytoma (PXA) is a rare localized glioma characterized by frequent BRAF V600E mutation and CDKN2A/B deletion. We explored the association of copy-number variants (CNVs) with BRAF mutations, tumor grade, and patient survival in a cohort of 41 PXA patients using OncoScan chromosomal microarray. Primary resection specimens were available in 38 cases, including 24 PXA and 14 anaplastic PXA (A-PXA), 23 BRAF V600E mutant tumors (61%). CNVs were identified in all cases and most frequently involved chromosome 9 with homozygous CDKN2A/B deletion (n = 33, 87%), a higher proportion than previously detected by comparative genomic hybridization (50%-60%) (37). CDKN2A/B deletion was present in similar proportion of PXA (83%), A-PXA (93%), BRAF V600E (87%), and wild-type (87%) tumors. Whole chromosome gains/losses were frequent, including gains +7 (n = 15), +2 (n = 11), +5 (n = 10), +21 (n = 10), +20 (n = 9), +12 (n = 8), +15 (n = 8), and losses -22 (n = 11), -14 (n = 7), -13 (n = 5). Losses and copy-neutral loss of heterozygosity were significantly more common in A-PXA, involving chromosomes 22 (P = 0.009) and 14 (P = 0.03). Amplification of 8p and 12q was identified in a single tumor. Histologic grade was a robust predictor of overall survival (P = 0.003), while other copy-number changes, including CDKN2A/B deletion, did not show significant association with survival. Distinct histologic patterns of anaplasia included increased mitotic activity in an otherwise classic PXA or associated with small cell, fibrillary, or epithelioid morphology, with loss of SMARCB1 expression in one case. In 10 cases, matched specimens were compared, including A-PXA with areas of distinct low- and high-grade morphology (n = 2), matched primary/tumor recurrence (n = 7), or both (n = 1). Copy-number changes on recurrence/anaplastic transformation were complex and highly variable, from nearly identical profiles to numerous copy-number changes. Overall, we confirm CDKN2A/B deletion as key a feature of PXA not associated with tumor grade or BRAF mutation, but central to the underlying genetics of PXA.\",\n \"corpus_id\": 3942062,\n \"score\": 0\n },\n {\n \"doc_id\": \"28607096\",\n \"title\": \"The somatic mutation landscape of premalignant colorectal adenoma.\",\n \"abstract\": \"OBJECTIVE: There are few studies which characterised the molecular alterations in premalignant colorectal adenomas. Our major goal was to establish colorectal adenoma genome atlas and identify molecular markers of progression from colorectal adenoma to adenocarcinoma. DESIGN: Whole-exome sequencing and targeted sequencing were carried out in 149 adenoma samples and paired blood from patients with conventional adenoma or sessile serrated adenoma to characterise the somatic mutation landscape for premalignant colorectal lesions. The identified somatic mutations were compared with those in colorectal cancer (CRC) samples from The Cancer Genome Atlas. A supervised random forest model was employed to identify gene panels differentiating adenoma from CRC. RESULTS: Similar somatic mutation frequencies, but distinctive driver mutations, were observed in sessile serrated adenomas and conventional adenomas. The final model included 20 genes and was able to separate the somatic mutation profile of colorectal adenoma and adenocarcinoma with an area under the curve of 0.941. CONCLUSION: The findings of this project hold potential to better identify patients with adenoma who may be candidates for targeted surveillance programmes and preventive interventions to reduce the incidence of CRC.\",\n \"corpus_id\": 5167455,\n \"score\": 0\n },\n {\n \"doc_id\": \"28710315\",\n \"title\": \"Shallow whole genome sequencing on circulating cell-free DNA allows reliable non-invasive copy number profiling in neuroblastoma patients.\",\n \"abstract\": \"PURPOSE: <p>Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of NB patients could offer a valuable alternative to primary tumor DNA for CNA profiling.</p> <br /><br />Experimental Design: <p>In 37 NB patients cfDNA analysis using shallow whole genome sequencing (sWGS) was compared to arrayCGH analysis of primary tumor tissue.</p> <br /><br />Results: <p>Comparison of CNA profiles on cfDNA showed highly concordant patterns, particularly in high-stage patients. Numerical chromosome imbalances as well as large and focal structural aberrations including MYCN and LIN28B amplification and ATRX deletion could be readily detected with sWGS using a low input of cfDNA.</p> <br /><br />Conclusions: <p>In conclusion, sWGS analysis on cfDNA offers a cost-effective, non-invasive, rapid, robust and sensitive alternative for tumor DNA copy number profiling in most NB patients.\",\n \"corpus_id\": 19774549,\n \"score\": 0\n },\n {\n \"doc_id\": \"28789476\",\n \"title\": \"Molecular Transition of an Adult Low-Grade Brain Tumor to an Atypical Teratoid/Rhabdoid Tumor Over a Time-Course of 14 Years.\",\n \"abstract\": \"Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system is a highly malignant, pediatric brain tumor typically arising de novo. Inactivation of SMARCB1 is a defining molecular event. We present here a rare case of an adult (35 years) low-grade SMARCB1-deleted brain tumor with transition into prototypical AT/RT over 14 years. Molecular analysis was performed for 3 tumor presentations including copy number analysis, DNA methylation analysis (450k), and whole exome sequencing. We detected the identical somatic SMARCB1 deletion at all 3 time-points. In an unsupervised hierarchical clustering of methylation data together with 127 reference cases comprising 9 brain tumor classes all 3 manifestations clustered with AT/RT. Exome sequencing revealed an increase of mutational burden over time. The acquired mutations and additional copy number changes did not affect known cancer genes. In conclusion, we demonstrate molecular changes associated with histological and clinical transition of a low-grade brain tumor to an adult AT/RT. Our observation of a stable disease course for nearly 10 years in a tumor with SMARCB1 loss and an AT/RT-like DNA methylation profile indicates that caution may be required in the diagnostic interpretation of such findings in adult patients.\",\n \"corpus_id\": 42816748,\n \"score\": 0\n },\n {\n \"doc_id\": \"29030356\",\n \"title\": \"Cell-Cycle and DNA-Damage Response Pathway Is Involved in Leptomeningeal Metastasis of Non-Small Cell Lung Cancer.\",\n \"abstract\": \"Purpose: Leptomeningeal metastasis (LM) is a detrimental complication of non-small cell lung cancer (NSCLC) and associated with poor prognosis. However, the underlying mechanisms of the metastasis process are still poorly understood. Experimental Design: We performed next-generation panel sequencing of primary tumor tissue, cerebrospinal fluid (CSF), and matched normal controls from epidermal growth factor receptor (EGFR) mutation-positive NSCLC patients with LM.Results: The status of EGFR-activating mutations was highly concordant between primary tumor and CSF. PIK3CA aberrations were high in these patients, implicating an association with LM risk. Intriguingly, low overlapping of somatic protein-changing variants was observed between paired CSF and primary lesions, exhibiting tumor heterogeneity and genetic divergence. Moreover, genes with CSF-recurrent genomic alterations were predominantly involved in cell-cycle regulation and DNA-damage response (DDR), suggesting a role of the pathway in LM development. Conclusions: Our study has shed light on the genomic variations of NSCLC-LM, demonstrated genetic heterogeneity and divergence, uncovered involvement of cell-cycle and DDR pathway, and paved the way for potential therapeutic approaches to this unmet medical need. Clin Cancer Res; 24(1); 209-16. ©2017 AACR.\",\n \"corpus_id\": 11055603,\n \"score\": 0\n },\n {\n \"doc_id\": \"29351916\",\n \"title\": \"Pathways Impacted by Genomic Alterations in Pulmonary Carcinoid Tumors.\",\n \"abstract\": \"Purpose: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors. Experimental Design: We performed integrated genomic analysis of carcinoid tumors comprising whole genome and exome sequencing, mRNA expression profiling and SNP genotyping of specimens from normal lung, TC and AC, and small cell lung carcinoma (SCLC) to fully represent the lung neuroendocrine tumor spectrum. Results: Analysis of sequencing data found recurrent mutations in cancer genes including ATP1A2, CNNM1, MACF1, RAB38, NF1, RAD51C, TAF1L, EPHB2, POLR3B, and AGFG1 The mutated genes are involved in biological processes including cellular metabolism, cell division cycle, cell death, apoptosis, and immune regulation. The top most significantly mutated genes were TMEM41B, DEFB127, WDYHV1, and TBPL1 Pathway analysis of significantly mutated and cancer driver genes implicated MAPK/ERK and amyloid beta precursor protein (APP) pathways whereas analysis of CNV and gene expression data suggested deregulation of the NF-κB and MAPK/ERK pathways. The mutation signature was predominantly C>T and T>C transitions with a minor contribution of T>G transversions. Conclusions: This study identified mutated genes affecting cancer relevant pathways and biological processes that could provide opportunities for developing targeted therapies for pulmonary carcinoid tumors. Clin Cancer Res; 24(7); 1691-704. ©2018 AACR.\",\n \"corpus_id\": 4584205,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":81,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29535149\",\n \"title\": \"SvABA: genome-wide detection of structural variants and indels by local assembly.\",\n \"abstract\": \"Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA's performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs and substantially improves detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (<1000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types and found that short templated-sequence insertions occur in ∼4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized (50-300 bp) SVs.\",\n \"corpus_id\": 3870389\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19593373","title":"Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.","abstract":"The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen), with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs). SV reconstruction is considered the most challenging step in human genome re-sequencing. ( It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome.) To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost.","corpus_id":1865945,"score":2},{"doc_id":"19668202","title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.","abstract":"Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations. We examined BreakDancer's performance in simulation, in comparison with other methods and in analyses of a sample from an individual with acute myeloid leukemia and of samples from the 1,000 Genomes trio individuals. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.","corpus_id":887817,"score":2},{"doc_id":"20308636","title":"Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.","abstract":"Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.","corpus_id":4506651,"score":2},{"doc_id":"21785424","title":"Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.","abstract":"Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.","corpus_id":11830481,"score":2},{"doc_id":"21787423","title":"Identification of genomic indels and structural variations using split reads.","abstract":"BACKGROUND: Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection. RESULTS: We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions vs. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs. CONCLUSIONS: Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for deletions. Moreover, with the advent of the third-generation sequencing technologies that produce longer reads, we expect our method to be even more useful.","corpus_id":7472166,"score":2},{"doc_id":"22156294","title":"Efficient de novo assembly of large genomes using compressed data structures.","abstract":"De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a reference-unbiased way. We present memory efficient data structures and algorithms for assembly using the FM-index derived from the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA (String Graph Assembler). We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs <200 bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster.","corpus_id":8954687,"score":2},{"doc_id":"22179552","title":"Detection of structural variants and indels within exome data.","abstract":"We report an algorithm to detect structural variation and indels from 1 base pair (bp) to 1 Mbp within exome sequence data sets. Splitread uses one end-anchored placements to cluster the mappings of subsequences of unanchored ends to identify the size, content and location of variants with high specificity and sensitivity. The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods.","corpus_id":10153850,"score":2},{"doc_id":"22238266","title":"Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.","abstract":"MOTIVATION: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. RESULTS: Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant. AVAILABILITY: SplazerS is available from http://www.seqan.de/projects/ splazers. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":451429,"score":2},{"doc_id":"22962449","title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis.","abstract":"MOTIVATION: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs. RESULTS: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. AVAILABILITY: DELLY is available at www.korbel.embl.de/software.html CONTACT: tobias.rausch@embl.de.","corpus_id":18049007,"score":2},{"doc_id":"23060616","title":"CLEVER: clique-enumerating variant finder.","abstract":"MOTIVATION: Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. RESULTS: Here, we present a novel internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. A novel algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions. For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present relevant performance statistics. We achieve superior performance, in particular, for deletions or insertions (indels) of length 20-100 nt. This has been previously identified as a remaining major challenge in structural variation discovery, in particular, for insert size based approaches. In this size range, we even outperform split-read aligners. We achieve competitive results also on biological data, where our method is the only one to make a substantial amount of correct predictions, which, additionally, are disjoint from those by split-read aligners. AVAILABILITY: CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com. CONTACT: as@cwi.nl or tm@cwi.nl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":14262460,"score":2},{"doc_id":"23144753","title":"A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.","abstract":"Defining the architecture of a specific cancer genome, including its structural variants, is essential for understanding tumor biology, mechanisms of oncogenesis, and for designing effective personalized therapies. Short read paired-end sequencing is currently the most sensitive method for detecting somatic mutations that arise during tumor development. However, mapping structural variants using this method leads to a large number of false positive calls, mostly due to the repetitive nature of the genome and the difficulty of assigning correct mapping positions to short reads. This study describes a method to efficiently identify large tumor-specific deletions, inversions, duplications and translocations from low coverage data using SVDetect or BreakDancer software and a set of novel filtering procedures designed to reduce false positive calls. Applying our method to a spontaneous T cell lymphoma arising in a core RAG2/p53-deficient mouse, we identified 40 validated tumor-specific structural rearrangements supported by as few as 2 independent read pairs.","corpus_id":15648796,"score":2},{"doc_id":"23966565","title":"Assembler for de novo assembly of large genomes.","abstract":"Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for \"jumping\" extension and read \"remapping.\" First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read extension process, which expedites the extension process and can jump over short repeats. Third, it uses a dynamic back trimming process to avoid extension termination due to sequencing errors. Fourth, it remaps reads to each assembled sequence, and if an assembly error occurs by the presence of a repeat, it breaks the contig at the repeat boundaries. Fifth, it applies a less stringent extension criterion to connect low-coverage regions. Finally, it merges contigs by unused reads. An extensive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less central processing unit time, especially for large genomes. Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use and central processing unit time than most current assemblers when the read length is 150 bp or longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the read length increases with advances in next generation sequencing technology.","corpus_id":35531956,"score":2},{"doc_id":"24552580","title":"Detection of structural variants involving repetitive regions in the reference genome.","abstract":"Next-generation sequencing techniques are now commonly used to characterize structural variations (SVs) in population genomics and elucidate their associations with phenotypes. Many of the computational tools developed for detecting structural variations work by mapping paired-end reads to a reference genome and identifying the discordant read-pairs whose mapped loci in the reference genome deviate from the expected insert size and orientation. However, repetitive regions in the reference genome represent a major challenge in SV detection, because the paired-end reads from these regions may be mapped to multiple loci in the reference genome, resulting in spuriously discordant read-pairs. To address this issue, we have developed an algorithmic approach for read mapping and SV detection based on the framework of A-Bruijn graphs. Instead of mapping reads to a linear sequence of the reference genome, we propose to map reads onto the A-Bruijn graph constructed from the reference genome in which all instances of the same repeat are collapsed into a single edge. As a result, any given read, either from repetitive regions or not, will be mapped to a unique location in the A-Bruijn graph, and each discordant read-pair in the A-Bruijn graph indicates a potentially true SV event. We also developed a simple clustering algorithm to derive valid clusters of these discordant read-pairs, each supporting a different SV event. Finally, we demonstrate the performance of this approach, compared to existing approaches, by identifying transposition events of insertion sequence (IS) elements, a class of simple mobile genetic elements (MGEs), in E. coli by using simulated and real paired-end sequence data acquired from E. coli mutation accumulation lines.","corpus_id":22235709,"score":2},{"doc_id":"24564972","title":"iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.","abstract":"BACKGROUND: Structural variations (SVs), such as insertions, deletions, inversions, and duplications, are a common feature in human genomes, and a number of studies have reported that such SVs are associated with human diseases. Although the progress of next generation sequencing (NGS) technologies has led to the discovery of a large number of SVs, accurate and genome-wide detection of SVs remains challenging. Thus far, various calling algorithms based on NGS data have been proposed. However, their strategies are diverse and there is no tool able to detect a full range of SVs accurately. RESULTS: We focused on evaluating the performance of existing deletion calling algorithms for various spanning ranges from low- to high-coverage simulation data. The simulation data was generated from a whole genome sequence with artificial SVs constructed based on the distribution of variants obtained from the 1000 Genomes Project. From the simulation analysis, deletion calls of various deletion sizes were obtained with each caller, and it was found that the performance was quite different according to the type of algorithms and targeting deletion size. Based on these results, we propose an integrated structural variant calling pipeline (iSVP) that combines existing methods with a newly devised filtering and merging processes. It achieved highly accurate deletion calling with >90% precision and >90% recall on the 30× read data for a broad range of size. We applied iSVP to the whole-genome sequence data of a CEU HapMap sample, and detected a large number of deletions, including notable peaks around 300 bp and 6,000 bp, which corresponded to Alus and long interspersed nuclear elements, respectively. In addition, many of the predicted deletions were highly consistent with experimentally validated ones by other studies. CONCLUSIONS: We present iSVP, a new deletion calling pipeline to obtain a genome-wide landscape of deletions in a highly accurate manner. From simulation and real data analysis, we show that iSVP is broadly applicable to human whole-genome sequencing data, which will elucidate relationships between SVs across genomes and associated diseases or biological functions.","corpus_id":11871023,"score":2},{"doc_id":"24907369","title":"ABRA: improved coding indel detection via assembly-based realignment.","abstract":"MOTIVATION: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative. RESULTS: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation. AVAILABILITY AND IMPLEMENTATION: ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.","corpus_id":16470026,"score":2},{"doc_id":"25355789","title":"Characterization of structural variants with single molecule and hybrid sequencing approaches.","abstract":"MOTIVATION: Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS: We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.","corpus_id":13580950,"score":2},{"doc_id":"25380961","title":"Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.","abstract":"MOTIVATION: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. RESULTS: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes.","corpus_id":10043658,"score":2},{"doc_id":"25423315","title":"GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.","abstract":"Insertions and deletions (indels) are important types of structural variations. Obtaining accurate genotypes of indels may facilitate further genetic study. There are a few existing methods for calling indel genotypes from sequence reads. However, none of these tools can accurately call indel genotypes for indels of all lengths, especially for low coverage sequence data. In this paper, we present GINDEL, an approach for calling genotypes of both insertions and deletions from sequence reads. GINDEL uses a machine learning approach which combines multiple features extracted from next generation sequencing data. We test our approach on both simulated and real data and compare with existing tools, including Genome STRiP, Pindel and Clever-sv. Results show that GINDEL works well for deletions larger than 50 bp on both high and low coverage data. Also, GINDEL performs well for insertion genotyping on both simulated and real data. For comparison, Genome STRiP performs less well for shorter deletions (50-200 bp) on both simulated and real sequence data from the 1000 Genomes Project. Clever-sv performs well for intermediate deletions (200-1500 bp) but is less accurate when coverage is low. Pindel only works well for high coverage data, but does not perform well at low coverage. To summarize, we show that GINDEL not only can call genotypes of insertions and deletions (both short and long) for high and low coverage population sequence data, but also is more accurate and efficient than other approaches. The program GINDEL can be downloaded at: http://sourceforge.net/p/gindel.","corpus_id":7907662,"score":2},{"doc_id":"25671094","title":"Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology.","abstract":"BACKGROUND: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. RESULTS: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger than 1 kb. Excluding the 59 SVs (54 insertions/deletions, 5 inversions) that overlap with N-base gaps in the reference assembly hg19, 666 non-gap SVs remained, and 396 of them (60%) were verified by paired-end data from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides valuable information for complex regions with haplotypes in a straightforward fashion. In addition, with long single-molecule labeling patterns, exogenous viral sequences were mapped on a whole-genome scale, and sample heterogeneity was analyzed at a new level. CONCLUSION: Our study highlights genome mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome.","corpus_id":4673983,"score":2},{"doc_id":"25886820","title":"Assessing structural variation in a personal genome-towards a human reference diploid genome.","abstract":"BACKGROUND: Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods. RESULTS: We demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus. CONCLUSIONS: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.","corpus_id":207448,"score":2},{"doc_id":"26319364","title":"Amplicon Indel Hunter Is a Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based Next-Generation Sequencing Data.","abstract":"Amplicon-based targeted next-generation sequencing assays are used widely to test for clinically relevant somatic mutations in cancer. However, accurate detection of large insertions and deletions (indels) via these assays remains challenging. Sequencing reads that cover these anomalies are, by definition, different from the reference sequence, and lead to variable performance of alignment algorithms. Reads with large indels may be aligned incorrectly, causing incorrect calls, or may remain unmapped and essentially ignored by downstream informatics pipeline sub-processes. Herein, we describe Amplicon Indel Hunter (AIH), a novel large (>5-bp) indel detection method that is reference genome independent and highly sensitive for the identification of somatic indels in amplicon-based, paired-end, next-generation sequencing data. We validated the algorithm for sensitivity and specificity using a set of clinical cancer samples with Clinical Laboratory Improvement Amendment-confirmed indels as well as in silico mutated data sets. The AIH detected 100% of tested large indels with relatively higher mutant allele frequencies compared with a variety of traditional aligners, which showed variably reduced sensitivity and specificity by comparison. The AIH especially outperformed alignment-based methods for detection of all tested FLT3 internal tandem duplications up to 102 bp. Because AIH runs in parallel to traditional alignment-based informatics pathways, it can be readily incorporated into nearly any analysis pipeline for somatic mutation detection in paired-end amplicon-based data.","corpus_id":30520539,"score":2},{"doc_id":"26643039","title":"ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.","abstract":"Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel .","corpus_id":713655,"score":2},{"doc_id":"26647377","title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.","abstract":": We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. AVAILABILITY AND IMPLEMENTATION: Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta. CONTACT: csaunders@illumina.comSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":7620813,"score":2},{"doc_id":"26740523","title":"SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.","abstract":"MOTIVATION: Whole genome sequencing of paired-end reads can be applied to characterize the landscape of large somatic rearrangements of cancer genomes. Several methods for detecting structural variants with whole genome sequencing data have been developed. So far, none of these methods has combined information about abnormally mapped read pairs connecting rearranged regions and associated global copy number changes automatically inferred from the same sequencing data file. Our aim was to create a computational method that could use both types of information, i.e. normal and abnormal reads, and demonstrate that by doing so we can highly improve both sensitivity and specificity rates of structural variant prediction. RESULTS: We developed a computational method, SV-Bay, to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach. This approach takes into account depth of coverage by normal reads and abnormalities in read pair mappings. To estimate the model likelihood, SV-Bay considers GC-content and read mappability of the genome, thus making important corrections to the expected read count. For the detection of somatic variants, SV-Bay makes use of a matched normal sample when it is available. We validated SV-Bay on simulated datasets and an experimental mate-pair dataset for the CLB-GA neuroblastoma cell line. The comparison of SV-Bay with several other methods for structural variant detection demonstrated that SV-Bay has better prediction accuracy both in terms of sensitivity and false-positive detection rate. AVAILABILITY AND IMPLEMENTATION: https://github.com/InstitutCurie/SV-Bay CONTACT: valentina.boeva@inserm.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":12556366,"score":2},{"doc_id":"26772178","title":"svclassify: a method to establish benchmark structural variant calls.","abstract":"BACKGROUND: The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). High-quality benchmark small variant calls for the pilot National Institute of Standards and Technology (NIST) Reference Material (NA12878) have been developed by the Genome in a Bottle Consortium, but no similar high-quality benchmark SV calls exist for this genome. Since SV callers output highly discordant results, we developed methods to combine multiple forms of evidence from multiple sequencing technologies to classify candidate SVs into likely true or false positives. Our method (svclassify) calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate SVs as likely true or false positives. RESULTS: We first used pedigree analysis to develop a set of high-confidence breakpoint-resolved large deletions. We then used svclassify to cluster and classify these deletions as well as a set of high-confidence deletions from the 1000 Genomes Project and a set of breakpoint-resolved complex insertions from Spiral Genetics. We find that likely SVs cluster separately from likely non-SVs based on our annotations, and that the SVs cluster into different types of deletions. We then developed a supervised one-class classification method that uses a training set of random non-SV regions to determine whether candidate SVs have abnormal annotations different from most of the genome. To test this classification method, we use our pedigree-based breakpoint-resolved SVs, SVs validated by the 1000 Genomes Project, and assembly-based breakpoint-resolved insertions, along with semi-automated visualization using svviz. CONCLUSIONS: We find that candidate SVs with high scores from multiple technologies have high concordance with PCR validation and an orthogonal consensus method MetaSV (99.7 % concordant), and candidate SVs with low scores are questionable. We distribute a set of 2676 high-confidence deletions and 68 high-confidence insertions with high svclassify scores from these call sets for benchmarking SV callers. We expect these methods to be particularly useful for establishing high-confidence SV calls for benchmark samples that have been characterized by multiple technologies.","corpus_id":1305594,"score":2},{"doc_id":"26787508","title":"Nanopore sequencing detects structural variants in cancer.","abstract":"Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.","corpus_id":13902299,"score":2},{"doc_id":"27079510","title":"mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development.","abstract":"BACKGROUND: Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data generation, and enabled genome-wide identification of insertion and deletion variation. However, current NGS-based InDel mining tools, such as Samtools, GATK and Atlas2, all rely on a reference genome for variant calling which hinders their application on unsequenced organisms and the output of short InDels compromised their use on gel-based genotyping platforms. To address these issues, an enhanced platform is needed to identify longer InDels and develop markers in absence of a reference genome. RESULTS: Here we present mInDel (multiple InDel), a next-generation variant calling tool specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, this software identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable. By providing an option of combining multiple discovered InDels as output, mInDel is amiable to gel-based genotyping platforms where markers with large polymorphisms are preferred. We demonstrated the usability and performance of this software through a case study using a set of maize NGS data, and experimentally validated the accuracy of markers generated from mInDel. CONCLUSIONS: mInDel is a novel and practical tool that enables rapid genome-wide InDel marker discovery. The features of being independent from a reference genome and the flexibility with downstream genotyping platforms will allow a broad range of applications across genetics research and plant breeding. The mInDel pipeline is freely available at www.github.com/lyd0527/mInDel .","corpus_id":2422565,"score":2},{"doc_id":"27634948","title":"Seeksv: an accurate tool for somatic structural variation and virus integration detection.","abstract":"MOTIVATION: Many forms of variations exist in the human genome including single nucleotide polymorphism, small insert/deletion (DEL) (indel) and structural variation (SV). Somatically acquired SV may regulate the expression of tumor-related genes and result in cell proliferation and uncontrolled growth, eventually inducing tumor formation. Virus integration with host genome sequence is a type of SV that causes the related gene instability and normal cells to transform into tumor cells. Cancer SVs and viral integration sites must be discovered in a genome-wide scale for clarifying the mechanism of tumor occurrence and development. RESULTS: In this paper, we propose a new tool called seeksv to detect somatic SVs and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and the fragment with two ends unmapped. Seeksv can detect DEL, insertion, inversion and inter-chromosome transfer at single-nucleotide resolution. Different types of sequencing data, such as single-end sequencing data or paired-end sequencing data can accommodate to detect SV. Seeksv develops a rescue model for SV with breakpoints located in sequence homology regions. Results on simulated and real data from the 1000 Genomes Project and esophageal squamous cell carcinoma samples show that seeksv has higher efficiency and precision compared with other similar software in detecting SVs. For the discovery of hepatitis B virus integration sites from probe capture data, the verified experiments show that more than 90% viral integration sequences detected by seeksv are true. AVAILABILITY AND IMPLEMENTATION: seeksv is implemented in C ++ and can be downloaded from https://github.com/qkl871118/seeksv CONTACT: : dragonbw@163.comSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":6647775,"score":2},{"doc_id":"27892959","title":"novoBreak: local assembly for breakpoint detection in cancer genomes.","abstract":"We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions.","corpus_id":3541000,"score":2},{"doc_id":"27895111","title":"Discovery and genotyping of structural variation from long-read haploid genome sequence data.","abstract":"In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.","corpus_id":22109251,"score":2},{"doc_id":"28056804","title":"INDELseek: detection of complex insertions and deletions from next-generation sequencing data.","abstract":"BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of \"pileup\" of each reference position across multiple alignments. In benchmarking against the reference material NA12878 genome (n = 160 derived from high-confidence variant calls), GATK, SAMtools and INDELseek showed complex indel detection sensitivities of 0%, 0% and 100%, respectively. INDELseek also detected all known germline (BRCA1 and BRCA2) and somatic (CALR and JAK2) complex indels in human clinical samples (n = 8). Further experiments validated all 10 detected KIT complex indels in a discovery cohort of clinical samples. In silico semi-simulation showed sensitivities of 93.7-96.2% based on 8671 unique complex indels in >5000 genes from dbSNP and COSMIC. We also demonstrated the importance of complex indel detection in accurately annotating BRCA1, BRCA2 and TP53 mutations with gained or rescued protein-truncating effects. CONCLUSIONS: INDELseek is an accurate and versatile tool for complex indel detection in NGS data. It complements other variant callers in NGS-based genomics studies targeting a wide spectrum of genetic variations.","corpus_id":19801079,"score":2},{"doc_id":"28104618","title":"HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.","abstract":"Achieving complete, accurate, and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a Hybrid Structural variant Assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variants (SVs) in human genomes. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance the assembly of structurally altered regions in human genomes. We used data generated from a haploid hydatidiform mole genome (CHM1) and a diploid human genome (NA12878) to test our approach. The result showed that, compared with existing methods, our approach had a low false discovery rate and substantially improved the detection of many types of SVs, particularly novel large insertions, small indels (10-50 bp), and short tandem repeat expansions and contractions. Our work highlights the strengths and limitations of current approaches and provides an effective solution for extending the power of existing sequencing technologies for SV discovery.","corpus_id":17631100,"score":2},{"doc_id":"28714986","title":"Genome-wide reconstruction of complex structural variants using read clouds.","abstract":"In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets. Compared with short-fragment sequencing, GROC-SVs substantially improves the specificity of breakpoint detection at comparable sensitivity. This approach also performs sequence assembly across multiple breakpoints simultaneously, enabling the reconstruction of events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nucleotide variants and SVs are not correlated. Our results support the use of read cloud approaches to advance the characterization of large and complex structural variation.","corpus_id":16198659,"score":2},{"doc_id":"29048532","title":"Lightning-fast genome variant detection with GROM.","abstract":"Current human whole genome sequencing projects produce massive amounts of data, often creating significant computational challenges. Different approaches have been developed for each type of genome variant and method of its detection, necessitating users to run multiple algorithms to find variants. We present Genome Rearrangement OmniMapper (GROM), a novel comprehensive variant detection algorithm accepting aligned read files as input and finding SNVs, indels, structural variants (SVs), and copy number variants (CNVs). We show that GROM outperforms state-of-the-art methods on 7 validated benchmarks using 2 whole genome sequencing (WGS) data sets. Additionally, GROM boasts lightning-fast run times, analyzing a 50× WGS human data set (NA12878) on commonly available computer hardware in 11 minutes, more than an order of magnitude (up to 72 times) faster than tools detecting a similar range of variants. Addressing the needs of big data analysis, GROM combines in 1 algorithm SNV, indel, SV, and CNV detection, providing superior speed, sensitivity, and precision. GROM is also able to detect CNVs, SNVs, and indels in non-paired-read WGS libraries, as well as SNVs and indels in whole exome or RNA sequencing data sets.","corpus_id":29395223,"score":2},{"doc_id":"29097403","title":"GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.","abstract":"The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.","corpus_id":2824411,"score":2},{"doc_id":"29109544","title":"Mapping and phasing of structural variation in patient genomes using nanopore sequencing.","abstract":"Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.","corpus_id":10597633,"score":2},{"doc_id":"29123647","title":"Tools for annotation and comparison of structural variation.","abstract":"The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop.","corpus_id":2785318,"score":2},{"doc_id":"29590294","title":"Leveraging known genomic variants to improve detection of variants, especially close-by Indels.","abstract":"Motivation: The detection of genomic variants has great significance in genomics, bioinformatics, biomedical research and its applications. However, despite a lot of effort, Indels and structural variants are still under-characterized compared to SNPs. Current approaches based on next-generation sequencing data usually require large numbers of reads (high coverage) to be able to detect such types of variants accurately. However Indels, especially those close to each other, are still hard to detect accurately. Results: We introduce a novel approach that leverages known variant information, e.g. provided by dbSNP, dbVar, ExAC or the 1000 Genomes Project, to improve sensitivity of detecting variants, especially close-by Indels. In our approach, the standard reference genome and the known variants are combined to build a meta-reference, which is expected to be probabilistically closer to the subject genomes than the standard reference. An alignment algorithm, which can take into account known variant information, is developed to accurately align reads to the meta-reference. This strategy resulted in accurate alignment and variant calling even with low coverage data. We showed that compared to popular methods such as GATK and SAMtools, our method significantly improves the sensitivity of detecting variants, especially Indels that are close to each other. In particular, our method was able to call these close-by Indels at a 15-20% higher sensitivity than other methods at low coverage, and still get 1-5% higher sensitivity at high coverage, at competitive precision. These results were validated using simulated data with variant profiles extracted from the 1000 Genomes Project data, and real data from the Illumina Platinum Genomes Project and ExAC database. Our finding suggests that by incorporating known variant information in an appropriate manner, sensitive variant calling is possible at a low cost. Availability and implementation: Implementation can be found in our public code repository https://github.com/namsyvo/IVC. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4306823,"score":2},{"doc_id":"29618752","title":"IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.","abstract":"Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease.","corpus_id":52807469,"score":2},{"doc_id":"29713081","title":"Picky comprehensively detects high-resolution structural variants in nanopore long reads.","abstract":"Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.","corpus_id":14038771,"score":2},{"doc_id":"19439515","title":"Mobile elements create structural variation: analysis of a complete human genome.","abstract":"Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed approximately 126 kb of sequence from the HuRef genome. Overall, approximately 10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation.","corpus_id":10407859,"score":1},{"doc_id":"19657104","title":"Sensitive and accurate detection of copy number variants using read depth of coverage.","abstract":"Methods for the direct detection of copy number variation (CNV) genome-wide have become effective instruments for identifying genetic risk factors for disease. The application of next-generation sequencing platforms to genetic studies promises to improve sensitivity to detect CNVs as well as inversions, indels, and SNPs. New computational approaches are needed to systematically detect these variants from genome sequence data. Existing sequence-based approaches for CNV detection are primarily based on paired-end read mapping (PEM) as reported previously by Tuzun et al. and Korbel et al. Due to limitations of the PEM approach, some classes of CNVs are difficult to ascertain, including large insertions and variants located within complex genomic regions. To overcome these limitations, we developed a method for CNV detection using read depth of coverage. Event-wise testing (EWT) is a method based on significance testing. In contrast to standard segmentation algorithms that typically operate by performing likelihood evaluation for every point in the genome, EWT works on intervals of data points, rapidly searching for specific classes of events. Overall false-positive rate is controlled by testing the significance of each possible event and adjusting for multiple testing. Deletions and duplications detected in an individual genome by EWT are examined across multiple genomes to identify polymorphism between individuals. We estimated error rates using simulations based on real data, and we applied EWT to the analysis of chromosome 1 from paired-end shotgun sequence data (30x) on five individuals. Our results suggest that analysis of read depth is an effective approach for the detection of CNVs, and it captures structural variants that are refractory to established PEM-based methods.","corpus_id":23734995,"score":1},{"doc_id":"19907642","title":"BFAST: an alignment tool for large scale genome resequencing.","abstract":"BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net).","corpus_id":13516642,"score":1},{"doc_id":"20305016","title":"Genome assembly quality: assessment and improvement using the neutral indel model.","abstract":"We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. Thus, the method is well-suited to assessing fine-scale sequence quality within single assemblies, between different assemblies of a single set of reads, and between genome assemblies for different species. When applying this approach to four primate genome assemblies, we found that average gap error rates per base varied considerably, by up to sixfold. As expected, bacterial artificial chromosome (BAC) sequences contained lower, but still substantial, predicted numbers of errors, arguing for caution in regarding BACs as the epitome of genome fidelity. We then mapped short reads, at approximately 10-fold statistical coverage, from a Bornean orangutan onto the Sumatran orangutan genome assembly originally constructed from capillary reads. This resulted in a reduced gap error rate and a separation of error-prone from high-fidelity sequence. Over 5000 predicted indel errors in protein-coding sequence were corrected in a hybrid assembly. Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies.","corpus_id":18258915,"score":1},{"doc_id":"21291514","title":"Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.","abstract":"BACKGROUND: Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken. RESULTS: We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome. CONCLUSION: We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.","corpus_id":742609,"score":1},{"doc_id":"21653520","title":"A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.","abstract":"MOTIVATION: High-throughput sequencing technologies have made population-scale studies of human genetic variation possible. Accurate and comprehensive detection of DNA sequence variants is crucial for the success of these studies. Small insertions and deletions represent the second most frequent class of variation in the human genome after single nucleotide polymorphisms (SNPs). Although several alignment tools for the gapped alignment of sequence reads to a reference genome are available, computational methods for discriminating indels from sequencing errors and genotyping indels directly from sequence reads are needed. RESULTS: We describe a probabilistic method for the accurate detection and genotyping of short indels from population-scale sequence data. In this approach, aligned sequence reads from a population of individuals are used to automatically account for context-specific sequencing errors associated with indels. We applied this approach to population sequence datasets from the 1000 Genomes exon pilot project generated using the Roche 454 and Illumina sequencing platforms, and were able to detect a significantly greater number of indels than reported previously. Comparison to indels identified in the 1000 Genomes pilot project demonstrated the sensitivity of our method. The consistency in the number of indels and the fraction of indels whose length is a multiple of three across different human populations and two different sequencing platforms indicated that our method has a low false discovery rate. Finally, the method represents a general approach for the detection and genotyping of small-scale DNA sequence variants for population-scale sequencing projects. AVAILABILITY: A program implementing this method is available at http://polymorphism.scripps.edu/~vbansal/software/piCALL/","corpus_id":263602155,"score":1},{"doc_id":"22439878","title":"The fine-scale architecture of structural variants in 17 mouse genomes.","abstract":"BACKGROUND: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. RESULTS: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. CONCLUSIONS: An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.","corpus_id":933467,"score":1},{"doc_id":"22537045","title":"An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.","abstract":"BACKGROUND: Recent advances in sequencing technologies make it possible to comprehensively study structural variations (SVs) using sequence data of large-scale populations. Currently, more efforts have been taken to develop methods that call SVs with exact breakpoints. Among these approaches, split-read mapping methods can be applied on low-coverage sequence data. With increasing amount of data generated, more efficient split-read mapping methods are still needed. Also, since sequence errors can not be avoided for the current sequencing technologies, more accurate split-read mapping methods are still needed to better handle sequence errors. RESULTS: In this paper, we present a split-read mapping method implemented in the program SVseq2 which improves our previous work SVseq1. Similar to SVseq1, SVseq2 calls deletions (and insertions) with exact breakpoints. SVseq2 achieves more accurate calling through split-read mapping within focal regions. SVseq2 also has a much desired feature: there is no need to specify the maximum deletion size, while some existing split-read mapping methods need more memory and longer running time when larger maximum deletion size is chosen. SVseq2 is also much faster because it only needs to examine a small number of ways of splitting the reads. Moreover, SVseq2 supports insertion calling from low-coverage sequence data, while SVseq1 only supports deletion finding. The program SVseq2 can be downloaded at http://www.engr.uconn.edu/~jiz08001/. CONCLUSIONS: SVseq2 enables accurate and efficient SV calling through split-read mapping within focal regions using paired-end reads. For many simulated data and real sequence data, SVseq2 outperforms some other existing approaches in accuracy and efficiency, especially when sequence coverage is low.","corpus_id":1870009,"score":1},{"doc_id":"25123898","title":"MindTheGap: integrated detection and assembly of short and long insertions.","abstract":"MOTIVATION: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. RESULTS: We propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MindTheGap uses an efficient k-mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. MindTheGap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, MindTheGap detected and correctly assembled insertions >1 kb, using at most 14 GB of memory.","corpus_id":1616078,"score":1},{"doc_id":"25409509","title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.","abstract":"Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3-5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.","corpus_id":7422811,"score":1},{"doc_id":"25861968","title":"MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.","abstract":"UNLABELLED: Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes. AVAILABILITY AND IMPLEMENTATION: Code in Python is at http://bioinform.github.io/metasv/. CONTACT: rd@bina.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":2109057,"score":1},{"doc_id":"25926346","title":"PopIns: population-scale detection of novel sequence insertions.","abstract":"MOTIVATION: The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome, have received less attention than other types of SVs due to the computational challenges in their detection from short read sequencing data, which inherently involves de novo assembly. De novo assembly is not only computationally challenging, but also requires high-quality data. Although the reads from a single individual may not always meet this requirement, using reads from multiple individuals can increase power to detect novel insertions. RESULTS: We have developed the program PopIns, which can discover and characterize non-reference insertions of 100 bp or longer on a population scale. In this article, we describe the approach we implemented in PopIns. It takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs of different individuals into high-confidence sequences, anchors the merged sequences into the reference genome, and finally genotypes all individuals for the discovered insertions. Our tests on simulated data indicate that the merging step greatly improves the quality and reliability of predicted insertions and that PopIns shows significantly better recall and precision than the recent tool MindTheGap. Preliminary results on a dataset of 305 Icelanders demonstrate the practicality of the new approach. AVAILABILITY AND IMPLEMENTATION: The source code of PopIns is available from http://github.com/bkehr/popins. CONTACT: birte.kehr@decode.is Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":17881554,"score":1},{"doc_id":"27708267","title":"A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.","abstract":"Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.","corpus_id":494337,"score":1},{"doc_id":"27854363","title":"Indel variant analysis of short-read sequencing data with Scalpel.","abstract":"As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ∼5 h after read mapping.","corpus_id":14947825,"score":1},{"doc_id":"28267569","title":"The challenge of detecting indels in bacterial genomes from short-read sequencing data.","abstract":"We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1-2321bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size. All tools tested were able to detect short indels (≤29 basepairs) at sensitivities close to 100%, albeit Pindel reported up to 20% false calls. In contrast, gapped-alignment and split-read tools failed to recover large proportions of long indels (>29bp) even at 120-fold coverage, and again, Pindel produced significant numbers of false-positive calls. Outstandingly, ScanIndel detected and reconstructed 97% of long indels on average (95% confidence intervals, 88%-99%) and, at the same time, produced negligible amounts of false calls. Hence, the combinatorial approach implemented in ScanIndel was able to recover the positions, types and sequences of indels with excellent sensitivity and false-discovery rate, by encompassing the full indel length spectrum present in the datasets.","corpus_id":205747913,"score":1},{"doc_id":"28986857","title":"Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads.","abstract":"BACKGROUND: Diagnostic genetic testing programmes based on next-generation DNA sequencing have resulted in the accrual of large datasets of targeted raw sequence data. Most diagnostic laboratories process these data through an automated variant-calling pipeline. Validation of the chosen analytical methods typically depends on confirming the detection of known sequence variants. Despite improvements in short-read alignment methods, current pipelines are known to be comparatively poor at detecting large insertion/deletion mutations. METHODS: We performed clinical validation of a local reassembly tool, ABRA (assembly-based realigner), through retrospective reanalysis of a cohort of more than 2000 hereditary cancer cases. RESULTS: ABRA enabled detection of a 96-bp deletion, 4-bp insertion mutation in PMS2 that had been initially identified using a comparative read-depth approach. We applied an updated pipeline incorporating ABRA to the entire cohort of 2000 cases and identified one previously undetected pathogenic variant, a 23-bp duplication in PTEN. We demonstrate the effect of read length on the ability to detect insertion/deletion variants by comparing HiSeq2500 (2 × 101-bp) and NextSeq500 (2 × 151-bp) sequence data for a range of variants and thereby show that the limitations of shorter read lengths can be mitigated using appropriate informatics tools. CONCLUSIONS: This work highlights the need for ongoing development of diagnostic pipelines to maximize test sensitivity. We also draw attention to the large differences in computational infrastructure required to perform day-to-day versus large-scale reprocessing tasks.","corpus_id":19819877,"score":1},{"doc_id":"29673323","title":"Indel detection from DNA and RNA sequencing data with transIndel.","abstract":"BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data. TransIndel exhibits competitive or superior performance over eight state-of-the-art indel detection tools on benchmarks using both synthetic and real DNA-seq data. Additionally, we applied transIndel to DNA-seq and RNA-seq datasets from 333 primary prostate cancer patients from The Cancer Genome Atlas (TCGA) and 59 metastatic prostate cancer patients from AACR-PCF Stand-Up- To-Cancer (SU2C) studies. TransIndel enhanced the taxonomy of DNA- and RNA-level alterations in prostate cancer by identifying recurrent FOXA1 indels as well as exitron splicing in genes implicated in disease progression. CONCLUSIONS: Our study demonstrates that transIndel is a robust tool for elucidation of medium- and large-sized indels from DNA-seq and RNA-seq data. Including RNA-seq in indel discovery efforts leads to significant improvements in sensitivity for identification of med-sized and large indels missed by DNA-seq, and reveals non-canonical RNA-splicing events in genes associated with disease pathology.","corpus_id":4984662,"score":1},{"doc_id":"26130710","title":"The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection.","abstract":"With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Furthermore, there is evidence that indels are often severely under-reported. In this manuscript we derive the total number of indel variants in a human genome by combining data from different sequencing technologies, while assessing the indel detection accuracy. Our estimate of approximately 1 million indels in a Yoruban genome is much higher than the results reported in several recent HTS studies. We identify two key sources of difficulties in indel detection: the insufficient coverage, read length or alignment quality; and the presence of repeats, including short interspersed elements and homopolymers/dimers. We quantify the effect of these factors on indel detection. The quality of sequencing data plays a major role in improving indel detection by HTS methods. However, many indels exist in long homopolymers and repeats, where their detection is severely impeded. The true number of indel events is likely even higher than our current estimates, and new techniques and technologies will be required to detect them.","corpus_id":5655939,"score":0},{"doc_id":"27473065","title":"Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.","abstract":"Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Although single-nucleotide variants (SNVs) can be easily identified from RNA-seq, intermediate long insertions/deletions (indels > 2 bases and less than sequence reads) cause significant challenges and are ignored by most RNA-seq analysis tools. This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known indels. The aim is to develop strategies for accurate indel detection. Our results show that the RNA-seq alignment is the most important step for indel identification and the evaluated programs have a wide range of sensitivity to map sequence reads with indels, from not at all to decently sensitive. The sensitivity is impacted by sequence read lengths. Most variant calling programs rely on hard evidence indels marked in the alignment and the programs with realignment may use soft-clipped reads for indel inferencing. Based on the observations, we have provided practical recommendations for indel detection when different RNA-seq aligners are used and demonstrated the best option with highly reliable results. With careful customization of bioinformatics algorithms, RNA-seq can be reliably used for both SNV and indel mutation detection that can be used for clinical decision-making.","corpus_id":23329451,"score":0},{"doc_id":"28423598","title":"Next generation mapping reveals novel large genomic rearrangements in prostate cancer.","abstract":"Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.","corpus_id":11207462,"score":0}],"string":"[\n {\n \"doc_id\": \"19593373\",\n \"title\": \"Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.\",\n \"abstract\": \"The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen), with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs). SV reconstruction is considered the most challenging step in human genome re-sequencing. ( It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome.) To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost.\",\n \"corpus_id\": 1865945,\n \"score\": 2\n },\n {\n \"doc_id\": \"19668202\",\n \"title\": \"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.\",\n \"abstract\": \"Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations. We examined BreakDancer's performance in simulation, in comparison with other methods and in analyses of a sample from an individual with acute myeloid leukemia and of samples from the 1,000 Genomes trio individuals. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.\",\n \"corpus_id\": 887817,\n \"score\": 2\n },\n {\n \"doc_id\": \"20308636\",\n \"title\": \"Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.\",\n \"abstract\": \"Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.\",\n \"corpus_id\": 4506651,\n \"score\": 2\n },\n {\n \"doc_id\": \"21785424\",\n \"title\": \"Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.\",\n \"abstract\": \"Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.\",\n \"corpus_id\": 11830481,\n \"score\": 2\n },\n {\n \"doc_id\": \"21787423\",\n \"title\": \"Identification of genomic indels and structural variations using split reads.\",\n \"abstract\": \"BACKGROUND: Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection. RESULTS: We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions vs. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs. CONCLUSIONS: Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for deletions. Moreover, with the advent of the third-generation sequencing technologies that produce longer reads, we expect our method to be even more useful.\",\n \"corpus_id\": 7472166,\n \"score\": 2\n },\n {\n \"doc_id\": \"22156294\",\n \"title\": \"Efficient de novo assembly of large genomes using compressed data structures.\",\n \"abstract\": \"De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a reference-unbiased way. We present memory efficient data structures and algorithms for assembly using the FM-index derived from the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA (String Graph Assembler). We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs <200 bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster.\",\n \"corpus_id\": 8954687,\n \"score\": 2\n },\n {\n \"doc_id\": \"22179552\",\n \"title\": \"Detection of structural variants and indels within exome data.\",\n \"abstract\": \"We report an algorithm to detect structural variation and indels from 1 base pair (bp) to 1 Mbp within exome sequence data sets. Splitread uses one end-anchored placements to cluster the mappings of subsequences of unanchored ends to identify the size, content and location of variants with high specificity and sensitivity. The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods.\",\n \"corpus_id\": 10153850,\n \"score\": 2\n },\n {\n \"doc_id\": \"22238266\",\n \"title\": \"Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.\",\n \"abstract\": \"MOTIVATION: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. RESULTS: Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant. AVAILABILITY: SplazerS is available from http://www.seqan.de/projects/ splazers. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 451429,\n \"score\": 2\n },\n {\n \"doc_id\": \"22962449\",\n \"title\": \"DELLY: structural variant discovery by integrated paired-end and split-read analysis.\",\n \"abstract\": \"MOTIVATION: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs. RESULTS: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. AVAILABILITY: DELLY is available at www.korbel.embl.de/software.html CONTACT: tobias.rausch@embl.de.\",\n \"corpus_id\": 18049007,\n \"score\": 2\n },\n {\n \"doc_id\": \"23060616\",\n \"title\": \"CLEVER: clique-enumerating variant finder.\",\n \"abstract\": \"MOTIVATION: Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. RESULTS: Here, we present a novel internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. A novel algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions. For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present relevant performance statistics. We achieve superior performance, in particular, for deletions or insertions (indels) of length 20-100 nt. This has been previously identified as a remaining major challenge in structural variation discovery, in particular, for insert size based approaches. In this size range, we even outperform split-read aligners. We achieve competitive results also on biological data, where our method is the only one to make a substantial amount of correct predictions, which, additionally, are disjoint from those by split-read aligners. AVAILABILITY: CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com. CONTACT: as@cwi.nl or tm@cwi.nl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 14262460,\n \"score\": 2\n },\n {\n \"doc_id\": \"23144753\",\n \"title\": \"A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.\",\n \"abstract\": \"Defining the architecture of a specific cancer genome, including its structural variants, is essential for understanding tumor biology, mechanisms of oncogenesis, and for designing effective personalized therapies. Short read paired-end sequencing is currently the most sensitive method for detecting somatic mutations that arise during tumor development. However, mapping structural variants using this method leads to a large number of false positive calls, mostly due to the repetitive nature of the genome and the difficulty of assigning correct mapping positions to short reads. This study describes a method to efficiently identify large tumor-specific deletions, inversions, duplications and translocations from low coverage data using SVDetect or BreakDancer software and a set of novel filtering procedures designed to reduce false positive calls. Applying our method to a spontaneous T cell lymphoma arising in a core RAG2/p53-deficient mouse, we identified 40 validated tumor-specific structural rearrangements supported by as few as 2 independent read pairs.\",\n \"corpus_id\": 15648796,\n \"score\": 2\n },\n {\n \"doc_id\": \"23966565\",\n \"title\": \"Assembler for de novo assembly of large genomes.\",\n \"abstract\": \"Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for \\\"jumping\\\" extension and read \\\"remapping.\\\" First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read extension process, which expedites the extension process and can jump over short repeats. Third, it uses a dynamic back trimming process to avoid extension termination due to sequencing errors. Fourth, it remaps reads to each assembled sequence, and if an assembly error occurs by the presence of a repeat, it breaks the contig at the repeat boundaries. Fifth, it applies a less stringent extension criterion to connect low-coverage regions. Finally, it merges contigs by unused reads. An extensive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less central processing unit time, especially for large genomes. Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use and central processing unit time than most current assemblers when the read length is 150 bp or longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the read length increases with advances in next generation sequencing technology.\",\n \"corpus_id\": 35531956,\n \"score\": 2\n },\n {\n \"doc_id\": \"24552580\",\n \"title\": \"Detection of structural variants involving repetitive regions in the reference genome.\",\n \"abstract\": \"Next-generation sequencing techniques are now commonly used to characterize structural variations (SVs) in population genomics and elucidate their associations with phenotypes. Many of the computational tools developed for detecting structural variations work by mapping paired-end reads to a reference genome and identifying the discordant read-pairs whose mapped loci in the reference genome deviate from the expected insert size and orientation. However, repetitive regions in the reference genome represent a major challenge in SV detection, because the paired-end reads from these regions may be mapped to multiple loci in the reference genome, resulting in spuriously discordant read-pairs. To address this issue, we have developed an algorithmic approach for read mapping and SV detection based on the framework of A-Bruijn graphs. Instead of mapping reads to a linear sequence of the reference genome, we propose to map reads onto the A-Bruijn graph constructed from the reference genome in which all instances of the same repeat are collapsed into a single edge. As a result, any given read, either from repetitive regions or not, will be mapped to a unique location in the A-Bruijn graph, and each discordant read-pair in the A-Bruijn graph indicates a potentially true SV event. We also developed a simple clustering algorithm to derive valid clusters of these discordant read-pairs, each supporting a different SV event. Finally, we demonstrate the performance of this approach, compared to existing approaches, by identifying transposition events of insertion sequence (IS) elements, a class of simple mobile genetic elements (MGEs), in E. coli by using simulated and real paired-end sequence data acquired from E. coli mutation accumulation lines.\",\n \"corpus_id\": 22235709,\n \"score\": 2\n },\n {\n \"doc_id\": \"24564972\",\n \"title\": \"iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.\",\n \"abstract\": \"BACKGROUND: Structural variations (SVs), such as insertions, deletions, inversions, and duplications, are a common feature in human genomes, and a number of studies have reported that such SVs are associated with human diseases. Although the progress of next generation sequencing (NGS) technologies has led to the discovery of a large number of SVs, accurate and genome-wide detection of SVs remains challenging. Thus far, various calling algorithms based on NGS data have been proposed. However, their strategies are diverse and there is no tool able to detect a full range of SVs accurately. RESULTS: We focused on evaluating the performance of existing deletion calling algorithms for various spanning ranges from low- to high-coverage simulation data. The simulation data was generated from a whole genome sequence with artificial SVs constructed based on the distribution of variants obtained from the 1000 Genomes Project. From the simulation analysis, deletion calls of various deletion sizes were obtained with each caller, and it was found that the performance was quite different according to the type of algorithms and targeting deletion size. Based on these results, we propose an integrated structural variant calling pipeline (iSVP) that combines existing methods with a newly devised filtering and merging processes. It achieved highly accurate deletion calling with >90% precision and >90% recall on the 30× read data for a broad range of size. We applied iSVP to the whole-genome sequence data of a CEU HapMap sample, and detected a large number of deletions, including notable peaks around 300 bp and 6,000 bp, which corresponded to Alus and long interspersed nuclear elements, respectively. In addition, many of the predicted deletions were highly consistent with experimentally validated ones by other studies. CONCLUSIONS: We present iSVP, a new deletion calling pipeline to obtain a genome-wide landscape of deletions in a highly accurate manner. From simulation and real data analysis, we show that iSVP is broadly applicable to human whole-genome sequencing data, which will elucidate relationships between SVs across genomes and associated diseases or biological functions.\",\n \"corpus_id\": 11871023,\n \"score\": 2\n },\n {\n \"doc_id\": \"24907369\",\n \"title\": \"ABRA: improved coding indel detection via assembly-based realignment.\",\n \"abstract\": \"MOTIVATION: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative. RESULTS: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation. AVAILABILITY AND IMPLEMENTATION: ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.\",\n \"corpus_id\": 16470026,\n \"score\": 2\n },\n {\n \"doc_id\": \"25355789\",\n \"title\": \"Characterization of structural variants with single molecule and hybrid sequencing approaches.\",\n \"abstract\": \"MOTIVATION: Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS: We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.\",\n \"corpus_id\": 13580950,\n \"score\": 2\n },\n {\n \"doc_id\": \"25380961\",\n \"title\": \"Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.\",\n \"abstract\": \"MOTIVATION: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. RESULTS: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes.\",\n \"corpus_id\": 10043658,\n \"score\": 2\n },\n {\n \"doc_id\": \"25423315\",\n \"title\": \"GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.\",\n \"abstract\": \"Insertions and deletions (indels) are important types of structural variations. Obtaining accurate genotypes of indels may facilitate further genetic study. There are a few existing methods for calling indel genotypes from sequence reads. However, none of these tools can accurately call indel genotypes for indels of all lengths, especially for low coverage sequence data. In this paper, we present GINDEL, an approach for calling genotypes of both insertions and deletions from sequence reads. GINDEL uses a machine learning approach which combines multiple features extracted from next generation sequencing data. We test our approach on both simulated and real data and compare with existing tools, including Genome STRiP, Pindel and Clever-sv. Results show that GINDEL works well for deletions larger than 50 bp on both high and low coverage data. Also, GINDEL performs well for insertion genotyping on both simulated and real data. For comparison, Genome STRiP performs less well for shorter deletions (50-200 bp) on both simulated and real sequence data from the 1000 Genomes Project. Clever-sv performs well for intermediate deletions (200-1500 bp) but is less accurate when coverage is low. Pindel only works well for high coverage data, but does not perform well at low coverage. To summarize, we show that GINDEL not only can call genotypes of insertions and deletions (both short and long) for high and low coverage population sequence data, but also is more accurate and efficient than other approaches. The program GINDEL can be downloaded at: http://sourceforge.net/p/gindel.\",\n \"corpus_id\": 7907662,\n \"score\": 2\n },\n {\n \"doc_id\": \"25671094\",\n \"title\": \"Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology.\",\n \"abstract\": \"BACKGROUND: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. RESULTS: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger than 1 kb. Excluding the 59 SVs (54 insertions/deletions, 5 inversions) that overlap with N-base gaps in the reference assembly hg19, 666 non-gap SVs remained, and 396 of them (60%) were verified by paired-end data from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides valuable information for complex regions with haplotypes in a straightforward fashion. In addition, with long single-molecule labeling patterns, exogenous viral sequences were mapped on a whole-genome scale, and sample heterogeneity was analyzed at a new level. CONCLUSION: Our study highlights genome mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome.\",\n \"corpus_id\": 4673983,\n \"score\": 2\n },\n {\n \"doc_id\": \"25886820\",\n \"title\": \"Assessing structural variation in a personal genome-towards a human reference diploid genome.\",\n \"abstract\": \"BACKGROUND: Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods. RESULTS: We demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus. CONCLUSIONS: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.\",\n \"corpus_id\": 207448,\n \"score\": 2\n },\n {\n \"doc_id\": \"26319364\",\n \"title\": \"Amplicon Indel Hunter Is a Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based Next-Generation Sequencing Data.\",\n \"abstract\": \"Amplicon-based targeted next-generation sequencing assays are used widely to test for clinically relevant somatic mutations in cancer. However, accurate detection of large insertions and deletions (indels) via these assays remains challenging. Sequencing reads that cover these anomalies are, by definition, different from the reference sequence, and lead to variable performance of alignment algorithms. Reads with large indels may be aligned incorrectly, causing incorrect calls, or may remain unmapped and essentially ignored by downstream informatics pipeline sub-processes. Herein, we describe Amplicon Indel Hunter (AIH), a novel large (>5-bp) indel detection method that is reference genome independent and highly sensitive for the identification of somatic indels in amplicon-based, paired-end, next-generation sequencing data. We validated the algorithm for sensitivity and specificity using a set of clinical cancer samples with Clinical Laboratory Improvement Amendment-confirmed indels as well as in silico mutated data sets. The AIH detected 100% of tested large indels with relatively higher mutant allele frequencies compared with a variety of traditional aligners, which showed variably reduced sensitivity and specificity by comparison. The AIH especially outperformed alignment-based methods for detection of all tested FLT3 internal tandem duplications up to 102 bp. Because AIH runs in parallel to traditional alignment-based informatics pathways, it can be readily incorporated into nearly any analysis pipeline for somatic mutation detection in paired-end amplicon-based data.\",\n \"corpus_id\": 30520539,\n \"score\": 2\n },\n {\n \"doc_id\": \"26643039\",\n \"title\": \"ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.\",\n \"abstract\": \"Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel .\",\n \"corpus_id\": 713655,\n \"score\": 2\n },\n {\n \"doc_id\": \"26647377\",\n \"title\": \"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.\",\n \"abstract\": \": We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. AVAILABILITY AND IMPLEMENTATION: Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta. CONTACT: csaunders@illumina.comSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 7620813,\n \"score\": 2\n },\n {\n \"doc_id\": \"26740523\",\n \"title\": \"SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.\",\n \"abstract\": \"MOTIVATION: Whole genome sequencing of paired-end reads can be applied to characterize the landscape of large somatic rearrangements of cancer genomes. Several methods for detecting structural variants with whole genome sequencing data have been developed. So far, none of these methods has combined information about abnormally mapped read pairs connecting rearranged regions and associated global copy number changes automatically inferred from the same sequencing data file. Our aim was to create a computational method that could use both types of information, i.e. normal and abnormal reads, and demonstrate that by doing so we can highly improve both sensitivity and specificity rates of structural variant prediction. RESULTS: We developed a computational method, SV-Bay, to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach. This approach takes into account depth of coverage by normal reads and abnormalities in read pair mappings. To estimate the model likelihood, SV-Bay considers GC-content and read mappability of the genome, thus making important corrections to the expected read count. For the detection of somatic variants, SV-Bay makes use of a matched normal sample when it is available. We validated SV-Bay on simulated datasets and an experimental mate-pair dataset for the CLB-GA neuroblastoma cell line. The comparison of SV-Bay with several other methods for structural variant detection demonstrated that SV-Bay has better prediction accuracy both in terms of sensitivity and false-positive detection rate. AVAILABILITY AND IMPLEMENTATION: https://github.com/InstitutCurie/SV-Bay CONTACT: valentina.boeva@inserm.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 12556366,\n \"score\": 2\n },\n {\n \"doc_id\": \"26772178\",\n \"title\": \"svclassify: a method to establish benchmark structural variant calls.\",\n \"abstract\": \"BACKGROUND: The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). High-quality benchmark small variant calls for the pilot National Institute of Standards and Technology (NIST) Reference Material (NA12878) have been developed by the Genome in a Bottle Consortium, but no similar high-quality benchmark SV calls exist for this genome. Since SV callers output highly discordant results, we developed methods to combine multiple forms of evidence from multiple sequencing technologies to classify candidate SVs into likely true or false positives. Our method (svclassify) calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate SVs as likely true or false positives. RESULTS: We first used pedigree analysis to develop a set of high-confidence breakpoint-resolved large deletions. We then used svclassify to cluster and classify these deletions as well as a set of high-confidence deletions from the 1000 Genomes Project and a set of breakpoint-resolved complex insertions from Spiral Genetics. We find that likely SVs cluster separately from likely non-SVs based on our annotations, and that the SVs cluster into different types of deletions. We then developed a supervised one-class classification method that uses a training set of random non-SV regions to determine whether candidate SVs have abnormal annotations different from most of the genome. To test this classification method, we use our pedigree-based breakpoint-resolved SVs, SVs validated by the 1000 Genomes Project, and assembly-based breakpoint-resolved insertions, along with semi-automated visualization using svviz. CONCLUSIONS: We find that candidate SVs with high scores from multiple technologies have high concordance with PCR validation and an orthogonal consensus method MetaSV (99.7 % concordant), and candidate SVs with low scores are questionable. We distribute a set of 2676 high-confidence deletions and 68 high-confidence insertions with high svclassify scores from these call sets for benchmarking SV callers. We expect these methods to be particularly useful for establishing high-confidence SV calls for benchmark samples that have been characterized by multiple technologies.\",\n \"corpus_id\": 1305594,\n \"score\": 2\n },\n {\n \"doc_id\": \"26787508\",\n \"title\": \"Nanopore sequencing detects structural variants in cancer.\",\n \"abstract\": \"Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.\",\n \"corpus_id\": 13902299,\n \"score\": 2\n },\n {\n \"doc_id\": \"27079510\",\n \"title\": \"mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development.\",\n \"abstract\": \"BACKGROUND: Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data generation, and enabled genome-wide identification of insertion and deletion variation. However, current NGS-based InDel mining tools, such as Samtools, GATK and Atlas2, all rely on a reference genome for variant calling which hinders their application on unsequenced organisms and the output of short InDels compromised their use on gel-based genotyping platforms. To address these issues, an enhanced platform is needed to identify longer InDels and develop markers in absence of a reference genome. RESULTS: Here we present mInDel (multiple InDel), a next-generation variant calling tool specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, this software identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable. By providing an option of combining multiple discovered InDels as output, mInDel is amiable to gel-based genotyping platforms where markers with large polymorphisms are preferred. We demonstrated the usability and performance of this software through a case study using a set of maize NGS data, and experimentally validated the accuracy of markers generated from mInDel. CONCLUSIONS: mInDel is a novel and practical tool that enables rapid genome-wide InDel marker discovery. The features of being independent from a reference genome and the flexibility with downstream genotyping platforms will allow a broad range of applications across genetics research and plant breeding. The mInDel pipeline is freely available at www.github.com/lyd0527/mInDel .\",\n \"corpus_id\": 2422565,\n \"score\": 2\n },\n {\n \"doc_id\": \"27634948\",\n \"title\": \"Seeksv: an accurate tool for somatic structural variation and virus integration detection.\",\n \"abstract\": \"MOTIVATION: Many forms of variations exist in the human genome including single nucleotide polymorphism, small insert/deletion (DEL) (indel) and structural variation (SV). Somatically acquired SV may regulate the expression of tumor-related genes and result in cell proliferation and uncontrolled growth, eventually inducing tumor formation. Virus integration with host genome sequence is a type of SV that causes the related gene instability and normal cells to transform into tumor cells. Cancer SVs and viral integration sites must be discovered in a genome-wide scale for clarifying the mechanism of tumor occurrence and development. RESULTS: In this paper, we propose a new tool called seeksv to detect somatic SVs and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and the fragment with two ends unmapped. Seeksv can detect DEL, insertion, inversion and inter-chromosome transfer at single-nucleotide resolution. Different types of sequencing data, such as single-end sequencing data or paired-end sequencing data can accommodate to detect SV. Seeksv develops a rescue model for SV with breakpoints located in sequence homology regions. Results on simulated and real data from the 1000 Genomes Project and esophageal squamous cell carcinoma samples show that seeksv has higher efficiency and precision compared with other similar software in detecting SVs. For the discovery of hepatitis B virus integration sites from probe capture data, the verified experiments show that more than 90% viral integration sequences detected by seeksv are true. AVAILABILITY AND IMPLEMENTATION: seeksv is implemented in C ++ and can be downloaded from https://github.com/qkl871118/seeksv CONTACT: : dragonbw@163.comSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 6647775,\n \"score\": 2\n },\n {\n \"doc_id\": \"27892959\",\n \"title\": \"novoBreak: local assembly for breakpoint detection in cancer genomes.\",\n \"abstract\": \"We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions.\",\n \"corpus_id\": 3541000,\n \"score\": 2\n },\n {\n \"doc_id\": \"27895111\",\n \"title\": \"Discovery and genotyping of structural variation from long-read haploid genome sequence data.\",\n \"abstract\": \"In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.\",\n \"corpus_id\": 22109251,\n \"score\": 2\n },\n {\n \"doc_id\": \"28056804\",\n \"title\": \"INDELseek: detection of complex insertions and deletions from next-generation sequencing data.\",\n \"abstract\": \"BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of \\\"pileup\\\" of each reference position across multiple alignments. In benchmarking against the reference material NA12878 genome (n = 160 derived from high-confidence variant calls), GATK, SAMtools and INDELseek showed complex indel detection sensitivities of 0%, 0% and 100%, respectively. INDELseek also detected all known germline (BRCA1 and BRCA2) and somatic (CALR and JAK2) complex indels in human clinical samples (n = 8). Further experiments validated all 10 detected KIT complex indels in a discovery cohort of clinical samples. In silico semi-simulation showed sensitivities of 93.7-96.2% based on 8671 unique complex indels in >5000 genes from dbSNP and COSMIC. We also demonstrated the importance of complex indel detection in accurately annotating BRCA1, BRCA2 and TP53 mutations with gained or rescued protein-truncating effects. CONCLUSIONS: INDELseek is an accurate and versatile tool for complex indel detection in NGS data. It complements other variant callers in NGS-based genomics studies targeting a wide spectrum of genetic variations.\",\n \"corpus_id\": 19801079,\n \"score\": 2\n },\n {\n \"doc_id\": \"28104618\",\n \"title\": \"HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.\",\n \"abstract\": \"Achieving complete, accurate, and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a Hybrid Structural variant Assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variants (SVs) in human genomes. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance the assembly of structurally altered regions in human genomes. We used data generated from a haploid hydatidiform mole genome (CHM1) and a diploid human genome (NA12878) to test our approach. The result showed that, compared with existing methods, our approach had a low false discovery rate and substantially improved the detection of many types of SVs, particularly novel large insertions, small indels (10-50 bp), and short tandem repeat expansions and contractions. Our work highlights the strengths and limitations of current approaches and provides an effective solution for extending the power of existing sequencing technologies for SV discovery.\",\n \"corpus_id\": 17631100,\n \"score\": 2\n },\n {\n \"doc_id\": \"28714986\",\n \"title\": \"Genome-wide reconstruction of complex structural variants using read clouds.\",\n \"abstract\": \"In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets. Compared with short-fragment sequencing, GROC-SVs substantially improves the specificity of breakpoint detection at comparable sensitivity. This approach also performs sequence assembly across multiple breakpoints simultaneously, enabling the reconstruction of events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nucleotide variants and SVs are not correlated. Our results support the use of read cloud approaches to advance the characterization of large and complex structural variation.\",\n \"corpus_id\": 16198659,\n \"score\": 2\n },\n {\n \"doc_id\": \"29048532\",\n \"title\": \"Lightning-fast genome variant detection with GROM.\",\n \"abstract\": \"Current human whole genome sequencing projects produce massive amounts of data, often creating significant computational challenges. Different approaches have been developed for each type of genome variant and method of its detection, necessitating users to run multiple algorithms to find variants. We present Genome Rearrangement OmniMapper (GROM), a novel comprehensive variant detection algorithm accepting aligned read files as input and finding SNVs, indels, structural variants (SVs), and copy number variants (CNVs). We show that GROM outperforms state-of-the-art methods on 7 validated benchmarks using 2 whole genome sequencing (WGS) data sets. Additionally, GROM boasts lightning-fast run times, analyzing a 50× WGS human data set (NA12878) on commonly available computer hardware in 11 minutes, more than an order of magnitude (up to 72 times) faster than tools detecting a similar range of variants. Addressing the needs of big data analysis, GROM combines in 1 algorithm SNV, indel, SV, and CNV detection, providing superior speed, sensitivity, and precision. GROM is also able to detect CNVs, SNVs, and indels in non-paired-read WGS libraries, as well as SNVs and indels in whole exome or RNA sequencing data sets.\",\n \"corpus_id\": 29395223,\n \"score\": 2\n },\n {\n \"doc_id\": \"29097403\",\n \"title\": \"GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.\",\n \"abstract\": \"The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.\",\n \"corpus_id\": 2824411,\n \"score\": 2\n },\n {\n \"doc_id\": \"29109544\",\n \"title\": \"Mapping and phasing of structural variation in patient genomes using nanopore sequencing.\",\n \"abstract\": \"Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.\",\n \"corpus_id\": 10597633,\n \"score\": 2\n },\n {\n \"doc_id\": \"29123647\",\n \"title\": \"Tools for annotation and comparison of structural variation.\",\n \"abstract\": \"The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop.\",\n \"corpus_id\": 2785318,\n \"score\": 2\n },\n {\n \"doc_id\": \"29590294\",\n \"title\": \"Leveraging known genomic variants to improve detection of variants, especially close-by Indels.\",\n \"abstract\": \"Motivation: The detection of genomic variants has great significance in genomics, bioinformatics, biomedical research and its applications. However, despite a lot of effort, Indels and structural variants are still under-characterized compared to SNPs. Current approaches based on next-generation sequencing data usually require large numbers of reads (high coverage) to be able to detect such types of variants accurately. However Indels, especially those close to each other, are still hard to detect accurately. Results: We introduce a novel approach that leverages known variant information, e.g. provided by dbSNP, dbVar, ExAC or the 1000 Genomes Project, to improve sensitivity of detecting variants, especially close-by Indels. In our approach, the standard reference genome and the known variants are combined to build a meta-reference, which is expected to be probabilistically closer to the subject genomes than the standard reference. An alignment algorithm, which can take into account known variant information, is developed to accurately align reads to the meta-reference. This strategy resulted in accurate alignment and variant calling even with low coverage data. We showed that compared to popular methods such as GATK and SAMtools, our method significantly improves the sensitivity of detecting variants, especially Indels that are close to each other. In particular, our method was able to call these close-by Indels at a 15-20% higher sensitivity than other methods at low coverage, and still get 1-5% higher sensitivity at high coverage, at competitive precision. These results were validated using simulated data with variant profiles extracted from the 1000 Genomes Project data, and real data from the Illumina Platinum Genomes Project and ExAC database. Our finding suggests that by incorporating known variant information in an appropriate manner, sensitive variant calling is possible at a low cost. Availability and implementation: Implementation can be found in our public code repository https://github.com/namsyvo/IVC. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4306823,\n \"score\": 2\n },\n {\n \"doc_id\": \"29618752\",\n \"title\": \"IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.\",\n \"abstract\": \"Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease.\",\n \"corpus_id\": 52807469,\n \"score\": 2\n },\n {\n \"doc_id\": \"29713081\",\n \"title\": \"Picky comprehensively detects high-resolution structural variants in nanopore long reads.\",\n \"abstract\": \"Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.\",\n \"corpus_id\": 14038771,\n \"score\": 2\n },\n {\n \"doc_id\": \"19439515\",\n \"title\": \"Mobile elements create structural variation: analysis of a complete human genome.\",\n \"abstract\": \"Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed approximately 126 kb of sequence from the HuRef genome. Overall, approximately 10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation.\",\n \"corpus_id\": 10407859,\n \"score\": 1\n },\n {\n \"doc_id\": \"19657104\",\n \"title\": \"Sensitive and accurate detection of copy number variants using read depth of coverage.\",\n \"abstract\": \"Methods for the direct detection of copy number variation (CNV) genome-wide have become effective instruments for identifying genetic risk factors for disease. The application of next-generation sequencing platforms to genetic studies promises to improve sensitivity to detect CNVs as well as inversions, indels, and SNPs. New computational approaches are needed to systematically detect these variants from genome sequence data. Existing sequence-based approaches for CNV detection are primarily based on paired-end read mapping (PEM) as reported previously by Tuzun et al. and Korbel et al. Due to limitations of the PEM approach, some classes of CNVs are difficult to ascertain, including large insertions and variants located within complex genomic regions. To overcome these limitations, we developed a method for CNV detection using read depth of coverage. Event-wise testing (EWT) is a method based on significance testing. In contrast to standard segmentation algorithms that typically operate by performing likelihood evaluation for every point in the genome, EWT works on intervals of data points, rapidly searching for specific classes of events. Overall false-positive rate is controlled by testing the significance of each possible event and adjusting for multiple testing. Deletions and duplications detected in an individual genome by EWT are examined across multiple genomes to identify polymorphism between individuals. We estimated error rates using simulations based on real data, and we applied EWT to the analysis of chromosome 1 from paired-end shotgun sequence data (30x) on five individuals. Our results suggest that analysis of read depth is an effective approach for the detection of CNVs, and it captures structural variants that are refractory to established PEM-based methods.\",\n \"corpus_id\": 23734995,\n \"score\": 1\n },\n {\n \"doc_id\": \"19907642\",\n \"title\": \"BFAST: an alignment tool for large scale genome resequencing.\",\n \"abstract\": \"BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net).\",\n \"corpus_id\": 13516642,\n \"score\": 1\n },\n {\n \"doc_id\": \"20305016\",\n \"title\": \"Genome assembly quality: assessment and improvement using the neutral indel model.\",\n \"abstract\": \"We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. Thus, the method is well-suited to assessing fine-scale sequence quality within single assemblies, between different assemblies of a single set of reads, and between genome assemblies for different species. When applying this approach to four primate genome assemblies, we found that average gap error rates per base varied considerably, by up to sixfold. As expected, bacterial artificial chromosome (BAC) sequences contained lower, but still substantial, predicted numbers of errors, arguing for caution in regarding BACs as the epitome of genome fidelity. We then mapped short reads, at approximately 10-fold statistical coverage, from a Bornean orangutan onto the Sumatran orangutan genome assembly originally constructed from capillary reads. This resulted in a reduced gap error rate and a separation of error-prone from high-fidelity sequence. Over 5000 predicted indel errors in protein-coding sequence were corrected in a hybrid assembly. Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies.\",\n \"corpus_id\": 18258915,\n \"score\": 1\n },\n {\n \"doc_id\": \"21291514\",\n \"title\": \"Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.\",\n \"abstract\": \"BACKGROUND: Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken. RESULTS: We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome. CONCLUSION: We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.\",\n \"corpus_id\": 742609,\n \"score\": 1\n },\n {\n \"doc_id\": \"21653520\",\n \"title\": \"A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.\",\n \"abstract\": \"MOTIVATION: High-throughput sequencing technologies have made population-scale studies of human genetic variation possible. Accurate and comprehensive detection of DNA sequence variants is crucial for the success of these studies. Small insertions and deletions represent the second most frequent class of variation in the human genome after single nucleotide polymorphisms (SNPs). Although several alignment tools for the gapped alignment of sequence reads to a reference genome are available, computational methods for discriminating indels from sequencing errors and genotyping indels directly from sequence reads are needed. RESULTS: We describe a probabilistic method for the accurate detection and genotyping of short indels from population-scale sequence data. In this approach, aligned sequence reads from a population of individuals are used to automatically account for context-specific sequencing errors associated with indels. We applied this approach to population sequence datasets from the 1000 Genomes exon pilot project generated using the Roche 454 and Illumina sequencing platforms, and were able to detect a significantly greater number of indels than reported previously. Comparison to indels identified in the 1000 Genomes pilot project demonstrated the sensitivity of our method. The consistency in the number of indels and the fraction of indels whose length is a multiple of three across different human populations and two different sequencing platforms indicated that our method has a low false discovery rate. Finally, the method represents a general approach for the detection and genotyping of small-scale DNA sequence variants for population-scale sequencing projects. AVAILABILITY: A program implementing this method is available at http://polymorphism.scripps.edu/~vbansal/software/piCALL/\",\n \"corpus_id\": 263602155,\n \"score\": 1\n },\n {\n \"doc_id\": \"22439878\",\n \"title\": \"The fine-scale architecture of structural variants in 17 mouse genomes.\",\n \"abstract\": \"BACKGROUND: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. RESULTS: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. CONCLUSIONS: An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.\",\n \"corpus_id\": 933467,\n \"score\": 1\n },\n {\n \"doc_id\": \"22537045\",\n \"title\": \"An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.\",\n \"abstract\": \"BACKGROUND: Recent advances in sequencing technologies make it possible to comprehensively study structural variations (SVs) using sequence data of large-scale populations. Currently, more efforts have been taken to develop methods that call SVs with exact breakpoints. Among these approaches, split-read mapping methods can be applied on low-coverage sequence data. With increasing amount of data generated, more efficient split-read mapping methods are still needed. Also, since sequence errors can not be avoided for the current sequencing technologies, more accurate split-read mapping methods are still needed to better handle sequence errors. RESULTS: In this paper, we present a split-read mapping method implemented in the program SVseq2 which improves our previous work SVseq1. Similar to SVseq1, SVseq2 calls deletions (and insertions) with exact breakpoints. SVseq2 achieves more accurate calling through split-read mapping within focal regions. SVseq2 also has a much desired feature: there is no need to specify the maximum deletion size, while some existing split-read mapping methods need more memory and longer running time when larger maximum deletion size is chosen. SVseq2 is also much faster because it only needs to examine a small number of ways of splitting the reads. Moreover, SVseq2 supports insertion calling from low-coverage sequence data, while SVseq1 only supports deletion finding. The program SVseq2 can be downloaded at http://www.engr.uconn.edu/~jiz08001/. CONCLUSIONS: SVseq2 enables accurate and efficient SV calling through split-read mapping within focal regions using paired-end reads. For many simulated data and real sequence data, SVseq2 outperforms some other existing approaches in accuracy and efficiency, especially when sequence coverage is low.\",\n \"corpus_id\": 1870009,\n \"score\": 1\n },\n {\n \"doc_id\": \"25123898\",\n \"title\": \"MindTheGap: integrated detection and assembly of short and long insertions.\",\n \"abstract\": \"MOTIVATION: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. RESULTS: We propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MindTheGap uses an efficient k-mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. MindTheGap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, MindTheGap detected and correctly assembled insertions >1 kb, using at most 14 GB of memory.\",\n \"corpus_id\": 1616078,\n \"score\": 1\n },\n {\n \"doc_id\": \"25409509\",\n \"title\": \"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.\",\n \"abstract\": \"Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3-5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.\",\n \"corpus_id\": 7422811,\n \"score\": 1\n },\n {\n \"doc_id\": \"25861968\",\n \"title\": \"MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.\",\n \"abstract\": \"UNLABELLED: Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes. AVAILABILITY AND IMPLEMENTATION: Code in Python is at http://bioinform.github.io/metasv/. CONTACT: rd@bina.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 2109057,\n \"score\": 1\n },\n {\n \"doc_id\": \"25926346\",\n \"title\": \"PopIns: population-scale detection of novel sequence insertions.\",\n \"abstract\": \"MOTIVATION: The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome, have received less attention than other types of SVs due to the computational challenges in their detection from short read sequencing data, which inherently involves de novo assembly. De novo assembly is not only computationally challenging, but also requires high-quality data. Although the reads from a single individual may not always meet this requirement, using reads from multiple individuals can increase power to detect novel insertions. RESULTS: We have developed the program PopIns, which can discover and characterize non-reference insertions of 100 bp or longer on a population scale. In this article, we describe the approach we implemented in PopIns. It takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs of different individuals into high-confidence sequences, anchors the merged sequences into the reference genome, and finally genotypes all individuals for the discovered insertions. Our tests on simulated data indicate that the merging step greatly improves the quality and reliability of predicted insertions and that PopIns shows significantly better recall and precision than the recent tool MindTheGap. Preliminary results on a dataset of 305 Icelanders demonstrate the practicality of the new approach. AVAILABILITY AND IMPLEMENTATION: The source code of PopIns is available from http://github.com/bkehr/popins. CONTACT: birte.kehr@decode.is Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 17881554,\n \"score\": 1\n },\n {\n \"doc_id\": \"27708267\",\n \"title\": \"A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.\",\n \"abstract\": \"Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.\",\n \"corpus_id\": 494337,\n \"score\": 1\n },\n {\n \"doc_id\": \"27854363\",\n \"title\": \"Indel variant analysis of short-read sequencing data with Scalpel.\",\n \"abstract\": \"As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ∼5 h after read mapping.\",\n \"corpus_id\": 14947825,\n \"score\": 1\n },\n {\n \"doc_id\": \"28267569\",\n \"title\": \"The challenge of detecting indels in bacterial genomes from short-read sequencing data.\",\n \"abstract\": \"We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1-2321bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size. All tools tested were able to detect short indels (≤29 basepairs) at sensitivities close to 100%, albeit Pindel reported up to 20% false calls. In contrast, gapped-alignment and split-read tools failed to recover large proportions of long indels (>29bp) even at 120-fold coverage, and again, Pindel produced significant numbers of false-positive calls. Outstandingly, ScanIndel detected and reconstructed 97% of long indels on average (95% confidence intervals, 88%-99%) and, at the same time, produced negligible amounts of false calls. Hence, the combinatorial approach implemented in ScanIndel was able to recover the positions, types and sequences of indels with excellent sensitivity and false-discovery rate, by encompassing the full indel length spectrum present in the datasets.\",\n \"corpus_id\": 205747913,\n \"score\": 1\n },\n {\n \"doc_id\": \"28986857\",\n \"title\": \"Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads.\",\n \"abstract\": \"BACKGROUND: Diagnostic genetic testing programmes based on next-generation DNA sequencing have resulted in the accrual of large datasets of targeted raw sequence data. Most diagnostic laboratories process these data through an automated variant-calling pipeline. Validation of the chosen analytical methods typically depends on confirming the detection of known sequence variants. Despite improvements in short-read alignment methods, current pipelines are known to be comparatively poor at detecting large insertion/deletion mutations. METHODS: We performed clinical validation of a local reassembly tool, ABRA (assembly-based realigner), through retrospective reanalysis of a cohort of more than 2000 hereditary cancer cases. RESULTS: ABRA enabled detection of a 96-bp deletion, 4-bp insertion mutation in PMS2 that had been initially identified using a comparative read-depth approach. We applied an updated pipeline incorporating ABRA to the entire cohort of 2000 cases and identified one previously undetected pathogenic variant, a 23-bp duplication in PTEN. We demonstrate the effect of read length on the ability to detect insertion/deletion variants by comparing HiSeq2500 (2 × 101-bp) and NextSeq500 (2 × 151-bp) sequence data for a range of variants and thereby show that the limitations of shorter read lengths can be mitigated using appropriate informatics tools. CONCLUSIONS: This work highlights the need for ongoing development of diagnostic pipelines to maximize test sensitivity. We also draw attention to the large differences in computational infrastructure required to perform day-to-day versus large-scale reprocessing tasks.\",\n \"corpus_id\": 19819877,\n \"score\": 1\n },\n {\n \"doc_id\": \"29673323\",\n \"title\": \"Indel detection from DNA and RNA sequencing data with transIndel.\",\n \"abstract\": \"BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data. TransIndel exhibits competitive or superior performance over eight state-of-the-art indel detection tools on benchmarks using both synthetic and real DNA-seq data. Additionally, we applied transIndel to DNA-seq and RNA-seq datasets from 333 primary prostate cancer patients from The Cancer Genome Atlas (TCGA) and 59 metastatic prostate cancer patients from AACR-PCF Stand-Up- To-Cancer (SU2C) studies. TransIndel enhanced the taxonomy of DNA- and RNA-level alterations in prostate cancer by identifying recurrent FOXA1 indels as well as exitron splicing in genes implicated in disease progression. CONCLUSIONS: Our study demonstrates that transIndel is a robust tool for elucidation of medium- and large-sized indels from DNA-seq and RNA-seq data. Including RNA-seq in indel discovery efforts leads to significant improvements in sensitivity for identification of med-sized and large indels missed by DNA-seq, and reveals non-canonical RNA-splicing events in genes associated with disease pathology.\",\n \"corpus_id\": 4984662,\n \"score\": 1\n },\n {\n \"doc_id\": \"26130710\",\n \"title\": \"The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection.\",\n \"abstract\": \"With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Furthermore, there is evidence that indels are often severely under-reported. In this manuscript we derive the total number of indel variants in a human genome by combining data from different sequencing technologies, while assessing the indel detection accuracy. Our estimate of approximately 1 million indels in a Yoruban genome is much higher than the results reported in several recent HTS studies. We identify two key sources of difficulties in indel detection: the insufficient coverage, read length or alignment quality; and the presence of repeats, including short interspersed elements and homopolymers/dimers. We quantify the effect of these factors on indel detection. The quality of sequencing data plays a major role in improving indel detection by HTS methods. However, many indels exist in long homopolymers and repeats, where their detection is severely impeded. The true number of indel events is likely even higher than our current estimates, and new techniques and technologies will be required to detect them.\",\n \"corpus_id\": 5655939,\n \"score\": 0\n },\n {\n \"doc_id\": \"27473065\",\n \"title\": \"Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.\",\n \"abstract\": \"Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Although single-nucleotide variants (SNVs) can be easily identified from RNA-seq, intermediate long insertions/deletions (indels > 2 bases and less than sequence reads) cause significant challenges and are ignored by most RNA-seq analysis tools. This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known indels. The aim is to develop strategies for accurate indel detection. Our results show that the RNA-seq alignment is the most important step for indel identification and the evaluated programs have a wide range of sensitivity to map sequence reads with indels, from not at all to decently sensitive. The sensitivity is impacted by sequence read lengths. Most variant calling programs rely on hard evidence indels marked in the alignment and the programs with realignment may use soft-clipped reads for indel inferencing. Based on the observations, we have provided practical recommendations for indel detection when different RNA-seq aligners are used and demonstrated the best option with highly reliable results. With careful customization of bioinformatics algorithms, RNA-seq can be reliably used for both SNV and indel mutation detection that can be used for clinical decision-making.\",\n \"corpus_id\": 23329451,\n \"score\": 0\n },\n {\n \"doc_id\": \"28423598\",\n \"title\": \"Next generation mapping reveals novel large genomic rearrangements in prostate cancer.\",\n \"abstract\": \"Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.\",\n \"corpus_id\": 11207462,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":82,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28104717\",\n \"title\": \"Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors.\",\n \"abstract\": \"BACKGROUND: Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established. METHODS: Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels. Alterations were annotated (Tiers 1-4) based on clinical significance, with Tier 1 alterations having well-established clinical utility. OncoCopy, a clinical genome-wide array comparative genomic hybridization (aCGH) assay, was also performed to evaluate copy number alterations and better define rearrangement breakpoints. RESULTS: Cancer genomes of 203 pediatric brain tumors were profiled across histological subtypes, including 117 samples analyzed by OncoPanel, 146 by OncoCopy, and 60 tumors subjected to both methodologies. OncoPanel revealed clinically relevant alterations in 56% of patients (44 cancer mutations and 20 rearrangements), including BRAF alterations that directed the use of targeted inhibitors. Rearrangements in MYB-QKI, MYBL1, BRAF, and FGFR1 were also detected. Furthermore, while copy number profiles differed across histologies, the combined use of OncoPanel and OncoCopy identified subgroup-specific alterations in 89% (17/19) of medulloblastomas. CONCLUSION: The combination of OncoPanel and OncoCopy multiplex genomic assays can identify critical diagnostic, prognostic, and treatment-relevant alterations and represents an effective precision medicine approach for clinical evaluation of pediatric brain tumors.\",\n \"corpus_id\": 3751907\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"21979893","title":"Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling.","abstract":"Medulloblastoma (MB) is a WHO grade IV, invasive embryonal CNS tumor that mainly affects children. The aggressiveness and response to therapy can vary considerably between cases, and despite treatment, ~30% of patients die within 2 years from diagnosis. Furthermore, the majority of survivors suffer long-term side-effects due to severe management modalities. Several distinct morphological features have been associated with differences in biological behavior, but improved molecular-based criteria that better reflect the underlying tumor biology are in great demand. In this study, we profiled a series of 25 MB with a 32K BAC array covering 99% of the current assembly of the human genome for the identification of genetic copy number alterations possibly important in MB. Previously known aberrations as well as several novel focally amplified loci could be identified. As expected, the most frequently observed alteration was the combination of 17p loss and 17q gain, which was detected in both high- and standard-risk patients. We also defined minimal overlapping regions of aberrations, including 16 regions of gain and 18 regions of loss in various chromosomes. A few noteworthy narrow amplified loci were identified on autosomes 1 (38.89-41.97 and 84.89-90.76 Mb), 3 (27.64-28.20 and 35.80-43.50 Mb), and 8 (119.66-139.79 Mb), aberrations that were verified with an alternative platform (Illumina 610Q chips). Gene expression levels were also established for these samples using Affymetrix U133Plus2.0 arrays. Several interesting genes encompassed within the amplified regions and presenting with transcript upregulation were identified. These data contribute to the characterization of this malignant childhood brain tumor and confirm its genetic heterogeneity.","corpus_id":30840874,"score":2},{"doc_id":"22585170","title":"High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.","abstract":"UNLABELLED: Knowledge of \"actionable\" somatic genomic alterations present in each tumor (e.g., point mutations, small insertions/deletions, and copy-number alterations that direct therapeutic options) should facilitate individualized approaches to cancer treatment. However, clinical implementation of systematic genomic profiling has rarely been achieved beyond limited numbers of oncogene point mutations. To address this challenge, we utilized a targeted, massively parallel sequencing approach to detect tumor genomic alterations in formalin-fixed, paraffin-embedded (FFPE) tumor samples. Nearly 400-fold mean sequence coverage was achieved, and single-nucleotide sequence variants, small insertions/deletions, and chromosomal copynumber alterations were detected simultaneously with high accuracy compared with other methods in clinical use. Putatively actionable genomic alterations, including those that predict sensitivity or resistance to established and experimental therapies, were detected in each tumor sample tested. Thus, targeted deep sequencing of clinical tumor material may enable mutation-driven clinical trials and, ultimately, \"personalized\" cancer treatment. SIGNIFICANCE: Despite the rapid proliferation of targeted therapeutic agents, systematic methods to profile clinically relevant tumor genomic alterations remain underdeveloped. We describe a sequencingbased approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.","corpus_id":10714052,"score":2},{"doc_id":"23633565","title":"Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1.","abstract":"Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from BRAF kinase mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. We performed high-resolution copy-number analysis on 44 formalin-fixed, paraffin-embedded diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gain, was observed in 28% of diffuse astrocytoma grade IIs and resulted in partial duplication of the transcription factor MYBL1 with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene v-myb avian myeloblastosis viral oncogene homolog (MYB) on 6q23.3. Whole-genome sequencing of a MYBL1-rearranged diffuse astrocytoma grade II demonstrated MYBL1 tandem duplication and few other events. Truncated MYBL1 transcripts identified in this tumor induced anchorage-independent growth in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with MYBL1 partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.","corpus_id":2023523,"score":2},{"doc_id":"24767714","title":"Diagnostic application of high resolution single nucleotide polymorphism array analysis for children with brain tumors.","abstract":"Single nucleotide polymorphism (SNP) array analysis is currently used as a first tier test for pediatric brain tumors at The Children's Hospital of Philadelphia. The results from 100 consecutive patients are summarized in the present report. Eighty-seven percent of the tumors had at least one pathogenic copy number alteration. Nineteen of 56 low grade gliomas (LGGs) demonstrated a duplication in 7q34, which resulted in a KIAA1549-BRAF fusion. Chromosome band 7q34 deletions, which resulted in a FAM131B-BRAF fusion, were identified in one pilocytic astrocytoma (PA) and one dysembryoplastic neuroepithelial tumor (DNT). One ganglioglioma (GG) demonstrated a 6q23.3q26 deletion that was predicted to result in a MYB-QKI fusion. Gains of chromosomes 5, 6, 7, 11, and 20 were seen in a subset of LGGs. Monosomy 6, deletion of 9q and 10q, and an i(17)(q10) were each detected in the medulloblastomas (MBs). Deletions and regions of loss of heterozygosity that encompassed TP53, RB1, CDKN2A/B, CHEK2, NF1, and NF2 were identified in a variety of tumors, which led to a recommendation for germline testing. A BRAF p.Thr599dup or p.V600E mutation was identified by Sanger sequencing in one and five gliomas, respectively, and a somatic TP53 mutation was identified in a fibrillary astrocytoma. No TP53 hot-spot mutations were detected in the MBs. SNP array analysis of pediatric brain tumors can be combined with pathologic examination and molecular analyses to further refine diagnoses, offer more accurate prognostic assessments, and identify patients who should be referred for cancer risk assessment.","corpus_id":22298017,"score":2},{"doc_id":"24959384","title":"Genome-wide copy number analysis in pediatric glioblastoma multiforme.","abstract":"Glioblastoma (GBM) is a very aggressive and lethal brain tumor with poor prognosis. Despite new treatment strategies, patients' median survival is still less than 1 year in most cases. Few studies have focused exclusively on this disease in children and most of our understanding of the disease process and its clinical outcome has come from studies on malignant gliomas in childhood, combining children with the diagnosis of GBM with other pediatric patients harboring high grade malignant tumors other than GBM. In this study we investigated, using array-CGH platforms, children (median age of 9 years) affected by GBM (WHO-grade IV). We identified recurrent Copy Number Alterations demonstrating that different chromosome regions are involved, in various combinations. These observations suggest a condition of strong genomic instability. Since cancer is an acquired disease and inherited factors play a significant role, we compared for the first time the constitutional Copy Number Variations with the Copy Number Alterations found in tumor biopsy. We speculate that genes included in the recurrent 9p21.3 and 16p13.3 deletions and 1q32.1-q44 duplication play a crucial role for tumorigenesis and/or progression. In particular we suggest that the A2BP1 gene (16p13.3) is one possible culprit of the disease. Given the rarity of the disease, the poor quality and quantity of bioptic material and the scarcity of data in the literature, our findings may better elucidate the genomic background of these tumors. The recognition of candidate genes underlying this disease could then improve treatment strategies for this devastating tumor.","corpus_id":7998376,"score":2},{"doc_id":"25626406","title":"Clinical actionability enhanced through deep targeted sequencing of solid tumors.","abstract":"BACKGROUND: Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is present and whether it may affect clinical decision-making. To study this question, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples. METHODS: We assayed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer-related genes. Mutations, indels, and copy number data were reported. RESULTS: We obtained a 1000-fold mean sequencing depth and identified 4794 nonsynonymous mutations in the samples analyzed, of which 15.2% were present at <10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) otherwise would have been unactionable. In addition, acquiring ultrahigh depth also ensured a low false discovery rate (<2.2%) from FFPE samples. CONCLUSIONS: Our results were as accurate as a commercially available CLIA-compliant hotspot panel but allowed the detection of a higher number of mutations in actionable genes. Our study reveals the critical importance of acquiring and utilizing high sequencing depth in profiling clinical tumor samples and presents a very useful platform for implementing routine sequencing in a cancer care institution.","corpus_id":8474215,"score":2},{"doc_id":"25754088","title":"Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma.","abstract":"BACKGROUND: Multidimensional genotyping of formalin-fixed paraffin-embedded (FFPE) samples has the potential to improve diagnostics and clinical trials for brain tumors, but prospective use in the clinical setting is not yet routine. We report our experience with implementing a multiplexed copy number and mutation-testing program in a diagnostic laboratory certified by the Clinical Laboratory Improvement Amendments. METHODS: We collected and analyzed clinical testing results from whole-genome array comparative genomic hybridization (OncoCopy) of 420 brain tumors, including 148 glioblastomas. Mass spectrometry-based mutation genotyping (OncoMap, 471 mutations) was performed on 86 glioblastomas. RESULTS: OncoCopy was successful in 99% of samples for which sufficient DNA was obtained (n = 415). All clinically relevant loci for glioblastomas were detected, including amplifications (EGFR, PDGFRA, MET) and deletions (EGFRvIII, PTEN, 1p/19q). Glioblastoma patients ≤40 years old had distinct profiles compared with patients >40 years. OncoMap testing reliably identified mutations in IDH1, TP53, and PTEN. Seventy-seven glioblastoma patients enrolled on trials, of whom 51% participated in targeted therapeutic trials where multiplex data informed eligibility or outcomes. Data integration identified patients with complete tumor suppressor inactivation, albeit rarely (5% of patients) due to lack of whole-gene coverage in OncoMap. CONCLUSIONS: Combined use of multiplexed copy number and mutation detection from FFPE samples in the clinical setting can efficiently replace singleton tests for clinical diagnosis and prognosis in most settings. Our results support incorporation of these assays into clinical trials as integral biomarkers and their potential to impact interpretation of results. Limited tumor suppressor variant capture by targeted genotyping highlights the need for whole-gene sequencing in glioblastoma.","corpus_id":24699053,"score":2},{"doc_id":"26681766","title":"Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors.","abstract":"BACKGROUND: Identification of genetic changes in CNS tumors is important for the appropriate clinical management of patients. Our objective was to develop a next-generation sequencing (NGS) assay for simultaneously detecting the various types of genetic alterations characteristic for adult and pediatric CNS tumors that can be applied to small brain biopsies. METHODS: We report an amplification-based targeted NGS assay (GlioSeq) that analyzes 30 genes for single nucleotide variants (SNVs) and indels, 24 genes for copy number variations (CNVs), and 14 types of structural alterations in BRAF, EGFR, and FGFR3 genes in a single workflow. GlioSeq performance was evaluated in 54 adult and pediatric CNS tumors, and the results were compared with fluorescence in-situ hybridization, Sanger sequencing, and reverse transcription PCR. RESULTS: GlioSeq correctly identified 71/71 (100%) genetic alterations known to be present by conventional techniques, including 56 SNVs/indels, 9 CNVs, 3 EGFRvIII, and 3 KIAA1549-BRAF fusions. Only 20 ng of DNA and 10 ng of RNA were required for successful sequencing of 100% frozen and 96% formalin-fixed, paraffin-embedded tissue specimens. The assay sensitivity was 3%-5% of mutant alleles for SNVs and 1%-5% for gene fusions. The most commonly detected alterations were IDH1, TP53, TERT, ATRX. CDKN2A, and PTEN in high-grade gliomas, followed by BRAF fusions in low-grade gliomas and H3F3A mutations in pediatric gliomas. CONCLUSIONS: GlioSeq NGS assay offers accurate and sensitive detection of a wide range of genetic alterations in a single workflow. It allows rapid and cost-effective profiling of brain tumor specimens and thus provides valuable information for patient management.","corpus_id":1938530,"score":2},{"doc_id":"26794043","title":"Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.","abstract":"In the pediatric cancer neuroblastoma, analysis of recurrent chromosomal aberrations such as loss of chromosome 1p, 11q, gain of 17q and MYCN amplification are used for patient stratification and subsequent therapy decision making. Different analysis techniques have been used for detection of segmental abnormalities, including fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH)-microarrays and multiplex ligation-dependent probe amplification (MLPA). However, as next-generation sequencing becomes available for clinical use, this technique could also be used for assessment of copy number alterations simultaneously with mutational analysis. In this study we compare genomic profiles generated through exome sequencing data with profiles generated from high resolution Affymetrix single nucleotide polymorphism (SNP) microarrays on 30 neuroblastoma tumors of different stages. Normalized coverage reads for tumors were calculated using Control-FREEC software and visualized through a web based Shiny application, prior to comparison with corresponding SNP-microarray data. The two methods show high-level agreement for breakpoints and copy number of larger segmental aberrations and numerical aneuploidies. However, several smaller gene containing deletions that could not readily be detected through the SNP-microarray analyses were identified through exome profiling, most likely due to difference between spatial distribution of microarray probes and targeted regions of the exome capture. These smaller aberrations included focal ATRX deletion in two tumors and three cases of novel deletions in chromosomal region 19q13.2 causing homozygous loss of multiple genes including the CIC (Capicua) gene. In conclusion, genomic profiles generated from normalized coverage of exome sequencing show concordance with SNP microarray generated genomic profiles. Exome sequencing is therefore a useful diagnostic tool for copy number variant (CNV) detection in neuroblastoma tumors, especially considering the combination with mutational screening. This enables detection of theranostic targets such as ALK and ATRX together with detection of significant segmental aneuploidies, such as 2p-gain, 17q-gain, 11q-deletion as well as MYCN amplification.","corpus_id":207753089,"score":2},{"doc_id":"26994145","title":"MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research.","abstract":"PURPOSE: We undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers to determine the feasibility of genome-guided precision therapy. EXPERIMENTAL DESIGN: Patients with non-central nervous system solid tumors underwent a combination of whole exome sequencing (WES), whole transcriptome sequencing (WTS), and high-density single-nucleotide polymorphism array analysis of the tumor, with WES of matched germline DNA. Clinically actionable alterations were identified as a reportable germline mutation, a diagnosis change, or a somatic event (including a single nucleotide variant, an indel, an amplification, a deletion, or a fusion gene), which could be targeted with drugs in existing clinical trials or with FDA-approved drugs. RESULTS: Fifty-nine patients in 20 diagnostic categories were enrolled from 2010 to 2014. Ages ranged from 7 months to 25 years old. Seventy-three percent of the patients had prior chemotherapy, and the tumors from these patients with relapsed or refractory cancers had a higher mutational burden than that reported in the literature. Thirty patients (51% of total) had clinically actionable mutations, of which 24 (41%) had a mutation that was currently targetable in a clinical trial setting, 4 patients (7%) had a change in diagnosis, and 7 patients (12%) had a reportable germline mutation. CONCLUSIONS: We found a remarkably high number of clinically actionable mutations in 51% of the patients, and 12% with significant germline mutations. We demonstrated the clinical feasibility of next-generation sequencing in a diverse population of relapsed and refractory pediatric solid tumors. Clin Cancer Res; 22(15); 3810-20. ©2016 AACR.","corpus_id":23308352,"score":2},{"doc_id":"27026619","title":"IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.","abstract":"OBJECTIVE: Currently, there is a disconnect between finding a patient's relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics. METHODS AND MATERIALS: The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment. RESULTS: IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies. CONCLUSION: IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine. IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT.","corpus_id":10050676,"score":2},{"doc_id":"27167109","title":"A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine.","abstract":"Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed. We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers. The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens.","corpus_id":14194200,"score":2},{"doc_id":"27245685","title":"Development and clinical application of an integrative genomic approach to personalized cancer therapy.","abstract":"BACKGROUND: Personalized therapy provides the best outcome of cancer care and its implementation in the clinic has been greatly facilitated by recent convergence of enormous progress in basic cancer research, rapid advancement of new tumor profiling technologies, and an expanding compendium of targeted cancer therapeutics. METHODS: We developed a personalized cancer therapy (PCT) program in a clinical setting, using an integrative genomics approach to fully characterize the complexity of each tumor. We carried out whole exome sequencing (WES) and single-nucleotide polymorphism (SNP) microarray genotyping on DNA from tumor and patient-matched normal specimens, as well as RNA sequencing (RNA-Seq) on available frozen specimens, to identify somatic (tumor-specific) mutations, copy number alterations (CNAs), gene expression changes, gene fusions, and also germline variants. To provide high sensitivity in known cancer mutation hotspots, Ion AmpliSeq Cancer Hotspot Panel v2 (CHPv2) was also employed. We integrated the resulting data with cancer knowledge bases and developed a specific workflow for each cancer type to improve interpretation of genomic data. RESULTS: We returned genomics findings to 46 patients and their physicians describing somatic alterations and predicting drug response, toxicity, and prognosis. Mean 17.3 cancer-relevant somatic mutations per patient were identified, 13.3-fold, 6.9-fold, and 4.7-fold more than could have been detected using CHPv2, Oncomine Cancer Panel (OCP), and FoundationOne, respectively. Our approach delineated the underlying genetic drivers at the pathway level and provided meaningful predictions of therapeutic efficacy and toxicity. Actionable alterations were found in 91 % of patients (mean 4.9 per patient, including somatic mutations, copy number alterations, gene expression alterations, and germline variants), a 7.5-fold, 2.0-fold, and 1.9-fold increase over what could have been uncovered by CHPv2, OCP, and FoundationOne, respectively. The findings altered the course of treatment in four cases. CONCLUSIONS: These results show that a comprehensive, integrative genomic approach as outlined above significantly enhanced genomics-based PCT strategies.","corpus_id":12296984,"score":2},{"doc_id":"28007021","title":"Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations.","abstract":"BACKGROUND: Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. METHODS: The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient's electronic medical record. RESULTS: NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. CONCLUSIONS: Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.","corpus_id":8576826,"score":2},{"doc_id":"28453743","title":"Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy.","abstract":"Background: Molecular profiling is revolutionizing cancer diagnostics and leading to personalized therapeutic approaches. Herein we describe our clinical experience performing targeted sequencing for 31 pediatric neuro-oncology patients. Methods: We sequenced 510 cancer-associated genes from tumor and peripheral blood to identify germline and somatic mutations, structural variants, and copy number changes. Results: Genomic profiling was performed on 31 patients with tumors including 11 high-grade gliomas, 8 medulloblastomas, 6 low-grade gliomas, 1 embryonal tumor with multilayered rosettes, 1 pineoblastoma, 1 uveal ganglioneuroma, 1 choroid plexus carcinoma, 1 chordoma, and 1 high-grade neuroepithelial tumor. In 25 cases (81%), results impacted patient management by: (i) clarifying diagnosis, (ii) identifying pathogenic germline mutations, or (iii) detecting potentially targetable alterations. The pathologic diagnosis was amended after genomic profiling for 6 patients (19%), including a high-grade glioma to pilocytic astrocytoma, medulloblastoma to pineoblastoma, ependymoma to high-grade glioma, and medulloblastoma to CNS high-grade neuroepithelial tumor with BCOR alteration. Multiple patients had pathogenic germline mutations, many of which were previously unsuspected. Potentially targetable alterations were identified in 19 patients (61%). Additionally, novel likely pathogenic alterations were identified in 3 cases: an in-frame RAF1 fusion in a BRAF wild-type pleomorphic xanthoastrocytoma, an inactivating ASXL1 mutation in a histone H3 wild-type diffuse pontine glioma, and an in-frame deletion within exon 2 of MAP2K1 in a low-grade astrocytic neoplasm. Conclusions: Our experience demonstrates the significant impact of molecular profiling on diagnosis and treatment of pediatric brain tumors and confirms its feasibility for use at the time of diagnosis or recurrence.","corpus_id":3917526,"score":2},{"doc_id":"28567303","title":"Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.","abstract":"The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.","corpus_id":8998250,"score":2},{"doc_id":"28574513","title":"Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.","abstract":"PURPOSE: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10-20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. METHODS: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. RESULTS: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to -5.8% per disorder). CONCLUSIONS: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016.","corpus_id":-1,"score":2},{"doc_id":"28597942","title":"Copy number alterations determined by single nucleotide polymorphism array testing in the clinical laboratory are indicative of gene fusions in pediatric cancer patients.","abstract":"Gene fusions resulting from structural rearrangements are an established mechanism of tumorigenesis in pediatric cancer. In this clinical cohort, 1,350 single nucleotide polymorphism (SNP)-based chromosomal microarrays from 1,211 pediatric cancer patients were evaluated for copy number alterations (CNAs) associated with gene fusions. Karyotype or fluorescence in situ hybridization studies were performed in 42% of the patients. Ten percent of the bone marrow or solid tumor specimens had SNP array-associated CNAs suggestive of a gene fusion. Alterations involving ETV6, ABL1-NUP214, EBF1-PDGFRB, KMT2A(MLL), LMO2-RAG, MYH11-CBFB, NSD1-NUP98, PBX1, STIL-TAL1, ZNF384-TCF3, P2RY8-CRLF2, and RUNX1T1-RUNX1 fusions were detected in the bone marrow samples. The most common alteration among the low-grade gliomas was a 7q34 tandem duplication resulting in a KIAA1549-BRAF fusion. Additional fusions identified in the pediatric brain tumors included FAM131B-BRAF and RAF1-QKI. COL1A1-PDGFB, CRTC1-MAML2, EWSR1, HEY1, PAX3- and PAX7-FOXO1, and PLAG1 fusions were determined in a variety of solid tumors and a novel potential gene fusion, FGFR1-USP6, was detected in an aneurysmal bone cyst. The identification of these gene fusions was instrumental in tumor diagnosis. In contrast to hematologic and solid tumors in adults that are predominantly driven by mutations, the majority of hematologic and solid tumors in children are characterized by CNAs and gene fusions. Chromosomal microarray analysis is therefore a robust platform to identify diagnostic and prognostic markers in the clinical setting.","corpus_id":4452423,"score":2},{"doc_id":"28638988","title":"Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.","abstract":"Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It outperforms hybridization-based and current sequencing technologies with respect to time to diagnosis and required laboratory equipment and expertise, aiming to make precision medicine possible for every cancer patient, even in resource-restricted settings.","corpus_id":2065740,"score":2},{"doc_id":"28640705","title":"Genomic Analysis of Childhood Brain Tumors: Methods for Genome-Wide Discovery and Precision Medicine Become Mainstream.","abstract":"Recent breakthroughs in next-generation sequencing technology and complementary genomic platforms have transformed our capacity to interrogate the molecular landscapes of human cancers, including childhood brain tumors. Numerous high-throughput genomic studies have been reported for the major histologic brain tumor entities diagnosed in children, including interrogations at the level of the genome, epigenome, and transcriptome, many of which have yielded essential new insights into disease biology. The nature of these discoveries has been largely platform dependent, exemplifying the usefulness of applying different genomic and computational strategies, or integrative approaches, to address specific biologic and/or clinical questions. The goal of this article is to summarize the spectrum of molecular profiling methods available for investigating genomic aspects of childhood brain tumors in both the research and the clinical setting. We provide an overview of the main next-generation sequencing and array-based technologies currently being applied in this field and draw from key examples in the recent neuro-oncology literature to illustrate how these genomic approaches have profoundly advanced our understanding of individual tumor entities. Moreover, we discuss the current status of genomic profiling in the clinic and how different platforms are being used to improve patient diagnosis and stratification, as well as to identify actionable targets for informing molecularly guided therapies, especially for patients for whom conventional standard-of-care treatments have failed. Both the demand for genomic testing and the main challenges associated with incorporating genomics into the clinical management of pediatric patients with brain tumors are discussed, as are recommendations for incorporating these assays into future clinical trials.","corpus_id":29219175,"score":2},{"doc_id":"28844173","title":"Clinical Application of Whole Genome Array Improves the Diagnosis of Pediatric Brain Tumors.","abstract":"Pediatric brain tumors are the leading cause of childhood cancer mortality. Recurring genetic abnormalities play an essential role in the diagnosis and prognosis of pediatric brain tumors. However, clinical workup has not routinely included whole genome assessment. Here, we present high resolution whole genome array results in 11 pediatric brain tumors. Array identified clinically relevant abnormalities in all samples. Copy number aberrations with targeted therapy implication, GOPC-ROS1 fusion, CDK4 amplification, and NF1 deletion, were detected in 3 cases. In addition, array detected recurring genetic abnormalities, including KIAA1549-BRAF fusion, 19q13.42 amplification, i(17q), and monosomy 6, which assisted accurate histological diagnosis in pediatric brain tumors. In conclusion, our results show that whole genome high-resolution array detects diagnostic and treatment-relevant copy number abnormalities in pediatric brain tumors.","corpus_id":32741163,"score":2},{"doc_id":"28912153","title":"Comprehensive Genomic Profiling of 282 Pediatric Low- and High-Grade Gliomas Reveals Genomic Drivers, Tumor Mutational Burden, and Hypermutation Signatures.","abstract":"BACKGROUND: Pediatric brain tumors are the leading cause of death for children with cancer in the U.S. Incorporating next-generation sequencing data for both pediatric low-grade (pLGGs) and high-grade gliomas (pHGGs) can inform diagnostic, prognostic, and therapeutic decision-making. MATERIALS AND METHODS: We performed comprehensive genomic profiling on 282 pediatric gliomas (157 pHGGs, 125 pLGGs), sequencing 315 cancer-related genes and calculating the tumor mutational burden (TMB; mutations per megabase [Mb]). RESULTS: In pLGGs, we detected genomic alterations (GA) in 95.2% (119/125) of tumors. BRAF was most frequently altered (48%; 60/125), and FGFR1 missense (17.6%; 22/125), NF1 loss of function (8.8%; 11/125), and TP53 (5.6%; 7/125) mutations were also detected. Rearrangements were identified in 35% of pLGGs, including KIAA1549-BRAF, QKI-RAF1, FGFR3-TACC3, CEP85L-ROS1, and GOPC-ROS1 fusions. Among pHGGs, GA were identified in 96.8% (152/157). The genes most frequently mutated were TP53 (49%; 77/157), H3F3A (37.6%; 59/157), ATRX (24.2%; 38/157), NF1 (22.2%; 35/157), and PDGFRA (21.7%; 34/157). Interestingly, most H3F3A mutations (81.4%; 35/43) were the variant K28M. Midline tumor analysis revealed H3F3A mutations (40%; 40/100) consisted solely of the K28M variant. Pediatric high-grade gliomas harbored oncogenic EML4-ALK, DGKB-ETV1, ATG7-RAF1, and EWSR1-PATZ1 fusions. Six percent (9/157) of pHGGs were hypermutated (TMB >20 mutations per Mb; range 43-581 mutations per Mb), harboring mutations deleterious for DNA repair in MSH6, MSH2, MLH1, PMS2, POLE, and POLD1 genes (78% of cases). CONCLUSION: Comprehensive genomic profiling of pediatric gliomas provides objective data that promote diagnostic accuracy and enhance clinical decision-making. Additionally, TMB could be a biomarker to identify pediatric glioblastoma (GBM) patients who may benefit from immunotherapy. IMPLICATIONS FOR PRACTICE: By providing objective data to support diagnostic, prognostic, and therapeutic decision-making, comprehensive genomic profiling is necessary for advancing care for pediatric neuro-oncology patients. This article presents the largest cohort of pediatric low- and high-grade gliomas profiled by next-generation sequencing. Reportable alterations were detected in 95% of patients, including diagnostically relevant lesions as well as novel oncogenic fusions and mutations. Additionally, tumor mutational burden (TMB) is reported, which identifies a subpopulation of hypermutated glioblastomas that harbor deleterious mutations in DNA repair genes. This provides support for TMB as a potential biomarker to identify patients who may preferentially benefit from immune checkpoint inhibitors.","corpus_id":29864055,"score":2},{"doc_id":"29285848","title":"Implementation of \"clinical sequencing\" in cancer genome medicine in Japan.","abstract":"In oncology, actionable mutations (alterations) in cancer-associated genes are critical in terms of the selection of therapeutic approaches. Next-generation sequencing of tumor sample DNA (ie, clinical sequencing) can guide clinical management by providing diagnostic or prognostic data, and facilitating the identification of potential treatment regimens, such as molecular-targeted and immune checkpoint blockade therapies. In the USA, a variety of tumor-profiling multiplex gene panels have been developed and implemented for this purpose. In Japan, several academic institutions have now carried out detailed investigations of the feasibility and value of clinical sequencing, and cancer societies have issued consensus clinical practice guidance for next-generation sequencing-based gene panel tests. These efforts will facilitate the implementation of cancer genome medicine in Japan.","corpus_id":3749177,"score":2},{"doc_id":"19276269","title":"Genomic analysis using high-density single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors.","abstract":"PURPOSE: A high-resolution genomic profiling and comprehensive targeted analysis of INI1/SMARCB1 of a large series of pediatric rhabdoid tumors was done. The aim was to identify regions of copy number change and loss of heterozygosity (LOH) that might pinpoint additional loci involved in the development or progression of rhabdoid tumors and define the spectrum of genomic alterations of INI1 in this malignancy. EXPERIMENTAL DESIGN: A multiplatform approach using Illumina single nucleotide polymorphism-based oligonucleotide arrays, multiplex ligation-dependent probe amplification, fluorescence in situ hybridization, and coding sequence analysis was used to characterize genome-wide copy number changes, LOH, and genomic alterations of INI1/SMARCB1 in a series of pediatric rhabdoid tumors. RESULTS: The biallelic alterations of INI1 that led to inactivation were elucidated in 50 of 51 tumors. INI1 inactivation was shown by a variety of mechanisms, including deletions, mutations, and LOH. The results from the array studies highlighted the complexity of rearrangements of chromosome 22 compared with the low frequency of alterations involving the other chromosomes. CONCLUSIONS: The results from the genome-wide single nucleotide polymorphism array analysis suggest that INI1 is the primary tumor suppressor gene involved in the development of rhabdoid tumors with no second locus identified. In addition, we did not identify hotspots for the breakpoints in sporadic tumors with deletions of chromosome 22q11.2. By employing a multimodality approach, the wide spectrum of alterations of INI1 can be identified in the majority of patients, which increases the clinical utility of molecular diagnostic testing.","corpus_id":7290742,"score":1},{"doc_id":"22131877","title":"Detection of somatic copy number alterations in cancer using targeted exome capture sequencing.","abstract":"The research community at large is expending considerable resources to sequence the coding region of the genomes of tumors and other human diseases using targeted exome capture (i.e., \"whole exome sequencing\"). The primary goal of targeted exome sequencing is to identify nonsynonymous mutations that potentially have functional consequences. Here, we demonstrate that whole-exome sequencing data can also be analyzed for comprehensively monitoring somatic copy number alterations (CNAs) by benchmarking the technique against conventional array CGH. A series of 17 matched tumor and normal tissues from patients with metastatic castrate-resistant prostate cancer was used for this assessment. We show that targeted exome sequencing reliably identifies CNAs that are common in advanced prostate cancer, such as androgen receptor (AR) gain and PTEN loss. Taken together, these data suggest that targeted exome sequencing data can be effectively leveraged for the detection of somatic CNAs in cancer.","corpus_id":27717232,"score":1},{"doc_id":"22140474","title":"Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.","abstract":"Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications.","corpus_id":834007,"score":1},{"doc_id":"22313367","title":"Genome-wide copy number analysis in primary breast cancer.","abstract":"INTRODUCTION: Carcinogenesis is considered to be a multistep process that may involve cumulative genomic alterations. Loss of chromosomal material would inactivate tumor suppressor genes and gain of chromosomal material has the potential to activate tumor-promoting genes. AREAS COVERED: Recent intensive studies by array comparative genomic hybridization (aCGH) have demonstrated frequent alterations in multiple regions of the genome. This suggests that these regions contain a variety of oncogenes and tumor suppressor genes associated with breast cancer development. The patterns of copy number variations (CNVs) have been suggested to be associated with breast cancer subtypes, indicating the importance of genomic instability in the development of breast cancer. EXPERT OPINION: To further clarify the complexity of gene alterations, one approach is to employ a CNV-targeted platform that harbors a large number of direct CNV markers located in the repeat-rich unstable regions of the human genome. Next generation sequencing is another approach to overcome the limitations of aCGH such as the repeat-rich regions. Genomic analysis should be combined with expression analysis to elucidate individual genes relevant to breast cancer development and progression. The elucidation of the functions of the affected genes would lead to identification of new molecular targets for breast cancer eradication.","corpus_id":3254274,"score":1},{"doc_id":"23284693","title":"Estimation of copy number alterations from exome sequencing data.","abstract":"Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.","corpus_id":14457367,"score":1},{"doc_id":"23893877","title":"Detection of clinically relevant copy number variants with whole-exome sequencing.","abstract":"Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. This has resulted in the widespread application of genomic microarrays as a first-tier diagnostic tool for CNV detection. More recently, whole-exome sequencing (WES) has been proven successful for the detection of clinically relevant point mutations and small insertion-deletions exome wide. We evaluate the utility of short-read WES (SOLiD 5500xl) to detect clinically relevant CNVs in DNA from 10 patients with intellectual disability and compare these results to data from two independent high-resolution microarrays. Eleven of the 12 clinically relevant CNVs were detected via read-depth analysis of WES data; a heterozygous single-exon deletion remained undetected by all algorithms evaluated. Although the detection power of WES for small CNVs currently does not match that of high-resolution microarray platforms, we show that the majority (88%) of rare coding CNVs containing three or more exons are successfully identified by WES. These results show that the CNV detection resolution of WES is comparable to that of medium-resolution genomic microarrays commonly used as clinical assays. The combined detection of point mutations, indels, and CNVs makes WES a very attractive first-tier diagnostic test for genetically heterogeneous disorders.","corpus_id":7491601,"score":1},{"doc_id":"24634382","title":"Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment.","abstract":"BACKGROUND: Current technology permits an unbiased massive analysis of somatic genetic alterations from tumor DNA as well as the generation of individualized mouse xenografts (Avatar models). This work aimed to evaluate our experience integrating these two strategies to personalize the treatment of patients with cancer. METHODS: We performed whole-exome sequencing analysis of 25 patients with advanced solid tumors to identify putatively actionable tumor-specific genomic alterations. Avatar models were used as an in vivo platform to test proposed treatment strategies. RESULTS: Successful exome sequencing analyses have been obtained for 23 patients. Tumor-specific mutations and copy-number variations were identified. All samples profiled contained relevant genomic alterations. Tumor was implanted to create an Avatar model from 14 patients and 10 succeeded. Occasionally, actionable alterations such as mutations in NF1, PI3KA, and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and, accordingly, treatment of the patients with these drugs was not effective. To date, 13 patients have received a personalized treatment and 6 achieved durable partial remissions. Prior testing of candidate treatments in Avatar models correlated with clinical response and helped to select empirical treatments in some patients with no actionable mutations. CONCLUSION: The use of full genomic analysis for cancer care is encouraging but presents important challenges that will need to be solved for broad clinical application. Avatar models are a promising investigational platform for therapeutic decision making. While limitations still exist, this strategy should be further tested.","corpus_id":11008577,"score":1},{"doc_id":"24710307","title":"A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practice.","abstract":"The aim of this study was to assess the frequency of potentially actionable genomic alterations in breast cancer that could be targeted with approved agents or investigational drugs in clinical trials using a next-generation sequencing-based genomic profiling assay performed in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited commercial laboratory. Methods. Fifty-one breast cancers were analyzed, including primary tumor biopsies of 33 stage I-II and 18 stage IV cancers (13 soft tissue, 3 liver, and 2 bone metastases). We assessed 3,230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was 1,154×. Results. We observed 158 genomic alterations in 55 genes in 48 of 51 (94%) tumors (mean 3.1, range 0-9). The average number of potentially therapeutically relevant alterations was similar in primary (1.6, range 0-4) and in heavily pretreated metastatic cancers (2.0, range 0-4) (p = .24). The most common actionable alterations were in PIK3CA (n = 9, phosphatidylinositol 3-kinase [PI3K]/mammalian target of rapamycin [mTOR] inhibitors), NF1 (n = 7, PI3K/mTOR/mitogen-activated protein kinase inhibitors), v-akt murine thymoma viral oncogene homolog 1-3 (n = 7, PI3K/mTOR/AKT inhibitors), BRCA1/2 (n = 6, poly[ADP-ribose] polymerase inhibitors), and CCND1,2 and CCNE (n = 8)/cycline dependent kinase (CDK)6 (n = 1) (CDK4/6 inhibitors), KIT (n = 1, imatinib/sunitinib), ALK (n = 1, crizotinib), FGFR1,2 (n = 5, fibroblast growth factor receptor inhibitors), and EGFR (n = 2, epidermal growth factor receptor inhibitors). Our sequencing assay also correctly identified all six cases with HER2 (ERBB2) amplification by fluorescence in situ hybridization when tumor content was adequate. In addition, two known activating HER2 mutations were identified, both in unamplified cases. Conclusion. Overall, 84% of cancers harbored at least one genomic alteration linked to potential treatment options. Systematic evaluation of the predictive value of these genomic alterations is critically important for further progress in this field.","corpus_id":21190797,"score":1},{"doc_id":"25356966","title":"Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort.","abstract":"PURPOSE: Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. METHODS: Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. RESULTS: In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. CONCLUSION: These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array. Genet Med 17 8, 623-629.","corpus_id":21899706,"score":1},{"doc_id":"26088785","title":"Exome sequencing and whole genome sequencing for the detection of copy number variation.","abstract":"Many laboratories now use genomic microarrays as their first-tier diagnostic test for copy number variation (CNV) detection. In addition, whole exome sequencing is increasingly being offered as a diagnostic test for heterogeneous disorders. Although mostly used for the detection of point mutations and small insertion-deletions, exome sequencing can also be used to call CNVs, allowing combined small and large variant analysis. Whole genome sequencing in addition to these advantages also offers the potential to characterize CNVs to unprecedented levels of accuracy, providing position and orientation information. In this review, we discuss the clinical potential of CNV identification in whole exome sequencing and whole genome sequencing data and the implications this has on diagnostic laboratories.","corpus_id":6979431,"score":1},{"doc_id":"26181256","title":"Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.","abstract":"IMPORTANCE: Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer. OBJECTIVE: To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response. DESIGN, SETTING, AND PATIENTS: Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response. MAIN OUTCOMES AND MEASURES: Feasibility, use of WES for decision making, and identification of novel biomarkers. RESULTS: A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95X and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response. CONCLUSIONS AND RELEVANCE: The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.","corpus_id":205126404,"score":1},{"doc_id":"26598538","title":"Seeking the driver in tumours with apparent normal molecular profile on comparative genomic hybridization and targeted gene panel sequencing: what is the added value of whole exome sequencing?","abstract":"BACKGROUND: Molecular tumour profiling technologies have become increasingly important in the era of precision medicine, but their routine use is limited by their accessibility, cost, and tumour material availability. It is therefore crucial to assess their relative added value to optimize the sequence and combination of such technologies. PATIENTS AND METHODS: Within the MOSCATO-01 trial, we investigated the added value of whole exome sequencing (WES) in patients that did not present any molecular abnormality on array comparative genomic hybridization (aCGH) and targeted gene panel sequencing (TGPS) using cancer specific panels. The pathogenicity potential and actionability of mutations detected on WES was assessed. RESULTS: Among 420 patients enrolled between December 2011 and December 2013, 283 (67%) patients were analysed for both TGPS and aCGH. The tumour sample of 25 (8.8%) of them presented a flat (or low-dynamic) aCGH profile and no pathogenic mutation on TGPS. We selected the first eligible 10 samples-corresponding to a heterogeneous cohort of different tumour types-to perform WES. This allowed identifying eight mutations of interest in two patients: FGFR3, PDGFRB, and CREBBP missense single-nucleotide variants (SNVs) in an urothelial carcinoma; FGFR2, FBXW7, TP53, and MLH1 missense SNVs as well as an ATM frameshift mutation in a squamous cell carcinoma of the tongue. The FGFR3 alteration had been previously described as an actionable activating mutation and might have resulted in treatment by an FGFR inhibitor. CREBBP and ATM alterations might also have suggested a therapeutic orientation towards epigenetic modifiers and ataxia-telangectasia and Rad3-related inhibitors, respectively. CONCLUSION: The therapeutic added value of performing WES on tumour samples that do not harbour any genetic abnormality on TGPS and aCGH might be limited and variable according to the histotype. Alternative techniques, including RNASeq and methylome analysis, might be more informative in selected cases.","corpus_id":4679077,"score":1},{"doc_id":"26662885","title":"Application of whole-exome sequencing for detecting copy number variants in CMT1A/HNPP.","abstract":"Large insertions and deletions (indels), including copy number variations (CNVs), are commonly seen in many diseases. Standard approaches for indel detection rely on well-established methods such as qPCR or short tandem repeat (STR) markers. Recently, a number of tools for CNV detection based on next-generation sequencing (NGS) data have also been developed; however, use of these methods is limited. Here, we used whole-exome sequencing (WES) in patients previously diagnosed with CMT1A or HNPP using STR markers to evaluate the ability of WES to improve the clinical diagnosis. Patients were evaluated utilizing three CNV detection tools including CONIFER, ExomeCNV and CEQer, and array comparative genomic hybridization (aCGH). We identified a breakpoint region at 17p11.2-p12 in patients with CMT1A and HNPP. CNV detection levels were similar in both 6 Gb (mean read depth=80×) and 17 Gb (mean read depth=190×) data. Taken together, these data suggest that 6 Gb WES data are sufficient to reveal the genetic causes of various diseases and can be used to estimate single mutations, indels, and CNVs simultaneously. Furthermore, our data strongly indicate that CNV detection by NGS is a rapid and cost-effective method for clinical diagnosis of genetically heterogeneous disorders such as CMT neuropathy.","corpus_id":45479243,"score":1},{"doc_id":"27100738","title":"CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.","abstract":"Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.","corpus_id":3651442,"score":1},{"doc_id":"27197880","title":"Precision Oncology Medicine: The Clinical Relevance of Patient-Specific Biomarkers Used to Optimize Cancer Treatment.","abstract":"Precision medicine in oncology is the result of an increasing awareness of patient-specific clinical features coupled with the development of genomic-based diagnostics and targeted therapeutics. Companion diagnostics designed for specific drug-target pairs were the first to widely utilize clinically applicable tumor biomarkers (eg, HER2, EGFR), directing treatment for patients whose tumors exhibit a mutation susceptible to an FDA-approved targeted therapy (eg, trastuzumab, erlotinib). Clinically relevant germline mutations in drug-metabolizing enzymes and transporters (eg, TPMT, DPYD) have been shown to impact drug response, providing a rationale for individualized dosing to optimize treatment. The use of multigene expression-based assays to analyze an array of prognostic biomarkers has been shown to help direct treatment decisions, especially in breast cancer (eg, Oncotype DX). More recently, the use of next-generation sequencing to detect many potential \"actionable\" cancer molecular alterations is further shifting the 1 gene-1 drug paradigm toward a more comprehensive, multigene approach. Currently, many clinical trials (eg, NCI-MATCH, NCI-MPACT) are assessing novel diagnostic tools with a combination of different targeted therapeutics while also examining tumor biomarkers that were previously unexplored in a variety of cancer histologies. Results from ongoing trials such as the NCI-MATCH will help determine the clinical utility and future development of the precision-medicine approach.","corpus_id":19759664,"score":1},{"doc_id":"27425854","title":"Genomic characterization of recurrent high-grade astroblastoma.","abstract":"Astroblastomas are rare primary brain tumors, diagnosed based on histologic features. Not currently assigned a WHO grade, they typically display indolent behavior, with occasional variants taking a more aggressive course. We characterized the immunohistochemical characteristics, copy number (high-resolution array comparative genomic hybridization, OncoCopy) and mutational profile (targeted next-generation exome sequencing, OncoPanel) of a cohort of seven biopsies from four patients to identify recurrent genomic events that may help distinguish astroblastomas from other more common high-grade gliomas. We found that tumor histology was variable across patients and between primary and recurrent tumor samples. No common molecular features were identified among the four tumors. Mutations commonly observed in astrocytic tumors (IDH1/2, TP53, ATRX, and PTEN) or ependymoma were not identified. However one case with rapid clinical progression displayed mutations more commonly associated with GBM (NF1(N1054H/K63)*, PIK3CA(R38H) and ERG(A403T)). Conversely, another case, originally classified as glioblastoma with nine-year survival before recurrence, lacked a GBM mutational profile. Other mutations frequently seen in lower grade gliomas (BCOR, BCORL1, ERBB3, MYB, ATM) were also present in several tumors. Copy number changes were variable across tumors. Our findings indicate that astroblastomas have variable growth patterns and morphologic features, posing significant challenges to accurate classification in the absence of diagnostically specific copy number alterations and molecular features. Their histopathologic overlap with glioblastoma will likely confound the observation of long-term GBM \"survivors\". Further genomic profiling is needed to determine whether these tumors represent a distinct entity and to guide management strategies.","corpus_id":32365824,"score":1},{"doc_id":"27440268","title":"Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma.","abstract":"PURPOSE: The tumor genomic copy number profile is of prognostic significance in neuroblastoma patients. We have studied the genomic copy number profile of cell-free DNA (cfDNA) and compared this with primary tumor arrayCGH (aCGH) at diagnosis. EXPERIMENTAL DESIGN: In 70 patients, cfDNA genomic copy number profiling was performed using the OncoScan platform. The profiles were classified according to the overall pattern, including numerical chromosome alterations (NCA), segmental chromosome alterations (SCA), and MYCN amplification (MNA). RESULTS: Interpretable and dynamic cfDNA profiles were obtained in 66 of 70 and 52 of 70 cases, respectively. An overall identical genomic profile between tumor aCGH and cfDNA was observed in 47 cases (3 NCAs, 22 SCAs, 22 MNAs). In one case, cfDNA showed an additional SCA not detected by tumor aCGH. In 4 of 8 cases with a silent tumor aCGH profile, cfDNA analysis revealed a dynamic profile (3 SCAs, 1 NCA). In 14 cases, cfDNA analysis did not reveal any copy number changes. A total of 378 breakpoints common to the primary tumor and cfDNA of any given patient were identified, 27 breakpoints were seen by tumor aCGH, and 54 breakpoints were seen in cfDNA only, including two cases with interstitial IGFR1 gains and two alterations targeting TERT CONCLUSIONS: These results demonstrate the feasibility of cfDNA copy number profiling in neuroblastoma patients, with a concordance of the overall genomic profile in aCGH and cfDNA dynamic cases of 97% and a sensitivity of 77%, respectively. Furthermore, neuroblastoma heterogeneity is highlighted, suggesting that cfDNA might reflect genetic alterations of more aggressive cell clones. Clin Cancer Res; 22(22); 5564-73. ©2016 AACRSee related commentary by Janku and Kurzrock, p. 5400.","corpus_id":374560,"score":1},{"doc_id":"27765906","title":"Targeted NGS, array-CGH, and patient-derived tumor xenografts for precision medicine in advanced breast cancer: a single-center prospective study.","abstract":"BACKGROUND: Routine feasibility and clinical impact of genomics-based tumor profiling in advanced breast cancer (aBC) remains to be determined. We conducted a pilot study to evaluate whether precision medicine could be prospectively implemented for aBC patients in a single center and to examine whether patient-derived tumor xenografts (PDX) could be obtained in this population. RESULTS: Thirty-four aBC patients were included. Actionable targets were found in 28 patients (82%). A targeted therapy could be proposed to 22 patients (64%), either through a clinical trial (n=15) and/or using already registered drugs (n=21). Ten patients (29%) eventually received targeted treatment, 2 of them deriving clinical benefit. Of 22 patients subjected to mouse implantation, 10 had successful xenografting (45%), mostly in triple-negative aBC. METHODS: aBC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Genomic profiling was established by whole-genome array comparative genomic hybridization (aCGH) and targeted next-generation sequencing (NGS) of 365 candidate cancer genes. For a subset of patients, a sample of fresh tumor was orthotopically implanted in humanized cleared fat pads of NSG mice for establishing PDX. CONCLUSIONS: Precision medicine can be implemented in a single center in the context of clinical practice and may allow genomic-driven treatment in approximately 30% of aBC patients. PDX may be obtained in a significant fraction of cases.","corpus_id":3447760,"score":1},{"doc_id":"28007036","title":"Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine.","abstract":"BACKGROUND: Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been limited to Western populations. In order to understand possible ethnic and geographic differences and to explore the broader application of CGS to other populations, we sequenced a panel of 415 important cancer genes to characterize clinically actionable genomic driver events in 201 Japanese patients with colorectal cancer (CRC). METHODS: Using next-generation sequencing methods, we examined all exons of 415 known cancer genes in Japanese CRC patients (n = 201) and evaluated for concordance among independent data obtained from US patients with CRC (n = 108) and from The Cancer Genome Atlas-CRC whole exome sequencing (WES) database (n = 224). Mutation data from non-hypermutated Japanese CRC patients were extracted and clustered by gene mutation patterns. Two different sets of genes from the 415-gene panel were used for clustering: 61 genes with frequent alteration in CRC and 26 genes that are clinically actionable in CRC. RESULTS: The 415-gene panel is able to identify all of the critical mutations in tumor samples as well as WES, including identifying hypermutated tumors. Although the overall mutation spectrum of the Japanese patients is similar to that of the Western population, we found significant differences in the frequencies of mutations in ERBB2 and BRAF. We show that the 415-gene panel identifies a number of clinically actionable mutations in KRAS, NRAS, and BRAF that are not detected by hot-spot testing. We also discovered that 26% of cases have mutations in genes involved in DNA double-strand break repair pathway. Unsupervised clustering revealed that a panel of 26 genes can be used to classify the patients into eight different categories, each of which can optimally be treated with a particular combination therapy. CONCLUSIONS: Use of a panel of 415 genes can reliably identify all of the critical mutations in CRC patients and this information of CGS can be used to determine the most optimal treatment for patients of all ethnicities.","corpus_id":2480750,"score":1},{"doc_id":"28231819","title":"Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies.","abstract":"BACKGROUND: The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic options has been revived. Current data suggest that each tumor contains a unique set of mutations (mutanome), thus requiring the creation of individualized cancer vaccines. However, rigorous analysis of non-individualized cancer immunotherapy approaches across multiple cancer types and in the context of known driver alterations has yet to be reported. We therefore set out to determine the feasibility of a generalizable cancer vaccine strategy based on targeting multiple neoantigens in an HLA-A/B subtype-directed manner. METHODS: A cancer gene-focused, hybrid capture-based genomic analysis was performed on 63,220 unique tumors. Neoantigens were predicted using a combined peptide processing and MHC-I binding prediction tool (IEDB) for all recurrent (>10 tumors) missense alterations and non-frameshift indels for the two most common HLA-A/B subtypes in North American/European populations. RESULTS: Despite being overwhelmingly unique overall, many mutanomes (~45%) contain at least one mutation from a set of ten mutations chosen to maximize the number of unique tumors. This held true for tumors driven by KRAS G12C (n = 1799), PIK3CA E545K (n = 1713), or EGFR L858R (n = 478) alterations, which define distinct sample subsets. We therefore hypothesized that sets of carefully selected mutations/neoantigens may allow the development of broadly applicable semi-universal cancer vaccines. To test the feasibility of such an approach, antigen processing and MHC-I binding prediction was applied for HLA subtypes A*01:01/B*08:01 and A*02:01/B*44:02. In tumors with a specific HLA type, 0.7 and 2.5% harbored at least one of a set of ten neoantigens predicted to bind to each subtype, respectively. In comparison, KRAS G12C-driven tumors produced similar results (0.8 and 2.6% for each HLA subtype, respectively), indicating that neoantigen targets still remain highly diverse even within the context of major driver mutations. CONCLUSIONS: This \"best case scenario\" analysis of a large tumor set across multiple cancer types and in the context of driver alterations reveals that semi-universal, HLA-specific cancer vaccine strategies will be relevant to only a small subset of the general population. Similar analysis of whole exome/genome sequencing, although not currently feasible at scale in a clinical setting, will likely uncover further diversity.","corpus_id":2426402,"score":1},{"doc_id":"28460482","title":"Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data.","abstract":"Accurate detection of copy number alterations (CNAs) using next-generation sequencing technology is essential for the development and application of more precise medical treatments for human cancer. Here, we evaluated seven CNA estimation tools (ExomeCNV, CoNIFER, VarScan2, CODEX, ngCGH, saasCNV, and falcon) using whole-exome sequencing data from 419 breast cancer tumor-normal sample pairs from The Cancer Genome Atlas. Estimations generated using each tool were converted into gene-based copy numbers; concordance for gains and losses and the sensitivity and specificity of each tool were compared to validated copy numbers from a single nucleotide polymorphism reference array. The concordance and sensitivity of the tumor-normal pair methods for estimating CNAs (saasCNV, ExomeCNV, and VarScan2) were better than those of the tumor batch methods (CoNIFER and CODEX). SaasCNV had the highest gain and loss concordances (65.0%), sensitivity (69.4%), and specificity (89.1%) for estimating copy number gains or losses. These findings indicate that improved CNA detection algorithms are needed to more accurately interpret whole-exome sequencing results in human cancer.","corpus_id":3668344,"score":1},{"doc_id":"28554745","title":"Genomic profiling of esophageal squamous cell carcinoma (ESCC)-Basis for precision medicine.","abstract":"PURPOSE: Preparing for precision medicine, we surveyed genomic alterations in esophageal squamous cell carcinoma (ESCC) and identified candidate therapeutic targets by genomic profiling using next-generation sequencing (NGS). MATERIALS AND METHODS: Single-nucleotide variations, indels, and copy number variations in 80 genes were evaluated by targeted deep sequencing in 24 surgically resected ESCC specimens. Immunohistochemistry analyses and silver in situ hybridization for ERBB2 (HER2) were conducted to verify the NGS results. Associations between clinicopathological factors and detected genomic alterations were estimated. RESULTS: The mean coverage of sequencing of the tumor tissues from 24 patients was 464.8X with 85.1% over 100X. We detected a total of 115 genetic alterations and more than one genetic alteration was detected in most patients (23/24, 95.8%). Genes with genetic alterations detected in more than 20% of cases included TP53 (20/24, 83%), NOTCH1 (7/24, 29%), and MTOR (6/24, 25%). Amplification of 7 genes was detected in 8 cases. Genes showing amplification included AKT2 (1/24, 4.2%), EGFR (2/24, 8.3%), ERBB2 (HER2; 1/24, 4.2%), FGFR1 (1/24, 4.2%), KRAS (1/24, 4.2%), MDM2 (1/24, 4.2%), and PIK3CA (1/24, 4.2%). The ERBB2 alteration was confirmed by immunohistochemistry and silver in situ hybridization. Patients with NF1 and ARID1A mutations were younger than the patients without the mutations. ( p=0.024 and 0.014, respectively). NOTCH1 mutation and EGFR genetic alteration were associated with a larger tumor size (p=0.019) and lesser invasion depth (p=0.005), respectively. CONCLUSION: This study revealed the genetic profiles of ESCC, which may provide a foundation for the development of novel targeted therapy and precision medicine.","corpus_id":207438895,"score":1},{"doc_id":"28557599","title":"Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer.","abstract":"CONTEXT: - The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. OBJECTIVE: - To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. DESIGN: - OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies. RESULTS: - OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50× coverage. CONCLUSIONS: - The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology.","corpus_id":207534585,"score":1},{"doc_id":"28717660","title":"A novel molecular diagnostics platform for somatic and germline precision oncology.","abstract":"BACKGROUND: Next-generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies. METHODS: Next-generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug-related rearrangements, were prepared from 39 tumors (paraffin-embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines. RESULTS: The platform detects single-nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy-number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent. CONCLUSION: With an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.","corpus_id":22316127,"score":1},{"doc_id":"28751446","title":"Gene Copy Number Estimation From Targeted Next Generation Sequencing Of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification.","abstract":"Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach.</p> <p>Results</p> <p>We showed that this method produced highly reproducible CNA results (r=0.92), with the use of pooled germline DNA as a coverage reference supporting precise CNA estimation. CNA estimates from targeted next generation sequencing were comparable with WES (r=0.86) and aCGH (r=0.7); for key selected genes (BRCA2, MYC, PIK3CA, PTEN and RB1) CNA estimation correlated well with WES (r = 0.91) and aCGH (r = 0.84) results.</p> <p>The frequency of CNAs in our population was comparable to that previously described (ie. deep deletions: BRCA2 4.5%; RB1 8.2%; PTEN 15.5%; amplification: AR 45.5%; gain: MYC 31.8%). We also showed, utilizing FISH, that CNA estimation can be impacted by intra-tumor heterogeneity and demonstrated that tumor microdissection allows NGS to provide more precise CNA estimates.</p> <p>Conclusion</p> <p>Targeted NGS and CNVkit based analyses provide a robust, precise, high throughput and cost effective method for CNA estimation for the delivery of more precise patient care.","corpus_id":19052648,"score":1},{"doc_id":"20156996","title":"Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays.","abstract":"The detection of copy number variants (CNV) by array-based platforms provides valuable insight into understanding human diversity. However, suboptimal study design and data processing negatively affect CNV assessment. We quantitatively evaluate their impact when short-sequence oligonucleotide arrays are applied (Affymetrix Genome-Wide Human SNP Array 6.0) by evaluating 42 HapMap samples for CNV detection. Several processing and segmentation strategies are implemented, and results are compared to CNV assessment obtained using an oligonucleotide array CGH platform designed to query CNVs at high resolution (Agilent). We quantitatively demonstrate that different reference models (e.g. single versus pooled sample reference) used to detect CNVs are a major source of inter-platform discrepancy (up to 30%) and that CNVs residing within segmental duplication regions (higher reference copy number) are significantly harder to detect (P < 0.0001). After adjusting Affymetrix data to mimic the Agilent experimental design (reference sample effect), we applied several common segmentation approaches and evaluated differential sensitivity and specificity for CNV detection, ranging 39-77% and 86-100% for non-segmental duplication regions, respectively, and 18-55% and 39-77% for segmental duplications. Our results are relevant to any array-based CNV study and provide guidelines to optimize performance based on study-specific objectives.","corpus_id":8315727,"score":0},{"doc_id":"21272361","title":"The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.","abstract":"BACKGROUND: Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel next generation sequencing, which enables the discovery of such changes, uses considerable quantities of genomic DNA (> 5 ug), a serious limitation in ever smaller clinical samples. However, a commonly available microarray platforms such as array comparative genomic hybridization (array CGH) allows the characterization of gene copy number at a single gene resolution using much smaller amounts of genomic DNA. In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities. METHODS: We performed array CGH on whole genome amplified and not amplified genomic DNA from MCF-7 breast cancer cells, using 244 K and 1 M Agilent arrays. The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length. RESULTS: DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length. The 4-fold extra resolution of the 1 M array platform relative to the less dense 244 K array platform, led to the improved detection of copy number variations (CNVs) and micro-CNAs. The identification of intra-genic breakpoints in areas of DNA copy number gain signaled the possible presence of gene fusion events. However, the ultra-dense platforms, especially the densest 1 M array, detect artifacts inherent to whole genome amplification and should be used only with non-amplified DNA samples. CONCLUSIONS: This is a first report using 1 M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification.","corpus_id":10742867,"score":0},{"doc_id":"23368785","title":"CoNVEX: copy number variation estimation in exome sequencing data using HMM.","abstract":"BACKGROUND: One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequencing (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic variations. However, finding CNV in Cancer samples using WES data has not been fully explored. RESULTS: We present a new method, called CoNVEX, to estimate copy number variation in whole exome sequencing data. It uses ratio of tumour and matched normal average read depths at each exonic region, to predict the copy gain or loss. The useful signal produced by WES data will be hindered by the intrinsic noise present in the data itself. This limits its capacity to be used as a highly reliable CNV detection source. Here, we propose a method that consists of discrete wavelet transform (DWT) to reduce noise. The identification of copy number gains/losses of each targeted region is performed by a Hidden Markov Model (HMM). CONCLUSION: HMM is frequently used to identify CNV in data produced by various technologies including Array Comparative Genomic Hybridization (aCGH) and WGS. Here, we propose an HMM to detect CNV in cancer exome data. We used modified data from 1000 Genomes project to evaluate the performance of the proposed method. Using these data we have shown that CoNVEX outperforms the existing methods significantly in terms of precision. Overall, CoNVEX achieved a sensitivity of more than 92% and a precision of more than 50%.","corpus_id":8393487,"score":0},{"doc_id":"25102989","title":"Identification of copy number variants from exome sequence data.","abstract":"BACKGROUND: With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task. Whilst numerous programs are available, they have different sensitivities, and have low sensitivity to detect smaller CNVs (1-4 exons). Additionally, exonic CNV discovery using standard aCGH has limitations due to the low probe density over exonic regions. The goal of our study was to develop a protocol to detect exonic CNVs (including shorter CNVs that cover 1-4 exons), combining computational prediction algorithms and a high-resolution custom CGH array. RESULTS: We used six published CNV prediction programs (ExomeCNV, CONTRA, ExomeCopy, ExomeDepth, CoNIFER, XHMM) and an in-house modification to ExomeCopy and ExomeDepth (ExCopyDepth) for computational CNV prediction on 30 exomes from the 1000 genomes project and 9 exomes from primary immunodeficiency patients. CNV predictions were tested using a custom CGH array designed to capture all exons (exaCGH). After this validation, we next evaluated the computational prediction of shorter CNVs. ExomeCopy and the in-house modified algorithm, ExCopyDepth, showed the highest capability in detecting shorter CNVs. Finally, the performance of each computational program was assessed by calculating the sensitivity and false positive rate. CONCLUSIONS: In this paper, we assessed the ability of 6 computational programs to predict CNVs, focussing on short (1-4 exon) CNVs. We also tested these predictions using a custom array targeting exons. Based on these results, we propose a protocol to identify and confirm shorter exonic CNVs combining computational prediction algorithms and custom aCGH experiments.","corpus_id":1781103,"score":0},{"doc_id":"25319062","title":"Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.","abstract":"BACKGROUND: Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS: We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS: Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. CONCLUSIONS: The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.","corpus_id":-1,"score":0},{"doc_id":"26110913","title":"Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.","abstract":"Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy-number variant calling when evaluated against a single-nucleotide polymorphism array. This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.","corpus_id":4103107,"score":0},{"doc_id":"26258935","title":"A sparse model based detection of copy number variations from exome sequencing data.","abstract":"GOAL: Whole-exome sequencing provides a more cost-effective way than whole-genome sequencing for detecting genetic variants such as copy number variations (CNVs). Although a number of approaches have been proposed to detect CNVs from whole-genome sequencing, a direct adoption of these approaches to whole-exome sequencing will often fail because exons are separately located along a genome. Therefore, an appropriate method is needed to target the specific features of exome sequencing data. METHODS: In this paper a novel sparse model based method is proposed to discover CNVs from multiple exome sequencing data. First, exome sequencing data are represented with a penalized matrix approximation, and technical variability and random sequencing errors are assumed to follow a generalized Gaussian distribution. Second, an iteratively reweighted least squares algorithm is used to estimate the solution. RESULTS: The method is tested and validated on both synthetic and real data, and compared with other approaches including CoNIFER, XHMM and cn. MOPS. The test demonstrates that the proposed method outperform other approaches. CONCLUSION: The proposed sparse model can detect CNVs from exome sequencing data with high power and precision. SIGNIFICANCE: Sparse model can target the specific features of exome sequencing data. The software codes are freely available at http://www.tulane.edu/ wyp/software/Exon CNV.m.","corpus_id":2111111,"score":0},{"doc_id":"27028851","title":"Comparative genomic analysis of primary tumors and metastases in breast cancer.","abstract":"Personalized medicine uses genomic information for selecting therapy in patients with metastatic cancer. An issue is the optimal tissue source (primary tumor or metastasis) for testing. We compared the DNA copy number and mutational profiles of primary breast cancers and paired metastases from 23 patients using whole-genome array-comparative genomic hybridization and next-generation sequencing of 365 \"cancer-associated\" genes. Primary tumors and metastases harbored copy number alterations (CNAs) and mutations common in breast cancer and showed concordant profiles. The global concordance regarding CNAs was shown by clustering and correlation matrix, which showed that each metastasis correlated more strongly with its paired tumor than with other samples. Genes with recurrent amplifications in breast cancer showed 100% (ERBB2, FGFR1), 96% (CCND1), and 88% (MYC) concordance for the amplified/non-amplified status. Among all samples, 499 mutations were identified, including 39 recurrent (AKT1, ERBB2, PIK3CA, TP53) and 460 non-recurrent variants. The tumors/metastases concordance of variants was 75%, higher for recurrent (92%) than for non-recurrent (73%) variants. Further mutational discordance came from very different variant allele frequencies for some variants. We showed that the chosen targeted therapy in two clinical trials of personalized medicine would be concordant in all but one patient (96%) when based on the molecular profiling of tumor and paired metastasis. Our results suggest that the genotyping of primary tumor may be acceptable to guide systemic treatment if the metastatic sample is not obtainable. However, given the rare but potentially relevant divergences for some actionable driver genes, the profiling of metastatic sample is recommended.","corpus_id":20868599,"score":0},{"doc_id":"27851748","title":"Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis.","abstract":"Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression. To that end, we developed a single cell Copy Number Variation (CNV) Assay to evaluate genomic instability and CNVs in patient CTCs. For proof of concept, prostate cancer cell lines, LNCaP, PC3 and VCaP, were spiked into healthy donor blood to create mock patient-like samples for downstream single cell genomic analysis. In addition, samples from seven metastatic castration resistant prostate cancer (mCRPC) patients were included to evaluate clinical feasibility. CTCs were enumerated and characterized using the Epic Sciences CTC Platform. Identified single CTCs were recovered, whole genome amplified, and sequenced using an Illumina NextSeq 500. CTCs were then analyzed for genome-wide copy number variations, followed by genomic instability analyses. Large-scale state transitions (LSTs) were measured as surrogates of genomic instability. Genomic instability scores were determined reproducibly for LNCaP, PC3, and VCaP, and were higher than white blood cell (WBC) controls from healthy donors. A wide range of LST scores were observed within and among the seven mCRPC patient samples. On the gene level, loss of the PTEN tumor suppressor was observed in PC3 and 5/7 (71%) patients. Amplification of the androgen receptor (AR) gene was observed in VCaP cells and 5/7 (71%) mCRPC patients. Using an in silico down-sampling approach, we determined that DNA copy number and genomic instability can be detected with as few as 350K sequencing reads. The data shown here demonstrate the feasibility of detecting genomic instabilities at the single cell level using the Epic Sciences CTC Platform. Understanding CTC heterogeneity has great potential for patient stratification prior to treatment with targeted therapies and for monitoring disease evolution during treatment.","corpus_id":824781,"score":0},{"doc_id":"28002793","title":"Next generation sequencing of vitreoretinal lymphomas from small-volume intraocular liquid biopsies: new routes to targeted therapies.","abstract":"BACKGROUND: Vitreoretinal lymphoma (VRL), the most common lymphoma of the eye, is a rare form of primary CNS lymphoma (PCNSL). Most frequently a high-grade diffuse large B cell lymphoma, VRL can cause vision loss and its prognosis remains dismal: the overall survival time is 3 years after diagnosis. Radiotherapy and chemotherapy are used but remain frequently ineffective, and no standardized treatment regimen exists. Furthermore, no biologically targeted treatments, based on the genetic profile of the tumor, are available, as VRL has hitherto not comprehensively been profiled. To address these unmet needs, we hypothesized that a next generation sequencing (NGS)-based, National Cancer Institute (NCI) MATCH Trial-modified panel would be able to identify actionable genomic alterations from small-volume, intraocular liquid biopsies. METHODS AND FINDINGS: In this retrospective study, we collected diluted vitreous biopsies from 4 patients with a high suspicion for VRL. Following cytological confirmation of lymphoma (all were diffuse large B cell lymphomas), we subjected genomic DNA from the biopsies to NGS, using a panel containing 126 genes (3,435 amplicons across several hotspots per gene), which was modified from that of the NCI MATCH Trial, a new trial that has matched patients with cancers that have not responded (or never responded), to investigational therapeutics based on their prioritized mutation profile rather than site of tumor origin. Using a validated bioinformatics pipeline, we assessed for the presence of actionable mutations and copy number alterations. In all four small-volume, intraocular liquid biopsies, we obtained sufficient genomic DNA for analysis, even in diluted samples in which the undiluted vitreous was used for cytology and flow cytometry. Using NGS, we found targetable heterozygous gain-of-function mutations in the MYD88 oncogene, and confirmed in our cohort the presence the L265 mutations, previously described using PCR-based assays. For the first time in VRL, we also identified the MYD88 S243N mutation. We also identified two-copy copy number losses in the tumor suppressor CDKN2A in all four cases, and one copy loss of the tumor suppressor PTEN in one sample. In one case, in which vitreous biopsies were originally read as cytologically negative, but which was confirmed as lymphoma when a lesion appeared in the brain two years later, our NGS-based approach detected tumoral DNA in the banked, original liquid biopsy. CONCLUSIONS: We performed the first systematic exploration of the actionable cancer genome in VRL. Our NGS-based approach identified exploitable genomic alterations such as gain-of-function MYD88 oncogene mutations and loss of the tumor suppressor CDKN2A, and thus illuminates new routes to biologically targeted therapies for VRL, a cancer with a dismal prognosis. This precision medicine strategy could be used to nominate novel, targeted therapies in lymphomas and other blinding and deadly ocular, orbital, and ocular adnexal diseases for which few treatments exist.","corpus_id":3661857,"score":0},{"doc_id":"28034454","title":"Comprehensive genomic sequencing and the molecular profiles of clinically advanced breast cancer.","abstract":"Targeting specific mutations that have arisen within a tumour is a promising means of increasing the efficacy of treatments, and breast cancer is no exception to this new paradigm of personalised medicine. Traditional DNA sequencing methods used to characterise clinical cancer specimens and impact treatment decisions are highly sensitive, but are often limited in their scope to known mutational hot spots. Next-generation sequencing (NGS) technologies can also test for these well-known hot spots, as well as identifying insertions and deletions, copy number changes such as ERBB2 (HER2) gene amplification, and a wide array of fusion or rearrangement events. By rapidly analysing many genes in parallel, NGS technologies can make efficient use of precious biopsy material. Comprehensive genomic profiling (CGP) by NGS can reveal targetable, clinically relevant genomic alterations that can stratify tumours by predicted sensitivity to a variety of therapies, including HER2- or MTOR-targeted therapies, immunotherapies, and other kinase inhibitors. Many clinically relevant genomic alterations would not be identified by IHC or hotspot testing, but can be detected by NGS. In addition to the most common breast carcinoma subtypes, rare subtypes analysed with CGP also harbour clinically relevant genomic alterations that can potentially direct therapy selection, illustrating that CGP is a powerful tool for guiding treatment across all breast cancer subtypes.","corpus_id":42872352,"score":0},{"doc_id":"28666423","title":"Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications.","abstract":"BACKGROUND: Sequencing analysis of circulating tumor cells (CTCs) enables \"liquid biopsy\" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies. METHODS: Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score. RESULTS: Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA. CONCLUSION: The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5-10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template.","corpus_id":870354,"score":0}],"string":"[\n {\n \"doc_id\": \"21979893\",\n \"title\": \"Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling.\",\n \"abstract\": \"Medulloblastoma (MB) is a WHO grade IV, invasive embryonal CNS tumor that mainly affects children. The aggressiveness and response to therapy can vary considerably between cases, and despite treatment, ~30% of patients die within 2 years from diagnosis. Furthermore, the majority of survivors suffer long-term side-effects due to severe management modalities. Several distinct morphological features have been associated with differences in biological behavior, but improved molecular-based criteria that better reflect the underlying tumor biology are in great demand. In this study, we profiled a series of 25 MB with a 32K BAC array covering 99% of the current assembly of the human genome for the identification of genetic copy number alterations possibly important in MB. Previously known aberrations as well as several novel focally amplified loci could be identified. As expected, the most frequently observed alteration was the combination of 17p loss and 17q gain, which was detected in both high- and standard-risk patients. We also defined minimal overlapping regions of aberrations, including 16 regions of gain and 18 regions of loss in various chromosomes. A few noteworthy narrow amplified loci were identified on autosomes 1 (38.89-41.97 and 84.89-90.76 Mb), 3 (27.64-28.20 and 35.80-43.50 Mb), and 8 (119.66-139.79 Mb), aberrations that were verified with an alternative platform (Illumina 610Q chips). Gene expression levels were also established for these samples using Affymetrix U133Plus2.0 arrays. Several interesting genes encompassed within the amplified regions and presenting with transcript upregulation were identified. These data contribute to the characterization of this malignant childhood brain tumor and confirm its genetic heterogeneity.\",\n \"corpus_id\": 30840874,\n \"score\": 2\n },\n {\n \"doc_id\": \"22585170\",\n \"title\": \"High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.\",\n \"abstract\": \"UNLABELLED: Knowledge of \\\"actionable\\\" somatic genomic alterations present in each tumor (e.g., point mutations, small insertions/deletions, and copy-number alterations that direct therapeutic options) should facilitate individualized approaches to cancer treatment. However, clinical implementation of systematic genomic profiling has rarely been achieved beyond limited numbers of oncogene point mutations. To address this challenge, we utilized a targeted, massively parallel sequencing approach to detect tumor genomic alterations in formalin-fixed, paraffin-embedded (FFPE) tumor samples. Nearly 400-fold mean sequence coverage was achieved, and single-nucleotide sequence variants, small insertions/deletions, and chromosomal copynumber alterations were detected simultaneously with high accuracy compared with other methods in clinical use. Putatively actionable genomic alterations, including those that predict sensitivity or resistance to established and experimental therapies, were detected in each tumor sample tested. Thus, targeted deep sequencing of clinical tumor material may enable mutation-driven clinical trials and, ultimately, \\\"personalized\\\" cancer treatment. SIGNIFICANCE: Despite the rapid proliferation of targeted therapeutic agents, systematic methods to profile clinically relevant tumor genomic alterations remain underdeveloped. We describe a sequencingbased approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.\",\n \"corpus_id\": 10714052,\n \"score\": 2\n },\n {\n \"doc_id\": \"23633565\",\n \"title\": \"Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1.\",\n \"abstract\": \"Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from BRAF kinase mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. We performed high-resolution copy-number analysis on 44 formalin-fixed, paraffin-embedded diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gain, was observed in 28% of diffuse astrocytoma grade IIs and resulted in partial duplication of the transcription factor MYBL1 with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene v-myb avian myeloblastosis viral oncogene homolog (MYB) on 6q23.3. Whole-genome sequencing of a MYBL1-rearranged diffuse astrocytoma grade II demonstrated MYBL1 tandem duplication and few other events. Truncated MYBL1 transcripts identified in this tumor induced anchorage-independent growth in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with MYBL1 partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.\",\n \"corpus_id\": 2023523,\n \"score\": 2\n },\n {\n \"doc_id\": \"24767714\",\n \"title\": \"Diagnostic application of high resolution single nucleotide polymorphism array analysis for children with brain tumors.\",\n \"abstract\": \"Single nucleotide polymorphism (SNP) array analysis is currently used as a first tier test for pediatric brain tumors at The Children's Hospital of Philadelphia. The results from 100 consecutive patients are summarized in the present report. Eighty-seven percent of the tumors had at least one pathogenic copy number alteration. Nineteen of 56 low grade gliomas (LGGs) demonstrated a duplication in 7q34, which resulted in a KIAA1549-BRAF fusion. Chromosome band 7q34 deletions, which resulted in a FAM131B-BRAF fusion, were identified in one pilocytic astrocytoma (PA) and one dysembryoplastic neuroepithelial tumor (DNT). One ganglioglioma (GG) demonstrated a 6q23.3q26 deletion that was predicted to result in a MYB-QKI fusion. Gains of chromosomes 5, 6, 7, 11, and 20 were seen in a subset of LGGs. Monosomy 6, deletion of 9q and 10q, and an i(17)(q10) were each detected in the medulloblastomas (MBs). Deletions and regions of loss of heterozygosity that encompassed TP53, RB1, CDKN2A/B, CHEK2, NF1, and NF2 were identified in a variety of tumors, which led to a recommendation for germline testing. A BRAF p.Thr599dup or p.V600E mutation was identified by Sanger sequencing in one and five gliomas, respectively, and a somatic TP53 mutation was identified in a fibrillary astrocytoma. No TP53 hot-spot mutations were detected in the MBs. SNP array analysis of pediatric brain tumors can be combined with pathologic examination and molecular analyses to further refine diagnoses, offer more accurate prognostic assessments, and identify patients who should be referred for cancer risk assessment.\",\n \"corpus_id\": 22298017,\n \"score\": 2\n },\n {\n \"doc_id\": \"24959384\",\n \"title\": \"Genome-wide copy number analysis in pediatric glioblastoma multiforme.\",\n \"abstract\": \"Glioblastoma (GBM) is a very aggressive and lethal brain tumor with poor prognosis. Despite new treatment strategies, patients' median survival is still less than 1 year in most cases. Few studies have focused exclusively on this disease in children and most of our understanding of the disease process and its clinical outcome has come from studies on malignant gliomas in childhood, combining children with the diagnosis of GBM with other pediatric patients harboring high grade malignant tumors other than GBM. In this study we investigated, using array-CGH platforms, children (median age of 9 years) affected by GBM (WHO-grade IV). We identified recurrent Copy Number Alterations demonstrating that different chromosome regions are involved, in various combinations. These observations suggest a condition of strong genomic instability. Since cancer is an acquired disease and inherited factors play a significant role, we compared for the first time the constitutional Copy Number Variations with the Copy Number Alterations found in tumor biopsy. We speculate that genes included in the recurrent 9p21.3 and 16p13.3 deletions and 1q32.1-q44 duplication play a crucial role for tumorigenesis and/or progression. In particular we suggest that the A2BP1 gene (16p13.3) is one possible culprit of the disease. Given the rarity of the disease, the poor quality and quantity of bioptic material and the scarcity of data in the literature, our findings may better elucidate the genomic background of these tumors. The recognition of candidate genes underlying this disease could then improve treatment strategies for this devastating tumor.\",\n \"corpus_id\": 7998376,\n \"score\": 2\n },\n {\n \"doc_id\": \"25626406\",\n \"title\": \"Clinical actionability enhanced through deep targeted sequencing of solid tumors.\",\n \"abstract\": \"BACKGROUND: Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is present and whether it may affect clinical decision-making. To study this question, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples. METHODS: We assayed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer-related genes. Mutations, indels, and copy number data were reported. RESULTS: We obtained a 1000-fold mean sequencing depth and identified 4794 nonsynonymous mutations in the samples analyzed, of which 15.2% were present at <10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) otherwise would have been unactionable. In addition, acquiring ultrahigh depth also ensured a low false discovery rate (<2.2%) from FFPE samples. CONCLUSIONS: Our results were as accurate as a commercially available CLIA-compliant hotspot panel but allowed the detection of a higher number of mutations in actionable genes. Our study reveals the critical importance of acquiring and utilizing high sequencing depth in profiling clinical tumor samples and presents a very useful platform for implementing routine sequencing in a cancer care institution.\",\n \"corpus_id\": 8474215,\n \"score\": 2\n },\n {\n \"doc_id\": \"25754088\",\n \"title\": \"Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma.\",\n \"abstract\": \"BACKGROUND: Multidimensional genotyping of formalin-fixed paraffin-embedded (FFPE) samples has the potential to improve diagnostics and clinical trials for brain tumors, but prospective use in the clinical setting is not yet routine. We report our experience with implementing a multiplexed copy number and mutation-testing program in a diagnostic laboratory certified by the Clinical Laboratory Improvement Amendments. METHODS: We collected and analyzed clinical testing results from whole-genome array comparative genomic hybridization (OncoCopy) of 420 brain tumors, including 148 glioblastomas. Mass spectrometry-based mutation genotyping (OncoMap, 471 mutations) was performed on 86 glioblastomas. RESULTS: OncoCopy was successful in 99% of samples for which sufficient DNA was obtained (n = 415). All clinically relevant loci for glioblastomas were detected, including amplifications (EGFR, PDGFRA, MET) and deletions (EGFRvIII, PTEN, 1p/19q). Glioblastoma patients ≤40 years old had distinct profiles compared with patients >40 years. OncoMap testing reliably identified mutations in IDH1, TP53, and PTEN. Seventy-seven glioblastoma patients enrolled on trials, of whom 51% participated in targeted therapeutic trials where multiplex data informed eligibility or outcomes. Data integration identified patients with complete tumor suppressor inactivation, albeit rarely (5% of patients) due to lack of whole-gene coverage in OncoMap. CONCLUSIONS: Combined use of multiplexed copy number and mutation detection from FFPE samples in the clinical setting can efficiently replace singleton tests for clinical diagnosis and prognosis in most settings. Our results support incorporation of these assays into clinical trials as integral biomarkers and their potential to impact interpretation of results. Limited tumor suppressor variant capture by targeted genotyping highlights the need for whole-gene sequencing in glioblastoma.\",\n \"corpus_id\": 24699053,\n \"score\": 2\n },\n {\n \"doc_id\": \"26681766\",\n \"title\": \"Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors.\",\n \"abstract\": \"BACKGROUND: Identification of genetic changes in CNS tumors is important for the appropriate clinical management of patients. Our objective was to develop a next-generation sequencing (NGS) assay for simultaneously detecting the various types of genetic alterations characteristic for adult and pediatric CNS tumors that can be applied to small brain biopsies. METHODS: We report an amplification-based targeted NGS assay (GlioSeq) that analyzes 30 genes for single nucleotide variants (SNVs) and indels, 24 genes for copy number variations (CNVs), and 14 types of structural alterations in BRAF, EGFR, and FGFR3 genes in a single workflow. GlioSeq performance was evaluated in 54 adult and pediatric CNS tumors, and the results were compared with fluorescence in-situ hybridization, Sanger sequencing, and reverse transcription PCR. RESULTS: GlioSeq correctly identified 71/71 (100%) genetic alterations known to be present by conventional techniques, including 56 SNVs/indels, 9 CNVs, 3 EGFRvIII, and 3 KIAA1549-BRAF fusions. Only 20 ng of DNA and 10 ng of RNA were required for successful sequencing of 100% frozen and 96% formalin-fixed, paraffin-embedded tissue specimens. The assay sensitivity was 3%-5% of mutant alleles for SNVs and 1%-5% for gene fusions. The most commonly detected alterations were IDH1, TP53, TERT, ATRX. CDKN2A, and PTEN in high-grade gliomas, followed by BRAF fusions in low-grade gliomas and H3F3A mutations in pediatric gliomas. CONCLUSIONS: GlioSeq NGS assay offers accurate and sensitive detection of a wide range of genetic alterations in a single workflow. It allows rapid and cost-effective profiling of brain tumor specimens and thus provides valuable information for patient management.\",\n \"corpus_id\": 1938530,\n \"score\": 2\n },\n {\n \"doc_id\": \"26794043\",\n \"title\": \"Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.\",\n \"abstract\": \"In the pediatric cancer neuroblastoma, analysis of recurrent chromosomal aberrations such as loss of chromosome 1p, 11q, gain of 17q and MYCN amplification are used for patient stratification and subsequent therapy decision making. Different analysis techniques have been used for detection of segmental abnormalities, including fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH)-microarrays and multiplex ligation-dependent probe amplification (MLPA). However, as next-generation sequencing becomes available for clinical use, this technique could also be used for assessment of copy number alterations simultaneously with mutational analysis. In this study we compare genomic profiles generated through exome sequencing data with profiles generated from high resolution Affymetrix single nucleotide polymorphism (SNP) microarrays on 30 neuroblastoma tumors of different stages. Normalized coverage reads for tumors were calculated using Control-FREEC software and visualized through a web based Shiny application, prior to comparison with corresponding SNP-microarray data. The two methods show high-level agreement for breakpoints and copy number of larger segmental aberrations and numerical aneuploidies. However, several smaller gene containing deletions that could not readily be detected through the SNP-microarray analyses were identified through exome profiling, most likely due to difference between spatial distribution of microarray probes and targeted regions of the exome capture. These smaller aberrations included focal ATRX deletion in two tumors and three cases of novel deletions in chromosomal region 19q13.2 causing homozygous loss of multiple genes including the CIC (Capicua) gene. In conclusion, genomic profiles generated from normalized coverage of exome sequencing show concordance with SNP microarray generated genomic profiles. Exome sequencing is therefore a useful diagnostic tool for copy number variant (CNV) detection in neuroblastoma tumors, especially considering the combination with mutational screening. This enables detection of theranostic targets such as ALK and ATRX together with detection of significant segmental aneuploidies, such as 2p-gain, 17q-gain, 11q-deletion as well as MYCN amplification.\",\n \"corpus_id\": 207753089,\n \"score\": 2\n },\n {\n \"doc_id\": \"26994145\",\n \"title\": \"MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research.\",\n \"abstract\": \"PURPOSE: We undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers to determine the feasibility of genome-guided precision therapy. EXPERIMENTAL DESIGN: Patients with non-central nervous system solid tumors underwent a combination of whole exome sequencing (WES), whole transcriptome sequencing (WTS), and high-density single-nucleotide polymorphism array analysis of the tumor, with WES of matched germline DNA. Clinically actionable alterations were identified as a reportable germline mutation, a diagnosis change, or a somatic event (including a single nucleotide variant, an indel, an amplification, a deletion, or a fusion gene), which could be targeted with drugs in existing clinical trials or with FDA-approved drugs. RESULTS: Fifty-nine patients in 20 diagnostic categories were enrolled from 2010 to 2014. Ages ranged from 7 months to 25 years old. Seventy-three percent of the patients had prior chemotherapy, and the tumors from these patients with relapsed or refractory cancers had a higher mutational burden than that reported in the literature. Thirty patients (51% of total) had clinically actionable mutations, of which 24 (41%) had a mutation that was currently targetable in a clinical trial setting, 4 patients (7%) had a change in diagnosis, and 7 patients (12%) had a reportable germline mutation. CONCLUSIONS: We found a remarkably high number of clinically actionable mutations in 51% of the patients, and 12% with significant germline mutations. We demonstrated the clinical feasibility of next-generation sequencing in a diverse population of relapsed and refractory pediatric solid tumors. Clin Cancer Res; 22(15); 3810-20. ©2016 AACR.\",\n \"corpus_id\": 23308352,\n \"score\": 2\n },\n {\n \"doc_id\": \"27026619\",\n \"title\": \"IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.\",\n \"abstract\": \"OBJECTIVE: Currently, there is a disconnect between finding a patient's relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics. METHODS AND MATERIALS: The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment. RESULTS: IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies. CONCLUSION: IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine. IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT.\",\n \"corpus_id\": 10050676,\n \"score\": 2\n },\n {\n \"doc_id\": \"27167109\",\n \"title\": \"A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine.\",\n \"abstract\": \"Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed. We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers. The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens.\",\n \"corpus_id\": 14194200,\n \"score\": 2\n },\n {\n \"doc_id\": \"27245685\",\n \"title\": \"Development and clinical application of an integrative genomic approach to personalized cancer therapy.\",\n \"abstract\": \"BACKGROUND: Personalized therapy provides the best outcome of cancer care and its implementation in the clinic has been greatly facilitated by recent convergence of enormous progress in basic cancer research, rapid advancement of new tumor profiling technologies, and an expanding compendium of targeted cancer therapeutics. METHODS: We developed a personalized cancer therapy (PCT) program in a clinical setting, using an integrative genomics approach to fully characterize the complexity of each tumor. We carried out whole exome sequencing (WES) and single-nucleotide polymorphism (SNP) microarray genotyping on DNA from tumor and patient-matched normal specimens, as well as RNA sequencing (RNA-Seq) on available frozen specimens, to identify somatic (tumor-specific) mutations, copy number alterations (CNAs), gene expression changes, gene fusions, and also germline variants. To provide high sensitivity in known cancer mutation hotspots, Ion AmpliSeq Cancer Hotspot Panel v2 (CHPv2) was also employed. We integrated the resulting data with cancer knowledge bases and developed a specific workflow for each cancer type to improve interpretation of genomic data. RESULTS: We returned genomics findings to 46 patients and their physicians describing somatic alterations and predicting drug response, toxicity, and prognosis. Mean 17.3 cancer-relevant somatic mutations per patient were identified, 13.3-fold, 6.9-fold, and 4.7-fold more than could have been detected using CHPv2, Oncomine Cancer Panel (OCP), and FoundationOne, respectively. Our approach delineated the underlying genetic drivers at the pathway level and provided meaningful predictions of therapeutic efficacy and toxicity. Actionable alterations were found in 91 % of patients (mean 4.9 per patient, including somatic mutations, copy number alterations, gene expression alterations, and germline variants), a 7.5-fold, 2.0-fold, and 1.9-fold increase over what could have been uncovered by CHPv2, OCP, and FoundationOne, respectively. The findings altered the course of treatment in four cases. CONCLUSIONS: These results show that a comprehensive, integrative genomic approach as outlined above significantly enhanced genomics-based PCT strategies.\",\n \"corpus_id\": 12296984,\n \"score\": 2\n },\n {\n \"doc_id\": \"28007021\",\n \"title\": \"Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations.\",\n \"abstract\": \"BACKGROUND: Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. METHODS: The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient's electronic medical record. RESULTS: NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. CONCLUSIONS: Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.\",\n \"corpus_id\": 8576826,\n \"score\": 2\n },\n {\n \"doc_id\": \"28453743\",\n \"title\": \"Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy.\",\n \"abstract\": \"Background: Molecular profiling is revolutionizing cancer diagnostics and leading to personalized therapeutic approaches. Herein we describe our clinical experience performing targeted sequencing for 31 pediatric neuro-oncology patients. Methods: We sequenced 510 cancer-associated genes from tumor and peripheral blood to identify germline and somatic mutations, structural variants, and copy number changes. Results: Genomic profiling was performed on 31 patients with tumors including 11 high-grade gliomas, 8 medulloblastomas, 6 low-grade gliomas, 1 embryonal tumor with multilayered rosettes, 1 pineoblastoma, 1 uveal ganglioneuroma, 1 choroid plexus carcinoma, 1 chordoma, and 1 high-grade neuroepithelial tumor. In 25 cases (81%), results impacted patient management by: (i) clarifying diagnosis, (ii) identifying pathogenic germline mutations, or (iii) detecting potentially targetable alterations. The pathologic diagnosis was amended after genomic profiling for 6 patients (19%), including a high-grade glioma to pilocytic astrocytoma, medulloblastoma to pineoblastoma, ependymoma to high-grade glioma, and medulloblastoma to CNS high-grade neuroepithelial tumor with BCOR alteration. Multiple patients had pathogenic germline mutations, many of which were previously unsuspected. Potentially targetable alterations were identified in 19 patients (61%). Additionally, novel likely pathogenic alterations were identified in 3 cases: an in-frame RAF1 fusion in a BRAF wild-type pleomorphic xanthoastrocytoma, an inactivating ASXL1 mutation in a histone H3 wild-type diffuse pontine glioma, and an in-frame deletion within exon 2 of MAP2K1 in a low-grade astrocytic neoplasm. Conclusions: Our experience demonstrates the significant impact of molecular profiling on diagnosis and treatment of pediatric brain tumors and confirms its feasibility for use at the time of diagnosis or recurrence.\",\n \"corpus_id\": 3917526,\n \"score\": 2\n },\n {\n \"doc_id\": \"28567303\",\n \"title\": \"Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.\",\n \"abstract\": \"The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.\",\n \"corpus_id\": 8998250,\n \"score\": 2\n },\n {\n \"doc_id\": \"28574513\",\n \"title\": \"Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.\",\n \"abstract\": \"PURPOSE: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10-20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. METHODS: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. RESULTS: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to -5.8% per disorder). CONCLUSIONS: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28597942\",\n \"title\": \"Copy number alterations determined by single nucleotide polymorphism array testing in the clinical laboratory are indicative of gene fusions in pediatric cancer patients.\",\n \"abstract\": \"Gene fusions resulting from structural rearrangements are an established mechanism of tumorigenesis in pediatric cancer. In this clinical cohort, 1,350 single nucleotide polymorphism (SNP)-based chromosomal microarrays from 1,211 pediatric cancer patients were evaluated for copy number alterations (CNAs) associated with gene fusions. Karyotype or fluorescence in situ hybridization studies were performed in 42% of the patients. Ten percent of the bone marrow or solid tumor specimens had SNP array-associated CNAs suggestive of a gene fusion. Alterations involving ETV6, ABL1-NUP214, EBF1-PDGFRB, KMT2A(MLL), LMO2-RAG, MYH11-CBFB, NSD1-NUP98, PBX1, STIL-TAL1, ZNF384-TCF3, P2RY8-CRLF2, and RUNX1T1-RUNX1 fusions were detected in the bone marrow samples. The most common alteration among the low-grade gliomas was a 7q34 tandem duplication resulting in a KIAA1549-BRAF fusion. Additional fusions identified in the pediatric brain tumors included FAM131B-BRAF and RAF1-QKI. COL1A1-PDGFB, CRTC1-MAML2, EWSR1, HEY1, PAX3- and PAX7-FOXO1, and PLAG1 fusions were determined in a variety of solid tumors and a novel potential gene fusion, FGFR1-USP6, was detected in an aneurysmal bone cyst. The identification of these gene fusions was instrumental in tumor diagnosis. In contrast to hematologic and solid tumors in adults that are predominantly driven by mutations, the majority of hematologic and solid tumors in children are characterized by CNAs and gene fusions. Chromosomal microarray analysis is therefore a robust platform to identify diagnostic and prognostic markers in the clinical setting.\",\n \"corpus_id\": 4452423,\n \"score\": 2\n },\n {\n \"doc_id\": \"28638988\",\n \"title\": \"Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.\",\n \"abstract\": \"Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It outperforms hybridization-based and current sequencing technologies with respect to time to diagnosis and required laboratory equipment and expertise, aiming to make precision medicine possible for every cancer patient, even in resource-restricted settings.\",\n \"corpus_id\": 2065740,\n \"score\": 2\n },\n {\n \"doc_id\": \"28640705\",\n \"title\": \"Genomic Analysis of Childhood Brain Tumors: Methods for Genome-Wide Discovery and Precision Medicine Become Mainstream.\",\n \"abstract\": \"Recent breakthroughs in next-generation sequencing technology and complementary genomic platforms have transformed our capacity to interrogate the molecular landscapes of human cancers, including childhood brain tumors. Numerous high-throughput genomic studies have been reported for the major histologic brain tumor entities diagnosed in children, including interrogations at the level of the genome, epigenome, and transcriptome, many of which have yielded essential new insights into disease biology. The nature of these discoveries has been largely platform dependent, exemplifying the usefulness of applying different genomic and computational strategies, or integrative approaches, to address specific biologic and/or clinical questions. The goal of this article is to summarize the spectrum of molecular profiling methods available for investigating genomic aspects of childhood brain tumors in both the research and the clinical setting. We provide an overview of the main next-generation sequencing and array-based technologies currently being applied in this field and draw from key examples in the recent neuro-oncology literature to illustrate how these genomic approaches have profoundly advanced our understanding of individual tumor entities. Moreover, we discuss the current status of genomic profiling in the clinic and how different platforms are being used to improve patient diagnosis and stratification, as well as to identify actionable targets for informing molecularly guided therapies, especially for patients for whom conventional standard-of-care treatments have failed. Both the demand for genomic testing and the main challenges associated with incorporating genomics into the clinical management of pediatric patients with brain tumors are discussed, as are recommendations for incorporating these assays into future clinical trials.\",\n \"corpus_id\": 29219175,\n \"score\": 2\n },\n {\n \"doc_id\": \"28844173\",\n \"title\": \"Clinical Application of Whole Genome Array Improves the Diagnosis of Pediatric Brain Tumors.\",\n \"abstract\": \"Pediatric brain tumors are the leading cause of childhood cancer mortality. Recurring genetic abnormalities play an essential role in the diagnosis and prognosis of pediatric brain tumors. However, clinical workup has not routinely included whole genome assessment. Here, we present high resolution whole genome array results in 11 pediatric brain tumors. Array identified clinically relevant abnormalities in all samples. Copy number aberrations with targeted therapy implication, GOPC-ROS1 fusion, CDK4 amplification, and NF1 deletion, were detected in 3 cases. In addition, array detected recurring genetic abnormalities, including KIAA1549-BRAF fusion, 19q13.42 amplification, i(17q), and monosomy 6, which assisted accurate histological diagnosis in pediatric brain tumors. In conclusion, our results show that whole genome high-resolution array detects diagnostic and treatment-relevant copy number abnormalities in pediatric brain tumors.\",\n \"corpus_id\": 32741163,\n \"score\": 2\n },\n {\n \"doc_id\": \"28912153\",\n \"title\": \"Comprehensive Genomic Profiling of 282 Pediatric Low- and High-Grade Gliomas Reveals Genomic Drivers, Tumor Mutational Burden, and Hypermutation Signatures.\",\n \"abstract\": \"BACKGROUND: Pediatric brain tumors are the leading cause of death for children with cancer in the U.S. Incorporating next-generation sequencing data for both pediatric low-grade (pLGGs) and high-grade gliomas (pHGGs) can inform diagnostic, prognostic, and therapeutic decision-making. MATERIALS AND METHODS: We performed comprehensive genomic profiling on 282 pediatric gliomas (157 pHGGs, 125 pLGGs), sequencing 315 cancer-related genes and calculating the tumor mutational burden (TMB; mutations per megabase [Mb]). RESULTS: In pLGGs, we detected genomic alterations (GA) in 95.2% (119/125) of tumors. BRAF was most frequently altered (48%; 60/125), and FGFR1 missense (17.6%; 22/125), NF1 loss of function (8.8%; 11/125), and TP53 (5.6%; 7/125) mutations were also detected. Rearrangements were identified in 35% of pLGGs, including KIAA1549-BRAF, QKI-RAF1, FGFR3-TACC3, CEP85L-ROS1, and GOPC-ROS1 fusions. Among pHGGs, GA were identified in 96.8% (152/157). The genes most frequently mutated were TP53 (49%; 77/157), H3F3A (37.6%; 59/157), ATRX (24.2%; 38/157), NF1 (22.2%; 35/157), and PDGFRA (21.7%; 34/157). Interestingly, most H3F3A mutations (81.4%; 35/43) were the variant K28M. Midline tumor analysis revealed H3F3A mutations (40%; 40/100) consisted solely of the K28M variant. Pediatric high-grade gliomas harbored oncogenic EML4-ALK, DGKB-ETV1, ATG7-RAF1, and EWSR1-PATZ1 fusions. Six percent (9/157) of pHGGs were hypermutated (TMB >20 mutations per Mb; range 43-581 mutations per Mb), harboring mutations deleterious for DNA repair in MSH6, MSH2, MLH1, PMS2, POLE, and POLD1 genes (78% of cases). CONCLUSION: Comprehensive genomic profiling of pediatric gliomas provides objective data that promote diagnostic accuracy and enhance clinical decision-making. Additionally, TMB could be a biomarker to identify pediatric glioblastoma (GBM) patients who may benefit from immunotherapy. IMPLICATIONS FOR PRACTICE: By providing objective data to support diagnostic, prognostic, and therapeutic decision-making, comprehensive genomic profiling is necessary for advancing care for pediatric neuro-oncology patients. This article presents the largest cohort of pediatric low- and high-grade gliomas profiled by next-generation sequencing. Reportable alterations were detected in 95% of patients, including diagnostically relevant lesions as well as novel oncogenic fusions and mutations. Additionally, tumor mutational burden (TMB) is reported, which identifies a subpopulation of hypermutated glioblastomas that harbor deleterious mutations in DNA repair genes. This provides support for TMB as a potential biomarker to identify patients who may preferentially benefit from immune checkpoint inhibitors.\",\n \"corpus_id\": 29864055,\n \"score\": 2\n },\n {\n \"doc_id\": \"29285848\",\n \"title\": \"Implementation of \\\"clinical sequencing\\\" in cancer genome medicine in Japan.\",\n \"abstract\": \"In oncology, actionable mutations (alterations) in cancer-associated genes are critical in terms of the selection of therapeutic approaches. Next-generation sequencing of tumor sample DNA (ie, clinical sequencing) can guide clinical management by providing diagnostic or prognostic data, and facilitating the identification of potential treatment regimens, such as molecular-targeted and immune checkpoint blockade therapies. In the USA, a variety of tumor-profiling multiplex gene panels have been developed and implemented for this purpose. In Japan, several academic institutions have now carried out detailed investigations of the feasibility and value of clinical sequencing, and cancer societies have issued consensus clinical practice guidance for next-generation sequencing-based gene panel tests. These efforts will facilitate the implementation of cancer genome medicine in Japan.\",\n \"corpus_id\": 3749177,\n \"score\": 2\n },\n {\n \"doc_id\": \"19276269\",\n \"title\": \"Genomic analysis using high-density single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors.\",\n \"abstract\": \"PURPOSE: A high-resolution genomic profiling and comprehensive targeted analysis of INI1/SMARCB1 of a large series of pediatric rhabdoid tumors was done. The aim was to identify regions of copy number change and loss of heterozygosity (LOH) that might pinpoint additional loci involved in the development or progression of rhabdoid tumors and define the spectrum of genomic alterations of INI1 in this malignancy. EXPERIMENTAL DESIGN: A multiplatform approach using Illumina single nucleotide polymorphism-based oligonucleotide arrays, multiplex ligation-dependent probe amplification, fluorescence in situ hybridization, and coding sequence analysis was used to characterize genome-wide copy number changes, LOH, and genomic alterations of INI1/SMARCB1 in a series of pediatric rhabdoid tumors. RESULTS: The biallelic alterations of INI1 that led to inactivation were elucidated in 50 of 51 tumors. INI1 inactivation was shown by a variety of mechanisms, including deletions, mutations, and LOH. The results from the array studies highlighted the complexity of rearrangements of chromosome 22 compared with the low frequency of alterations involving the other chromosomes. CONCLUSIONS: The results from the genome-wide single nucleotide polymorphism array analysis suggest that INI1 is the primary tumor suppressor gene involved in the development of rhabdoid tumors with no second locus identified. In addition, we did not identify hotspots for the breakpoints in sporadic tumors with deletions of chromosome 22q11.2. By employing a multimodality approach, the wide spectrum of alterations of INI1 can be identified in the majority of patients, which increases the clinical utility of molecular diagnostic testing.\",\n \"corpus_id\": 7290742,\n \"score\": 1\n },\n {\n \"doc_id\": \"22131877\",\n \"title\": \"Detection of somatic copy number alterations in cancer using targeted exome capture sequencing.\",\n \"abstract\": \"The research community at large is expending considerable resources to sequence the coding region of the genomes of tumors and other human diseases using targeted exome capture (i.e., \\\"whole exome sequencing\\\"). The primary goal of targeted exome sequencing is to identify nonsynonymous mutations that potentially have functional consequences. Here, we demonstrate that whole-exome sequencing data can also be analyzed for comprehensively monitoring somatic copy number alterations (CNAs) by benchmarking the technique against conventional array CGH. A series of 17 matched tumor and normal tissues from patients with metastatic castrate-resistant prostate cancer was used for this assessment. We show that targeted exome sequencing reliably identifies CNAs that are common in advanced prostate cancer, such as androgen receptor (AR) gain and PTEN loss. Taken together, these data suggest that targeted exome sequencing data can be effectively leveraged for the detection of somatic CNAs in cancer.\",\n \"corpus_id\": 27717232,\n \"score\": 1\n },\n {\n \"doc_id\": \"22140474\",\n \"title\": \"Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.\",\n \"abstract\": \"Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications.\",\n \"corpus_id\": 834007,\n \"score\": 1\n },\n {\n \"doc_id\": \"22313367\",\n \"title\": \"Genome-wide copy number analysis in primary breast cancer.\",\n \"abstract\": \"INTRODUCTION: Carcinogenesis is considered to be a multistep process that may involve cumulative genomic alterations. Loss of chromosomal material would inactivate tumor suppressor genes and gain of chromosomal material has the potential to activate tumor-promoting genes. AREAS COVERED: Recent intensive studies by array comparative genomic hybridization (aCGH) have demonstrated frequent alterations in multiple regions of the genome. This suggests that these regions contain a variety of oncogenes and tumor suppressor genes associated with breast cancer development. The patterns of copy number variations (CNVs) have been suggested to be associated with breast cancer subtypes, indicating the importance of genomic instability in the development of breast cancer. EXPERT OPINION: To further clarify the complexity of gene alterations, one approach is to employ a CNV-targeted platform that harbors a large number of direct CNV markers located in the repeat-rich unstable regions of the human genome. Next generation sequencing is another approach to overcome the limitations of aCGH such as the repeat-rich regions. Genomic analysis should be combined with expression analysis to elucidate individual genes relevant to breast cancer development and progression. The elucidation of the functions of the affected genes would lead to identification of new molecular targets for breast cancer eradication.\",\n \"corpus_id\": 3254274,\n \"score\": 1\n },\n {\n \"doc_id\": \"23284693\",\n \"title\": \"Estimation of copy number alterations from exome sequencing data.\",\n \"abstract\": \"Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.\",\n \"corpus_id\": 14457367,\n \"score\": 1\n },\n {\n \"doc_id\": \"23893877\",\n \"title\": \"Detection of clinically relevant copy number variants with whole-exome sequencing.\",\n \"abstract\": \"Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. This has resulted in the widespread application of genomic microarrays as a first-tier diagnostic tool for CNV detection. More recently, whole-exome sequencing (WES) has been proven successful for the detection of clinically relevant point mutations and small insertion-deletions exome wide. We evaluate the utility of short-read WES (SOLiD 5500xl) to detect clinically relevant CNVs in DNA from 10 patients with intellectual disability and compare these results to data from two independent high-resolution microarrays. Eleven of the 12 clinically relevant CNVs were detected via read-depth analysis of WES data; a heterozygous single-exon deletion remained undetected by all algorithms evaluated. Although the detection power of WES for small CNVs currently does not match that of high-resolution microarray platforms, we show that the majority (88%) of rare coding CNVs containing three or more exons are successfully identified by WES. These results show that the CNV detection resolution of WES is comparable to that of medium-resolution genomic microarrays commonly used as clinical assays. The combined detection of point mutations, indels, and CNVs makes WES a very attractive first-tier diagnostic test for genetically heterogeneous disorders.\",\n \"corpus_id\": 7491601,\n \"score\": 1\n },\n {\n \"doc_id\": \"24634382\",\n \"title\": \"Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment.\",\n \"abstract\": \"BACKGROUND: Current technology permits an unbiased massive analysis of somatic genetic alterations from tumor DNA as well as the generation of individualized mouse xenografts (Avatar models). This work aimed to evaluate our experience integrating these two strategies to personalize the treatment of patients with cancer. METHODS: We performed whole-exome sequencing analysis of 25 patients with advanced solid tumors to identify putatively actionable tumor-specific genomic alterations. Avatar models were used as an in vivo platform to test proposed treatment strategies. RESULTS: Successful exome sequencing analyses have been obtained for 23 patients. Tumor-specific mutations and copy-number variations were identified. All samples profiled contained relevant genomic alterations. Tumor was implanted to create an Avatar model from 14 patients and 10 succeeded. Occasionally, actionable alterations such as mutations in NF1, PI3KA, and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and, accordingly, treatment of the patients with these drugs was not effective. To date, 13 patients have received a personalized treatment and 6 achieved durable partial remissions. Prior testing of candidate treatments in Avatar models correlated with clinical response and helped to select empirical treatments in some patients with no actionable mutations. CONCLUSION: The use of full genomic analysis for cancer care is encouraging but presents important challenges that will need to be solved for broad clinical application. Avatar models are a promising investigational platform for therapeutic decision making. While limitations still exist, this strategy should be further tested.\",\n \"corpus_id\": 11008577,\n \"score\": 1\n },\n {\n \"doc_id\": \"24710307\",\n \"title\": \"A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practice.\",\n \"abstract\": \"The aim of this study was to assess the frequency of potentially actionable genomic alterations in breast cancer that could be targeted with approved agents or investigational drugs in clinical trials using a next-generation sequencing-based genomic profiling assay performed in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited commercial laboratory. Methods. Fifty-one breast cancers were analyzed, including primary tumor biopsies of 33 stage I-II and 18 stage IV cancers (13 soft tissue, 3 liver, and 2 bone metastases). We assessed 3,230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was 1,154×. Results. We observed 158 genomic alterations in 55 genes in 48 of 51 (94%) tumors (mean 3.1, range 0-9). The average number of potentially therapeutically relevant alterations was similar in primary (1.6, range 0-4) and in heavily pretreated metastatic cancers (2.0, range 0-4) (p = .24). The most common actionable alterations were in PIK3CA (n = 9, phosphatidylinositol 3-kinase [PI3K]/mammalian target of rapamycin [mTOR] inhibitors), NF1 (n = 7, PI3K/mTOR/mitogen-activated protein kinase inhibitors), v-akt murine thymoma viral oncogene homolog 1-3 (n = 7, PI3K/mTOR/AKT inhibitors), BRCA1/2 (n = 6, poly[ADP-ribose] polymerase inhibitors), and CCND1,2 and CCNE (n = 8)/cycline dependent kinase (CDK)6 (n = 1) (CDK4/6 inhibitors), KIT (n = 1, imatinib/sunitinib), ALK (n = 1, crizotinib), FGFR1,2 (n = 5, fibroblast growth factor receptor inhibitors), and EGFR (n = 2, epidermal growth factor receptor inhibitors). Our sequencing assay also correctly identified all six cases with HER2 (ERBB2) amplification by fluorescence in situ hybridization when tumor content was adequate. In addition, two known activating HER2 mutations were identified, both in unamplified cases. Conclusion. Overall, 84% of cancers harbored at least one genomic alteration linked to potential treatment options. Systematic evaluation of the predictive value of these genomic alterations is critically important for further progress in this field.\",\n \"corpus_id\": 21190797,\n \"score\": 1\n },\n {\n \"doc_id\": \"25356966\",\n \"title\": \"Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort.\",\n \"abstract\": \"PURPOSE: Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. METHODS: Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. RESULTS: In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. CONCLUSION: These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array. Genet Med 17 8, 623-629.\",\n \"corpus_id\": 21899706,\n \"score\": 1\n },\n {\n \"doc_id\": \"26088785\",\n \"title\": \"Exome sequencing and whole genome sequencing for the detection of copy number variation.\",\n \"abstract\": \"Many laboratories now use genomic microarrays as their first-tier diagnostic test for copy number variation (CNV) detection. In addition, whole exome sequencing is increasingly being offered as a diagnostic test for heterogeneous disorders. Although mostly used for the detection of point mutations and small insertion-deletions, exome sequencing can also be used to call CNVs, allowing combined small and large variant analysis. Whole genome sequencing in addition to these advantages also offers the potential to characterize CNVs to unprecedented levels of accuracy, providing position and orientation information. In this review, we discuss the clinical potential of CNV identification in whole exome sequencing and whole genome sequencing data and the implications this has on diagnostic laboratories.\",\n \"corpus_id\": 6979431,\n \"score\": 1\n },\n {\n \"doc_id\": \"26181256\",\n \"title\": \"Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.\",\n \"abstract\": \"IMPORTANCE: Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer. OBJECTIVE: To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response. DESIGN, SETTING, AND PATIENTS: Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response. MAIN OUTCOMES AND MEASURES: Feasibility, use of WES for decision making, and identification of novel biomarkers. RESULTS: A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95X and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response. CONCLUSIONS AND RELEVANCE: The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.\",\n \"corpus_id\": 205126404,\n \"score\": 1\n },\n {\n \"doc_id\": \"26598538\",\n \"title\": \"Seeking the driver in tumours with apparent normal molecular profile on comparative genomic hybridization and targeted gene panel sequencing: what is the added value of whole exome sequencing?\",\n \"abstract\": \"BACKGROUND: Molecular tumour profiling technologies have become increasingly important in the era of precision medicine, but their routine use is limited by their accessibility, cost, and tumour material availability. It is therefore crucial to assess their relative added value to optimize the sequence and combination of such technologies. PATIENTS AND METHODS: Within the MOSCATO-01 trial, we investigated the added value of whole exome sequencing (WES) in patients that did not present any molecular abnormality on array comparative genomic hybridization (aCGH) and targeted gene panel sequencing (TGPS) using cancer specific panels. The pathogenicity potential and actionability of mutations detected on WES was assessed. RESULTS: Among 420 patients enrolled between December 2011 and December 2013, 283 (67%) patients were analysed for both TGPS and aCGH. The tumour sample of 25 (8.8%) of them presented a flat (or low-dynamic) aCGH profile and no pathogenic mutation on TGPS. We selected the first eligible 10 samples-corresponding to a heterogeneous cohort of different tumour types-to perform WES. This allowed identifying eight mutations of interest in two patients: FGFR3, PDGFRB, and CREBBP missense single-nucleotide variants (SNVs) in an urothelial carcinoma; FGFR2, FBXW7, TP53, and MLH1 missense SNVs as well as an ATM frameshift mutation in a squamous cell carcinoma of the tongue. The FGFR3 alteration had been previously described as an actionable activating mutation and might have resulted in treatment by an FGFR inhibitor. CREBBP and ATM alterations might also have suggested a therapeutic orientation towards epigenetic modifiers and ataxia-telangectasia and Rad3-related inhibitors, respectively. CONCLUSION: The therapeutic added value of performing WES on tumour samples that do not harbour any genetic abnormality on TGPS and aCGH might be limited and variable according to the histotype. Alternative techniques, including RNASeq and methylome analysis, might be more informative in selected cases.\",\n \"corpus_id\": 4679077,\n \"score\": 1\n },\n {\n \"doc_id\": \"26662885\",\n \"title\": \"Application of whole-exome sequencing for detecting copy number variants in CMT1A/HNPP.\",\n \"abstract\": \"Large insertions and deletions (indels), including copy number variations (CNVs), are commonly seen in many diseases. Standard approaches for indel detection rely on well-established methods such as qPCR or short tandem repeat (STR) markers. Recently, a number of tools for CNV detection based on next-generation sequencing (NGS) data have also been developed; however, use of these methods is limited. Here, we used whole-exome sequencing (WES) in patients previously diagnosed with CMT1A or HNPP using STR markers to evaluate the ability of WES to improve the clinical diagnosis. Patients were evaluated utilizing three CNV detection tools including CONIFER, ExomeCNV and CEQer, and array comparative genomic hybridization (aCGH). We identified a breakpoint region at 17p11.2-p12 in patients with CMT1A and HNPP. CNV detection levels were similar in both 6 Gb (mean read depth=80×) and 17 Gb (mean read depth=190×) data. Taken together, these data suggest that 6 Gb WES data are sufficient to reveal the genetic causes of various diseases and can be used to estimate single mutations, indels, and CNVs simultaneously. Furthermore, our data strongly indicate that CNV detection by NGS is a rapid and cost-effective method for clinical diagnosis of genetically heterogeneous disorders such as CMT neuropathy.\",\n \"corpus_id\": 45479243,\n \"score\": 1\n },\n {\n \"doc_id\": \"27100738\",\n \"title\": \"CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.\",\n \"abstract\": \"Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.\",\n \"corpus_id\": 3651442,\n \"score\": 1\n },\n {\n \"doc_id\": \"27197880\",\n \"title\": \"Precision Oncology Medicine: The Clinical Relevance of Patient-Specific Biomarkers Used to Optimize Cancer Treatment.\",\n \"abstract\": \"Precision medicine in oncology is the result of an increasing awareness of patient-specific clinical features coupled with the development of genomic-based diagnostics and targeted therapeutics. Companion diagnostics designed for specific drug-target pairs were the first to widely utilize clinically applicable tumor biomarkers (eg, HER2, EGFR), directing treatment for patients whose tumors exhibit a mutation susceptible to an FDA-approved targeted therapy (eg, trastuzumab, erlotinib). Clinically relevant germline mutations in drug-metabolizing enzymes and transporters (eg, TPMT, DPYD) have been shown to impact drug response, providing a rationale for individualized dosing to optimize treatment. The use of multigene expression-based assays to analyze an array of prognostic biomarkers has been shown to help direct treatment decisions, especially in breast cancer (eg, Oncotype DX). More recently, the use of next-generation sequencing to detect many potential \\\"actionable\\\" cancer molecular alterations is further shifting the 1 gene-1 drug paradigm toward a more comprehensive, multigene approach. Currently, many clinical trials (eg, NCI-MATCH, NCI-MPACT) are assessing novel diagnostic tools with a combination of different targeted therapeutics while also examining tumor biomarkers that were previously unexplored in a variety of cancer histologies. Results from ongoing trials such as the NCI-MATCH will help determine the clinical utility and future development of the precision-medicine approach.\",\n \"corpus_id\": 19759664,\n \"score\": 1\n },\n {\n \"doc_id\": \"27425854\",\n \"title\": \"Genomic characterization of recurrent high-grade astroblastoma.\",\n \"abstract\": \"Astroblastomas are rare primary brain tumors, diagnosed based on histologic features. Not currently assigned a WHO grade, they typically display indolent behavior, with occasional variants taking a more aggressive course. We characterized the immunohistochemical characteristics, copy number (high-resolution array comparative genomic hybridization, OncoCopy) and mutational profile (targeted next-generation exome sequencing, OncoPanel) of a cohort of seven biopsies from four patients to identify recurrent genomic events that may help distinguish astroblastomas from other more common high-grade gliomas. We found that tumor histology was variable across patients and between primary and recurrent tumor samples. No common molecular features were identified among the four tumors. Mutations commonly observed in astrocytic tumors (IDH1/2, TP53, ATRX, and PTEN) or ependymoma were not identified. However one case with rapid clinical progression displayed mutations more commonly associated with GBM (NF1(N1054H/K63)*, PIK3CA(R38H) and ERG(A403T)). Conversely, another case, originally classified as glioblastoma with nine-year survival before recurrence, lacked a GBM mutational profile. Other mutations frequently seen in lower grade gliomas (BCOR, BCORL1, ERBB3, MYB, ATM) were also present in several tumors. Copy number changes were variable across tumors. Our findings indicate that astroblastomas have variable growth patterns and morphologic features, posing significant challenges to accurate classification in the absence of diagnostically specific copy number alterations and molecular features. Their histopathologic overlap with glioblastoma will likely confound the observation of long-term GBM \\\"survivors\\\". Further genomic profiling is needed to determine whether these tumors represent a distinct entity and to guide management strategies.\",\n \"corpus_id\": 32365824,\n \"score\": 1\n },\n {\n \"doc_id\": \"27440268\",\n \"title\": \"Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma.\",\n \"abstract\": \"PURPOSE: The tumor genomic copy number profile is of prognostic significance in neuroblastoma patients. We have studied the genomic copy number profile of cell-free DNA (cfDNA) and compared this with primary tumor arrayCGH (aCGH) at diagnosis. EXPERIMENTAL DESIGN: In 70 patients, cfDNA genomic copy number profiling was performed using the OncoScan platform. The profiles were classified according to the overall pattern, including numerical chromosome alterations (NCA), segmental chromosome alterations (SCA), and MYCN amplification (MNA). RESULTS: Interpretable and dynamic cfDNA profiles were obtained in 66 of 70 and 52 of 70 cases, respectively. An overall identical genomic profile between tumor aCGH and cfDNA was observed in 47 cases (3 NCAs, 22 SCAs, 22 MNAs). In one case, cfDNA showed an additional SCA not detected by tumor aCGH. In 4 of 8 cases with a silent tumor aCGH profile, cfDNA analysis revealed a dynamic profile (3 SCAs, 1 NCA). In 14 cases, cfDNA analysis did not reveal any copy number changes. A total of 378 breakpoints common to the primary tumor and cfDNA of any given patient were identified, 27 breakpoints were seen by tumor aCGH, and 54 breakpoints were seen in cfDNA only, including two cases with interstitial IGFR1 gains and two alterations targeting TERT CONCLUSIONS: These results demonstrate the feasibility of cfDNA copy number profiling in neuroblastoma patients, with a concordance of the overall genomic profile in aCGH and cfDNA dynamic cases of 97% and a sensitivity of 77%, respectively. Furthermore, neuroblastoma heterogeneity is highlighted, suggesting that cfDNA might reflect genetic alterations of more aggressive cell clones. Clin Cancer Res; 22(22); 5564-73. ©2016 AACRSee related commentary by Janku and Kurzrock, p. 5400.\",\n \"corpus_id\": 374560,\n \"score\": 1\n },\n {\n \"doc_id\": \"27765906\",\n \"title\": \"Targeted NGS, array-CGH, and patient-derived tumor xenografts for precision medicine in advanced breast cancer: a single-center prospective study.\",\n \"abstract\": \"BACKGROUND: Routine feasibility and clinical impact of genomics-based tumor profiling in advanced breast cancer (aBC) remains to be determined. We conducted a pilot study to evaluate whether precision medicine could be prospectively implemented for aBC patients in a single center and to examine whether patient-derived tumor xenografts (PDX) could be obtained in this population. RESULTS: Thirty-four aBC patients were included. Actionable targets were found in 28 patients (82%). A targeted therapy could be proposed to 22 patients (64%), either through a clinical trial (n=15) and/or using already registered drugs (n=21). Ten patients (29%) eventually received targeted treatment, 2 of them deriving clinical benefit. Of 22 patients subjected to mouse implantation, 10 had successful xenografting (45%), mostly in triple-negative aBC. METHODS: aBC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Genomic profiling was established by whole-genome array comparative genomic hybridization (aCGH) and targeted next-generation sequencing (NGS) of 365 candidate cancer genes. For a subset of patients, a sample of fresh tumor was orthotopically implanted in humanized cleared fat pads of NSG mice for establishing PDX. CONCLUSIONS: Precision medicine can be implemented in a single center in the context of clinical practice and may allow genomic-driven treatment in approximately 30% of aBC patients. PDX may be obtained in a significant fraction of cases.\",\n \"corpus_id\": 3447760,\n \"score\": 1\n },\n {\n \"doc_id\": \"28007036\",\n \"title\": \"Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine.\",\n \"abstract\": \"BACKGROUND: Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been limited to Western populations. In order to understand possible ethnic and geographic differences and to explore the broader application of CGS to other populations, we sequenced a panel of 415 important cancer genes to characterize clinically actionable genomic driver events in 201 Japanese patients with colorectal cancer (CRC). METHODS: Using next-generation sequencing methods, we examined all exons of 415 known cancer genes in Japanese CRC patients (n = 201) and evaluated for concordance among independent data obtained from US patients with CRC (n = 108) and from The Cancer Genome Atlas-CRC whole exome sequencing (WES) database (n = 224). Mutation data from non-hypermutated Japanese CRC patients were extracted and clustered by gene mutation patterns. Two different sets of genes from the 415-gene panel were used for clustering: 61 genes with frequent alteration in CRC and 26 genes that are clinically actionable in CRC. RESULTS: The 415-gene panel is able to identify all of the critical mutations in tumor samples as well as WES, including identifying hypermutated tumors. Although the overall mutation spectrum of the Japanese patients is similar to that of the Western population, we found significant differences in the frequencies of mutations in ERBB2 and BRAF. We show that the 415-gene panel identifies a number of clinically actionable mutations in KRAS, NRAS, and BRAF that are not detected by hot-spot testing. We also discovered that 26% of cases have mutations in genes involved in DNA double-strand break repair pathway. Unsupervised clustering revealed that a panel of 26 genes can be used to classify the patients into eight different categories, each of which can optimally be treated with a particular combination therapy. CONCLUSIONS: Use of a panel of 415 genes can reliably identify all of the critical mutations in CRC patients and this information of CGS can be used to determine the most optimal treatment for patients of all ethnicities.\",\n \"corpus_id\": 2480750,\n \"score\": 1\n },\n {\n \"doc_id\": \"28231819\",\n \"title\": \"Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies.\",\n \"abstract\": \"BACKGROUND: The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic options has been revived. Current data suggest that each tumor contains a unique set of mutations (mutanome), thus requiring the creation of individualized cancer vaccines. However, rigorous analysis of non-individualized cancer immunotherapy approaches across multiple cancer types and in the context of known driver alterations has yet to be reported. We therefore set out to determine the feasibility of a generalizable cancer vaccine strategy based on targeting multiple neoantigens in an HLA-A/B subtype-directed manner. METHODS: A cancer gene-focused, hybrid capture-based genomic analysis was performed on 63,220 unique tumors. Neoantigens were predicted using a combined peptide processing and MHC-I binding prediction tool (IEDB) for all recurrent (>10 tumors) missense alterations and non-frameshift indels for the two most common HLA-A/B subtypes in North American/European populations. RESULTS: Despite being overwhelmingly unique overall, many mutanomes (~45%) contain at least one mutation from a set of ten mutations chosen to maximize the number of unique tumors. This held true for tumors driven by KRAS G12C (n = 1799), PIK3CA E545K (n = 1713), or EGFR L858R (n = 478) alterations, which define distinct sample subsets. We therefore hypothesized that sets of carefully selected mutations/neoantigens may allow the development of broadly applicable semi-universal cancer vaccines. To test the feasibility of such an approach, antigen processing and MHC-I binding prediction was applied for HLA subtypes A*01:01/B*08:01 and A*02:01/B*44:02. In tumors with a specific HLA type, 0.7 and 2.5% harbored at least one of a set of ten neoantigens predicted to bind to each subtype, respectively. In comparison, KRAS G12C-driven tumors produced similar results (0.8 and 2.6% for each HLA subtype, respectively), indicating that neoantigen targets still remain highly diverse even within the context of major driver mutations. CONCLUSIONS: This \\\"best case scenario\\\" analysis of a large tumor set across multiple cancer types and in the context of driver alterations reveals that semi-universal, HLA-specific cancer vaccine strategies will be relevant to only a small subset of the general population. Similar analysis of whole exome/genome sequencing, although not currently feasible at scale in a clinical setting, will likely uncover further diversity.\",\n \"corpus_id\": 2426402,\n \"score\": 1\n },\n {\n \"doc_id\": \"28460482\",\n \"title\": \"Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data.\",\n \"abstract\": \"Accurate detection of copy number alterations (CNAs) using next-generation sequencing technology is essential for the development and application of more precise medical treatments for human cancer. Here, we evaluated seven CNA estimation tools (ExomeCNV, CoNIFER, VarScan2, CODEX, ngCGH, saasCNV, and falcon) using whole-exome sequencing data from 419 breast cancer tumor-normal sample pairs from The Cancer Genome Atlas. Estimations generated using each tool were converted into gene-based copy numbers; concordance for gains and losses and the sensitivity and specificity of each tool were compared to validated copy numbers from a single nucleotide polymorphism reference array. The concordance and sensitivity of the tumor-normal pair methods for estimating CNAs (saasCNV, ExomeCNV, and VarScan2) were better than those of the tumor batch methods (CoNIFER and CODEX). SaasCNV had the highest gain and loss concordances (65.0%), sensitivity (69.4%), and specificity (89.1%) for estimating copy number gains or losses. These findings indicate that improved CNA detection algorithms are needed to more accurately interpret whole-exome sequencing results in human cancer.\",\n \"corpus_id\": 3668344,\n \"score\": 1\n },\n {\n \"doc_id\": \"28554745\",\n \"title\": \"Genomic profiling of esophageal squamous cell carcinoma (ESCC)-Basis for precision medicine.\",\n \"abstract\": \"PURPOSE: Preparing for precision medicine, we surveyed genomic alterations in esophageal squamous cell carcinoma (ESCC) and identified candidate therapeutic targets by genomic profiling using next-generation sequencing (NGS). MATERIALS AND METHODS: Single-nucleotide variations, indels, and copy number variations in 80 genes were evaluated by targeted deep sequencing in 24 surgically resected ESCC specimens. Immunohistochemistry analyses and silver in situ hybridization for ERBB2 (HER2) were conducted to verify the NGS results. Associations between clinicopathological factors and detected genomic alterations were estimated. RESULTS: The mean coverage of sequencing of the tumor tissues from 24 patients was 464.8X with 85.1% over 100X. We detected a total of 115 genetic alterations and more than one genetic alteration was detected in most patients (23/24, 95.8%). Genes with genetic alterations detected in more than 20% of cases included TP53 (20/24, 83%), NOTCH1 (7/24, 29%), and MTOR (6/24, 25%). Amplification of 7 genes was detected in 8 cases. Genes showing amplification included AKT2 (1/24, 4.2%), EGFR (2/24, 8.3%), ERBB2 (HER2; 1/24, 4.2%), FGFR1 (1/24, 4.2%), KRAS (1/24, 4.2%), MDM2 (1/24, 4.2%), and PIK3CA (1/24, 4.2%). The ERBB2 alteration was confirmed by immunohistochemistry and silver in situ hybridization. Patients with NF1 and ARID1A mutations were younger than the patients without the mutations. ( p=0.024 and 0.014, respectively). NOTCH1 mutation and EGFR genetic alteration were associated with a larger tumor size (p=0.019) and lesser invasion depth (p=0.005), respectively. CONCLUSION: This study revealed the genetic profiles of ESCC, which may provide a foundation for the development of novel targeted therapy and precision medicine.\",\n \"corpus_id\": 207438895,\n \"score\": 1\n },\n {\n \"doc_id\": \"28557599\",\n \"title\": \"Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer.\",\n \"abstract\": \"CONTEXT: - The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. OBJECTIVE: - To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. DESIGN: - OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies. RESULTS: - OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50× coverage. CONCLUSIONS: - The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology.\",\n \"corpus_id\": 207534585,\n \"score\": 1\n },\n {\n \"doc_id\": \"28717660\",\n \"title\": \"A novel molecular diagnostics platform for somatic and germline precision oncology.\",\n \"abstract\": \"BACKGROUND: Next-generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies. METHODS: Next-generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug-related rearrangements, were prepared from 39 tumors (paraffin-embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines. RESULTS: The platform detects single-nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy-number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent. CONCLUSION: With an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.\",\n \"corpus_id\": 22316127,\n \"score\": 1\n },\n {\n \"doc_id\": \"28751446\",\n \"title\": \"Gene Copy Number Estimation From Targeted Next Generation Sequencing Of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification.\",\n \"abstract\": \"Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach.</p> <p>Results</p> <p>We showed that this method produced highly reproducible CNA results (r=0.92), with the use of pooled germline DNA as a coverage reference supporting precise CNA estimation. CNA estimates from targeted next generation sequencing were comparable with WES (r=0.86) and aCGH (r=0.7); for key selected genes (BRCA2, MYC, PIK3CA, PTEN and RB1) CNA estimation correlated well with WES (r = 0.91) and aCGH (r = 0.84) results.</p> <p>The frequency of CNAs in our population was comparable to that previously described (ie. deep deletions: BRCA2 4.5%; RB1 8.2%; PTEN 15.5%; amplification: AR 45.5%; gain: MYC 31.8%). We also showed, utilizing FISH, that CNA estimation can be impacted by intra-tumor heterogeneity and demonstrated that tumor microdissection allows NGS to provide more precise CNA estimates.</p> <p>Conclusion</p> <p>Targeted NGS and CNVkit based analyses provide a robust, precise, high throughput and cost effective method for CNA estimation for the delivery of more precise patient care.\",\n \"corpus_id\": 19052648,\n \"score\": 1\n },\n {\n \"doc_id\": \"20156996\",\n \"title\": \"Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays.\",\n \"abstract\": \"The detection of copy number variants (CNV) by array-based platforms provides valuable insight into understanding human diversity. However, suboptimal study design and data processing negatively affect CNV assessment. We quantitatively evaluate their impact when short-sequence oligonucleotide arrays are applied (Affymetrix Genome-Wide Human SNP Array 6.0) by evaluating 42 HapMap samples for CNV detection. Several processing and segmentation strategies are implemented, and results are compared to CNV assessment obtained using an oligonucleotide array CGH platform designed to query CNVs at high resolution (Agilent). We quantitatively demonstrate that different reference models (e.g. single versus pooled sample reference) used to detect CNVs are a major source of inter-platform discrepancy (up to 30%) and that CNVs residing within segmental duplication regions (higher reference copy number) are significantly harder to detect (P < 0.0001). After adjusting Affymetrix data to mimic the Agilent experimental design (reference sample effect), we applied several common segmentation approaches and evaluated differential sensitivity and specificity for CNV detection, ranging 39-77% and 86-100% for non-segmental duplication regions, respectively, and 18-55% and 39-77% for segmental duplications. Our results are relevant to any array-based CNV study and provide guidelines to optimize performance based on study-specific objectives.\",\n \"corpus_id\": 8315727,\n \"score\": 0\n },\n {\n \"doc_id\": \"21272361\",\n \"title\": \"The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.\",\n \"abstract\": \"BACKGROUND: Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel next generation sequencing, which enables the discovery of such changes, uses considerable quantities of genomic DNA (> 5 ug), a serious limitation in ever smaller clinical samples. However, a commonly available microarray platforms such as array comparative genomic hybridization (array CGH) allows the characterization of gene copy number at a single gene resolution using much smaller amounts of genomic DNA. In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities. METHODS: We performed array CGH on whole genome amplified and not amplified genomic DNA from MCF-7 breast cancer cells, using 244 K and 1 M Agilent arrays. The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length. RESULTS: DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length. The 4-fold extra resolution of the 1 M array platform relative to the less dense 244 K array platform, led to the improved detection of copy number variations (CNVs) and micro-CNAs. The identification of intra-genic breakpoints in areas of DNA copy number gain signaled the possible presence of gene fusion events. However, the ultra-dense platforms, especially the densest 1 M array, detect artifacts inherent to whole genome amplification and should be used only with non-amplified DNA samples. CONCLUSIONS: This is a first report using 1 M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification.\",\n \"corpus_id\": 10742867,\n \"score\": 0\n },\n {\n \"doc_id\": \"23368785\",\n \"title\": \"CoNVEX: copy number variation estimation in exome sequencing data using HMM.\",\n \"abstract\": \"BACKGROUND: One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequencing (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic variations. However, finding CNV in Cancer samples using WES data has not been fully explored. RESULTS: We present a new method, called CoNVEX, to estimate copy number variation in whole exome sequencing data. It uses ratio of tumour and matched normal average read depths at each exonic region, to predict the copy gain or loss. The useful signal produced by WES data will be hindered by the intrinsic noise present in the data itself. This limits its capacity to be used as a highly reliable CNV detection source. Here, we propose a method that consists of discrete wavelet transform (DWT) to reduce noise. The identification of copy number gains/losses of each targeted region is performed by a Hidden Markov Model (HMM). CONCLUSION: HMM is frequently used to identify CNV in data produced by various technologies including Array Comparative Genomic Hybridization (aCGH) and WGS. Here, we propose an HMM to detect CNV in cancer exome data. We used modified data from 1000 Genomes project to evaluate the performance of the proposed method. Using these data we have shown that CoNVEX outperforms the existing methods significantly in terms of precision. Overall, CoNVEX achieved a sensitivity of more than 92% and a precision of more than 50%.\",\n \"corpus_id\": 8393487,\n \"score\": 0\n },\n {\n \"doc_id\": \"25102989\",\n \"title\": \"Identification of copy number variants from exome sequence data.\",\n \"abstract\": \"BACKGROUND: With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task. Whilst numerous programs are available, they have different sensitivities, and have low sensitivity to detect smaller CNVs (1-4 exons). Additionally, exonic CNV discovery using standard aCGH has limitations due to the low probe density over exonic regions. The goal of our study was to develop a protocol to detect exonic CNVs (including shorter CNVs that cover 1-4 exons), combining computational prediction algorithms and a high-resolution custom CGH array. RESULTS: We used six published CNV prediction programs (ExomeCNV, CONTRA, ExomeCopy, ExomeDepth, CoNIFER, XHMM) and an in-house modification to ExomeCopy and ExomeDepth (ExCopyDepth) for computational CNV prediction on 30 exomes from the 1000 genomes project and 9 exomes from primary immunodeficiency patients. CNV predictions were tested using a custom CGH array designed to capture all exons (exaCGH). After this validation, we next evaluated the computational prediction of shorter CNVs. ExomeCopy and the in-house modified algorithm, ExCopyDepth, showed the highest capability in detecting shorter CNVs. Finally, the performance of each computational program was assessed by calculating the sensitivity and false positive rate. CONCLUSIONS: In this paper, we assessed the ability of 6 computational programs to predict CNVs, focussing on short (1-4 exon) CNVs. We also tested these predictions using a custom array targeting exons. Based on these results, we propose a protocol to identify and confirm shorter exonic CNVs combining computational prediction algorithms and custom aCGH experiments.\",\n \"corpus_id\": 1781103,\n \"score\": 0\n },\n {\n \"doc_id\": \"25319062\",\n \"title\": \"Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.\",\n \"abstract\": \"BACKGROUND: Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS: We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS: Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. CONCLUSIONS: The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"26110913\",\n \"title\": \"Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.\",\n \"abstract\": \"Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy-number variant calling when evaluated against a single-nucleotide polymorphism array. This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.\",\n \"corpus_id\": 4103107,\n \"score\": 0\n },\n {\n \"doc_id\": \"26258935\",\n \"title\": \"A sparse model based detection of copy number variations from exome sequencing data.\",\n \"abstract\": \"GOAL: Whole-exome sequencing provides a more cost-effective way than whole-genome sequencing for detecting genetic variants such as copy number variations (CNVs). Although a number of approaches have been proposed to detect CNVs from whole-genome sequencing, a direct adoption of these approaches to whole-exome sequencing will often fail because exons are separately located along a genome. Therefore, an appropriate method is needed to target the specific features of exome sequencing data. METHODS: In this paper a novel sparse model based method is proposed to discover CNVs from multiple exome sequencing data. First, exome sequencing data are represented with a penalized matrix approximation, and technical variability and random sequencing errors are assumed to follow a generalized Gaussian distribution. Second, an iteratively reweighted least squares algorithm is used to estimate the solution. RESULTS: The method is tested and validated on both synthetic and real data, and compared with other approaches including CoNIFER, XHMM and cn. MOPS. The test demonstrates that the proposed method outperform other approaches. CONCLUSION: The proposed sparse model can detect CNVs from exome sequencing data with high power and precision. SIGNIFICANCE: Sparse model can target the specific features of exome sequencing data. The software codes are freely available at http://www.tulane.edu/ wyp/software/Exon CNV.m.\",\n \"corpus_id\": 2111111,\n \"score\": 0\n },\n {\n \"doc_id\": \"27028851\",\n \"title\": \"Comparative genomic analysis of primary tumors and metastases in breast cancer.\",\n \"abstract\": \"Personalized medicine uses genomic information for selecting therapy in patients with metastatic cancer. An issue is the optimal tissue source (primary tumor or metastasis) for testing. We compared the DNA copy number and mutational profiles of primary breast cancers and paired metastases from 23 patients using whole-genome array-comparative genomic hybridization and next-generation sequencing of 365 \\\"cancer-associated\\\" genes. Primary tumors and metastases harbored copy number alterations (CNAs) and mutations common in breast cancer and showed concordant profiles. The global concordance regarding CNAs was shown by clustering and correlation matrix, which showed that each metastasis correlated more strongly with its paired tumor than with other samples. Genes with recurrent amplifications in breast cancer showed 100% (ERBB2, FGFR1), 96% (CCND1), and 88% (MYC) concordance for the amplified/non-amplified status. Among all samples, 499 mutations were identified, including 39 recurrent (AKT1, ERBB2, PIK3CA, TP53) and 460 non-recurrent variants. The tumors/metastases concordance of variants was 75%, higher for recurrent (92%) than for non-recurrent (73%) variants. Further mutational discordance came from very different variant allele frequencies for some variants. We showed that the chosen targeted therapy in two clinical trials of personalized medicine would be concordant in all but one patient (96%) when based on the molecular profiling of tumor and paired metastasis. Our results suggest that the genotyping of primary tumor may be acceptable to guide systemic treatment if the metastatic sample is not obtainable. However, given the rare but potentially relevant divergences for some actionable driver genes, the profiling of metastatic sample is recommended.\",\n \"corpus_id\": 20868599,\n \"score\": 0\n },\n {\n \"doc_id\": \"27851748\",\n \"title\": \"Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis.\",\n \"abstract\": \"Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression. To that end, we developed a single cell Copy Number Variation (CNV) Assay to evaluate genomic instability and CNVs in patient CTCs. For proof of concept, prostate cancer cell lines, LNCaP, PC3 and VCaP, were spiked into healthy donor blood to create mock patient-like samples for downstream single cell genomic analysis. In addition, samples from seven metastatic castration resistant prostate cancer (mCRPC) patients were included to evaluate clinical feasibility. CTCs were enumerated and characterized using the Epic Sciences CTC Platform. Identified single CTCs were recovered, whole genome amplified, and sequenced using an Illumina NextSeq 500. CTCs were then analyzed for genome-wide copy number variations, followed by genomic instability analyses. Large-scale state transitions (LSTs) were measured as surrogates of genomic instability. Genomic instability scores were determined reproducibly for LNCaP, PC3, and VCaP, and were higher than white blood cell (WBC) controls from healthy donors. A wide range of LST scores were observed within and among the seven mCRPC patient samples. On the gene level, loss of the PTEN tumor suppressor was observed in PC3 and 5/7 (71%) patients. Amplification of the androgen receptor (AR) gene was observed in VCaP cells and 5/7 (71%) mCRPC patients. Using an in silico down-sampling approach, we determined that DNA copy number and genomic instability can be detected with as few as 350K sequencing reads. The data shown here demonstrate the feasibility of detecting genomic instabilities at the single cell level using the Epic Sciences CTC Platform. Understanding CTC heterogeneity has great potential for patient stratification prior to treatment with targeted therapies and for monitoring disease evolution during treatment.\",\n \"corpus_id\": 824781,\n \"score\": 0\n },\n {\n \"doc_id\": \"28002793\",\n \"title\": \"Next generation sequencing of vitreoretinal lymphomas from small-volume intraocular liquid biopsies: new routes to targeted therapies.\",\n \"abstract\": \"BACKGROUND: Vitreoretinal lymphoma (VRL), the most common lymphoma of the eye, is a rare form of primary CNS lymphoma (PCNSL). Most frequently a high-grade diffuse large B cell lymphoma, VRL can cause vision loss and its prognosis remains dismal: the overall survival time is 3 years after diagnosis. Radiotherapy and chemotherapy are used but remain frequently ineffective, and no standardized treatment regimen exists. Furthermore, no biologically targeted treatments, based on the genetic profile of the tumor, are available, as VRL has hitherto not comprehensively been profiled. To address these unmet needs, we hypothesized that a next generation sequencing (NGS)-based, National Cancer Institute (NCI) MATCH Trial-modified panel would be able to identify actionable genomic alterations from small-volume, intraocular liquid biopsies. METHODS AND FINDINGS: In this retrospective study, we collected diluted vitreous biopsies from 4 patients with a high suspicion for VRL. Following cytological confirmation of lymphoma (all were diffuse large B cell lymphomas), we subjected genomic DNA from the biopsies to NGS, using a panel containing 126 genes (3,435 amplicons across several hotspots per gene), which was modified from that of the NCI MATCH Trial, a new trial that has matched patients with cancers that have not responded (or never responded), to investigational therapeutics based on their prioritized mutation profile rather than site of tumor origin. Using a validated bioinformatics pipeline, we assessed for the presence of actionable mutations and copy number alterations. In all four small-volume, intraocular liquid biopsies, we obtained sufficient genomic DNA for analysis, even in diluted samples in which the undiluted vitreous was used for cytology and flow cytometry. Using NGS, we found targetable heterozygous gain-of-function mutations in the MYD88 oncogene, and confirmed in our cohort the presence the L265 mutations, previously described using PCR-based assays. For the first time in VRL, we also identified the MYD88 S243N mutation. We also identified two-copy copy number losses in the tumor suppressor CDKN2A in all four cases, and one copy loss of the tumor suppressor PTEN in one sample. In one case, in which vitreous biopsies were originally read as cytologically negative, but which was confirmed as lymphoma when a lesion appeared in the brain two years later, our NGS-based approach detected tumoral DNA in the banked, original liquid biopsy. CONCLUSIONS: We performed the first systematic exploration of the actionable cancer genome in VRL. Our NGS-based approach identified exploitable genomic alterations such as gain-of-function MYD88 oncogene mutations and loss of the tumor suppressor CDKN2A, and thus illuminates new routes to biologically targeted therapies for VRL, a cancer with a dismal prognosis. This precision medicine strategy could be used to nominate novel, targeted therapies in lymphomas and other blinding and deadly ocular, orbital, and ocular adnexal diseases for which few treatments exist.\",\n \"corpus_id\": 3661857,\n \"score\": 0\n },\n {\n \"doc_id\": \"28034454\",\n \"title\": \"Comprehensive genomic sequencing and the molecular profiles of clinically advanced breast cancer.\",\n \"abstract\": \"Targeting specific mutations that have arisen within a tumour is a promising means of increasing the efficacy of treatments, and breast cancer is no exception to this new paradigm of personalised medicine. Traditional DNA sequencing methods used to characterise clinical cancer specimens and impact treatment decisions are highly sensitive, but are often limited in their scope to known mutational hot spots. Next-generation sequencing (NGS) technologies can also test for these well-known hot spots, as well as identifying insertions and deletions, copy number changes such as ERBB2 (HER2) gene amplification, and a wide array of fusion or rearrangement events. By rapidly analysing many genes in parallel, NGS technologies can make efficient use of precious biopsy material. Comprehensive genomic profiling (CGP) by NGS can reveal targetable, clinically relevant genomic alterations that can stratify tumours by predicted sensitivity to a variety of therapies, including HER2- or MTOR-targeted therapies, immunotherapies, and other kinase inhibitors. Many clinically relevant genomic alterations would not be identified by IHC or hotspot testing, but can be detected by NGS. In addition to the most common breast carcinoma subtypes, rare subtypes analysed with CGP also harbour clinically relevant genomic alterations that can potentially direct therapy selection, illustrating that CGP is a powerful tool for guiding treatment across all breast cancer subtypes.\",\n \"corpus_id\": 42872352,\n \"score\": 0\n },\n {\n \"doc_id\": \"28666423\",\n \"title\": \"Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications.\",\n \"abstract\": \"BACKGROUND: Sequencing analysis of circulating tumor cells (CTCs) enables \\\"liquid biopsy\\\" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies. METHODS: Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score. RESULTS: Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA. CONCLUSION: The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5-10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template.\",\n \"corpus_id\": 870354,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":83,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27479325\",\n \"title\": \"DWARF14 is a non-canonical hormone receptor for strigolactone.\",\n \"abstract\": \"Classical hormone receptors reversibly and non-covalently bind active hormone molecules, which are generated by biosynthetic enzymes, to trigger signal transduction. The α/β hydrolase DWARF14 (D14), which hydrolyses the plant branching hormone strigolactone and interacts with the F-box protein D3/MAX2, is probably involved in strigolactone detection. However, the active form of strigolactone has yet to be identified and it is unclear which protein directly binds the active form of strigolactone, and in which manner, to act as the genuine strigolactone receptor. Here we report the crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex, reveal that Arabidopsis thaliana (At)D14 undergoes an open-to-closed state transition to trigger strigolactone signalling, and demonstrate that strigolactone is hydrolysed into a covalently linked intermediate molecule (CLIM) to initiate a conformational change of AtD14 to facilitate interaction with D3. Notably, analyses of a highly branched Arabidopsis mutant d14-5 show that the AtD14(G158E) mutant maintains enzyme activity to hydrolyse strigolactone, but fails to efficiently interact with D3/MAX2 and loses the ability to act as a receptor that triggers strigolactone signalling in planta. These findings uncover a mechanism underlying the allosteric activation of AtD14 by strigolactone hydrolysis into CLIM, and define AtD14 as a non-canonical hormone receptor with dual functions to generate and sense the active form of strigolactone.\",\n \"corpus_id\": 4469412\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18690209","title":"Strigolactone inhibition of shoot branching.","abstract":"A carotenoid-derived hormonal signal that inhibits shoot branching in plants has long escaped identification. Strigolactones are compounds thought to be derived from carotenoids and are known to trigger the germination of parasitic plant seeds and stimulate symbiotic fungi. Here we present evidence that carotenoid cleavage dioxygenase 8 shoot branching mutants of pea are strigolactone deficient and that strigolactone application restores the wild-type branching phenotype to ccd8 mutants. Moreover, we show that other branching mutants previously characterized as lacking a response to the branching inhibition signal also lack strigolactone response, and are not deficient in strigolactones. These responses are conserved in Arabidopsis. In agreement with the expected properties of the hormonal signal, exogenous strigolactone can be transported in shoots and act at low concentrations. We suggest that endogenous strigolactones or related compounds inhibit shoot branching in plants. Furthermore, ccd8 mutants demonstrate the diverse effects of strigolactones in shoot branching, mycorrhizal symbiosis and parasitic weed interaction.","corpus_id":205214618,"score":2},{"doc_id":"19542179","title":"d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers.","abstract":"Recent studies using highly branched mutants of pea, Arabidopsis and rice have demonstrated that strigolactones, a group of terpenoid lactones, act as a new hormone class, or its biosynthetic precursors, in inhibiting shoot branching. Here, we provide evidence that DWARF14 (D14) inhibits rice tillering and may act as a new compo-nent of the strigolactone-dependent branching inhibition pathway. The d14 mutant exhibits increased shoot branch-ing with reduced plant height like the previously characterized strigolactone-deficient and -insensitive mutants d10 and d3, respectively. The d10-1 d14-1 double mutant is phenotypically indistinguishable from the d10-1 and d14-1 single mutants, consistent with the idea that D10 and D14 function in the same pathway. However, unlike with d10, the d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2'-epi-5-deoxystrigol than the wild type. Positional cloning revealed that D14 encodes a protein of the alpha/beta-fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones. We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form.","corpus_id":11534217,"score":2},{"doc_id":"19726222","title":"Strigolactones: a new hormone with a past.","abstract":"The recent discovery of an endogenous hormonal activity for strigolactones in shoot branching was surprising since these molecules were thought to mostly play roles as signaling molecules between organisms. Even in the context of plant hormones, strigolactones appear to be different in that their role in plant development is quite restricted. This most probably reflects early days and new hormonal functions will most probably be found for these compounds in the future. In this respect, the exogenous role of strigolactones in parasitic plant seed germination may hint to functions of this compound in seed development. However, showing new roles for strigolactones in the seed or any other aspect of plant development for that matter will require developing assays in model genetic systems such as Arabidopsis and rice where we can take full advantage of the experimental tools that are available.","corpus_id":21288092,"score":2},{"doc_id":"19913454","title":"New genes in the strigolactone-related shoot branching pathway.","abstract":"Shoot branching is controlled by the formation and subsequent outgrowth of axillary buds in the axils of leaves. Axillary buds are indeterminate structures that can be arrested and await endogenous or environmental cues for outgrowth. A major breakthrough in this area of plant development has been the discovery that a specific group of terpenoid lactones, named strigolactones, can directly or indirectly, inhibit axillary bud outgrowth. Since that discovery, new branching mutants have been identified with reduced strigolactone levels or which are defective in strigolactone regulation or response. DWARF27 and DWARF14 probably act on strigolactone biosynthesis and strigolactone metabolism or signal transduction, respectively. Auxin signaling mutants have also been useful in demonstrating that strigolactone levels are mediated by a classical auxin signal transduction pathway. The discovery and characterization of these mutants is an important first step toward understanding the mechanisms of strigolactone biosynthesis and signaling and their importance in regulating shoot branching.","corpus_id":22923139,"score":2},{"doc_id":"21119045","title":"Strigolactones are transported through the xylem and play a key role in shoot architectural response to phosphate deficiency in nonarbuscular mycorrhizal host Arabidopsis.","abstract":"The biosynthesis of the recently identified novel class of plant hormones, strigolactones, is up-regulated upon phosphate deficiency in many plant species. It is generally accepted that the evolutionary origin of strigolactone up-regulation is their function as a rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi. In this work, we demonstrate that this induction is conserved in Arabidopsis (Arabidopsis thaliana), although Arabidopsis is not a host for arbuscular mycorrhizal fungi. We demonstrate that the increase in strigolactone production contributes to the changes in shoot architecture observed in response to phosphate deficiency. Using high-performance liquid chromatography, column chromatography, and multiple reaction monitoring-liquid chromatography-tandem mass spectrometry analysis, we identified two strigolactones (orobanchol and orobanchyl acetate) in Arabidopsis and have evidence of the presence of a third (5-deoxystrigol). We show that at least one of them (orobanchol) is strongly reduced in the putative strigolactone biosynthetic mutants more axillary growth1 (max1) and max4 but not in the signal transduction mutant max2. Orobanchol was also detected in xylem sap and up-regulated under phosphate deficiency, which is consistent with the idea that root-derived strigolactones are transported to the shoot, where they regulate branching. Moreover, two additional putative strigolactone-like compounds were detected in xylem sap, one of which was not detected in root exudates. Together, these results show that xylem-transported strigolactones contribute to the regulation of shoot architectural response to phosphate-limiting conditions.","corpus_id":13264036,"score":2},{"doc_id":"21555559","title":"F-box protein MAX2 has dual roles in karrikin and strigolactone signaling in Arabidopsis thaliana.","abstract":"Smoke is an important abiotic cue for plant regeneration in postfire landscapes. Karrikins are a class of compounds discovered in smoke that promote seed germination and influence early development of many plants by an unknown mechanism. A genetic screen for karrikin-insensitive mutants in Arabidopsis thaliana revealed that karrikin signaling requires the F-box protein MAX2, which also mediates responses to the structurally-related strigolactone family of phytohormones. Karrikins and the synthetic strigolactone GR24 trigger similar effects on seed germination, seedling photomorphogenesis, and expression of a small set of genes during these developmental stages. Karrikins also repress MAX4 and IAA1 transcripts, which show negative feedback regulation by strigolactone. We demonstrate that all of these common responses are abolished in max2 mutants. Unlike strigolactones, however, karrikins do not inhibit shoot branching in Arabidopsis or pea, indicating that plants can distinguish between these signals. These results suggest that a MAX2-dependent signal transduction mechanism was adapted to mediate responses to two chemical cues with distinct roles in plant ecology and development.","corpus_id":11583709,"score":2},{"doc_id":"22357928","title":"Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis.","abstract":"Karrikins are butenolides derived from burnt vegetation that stimulate seed germination and enhance seedling responses to light. Strigolactones are endogenous butenolide hormones that regulate shoot and root architecture, and stimulate the branching of arbuscular mycorrhizal fungi. Thus, karrikins and strigolactones are structurally similar but physiologically distinct plant growth regulators. In Arabidopsis thaliana, responses to both classes of butenolides require the F-box protein MAX2, but it remains unclear how discrete responses to karrikins and strigolactones are achieved. In rice, the DWARF14 protein is required for strigolactone-dependent inhibition of shoot branching. Here, we show that the Arabidopsis DWARF14 orthologue, AtD14, is also necessary for normal strigolactone responses in seedlings and adult plants. However, the AtD14 paralogue KARRIKIN INSENSITIVE 2 (KAI2) is specifically required for responses to karrikins, and not to strigolactones. Phylogenetic analysis indicates that KAI2 is ancestral and that AtD14 functional specialisation has evolved subsequently. Atd14 and kai2 mutants exhibit distinct subsets of max2 phenotypes, and expression patterns of AtD14 and KAI2 are consistent with the capacity to respond to either strigolactones or karrikins at different stages of plant development. We propose that AtD14 and KAI2 define a class of proteins that permit the separate regulation of karrikin and strigolactone signalling by MAX2. Our results support the existence of an endogenous, butenolide-based signalling mechanism that is distinct from the strigolactone pathway, providing a molecular basis for the adaptive response of plants to smoke.","corpus_id":9432783,"score":2},{"doc_id":"22713366","title":"The computational-based structure of Dwarf14 provides evidence for its role as potential strigolactone receptor in plants.","abstract":"BACKGROUND: Strigolactones (SLs) are recently identified plant hormones modulating root and shoot branching. Besides their endogenous role within the producing organism, SLs are also key molecules in the communication of plants with arbuscular mycorrhizal (AM) fungi and parasitic weeds. In fact SLs are exuded into the rhizosphere where they act as a host-derived signal, stimulating the germination of the seeds of parasitic plants which would not survive in the absence of a host root to colonize. Similarly, their perception by AM fungi causes extensive hyphal branching; this is a prerequisite for effective root colonization, since it increases the number of potential contact points with the host surface. In spite of the crucial and multifaceted biological role of SLs, there is no information on the receptor(s) which bind(s) such active molecules, neither in the producing plants, or in parasitic weeds or AM fungi. RESULTS: In this work, we applied homology modelling techniques to investigate the structure of the protein encoded by the gene Dwarf14, which was first identified in rice as conferring SLs insensitivity when mutated. The best sequence identity was with bacterial RsbQ. Both proteins belong to the superfamily of alpha/beta-fold hydrolases, some members of which play a role in the metabolism or signalling of plant hormones. The Dwarf14 (D14) structure was refined by means of molecular dynamics simulations. In order to support the hypothesis that D14 could be an endogenous SLs receptor, we performed docking experiments with a natural ligand. CONCLUSIONS: It is suggested that D14 interacts with and thereby may act as a receptor for SLs in plants. This hypothesis offers a starting point to experimentally study the mechanism of its activity in vivo by means of structural, molecular and genetic approaches. Lastly, knowledge of the putative receptor structure will boost the research on analogues of the natural substrates as required for agricultural applications.","corpus_id":12136692,"score":2},{"doc_id":"22959345","title":"DAD2 is an α/β hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone.","abstract":"Strigolactones are a recently discovered class of plant hormone involved in branching, leaf senescence, root development, and plant-microbe interactions. They are carotenoid-derived lactones, synthesized in the roots and transported acropetally to modulate axillary bud outgrowth (i.e., branching). However, a receptor for strigolactones has not been identified. We have identified the DAD2 gene from petunia, an ortholog of the rice and Arabidopsis D14 genes, and present evidence for its roles in strigolactone perception and signaling. DAD2 acts in the strigolactone pathway, and the dad2 mutant is insensitive to the strigolactone analog GR24. The crystal structure of DAD2 reveals an α/β hydrolase fold containing a canonical catalytic triad with a large internal cavity capable of accommodating strigolactones. In the presence of GR24 DAD2 interacts with PhMAX2A, a central component of strigolactone signaling, in a GR24 concentration-dependent manner. DAD2 can hydrolyze GR24, with mutants of the catalytic triad abolishing both this activity and the ability of DAD2 to interact with PhMAX2A. The hydrolysis products can neither stimulate the protein-protein interaction nor modulate branching. These observations suggest that DAD2 acts to bind the mobile strigolactone signal and then interacts with PhMAX2A during catalysis to initiate an SCF-mediated signal transduction pathway.","corpus_id":15616452,"score":2},{"doc_id":"23025475","title":"The D3 F-box protein is a key component in host strigolactone responses essential for arbuscular mycorrhizal symbiosis.","abstract":"Arbuscular mycorrhiza (AM) represents an ancient endosymbiosis between plant roots and Glomeromycota fungi. Strigolactones (SLs), plant-derived terpenoid lactones, activate hyphal branching of AM fungi before physical contact. Lack of SL biosynthesis results in lower colonization of AM fungi. The F-box protein, DWARF3 (D3), and the hydrolase family protein DWARF14 (D14) are crucial for SL responses in rice. Here we conducted AM fungal colonization assays with the SL-insensitive d3 and d14 mutants. The d3 mutant exhibited strong defects in AM fungal colonization, whereas the d14 mutant showed higher AM fungal colonization. As D14 has a homologous protein, D14-LIKE, we generated D14-LIKE knockdown lines by RNA interference in the wildtype and d14 background. D14 and D14-LIKE double knockdown lines exhibited similar colonization rates as those of the d14-1 mutant. D3 is crucial for establishing AM symbiosis in rice, whereas D14 and D14-LIKE are not. Our results suggest distinct roles for these SL-related components in AM symbiosis.","corpus_id":41759016,"score":2},{"doc_id":"23182342","title":"The biology of strigolactones.","abstract":"The strigolactones are rhizosphere signaling molecules as well as a new class of plant hormones with a still increasing number of biological functions being uncovered. Here, we review a recent major breakthrough in our understanding of strigolactone biosynthesis, which has revealed the unexpected simplicity of the originally postulated complex pathway. Moreover, the discovery and localization of a strigolactone exporter sheds new light on putative strigolactone fluxes to the rhizosphere as well as within the plant. The combination of these data with information on the expression and regulation of strigolactone biosynthetic and downstream signaling genes provides new insights into how strigolactones control the many different aspects of plant development and how their rhizosphere signaling role may have evolved.","corpus_id":9546410,"score":2},{"doc_id":"23204501","title":"Selective mimics of strigolactone actions and their potential use for controlling damage caused by root parasitic weeds.","abstract":"Strigolactones (SLs) are a novel class of plant hormones and rhizosphere communication signals, although the molecular mechanisms underlying their activities have not yet been fully determined. Nor is their application in agriculture well developed. The importance of plant hormone agonists has been demonstrated in both basic and applied research, and chemicals that mimic strigolactone functions should greatly facilitate strigolactone research. Here, we report our discovery of a new phenoxyfuranone compound, 4-Br debranone (4BD), that shows similar activity to that of the major strigolactone (SL) analog GR24 in many aspects of a biological assay on plants. 4BD strongly inhibited tiller bud outgrowth in the SL-deficient rice mutant d10 at the same concentration as GR24, with no adverse effects, even during prolonged cultivation. This result was also observed in the Arabidopsis thaliana SL-deficient mutants max1, max3, and max4. However, the application of 4BD to the Arabidopsis SL-insensitive mutant max2 induced no morphological changes in it. The expression of SL biosynthetic genes was also reduced by 4BD treatment, probably via negative feedback regulation. However, in a seed germination assay on Striga hermonthica, a root parasitic plant, 4BD showed far less activity than GR24. These results suggest that 4BD is the first plant-specific strigolactone mimic.","corpus_id":21193103,"score":2},{"doc_id":"23293648","title":"Strigolactone and karrikin signal perception: receptors, enzymes, or both?","abstract":"The signaling molecules strigolactone (SL) and karrikin are involved in seed germination, development of axillary meristems, senescence of leaves, and interactions with arbuscular mycorrhizal fungi. The signal transduction pathways for both SLs and karrikins require the same F-box protein (MAX2) and closely related α/β hydrolase fold proteins (DAD2 and KAI2). The crystal structure of DAD2 has been solved revealing an α/β hydrolase fold protein with an internal cavity capable of accommodating SLs. DAD2 responds to the SL analog GR24 by changing conformation and binding to MAX2 in a GR24 concentration-dependent manner. DAD2 can also catalyze hydrolysis of GR24. Structure activity relationships of analogs indicate that the butenolide ring common to both SLs and karrikins is essential for biological activity, but the remainder of the molecules can be significantly modified without loss of activity. The combination of data from the study of DAD2, KAI2, and chemical analogs of SLs and karrikins suggests a model for binding that requires nucleophilic attack by the active site serine of the hydrolase at the carbonyl atom of the butenolide ring. A conformational change occurs in the hydrolase that results in interaction with the F-box protein MAX2. Downstream signal transduction is then likely to occur via SCF (Skp-Cullin-F-box) complex-mediated ubiquitination of target proteins and their subsequent degradation. The role of the catalytic activity of the hydrolase is unclear but it may be integral in binding as well as possibly allowing the signal to be cleared from the receptor. The α/β hydrolase fold family consists mostly of active enzymes, with a few notable exceptions. We suggest that DAD2 and KAI2 represent an intermediate stage where some catalytic activity is retained at the same time as a receptor role has evolved.","corpus_id":18476075,"score":2},{"doc_id":"23301669","title":"Structures of D14 and D14L in the strigolactone and karrikin signaling pathways.","abstract":"Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/β-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between β6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long β6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/β-fold hydrolases.","corpus_id":205150729,"score":2},{"doc_id":"23382651","title":"Strigolactone can promote or inhibit shoot branching by triggering rapid depletion of the auxin efflux protein PIN1 from the plasma membrane.","abstract":"Plants continuously extend their root and shoot systems through the action of meristems at their growing tips. By regulating which meristems are active, plants adjust their body plans to suit local environmental conditions. The transport network of the phytohormone auxin has been proposed to mediate this systemic growth coordination, due to its self-organising, environmentally sensitive properties. In particular, a positive feedback mechanism termed auxin transport canalization, which establishes auxin flow from active shoot meristems (auxin sources) to the roots (auxin sinks), has been proposed to mediate competition between shoot meristems and to balance shoot and root growth. Here we provide strong support for this hypothesis by demonstrating that a second hormone, strigolactone, regulates growth redistribution in the shoot by rapidly modulating auxin transport. A computational model in which strigolactone action is represented as an increase in the rate of removal of the auxin export protein, PIN1, from the plasma membrane can reproduce both the auxin transport and shoot branching phenotypes observed in various mutant combinations and strigolactone treatments, including the counterintuitive ability of strigolactones either to promote or inhibit shoot branching, depending on the auxin transport status of the plant. Consistent with this predicted mode of action, strigolactone signalling was found to trigger PIN1 depletion from the plasma membrane of xylem parenchyma cells in the stem. This effect could be detected within 10 minutes of strigolactone treatment and was independent of protein synthesis but dependent on clathrin-mediated membrane trafficking. Together these results support the hypothesis that growth across the plant shoot system is balanced by competition between shoot apices for a common auxin transport path to the root and that strigolactones regulate shoot branching by modulating this competition.","corpus_id":8836606,"score":2},{"doc_id":"23424248","title":"A role for more axillary growth1 (MAX1) in evolutionary diversity in strigolactone signaling upstream of MAX2.","abstract":"Strigolactones (SLs) are carotenoid-derived phytohormones with diverse roles. They are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. To date, six genes associated with SL synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of Arabidopsis (Arabidopsis thaliana) and dwarf (d) of rice (Oryza sativa). Here, we present a phylogenetic analysis of the MAX/D genes to clarify the relationships of each gene with its wider family and to allow the correlation of events in the evolution of the genes with the evolution of SL function. Our analysis suggests that the notion of a distinct SL pathway is inappropriate. Instead, there may be a diversity of SL-like compounds, the response to which requires a D14/D14-like protein. This ancestral system could have been refined toward distinct ligand-specific pathways channeled through MAX2, the most downstream known component of SL signaling. MAX2 is tightly conserved among land plants and is more diverged from its nearest sister clade than any other SL-related gene, suggesting a pivotal role in the evolution of SL signaling. By contrast, the evidence suggests much greater flexibility upstream of MAX2. The MAX1 gene is a particularly strong candidate for contributing to diversification of inputs upstream of MAX2. Our functional analysis of the MAX1 family demonstrates the early origin of its catalytic function and both redundancy and functional diversification associated with its duplication in angiosperm lineages.","corpus_id":24729313,"score":2},{"doc_id":"23773129","title":"Carlactone-independent seedling morphogenesis in Arabidopsis.","abstract":"Strigolactone hormones are derived from carotenoids via carlactone, and act through the α/β-hydrolase D14 and the F-box protein D3/MAX2 to repress plant shoot branching. While MAX2 is also necessary for normal seedling development, D14 and the known strigolactone biosynthesis genes are not, raising the question of whether endogenous, canonical strigolactones derived from carlactone have a role in seedling morphogenesis. Here, we report the chemical synthesis of the strigolactone precursor carlactone, and show that it represses Arabidopsis shoot branching and influences leaf morphogenesis via a mechanism that is dependent on the cytochrome P450 MAX1. In contrast, both physiologically active Z-carlactone and the non-physiological E isomer exhibit similar weak activity in seedlings, and predominantly signal through D14 rather than its paralogue KAI2, in a MAX2-dependent but MAX1-independent manner. KAI2 is essential for seedling morphogenesis, and hence this early-stage development employs carlactone-independent morphogens for which karrikins from wildfire smoke are specific surrogates. While the commonly employed synthetic strigolactone GR24 acts non-specifically through both D14 and KAI2, carlactone is a specific effector of strigolactone signalling that acts through MAX1 and D14.","corpus_id":3481094,"score":2},{"doc_id":"24131983","title":"Molecular mechanism of strigolactone perception by DWARF14.","abstract":"Strigolactones (SLs) are phytohormones that inhibit shoot branching and function in the rhizospheric communication with symbiotic fungi and parasitic weeds. An α/β-hydrolase protein, DWARF14 (D14), has been recognized to be an essential component of plant SL signalling, although its precise function remains unknown. Here we present the SL-dependent interaction of D14 with a gibberellin signalling repressor SLR1 and a possible mechanism of phytohormone perception in D14-mediated SL signalling. D14 functions as a cleavage enzyme of SLs, and the cleavage reaction induces the interaction with SLR1. The crystal structure of D14 shows that 5-hydroxy-3-methylbutenolide (D-OH), which is a reaction product of SLs, is trapped in the catalytic cavity of D14 to form an altered surface. The D14 residues recognizing D-OH are critical for the SL-dependent D14-SLR1 interaction. These results provide new insight into crosstalk between gibberellin and SL signalling pathways.","corpus_id":28987166,"score":2},{"doc_id":"24336200","title":"DWARF 53 acts as a repressor of strigolactone signalling in rice.","abstract":"Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.","corpus_id":4383175,"score":2},{"doc_id":"24336215","title":"D14-SCF(D3)-dependent degradation of D53 regulates strigolactone signalling.","abstract":"Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the α/β hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.","corpus_id":4407338,"score":2},{"doc_id":"24483232","title":"Striga hermonthica MAX2 restores branching but not the Very Low Fluence Response in the Arabidopsis thaliana max2 mutant.","abstract":"Seed germination of Striga spp. ( witchweeds), one of the world's most destructive parasitic weeds, cannot be induced by light but is specifically induced by strigolactones. It is not known whether Striga uses the same components for strigolactone signaling as host plants, whether it has endogenous strigolactone biosynthesis and whether there is post-germination strigolactone signaling in Striga. Strigolactones could not be detected in in vitro grown Striga, while for host-grown Striga, the strigolactone profile is dominated by a subset of the strigolactones present in the host. Branching of in vitro grown Striga is affected by strigolactone biosynthesis inhibitors. ShMAX2, the Striga ortholog of Arabidopsis MORE AXILLARY BRANCHING 2 (AtMAX2) - which mediates strigolactone signaling - complements several of the Arabidopsis max2-1 phenotypes, including the root and shoot phenotype, the High Irradiance Response and the response to strigolactones. Seed germination of max2-1 complemented with ShMAX2 showed no complementation of the Very Low Fluence Response phenotype of max2-1. Results provide indirect evidence for ShMAX2 functions in Striga. A putative role of ShMAX2 in strigolactone-dependent seed germination of Striga is discussed.","corpus_id":22158546,"score":2},{"doc_id":"24610723","title":"Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis.","abstract":"Strigolactones (SLs) are phytohormones that play a central role in regulating shoot branching. SL perception and signaling involves the F-box protein MAX2 and the hydrolase DWARF14 (D14), proposed to act as an SL receptor. We used strong loss-of-function alleles of the Arabidopsis thaliana D14 gene to characterize D14 function from early axillary bud development through to lateral shoot outgrowth and demonstrated a role of this gene in the control of flowering time. Our data show that D14 distribution in vivo overlaps with that reported for MAX2 at both the tissue and subcellular levels, allowing physical interactions between these proteins. Our grafting studies indicate that neither D14 mRNA nor the protein move over a long range upwards in the plant. Like MAX2, D14 is required locally in the aerial part of the plant to suppress shoot branching. We also identified a mechanism of SL-induced, MAX2-dependent proteasome-mediated degradation of D14. This negative feedback loop would cause a substantial drop in SL perception, which would effectively limit SL signaling duration and intensity.","corpus_id":7000577,"score":2},{"doc_id":"24616269","title":"DWARF3 participates in an SCF complex and associates with DWARF14 to suppress rice shoot branching.","abstract":"Strigolactones (SLs) are a novel class of plant hormones that inhibit shoot branching. Currently, two proteins in rice are thought to play crucial roles in SL signal transduction. DWARF14 (D14), an α/β hydrolase, is responsible for SL perception, while DWARF3 (D3), an F-box protein with leucine-rich repeats, is essential for SL signal transduction. However, how these two proteins transmit SL signals to downstream factors remains unclear. Here, we characterized a high-tillering dwarf rice mutant, gsor300097, which is insensitive to GR24, a synthetic analog of SL. Mapping and sequencing analysis showed that gsor300097 is a novel allelic mutant of D3, in which a nonsense mutation truncates the protein from 720 to 527 amino acids. The D3 gene was strongly expressed in root, leaf, shoot base and panicle. Nuclear-localized F-box protein D3 played a role in the SCF complex by interacting with OSK1, OSK5 or OSK20 and OsCullin1. In addition, D3 associated with D14 in a GR24-dependent manner in vivo. Taken together, our findings suggested that D3 assembled into an SCF(D3) complex and associated with D14 to suppress rice shoot branching.","corpus_id":14189899,"score":2},{"doc_id":"24981923","title":"Strigolactone biosynthesis and perception.","abstract":"Strigolactones (SLs) are plant hormones that regulate shoot branching as well as known as root-derived signals for parasitic and symbiotic interactions. Since the first discovery of a naturally occurring SL, strigol, more than 40 years ago, the biosynthetic pathway has remained elusive. Recently, it was partially uncovered through the functional analysis of some biosynthetic components that were discovered from genetic studies using SL-deficient mutants. In addition, a perception component was also characterized through genetic and biochemical studies of a rice SL-insensitive mutant, dwarf14. In this review, we describe new findings on SL biosynthesis and focus on a recently identified SL precursor, carlactone. We also describe the perception mechanisms by an α/β-fold hydrolase family protein.","corpus_id":42603521,"score":2},{"doc_id":"24996032","title":"Signalling and responses to strigolactones and karrikins.","abstract":"Strigolactone (SL) and karrikin (KAR) signalling control many aspects of plant growth and development through similar mechanisms employing related α/β-fold hydrolase-receptors and a common F-box protein named MORE AXILARY GROWTH2 (MAX2) in Arabidopsis or DWARF3 (D3) in rice. D3 mediates SL-dependent ubiquitination and proteolysis of DWARF53 (D53) protein, thought to be involved in the control of gene expression, while a related protein SUPPRESSOR OF MAX2-1 (SMAX1) is implicated in the response to KAR in Arabidopsis. Different members of the D53/SMAX1 multigene family likely mediate different responses in plant growth and development. Analysis of responses to SL or KAR has identified many genes regulated by these compounds. Crosstalk with other signalling systems including light, hormones and abiotic stress has also been identified. Here we critically analyse how to progress towards a clearer understanding of the targets and functions of the SL and KAR signalling systems.","corpus_id":2437,"score":2},{"doc_id":"25126711","title":"Detection of parasitic plant suicide germination compounds using a high-throughput Arabidopsis HTL/KAI2 strigolactone perception system.","abstract":"Strigolactones are terpenoid-based plant hormones that act as communication signals within a plant, between plants and fungi, and between parasitic plants and their hosts. Here we show that an active enantiomer form of the strigolactone GR24, the germination stimulant karrikin, and a number of structurally related small molecules called cotylimides all bind the HTL/KAI2 α/β hydrolase in Arabidopsis. Strigolactones and cotylimides also promoted an interaction between HTL/KAI2 and the F-box protein MAX2 in yeast. Identification of this chemically dependent protein-protein interaction prompted the development of a yeast-based, high-throughput chemical screen for potential strigolactone mimics. Of the 40 lead compounds identified, three were found to have in planta strigolactone activity using Arabidopsis-based assays. More importantly, these three compounds were all found to stimulate suicide germination of the obligate parasitic plant Striga hermonthica. These results suggest that screening strategies involving yeast/Arabidopsis models may be useful in combating parasitic plant infestations.","corpus_id":6213043,"score":2},{"doc_id":"25179782","title":"Strigolactone signalling: standing on the shoulders of DWARFs.","abstract":"Strigolactones are an ancient and major class of endogenous plant growth regulators. Although only recently identified, rapid progress has been made in understanding strigolactone biology, including the identification of a signalling pathway involving DWARF14 α/β-fold proteins, the SCF(MAX2) ubiquitin ligase and SMAX1-LIKE (SMXL) family of chaperonin-like proteins. Several rapid effects of strigolactone signalling have also been identified, including endocytosis of the PIN-FORMED1 (PIN1) auxin efflux carrier and transcript accumulation of the BRANCHED1 (BRC1) transcription factor. Here we assess our current knowledge of strigolactone signalling, and discuss how increased understanding of the cell biology of the system can help to resolve some of the current uncertainties in the field.","corpus_id":37952801,"score":2},{"doc_id":"25425668","title":"Carlactone is converted to carlactonoic acid by MAX1 in Arabidopsis and its methyl ester can directly interact with AtD14 in vitro.","abstract":"Strigolactones (SLs) stimulate seed germination of root parasitic plants and induce hyphal branching of arbuscular mycorrhizal fungi in the rhizosphere. In addition, they have been classified as a new group of plant hormones essential for shoot branching inhibition. It has been demonstrated thus far that SLs are derived from carotenoid via a biosynthetic precursor carlactone (CL), which is produced by sequential reactions of DWARF27 (D27) enzyme and two carotenoid cleavage dioxygenases CCD7 and CCD8. We previously found an extreme accumulation of CL in the more axillary growth1 (max1) mutant of Arabidopsis, which exhibits increased lateral inflorescences due to SL deficiency, indicating that CL is a probable substrate for MAX1 (CYP711A1), a cytochrome P450 monooxygenase. To elucidate the enzymatic function of MAX1 in SL biosynthesis, we incubated CL with a recombinant MAX1 protein expressed in yeast microsomes. MAX1 catalyzed consecutive oxidations at C-19 of CL to convert the C-19 methyl group into carboxylic acid, 9-desmethyl-9-carboxy-CL [designated as carlactonoic acid (CLA)]. We also identified endogenous CLA and its methyl ester [methyl carlactonoate (MeCLA)] in Arabidopsis plants using LC-MS/MS. Although an exogenous application of either CLA or MeCLA suppressed the growth of lateral inflorescences of the max1 mutant, MeCLA, but not CLA, interacted with Arabidopsis thaliana DWARF14 (AtD14) protein, a putative SL receptor, as shown by differential scanning fluorimetry and hydrolysis activity tests. These results indicate that not only known SLs but also MeCLA are biologically active in inhibiting shoot branching in Arabidopsis.","corpus_id":2266658,"score":2},{"doc_id":"26175507","title":"A Selaginella moellendorffii Ortholog of KARRIKIN INSENSITIVE2 Functions in Arabidopsis Development but Cannot Mediate Responses to Karrikins or Strigolactones.","abstract":"In Arabidopsis thaliana, the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) is essential for normal seed germination, seedling development, and leaf morphogenesis, as well as for responses to karrikins. KAI2 is a paralog of DWARF14 (D14), the proposed strigolactone receptor, but the evolutionary timing of functional divergence between the KAI2 and D14 clades has not been established. By swapping gene promoters, we show that Arabidopsis KAI2 and D14 proteins are functionally distinct. We show that the catalytic serine of KAI2 is essential for function in plants and for biochemical activity in vitro. We identified two KAI2 homologs from Selaginella moellendorffii and two from Marchantia polymorpha. One from each species could hydrolyze the strigolactone analog GR24 in vitro, but when tested for their ability to complement Arabidopsis d14 and kai2 mutants, neither of these homologs was effective. However, the second KAI2 homolog from S. moellendorffii was able to complement the seedling and leaf development phenotypes of Arabidopsis kai2. This homolog could not transduce signals from exogenous karrikins, strigolactone analogs, or carlactone, but its activity did depend on the conserved catalytic serine. We conclude that KAI2, and most likely the endogenous signal to which it responds, has been conserved since the divergence of lycophytes and angiosperm lineages, despite their major developmental and morphogenic differences.","corpus_id":22057851,"score":2},{"doc_id":"26228149","title":"PLANT EVOLUTION. Convergent evolution of strigolactone perception enabled host detection in parasitic plants.","abstract":"Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.","corpus_id":206637320,"score":2},{"doc_id":"26293962","title":"PARASITIC PLANTS. Probing strigolactone receptors in Striga hermonthica with fluorescence.","abstract":"Elucidating the signaling mechanism of strigolactones has been the key to controlling the devastating problem caused by the parasitic plant Striga hermonthica. To overcome the genetic intractability that has previously interfered with identification of the strigolactone receptor, we developed a fluorescence turn-on probe, Yoshimulactone Green (YLG), which activates strigolactone signaling and illuminates signal perception by the strigolactone receptors. Here we describe how strigolactones bind to and act via ShHTLs, the diverged family of α/β hydrolase-fold proteins in Striga. Live imaging using YLGs revealed that a dynamic wavelike propagation of strigolactone perception wakes up Striga seeds. We conclude that ShHTLs function as the strigolactone receptors mediating seed germination in Striga. Our findings enable access to strigolactone receptors and observation of the regulatory dynamics for strigolactone signal transduction in Striga.","corpus_id":9968741,"score":2},{"doc_id":"26450211","title":"Structure-function analysis identifies highly sensitive strigolactone receptors in Striga.","abstract":"Strigolactones are naturally occurring signaling molecules that affect plant development, fungi-plant interactions, and parasitic plant infestations. We characterized the function of 11 strigolactone receptors from the parasitic plant Striga hermonthica using chemical and structural biology. We found a clade of polyspecific receptors, including one that is sensitive to picomolar concentrations of strigolactone. A crystal structure of a highly sensitive strigolactone receptor from Striga revealed a larger binding pocket than that of the Arabidopsis receptor, which could explain the increased range of strigolactone sensitivity. Thus, the sensitivity of Striga to strigolactones from host plants is driven by receptor sensitivity. By expressing strigolactone receptors in Arabidopsis, we developed a bioassay that can be used to identify chemicals and crops with altered strigolactone levels.","corpus_id":24993088,"score":2},{"doc_id":"26470846","title":"Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.","abstract":"Strigolactones (SLs) are endogenous hormones and exuded signaling molecules in plant responses to low levels of mineral nutrients. Key mediators of the SL signaling pathway in rice include the α/β-fold hydrolase DWARF 14 (D14) and the F-box component DWARF 3 (D3) of the ubiquitin ligase SCF(D3) that mediate ligand-dependent degradation of downstream signaling repressors. One perplexing feature is that D14 not only functions as the SL receptor but is also an active enzyme that slowly hydrolyzes diverse natural and synthetic SLs including GR24, preventing the crystallization of a binary complex of D14 with an intact SL as well as the ternary D14/SL/D3 complex. Here we overcome these barriers to derive a structural model of D14 bound to intact GR24 and identify the interface that is required for GR24-mediated D14-D3 interaction. The mode of GR24-mediated signaling, including ligand recognition, hydrolysis by D14, and ligand-mediated D14-D3 interaction, is conserved in structurally diverse SLs. More importantly, D14 is destabilized upon the binding of ligands and D3, thus revealing an unusual mechanism of SL recognition and signaling, in which the hormone, the receptor, and the downstream effectors are systematically destabilized during the signal transduction process.","corpus_id":34622367,"score":2},{"doc_id":"26546446","title":"Strigolactone Signaling in Arabidopsis Regulates Shoot Development by Targeting D53-Like SMXL Repressor Proteins for Ubiquitination and Degradation.","abstract":"Strigolactones (SLs) are carotenoid-derived phytohormones that control many aspects of plant development, including shoot branching, leaf shape, stem secondary thickening, and lateral root growth. In rice (Oryza sativa), SL signaling requires the degradation of DWARF53 (D53), mediated by a complex including D14 and D3, but in Arabidopsis thaliana, the components and mechanism of SL signaling involving the D3 ortholog MORE AXILLARY GROWTH2 (MAX2) are unknown. Here, we show that SL-dependent regulation of shoot branching in Arabidopsis requires three D53-like proteins, SUPPRESSOR OF MORE AXILLARY GROWTH2-LIKE6 (SMXL6), SMXL7, and SMXL8. The smxl6 smxl7 smxl8 triple mutant suppresses the highly branched phenotypes of max2 and the SL-deficient mutant max3. Overexpression of a mutant form of SMXL6 that is resistant to SL-induced ubiquitination and degradation enhances shoot branching. Exogenous application of the SL analog rac-GR24 causes ubiquitination and degradation of SMXL6, 7, and 8; this requires D14 and MAX2. D53-like SMXLs form complexes with MAX2 and TOPLESS-RELATED PROTEIN2 (TPR2) and interact with D14 in a GR24-responsive manner. Furthermore, D53-like SMXLs exhibit TPR2-dependent transcriptional repression activity and repress the expression of BRANCHED1. Our findings reveal that in Arabidopsis, D53-like SMXLs act with TPR2 to repress transcription and so allow lateral bud outgrowth but that SL-induced degradation of D53-like proteins activates transcription to inhibit outgrowth.","corpus_id":23978379,"score":2},{"doc_id":"26546447","title":"SMAX1-LIKE/D53 Family Members Enable Distinct MAX2-Dependent Responses to Strigolactones and Karrikins in Arabidopsis.","abstract":"The plant hormones strigolactones and smoke-derived karrikins are butenolide signals that control distinct aspects of plant development. Perception of both molecules in Arabidopsis thaliana requires the F-box protein MORE AXILLARY GROWTH2 (MAX2). Recent studies suggest that the homologous SUPPRESSOR OF MAX2 1 (SMAX1) in Arabidopsis and DWARF53 (D53) in rice (Oryza sativa) are downstream targets of MAX2. Through an extensive analysis of loss-of-function mutants, we demonstrate that the Arabidopsis SMAX1-LIKE genes SMXL6, SMXL7, and SMXL8 are co-orthologs of rice D53 that promote shoot branching. SMXL7 is degraded rapidly after treatment with the synthetic strigolactone mixture rac-GR24. Like D53, SMXL7 degradation is MAX2- and D14-dependent and can be prevented by deletion of a putative P-loop. Loss of SMXL6,7,8 suppresses several other strigolactone-related phenotypes in max2, including increased auxin transport and PIN1 accumulation, and increased lateral root density. Although only SMAX1 regulates germination and hypocotyl elongation, SMAX1 and SMXL6,7,8 have complementary roles in the control of leaf morphology. Our data indicate that SMAX1 and SMXL6,7,8 repress karrikin and strigolactone signaling, respectively, and suggest that all MAX2-dependent growth effects are mediated by degradation of SMAX1/SMXL proteins. We propose that functional diversification within the SMXL family enabled responses to different butenolide signals through a shared regulatory mechanism.","corpus_id":7658561,"score":2},{"doc_id":"26779242","title":"Evidence that KARRIKIN-INSENSITIVE2 (KAI2) Receptors may Perceive an Unknown Signal that is not Karrikin or Strigolactone.","abstract":"The α/β-hydrolases KAI2 and D14 are paralogous receptors for karrikins and strigolactones, two classes of plant growth regulators with butenolide moieties. KAI2 and D14 act in parallel signaling pathways that share a requirement for the F-box protein MAX2, but produce distinct growth responses by regulating different members of the SMAX1-LIKE/D53 family. kai2 and max2 mutants share seed germination, seedling growth, leaf shape, and petiole orientation phenotypes that are not found in d14 or SL-deficient mutants. This implies that KAI2 recognizes an unknown, endogenous signal, herein termed KAI2 ligand (KL). Recent studies of ligand-specificity among KAI2 paralogs in basal land plants and root parasitic plants suggest that karrikin and strigolactone perception may be evolutionary adaptations of KL receptors. Here we demonstrate that evolutionarily conserved KAI2c genes from two parasite species rescue multiple phenotypes of the Arabidopsis kai2 mutant, unlike karrikin-, and strigolactone-specific KAI2 paralogs. We hypothesize that KAI2c proteins recognize KL, which could be an undiscovered hormone.","corpus_id":16787226,"score":2},{"doc_id":"26838034","title":"Strigolactones: new plant hormones in action.","abstract":"MAIN CONCLUSION: The key step in the mode of action of strigolactones is the enzymatic detachment of the D-ring. The thus formed hydroxy butenolide induces conformational changes of the receptor pocket which trigger a cascade of reactions in the signal transduction. Strigolactones (SLs) constitute a new class of plant hormones which are of increasing importance in plant science. For the last 60 years, they have been known as germination stimulants for parasitic plants. Recently, several new bio-properties of SLs have been discovered such as the branching factor for arbuscular mycorrhizal fungi, regulation of plant architecture (inhibition of bud outgrowth and of shoot branching) and the response to abiotic factors, etc. To broaden horizons and encourage new ideas for identifying and synthesising new and structurally simple SLs, this review is focused on molecular aspects of this new class of plant hormones. Special attention has been given to structural features, the mode of action of these phytohormones in various biological actions, the design of SL analogs and their applications.","corpus_id":14113210,"score":2},{"doc_id":"26851153","title":"Smoke and Hormone Mirrors: Action and Evolution of Karrikin and Strigolactone Signaling.","abstract":"Karrikins and strigolactones are two classes of butenolide molecules that have diverse effects on plant growth. Karrikins are found in smoke and strigolactones are plant hormones, yet both molecules are likely recognized through highly similar signaling mechanisms. Here we review the most recent discoveries of karrikin and strigolactone perception and signal transduction. Two paralogous α/β hydrolases, KAI2 and D14, are respectively karrikin and strigolactone receptors. D14 acts with an F-box protein, MAX2, to target SMXL/D53 family proteins for proteasomal degradation, and genetic data suggest that KAI2 acts similarly. There are striking parallels in the signaling mechanisms of karrikins, strigolactones, and other plant hormones, including auxins, jasmonates, and gibberellins. Recent investigations of host perception in parasitic plants have demonstrated that strigolactone recognition can evolve following gene duplication of KAI2.","corpus_id":10825561,"score":2},{"doc_id":"26875827","title":"Characterization of DWARF14 Genes in Populus.","abstract":"Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching mutants in herbaceous plants have identified several key genes involved in strigolactone biosynthesis or signaling. The strigolactone signal is perceived by a member of the α/β-fold hydrolase superfamily, known as DWARF14 (D14). However, little is known about D14 genes in the woody perennial plants. Here we report the identification of D14 homologs in the model woody plant Populus trichocarpa. We showed that there are two D14 homologs in P. trichocarpa, designated as PtD14a and PtD14b that are over 95% similar at the amino acid level. Expression analysis indicated that the transcript level of PtD14a is generally more abundant than that of PtD14b. However, only PtD14a was able to complement Arabidopsis d14 mutants, suggesting that PtD14a is the functional D14 ortholog. Amino acid alignment and structural modeling revealed substitutions of several highly conserved amino acids in the PtD14b protein including a phenylalanine near the catalytic triad of D14 proteins. This study lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants.","corpus_id":18561879,"score":2},{"doc_id":"26979323","title":"Structural modelling and transcriptional responses highlight a clade of PpKAI2-LIKE genes as candidate receptors for strigolactones in Physcomitrella patens.","abstract":"MAIN CONCLUSION: A set of PpKAI2 - LIKE paralogs that may encode strigolactone receptors in Physcomitrella patens were identified through evolutionary, structural, and transcriptional analyses, suggesting that strigolactone perception may have evolved independently in basal land plants in a similar manner as spermatophytes. Carotenoid-derived compounds known as strigolactones are a new class of plant hormones that modulate development and interactions with parasitic plants and arbuscular mycorrhizal fungi. The strigolactone receptor protein DWARF14 (D14) belongs to the α/β hydrolase family. D14 is closely related to KARRIKIN INSENSITIVE2 (KAI2), a receptor of smoke-derived germination stimulants called karrikins. Strigolactone and karrikin structures share a butenolide ring that is necessary for bioactivity. Charophyte algae and basal land plants produce strigolactones that influence their development. However phylogenetic studies suggest that D14 is absent from algae, moss, and liverwort genomes, raising the question of how these basal plants perceive strigolactones. Strigolactone perception during seed germination putatively evolved in parasitic plants through gene duplication and neofunctionalization of KAI2 paralogs. The moss Physcomitrella patens shows an increase in KAI2 gene copy number, similar to parasitic plants. In this study we investigated whether P. patens KAI2-LIKE (PpKAI2L) genes may contribute to strigolactone perception. Based on phylogenetic analyses and homology modelling, we predict that a clade of PpKAI2L proteins have enlarged ligand-binding cavities, similar to D14. We observed that some PpKAI2L genes have transcriptional responses to the synthetic strigolactone GR24 racemate or its enantiomers. These responses were influenced by light and dark conditions. Moreover, (+)-GR24 seems to be the active enantiomer that induces the transcriptional responses of PpKAI2L genes. We hypothesize that members of specific PpKAI2L clades are candidate strigolactone receptors in moss.","corpus_id":14269467,"score":2},{"doc_id":"27194725","title":"LATERAL BRANCHING OXIDOREDUCTASE acts in the final stages of strigolactone biosynthesis in Arabidopsis.","abstract":"Strigolactones are a group of plant compounds of diverse but related chemical structures. They have similar bioactivity across a broad range of plant species, act to optimize plant growth and development, and promote soil microbe interactions. Carlactone, a common precursor to strigolactones, is produced by conserved enzymes found in a number of diverse species. Versions of the MORE AXILLARY GROWTH1 (MAX1) cytochrome P450 from rice and Arabidopsis thaliana make specific subsets of strigolactones from carlactone. However, the diversity of natural strigolactones suggests that additional enzymes are involved and remain to be discovered. Here, we use an innovative method that has revealed a missing enzyme involved in strigolactone metabolism. By using a transcriptomics approach involving a range of treatments that modify strigolactone biosynthesis gene expression coupled with reverse genetics, we identified LATERAL BRANCHING OXIDOREDUCTASE (LBO), a gene encoding an oxidoreductase-like enzyme of the 2-oxoglutarate and Fe(II)-dependent dioxygenase superfamily. Arabidopsis lbo mutants exhibited increased shoot branching, but the lbo mutation did not enhance the max mutant phenotype. Grafting indicated that LBO is required for a graft-transmissible signal that, in turn, requires a product of MAX1. Mutant lbo backgrounds showed reduced responses to carlactone, the substrate of MAX1, and methyl carlactonoate (MeCLA), a product downstream of MAX1. Furthermore, lbo mutants contained increased amounts of these compounds, and the LBO protein specifically converts MeCLA to an unidentified strigolactone-like compound. Thus, LBO function may be important in the later steps of strigolactone biosynthesis to inhibit shoot branching in Arabidopsis and other seed plants.","corpus_id":38452643,"score":2},{"doc_id":"27317673","title":"SMAX1-LIKE7 Signals from the Nucleus to Regulate Shoot Development in Arabidopsis via Partially EAR Motif-Independent Mechanisms.","abstract":"Strigolactones (SLs) are hormonal signals that regulate multiple aspects of shoot architecture, including shoot branching. Like many plant hormonal signaling systems, SLs act by promoting ubiquitination of target proteins and their subsequent proteasome-mediated degradation. Recently, SMXL6, SMXL7, and SMXL8, members of the SMAX1-LIKE (SMXL) family of chaperonin-like proteins, have been identified as proteolytic targets of SL signaling in Arabidopsis thaliana However, the mechanisms by which these proteins regulate downstream events remain largely unclear. Here, we show that SMXL7 functions in the nucleus, as does the SL receptor, DWARF14 (D14). We show that nucleus-localized D14 can physically interact with both SMXL7 and the MAX2 F-box protein in a SL-dependent manner and that disruption of specific conserved domains in SMXL7 affects its localization, SL-induced degradation, and activity. By expressing and overexpressing these SMXL7 protein variants, we show that shoot tissues are broadly sensitive to SMXL7 activity, but degradation normally buffers the effect of increasing SMXL7 expression. SMXL7 contains a well-conserved EAR (ETHYLENE-RESPONSE FACTOR Amphiphilic Repression) motif, which contributes to, but is not essential for, SMXL7 functionality. Intriguingly, different developmental processes show differential sensitivity to the loss of the EAR motif, raising the possibility that there may be several distinct mechanisms at play downstream of SMXL7.","corpus_id":11073468,"score":2},{"doc_id":"27318656","title":"Strigolactones, super hormones in the fight against Striga.","abstract":"Strigolactones are plant hormones that control diverse aspects of plant growth, but are also exuded into soil as recruitment signals for arbuscular mycorrhizal fungi interactions. Highly damaging parasitic weeds in the Orobanchaceae family have coopted strigolactones as germination cues that indicate the presence of a host. Recent studies have established how strigolactones are actively transported within and out of plants. Key components of the strigolactone signaling system have been identified, including strigolactone receptors in angiosperms and parasites, as well as downstream targets that are polyubiquitinated and proteolyzed following strigolactone perception. The basis for protein-protein interactions among these signaling components has also been explored. We propose several strategies to translate current knowledge of strigolactone transport and signaling into parasite control methods.","corpus_id":3495518,"score":2},{"doc_id":"27479744","title":"An histidine covalent receptor and butenolide complex mediates strigolactone perception.","abstract":"Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand.","corpus_id":19600033,"score":2},{"doc_id":"27602041","title":"Perception and Signaling of Strigolactones.","abstract":"Strigolactones (SLs), a recently discovered class of phytohormones, are important regulators of plant growth and development. While the biosynthetic pathway of these molecules is well documented, until recently there was not much known about the molecular mechanisms underlying SL perception and signal transduction in plants. Certain aspects of their perception and signaling, including the hormone-mediated interaction between receptor and F-box protein, degradation of suppressor proteins and activation of transcription factors, are also found in other phytohormones. However, some of SL signaling features seem to be specific for the SL signaling pathway. These include the enzymatic activity of the SL receptor and its destabilization caused by SLs. This review summarizes the current knowledge about SL signaling pathway in plants.","corpus_id":5715306,"score":2},{"doc_id":"27670819","title":"Phloem Transport of the Receptor DWARF14 Protein Is Required for Full Function of Strigolactones.","abstract":"The cell-to-cell transport of signaling molecules is essential for multicellular organisms to coordinate the action of their cells. Recent studies identified DWARF14 (D14) as a receptor of strigolactones (SLs), molecules that act as plant hormones and inhibit shoot branching. Here, we demonstrate that RAMOSUS3, a pea ortholog of D14, works as a graft-transmissible signal to suppress shoot branching. In addition, we show that D14 protein is contained in phloem sap and transported through the phloem to axillary buds in rice. SLs are not required for the transport of D14 protein. Disruption of D14 transport weakens the suppression of axillary bud outgrowth of rice. Taken together, we conclude that the D14 protein works as an intercellular signaling molecule to fine-tune SL function. Our findings provide evidence that the intercellular transport of a receptor can regulate the action of plant hormones.","corpus_id":33994659,"score":2},{"doc_id":"27760882","title":"Low-Phosphate Induction of Plastidal Stromules Is Dependent on Strigolactones But Not on the Canonical Strigolactone Signaling Component MAX2.","abstract":"Stromules are highly dynamic protrusions of the plastids in plants. Several factors, such as drought and light conditions, influence the stromule frequency (SF) in a positive or negative way. A relatively recently discovered class of plant hormones are the strigolactones; strigolactones inhibit branching of the shoots and promote beneficial interactions between roots and arbuscular mycorrhizal fungi. Here, we investigate the link between the formation of stromules and strigolactones. This research shows a strong link between strigolactones and the formation of stromules: SF correlates with strigolactone levels in the wild type and strigolactone mutants (max2-1 max3-9), and SF is stimulated by strigolactone GR24 and reduced by strigolactone inhibitor D2.","corpus_id":34099988,"score":2},{"doc_id":"27793831","title":"Strigolactone regulates shoot development through a core signalling pathway.","abstract":"Strigolactones are a recently identified class of hormone that regulate multiple aspects of plant development. The DWARF14 (D14) α/β fold protein has been identified as a strigolactone receptor, which can act through the SCF(MAX2) ubiquitin ligase, but the universality of this mechanism is not clear. Multiple proteins have been suggested as targets for strigolactone signalling, including both direct proteolytic targets of SCF(MAX2), and downstream targets. However, the relevance and importance of these proteins to strigolactone signalling in many cases has not been fully established. Here we assess the contribution of these targets to strigolactone signalling in adult shoot developmental responses. We find that all examined strigolactone responses are regulated by SCF(MAX2) and D14, and not by other D14-like proteins. We further show that all examined strigolactone responses likely depend on degradation of SMXL proteins in the SMXL6 clade, and not on the other proposed proteolytic targets BES1 or DELLAs. Taken together, our results suggest that in the adult shoot, the dominant mode of strigolactone signalling is D14-initiated, MAX2-mediated degradation of SMXL6-related proteins. We confirm that the BRANCHED1 transcription factor and the PIN-FORMED1 auxin efflux carrier are plausible downstream targets of this pathway in the regulation of shoot branching, and show that BRC1 likely acts in parallel to PIN1.","corpus_id":7622552,"score":2},{"doc_id":"28392107","title":"Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation.","abstract":"Plant stem cell niches, the meristems, require long-distance transport of energy metabolites and signaling molecules along the phloem tissue. However, currently it is unclear how specification of phloem cells is controlled. Here we show that the genes SUPPRESSOR OF MAX2 1-LIKE3 (SMXL3), SMXL4, and SMXL5 act as cell-autonomous key regulators of phloem formation in Arabidopsis thaliana. The three genes form an uncharacterized subclade of the SMXL gene family that mediates hormonal strigolactone and karrikin signaling. Strigolactones are endogenous signaling molecules regulating shoot and root branching [1] whereas exogenous karrikin molecules induce germination after wildfires [2]. Both activities depend on the F-box protein and SCF (Skp, Cullin, F-box) complex component MORE AXILLARY GROWTH2 (MAX2) [3-5]. Strigolactone and karrikin perception leads to MAX2-dependent degradation of distinct SMXL protein family members, which is key for mediating hormonal effects [6-12]. However, the nature of events immediately downstream of SMXL protein degradation and whether all SMXL proteins mediate strigolactone or karrikin signaling is unknown. In this study we demonstrate that, within the SMXL gene family, specifically SMXL3/4/5 deficiency results in strong defects in phloem formation, altered sugar accumulation, and seedling lethality. By comparing protein stabilities, we show that SMXL3/4/5 proteins function differently to canonical strigolactone and karrikin signaling mediators, although being functionally interchangeable with those under low strigolactone/karrikin signaling conditions. Our observations reveal a fundamental mechanism of phloem formation and indicate that diversity of SMXL protein functions is essential for a steady fuelling of plant meristems.","corpus_id":13456775,"score":2},{"doc_id":"28558130","title":"Strigolactones, karrikins and beyond.","abstract":"The plant hormones strigolactones are synthesized from carotenoids and signal via the α/β hydrolase DWARF 14 (D14) and the F-box protein MORE AXILLARY GROWTH 2 (MAX2). Karrikins, molecules produced upon fire, share MAX2 for signalling, but depend on the D14 paralog KARRIKIN INSENSITIVE 2 (KAI2) for perception with strong evidence that the MAX2-KAI2 protein complex might also recognize so far unknown plant-made karrikin-like molecules. Thus, the phenotypes of the max2 mutants are the complex consequence of a loss of both D14-dependent and KAI2-dependent signalling, hence, the reason why some biological roles, attributed to strigolactones based on max2 phenotypes, could never be observed in d14 or in the strigolactone-deficient max3 and max4 mutants. Moreover, the broadly used synthetic strigolactone analog rac-GR24 has been shown to mimic strigolactone as well as karrikin(-like) signals, providing an extra level of complexity in the distinction of the unique and common roles of both molecules in plant biology. Here, a critical overview is provided of the diverse biological processes regulated by strigolactones and/or karrikins. These two growth regulators are considered beyond their boundaries, and the importance of the yet unknown karrikin-like molecules is discussed as well.","corpus_id":5158228,"score":2},{"doc_id":"28662667","title":"Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.","abstract":"BACKGROUND: Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. RESULTS: We have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analysed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We show that eu-KAI2 proteins are highly conserved, and have unique features not found in DDK proteins. Conversely, we show that DDK proteins show considerable sequence and structural variation to each other, and lack clearly definable characteristics. We use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2 and that SL receptors in non-seed plants likely do not have D14-like structure. We also show that certain groups of DDK proteins lack the otherwise conserved MORE AXILLARY GROWTH2 (MAX2) interface, and may thus function independently of MAX2, which we show is highly conserved throughout land plant evolution. CONCLUSIONS: Our results suggest that D14-like structure is not required for SL perception, and that SL perception has relatively relaxed structural requirements compared to KAI2-mediated signalling. We suggest that SL perception gradually evolved by neo-functionalization within the DDK lineage, and that the transition from KAI2-like to D14-like protein may have been driven by interactions with protein partners, rather than being required for SL perception per se.","corpus_id":1176031,"score":2},{"doc_id":"28970845","title":"Comprehensive Analysis of DWARF14-LIKE2 (DLK2) Reveals Its Functional Divergence from Strigolactone-Related Paralogs.","abstract":"Strigolactones (SLs) and related butenolides, originally identified as active seed germination stimulants of parasitic weeds, play important roles in many aspects of plant development. Two members of the D14 α/β hydrolase protein family, DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are essential for SL/butenolide signaling. The third member of the family in Arabidopsis, DWARF 14-LIKE2 (DLK2) is structurally very similar to D14 and KAI2, but its function is unknown. We demonstrated that DLK2 does not bind nor hydrolyze natural (+)5-deoxystrigol [(+)5DS], and weakly hydrolyzes non-natural strigolactone (-)5DS. A detailed genetic analysis revealed that DLK2 does not affect SL responses and can regulate seedling photomorphogenesis. DLK2 is upregulated in the dark dependent upon KAI2 and PHYTOCHROME INTERACTING FACTORS (PIFs), indicating that DLK2 might function in light signaling pathways. In addition, unlike its paralog proteins, DLK2 is not subject to rac-GR24-induced degradation, suggesting that DLK2 acts independently of MORE AXILLARY GROWTH2 (MAX2); however, regulation of DLK2 transcription is mostly accomplished through MAX2. In conclusion, these data suggest that DLK2 represents a divergent member of the DWARF14 family.","corpus_id":23801725,"score":2},{"doc_id":"29170677","title":"DWARF14, A Receptor Covalently Linked with the Active Form of Strigolactones, Undergoes Strigolactone-Dependent Degradation in Rice.","abstract":"Strigolactones (SLs) are the latest confirmed phytohormones that regulate shoot branching by inhibiting bud outgrowth in higher plants. Perception of SLs depends on a novel mechanism employing an enzyme-receptor DWARF14 (D14) that hydrolyzes SLs and becomes covalently modified. This stimulates the interaction between D14 and D3, leading to the ubiquitination and degradation of the transcriptional repressor protein D53. However, the regulation of SL perception in rice remains elusive. In this study, we provide evidences that D14 is ubiquitinated after SL treatment and degraded through the 26S proteasome system. The Lys280 site of the D14 amino acid sequence was important for SL-induced D14 degradation, but did not change the subcellular localization of D14 nor disturbed the interaction between D14 and D3, nor D53 degradation. Biochemical and genetic analysis indicated that the key amino acids in the catalytic center of D14 were essential for D14 degradation. We further showed that D14 degradation is dependent on D3 and is tightly correlated with protein levels of D53. These findings revealed that D14 degradation takes place following D53 degradation and functions as an important feedback regulation mechanism of SL perception in rice.","corpus_id":5617131,"score":2},{"doc_id":"29365172","title":"Rice DWARF14 acts as an unconventional hormone receptor for strigolactone.","abstract":"Strigolactones (SLs) act as an important class of phytohormones to regulate plant shoot branching, and also serve as rhizosphere signals to mediate interactions of host plants with soil microbes and parasitic weeds. SL receptors in dicots, such as DWARF14 in Arabidopsis (AtD14), RMS3 in pea, and ShHTL7 in Striga, serve as unconventional receptors that hydrolyze SLs into a D-ring-derived intermediate CLIM and irreversibly bind CLIM to trigger SL signal transduction. Here, we show that D14 from the monocot rice can complement Arabidopsis d14 mutant and interact with the SL signaling components in Arabidopsis. Our results further reveal that rice D14, similar to SL receptors in dicots, also serves as an unconventional hormone receptor that generates and irreversibly binds the active form of SLs. These findings uncover the conserved functions of D14 proteins in monocots and dicots.","corpus_id":13774480,"score":2},{"doc_id":"29394369","title":"The elusive ligand complexes of the DWARF14 strigolactone receptor.","abstract":"Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.","corpus_id":7569217,"score":2},{"doc_id":"29522151","title":"Which are the major players, canonical or non-canonical strigolactones?","abstract":"Strigolactones (SLs) can be classified into two structurally distinct groups: canonical and non-canonical SLs. Canonical SLs contain the ABCD ring system, and non-canonical SLs lack the A, B, or C ring but have the enol ether-D ring moiety, which is essential for biological activities. The simplest non-canonical SL is the SL biosynthetic intermediate carlactone. In plants, carlactone and its oxidized metabolites, such as carlactonoic acid and methyl carlactonoate, are present in root and shoot tissues. In some plant species, including black oat (Avena strigosa), sunflower (Helianthus annuus), and maize (Zea mays), non-canonical SLs in the root exudates are major germination stimulants. Various plant species, such as tomato (Solanum lycopersicum), Arabidopsis, and poplar (Populus spp.), release carlactonoic acid into the rhizosphere. These observations suggest that both canonical and non-canonical SLs act as host-recognition signals in the rhizosphere. In contrast, the limited distribution of canonical SLs in the plant kingdom, and the structure-specific and stereospecific transportation of canonical SLs from roots to shoots, suggest that plant hormones inhibiting shoot branching are not canonical SLs but, rather, are non-canonical SLs.","corpus_id":27076314,"score":2},{"doc_id":"29532023","title":"Discovery of Shoot Branching Regulator Targeting Strigolactone Receptor DWARF14.","abstract":"DWARF14 (D14) is a strigolactone receptor that plays a central role in suppression of shoot branching, and hence is a potential target to increase crop productions and biomass. Recently, we reported a fluorescence turn-on probe, Yoshimulactone Green (YLG), which generates a strong fluorescence upon the hydrolysis by D14-type strigolactone receptors. Herein, we applied a YLG-based in vitro assay to a high-throughput chemical screening and identified a novel small molecule DL1 as a potent inhibitor of D14. DL1 competes with endogenous strigolactones, thereby increasing the number of shoot branching in a model plant Arabidopsis as well as in rice. Thus, DL1 is expected to be useful not only as a tool to understand the biological roles of D14 receptors in plant growth and development, but also as a potent agrochemical to improve the crop yield.","corpus_id":3888246,"score":2},{"doc_id":"29554337","title":"Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay.","abstract":"Strigolactones (SLs) are plant hormones with various functions in development, responses to stress, and interactions with (micro)organisms in the rhizosphere, including with seeds of parasitic plants. Their perception for hormonal functions requires an α,β-hydrolase belonging to the D14 clade in higher plants; perception of host-produced SLs by parasitic seeds relies on similar but phylogenetically distinct proteins (D14-like). D14 and D14-like proteins are peculiar receptors, because they cleave SLs before undergoing a conformational change that elicits downstream events. Structure-activity relationship data show that the butenolide D-ring is crucial for bioactivity. We applied a bioisosteric approach to the structure of SLs by synthetizing analogues and mimics of natural SLs in which the D-ring was changed from a butenolide to a lactam and then evaluating their bioactivity. This was done by using a novel bioassay based on Arabidopsis transgenic lines expressing AtD14 fused to firefly luciferase, in parallel with the quantification of germination-inducing activity on parasitic seeds. The results obtained showed that the in planta bioassay is robust and quantitative, and thus can be confidently added to the SL-survey toolbox. The results also showed that modification of the butenolide ring into a lactam one significantly hampers the biological activity exhibited by SLs possessing a canonical lactonic D-ring.","corpus_id":4045211,"score":2},{"doc_id":"29727000","title":"Rationally Designed Strigolactone Analogs as Antagonists of the D14 Receptor.","abstract":"Strigolactones (SLs) are plant hormones that inhibit shoot branching and act as signals in communications with symbiotic fungi and parasitic weeds in the rhizosphere. SL signaling is mediated by DWARF14 (D14), which is an α/β-hydrolase that cleaves SLs into an ABC tricyclic lactone and a butenolide group (i.e. D-ring). This cleavage reaction (hydrolysis and dissociation) is important for inducing the interaction between D14 and its target proteins, including D3 and D53. In this study, a hydrolysis-resistant SL analog was predicted to inhibit the activation of the D14 receptor, thereby disrupting the SL signaling pathway. To test this prediction, carba-SL compounds, in which the ether oxygen of the D-ring or the phenol ether oxygen of the SL agonist (GR24 or 4-bromo debranone) was replaced with a methylene group, were synthesized as novel D14 antagonists. Subsequent biochemical and physiological studies indicated that carba-SLs blocked the interaction between D14 and D53 by inhibiting D14 hydrolytic activity. They also suppressed the SL-induced inhibition of rice tiller outgrowths. Additionally, carba-SLs antagonized the SL response in a Striga parasitic weed species. Structural analyses revealed that the D-ring of 7'-carba-4BD was hydrolyzed by D14 but did not dissociate from the 4BD skeleton. Thus, 7'-carba-4BD functioned as an antagonist rather than an agonist. Thus, the hydrolysis of the D-ring of SLs may be insufficient for activating the receptor. This study provides data relevant to designing SL receptor antagonists.","corpus_id":19126937,"score":2},{"doc_id":"26308901","title":"Allosteric receptor activation by the plant peptide hormone phytosulfokine.","abstract":"Phytosulfokine (PSK) is a disulfated pentapeptide that has a ubiquitous role in plant growth and development. PSK is perceived by its receptor PSKR, a leucine-rich repeat receptor kinase (LRR-RK). The mechanisms underlying the recognition of PSK, the activation of PSKR and the identity of the components downstream of the initial binding remain elusive. Here we report the crystal structures of the extracellular LRR domain of PSKR in free, PSK- and co-receptor-bound forms. The structures reveal that PSK interacts mainly with a β-strand from the island domain of PSKR, forming an anti-β-sheet. The two sulfate moieties of PSK interact directly with PSKR, sensitizing PSKR recognition of PSK. Supported by biochemical, structural and genetic evidence, PSK binding enhances PSKR heterodimerization with the somatic embryogenesis receptor-like kinases (SERKs). However, PSK is not directly involved in PSKR-SERK interaction but stabilizes PSKR island domain for recruitment of a SERK. Our data reveal the structural basis for PSKR recognition of PSK and allosteric activation of PSKR by PSK, opening up new avenues for the design of PSKR-specific small molecules.","corpus_id":4467542,"score":0}],"string":"[\n {\n \"doc_id\": \"18690209\",\n \"title\": \"Strigolactone inhibition of shoot branching.\",\n \"abstract\": \"A carotenoid-derived hormonal signal that inhibits shoot branching in plants has long escaped identification. Strigolactones are compounds thought to be derived from carotenoids and are known to trigger the germination of parasitic plant seeds and stimulate symbiotic fungi. Here we present evidence that carotenoid cleavage dioxygenase 8 shoot branching mutants of pea are strigolactone deficient and that strigolactone application restores the wild-type branching phenotype to ccd8 mutants. Moreover, we show that other branching mutants previously characterized as lacking a response to the branching inhibition signal also lack strigolactone response, and are not deficient in strigolactones. These responses are conserved in Arabidopsis. In agreement with the expected properties of the hormonal signal, exogenous strigolactone can be transported in shoots and act at low concentrations. We suggest that endogenous strigolactones or related compounds inhibit shoot branching in plants. Furthermore, ccd8 mutants demonstrate the diverse effects of strigolactones in shoot branching, mycorrhizal symbiosis and parasitic weed interaction.\",\n \"corpus_id\": 205214618,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542179\",\n \"title\": \"d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers.\",\n \"abstract\": \"Recent studies using highly branched mutants of pea, Arabidopsis and rice have demonstrated that strigolactones, a group of terpenoid lactones, act as a new hormone class, or its biosynthetic precursors, in inhibiting shoot branching. Here, we provide evidence that DWARF14 (D14) inhibits rice tillering and may act as a new compo-nent of the strigolactone-dependent branching inhibition pathway. The d14 mutant exhibits increased shoot branch-ing with reduced plant height like the previously characterized strigolactone-deficient and -insensitive mutants d10 and d3, respectively. The d10-1 d14-1 double mutant is phenotypically indistinguishable from the d10-1 and d14-1 single mutants, consistent with the idea that D10 and D14 function in the same pathway. However, unlike with d10, the d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2'-epi-5-deoxystrigol than the wild type. Positional cloning revealed that D14 encodes a protein of the alpha/beta-fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones. We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form.\",\n \"corpus_id\": 11534217,\n \"score\": 2\n },\n {\n \"doc_id\": \"19726222\",\n \"title\": \"Strigolactones: a new hormone with a past.\",\n \"abstract\": \"The recent discovery of an endogenous hormonal activity for strigolactones in shoot branching was surprising since these molecules were thought to mostly play roles as signaling molecules between organisms. Even in the context of plant hormones, strigolactones appear to be different in that their role in plant development is quite restricted. This most probably reflects early days and new hormonal functions will most probably be found for these compounds in the future. In this respect, the exogenous role of strigolactones in parasitic plant seed germination may hint to functions of this compound in seed development. However, showing new roles for strigolactones in the seed or any other aspect of plant development for that matter will require developing assays in model genetic systems such as Arabidopsis and rice where we can take full advantage of the experimental tools that are available.\",\n \"corpus_id\": 21288092,\n \"score\": 2\n },\n {\n \"doc_id\": \"19913454\",\n \"title\": \"New genes in the strigolactone-related shoot branching pathway.\",\n \"abstract\": \"Shoot branching is controlled by the formation and subsequent outgrowth of axillary buds in the axils of leaves. Axillary buds are indeterminate structures that can be arrested and await endogenous or environmental cues for outgrowth. A major breakthrough in this area of plant development has been the discovery that a specific group of terpenoid lactones, named strigolactones, can directly or indirectly, inhibit axillary bud outgrowth. Since that discovery, new branching mutants have been identified with reduced strigolactone levels or which are defective in strigolactone regulation or response. DWARF27 and DWARF14 probably act on strigolactone biosynthesis and strigolactone metabolism or signal transduction, respectively. Auxin signaling mutants have also been useful in demonstrating that strigolactone levels are mediated by a classical auxin signal transduction pathway. The discovery and characterization of these mutants is an important first step toward understanding the mechanisms of strigolactone biosynthesis and signaling and their importance in regulating shoot branching.\",\n \"corpus_id\": 22923139,\n \"score\": 2\n },\n {\n \"doc_id\": \"21119045\",\n \"title\": \"Strigolactones are transported through the xylem and play a key role in shoot architectural response to phosphate deficiency in nonarbuscular mycorrhizal host Arabidopsis.\",\n \"abstract\": \"The biosynthesis of the recently identified novel class of plant hormones, strigolactones, is up-regulated upon phosphate deficiency in many plant species. It is generally accepted that the evolutionary origin of strigolactone up-regulation is their function as a rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi. In this work, we demonstrate that this induction is conserved in Arabidopsis (Arabidopsis thaliana), although Arabidopsis is not a host for arbuscular mycorrhizal fungi. We demonstrate that the increase in strigolactone production contributes to the changes in shoot architecture observed in response to phosphate deficiency. Using high-performance liquid chromatography, column chromatography, and multiple reaction monitoring-liquid chromatography-tandem mass spectrometry analysis, we identified two strigolactones (orobanchol and orobanchyl acetate) in Arabidopsis and have evidence of the presence of a third (5-deoxystrigol). We show that at least one of them (orobanchol) is strongly reduced in the putative strigolactone biosynthetic mutants more axillary growth1 (max1) and max4 but not in the signal transduction mutant max2. Orobanchol was also detected in xylem sap and up-regulated under phosphate deficiency, which is consistent with the idea that root-derived strigolactones are transported to the shoot, where they regulate branching. Moreover, two additional putative strigolactone-like compounds were detected in xylem sap, one of which was not detected in root exudates. Together, these results show that xylem-transported strigolactones contribute to the regulation of shoot architectural response to phosphate-limiting conditions.\",\n \"corpus_id\": 13264036,\n \"score\": 2\n },\n {\n \"doc_id\": \"21555559\",\n \"title\": \"F-box protein MAX2 has dual roles in karrikin and strigolactone signaling in Arabidopsis thaliana.\",\n \"abstract\": \"Smoke is an important abiotic cue for plant regeneration in postfire landscapes. Karrikins are a class of compounds discovered in smoke that promote seed germination and influence early development of many plants by an unknown mechanism. A genetic screen for karrikin-insensitive mutants in Arabidopsis thaliana revealed that karrikin signaling requires the F-box protein MAX2, which also mediates responses to the structurally-related strigolactone family of phytohormones. Karrikins and the synthetic strigolactone GR24 trigger similar effects on seed germination, seedling photomorphogenesis, and expression of a small set of genes during these developmental stages. Karrikins also repress MAX4 and IAA1 transcripts, which show negative feedback regulation by strigolactone. We demonstrate that all of these common responses are abolished in max2 mutants. Unlike strigolactones, however, karrikins do not inhibit shoot branching in Arabidopsis or pea, indicating that plants can distinguish between these signals. These results suggest that a MAX2-dependent signal transduction mechanism was adapted to mediate responses to two chemical cues with distinct roles in plant ecology and development.\",\n \"corpus_id\": 11583709,\n \"score\": 2\n },\n {\n \"doc_id\": \"22357928\",\n \"title\": \"Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis.\",\n \"abstract\": \"Karrikins are butenolides derived from burnt vegetation that stimulate seed germination and enhance seedling responses to light. Strigolactones are endogenous butenolide hormones that regulate shoot and root architecture, and stimulate the branching of arbuscular mycorrhizal fungi. Thus, karrikins and strigolactones are structurally similar but physiologically distinct plant growth regulators. In Arabidopsis thaliana, responses to both classes of butenolides require the F-box protein MAX2, but it remains unclear how discrete responses to karrikins and strigolactones are achieved. In rice, the DWARF14 protein is required for strigolactone-dependent inhibition of shoot branching. Here, we show that the Arabidopsis DWARF14 orthologue, AtD14, is also necessary for normal strigolactone responses in seedlings and adult plants. However, the AtD14 paralogue KARRIKIN INSENSITIVE 2 (KAI2) is specifically required for responses to karrikins, and not to strigolactones. Phylogenetic analysis indicates that KAI2 is ancestral and that AtD14 functional specialisation has evolved subsequently. Atd14 and kai2 mutants exhibit distinct subsets of max2 phenotypes, and expression patterns of AtD14 and KAI2 are consistent with the capacity to respond to either strigolactones or karrikins at different stages of plant development. We propose that AtD14 and KAI2 define a class of proteins that permit the separate regulation of karrikin and strigolactone signalling by MAX2. Our results support the existence of an endogenous, butenolide-based signalling mechanism that is distinct from the strigolactone pathway, providing a molecular basis for the adaptive response of plants to smoke.\",\n \"corpus_id\": 9432783,\n \"score\": 2\n },\n {\n \"doc_id\": \"22713366\",\n \"title\": \"The computational-based structure of Dwarf14 provides evidence for its role as potential strigolactone receptor in plants.\",\n \"abstract\": \"BACKGROUND: Strigolactones (SLs) are recently identified plant hormones modulating root and shoot branching. Besides their endogenous role within the producing organism, SLs are also key molecules in the communication of plants with arbuscular mycorrhizal (AM) fungi and parasitic weeds. In fact SLs are exuded into the rhizosphere where they act as a host-derived signal, stimulating the germination of the seeds of parasitic plants which would not survive in the absence of a host root to colonize. Similarly, their perception by AM fungi causes extensive hyphal branching; this is a prerequisite for effective root colonization, since it increases the number of potential contact points with the host surface. In spite of the crucial and multifaceted biological role of SLs, there is no information on the receptor(s) which bind(s) such active molecules, neither in the producing plants, or in parasitic weeds or AM fungi. RESULTS: In this work, we applied homology modelling techniques to investigate the structure of the protein encoded by the gene Dwarf14, which was first identified in rice as conferring SLs insensitivity when mutated. The best sequence identity was with bacterial RsbQ. Both proteins belong to the superfamily of alpha/beta-fold hydrolases, some members of which play a role in the metabolism or signalling of plant hormones. The Dwarf14 (D14) structure was refined by means of molecular dynamics simulations. In order to support the hypothesis that D14 could be an endogenous SLs receptor, we performed docking experiments with a natural ligand. CONCLUSIONS: It is suggested that D14 interacts with and thereby may act as a receptor for SLs in plants. This hypothesis offers a starting point to experimentally study the mechanism of its activity in vivo by means of structural, molecular and genetic approaches. Lastly, knowledge of the putative receptor structure will boost the research on analogues of the natural substrates as required for agricultural applications.\",\n \"corpus_id\": 12136692,\n \"score\": 2\n },\n {\n \"doc_id\": \"22959345\",\n \"title\": \"DAD2 is an α/β hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone.\",\n \"abstract\": \"Strigolactones are a recently discovered class of plant hormone involved in branching, leaf senescence, root development, and plant-microbe interactions. They are carotenoid-derived lactones, synthesized in the roots and transported acropetally to modulate axillary bud outgrowth (i.e., branching). However, a receptor for strigolactones has not been identified. We have identified the DAD2 gene from petunia, an ortholog of the rice and Arabidopsis D14 genes, and present evidence for its roles in strigolactone perception and signaling. DAD2 acts in the strigolactone pathway, and the dad2 mutant is insensitive to the strigolactone analog GR24. The crystal structure of DAD2 reveals an α/β hydrolase fold containing a canonical catalytic triad with a large internal cavity capable of accommodating strigolactones. In the presence of GR24 DAD2 interacts with PhMAX2A, a central component of strigolactone signaling, in a GR24 concentration-dependent manner. DAD2 can hydrolyze GR24, with mutants of the catalytic triad abolishing both this activity and the ability of DAD2 to interact with PhMAX2A. The hydrolysis products can neither stimulate the protein-protein interaction nor modulate branching. These observations suggest that DAD2 acts to bind the mobile strigolactone signal and then interacts with PhMAX2A during catalysis to initiate an SCF-mediated signal transduction pathway.\",\n \"corpus_id\": 15616452,\n \"score\": 2\n },\n {\n \"doc_id\": \"23025475\",\n \"title\": \"The D3 F-box protein is a key component in host strigolactone responses essential for arbuscular mycorrhizal symbiosis.\",\n \"abstract\": \"Arbuscular mycorrhiza (AM) represents an ancient endosymbiosis between plant roots and Glomeromycota fungi. Strigolactones (SLs), plant-derived terpenoid lactones, activate hyphal branching of AM fungi before physical contact. Lack of SL biosynthesis results in lower colonization of AM fungi. The F-box protein, DWARF3 (D3), and the hydrolase family protein DWARF14 (D14) are crucial for SL responses in rice. Here we conducted AM fungal colonization assays with the SL-insensitive d3 and d14 mutants. The d3 mutant exhibited strong defects in AM fungal colonization, whereas the d14 mutant showed higher AM fungal colonization. As D14 has a homologous protein, D14-LIKE, we generated D14-LIKE knockdown lines by RNA interference in the wildtype and d14 background. D14 and D14-LIKE double knockdown lines exhibited similar colonization rates as those of the d14-1 mutant. D3 is crucial for establishing AM symbiosis in rice, whereas D14 and D14-LIKE are not. Our results suggest distinct roles for these SL-related components in AM symbiosis.\",\n \"corpus_id\": 41759016,\n \"score\": 2\n },\n {\n \"doc_id\": \"23182342\",\n \"title\": \"The biology of strigolactones.\",\n \"abstract\": \"The strigolactones are rhizosphere signaling molecules as well as a new class of plant hormones with a still increasing number of biological functions being uncovered. Here, we review a recent major breakthrough in our understanding of strigolactone biosynthesis, which has revealed the unexpected simplicity of the originally postulated complex pathway. Moreover, the discovery and localization of a strigolactone exporter sheds new light on putative strigolactone fluxes to the rhizosphere as well as within the plant. The combination of these data with information on the expression and regulation of strigolactone biosynthetic and downstream signaling genes provides new insights into how strigolactones control the many different aspects of plant development and how their rhizosphere signaling role may have evolved.\",\n \"corpus_id\": 9546410,\n \"score\": 2\n },\n {\n \"doc_id\": \"23204501\",\n \"title\": \"Selective mimics of strigolactone actions and their potential use for controlling damage caused by root parasitic weeds.\",\n \"abstract\": \"Strigolactones (SLs) are a novel class of plant hormones and rhizosphere communication signals, although the molecular mechanisms underlying their activities have not yet been fully determined. Nor is their application in agriculture well developed. The importance of plant hormone agonists has been demonstrated in both basic and applied research, and chemicals that mimic strigolactone functions should greatly facilitate strigolactone research. Here, we report our discovery of a new phenoxyfuranone compound, 4-Br debranone (4BD), that shows similar activity to that of the major strigolactone (SL) analog GR24 in many aspects of a biological assay on plants. 4BD strongly inhibited tiller bud outgrowth in the SL-deficient rice mutant d10 at the same concentration as GR24, with no adverse effects, even during prolonged cultivation. This result was also observed in the Arabidopsis thaliana SL-deficient mutants max1, max3, and max4. However, the application of 4BD to the Arabidopsis SL-insensitive mutant max2 induced no morphological changes in it. The expression of SL biosynthetic genes was also reduced by 4BD treatment, probably via negative feedback regulation. However, in a seed germination assay on Striga hermonthica, a root parasitic plant, 4BD showed far less activity than GR24. These results suggest that 4BD is the first plant-specific strigolactone mimic.\",\n \"corpus_id\": 21193103,\n \"score\": 2\n },\n {\n \"doc_id\": \"23293648\",\n \"title\": \"Strigolactone and karrikin signal perception: receptors, enzymes, or both?\",\n \"abstract\": \"The signaling molecules strigolactone (SL) and karrikin are involved in seed germination, development of axillary meristems, senescence of leaves, and interactions with arbuscular mycorrhizal fungi. The signal transduction pathways for both SLs and karrikins require the same F-box protein (MAX2) and closely related α/β hydrolase fold proteins (DAD2 and KAI2). The crystal structure of DAD2 has been solved revealing an α/β hydrolase fold protein with an internal cavity capable of accommodating SLs. DAD2 responds to the SL analog GR24 by changing conformation and binding to MAX2 in a GR24 concentration-dependent manner. DAD2 can also catalyze hydrolysis of GR24. Structure activity relationships of analogs indicate that the butenolide ring common to both SLs and karrikins is essential for biological activity, but the remainder of the molecules can be significantly modified without loss of activity. The combination of data from the study of DAD2, KAI2, and chemical analogs of SLs and karrikins suggests a model for binding that requires nucleophilic attack by the active site serine of the hydrolase at the carbonyl atom of the butenolide ring. A conformational change occurs in the hydrolase that results in interaction with the F-box protein MAX2. Downstream signal transduction is then likely to occur via SCF (Skp-Cullin-F-box) complex-mediated ubiquitination of target proteins and their subsequent degradation. The role of the catalytic activity of the hydrolase is unclear but it may be integral in binding as well as possibly allowing the signal to be cleared from the receptor. The α/β hydrolase fold family consists mostly of active enzymes, with a few notable exceptions. We suggest that DAD2 and KAI2 represent an intermediate stage where some catalytic activity is retained at the same time as a receptor role has evolved.\",\n \"corpus_id\": 18476075,\n \"score\": 2\n },\n {\n \"doc_id\": \"23301669\",\n \"title\": \"Structures of D14 and D14L in the strigolactone and karrikin signaling pathways.\",\n \"abstract\": \"Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/β-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between β6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long β6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/β-fold hydrolases.\",\n \"corpus_id\": 205150729,\n \"score\": 2\n },\n {\n \"doc_id\": \"23382651\",\n \"title\": \"Strigolactone can promote or inhibit shoot branching by triggering rapid depletion of the auxin efflux protein PIN1 from the plasma membrane.\",\n \"abstract\": \"Plants continuously extend their root and shoot systems through the action of meristems at their growing tips. By regulating which meristems are active, plants adjust their body plans to suit local environmental conditions. The transport network of the phytohormone auxin has been proposed to mediate this systemic growth coordination, due to its self-organising, environmentally sensitive properties. In particular, a positive feedback mechanism termed auxin transport canalization, which establishes auxin flow from active shoot meristems (auxin sources) to the roots (auxin sinks), has been proposed to mediate competition between shoot meristems and to balance shoot and root growth. Here we provide strong support for this hypothesis by demonstrating that a second hormone, strigolactone, regulates growth redistribution in the shoot by rapidly modulating auxin transport. A computational model in which strigolactone action is represented as an increase in the rate of removal of the auxin export protein, PIN1, from the plasma membrane can reproduce both the auxin transport and shoot branching phenotypes observed in various mutant combinations and strigolactone treatments, including the counterintuitive ability of strigolactones either to promote or inhibit shoot branching, depending on the auxin transport status of the plant. Consistent with this predicted mode of action, strigolactone signalling was found to trigger PIN1 depletion from the plasma membrane of xylem parenchyma cells in the stem. This effect could be detected within 10 minutes of strigolactone treatment and was independent of protein synthesis but dependent on clathrin-mediated membrane trafficking. Together these results support the hypothesis that growth across the plant shoot system is balanced by competition between shoot apices for a common auxin transport path to the root and that strigolactones regulate shoot branching by modulating this competition.\",\n \"corpus_id\": 8836606,\n \"score\": 2\n },\n {\n \"doc_id\": \"23424248\",\n \"title\": \"A role for more axillary growth1 (MAX1) in evolutionary diversity in strigolactone signaling upstream of MAX2.\",\n \"abstract\": \"Strigolactones (SLs) are carotenoid-derived phytohormones with diverse roles. They are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. To date, six genes associated with SL synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of Arabidopsis (Arabidopsis thaliana) and dwarf (d) of rice (Oryza sativa). Here, we present a phylogenetic analysis of the MAX/D genes to clarify the relationships of each gene with its wider family and to allow the correlation of events in the evolution of the genes with the evolution of SL function. Our analysis suggests that the notion of a distinct SL pathway is inappropriate. Instead, there may be a diversity of SL-like compounds, the response to which requires a D14/D14-like protein. This ancestral system could have been refined toward distinct ligand-specific pathways channeled through MAX2, the most downstream known component of SL signaling. MAX2 is tightly conserved among land plants and is more diverged from its nearest sister clade than any other SL-related gene, suggesting a pivotal role in the evolution of SL signaling. By contrast, the evidence suggests much greater flexibility upstream of MAX2. The MAX1 gene is a particularly strong candidate for contributing to diversification of inputs upstream of MAX2. Our functional analysis of the MAX1 family demonstrates the early origin of its catalytic function and both redundancy and functional diversification associated with its duplication in angiosperm lineages.\",\n \"corpus_id\": 24729313,\n \"score\": 2\n },\n {\n \"doc_id\": \"23773129\",\n \"title\": \"Carlactone-independent seedling morphogenesis in Arabidopsis.\",\n \"abstract\": \"Strigolactone hormones are derived from carotenoids via carlactone, and act through the α/β-hydrolase D14 and the F-box protein D3/MAX2 to repress plant shoot branching. While MAX2 is also necessary for normal seedling development, D14 and the known strigolactone biosynthesis genes are not, raising the question of whether endogenous, canonical strigolactones derived from carlactone have a role in seedling morphogenesis. Here, we report the chemical synthesis of the strigolactone precursor carlactone, and show that it represses Arabidopsis shoot branching and influences leaf morphogenesis via a mechanism that is dependent on the cytochrome P450 MAX1. In contrast, both physiologically active Z-carlactone and the non-physiological E isomer exhibit similar weak activity in seedlings, and predominantly signal through D14 rather than its paralogue KAI2, in a MAX2-dependent but MAX1-independent manner. KAI2 is essential for seedling morphogenesis, and hence this early-stage development employs carlactone-independent morphogens for which karrikins from wildfire smoke are specific surrogates. While the commonly employed synthetic strigolactone GR24 acts non-specifically through both D14 and KAI2, carlactone is a specific effector of strigolactone signalling that acts through MAX1 and D14.\",\n \"corpus_id\": 3481094,\n \"score\": 2\n },\n {\n \"doc_id\": \"24131983\",\n \"title\": \"Molecular mechanism of strigolactone perception by DWARF14.\",\n \"abstract\": \"Strigolactones (SLs) are phytohormones that inhibit shoot branching and function in the rhizospheric communication with symbiotic fungi and parasitic weeds. An α/β-hydrolase protein, DWARF14 (D14), has been recognized to be an essential component of plant SL signalling, although its precise function remains unknown. Here we present the SL-dependent interaction of D14 with a gibberellin signalling repressor SLR1 and a possible mechanism of phytohormone perception in D14-mediated SL signalling. D14 functions as a cleavage enzyme of SLs, and the cleavage reaction induces the interaction with SLR1. The crystal structure of D14 shows that 5-hydroxy-3-methylbutenolide (D-OH), which is a reaction product of SLs, is trapped in the catalytic cavity of D14 to form an altered surface. The D14 residues recognizing D-OH are critical for the SL-dependent D14-SLR1 interaction. These results provide new insight into crosstalk between gibberellin and SL signalling pathways.\",\n \"corpus_id\": 28987166,\n \"score\": 2\n },\n {\n \"doc_id\": \"24336200\",\n \"title\": \"DWARF 53 acts as a repressor of strigolactone signalling in rice.\",\n \"abstract\": \"Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.\",\n \"corpus_id\": 4383175,\n \"score\": 2\n },\n {\n \"doc_id\": \"24336215\",\n \"title\": \"D14-SCF(D3)-dependent degradation of D53 regulates strigolactone signalling.\",\n \"abstract\": \"Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the α/β hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.\",\n \"corpus_id\": 4407338,\n \"score\": 2\n },\n {\n \"doc_id\": \"24483232\",\n \"title\": \"Striga hermonthica MAX2 restores branching but not the Very Low Fluence Response in the Arabidopsis thaliana max2 mutant.\",\n \"abstract\": \"Seed germination of Striga spp. ( witchweeds), one of the world's most destructive parasitic weeds, cannot be induced by light but is specifically induced by strigolactones. It is not known whether Striga uses the same components for strigolactone signaling as host plants, whether it has endogenous strigolactone biosynthesis and whether there is post-germination strigolactone signaling in Striga. Strigolactones could not be detected in in vitro grown Striga, while for host-grown Striga, the strigolactone profile is dominated by a subset of the strigolactones present in the host. Branching of in vitro grown Striga is affected by strigolactone biosynthesis inhibitors. ShMAX2, the Striga ortholog of Arabidopsis MORE AXILLARY BRANCHING 2 (AtMAX2) - which mediates strigolactone signaling - complements several of the Arabidopsis max2-1 phenotypes, including the root and shoot phenotype, the High Irradiance Response and the response to strigolactones. Seed germination of max2-1 complemented with ShMAX2 showed no complementation of the Very Low Fluence Response phenotype of max2-1. Results provide indirect evidence for ShMAX2 functions in Striga. A putative role of ShMAX2 in strigolactone-dependent seed germination of Striga is discussed.\",\n \"corpus_id\": 22158546,\n \"score\": 2\n },\n {\n \"doc_id\": \"24610723\",\n \"title\": \"Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis.\",\n \"abstract\": \"Strigolactones (SLs) are phytohormones that play a central role in regulating shoot branching. SL perception and signaling involves the F-box protein MAX2 and the hydrolase DWARF14 (D14), proposed to act as an SL receptor. We used strong loss-of-function alleles of the Arabidopsis thaliana D14 gene to characterize D14 function from early axillary bud development through to lateral shoot outgrowth and demonstrated a role of this gene in the control of flowering time. Our data show that D14 distribution in vivo overlaps with that reported for MAX2 at both the tissue and subcellular levels, allowing physical interactions between these proteins. Our grafting studies indicate that neither D14 mRNA nor the protein move over a long range upwards in the plant. Like MAX2, D14 is required locally in the aerial part of the plant to suppress shoot branching. We also identified a mechanism of SL-induced, MAX2-dependent proteasome-mediated degradation of D14. This negative feedback loop would cause a substantial drop in SL perception, which would effectively limit SL signaling duration and intensity.\",\n \"corpus_id\": 7000577,\n \"score\": 2\n },\n {\n \"doc_id\": \"24616269\",\n \"title\": \"DWARF3 participates in an SCF complex and associates with DWARF14 to suppress rice shoot branching.\",\n \"abstract\": \"Strigolactones (SLs) are a novel class of plant hormones that inhibit shoot branching. Currently, two proteins in rice are thought to play crucial roles in SL signal transduction. DWARF14 (D14), an α/β hydrolase, is responsible for SL perception, while DWARF3 (D3), an F-box protein with leucine-rich repeats, is essential for SL signal transduction. However, how these two proteins transmit SL signals to downstream factors remains unclear. Here, we characterized a high-tillering dwarf rice mutant, gsor300097, which is insensitive to GR24, a synthetic analog of SL. Mapping and sequencing analysis showed that gsor300097 is a novel allelic mutant of D3, in which a nonsense mutation truncates the protein from 720 to 527 amino acids. The D3 gene was strongly expressed in root, leaf, shoot base and panicle. Nuclear-localized F-box protein D3 played a role in the SCF complex by interacting with OSK1, OSK5 or OSK20 and OsCullin1. In addition, D3 associated with D14 in a GR24-dependent manner in vivo. Taken together, our findings suggested that D3 assembled into an SCF(D3) complex and associated with D14 to suppress rice shoot branching.\",\n \"corpus_id\": 14189899,\n \"score\": 2\n },\n {\n \"doc_id\": \"24981923\",\n \"title\": \"Strigolactone biosynthesis and perception.\",\n \"abstract\": \"Strigolactones (SLs) are plant hormones that regulate shoot branching as well as known as root-derived signals for parasitic and symbiotic interactions. Since the first discovery of a naturally occurring SL, strigol, more than 40 years ago, the biosynthetic pathway has remained elusive. Recently, it was partially uncovered through the functional analysis of some biosynthetic components that were discovered from genetic studies using SL-deficient mutants. In addition, a perception component was also characterized through genetic and biochemical studies of a rice SL-insensitive mutant, dwarf14. In this review, we describe new findings on SL biosynthesis and focus on a recently identified SL precursor, carlactone. We also describe the perception mechanisms by an α/β-fold hydrolase family protein.\",\n \"corpus_id\": 42603521,\n \"score\": 2\n },\n {\n \"doc_id\": \"24996032\",\n \"title\": \"Signalling and responses to strigolactones and karrikins.\",\n \"abstract\": \"Strigolactone (SL) and karrikin (KAR) signalling control many aspects of plant growth and development through similar mechanisms employing related α/β-fold hydrolase-receptors and a common F-box protein named MORE AXILARY GROWTH2 (MAX2) in Arabidopsis or DWARF3 (D3) in rice. D3 mediates SL-dependent ubiquitination and proteolysis of DWARF53 (D53) protein, thought to be involved in the control of gene expression, while a related protein SUPPRESSOR OF MAX2-1 (SMAX1) is implicated in the response to KAR in Arabidopsis. Different members of the D53/SMAX1 multigene family likely mediate different responses in plant growth and development. Analysis of responses to SL or KAR has identified many genes regulated by these compounds. Crosstalk with other signalling systems including light, hormones and abiotic stress has also been identified. Here we critically analyse how to progress towards a clearer understanding of the targets and functions of the SL and KAR signalling systems.\",\n \"corpus_id\": 2437,\n \"score\": 2\n },\n {\n \"doc_id\": \"25126711\",\n \"title\": \"Detection of parasitic plant suicide germination compounds using a high-throughput Arabidopsis HTL/KAI2 strigolactone perception system.\",\n \"abstract\": \"Strigolactones are terpenoid-based plant hormones that act as communication signals within a plant, between plants and fungi, and between parasitic plants and their hosts. Here we show that an active enantiomer form of the strigolactone GR24, the germination stimulant karrikin, and a number of structurally related small molecules called cotylimides all bind the HTL/KAI2 α/β hydrolase in Arabidopsis. Strigolactones and cotylimides also promoted an interaction between HTL/KAI2 and the F-box protein MAX2 in yeast. Identification of this chemically dependent protein-protein interaction prompted the development of a yeast-based, high-throughput chemical screen for potential strigolactone mimics. Of the 40 lead compounds identified, three were found to have in planta strigolactone activity using Arabidopsis-based assays. More importantly, these three compounds were all found to stimulate suicide germination of the obligate parasitic plant Striga hermonthica. These results suggest that screening strategies involving yeast/Arabidopsis models may be useful in combating parasitic plant infestations.\",\n \"corpus_id\": 6213043,\n \"score\": 2\n },\n {\n \"doc_id\": \"25179782\",\n \"title\": \"Strigolactone signalling: standing on the shoulders of DWARFs.\",\n \"abstract\": \"Strigolactones are an ancient and major class of endogenous plant growth regulators. Although only recently identified, rapid progress has been made in understanding strigolactone biology, including the identification of a signalling pathway involving DWARF14 α/β-fold proteins, the SCF(MAX2) ubiquitin ligase and SMAX1-LIKE (SMXL) family of chaperonin-like proteins. Several rapid effects of strigolactone signalling have also been identified, including endocytosis of the PIN-FORMED1 (PIN1) auxin efflux carrier and transcript accumulation of the BRANCHED1 (BRC1) transcription factor. Here we assess our current knowledge of strigolactone signalling, and discuss how increased understanding of the cell biology of the system can help to resolve some of the current uncertainties in the field.\",\n \"corpus_id\": 37952801,\n \"score\": 2\n },\n {\n \"doc_id\": \"25425668\",\n \"title\": \"Carlactone is converted to carlactonoic acid by MAX1 in Arabidopsis and its methyl ester can directly interact with AtD14 in vitro.\",\n \"abstract\": \"Strigolactones (SLs) stimulate seed germination of root parasitic plants and induce hyphal branching of arbuscular mycorrhizal fungi in the rhizosphere. In addition, they have been classified as a new group of plant hormones essential for shoot branching inhibition. It has been demonstrated thus far that SLs are derived from carotenoid via a biosynthetic precursor carlactone (CL), which is produced by sequential reactions of DWARF27 (D27) enzyme and two carotenoid cleavage dioxygenases CCD7 and CCD8. We previously found an extreme accumulation of CL in the more axillary growth1 (max1) mutant of Arabidopsis, which exhibits increased lateral inflorescences due to SL deficiency, indicating that CL is a probable substrate for MAX1 (CYP711A1), a cytochrome P450 monooxygenase. To elucidate the enzymatic function of MAX1 in SL biosynthesis, we incubated CL with a recombinant MAX1 protein expressed in yeast microsomes. MAX1 catalyzed consecutive oxidations at C-19 of CL to convert the C-19 methyl group into carboxylic acid, 9-desmethyl-9-carboxy-CL [designated as carlactonoic acid (CLA)]. We also identified endogenous CLA and its methyl ester [methyl carlactonoate (MeCLA)] in Arabidopsis plants using LC-MS/MS. Although an exogenous application of either CLA or MeCLA suppressed the growth of lateral inflorescences of the max1 mutant, MeCLA, but not CLA, interacted with Arabidopsis thaliana DWARF14 (AtD14) protein, a putative SL receptor, as shown by differential scanning fluorimetry and hydrolysis activity tests. These results indicate that not only known SLs but also MeCLA are biologically active in inhibiting shoot branching in Arabidopsis.\",\n \"corpus_id\": 2266658,\n \"score\": 2\n },\n {\n \"doc_id\": \"26175507\",\n \"title\": \"A Selaginella moellendorffii Ortholog of KARRIKIN INSENSITIVE2 Functions in Arabidopsis Development but Cannot Mediate Responses to Karrikins or Strigolactones.\",\n \"abstract\": \"In Arabidopsis thaliana, the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) is essential for normal seed germination, seedling development, and leaf morphogenesis, as well as for responses to karrikins. KAI2 is a paralog of DWARF14 (D14), the proposed strigolactone receptor, but the evolutionary timing of functional divergence between the KAI2 and D14 clades has not been established. By swapping gene promoters, we show that Arabidopsis KAI2 and D14 proteins are functionally distinct. We show that the catalytic serine of KAI2 is essential for function in plants and for biochemical activity in vitro. We identified two KAI2 homologs from Selaginella moellendorffii and two from Marchantia polymorpha. One from each species could hydrolyze the strigolactone analog GR24 in vitro, but when tested for their ability to complement Arabidopsis d14 and kai2 mutants, neither of these homologs was effective. However, the second KAI2 homolog from S. moellendorffii was able to complement the seedling and leaf development phenotypes of Arabidopsis kai2. This homolog could not transduce signals from exogenous karrikins, strigolactone analogs, or carlactone, but its activity did depend on the conserved catalytic serine. We conclude that KAI2, and most likely the endogenous signal to which it responds, has been conserved since the divergence of lycophytes and angiosperm lineages, despite their major developmental and morphogenic differences.\",\n \"corpus_id\": 22057851,\n \"score\": 2\n },\n {\n \"doc_id\": \"26228149\",\n \"title\": \"PLANT EVOLUTION. Convergent evolution of strigolactone perception enabled host detection in parasitic plants.\",\n \"abstract\": \"Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.\",\n \"corpus_id\": 206637320,\n \"score\": 2\n },\n {\n \"doc_id\": \"26293962\",\n \"title\": \"PARASITIC PLANTS. Probing strigolactone receptors in Striga hermonthica with fluorescence.\",\n \"abstract\": \"Elucidating the signaling mechanism of strigolactones has been the key to controlling the devastating problem caused by the parasitic plant Striga hermonthica. To overcome the genetic intractability that has previously interfered with identification of the strigolactone receptor, we developed a fluorescence turn-on probe, Yoshimulactone Green (YLG), which activates strigolactone signaling and illuminates signal perception by the strigolactone receptors. Here we describe how strigolactones bind to and act via ShHTLs, the diverged family of α/β hydrolase-fold proteins in Striga. Live imaging using YLGs revealed that a dynamic wavelike propagation of strigolactone perception wakes up Striga seeds. We conclude that ShHTLs function as the strigolactone receptors mediating seed germination in Striga. Our findings enable access to strigolactone receptors and observation of the regulatory dynamics for strigolactone signal transduction in Striga.\",\n \"corpus_id\": 9968741,\n \"score\": 2\n },\n {\n \"doc_id\": \"26450211\",\n \"title\": \"Structure-function analysis identifies highly sensitive strigolactone receptors in Striga.\",\n \"abstract\": \"Strigolactones are naturally occurring signaling molecules that affect plant development, fungi-plant interactions, and parasitic plant infestations. We characterized the function of 11 strigolactone receptors from the parasitic plant Striga hermonthica using chemical and structural biology. We found a clade of polyspecific receptors, including one that is sensitive to picomolar concentrations of strigolactone. A crystal structure of a highly sensitive strigolactone receptor from Striga revealed a larger binding pocket than that of the Arabidopsis receptor, which could explain the increased range of strigolactone sensitivity. Thus, the sensitivity of Striga to strigolactones from host plants is driven by receptor sensitivity. By expressing strigolactone receptors in Arabidopsis, we developed a bioassay that can be used to identify chemicals and crops with altered strigolactone levels.\",\n \"corpus_id\": 24993088,\n \"score\": 2\n },\n {\n \"doc_id\": \"26470846\",\n \"title\": \"Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.\",\n \"abstract\": \"Strigolactones (SLs) are endogenous hormones and exuded signaling molecules in plant responses to low levels of mineral nutrients. Key mediators of the SL signaling pathway in rice include the α/β-fold hydrolase DWARF 14 (D14) and the F-box component DWARF 3 (D3) of the ubiquitin ligase SCF(D3) that mediate ligand-dependent degradation of downstream signaling repressors. One perplexing feature is that D14 not only functions as the SL receptor but is also an active enzyme that slowly hydrolyzes diverse natural and synthetic SLs including GR24, preventing the crystallization of a binary complex of D14 with an intact SL as well as the ternary D14/SL/D3 complex. Here we overcome these barriers to derive a structural model of D14 bound to intact GR24 and identify the interface that is required for GR24-mediated D14-D3 interaction. The mode of GR24-mediated signaling, including ligand recognition, hydrolysis by D14, and ligand-mediated D14-D3 interaction, is conserved in structurally diverse SLs. More importantly, D14 is destabilized upon the binding of ligands and D3, thus revealing an unusual mechanism of SL recognition and signaling, in which the hormone, the receptor, and the downstream effectors are systematically destabilized during the signal transduction process.\",\n \"corpus_id\": 34622367,\n \"score\": 2\n },\n {\n \"doc_id\": \"26546446\",\n \"title\": \"Strigolactone Signaling in Arabidopsis Regulates Shoot Development by Targeting D53-Like SMXL Repressor Proteins for Ubiquitination and Degradation.\",\n \"abstract\": \"Strigolactones (SLs) are carotenoid-derived phytohormones that control many aspects of plant development, including shoot branching, leaf shape, stem secondary thickening, and lateral root growth. In rice (Oryza sativa), SL signaling requires the degradation of DWARF53 (D53), mediated by a complex including D14 and D3, but in Arabidopsis thaliana, the components and mechanism of SL signaling involving the D3 ortholog MORE AXILLARY GROWTH2 (MAX2) are unknown. Here, we show that SL-dependent regulation of shoot branching in Arabidopsis requires three D53-like proteins, SUPPRESSOR OF MORE AXILLARY GROWTH2-LIKE6 (SMXL6), SMXL7, and SMXL8. The smxl6 smxl7 smxl8 triple mutant suppresses the highly branched phenotypes of max2 and the SL-deficient mutant max3. Overexpression of a mutant form of SMXL6 that is resistant to SL-induced ubiquitination and degradation enhances shoot branching. Exogenous application of the SL analog rac-GR24 causes ubiquitination and degradation of SMXL6, 7, and 8; this requires D14 and MAX2. D53-like SMXLs form complexes with MAX2 and TOPLESS-RELATED PROTEIN2 (TPR2) and interact with D14 in a GR24-responsive manner. Furthermore, D53-like SMXLs exhibit TPR2-dependent transcriptional repression activity and repress the expression of BRANCHED1. Our findings reveal that in Arabidopsis, D53-like SMXLs act with TPR2 to repress transcription and so allow lateral bud outgrowth but that SL-induced degradation of D53-like proteins activates transcription to inhibit outgrowth.\",\n \"corpus_id\": 23978379,\n \"score\": 2\n },\n {\n \"doc_id\": \"26546447\",\n \"title\": \"SMAX1-LIKE/D53 Family Members Enable Distinct MAX2-Dependent Responses to Strigolactones and Karrikins in Arabidopsis.\",\n \"abstract\": \"The plant hormones strigolactones and smoke-derived karrikins are butenolide signals that control distinct aspects of plant development. Perception of both molecules in Arabidopsis thaliana requires the F-box protein MORE AXILLARY GROWTH2 (MAX2). Recent studies suggest that the homologous SUPPRESSOR OF MAX2 1 (SMAX1) in Arabidopsis and DWARF53 (D53) in rice (Oryza sativa) are downstream targets of MAX2. Through an extensive analysis of loss-of-function mutants, we demonstrate that the Arabidopsis SMAX1-LIKE genes SMXL6, SMXL7, and SMXL8 are co-orthologs of rice D53 that promote shoot branching. SMXL7 is degraded rapidly after treatment with the synthetic strigolactone mixture rac-GR24. Like D53, SMXL7 degradation is MAX2- and D14-dependent and can be prevented by deletion of a putative P-loop. Loss of SMXL6,7,8 suppresses several other strigolactone-related phenotypes in max2, including increased auxin transport and PIN1 accumulation, and increased lateral root density. Although only SMAX1 regulates germination and hypocotyl elongation, SMAX1 and SMXL6,7,8 have complementary roles in the control of leaf morphology. Our data indicate that SMAX1 and SMXL6,7,8 repress karrikin and strigolactone signaling, respectively, and suggest that all MAX2-dependent growth effects are mediated by degradation of SMAX1/SMXL proteins. We propose that functional diversification within the SMXL family enabled responses to different butenolide signals through a shared regulatory mechanism.\",\n \"corpus_id\": 7658561,\n \"score\": 2\n },\n {\n \"doc_id\": \"26779242\",\n \"title\": \"Evidence that KARRIKIN-INSENSITIVE2 (KAI2) Receptors may Perceive an Unknown Signal that is not Karrikin or Strigolactone.\",\n \"abstract\": \"The α/β-hydrolases KAI2 and D14 are paralogous receptors for karrikins and strigolactones, two classes of plant growth regulators with butenolide moieties. KAI2 and D14 act in parallel signaling pathways that share a requirement for the F-box protein MAX2, but produce distinct growth responses by regulating different members of the SMAX1-LIKE/D53 family. kai2 and max2 mutants share seed germination, seedling growth, leaf shape, and petiole orientation phenotypes that are not found in d14 or SL-deficient mutants. This implies that KAI2 recognizes an unknown, endogenous signal, herein termed KAI2 ligand (KL). Recent studies of ligand-specificity among KAI2 paralogs in basal land plants and root parasitic plants suggest that karrikin and strigolactone perception may be evolutionary adaptations of KL receptors. Here we demonstrate that evolutionarily conserved KAI2c genes from two parasite species rescue multiple phenotypes of the Arabidopsis kai2 mutant, unlike karrikin-, and strigolactone-specific KAI2 paralogs. We hypothesize that KAI2c proteins recognize KL, which could be an undiscovered hormone.\",\n \"corpus_id\": 16787226,\n \"score\": 2\n },\n {\n \"doc_id\": \"26838034\",\n \"title\": \"Strigolactones: new plant hormones in action.\",\n \"abstract\": \"MAIN CONCLUSION: The key step in the mode of action of strigolactones is the enzymatic detachment of the D-ring. The thus formed hydroxy butenolide induces conformational changes of the receptor pocket which trigger a cascade of reactions in the signal transduction. Strigolactones (SLs) constitute a new class of plant hormones which are of increasing importance in plant science. For the last 60 years, they have been known as germination stimulants for parasitic plants. Recently, several new bio-properties of SLs have been discovered such as the branching factor for arbuscular mycorrhizal fungi, regulation of plant architecture (inhibition of bud outgrowth and of shoot branching) and the response to abiotic factors, etc. To broaden horizons and encourage new ideas for identifying and synthesising new and structurally simple SLs, this review is focused on molecular aspects of this new class of plant hormones. Special attention has been given to structural features, the mode of action of these phytohormones in various biological actions, the design of SL analogs and their applications.\",\n \"corpus_id\": 14113210,\n \"score\": 2\n },\n {\n \"doc_id\": \"26851153\",\n \"title\": \"Smoke and Hormone Mirrors: Action and Evolution of Karrikin and Strigolactone Signaling.\",\n \"abstract\": \"Karrikins and strigolactones are two classes of butenolide molecules that have diverse effects on plant growth. Karrikins are found in smoke and strigolactones are plant hormones, yet both molecules are likely recognized through highly similar signaling mechanisms. Here we review the most recent discoveries of karrikin and strigolactone perception and signal transduction. Two paralogous α/β hydrolases, KAI2 and D14, are respectively karrikin and strigolactone receptors. D14 acts with an F-box protein, MAX2, to target SMXL/D53 family proteins for proteasomal degradation, and genetic data suggest that KAI2 acts similarly. There are striking parallels in the signaling mechanisms of karrikins, strigolactones, and other plant hormones, including auxins, jasmonates, and gibberellins. Recent investigations of host perception in parasitic plants have demonstrated that strigolactone recognition can evolve following gene duplication of KAI2.\",\n \"corpus_id\": 10825561,\n \"score\": 2\n },\n {\n \"doc_id\": \"26875827\",\n \"title\": \"Characterization of DWARF14 Genes in Populus.\",\n \"abstract\": \"Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching mutants in herbaceous plants have identified several key genes involved in strigolactone biosynthesis or signaling. The strigolactone signal is perceived by a member of the α/β-fold hydrolase superfamily, known as DWARF14 (D14). However, little is known about D14 genes in the woody perennial plants. Here we report the identification of D14 homologs in the model woody plant Populus trichocarpa. We showed that there are two D14 homologs in P. trichocarpa, designated as PtD14a and PtD14b that are over 95% similar at the amino acid level. Expression analysis indicated that the transcript level of PtD14a is generally more abundant than that of PtD14b. However, only PtD14a was able to complement Arabidopsis d14 mutants, suggesting that PtD14a is the functional D14 ortholog. Amino acid alignment and structural modeling revealed substitutions of several highly conserved amino acids in the PtD14b protein including a phenylalanine near the catalytic triad of D14 proteins. This study lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants.\",\n \"corpus_id\": 18561879,\n \"score\": 2\n },\n {\n \"doc_id\": \"26979323\",\n \"title\": \"Structural modelling and transcriptional responses highlight a clade of PpKAI2-LIKE genes as candidate receptors for strigolactones in Physcomitrella patens.\",\n \"abstract\": \"MAIN CONCLUSION: A set of PpKAI2 - LIKE paralogs that may encode strigolactone receptors in Physcomitrella patens were identified through evolutionary, structural, and transcriptional analyses, suggesting that strigolactone perception may have evolved independently in basal land plants in a similar manner as spermatophytes. Carotenoid-derived compounds known as strigolactones are a new class of plant hormones that modulate development and interactions with parasitic plants and arbuscular mycorrhizal fungi. The strigolactone receptor protein DWARF14 (D14) belongs to the α/β hydrolase family. D14 is closely related to KARRIKIN INSENSITIVE2 (KAI2), a receptor of smoke-derived germination stimulants called karrikins. Strigolactone and karrikin structures share a butenolide ring that is necessary for bioactivity. Charophyte algae and basal land plants produce strigolactones that influence their development. However phylogenetic studies suggest that D14 is absent from algae, moss, and liverwort genomes, raising the question of how these basal plants perceive strigolactones. Strigolactone perception during seed germination putatively evolved in parasitic plants through gene duplication and neofunctionalization of KAI2 paralogs. The moss Physcomitrella patens shows an increase in KAI2 gene copy number, similar to parasitic plants. In this study we investigated whether P. patens KAI2-LIKE (PpKAI2L) genes may contribute to strigolactone perception. Based on phylogenetic analyses and homology modelling, we predict that a clade of PpKAI2L proteins have enlarged ligand-binding cavities, similar to D14. We observed that some PpKAI2L genes have transcriptional responses to the synthetic strigolactone GR24 racemate or its enantiomers. These responses were influenced by light and dark conditions. Moreover, (+)-GR24 seems to be the active enantiomer that induces the transcriptional responses of PpKAI2L genes. We hypothesize that members of specific PpKAI2L clades are candidate strigolactone receptors in moss.\",\n \"corpus_id\": 14269467,\n \"score\": 2\n },\n {\n \"doc_id\": \"27194725\",\n \"title\": \"LATERAL BRANCHING OXIDOREDUCTASE acts in the final stages of strigolactone biosynthesis in Arabidopsis.\",\n \"abstract\": \"Strigolactones are a group of plant compounds of diverse but related chemical structures. They have similar bioactivity across a broad range of plant species, act to optimize plant growth and development, and promote soil microbe interactions. Carlactone, a common precursor to strigolactones, is produced by conserved enzymes found in a number of diverse species. Versions of the MORE AXILLARY GROWTH1 (MAX1) cytochrome P450 from rice and Arabidopsis thaliana make specific subsets of strigolactones from carlactone. However, the diversity of natural strigolactones suggests that additional enzymes are involved and remain to be discovered. Here, we use an innovative method that has revealed a missing enzyme involved in strigolactone metabolism. By using a transcriptomics approach involving a range of treatments that modify strigolactone biosynthesis gene expression coupled with reverse genetics, we identified LATERAL BRANCHING OXIDOREDUCTASE (LBO), a gene encoding an oxidoreductase-like enzyme of the 2-oxoglutarate and Fe(II)-dependent dioxygenase superfamily. Arabidopsis lbo mutants exhibited increased shoot branching, but the lbo mutation did not enhance the max mutant phenotype. Grafting indicated that LBO is required for a graft-transmissible signal that, in turn, requires a product of MAX1. Mutant lbo backgrounds showed reduced responses to carlactone, the substrate of MAX1, and methyl carlactonoate (MeCLA), a product downstream of MAX1. Furthermore, lbo mutants contained increased amounts of these compounds, and the LBO protein specifically converts MeCLA to an unidentified strigolactone-like compound. Thus, LBO function may be important in the later steps of strigolactone biosynthesis to inhibit shoot branching in Arabidopsis and other seed plants.\",\n \"corpus_id\": 38452643,\n \"score\": 2\n },\n {\n \"doc_id\": \"27317673\",\n \"title\": \"SMAX1-LIKE7 Signals from the Nucleus to Regulate Shoot Development in Arabidopsis via Partially EAR Motif-Independent Mechanisms.\",\n \"abstract\": \"Strigolactones (SLs) are hormonal signals that regulate multiple aspects of shoot architecture, including shoot branching. Like many plant hormonal signaling systems, SLs act by promoting ubiquitination of target proteins and their subsequent proteasome-mediated degradation. Recently, SMXL6, SMXL7, and SMXL8, members of the SMAX1-LIKE (SMXL) family of chaperonin-like proteins, have been identified as proteolytic targets of SL signaling in Arabidopsis thaliana However, the mechanisms by which these proteins regulate downstream events remain largely unclear. Here, we show that SMXL7 functions in the nucleus, as does the SL receptor, DWARF14 (D14). We show that nucleus-localized D14 can physically interact with both SMXL7 and the MAX2 F-box protein in a SL-dependent manner and that disruption of specific conserved domains in SMXL7 affects its localization, SL-induced degradation, and activity. By expressing and overexpressing these SMXL7 protein variants, we show that shoot tissues are broadly sensitive to SMXL7 activity, but degradation normally buffers the effect of increasing SMXL7 expression. SMXL7 contains a well-conserved EAR (ETHYLENE-RESPONSE FACTOR Amphiphilic Repression) motif, which contributes to, but is not essential for, SMXL7 functionality. Intriguingly, different developmental processes show differential sensitivity to the loss of the EAR motif, raising the possibility that there may be several distinct mechanisms at play downstream of SMXL7.\",\n \"corpus_id\": 11073468,\n \"score\": 2\n },\n {\n \"doc_id\": \"27318656\",\n \"title\": \"Strigolactones, super hormones in the fight against Striga.\",\n \"abstract\": \"Strigolactones are plant hormones that control diverse aspects of plant growth, but are also exuded into soil as recruitment signals for arbuscular mycorrhizal fungi interactions. Highly damaging parasitic weeds in the Orobanchaceae family have coopted strigolactones as germination cues that indicate the presence of a host. Recent studies have established how strigolactones are actively transported within and out of plants. Key components of the strigolactone signaling system have been identified, including strigolactone receptors in angiosperms and parasites, as well as downstream targets that are polyubiquitinated and proteolyzed following strigolactone perception. The basis for protein-protein interactions among these signaling components has also been explored. We propose several strategies to translate current knowledge of strigolactone transport and signaling into parasite control methods.\",\n \"corpus_id\": 3495518,\n \"score\": 2\n },\n {\n \"doc_id\": \"27479744\",\n \"title\": \"An histidine covalent receptor and butenolide complex mediates strigolactone perception.\",\n \"abstract\": \"Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand.\",\n \"corpus_id\": 19600033,\n \"score\": 2\n },\n {\n \"doc_id\": \"27602041\",\n \"title\": \"Perception and Signaling of Strigolactones.\",\n \"abstract\": \"Strigolactones (SLs), a recently discovered class of phytohormones, are important regulators of plant growth and development. While the biosynthetic pathway of these molecules is well documented, until recently there was not much known about the molecular mechanisms underlying SL perception and signal transduction in plants. Certain aspects of their perception and signaling, including the hormone-mediated interaction between receptor and F-box protein, degradation of suppressor proteins and activation of transcription factors, are also found in other phytohormones. However, some of SL signaling features seem to be specific for the SL signaling pathway. These include the enzymatic activity of the SL receptor and its destabilization caused by SLs. This review summarizes the current knowledge about SL signaling pathway in plants.\",\n \"corpus_id\": 5715306,\n \"score\": 2\n },\n {\n \"doc_id\": \"27670819\",\n \"title\": \"Phloem Transport of the Receptor DWARF14 Protein Is Required for Full Function of Strigolactones.\",\n \"abstract\": \"The cell-to-cell transport of signaling molecules is essential for multicellular organisms to coordinate the action of their cells. Recent studies identified DWARF14 (D14) as a receptor of strigolactones (SLs), molecules that act as plant hormones and inhibit shoot branching. Here, we demonstrate that RAMOSUS3, a pea ortholog of D14, works as a graft-transmissible signal to suppress shoot branching. In addition, we show that D14 protein is contained in phloem sap and transported through the phloem to axillary buds in rice. SLs are not required for the transport of D14 protein. Disruption of D14 transport weakens the suppression of axillary bud outgrowth of rice. Taken together, we conclude that the D14 protein works as an intercellular signaling molecule to fine-tune SL function. Our findings provide evidence that the intercellular transport of a receptor can regulate the action of plant hormones.\",\n \"corpus_id\": 33994659,\n \"score\": 2\n },\n {\n \"doc_id\": \"27760882\",\n \"title\": \"Low-Phosphate Induction of Plastidal Stromules Is Dependent on Strigolactones But Not on the Canonical Strigolactone Signaling Component MAX2.\",\n \"abstract\": \"Stromules are highly dynamic protrusions of the plastids in plants. Several factors, such as drought and light conditions, influence the stromule frequency (SF) in a positive or negative way. A relatively recently discovered class of plant hormones are the strigolactones; strigolactones inhibit branching of the shoots and promote beneficial interactions between roots and arbuscular mycorrhizal fungi. Here, we investigate the link between the formation of stromules and strigolactones. This research shows a strong link between strigolactones and the formation of stromules: SF correlates with strigolactone levels in the wild type and strigolactone mutants (max2-1 max3-9), and SF is stimulated by strigolactone GR24 and reduced by strigolactone inhibitor D2.\",\n \"corpus_id\": 34099988,\n \"score\": 2\n },\n {\n \"doc_id\": \"27793831\",\n \"title\": \"Strigolactone regulates shoot development through a core signalling pathway.\",\n \"abstract\": \"Strigolactones are a recently identified class of hormone that regulate multiple aspects of plant development. The DWARF14 (D14) α/β fold protein has been identified as a strigolactone receptor, which can act through the SCF(MAX2) ubiquitin ligase, but the universality of this mechanism is not clear. Multiple proteins have been suggested as targets for strigolactone signalling, including both direct proteolytic targets of SCF(MAX2), and downstream targets. However, the relevance and importance of these proteins to strigolactone signalling in many cases has not been fully established. Here we assess the contribution of these targets to strigolactone signalling in adult shoot developmental responses. We find that all examined strigolactone responses are regulated by SCF(MAX2) and D14, and not by other D14-like proteins. We further show that all examined strigolactone responses likely depend on degradation of SMXL proteins in the SMXL6 clade, and not on the other proposed proteolytic targets BES1 or DELLAs. Taken together, our results suggest that in the adult shoot, the dominant mode of strigolactone signalling is D14-initiated, MAX2-mediated degradation of SMXL6-related proteins. We confirm that the BRANCHED1 transcription factor and the PIN-FORMED1 auxin efflux carrier are plausible downstream targets of this pathway in the regulation of shoot branching, and show that BRC1 likely acts in parallel to PIN1.\",\n \"corpus_id\": 7622552,\n \"score\": 2\n },\n {\n \"doc_id\": \"28392107\",\n \"title\": \"Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation.\",\n \"abstract\": \"Plant stem cell niches, the meristems, require long-distance transport of energy metabolites and signaling molecules along the phloem tissue. However, currently it is unclear how specification of phloem cells is controlled. Here we show that the genes SUPPRESSOR OF MAX2 1-LIKE3 (SMXL3), SMXL4, and SMXL5 act as cell-autonomous key regulators of phloem formation in Arabidopsis thaliana. The three genes form an uncharacterized subclade of the SMXL gene family that mediates hormonal strigolactone and karrikin signaling. Strigolactones are endogenous signaling molecules regulating shoot and root branching [1] whereas exogenous karrikin molecules induce germination after wildfires [2]. Both activities depend on the F-box protein and SCF (Skp, Cullin, F-box) complex component MORE AXILLARY GROWTH2 (MAX2) [3-5]. Strigolactone and karrikin perception leads to MAX2-dependent degradation of distinct SMXL protein family members, which is key for mediating hormonal effects [6-12]. However, the nature of events immediately downstream of SMXL protein degradation and whether all SMXL proteins mediate strigolactone or karrikin signaling is unknown. In this study we demonstrate that, within the SMXL gene family, specifically SMXL3/4/5 deficiency results in strong defects in phloem formation, altered sugar accumulation, and seedling lethality. By comparing protein stabilities, we show that SMXL3/4/5 proteins function differently to canonical strigolactone and karrikin signaling mediators, although being functionally interchangeable with those under low strigolactone/karrikin signaling conditions. Our observations reveal a fundamental mechanism of phloem formation and indicate that diversity of SMXL protein functions is essential for a steady fuelling of plant meristems.\",\n \"corpus_id\": 13456775,\n \"score\": 2\n },\n {\n \"doc_id\": \"28558130\",\n \"title\": \"Strigolactones, karrikins and beyond.\",\n \"abstract\": \"The plant hormones strigolactones are synthesized from carotenoids and signal via the α/β hydrolase DWARF 14 (D14) and the F-box protein MORE AXILLARY GROWTH 2 (MAX2). Karrikins, molecules produced upon fire, share MAX2 for signalling, but depend on the D14 paralog KARRIKIN INSENSITIVE 2 (KAI2) for perception with strong evidence that the MAX2-KAI2 protein complex might also recognize so far unknown plant-made karrikin-like molecules. Thus, the phenotypes of the max2 mutants are the complex consequence of a loss of both D14-dependent and KAI2-dependent signalling, hence, the reason why some biological roles, attributed to strigolactones based on max2 phenotypes, could never be observed in d14 or in the strigolactone-deficient max3 and max4 mutants. Moreover, the broadly used synthetic strigolactone analog rac-GR24 has been shown to mimic strigolactone as well as karrikin(-like) signals, providing an extra level of complexity in the distinction of the unique and common roles of both molecules in plant biology. Here, a critical overview is provided of the diverse biological processes regulated by strigolactones and/or karrikins. These two growth regulators are considered beyond their boundaries, and the importance of the yet unknown karrikin-like molecules is discussed as well.\",\n \"corpus_id\": 5158228,\n \"score\": 2\n },\n {\n \"doc_id\": \"28662667\",\n \"title\": \"Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.\",\n \"abstract\": \"BACKGROUND: Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. RESULTS: We have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analysed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We show that eu-KAI2 proteins are highly conserved, and have unique features not found in DDK proteins. Conversely, we show that DDK proteins show considerable sequence and structural variation to each other, and lack clearly definable characteristics. We use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2 and that SL receptors in non-seed plants likely do not have D14-like structure. We also show that certain groups of DDK proteins lack the otherwise conserved MORE AXILLARY GROWTH2 (MAX2) interface, and may thus function independently of MAX2, which we show is highly conserved throughout land plant evolution. CONCLUSIONS: Our results suggest that D14-like structure is not required for SL perception, and that SL perception has relatively relaxed structural requirements compared to KAI2-mediated signalling. We suggest that SL perception gradually evolved by neo-functionalization within the DDK lineage, and that the transition from KAI2-like to D14-like protein may have been driven by interactions with protein partners, rather than being required for SL perception per se.\",\n \"corpus_id\": 1176031,\n \"score\": 2\n },\n {\n \"doc_id\": \"28970845\",\n \"title\": \"Comprehensive Analysis of DWARF14-LIKE2 (DLK2) Reveals Its Functional Divergence from Strigolactone-Related Paralogs.\",\n \"abstract\": \"Strigolactones (SLs) and related butenolides, originally identified as active seed germination stimulants of parasitic weeds, play important roles in many aspects of plant development. Two members of the D14 α/β hydrolase protein family, DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are essential for SL/butenolide signaling. The third member of the family in Arabidopsis, DWARF 14-LIKE2 (DLK2) is structurally very similar to D14 and KAI2, but its function is unknown. We demonstrated that DLK2 does not bind nor hydrolyze natural (+)5-deoxystrigol [(+)5DS], and weakly hydrolyzes non-natural strigolactone (-)5DS. A detailed genetic analysis revealed that DLK2 does not affect SL responses and can regulate seedling photomorphogenesis. DLK2 is upregulated in the dark dependent upon KAI2 and PHYTOCHROME INTERACTING FACTORS (PIFs), indicating that DLK2 might function in light signaling pathways. In addition, unlike its paralog proteins, DLK2 is not subject to rac-GR24-induced degradation, suggesting that DLK2 acts independently of MORE AXILLARY GROWTH2 (MAX2); however, regulation of DLK2 transcription is mostly accomplished through MAX2. In conclusion, these data suggest that DLK2 represents a divergent member of the DWARF14 family.\",\n \"corpus_id\": 23801725,\n \"score\": 2\n },\n {\n \"doc_id\": \"29170677\",\n \"title\": \"DWARF14, A Receptor Covalently Linked with the Active Form of Strigolactones, Undergoes Strigolactone-Dependent Degradation in Rice.\",\n \"abstract\": \"Strigolactones (SLs) are the latest confirmed phytohormones that regulate shoot branching by inhibiting bud outgrowth in higher plants. Perception of SLs depends on a novel mechanism employing an enzyme-receptor DWARF14 (D14) that hydrolyzes SLs and becomes covalently modified. This stimulates the interaction between D14 and D3, leading to the ubiquitination and degradation of the transcriptional repressor protein D53. However, the regulation of SL perception in rice remains elusive. In this study, we provide evidences that D14 is ubiquitinated after SL treatment and degraded through the 26S proteasome system. The Lys280 site of the D14 amino acid sequence was important for SL-induced D14 degradation, but did not change the subcellular localization of D14 nor disturbed the interaction between D14 and D3, nor D53 degradation. Biochemical and genetic analysis indicated that the key amino acids in the catalytic center of D14 were essential for D14 degradation. We further showed that D14 degradation is dependent on D3 and is tightly correlated with protein levels of D53. These findings revealed that D14 degradation takes place following D53 degradation and functions as an important feedback regulation mechanism of SL perception in rice.\",\n \"corpus_id\": 5617131,\n \"score\": 2\n },\n {\n \"doc_id\": \"29365172\",\n \"title\": \"Rice DWARF14 acts as an unconventional hormone receptor for strigolactone.\",\n \"abstract\": \"Strigolactones (SLs) act as an important class of phytohormones to regulate plant shoot branching, and also serve as rhizosphere signals to mediate interactions of host plants with soil microbes and parasitic weeds. SL receptors in dicots, such as DWARF14 in Arabidopsis (AtD14), RMS3 in pea, and ShHTL7 in Striga, serve as unconventional receptors that hydrolyze SLs into a D-ring-derived intermediate CLIM and irreversibly bind CLIM to trigger SL signal transduction. Here, we show that D14 from the monocot rice can complement Arabidopsis d14 mutant and interact with the SL signaling components in Arabidopsis. Our results further reveal that rice D14, similar to SL receptors in dicots, also serves as an unconventional hormone receptor that generates and irreversibly binds the active form of SLs. These findings uncover the conserved functions of D14 proteins in monocots and dicots.\",\n \"corpus_id\": 13774480,\n \"score\": 2\n },\n {\n \"doc_id\": \"29394369\",\n \"title\": \"The elusive ligand complexes of the DWARF14 strigolactone receptor.\",\n \"abstract\": \"Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.\",\n \"corpus_id\": 7569217,\n \"score\": 2\n },\n {\n \"doc_id\": \"29522151\",\n \"title\": \"Which are the major players, canonical or non-canonical strigolactones?\",\n \"abstract\": \"Strigolactones (SLs) can be classified into two structurally distinct groups: canonical and non-canonical SLs. Canonical SLs contain the ABCD ring system, and non-canonical SLs lack the A, B, or C ring but have the enol ether-D ring moiety, which is essential for biological activities. The simplest non-canonical SL is the SL biosynthetic intermediate carlactone. In plants, carlactone and its oxidized metabolites, such as carlactonoic acid and methyl carlactonoate, are present in root and shoot tissues. In some plant species, including black oat (Avena strigosa), sunflower (Helianthus annuus), and maize (Zea mays), non-canonical SLs in the root exudates are major germination stimulants. Various plant species, such as tomato (Solanum lycopersicum), Arabidopsis, and poplar (Populus spp.), release carlactonoic acid into the rhizosphere. These observations suggest that both canonical and non-canonical SLs act as host-recognition signals in the rhizosphere. In contrast, the limited distribution of canonical SLs in the plant kingdom, and the structure-specific and stereospecific transportation of canonical SLs from roots to shoots, suggest that plant hormones inhibiting shoot branching are not canonical SLs but, rather, are non-canonical SLs.\",\n \"corpus_id\": 27076314,\n \"score\": 2\n },\n {\n \"doc_id\": \"29532023\",\n \"title\": \"Discovery of Shoot Branching Regulator Targeting Strigolactone Receptor DWARF14.\",\n \"abstract\": \"DWARF14 (D14) is a strigolactone receptor that plays a central role in suppression of shoot branching, and hence is a potential target to increase crop productions and biomass. Recently, we reported a fluorescence turn-on probe, Yoshimulactone Green (YLG), which generates a strong fluorescence upon the hydrolysis by D14-type strigolactone receptors. Herein, we applied a YLG-based in vitro assay to a high-throughput chemical screening and identified a novel small molecule DL1 as a potent inhibitor of D14. DL1 competes with endogenous strigolactones, thereby increasing the number of shoot branching in a model plant Arabidopsis as well as in rice. Thus, DL1 is expected to be useful not only as a tool to understand the biological roles of D14 receptors in plant growth and development, but also as a potent agrochemical to improve the crop yield.\",\n \"corpus_id\": 3888246,\n \"score\": 2\n },\n {\n \"doc_id\": \"29554337\",\n \"title\": \"Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay.\",\n \"abstract\": \"Strigolactones (SLs) are plant hormones with various functions in development, responses to stress, and interactions with (micro)organisms in the rhizosphere, including with seeds of parasitic plants. Their perception for hormonal functions requires an α,β-hydrolase belonging to the D14 clade in higher plants; perception of host-produced SLs by parasitic seeds relies on similar but phylogenetically distinct proteins (D14-like). D14 and D14-like proteins are peculiar receptors, because they cleave SLs before undergoing a conformational change that elicits downstream events. Structure-activity relationship data show that the butenolide D-ring is crucial for bioactivity. We applied a bioisosteric approach to the structure of SLs by synthetizing analogues and mimics of natural SLs in which the D-ring was changed from a butenolide to a lactam and then evaluating their bioactivity. This was done by using a novel bioassay based on Arabidopsis transgenic lines expressing AtD14 fused to firefly luciferase, in parallel with the quantification of germination-inducing activity on parasitic seeds. The results obtained showed that the in planta bioassay is robust and quantitative, and thus can be confidently added to the SL-survey toolbox. The results also showed that modification of the butenolide ring into a lactam one significantly hampers the biological activity exhibited by SLs possessing a canonical lactonic D-ring.\",\n \"corpus_id\": 4045211,\n \"score\": 2\n },\n {\n \"doc_id\": \"29727000\",\n \"title\": \"Rationally Designed Strigolactone Analogs as Antagonists of the D14 Receptor.\",\n \"abstract\": \"Strigolactones (SLs) are plant hormones that inhibit shoot branching and act as signals in communications with symbiotic fungi and parasitic weeds in the rhizosphere. SL signaling is mediated by DWARF14 (D14), which is an α/β-hydrolase that cleaves SLs into an ABC tricyclic lactone and a butenolide group (i.e. D-ring). This cleavage reaction (hydrolysis and dissociation) is important for inducing the interaction between D14 and its target proteins, including D3 and D53. In this study, a hydrolysis-resistant SL analog was predicted to inhibit the activation of the D14 receptor, thereby disrupting the SL signaling pathway. To test this prediction, carba-SL compounds, in which the ether oxygen of the D-ring or the phenol ether oxygen of the SL agonist (GR24 or 4-bromo debranone) was replaced with a methylene group, were synthesized as novel D14 antagonists. Subsequent biochemical and physiological studies indicated that carba-SLs blocked the interaction between D14 and D53 by inhibiting D14 hydrolytic activity. They also suppressed the SL-induced inhibition of rice tiller outgrowths. Additionally, carba-SLs antagonized the SL response in a Striga parasitic weed species. Structural analyses revealed that the D-ring of 7'-carba-4BD was hydrolyzed by D14 but did not dissociate from the 4BD skeleton. Thus, 7'-carba-4BD functioned as an antagonist rather than an agonist. Thus, the hydrolysis of the D-ring of SLs may be insufficient for activating the receptor. This study provides data relevant to designing SL receptor antagonists.\",\n \"corpus_id\": 19126937,\n \"score\": 2\n },\n {\n \"doc_id\": \"26308901\",\n \"title\": \"Allosteric receptor activation by the plant peptide hormone phytosulfokine.\",\n \"abstract\": \"Phytosulfokine (PSK) is a disulfated pentapeptide that has a ubiquitous role in plant growth and development. PSK is perceived by its receptor PSKR, a leucine-rich repeat receptor kinase (LRR-RK). The mechanisms underlying the recognition of PSK, the activation of PSKR and the identity of the components downstream of the initial binding remain elusive. Here we report the crystal structures of the extracellular LRR domain of PSKR in free, PSK- and co-receptor-bound forms. The structures reveal that PSK interacts mainly with a β-strand from the island domain of PSKR, forming an anti-β-sheet. The two sulfate moieties of PSK interact directly with PSKR, sensitizing PSKR recognition of PSK. Supported by biochemical, structural and genetic evidence, PSK binding enhances PSKR heterodimerization with the somatic embryogenesis receptor-like kinases (SERKs). However, PSK is not directly involved in PSKR-SERK interaction but stabilizes PSKR island domain for recruitment of a SERK. Our data reveal the structural basis for PSKR recognition of PSK and allosteric activation of PSKR by PSK, opening up new avenues for the design of PSKR-specific small molecules.\",\n \"corpus_id\": 4467542,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":84,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26773146\",\n \"title\": \"Swift and Strong NK Cell Responses Protect 129 Mice against High-Dose Influenza Virus Infection.\",\n \"abstract\": \"It is generally unclear what roles NK cells play during influenza virus infection with regard to different host genetic backgrounds. In this study, we show that in six inbred mouse strains, NK cells play an important protective role only in 129 mice during high-dose influenza A H1N1 virus infection. Swift and strong NK cell responses efficiently control early pulmonary viral replication in 129 mice, providing survival privilege. In addition, we identified that early activation of TLRs and RIG-I signaling in 129 mice resulted in quick production of type 1 IFNs and inflammatory cytokines, which are important reasons for the swift kinetics of NK cell responses post influenza virus infection. Thus, under different microenvironments, NK cells play differential roles against viral infections. The kinetics and magnitude of NK cell responses correlate with the distinct roles that NK cells play against influenza virus infections. Thus, our works further our understandings about the complex role of NK cells during influenza virus infection.\",\n \"corpus_id\": 26114617\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18304606","title":"Characterization of age-related changes in natural killer cells during primary influenza infection in mice.","abstract":"The current investigation examined the importance of natural killer (NK) cells during the innate immune response to primary influenza infection in young and aged mice. Young (6-8 weeks) and aged (22 months) C57BL/6 mice were infected intranasally with influenza A virus, and NK cell-mediated cytotoxicity was determined in lung and spleen during the first 4 days of infection. Aged mice demonstrated both a decrease in influenza-inducible NK activity and a reduction in the percentage and number of NK1.1+ cells in response to primary influenza infection, relative to young mice. In order to further establish a role for NK cells in controlling influenza infection, young mice were depleted of NK cells in vivo by injecting rabbit anit-NK1.1 antibody 2 days and 1 day prior to influenza infection. Young mice depleted of NK cells exhibited increased weight loss and lung virus titers during the course of infection, compared to young mice infected with influenza virus. These data indicate that NK cell function is impaired in response to primary influenza infection in aged mice. More importantly, these results underscore the essential role of NK cells in controlling virus titers in lung during the early course of influenza infection, regardless of age.","corpus_id":5478837,"score":2},{"doc_id":"19293935","title":"Host genetic background strongly influences the response to influenza a virus infections.","abstract":"The genetic make-up of the host has a major influence on its response to combat pathogens. For influenza A virus, several single gene mutations have been described which contribute to survival, the immune response and clearance of the pathogen by the host organism. Here, we have studied the influence of the genetic background to influenza A H1N1 (PR8) and H7N7 (SC35M) viruses. The seven inbred laboratory strains of mice analyzed exhibited different weight loss kinetics and survival rates after infection with PR8. Two strains in particular, DBA/2J and A/J, showed very high susceptibility to viral infections compared to all other strains. The LD(50) to the influenza virus PR8 in DBA/2J mice was more than 1000-fold lower than in C57BL/6J mice. High susceptibility in DBA/2J mice was also observed after infection with influenza strain SC35M. In addition, infected DBA/2J mice showed a higher viral load in their lungs, elevated expression of cytokines and chemokines, and a more severe and extended lung pathology compared to infected C57BL/6J mice. These findings indicate a major contribution of the genetic background of the host to influenza A virus infections. The overall response in highly susceptible DBA/2J mice resembled the pathology described for infections with the highly virulent influenza H1N1-1918 and newly emerged H5N1 viruses.","corpus_id":17996944,"score":2},{"doc_id":"19721456","title":"The functional impairment of natural killer cells during influenza virus infection.","abstract":"Natural killer (NK) cells have a critical role in clearing influenza virus, which primarily infects the lung epithelial cells. However, the ability of influenza virus to infect and manipulate NK cells has not been studied. In this context, we hypothesized that influenza virus can target NK cells leading to a functional impairment in their ability to mediate cytotoxicity and cytokine/chemokine generations. Here, we show influenza virus, PR8, can enter and infect NK cells. This infection did not alter the expression levels of activating, inhibitory or developmental receptors of NK cells. However, infection of NK cells by PR8 reduced the cytotoxicity to tumor cells that represent 'induced-self' and 'missing-self'. PR8-infection also significantly downregulated the NCR1, NKG2D, Nkpr1c, Ly49D and CD244 receptors-mediated generation of pro-inflammatory cytokines and chemokines. Mutations in the non-structural protein 1 (NS1) of influenza virus further augmented the functional impairment of NK cells. Our observations show the presence of a new, but yet to be explored, mechanism by which the influenza virus can evade immune detection.","corpus_id":20495343,"score":2},{"doc_id":"20083661","title":"Influenza infection leads to increased susceptibility to subsequent bacterial superinfection by impairing NK cell responses in the lung.","abstract":"Influenza viral infection is well-known to predispose to subsequent bacterial superinfection in the lung but the mechanisms have remained poorly defined. We have established a murine model of heterologous infections by an H1N1 influenza virus and Staphylococcus aureus. We found that indeed prior influenza infection markedly increased the susceptibility of mice to secondary S. aureus superinfection. Severe sickness and heightened bacterial infection in flu and S. aureus dual-infected animals were associated with severe immunopathology in the lung. We further found that flu-experienced lungs had an impaired NK cell response in the airway to subsequent S. aureus bacterial infection. Thus, adoptive transfer of naive NK cells to the airway of prior flu-infected mice restored flu-impaired antibacterial host defense. We identified that TNF-alpha production of NK cells played an important role in NK cell-mediated antibacterial host defense as NK cells in flu-experienced lungs had reduced TNF-alpha expression and adoptive transfer of TNF-alpha-deficient NK cells to the airway of flu-infected mice failed to restore flu-impaired antibacterial host defense. Defected NK cell function was found to be an upstream mechanism of depressed antibacterial activities by alveolar macrophages as contrast to naive wild-type NK cells, the NK cells from flu-infected or TNF-alpha-deficient mice failed to enhance S. aureus phagocytosis by alveolar macrophages. Together, our study identifies the weakened NK cell response in the lung to be a novel critical mechanism for flu-mediated susceptibility to bacterial superinfection.","corpus_id":1977042,"score":2},{"doc_id":"20121698","title":"The role of Toll-like receptors in regulating the immune response against respiratory syncytial virus.","abstract":"Toll-like receptors (TLRs) play a distinct role in battling respiratory syncytial virus (RSV) infections. However, due to a lack of representative animal models and several early controversies, the field is unclear. In this systematic review, we have elucidated conflicting results and outlined important factors that might affect study outcomes. We reviewed studies that used different doses/viral strains, performed virus propagation in different cell lines, or used different mice strains. The following firm conclusions can be drawn: multiple TLRs activate innate immunity upon RSV infection; TLR4 can influence TLR2 expression, suggesting that optimal induction of multiple signaling pathways is required to elicit protective, rather than deleterious innate immune responses following infection; in mice, TLR4, TLR2/-6, and TLR7 have immune-stimulating properties, while TLR3 activation occurs later and appears to downregulate immune responses; in humans, polymorphism studies have demonstrated an important role for TLR4-signaling; and activation of TLR-signaling leads to antiviral cytokine production, such as TNF-a and IFNs. Viral factors may block these pathways, thereby contributing to immune evasion and RSV survival. A better understanding of the complex interplay between TLRs and severe RSV infections might lead to efficient prophylactic and therapeutic treatments, as well as the development of adequate vaccines combined with TLR adjuvants.","corpus_id":13007136,"score":2},{"doc_id":"20130050","title":"Killing of avian and Swine influenza virus by natural killer cells.","abstract":"Today, global attention is focused on two influenza virus strains: the current pandemic strain, swine origin influenza virus (H1N1-2009), and the highly pathogenic avian influenza virus, H5N1. At present, the infection caused by the H1N1-2009 is moderate, with mortality rates of less <1%. In contrast, infection with the H5N1 virus resulted in high mortality rates, and ca. 60% of the infected patients succumb to the infection. Thus, one of the world greatest concerns is that the H5N1 virus will evolve to allow an efficient human infection and human-to-human transmission. Natural killer (NK) cells are one of the innate immune components playing an important role in fighting against influenza viruses. One of the major NK activating receptors involved in NK cell cytotoxicity is NKp46. We previously demonstrated that NKp46 recognizes the hemagglutinin proteins of B and A influenza virus strains. Whether NKp46 could also interact with H1N1-2009 virus or with the avian influenza virus is still unknown. We analyzed the immunological properties of both the avian and the H1N1-2009 influenza viruses. We show that NKp46 recognizes the hemagglutinins of H1N1-2009 and H5 and that this recognition leads to virus killing both in vitro and in vivo. However, importantly, while the swine H1-NKp46 interactions lead to the direct killing of the infected cells, the H5-NKp46 interactions were unable to elicit direct killing, probably because the NKp46 binding sites for these two viruses are different.","corpus_id":206811398,"score":2},{"doc_id":"20235626","title":"IFN-gamma treatment at early stages of influenza virus infection protects mice from death in a NK cell-dependent manner.","abstract":"Influenza pandemics are imminent and represent a major world health concern. Since vaccinations are expected to be less efficient in the coming years due to newly emerging influenza virus strains, novel antiviral therapies are urgently needed. Here, we show that influenza-infected mice, capable of clearing the virus in the early stages of infection, failed to control inflammation and death. Sequential administration of Interferon-gamma (IFN-gamma) at early stage of the infection protected infected mice from death in a NK cell-dependent manner. IFN-gamma treatment stimulated NK cell proliferation and function and increased their number in the bone marrow, blood, spleen, and infected lungs, keeping viral clearance intact. In parallel, IFN-gamma treatment significantly reduced the number of T cells and NKT cells in the lungs at the inflammatory phase following infection. Thus, rapidly clearing the virus and reducing inflammation by shaping the cellular and cytokine profiles in the early stages of infection may favorably change the fate of influenza pathogenesis.","corpus_id":5686206,"score":2},{"doc_id":"21543489","title":"Viral replication and innate host responses in primary human alveolar epithelial cells and alveolar macrophages infected with influenza H5N1 and H1N1 viruses.","abstract":"Highly pathogenic influenza H5N1 virus continues to pose a threat to public health. Although the mechanisms underlying the pathogenesis of the H5N1 virus have not been fully defined, it has been suggested that cytokine dysregulation plays an important role. As the human respiratory epithelium is the primary target cell for influenza viruses, elucidating the viral tropism and innate immune responses of influenza H5N1 virus in the alveolar epithelium may help us to understand the pathogenesis of the severe pneumonia associated with H5N1 disease. Here we used primary cultures of differentiated human alveolar type II cells, alveolar type I-like cells, and alveolar macrophages isolated from the same individual to investigate viral replication competence and host innate immune responses to influenza H5N1 (A/HK/483/97) and H1N1 (A/HK/54/98) virus infection. The viral replication kinetics and cytokine and chemokine responses were compared by quantitative PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA). We demonstrated that influenza H1N1 and H5N1 viruses replicated productively in type II cells and type I-like cells although with different kinetics. The H5N1 virus replicated productively in alveolar macrophages, whereas the H1N1 virus led to an abortive infection. The H5N1 virus was a more potent inducer of proinflammatory cytokines and chemokines than the H1N1 virus in all cell types. However, higher levels of cytokine expression were observed for peripheral blood monocyte-derived macrophages than for alveolar macrophages in response to H5N1 virus infection. Our findings provide important insights into the viral tropisms and host responses of different cell types found in the lung and are relevant to an understanding of the pathogenesis of severe human influenza disease.","corpus_id":961092,"score":2},{"doc_id":"21896679","title":"H5N1 influenza virus pathogenesis in genetically diverse mice is mediated at the level of viral load.","abstract":"UNLABELLED: The genotype of the host is one of several factors involved in the pathogenesis of an infectious disease and may be a key parameter in the epidemiology of highly pathogenic H5N1 influenza virus infection in humans. Gene polymorphisms may affect the viral replication rate or alter the host's immune response to the virus. In humans, it is unclear which aspect dictates the severity of H5N1 virus disease. To identify the mechanism underlying differential responses to H5N1 virus infection in a genetically diverse population, we assessed the host responses and lung viral loads in 21 inbred mouse strains upon intranasal inoculation with A/Hong Kong/213/03 (H5N1). Resistant mouse strains survived large inocula while susceptible strains succumbed to infection with 1,000- to 10,000-fold-lower doses. Quantitative analysis of the viral load after inoculation with an intermediate dose found significant associations with lethality as early as 2 days postinoculation, earlier than any other disease indicator. The increased viral titers in the highly susceptible strains mediated a hyperinflamed environment, indicated by the distinct expression profiles and increased production of inflammatory mediators on day 3. Supporting the hypothesis that viral load rather than an inappropriate response to the virus was the key severity-determining factor, we performed quantitative real-time PCR measuring the cytokine/viral RNA ratio. No significant differences between susceptible and resistant mouse strains were detected, confirming that it is the host genetic component controlling viral load, and therefore replication dynamics, that is primarily responsible for a host's susceptibility to a given H5N1 virus. IMPORTANCE: Highly pathogenic H5N1 influenza virus has circulated in Southeast Asia since 2003 but has been confirmed in relatively few individuals. It has been postulated that host genetic polymorphisms increase the susceptibility to infection and severe disease. The mechanisms and host proteins affected during severe disease are unknown. Inbred mouse strains vary considerably in their ability to resist H5N1 virus and were used to identify the primary mechanism determining disease severity. After inoculation with H5N1, resistant mouse strains had reduced amounts of virus in their lungs, which subsequently resulted in lower production of proinflammatory mediators and less pathology. We therefore conclude that the host genetic component controlling disease severity is primarily influencing viral replication. This is an important concept, as it emphasizes the need to limit virus replication through antiviral therapies and it shows that the hyperinflammatory environment is simply a reflection of more viral genetic material inducing a response.","corpus_id":14567885,"score":2},{"doc_id":"21966414","title":"Changes in cytokine levels and NK cell activation associated with influenza.","abstract":"Several studies have highlighted the important role played by murine natural killer (NK) cells in the control of influenza infection. However, human NK cell responses in acute influenza infection, including infection with the 2009 pandemic H1N1 influenza virus, are poorly documented. Here, we examined changes in NK cell phenotype and function and plasma cytokine levels associated with influenza infection and vaccination. We show that absolute numbers of peripheral blood NK cells, and particularly those of CD56(bright) NK cells, decreased upon acute influenza infection while this NK cell subset expanded following intramuscular influenza vaccination. NK cells exposed to influenza antigens were activated, with higher proportions of NK cells expressing CD69 in study subjects infected with seasonal influenza strains. Vaccination led to increased levels of CD25+ NK cells, and notably CD56(bright) CD25+ NK cells, whereas decreased amounts of this subset were present in the peripheral blood of influenza infected individuals, and predominantly in study subjects infected with the 2009 pandemic H1N1 influenza virus. Finally, acute influenza infection was associated with low plasma concentrations of inflammatory cytokines, including IFN-γ, MIP-1β, IL-2 and IL-15, and high levels of the anti-inflammatory cytokines IL-10 and IL-1ra. Altogether, these data suggest a role for the CD56(bright) NK cell subset in the response to influenza, potentially involving their recruitment to infected tissues and a local production and/or uptake of inflammatory cytokines.","corpus_id":1347000,"score":2},{"doc_id":"22134539","title":"Mice with asthma are more resistant to influenza virus infection and NK cells activated by the induction of asthma have potentially protective effects.","abstract":"PURPOSE: This study was conducted in order to investigate whether the virulence of the influenza virus infection is affected by asthma in mice. METHODS: Mice with asthma or control mice were infected with influenza virus. The survival rate, body weight, virus titer, cytokine profile, and cell infiltration in bronchoalveolar lavage fluid (BALF) were measured. The NK cell cytotoxicity was determined by a co-culture system with YAC-1 cells, and the effects of NK cells were observed by depletion of NK cells using anti-asialoGM1 serum. The virus-specific CD8(+) T cell killing assay was also performed. RESULTS: When asthmatic or control mice were infected with non- and sub-lethal doses of influenza virus, the asthmatic mice were more resistant to the virus than control mice with regard to the survival rate, the remission of body weight loss, and the virus burden. Anti-viral cytokines and the NK cell number were increased in the BALF of asthmatic mice before the infection. The NK cell cytotoxicity in the asthmatic mice was significantly enhanced compared to that in control mice, and the depletion of NK cells in asthmatic mice was abrogated both the improved survival rate and the recovery of the body weight loss. The antigen-specific CD8(+) T cell killing activity in asthmatic mice was also significantly increased following the infection compared to that in control mice. CONCLUSION: NK cell activated by the induction of asthma and the subsequently activated antigen-specific CD8(+) T cells could promptly eliminate the viral-infected cells, thus leading to improvements in the morbidity and mortality of influenza virus infection.","corpus_id":1499968,"score":2},{"doc_id":"22442495","title":"Highly pathogenic avian influenza viruses inhibit effective immune responses of human blood-derived macrophages.","abstract":"Systemic infections with HPAIVs, such as H5N1, are characterized by cytokine burst and sepsis. We investigated the role of human monocyte-derived macrophages in these events after infection with different influenza virus strains. Macrophages were infected with low pathogenic H1N1 (PR8) or high pathogenic H7N7 (FPV) and H5N1 (KAN-1) subtypes. Macrophages were found to be nonpermissive for influenza virus propagation. Surprisingly, transcriptome analysis revealed an insufficient innate immune response of macrophages only to HPAIV infections. Induction of inflammatory cytokines, as well as type I IFNs, was significantly attenuated in H5N1- and H7N7-infected cells, contradicting a primary role of macrophages for the cytokine burst. Furthermore, inflammasome activation was impaired significantly in HPAIV-infected macrophages. Interestingly, this finding correlated with a complete suppression of viral protein M2 expression after HPAIV infection, which is known to be involved in influenza viral inflammasome activation. In summary, our data provide first evidences for a strategy of how HPAIVs avoid initial inflammatory responses of macrophages facilitating virus spreading and progression to the systemic stage of disease.","corpus_id":206996747,"score":2},{"doc_id":"22624047","title":"IL-15 participates in the respiratory innate immune response to influenza virus infection.","abstract":"Following influenza infection, natural killer (NK) cells function as interim effectors by suppressing viral replication until CD8 T cells are activated, proliferate, and are mobilized within the respiratory tract. Thus, NK cells are an important first line of defense against influenza virus. Here, in a murine model of influenza, we show that virally-induced IL-15 facilitates the trafficking of NK cells into the lung airways. Blocking IL-15 delays NK cell entry to the site of infection and results in a disregulated control of early viral replication. By the same principle, viral control by NK cells can be therapeutically enhanced via intranasal administration of exogenous IL-15 in the early days post influenza infection. In addition to controlling early viral replication, this IL-15-induced mobilization of NK cells to the lung airways has important downstream consequences on adaptive responses. Primarily, depletion of responding NK1.1+ NK cells is associated with reduced immigration of influenza-specific CD8 T cells to the site of infection. Together this work suggests that local deposits of IL-15 in the lung airways regulate the coordinated innate and adaptive immune responses to influenza infection and may represent an important point of immune intervention.","corpus_id":16114244,"score":2},{"doc_id":"22869906","title":"NK cells regulate CD8+ T cell priming and dendritic cell migration during influenza A infection by IFN-γ and perforin-dependent mechanisms.","abstract":"An effective immune response against influenza A infection depends on the generation of virus-specific T cells. NK cells are one of the first-line defenses against influenza A infection. We set out to delineate the role of NK cells in T cell immunity using a murine model of influenza A infection with A/PR/8/34. We show that early T cell recruitment mainly occurs in the posterior mediastinal lymph node (pMLN). Depletion of NK cells significantly impaired both dendritic cell (DC) and T cell recruitment into the pMLN. A similar reduction of T cell recruitment was observed when migration was blocked by pertussis toxin, suggesting that migration of pulmonary NK cells and DCs regulates cell recruitment to the pMLN. T cell recruitment was dependent on IFN-γ, and transfer of IFN-γ-competent naive NK cells into IFN-γ-/- mice restored T cell recruitment, whereas IFN-γ-deficient NK cells failed to do so. In addition, NK cell depletion reduced the uptake and transport of influenza A virus by DCs, and significantly impaired the virus-specific T cell response. Both IFN-γ-/- and perforin-/- mice showed reduced viral Ag transport by DCs, suggesting that the ability of NK cells to influence virus transport depends on IFN-γ and perforin. In summary, our data suggest that NK cells play a critical role in the initiation and shaping of the T cell response after influenza A infection.","corpus_id":24236105,"score":2},{"doc_id":"23185463","title":"Influenza A(H1N1)pdm09 virus suppresses RIG-I initiated innate antiviral responses in the human lung.","abstract":"Influenza infection is a major cause of morbidity and mortality. Retinoic acid-inducible gene I (RIG-I) is believed to play an important role in the recognition of, and response to, influenza virus and other RNA viruses. Our study focuses on the hypothesis that pandemic H1N1/09 influenza virus alters the influenza-induced proinflammatory response and suppresses host antiviral activity. We first compared the innate response to a clinical isolate of influenza A(H1N1)pdm09 virus, OK/09, a clinical isolate of seasonal H3N2 virus, OK/06, and to a laboratory adapted seasonal H1N1 virus, PR8, using a unique human lung organ culture model. Exposure of human lung tissue to either pandemic or seasonal influenza virus resulted in infection and replication in alveolar epithelial cells. Pandemic virus induces a diminished RIG-I mRNA and antiviral cytokine response than seasonal virus in human lung. The suppression of antiviral response and RIG-I mRNA expression was confirmed at the protein level by ELISA and western blot. We performed a time course of RIG-I and interferon-β (IFN-β) mRNA induction by the two viruses. RIG-I and IFN-β induction by OK/09 was of lower amplitude and shorter duration than that caused by PR8. In contrast, the pandemic virus OK/09 caused similar induction of proinflammatory cytokines, IL-8 and IL-6, at both the transcriptional and translational level as PR8 in human lung. Differential antiviral responses did not appear to be due to a difference in cellular infectivity as immunohistochemistry showed that both viruses infected alveolar macrophages and epithelial cells. These findings show that influenza A(H1N1)pdm09 virus suppresses anti-viral immune responses in infected human lung through inhibition of viral-mediated induction of the pattern recognition receptor, RIG-I, though proinflammatory cytokine induction was unaltered. This immunosuppression of the host antiviral response by pandemic virus may have contributed to the more serious lung infections that occurred in the H1N1 pandemic of 2009.","corpus_id":18883954,"score":2},{"doc_id":"23272202","title":"CCR2 defines a distinct population of NK cells and mediates their migration during influenza virus infection in mice.","abstract":"Natural killer (NK) cells are innate lymphocytes that play an important role in control of viral infections. We recently showed that intranasal infection of mice with influenza virus induced the accumulation of NK cells in the airways. NK cells however did not proliferate in the airways or in the draining lymph node, but in the bone marrow mainly. As also monocyte-precursors undergo vigorous proliferation in the bone marrow (BM) during infections and then egress CCR2-dependently, we decided to determine the role of CCR2 in NK cell migration during intranasal influenza virus infection. We show that a unique population of NK cells in the BM expressed CCR2 and that monocyte chemotactic protein-1 (MCP-1), one of the CCR2 ligands, was produced in the airways of influenza virus infected mice. Analysis of BM chimeric mice reconstituted with a mix of wild-type (wt) and CCR2-deficient BM cells showed that upon influenza virus infection, a significantly lower proportion of CCR2-deficient than wt NK cells was recovered from the bronchoalveolar lavage (BAL). Taken together, our data demonstrate that during influenza virus infection a proportion of NK cells migrate in a CCR2-dependent fashion.","corpus_id":18043084,"score":2},{"doc_id":"23300570","title":"Activation mechanisms of natural killer cells during influenza virus infection.","abstract":"During early viral infection, activation of natural killer (NK) cells elicits the effector functions of target cell lysis and cytokine production. However, the cellular and molecular mechanisms leading to NK cell activation during viral infections are incompletely understood. In this study, using a model of acute viral infection, we investigated the mechanisms controlling cytotoxic activity and cytokine production in response to influenza (flu) virus. Analysis of cytokine receptor deficient mice demonstrated that type I interferons (IFNs), but not IL-12 or IL-18, were critical for the NK cell expression of both IFN-γ and granzyme B in response to flu infection. Further, adoptive transfer experiments revealed that NK cell activation was mediated by type I IFNs acting directly on NK cells. Analysis of signal transduction molecules showed that during flu infection, STAT1 activation in NK cells was completely dependent on direct type I IFN signaling, whereas STAT4 activation was only partially dependent. In addition, granzyme B induction in NK cells was mediated by signaling primarily through STAT1, but not STAT4, while IFN-γ production was mediated by signaling through STAT4, but not STAT1. Therefore, our findings demonstrate the importance of direct action of type I IFNs on NK cells to mount effective NK cell responses in the context of flu infection and delineate NK cell signaling pathways responsible for controlling cytotoxic activity and cytokine production.","corpus_id":6895012,"score":2},{"doc_id":"23436540","title":"NK cells exacerbate the pathology of influenza virus infection in mice.","abstract":"NK cells offer a first line of defense against viruses and are considered beneficial to the host during infection. Nevertheless, little is understood regarding the phenotype and function of NK cells in the lung during influenza virus infection. We found that the frequency of NK cells in mouse lung increased during influenza infection, with the majority of a mature phenotype. Cell surface CD107a and intracellular IFN-γ were detected in cells expressing multiple NK-cell receptors in infected lung, suggesting that NK cells were activated during infection. The activating receptor NKp46 was predominantly negative on such cells, possibly as a result of encountering influenza HA. Depletion of NK cells in vivo with anti-asialo GM1 or anti-NK1.1 reduced mortality from influenza infection and surviving mice recovered their body weight. Pathology induced by NK cells was only observed with high, not medium or low-dose influenza infection, indicating that the severity of infection influences NK-cell-mediated pathology. Furthermore, adoptive transfer of NK cells from influenza-infected lung, but not uninfected lung, resulted in more rapid weight loss and increased mortality of influenza-infected mice. Our results indicate that during severe influenza infection of the lung, NK cells have a deleterious impact on the host, promoting mortality.","corpus_id":5522473,"score":2},{"doc_id":"23963354","title":"Differential lung NK cell responses in avian influenza virus infected chickens correlate with pathogenicity.","abstract":"Infection of chickens with low pathogenicity avian influenza (LPAI) virus results in mild clinical signs while infection with highly pathogenic avian influenza (HPAI) viruses causes death of the birds within 36-48 hours. Since natural killer (NK) cells have been shown to play an important role in influenza-specific immunity, we hypothesise that NK cells are involved in this difference in pathogenicity. To investigate this, the role of chicken NK-cells in LPAI virus infection was studied. Next activation of lung NK cells upon HPAI virus infection was analysed. Infection with a H9N2 LPAI virus resulted in the presence of viral RNA in the lungs which coincided with enhanced activation of lung NK cells. The presence of H5N1 viruses, measured by detection of viral RNA, did not induce activation of lung NK cells. This suggests that decreased NK-cell activation may be one of the mechanisms associated with the enhanced pathogenicity of H5N1 viruses.","corpus_id":261351984,"score":2},{"doc_id":"24373231","title":"Inhibition of the inflammatory cytokine tumor necrosis factor-alpha with etanercept provides protection against lethal H1N1 influenza infection in mice.","abstract":"INTRODUCTION: Factors implicated in influenza-mediated morbidity and mortality include robust cytokine production (cytokine storm), excessive inflammatory infiltrates, and virus-induced tissue destruction. Tumor necrosis factor-alpha (TNF-α) is an important pro-inflammatory cytokine present during influenza infection, but it is unclear whether direct inhibition of TNF-α can elicit protection against influenza infection. METHODS: In this study, the commercially available TNF-α inhibitor etanercept was used to inhibit TNF-α induced by lethal A/FM/1/47 (H1N1) influenza virus infection of mice. The effects of TNF-α inhibition on mouse survival, pathologic changes, immune cell infiltration, inflammatory cytokine secretion, Toll-like receptor expression, and activation of the NF-κB (nuclear factor kappa B) signaling pathway were evaluated. RESULTS: The intranasal delivery of etanercept provided significant protection against mortality (30% of mice survived up to 14 days after infection) in mice treated with etanercept. In contrast, no survivors were found beyond 6 days in mice treated with saline after lethal challenge with H1N1 influenza virus. It was observed that etanercept significantly reduced inflammatory cell infiltration (for example, macrophages and neutrophils), inflammatory cytokine secretion (for example, interleukin-6, TNF-α, and interferon gamma), and expression of Toll-like receptors (TLR-3, TLR-4, and TLR-7). Etanercept also downregulated and inhibited the cascade proteins of the NF-κB signaling pathway (for example, MyD88, TRIF, NF-κB, and p65), as well as enhanced host control of virus replication. CONCLUSIONS: These findings indicate that etanercept, by blocking TNF-α, can significantly downregulate excessive inflammatory immune responses and provide protection against lethal influenza infection, making its use a novel strategy for controlling severe influenza-induced viral pneumonia.","corpus_id":7979949,"score":2},{"doc_id":"24435166","title":"Type I interferon plays opposing roles in cytotoxicity and interferon-γ production by natural killer and CD8 T cells after influenza A virus infection in mice.","abstract":"Type I interferons (IFNs) promote natural killer (NK) and CD8(+) T-cell responses, which play a role not only in the resolution of infection but also in the induction of acute lung injury following influenza A virus infection. We show here that IFN-α receptor knock-out (Ifnar1(-/-)) mice exhibited impaired cytotoxic activity as well as an increased ability of NK and CD8(+) T cells to produce IFN-γ after infection with influenza virus A/FM/1/47 (H1N1, a mouse-adapted strain). A deficiency in IFNAR signaling significantly impaired IL-10 production in influenza virus-infected lungs and enhanced IFN-γ production by NK cells, which were suppressed by exogenous IL-10. Depletion of NK cells but not CD8(+) T cells in Ifnar1(-/-) mice improved the survival rate after A/FM/1/47 infection, indicating that NK cells are responsible for acute lung injury in Ifnar1(-/-) mice following influenza A virus infection, although the depletion of IFN-γ did not improve the outcome. Thus, type I IFN signaling plays a role not only in the upregulation of cytotoxicity but also in the downregulation of some effector mechanisms including IFN-γ production by NK and CD8(+) T cells via IL-10 production.","corpus_id":8881230,"score":2},{"doc_id":"24567377","title":"Toll-like receptor 10 is involved in induction of innate immune responses to influenza virus infection.","abstract":"Toll-like receptors (TLRs) play key roles in innate immune recognition of pathogen-associated molecular patterns of invading microbes. Among the 10 TLR family members identified in humans, TLR10 remains an orphan receptor without known agonist or function. TLR10 is a pseudogene in mice and mouse models are noninformative in this regard. Using influenza virus infection in primary human peripheral blood monocyte-derived macrophages and a human monocytic cell line, we now provide previously unidentified evidence that TLR10 plays a role in innate immune responses following viral infection. Influenza virus infection increased TLR10 expression and TLR10 contributed to innate immune sensing of viral infection leading to cytokine induction, including proinflammatory cytokines and interferons. TLR10 induction is more pronounced following infection with highly pathogenic avian influenza H5N1 virus compared with a low pathogenic H1N1 virus. Induction of TLR10 by virus infection requires active virus replication and de novo protein synthesis. Culture supernatants of virus-infected cells modestly up-regulate TLR10 expression in nonvirus-infected cells. Signaling via TLR10 was activated by the functional RNA-protein complex of influenza virus leading to robust induction of cytokine expression. Taken together, our findings identify TLR10 as an important innate immune sensor of viral infection and its role in innate immune defense and immunopathology following viral and bacterial pathogens deserves attention.","corpus_id":656618,"score":2},{"doc_id":"24903089","title":"Type-I interferon response affects an inoculation dose-independent mortality in mice following Japanese encephalitis virus infection.","abstract":"BACKGROUND: The laboratory mouse model is commonly employed to study the pathogenesis of encephalitic flaviviruses such as Japanese encephalitis virus (JEV). However, it is known that some strains of these viruses do not elicit a typical mortality dose response curve from this organism after peripheral infection and the reason for it has not yet been fully understood. It is suggested that induction of more vigorous Type-I IFN (IFN-I) response might control early virus dissemination following increasing infectious challenge doses of the virus. Thus, the objective of this study was to examine this suggested role of IFN-I in the mortality of mice infected with various doses of JEV. METHODS: Inbred 129 mice and their IFNAR KO (A129) mice were subcutaneously inoculated with 100, 102, 104 or 106 pfu of JaOArS982 strain of JEV. Mice were weighed daily and observed for clinical signs. Virus titers in the brains and spleens of JEV-infected mice were determined by plaque forming assays. The upregulated mRNA levels of genes related to IFN-I response of mice were examined by real-time PCR. RESULTS: The mortality rates of 129 mice infected with JaOArS982 did not significantly increase despite the increase in inoculation dose and no significant difference of viral loads was observed between their brains. However, there was clear elevation of the mRNA levels of interferon regulatory factor (IRF)3, IRF7, IRF9, MDA5 and RIG-I at 24 hours post-infection depending on the inoculation dose. In A129 mice, length of survival days and the viral loads of spleen and brain were observed to be inoculation dose-dependent. CONCLUSIONS: From these results, it is suggested that early IFN-I response elicited by high inoculation doses of JEV provides an anti-viral effect during the early phase of infection. Accordingly, virus replication is counteracted by IFN-I response at each increasing inoculation dose resulting in the interference of impending severe disease course or fatal outcome; hence, this might explain the inoculation dose-independent mortality in mice caused by Japanese encephalitis virus.","corpus_id":8275808,"score":2},{"doc_id":"24951819","title":"Klebsiella pneumoniae alleviates influenza-induced acute lung injury via limiting NK cell expansion.","abstract":"A protective effect induced by bacterial preinfection upon a subsequent lethal influenza virus infection has been observed, but the underlying immune mechanisms have not yet been fully elucidated. In this study, we used a mouse model of Klebsiella pneumoniae preinfection to gain insight into how bacterial preinfection influences the subsequent lethal influenza virus infection. We found that K. pneumoniae preinfection significantly attenuated lung immune injury and decreased mortality during influenza virus infection, but K. pneumoniae-specific immunity was not involved in this cross-protection against influenza virus. K. pneumoniae preinfection limited NK cell expansion, which was involved in influenza-induced immune injury and death. Furthermore, K. pneumoniae preinfection could not control NK cell expansion and death during influenza virus infection in Rag1(-/-) mice, but adoptive transfer of T cells from wild-type mice was able to restore this protective effect. Our data suggest that the adaptive immune response activated by bacterial infection limits the excessive innate immune response induced by a subsequent influenza infection, ultimately protecting mice from death.","corpus_id":23402303,"score":2},{"doc_id":"24992894","title":"Role of NK cells in influenza infection.","abstract":"Within days after infection, natural killer (NK) cells are recruited to the lungs and play an essential role in the immune response against influenza infection. Through interactions with the virus itself, as well as viral-infected cells, NK cells secrete a variety of cytokines and can contain viral replication by killing infected cells early after influenza infection. However, the virus has means of evading NK cell responses, including escaping NK cell recognition through mutation of the viral hemagglutinin (HA) protein, regulating HA levels, and by directly infecting and destroying NK cells. Although much of our understanding of NK cell role in influenza infection has come from animal models, there is increasing information from human infection. Studies conducted during the 2009 H1N1 pandemic provided much needed information on the importance of NK cells during human infection and suggest that NK lymphopenia may correlate with increased disease severity. However, more information on how different influenza virus subtypes influence NK cell levels and activities, the role of the different NK cell receptors in infection, and the impact of NK cells on human infection, particularly in high risk populations is needed.","corpus_id":37673946,"score":2},{"doc_id":"25404045","title":"NK cells and their ability to modulate T cells during virus infections.","abstract":"Natural killer (NK) cells are important in protection against virus infections, and many viruses have evolved mechanisms to thwart NK cell activity. NK cells respond to inflammatory signals at an early stage of virus infection, resulting in proliferation, cytokine production, and cytolytic activity that can reduce virus loads. Moreover, the rapid kinetics of the NK cell response enables NK cells to influence other populations of innate immune cells, affect the inflammatory milieu, and guide adaptive immune responses to infection. Early NK cell interactions with other leukocytes can have long-lasting effects on the number and quality of memory T cells, as well as impact the exhaustion of T cells during chronic infections. The ability of NK cells to modulate T cell responses can be mediated through direct T-NK interactions, cytokine production, or indirectly through dendritic cells and other cell types. Herein, we summarize our current understanding of how NK cells interact with T cells, dendritic cells, B cells, and other cell types involved in adaptive immune responses to virus infection. We outline several mechanisms by which NK cells enhance or suppress adaptive immune response and long-lived immunological memory.","corpus_id":41304022,"score":2},{"doc_id":"25418976","title":"A novel genetic locus linked to pro-inflammatory cytokines after virulent H5N1 virus infection in mice.","abstract":"BACKGROUND: Genetic variation in the human population is a key determinant of influenza disease severity. A single nucleotide polymorphism in the antiviral gene IFITM3 was linked to outcomes during the 2009 H1N1 pandemic. To identify variant host genes associated with increased virus replication and severe disease, we performed a quantitative trait locus analysis on pro-inflammatory cytokine production 48 hours after intranasal infection with highly pathogenic H5N1 influenza virus. RESULTS: Pro-inflammatory cytokines CCL2, TNFα and IFN-α, were measured by ELISA in lung homogenates of DBA/2J (D2), C57BL/6J (B6) and 44 different BXD recombinant inbred mouse strains. Virus titer was also assessed in a subset of these animals. CCL2 (8-fold), TNFα (24-fold) and IFN-α (8-fold) concentrations varied significantly among the different BXD RI strains. Importantly, cytokine concentration correlated very well (r =0.86-0.96, P <0.0001) with virus titer suggesting that early cytokine production is due to increased virus infection and replication. Linkage analysis of cytokine concentration revealed a significant locus on chromosome 6 associated with differences in TNFα, IFN-α and CCL2 cytokine concentration (LRS =26). This locus accounted for nearly 20% of the observed phenotypic variation in the BXD population studied. Sequence and RNA expression analysis identified several candidate host genes containing missense mutations or deletions; Samd9l, Ica1, and Slc25a13. To study the role of Slc25a13, we obtained Slc25a13 knockout line, but upon challenge with H5N1 influenza virus observed no effect on CCL2 production, or morbidity and mortality. CONCLUSION: A novel genetic locus on chromosome 6 modulates early pro-inflammatory cytokine production and virus replication after highly pathogenic influenza virus infection. Candidate genes, Samd9l and Ica1, may be important for the control of influenza virus infection and pathogenesis.","corpus_id":6917249,"score":2},{"doc_id":"26202236","title":"Protection from Severe Influenza Virus Infections in Mice Carrying the Mx1 Influenza Virus Resistance Gene Strongly Depends on Genetic Background.","abstract":"UNLABELLED: Influenza virus infections represent a serious threat to human health. Both extrinsic and intrinsic factors determine the severity of influenza. The MX dynamin-like GTPase 1 (Mx1) gene has been shown to confer strong resistance to influenza A virus infections in mice. Most laboratory mouse strains, including C57BL/6J, carry nonsense or deletion mutations in Mx1 and thus a nonfunctional allele, whereas wild-derived mouse strains carry a wild-type Mx1 allele. Congenic C57BL/6J (B6-Mx1(r/r)) mice expressing a wild-type allele from the A2G mouse strain are highly resistant to influenza A virus infections, to both mono- and polybasic subtypes. Furthermore, in genetic mapping studies, Mx1 was identified as the major locus of resistance to influenza virus infections. Here, we investigated whether the Mx1 protective function is influenced by the genetic background. For this, we generated a congenic mouse strain carrying the A2G wild-type Mx1 resistance allele on a DBA/2J background (D2-Mx1(r/r)). Most remarkably, congenic D2-Mx1(r/r) mice expressing a functional Mx1 wild-type allele are still highly susceptible to H1N1 virus. However, pretreatment of D2-Mx1(r/r) mice with alpha interferon protected them from lethal infections. Our results showed, for the first time, that the presence of an Mx1 wild-type allele from A2G as such does not fully protect mice from lethal influenza A virus infections. These observations are also highly relevant for susceptibility to influenza virus infections in humans. IMPORTANCE: Influenza A virus represents a major health threat to humans. Seasonal influenza epidemics cause high economic loss, morbidity, and deaths each year. Genetic factors of the host strongly influence susceptibility and resistance to virus infections. The Mx1 (MX dynamin-like GTPase 1) gene has been described as a major resistance gene in mice and humans. Most inbred laboratory mouse strains are deficient in Mx1, but congenic B6-Mx1(r/r) mice that carry the wild-type Mx1 gene from the A2G mouse strain are highly resistant. Here, we show that, very unexpectedly, congenic D2-Mx1(r/r) mice carrying the wild-type Mx1 gene from the A2G strain are not fully protected against lethal influenza virus infections. These observations demonstrate that the genetic background is very important for the protective function of the Mx1 resistance gene. Our results are also highly relevant for understanding genetic susceptibility to influenza virus infections in humans.","corpus_id":16032096,"score":2},{"doc_id":"26329040","title":"RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.","abstract":"BACKGROUND: The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual mouse after H1N1 infection. RESULTS: We performed a detailed expression analysis to identify (i) correlations between changes in expression of host and virus genes, (ii) host genes involved in viral replication, and (iii) genes showing differential expression between two mouse strains that strongly differ in resistance to influenza infections. These genes may be key players involved in regulating the differences in pathogenesis and host defense mechanisms after influenza A infections. Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements. Furthermore, we investigated the functional role of two genes, Reg3g and Irf7, in knock-out mice and found that deletion of the Irf7 gene renders the host highly susceptible to H1N1 infection. CONCLUSIONS: Using RNAseq analysis we identified novel genes important for viral replication or the host defense. This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.","corpus_id":15338495,"score":2},{"doc_id":"26346306","title":"Natural Killer Cells are involved in Thymic Atrophy induced by Influenza A Virus Infection.","abstract":"Natural killer (NK) cells have traditionally been viewed as innate effector lymphocytes that serve as a first-line defense against a range of viruses and tumors. More recently, the importance of NK cell immunoregulatory functions has been highlighted. NK cells can inhibit antiviral T cell responses and also play an important role in controlling harmful T cell activity in autoimmunity and transplantation settings. Moreover, immunopathological effects of NK cells during infection have been reported. Nevertheless, the phenotype and function of NK cells in the thymus during influenza virus infection is not understood. In the present study, we demonstrated that influenza A virus (IAV) infection in mice led to severe thymic atrophy caused by increased thymic T cell apoptosis and suppressed proliferation. We found that NK cells played a critical role in this phenotype. IFN-γ production by NK cells was a contributing factor for thymic atrophy during IAV infection. Taken together, our data indicate that NK cells are involved in the thymic atrophy associated with IAV infection.","corpus_id":20509718,"score":2},{"doc_id":"27438481","title":"RIG-I Signaling Is Critical for Efficient Polyfunctional T Cell Responses during Influenza Virus Infection.","abstract":"Retinoic acid inducible gene-I (RIG-I) is an innate RNA sensor that recognizes the influenza A virus (IAV) RNA genome and activates antiviral host responses. Here, we demonstrate that RIG-I signaling plays a crucial role in restricting IAV tropism and regulating host immune responses. Mice deficient in the RIG-I-MAVS pathway show defects in migratory dendritic cell (DC) activation, viral antigen presentation, and priming of CD8+ and CD4+ T cell responses during IAV infection. These defects result in decreased frequency of polyfunctional effector T cells and lowered protection against heterologous IAV challenge. In addition, our data show that RIG-I activation is essential for protecting epithelial cells and hematopoietic cells from IAV infection. These diverse effects of RIG-I signaling are likely imparted by the actions of type I interferon (IFN), as addition of exogenous type I IFN is sufficient to overcome the defects in antigen presentation by RIG-I deficient BMDC. Moreover, the in vivo T cell defects in RIG-I deficient mice can be overcome by the activation of MDA5 -MAVS via poly I:C treatment. Taken together, these findings demonstrate that RIG-I signaling through MAVS is critical for determining the quality of polyfunctional T cell responses against IAV and for providing protection against subsequent infection from heterologous or novel pandemic IAV strains.","corpus_id":10918951,"score":2},{"doc_id":"27531368","title":"Antimicrobial peptides alter early immune response to influenza A virus infection in C57BL/6 mice.","abstract":"Influenza is a disease of the respiratory system caused by single stranded RNA viruses with varying genotypes. Immunopathogenesis to influenza viruses differs based on virus strain, dose, and mouse strain used in laboratory models. Although effective mucosal immune defenses are important in early host defense against influenza, information on the kinetics of these immune defense mechanisms during the course of influenza infection is limited. We investigated changes to antimicrobial peptides and primary innate immune cells at early time points after infection and compared these variables between two prominent H1N1 influenza A virus (IAV) strains, A/CA/04/2009 and A/PR/08/1934 in C57BL/6 mice. Alveolar and parenchymal macrophage ratios were altered after IAV infection and pro-inflammatory cytokine production in macrophages was induced after IAV infection. Genes encoding antimicrobial peptides, β-defensin (Defb4), bactericidal-permeability increasing protein (Bpifa1), and cathelicidin antimicrobial peptide (Camp), were differentially regulated after IAV infection and the kinetics of Defb4 expression differed in response to each virus strain. Beta-defensin reduced infectivity of A/CA/04/2009 virus but not A/PR/08/1934. Beta defensins also changed the innate immune cell profile wherein mice pre-treated with β-defensin had increased alveolar macrophages and CD103(+) dendritic cells, and reduced CD11b(+) dendritic cells and neutrophils. In addition to highlighting that immune responses may vary based on influenza virus strain used, our data suggest an important role for antimicrobial peptides in host defense against influenza virus.","corpus_id":4926733,"score":2},{"doc_id":"28585438","title":"Pulmonary immune cells and inflammatory cytokine dysregulation are associated with mortality of IL-1R1 (-/-)mice infected with influenza virus (H1N1).","abstract":"Respirovirus infection can cause viral pneumonia and acute lung injury (ALI). The interleukin-1 (IL-1) family consists of proinflammatory cytokines that play essential roles in regulating immune and inflammatory responses in vivo. IL-1 signaling is associated with protection against respiratory influenza virus infection by mediation of the pulmonary anti-viral immune response and inflammation. We analyzed the infiltration lung immune leukocytes and cytokines that contribute to inflammatory lung pathology and mortality of fatal H1N1 virus-infected IL-1 receptor 1 (IL-1R1) deficient mice. Results showed that early innate immune cells and cytokine/chemokine dysregulation were observed with significantly decreased neutrophil infiltration and IL-6, TNF-α, G-CSF, KC, and MIP-2 cytokine levels in the bronchoalveolar lavage fluid of infected IL-1R1 (-/-) mice in comparison with that of wild type infected mice. The adaptive immune response against the H1N1 virus in IL-1R1 (-/-) mice was impaired with downregulated anti-viral Th1 cell, CD8+ cell, and antibody functions, which contributes to attenuated viral clearance. Histological analysis revealed reduced lung inflammation during early infection but severe lung pathology in late infection in IL-1R1 (-/-) mice compared with that in WT infected mice. Moreover, the infected IL-1R1 (-/-) mice showed markedly reduced neutrophil generation in bone marrow and neutrophil recruitment to the inflamed lung. Together, these results suggest that IL-1 signaling is associated with pulmonary anti-influenza immune response and inflammatory lung injury, particularly via the influence on neutrophil mobilization and inflammatory cytokine/chemokine production.","corpus_id":3648567,"score":2},{"doc_id":"28904191","title":"Dose of Retroviral Infection Determines Induction of Antiviral NK Cell Responses.","abstract":"Natural killer (NK) cells are part of the innate immune system and recognize virus-infected cells as well as tumor cells. Conflicting data about the beneficial or even detrimental role of NK cells in different infectious diseases have been described previously. While the type of pathogen strongly influences NK cell functionality, less is known about how the infection dose influences the quality of a NK cell response against retroviruses. In this study, we used the well-established Friend retrovirus (FV) mouse model to investigate the impact of virus dose on the induction of antiviral NK cell functions. High-dose virus inoculation increased initial virus replication compared to that with medium- or low-dose viral challenge and significantly improved NK cell activation. Antiviral NK cell activity, including in vivo cytotoxicity toward infected target cells, was also enhanced by high-dose virus infection. NK cell activation following high-dose viral challenge was likely mediated by activated dendritic cells (DCs) and macrophages and the NK cell-stimulating cytokines interleukin 15 (IL-15) and IL-18. Neutralization of these cytokines decreased NK cell functions and increased viral loads, whereas IL-15 and IL-18 therapy improved NK cell activity. Here we demonstrate that virus dose positively correlates with antiviral NK cell activity and function, which are at least partly driven by IL-15 and IL-18. Our results suggest that NK cell activity may be therapeutically enhanced by administering IL-15 and IL-18 in virus infections that inadequately activate NK cells. IMPORTANCE In infections with retroviruses, like HIV and FV infection of mice, NK cells clearly mediate antiviral activities, but they are usually not sufficient to prevent severe pathology. Here we show that the initial infection dose impacts the induction of an antiviral NK cell response during an acute retroviral infection, which had not investigated before. High-dose infection resulted in a strong NK cell functionality, whereas no antiviral activities were detected after low- or medium-dose infection. Interestingly, DCs and macrophages were highly activated after high-dose FV challenge, which corresponded with increased levels of NK cell-stimulating cytokines IL-15 and IL-18. IL-15 and IL-18 neutralization decreased NK cell functions, whereas IL-15 and IL-18 therapy improved NK cell activity. Here we show the importance of cytokines for NK cell activation in retroviral infections; our findings suggest that immunotherapy combining the well-tolerated cytokines IL-15 and IL-18 might be an interesting approach for antiretroviral treatment.","corpus_id":4628503,"score":2},{"doc_id":"19200852","title":"Activation of toll-like receptor signaling pathway for protection against influenza virus infection.","abstract":"This study aims to evaluate the antiviral role of nucleic acid-based agonists for the activation of toll-like receptor (TLR) signaling pathways, and its protective role in respiratory influenza A virus infections. TLR-3 is expressed on myeloid dendritic cells, respiratory epithelium, and macrophages, and appears to play a central role in mediating both the antiviral and inflammatory responses of the innate immunity in combating viral infections. Influenza viruses can effectively inhibit the host's ability to produce interferons, and thereby suppress the immune system's antiviral defence mechanisms. Poly ICLC is a synthetic double stranded RNA comprising of polyriboinosinic-poly ribocytidylic acid (Poly IC) stabilized with l-lysine (L) and carboxymethylcellulose (C). Poly ICLC and liposome-encapsulated Poly ICLC (LE Poly ICLC) are TLR-3 agonists and are potent inducer of interferons and natural killer cells. Intranasal pre-treatment of mice with Poly ICLC and LE Poly ICLC provided high level of protection against lethal challenge with a highly lethal avian H5N1 influenza (HPAI) strain (A/H5N1/chicken/Henan clade 2), and against lethal seasonal influenza A/PR/8/34 [H1N1] and A/Aichi/2 [H3N2] virus strains. The duration of protective antiviral immunity to multiple lethal doses of influenza virus A/PR/8/34 virus had been previously found to persist for up to 3 weeks in mice for LE Poly ICLC and 2 weeks for Poly ICLC. Similarly, pre-treatment of mice with CpG oligonucleotides (TLR-9 agonist) was also found to provide complete protection against influenza A/PR/8/34 infection in mice. RT-PCR analysis of lung tissues of mice treated with Poly ICLC and LE Poly ICLC revealed upregulation of TLR-3 mRNAs gene expression. Taken together, these results do support the potential role of TLR-3 and TLR-9 agonists such as Poly ICLC and LE Poly ICLC in protection against lethal seasonal and HPAI virus infection.","corpus_id":37319142,"score":1},{"doc_id":"19922665","title":"Impaired immune responses in the lungs of aged mice following influenza infection.","abstract":"BACKGROUND: Each year, influenza virus infection causes severe morbidity and mortality, particularly in the most susceptible groups including children, the elderly (>65 years-old) and people with chronic respiratory diseases. Among the several factors that contribute to the increased susceptibility in elderly populations are the higher prevalence of chronic diseases (e.g. diabetes) and the senescence of the immune system. METHODS: In this study, aged and adult mice were infected with sublethal doses of influenza virus (A/Puerto Rico/8/1934). Differences in weight loss, morbidity, virus titer and the kinetics of lung infiltration with cells of the innate and adaptive immune responses were analyzed. Additionally, the main cytokines and chemokines produced by these cells were also assayed. RESULTS: Compared to adult mice, aged mice had higher morbidity, lost weight more rapidly, and recovered more slowly from infection. There was a delay in the accumulation of granulocytic cells and conventional dendritic cells (cDCs), but not macrophages in the lungs of aged mice compared to adult animals. The delayed infiltration kinetics of APCs in aged animals correlated with alteration in their activation (CD40 expression), which also correlated with a delayed detection of cytokines and chemokines in lung homogenates. This was associated with retarded lung infiltration by natural killer (NK), CD4+ and CD8+ T-cells. Furthermore, the percentage of activated (CD69+) influenza-specific and IL-2 producer CD8+ T-cells was higher in adult mice compared to aged ones. Additionally, activation (CD69+) of adult B-cells was earlier and correlated with a quicker development of neutralizing antibodies in adult animals. CONCLUSION: Overall, alterations in APC priming and activation lead to delayed production of cytokines and chemokines in the lungs that ultimately affected the infiltration of immune cells following influenza infection. This resulted in delayed activation of the adaptive immune response and subsequent delay in clearance of virus and prolonged illness in aged animals. Since the elderly are the fastest growing segment of the population in developed countries, a better understanding of the changes that occur in the immune system during the aging process is a priority for the development of new vaccines and adjuvants to improve the immune responses in this population.","corpus_id":-1,"score":1},{"doc_id":"20033657","title":"Studying NK cell responses to ectromelia virus infections in mice.","abstract":"Here we describe methods for the in vivo study of antiviral NK cell responses using the mouse Orthopoxvirus ectromelia virus as a model, the agent of mousepox. The methods include those specific for the preparation and use of ectromelia virus such as the production of virus stocks in tissue culture and in live mice, the purification of virus stocks, the titration of virus stocks and virus loads in organs, and the infection of mice. The chapter also includes methods for the specific study of NK cell responses in infected mice such as the preparation of organs (lymph nodes, spleen, and liver) for analysis, the study of NK cell responses by flow cytometry, the adoptive transfer of NK cells, the measurement of NK cell cytolytic activity ex vivo and in vivo, and the determination of NK cell proliferation by bromodeoxyuridine loading or by dilution of carboxyfluorescein diacetate succinimidyl ester (CFSE).","corpus_id":10863468,"score":1},{"doc_id":"20855097","title":"IFN-γ production downstream of NKT cell activation in mice infected with influenza virus enhances the cytolytic activities of both NK cells and viral antigen-specific CD8+ T cells.","abstract":"Natural killer T (NKT) cell activation is responsible for eliminating pathogens. However, the biological functions of NKT cells against influenza virus are not fully understood. We therefore investigated the effects of NKT cells in viral infection using CD1d knockout (KO) mice. When CD1d KO or wild-type (WT) mice were infected with a sub-lethal dosage of the influenza virus, the survival rate of CD1d KO mice was significantly lower than for WT mice in association with delayed viral clearance in the lungs. Consistently, IFN-γ production in bronchoalveolar lavage fluid of CD1d KO mice was largely reduced compared to WT mice during infection. Moreover, the cytotoxic activities of NK cells and viral antigen-specific CD8(+) T cells were impaired in CD1d KO mice. It was concluded that activated NKT cell-induced IFN-γ release enhances both NK-cell activity and antigen-specific CD8(+) T cells to eliminate the influenza virus, thus leading to an enhanced survival.","corpus_id":205645431,"score":1},{"doc_id":"20943980","title":"MyD88 signaling is indispensable for primary influenza A virus infection but dispensable for secondary infection.","abstract":"Recent studies have revealed that innate immunity is involved in the development of adaptive immune responses; however, its role in protection is not clear. In order to elucidate the exact role of Toll-like receptor (TLR) or RIG-I-like receptor (RLR) signaling on immunogenicity and protective efficacy against influenza A virus infection (A/PR/8/34 [PR8]; H1N1), we adapted several innate signal-deficient mice (e.g., TRIF(-/-), MyD88(-/-), MyD88(-/-) TRIF(-/-), TLR3(-/-) TLR7(-/-), and IPS-1(-/-)). In this study, we found that MyD88 signaling was required for recruitment of CD11b(+) granulocytes, production of early inflammatory cytokines, optimal proliferation of CD4 T cells, and production of Th1 cytokines by T cells. However, PR8 virus-specific IgG and IgA antibody levels in both systemic and mucosal compartments were normal in TLR- and RLR-deficient mice. To further assess the susceptibility of these mice to influenza virus infection, protective efficacy was determined after primary or secondary lethal challenge. We found that MyD88(-/-) and MyD88(-/-) TRIF(-/-) mice were more susceptible to primary influenza virus infection than the B6 mice but were fully protected against homologous (H1N1) and heterosubtypic (H5N2) secondary infection when primed with a nonlethal dose of PR8 virus. Taken together, these results show that MyD88 signaling plays an important role for resisting primary influenza virus infection but is dispensable for protection against a secondary lethal challenge.","corpus_id":24306635,"score":1},{"doc_id":"22098223","title":"Heat-killed Lactobacillus gasseri TMC0356 protects mice against influenza virus infection by stimulating gut and respiratory immune responses.","abstract":"This study investigated whether heat-killed Lactobacillus protects host animal against influenza virus infection and stimulates their immunity. Heat-killed Lactobacillus gasseri TMC0356 was orally administered to BALB/c mice for 19 days; the mice were intranasally infected with Flu A/PR/8/34 (H1N1) on day 14, and clinical symptoms were monitored. After 6 days, the mice were sacrificed, and pulmonary virus titres were determined. Splenic activation of natural killer (NK) cells and the mRNA expression of cytokines and other immune molecules in the lung and Peyer's patch (PP) were analysed. Clinical symptom scores of mice orally fed TMC0356 ameliorated significantly (P < 0.01); their pulmonary virus titres decreased significantly compared with those of control mice (P < 0.05); their mRNA expression of interleukin (IL)-12, IL-15 and IL-21 in PP and the pulmonary mRNA expression of IFN-γ, TNF, IL-12a, IL-12rbl, IL-2rb and perforin 1 increased significantly (P < 0.05). Oral administration of heat-killed lactobacilli may protect against influenza virus infection by stimulating local and systemic immune responses. Cellular components of lactobacilli may be pivotal in protecting against viral infection by enhancing gut and respiratory immune responses.","corpus_id":24538140,"score":1},{"doc_id":"22294696","title":"Interleukin-22 is produced by invariant natural killer T lymphocytes during influenza A virus infection: potential role in protection against lung epithelial damages.","abstract":"Invariant natural killer T (iNKT) cells are non-conventional lipid-reactive αβ T lymphocytes that play a key role in host responses during viral infections, in particular through the swift production of cytokines. Their beneficial role during experimental influenza A virus (IAV) infection has recently been proposed, although the mechanisms involved remain elusive. Here we show that during in vivo IAV infection, mouse pulmonary iNKT cells produce IFN-γ and IL-22, a Th17-related cytokine critical in mucosal immunity. Although permissive to viral replication, IL-22 production by iNKT cells is not due to IAV infection per se of these cells but is indirectly mediated by IAV-infected dendritic cells (DCs). We show that activation of the viral RNA sensors TLR7 and RIG-I in DCs is important for triggering IL-22 secretion by iNKT cells, whereas the NOD-like receptors NOD2 and NLRP3 are dispensable. Invariant NKT cells respond to IL-1β and IL-23 provided by infected DCs independently of the CD1d molecule to release IL-22. In vitro, IL-22 protects IAV-infected airway epithelial cells against mortality but has no role on viral replication. Finally, during early IAV infection, IL-22 plays a positive role in the control of lung epithelial damages. Overall, IAV infection of DCs activates iNKT cells, providing a rapid source of IL-22 that might be beneficial to preserve the lung epithelium integrity.","corpus_id":30142675,"score":1},{"doc_id":"22467655","title":"NKG2D mediates NK cell hyperresponsiveness and influenza-induced pathologies in a mouse model of chronic obstructive pulmonary disease.","abstract":"Chronic obstructive pulmonary disease (COPD) is characterized by peribronchial and perivascular inflammation and largely irreversible airflow obstruction. Acute disease exacerbations, due frequently to viral infections, lead to enhanced disease symptoms and contribute to long-term progression of COPD pathology. Previously, we demonstrated that NK cells from cigarette smoke (CS)-exposed mice exhibit enhanced effector functions in response to stimulating cytokines or TLR ligands. In this article, we show that the activating receptor NKG2D is a key mediator for CS-stimulated NK cell hyperresponsiveness, because CS-exposed NKG2D-deficient mice (Klrk1(-/-)) did not exhibit enhanced effector functions as assessed by cytokine responsiveness. NK cell cytotoxicity against MHC class I-deficient targets was not affected in a COPD model. However, NK cells from CS-exposed mice exhibit greater cytotoxic activity toward cells that express the NKG2D ligand RAET1ε. We also demonstrate that NKG2D-deficient mice exhibit diminished airway damage and reduced inflammation in a model of viral COPD exacerbation, which do not affect viral clearance. Furthermore, adoptive transfer of NKG2D(+) NK cells into CS-exposed, influenza-infected NKG2D-deficient mice recapitulated the phenotypes observed in CS-exposed, influenza-infected wild-type mice. Our findings indicate that NKG2D stimulation during long-term CS exposure is a central pathway in the development of NK cell hyperresponsiveness and influenza-mediated exacerbations of COPD.","corpus_id":207426531,"score":1},{"doc_id":"23200185","title":"Effect of dietary supplementation with white button mushrooms on host resistance to influenza infection and immune function in mice.","abstract":"Previously, we showed that mice fed white button mushrooms (WBM) had enhanced immune functions known to help the body's antiviral defence. In the present study, we tested whether WBM conferred protection against viral infection. Young (4-month-old) and old (22-month-old) C57BL/6 mice were fed a diet containing 0, 2 or 10 % WBM powder for 8 weeks. Mice were then infected with influenza Puerto Rico/8/34 (H1N1), and killed at day 0 (uninfected), 2, 5 or 7 post-infection. The primary outcomes of the study were viral titre and body weight. Secondary outcomes were natural killer (NK) cell activity, lymphocyte proliferation and cytokine production. The results showed that WBM did not affect viral titre, nor did it prevent infection-induced weight loss. WBM supplementation was found to enhance NK cell activity in old mice and to increase interferon (IFN)-γ production in young and old mice under naive (uninfected) conditions, but it had no such effect after infection. The lack of a mushroom supplementation effect on NK activity and concanavalin A-stimulated IFN-γ production after infection may explain the immune system's failure to reduce viral load and weight loss in mice after influenza infection. WBM supplementation, however, did induce changes in other aspects of the immune response: it significantly increased the production of T-helper type 2 cytokines IL-4 and IL-10 in uninfected mice and pro-inflammatory cytokines IL-1β and TNF-α in infected mice. These mushroom-induced systemic changes, however, were not adequate to confer a protective effect against influenza infection.","corpus_id":4417272,"score":1},{"doc_id":"23739563","title":"[Screening for genes associated with natural killer cell mediated cytotoxicity in pneumonia mice infected with influenza virus and regulation of two herbal anti-virus formulas].","abstract":"OBJECTIVE: To investigate the regulation of two herbal anti-virus formulas on gene expression profile associated with natural killer cell (NK cell) mediated cytotoxicity in pneumonia mice infected with influenza virus. METHODS: According to random number table, 90 ICR mice were divided into nine groups with 10 mice in each group: normal group (N), model group (M), oseltamivir group (control group, C), low-dose, medium-dose and high-dose Shufeng Xuanfei formula groups (SL, SM, SH groups), and low-dose, medium-dose and high-dose Jiebiao Qingli formula groups (JL, JM, JH groups). The model of pneumonia was reproduced by nasal dropping influenza virus A (FM1) in mice. N group was given isotonic saline 0.05 ml in nasal drops. After 2 hours of model-building, C group was received 11.375 mg×kg⁻¹×d⁻¹ oseltamivir phosphate. Shufeng Xuanfei formula (mainly honeysuckle, forsythia and radix isatidis, etc.) with 3.76, 1.88 and 0.94 g×kg⁻¹×d were administrated to SH, SM and SL groups by gastric irrigation respectively. Jiebiao Qingli formula (mainly ephedra, gypsum, glycyrrhiza glabra, etc.) with 4.36, 2.18 and 1.09 g×kg⁻¹×d⁻¹ were administrated to JH, JM and JL groups by gastric irrigation respectively. In N and M groups, normal saline was administrated with gastric perfusion. Each group was in equal dose of 0.2 ml daily over a 4-day period. Total RNA in lung tissue of mice were extracted in each group, then gene chips were used to screen these RNA samples. Some genes involved NK cell mediated cytotoxicity were selected, with \"I\" representing of signal intensity. These candidate genes were verified by real-time fluorescent quantitation polymerase chain reaction (PCR) and Western blotting. RESULTS: In the pathway of NK cell mediated cytotoxicity, M group up-regulated 43 genes expression, and 36, 29, 22, 21, 20 and 10 genes showed down-regulation in SM, JM, SL, JH, SH and JL groups, respectively. Apart from gene co-expression network in SH, SL, JH, JM and JL, SM also expressed other differential genes which SH, SL, JH, JM and JL did not. So medium-does Shufeng Xuanfei formula had the most significant regulation in gene expression of NK cell mediated cytotoxicity. By real-time PCR and Western blotting experiments showed that compared with the M group, mRNA and protein expression of tumor necrosis factor-α (TNF-α) in these two formula groups were significantly down-regulated, especially prominent in SM group and JM group (TNF-α mRNA: 1.07 ± 0.19, 1.19 ± 0.14 vs. 3.20 ± 0.56, both P<0.01). CONCLUSIONS: Influenza viral replication in host cell, which means influenza antigens exposure in infected cells as target cells. NK cells recognize and exert cell mediated cytotoxic function against influenza antigens. Genes associated with NK cell mediated cytotoxicity in influenza infection were up-regulated. Shufeng Xuanfei and Jiebiao Qingli formulas could down-regulate these genes. The mechanism of down-regulated genes is that the number of influenza infected cells and NK cells activation decreases in treatment with two formulas.","corpus_id":38787508,"score":1},{"doc_id":"24053449","title":"Cross-protective immunity against influenza A/H1N1 virus challenge in mice immunized with recombinant vaccine expressing HA gene of influenza A/H5N1 virus.","abstract":"BACKGROUND: Influenza virus undergoes constant antigenic evolution, and therefore influenza vaccines must be reformulated each year. Time is necessary to produce a vaccine that is antigenically matched to a pandemic strain. A goal of many research works is to produce universal vaccines that can induce protective immunity to influenza A viruses of various subtypes. Despite intensive studies, the precise mechanisms of heterosubtypic immunity (HSI) remain ambiguous. METHOD: In this study, mice were vaccinated with recombinant virus vaccine (rL H5), in which the hemagglutinin (HA) gene of influenza A/H5N1 virus was inserted into the LaSota Newcastle disease virus (NDV) vaccine strain. Following a challenge with influenza A/H1N1 virus, survival rates and lung index of mice were observed. The antibodies to influenza virus were detected using hemagglutination inhibition (HI). The lung viral loads, lung cytokine levels and the percentages of both IFN-γ+CD4+ and IFN-γ+CD8+ T cells in spleen were detected using real-time RT-PCR, ELISA and flow cytometry respectively. RESULTS: In comparison with the group of mice given phosphate-buffered saline (PBS), the mice vaccinated with rL H5 showed reductions in lung index and viral replication in the lungs after a challenge with influenza A/H1N1 virus. The antibody titer in group 3 (H1N1-H1N1) was significantly higher than that in other groups which only low levels of antibody were detected. IFN-γ levels increased in both group 1 (rL H5-H1N1) and group 2 (rL H5 + IL-2-H1N1). And the IFN-γ level of group 2 was significantly higher than that of group 1. The percentages of both IFN-γ+CD4+ and IFN-γ+CD8+ T cells in group 1 (rL H5-H1N1) and group 2 (rL H5 + IL-2-H1N1) increased significantly, as measured by flow cytometry. CONCLUSION: After the mice were vaccinated with rL H5, cross-protective immune response was induced, which was against heterosubtypic influenza A/H1N1 virus. To some extent, cross-protective immune response can be enhanced by IL-2 as an adjuvant. Cellular immune responses may play an important role in HSI against influenza virus.","corpus_id":1756782,"score":1},{"doc_id":"24187666","title":"Influenza virus specific CD8⁺ T cells exacerbate infection following high dose influenza challenge of aged mice.","abstract":"Influenza viruses cause severe illnesses and death, mainly in the aged population. Protection afforded by licensed vaccines through subtype-specific neutralizing antibodies is incomplete, especially when the vaccine antigens fail to closely match those of the circulating viral strains. Efforts are underway to generate a so-called universal influenza vaccine expressing conserved viral sequences that induce broad protection to multiple strains of influenza virus through the induction of CD8⁺ T cells. Here we assess the effect of a potent antiviral CD8⁺ T cell response on influenza virus infection of young and aged mice. Our results show that CD8⁺ T cell-inducing vaccines can provide some protection to young mice, but they exacerbate influenza virus-associated disease in aged mice, causing extensive lung pathology and death.","corpus_id":553495,"score":1},{"doc_id":"24201084","title":"Lactobacillus fermentum CJL-112 protects mice against influenza virus infection by activating T-helper 1 and eliciting a protective immune response.","abstract":"We have previously reported that nasally administered Lactobacillus fermentum CJL-112 (CJL-112) efficiently improves resistance against lethal influenza infection in both mice and chicken. The aim of the present study was to understand the underlying mechanisms of the significant anti-influenza activity of this lactobacilli strain. In vitro, co-culturing of the chicken macrophage cell line HD-11 with CJL-112 significantly increased nitric oxide (NO) production. In vivo, CJL-112 was nasally administered to BALB/c mice for 21 days prior to influenza A/NWS/33 (H1N1) virus (IFV) infection. Significant up-regulation of T-helper 1 (Th1) cytokines (IL-2, IFN-γ) was observed, while the levels of T-helper 2 (Th2) cytokines (IL-4, IL-5, IL-10) was either reduced or unchanged than that in control mice were. Furthermore, IgA and specific anti-influenza IgA levels increased significantly in the treated mice than those in untreated mice. Therefore, CJL-112 likely protects the mice against lethal IFV infection via stimulation of macrophages, activation of Th1 and augmentation of IgA production, when directly delivered into the respiratory tract.","corpus_id":27306300,"score":1},{"doc_id":"24385240","title":"Ability of recombinant human catalase to suppress inflammation of the murine lung induced by influenza A.","abstract":"Influenza A virus pandemics and emerging antiviral resistance highlight the urgent need for novel generic pharmacological strategies that reduce both viral replication and inflammation of the lung. We have previously investigated the therapeutic efficacy of recombinant human catalase (rhCAT) against viral pneumonia in mice, but the protection mechanisms involved were not explored. In the present study, we have performed a more in-depth analysis covering survival, lung inflammation, immune cell responses, production of cytokines, and inflammation signaling pathways in mice. Male imprinting control region mice were infected intranasally with high pathogenicity (H1N1) influenza A virus followed by treatment with recombinant human catalase. The administration of rhCAT resulted in a significant reduction in inflammatory cell infiltration (e.g., macrophages and neutrophils), inflammatory cytokine levels (e.g., IL-2, IL-6, TNF-α, IFN-γ), the level of the intercellular adhesion molecule 1 chemokine and the mRNA levels of toll-like receptors TLR-4, TLR-7, and NF-κB, as well as partially maintaining the activity of the antioxidant enzymes system. These findings indicated that rhCAT might play a key protective role in viral pneumonia of mice via suppression of inflammatory immune responses.","corpus_id":12963207,"score":1},{"doc_id":"24509810","title":"Pretreatment of mice with oligonucleotide prop5 protects them from influenza virus infections.","abstract":"Influenza A virus is a successful parasite and requires host factors to complete its life cycle. Prop5 is an antisense oligonucleotide, targeting programmed cell death protein 5 (PDCD5). In this study, we tested the antiviral activity of prop5 against mouse-adapted A/FM/1/47 strain of influenza A virus in a mouse model. Prop5 intranasally administered the mice at dosages of 10 and 20 mg/kg/d at 24 h and 30 min before infection, provided 80% and 100% survival rates and prolonged mean survival days in comparison with influenza virus-infected mice (both p < 0.01). Moreover, viral titres in mice pretreated with prop5, at dose of 10 and 20 mg/kg/d, had declined significantly on day two, four, and six post-infection compared with the yields in infected mice (p < 0.05 or p < 0.01); lung index in mice pretreated with prop5 (20 mg/kg/d) had been inhibited on day six post-infection (p < 0.05). Western blotting and immunohistochemistry showed that prop5 could down-regulate the PDCD5 protein expression levels in lung tissues of infected mice. These data indicate that antisense oligonucleotide prop5 is a promising drug for prophylaxis and control influenza virus infections and provides an insight into the host-pathogen interaction.","corpus_id":14021146,"score":1},{"doc_id":"24676773","title":"Protective effect of fluvastatin on influenza virus infection.","abstract":"Statins are 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors and have pleiotropic effects. It has been suggested that statins may be a potential treatment during the next influenza pandemic. In a previous study we found that a statin/caffeine combination protects BALB/c mice against Influenza A, subtypes haemagglutinin type 5 and neuraminidase type 1 (H5N1), H3N2 and H1N1 infection. The effect of statins alone on influenza virus infection, however, is not known. In this study, it was investigated whether fluvastatin is capable of inhibiting influenza A virus replication in vitro. The results demonstrated that the synthesis of viral RNA and protein was affected by fluvastatin treatment. Virus production was markedly reduced when fluvastatin was administered simultaneously with the virus; however, a greater inhibition was observed when fluvastatin was added following viral adsorption. The selectivity index [SI; 50% cytotoxic concentration (CC50)/50% inhibition concentration (IC50)], however, was only 21. It was further demonstrated that fluvastatin protects host cells against influenza-induced inflammation by reducing the production of tumour necrosis factor-α, interleukin 8 and interferon γ. In conclusion, the results demonstrated that fluvastatin exerted a minor inhibitory effect on influenza virus infection, which involved anti-inflammatory activities.","corpus_id":25942052,"score":1},{"doc_id":"24725777","title":"Pulmonary immune responses to 2009 pandemic influenza A (H1N1) virus in mice.","abstract":"BACKGROUND: Well-characterized mice models will afford a cheaper, easy-handling opportunity for a more comprehensive understanding of 2009 influenza A (H1N1) virus's pathogenesis potential. We aimed to provide a robust description of pulmonary immune responses in the mice infected by the virus. METHODS: BALB/c mice were inoculated intranasally with A/Beijing/501/2009(H1N1) (BJ501) and A/PR/8/34(H1N1) (PR8) viruses and compared for survival rate, viral replication, and kinetics of pulmonary immune responses. RESULTS: BJ501 virus replicated less efficiently in the lungs than PR8, and both caused lethal illness in the mice. The transient increases of pulmonary TNF-α 2 days post infection for BJ501 and of INF-γ and IL-10 at 6 days post infection for PR8 were observed. IL-2+ and IL-4+ secreting cells showed significant increase 12 days post infection, while IFN-γ+, IgG+ and IgA+ secreting cells increased 6 days post infection. The different patterns of pulmonary immunological parameters between two viruses were at most seen in IL-6, IL-17 secretion and IgG1/IgG2a ratio. CONCLUSIONS: The BALB/c mouse is evaluated as a good pathogenic model for studying BJ501 2009 H1N1 virus. The work provided some basic and detailed data, which might be referred when further evaluating innate and adapted pulmonary immune responses and local viral load in mice.","corpus_id":1014640,"score":1},{"doc_id":"24774068","title":"Bovine colostrum enhances natural killer cell activity and immune response in a mouse model of influenza infection and mediates intestinal immunity through toll-like receptors 2 and 4.","abstract":"Oral administration of bovine colostrum affects intestinal immunity, including an increased percentage of natural killer (NK) cells. However, effects on NK cell cytotoxic activity and resistance to infection as well as a potential mechanism remain unclear. Therefore, we investigated the effects of bovine colostrum (La Belle, Inc, Bellingham, WA) on the NK cytotoxic response to influenza infection and on toll-like receptor (TLR) activity in a primary intestinal epithelial cell culture. We hypothesized that colostrum would increase NK cell activity and that TLR-2 and TLR-4 blocking would reduce interleukin 6 production by epithelial cells in response to contact stimulation with colostrum. Four-month-old female C57BL/6 mice were supplemented with 1 g of colostrum per kilogram of body weight before and after infection with influenza A virus (H1N1). Animals were assessed for weight loss, splenic NK cell activity, and lung virus titers. Colostrum-supplemented mice demonstrated less reduction in body weight after influenza infection, indicating a less severe infection, increased NK cell cytotoxicity, and less virus burden in the lungs compared with controls. Colostrum supplementation enhanced NK cell cytotoxicity and improved the immune response to primary influenza virus infection in mice. To investigate a potential mechanism, a primary culture of small intestine epithelial cells was then stimulated with colostrum. Direct activation of epithelial cells resulted in increased interleukin 6 production, which was inhibited with TLR-2 and TLR-4 blocking antibodies. The interaction between colostrum and immunity may be dependent, in part, on the interaction of colostrum components with innate receptors at the intestinal epithelium, including TLR-2 and TLR-4.","corpus_id":45561707,"score":1},{"doc_id":"25400245","title":"Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model.","abstract":"Bifidobacterium, one of the major components of intestinal microflora, shows anti-influenza virus (IFV) potential as a probiotic, partly through enhancement of innate immunity by modulation of the intestinal immune system. Bifidobacterium longum MM-2 (MM-2), a very safe bacterium in humans, was isolated from healthy humans and its protective effect against IFV infection in a murine model shown. In mice that were intranasally inoculated with IFV, oral administration of MM-2 for 17 consecutive days improved clinical symptoms, reduced mortality, suppressed inflammation in the lower respiratory tract, and decreased virus titers, cell death, and pro-inflammatory cytokines such as IL-6 and TNF-α in bronchoalveolar lavage fluid. The anti-IFV mechanism of MM-2 involves innate immunity through significant increases in NK cell activities in the lungs and spleen and a significant increase in pulmonary gene expression of NK cell activators such as IFN-γ, IL-2, IL-12 and IL-18. Even in non-infected mice, MM-2 administration also induced significant enhancement of both IFN-γ production by Peyer's patch cells (PPs) and splenetic NK cell activity. Oral administration of MM-2 for 17 days activates systemic immunoreactivity in PPs, which contributes to innate immunity, including NK cell activation, resulting in an anti-IFV effect. MM-2 as a probiotic may function as a prophylactic agent in the management of an IFV epidemic.","corpus_id":25087026,"score":1},{"doc_id":"25422494","title":"Cytomegalovirus generates long-lived antigen-specific NK cells with diminished bystander activation to heterologous infection.","abstract":"Natural killer (NK) cells play a key role in the host response to cytomegalovirus (CMV) and can mediate an enhanced response to secondary challenge with CMV. We assessed the ability of mouse CMV (MCMV)-induced memory Ly49H(+) NK cells to respond to challenges with influenza, an acute viral infection localized to the lung, and Listeria monocytogenes, a systemic bacterial infection. MCMV-memory NK cells did not display enhanced activation or proliferation after infection with influenza or Listeria, as compared with naive Ly49H(+) or Ly49H(-) NK cells. Memory NK cells also showed impaired activation compared with naive cells when challenged with a mutant MCMV lacking m157, highlighting their antigen-specific response. Ex vivo, MCMV-memory NK cells displayed reduced phosphorylation of STAT4 and STAT1 in response to stimulation by IL-12 and type I interferon (IFN), respectively, and IFN-γ production was reduced in response to IL-12 + IL-18 compared with naive NK cells. However, costimulation of MCMV-memory NK cells with IL-12 and m157 antigen rescues their impaired response compared with cytokines alone. These findings reveal that MCMV-primed memory NK cells are diminished in their response to cytokine-driven bystander responses to heterologous infections as they become specialized and antigen-specific for the control of MCMV upon rechallenge.","corpus_id":18341735,"score":1},{"doc_id":"26437715","title":"Intranasal administration of poly-gamma glutamate induced antiviral activity and protective immune responses against H1N1 influenza A virus infection.","abstract":"BACKGROUND: The global outbreak of a novel swine-origin strain of the 2009 H1N1 influenza A virus and the sudden, worldwide increase in oseltamivir-resistant H1N1 influenza A viruses highlight the urgent need for novel antiviral therapy. METHODS: Here, we investigated the antiviral efficacy of poly-gamma glutamate (γ-PGA), a safe and edible biomaterial that is naturally synthesized by Bacillus subtilis, against A/Puerto Rico/8/1934 (PR8) and A/California/04/2009 (CA04) H1N1 influenza A virus infections in C57BL/6 mice. RESULTS: Intranasal administration of γ-PGA for 5 days post-infection improved survival, increased production of antiviral cytokines including interferon-beta (IFN-β) and interleukin-12 (IL-12), and enhanced activation of natural killer (NK) cells and influenza antigen-specific cytotoxic T lymphocytes (CTL) activity. CONCLUSIONS: These results suggest that γ-PGA protects mice against H1N1 influenza A virus by enhancing antiviral immune responses.","corpus_id":8002821,"score":1},{"doc_id":"28031334","title":"Respiratory Influenza Virus Infection Induces Memory-like Liver NK Cells in Mice.","abstract":"Although NK cells are classified as innate immune cells, recent studies have demonstrated the transformation of NK cells into long-lived memory cells that contribute to secondary immune responses in certain mouse models. However, whether NK cells mount an Ag-specific memory response to acute influenza virus infection has not yet been examined. Here, we show that, consistent with previous studies, lung NK cells play an important role in controlling viral proliferation after primary influenza virus infection. However, although lung NK cells display a memory phenotype at the late stage of infection, these cells do not protect mice against secondary influenza virus infection. Interestingly, liver NK cells from influenza virus-infected mice possess a memory phenotype and protect mice against secondary influenza virus infection. Memory-like liver NK cells display a CD49a(+)DX5(-) phenotype, and the adoptive transfer of purified liver CD49a(+)DX5(-) NK cells into naive mice followed by viral infection results in protective immunity and decreased viral titer. Moreover, we demonstrate that primary inactivated influenza virus induces memory NK cells residing in the liver of Rag1(-/-) mice. Collectively, these data suggest that liver CD49a(+)DX5(-) NK cells remember encountered Ag from influenza virus after primary infection and are more protective upon subsequent infection.","corpus_id":19765445,"score":1},{"doc_id":"28865477","title":"RIG-I overexpression decreases mortality of cigarette smoke exposed mice during influenza A virus infection.","abstract":"BACKGROUND: Retinoic acid-inducible gene I (RIG-I) is an important regulator of virus-induced antiviral interferons (IFNs) and proinflammatory cytokines which participate in clearing viral infections. Cigarette smoke (CS) exposure increases the frequency and severity of respiratory tract infections. METHODS: We generated a RIG-I transgenic (TG) mouse strain that expresses the RIG-I gene product under the control of the human lung specific surfactant protein C promoter. We compared the mortality and host immune responses of RIG-I TG mice and their litter-matched wild type (WT) mice following challenge with influenza A virus (IAV). RESULTS: RIG-I overexpression increased survival of IAV-infected mice. CS exposure increased mortality in WT mice infected with IAV. Remarkably, the effect of RIG-I overexpression on survival during IAV infection was enhanced in CS-exposed animals. CS-exposed IAV-infected WT mice had a suppressed innate response profile in the lung compared to sham-exposed IAV-infected WT mice in terms of the protein concentration, total cell count and inflammatory cell composition in the bronchoalveolar lavage fluid. RIG-I overexpression restored the innate immune response in CS-exposed mice to that seen in sham-exposed WT mice during IAV infection, and is likely responsible for enhanced survival in RIG-I TG mice as restoration preceded death of the animals. CONCLUSIONS: Our results demonstrate that RIG-I overexpression in mice is protective for CS enhanced susceptibility of smokers to influenza infection, and that CS mediated RIG-I suppression may be partially responsible for the increased morbidity and mortality of the mice exposed to IAV. Thus, optimizing the RIG-I response may be an important treatment strategy for CS-enhanced lung infections, particularly those due to IAV.","corpus_id":8485639,"score":1},{"doc_id":"23189830","title":"[Analysis of the application of host innate immune response to control and prevent infection].","abstract":"The baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) has been widely used not only to achieve a high level of foreign gene expression in insect cells but also for efficient gene transduction into mammalian cells without any replication. In addition to the efficient gene delivery, baculovirus has been shown to induce host innate immune responses in various mammalian cells and in mice. The baculovirus has abundant CpG motifs in the viral genome and is capable of inducing pro-inflammatory cytokines and interferons (IFNs) through Toll-like receptor (TLR)-dependent and -independent signaling pathways in a cell-type-specific manner. The cytoplasmic helicase proteins RIG-I (retinoic-acid-inducible protein I) and MDA5 (melanoma-differentiation-associated gene 5) have been identified as viral dsRNA detectors and the adaptor IPS-1 (IFN-beta promoter stimulator-1) interacts with RIG-I and MDA5 to facilitate type-I IFN production mediated interferon regulatory factor 3 (IRF3) and 7 (IRF7). These helicases and IPS-1, however, were not essential for the type-I IFN and inflammatory cytokine responses to baculovirus. The baculovirus also has a strong adjuvant activity, and recombinant baculoviruses encoding neutralization epitopes elicit protective immunity in mice. This review deals with the current status of our knowledge of the induction of host innate immune responses by baculovirus and discusses the future prospects for baculovirus vectors.","corpus_id":29176319,"score":0},{"doc_id":"23627014","title":"[Prior infected influenza virus could protect mice from challenge of lethal influenza virus].","abstract":"OBJECTIVE: To determine whether it could protect mice from challenge of lethal influenza virus which group prior infected A(H1N1) pdm09 and H9N2 virus respectively. METHODS: 150 BALB/c mice are divided into three groups. Mice are infected A(H1N1) pdm09 virus (pCA07) and poultry H9N2 virus (GZ333) respectively. Infected mice are challenged with 10 times of lethal dose virus (PR8) then compare the viral load, antibody and survival of the two group mice before and after challenged. RESULTS: Both experimental group mice survived after challenge of lethal influenza virus and lung viral load are lower than that of the first infection. Antibodies derived from the infective virus and challenge virus. CONCLUSION: Prior infected A(H1N1) pdm09 and H9N2 virus could protect mice from challenge of lethal influenza virus.","corpus_id":41469081,"score":0},{"doc_id":"27354005","title":"Cyclophilin A protects mice against infection by influenza A virus.","abstract":"Our previous studies indicate that Cyclophilin A (CypA) impairs the replication of influenza A virus in vitro. To further evaluate the antiviral functions of CypA and explore its mechanism, transgenic mice with overexpression of CypA by two specific promoters with SPC (CypA-SPC) or CMV (CypA-CMV) were developed. After challenge with the A/WSN/33(H1N1) influenza virus, CypA-SPC and CypA-CMV transgenic mice displayed nearly 2.5- and 3.8-fold stronger disease resistance to virus infection, respectively, compared to wild-type animals. Virus replication, pathological lesions and inflammatory cytokines were substantially reduced in both lines of transgenic mice. In addition, after infection there was an upregulation of genes associated with cell migration, immune function, and organ development; and a downregulation of genes associated with the positive regulation of immune cells and apoptosis in the peritoneal macrophages of CypA-overexpressing transgenic mice (CypA+). These results indicate that CypA is a key modulator of influenza virus resistance in mice, and that CypA+ mice constitutes an important model to study the roles of CypA in the regulation of immune responses and infections.","corpus_id":8155910,"score":0}],"string":"[\n {\n \"doc_id\": \"18304606\",\n \"title\": \"Characterization of age-related changes in natural killer cells during primary influenza infection in mice.\",\n \"abstract\": \"The current investigation examined the importance of natural killer (NK) cells during the innate immune response to primary influenza infection in young and aged mice. Young (6-8 weeks) and aged (22 months) C57BL/6 mice were infected intranasally with influenza A virus, and NK cell-mediated cytotoxicity was determined in lung and spleen during the first 4 days of infection. Aged mice demonstrated both a decrease in influenza-inducible NK activity and a reduction in the percentage and number of NK1.1+ cells in response to primary influenza infection, relative to young mice. In order to further establish a role for NK cells in controlling influenza infection, young mice were depleted of NK cells in vivo by injecting rabbit anit-NK1.1 antibody 2 days and 1 day prior to influenza infection. Young mice depleted of NK cells exhibited increased weight loss and lung virus titers during the course of infection, compared to young mice infected with influenza virus. These data indicate that NK cell function is impaired in response to primary influenza infection in aged mice. More importantly, these results underscore the essential role of NK cells in controlling virus titers in lung during the early course of influenza infection, regardless of age.\",\n \"corpus_id\": 5478837,\n \"score\": 2\n },\n {\n \"doc_id\": \"19293935\",\n \"title\": \"Host genetic background strongly influences the response to influenza a virus infections.\",\n \"abstract\": \"The genetic make-up of the host has a major influence on its response to combat pathogens. For influenza A virus, several single gene mutations have been described which contribute to survival, the immune response and clearance of the pathogen by the host organism. Here, we have studied the influence of the genetic background to influenza A H1N1 (PR8) and H7N7 (SC35M) viruses. The seven inbred laboratory strains of mice analyzed exhibited different weight loss kinetics and survival rates after infection with PR8. Two strains in particular, DBA/2J and A/J, showed very high susceptibility to viral infections compared to all other strains. The LD(50) to the influenza virus PR8 in DBA/2J mice was more than 1000-fold lower than in C57BL/6J mice. High susceptibility in DBA/2J mice was also observed after infection with influenza strain SC35M. In addition, infected DBA/2J mice showed a higher viral load in their lungs, elevated expression of cytokines and chemokines, and a more severe and extended lung pathology compared to infected C57BL/6J mice. These findings indicate a major contribution of the genetic background of the host to influenza A virus infections. The overall response in highly susceptible DBA/2J mice resembled the pathology described for infections with the highly virulent influenza H1N1-1918 and newly emerged H5N1 viruses.\",\n \"corpus_id\": 17996944,\n \"score\": 2\n },\n {\n \"doc_id\": \"19721456\",\n \"title\": \"The functional impairment of natural killer cells during influenza virus infection.\",\n \"abstract\": \"Natural killer (NK) cells have a critical role in clearing influenza virus, which primarily infects the lung epithelial cells. However, the ability of influenza virus to infect and manipulate NK cells has not been studied. In this context, we hypothesized that influenza virus can target NK cells leading to a functional impairment in their ability to mediate cytotoxicity and cytokine/chemokine generations. Here, we show influenza virus, PR8, can enter and infect NK cells. This infection did not alter the expression levels of activating, inhibitory or developmental receptors of NK cells. However, infection of NK cells by PR8 reduced the cytotoxicity to tumor cells that represent 'induced-self' and 'missing-self'. PR8-infection also significantly downregulated the NCR1, NKG2D, Nkpr1c, Ly49D and CD244 receptors-mediated generation of pro-inflammatory cytokines and chemokines. Mutations in the non-structural protein 1 (NS1) of influenza virus further augmented the functional impairment of NK cells. Our observations show the presence of a new, but yet to be explored, mechanism by which the influenza virus can evade immune detection.\",\n \"corpus_id\": 20495343,\n \"score\": 2\n },\n {\n \"doc_id\": \"20083661\",\n \"title\": \"Influenza infection leads to increased susceptibility to subsequent bacterial superinfection by impairing NK cell responses in the lung.\",\n \"abstract\": \"Influenza viral infection is well-known to predispose to subsequent bacterial superinfection in the lung but the mechanisms have remained poorly defined. We have established a murine model of heterologous infections by an H1N1 influenza virus and Staphylococcus aureus. We found that indeed prior influenza infection markedly increased the susceptibility of mice to secondary S. aureus superinfection. Severe sickness and heightened bacterial infection in flu and S. aureus dual-infected animals were associated with severe immunopathology in the lung. We further found that flu-experienced lungs had an impaired NK cell response in the airway to subsequent S. aureus bacterial infection. Thus, adoptive transfer of naive NK cells to the airway of prior flu-infected mice restored flu-impaired antibacterial host defense. We identified that TNF-alpha production of NK cells played an important role in NK cell-mediated antibacterial host defense as NK cells in flu-experienced lungs had reduced TNF-alpha expression and adoptive transfer of TNF-alpha-deficient NK cells to the airway of flu-infected mice failed to restore flu-impaired antibacterial host defense. Defected NK cell function was found to be an upstream mechanism of depressed antibacterial activities by alveolar macrophages as contrast to naive wild-type NK cells, the NK cells from flu-infected or TNF-alpha-deficient mice failed to enhance S. aureus phagocytosis by alveolar macrophages. Together, our study identifies the weakened NK cell response in the lung to be a novel critical mechanism for flu-mediated susceptibility to bacterial superinfection.\",\n \"corpus_id\": 1977042,\n \"score\": 2\n },\n {\n \"doc_id\": \"20121698\",\n \"title\": \"The role of Toll-like receptors in regulating the immune response against respiratory syncytial virus.\",\n \"abstract\": \"Toll-like receptors (TLRs) play a distinct role in battling respiratory syncytial virus (RSV) infections. However, due to a lack of representative animal models and several early controversies, the field is unclear. In this systematic review, we have elucidated conflicting results and outlined important factors that might affect study outcomes. We reviewed studies that used different doses/viral strains, performed virus propagation in different cell lines, or used different mice strains. The following firm conclusions can be drawn: multiple TLRs activate innate immunity upon RSV infection; TLR4 can influence TLR2 expression, suggesting that optimal induction of multiple signaling pathways is required to elicit protective, rather than deleterious innate immune responses following infection; in mice, TLR4, TLR2/-6, and TLR7 have immune-stimulating properties, while TLR3 activation occurs later and appears to downregulate immune responses; in humans, polymorphism studies have demonstrated an important role for TLR4-signaling; and activation of TLR-signaling leads to antiviral cytokine production, such as TNF-a and IFNs. Viral factors may block these pathways, thereby contributing to immune evasion and RSV survival. A better understanding of the complex interplay between TLRs and severe RSV infections might lead to efficient prophylactic and therapeutic treatments, as well as the development of adequate vaccines combined with TLR adjuvants.\",\n \"corpus_id\": 13007136,\n \"score\": 2\n },\n {\n \"doc_id\": \"20130050\",\n \"title\": \"Killing of avian and Swine influenza virus by natural killer cells.\",\n \"abstract\": \"Today, global attention is focused on two influenza virus strains: the current pandemic strain, swine origin influenza virus (H1N1-2009), and the highly pathogenic avian influenza virus, H5N1. At present, the infection caused by the H1N1-2009 is moderate, with mortality rates of less <1%. In contrast, infection with the H5N1 virus resulted in high mortality rates, and ca. 60% of the infected patients succumb to the infection. Thus, one of the world greatest concerns is that the H5N1 virus will evolve to allow an efficient human infection and human-to-human transmission. Natural killer (NK) cells are one of the innate immune components playing an important role in fighting against influenza viruses. One of the major NK activating receptors involved in NK cell cytotoxicity is NKp46. We previously demonstrated that NKp46 recognizes the hemagglutinin proteins of B and A influenza virus strains. Whether NKp46 could also interact with H1N1-2009 virus or with the avian influenza virus is still unknown. We analyzed the immunological properties of both the avian and the H1N1-2009 influenza viruses. We show that NKp46 recognizes the hemagglutinins of H1N1-2009 and H5 and that this recognition leads to virus killing both in vitro and in vivo. However, importantly, while the swine H1-NKp46 interactions lead to the direct killing of the infected cells, the H5-NKp46 interactions were unable to elicit direct killing, probably because the NKp46 binding sites for these two viruses are different.\",\n \"corpus_id\": 206811398,\n \"score\": 2\n },\n {\n \"doc_id\": \"20235626\",\n \"title\": \"IFN-gamma treatment at early stages of influenza virus infection protects mice from death in a NK cell-dependent manner.\",\n \"abstract\": \"Influenza pandemics are imminent and represent a major world health concern. Since vaccinations are expected to be less efficient in the coming years due to newly emerging influenza virus strains, novel antiviral therapies are urgently needed. Here, we show that influenza-infected mice, capable of clearing the virus in the early stages of infection, failed to control inflammation and death. Sequential administration of Interferon-gamma (IFN-gamma) at early stage of the infection protected infected mice from death in a NK cell-dependent manner. IFN-gamma treatment stimulated NK cell proliferation and function and increased their number in the bone marrow, blood, spleen, and infected lungs, keeping viral clearance intact. In parallel, IFN-gamma treatment significantly reduced the number of T cells and NKT cells in the lungs at the inflammatory phase following infection. Thus, rapidly clearing the virus and reducing inflammation by shaping the cellular and cytokine profiles in the early stages of infection may favorably change the fate of influenza pathogenesis.\",\n \"corpus_id\": 5686206,\n \"score\": 2\n },\n {\n \"doc_id\": \"21543489\",\n \"title\": \"Viral replication and innate host responses in primary human alveolar epithelial cells and alveolar macrophages infected with influenza H5N1 and H1N1 viruses.\",\n \"abstract\": \"Highly pathogenic influenza H5N1 virus continues to pose a threat to public health. Although the mechanisms underlying the pathogenesis of the H5N1 virus have not been fully defined, it has been suggested that cytokine dysregulation plays an important role. As the human respiratory epithelium is the primary target cell for influenza viruses, elucidating the viral tropism and innate immune responses of influenza H5N1 virus in the alveolar epithelium may help us to understand the pathogenesis of the severe pneumonia associated with H5N1 disease. Here we used primary cultures of differentiated human alveolar type II cells, alveolar type I-like cells, and alveolar macrophages isolated from the same individual to investigate viral replication competence and host innate immune responses to influenza H5N1 (A/HK/483/97) and H1N1 (A/HK/54/98) virus infection. The viral replication kinetics and cytokine and chemokine responses were compared by quantitative PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA). We demonstrated that influenza H1N1 and H5N1 viruses replicated productively in type II cells and type I-like cells although with different kinetics. The H5N1 virus replicated productively in alveolar macrophages, whereas the H1N1 virus led to an abortive infection. The H5N1 virus was a more potent inducer of proinflammatory cytokines and chemokines than the H1N1 virus in all cell types. However, higher levels of cytokine expression were observed for peripheral blood monocyte-derived macrophages than for alveolar macrophages in response to H5N1 virus infection. Our findings provide important insights into the viral tropisms and host responses of different cell types found in the lung and are relevant to an understanding of the pathogenesis of severe human influenza disease.\",\n \"corpus_id\": 961092,\n \"score\": 2\n },\n {\n \"doc_id\": \"21896679\",\n \"title\": \"H5N1 influenza virus pathogenesis in genetically diverse mice is mediated at the level of viral load.\",\n \"abstract\": \"UNLABELLED: The genotype of the host is one of several factors involved in the pathogenesis of an infectious disease and may be a key parameter in the epidemiology of highly pathogenic H5N1 influenza virus infection in humans. Gene polymorphisms may affect the viral replication rate or alter the host's immune response to the virus. In humans, it is unclear which aspect dictates the severity of H5N1 virus disease. To identify the mechanism underlying differential responses to H5N1 virus infection in a genetically diverse population, we assessed the host responses and lung viral loads in 21 inbred mouse strains upon intranasal inoculation with A/Hong Kong/213/03 (H5N1). Resistant mouse strains survived large inocula while susceptible strains succumbed to infection with 1,000- to 10,000-fold-lower doses. Quantitative analysis of the viral load after inoculation with an intermediate dose found significant associations with lethality as early as 2 days postinoculation, earlier than any other disease indicator. The increased viral titers in the highly susceptible strains mediated a hyperinflamed environment, indicated by the distinct expression profiles and increased production of inflammatory mediators on day 3. Supporting the hypothesis that viral load rather than an inappropriate response to the virus was the key severity-determining factor, we performed quantitative real-time PCR measuring the cytokine/viral RNA ratio. No significant differences between susceptible and resistant mouse strains were detected, confirming that it is the host genetic component controlling viral load, and therefore replication dynamics, that is primarily responsible for a host's susceptibility to a given H5N1 virus. IMPORTANCE: Highly pathogenic H5N1 influenza virus has circulated in Southeast Asia since 2003 but has been confirmed in relatively few individuals. It has been postulated that host genetic polymorphisms increase the susceptibility to infection and severe disease. The mechanisms and host proteins affected during severe disease are unknown. Inbred mouse strains vary considerably in their ability to resist H5N1 virus and were used to identify the primary mechanism determining disease severity. After inoculation with H5N1, resistant mouse strains had reduced amounts of virus in their lungs, which subsequently resulted in lower production of proinflammatory mediators and less pathology. We therefore conclude that the host genetic component controlling disease severity is primarily influencing viral replication. This is an important concept, as it emphasizes the need to limit virus replication through antiviral therapies and it shows that the hyperinflammatory environment is simply a reflection of more viral genetic material inducing a response.\",\n \"corpus_id\": 14567885,\n \"score\": 2\n },\n {\n \"doc_id\": \"21966414\",\n \"title\": \"Changes in cytokine levels and NK cell activation associated with influenza.\",\n \"abstract\": \"Several studies have highlighted the important role played by murine natural killer (NK) cells in the control of influenza infection. However, human NK cell responses in acute influenza infection, including infection with the 2009 pandemic H1N1 influenza virus, are poorly documented. Here, we examined changes in NK cell phenotype and function and plasma cytokine levels associated with influenza infection and vaccination. We show that absolute numbers of peripheral blood NK cells, and particularly those of CD56(bright) NK cells, decreased upon acute influenza infection while this NK cell subset expanded following intramuscular influenza vaccination. NK cells exposed to influenza antigens were activated, with higher proportions of NK cells expressing CD69 in study subjects infected with seasonal influenza strains. Vaccination led to increased levels of CD25+ NK cells, and notably CD56(bright) CD25+ NK cells, whereas decreased amounts of this subset were present in the peripheral blood of influenza infected individuals, and predominantly in study subjects infected with the 2009 pandemic H1N1 influenza virus. Finally, acute influenza infection was associated with low plasma concentrations of inflammatory cytokines, including IFN-γ, MIP-1β, IL-2 and IL-15, and high levels of the anti-inflammatory cytokines IL-10 and IL-1ra. Altogether, these data suggest a role for the CD56(bright) NK cell subset in the response to influenza, potentially involving their recruitment to infected tissues and a local production and/or uptake of inflammatory cytokines.\",\n \"corpus_id\": 1347000,\n \"score\": 2\n },\n {\n \"doc_id\": \"22134539\",\n \"title\": \"Mice with asthma are more resistant to influenza virus infection and NK cells activated by the induction of asthma have potentially protective effects.\",\n \"abstract\": \"PURPOSE: This study was conducted in order to investigate whether the virulence of the influenza virus infection is affected by asthma in mice. METHODS: Mice with asthma or control mice were infected with influenza virus. The survival rate, body weight, virus titer, cytokine profile, and cell infiltration in bronchoalveolar lavage fluid (BALF) were measured. The NK cell cytotoxicity was determined by a co-culture system with YAC-1 cells, and the effects of NK cells were observed by depletion of NK cells using anti-asialoGM1 serum. The virus-specific CD8(+) T cell killing assay was also performed. RESULTS: When asthmatic or control mice were infected with non- and sub-lethal doses of influenza virus, the asthmatic mice were more resistant to the virus than control mice with regard to the survival rate, the remission of body weight loss, and the virus burden. Anti-viral cytokines and the NK cell number were increased in the BALF of asthmatic mice before the infection. The NK cell cytotoxicity in the asthmatic mice was significantly enhanced compared to that in control mice, and the depletion of NK cells in asthmatic mice was abrogated both the improved survival rate and the recovery of the body weight loss. The antigen-specific CD8(+) T cell killing activity in asthmatic mice was also significantly increased following the infection compared to that in control mice. CONCLUSION: NK cell activated by the induction of asthma and the subsequently activated antigen-specific CD8(+) T cells could promptly eliminate the viral-infected cells, thus leading to improvements in the morbidity and mortality of influenza virus infection.\",\n \"corpus_id\": 1499968,\n \"score\": 2\n },\n {\n \"doc_id\": \"22442495\",\n \"title\": \"Highly pathogenic avian influenza viruses inhibit effective immune responses of human blood-derived macrophages.\",\n \"abstract\": \"Systemic infections with HPAIVs, such as H5N1, are characterized by cytokine burst and sepsis. We investigated the role of human monocyte-derived macrophages in these events after infection with different influenza virus strains. Macrophages were infected with low pathogenic H1N1 (PR8) or high pathogenic H7N7 (FPV) and H5N1 (KAN-1) subtypes. Macrophages were found to be nonpermissive for influenza virus propagation. Surprisingly, transcriptome analysis revealed an insufficient innate immune response of macrophages only to HPAIV infections. Induction of inflammatory cytokines, as well as type I IFNs, was significantly attenuated in H5N1- and H7N7-infected cells, contradicting a primary role of macrophages for the cytokine burst. Furthermore, inflammasome activation was impaired significantly in HPAIV-infected macrophages. Interestingly, this finding correlated with a complete suppression of viral protein M2 expression after HPAIV infection, which is known to be involved in influenza viral inflammasome activation. In summary, our data provide first evidences for a strategy of how HPAIVs avoid initial inflammatory responses of macrophages facilitating virus spreading and progression to the systemic stage of disease.\",\n \"corpus_id\": 206996747,\n \"score\": 2\n },\n {\n \"doc_id\": \"22624047\",\n \"title\": \"IL-15 participates in the respiratory innate immune response to influenza virus infection.\",\n \"abstract\": \"Following influenza infection, natural killer (NK) cells function as interim effectors by suppressing viral replication until CD8 T cells are activated, proliferate, and are mobilized within the respiratory tract. Thus, NK cells are an important first line of defense against influenza virus. Here, in a murine model of influenza, we show that virally-induced IL-15 facilitates the trafficking of NK cells into the lung airways. Blocking IL-15 delays NK cell entry to the site of infection and results in a disregulated control of early viral replication. By the same principle, viral control by NK cells can be therapeutically enhanced via intranasal administration of exogenous IL-15 in the early days post influenza infection. In addition to controlling early viral replication, this IL-15-induced mobilization of NK cells to the lung airways has important downstream consequences on adaptive responses. Primarily, depletion of responding NK1.1+ NK cells is associated with reduced immigration of influenza-specific CD8 T cells to the site of infection. Together this work suggests that local deposits of IL-15 in the lung airways regulate the coordinated innate and adaptive immune responses to influenza infection and may represent an important point of immune intervention.\",\n \"corpus_id\": 16114244,\n \"score\": 2\n },\n {\n \"doc_id\": \"22869906\",\n \"title\": \"NK cells regulate CD8+ T cell priming and dendritic cell migration during influenza A infection by IFN-γ and perforin-dependent mechanisms.\",\n \"abstract\": \"An effective immune response against influenza A infection depends on the generation of virus-specific T cells. NK cells are one of the first-line defenses against influenza A infection. We set out to delineate the role of NK cells in T cell immunity using a murine model of influenza A infection with A/PR/8/34. We show that early T cell recruitment mainly occurs in the posterior mediastinal lymph node (pMLN). Depletion of NK cells significantly impaired both dendritic cell (DC) and T cell recruitment into the pMLN. A similar reduction of T cell recruitment was observed when migration was blocked by pertussis toxin, suggesting that migration of pulmonary NK cells and DCs regulates cell recruitment to the pMLN. T cell recruitment was dependent on IFN-γ, and transfer of IFN-γ-competent naive NK cells into IFN-γ-/- mice restored T cell recruitment, whereas IFN-γ-deficient NK cells failed to do so. In addition, NK cell depletion reduced the uptake and transport of influenza A virus by DCs, and significantly impaired the virus-specific T cell response. Both IFN-γ-/- and perforin-/- mice showed reduced viral Ag transport by DCs, suggesting that the ability of NK cells to influence virus transport depends on IFN-γ and perforin. In summary, our data suggest that NK cells play a critical role in the initiation and shaping of the T cell response after influenza A infection.\",\n \"corpus_id\": 24236105,\n \"score\": 2\n },\n {\n \"doc_id\": \"23185463\",\n \"title\": \"Influenza A(H1N1)pdm09 virus suppresses RIG-I initiated innate antiviral responses in the human lung.\",\n \"abstract\": \"Influenza infection is a major cause of morbidity and mortality. Retinoic acid-inducible gene I (RIG-I) is believed to play an important role in the recognition of, and response to, influenza virus and other RNA viruses. Our study focuses on the hypothesis that pandemic H1N1/09 influenza virus alters the influenza-induced proinflammatory response and suppresses host antiviral activity. We first compared the innate response to a clinical isolate of influenza A(H1N1)pdm09 virus, OK/09, a clinical isolate of seasonal H3N2 virus, OK/06, and to a laboratory adapted seasonal H1N1 virus, PR8, using a unique human lung organ culture model. Exposure of human lung tissue to either pandemic or seasonal influenza virus resulted in infection and replication in alveolar epithelial cells. Pandemic virus induces a diminished RIG-I mRNA and antiviral cytokine response than seasonal virus in human lung. The suppression of antiviral response and RIG-I mRNA expression was confirmed at the protein level by ELISA and western blot. We performed a time course of RIG-I and interferon-β (IFN-β) mRNA induction by the two viruses. RIG-I and IFN-β induction by OK/09 was of lower amplitude and shorter duration than that caused by PR8. In contrast, the pandemic virus OK/09 caused similar induction of proinflammatory cytokines, IL-8 and IL-6, at both the transcriptional and translational level as PR8 in human lung. Differential antiviral responses did not appear to be due to a difference in cellular infectivity as immunohistochemistry showed that both viruses infected alveolar macrophages and epithelial cells. These findings show that influenza A(H1N1)pdm09 virus suppresses anti-viral immune responses in infected human lung through inhibition of viral-mediated induction of the pattern recognition receptor, RIG-I, though proinflammatory cytokine induction was unaltered. This immunosuppression of the host antiviral response by pandemic virus may have contributed to the more serious lung infections that occurred in the H1N1 pandemic of 2009.\",\n \"corpus_id\": 18883954,\n \"score\": 2\n },\n {\n \"doc_id\": \"23272202\",\n \"title\": \"CCR2 defines a distinct population of NK cells and mediates their migration during influenza virus infection in mice.\",\n \"abstract\": \"Natural killer (NK) cells are innate lymphocytes that play an important role in control of viral infections. We recently showed that intranasal infection of mice with influenza virus induced the accumulation of NK cells in the airways. NK cells however did not proliferate in the airways or in the draining lymph node, but in the bone marrow mainly. As also monocyte-precursors undergo vigorous proliferation in the bone marrow (BM) during infections and then egress CCR2-dependently, we decided to determine the role of CCR2 in NK cell migration during intranasal influenza virus infection. We show that a unique population of NK cells in the BM expressed CCR2 and that monocyte chemotactic protein-1 (MCP-1), one of the CCR2 ligands, was produced in the airways of influenza virus infected mice. Analysis of BM chimeric mice reconstituted with a mix of wild-type (wt) and CCR2-deficient BM cells showed that upon influenza virus infection, a significantly lower proportion of CCR2-deficient than wt NK cells was recovered from the bronchoalveolar lavage (BAL). Taken together, our data demonstrate that during influenza virus infection a proportion of NK cells migrate in a CCR2-dependent fashion.\",\n \"corpus_id\": 18043084,\n \"score\": 2\n },\n {\n \"doc_id\": \"23300570\",\n \"title\": \"Activation mechanisms of natural killer cells during influenza virus infection.\",\n \"abstract\": \"During early viral infection, activation of natural killer (NK) cells elicits the effector functions of target cell lysis and cytokine production. However, the cellular and molecular mechanisms leading to NK cell activation during viral infections are incompletely understood. In this study, using a model of acute viral infection, we investigated the mechanisms controlling cytotoxic activity and cytokine production in response to influenza (flu) virus. Analysis of cytokine receptor deficient mice demonstrated that type I interferons (IFNs), but not IL-12 or IL-18, were critical for the NK cell expression of both IFN-γ and granzyme B in response to flu infection. Further, adoptive transfer experiments revealed that NK cell activation was mediated by type I IFNs acting directly on NK cells. Analysis of signal transduction molecules showed that during flu infection, STAT1 activation in NK cells was completely dependent on direct type I IFN signaling, whereas STAT4 activation was only partially dependent. In addition, granzyme B induction in NK cells was mediated by signaling primarily through STAT1, but not STAT4, while IFN-γ production was mediated by signaling through STAT4, but not STAT1. Therefore, our findings demonstrate the importance of direct action of type I IFNs on NK cells to mount effective NK cell responses in the context of flu infection and delineate NK cell signaling pathways responsible for controlling cytotoxic activity and cytokine production.\",\n \"corpus_id\": 6895012,\n \"score\": 2\n },\n {\n \"doc_id\": \"23436540\",\n \"title\": \"NK cells exacerbate the pathology of influenza virus infection in mice.\",\n \"abstract\": \"NK cells offer a first line of defense against viruses and are considered beneficial to the host during infection. Nevertheless, little is understood regarding the phenotype and function of NK cells in the lung during influenza virus infection. We found that the frequency of NK cells in mouse lung increased during influenza infection, with the majority of a mature phenotype. Cell surface CD107a and intracellular IFN-γ were detected in cells expressing multiple NK-cell receptors in infected lung, suggesting that NK cells were activated during infection. The activating receptor NKp46 was predominantly negative on such cells, possibly as a result of encountering influenza HA. Depletion of NK cells in vivo with anti-asialo GM1 or anti-NK1.1 reduced mortality from influenza infection and surviving mice recovered their body weight. Pathology induced by NK cells was only observed with high, not medium or low-dose influenza infection, indicating that the severity of infection influences NK-cell-mediated pathology. Furthermore, adoptive transfer of NK cells from influenza-infected lung, but not uninfected lung, resulted in more rapid weight loss and increased mortality of influenza-infected mice. Our results indicate that during severe influenza infection of the lung, NK cells have a deleterious impact on the host, promoting mortality.\",\n \"corpus_id\": 5522473,\n \"score\": 2\n },\n {\n \"doc_id\": \"23963354\",\n \"title\": \"Differential lung NK cell responses in avian influenza virus infected chickens correlate with pathogenicity.\",\n \"abstract\": \"Infection of chickens with low pathogenicity avian influenza (LPAI) virus results in mild clinical signs while infection with highly pathogenic avian influenza (HPAI) viruses causes death of the birds within 36-48 hours. Since natural killer (NK) cells have been shown to play an important role in influenza-specific immunity, we hypothesise that NK cells are involved in this difference in pathogenicity. To investigate this, the role of chicken NK-cells in LPAI virus infection was studied. Next activation of lung NK cells upon HPAI virus infection was analysed. Infection with a H9N2 LPAI virus resulted in the presence of viral RNA in the lungs which coincided with enhanced activation of lung NK cells. The presence of H5N1 viruses, measured by detection of viral RNA, did not induce activation of lung NK cells. This suggests that decreased NK-cell activation may be one of the mechanisms associated with the enhanced pathogenicity of H5N1 viruses.\",\n \"corpus_id\": 261351984,\n \"score\": 2\n },\n {\n \"doc_id\": \"24373231\",\n \"title\": \"Inhibition of the inflammatory cytokine tumor necrosis factor-alpha with etanercept provides protection against lethal H1N1 influenza infection in mice.\",\n \"abstract\": \"INTRODUCTION: Factors implicated in influenza-mediated morbidity and mortality include robust cytokine production (cytokine storm), excessive inflammatory infiltrates, and virus-induced tissue destruction. Tumor necrosis factor-alpha (TNF-α) is an important pro-inflammatory cytokine present during influenza infection, but it is unclear whether direct inhibition of TNF-α can elicit protection against influenza infection. METHODS: In this study, the commercially available TNF-α inhibitor etanercept was used to inhibit TNF-α induced by lethal A/FM/1/47 (H1N1) influenza virus infection of mice. The effects of TNF-α inhibition on mouse survival, pathologic changes, immune cell infiltration, inflammatory cytokine secretion, Toll-like receptor expression, and activation of the NF-κB (nuclear factor kappa B) signaling pathway were evaluated. RESULTS: The intranasal delivery of etanercept provided significant protection against mortality (30% of mice survived up to 14 days after infection) in mice treated with etanercept. In contrast, no survivors were found beyond 6 days in mice treated with saline after lethal challenge with H1N1 influenza virus. It was observed that etanercept significantly reduced inflammatory cell infiltration (for example, macrophages and neutrophils), inflammatory cytokine secretion (for example, interleukin-6, TNF-α, and interferon gamma), and expression of Toll-like receptors (TLR-3, TLR-4, and TLR-7). Etanercept also downregulated and inhibited the cascade proteins of the NF-κB signaling pathway (for example, MyD88, TRIF, NF-κB, and p65), as well as enhanced host control of virus replication. CONCLUSIONS: These findings indicate that etanercept, by blocking TNF-α, can significantly downregulate excessive inflammatory immune responses and provide protection against lethal influenza infection, making its use a novel strategy for controlling severe influenza-induced viral pneumonia.\",\n \"corpus_id\": 7979949,\n \"score\": 2\n },\n {\n \"doc_id\": \"24435166\",\n \"title\": \"Type I interferon plays opposing roles in cytotoxicity and interferon-γ production by natural killer and CD8 T cells after influenza A virus infection in mice.\",\n \"abstract\": \"Type I interferons (IFNs) promote natural killer (NK) and CD8(+) T-cell responses, which play a role not only in the resolution of infection but also in the induction of acute lung injury following influenza A virus infection. We show here that IFN-α receptor knock-out (Ifnar1(-/-)) mice exhibited impaired cytotoxic activity as well as an increased ability of NK and CD8(+) T cells to produce IFN-γ after infection with influenza virus A/FM/1/47 (H1N1, a mouse-adapted strain). A deficiency in IFNAR signaling significantly impaired IL-10 production in influenza virus-infected lungs and enhanced IFN-γ production by NK cells, which were suppressed by exogenous IL-10. Depletion of NK cells but not CD8(+) T cells in Ifnar1(-/-) mice improved the survival rate after A/FM/1/47 infection, indicating that NK cells are responsible for acute lung injury in Ifnar1(-/-) mice following influenza A virus infection, although the depletion of IFN-γ did not improve the outcome. Thus, type I IFN signaling plays a role not only in the upregulation of cytotoxicity but also in the downregulation of some effector mechanisms including IFN-γ production by NK and CD8(+) T cells via IL-10 production.\",\n \"corpus_id\": 8881230,\n \"score\": 2\n },\n {\n \"doc_id\": \"24567377\",\n \"title\": \"Toll-like receptor 10 is involved in induction of innate immune responses to influenza virus infection.\",\n \"abstract\": \"Toll-like receptors (TLRs) play key roles in innate immune recognition of pathogen-associated molecular patterns of invading microbes. Among the 10 TLR family members identified in humans, TLR10 remains an orphan receptor without known agonist or function. TLR10 is a pseudogene in mice and mouse models are noninformative in this regard. Using influenza virus infection in primary human peripheral blood monocyte-derived macrophages and a human monocytic cell line, we now provide previously unidentified evidence that TLR10 plays a role in innate immune responses following viral infection. Influenza virus infection increased TLR10 expression and TLR10 contributed to innate immune sensing of viral infection leading to cytokine induction, including proinflammatory cytokines and interferons. TLR10 induction is more pronounced following infection with highly pathogenic avian influenza H5N1 virus compared with a low pathogenic H1N1 virus. Induction of TLR10 by virus infection requires active virus replication and de novo protein synthesis. Culture supernatants of virus-infected cells modestly up-regulate TLR10 expression in nonvirus-infected cells. Signaling via TLR10 was activated by the functional RNA-protein complex of influenza virus leading to robust induction of cytokine expression. Taken together, our findings identify TLR10 as an important innate immune sensor of viral infection and its role in innate immune defense and immunopathology following viral and bacterial pathogens deserves attention.\",\n \"corpus_id\": 656618,\n \"score\": 2\n },\n {\n \"doc_id\": \"24903089\",\n \"title\": \"Type-I interferon response affects an inoculation dose-independent mortality in mice following Japanese encephalitis virus infection.\",\n \"abstract\": \"BACKGROUND: The laboratory mouse model is commonly employed to study the pathogenesis of encephalitic flaviviruses such as Japanese encephalitis virus (JEV). However, it is known that some strains of these viruses do not elicit a typical mortality dose response curve from this organism after peripheral infection and the reason for it has not yet been fully understood. It is suggested that induction of more vigorous Type-I IFN (IFN-I) response might control early virus dissemination following increasing infectious challenge doses of the virus. Thus, the objective of this study was to examine this suggested role of IFN-I in the mortality of mice infected with various doses of JEV. METHODS: Inbred 129 mice and their IFNAR KO (A129) mice were subcutaneously inoculated with 100, 102, 104 or 106 pfu of JaOArS982 strain of JEV. Mice were weighed daily and observed for clinical signs. Virus titers in the brains and spleens of JEV-infected mice were determined by plaque forming assays. The upregulated mRNA levels of genes related to IFN-I response of mice were examined by real-time PCR. RESULTS: The mortality rates of 129 mice infected with JaOArS982 did not significantly increase despite the increase in inoculation dose and no significant difference of viral loads was observed between their brains. However, there was clear elevation of the mRNA levels of interferon regulatory factor (IRF)3, IRF7, IRF9, MDA5 and RIG-I at 24 hours post-infection depending on the inoculation dose. In A129 mice, length of survival days and the viral loads of spleen and brain were observed to be inoculation dose-dependent. CONCLUSIONS: From these results, it is suggested that early IFN-I response elicited by high inoculation doses of JEV provides an anti-viral effect during the early phase of infection. Accordingly, virus replication is counteracted by IFN-I response at each increasing inoculation dose resulting in the interference of impending severe disease course or fatal outcome; hence, this might explain the inoculation dose-independent mortality in mice caused by Japanese encephalitis virus.\",\n \"corpus_id\": 8275808,\n \"score\": 2\n },\n {\n \"doc_id\": \"24951819\",\n \"title\": \"Klebsiella pneumoniae alleviates influenza-induced acute lung injury via limiting NK cell expansion.\",\n \"abstract\": \"A protective effect induced by bacterial preinfection upon a subsequent lethal influenza virus infection has been observed, but the underlying immune mechanisms have not yet been fully elucidated. In this study, we used a mouse model of Klebsiella pneumoniae preinfection to gain insight into how bacterial preinfection influences the subsequent lethal influenza virus infection. We found that K. pneumoniae preinfection significantly attenuated lung immune injury and decreased mortality during influenza virus infection, but K. pneumoniae-specific immunity was not involved in this cross-protection against influenza virus. K. pneumoniae preinfection limited NK cell expansion, which was involved in influenza-induced immune injury and death. Furthermore, K. pneumoniae preinfection could not control NK cell expansion and death during influenza virus infection in Rag1(-/-) mice, but adoptive transfer of T cells from wild-type mice was able to restore this protective effect. Our data suggest that the adaptive immune response activated by bacterial infection limits the excessive innate immune response induced by a subsequent influenza infection, ultimately protecting mice from death.\",\n \"corpus_id\": 23402303,\n \"score\": 2\n },\n {\n \"doc_id\": \"24992894\",\n \"title\": \"Role of NK cells in influenza infection.\",\n \"abstract\": \"Within days after infection, natural killer (NK) cells are recruited to the lungs and play an essential role in the immune response against influenza infection. Through interactions with the virus itself, as well as viral-infected cells, NK cells secrete a variety of cytokines and can contain viral replication by killing infected cells early after influenza infection. However, the virus has means of evading NK cell responses, including escaping NK cell recognition through mutation of the viral hemagglutinin (HA) protein, regulating HA levels, and by directly infecting and destroying NK cells. Although much of our understanding of NK cell role in influenza infection has come from animal models, there is increasing information from human infection. Studies conducted during the 2009 H1N1 pandemic provided much needed information on the importance of NK cells during human infection and suggest that NK lymphopenia may correlate with increased disease severity. However, more information on how different influenza virus subtypes influence NK cell levels and activities, the role of the different NK cell receptors in infection, and the impact of NK cells on human infection, particularly in high risk populations is needed.\",\n \"corpus_id\": 37673946,\n \"score\": 2\n },\n {\n \"doc_id\": \"25404045\",\n \"title\": \"NK cells and their ability to modulate T cells during virus infections.\",\n \"abstract\": \"Natural killer (NK) cells are important in protection against virus infections, and many viruses have evolved mechanisms to thwart NK cell activity. NK cells respond to inflammatory signals at an early stage of virus infection, resulting in proliferation, cytokine production, and cytolytic activity that can reduce virus loads. Moreover, the rapid kinetics of the NK cell response enables NK cells to influence other populations of innate immune cells, affect the inflammatory milieu, and guide adaptive immune responses to infection. Early NK cell interactions with other leukocytes can have long-lasting effects on the number and quality of memory T cells, as well as impact the exhaustion of T cells during chronic infections. The ability of NK cells to modulate T cell responses can be mediated through direct T-NK interactions, cytokine production, or indirectly through dendritic cells and other cell types. Herein, we summarize our current understanding of how NK cells interact with T cells, dendritic cells, B cells, and other cell types involved in adaptive immune responses to virus infection. We outline several mechanisms by which NK cells enhance or suppress adaptive immune response and long-lived immunological memory.\",\n \"corpus_id\": 41304022,\n \"score\": 2\n },\n {\n \"doc_id\": \"25418976\",\n \"title\": \"A novel genetic locus linked to pro-inflammatory cytokines after virulent H5N1 virus infection in mice.\",\n \"abstract\": \"BACKGROUND: Genetic variation in the human population is a key determinant of influenza disease severity. A single nucleotide polymorphism in the antiviral gene IFITM3 was linked to outcomes during the 2009 H1N1 pandemic. To identify variant host genes associated with increased virus replication and severe disease, we performed a quantitative trait locus analysis on pro-inflammatory cytokine production 48 hours after intranasal infection with highly pathogenic H5N1 influenza virus. RESULTS: Pro-inflammatory cytokines CCL2, TNFα and IFN-α, were measured by ELISA in lung homogenates of DBA/2J (D2), C57BL/6J (B6) and 44 different BXD recombinant inbred mouse strains. Virus titer was also assessed in a subset of these animals. CCL2 (8-fold), TNFα (24-fold) and IFN-α (8-fold) concentrations varied significantly among the different BXD RI strains. Importantly, cytokine concentration correlated very well (r =0.86-0.96, P <0.0001) with virus titer suggesting that early cytokine production is due to increased virus infection and replication. Linkage analysis of cytokine concentration revealed a significant locus on chromosome 6 associated with differences in TNFα, IFN-α and CCL2 cytokine concentration (LRS =26). This locus accounted for nearly 20% of the observed phenotypic variation in the BXD population studied. Sequence and RNA expression analysis identified several candidate host genes containing missense mutations or deletions; Samd9l, Ica1, and Slc25a13. To study the role of Slc25a13, we obtained Slc25a13 knockout line, but upon challenge with H5N1 influenza virus observed no effect on CCL2 production, or morbidity and mortality. CONCLUSION: A novel genetic locus on chromosome 6 modulates early pro-inflammatory cytokine production and virus replication after highly pathogenic influenza virus infection. Candidate genes, Samd9l and Ica1, may be important for the control of influenza virus infection and pathogenesis.\",\n \"corpus_id\": 6917249,\n \"score\": 2\n },\n {\n \"doc_id\": \"26202236\",\n \"title\": \"Protection from Severe Influenza Virus Infections in Mice Carrying the Mx1 Influenza Virus Resistance Gene Strongly Depends on Genetic Background.\",\n \"abstract\": \"UNLABELLED: Influenza virus infections represent a serious threat to human health. Both extrinsic and intrinsic factors determine the severity of influenza. The MX dynamin-like GTPase 1 (Mx1) gene has been shown to confer strong resistance to influenza A virus infections in mice. Most laboratory mouse strains, including C57BL/6J, carry nonsense or deletion mutations in Mx1 and thus a nonfunctional allele, whereas wild-derived mouse strains carry a wild-type Mx1 allele. Congenic C57BL/6J (B6-Mx1(r/r)) mice expressing a wild-type allele from the A2G mouse strain are highly resistant to influenza A virus infections, to both mono- and polybasic subtypes. Furthermore, in genetic mapping studies, Mx1 was identified as the major locus of resistance to influenza virus infections. Here, we investigated whether the Mx1 protective function is influenced by the genetic background. For this, we generated a congenic mouse strain carrying the A2G wild-type Mx1 resistance allele on a DBA/2J background (D2-Mx1(r/r)). Most remarkably, congenic D2-Mx1(r/r) mice expressing a functional Mx1 wild-type allele are still highly susceptible to H1N1 virus. However, pretreatment of D2-Mx1(r/r) mice with alpha interferon protected them from lethal infections. Our results showed, for the first time, that the presence of an Mx1 wild-type allele from A2G as such does not fully protect mice from lethal influenza A virus infections. These observations are also highly relevant for susceptibility to influenza virus infections in humans. IMPORTANCE: Influenza A virus represents a major health threat to humans. Seasonal influenza epidemics cause high economic loss, morbidity, and deaths each year. Genetic factors of the host strongly influence susceptibility and resistance to virus infections. The Mx1 (MX dynamin-like GTPase 1) gene has been described as a major resistance gene in mice and humans. Most inbred laboratory mouse strains are deficient in Mx1, but congenic B6-Mx1(r/r) mice that carry the wild-type Mx1 gene from the A2G mouse strain are highly resistant. Here, we show that, very unexpectedly, congenic D2-Mx1(r/r) mice carrying the wild-type Mx1 gene from the A2G strain are not fully protected against lethal influenza virus infections. These observations demonstrate that the genetic background is very important for the protective function of the Mx1 resistance gene. Our results are also highly relevant for understanding genetic susceptibility to influenza virus infections in humans.\",\n \"corpus_id\": 16032096,\n \"score\": 2\n },\n {\n \"doc_id\": \"26329040\",\n \"title\": \"RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.\",\n \"abstract\": \"BACKGROUND: The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual mouse after H1N1 infection. RESULTS: We performed a detailed expression analysis to identify (i) correlations between changes in expression of host and virus genes, (ii) host genes involved in viral replication, and (iii) genes showing differential expression between two mouse strains that strongly differ in resistance to influenza infections. These genes may be key players involved in regulating the differences in pathogenesis and host defense mechanisms after influenza A infections. Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements. Furthermore, we investigated the functional role of two genes, Reg3g and Irf7, in knock-out mice and found that deletion of the Irf7 gene renders the host highly susceptible to H1N1 infection. CONCLUSIONS: Using RNAseq analysis we identified novel genes important for viral replication or the host defense. This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.\",\n \"corpus_id\": 15338495,\n \"score\": 2\n },\n {\n \"doc_id\": \"26346306\",\n \"title\": \"Natural Killer Cells are involved in Thymic Atrophy induced by Influenza A Virus Infection.\",\n \"abstract\": \"Natural killer (NK) cells have traditionally been viewed as innate effector lymphocytes that serve as a first-line defense against a range of viruses and tumors. More recently, the importance of NK cell immunoregulatory functions has been highlighted. NK cells can inhibit antiviral T cell responses and also play an important role in controlling harmful T cell activity in autoimmunity and transplantation settings. Moreover, immunopathological effects of NK cells during infection have been reported. Nevertheless, the phenotype and function of NK cells in the thymus during influenza virus infection is not understood. In the present study, we demonstrated that influenza A virus (IAV) infection in mice led to severe thymic atrophy caused by increased thymic T cell apoptosis and suppressed proliferation. We found that NK cells played a critical role in this phenotype. IFN-γ production by NK cells was a contributing factor for thymic atrophy during IAV infection. Taken together, our data indicate that NK cells are involved in the thymic atrophy associated with IAV infection.\",\n \"corpus_id\": 20509718,\n \"score\": 2\n },\n {\n \"doc_id\": \"27438481\",\n \"title\": \"RIG-I Signaling Is Critical for Efficient Polyfunctional T Cell Responses during Influenza Virus Infection.\",\n \"abstract\": \"Retinoic acid inducible gene-I (RIG-I) is an innate RNA sensor that recognizes the influenza A virus (IAV) RNA genome and activates antiviral host responses. Here, we demonstrate that RIG-I signaling plays a crucial role in restricting IAV tropism and regulating host immune responses. Mice deficient in the RIG-I-MAVS pathway show defects in migratory dendritic cell (DC) activation, viral antigen presentation, and priming of CD8+ and CD4+ T cell responses during IAV infection. These defects result in decreased frequency of polyfunctional effector T cells and lowered protection against heterologous IAV challenge. In addition, our data show that RIG-I activation is essential for protecting epithelial cells and hematopoietic cells from IAV infection. These diverse effects of RIG-I signaling are likely imparted by the actions of type I interferon (IFN), as addition of exogenous type I IFN is sufficient to overcome the defects in antigen presentation by RIG-I deficient BMDC. Moreover, the in vivo T cell defects in RIG-I deficient mice can be overcome by the activation of MDA5 -MAVS via poly I:C treatment. Taken together, these findings demonstrate that RIG-I signaling through MAVS is critical for determining the quality of polyfunctional T cell responses against IAV and for providing protection against subsequent infection from heterologous or novel pandemic IAV strains.\",\n \"corpus_id\": 10918951,\n \"score\": 2\n },\n {\n \"doc_id\": \"27531368\",\n \"title\": \"Antimicrobial peptides alter early immune response to influenza A virus infection in C57BL/6 mice.\",\n \"abstract\": \"Influenza is a disease of the respiratory system caused by single stranded RNA viruses with varying genotypes. Immunopathogenesis to influenza viruses differs based on virus strain, dose, and mouse strain used in laboratory models. Although effective mucosal immune defenses are important in early host defense against influenza, information on the kinetics of these immune defense mechanisms during the course of influenza infection is limited. We investigated changes to antimicrobial peptides and primary innate immune cells at early time points after infection and compared these variables between two prominent H1N1 influenza A virus (IAV) strains, A/CA/04/2009 and A/PR/08/1934 in C57BL/6 mice. Alveolar and parenchymal macrophage ratios were altered after IAV infection and pro-inflammatory cytokine production in macrophages was induced after IAV infection. Genes encoding antimicrobial peptides, β-defensin (Defb4), bactericidal-permeability increasing protein (Bpifa1), and cathelicidin antimicrobial peptide (Camp), were differentially regulated after IAV infection and the kinetics of Defb4 expression differed in response to each virus strain. Beta-defensin reduced infectivity of A/CA/04/2009 virus but not A/PR/08/1934. Beta defensins also changed the innate immune cell profile wherein mice pre-treated with β-defensin had increased alveolar macrophages and CD103(+) dendritic cells, and reduced CD11b(+) dendritic cells and neutrophils. In addition to highlighting that immune responses may vary based on influenza virus strain used, our data suggest an important role for antimicrobial peptides in host defense against influenza virus.\",\n \"corpus_id\": 4926733,\n \"score\": 2\n },\n {\n \"doc_id\": \"28585438\",\n \"title\": \"Pulmonary immune cells and inflammatory cytokine dysregulation are associated with mortality of IL-1R1 (-/-)mice infected with influenza virus (H1N1).\",\n \"abstract\": \"Respirovirus infection can cause viral pneumonia and acute lung injury (ALI). The interleukin-1 (IL-1) family consists of proinflammatory cytokines that play essential roles in regulating immune and inflammatory responses in vivo. IL-1 signaling is associated with protection against respiratory influenza virus infection by mediation of the pulmonary anti-viral immune response and inflammation. We analyzed the infiltration lung immune leukocytes and cytokines that contribute to inflammatory lung pathology and mortality of fatal H1N1 virus-infected IL-1 receptor 1 (IL-1R1) deficient mice. Results showed that early innate immune cells and cytokine/chemokine dysregulation were observed with significantly decreased neutrophil infiltration and IL-6, TNF-α, G-CSF, KC, and MIP-2 cytokine levels in the bronchoalveolar lavage fluid of infected IL-1R1 (-/-) mice in comparison with that of wild type infected mice. The adaptive immune response against the H1N1 virus in IL-1R1 (-/-) mice was impaired with downregulated anti-viral Th1 cell, CD8+ cell, and antibody functions, which contributes to attenuated viral clearance. Histological analysis revealed reduced lung inflammation during early infection but severe lung pathology in late infection in IL-1R1 (-/-) mice compared with that in WT infected mice. Moreover, the infected IL-1R1 (-/-) mice showed markedly reduced neutrophil generation in bone marrow and neutrophil recruitment to the inflamed lung. Together, these results suggest that IL-1 signaling is associated with pulmonary anti-influenza immune response and inflammatory lung injury, particularly via the influence on neutrophil mobilization and inflammatory cytokine/chemokine production.\",\n \"corpus_id\": 3648567,\n \"score\": 2\n },\n {\n \"doc_id\": \"28904191\",\n \"title\": \"Dose of Retroviral Infection Determines Induction of Antiviral NK Cell Responses.\",\n \"abstract\": \"Natural killer (NK) cells are part of the innate immune system and recognize virus-infected cells as well as tumor cells. Conflicting data about the beneficial or even detrimental role of NK cells in different infectious diseases have been described previously. While the type of pathogen strongly influences NK cell functionality, less is known about how the infection dose influences the quality of a NK cell response against retroviruses. In this study, we used the well-established Friend retrovirus (FV) mouse model to investigate the impact of virus dose on the induction of antiviral NK cell functions. High-dose virus inoculation increased initial virus replication compared to that with medium- or low-dose viral challenge and significantly improved NK cell activation. Antiviral NK cell activity, including in vivo cytotoxicity toward infected target cells, was also enhanced by high-dose virus infection. NK cell activation following high-dose viral challenge was likely mediated by activated dendritic cells (DCs) and macrophages and the NK cell-stimulating cytokines interleukin 15 (IL-15) and IL-18. Neutralization of these cytokines decreased NK cell functions and increased viral loads, whereas IL-15 and IL-18 therapy improved NK cell activity. Here we demonstrate that virus dose positively correlates with antiviral NK cell activity and function, which are at least partly driven by IL-15 and IL-18. Our results suggest that NK cell activity may be therapeutically enhanced by administering IL-15 and IL-18 in virus infections that inadequately activate NK cells. IMPORTANCE In infections with retroviruses, like HIV and FV infection of mice, NK cells clearly mediate antiviral activities, but they are usually not sufficient to prevent severe pathology. Here we show that the initial infection dose impacts the induction of an antiviral NK cell response during an acute retroviral infection, which had not investigated before. High-dose infection resulted in a strong NK cell functionality, whereas no antiviral activities were detected after low- or medium-dose infection. Interestingly, DCs and macrophages were highly activated after high-dose FV challenge, which corresponded with increased levels of NK cell-stimulating cytokines IL-15 and IL-18. IL-15 and IL-18 neutralization decreased NK cell functions, whereas IL-15 and IL-18 therapy improved NK cell activity. Here we show the importance of cytokines for NK cell activation in retroviral infections; our findings suggest that immunotherapy combining the well-tolerated cytokines IL-15 and IL-18 might be an interesting approach for antiretroviral treatment.\",\n \"corpus_id\": 4628503,\n \"score\": 2\n },\n {\n \"doc_id\": \"19200852\",\n \"title\": \"Activation of toll-like receptor signaling pathway for protection against influenza virus infection.\",\n \"abstract\": \"This study aims to evaluate the antiviral role of nucleic acid-based agonists for the activation of toll-like receptor (TLR) signaling pathways, and its protective role in respiratory influenza A virus infections. TLR-3 is expressed on myeloid dendritic cells, respiratory epithelium, and macrophages, and appears to play a central role in mediating both the antiviral and inflammatory responses of the innate immunity in combating viral infections. Influenza viruses can effectively inhibit the host's ability to produce interferons, and thereby suppress the immune system's antiviral defence mechanisms. Poly ICLC is a synthetic double stranded RNA comprising of polyriboinosinic-poly ribocytidylic acid (Poly IC) stabilized with l-lysine (L) and carboxymethylcellulose (C). Poly ICLC and liposome-encapsulated Poly ICLC (LE Poly ICLC) are TLR-3 agonists and are potent inducer of interferons and natural killer cells. Intranasal pre-treatment of mice with Poly ICLC and LE Poly ICLC provided high level of protection against lethal challenge with a highly lethal avian H5N1 influenza (HPAI) strain (A/H5N1/chicken/Henan clade 2), and against lethal seasonal influenza A/PR/8/34 [H1N1] and A/Aichi/2 [H3N2] virus strains. The duration of protective antiviral immunity to multiple lethal doses of influenza virus A/PR/8/34 virus had been previously found to persist for up to 3 weeks in mice for LE Poly ICLC and 2 weeks for Poly ICLC. Similarly, pre-treatment of mice with CpG oligonucleotides (TLR-9 agonist) was also found to provide complete protection against influenza A/PR/8/34 infection in mice. RT-PCR analysis of lung tissues of mice treated with Poly ICLC and LE Poly ICLC revealed upregulation of TLR-3 mRNAs gene expression. Taken together, these results do support the potential role of TLR-3 and TLR-9 agonists such as Poly ICLC and LE Poly ICLC in protection against lethal seasonal and HPAI virus infection.\",\n \"corpus_id\": 37319142,\n \"score\": 1\n },\n {\n \"doc_id\": \"19922665\",\n \"title\": \"Impaired immune responses in the lungs of aged mice following influenza infection.\",\n \"abstract\": \"BACKGROUND: Each year, influenza virus infection causes severe morbidity and mortality, particularly in the most susceptible groups including children, the elderly (>65 years-old) and people with chronic respiratory diseases. Among the several factors that contribute to the increased susceptibility in elderly populations are the higher prevalence of chronic diseases (e.g. diabetes) and the senescence of the immune system. METHODS: In this study, aged and adult mice were infected with sublethal doses of influenza virus (A/Puerto Rico/8/1934). Differences in weight loss, morbidity, virus titer and the kinetics of lung infiltration with cells of the innate and adaptive immune responses were analyzed. Additionally, the main cytokines and chemokines produced by these cells were also assayed. RESULTS: Compared to adult mice, aged mice had higher morbidity, lost weight more rapidly, and recovered more slowly from infection. There was a delay in the accumulation of granulocytic cells and conventional dendritic cells (cDCs), but not macrophages in the lungs of aged mice compared to adult animals. The delayed infiltration kinetics of APCs in aged animals correlated with alteration in their activation (CD40 expression), which also correlated with a delayed detection of cytokines and chemokines in lung homogenates. This was associated with retarded lung infiltration by natural killer (NK), CD4+ and CD8+ T-cells. Furthermore, the percentage of activated (CD69+) influenza-specific and IL-2 producer CD8+ T-cells was higher in adult mice compared to aged ones. Additionally, activation (CD69+) of adult B-cells was earlier and correlated with a quicker development of neutralizing antibodies in adult animals. CONCLUSION: Overall, alterations in APC priming and activation lead to delayed production of cytokines and chemokines in the lungs that ultimately affected the infiltration of immune cells following influenza infection. This resulted in delayed activation of the adaptive immune response and subsequent delay in clearance of virus and prolonged illness in aged animals. Since the elderly are the fastest growing segment of the population in developed countries, a better understanding of the changes that occur in the immune system during the aging process is a priority for the development of new vaccines and adjuvants to improve the immune responses in this population.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"20033657\",\n \"title\": \"Studying NK cell responses to ectromelia virus infections in mice.\",\n \"abstract\": \"Here we describe methods for the in vivo study of antiviral NK cell responses using the mouse Orthopoxvirus ectromelia virus as a model, the agent of mousepox. The methods include those specific for the preparation and use of ectromelia virus such as the production of virus stocks in tissue culture and in live mice, the purification of virus stocks, the titration of virus stocks and virus loads in organs, and the infection of mice. The chapter also includes methods for the specific study of NK cell responses in infected mice such as the preparation of organs (lymph nodes, spleen, and liver) for analysis, the study of NK cell responses by flow cytometry, the adoptive transfer of NK cells, the measurement of NK cell cytolytic activity ex vivo and in vivo, and the determination of NK cell proliferation by bromodeoxyuridine loading or by dilution of carboxyfluorescein diacetate succinimidyl ester (CFSE).\",\n \"corpus_id\": 10863468,\n \"score\": 1\n },\n {\n \"doc_id\": \"20855097\",\n \"title\": \"IFN-γ production downstream of NKT cell activation in mice infected with influenza virus enhances the cytolytic activities of both NK cells and viral antigen-specific CD8+ T cells.\",\n \"abstract\": \"Natural killer T (NKT) cell activation is responsible for eliminating pathogens. However, the biological functions of NKT cells against influenza virus are not fully understood. We therefore investigated the effects of NKT cells in viral infection using CD1d knockout (KO) mice. When CD1d KO or wild-type (WT) mice were infected with a sub-lethal dosage of the influenza virus, the survival rate of CD1d KO mice was significantly lower than for WT mice in association with delayed viral clearance in the lungs. Consistently, IFN-γ production in bronchoalveolar lavage fluid of CD1d KO mice was largely reduced compared to WT mice during infection. Moreover, the cytotoxic activities of NK cells and viral antigen-specific CD8(+) T cells were impaired in CD1d KO mice. It was concluded that activated NKT cell-induced IFN-γ release enhances both NK-cell activity and antigen-specific CD8(+) T cells to eliminate the influenza virus, thus leading to an enhanced survival.\",\n \"corpus_id\": 205645431,\n \"score\": 1\n },\n {\n \"doc_id\": \"20943980\",\n \"title\": \"MyD88 signaling is indispensable for primary influenza A virus infection but dispensable for secondary infection.\",\n \"abstract\": \"Recent studies have revealed that innate immunity is involved in the development of adaptive immune responses; however, its role in protection is not clear. In order to elucidate the exact role of Toll-like receptor (TLR) or RIG-I-like receptor (RLR) signaling on immunogenicity and protective efficacy against influenza A virus infection (A/PR/8/34 [PR8]; H1N1), we adapted several innate signal-deficient mice (e.g., TRIF(-/-), MyD88(-/-), MyD88(-/-) TRIF(-/-), TLR3(-/-) TLR7(-/-), and IPS-1(-/-)). In this study, we found that MyD88 signaling was required for recruitment of CD11b(+) granulocytes, production of early inflammatory cytokines, optimal proliferation of CD4 T cells, and production of Th1 cytokines by T cells. However, PR8 virus-specific IgG and IgA antibody levels in both systemic and mucosal compartments were normal in TLR- and RLR-deficient mice. To further assess the susceptibility of these mice to influenza virus infection, protective efficacy was determined after primary or secondary lethal challenge. We found that MyD88(-/-) and MyD88(-/-) TRIF(-/-) mice were more susceptible to primary influenza virus infection than the B6 mice but were fully protected against homologous (H1N1) and heterosubtypic (H5N2) secondary infection when primed with a nonlethal dose of PR8 virus. Taken together, these results show that MyD88 signaling plays an important role for resisting primary influenza virus infection but is dispensable for protection against a secondary lethal challenge.\",\n \"corpus_id\": 24306635,\n \"score\": 1\n },\n {\n \"doc_id\": \"22098223\",\n \"title\": \"Heat-killed Lactobacillus gasseri TMC0356 protects mice against influenza virus infection by stimulating gut and respiratory immune responses.\",\n \"abstract\": \"This study investigated whether heat-killed Lactobacillus protects host animal against influenza virus infection and stimulates their immunity. Heat-killed Lactobacillus gasseri TMC0356 was orally administered to BALB/c mice for 19 days; the mice were intranasally infected with Flu A/PR/8/34 (H1N1) on day 14, and clinical symptoms were monitored. After 6 days, the mice were sacrificed, and pulmonary virus titres were determined. Splenic activation of natural killer (NK) cells and the mRNA expression of cytokines and other immune molecules in the lung and Peyer's patch (PP) were analysed. Clinical symptom scores of mice orally fed TMC0356 ameliorated significantly (P < 0.01); their pulmonary virus titres decreased significantly compared with those of control mice (P < 0.05); their mRNA expression of interleukin (IL)-12, IL-15 and IL-21 in PP and the pulmonary mRNA expression of IFN-γ, TNF, IL-12a, IL-12rbl, IL-2rb and perforin 1 increased significantly (P < 0.05). Oral administration of heat-killed lactobacilli may protect against influenza virus infection by stimulating local and systemic immune responses. Cellular components of lactobacilli may be pivotal in protecting against viral infection by enhancing gut and respiratory immune responses.\",\n \"corpus_id\": 24538140,\n \"score\": 1\n },\n {\n \"doc_id\": \"22294696\",\n \"title\": \"Interleukin-22 is produced by invariant natural killer T lymphocytes during influenza A virus infection: potential role in protection against lung epithelial damages.\",\n \"abstract\": \"Invariant natural killer T (iNKT) cells are non-conventional lipid-reactive αβ T lymphocytes that play a key role in host responses during viral infections, in particular through the swift production of cytokines. Their beneficial role during experimental influenza A virus (IAV) infection has recently been proposed, although the mechanisms involved remain elusive. Here we show that during in vivo IAV infection, mouse pulmonary iNKT cells produce IFN-γ and IL-22, a Th17-related cytokine critical in mucosal immunity. Although permissive to viral replication, IL-22 production by iNKT cells is not due to IAV infection per se of these cells but is indirectly mediated by IAV-infected dendritic cells (DCs). We show that activation of the viral RNA sensors TLR7 and RIG-I in DCs is important for triggering IL-22 secretion by iNKT cells, whereas the NOD-like receptors NOD2 and NLRP3 are dispensable. Invariant NKT cells respond to IL-1β and IL-23 provided by infected DCs independently of the CD1d molecule to release IL-22. In vitro, IL-22 protects IAV-infected airway epithelial cells against mortality but has no role on viral replication. Finally, during early IAV infection, IL-22 plays a positive role in the control of lung epithelial damages. Overall, IAV infection of DCs activates iNKT cells, providing a rapid source of IL-22 that might be beneficial to preserve the lung epithelium integrity.\",\n \"corpus_id\": 30142675,\n \"score\": 1\n },\n {\n \"doc_id\": \"22467655\",\n \"title\": \"NKG2D mediates NK cell hyperresponsiveness and influenza-induced pathologies in a mouse model of chronic obstructive pulmonary disease.\",\n \"abstract\": \"Chronic obstructive pulmonary disease (COPD) is characterized by peribronchial and perivascular inflammation and largely irreversible airflow obstruction. Acute disease exacerbations, due frequently to viral infections, lead to enhanced disease symptoms and contribute to long-term progression of COPD pathology. Previously, we demonstrated that NK cells from cigarette smoke (CS)-exposed mice exhibit enhanced effector functions in response to stimulating cytokines or TLR ligands. In this article, we show that the activating receptor NKG2D is a key mediator for CS-stimulated NK cell hyperresponsiveness, because CS-exposed NKG2D-deficient mice (Klrk1(-/-)) did not exhibit enhanced effector functions as assessed by cytokine responsiveness. NK cell cytotoxicity against MHC class I-deficient targets was not affected in a COPD model. However, NK cells from CS-exposed mice exhibit greater cytotoxic activity toward cells that express the NKG2D ligand RAET1ε. We also demonstrate that NKG2D-deficient mice exhibit diminished airway damage and reduced inflammation in a model of viral COPD exacerbation, which do not affect viral clearance. Furthermore, adoptive transfer of NKG2D(+) NK cells into CS-exposed, influenza-infected NKG2D-deficient mice recapitulated the phenotypes observed in CS-exposed, influenza-infected wild-type mice. Our findings indicate that NKG2D stimulation during long-term CS exposure is a central pathway in the development of NK cell hyperresponsiveness and influenza-mediated exacerbations of COPD.\",\n \"corpus_id\": 207426531,\n \"score\": 1\n },\n {\n \"doc_id\": \"23200185\",\n \"title\": \"Effect of dietary supplementation with white button mushrooms on host resistance to influenza infection and immune function in mice.\",\n \"abstract\": \"Previously, we showed that mice fed white button mushrooms (WBM) had enhanced immune functions known to help the body's antiviral defence. In the present study, we tested whether WBM conferred protection against viral infection. Young (4-month-old) and old (22-month-old) C57BL/6 mice were fed a diet containing 0, 2 or 10 % WBM powder for 8 weeks. Mice were then infected with influenza Puerto Rico/8/34 (H1N1), and killed at day 0 (uninfected), 2, 5 or 7 post-infection. The primary outcomes of the study were viral titre and body weight. Secondary outcomes were natural killer (NK) cell activity, lymphocyte proliferation and cytokine production. The results showed that WBM did not affect viral titre, nor did it prevent infection-induced weight loss. WBM supplementation was found to enhance NK cell activity in old mice and to increase interferon (IFN)-γ production in young and old mice under naive (uninfected) conditions, but it had no such effect after infection. The lack of a mushroom supplementation effect on NK activity and concanavalin A-stimulated IFN-γ production after infection may explain the immune system's failure to reduce viral load and weight loss in mice after influenza infection. WBM supplementation, however, did induce changes in other aspects of the immune response: it significantly increased the production of T-helper type 2 cytokines IL-4 and IL-10 in uninfected mice and pro-inflammatory cytokines IL-1β and TNF-α in infected mice. These mushroom-induced systemic changes, however, were not adequate to confer a protective effect against influenza infection.\",\n \"corpus_id\": 4417272,\n \"score\": 1\n },\n {\n \"doc_id\": \"23739563\",\n \"title\": \"[Screening for genes associated with natural killer cell mediated cytotoxicity in pneumonia mice infected with influenza virus and regulation of two herbal anti-virus formulas].\",\n \"abstract\": \"OBJECTIVE: To investigate the regulation of two herbal anti-virus formulas on gene expression profile associated with natural killer cell (NK cell) mediated cytotoxicity in pneumonia mice infected with influenza virus. METHODS: According to random number table, 90 ICR mice were divided into nine groups with 10 mice in each group: normal group (N), model group (M), oseltamivir group (control group, C), low-dose, medium-dose and high-dose Shufeng Xuanfei formula groups (SL, SM, SH groups), and low-dose, medium-dose and high-dose Jiebiao Qingli formula groups (JL, JM, JH groups). The model of pneumonia was reproduced by nasal dropping influenza virus A (FM1) in mice. N group was given isotonic saline 0.05 ml in nasal drops. After 2 hours of model-building, C group was received 11.375 mg×kg⁻¹×d⁻¹ oseltamivir phosphate. Shufeng Xuanfei formula (mainly honeysuckle, forsythia and radix isatidis, etc.) with 3.76, 1.88 and 0.94 g×kg⁻¹×d were administrated to SH, SM and SL groups by gastric irrigation respectively. Jiebiao Qingli formula (mainly ephedra, gypsum, glycyrrhiza glabra, etc.) with 4.36, 2.18 and 1.09 g×kg⁻¹×d⁻¹ were administrated to JH, JM and JL groups by gastric irrigation respectively. In N and M groups, normal saline was administrated with gastric perfusion. Each group was in equal dose of 0.2 ml daily over a 4-day period. Total RNA in lung tissue of mice were extracted in each group, then gene chips were used to screen these RNA samples. Some genes involved NK cell mediated cytotoxicity were selected, with \\\"I\\\" representing of signal intensity. These candidate genes were verified by real-time fluorescent quantitation polymerase chain reaction (PCR) and Western blotting. RESULTS: In the pathway of NK cell mediated cytotoxicity, M group up-regulated 43 genes expression, and 36, 29, 22, 21, 20 and 10 genes showed down-regulation in SM, JM, SL, JH, SH and JL groups, respectively. Apart from gene co-expression network in SH, SL, JH, JM and JL, SM also expressed other differential genes which SH, SL, JH, JM and JL did not. So medium-does Shufeng Xuanfei formula had the most significant regulation in gene expression of NK cell mediated cytotoxicity. By real-time PCR and Western blotting experiments showed that compared with the M group, mRNA and protein expression of tumor necrosis factor-α (TNF-α) in these two formula groups were significantly down-regulated, especially prominent in SM group and JM group (TNF-α mRNA: 1.07 ± 0.19, 1.19 ± 0.14 vs. 3.20 ± 0.56, both P<0.01). CONCLUSIONS: Influenza viral replication in host cell, which means influenza antigens exposure in infected cells as target cells. NK cells recognize and exert cell mediated cytotoxic function against influenza antigens. Genes associated with NK cell mediated cytotoxicity in influenza infection were up-regulated. Shufeng Xuanfei and Jiebiao Qingli formulas could down-regulate these genes. The mechanism of down-regulated genes is that the number of influenza infected cells and NK cells activation decreases in treatment with two formulas.\",\n \"corpus_id\": 38787508,\n \"score\": 1\n },\n {\n \"doc_id\": \"24053449\",\n \"title\": \"Cross-protective immunity against influenza A/H1N1 virus challenge in mice immunized with recombinant vaccine expressing HA gene of influenza A/H5N1 virus.\",\n \"abstract\": \"BACKGROUND: Influenza virus undergoes constant antigenic evolution, and therefore influenza vaccines must be reformulated each year. Time is necessary to produce a vaccine that is antigenically matched to a pandemic strain. A goal of many research works is to produce universal vaccines that can induce protective immunity to influenza A viruses of various subtypes. Despite intensive studies, the precise mechanisms of heterosubtypic immunity (HSI) remain ambiguous. METHOD: In this study, mice were vaccinated with recombinant virus vaccine (rL H5), in which the hemagglutinin (HA) gene of influenza A/H5N1 virus was inserted into the LaSota Newcastle disease virus (NDV) vaccine strain. Following a challenge with influenza A/H1N1 virus, survival rates and lung index of mice were observed. The antibodies to influenza virus were detected using hemagglutination inhibition (HI). The lung viral loads, lung cytokine levels and the percentages of both IFN-γ+CD4+ and IFN-γ+CD8+ T cells in spleen were detected using real-time RT-PCR, ELISA and flow cytometry respectively. RESULTS: In comparison with the group of mice given phosphate-buffered saline (PBS), the mice vaccinated with rL H5 showed reductions in lung index and viral replication in the lungs after a challenge with influenza A/H1N1 virus. The antibody titer in group 3 (H1N1-H1N1) was significantly higher than that in other groups which only low levels of antibody were detected. IFN-γ levels increased in both group 1 (rL H5-H1N1) and group 2 (rL H5 + IL-2-H1N1). And the IFN-γ level of group 2 was significantly higher than that of group 1. The percentages of both IFN-γ+CD4+ and IFN-γ+CD8+ T cells in group 1 (rL H5-H1N1) and group 2 (rL H5 + IL-2-H1N1) increased significantly, as measured by flow cytometry. CONCLUSION: After the mice were vaccinated with rL H5, cross-protective immune response was induced, which was against heterosubtypic influenza A/H1N1 virus. To some extent, cross-protective immune response can be enhanced by IL-2 as an adjuvant. Cellular immune responses may play an important role in HSI against influenza virus.\",\n \"corpus_id\": 1756782,\n \"score\": 1\n },\n {\n \"doc_id\": \"24187666\",\n \"title\": \"Influenza virus specific CD8⁺ T cells exacerbate infection following high dose influenza challenge of aged mice.\",\n \"abstract\": \"Influenza viruses cause severe illnesses and death, mainly in the aged population. Protection afforded by licensed vaccines through subtype-specific neutralizing antibodies is incomplete, especially when the vaccine antigens fail to closely match those of the circulating viral strains. Efforts are underway to generate a so-called universal influenza vaccine expressing conserved viral sequences that induce broad protection to multiple strains of influenza virus through the induction of CD8⁺ T cells. Here we assess the effect of a potent antiviral CD8⁺ T cell response on influenza virus infection of young and aged mice. Our results show that CD8⁺ T cell-inducing vaccines can provide some protection to young mice, but they exacerbate influenza virus-associated disease in aged mice, causing extensive lung pathology and death.\",\n \"corpus_id\": 553495,\n \"score\": 1\n },\n {\n \"doc_id\": \"24201084\",\n \"title\": \"Lactobacillus fermentum CJL-112 protects mice against influenza virus infection by activating T-helper 1 and eliciting a protective immune response.\",\n \"abstract\": \"We have previously reported that nasally administered Lactobacillus fermentum CJL-112 (CJL-112) efficiently improves resistance against lethal influenza infection in both mice and chicken. The aim of the present study was to understand the underlying mechanisms of the significant anti-influenza activity of this lactobacilli strain. In vitro, co-culturing of the chicken macrophage cell line HD-11 with CJL-112 significantly increased nitric oxide (NO) production. In vivo, CJL-112 was nasally administered to BALB/c mice for 21 days prior to influenza A/NWS/33 (H1N1) virus (IFV) infection. Significant up-regulation of T-helper 1 (Th1) cytokines (IL-2, IFN-γ) was observed, while the levels of T-helper 2 (Th2) cytokines (IL-4, IL-5, IL-10) was either reduced or unchanged than that in control mice were. Furthermore, IgA and specific anti-influenza IgA levels increased significantly in the treated mice than those in untreated mice. Therefore, CJL-112 likely protects the mice against lethal IFV infection via stimulation of macrophages, activation of Th1 and augmentation of IgA production, when directly delivered into the respiratory tract.\",\n \"corpus_id\": 27306300,\n \"score\": 1\n },\n {\n \"doc_id\": \"24385240\",\n \"title\": \"Ability of recombinant human catalase to suppress inflammation of the murine lung induced by influenza A.\",\n \"abstract\": \"Influenza A virus pandemics and emerging antiviral resistance highlight the urgent need for novel generic pharmacological strategies that reduce both viral replication and inflammation of the lung. We have previously investigated the therapeutic efficacy of recombinant human catalase (rhCAT) against viral pneumonia in mice, but the protection mechanisms involved were not explored. In the present study, we have performed a more in-depth analysis covering survival, lung inflammation, immune cell responses, production of cytokines, and inflammation signaling pathways in mice. Male imprinting control region mice were infected intranasally with high pathogenicity (H1N1) influenza A virus followed by treatment with recombinant human catalase. The administration of rhCAT resulted in a significant reduction in inflammatory cell infiltration (e.g., macrophages and neutrophils), inflammatory cytokine levels (e.g., IL-2, IL-6, TNF-α, IFN-γ), the level of the intercellular adhesion molecule 1 chemokine and the mRNA levels of toll-like receptors TLR-4, TLR-7, and NF-κB, as well as partially maintaining the activity of the antioxidant enzymes system. These findings indicated that rhCAT might play a key protective role in viral pneumonia of mice via suppression of inflammatory immune responses.\",\n \"corpus_id\": 12963207,\n \"score\": 1\n },\n {\n \"doc_id\": \"24509810\",\n \"title\": \"Pretreatment of mice with oligonucleotide prop5 protects them from influenza virus infections.\",\n \"abstract\": \"Influenza A virus is a successful parasite and requires host factors to complete its life cycle. Prop5 is an antisense oligonucleotide, targeting programmed cell death protein 5 (PDCD5). In this study, we tested the antiviral activity of prop5 against mouse-adapted A/FM/1/47 strain of influenza A virus in a mouse model. Prop5 intranasally administered the mice at dosages of 10 and 20 mg/kg/d at 24 h and 30 min before infection, provided 80% and 100% survival rates and prolonged mean survival days in comparison with influenza virus-infected mice (both p < 0.01). Moreover, viral titres in mice pretreated with prop5, at dose of 10 and 20 mg/kg/d, had declined significantly on day two, four, and six post-infection compared with the yields in infected mice (p < 0.05 or p < 0.01); lung index in mice pretreated with prop5 (20 mg/kg/d) had been inhibited on day six post-infection (p < 0.05). Western blotting and immunohistochemistry showed that prop5 could down-regulate the PDCD5 protein expression levels in lung tissues of infected mice. These data indicate that antisense oligonucleotide prop5 is a promising drug for prophylaxis and control influenza virus infections and provides an insight into the host-pathogen interaction.\",\n \"corpus_id\": 14021146,\n \"score\": 1\n },\n {\n \"doc_id\": \"24676773\",\n \"title\": \"Protective effect of fluvastatin on influenza virus infection.\",\n \"abstract\": \"Statins are 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors and have pleiotropic effects. It has been suggested that statins may be a potential treatment during the next influenza pandemic. In a previous study we found that a statin/caffeine combination protects BALB/c mice against Influenza A, subtypes haemagglutinin type 5 and neuraminidase type 1 (H5N1), H3N2 and H1N1 infection. The effect of statins alone on influenza virus infection, however, is not known. In this study, it was investigated whether fluvastatin is capable of inhibiting influenza A virus replication in vitro. The results demonstrated that the synthesis of viral RNA and protein was affected by fluvastatin treatment. Virus production was markedly reduced when fluvastatin was administered simultaneously with the virus; however, a greater inhibition was observed when fluvastatin was added following viral adsorption. The selectivity index [SI; 50% cytotoxic concentration (CC50)/50% inhibition concentration (IC50)], however, was only 21. It was further demonstrated that fluvastatin protects host cells against influenza-induced inflammation by reducing the production of tumour necrosis factor-α, interleukin 8 and interferon γ. In conclusion, the results demonstrated that fluvastatin exerted a minor inhibitory effect on influenza virus infection, which involved anti-inflammatory activities.\",\n \"corpus_id\": 25942052,\n \"score\": 1\n },\n {\n \"doc_id\": \"24725777\",\n \"title\": \"Pulmonary immune responses to 2009 pandemic influenza A (H1N1) virus in mice.\",\n \"abstract\": \"BACKGROUND: Well-characterized mice models will afford a cheaper, easy-handling opportunity for a more comprehensive understanding of 2009 influenza A (H1N1) virus's pathogenesis potential. We aimed to provide a robust description of pulmonary immune responses in the mice infected by the virus. METHODS: BALB/c mice were inoculated intranasally with A/Beijing/501/2009(H1N1) (BJ501) and A/PR/8/34(H1N1) (PR8) viruses and compared for survival rate, viral replication, and kinetics of pulmonary immune responses. RESULTS: BJ501 virus replicated less efficiently in the lungs than PR8, and both caused lethal illness in the mice. The transient increases of pulmonary TNF-α 2 days post infection for BJ501 and of INF-γ and IL-10 at 6 days post infection for PR8 were observed. IL-2+ and IL-4+ secreting cells showed significant increase 12 days post infection, while IFN-γ+, IgG+ and IgA+ secreting cells increased 6 days post infection. The different patterns of pulmonary immunological parameters between two viruses were at most seen in IL-6, IL-17 secretion and IgG1/IgG2a ratio. CONCLUSIONS: The BALB/c mouse is evaluated as a good pathogenic model for studying BJ501 2009 H1N1 virus. The work provided some basic and detailed data, which might be referred when further evaluating innate and adapted pulmonary immune responses and local viral load in mice.\",\n \"corpus_id\": 1014640,\n \"score\": 1\n },\n {\n \"doc_id\": \"24774068\",\n \"title\": \"Bovine colostrum enhances natural killer cell activity and immune response in a mouse model of influenza infection and mediates intestinal immunity through toll-like receptors 2 and 4.\",\n \"abstract\": \"Oral administration of bovine colostrum affects intestinal immunity, including an increased percentage of natural killer (NK) cells. However, effects on NK cell cytotoxic activity and resistance to infection as well as a potential mechanism remain unclear. Therefore, we investigated the effects of bovine colostrum (La Belle, Inc, Bellingham, WA) on the NK cytotoxic response to influenza infection and on toll-like receptor (TLR) activity in a primary intestinal epithelial cell culture. We hypothesized that colostrum would increase NK cell activity and that TLR-2 and TLR-4 blocking would reduce interleukin 6 production by epithelial cells in response to contact stimulation with colostrum. Four-month-old female C57BL/6 mice were supplemented with 1 g of colostrum per kilogram of body weight before and after infection with influenza A virus (H1N1). Animals were assessed for weight loss, splenic NK cell activity, and lung virus titers. Colostrum-supplemented mice demonstrated less reduction in body weight after influenza infection, indicating a less severe infection, increased NK cell cytotoxicity, and less virus burden in the lungs compared with controls. Colostrum supplementation enhanced NK cell cytotoxicity and improved the immune response to primary influenza virus infection in mice. To investigate a potential mechanism, a primary culture of small intestine epithelial cells was then stimulated with colostrum. Direct activation of epithelial cells resulted in increased interleukin 6 production, which was inhibited with TLR-2 and TLR-4 blocking antibodies. The interaction between colostrum and immunity may be dependent, in part, on the interaction of colostrum components with innate receptors at the intestinal epithelium, including TLR-2 and TLR-4.\",\n \"corpus_id\": 45561707,\n \"score\": 1\n },\n {\n \"doc_id\": \"25400245\",\n \"title\": \"Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model.\",\n \"abstract\": \"Bifidobacterium, one of the major components of intestinal microflora, shows anti-influenza virus (IFV) potential as a probiotic, partly through enhancement of innate immunity by modulation of the intestinal immune system. Bifidobacterium longum MM-2 (MM-2), a very safe bacterium in humans, was isolated from healthy humans and its protective effect against IFV infection in a murine model shown. In mice that were intranasally inoculated with IFV, oral administration of MM-2 for 17 consecutive days improved clinical symptoms, reduced mortality, suppressed inflammation in the lower respiratory tract, and decreased virus titers, cell death, and pro-inflammatory cytokines such as IL-6 and TNF-α in bronchoalveolar lavage fluid. The anti-IFV mechanism of MM-2 involves innate immunity through significant increases in NK cell activities in the lungs and spleen and a significant increase in pulmonary gene expression of NK cell activators such as IFN-γ, IL-2, IL-12 and IL-18. Even in non-infected mice, MM-2 administration also induced significant enhancement of both IFN-γ production by Peyer's patch cells (PPs) and splenetic NK cell activity. Oral administration of MM-2 for 17 days activates systemic immunoreactivity in PPs, which contributes to innate immunity, including NK cell activation, resulting in an anti-IFV effect. MM-2 as a probiotic may function as a prophylactic agent in the management of an IFV epidemic.\",\n \"corpus_id\": 25087026,\n \"score\": 1\n },\n {\n \"doc_id\": \"25422494\",\n \"title\": \"Cytomegalovirus generates long-lived antigen-specific NK cells with diminished bystander activation to heterologous infection.\",\n \"abstract\": \"Natural killer (NK) cells play a key role in the host response to cytomegalovirus (CMV) and can mediate an enhanced response to secondary challenge with CMV. We assessed the ability of mouse CMV (MCMV)-induced memory Ly49H(+) NK cells to respond to challenges with influenza, an acute viral infection localized to the lung, and Listeria monocytogenes, a systemic bacterial infection. MCMV-memory NK cells did not display enhanced activation or proliferation after infection with influenza or Listeria, as compared with naive Ly49H(+) or Ly49H(-) NK cells. Memory NK cells also showed impaired activation compared with naive cells when challenged with a mutant MCMV lacking m157, highlighting their antigen-specific response. Ex vivo, MCMV-memory NK cells displayed reduced phosphorylation of STAT4 and STAT1 in response to stimulation by IL-12 and type I interferon (IFN), respectively, and IFN-γ production was reduced in response to IL-12 + IL-18 compared with naive NK cells. However, costimulation of MCMV-memory NK cells with IL-12 and m157 antigen rescues their impaired response compared with cytokines alone. These findings reveal that MCMV-primed memory NK cells are diminished in their response to cytokine-driven bystander responses to heterologous infections as they become specialized and antigen-specific for the control of MCMV upon rechallenge.\",\n \"corpus_id\": 18341735,\n \"score\": 1\n },\n {\n \"doc_id\": \"26437715\",\n \"title\": \"Intranasal administration of poly-gamma glutamate induced antiviral activity and protective immune responses against H1N1 influenza A virus infection.\",\n \"abstract\": \"BACKGROUND: The global outbreak of a novel swine-origin strain of the 2009 H1N1 influenza A virus and the sudden, worldwide increase in oseltamivir-resistant H1N1 influenza A viruses highlight the urgent need for novel antiviral therapy. METHODS: Here, we investigated the antiviral efficacy of poly-gamma glutamate (γ-PGA), a safe and edible biomaterial that is naturally synthesized by Bacillus subtilis, against A/Puerto Rico/8/1934 (PR8) and A/California/04/2009 (CA04) H1N1 influenza A virus infections in C57BL/6 mice. RESULTS: Intranasal administration of γ-PGA for 5 days post-infection improved survival, increased production of antiviral cytokines including interferon-beta (IFN-β) and interleukin-12 (IL-12), and enhanced activation of natural killer (NK) cells and influenza antigen-specific cytotoxic T lymphocytes (CTL) activity. CONCLUSIONS: These results suggest that γ-PGA protects mice against H1N1 influenza A virus by enhancing antiviral immune responses.\",\n \"corpus_id\": 8002821,\n \"score\": 1\n },\n {\n \"doc_id\": \"28031334\",\n \"title\": \"Respiratory Influenza Virus Infection Induces Memory-like Liver NK Cells in Mice.\",\n \"abstract\": \"Although NK cells are classified as innate immune cells, recent studies have demonstrated the transformation of NK cells into long-lived memory cells that contribute to secondary immune responses in certain mouse models. However, whether NK cells mount an Ag-specific memory response to acute influenza virus infection has not yet been examined. Here, we show that, consistent with previous studies, lung NK cells play an important role in controlling viral proliferation after primary influenza virus infection. However, although lung NK cells display a memory phenotype at the late stage of infection, these cells do not protect mice against secondary influenza virus infection. Interestingly, liver NK cells from influenza virus-infected mice possess a memory phenotype and protect mice against secondary influenza virus infection. Memory-like liver NK cells display a CD49a(+)DX5(-) phenotype, and the adoptive transfer of purified liver CD49a(+)DX5(-) NK cells into naive mice followed by viral infection results in protective immunity and decreased viral titer. Moreover, we demonstrate that primary inactivated influenza virus induces memory NK cells residing in the liver of Rag1(-/-) mice. Collectively, these data suggest that liver CD49a(+)DX5(-) NK cells remember encountered Ag from influenza virus after primary infection and are more protective upon subsequent infection.\",\n \"corpus_id\": 19765445,\n \"score\": 1\n },\n {\n \"doc_id\": \"28865477\",\n \"title\": \"RIG-I overexpression decreases mortality of cigarette smoke exposed mice during influenza A virus infection.\",\n \"abstract\": \"BACKGROUND: Retinoic acid-inducible gene I (RIG-I) is an important regulator of virus-induced antiviral interferons (IFNs) and proinflammatory cytokines which participate in clearing viral infections. Cigarette smoke (CS) exposure increases the frequency and severity of respiratory tract infections. METHODS: We generated a RIG-I transgenic (TG) mouse strain that expresses the RIG-I gene product under the control of the human lung specific surfactant protein C promoter. We compared the mortality and host immune responses of RIG-I TG mice and their litter-matched wild type (WT) mice following challenge with influenza A virus (IAV). RESULTS: RIG-I overexpression increased survival of IAV-infected mice. CS exposure increased mortality in WT mice infected with IAV. Remarkably, the effect of RIG-I overexpression on survival during IAV infection was enhanced in CS-exposed animals. CS-exposed IAV-infected WT mice had a suppressed innate response profile in the lung compared to sham-exposed IAV-infected WT mice in terms of the protein concentration, total cell count and inflammatory cell composition in the bronchoalveolar lavage fluid. RIG-I overexpression restored the innate immune response in CS-exposed mice to that seen in sham-exposed WT mice during IAV infection, and is likely responsible for enhanced survival in RIG-I TG mice as restoration preceded death of the animals. CONCLUSIONS: Our results demonstrate that RIG-I overexpression in mice is protective for CS enhanced susceptibility of smokers to influenza infection, and that CS mediated RIG-I suppression may be partially responsible for the increased morbidity and mortality of the mice exposed to IAV. Thus, optimizing the RIG-I response may be an important treatment strategy for CS-enhanced lung infections, particularly those due to IAV.\",\n \"corpus_id\": 8485639,\n \"score\": 1\n },\n {\n \"doc_id\": \"23189830\",\n \"title\": \"[Analysis of the application of host innate immune response to control and prevent infection].\",\n \"abstract\": \"The baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) has been widely used not only to achieve a high level of foreign gene expression in insect cells but also for efficient gene transduction into mammalian cells without any replication. In addition to the efficient gene delivery, baculovirus has been shown to induce host innate immune responses in various mammalian cells and in mice. The baculovirus has abundant CpG motifs in the viral genome and is capable of inducing pro-inflammatory cytokines and interferons (IFNs) through Toll-like receptor (TLR)-dependent and -independent signaling pathways in a cell-type-specific manner. The cytoplasmic helicase proteins RIG-I (retinoic-acid-inducible protein I) and MDA5 (melanoma-differentiation-associated gene 5) have been identified as viral dsRNA detectors and the adaptor IPS-1 (IFN-beta promoter stimulator-1) interacts with RIG-I and MDA5 to facilitate type-I IFN production mediated interferon regulatory factor 3 (IRF3) and 7 (IRF7). These helicases and IPS-1, however, were not essential for the type-I IFN and inflammatory cytokine responses to baculovirus. The baculovirus also has a strong adjuvant activity, and recombinant baculoviruses encoding neutralization epitopes elicit protective immunity in mice. This review deals with the current status of our knowledge of the induction of host innate immune responses by baculovirus and discusses the future prospects for baculovirus vectors.\",\n \"corpus_id\": 29176319,\n \"score\": 0\n },\n {\n \"doc_id\": \"23627014\",\n \"title\": \"[Prior infected influenza virus could protect mice from challenge of lethal influenza virus].\",\n \"abstract\": \"OBJECTIVE: To determine whether it could protect mice from challenge of lethal influenza virus which group prior infected A(H1N1) pdm09 and H9N2 virus respectively. METHODS: 150 BALB/c mice are divided into three groups. Mice are infected A(H1N1) pdm09 virus (pCA07) and poultry H9N2 virus (GZ333) respectively. Infected mice are challenged with 10 times of lethal dose virus (PR8) then compare the viral load, antibody and survival of the two group mice before and after challenged. RESULTS: Both experimental group mice survived after challenge of lethal influenza virus and lung viral load are lower than that of the first infection. Antibodies derived from the infective virus and challenge virus. CONCLUSION: Prior infected A(H1N1) pdm09 and H9N2 virus could protect mice from challenge of lethal influenza virus.\",\n \"corpus_id\": 41469081,\n \"score\": 0\n },\n {\n \"doc_id\": \"27354005\",\n \"title\": \"Cyclophilin A protects mice against infection by influenza A virus.\",\n \"abstract\": \"Our previous studies indicate that Cyclophilin A (CypA) impairs the replication of influenza A virus in vitro. To further evaluate the antiviral functions of CypA and explore its mechanism, transgenic mice with overexpression of CypA by two specific promoters with SPC (CypA-SPC) or CMV (CypA-CMV) were developed. After challenge with the A/WSN/33(H1N1) influenza virus, CypA-SPC and CypA-CMV transgenic mice displayed nearly 2.5- and 3.8-fold stronger disease resistance to virus infection, respectively, compared to wild-type animals. Virus replication, pathological lesions and inflammatory cytokines were substantially reduced in both lines of transgenic mice. In addition, after infection there was an upregulation of genes associated with cell migration, immune function, and organ development; and a downregulation of genes associated with the positive regulation of immune cells and apoptosis in the peritoneal macrophages of CypA-overexpressing transgenic mice (CypA+). These results indicate that CypA is a key modulator of influenza virus resistance in mice, and that CypA+ mice constitutes an important model to study the roles of CypA in the regulation of immune responses and infections.\",\n \"corpus_id\": 8155910,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":85,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24862879\",\n \"title\": \"A novel P700 redox kinetics probe for rapid, non-intrusive and whole-tissue determination of photosystem II functionality, and the stoichiometry of the two photosystems in vivo.\",\n \"abstract\": \"We sought a rapid, non-intrusive, whole-tissue measure of the functional photosystem II (PS II) content in leaves. Summation of electrons, delivered by a single-turnover flash to P700(+) (oxidized PS I primary donor) in continuous background far-red light, gave a parameter S in absorbance units after taking into account an experimentally determined basal electron flux that affects P700 redox kinetics. S was linearly correlated with the functional PS II content measured by the O(2) yield per single-turnover repetitive flash in Arabidopsis thaliana expressing an antisense construct to the PsbO (manganese-stabilizing protein in PS II) proteins of PS II (PsbO mutants). The ratio of S to z(max) (total PS I content in absorbance units) was comparable to the PS II/PS I reaction-center ratio in wild-type A. thaliana and in control Spinacea oleracea. Both S and S/z(max) decreased in photoinhibited spinach leaf discs. The whole-tissue functional PS II content and the PS II/photosystem I (PS I) ratio can be non-intrusively monitored by S and S/z(max), respectively, using a quick P700 absorbance protocol compatible with modern P700 instruments.\",\n \"corpus_id\": 38948168\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18251867","title":"A rapid, whole-tissue determination of the functional fraction of PSII after photoinhibition of leaves based on flash-induced P700 redox kinetics.","abstract":"Assaying the number of functional PSII complexes by the oxygen yield from leaf tissue per saturating, single-turnover flash, assuming that each functional PSII evolves one oxygen molecule after four flashes, is one of the most direct methods but time-consuming. The ratio of variable to maximum Chl fluorescence yield (F(v)/F(m)) in leaves can be correlated with the oxygen yield per flash during a progressive loss of PSII activity associated with high-light stress and is rapid and non-intrusive, but suffers from being representative of chloroplasts near the measured leaf surface; consequently, the exact correlation depends on the internal leaf structure and on which leaf surface is being measured. Our results show that the average F(v)/F(m) of the adaxial and abaxial surfaces has a reasonable linear correlation with the oxygen yield per flash after varied extents of photoinactivation of PSII. However, we obtained an even better linear correlation between (1) the integrated, transient electron flow (Sigma) to P700+, the dimeric Chl cation in PSI, after superimposing a single-turnover flash on steady background far-red light and (2) the relative oxygen yield per flash. Leaves of C3 and C4 plants, woody and herbaceous species, wild-type and a Chl-b-less mutant, and monocot and dicot plants gave a single straight line, which seems to be a universal relation for predicting the relative oxygen yield per flash from Sigma. Measurement of Sigma is non-intrusive, representative of the whole leaf tissue, rapid and applicable to attached leaves; it may even be applicable in the field.","corpus_id":36144041,"score":2},{"doc_id":"19495738","title":"Novel effects of methyl viologen on photosystem II function in spinach leaves.","abstract":"Methyl viologen (MV) is a well-known electron mediator that works on the acceptor side of photosystem I. We investigated the little-known, MV-induced inhibition of linear electron flow through photosystem II (PS II) in spinach-leaf discs. Even a low [MV] decreased the (1) average, light-adapted photochemical efficiency of PS II traps, (2) oxidation state of the primary quinone acceptor Q(A) in PS II during illumination, (3) photochemical efficiency of light-adapted open PS II traps, (4) fraction of absorbed light energy dissipated constitutively in a light-independent manner or as chlorophyll (Chl) a fluorescence emission, (5) Chl a fluorescence yield corresponding to dark-adapted open reaction-center traps (F (o)) and closed reaction-center traps (F (m)), and (6) half-time for re-oxidation of Q (A) (-) in PS II after a single-turnover flash. These effects suggest that the presence of MV accelerates various \"downhill\" electron-transfer steps in PS II. Therefore, when using the MV to quantify cyclic electron flow, the inhibitory effect of MV on PS II should be taken into account.","corpus_id":39063567,"score":2},{"doc_id":"20039131","title":"Fast cyclic electron transport around photosystem I in leaves under far-red light: a proton-uncoupled pathway?","abstract":"Fast cyclic electron transport (CET) around photosystem I (PS I) was observed in sunflower (Helianthus annuus L.) leaves under intense far-red light (FRL) of up to 200 mumol quanta m(-2) s(-1). The electron transport rate (ETR) through PS I was found from the FRL-dark transmittance change at 810 and 950 nm, which was deconvoluted into redox states and pool sizes of P700, plastocyanin (PC) and cytochrome f (Cyt f). PC and P700 were in redox equilibrium with K(e) = 35 (ΔE(m) = 90 mV). PS II ETR was based on O(2) evolution. CET [(PS I ETR) - (PS II ETR)] increased to 50-70 mumol e(-) m(-2) s(-1) when linear electron transport (LET) under FRL was limited to 5 mumol e(-) m(-2) s(-1) in a gas phase containing 20-40 mumol CO(2) mol(-1) and 20 mumol O(2) mol(-1). Under these conditions, pulse-saturated fluorescence yield F(m) was non-photochemically quenched; however, F(m) was similarly quenched when LET was driven by low green or white light, which energetically precluded the possibility for active CET. We suggest that under FRL, CET is rather not coupled to transmembrane proton translocation than the CET-coupled protons are short-circuited via proton channels regulated to open at high ΔpH. A kinetic analysis of CET electron donors and acceptors suggests the CET pathway is that of the reversed Q-cycle: Fd -> (FNR) -> Cyt c(n) -> Cyt b(h) -> Cyt b(l) -> Rieske FeS -> Cyt f -> PC -> P700 ->-> Fd. CET is activated when PQH(2) oxidation is opposed by high ΔpH, and ferredoxin (Fd) is reduced due to low availability of e(-) acceptors. The physiological significance of CET may be photoprotective, as CET may be regarded as a mechanism of energy dissipation under stress conditions.","corpus_id":24601177,"score":2},{"doc_id":"20359461","title":"Photoelectrochemical control of the balance between cyclic- and linear electron transport in photosystem I. Algorithm for P700+ induction kinetics.","abstract":"Redox transients of chlorophyll P700, monitored as absorbance changes DeltaA810, were measured during and after exclusive PSI excitation with far-red (FR) light in pea (Pisum sativum, cv. Premium) leaves under various pre-excitation conditions. Prolonged adaptation in the dark terminated by a short PSII+PSI- exciting light pulse guarantees pre-conditions in which the initial photochemical events in PSI RCs are carried out by cyclic electron transfer (CET). Pre-excitation with one or more 10s FR pulses creates conditions for induction of linear electron transport (LET). These converse conditions give rise to totally different, but reproducible responses of P700- oxidation. System analyses of these responses were made based on quantitative solutions of the rate equations dictated by the associated reaction scheme for each of the relevant conditions. These provide the mathematical elements of the P700 induction algorithm (PIA) with which the distinguishable components of the P700+ response can be resolved and interpreted. It enables amongst others the interpretation and understanding of the characteristic kinetic profile of the P700+ response in intact leaves upon 10s illumination with far-red light under the promotive condition for CET. The system analysis provides evidence that this unique kinetic pattern with a non-responsive delay followed by a steep S-shaped signal increase is caused by a photoelectrochemically controlled suppression of the electron transport from Fd to the PQ-reducing Qr site of the cytb6f complex in the cyclic pathway. The photoelectrochemical control is exerted by the PSI-powered proton pump associated with CET. It shows strong similarities with the photoelectrochemical control of LET at the acceptor side of PSII which is reflected by release of photoelectrochemical quenching of chlorophyll a fluorescence.","corpus_id":10773023,"score":2},{"doc_id":"22638914","title":"Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments: approaches and approximations.","abstract":"Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. ( 1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. ( 2) The gross O(2) yield per single-turnover flash in CO(2)-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O(2) molecule after four flashes. However, the gross O(2) yield per single-turnover flash (multiplied by four) could over-estimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. ( 3) The cumulative delivery of electrons from PS II to P700(+) (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field.","corpus_id":16079792,"score":2},{"doc_id":"23589088","title":"Whole-tissue determination of the rate coefficients of photoinactivation and repair of photosystem II in cotton leaf discs based on flash-induced P700 redox kinetics.","abstract":"Using radioactively labelled amino acids to investigate repair of photoinactivated photosystem II (PS II) gives only a relative rate of repair, while using chlorophyll fluorescence parameters yields a repair rate coefficient for an undefined, variable location within the leaf tissue. Here, we report on a whole-tissue determination of the rate coefficient of photoinactivation k i , and that of repair k r in cotton leaf discs. The method assays functional PS II via a P700 kinetics area associated with PS I, as induced by a single-turnover, saturating flash superimposed on continuous background far-red light. The P700 kinetics area, directly proportional to the oxygen yield per single-turnover, saturating flash, was used to obtain both k i and k r . The value of k i , directly proportional to irradiance, was slightly higher when CO2 diffusion into the abaxial surface (richer in stomata) was blocked by contact with water. The value of k r , sizable in darkness, changed in the light depending on which surface was blocked by contact with water. When the abaxial surface was blocked, k r first peaked at moderate irradiance and then decreased at high irradiance. When the adaxial surface was blocked, k r first increased at low irradiance, then plateaued, before increasing markedly at high irradiance. At the highest irradiance, k r differed by an order of magnitude between the two orientations, attributable to different extents of oxidative stress affecting repair (Nishiyama et al., EMBO J 20: 5587-5594, 2001). The method is a whole-tissue, convenient determination of the rate coefficient of photoinactivation k i and that of repair k r .","corpus_id":18234197,"score":2},{"doc_id":"26297354","title":"Multiple roles of oxygen in the photoinactivation and dynamic repair of Photosystem II in spinach leaves.","abstract":"Oxygen effects have long been ambiguous: exacerbating, being indifferent to, or ameliorating the net photoinactivation of Photosystem II (PS II). We scrutinized the time course of PS II photoinactivation (characterized by rate coefficient k i) in the absence of repair, or when recovery (characterized by k r) occurred simultaneously in CO2 ± O2. Oxygen exacerbated photoinactivation per se, but alleviated it by mediating the utilization of electrons. With repair permitted, the gradual net loss of functional PS II during illumination of leaves was better described phenomenologically by introducing τ, the time for an initial k r to decrease by half. At 1500 μmol photons m(-2) s(-1), oxygen decreased the initial k r but increased τ. Similarly, at even higher irradiance in air, there was a further decrease in the initial k r and increase in τ. These observations are consistent with an empirical model that (1) oxygen increased k i via oxidative stress but decreased it by mediating the utilization of electrons; and (2) reactive oxygen species stimulated the degradation of photodamaged D1 protein in PS II (characterized by k d), but inhibited the de novo synthesis of D1 (characterized by k s), and that the balance between these effects determines the net effect of O2 on PS II functionality.","corpus_id":8616988,"score":2},{"doc_id":"29535751","title":"Cyclic Electron Flow around Photosystem I Promotes ATP Synthesis Possibly Helping the Rapid Repair of Photodamaged Photosystem II at Low Light.","abstract":"In higher plants, moderate photoinhibition of photosystem II (PSII) leads to a stimulation of cyclic electron flow (CEF) at low light, which is accompanied by an increase in the P700 oxidation ratio. However, the specific role of CEF stimulation at low light is not well known. Furthermore, the mechanism underlying this increase in P700 oxidation ratio at low light is unclear. To address these questions, intact leaves of the shade-adapted plant Panax notoginseng were treated at 2258 μmol photons m-2 s-1 for 30 min to induce PSII photoinhibition. Before and after this high-light treatment, PSI and PSII activity, the energy quenching in PSII, the redox state of PSI and proton motive force (pmf) at a low light of 54 μmol photons m-2 s-1 were determined at the steady state. After high-light treatment, electron flow through PSII (ETRII) significantly decreased but CEF was remarkably stimulated. The P700 oxidation ratio significantly increased but non-photochemical quenching changed negligibly. Concomitantly, the total pmf decreased significantly and the proton gradient (ΔpH) across the thylakoid membrane remained stable. Furthermore, the P700 oxidation ratio was negatively correlated with the value of ETRII. These results suggest that upon PSII photoinhibition, CEF is stimulated to increase the ATP synthesis, facilitating the rapid repair of photodamaged PSII. The increase in P700 oxidation ratio at low light cannot be explained by the change in pmf, but is primarily controlled by electron transfer from PSII.","corpus_id":3533046,"score":2},{"doc_id":"18385893","title":"Heat-induced changes in photosystem I activity as measured with different electron donors in isolated spinach thylakoid membranes.","abstract":"Heat-induced changes in photosystem I (PSI) have been studied in terms of rates of oxygen consumption using various donors (DCPIPH2, TMPDred and DADred), formation of photo-oxidized P700 and changes in Chl a fluorescence emission at 77 K. Linear heating of thylakoid membranes from 35 degrees C to 70 degrees C caused an enhancement in PSI-mediated electron transfer rates (DCPIPH2-->MV) up to 55 degrees C. However, no change was observed in PSI rates when other electron donors were used (TMPDred and DADred). Similarly, Chl a fluorescence emission spectra at 77 K of heat-treated thylakoid membranes did not show any increase in peak at 735 nm, however, a significant decrease was observed as a function of temperature in the peaks at 685 and 694 nm. In DCMU-treated control thylakoid membranes maximum photo-oxidized P700 was generated at g = 2.0025. In heat-treated thylakoid membranes maximum intensity of photo-oxidized P700 signal was observed at approximately 50-55 degrees C without DCMU treatment. The steady-state signal of the photo-oxidized P700 was studied in the presence of DCPIPH2 and TMPDred as electron donors in DCMU-treated control and in 50 degrees C treated thylakoid membranes. We present here the first of such comparative study of PSI activity in terms of the rates of oxygen consumption and re-reduction kinetics of photo-oxidized P700 in the presence of different electron donors. It appears that the formation of the P700+ signal in heat-treated thylakoid membranes is due to an inhibited electron supply from PSII and not due to spillover or antenna migration.","corpus_id":36166450,"score":1},{"doc_id":"18426807","title":"Separation of light-induced linear, cyclic and stroma-sourced electron fluxes to P700+ in cucumber leaf discs after pre-illumination at a chilling temperature.","abstract":"Pre-illumination of cucumber leaf discs at 4 degrees C with low-irradiance white light (i) led to a marked decrease in the extent of photo-oxidation of P700 (the special chlorophyll pair in the PSI reaction center) in actinic light at room temperature and (ii) hastened the post-illumination re-reduction of P700+. Quantifying the linear, cyclic and stroma-sourced electron fluxes to P700+ in two actinic light regimes, we found that there was no increase in cyclic or linear electron fluxes to account for these changes. Rather, we observed a decrease in the maximum extent of P700 photo-oxidation assayed by a strong flash superimposed on continuous, background light of wavelength 723 nm, which we interpret to represent a loss of stable charge separation in PSI due to enhanced charge recombination as a result of the pre-illumination treatment. The funneling of electrons towards fewer non-damaged PSI complexes could explain the hastened post-illumination re-reduction of P700+, aided by a slight increase in a stroma-sourced electron flux after prolonged pre-illumination at 4 degrees C. Quantifying the separate fluxes to P700+ helps to elucidate the effects of chilling of cucumber leaf discs in the light and the reasons for the hastened post-illumination re-reduction of P700+.","corpus_id":15565694,"score":1},{"doc_id":"18445472","title":"Competitive inhibition of electron donation to photosystem 1 by metal-substituted plastocyanin.","abstract":"The electron transfer from wild-type spinach plastocyanin (Pc) to photosystem 1 has been studied by flash-induced absorption changes at 830 nm. The decay kinetics of photo-oxidized P700 are drastically slower in the presence of Ag(I)-substituted Pc, while addition of Zn(II)-substituted Pc has a weaker effect. The metal-substituted forms of Pc act as competitive inhibitors of the reaction between normal, Cu-containing, Pc and P700. The inhibition constants obtained from an analysis of the kinetic data were 30 and 410 microM for Ag(I)- and Zn(II)-substituted Pc, respectively. When the Gly8Asp mutant form of Pc was used instead of the wild-type form, the corresponding values were found to be 77 and 442 microM. If the Ag- and Zn-derivatives can be considered as structural mimics of reduced and oxidized CuPc, respectively, our results imply that there is a redox-induced decrease in the affinity between Pc and photosystem 1 that follows the electron donation to P700. Our data also imply that the Gly8Asp mutation can diminish the magnitude of this change. The findings reported here are consistent with a reaction mechanism where the electron transfer in the complex between Pc and photosystem 1 is assumed to be reversible.","corpus_id":24078152,"score":1},{"doc_id":"18563623","title":"Elucidating the site of action of oxalate in photosynthetic electron transport chain in spinach thylakoid membranes.","abstract":"The effects of oxalate on PS II and PS I photochemistry were studied. The results suggested that in chloride-deficient thylakoid membranes, oxalate inhibited activity of PS II as well as PS I. To our knowledge, this is the only anion so far known which inhibits both the photosystems. Measurements of fluorescence induction kinetics, YZ* decay, and S2 state multiline EPR signal suggested that oxalate inhibited PS II at the donor side most likely on the oxygen evolving complex. Measurements of re-reduction of P700+ signal in isolated PS I particles in oxalate-treated samples suggested a binding site of oxalate on the donor, as well as the acceptor side of PS I.","corpus_id":11340623,"score":1},{"doc_id":"18688503","title":"Quantum yield of P700+ photodestruction in isolated photosystem I complexes of the cyanobacterium Arthrospira platensis.","abstract":"The photostability of P700 cation radical (P700+) was studied by evaluating the quantum yields of P700(+) photodestruction in photosystem I (PSI) complexes of the cyanobacterium Arthrospira platensis. The time courses of P700+ photodestruction in PSI trimers and monomers have been measured in aerobic conditions under selective excitation of far-red absorption band of P700+ by intense light of laser diodes. Long-term exposure of PSI complexes to 808 or 870 nm laser light caused destruction of P700+ and antenna chlorophylls. The true integral quantum yield of P700+ photodestruction calculated from these data was less than 0.7-1.4 x 10(-8). Illumination of PSI complexes by 650 nm light caused destruction of antenna chlorophylls with true quantum yield of about 6-7 x 10(-6) and damage of P700 with apparent quantum yield 2-3 x 10(-8). Preferential photodestruction of the long-wavelength antenna chlorophyll absorbing at 710 nm as compared with bulk chlorophylls was observed. About three orders of difference in magnitude between quantum yields of P700+ and bulk chlorophyll photodestruction indicates that P700+ is extremely photostable for functioning as an efficient quencher of singlet excitation energy in PSI.","corpus_id":205707552,"score":1},{"doc_id":"18975133","title":"Reduction of the primary donor P700 of photosystem I during steady-state photosynthesis under low light in Arabidopsis.","abstract":"During steady-state photosynthesis in low-light, 830-nm absorption (A(830)) by leaves was close to that in darkness in Arabidopsis, indicating that the primary donor P700 in the reaction center of photosystem I (PSI) was in reduced form. However, P700 was not fully oxidized by a saturating light pulse, suggesting the presence of a population of PSI centers with reduced P700 that remains thermodynamically stable during the application of the saturating light pulse (i.e., reduced-inactive P700). To substantiate this, the effects of methyl viologen (MV) and far-red light on P700 oxidation by the saturating light pulse were analyzed, and the cumulative effects of repetitive application of the saturating light pulse on photosynthesis were analyzed using a mutant crr2-2 with impaired PSI cyclic electron flow. We concluded that the reduced-inactive P700 in low-light as revealed by saturating light pulse indicates limitations of electron flow at the PSI acceptor side.","corpus_id":723157,"score":1},{"doc_id":"19289096","title":"Functional complementation of the Arabidopsis thaliana psbo1 mutant phenotype with an N-terminally His6-tagged PsbO-1 protein in photosystem II.","abstract":"The Arabidopsis thaliana mutant psbo1 has recently been described and characterized. Loss of expression of the PsbO-1 protein leads to a variety of functional perturbations including elevated levels of the PsbO-2 protein and defects on both the oxidizing- and reducing-sides of Photosystem II. In this communication, two plant lines were produced using the psbo1 mutant as transgenic host, which contained an N-terminally histidine(6)-tagged PsbO-1 protein. This protein was expressed and correctly targeted into the thylakoid lumen. Immunological analysis indicated that different levels of expression of the modified PsbO-1 protein were obtained in different transgenic plant lines and that the level of expression in each line was stable over several generations. Examination of the Photosystem II closure kinetics demonstrated that the defective double reduction of Q(B) and the delayed exchange of Q(B)H(2) with the plastoquinone pool which were observed during the characterization of the psbo1 mutant were effectively restored to wild-type levels by the His(6)-tagged PsbO-1 protein. Flash fluorescence induction and decay were also examined. Our results indicated that high expression of the modified PsbO-1 was required to increase the ratio of PS II(alpha)/PS II(beta) reaction centers to wild-type levels. Fluorescence decay kinetics in the absence of DCMU indicated that the expression of the His(6)-tagged PsbO-1 protein restored efficient electron transfer to Q(B), while in the presence of DCMU, charge recombination between Q(A)(-) and the S(2) state of the oxygen-evolving complex occurred at near wild-type rates. Our results indicate that high expression of the His(6)-tagged PsbO-1 protein efficiently complements nearly all of the photochemical defects observed in the psbo1 mutant. Additionally, this study establishes a platform on which the in vivo consequences of site-directed mutagenesis of the PsbO-1 protein can be examined.","corpus_id":34270486,"score":1},{"doc_id":"19761751","title":"Effect of the P700 pre-oxidation and point mutations near A(0) on the reversibility of the primary charge separation in Photosystem I from Chlamydomonas reinhardtii.","abstract":"Time-resolved fluorescence studies with a 3-ps temporal resolution were performed in order to: (1) test the recent model of the reversible primary charge separation in Photosystem I (Müller et al., 2003; Holwzwarth et al., 2005, 2006), and (2) to reconcile this model with a mechanism of excitation energy quenching by closed Photosystem I (with P700 pre-oxidized to P700+). For these purposes, we performed experiments using Photosystem I core samples isolated from Chlamydomonas reinhardtii wild type, and two mutants in which the methionine axial ligand to primary electron acceptor, A(0), has been change to either histidine or serine. The temporal evolution of fluorescence spectra was recorded for each preparation under conditions where the \"primary electron donor,\" P700, was either neutral or chemically pre-oxidized to P700+. For all the preparations under study, and under neutral and oxidizing conditions, we observed multiexponential fluorescence decay with the major phases of approximately 7 ps and approximately 25 ps. The relative amplitudes and, to a minor extent the lifetimes, of these two phases were modulated by the redox state of P700 and by the mutations near A(0): both pre-oxidation of P700 and mutations caused slight deceleration of the excited state decay. These results are consistent with a model in which P700 is not the primary electron donor, but rather a secondary electron donor, with the primary charge separation event occurring between the accessory chlorophyll, A, and A(0). We assign the faster phase to the equilibration process between the excited state of the antenna/reaction center ensemble and the primary radical pair, and the slower phase to the secondary electron transfer reaction. The pre-oxidation of P700 shifts the equilibrium between the excited state and the primary radical pair towards the excited state. This shift is proposed to be induced by the presence of the positive charge on P700+. The same charge is proposed to be responsible for the fast A+A(0)(-)-->AA(0) charge recombination to the ground state and, in consequence, excitation quenching in closed reaction centers. Mutations of the A(0) axial ligand shift the equilibrium in the same direction as pre-oxidation of P700 due to the up-shift of the free energy level of the state A+A(0)(-).","corpus_id":205795038,"score":1},{"doc_id":"20480090","title":"Evidence that pH can drive state transitions in isolated thylakoid membranes from spinach.","abstract":"Our observation that the F735/F685 ratio at 77 K increased when the lumenal pH decreased led us to investigate the role of pH in explaining the mechanism of state transitions in spinach (Spinacea oleracea L.) thylakoid membranes. As the lumenal pH was changed from pH 7.5 to 5.5, the quantum yield of PS II decreased, while that of PS I increased. In the presence of an uncoupler, NH(4)Cl, which sequesters protons, a reversal of the effects observed at pH 5.5 were noticed. The thylakoid membranes treated with NaF at pH 5.5, when suspended in a buffer of pH 7.5, showed enhanced PS II fluorescence and a decreased PS I fluorescence, suggesting migration of LHC II back to PS II from PS I. The results presented here suggest for the first time that the lumenal pH of thylakoid membranes regulates the migration of antenna, and hence the energy distribution, between the two photosystems, i.e. a low lumenal pH (pH 5.5) favors antenna migration from PS II to PS I. At pH 7.5, the deprotonation of LHC II antenna attached to PS I leads to back migration of LHC II to PS II.","corpus_id":13539122,"score":1},{"doc_id":"20643811","title":"Short flashes and continuous light have similar photoinhibitory efficiency in intact leaves.","abstract":"Lincomycin-treated pumpkin leaves were illuminated with either continuous light or saturating single-turnover xenon flashes to study the dependence of photoinactivation of photosystem II (PSII) on the mode of delivery of light. The flash energy and the time interval between the flashes were varied between the experiments, and photoinactivation was measured with oxygen evolution and the ratio of variable to maximum fluorescence (F(v)/F(m)). The photoinhibitory efficiency of saturating xenon flashes was found to be directly proportional to flash energy and independent of the time interval between the flashes. These findings indicate that a low-light-specific mechanism, based on charge recombination between PSII electron acceptors and the oxygen-evolving complex, is not the main cause of photoinactivation caused by short flashes in vivo. Furthermore, the relationship between the rate constant of photoinactivation and photon flux density was similar for flashes and continuous light when F(v)/F(m) was used to quantify photoinactivation, suggesting that continuous-light photoinactivation has a mechanism in which the quantum yield does not depend on the mode of delivery of light. A similar quantum yield of photoinhibition for flashes and continuous light is compatible with the manganese-based photoinhibition mechanism and with mechanisms in which singlet oxygen, produced via a direct photosensitization reaction, is the agent of damage. However, the classical acceptor-side and donor-side mechanisms do not predict a similar quantum yield for flashes and continuous light.","corpus_id":100069,"score":1},{"doc_id":"20705115","title":"Computational analysis of fluorescence induction curves in intact spinach leaves treated at different pH.","abstract":"Effects of change in pH have been investigated on spinach leaf discs by measuring fluorescence induction kinetics using plant efficiency analyzer (PEA). On the basis of computational analysis of the results, we have reported that acidic pH causes a significant inhibition of the donor and the acceptor side of PS II. Energy flux models have been presented using the software Biolyzer HP 3. Effects of pH were investigated on the antenna size heterogeneity of PS II and a relative change in the proportions of α, β, and γ centers was observed.","corpus_id":39301839,"score":1},{"doc_id":"20951762","title":"PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies.","abstract":"Our recently presented PS II model (Belyaeva et al., 2008) was improved in order to permit a consistent simulation of Single Flash Induced Transient Fluorescence Yield (SFITFY) traces that were earlier measured by Steffen et al. (2005) on whole leaves of Arabidopsis (A.) thaliana at four different energies of the actinic flash. As the essential modification, the shape of the actinic flash was explicitly taken into account assuming that an exponentially decaying rate simulates the time dependent excitation of PS II by the 10 ns actinic flash. The maximum amplitude of this excitation exceeds that of the measuring light by 9 orders of magnitude. A very good fit of the SFITFY data was achieved in the time domain from 100 ns to 10s for all actinic flash energies (the maximum energy of 7.5 × 10¹⁶ photons/(cm²flash) is set to 100%, the relative energies of weaker actinic flashes were of ∼8%, 4%, ∼1%). Our model allows the calculation and visualization of the transient PS II redox state populations ranging from the dark adapted state, via excitation energy and electron transfer steps induced by pulse excitation, followed by final relaxation into the stationary state eventually attained under the measuring light. It turned out that the rate constants of electron transfer steps are invariant to intensity of the actinic laser flash. In marked contrast, an increase of the actinic flash energy by more than two orders of magnitude from 5.4×10¹⁴ photons/(cm²flash) to 7.5×10¹⁶ photons/(cm²flash), leads to an increase of the extent of fluorescence quenching due to carotenoid triplet (³Car) formation by a factor of 14 and of the recombination reaction between reduced primary pheophytin (Phe(-)) and P680(+) by a factor of 3 while the heat dissipation in the antenna complex remains virtually constant. The modified PS II model offers new opportunities to compare electron transfer and dissipative parameters for different species (e.g. for the green algae and the higher plant) under varying illumination conditions.","corpus_id":10270339,"score":1},{"doc_id":"21238459","title":"Structural investigation of PsbO from plant and cyanobacterial photosystem II.","abstract":"The manganese-stabilizing protein PsbO is associated with the luminal side of thylakoids close to the redox-active Mn(4)Ca cluster at the catalytically active site of photosystem II (PSII). PsbO is believed to increase the efficiency of oxygen evolution and to stabilize the Mn(4)Ca cluster against photoinhibition. Using small-angle X-ray scattering, we investigated the low-resolution structure of wild-type spinach PsbO and that of chimeric spinach PsbO fused with maltose-binding protein. Small-angle X-ray scattering data revealed that both proteins are monomeric in solution, and that plant and cyanobacterial PsbO have similar structures. We show a highly efficient expression system that allows recombinant production of the active wild type and the chimeric PsbO from spinach and cyanobacteria, with yields compatible with biophysical and structural studies. The binding of spinach PsbO fused with maltose-binding protein to PSII depleted of extrinsic subunits (PSII-ΔpsbO,P,Q) was confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The reconstituted PSII was shown to have similar oxygen evolution rates as obtained with wild-type spinach PsbO.","corpus_id":11610246,"score":1},{"doc_id":"21357184","title":"The physiological role of ascorbate as photosystem II electron donor: protection against photoinactivation in heat-stressed leaves.","abstract":"Previously, we showed that ascorbate (Asc), by donating electrons to photosystem II (PSII), supports a sustained electron transport activity in leaves in which the oxygen-evolving complexes were inactivated with a heat pulse (49°C, 40 s). Here, by using wild-type, Asc-overproducing, and -deficient Arabidopsis (Arabidopsis thaliana) mutants (miox4 and vtc2-3, respectively), we investigated the physiological role of Asc as PSII electron donor in heat-stressed leaves (40°C, 15 min), lacking active oxygen-evolving complexes. Chlorophyll-a fluorescence transients show that in leaves excited with trains of saturating single-turnover flashes spaced 200 ms apart, allowing continual electron donation from Asc to PSII, the reaction centers remained functional even after thousands of turnovers. Higher flash frequencies or continuous illumination (300 μmol photons m(-2) s(-1)) gradually inactivated them, a process that appeared to be initiated by a dramatic deceleration of the electron transfer from Tyr(Z) to P680(+), followed by the complete loss of charge separation activity. These processes occurred with half-times of 1.2 and 10 min, 2.8 and 23 min, and 4.1 and 51 min in vtc2-3, the wild type, and miox4, respectively, indicating that the rate of inactivation strongly depended on the Asc content of the leaves. The recovery of PSII activity, following the degradation of PSII proteins (D1, CP43, and PsbO), in moderate light (100 μmol photons m(-2) s(-1), comparable to growth light), was also retarded in the Asc-deficient mutant. These data show that high Asc content of leaves contributes significantly to the ability of plants to withstand heat-stress conditions.","corpus_id":20815127,"score":1},{"doc_id":"21429906","title":"Species dependence of the redox potential of the primary electron donor p700 in photosystem I of oxygenic photosynthetic organisms revealed by spectroelectrochemistry.","abstract":"The redox potential of the primary electron donor P700, E(m)(P700/P700(+)), of Photosystem I (PSI) has been determined for 10 oxygenic photosynthesis organisms, ranging from cyanobacteria, red algae, green algae to higher plants, by spectroelectrochemistry with an optically transparent thin-layer electrode (OTTLE) cell to elucidate the scattering by as much as 150 mV in reported values of E(m)(P700/P700(+)). The E(m)(P700/P700(+)) values determined within error ranges of ± 1-4 mV exhibited a significant species dependence, with a span >70 mV, from +398 to +470 mV vs. the standard hydrogen electrode (SHE). The E(m)(P700/P700(+)) value appears to change systematically in going from cyanobacteria and primitive eukaryotic red algae, then to green algae and higher plants. From an evolutionary point of view, this result suggests that the species believed to appear later in evolution of photosynthetic organisms exhibit higher values of E(m)(P700/P700(+)). Further, the species dependence of E(m)(P700/P700(+)) seems to originate in the species-dependent redox potentials of soluble metalloproteins, Cyt c(6) and plastocyanin, which re-reduce the oxidized P700 in the electron transfer chain.","corpus_id":21548127,"score":1},{"doc_id":"21546369","title":"Cold stress effects on PSI photochemistry in Zea mays: differential increase of FQR-dependent cyclic electron flow and functional implications.","abstract":"Cold-induced inhibition of CO(2) assimilation in maize (Zea mays L.) is associated with a persistent depression of the photochemical efficiency of PSII. However, very limited information is available on PSI photochemistry and PSI-dependent electron flow in cold-stressed maize. The extent of the absorbance change (ΔA(820)) used for in vivo quantitative estimation of photooxidizable P700(+) indicated a 32% lower steady-state oxidation level of the PSI reaction center P700 (P700(+)) in cold-stressed compared with control maize leaves. This was accompanied by a 2-fold faster re-reduction rate of P700(+) in the dark, indicating a higher capacity for cyclic electron flow (CEF) around PSI in cold-stressed maize leaves. Furthermore, the increased PSI-dependent CEF(s) was associated with a much higher stromal electron pool size and 56% lower capacity for state transitions compared with control plants. To examine NADP(H) dehydrogenase (NDH)- and ferredoxin:plastoquinone oxidoreductase (FQR)-dependent CEF in vivo, the post-illumination transient increase of F(o)' was measured in the presence of electron transport inhibitors. The results indicate that under optimal growth conditions the relatively low CEF in the maize mesophyll cells is mostly due to the NDH-dependent pathway. However, the increased CEF in cold-stressed plants appears to originate from the up-regulated FQR pathway. The physiological role of PSI down-regulation, the increased capacity for CEF and the shift of preferred CEF mode in modulating the photosynthetic electron fluxes and distribution of excitation light energy in maize plants under cold stress conditions are discussed.","corpus_id":10623255,"score":1},{"doc_id":"21777563","title":"Fluorescence of the various red antenna states in photosystem I complexes from cyanobacteria is affected differently by the redox state of P700.","abstract":"Photosystem I of cyanobacteria contains different spectral pools of chlorophylls called red or long-wavelength chlorophylls that absorb at longer wavelengths than the primary electron donor P700. We measured the fluorescence spectra at the ensemble and the single-molecule level at low temperatures in the presence of oxidized and reduced P700. In accordance with the literature, it was observed that the fluorescence is quenched by P700(+). However, the efficiency of the fluorescence quenching by oxidized P700(+) was found to be extremely different for the various red states in PS I from different cyanobacteria. The emission of the longest-wavelength absorbing antenna state in PS I trimers from Thermosynechococcus elongatus (absorption maximum at 5K: ≈ 719nm; emission maximum at 5K: ≈ 740nm) was found to be strongly quenched by P700(+) similar to the reddest state in PS I trimers from Arthrospira platensis emitting at 760nm at 5K. The fluorescence of these red states is diminished by more than a factor of 10 in the presence of oxidized P700. For the first time, the emission of the reddest states in A. platensis and T. elongatus has been monitored using single-molecule fluorescence techniques.","corpus_id":21898417,"score":1},{"doc_id":"21910736","title":"Thermoluminescence and P700 redox kinetics as complementary tools to investigate the cyclic/chlororespiratory electron pathways in stress conditions in barley leaves.","abstract":"Cyclic electron flow around photosystem I drives additional proton pumping into the thylakoid lumen, which enhances the protective non-photochemical quenching and increases ATP synthesis. It involves several pathways activated independently. In whole barley leaves, P700 oxidation under far-red illumination and subsequent P700(+) dark reduction kinetics provide a major probe of the activation of cyclic pathways. Two 'intermediate' and 'slow' exponential reduction phases are always observed and they become faster after high light illumination, but dark inactivation of the Benson-Calvin cycle causes the emergence of both a transient in the P700 oxidation and a 'fast' phase in the P700(+) reduction. We investigate here the afterglow (AG) thermoluminescence emission as another tool to detect the activation of cyclic electron pathways from stroma reductants to the acceptor side of photosystem II. This transfer is activated by warming, yielding an AG band at about 45°C. However, treatments that accelerate the 'intermediate' and 'slow' P700(+) reduction phases (brief anoxia, hexose infiltration, fast dehydration of excised leaves) also produced a downshift of this AG band. This pathway ascribable to NADPH dehydrogenase (NDH) would be triggered by a deficit in ATP, while the 'fast' reduction phase corresponding to the ferredoxin plastoquinone reductase pathway is triggered by an overreduction of the photosystem I acceptor pool and is undetected in thermoluminescence. Contrastingly, slow dehydration of unwatered plants did not cause faster reduction of P700(+) nor temperature downshift of the AG band, that is no induction of the NDH pathway, whereas an increased intensity of the AG band indicated a strong NADPH + ATP assimilatory potential.","corpus_id":26725453,"score":1},{"doc_id":"22644475","title":"The time course of photoinactivation of photosystem II in leaves revisited.","abstract":"Since photosystem II (PS II) performs the demanding function of water oxidation using light energy, it is susceptible to photoinactivation during photosynthesis. The time course of photoinactivation of PS II yields useful information about the process. Depending on how PS II function is assayed, however, the time course seems to differ. Here, we revisit this problem by using two additional assays: (1) the quantum yield of oxygen evolution in limiting, continuous light and (2) the flash-induced cumulative delivery of PS II electrons to the oxidized primary donor (P700(+)) in PS I measured as a 'P700 kinetics area'. The P700 kinetics area is based on the fact that the two photosystems function in series: when P700 is completely photo-oxidized by a flash added to continuous far-red light, electrons delivered from PS II to PS I by the flash tend to re-reduce P700(+) transiently to an extent depending on the PS II functionality, while the far-red light photo-oxidizes P700 back to the steady-state concentration. The quantum yield of oxygen evolution in limiting, continuous light indeed decreased in a way that deviated from a single-negative exponential. However, measurement of the quantum yield of oxygen in limiting light may be complicated by changes in mitochondrial respiration between darkness and limiting light. Similarly, an assay based on chlorophyll fluorescence may be complicated by the varying depth in leaf tissue from which the signal is detected after progressive photoinactivation of PS II. On the other hand, the P700 kinetics area appears to be a reasonable assay, which is a measure of functional PS II in the whole leaf tissue and independent of changes in mitochondrial respiration. The P700 kinetics area decreased in a single-negative exponential fashion during progressive photoinactivation of PS II in a number of plant species, at least at functional PS II contents ≥6 % of the initial value, in agreement with the conclusion of Sarvikas et al. (Photosynth Res 103:7-17, 2010). That is, the single-negative-exponential time course does not provide evidence for photoprotection of functional PS II complexes by photoinactivated, connected neighbours.","corpus_id":13513107,"score":1},{"doc_id":"22922640","title":"Antisense reductions in the PsbO protein of photosystem II leads to decreased quantum yield but similar maximal photosynthetic rates.","abstract":"Photosystem (PS) II is the multisubunit complex which uses light energy to split water, providing the reducing equivalents needed for photosynthesis. The complex is susceptible to damage from environmental stresses such as excess excitation energy and high temperature. This research investigated the in vivo photosynthetic consequences of impairments to PSII in Arabidopsis thaliana (ecotype Columbia) expressing an antisense construct to the PsbO proteins of PSII. Transgenic lines were obtained with between 25 and 60% of wild-type (WT) total PsbO protein content, with the PsbO1 isoform being more strongly reduced than PsbO2. These changes coincided with a decrease in functional PSII content. Low PsbO (less than 50% WT) plants grew more slowly and had lower chlorophyll content per leaf area. There was no change in content per unit area of cytochrome b6f, ATP synthase, or Rubisco, whereas PSI decreased in proportion to the reduction in chlorophyll content. The irradiance response of photosynthetic oxygen evolution showed that low PsbO plants had a reduced quantum yield, but matched the oxygen evolution rates of WT plants at saturating irradiance. It is suggested that these plants had a smaller pool of PSII centres, which are inefficiently connected to antenna pigments resulting in reduced photochemical efficiency.","corpus_id":52837249,"score":1},{"doc_id":"23183256","title":"Excess manganese differentially inhibits photosystem I versus II in Arabidopsis thaliana.","abstract":"The effects of exposure to increasing manganese concentrations (50-1500 µM) from the start of the experiment on the functional performance of photosystem II (PSII) and photosystem I (PSI) and photosynthetic apparatus composition of Arabidopsis thaliana were compared. In agreement with earlier studies, excess Mn caused minimal changes in the PSII photochemical efficiency measured as F(v)/F(m), although the characteristic peak temperature of the S(2/3)Q(B) (-) charge recombinations was shifted to lower temperatures at the highest Mn concentration. SDS-PAGE and immunoblot analyses also did not exhibit any significant change in the relative abundance of PSII-associated polypeptides: PSII reaction centre protein D1, Lhcb1 (major light-harvesting protein of LHCII complex), and PsbO (OEC33, a 33 kDa protein of the oxygen-evolving complex). In addition, the abundance of Rubisco also did not change with Mn treatments. However, plants grown under excess Mn exhibited increased susceptibility to PSII photoinhibition. In contrast, in vivo measurements of the redox transients of PSI reaction centre (P700) showed a considerable gradual decrease in the extent of P700 photooxidation (P700(+)) under increased Mn concentrations compared to control. This was accompanied by a slower rate of P700(+) re-reduction indicating a downregulation of the PSI-dependent cyclic electron flow. The abundance of PSI reaction centre polypeptides (PsaA and PsaB) in plants under the highest Mn concentration was also significantly lower compared to the control. The results demonstrate for the first time that PSI is the major target of Mn toxicity within the photosynthetic apparatus of Arabidopsis plants. The possible involvement mechanisms of Mn toxicity targeting specifically PSI are discussed.","corpus_id":52809861,"score":1},{"doc_id":"23220185","title":"Damage of photosynthetic apparatus in the senescing basal leaf of Arabidopsis thaliana: a plausible mechanism of inactivation of reaction center II.","abstract":"Significant decline in oxygen evolution and DCPIP photoreduction and a marginal restoration of the later with DPC as an electron donor suggest the inactivation of reaction center of photosystem II. The declines in the height of thermoluminescence bands support the view and the damage of reaction center II could be central to the senescence process in Arabidopsis leaves. The enhancement in the number of reduced quinones, signifying a loss in redox homeostasis in the electron transport chain between photosystem II and I leads to the creation of an energy imbalance. The view is supported by the decline in actual quantum yield of photosystem II in the light adapted state and maximum quantum yield of primary photochemistry in the dark adapted state of chlorophyll fluorescence. An increase in chlorophyll a fluorescence polarization and decline in carotenoid to chlorophyll energy transfer efficiency suggest the perturbation in thylakoid structure. A plausible mechanism illustrating the senescence mediated inactivation of oxygen evolving complex has been proposed.","corpus_id":9647929,"score":1},{"doc_id":"23273864","title":"Photoinhibition of Photosystem II.","abstract":"Photoinhibition of Photosystem II (PSII) is the light-induced loss of PSII electron-transfer activity. Although photoinhibition has been studied for a long time, there is no consensus about its mechanism. On one hand, production of singlet oxygen ((1)O(2)) by PSII has promoted models in which this reactive oxygen species (ROS) is considered to act as the agent of photoinhibitory damage. These chemistry-based models have often not taken into account the photophysical features of photoinhibition-like light response and action spectrum. On the other hand, models that reproduce these basic photophysical features of the reaction have not considered the importance of data about ROS. In this chapter, it is shown that the evidence behind the chemistry-based models and the photophysically oriented models can be brought together to build a mechanism that confirms with all types of experimental data. A working hypothesis is proposed, starting with inhibition of the manganese complex by light. Inability of the manganese complex to reduce the primary donor promotes recombination between the oxidized primary donor and Q(A), the first stable quinone acceptor of PSII. (1)O(2) production due to this recombination may inhibit protein synthesis or spread the photoinhibitory damage to another PSII center. The production of (1)O(2) is transient because loss of activity of the oxygen-evolving complex induces an increase in the redox potential of Q(A), which lowers (1)O(2) production.","corpus_id":23331378,"score":1},{"doc_id":"23340737","title":"Probing the picosecond kinetics of the photosystem II core complex in vivo.","abstract":"Photosystems I (PSI) and II (PSII) are two major pigment-protein complexes of photosynthetic organisms that function in series to convert sunlight energy into chemical energy. We have studied the picosecond fluorescence behaviour of the core of both photosystems in vivo by using two Synechocystis PCC 6803 mutants: BE cells contain PSI but are lacking both PSII and the light-harvesting complexes called phycobilisomes (PBs) whereas PAL cells contain both PSI and PSII but lack the PBs. Measurements were performed at room temperature and at 77 K. The fluorescence kinetics of PSI and PSII can nicely be separated, en passant providing the PSI/PSII ratio. At room temperature, the PSI kinetics are identical to those of isolated PSI whereas the PSII kinetics can equally well be described by the in vitro trap-limited model of Y. Miloslavina, M. Szczepaniak, M. G. Muller, J. Sander, M. Nowaczyk, M. Rogner and A. R. Holzwarth, Biophys J., 2009, 96(2), 621-631, and by the transfer-to-the-trap-limited model of C. D. van der Weij-de Wit, J. P. Dekker, R. van Grondelle and I. H. M. van Stokkum, J. Phys. Chem. A, 2011, 115(16), 3947-3956, albeit that the in vivo kinetics turn out to be somewhat slower. At 77 K several low-energy pigments are observed in both photosystems which complicate the overall dynamics but the PSII kinetics can still be described by both a trap-limited and a transfer-to-the-trap-limited model.","corpus_id":6088644,"score":1},{"doc_id":"23747063","title":"How does iron deficiency disrupt the electron flow in photosystem I of lettuce leaves?","abstract":"The changes observed photosystem I activity of lettuce plants exposed to iron deficiency were investigated. Photooxidation/reduction kinetics of P700 monitored as ΔA820 in the presence and absence of electron transport inhibitors and acceptors demonstrated that deprivation in iron decreased the population of active photo-oxidizable P700. In the complete absence of iron, the addition of plant inhibitors (DCMU and MV) could not recover the full PSI activity owing to the abolition of a part of P700 centers. In leaves with total iron deprivation (0μM Fe), only 15% of photo-oxidizable P700 remained. In addition, iron deficiency appeared to affect the pool size of NADP(+) as shown by the decline in the magnitude of the first phase of the photooxidation kinetics of P700 by FR-light. Concomitantly, chlorophyll content gradually declined with the iron concentration added to culture medium. In addition, pronounced changes were found in chlorophyll fluorescence spectra. Also, the global fluorescence intensity was affected. The above changes led to an increased rate of cyclic electron transport around PSI mainly supported by stromal reductants.","corpus_id":33730978,"score":1},{"doc_id":"24553846","title":"Roles of the cyclic electron flow around PSI (CEF-PSI) and O₂-dependent alternative pathways in regulation of the photosynthetic electron flow in short-term fluctuating light in Arabidopsis thaliana.","abstract":"To assess the roles of the cyclic electron flow around PSI (CEF-PSI) and O₂-dependent alternative pathways including the water-water cycle in fluctuating light, we grew the wild type and pgr5 mutant of Arabidopsis thaliana in constant light, and measured Chl fluorescence and P700 parameters in their leaves in the fluctuating light alternating between 240 (HL) and 30 µmol photons m⁻² s⁻² (LL) every 2 min. At 20% O₂, the photochemical quantum yield of PSII decreased, in particular in the pgr5 plants, soon after the start of the fluctuating light treatment. PSI of the pgr5 plants was markedly photoinhibited by this treatment for 42 min. Slight PSI photoinhibition was also observed in the wild type. We measured energy sharing between PSII and PSI and estimated the PSI and PSII electron transport rates (ETRs). pgr5 showed larger energy allocation to PSI. In contrast to the wild type, the ratio of the PSI to the PSII ETR in pgr5 was higher in LL but lower in HL at 20% O₂ due to PSI acceptor-side limitation. At 2.7% or 0% O₂, the CEF-PSI of the pgr5 plants was enhanced, the acceptor-side limitation of PSI electron flow was released and PSI photoinhibition was not observed. The results suggest that the light fluctuation is a potent stress to PSI and that the CEF-PSI is essential to protect PSI from this stress.","corpus_id":26442906,"score":1},{"doc_id":"25008325","title":"The PsbP domain protein 1 functions in the assembly of lumenal domains in photosystem I.","abstract":"Photosystem I (PS I) is a multisubunit membrane protein complex that functions as a light-driven plastocyanin-ferredoxin oxidoreductase. The PsbP domain protein 1 (PPD1; At4g15510) is located in the thylakoid lumen of plant chloroplasts and is essential for photoautotrophy, functioning as a PS I assembly factor. In this work, RNAi was used to suppress PPD1 expression, yielding mutants displaying a range of phenotypes with respect to PS I accumulation and function. These PPD1 RNAi mutants showed a loss of assembled PS I that was correlated with loss of the PPD1 protein. In the most severely affected PPD1 RNAi lines, the accumulated PS I complexes exhibited defects in electron transfer from plastocyanin to the oxidized reaction center P700 (+). The defects in PS I assembly in the PPD1 RNAi mutants also had secondary effects with respect to the association of light-harvesting antenna complexes to PS I. Because of the imbalance in photosystem function in the PPD1 RNAi mutants, light-harvesting complex II associated with and acted as an antenna for the PS I complexes. These results provide new evidence for the role of PPD1 in PS I biogenesis, particularly as a factor essential for proper assembly of the lumenal portion of the complex.","corpus_id":30642262,"score":1},{"doc_id":"25023284","title":"Defining the far-red limit of photosystem I: the primary charge separation is functional to 840 nm.","abstract":"The far-red limit of photosystem I (PS I) photochemistry was studied by EPR spectroscopy using laser flashes between 730 and 850 nm. In manganese-depleted spinach thylakoid membranes, the primary donor in PS I, P700, was oxidized simultaneously with tyrosine Z, the secondary donor in PS II. It was found that at 295 K PS I photochemistry, observed as P700 (+) formation, was functional up to 840 nm. This is 30 nm further to the red region than was reported for PS II photochemistry (Thapper, A., Mamedov, F., Mokvist, F., Hammarström, L., and Styring, S. (2009) Plant Cell 21, 2391-2401). The same far-red limit for the P700 (+) formation was observed in a PS I reaction center core preparation from Nostoc punctiforme. The reduction of the acceptor side of PS I, observed as reduction of the iron-sulfur centers FA and FB by low temperature EPR measurements, was also functional at 15 K with light up to >830 nm. Taken together, these results, obtained from both plants and cyanobacteria, most likely rule out involvement of the red-absorbing antenna chlorophylls in this reaction. Instead we propose the existence of weak charge transfer bands absorbing in the far-red region in the ensemble of excitonically coupled chlorophyll a molecules around P700 similar to what has been found in the reaction center of PS II. These charge transfer bands could be responsible for the far-red light absorption leading to PS I photochemistry at wavelengths up to 840 nm.","corpus_id":24313038,"score":1},{"doc_id":"26101037","title":"Photoinactivation of Photosystem II in wild-type and chlorophyll b-less barley leaves: which mechanism dominates depends on experimental circumstances.","abstract":"Action spectra of photoinactivation of Photosystem II (PS II) in wild-type and chlorophyll b-less barley leaf segments were obtained. Photoinactivation of PS II was monitored by the delivery of electrons from PS II to PS I following single-turnover flashes superimposed on continuous far-red light, the time course of photoinactivation yielding a rate coefficient k i. Susceptibility of PS II to photoinactivation was quantified as the ratio of k i to the moderate irradiance (I) of light at each selected wavelength. k i/I was very much higher in blue light than in red light. The experimental conditions permitted little excess light energy absorbed by chlorophyll (not utilized in photochemical conversion or dissipated in controlled photoprotection) that could lead to photoinactivation of PS II. Therefore, direct absorption of light by Mn in PS II, rather than by chlorophyll, was more likely to have initiated the much more severe photoinactivation in blue light than in red light. Mutant leaves were ca. 1.5-fold more susceptible to photoinactivation than the wild type. Neither the excess-energy mechanism nor the Mn mechanism can explain this difference. Instead, the much lower chlorophyll content of mutant leaves could have exerted an exacerbating effect, possibly partly due to less mutual shading of chloroplasts in the mutant leaves. In general, which mechanism dominates depends on the experimental conditions.","corpus_id":10226888,"score":1},{"doc_id":"27053032","title":"Analysis of Photosystem I Donor and Acceptor Sides with a New Type of Online-Deconvoluting Kinetic LED-Array Spectrophotometer.","abstract":"The newly developed Dual/KLAS-NIR spectrophotometer, technical details of which were reported very recently, is used in measuring redox changes of P700, plastocyanin (PC) and ferredoxin (Fd) in intact leaves of Hedera helix, Taxus baccata and Brassica napus An overview of various light-/dark-induced changes of deconvoluted P700(+), PC(+) and Fd(-) signals is presented demonstrating the wealth of novel information and the consistency of the obtained results. Fd(-) changes are particularly large after dark adaptation. PC oxidation precedes P700 oxidation during dark-light induction and in steady-state light response curves. Fd reoxidation during induction correlates with the secondary decline of simultaneously measured fluorescence yield, both of which are eliminated by removal of O2 By determination of 100% redox changes, relative contents of PC/P700 and Fd/P700 can be assessed, which show considerable variations between different leaves, with a trend to higher values in sun leaves. Based on deconvoluted P700(+) signals, the complementary quantum yields of PSI, Y(I) (photochemical energy use), Y(ND) (non-photochemical loss due to oxidized primary donor) and Y(NA) (non-photochemical loss due to reduced acceptor) are determined as a function of light intensity and compared with the corresponding complementary quantum yields of PSII, Y(II) (photochemical energy use), Y(NPQ) (regulated non-photochemical loss) and Y(NO) (non-regulated non-photochemical loss). The ratio Y(I)/Y(II) increases with increasing intensities. In the low intensity range, a two-step increase of PC(+) is indicative of heterogeneous PC pools.","corpus_id":23923524,"score":1},{"doc_id":"27236700","title":"PSI photoinhibition is more related to electron transfer from PSII to PSI rather than PSI redox state in Psychotria rubra.","abstract":"Although it has been believed that wild-type plants are capable of protecting photosystem I (PSI) under high light, our previous study indicates that PSI is sensitive to high light in the shade-established tree species Psychotria rubra. However, the underlying physiological mechanisms are unclear. In this study, we examined the roles of electron transfer from PSII to PSI and PSI redox state in PSI photoinhibition in P. rubra by treatments with lincomycin (Lin), diuron (DCMU), and methyl viologen (MV). After exposure to 2000 μmol photons m(-2) s(-1) for 2 h, PSI activity decreased by 35, 29, 3, and 49 % in samples treated with H2O, Lin, DCMU, and MV, respectively. Meanwhile, the MV-treated samples showed higher P700 oxidation ratio than the H2O-treated samples, suggesting the PSI photoinhibition under high light was accompanied by high levels of P700 oxidation ratio. PSI photoinhibition was alleviated in the DCMU-treated samples but was accelerated in the MV-treated samples, suggesting that PSI photoinhibition in P. rubra was mainly controlled by electron transfer from PSII to PSI. Taking together, PSI photoinhibition is more related to electron transfer from PSII to PSI rather than PSI redox state in P. rubra, which is different from the mechanisms of PSI photoinhibition in Arabidopsis thaliana and cucumber.","corpus_id":17683775,"score":1},{"doc_id":"27613853","title":"Oxidation of P700 in Photosystem I Is Essential for the Growth of Cyanobacteria.","abstract":"The photoinhibition of photosystem I (PSI) is lethal to oxygenic phototrophs. Nevertheless, it is unclear how photodamage occurs or how oxygenic phototrophs prevent it. Here, we provide evidence that keeping P700 (the reaction center chlorophyll in PSI) oxidized protects PSI. Previous studies have suggested that PSI photoinhibition does not occur in the two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942, when photosynthetic CO2 fixation was suppressed under low CO2 partial pressure even in mutants deficient in flavodiiron protein (FLV), which mediates alternative electron flow. The lack of FLV in Synechococcus sp. PCC 7002 (S. 7002), however, is linked directly to reduced growth and PSI photodamage under CO2-limiting conditions. Unlike Synechocystis sp. PCC 6803 and S. elongatus PCC 7942, S. 7002 reduced P700 during CO2-limited illumination in the absence of FLV, resulting in decreases in both PSI and photosynthetic activities. Even at normal air CO2 concentration, the growth of S. 7002 mutant was retarded relative to that of the wild type. Therefore, P700 oxidation is essential for protecting PSI against photoinhibition. Here, we present various strategies to alleviate PSI photoinhibition in cyanobacteria.","corpus_id":44849856,"score":1},{"doc_id":"27738959","title":"In vitro kinetics of P700(+) reduction of Thermosynechococcus elongatus trimeric Photosystem I complexes by recombinant cytochrome c 6 using a Joliot-type LED spectrophotometer.","abstract":"The reduction rate of photo-oxidized Photosystem I (PSI) with various natural and artificial electron donors have been well studied by transient absorption spectroscopy. The electron transfer rate from various donors to P700(+) has been measured for a wide range of photosynthetic organisms encompassing cyanobacteria, algae, and plants. PSI can be a limiting component due to tedious extraction and purification methods required for this membrane protein. In this report, we have determined the in vivo, intracellular cytochrome c 6 (cyt c 6)/PSI ratio in Thermosynechococcus elongatus (T.e.) using quantitative Western blot analysis. This information permitted the determination of P700(+) reduction kinetics via recombinant cyt c 6 in a physiologically relevant ratio (cyt c 6: PSI) with a Joliot-type, LED-driven, pump-probe spectrophotometer. Dilute PSI samples were tested under varying cyt c 6 concentration, temperature, pH, and ionic strength, each of which shows similar trends to the reported literature utilizing much higher PSI concentrations with laser-based spectrophotometer. Our results do however indicate kinetic differences between actinic light sources (laser vs. LED), and we have attempted to resolve these effects by varying our LED light intensity and duration. The standardized configuration of this spectrophotometer will also allow a more uniform kinetic analysis of samples in different laboratories. We can conclude that our findings from the LED-based system display an added total protein concentration effect due to multiple turnover events of P700(+) reduction by cyt c 6 during the longer illumination regime.","corpus_id":25775424,"score":1},{"doc_id":"28235460","title":"Tyrozine D oxidation and redox equilibrium in photosystem II.","abstract":"Tyrosine D (TyrD) is an auxiliary redox active tyrosine residue in photosystem II (PSII). The mechanism of TyrD oxidation was investigated by EPR spectroscopy, flash-induced fluorescence decay and thermoluminescence measurements in PSII enriched membranes from spinach. PSII membranes were chemically treated with 3mM ascorbate and 1mM diaminodurene and subsequent washing, leading to the complete reduction of TyrD. TyrD oxidation kinetics and competing recombination reactions were measured after a single saturating flash in the absence and presence of DCMU (inhibitor of the QB-site) in the pH range of 4.7-8.5. Two kinetic phases of TyrD oxidation were observed by the time resolved EPR spectroscopy - the fast phase (msec-sec time range) and the pH dependent slow phase (tens of seconds time range). In the presence of DCMU, TyrD oxidation kinetics was monophasic in the entire pH range, i.e. only the fast kinetics was observed. The results obtained from the fluorescence and thermoluminescence analysis show that when forward electron transport is blocked in the presence of DCMU, the S2QA(-) recombination outcompetes the slow phase of TyrD oxidation by the S2 state. Modelling of the whole complex of these electron transfer events associated with TyrD oxidation fitted very well with our experimental data. Based on these data, structural information and theoretical considerations we confirm our assignment of the fast and slow oxidation kinetics to two populations of PSII centers with different water positions (proximal and distal) in the TyrD vicinity.","corpus_id":25063489,"score":1},{"doc_id":"28497192","title":"Redox changes of ferredoxin, P700, and plastocyanin measured simultaneously in intact leaves.","abstract":"Properties and performance of the recently introduced Dual/KLAS-NIR spectrophotometer for simultaneous measurements of ferredoxin (Fd), P700, and plastocyanin (PC) redox changes, together with whole leaf chlorophyll a (Chl) fluorescence (emission >760, 540 nm excitation) are outlined. Spectral information on in vivo Fd, P700, and PC in the near-infrared region (NIR, 780-1000 nm) is presented, on which the new approach is based. Examples of application focus on dark-light and light-dark transitions, where maximal redox changes of Fd occur. After dark-adaptation, Fd reduction induced by moderate light parallels the Kautsky effect of Chl fluorescence induction. Both signals are affected analogously by removal of O2. A rapid type of Fd reoxidation, observed after a short pulse of light before light activation of linear electron transport (LET), is more pronounced in C4 compared to C3 leaves and interpreted to reflect cyclic PS I (CET). Light activation of LET, as assessed via the rate of Fd reoxidation after short light pulses, occurs at very low intensities and is slowly reversed (half-time ca. 20 min). Illumination with strong far-red light (FR, 740 nm) reveals two fractions of PS I, PS I (LET), and PS I (CET), differing in the rates of Fd reoxidation upon FR-off and the apparent equilibrium constants between P700 and PC. Parallel information on oxidation of Fd and reduction of P700 plus PC proves essential for identification of CET. Comparison of maize (C4) with sunflower and ivy (C3) responses leads to the conclusion that segregation of two types of PS I may not only exist in C4 (mesophyll and bundle sheath cells), but also in C3 photosynthesis (grana margins plus end membranes and stroma lamellae).","corpus_id":12269864,"score":1},{"doc_id":"28823462","title":"Mechanism of adiabatic primary electron transfer in photosystem I: Femtosecond spectroscopy upon excitation of reaction center in the far-red edge of the QY band.","abstract":"The ultrafast primary charge separation in Photosystem I (PS I) excited by femtosecond pulses centered at 720 and 760nm was studied by pump-to-probe laser spectroscopy. The absorbance in the red edge of PS I absorption spectrum has an unusual exponential dependence on wavelength. The cutoff of short wavelength components of 760nm pulse allows direct excitation of reaction center chlorophyll molecules without involvement of light-harvesting antenna. The transient spectrum manifests the features of the primary ion-radical pair P700(+)A0(-) at time delay <180fs, followed by formation of the secondary pair P700(+)A1(-) with a characteristic time of 26ps. The obtained data are rationalized in the framework of adiabatic three-state model that includes the chlorophyll dimer P700 and two symmetrically arranged nearest chlorophyll molecules of A0. The arrangement of chlorophylls results in strong electronic coupling between P700 and A0. Excitation in the maximum of P700 absorption generates electronic states with the highest contribution from P700*, whereas excitation in the far-red edge predominantly generates charge transfer state P700(+)A0(-) in both branches of redox-cofactors. The three-level model accounts for a flat-bottomed potential surface of the excited state and adiabatic character of electron transfer between P700 and A0, providing a microscopic explanation of the ultrafast formation of P700(+)A0(-) and exponential decline of PS I absorption.","corpus_id":41849440,"score":1},{"doc_id":"29357086","title":"Photoinhibition of photosystem I in Nephrolepis falciformis depends on reactive oxygen species generated in the chloroplast stroma.","abstract":"We studied how high light causes photoinhibition of photosystem I (PSI) in the shade-demanding fern Nephrolepis falciformis, in an attempt to understand the mechanism of PSI photoinhibition under natural field conditions. Intact leaves were treated with constant high light and fluctuating light. Detached leaves were treated with constant high light in the presence and absence of methyl viologen (MV). Chlorophyll fluorescence and P700 signal were determined to estimate photoinhibition. PSI was highly oxidized under high light before treatments. N. falciformis showed significantly stronger photoinhibition of PSI and PSII under constant high light than fluctuating light. These results suggest that high levels of P700 oxidation ratio cannot prevent PSI photoinhibition under high light in N. falciformis. Furthermore, photoinhibition of PSI in N. falciformis was largely accelerated in the presence of MV that promotes the production of superoxide anion radicals in the chloroplast stroma by accepting electrons from PSI. From these results, we propose that photoinhibition of PSI in N. falciformis is mainly caused by superoxide radicals generated in the chloroplast stroma, which is different from the mechanism of PSI photoinhibition in Arabidopsis thaliana and spinach. Here, we provide some new insights into the PSI photoinhibition under natural field conditions.","corpus_id":23229486,"score":1},{"doc_id":"18667416","title":"The psbo1 mutant of Arabidopsis cannot efficiently use calcium in support of oxygen evolution by photosystem II.","abstract":"The Arabidopsis thaliana mutant psbo1 contains a point mutation in the psbO-1 gene (At5g66570) leading to the loss of expression of the PsbO-1 protein and overexpression of the PsbO-2 protein (Murakami, R., Ifuku, K., Takabayashi, A., Shikanai, T., Endo, T., and Sato, F. (2002) FEBS Lett. 523, 138-142). Previous characterization of fluorescence induction and decay kinetics by our laboratory documented defects on both the oxidizing and reducing sides of Photosystem II. Additionally, anomalous flash oxygen yield patterns indicated that the mutant contains a defective oxygen-evolving complex that appears to exhibit anomalously long-lived S(2) and S(3) oxidation states (Liu, H., Frankel, L. K., and Bricker, T. M. (2007) Biochemistry 46, 7607-7613). In this study, we have documented that the S(2) and S(3) states in psbo1 thylakoids decay very slowly. The total flash oxygen yield of the psbo1 mutant was also significantly reduced, as was its stability. Incubation of psbo1 thylakoids at high NaCl concentrations did not increase the rate of S(2) and S(3) state decay. The oxygen-evolving complexes of the mutant did, however, exhibit somewhat enhanced stability following this treatment. Incubation with CaCl(2) had a significantly more dramatic effect. Under this condition, both the S(2) and S(3) states of the mutant decayed at nearly the same rate as the wild type, and the total oxygen yield and its stability following CaCl(2) treatment were indistinguishable from that of the wild type. These results strongly suggest that the principal defect in the psbo1 mutant is an inability to effectively utilize the calcium associated with Photosystem II. We hypothesize that the PsbO-2 protein cannot effectively sequester calcium at the oxygen-evolving site.","corpus_id":19474734,"score":0},{"doc_id":"18791808","title":"The effects of simultaneous RNAi suppression of PsbO and PsbP protein expression in photosystem II of Arabidopsis.","abstract":"Interfering RNA was used to suppress simultaneously the expression of the four genes which encode the PsbO and PsbP proteins of Photosystem II in Arabidopsis (PsbO: At5g66570, At3g50820 and PsbP: At1g06680, At2g30790). A phenotypic series of transgenic plants was obtained that expressed variable amounts of the PsbO proteins and undetectable amounts of the PsbP proteins. Immunological studies indicated that the loss of PsbP expression was correlated with the loss of expression of the PsbQ, D2, and CP47 proteins, while the loss of PsbO expression was correlated with the loss of expression of the D1 and CP43 proteins. Q(A)(-) reoxidation kinetics in the absence of DCMU indicated that the slowing of electron transfer from Q(A)(-) to Q(B) was correlated with the loss of the PsbP protein. Q(A)(-) reoxidation kinetics in the presence of DCMU indicated that charge recombination between Q(A)(-) and donor side components of the photosystem was retarded in all of the mutants. Decreasing amounts of the PsbO protein in the absence of the PsbP component also led to a progressive loss of variable fluorescence yield (F(V)/F(M)). During fluorescence induction, the loss of PsbP was correlated with a more rapid O to J transition and a loss of the J to I transition. These results indicate that the losses of the PsbO and PsbP proteins differentially affect separate protein components and different PS II functions and can do so, apparently, in the same plant.","corpus_id":5674014,"score":0},{"doc_id":"18991552","title":"Oxygen as an alternative electron acceptor in the photosynthetic electron transport chain of C3 plants.","abstract":"This study deals with effects of oxygen on the kinetics of P(700) photoinduced redox transitions and on induction transients of chlorophyll fluorescence in leaves of C(3) plants Hibiscus rosa-sinensis and Vicia faba. It is shown that the removal of oxygen from the leaf environment has a conspicuous effect on photosynthetic electron transport. Under anaerobic conditions, the concentration of oxidized P700 centers in continuous white light was substantially lower than under aerobic conditions. The deficiency of oxygen released non-photochemical quenching of chlorophyll fluorescence, thus indicating a decrease in the trans-thylakoid pH gradient (DeltapH). Quantitative analysis of experimental data within the framework of an original mathematical model has shown that the steady-state electron flux toward oxygen in Chinese hibiscus leaves makes up to approximately 40% of the total electron flow passing through photosystem 1 (PS1). The decrease in P700+ content under anaerobic conditions can be due to two causes: i) the retardation of electron outflow from PS1, and ii) the release of photosynthetic control (acceleration of electron flow from PS2 to P700+) owing to lower acidification of the intra-thylakoid space. At the same time, cyclic electron transport around PS1 was not stimulated in the oxygen-free medium, although such stimulation seemed likely in view of possible rearrangement of electron flows on the acceptor side of PS1. This conclusion stems from observations that the rates of P700+ reduction in DCMU-poisoned samples, both under aerobic and anaerobic conditions, were negligibly small compared to rates of electron flow from PS2 toward P700+ in untreated samples.","corpus_id":12149860,"score":0},{"doc_id":"19700631","title":"Defining the far-red limit of photosystem II in spinach.","abstract":"The far-red limit of photosystem II (PSII) photochemistry was studied in PSII-enriched membranes and PSII core preparations from spinach (Spinacia oleracea) after application of laser flashes between 730 and 820 nm. Light up to 800 nm was found to drive PSII activity in both acceptor side reduction and oxidation of the water-oxidizing CaMn(4) cluster. Far-red illumination induced enhancement of, and slowed down decay kinetics of, variable fluorescence. Both effects reflect reduction of the acceptor side of PSII. The effects on the donor side of PSII were monitored using electron paramagnetic resonance spectroscopy. Signals from the S(2)-, S(3)-, and S(0)-states could be detected after one, two, and three far-red flashes, respectively, indicating that PSII underwent conventional S-state transitions. Full PSII turnover was demonstrated by far-red flash-induced oxygen release, with oxygen appearing on the third flash. In addition, both the pheophytin anion and the Tyr Z radical were formed by far-red flashes. The efficiency of this far-red photochemistry in PSII decreases with increasing wavelength. The upper limit for detectable photochemistry in PSII on a single flash was determined to be 780 nm. In photoaccumulation experiments, photochemistry was detectable up to 800 nm. Implications for the energetics and energy levels of the charge separated states in PSII are discussed in light of the presented results.","corpus_id":23237068,"score":0},{"doc_id":"20568728","title":"Function of PsbO, the photosystem II manganese-stabilizing protein: probing the role of aspartic acid 157.","abstract":"The D157N, D157E, and D157K mutations in the psbO gene encoding the photosystem II (PSII) manganese-stabilizing protein from spinach, exhibit near-wild-type PSII binding but are significantly impaired in O(2) evolution activity and Cl(-) retention by PSII [Popelkova et al. (2009) Biochemistry 48, 11920-11928]. To better characterize the role of PsbO-Asp157 in eukaryotic PSII, the effect of mutations in Asp157 on heat-induced changes in PsbO solution structure, O(2) release kinetics, and PSII redox reactions both within and outside the oxygen-evolving complex (OEC) have been examined. The data presented here show that Asn, Glu, or Lys mutations in PsbO-Asp157 modify PsbO thermostability in solution, which is consistent with the previously reported perturbation of the functional assembly of PsbO-Asp157 mutants into PSII that caused inefficient Cl(-) retention by PSII. Fluorescence decay signals from PSII reconstituted with Asp157 mutants indicate that that the Q(A)(-) to Q(B) transition on the PSII reducing side is unaffected, but complex alterations are detected on the PSII oxidizing side that affect the recombination of Q(A)(-) with the O(2)-evolving complex. In addition, oxygen yield on the first flash is increased, which indicates an impaired ability of mutant-reconstituted PSII samples to decay back to the S(1) state in the dark.","corpus_id":19192128,"score":0},{"doc_id":"21661738","title":"Binding stoichiometry and affinity of the manganese-stabilizing protein affects redox reactions on the oxidizing side of photosystem II.","abstract":"It has been reported previously that the two subunits of PsbO, the photosystem II (PSII) manganese stabilizing protein, have unique functions in relation to the Mn, Ca(2+), and Cl(-) cofactors in eukaryotic PSII [Popelkova; (2008) Biochemistry 47, 12593]. The experiments reported here utilize a set of N-terminal truncation mutants of PsbO, which exhibit altered subunit binding to PSII, to further characterize its role in establishing efficient O(2) evolution activity. The effects of PsbO binding stoichiometry, affinity, and specificity on Q(A)(-) reoxidation kinetics after a single turnover flash, S-state transitions, and O(2) release time have been examined. The data presented here show that weak rebinding of a single PsbO subunit to PsbO-depleted PSII repairs many of the defects in PSII resulting from the removal of the protein, but many of these are not sustainable, as indicated by low steady-state activities of the reconstituted samples [Popelkova; (2003) Biochemistry 42 , 6193]. High affinity binding of PsbO to PSII is required to produce more stable and efficient cycling of the water oxidation reaction. Reconstitution of the second PsbO subunit is needed to further optimize redox reactions on the PSII oxidizing side. Native PsbO and recombinant wild-type PsbO from spinach facilitate PSII redox reactions in a very similar manner, and nonspecific binding of PsbO to PSII has no significance in these reactions.","corpus_id":21663128,"score":0},{"doc_id":"22004756","title":"Cationic state distribution over the P700 chlorophyll pair in photosystem I.","abstract":"The primary electron donor P700 in photosystem I is composed of two chlorophylls, P(A) and P(B). P700 forms the cationic [P(A)/P(B)](•+) state as a result of light-induced electron transfer. We obtained a P(A)(•+)/P(B)(•+) ratio of 28:72 and a spin distribution of 22:78 for the entire PSI protein-pigment complex. By considering the influence of the protein components on the redox potential for one-electron oxidation of P(A)/P(B) monomers, we found that the following three factors significantly contributed to a large P(B)(•+) population relative to P(A)(•+): 1), Thr-A743 forming a H-bond with P(A); 2), P(A) as a chlorophyll a epimer; and 3), a conserved PsaA/PsaB pair, the Arg-A750/Ser-B734 residue. In addition, 4), the methyl-ester groups of the accessory chlorophylls A(-1A)/A(-1B) significantly stabilized the cationic [P(A)/P(B)](•+) state and 5), the methyl-ester group orientations were completely different in A(-1A) and A(-1B) as seen in the crystal structure. When the methyl-ester group was rotated, the spin-density distribution over P(A)/P(B) ranged from 22:78 to 15:85.","corpus_id":14695186,"score":0},{"doc_id":"22614952","title":"Probing the N-terminal sequence of spinach PsbO: evidence that essential threonine residues bind to different functional sites in eukaryotic photosystem II.","abstract":"The N-terminal ¹E-⁶L domain of the manganese-stabilizing protein (PsbO) from spinach prevents non-specific binding of the subunit to photosystem II (PSII) and deletions of the ¹E-⁷T or ¹E-¹⁵T sequences from the PsbO N-terminus reduce or impair, respectively, functional binding of PsbO to PSII (Popelkova et al., Biochemistry 42:6193-6200, 2003). The work presented here provides deeper insights into the interaction of PsbO with PSII. The data show that a single mutation, ¹⁵T → A in mature PsbO from spinach reduces the stoichiometry of its functional binding from two to one subunit per PSII and decreases reconstitution of activity to about 45 % of the wild-type control. Replacement of the ¹E-⁶L domain with ⁶M in the T15A PsbO mutant has no additional negative effect on recovery of O₂ evolution activity, but it significantly weakens both functional and nonspecific binding of the truncated mutant to PSII. These results suggest that the ¹⁵T side-chain by itself is essential for binding of one of two PsbO subunits to eukaryotic PSII and that specific PSII-binding sites for PsbO are distinguishable; one PSII-binding site does not require PsbO-¹⁵T and probably interacts with the other N-terminal domain of PsbO. Identity of the latter domain is revealed by a requirement for the presence of the ¹E-⁶L sequence that is shown here to be necessary for high-affinity binding of PsbO to PSII. When combined with previous results, the data presented here lead to a more detailed model for PsbO binding in eukaryotic PSII.","corpus_id":2549961,"score":0},{"doc_id":"23624674","title":"Gymnosperms have increased capacity for electron leakage to oxygen (Mehler and PTOX reactions) in photosynthesis compared with angiosperms.","abstract":"Oxygen plays an important role in photosynthesis by participating in a number of O2-consuming reactions. O2 inhibits CO2 fixation by stimulating photorespiration, thus reducing plant production. O2 interacts with photosynthetic electron transport in the chloroplasts' thylakoids in two main ways: by accepting electrons from PSI (Mehler reaction); and by accepting electrons from reduced plastoquinone (PQ) mediated by the plastid terminal oxidase (PTOX). In this study, we show, using 101 plant species, that there is a difference in the potential for photosynthetic electron flow to O2 between angiosperms and gymnosperms. We found, from measurements of Chl fluorescence and leaf absorbance at 830 nm, (i) that electron outflow from PSII, as determined by decay kinetics of Chl fluorescence after application of a saturating light pulse, is more rapid in gymnosperms than in angiosperms; (ii) that the reaction center Chl of PSI (P700) is rapidly and highly oxidized in gymnosperms during induction of photosynthesis; and (iii) that these differences are dependent on oxygen. Finally, rates of O2 uptake measured by mass spectrometry in the absence of photorespiration were significantly promoted by illumination in dark-adapted leaves of gymnosperms, but not in those of angiosperms. The light-stimulated O2 uptake was around 10% of the maximum O2 evolution in gymnosperms and 1% in angiosperms. These results suggest that gymnosperms have increased capacity for electron leakage to oxygen in photosynthesis compared with angiosperms. The involvement of the Mehler reaction and PTOX in the electron flow to O2 is discussed.","corpus_id":23679605,"score":0},{"doc_id":"24556534","title":"Model based analysis of transient fluorescence yield induced by actinic laser flashes in spinach leaves and cells of green alga Chlorella pyrenoidosa Chick.","abstract":"Measurements of Single Flash Induced Transient Fluorescence Yield (SFITFY) on spinach leaves and whole cells of green thermophilic alga Chlorella pyrenoidosa Chick were analyzed for electron transfer (ET) steps and coupled proton transfer (PT) on both the donor and the acceptor side of the reaction center (RC) of photosystem II (PS II). A specially developed PS II model (Belyaeva et al., 2008, 2011a) allowed the determination of ET steps that occur in a hierarchically ordered time scale from nanoseconds to several seconds. Our study demonstrates that our SFITFY data is consistent with the concept of the reduction of P680(+) by YZ in both leaves and algae (studied on spinach leaves and cells of Chlorella pyrenoidosa Chick). The multiphasic P680(+) reduction kinetics by YZ in PS II core complexes with high oxygen evolution capacity was seen in both algae and leaves. Model simulation to fit SFITFY curves for dark adapted species used here gives the rate constants to verify nanosecond kinetic stages of P680(+) reduction by YZ in the redox state S1 of the water oxidizing complex (WOC) shown in Kühn et al. (2004). Then a sequence of relaxation steps in the redox state S1, outlined by Renger (2012), occurs in both algae and leaves as a similar non-adiabatic ET reactions. Coupled PT is discussed briefly to understand a rearrangement of hydrogen bond protons in the protein matrix of the WOC (Umena et al., 2011). On the other hand, present studies showed a slower reoxidation of reduced QA by QB in algal cells as compared with that in a leaf that might be regarded as a consequence of differences of spatial domains at the QB-site in leaves compared to algae. Our comparative study helped to correlate theory with experimental data for molecular photosynthetic mechanisms in thylakoid membranes.","corpus_id":207392342,"score":0},{"doc_id":"26049407","title":"Modeling of the redox state dynamics in photosystem II of Chlorella pyrenoidosa Chick cells and leaves of spinach and Arabidopsis thaliana from single flash-induced fluorescence quantum yield changes on the 100 ns-10 s time scale.","abstract":"The time courses of the photosystem II (PSII) redox states were analyzed with a model scheme supposing a fraction of 11-25 % semiquinone (with reduced [Formula: see text]) RCs in the dark. Patterns of single flash-induced transient fluorescence yield (SFITFY) measured for leaves (spinach and Arabidopsis (A.) thaliana) and the thermophilic alga Chlorella (C.) pyrenoidosa Chick (Steffen et al. Biochemistry 44:3123-3132, 2005; Belyaeva et al. Photosynth Res 98:105-119, 2008, Plant Physiol Biochem 77:49-59, 2014) were fitted with the PSII model. The simulations show that at high-light conditions the flash generated triplet carotenoid (3)Car(t) population is the main NPQ regulator decaying in the time interval of 6-8 μs. So the SFITFY increase up to the maximum level [Formula: see text]/F 0 (at ~50 μs) depends mainly on the flash energy. Transient electron redistributions on the RC redox cofactors were displayed to explain the SFITFY measured by weak light pulses during the PSII relaxation by electron transfer (ET) steps and coupled proton transfer on both the donor and the acceptor side of the PSII. The contribution of non-radiative charge recombination was taken into account. Analytical expressions for the laser flash, the (3)Car(t) decay and the work of the water-oxidizing complex (WOC) were used to improve the modeled P680(+) reduction by YZ in the state S 1 of the WOC. All parameter values were compared between spinach, A. thaliana leaves and C. pyrenoidosa alga cells and at different laser flash energies. ET from [Formula: see text] slower in alga as compared to leaf samples was elucidated by the dynamics of [Formula: see text] fractions to fit SFITFY data. Low membrane energization after the 10 ns single turnover flash was modeled: the ∆Ψ(t) amplitude (20 mV) is found to be about 5-fold smaller than under the continuous light induction; the time-independent lumen pHL, stroma pHS are fitted close to dark estimates. Depending on the flash energy used at 1.4, 4, 100 % the pHS in stroma is fitted to 7.3, 7.4, and 7.7, respectively. The biggest ∆pH difference between stroma and lumen was found to be 1.2, thus pH- dependent NPQ was not considered.","corpus_id":17846716,"score":0},{"doc_id":"26151897","title":"Investigating changes in the redox state of Photosystem I at low pH.","abstract":"Changes in the redox state of Photosystem I (PSI) were studied in spinach leaf discs suspended in buffers of different pH (pH 7.5, 6.5, 5.5 and 4.5). By measuring absorbance changes at 820 nm, it was observed that under normal conditions, the electrons were supplied by Photosystem II (PSII) for the photo-oxidation of P700 while in the presence of DCMU when electrons coming from PSII are blocked, cyclic electron flow (CEF) around PSI was the major source for the absorbance changes observed at 820 nm. This was supported by complete inhibition in the reduction of both single turnover (ST) area and multiple turnover (MT) area, in the presence of DCMU, which is generally filled up by the electrons coming from PSII. In the absence of DCMU, the intersystem electron pool or plastoquinone (PQ) pool was increased at low pH which was probably due to enhanced cyclic electron flow around PSI. Our results also suggest that at low pH, in the absence of DCMU, the major contribution for faster dark re-reduction of P700(+) is attributed mainly by PSII and CEF PSI while in the presence of DCMU, the significant contribution is provided by CEF PSI and other stromal components.","corpus_id":24246756,"score":0},{"doc_id":"28432538","title":"Superoxide generated in the chloroplast stroma causes photoinhibition of photosystem I in the shade-establishing tree species Psychotria henryi.","abstract":"Our previous studies indicated that high light induced significant photoinhibition of photosystem I (PSI) in the shade-establishing tree species Psychotria henryi. However, the underlying mechanism has not been fully clarified. In the present study, in order to investigate the mechanism of PSI photoinhibition in P. henryi, we treated detached leaves with constant high light in the presence of methyl viologen (MV) or a soluble α-tocopherol analog, 2,2,5,7,8-pentamethyl-6-chromanol (PMC). We found that MV significantly depressed photochemical quantum yields in PSI and PSII when compared to PMC. On condition that no PSI photoinhibition happened, although cyclic electron flow (CEF) was abolished in the MV-treated samples, P700 oxidation ratio was maintain at higher levels than the PMC-treated samples. In the presence of PMC, PSI photoinhibition little changed but PSII photoinhibition was significantly alleviated. Importantly, PSI photoinhibition was largely accelerated in the presence of MV, which stimulates the production of superoxide and subsequently other reactive oxygen species at the chloroplast stroma by accepting electrons from PSI. Furthermore, MV largely aggravated PSII photoinhibition when compared to control. These results suggest that high P700 oxidation ratio cannot prevent PSI photoinhibition in P. henryi. Furthermore, the superoxide produced in the chloroplast stroma is critical for PSI photoinhibition in the higher plant P. henryi, which is opposite to the mechanism underlying PSI photoinhibition in Arabidopsis thaliana and spinach. These findings highlight a new mechanism of PSI photoinhibition in higher plants.","corpus_id":3758531,"score":0},{"doc_id":"28808836","title":"Excitation transfer and trapping kinetics in plant photosystem I probed by two-dimensional electronic spectroscopy.","abstract":"Photosystem I is a robust and highly efficient biological solar engine. Its capacity to utilize virtually every absorbed photon's energy in a photochemical reaction generates great interest in the kinetics and mechanisms of excitation energy transfer and charge separation. In this work, we have employed room-temperature coherent two-dimensional electronic spectroscopy and time-resolved fluorescence spectroscopy to follow exciton equilibration and excitation trapping in intact Photosystem I complexes as well as core complexes isolated from Pisum sativum. We performed two-dimensional electronic spectroscopy measurements with low excitation pulse energies to record excited-state kinetics free from singlet-singlet annihilation. Global lifetime analysis resolved energy transfer and trapping lifetimes closely matches the time-correlated single-photon counting data. Exciton energy equilibration in the core antenna occurred on a timescale of 0.5 ps. We further observed spectral equilibration component in the core complex with a 3-4 ps lifetime between the bulk Chl states and a state absorbing at 700 nm. Trapping in the core complex occurred with a 20 ps lifetime, which in the supercomplex split into two lifetimes, 16 ps and 67-75 ps. The experimental data could be modelled with two alternative models resulting in equally good fits-a transfer-to-trap-limited model and a trap-limited model. However, the former model is only possible if the 3-4 ps component is ascribed to equilibration with a \"red\" core antenna pool absorbing at 700 nm. Conversely, if these low-energy states are identified with the P700 reaction centre, the transfer-to-trap-model is ruled out in favour of a trap-limited model.","corpus_id":21492271,"score":0},{"doc_id":"28924898","title":"Formation of tyrosine radicals in photosystem II under far-red illumination.","abstract":"Photosystem II (PS II) contains two redox-active tyrosine residues on the donor side at symmetrical positions to the primary donor, P680. TyrZ, part of the water-oxidizing complex, is a preferential fast electron donor while TyrD is a slow auxiliary donor to P680+. We used PS II membranes from spinach which were depleted of the water oxidation complex (Mn-depleted PS II) to study electron donation from both tyrosines by time-resolved EPR spectroscopy under visible and far-red continuous light and laser flash illumination. Our results show that under both illumination regimes, oxidation of TyrD occurs via equilibrium with TyrZ• at pH 4.7 and 6.3. At pH 8.5 direct TyrD oxidation by P680+ occurs in the majority of the PS II centers. Under continuous far-red light illumination these reactions were less effective but still possible. Different photochemical steps were considered to explain the far-red light-induced electron donation from tyrosines and localization of the primary electron hole (P680+) on the ChlD1 in Mn-depleted PS II after the far-red light-induced charge separation at room temperature is suggested.","corpus_id":3887916,"score":0}],"string":"[\n {\n \"doc_id\": \"18251867\",\n \"title\": \"A rapid, whole-tissue determination of the functional fraction of PSII after photoinhibition of leaves based on flash-induced P700 redox kinetics.\",\n \"abstract\": \"Assaying the number of functional PSII complexes by the oxygen yield from leaf tissue per saturating, single-turnover flash, assuming that each functional PSII evolves one oxygen molecule after four flashes, is one of the most direct methods but time-consuming. The ratio of variable to maximum Chl fluorescence yield (F(v)/F(m)) in leaves can be correlated with the oxygen yield per flash during a progressive loss of PSII activity associated with high-light stress and is rapid and non-intrusive, but suffers from being representative of chloroplasts near the measured leaf surface; consequently, the exact correlation depends on the internal leaf structure and on which leaf surface is being measured. Our results show that the average F(v)/F(m) of the adaxial and abaxial surfaces has a reasonable linear correlation with the oxygen yield per flash after varied extents of photoinactivation of PSII. However, we obtained an even better linear correlation between (1) the integrated, transient electron flow (Sigma) to P700+, the dimeric Chl cation in PSI, after superimposing a single-turnover flash on steady background far-red light and (2) the relative oxygen yield per flash. Leaves of C3 and C4 plants, woody and herbaceous species, wild-type and a Chl-b-less mutant, and monocot and dicot plants gave a single straight line, which seems to be a universal relation for predicting the relative oxygen yield per flash from Sigma. Measurement of Sigma is non-intrusive, representative of the whole leaf tissue, rapid and applicable to attached leaves; it may even be applicable in the field.\",\n \"corpus_id\": 36144041,\n \"score\": 2\n },\n {\n \"doc_id\": \"19495738\",\n \"title\": \"Novel effects of methyl viologen on photosystem II function in spinach leaves.\",\n \"abstract\": \"Methyl viologen (MV) is a well-known electron mediator that works on the acceptor side of photosystem I. We investigated the little-known, MV-induced inhibition of linear electron flow through photosystem II (PS II) in spinach-leaf discs. Even a low [MV] decreased the (1) average, light-adapted photochemical efficiency of PS II traps, (2) oxidation state of the primary quinone acceptor Q(A) in PS II during illumination, (3) photochemical efficiency of light-adapted open PS II traps, (4) fraction of absorbed light energy dissipated constitutively in a light-independent manner or as chlorophyll (Chl) a fluorescence emission, (5) Chl a fluorescence yield corresponding to dark-adapted open reaction-center traps (F (o)) and closed reaction-center traps (F (m)), and (6) half-time for re-oxidation of Q (A) (-) in PS II after a single-turnover flash. These effects suggest that the presence of MV accelerates various \\\"downhill\\\" electron-transfer steps in PS II. Therefore, when using the MV to quantify cyclic electron flow, the inhibitory effect of MV on PS II should be taken into account.\",\n \"corpus_id\": 39063567,\n \"score\": 2\n },\n {\n \"doc_id\": \"20039131\",\n \"title\": \"Fast cyclic electron transport around photosystem I in leaves under far-red light: a proton-uncoupled pathway?\",\n \"abstract\": \"Fast cyclic electron transport (CET) around photosystem I (PS I) was observed in sunflower (Helianthus annuus L.) leaves under intense far-red light (FRL) of up to 200 mumol quanta m(-2) s(-1). The electron transport rate (ETR) through PS I was found from the FRL-dark transmittance change at 810 and 950 nm, which was deconvoluted into redox states and pool sizes of P700, plastocyanin (PC) and cytochrome f (Cyt f). PC and P700 were in redox equilibrium with K(e) = 35 (ΔE(m) = 90 mV). PS II ETR was based on O(2) evolution. CET [(PS I ETR) - (PS II ETR)] increased to 50-70 mumol e(-) m(-2) s(-1) when linear electron transport (LET) under FRL was limited to 5 mumol e(-) m(-2) s(-1) in a gas phase containing 20-40 mumol CO(2) mol(-1) and 20 mumol O(2) mol(-1). Under these conditions, pulse-saturated fluorescence yield F(m) was non-photochemically quenched; however, F(m) was similarly quenched when LET was driven by low green or white light, which energetically precluded the possibility for active CET. We suggest that under FRL, CET is rather not coupled to transmembrane proton translocation than the CET-coupled protons are short-circuited via proton channels regulated to open at high ΔpH. A kinetic analysis of CET electron donors and acceptors suggests the CET pathway is that of the reversed Q-cycle: Fd -> (FNR) -> Cyt c(n) -> Cyt b(h) -> Cyt b(l) -> Rieske FeS -> Cyt f -> PC -> P700 ->-> Fd. CET is activated when PQH(2) oxidation is opposed by high ΔpH, and ferredoxin (Fd) is reduced due to low availability of e(-) acceptors. The physiological significance of CET may be photoprotective, as CET may be regarded as a mechanism of energy dissipation under stress conditions.\",\n \"corpus_id\": 24601177,\n \"score\": 2\n },\n {\n \"doc_id\": \"20359461\",\n \"title\": \"Photoelectrochemical control of the balance between cyclic- and linear electron transport in photosystem I. Algorithm for P700+ induction kinetics.\",\n \"abstract\": \"Redox transients of chlorophyll P700, monitored as absorbance changes DeltaA810, were measured during and after exclusive PSI excitation with far-red (FR) light in pea (Pisum sativum, cv. Premium) leaves under various pre-excitation conditions. Prolonged adaptation in the dark terminated by a short PSII+PSI- exciting light pulse guarantees pre-conditions in which the initial photochemical events in PSI RCs are carried out by cyclic electron transfer (CET). Pre-excitation with one or more 10s FR pulses creates conditions for induction of linear electron transport (LET). These converse conditions give rise to totally different, but reproducible responses of P700- oxidation. System analyses of these responses were made based on quantitative solutions of the rate equations dictated by the associated reaction scheme for each of the relevant conditions. These provide the mathematical elements of the P700 induction algorithm (PIA) with which the distinguishable components of the P700+ response can be resolved and interpreted. It enables amongst others the interpretation and understanding of the characteristic kinetic profile of the P700+ response in intact leaves upon 10s illumination with far-red light under the promotive condition for CET. The system analysis provides evidence that this unique kinetic pattern with a non-responsive delay followed by a steep S-shaped signal increase is caused by a photoelectrochemically controlled suppression of the electron transport from Fd to the PQ-reducing Qr site of the cytb6f complex in the cyclic pathway. The photoelectrochemical control is exerted by the PSI-powered proton pump associated with CET. It shows strong similarities with the photoelectrochemical control of LET at the acceptor side of PSII which is reflected by release of photoelectrochemical quenching of chlorophyll a fluorescence.\",\n \"corpus_id\": 10773023,\n \"score\": 2\n },\n {\n \"doc_id\": \"22638914\",\n \"title\": \"Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments: approaches and approximations.\",\n \"abstract\": \"Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. ( 1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. ( 2) The gross O(2) yield per single-turnover flash in CO(2)-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O(2) molecule after four flashes. However, the gross O(2) yield per single-turnover flash (multiplied by four) could over-estimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. ( 3) The cumulative delivery of electrons from PS II to P700(+) (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field.\",\n \"corpus_id\": 16079792,\n \"score\": 2\n },\n {\n \"doc_id\": \"23589088\",\n \"title\": \"Whole-tissue determination of the rate coefficients of photoinactivation and repair of photosystem II in cotton leaf discs based on flash-induced P700 redox kinetics.\",\n \"abstract\": \"Using radioactively labelled amino acids to investigate repair of photoinactivated photosystem II (PS II) gives only a relative rate of repair, while using chlorophyll fluorescence parameters yields a repair rate coefficient for an undefined, variable location within the leaf tissue. Here, we report on a whole-tissue determination of the rate coefficient of photoinactivation k i , and that of repair k r in cotton leaf discs. The method assays functional PS II via a P700 kinetics area associated with PS I, as induced by a single-turnover, saturating flash superimposed on continuous background far-red light. The P700 kinetics area, directly proportional to the oxygen yield per single-turnover, saturating flash, was used to obtain both k i and k r . The value of k i , directly proportional to irradiance, was slightly higher when CO2 diffusion into the abaxial surface (richer in stomata) was blocked by contact with water. The value of k r , sizable in darkness, changed in the light depending on which surface was blocked by contact with water. When the abaxial surface was blocked, k r first peaked at moderate irradiance and then decreased at high irradiance. When the adaxial surface was blocked, k r first increased at low irradiance, then plateaued, before increasing markedly at high irradiance. At the highest irradiance, k r differed by an order of magnitude between the two orientations, attributable to different extents of oxidative stress affecting repair (Nishiyama et al., EMBO J 20: 5587-5594, 2001). The method is a whole-tissue, convenient determination of the rate coefficient of photoinactivation k i and that of repair k r .\",\n \"corpus_id\": 18234197,\n \"score\": 2\n },\n {\n \"doc_id\": \"26297354\",\n \"title\": \"Multiple roles of oxygen in the photoinactivation and dynamic repair of Photosystem II in spinach leaves.\",\n \"abstract\": \"Oxygen effects have long been ambiguous: exacerbating, being indifferent to, or ameliorating the net photoinactivation of Photosystem II (PS II). We scrutinized the time course of PS II photoinactivation (characterized by rate coefficient k i) in the absence of repair, or when recovery (characterized by k r) occurred simultaneously in CO2 ± O2. Oxygen exacerbated photoinactivation per se, but alleviated it by mediating the utilization of electrons. With repair permitted, the gradual net loss of functional PS II during illumination of leaves was better described phenomenologically by introducing τ, the time for an initial k r to decrease by half. At 1500 μmol photons m(-2) s(-1), oxygen decreased the initial k r but increased τ. Similarly, at even higher irradiance in air, there was a further decrease in the initial k r and increase in τ. These observations are consistent with an empirical model that (1) oxygen increased k i via oxidative stress but decreased it by mediating the utilization of electrons; and (2) reactive oxygen species stimulated the degradation of photodamaged D1 protein in PS II (characterized by k d), but inhibited the de novo synthesis of D1 (characterized by k s), and that the balance between these effects determines the net effect of O2 on PS II functionality.\",\n \"corpus_id\": 8616988,\n \"score\": 2\n },\n {\n \"doc_id\": \"29535751\",\n \"title\": \"Cyclic Electron Flow around Photosystem I Promotes ATP Synthesis Possibly Helping the Rapid Repair of Photodamaged Photosystem II at Low Light.\",\n \"abstract\": \"In higher plants, moderate photoinhibition of photosystem II (PSII) leads to a stimulation of cyclic electron flow (CEF) at low light, which is accompanied by an increase in the P700 oxidation ratio. However, the specific role of CEF stimulation at low light is not well known. Furthermore, the mechanism underlying this increase in P700 oxidation ratio at low light is unclear. To address these questions, intact leaves of the shade-adapted plant Panax notoginseng were treated at 2258 μmol photons m-2 s-1 for 30 min to induce PSII photoinhibition. Before and after this high-light treatment, PSI and PSII activity, the energy quenching in PSII, the redox state of PSI and proton motive force (pmf) at a low light of 54 μmol photons m-2 s-1 were determined at the steady state. After high-light treatment, electron flow through PSII (ETRII) significantly decreased but CEF was remarkably stimulated. The P700 oxidation ratio significantly increased but non-photochemical quenching changed negligibly. Concomitantly, the total pmf decreased significantly and the proton gradient (ΔpH) across the thylakoid membrane remained stable. Furthermore, the P700 oxidation ratio was negatively correlated with the value of ETRII. These results suggest that upon PSII photoinhibition, CEF is stimulated to increase the ATP synthesis, facilitating the rapid repair of photodamaged PSII. The increase in P700 oxidation ratio at low light cannot be explained by the change in pmf, but is primarily controlled by electron transfer from PSII.\",\n \"corpus_id\": 3533046,\n \"score\": 2\n },\n {\n \"doc_id\": \"18385893\",\n \"title\": \"Heat-induced changes in photosystem I activity as measured with different electron donors in isolated spinach thylakoid membranes.\",\n \"abstract\": \"Heat-induced changes in photosystem I (PSI) have been studied in terms of rates of oxygen consumption using various donors (DCPIPH2, TMPDred and DADred), formation of photo-oxidized P700 and changes in Chl a fluorescence emission at 77 K. Linear heating of thylakoid membranes from 35 degrees C to 70 degrees C caused an enhancement in PSI-mediated electron transfer rates (DCPIPH2-->MV) up to 55 degrees C. However, no change was observed in PSI rates when other electron donors were used (TMPDred and DADred). Similarly, Chl a fluorescence emission spectra at 77 K of heat-treated thylakoid membranes did not show any increase in peak at 735 nm, however, a significant decrease was observed as a function of temperature in the peaks at 685 and 694 nm. In DCMU-treated control thylakoid membranes maximum photo-oxidized P700 was generated at g = 2.0025. In heat-treated thylakoid membranes maximum intensity of photo-oxidized P700 signal was observed at approximately 50-55 degrees C without DCMU treatment. The steady-state signal of the photo-oxidized P700 was studied in the presence of DCPIPH2 and TMPDred as electron donors in DCMU-treated control and in 50 degrees C treated thylakoid membranes. We present here the first of such comparative study of PSI activity in terms of the rates of oxygen consumption and re-reduction kinetics of photo-oxidized P700 in the presence of different electron donors. It appears that the formation of the P700+ signal in heat-treated thylakoid membranes is due to an inhibited electron supply from PSII and not due to spillover or antenna migration.\",\n \"corpus_id\": 36166450,\n \"score\": 1\n },\n {\n \"doc_id\": \"18426807\",\n \"title\": \"Separation of light-induced linear, cyclic and stroma-sourced electron fluxes to P700+ in cucumber leaf discs after pre-illumination at a chilling temperature.\",\n \"abstract\": \"Pre-illumination of cucumber leaf discs at 4 degrees C with low-irradiance white light (i) led to a marked decrease in the extent of photo-oxidation of P700 (the special chlorophyll pair in the PSI reaction center) in actinic light at room temperature and (ii) hastened the post-illumination re-reduction of P700+. Quantifying the linear, cyclic and stroma-sourced electron fluxes to P700+ in two actinic light regimes, we found that there was no increase in cyclic or linear electron fluxes to account for these changes. Rather, we observed a decrease in the maximum extent of P700 photo-oxidation assayed by a strong flash superimposed on continuous, background light of wavelength 723 nm, which we interpret to represent a loss of stable charge separation in PSI due to enhanced charge recombination as a result of the pre-illumination treatment. The funneling of electrons towards fewer non-damaged PSI complexes could explain the hastened post-illumination re-reduction of P700+, aided by a slight increase in a stroma-sourced electron flux after prolonged pre-illumination at 4 degrees C. Quantifying the separate fluxes to P700+ helps to elucidate the effects of chilling of cucumber leaf discs in the light and the reasons for the hastened post-illumination re-reduction of P700+.\",\n \"corpus_id\": 15565694,\n \"score\": 1\n },\n {\n \"doc_id\": \"18445472\",\n \"title\": \"Competitive inhibition of electron donation to photosystem 1 by metal-substituted plastocyanin.\",\n \"abstract\": \"The electron transfer from wild-type spinach plastocyanin (Pc) to photosystem 1 has been studied by flash-induced absorption changes at 830 nm. The decay kinetics of photo-oxidized P700 are drastically slower in the presence of Ag(I)-substituted Pc, while addition of Zn(II)-substituted Pc has a weaker effect. The metal-substituted forms of Pc act as competitive inhibitors of the reaction between normal, Cu-containing, Pc and P700. The inhibition constants obtained from an analysis of the kinetic data were 30 and 410 microM for Ag(I)- and Zn(II)-substituted Pc, respectively. When the Gly8Asp mutant form of Pc was used instead of the wild-type form, the corresponding values were found to be 77 and 442 microM. If the Ag- and Zn-derivatives can be considered as structural mimics of reduced and oxidized CuPc, respectively, our results imply that there is a redox-induced decrease in the affinity between Pc and photosystem 1 that follows the electron donation to P700. Our data also imply that the Gly8Asp mutation can diminish the magnitude of this change. The findings reported here are consistent with a reaction mechanism where the electron transfer in the complex between Pc and photosystem 1 is assumed to be reversible.\",\n \"corpus_id\": 24078152,\n \"score\": 1\n },\n {\n \"doc_id\": \"18563623\",\n \"title\": \"Elucidating the site of action of oxalate in photosynthetic electron transport chain in spinach thylakoid membranes.\",\n \"abstract\": \"The effects of oxalate on PS II and PS I photochemistry were studied. The results suggested that in chloride-deficient thylakoid membranes, oxalate inhibited activity of PS II as well as PS I. To our knowledge, this is the only anion so far known which inhibits both the photosystems. Measurements of fluorescence induction kinetics, YZ* decay, and S2 state multiline EPR signal suggested that oxalate inhibited PS II at the donor side most likely on the oxygen evolving complex. Measurements of re-reduction of P700+ signal in isolated PS I particles in oxalate-treated samples suggested a binding site of oxalate on the donor, as well as the acceptor side of PS I.\",\n \"corpus_id\": 11340623,\n \"score\": 1\n },\n {\n \"doc_id\": \"18688503\",\n \"title\": \"Quantum yield of P700+ photodestruction in isolated photosystem I complexes of the cyanobacterium Arthrospira platensis.\",\n \"abstract\": \"The photostability of P700 cation radical (P700+) was studied by evaluating the quantum yields of P700(+) photodestruction in photosystem I (PSI) complexes of the cyanobacterium Arthrospira platensis. The time courses of P700+ photodestruction in PSI trimers and monomers have been measured in aerobic conditions under selective excitation of far-red absorption band of P700+ by intense light of laser diodes. Long-term exposure of PSI complexes to 808 or 870 nm laser light caused destruction of P700+ and antenna chlorophylls. The true integral quantum yield of P700+ photodestruction calculated from these data was less than 0.7-1.4 x 10(-8). Illumination of PSI complexes by 650 nm light caused destruction of antenna chlorophylls with true quantum yield of about 6-7 x 10(-6) and damage of P700 with apparent quantum yield 2-3 x 10(-8). Preferential photodestruction of the long-wavelength antenna chlorophyll absorbing at 710 nm as compared with bulk chlorophylls was observed. About three orders of difference in magnitude between quantum yields of P700+ and bulk chlorophyll photodestruction indicates that P700+ is extremely photostable for functioning as an efficient quencher of singlet excitation energy in PSI.\",\n \"corpus_id\": 205707552,\n \"score\": 1\n },\n {\n \"doc_id\": \"18975133\",\n \"title\": \"Reduction of the primary donor P700 of photosystem I during steady-state photosynthesis under low light in Arabidopsis.\",\n \"abstract\": \"During steady-state photosynthesis in low-light, 830-nm absorption (A(830)) by leaves was close to that in darkness in Arabidopsis, indicating that the primary donor P700 in the reaction center of photosystem I (PSI) was in reduced form. However, P700 was not fully oxidized by a saturating light pulse, suggesting the presence of a population of PSI centers with reduced P700 that remains thermodynamically stable during the application of the saturating light pulse (i.e., reduced-inactive P700). To substantiate this, the effects of methyl viologen (MV) and far-red light on P700 oxidation by the saturating light pulse were analyzed, and the cumulative effects of repetitive application of the saturating light pulse on photosynthesis were analyzed using a mutant crr2-2 with impaired PSI cyclic electron flow. We concluded that the reduced-inactive P700 in low-light as revealed by saturating light pulse indicates limitations of electron flow at the PSI acceptor side.\",\n \"corpus_id\": 723157,\n \"score\": 1\n },\n {\n \"doc_id\": \"19289096\",\n \"title\": \"Functional complementation of the Arabidopsis thaliana psbo1 mutant phenotype with an N-terminally His6-tagged PsbO-1 protein in photosystem II.\",\n \"abstract\": \"The Arabidopsis thaliana mutant psbo1 has recently been described and characterized. Loss of expression of the PsbO-1 protein leads to a variety of functional perturbations including elevated levels of the PsbO-2 protein and defects on both the oxidizing- and reducing-sides of Photosystem II. In this communication, two plant lines were produced using the psbo1 mutant as transgenic host, which contained an N-terminally histidine(6)-tagged PsbO-1 protein. This protein was expressed and correctly targeted into the thylakoid lumen. Immunological analysis indicated that different levels of expression of the modified PsbO-1 protein were obtained in different transgenic plant lines and that the level of expression in each line was stable over several generations. Examination of the Photosystem II closure kinetics demonstrated that the defective double reduction of Q(B) and the delayed exchange of Q(B)H(2) with the plastoquinone pool which were observed during the characterization of the psbo1 mutant were effectively restored to wild-type levels by the His(6)-tagged PsbO-1 protein. Flash fluorescence induction and decay were also examined. Our results indicated that high expression of the modified PsbO-1 was required to increase the ratio of PS II(alpha)/PS II(beta) reaction centers to wild-type levels. Fluorescence decay kinetics in the absence of DCMU indicated that the expression of the His(6)-tagged PsbO-1 protein restored efficient electron transfer to Q(B), while in the presence of DCMU, charge recombination between Q(A)(-) and the S(2) state of the oxygen-evolving complex occurred at near wild-type rates. Our results indicate that high expression of the His(6)-tagged PsbO-1 protein efficiently complements nearly all of the photochemical defects observed in the psbo1 mutant. Additionally, this study establishes a platform on which the in vivo consequences of site-directed mutagenesis of the PsbO-1 protein can be examined.\",\n \"corpus_id\": 34270486,\n \"score\": 1\n },\n {\n \"doc_id\": \"19761751\",\n \"title\": \"Effect of the P700 pre-oxidation and point mutations near A(0) on the reversibility of the primary charge separation in Photosystem I from Chlamydomonas reinhardtii.\",\n \"abstract\": \"Time-resolved fluorescence studies with a 3-ps temporal resolution were performed in order to: (1) test the recent model of the reversible primary charge separation in Photosystem I (Müller et al., 2003; Holwzwarth et al., 2005, 2006), and (2) to reconcile this model with a mechanism of excitation energy quenching by closed Photosystem I (with P700 pre-oxidized to P700+). For these purposes, we performed experiments using Photosystem I core samples isolated from Chlamydomonas reinhardtii wild type, and two mutants in which the methionine axial ligand to primary electron acceptor, A(0), has been change to either histidine or serine. The temporal evolution of fluorescence spectra was recorded for each preparation under conditions where the \\\"primary electron donor,\\\" P700, was either neutral or chemically pre-oxidized to P700+. For all the preparations under study, and under neutral and oxidizing conditions, we observed multiexponential fluorescence decay with the major phases of approximately 7 ps and approximately 25 ps. The relative amplitudes and, to a minor extent the lifetimes, of these two phases were modulated by the redox state of P700 and by the mutations near A(0): both pre-oxidation of P700 and mutations caused slight deceleration of the excited state decay. These results are consistent with a model in which P700 is not the primary electron donor, but rather a secondary electron donor, with the primary charge separation event occurring between the accessory chlorophyll, A, and A(0). We assign the faster phase to the equilibration process between the excited state of the antenna/reaction center ensemble and the primary radical pair, and the slower phase to the secondary electron transfer reaction. The pre-oxidation of P700 shifts the equilibrium between the excited state and the primary radical pair towards the excited state. This shift is proposed to be induced by the presence of the positive charge on P700+. The same charge is proposed to be responsible for the fast A+A(0)(-)-->AA(0) charge recombination to the ground state and, in consequence, excitation quenching in closed reaction centers. Mutations of the A(0) axial ligand shift the equilibrium in the same direction as pre-oxidation of P700 due to the up-shift of the free energy level of the state A+A(0)(-).\",\n \"corpus_id\": 205795038,\n \"score\": 1\n },\n {\n \"doc_id\": \"20480090\",\n \"title\": \"Evidence that pH can drive state transitions in isolated thylakoid membranes from spinach.\",\n \"abstract\": \"Our observation that the F735/F685 ratio at 77 K increased when the lumenal pH decreased led us to investigate the role of pH in explaining the mechanism of state transitions in spinach (Spinacea oleracea L.) thylakoid membranes. As the lumenal pH was changed from pH 7.5 to 5.5, the quantum yield of PS II decreased, while that of PS I increased. In the presence of an uncoupler, NH(4)Cl, which sequesters protons, a reversal of the effects observed at pH 5.5 were noticed. The thylakoid membranes treated with NaF at pH 5.5, when suspended in a buffer of pH 7.5, showed enhanced PS II fluorescence and a decreased PS I fluorescence, suggesting migration of LHC II back to PS II from PS I. The results presented here suggest for the first time that the lumenal pH of thylakoid membranes regulates the migration of antenna, and hence the energy distribution, between the two photosystems, i.e. a low lumenal pH (pH 5.5) favors antenna migration from PS II to PS I. At pH 7.5, the deprotonation of LHC II antenna attached to PS I leads to back migration of LHC II to PS II.\",\n \"corpus_id\": 13539122,\n \"score\": 1\n },\n {\n \"doc_id\": \"20643811\",\n \"title\": \"Short flashes and continuous light have similar photoinhibitory efficiency in intact leaves.\",\n \"abstract\": \"Lincomycin-treated pumpkin leaves were illuminated with either continuous light or saturating single-turnover xenon flashes to study the dependence of photoinactivation of photosystem II (PSII) on the mode of delivery of light. The flash energy and the time interval between the flashes were varied between the experiments, and photoinactivation was measured with oxygen evolution and the ratio of variable to maximum fluorescence (F(v)/F(m)). The photoinhibitory efficiency of saturating xenon flashes was found to be directly proportional to flash energy and independent of the time interval between the flashes. These findings indicate that a low-light-specific mechanism, based on charge recombination between PSII electron acceptors and the oxygen-evolving complex, is not the main cause of photoinactivation caused by short flashes in vivo. Furthermore, the relationship between the rate constant of photoinactivation and photon flux density was similar for flashes and continuous light when F(v)/F(m) was used to quantify photoinactivation, suggesting that continuous-light photoinactivation has a mechanism in which the quantum yield does not depend on the mode of delivery of light. A similar quantum yield of photoinhibition for flashes and continuous light is compatible with the manganese-based photoinhibition mechanism and with mechanisms in which singlet oxygen, produced via a direct photosensitization reaction, is the agent of damage. However, the classical acceptor-side and donor-side mechanisms do not predict a similar quantum yield for flashes and continuous light.\",\n \"corpus_id\": 100069,\n \"score\": 1\n },\n {\n \"doc_id\": \"20705115\",\n \"title\": \"Computational analysis of fluorescence induction curves in intact spinach leaves treated at different pH.\",\n \"abstract\": \"Effects of change in pH have been investigated on spinach leaf discs by measuring fluorescence induction kinetics using plant efficiency analyzer (PEA). On the basis of computational analysis of the results, we have reported that acidic pH causes a significant inhibition of the donor and the acceptor side of PS II. Energy flux models have been presented using the software Biolyzer HP 3. Effects of pH were investigated on the antenna size heterogeneity of PS II and a relative change in the proportions of α, β, and γ centers was observed.\",\n \"corpus_id\": 39301839,\n \"score\": 1\n },\n {\n \"doc_id\": \"20951762\",\n \"title\": \"PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies.\",\n \"abstract\": \"Our recently presented PS II model (Belyaeva et al., 2008) was improved in order to permit a consistent simulation of Single Flash Induced Transient Fluorescence Yield (SFITFY) traces that were earlier measured by Steffen et al. (2005) on whole leaves of Arabidopsis (A.) thaliana at four different energies of the actinic flash. As the essential modification, the shape of the actinic flash was explicitly taken into account assuming that an exponentially decaying rate simulates the time dependent excitation of PS II by the 10 ns actinic flash. The maximum amplitude of this excitation exceeds that of the measuring light by 9 orders of magnitude. A very good fit of the SFITFY data was achieved in the time domain from 100 ns to 10s for all actinic flash energies (the maximum energy of 7.5 × 10¹⁶ photons/(cm²flash) is set to 100%, the relative energies of weaker actinic flashes were of ∼8%, 4%, ∼1%). Our model allows the calculation and visualization of the transient PS II redox state populations ranging from the dark adapted state, via excitation energy and electron transfer steps induced by pulse excitation, followed by final relaxation into the stationary state eventually attained under the measuring light. It turned out that the rate constants of electron transfer steps are invariant to intensity of the actinic laser flash. In marked contrast, an increase of the actinic flash energy by more than two orders of magnitude from 5.4×10¹⁴ photons/(cm²flash) to 7.5×10¹⁶ photons/(cm²flash), leads to an increase of the extent of fluorescence quenching due to carotenoid triplet (³Car) formation by a factor of 14 and of the recombination reaction between reduced primary pheophytin (Phe(-)) and P680(+) by a factor of 3 while the heat dissipation in the antenna complex remains virtually constant. The modified PS II model offers new opportunities to compare electron transfer and dissipative parameters for different species (e.g. for the green algae and the higher plant) under varying illumination conditions.\",\n \"corpus_id\": 10270339,\n \"score\": 1\n },\n {\n \"doc_id\": \"21238459\",\n \"title\": \"Structural investigation of PsbO from plant and cyanobacterial photosystem II.\",\n \"abstract\": \"The manganese-stabilizing protein PsbO is associated with the luminal side of thylakoids close to the redox-active Mn(4)Ca cluster at the catalytically active site of photosystem II (PSII). PsbO is believed to increase the efficiency of oxygen evolution and to stabilize the Mn(4)Ca cluster against photoinhibition. Using small-angle X-ray scattering, we investigated the low-resolution structure of wild-type spinach PsbO and that of chimeric spinach PsbO fused with maltose-binding protein. Small-angle X-ray scattering data revealed that both proteins are monomeric in solution, and that plant and cyanobacterial PsbO have similar structures. We show a highly efficient expression system that allows recombinant production of the active wild type and the chimeric PsbO from spinach and cyanobacteria, with yields compatible with biophysical and structural studies. The binding of spinach PsbO fused with maltose-binding protein to PSII depleted of extrinsic subunits (PSII-ΔpsbO,P,Q) was confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The reconstituted PSII was shown to have similar oxygen evolution rates as obtained with wild-type spinach PsbO.\",\n \"corpus_id\": 11610246,\n \"score\": 1\n },\n {\n \"doc_id\": \"21357184\",\n \"title\": \"The physiological role of ascorbate as photosystem II electron donor: protection against photoinactivation in heat-stressed leaves.\",\n \"abstract\": \"Previously, we showed that ascorbate (Asc), by donating electrons to photosystem II (PSII), supports a sustained electron transport activity in leaves in which the oxygen-evolving complexes were inactivated with a heat pulse (49°C, 40 s). Here, by using wild-type, Asc-overproducing, and -deficient Arabidopsis (Arabidopsis thaliana) mutants (miox4 and vtc2-3, respectively), we investigated the physiological role of Asc as PSII electron donor in heat-stressed leaves (40°C, 15 min), lacking active oxygen-evolving complexes. Chlorophyll-a fluorescence transients show that in leaves excited with trains of saturating single-turnover flashes spaced 200 ms apart, allowing continual electron donation from Asc to PSII, the reaction centers remained functional even after thousands of turnovers. Higher flash frequencies or continuous illumination (300 μmol photons m(-2) s(-1)) gradually inactivated them, a process that appeared to be initiated by a dramatic deceleration of the electron transfer from Tyr(Z) to P680(+), followed by the complete loss of charge separation activity. These processes occurred with half-times of 1.2 and 10 min, 2.8 and 23 min, and 4.1 and 51 min in vtc2-3, the wild type, and miox4, respectively, indicating that the rate of inactivation strongly depended on the Asc content of the leaves. The recovery of PSII activity, following the degradation of PSII proteins (D1, CP43, and PsbO), in moderate light (100 μmol photons m(-2) s(-1), comparable to growth light), was also retarded in the Asc-deficient mutant. These data show that high Asc content of leaves contributes significantly to the ability of plants to withstand heat-stress conditions.\",\n \"corpus_id\": 20815127,\n \"score\": 1\n },\n {\n \"doc_id\": \"21429906\",\n \"title\": \"Species dependence of the redox potential of the primary electron donor p700 in photosystem I of oxygenic photosynthetic organisms revealed by spectroelectrochemistry.\",\n \"abstract\": \"The redox potential of the primary electron donor P700, E(m)(P700/P700(+)), of Photosystem I (PSI) has been determined for 10 oxygenic photosynthesis organisms, ranging from cyanobacteria, red algae, green algae to higher plants, by spectroelectrochemistry with an optically transparent thin-layer electrode (OTTLE) cell to elucidate the scattering by as much as 150 mV in reported values of E(m)(P700/P700(+)). The E(m)(P700/P700(+)) values determined within error ranges of ± 1-4 mV exhibited a significant species dependence, with a span >70 mV, from +398 to +470 mV vs. the standard hydrogen electrode (SHE). The E(m)(P700/P700(+)) value appears to change systematically in going from cyanobacteria and primitive eukaryotic red algae, then to green algae and higher plants. From an evolutionary point of view, this result suggests that the species believed to appear later in evolution of photosynthetic organisms exhibit higher values of E(m)(P700/P700(+)). Further, the species dependence of E(m)(P700/P700(+)) seems to originate in the species-dependent redox potentials of soluble metalloproteins, Cyt c(6) and plastocyanin, which re-reduce the oxidized P700 in the electron transfer chain.\",\n \"corpus_id\": 21548127,\n \"score\": 1\n },\n {\n \"doc_id\": \"21546369\",\n \"title\": \"Cold stress effects on PSI photochemistry in Zea mays: differential increase of FQR-dependent cyclic electron flow and functional implications.\",\n \"abstract\": \"Cold-induced inhibition of CO(2) assimilation in maize (Zea mays L.) is associated with a persistent depression of the photochemical efficiency of PSII. However, very limited information is available on PSI photochemistry and PSI-dependent electron flow in cold-stressed maize. The extent of the absorbance change (ΔA(820)) used for in vivo quantitative estimation of photooxidizable P700(+) indicated a 32% lower steady-state oxidation level of the PSI reaction center P700 (P700(+)) in cold-stressed compared with control maize leaves. This was accompanied by a 2-fold faster re-reduction rate of P700(+) in the dark, indicating a higher capacity for cyclic electron flow (CEF) around PSI in cold-stressed maize leaves. Furthermore, the increased PSI-dependent CEF(s) was associated with a much higher stromal electron pool size and 56% lower capacity for state transitions compared with control plants. To examine NADP(H) dehydrogenase (NDH)- and ferredoxin:plastoquinone oxidoreductase (FQR)-dependent CEF in vivo, the post-illumination transient increase of F(o)' was measured in the presence of electron transport inhibitors. The results indicate that under optimal growth conditions the relatively low CEF in the maize mesophyll cells is mostly due to the NDH-dependent pathway. However, the increased CEF in cold-stressed plants appears to originate from the up-regulated FQR pathway. The physiological role of PSI down-regulation, the increased capacity for CEF and the shift of preferred CEF mode in modulating the photosynthetic electron fluxes and distribution of excitation light energy in maize plants under cold stress conditions are discussed.\",\n \"corpus_id\": 10623255,\n \"score\": 1\n },\n {\n \"doc_id\": \"21777563\",\n \"title\": \"Fluorescence of the various red antenna states in photosystem I complexes from cyanobacteria is affected differently by the redox state of P700.\",\n \"abstract\": \"Photosystem I of cyanobacteria contains different spectral pools of chlorophylls called red or long-wavelength chlorophylls that absorb at longer wavelengths than the primary electron donor P700. We measured the fluorescence spectra at the ensemble and the single-molecule level at low temperatures in the presence of oxidized and reduced P700. In accordance with the literature, it was observed that the fluorescence is quenched by P700(+). However, the efficiency of the fluorescence quenching by oxidized P700(+) was found to be extremely different for the various red states in PS I from different cyanobacteria. The emission of the longest-wavelength absorbing antenna state in PS I trimers from Thermosynechococcus elongatus (absorption maximum at 5K: ≈ 719nm; emission maximum at 5K: ≈ 740nm) was found to be strongly quenched by P700(+) similar to the reddest state in PS I trimers from Arthrospira platensis emitting at 760nm at 5K. The fluorescence of these red states is diminished by more than a factor of 10 in the presence of oxidized P700. For the first time, the emission of the reddest states in A. platensis and T. elongatus has been monitored using single-molecule fluorescence techniques.\",\n \"corpus_id\": 21898417,\n \"score\": 1\n },\n {\n \"doc_id\": \"21910736\",\n \"title\": \"Thermoluminescence and P700 redox kinetics as complementary tools to investigate the cyclic/chlororespiratory electron pathways in stress conditions in barley leaves.\",\n \"abstract\": \"Cyclic electron flow around photosystem I drives additional proton pumping into the thylakoid lumen, which enhances the protective non-photochemical quenching and increases ATP synthesis. It involves several pathways activated independently. In whole barley leaves, P700 oxidation under far-red illumination and subsequent P700(+) dark reduction kinetics provide a major probe of the activation of cyclic pathways. Two 'intermediate' and 'slow' exponential reduction phases are always observed and they become faster after high light illumination, but dark inactivation of the Benson-Calvin cycle causes the emergence of both a transient in the P700 oxidation and a 'fast' phase in the P700(+) reduction. We investigate here the afterglow (AG) thermoluminescence emission as another tool to detect the activation of cyclic electron pathways from stroma reductants to the acceptor side of photosystem II. This transfer is activated by warming, yielding an AG band at about 45°C. However, treatments that accelerate the 'intermediate' and 'slow' P700(+) reduction phases (brief anoxia, hexose infiltration, fast dehydration of excised leaves) also produced a downshift of this AG band. This pathway ascribable to NADPH dehydrogenase (NDH) would be triggered by a deficit in ATP, while the 'fast' reduction phase corresponding to the ferredoxin plastoquinone reductase pathway is triggered by an overreduction of the photosystem I acceptor pool and is undetected in thermoluminescence. Contrastingly, slow dehydration of unwatered plants did not cause faster reduction of P700(+) nor temperature downshift of the AG band, that is no induction of the NDH pathway, whereas an increased intensity of the AG band indicated a strong NADPH + ATP assimilatory potential.\",\n \"corpus_id\": 26725453,\n \"score\": 1\n },\n {\n \"doc_id\": \"22644475\",\n \"title\": \"The time course of photoinactivation of photosystem II in leaves revisited.\",\n \"abstract\": \"Since photosystem II (PS II) performs the demanding function of water oxidation using light energy, it is susceptible to photoinactivation during photosynthesis. The time course of photoinactivation of PS II yields useful information about the process. Depending on how PS II function is assayed, however, the time course seems to differ. Here, we revisit this problem by using two additional assays: (1) the quantum yield of oxygen evolution in limiting, continuous light and (2) the flash-induced cumulative delivery of PS II electrons to the oxidized primary donor (P700(+)) in PS I measured as a 'P700 kinetics area'. The P700 kinetics area is based on the fact that the two photosystems function in series: when P700 is completely photo-oxidized by a flash added to continuous far-red light, electrons delivered from PS II to PS I by the flash tend to re-reduce P700(+) transiently to an extent depending on the PS II functionality, while the far-red light photo-oxidizes P700 back to the steady-state concentration. The quantum yield of oxygen evolution in limiting, continuous light indeed decreased in a way that deviated from a single-negative exponential. However, measurement of the quantum yield of oxygen in limiting light may be complicated by changes in mitochondrial respiration between darkness and limiting light. Similarly, an assay based on chlorophyll fluorescence may be complicated by the varying depth in leaf tissue from which the signal is detected after progressive photoinactivation of PS II. On the other hand, the P700 kinetics area appears to be a reasonable assay, which is a measure of functional PS II in the whole leaf tissue and independent of changes in mitochondrial respiration. The P700 kinetics area decreased in a single-negative exponential fashion during progressive photoinactivation of PS II in a number of plant species, at least at functional PS II contents ≥6 % of the initial value, in agreement with the conclusion of Sarvikas et al. (Photosynth Res 103:7-17, 2010). That is, the single-negative-exponential time course does not provide evidence for photoprotection of functional PS II complexes by photoinactivated, connected neighbours.\",\n \"corpus_id\": 13513107,\n \"score\": 1\n },\n {\n \"doc_id\": \"22922640\",\n \"title\": \"Antisense reductions in the PsbO protein of photosystem II leads to decreased quantum yield but similar maximal photosynthetic rates.\",\n \"abstract\": \"Photosystem (PS) II is the multisubunit complex which uses light energy to split water, providing the reducing equivalents needed for photosynthesis. The complex is susceptible to damage from environmental stresses such as excess excitation energy and high temperature. This research investigated the in vivo photosynthetic consequences of impairments to PSII in Arabidopsis thaliana (ecotype Columbia) expressing an antisense construct to the PsbO proteins of PSII. Transgenic lines were obtained with between 25 and 60% of wild-type (WT) total PsbO protein content, with the PsbO1 isoform being more strongly reduced than PsbO2. These changes coincided with a decrease in functional PSII content. Low PsbO (less than 50% WT) plants grew more slowly and had lower chlorophyll content per leaf area. There was no change in content per unit area of cytochrome b6f, ATP synthase, or Rubisco, whereas PSI decreased in proportion to the reduction in chlorophyll content. The irradiance response of photosynthetic oxygen evolution showed that low PsbO plants had a reduced quantum yield, but matched the oxygen evolution rates of WT plants at saturating irradiance. It is suggested that these plants had a smaller pool of PSII centres, which are inefficiently connected to antenna pigments resulting in reduced photochemical efficiency.\",\n \"corpus_id\": 52837249,\n \"score\": 1\n },\n {\n \"doc_id\": \"23183256\",\n \"title\": \"Excess manganese differentially inhibits photosystem I versus II in Arabidopsis thaliana.\",\n \"abstract\": \"The effects of exposure to increasing manganese concentrations (50-1500 µM) from the start of the experiment on the functional performance of photosystem II (PSII) and photosystem I (PSI) and photosynthetic apparatus composition of Arabidopsis thaliana were compared. In agreement with earlier studies, excess Mn caused minimal changes in the PSII photochemical efficiency measured as F(v)/F(m), although the characteristic peak temperature of the S(2/3)Q(B) (-) charge recombinations was shifted to lower temperatures at the highest Mn concentration. SDS-PAGE and immunoblot analyses also did not exhibit any significant change in the relative abundance of PSII-associated polypeptides: PSII reaction centre protein D1, Lhcb1 (major light-harvesting protein of LHCII complex), and PsbO (OEC33, a 33 kDa protein of the oxygen-evolving complex). In addition, the abundance of Rubisco also did not change with Mn treatments. However, plants grown under excess Mn exhibited increased susceptibility to PSII photoinhibition. In contrast, in vivo measurements of the redox transients of PSI reaction centre (P700) showed a considerable gradual decrease in the extent of P700 photooxidation (P700(+)) under increased Mn concentrations compared to control. This was accompanied by a slower rate of P700(+) re-reduction indicating a downregulation of the PSI-dependent cyclic electron flow. The abundance of PSI reaction centre polypeptides (PsaA and PsaB) in plants under the highest Mn concentration was also significantly lower compared to the control. The results demonstrate for the first time that PSI is the major target of Mn toxicity within the photosynthetic apparatus of Arabidopsis plants. The possible involvement mechanisms of Mn toxicity targeting specifically PSI are discussed.\",\n \"corpus_id\": 52809861,\n \"score\": 1\n },\n {\n \"doc_id\": \"23220185\",\n \"title\": \"Damage of photosynthetic apparatus in the senescing basal leaf of Arabidopsis thaliana: a plausible mechanism of inactivation of reaction center II.\",\n \"abstract\": \"Significant decline in oxygen evolution and DCPIP photoreduction and a marginal restoration of the later with DPC as an electron donor suggest the inactivation of reaction center of photosystem II. The declines in the height of thermoluminescence bands support the view and the damage of reaction center II could be central to the senescence process in Arabidopsis leaves. The enhancement in the number of reduced quinones, signifying a loss in redox homeostasis in the electron transport chain between photosystem II and I leads to the creation of an energy imbalance. The view is supported by the decline in actual quantum yield of photosystem II in the light adapted state and maximum quantum yield of primary photochemistry in the dark adapted state of chlorophyll fluorescence. An increase in chlorophyll a fluorescence polarization and decline in carotenoid to chlorophyll energy transfer efficiency suggest the perturbation in thylakoid structure. A plausible mechanism illustrating the senescence mediated inactivation of oxygen evolving complex has been proposed.\",\n \"corpus_id\": 9647929,\n \"score\": 1\n },\n {\n \"doc_id\": \"23273864\",\n \"title\": \"Photoinhibition of Photosystem II.\",\n \"abstract\": \"Photoinhibition of Photosystem II (PSII) is the light-induced loss of PSII electron-transfer activity. Although photoinhibition has been studied for a long time, there is no consensus about its mechanism. On one hand, production of singlet oxygen ((1)O(2)) by PSII has promoted models in which this reactive oxygen species (ROS) is considered to act as the agent of photoinhibitory damage. These chemistry-based models have often not taken into account the photophysical features of photoinhibition-like light response and action spectrum. On the other hand, models that reproduce these basic photophysical features of the reaction have not considered the importance of data about ROS. In this chapter, it is shown that the evidence behind the chemistry-based models and the photophysically oriented models can be brought together to build a mechanism that confirms with all types of experimental data. A working hypothesis is proposed, starting with inhibition of the manganese complex by light. Inability of the manganese complex to reduce the primary donor promotes recombination between the oxidized primary donor and Q(A), the first stable quinone acceptor of PSII. (1)O(2) production due to this recombination may inhibit protein synthesis or spread the photoinhibitory damage to another PSII center. The production of (1)O(2) is transient because loss of activity of the oxygen-evolving complex induces an increase in the redox potential of Q(A), which lowers (1)O(2) production.\",\n \"corpus_id\": 23331378,\n \"score\": 1\n },\n {\n \"doc_id\": \"23340737\",\n \"title\": \"Probing the picosecond kinetics of the photosystem II core complex in vivo.\",\n \"abstract\": \"Photosystems I (PSI) and II (PSII) are two major pigment-protein complexes of photosynthetic organisms that function in series to convert sunlight energy into chemical energy. We have studied the picosecond fluorescence behaviour of the core of both photosystems in vivo by using two Synechocystis PCC 6803 mutants: BE cells contain PSI but are lacking both PSII and the light-harvesting complexes called phycobilisomes (PBs) whereas PAL cells contain both PSI and PSII but lack the PBs. Measurements were performed at room temperature and at 77 K. The fluorescence kinetics of PSI and PSII can nicely be separated, en passant providing the PSI/PSII ratio. At room temperature, the PSI kinetics are identical to those of isolated PSI whereas the PSII kinetics can equally well be described by the in vitro trap-limited model of Y. Miloslavina, M. Szczepaniak, M. G. Muller, J. Sander, M. Nowaczyk, M. Rogner and A. R. Holzwarth, Biophys J., 2009, 96(2), 621-631, and by the transfer-to-the-trap-limited model of C. D. van der Weij-de Wit, J. P. Dekker, R. van Grondelle and I. H. M. van Stokkum, J. Phys. Chem. A, 2011, 115(16), 3947-3956, albeit that the in vivo kinetics turn out to be somewhat slower. At 77 K several low-energy pigments are observed in both photosystems which complicate the overall dynamics but the PSII kinetics can still be described by both a trap-limited and a transfer-to-the-trap-limited model.\",\n \"corpus_id\": 6088644,\n \"score\": 1\n },\n {\n \"doc_id\": \"23747063\",\n \"title\": \"How does iron deficiency disrupt the electron flow in photosystem I of lettuce leaves?\",\n \"abstract\": \"The changes observed photosystem I activity of lettuce plants exposed to iron deficiency were investigated. Photooxidation/reduction kinetics of P700 monitored as ΔA820 in the presence and absence of electron transport inhibitors and acceptors demonstrated that deprivation in iron decreased the population of active photo-oxidizable P700. In the complete absence of iron, the addition of plant inhibitors (DCMU and MV) could not recover the full PSI activity owing to the abolition of a part of P700 centers. In leaves with total iron deprivation (0μM Fe), only 15% of photo-oxidizable P700 remained. In addition, iron deficiency appeared to affect the pool size of NADP(+) as shown by the decline in the magnitude of the first phase of the photooxidation kinetics of P700 by FR-light. Concomitantly, chlorophyll content gradually declined with the iron concentration added to culture medium. In addition, pronounced changes were found in chlorophyll fluorescence spectra. Also, the global fluorescence intensity was affected. The above changes led to an increased rate of cyclic electron transport around PSI mainly supported by stromal reductants.\",\n \"corpus_id\": 33730978,\n \"score\": 1\n },\n {\n \"doc_id\": \"24553846\",\n \"title\": \"Roles of the cyclic electron flow around PSI (CEF-PSI) and O₂-dependent alternative pathways in regulation of the photosynthetic electron flow in short-term fluctuating light in Arabidopsis thaliana.\",\n \"abstract\": \"To assess the roles of the cyclic electron flow around PSI (CEF-PSI) and O₂-dependent alternative pathways including the water-water cycle in fluctuating light, we grew the wild type and pgr5 mutant of Arabidopsis thaliana in constant light, and measured Chl fluorescence and P700 parameters in their leaves in the fluctuating light alternating between 240 (HL) and 30 µmol photons m⁻² s⁻² (LL) every 2 min. At 20% O₂, the photochemical quantum yield of PSII decreased, in particular in the pgr5 plants, soon after the start of the fluctuating light treatment. PSI of the pgr5 plants was markedly photoinhibited by this treatment for 42 min. Slight PSI photoinhibition was also observed in the wild type. We measured energy sharing between PSII and PSI and estimated the PSI and PSII electron transport rates (ETRs). pgr5 showed larger energy allocation to PSI. In contrast to the wild type, the ratio of the PSI to the PSII ETR in pgr5 was higher in LL but lower in HL at 20% O₂ due to PSI acceptor-side limitation. At 2.7% or 0% O₂, the CEF-PSI of the pgr5 plants was enhanced, the acceptor-side limitation of PSI electron flow was released and PSI photoinhibition was not observed. The results suggest that the light fluctuation is a potent stress to PSI and that the CEF-PSI is essential to protect PSI from this stress.\",\n \"corpus_id\": 26442906,\n \"score\": 1\n },\n {\n \"doc_id\": \"25008325\",\n \"title\": \"The PsbP domain protein 1 functions in the assembly of lumenal domains in photosystem I.\",\n \"abstract\": \"Photosystem I (PS I) is a multisubunit membrane protein complex that functions as a light-driven plastocyanin-ferredoxin oxidoreductase. The PsbP domain protein 1 (PPD1; At4g15510) is located in the thylakoid lumen of plant chloroplasts and is essential for photoautotrophy, functioning as a PS I assembly factor. In this work, RNAi was used to suppress PPD1 expression, yielding mutants displaying a range of phenotypes with respect to PS I accumulation and function. These PPD1 RNAi mutants showed a loss of assembled PS I that was correlated with loss of the PPD1 protein. In the most severely affected PPD1 RNAi lines, the accumulated PS I complexes exhibited defects in electron transfer from plastocyanin to the oxidized reaction center P700 (+). The defects in PS I assembly in the PPD1 RNAi mutants also had secondary effects with respect to the association of light-harvesting antenna complexes to PS I. Because of the imbalance in photosystem function in the PPD1 RNAi mutants, light-harvesting complex II associated with and acted as an antenna for the PS I complexes. These results provide new evidence for the role of PPD1 in PS I biogenesis, particularly as a factor essential for proper assembly of the lumenal portion of the complex.\",\n \"corpus_id\": 30642262,\n \"score\": 1\n },\n {\n \"doc_id\": \"25023284\",\n \"title\": \"Defining the far-red limit of photosystem I: the primary charge separation is functional to 840 nm.\",\n \"abstract\": \"The far-red limit of photosystem I (PS I) photochemistry was studied by EPR spectroscopy using laser flashes between 730 and 850 nm. In manganese-depleted spinach thylakoid membranes, the primary donor in PS I, P700, was oxidized simultaneously with tyrosine Z, the secondary donor in PS II. It was found that at 295 K PS I photochemistry, observed as P700 (+) formation, was functional up to 840 nm. This is 30 nm further to the red region than was reported for PS II photochemistry (Thapper, A., Mamedov, F., Mokvist, F., Hammarström, L., and Styring, S. (2009) Plant Cell 21, 2391-2401). The same far-red limit for the P700 (+) formation was observed in a PS I reaction center core preparation from Nostoc punctiforme. The reduction of the acceptor side of PS I, observed as reduction of the iron-sulfur centers FA and FB by low temperature EPR measurements, was also functional at 15 K with light up to >830 nm. Taken together, these results, obtained from both plants and cyanobacteria, most likely rule out involvement of the red-absorbing antenna chlorophylls in this reaction. Instead we propose the existence of weak charge transfer bands absorbing in the far-red region in the ensemble of excitonically coupled chlorophyll a molecules around P700 similar to what has been found in the reaction center of PS II. These charge transfer bands could be responsible for the far-red light absorption leading to PS I photochemistry at wavelengths up to 840 nm.\",\n \"corpus_id\": 24313038,\n \"score\": 1\n },\n {\n \"doc_id\": \"26101037\",\n \"title\": \"Photoinactivation of Photosystem II in wild-type and chlorophyll b-less barley leaves: which mechanism dominates depends on experimental circumstances.\",\n \"abstract\": \"Action spectra of photoinactivation of Photosystem II (PS II) in wild-type and chlorophyll b-less barley leaf segments were obtained. Photoinactivation of PS II was monitored by the delivery of electrons from PS II to PS I following single-turnover flashes superimposed on continuous far-red light, the time course of photoinactivation yielding a rate coefficient k i. Susceptibility of PS II to photoinactivation was quantified as the ratio of k i to the moderate irradiance (I) of light at each selected wavelength. k i/I was very much higher in blue light than in red light. The experimental conditions permitted little excess light energy absorbed by chlorophyll (not utilized in photochemical conversion or dissipated in controlled photoprotection) that could lead to photoinactivation of PS II. Therefore, direct absorption of light by Mn in PS II, rather than by chlorophyll, was more likely to have initiated the much more severe photoinactivation in blue light than in red light. Mutant leaves were ca. 1.5-fold more susceptible to photoinactivation than the wild type. Neither the excess-energy mechanism nor the Mn mechanism can explain this difference. Instead, the much lower chlorophyll content of mutant leaves could have exerted an exacerbating effect, possibly partly due to less mutual shading of chloroplasts in the mutant leaves. In general, which mechanism dominates depends on the experimental conditions.\",\n \"corpus_id\": 10226888,\n \"score\": 1\n },\n {\n \"doc_id\": \"27053032\",\n \"title\": \"Analysis of Photosystem I Donor and Acceptor Sides with a New Type of Online-Deconvoluting Kinetic LED-Array Spectrophotometer.\",\n \"abstract\": \"The newly developed Dual/KLAS-NIR spectrophotometer, technical details of which were reported very recently, is used in measuring redox changes of P700, plastocyanin (PC) and ferredoxin (Fd) in intact leaves of Hedera helix, Taxus baccata and Brassica napus An overview of various light-/dark-induced changes of deconvoluted P700(+), PC(+) and Fd(-) signals is presented demonstrating the wealth of novel information and the consistency of the obtained results. Fd(-) changes are particularly large after dark adaptation. PC oxidation precedes P700 oxidation during dark-light induction and in steady-state light response curves. Fd reoxidation during induction correlates with the secondary decline of simultaneously measured fluorescence yield, both of which are eliminated by removal of O2 By determination of 100% redox changes, relative contents of PC/P700 and Fd/P700 can be assessed, which show considerable variations between different leaves, with a trend to higher values in sun leaves. Based on deconvoluted P700(+) signals, the complementary quantum yields of PSI, Y(I) (photochemical energy use), Y(ND) (non-photochemical loss due to oxidized primary donor) and Y(NA) (non-photochemical loss due to reduced acceptor) are determined as a function of light intensity and compared with the corresponding complementary quantum yields of PSII, Y(II) (photochemical energy use), Y(NPQ) (regulated non-photochemical loss) and Y(NO) (non-regulated non-photochemical loss). The ratio Y(I)/Y(II) increases with increasing intensities. In the low intensity range, a two-step increase of PC(+) is indicative of heterogeneous PC pools.\",\n \"corpus_id\": 23923524,\n \"score\": 1\n },\n {\n \"doc_id\": \"27236700\",\n \"title\": \"PSI photoinhibition is more related to electron transfer from PSII to PSI rather than PSI redox state in Psychotria rubra.\",\n \"abstract\": \"Although it has been believed that wild-type plants are capable of protecting photosystem I (PSI) under high light, our previous study indicates that PSI is sensitive to high light in the shade-established tree species Psychotria rubra. However, the underlying physiological mechanisms are unclear. In this study, we examined the roles of electron transfer from PSII to PSI and PSI redox state in PSI photoinhibition in P. rubra by treatments with lincomycin (Lin), diuron (DCMU), and methyl viologen (MV). After exposure to 2000 μmol photons m(-2) s(-1) for 2 h, PSI activity decreased by 35, 29, 3, and 49 % in samples treated with H2O, Lin, DCMU, and MV, respectively. Meanwhile, the MV-treated samples showed higher P700 oxidation ratio than the H2O-treated samples, suggesting the PSI photoinhibition under high light was accompanied by high levels of P700 oxidation ratio. PSI photoinhibition was alleviated in the DCMU-treated samples but was accelerated in the MV-treated samples, suggesting that PSI photoinhibition in P. rubra was mainly controlled by electron transfer from PSII to PSI. Taking together, PSI photoinhibition is more related to electron transfer from PSII to PSI rather than PSI redox state in P. rubra, which is different from the mechanisms of PSI photoinhibition in Arabidopsis thaliana and cucumber.\",\n \"corpus_id\": 17683775,\n \"score\": 1\n },\n {\n \"doc_id\": \"27613853\",\n \"title\": \"Oxidation of P700 in Photosystem I Is Essential for the Growth of Cyanobacteria.\",\n \"abstract\": \"The photoinhibition of photosystem I (PSI) is lethal to oxygenic phototrophs. Nevertheless, it is unclear how photodamage occurs or how oxygenic phototrophs prevent it. Here, we provide evidence that keeping P700 (the reaction center chlorophyll in PSI) oxidized protects PSI. Previous studies have suggested that PSI photoinhibition does not occur in the two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942, when photosynthetic CO2 fixation was suppressed under low CO2 partial pressure even in mutants deficient in flavodiiron protein (FLV), which mediates alternative electron flow. The lack of FLV in Synechococcus sp. PCC 7002 (S. 7002), however, is linked directly to reduced growth and PSI photodamage under CO2-limiting conditions. Unlike Synechocystis sp. PCC 6803 and S. elongatus PCC 7942, S. 7002 reduced P700 during CO2-limited illumination in the absence of FLV, resulting in decreases in both PSI and photosynthetic activities. Even at normal air CO2 concentration, the growth of S. 7002 mutant was retarded relative to that of the wild type. Therefore, P700 oxidation is essential for protecting PSI against photoinhibition. Here, we present various strategies to alleviate PSI photoinhibition in cyanobacteria.\",\n \"corpus_id\": 44849856,\n \"score\": 1\n },\n {\n \"doc_id\": \"27738959\",\n \"title\": \"In vitro kinetics of P700(+) reduction of Thermosynechococcus elongatus trimeric Photosystem I complexes by recombinant cytochrome c 6 using a Joliot-type LED spectrophotometer.\",\n \"abstract\": \"The reduction rate of photo-oxidized Photosystem I (PSI) with various natural and artificial electron donors have been well studied by transient absorption spectroscopy. The electron transfer rate from various donors to P700(+) has been measured for a wide range of photosynthetic organisms encompassing cyanobacteria, algae, and plants. PSI can be a limiting component due to tedious extraction and purification methods required for this membrane protein. In this report, we have determined the in vivo, intracellular cytochrome c 6 (cyt c 6)/PSI ratio in Thermosynechococcus elongatus (T.e.) using quantitative Western blot analysis. This information permitted the determination of P700(+) reduction kinetics via recombinant cyt c 6 in a physiologically relevant ratio (cyt c 6: PSI) with a Joliot-type, LED-driven, pump-probe spectrophotometer. Dilute PSI samples were tested under varying cyt c 6 concentration, temperature, pH, and ionic strength, each of which shows similar trends to the reported literature utilizing much higher PSI concentrations with laser-based spectrophotometer. Our results do however indicate kinetic differences between actinic light sources (laser vs. LED), and we have attempted to resolve these effects by varying our LED light intensity and duration. The standardized configuration of this spectrophotometer will also allow a more uniform kinetic analysis of samples in different laboratories. We can conclude that our findings from the LED-based system display an added total protein concentration effect due to multiple turnover events of P700(+) reduction by cyt c 6 during the longer illumination regime.\",\n \"corpus_id\": 25775424,\n \"score\": 1\n },\n {\n \"doc_id\": \"28235460\",\n \"title\": \"Tyrozine D oxidation and redox equilibrium in photosystem II.\",\n \"abstract\": \"Tyrosine D (TyrD) is an auxiliary redox active tyrosine residue in photosystem II (PSII). The mechanism of TyrD oxidation was investigated by EPR spectroscopy, flash-induced fluorescence decay and thermoluminescence measurements in PSII enriched membranes from spinach. PSII membranes were chemically treated with 3mM ascorbate and 1mM diaminodurene and subsequent washing, leading to the complete reduction of TyrD. TyrD oxidation kinetics and competing recombination reactions were measured after a single saturating flash in the absence and presence of DCMU (inhibitor of the QB-site) in the pH range of 4.7-8.5. Two kinetic phases of TyrD oxidation were observed by the time resolved EPR spectroscopy - the fast phase (msec-sec time range) and the pH dependent slow phase (tens of seconds time range). In the presence of DCMU, TyrD oxidation kinetics was monophasic in the entire pH range, i.e. only the fast kinetics was observed. The results obtained from the fluorescence and thermoluminescence analysis show that when forward electron transport is blocked in the presence of DCMU, the S2QA(-) recombination outcompetes the slow phase of TyrD oxidation by the S2 state. Modelling of the whole complex of these electron transfer events associated with TyrD oxidation fitted very well with our experimental data. Based on these data, structural information and theoretical considerations we confirm our assignment of the fast and slow oxidation kinetics to two populations of PSII centers with different water positions (proximal and distal) in the TyrD vicinity.\",\n \"corpus_id\": 25063489,\n \"score\": 1\n },\n {\n \"doc_id\": \"28497192\",\n \"title\": \"Redox changes of ferredoxin, P700, and plastocyanin measured simultaneously in intact leaves.\",\n \"abstract\": \"Properties and performance of the recently introduced Dual/KLAS-NIR spectrophotometer for simultaneous measurements of ferredoxin (Fd), P700, and plastocyanin (PC) redox changes, together with whole leaf chlorophyll a (Chl) fluorescence (emission >760, 540 nm excitation) are outlined. Spectral information on in vivo Fd, P700, and PC in the near-infrared region (NIR, 780-1000 nm) is presented, on which the new approach is based. Examples of application focus on dark-light and light-dark transitions, where maximal redox changes of Fd occur. After dark-adaptation, Fd reduction induced by moderate light parallels the Kautsky effect of Chl fluorescence induction. Both signals are affected analogously by removal of O2. A rapid type of Fd reoxidation, observed after a short pulse of light before light activation of linear electron transport (LET), is more pronounced in C4 compared to C3 leaves and interpreted to reflect cyclic PS I (CET). Light activation of LET, as assessed via the rate of Fd reoxidation after short light pulses, occurs at very low intensities and is slowly reversed (half-time ca. 20 min). Illumination with strong far-red light (FR, 740 nm) reveals two fractions of PS I, PS I (LET), and PS I (CET), differing in the rates of Fd reoxidation upon FR-off and the apparent equilibrium constants between P700 and PC. Parallel information on oxidation of Fd and reduction of P700 plus PC proves essential for identification of CET. Comparison of maize (C4) with sunflower and ivy (C3) responses leads to the conclusion that segregation of two types of PS I may not only exist in C4 (mesophyll and bundle sheath cells), but also in C3 photosynthesis (grana margins plus end membranes and stroma lamellae).\",\n \"corpus_id\": 12269864,\n \"score\": 1\n },\n {\n \"doc_id\": \"28823462\",\n \"title\": \"Mechanism of adiabatic primary electron transfer in photosystem I: Femtosecond spectroscopy upon excitation of reaction center in the far-red edge of the QY band.\",\n \"abstract\": \"The ultrafast primary charge separation in Photosystem I (PS I) excited by femtosecond pulses centered at 720 and 760nm was studied by pump-to-probe laser spectroscopy. The absorbance in the red edge of PS I absorption spectrum has an unusual exponential dependence on wavelength. The cutoff of short wavelength components of 760nm pulse allows direct excitation of reaction center chlorophyll molecules without involvement of light-harvesting antenna. The transient spectrum manifests the features of the primary ion-radical pair P700(+)A0(-) at time delay <180fs, followed by formation of the secondary pair P700(+)A1(-) with a characteristic time of 26ps. The obtained data are rationalized in the framework of adiabatic three-state model that includes the chlorophyll dimer P700 and two symmetrically arranged nearest chlorophyll molecules of A0. The arrangement of chlorophylls results in strong electronic coupling between P700 and A0. Excitation in the maximum of P700 absorption generates electronic states with the highest contribution from P700*, whereas excitation in the far-red edge predominantly generates charge transfer state P700(+)A0(-) in both branches of redox-cofactors. The three-level model accounts for a flat-bottomed potential surface of the excited state and adiabatic character of electron transfer between P700 and A0, providing a microscopic explanation of the ultrafast formation of P700(+)A0(-) and exponential decline of PS I absorption.\",\n \"corpus_id\": 41849440,\n \"score\": 1\n },\n {\n \"doc_id\": \"29357086\",\n \"title\": \"Photoinhibition of photosystem I in Nephrolepis falciformis depends on reactive oxygen species generated in the chloroplast stroma.\",\n \"abstract\": \"We studied how high light causes photoinhibition of photosystem I (PSI) in the shade-demanding fern Nephrolepis falciformis, in an attempt to understand the mechanism of PSI photoinhibition under natural field conditions. Intact leaves were treated with constant high light and fluctuating light. Detached leaves were treated with constant high light in the presence and absence of methyl viologen (MV). Chlorophyll fluorescence and P700 signal were determined to estimate photoinhibition. PSI was highly oxidized under high light before treatments. N. falciformis showed significantly stronger photoinhibition of PSI and PSII under constant high light than fluctuating light. These results suggest that high levels of P700 oxidation ratio cannot prevent PSI photoinhibition under high light in N. falciformis. Furthermore, photoinhibition of PSI in N. falciformis was largely accelerated in the presence of MV that promotes the production of superoxide anion radicals in the chloroplast stroma by accepting electrons from PSI. From these results, we propose that photoinhibition of PSI in N. falciformis is mainly caused by superoxide radicals generated in the chloroplast stroma, which is different from the mechanism of PSI photoinhibition in Arabidopsis thaliana and spinach. Here, we provide some new insights into the PSI photoinhibition under natural field conditions.\",\n \"corpus_id\": 23229486,\n \"score\": 1\n },\n {\n \"doc_id\": \"18667416\",\n \"title\": \"The psbo1 mutant of Arabidopsis cannot efficiently use calcium in support of oxygen evolution by photosystem II.\",\n \"abstract\": \"The Arabidopsis thaliana mutant psbo1 contains a point mutation in the psbO-1 gene (At5g66570) leading to the loss of expression of the PsbO-1 protein and overexpression of the PsbO-2 protein (Murakami, R., Ifuku, K., Takabayashi, A., Shikanai, T., Endo, T., and Sato, F. (2002) FEBS Lett. 523, 138-142). Previous characterization of fluorescence induction and decay kinetics by our laboratory documented defects on both the oxidizing and reducing sides of Photosystem II. Additionally, anomalous flash oxygen yield patterns indicated that the mutant contains a defective oxygen-evolving complex that appears to exhibit anomalously long-lived S(2) and S(3) oxidation states (Liu, H., Frankel, L. K., and Bricker, T. M. (2007) Biochemistry 46, 7607-7613). In this study, we have documented that the S(2) and S(3) states in psbo1 thylakoids decay very slowly. The total flash oxygen yield of the psbo1 mutant was also significantly reduced, as was its stability. Incubation of psbo1 thylakoids at high NaCl concentrations did not increase the rate of S(2) and S(3) state decay. The oxygen-evolving complexes of the mutant did, however, exhibit somewhat enhanced stability following this treatment. Incubation with CaCl(2) had a significantly more dramatic effect. Under this condition, both the S(2) and S(3) states of the mutant decayed at nearly the same rate as the wild type, and the total oxygen yield and its stability following CaCl(2) treatment were indistinguishable from that of the wild type. These results strongly suggest that the principal defect in the psbo1 mutant is an inability to effectively utilize the calcium associated with Photosystem II. We hypothesize that the PsbO-2 protein cannot effectively sequester calcium at the oxygen-evolving site.\",\n \"corpus_id\": 19474734,\n \"score\": 0\n },\n {\n \"doc_id\": \"18791808\",\n \"title\": \"The effects of simultaneous RNAi suppression of PsbO and PsbP protein expression in photosystem II of Arabidopsis.\",\n \"abstract\": \"Interfering RNA was used to suppress simultaneously the expression of the four genes which encode the PsbO and PsbP proteins of Photosystem II in Arabidopsis (PsbO: At5g66570, At3g50820 and PsbP: At1g06680, At2g30790). A phenotypic series of transgenic plants was obtained that expressed variable amounts of the PsbO proteins and undetectable amounts of the PsbP proteins. Immunological studies indicated that the loss of PsbP expression was correlated with the loss of expression of the PsbQ, D2, and CP47 proteins, while the loss of PsbO expression was correlated with the loss of expression of the D1 and CP43 proteins. Q(A)(-) reoxidation kinetics in the absence of DCMU indicated that the slowing of electron transfer from Q(A)(-) to Q(B) was correlated with the loss of the PsbP protein. Q(A)(-) reoxidation kinetics in the presence of DCMU indicated that charge recombination between Q(A)(-) and donor side components of the photosystem was retarded in all of the mutants. Decreasing amounts of the PsbO protein in the absence of the PsbP component also led to a progressive loss of variable fluorescence yield (F(V)/F(M)). During fluorescence induction, the loss of PsbP was correlated with a more rapid O to J transition and a loss of the J to I transition. These results indicate that the losses of the PsbO and PsbP proteins differentially affect separate protein components and different PS II functions and can do so, apparently, in the same plant.\",\n \"corpus_id\": 5674014,\n \"score\": 0\n },\n {\n \"doc_id\": \"18991552\",\n \"title\": \"Oxygen as an alternative electron acceptor in the photosynthetic electron transport chain of C3 plants.\",\n \"abstract\": \"This study deals with effects of oxygen on the kinetics of P(700) photoinduced redox transitions and on induction transients of chlorophyll fluorescence in leaves of C(3) plants Hibiscus rosa-sinensis and Vicia faba. It is shown that the removal of oxygen from the leaf environment has a conspicuous effect on photosynthetic electron transport. Under anaerobic conditions, the concentration of oxidized P700 centers in continuous white light was substantially lower than under aerobic conditions. The deficiency of oxygen released non-photochemical quenching of chlorophyll fluorescence, thus indicating a decrease in the trans-thylakoid pH gradient (DeltapH). Quantitative analysis of experimental data within the framework of an original mathematical model has shown that the steady-state electron flux toward oxygen in Chinese hibiscus leaves makes up to approximately 40% of the total electron flow passing through photosystem 1 (PS1). The decrease in P700+ content under anaerobic conditions can be due to two causes: i) the retardation of electron outflow from PS1, and ii) the release of photosynthetic control (acceleration of electron flow from PS2 to P700+) owing to lower acidification of the intra-thylakoid space. At the same time, cyclic electron transport around PS1 was not stimulated in the oxygen-free medium, although such stimulation seemed likely in view of possible rearrangement of electron flows on the acceptor side of PS1. This conclusion stems from observations that the rates of P700+ reduction in DCMU-poisoned samples, both under aerobic and anaerobic conditions, were negligibly small compared to rates of electron flow from PS2 toward P700+ in untreated samples.\",\n \"corpus_id\": 12149860,\n \"score\": 0\n },\n {\n \"doc_id\": \"19700631\",\n \"title\": \"Defining the far-red limit of photosystem II in spinach.\",\n \"abstract\": \"The far-red limit of photosystem II (PSII) photochemistry was studied in PSII-enriched membranes and PSII core preparations from spinach (Spinacia oleracea) after application of laser flashes between 730 and 820 nm. Light up to 800 nm was found to drive PSII activity in both acceptor side reduction and oxidation of the water-oxidizing CaMn(4) cluster. Far-red illumination induced enhancement of, and slowed down decay kinetics of, variable fluorescence. Both effects reflect reduction of the acceptor side of PSII. The effects on the donor side of PSII were monitored using electron paramagnetic resonance spectroscopy. Signals from the S(2)-, S(3)-, and S(0)-states could be detected after one, two, and three far-red flashes, respectively, indicating that PSII underwent conventional S-state transitions. Full PSII turnover was demonstrated by far-red flash-induced oxygen release, with oxygen appearing on the third flash. In addition, both the pheophytin anion and the Tyr Z radical were formed by far-red flashes. The efficiency of this far-red photochemistry in PSII decreases with increasing wavelength. The upper limit for detectable photochemistry in PSII on a single flash was determined to be 780 nm. In photoaccumulation experiments, photochemistry was detectable up to 800 nm. Implications for the energetics and energy levels of the charge separated states in PSII are discussed in light of the presented results.\",\n \"corpus_id\": 23237068,\n \"score\": 0\n },\n {\n \"doc_id\": \"20568728\",\n \"title\": \"Function of PsbO, the photosystem II manganese-stabilizing protein: probing the role of aspartic acid 157.\",\n \"abstract\": \"The D157N, D157E, and D157K mutations in the psbO gene encoding the photosystem II (PSII) manganese-stabilizing protein from spinach, exhibit near-wild-type PSII binding but are significantly impaired in O(2) evolution activity and Cl(-) retention by PSII [Popelkova et al. (2009) Biochemistry 48, 11920-11928]. To better characterize the role of PsbO-Asp157 in eukaryotic PSII, the effect of mutations in Asp157 on heat-induced changes in PsbO solution structure, O(2) release kinetics, and PSII redox reactions both within and outside the oxygen-evolving complex (OEC) have been examined. The data presented here show that Asn, Glu, or Lys mutations in PsbO-Asp157 modify PsbO thermostability in solution, which is consistent with the previously reported perturbation of the functional assembly of PsbO-Asp157 mutants into PSII that caused inefficient Cl(-) retention by PSII. Fluorescence decay signals from PSII reconstituted with Asp157 mutants indicate that that the Q(A)(-) to Q(B) transition on the PSII reducing side is unaffected, but complex alterations are detected on the PSII oxidizing side that affect the recombination of Q(A)(-) with the O(2)-evolving complex. In addition, oxygen yield on the first flash is increased, which indicates an impaired ability of mutant-reconstituted PSII samples to decay back to the S(1) state in the dark.\",\n \"corpus_id\": 19192128,\n \"score\": 0\n },\n {\n \"doc_id\": \"21661738\",\n \"title\": \"Binding stoichiometry and affinity of the manganese-stabilizing protein affects redox reactions on the oxidizing side of photosystem II.\",\n \"abstract\": \"It has been reported previously that the two subunits of PsbO, the photosystem II (PSII) manganese stabilizing protein, have unique functions in relation to the Mn, Ca(2+), and Cl(-) cofactors in eukaryotic PSII [Popelkova; (2008) Biochemistry 47, 12593]. The experiments reported here utilize a set of N-terminal truncation mutants of PsbO, which exhibit altered subunit binding to PSII, to further characterize its role in establishing efficient O(2) evolution activity. The effects of PsbO binding stoichiometry, affinity, and specificity on Q(A)(-) reoxidation kinetics after a single turnover flash, S-state transitions, and O(2) release time have been examined. The data presented here show that weak rebinding of a single PsbO subunit to PsbO-depleted PSII repairs many of the defects in PSII resulting from the removal of the protein, but many of these are not sustainable, as indicated by low steady-state activities of the reconstituted samples [Popelkova; (2003) Biochemistry 42 , 6193]. High affinity binding of PsbO to PSII is required to produce more stable and efficient cycling of the water oxidation reaction. Reconstitution of the second PsbO subunit is needed to further optimize redox reactions on the PSII oxidizing side. Native PsbO and recombinant wild-type PsbO from spinach facilitate PSII redox reactions in a very similar manner, and nonspecific binding of PsbO to PSII has no significance in these reactions.\",\n \"corpus_id\": 21663128,\n \"score\": 0\n },\n {\n \"doc_id\": \"22004756\",\n \"title\": \"Cationic state distribution over the P700 chlorophyll pair in photosystem I.\",\n \"abstract\": \"The primary electron donor P700 in photosystem I is composed of two chlorophylls, P(A) and P(B). P700 forms the cationic [P(A)/P(B)](•+) state as a result of light-induced electron transfer. We obtained a P(A)(•+)/P(B)(•+) ratio of 28:72 and a spin distribution of 22:78 for the entire PSI protein-pigment complex. By considering the influence of the protein components on the redox potential for one-electron oxidation of P(A)/P(B) monomers, we found that the following three factors significantly contributed to a large P(B)(•+) population relative to P(A)(•+): 1), Thr-A743 forming a H-bond with P(A); 2), P(A) as a chlorophyll a epimer; and 3), a conserved PsaA/PsaB pair, the Arg-A750/Ser-B734 residue. In addition, 4), the methyl-ester groups of the accessory chlorophylls A(-1A)/A(-1B) significantly stabilized the cationic [P(A)/P(B)](•+) state and 5), the methyl-ester group orientations were completely different in A(-1A) and A(-1B) as seen in the crystal structure. When the methyl-ester group was rotated, the spin-density distribution over P(A)/P(B) ranged from 22:78 to 15:85.\",\n \"corpus_id\": 14695186,\n \"score\": 0\n },\n {\n \"doc_id\": \"22614952\",\n \"title\": \"Probing the N-terminal sequence of spinach PsbO: evidence that essential threonine residues bind to different functional sites in eukaryotic photosystem II.\",\n \"abstract\": \"The N-terminal ¹E-⁶L domain of the manganese-stabilizing protein (PsbO) from spinach prevents non-specific binding of the subunit to photosystem II (PSII) and deletions of the ¹E-⁷T or ¹E-¹⁵T sequences from the PsbO N-terminus reduce or impair, respectively, functional binding of PsbO to PSII (Popelkova et al., Biochemistry 42:6193-6200, 2003). The work presented here provides deeper insights into the interaction of PsbO with PSII. The data show that a single mutation, ¹⁵T → A in mature PsbO from spinach reduces the stoichiometry of its functional binding from two to one subunit per PSII and decreases reconstitution of activity to about 45 % of the wild-type control. Replacement of the ¹E-⁶L domain with ⁶M in the T15A PsbO mutant has no additional negative effect on recovery of O₂ evolution activity, but it significantly weakens both functional and nonspecific binding of the truncated mutant to PSII. These results suggest that the ¹⁵T side-chain by itself is essential for binding of one of two PsbO subunits to eukaryotic PSII and that specific PSII-binding sites for PsbO are distinguishable; one PSII-binding site does not require PsbO-¹⁵T and probably interacts with the other N-terminal domain of PsbO. Identity of the latter domain is revealed by a requirement for the presence of the ¹E-⁶L sequence that is shown here to be necessary for high-affinity binding of PsbO to PSII. When combined with previous results, the data presented here lead to a more detailed model for PsbO binding in eukaryotic PSII.\",\n \"corpus_id\": 2549961,\n \"score\": 0\n },\n {\n \"doc_id\": \"23624674\",\n \"title\": \"Gymnosperms have increased capacity for electron leakage to oxygen (Mehler and PTOX reactions) in photosynthesis compared with angiosperms.\",\n \"abstract\": \"Oxygen plays an important role in photosynthesis by participating in a number of O2-consuming reactions. O2 inhibits CO2 fixation by stimulating photorespiration, thus reducing plant production. O2 interacts with photosynthetic electron transport in the chloroplasts' thylakoids in two main ways: by accepting electrons from PSI (Mehler reaction); and by accepting electrons from reduced plastoquinone (PQ) mediated by the plastid terminal oxidase (PTOX). In this study, we show, using 101 plant species, that there is a difference in the potential for photosynthetic electron flow to O2 between angiosperms and gymnosperms. We found, from measurements of Chl fluorescence and leaf absorbance at 830 nm, (i) that electron outflow from PSII, as determined by decay kinetics of Chl fluorescence after application of a saturating light pulse, is more rapid in gymnosperms than in angiosperms; (ii) that the reaction center Chl of PSI (P700) is rapidly and highly oxidized in gymnosperms during induction of photosynthesis; and (iii) that these differences are dependent on oxygen. Finally, rates of O2 uptake measured by mass spectrometry in the absence of photorespiration were significantly promoted by illumination in dark-adapted leaves of gymnosperms, but not in those of angiosperms. The light-stimulated O2 uptake was around 10% of the maximum O2 evolution in gymnosperms and 1% in angiosperms. These results suggest that gymnosperms have increased capacity for electron leakage to oxygen in photosynthesis compared with angiosperms. The involvement of the Mehler reaction and PTOX in the electron flow to O2 is discussed.\",\n \"corpus_id\": 23679605,\n \"score\": 0\n },\n {\n \"doc_id\": \"24556534\",\n \"title\": \"Model based analysis of transient fluorescence yield induced by actinic laser flashes in spinach leaves and cells of green alga Chlorella pyrenoidosa Chick.\",\n \"abstract\": \"Measurements of Single Flash Induced Transient Fluorescence Yield (SFITFY) on spinach leaves and whole cells of green thermophilic alga Chlorella pyrenoidosa Chick were analyzed for electron transfer (ET) steps and coupled proton transfer (PT) on both the donor and the acceptor side of the reaction center (RC) of photosystem II (PS II). A specially developed PS II model (Belyaeva et al., 2008, 2011a) allowed the determination of ET steps that occur in a hierarchically ordered time scale from nanoseconds to several seconds. Our study demonstrates that our SFITFY data is consistent with the concept of the reduction of P680(+) by YZ in both leaves and algae (studied on spinach leaves and cells of Chlorella pyrenoidosa Chick). The multiphasic P680(+) reduction kinetics by YZ in PS II core complexes with high oxygen evolution capacity was seen in both algae and leaves. Model simulation to fit SFITFY curves for dark adapted species used here gives the rate constants to verify nanosecond kinetic stages of P680(+) reduction by YZ in the redox state S1 of the water oxidizing complex (WOC) shown in Kühn et al. (2004). Then a sequence of relaxation steps in the redox state S1, outlined by Renger (2012), occurs in both algae and leaves as a similar non-adiabatic ET reactions. Coupled PT is discussed briefly to understand a rearrangement of hydrogen bond protons in the protein matrix of the WOC (Umena et al., 2011). On the other hand, present studies showed a slower reoxidation of reduced QA by QB in algal cells as compared with that in a leaf that might be regarded as a consequence of differences of spatial domains at the QB-site in leaves compared to algae. Our comparative study helped to correlate theory with experimental data for molecular photosynthetic mechanisms in thylakoid membranes.\",\n \"corpus_id\": 207392342,\n \"score\": 0\n },\n {\n \"doc_id\": \"26049407\",\n \"title\": \"Modeling of the redox state dynamics in photosystem II of Chlorella pyrenoidosa Chick cells and leaves of spinach and Arabidopsis thaliana from single flash-induced fluorescence quantum yield changes on the 100 ns-10 s time scale.\",\n \"abstract\": \"The time courses of the photosystem II (PSII) redox states were analyzed with a model scheme supposing a fraction of 11-25 % semiquinone (with reduced [Formula: see text]) RCs in the dark. Patterns of single flash-induced transient fluorescence yield (SFITFY) measured for leaves (spinach and Arabidopsis (A.) thaliana) and the thermophilic alga Chlorella (C.) pyrenoidosa Chick (Steffen et al. Biochemistry 44:3123-3132, 2005; Belyaeva et al. Photosynth Res 98:105-119, 2008, Plant Physiol Biochem 77:49-59, 2014) were fitted with the PSII model. The simulations show that at high-light conditions the flash generated triplet carotenoid (3)Car(t) population is the main NPQ regulator decaying in the time interval of 6-8 μs. So the SFITFY increase up to the maximum level [Formula: see text]/F 0 (at ~50 μs) depends mainly on the flash energy. Transient electron redistributions on the RC redox cofactors were displayed to explain the SFITFY measured by weak light pulses during the PSII relaxation by electron transfer (ET) steps and coupled proton transfer on both the donor and the acceptor side of the PSII. The contribution of non-radiative charge recombination was taken into account. Analytical expressions for the laser flash, the (3)Car(t) decay and the work of the water-oxidizing complex (WOC) were used to improve the modeled P680(+) reduction by YZ in the state S 1 of the WOC. All parameter values were compared between spinach, A. thaliana leaves and C. pyrenoidosa alga cells and at different laser flash energies. ET from [Formula: see text] slower in alga as compared to leaf samples was elucidated by the dynamics of [Formula: see text] fractions to fit SFITFY data. Low membrane energization after the 10 ns single turnover flash was modeled: the ∆Ψ(t) amplitude (20 mV) is found to be about 5-fold smaller than under the continuous light induction; the time-independent lumen pHL, stroma pHS are fitted close to dark estimates. Depending on the flash energy used at 1.4, 4, 100 % the pHS in stroma is fitted to 7.3, 7.4, and 7.7, respectively. The biggest ∆pH difference between stroma and lumen was found to be 1.2, thus pH- dependent NPQ was not considered.\",\n \"corpus_id\": 17846716,\n \"score\": 0\n },\n {\n \"doc_id\": \"26151897\",\n \"title\": \"Investigating changes in the redox state of Photosystem I at low pH.\",\n \"abstract\": \"Changes in the redox state of Photosystem I (PSI) were studied in spinach leaf discs suspended in buffers of different pH (pH 7.5, 6.5, 5.5 and 4.5). By measuring absorbance changes at 820 nm, it was observed that under normal conditions, the electrons were supplied by Photosystem II (PSII) for the photo-oxidation of P700 while in the presence of DCMU when electrons coming from PSII are blocked, cyclic electron flow (CEF) around PSI was the major source for the absorbance changes observed at 820 nm. This was supported by complete inhibition in the reduction of both single turnover (ST) area and multiple turnover (MT) area, in the presence of DCMU, which is generally filled up by the electrons coming from PSII. In the absence of DCMU, the intersystem electron pool or plastoquinone (PQ) pool was increased at low pH which was probably due to enhanced cyclic electron flow around PSI. Our results also suggest that at low pH, in the absence of DCMU, the major contribution for faster dark re-reduction of P700(+) is attributed mainly by PSII and CEF PSI while in the presence of DCMU, the significant contribution is provided by CEF PSI and other stromal components.\",\n \"corpus_id\": 24246756,\n \"score\": 0\n },\n {\n \"doc_id\": \"28432538\",\n \"title\": \"Superoxide generated in the chloroplast stroma causes photoinhibition of photosystem I in the shade-establishing tree species Psychotria henryi.\",\n \"abstract\": \"Our previous studies indicated that high light induced significant photoinhibition of photosystem I (PSI) in the shade-establishing tree species Psychotria henryi. However, the underlying mechanism has not been fully clarified. In the present study, in order to investigate the mechanism of PSI photoinhibition in P. henryi, we treated detached leaves with constant high light in the presence of methyl viologen (MV) or a soluble α-tocopherol analog, 2,2,5,7,8-pentamethyl-6-chromanol (PMC). We found that MV significantly depressed photochemical quantum yields in PSI and PSII when compared to PMC. On condition that no PSI photoinhibition happened, although cyclic electron flow (CEF) was abolished in the MV-treated samples, P700 oxidation ratio was maintain at higher levels than the PMC-treated samples. In the presence of PMC, PSI photoinhibition little changed but PSII photoinhibition was significantly alleviated. Importantly, PSI photoinhibition was largely accelerated in the presence of MV, which stimulates the production of superoxide and subsequently other reactive oxygen species at the chloroplast stroma by accepting electrons from PSI. Furthermore, MV largely aggravated PSII photoinhibition when compared to control. These results suggest that high P700 oxidation ratio cannot prevent PSI photoinhibition in P. henryi. Furthermore, the superoxide produced in the chloroplast stroma is critical for PSI photoinhibition in the higher plant P. henryi, which is opposite to the mechanism underlying PSI photoinhibition in Arabidopsis thaliana and spinach. These findings highlight a new mechanism of PSI photoinhibition in higher plants.\",\n \"corpus_id\": 3758531,\n \"score\": 0\n },\n {\n \"doc_id\": \"28808836\",\n \"title\": \"Excitation transfer and trapping kinetics in plant photosystem I probed by two-dimensional electronic spectroscopy.\",\n \"abstract\": \"Photosystem I is a robust and highly efficient biological solar engine. Its capacity to utilize virtually every absorbed photon's energy in a photochemical reaction generates great interest in the kinetics and mechanisms of excitation energy transfer and charge separation. In this work, we have employed room-temperature coherent two-dimensional electronic spectroscopy and time-resolved fluorescence spectroscopy to follow exciton equilibration and excitation trapping in intact Photosystem I complexes as well as core complexes isolated from Pisum sativum. We performed two-dimensional electronic spectroscopy measurements with low excitation pulse energies to record excited-state kinetics free from singlet-singlet annihilation. Global lifetime analysis resolved energy transfer and trapping lifetimes closely matches the time-correlated single-photon counting data. Exciton energy equilibration in the core antenna occurred on a timescale of 0.5 ps. We further observed spectral equilibration component in the core complex with a 3-4 ps lifetime between the bulk Chl states and a state absorbing at 700 nm. Trapping in the core complex occurred with a 20 ps lifetime, which in the supercomplex split into two lifetimes, 16 ps and 67-75 ps. The experimental data could be modelled with two alternative models resulting in equally good fits-a transfer-to-trap-limited model and a trap-limited model. However, the former model is only possible if the 3-4 ps component is ascribed to equilibration with a \\\"red\\\" core antenna pool absorbing at 700 nm. Conversely, if these low-energy states are identified with the P700 reaction centre, the transfer-to-trap-model is ruled out in favour of a trap-limited model.\",\n \"corpus_id\": 21492271,\n \"score\": 0\n },\n {\n \"doc_id\": \"28924898\",\n \"title\": \"Formation of tyrosine radicals in photosystem II under far-red illumination.\",\n \"abstract\": \"Photosystem II (PS II) contains two redox-active tyrosine residues on the donor side at symmetrical positions to the primary donor, P680. TyrZ, part of the water-oxidizing complex, is a preferential fast electron donor while TyrD is a slow auxiliary donor to P680+. We used PS II membranes from spinach which were depleted of the water oxidation complex (Mn-depleted PS II) to study electron donation from both tyrosines by time-resolved EPR spectroscopy under visible and far-red continuous light and laser flash illumination. Our results show that under both illumination regimes, oxidation of TyrD occurs via equilibrium with TyrZ• at pH 4.7 and 6.3. At pH 8.5 direct TyrD oxidation by P680+ occurs in the majority of the PS II centers. Under continuous far-red light illumination these reactions were less effective but still possible. Different photochemical steps were considered to explain the far-red light-induced electron donation from tyrosines and localization of the primary electron hole (P680+) on the ChlD1 in Mn-depleted PS II after the far-red light-induced charge separation at room temperature is suggested.\",\n \"corpus_id\": 3887916,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":86,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25339269\",\n \"title\": \"A proteome quality index.\",\n \"abstract\": \"We present the Proteome Quality Index (PQI; http://pqi-list.org), a much-needed resource for users of bacterial and eukaryotic proteomes. Completely sequenced genomes for which there is an available set of protein sequences (the proteome) are given a one- to five-star rating supported by 11 different metrics of quality. The database indexes over 3000 proteomes at the time of writing and is provided via a website for browsing, filtering and downloading. Previous to this work, there was no systematic way to account for the large variability in quality of the thousands of proteomes, and this is likely to have profoundly influenced the outcome of many published studies, in particular large-scale comparative analyses. The lack of a measure of proteome quality is likely due to the difficulty in producing one, a problem that we have approached by integrating multiple metrics. The continued development and improvement of the index will require the contribution of additional metrics by us and by others; the PQI provides a useful point of reference for the scientific community, but it is only the first step towards a 'standard' for the field.\",\n \"corpus_id\": 22675722\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18032431","title":"GenoList: an integrated environment for comparative analysis of microbial genomes.","abstract":"The multitude of bacterial genome sequences being determined has generated new requirements regarding the development of databases and graphical interfaces: these are needed to organize and retrieve biological information from the comparison of large sets of genomes. GenoList (http://genolist.pasteur.fr/GenoList) is an integrated environment dedicated to querying and analyzing genome data from bacterial species. GenoList inherits from the SubtiList database and web server, the reference data resource for the Bacillus subtilis genome. The data model was extended to hold information about relationships between genomes (e.g. protein families). The web user interface was designed to primarily take into account biologists' needs and modes of operation. Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis. One key feature is the integration of the many tools accessible in the environment. As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.","corpus_id":13844649,"score":2},{"doc_id":"18836194","title":"The Universal Protein Resource (UniProt) 2009.","abstract":"The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information that is essential for modern biological research. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute, the Protein Information Resource and the Swiss Institute of Bioinformatics. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, a user-friendly UniProt website and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. One of the key achievements of the UniProt consortium in 2008 is the completion of the first draft of the complete human proteome in UniProtKB/Swiss-Prot. This manually annotated representation of all currently known human protein-coding genes was made available in UniProt release 14.0 with 20 325 entries. UniProt is updated and distributed every three weeks and can be accessed online for searches or downloaded at www.uniprot.org.","corpus_id":14202205,"score":2},{"doc_id":"18849571","title":"HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.","abstract":"The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap).","corpus_id":1626367,"score":2},{"doc_id":"19457249","title":"EDGAR: a software framework for the comparative analysis of prokaryotic genomes.","abstract":"BACKGROUND: The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. RESULTS: To support these studies EDGAR - \"Efficient Database framework for comparative Genome Analyses using BLAST score Ratios\" - was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. CONCLUSION: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de, where the precomputed data sets can be browsed.","corpus_id":1041880,"score":2},{"doc_id":"19892825","title":"The comprehensive microbial resource.","abstract":"The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. At the gene level users can view the gene annotation and underlying evidence. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available. The data and tools on the CMR aid genomic research and analysis, and the CMR is included in over 200 scientific publications. The code underlying the CMR website and the CMR database are freely available for download with no license restrictions.","corpus_id":331367,"score":2},{"doc_id":"21556138","title":"Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.","abstract":"The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs), each selected from a Representative Proteome Group (RPG) containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT) are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55) most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains) and annotation information (93% of experimentally characterized proteins). All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.","corpus_id":18017470,"score":2},{"doc_id":"21584191","title":"MTB-PCDB: Mycobacterium tuberculosis proteome comparison database.","abstract":"UNLABELLED: The Mycobacterium tuberculosis Proteome Comparison Database (MTB-PCDB) is an online database providing integrated access to proteome sequence comparison data for five strains of Mycobacterium tuberculosis (H37Rv, H37Ra, CDC 1551, F11 and KZN 1435) sequenced completely so far. MTB-PCDB currently hosts 40252 protein sequence comparison data obtained through inter-strain proteome comparison of five different strains of MTB. 2373 proteins were found to be identical in all 5 strains using MTB H(37)Rv as reference strain. To enable wide use of this data, MTB-PCDB provides a set of tools for searching, browsing, analyzing and downloading the data. By bringing together, M. tuberculosis proteome comparison among virulent & avirulent strains and also drug susceptible & drug resistance strains MTB-PCDB provides a unique discovery platform for comparative proteomics among these strains which may give insights into the discovery & development of TB drugs, vaccines and biomarkers. AVAILABILITY: The database is available for free at http://www.bicjbtdrc-mgims.in/MTB-PCDB/","corpus_id":6143443,"score":2},{"doc_id":"21901743","title":"Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.","abstract":"OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that were pre-computed using the OrthoMCL algorithm. Version 4 of this database contained 116,536 ortholog groups clustered from 1,270,853 proteins obtained from 88 eukaryotic genomes, 16 archaean genomes, and 34 bacterial genomes. Future versions of OrthoMCL-DB will include more proteomes as more genomes are sequenced. Here, we describe how you can group your proteins of interest into ortholog clusters using two different means provided by the OrthoMCL system. The OrthoMCL-DB Web site has a tool for uploading and grouping a set of protein sequences, typically representing a proteome. This method maps the uploaded proteins to existing groups in OrthoMCL-DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install, and run the stand-alone OrthoMCL software.","corpus_id":31516519,"score":2},{"doc_id":"22180819","title":"Solving the Problem: Genome Annotation Standards before the Data Deluge.","abstract":"The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.","corpus_id":6814002,"score":2},{"doc_id":"23193269","title":"MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.","abstract":"MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.","corpus_id":18494847,"score":2},{"doc_id":"24163254","title":"Ensembl Genomes 2013: scaling up access to genome-wide data.","abstract":"Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.","corpus_id":137549,"score":2},{"doc_id":"24460813","title":"CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.","abstract":"BACKGROUND: The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult. RESULTS: We have developed CodaChrome (http://www.sourceforge.com/p/codachrome), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori. CONCLUSION: CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes.","corpus_id":6395529,"score":2},{"doc_id":"24723423","title":"OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.","abstract":"Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://www.orthomam.univ-montp2.fr/.","corpus_id":15030916,"score":2},{"doc_id":"25348405","title":"UniProt: a hub for protein information.","abstract":"UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.","corpus_id":16082970,"score":2},{"doc_id":"25378341","title":"diArk--the database for eukaryotic genome and transcriptome assemblies in 2014.","abstract":"Eukaryotic genomes are the basis for understanding the complexity of life from populations to the molecular level. Recent technological innovations have revolutionized the speed of data generation enabling the sequencing of eukaryotic genomes and transcriptomes within days. The database diArk (http://www.diark.org) has been developed with the aim to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes. In this new version of the database we have also integrated species, for which transcriptome assemblies are available, and we provide more analyses of assemblies.","corpus_id":15098268,"score":2},{"doc_id":"25429972","title":"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.","abstract":"The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.","corpus_id":1983307,"score":2},{"doc_id":"25435546","title":"Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.","abstract":"Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. The amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant genomics studies. The acquisition of information on protein structure can help elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. In this study, we calculated multiple physicochemical and secondary structural parameters of protein sequences, including length, hydrophobicity, the amount of secondary structure, the number of intrinsically disordered regions (IDRs) and the predicted presence of transmembrane helices and signal peptides, using a total of 208,333 protein sequences from the genomes of six representative plant species, Arabidopsis thaliana, Glycine max (soybean), Populus trichocarpa (poplar), Oryza sativa (rice), Physcomitrella patens (moss) and Cyanidioschyzon merolae (alga). Using the PASS tool and the Rosetta Stone method, we annotated the presence of novel functional regions in 1,732 protein sequences that included unannotated sequences from the Arabidopsis and rice proteomes. These results were organized into the Plant Protein Annotation Suite database (Plant-PrAS), which can be freely accessed online at http://plant-pras.riken.jp/.","corpus_id":11116254,"score":2},{"doc_id":"26673716","title":"The Pfam protein families database: towards a more sustainable future.","abstract":"In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.","corpus_id":9574721,"score":2},{"doc_id":"27153665","title":"DOGMA: domain-based transcriptome and proteome quality assessment.","abstract":"MOTIVATION: Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. RESULTS: We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. AVAILABILITY AND IMPLEMENTATION: DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":3187987,"score":2},{"doc_id":"18637161","title":"WildSilkbase: an EST database of wild silkmoths.","abstract":"BACKGROUND: Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed. DESCRIPTION: WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, Antheraea assama, an Indian tropical tasar silkmoth, A. mylitta and eri silkmoth, Samia cynthia ricini. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from http://www.cdfd.org.in/wildsilkbase/. CONCLUSION: A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.","corpus_id":13755501,"score":1},{"doc_id":"22524279","title":"Methods for visual mining of genomic and proteomic data atlases.","abstract":"BACKGROUND: As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. RESULTS: This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. CONCLUSIONS: The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations. Providing linked task specific views that allow a user to start from points of interest (from diseases to single genes) enables targeted exploration of thousands of spectra and genomes. As the composition of the atlases changes, and our understanding of the biology increase, new tasks will continually arise. It is therefore important to provide the means to make the data available in a suitable manner in as short a time as possible. We have done this through the use of common visualization workflows, into which we rapidly deploy visual tools. These visualizations follow common metaphors where possible to assist users in understanding the displayed data. Rapid development of tools and task specific views allows researchers to mine large-scale data almost as quickly as it is produced. Ultimately these visual tools enable new inferences, new analyses and further refinement of the large scale data being provided in atlases such as PeptideAtlas and The Cancer Genome Atlas.","corpus_id":16114676,"score":1},{"doc_id":"23203878","title":"D²P²: database of disordered protein predictions.","abstract":"We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D(2)P(2) will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life.","corpus_id":6164727,"score":1},{"doc_id":"23262288","title":"LepChorionDB, a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes.","abstract":"Chorion proteins of Lepidoptera have a tripartite structure, which consists of a central domain and two, more variable, flanking arms. The central domain is highly conserved and it is used for the classification of chorion proteins into two major classes, A and B. Annotated and unreviewed Lepidopteran chorion protein sequences are available in various databases. A database, named LepChorionDB, was constructed by searching 5 different protein databases using class A and B central domain-specific profile Hidden Markov Models (pHMMs), developed in this work. A total of 413 Lepidopteran chorion proteins from 9 moths and 1 butterfly species were retrieved. These data were enriched and organised in order to populate LepChorionDB, the first relational database, available on the web, containing Lepidopteran chorion proteins grouped in A and B classes. LepChorionDB may provide insights in future functional and evolutionary studies of Lepidopteran chorion proteins and thus, it will be a useful tool for the Lepidopteran scientific community and Lepidopteran genome annotators, since it also provides access to the two pHMMs developed in this work, which may be used to discriminate A and B class chorion proteins. LepChorionDB is freely available at http://bioinformatics.biol.uoa.gr/LepChorionDB.","corpus_id":23547009,"score":1},{"doc_id":"23409217","title":"The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.","abstract":"Variability in the extent of the descriptions of data ('metadata') held in public repositories forces users to assess the quality of records individually, which rapidly becomes impractical. The scoring of records on the richness of their description provides a simple, objective proxy measure for quality that enables filtering that supports downstream analysis. Pivotally, such descriptions should spur on improvements. Here, we introduce such a measure - the 'Metadata Coverage Index' (MCI): the percentage of available fields actually filled in a record or description. MCI scores can be calculated across a database, for individual records or for their component parts (e.g., fields of interest). There are many potential uses for this simple metric: for example; to filter, rank or search for records; to assess the metadata availability of an ad hoc collection; to determine the frequency with which fields in a particular record type are filled, especially with respect to standards compliance; to assess the utility of specific tools and resources, and of data capture practice more generally; to prioritize records for further curation; to serve as performance metrics of funded projects; or to quantify the value added by curation. Here we demonstrate the utility of MCI scores using metadata from the Genomes Online Database (GOLD), including records compliant with the 'Minimum Information about a Genome Sequence' (MIGS) standard developed by the Genomic Standards Consortium. We discuss challenges and address the further application of MCI scores; to show improvements in annotation quality over time, to inform the work of standards bodies and repository providers on the usability and popularity of their products, and to assess and credit the work of curators. Such an index provides a step towards putting metadata capture practices and in the future, standards compliance, into a quantitative and objective framework.","corpus_id":30896675,"score":1},{"doc_id":"24150944","title":"HRaP: database of occurrence of HomoRepeats and patterns in proteomes.","abstract":"We focus our attention on multiple repeats of one amino acid (homorepeats) and create a new database (named HRaP, at http://bioinfo.protres.ru/hrap/) of occurrence of homorepeats and disordered patterns in different proteomes. HRaP is aimed at understanding the amino acid tandem repeat function in different proteomes. Therefore, the database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kingdoms and 5 phyla of bacteria. The database includes 1,449,561 protein sequences and 771,786 sequences of proteins with GO annotations. We have determined homorepeats and patterns that are associated with some function. Through our web server, the user can do the following: (i) search for proteins with the given homorepeat in 122 proteomes, including GO annotation for these proteins; (ii) search for proteins with the given disordered pattern from the library of disordered patterns constructed on the clustered Protein Data Bank in 122 proteomes, including GO annotations for these proteins; (iii) analyze lengths of homorepeats in different proteomes; (iv) investigate disordered regions in the chosen proteins in 122 proteomes; (v) study the coupling of different homorepeats in one protein; (vi) determine longest runs for each amino acid inside each proteome; and (vii) download the full list of proteins with the given length of a homorepeat.","corpus_id":18523541,"score":1},{"doc_id":"24304897","title":"Plasma Proteome Database as a resource for proteomics research: 2014 update.","abstract":"Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.","corpus_id":11646204,"score":1},{"doc_id":"24498877","title":"PrionScan: an online database of predicted prion domains in complete proteomes.","abstract":"BACKGROUND: Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. DESCRIPTION: Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. CONCLUSIONS: It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.","corpus_id":14127536,"score":1},{"doc_id":"27153712","title":"Computational clustering for viral reference proteomes.","abstract":"MOTIVATION: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies. RESULTS: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt's curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs. AVAILABILITY AND IMPLEMENTATION: http://proteininformationresource.org/rps/viruses/ CONTACT: chenc@udel.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":18086674,"score":1},{"doc_id":"28317029","title":"Listeriomics: an Interactive Web Platform for Systems Biology of Listeria.","abstract":"As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach.","corpus_id":17356251,"score":1},{"doc_id":"18281347","title":"Information quality in proteomics.","abstract":"Proteomics, the study of the protein complement of a biological system, is generating increasing quantities of data from rapidly developing technologies employed in a variety of different experimental workflows. Experimental processes, e.g. for comparative 2D gel studies or LC-MS/MS analyses of complex protein mixtures, involve a number of steps: from experimental design, through wet and dry lab operations, to publication of data in repositories and finally to data annotation and maintenance. The presence of inaccuracies throughout the processing pipeline, however, results in data that can be untrustworthy, thus offsetting the benefits of high-throughput technology. While researchers and practitioners are generally aware of some of the information quality issues associated with public proteomics data, there are few accepted criteria and guidelines for dealing with them. In this article, we highlight factors that impact on the quality of experimental data and review current approaches to information quality management in proteomics. Data quality issues are considered throughout the lifecycle of a proteomics experiment, from experiment design and technique selection, through data analysis, to archiving and sharing.","corpus_id":11262766,"score":0},{"doc_id":"18314066","title":"Proteomics: methodologies and applications in oncology.","abstract":"Few technological developments have created as much excitement and skepticism as proteomics over their potential to change clinical diagnostic and prognostic procedures. Proteomics concerns itself with the characterization and function of all cellular proteins, the ultimate determinants of cellular function. As such, it represents the end result of all mechanisms of gene regulation and thus offers tremendous potential for characterizing biology. In much the same way as what has occurred with the genome, the scientific community is coming to grips with the fact that the proteome, although enormously complex, is finite. It is conceivable that we will learn the identity of all possible proteins, including all posttranslational modifications. The rate of protein discovery continues to accelerate in large part because of improvements in mass spectrometry-based technologies coupled with improved genomic databases and bioinformatic tools. In addition, there is reason to believe that proteomics is on the verge of moving from a methodology that requires repeated proteome \"discovery\" to one that can more systematically profile proteomes. This review discusses current proteomic-based technologies and the efforts of scientists to move them into the clinic for use in patients treated with radiotherapy and other modalities.","corpus_id":24486625,"score":0},{"doc_id":"18592171","title":"Plant proteomics.","abstract":"An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.","corpus_id":32604142,"score":0},{"doc_id":"18978022","title":"Sys-BodyFluid: a systematical database for human body fluid proteome research.","abstract":"Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.","corpus_id":694240,"score":0},{"doc_id":"19129418","title":"The proteome of seed development in the model legume Lotus japonicus.","abstract":"We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family.","corpus_id":7992872,"score":0},{"doc_id":"19541297","title":"PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison.","abstract":"Mitochondrial proteins associated with a wide spectrum of human diseases and currently large amounts of tissue or organ specific human mitochondrial proteome datasets are generated. However, high-throughput comparative proteomic methods have yet to be applied to extract subtle differences among mitochondria from different tissues or muscle types. The aim of this work was to provide an integrated way to identify and compare huge mitochondrial protein or peptide mass spectral data sets acquired from expert mitochondrial proteome or biomarker discovery community. Proteome comparison of human mitochondria (PCHM) is a web-based analysis environment for manual or automatic analysis of individual peptide mass fingerprints alongside a database of proteins and peptides identified in various organs for human mitochondrial proteins. PCHM provides a suite of graphical tools that allow the virtual plot of peptide mass fingerprinting (PMF) spectra and a fully automatic protein function classification based on gene ontology (GO) annotation system. The new virtual PMF plot is very useful to validate fragmented ion loses of any identical proteins and to remove unwanted foreign ion peaks. Fully automatic protein function classifier provides an easier way to compare the subtle differences of compositionally biased mitochondrial protein functions. PCHM also provides a variety of query algorithms aid in browsing, searching, and accessing complete annotations of data relevant to each mitochondrial protein of interest, which link external databases and users. PCHM will be a useful tool for the systematic and functional characterization of the mitochondrial proteins in relation to human diseases or biological research applications. PCHM can be accessed freely via a web interface http://pchm.inje.ac.kr.","corpus_id":31902462,"score":0},{"doc_id":"20837570","title":"A unified index of sequence quality and contig overlap for DNA barcoding.","abstract":"SUMMARY: Barcode quality index (B) is a novel, unified measure of sequence quality and contig overlap tailored to the needs of DNA barcoding. Re-analysis of published data demonstrates the utility of B. AVAILABILITY AND IMPLEMENTATION: A GPL PERL script is available for download (http://www.nybg.org/files/scientists/dlittle/B.html).","corpus_id":17620650,"score":0},{"doc_id":"21107258","title":"Proteomics beyond proteomics: toward clinical applications.","abstract":"PURPOSE OF REVIEW: There is an increasing interest in the application of proteomics in all areas of the life sciences, especially in the area of biomedical research wherein the analysis of biological fluids is very promising for biomarker discovery. The rapid development of proteomics as a field has depended upon substantial advances in instrumentation, methodologies, software and the availability of comprehensive sequence databases. However, progress has been slower than anticipated with respect to application in the realm of biomedicine. RECENT FINDINGS: We review some of the areas of importance for the development of proteomics and its applications to biomedical research. SUMMARY: One of the factors explaining the slow progress of candidate proteomics biomarkers through the translational pipeline has been the difficulty to develop validation and standardization of procedures to improve reproducibility, sensitivity and specificity. This challenge has now largely been met by large, consortium efforts, leading to the discovery of drug-specific protein biomarkers. The need for integrating complex protein patterns is now recognized in a new test classification by the US Food and Drug Administration termed 'in-vitro diagnostic multivariate index assays'. Further progress in clinical proteomics will depend upon continued collaborative efforts and infrastructure development by the proteomics community.","corpus_id":11110793,"score":0},{"doc_id":"21264403","title":"pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.","abstract":"pep2pro is a comprehensive proteome analysis database specifically suitable for flexible proteome data analysis. The pep2pro database schema offers solutions to the various challenges of developing a proteome data analysis database and because data integrated in pep2pro are in relational format, it enables flexible and detailed data analysis. The information provided here will facilitate building proteome data analysis databases for other organisms or applications. The capacity of the pep2pro database for the integration and analysis of large proteome datasets was demonstrated by creating the pep2pro dataset, which is an organ-specific characterisation of the Arabidopsis thaliana proteome containing 14 522 identified proteins based on 2.6 million peptide spectrum assignments. This dataset provides evidence of protein expression and reveals organ-specific processes. The high coverage and density of the dataset are essential for protein quantification by normalised spectral counting and allowed us to extract information that is usually not accessible in low-coverage datasets. With this quantitative protein information we analysed organ- and organelle-specific sub-proteomes. In addition we matched spectra to regions in the genome that were not predicted to have protein coding capacity and provide PCR validation for selected revised gene models. Furthermore, we analysed the peptide features that distinguish detected from non-detected peptides and found substantial disagreement between predicted and detected proteotypic peptides, suggesting that large-scale proteomics data are essential for efficient selection of proteotypic peptides in targeted proteomics surveys. The pep2pro dataset is available as a resource for plant systems biology at www.pep2pro.ethz.ch.","corpus_id":1044388,"score":0},{"doc_id":"21466708","title":"dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.","abstract":"BACKGROUND: Protein O-GlcNAcylation (or O-GlcNAc-ylation) is an O-linked glycosylation involving the transfer of β-N-acetylglucosamine to the hydroxyl group of serine or threonine residues of proteins. Growing evidences suggest that protein O-GlcNAcylation is common and is analogous to phosphorylation in modulating broad ranges of biological processes. However, compared to phosphorylation, the amount of protein O-GlcNAcylation data is relatively limited and its annotation in databases is scarce. Furthermore, a bioinformatics resource for O-GlcNAcylation is lacking, and an O-GlcNAcylation site prediction tool is much needed. DESCRIPTION: We developed a database of O-GlcNAcylated proteins and sites, dbOGAP, primarily based on literature published since O-GlcNAcylation was first described in 1984. The database currently contains ~800 proteins with experimental O-GlcNAcylation information, of which ~61% are of humans, and 172 proteins have a total of ~400 O-GlcNAcylation sites identified. The O-GlcNAcylated proteins are primarily nucleocytoplasmic, including membrane- and non-membrane bounded organelle-associated proteins. The known O-GlcNAcylated proteins exert a broad range of functions including transcriptional regulation, macromolecular complex assembly, intracellular transport, translation, and regulation of cell growth or death. The database also contains ~365 potential O-GlcNAcylated proteins inferred from known O-GlcNAcylated orthologs. Additional annotations, including other protein posttranslational modifications, biological pathways and disease information are integrated into the database. We developed an O-GlcNAcylation site prediction system, OGlcNAcScan, based on Support Vector Machine and trained using protein sequences with known O-GlcNAcylation sites from dbOGAP. The site prediction system achieved an area under ROC curve of 74.3% in five-fold cross-validation. The dbOGAP website was developed to allow for performing search and query on O-GlcNAcylated proteins and associated literature, as well as for browsing by gene names, organisms or pathways, and downloading of the database. Also available from the website, the OGlcNAcScan tool presents a list of predicted O-GlcNAcylation sites for given protein sequences. CONCLUSIONS: dbOGAP is the first public bioinformatics resource to allow systematic access to the O-GlcNAcylated proteins, and related functional information and bibliography, as well as to an O-GlcNAcylation site prediction tool. The resource will facilitate research on O-GlcNAcylation and its proteomic identification.","corpus_id":14550239,"score":0},{"doc_id":"21518215","title":"Proteomics of extremophiles.","abstract":"Functional genomic approaches, such as proteomics, greatly enhance the value of genome sequences by providing a global level assessment of which genes are expressed, when genes are expressed and at what cellular levels gene products are synthesized. With over 1000 complete genome sequences of different microorganisms available, and DNA sequencing for environmental samples (metagenomes) producing vast amounts of gene sequence data, there is a real opportunity and a clear need to generate associated functional genomic data to learn about the source microorganisms. In contrast to the technological advances that have led to the accelerated rate and ease at which DNA sequence data can be generated, mass spectrometry based proteomics remains a technically sophisticated and exacting science. In recognition of the need to make proteomics more accessible to a growing number of environmental microbiologists so that the 'functional genomics gap' may be bridged, this review strives to demystify proteomic technologies and describe ways in which they have been applied, and more importantly, can be applied to study the physiology and ecology of extremophiles.","corpus_id":27992723,"score":0},{"doc_id":"21538885","title":"A posteriori quality control for the curation and reuse of public proteomics data.","abstract":"Proteomics is a rapidly expanding field encompassing a multitude of complex techniques and data types. To date much effort has been devoted to achieving the highest possible coverage of proteomes with the aim to inform future developments in basic biology as well as in clinical settings. As a result, growing amounts of data have been deposited in publicly available proteomics databases. These data are in turn increasingly reused for orthogonal downstream purposes such as data mining and machine learning. These downstream uses however, need ways to a posteriori validate whether a particular data set is suitable for the envisioned purpose. Furthermore, the (semi-)automatic curation of repository data is dependent on analyses that can highlight misannotation and edge conditions for data sets. Such curation is an important prerequisite for efficient proteomics data reuse in the life sciences in general. We therefore present here a selection of quality control metrics and approaches for the a posteriori detection of potential issues encountered in typical proteomics data sets. We illustrate our metrics by relying on publicly available data from the Proteomics Identifications Database (PRIDE), and simultaneously show the usefulness of the large body of PRIDE data as a means to derive empirical background distributions for relevant metrics.","corpus_id":5224565,"score":0},{"doc_id":"22522798","title":"A proteomics performance standard to support measurement quality in proteomics.","abstract":"The emergence of MS-based proteomic platforms as a prominent technology utilized in biochemical and biomedical research has increased the need for high-quality MS measurements. To address this need, National Institute of Standards and Technology (NIST) reference material (RM) 8323 yeast protein extract is introduced as a proteomics quality control material for benchmarking the preanalytical and analytical performance of proteomics-based experimental workflows. RM 8323 yeast protein extract is based upon the well-characterized eukaryote Saccharomyces cerevisiae and can be utilized in the design and optimization of proteomics-based methodologies from sample preparation to data analysis. To demonstrate its utility as a proteomics quality control material, we coupled LC-MS/MS measurements of RM 8323 with the NIST MS Quality Control (MSQC) performance metrics to quantitatively assess the LC-MS/MS instrumentation parameters that influence measurement accuracy, repeatability, and reproducibility. Due to the complexity of the yeast proteome, we also demonstrate how NIST RM 8323, along with the NIST MSQC performance metrics, can be used in the evaluation and optimization of proteomics-based sample preparation methods.","corpus_id":31435450,"score":0},{"doc_id":"22682516","title":"ROCS: a reproducibility index and confidence score for interaction proteomics studies.","abstract":"BACKGROUND: Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. METHODS: To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. RESULTS: We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. CONCLUSIONS: Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called \"ROCS\", freely available from the CRAN repository http://cran.r-project.org/.","corpus_id":309294,"score":0},{"doc_id":"23153078","title":"P2TF: a comprehensive resource for analysis of prokaryotic transcription factors.","abstract":"BACKGROUND: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families according to their domain organisation. There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences. DESCRIPTION: P2TF (Predicted Prokaryotic Transcription Factors) is an integrated and comprehensive database relating to transcription factor proteins. The current version of the database contains 372,877 TFs from 1,987 completely sequenced prokaryotic genomes and 43 metagenomes. The database provides annotation, classification and visualisation of TF genes and their genetic context, providing researchers with a one-stop shop in which to investigate TFs. The P2TF database analyses TFs in both predicted proteomes and reconstituted ORFeomes, recovering approximately 3% more TF proteins than just screening predicted proteomes. Users are able to search the database with sequence or domain architecture queries, and resulting hits can be aligned to investigate evolutionary relationships and conservation of residues. To increase utility, all searches can be filtered by taxonomy, TF genes can be added to the P2TF cart, and gene lists can be exported for external analysis in a variety of formats. CONCLUSIONS: P2TF is an open resource for biologists, allowing exploration of all TFs within prokaryotic genomes and metagenomes. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access and download the data. The database is freely available at http://www.p2tf.org/.","corpus_id":5497004,"score":0},{"doc_id":"23246537","title":"Quality assessment for clinical proteomics.","abstract":"Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a quality by design paradigm, the variability of individual steps in experimental pipelines will be reduced, regularizing overall outcomes. This review discusses the evolution of quality assessment in 2D gel electrophoresis, mass spectrometry-based proteomic profiling, tandem mass spectrometry-based protein inventories, and proteomic quantitation. Taken together, the advances in each of these technologies are establishing databases that will be increasingly useful for decision-making in clinical experimentation.","corpus_id":25403695,"score":0},{"doc_id":"23256906","title":"CAPER: a chromosome-assembled human proteome browsER.","abstract":"High-throughput mass spectrometry and antibody-based experiments have begun to produce a large amount of proteomic data sets. Chromosome-based visualization of these data sets and their annotations can help effectively integrate, organize, and analyze them. Therefore, we developed a web-based, user-friendly Chromosome-Assembled human Proteome browsER (CAPER). To display proteomic data sets and related annotations comprehensively, CAPER employs two distinct visualization strategies: track-view for the sequence/site information and the correspondence between proteome, transcriptome, genome, and chromosome and heatmap-view for the qualitative and quantitative functional annotations. CAPER supports data browsing at multiple scales through Google Map-like smooth navigation, zooming, and positioning with chromosomes as the reference coordinate. Both track-view and heatmap-view can mutually switch, providing a high-quality user interface. Taken together, CAPER will greatly facilitate the complete annotation and functional interpretation of the human genome by proteomic approaches, thereby making a significant contribution to the Chromosome-Centric Human Proteome Project and even the human physiology/pathology research. CAPER can be accessed at http://www.bprc.ac.cn/CAPE .","corpus_id":38216842,"score":0},{"doc_id":"24105449","title":"Proteomics in radiation research: present status and future perspectives.","abstract":"Rapidly developing postgenome research has made proteins an attractive target for biological analysis. The well-established term of proteome is defined as the complete set of proteins expressed in a given cell, tissue or organism. Unlike the genome, a proteome is rapidly changing as it tends to adapt to microenvironmental signals. The systematic analysis of the proteome at a given time and state is referred to as proteomics. This technique provides information on the molecular and cellular mechanisms that regulate physiology and pathophysiology of the cell. Applications of proteome profiling in radiation research are increasing. However, the large-scale proteomics data sets generated need to be integrated into other fields of radiation biology to facilitate the interpretation of radiation-induced cellular and tissue effects. The aim of this review is to introduce the most recent developments in the field of radiation proteomics.","corpus_id":45488511,"score":0},{"doc_id":"24316359","title":"Proteomics quality and standard: from a regulatory perspective.","abstract":"Proteomics has emerged as a rapidly expanding field dealing with large-scale protein analyses. It is anticipated that proteomics data will be increasingly submitted to the U.S. Food and Drug Administration (FDA) for biomarker qualification or in conjunction with applications for the approval of drugs, medical devices, and other FDA-regulated consumer products. To date, however, no established guideline has been available regarding the generation, submission and assessment of the quality of proteomics data that will be reviewed by regulatory agencies for decision making. Therefore, this commentary is aimed at provoking some thoughts and debates towards developing a framework which can guide future proteomics data submission. The ultimate goal is to establish quality control standards for proteomics data generation and evaluation, and to prepare government agencies such as the FDA to meet future obligations utilizing proteomics data to support regulatory decision.","corpus_id":8789892,"score":0},{"doc_id":"24467687","title":"Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.","abstract":"BACKGROUND: Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. RESULTS: To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). CONCLUSIONS: Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.","corpus_id":1592784,"score":0},{"doc_id":"24648354","title":"Proteomics made more accessible.","abstract":"MS-based proteomics is a bioinformatic-intensive field. Additionally, the instruments and instrument-related and analytic software are expensive. Some free Internet-based proteomics tools have gained wide usage, but there have not been any single bioinformatic framework that in an easy and intuitive way guided the user through the whole process from analyses to submission. Together, these factors may have limited the expansion of proteomics analyses, and also the secondary use (reanalyses) of proteomic data. Vaudel et al. (Proteomics 2014, 14, 1001-1005) are now describing their Compomics framework that guides the user through all the main steps, from the database generation, via the analyses and validation, and through the submission process to PRIDE, a proteomic data bank. Vaudel et al. partly base the framework on tools that they have developed themselves, and partly they are integrating other freeware tools into the workflow. One of the most interesting aspects with the Compomics framework is the possibility of extending MS-based proteomics outside the MS laboratory itself. With the Compomics framework, any laboratory can handle large amounts of proteomic data, thereby facilitating collaboration and in-depth data analyses. The described software also opens the potential for any laboratory to reanalyze data deposited in PRIDE.","corpus_id":416164,"score":0},{"doc_id":"24833567","title":"Practice quality improvement during residency: where do we stand and where can we improve?","abstract":"RATIONALE AND OBJECTIVES: Completing a systems-based practice project, equivalent to a practice quality improvement project (PQI), is a residency requirement by the Accreditation Council for Graduate Medical Education and an American Board of Radiology milestone. The aim of this study was to assess the residents' perspectives on quality improvement projects in radiology. MATERIALS AND METHODS: Survey data were collected from 154 trainee members of the Association of University Radiologists to evaluate the residents' views on PQI. RESULTS: Most residents were aware of the requirement of completing a PQI project and had faculty mentors for their projects. Residents who thought it was difficult to find a mentor were more likely to start their project later in residency (P < .0001). Publication rates were low overall, and lack of time was considered the greatest obstacle. Having dedicated time for a PQI project was associated with increased likelihood of publishing or presenting the data (P = .0091). Residents who rated the five surveyed PQI steps (coming up with an idea, finding a mentor, designing a project, finding resources, and finding time) as difficult steps were more likely to not have initiated a PQI project (P < .0001 for the first four and P = .0046 for time). CONCLUSION: We present five practical areas of improvement to make PQI a valuable learning experience: 1) Increasing awareness of PQI and providing ideas for projects, 2) encouraging faculty mentorship and publication, 3) educating residents about project design and implementation, 4) providing resources such as books and funds, and 5) allowing dedicated time.","corpus_id":9490938,"score":0},{"doc_id":"25416467","title":"The quality/safety medical index: implementation and analysis.","abstract":"Medical analytics relating to quality and safety measures have become particularly timely and of high importance in contemporary medical practice. In medical imaging, the dynamic relationship between medical imaging quality and radiation safety creates challenges in quantifying quality or safety independently. By creating a standardized measurement which simultaneously accounts for quality and safety measures (i.e., quality safety index), one can in theory create a standardized method for combined quality and safety analysis, which in turn can be analyzed in the context of individual patient, exam, and clinical profiles. The derived index measures can be entered into a centralized database, which in turn can be used for comparative performance of individual and institutional service providers. In addition, data analytics can be used to create customizable educational resources for providers and patients, clinical decision support tools, technology performance analysis, and clinical/economic outcomes research.","corpus_id":23427235,"score":0},{"doc_id":"26590258","title":"MitoAge: a database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity.","abstract":"Mitochondria are the only organelles in the animal cells that have their own genome. Due to a key role in energy production, generation of damaging factors (ROS, heat), and apoptosis, mitochondria and mtDNA in particular have long been considered one of the major players in the mechanisms of aging, longevity and age-related diseases. The rapidly increasing number of species with fully sequenced mtDNA, together with accumulated data on longevity records, provides a new fascinating basis for comparative analysis of the links between mtDNA features and animal longevity. To facilitate such analyses and to support the scientific community in carrying these out, we developed the MitoAge database containing calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop) regions, and codon usage/amino acids frequency for each protein-coding gene. MitoAge includes 922 species with fully sequenced mtDNA and maximum lifespan records. The database is available through the MitoAge website (www.mitoage.org or www.mitoage.info), which provides the necessary tools for searching, browsing, comparing and downloading the data sets of interest for selected taxonomic groups across the Kingdom Animalia. The MitoAge website assists in statistical analysis of different features of the mtDNA and their correlative links to longevity.","corpus_id":21237600,"score":0},{"doc_id":"26974716","title":"Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics.","abstract":"Despite many technological and computational advances, the results of a mass spectrometry proteomics experiment are still subject to a large variability. For the understanding and evaluation of how technical variability affects the results of an experiment, several computationally derived quality control metrics have been introduced. However, despite the availability of these metrics, a systematic approach to quality control is often still lacking because the metrics are not fully understood and are hard to interpret. Here, we present a toolkit of powerful techniques to analyze and interpret multivariate quality control metrics to assess the quality of mass spectrometry proteomics experiments. We show how unsupervised techniques applied to these quality control metrics can provide an initial discrimination between low-quality experiments and high-quality experiments prior to manual investigation. Furthermore, we provide a technique to obtain detailed information on the quality control metrics that are related to the decreased performance, which can be used as actionable information to improve the experimental setup. Our toolkit is released as open-source and can be downloaded from https://bitbucket.org/proteinspector/qc_analysis/ .","corpus_id":20294295,"score":0},{"doc_id":"27577934","title":"Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.","abstract":"The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .","corpus_id":4572904,"score":0},{"doc_id":"27794554","title":"RNAcentral: a comprehensive database of non-coding RNA sequences.","abstract":"RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.","corpus_id":36012271,"score":0},{"doc_id":"27899569","title":"MEGARes: an antimicrobial resistance database for high throughput sequencing.","abstract":"Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.","corpus_id":17753684,"score":0},{"doc_id":"28025334","title":"Minimizing proteome redundancy in the UniProt Knowledgebase.","abstract":"Advances in high-throughput sequencing have led to an unprecedented growth in genome sequences being submitted to biological databases. In particular, the sequencing of large numbers of nearly identical bacterial genomes during infection outbreaks and for other large-scale studies has resulted in a high level of redundancy in nucleotide databases and consequently in the UniProt Knowledgebase (UniProtKB). Redundancy negatively impacts on database searches by causing slower searches, an increase in statistical bias and cumbersome result analysis. The redundancy combined with the large data volume increases the computational costs for most reuses of UniProtKB data. All of this poses challenges for effective discovery in this wealth of data. With the continuing development of sequencing technologies, it is clear that finding ways to minimize redundancy is crucial to maintaining UniProt's essential contribution to data interpretation by our users. We have developed a methodology to identify and remove highly redundant proteomes from UniProtKB. The procedure identifies redundant proteomes by performing pairwise alignments of sets of sequences for pairs of proteomes and subsequently, applies graph theory to find dominating sets that provide a set of non-redundant proteomes with a minimal loss of information. This method was implemented for bacteria in mid-2015, resulting in a removal of 50 million proteins in UniProtKB. With every new release, this procedure is used to filter new incoming proteomes, resulting in a more scalable and scientifically valuable growth of UniProtKB.Database URL: http://www.uniprot.org/proteomes/.","corpus_id":2231658,"score":0},{"doc_id":"28676234","title":"Computational proteomics tools for identification and quality control.","abstract":"Computational proteomics is a constantly growing field to support end users with powerful and reliable tools for performing several computational steps within an analytics workflow for proteomics experiments. Typically, after capturing with a mass spectrometer, the proteins have to be identified and quantified. After certain follow-up analyses, an optional targeted approach is suitable for validating the results. The de. NBI (German network for bioinformatics infrastructure) service center in Dortmund provides several software applications and platforms as services to meet these demands. In this work, we present our tools and services, which is the combination of SearchGUI and PeptideShaker. SearchGUI is a managing tool for several search engines to find peptide spectra matches for one or more complex MS(2) measurements. PeptideShaker combines all matches and creates a consensus list of identified proteins providing statistical confidence measures. In a next step, we are planning to release a web service for protein identification containing both tools. This system will be designed for high scalability and distributed computing using solutions like the Docker container system among others. As an additional service, we offer a web service oriented database providing all necessary high-quality and high-resolution data for starting targeted proteomics analyses. The user can easily select proteins of interest, review the according spectra and download both protein sequences and spectral library. All systems are designed to be intuitively and user-friendly operable.","corpus_id":10712225,"score":0},{"doc_id":"29124938","title":"Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.","abstract":"Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. We evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating six 2D LC-MS/MS data sets for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we derived a quantification confidence score based on the quality of each peptide-spectrum match to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS data sets collected over a 7-month period. This study provides the first quality assessment on long-term stability and technical considerations for study design of a large-scale clinical proteomics project.","corpus_id":3952058,"score":0}],"string":"[\n {\n \"doc_id\": \"18032431\",\n \"title\": \"GenoList: an integrated environment for comparative analysis of microbial genomes.\",\n \"abstract\": \"The multitude of bacterial genome sequences being determined has generated new requirements regarding the development of databases and graphical interfaces: these are needed to organize and retrieve biological information from the comparison of large sets of genomes. GenoList (http://genolist.pasteur.fr/GenoList) is an integrated environment dedicated to querying and analyzing genome data from bacterial species. GenoList inherits from the SubtiList database and web server, the reference data resource for the Bacillus subtilis genome. The data model was extended to hold information about relationships between genomes (e.g. protein families). The web user interface was designed to primarily take into account biologists' needs and modes of operation. Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis. One key feature is the integration of the many tools accessible in the environment. As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.\",\n \"corpus_id\": 13844649,\n \"score\": 2\n },\n {\n \"doc_id\": \"18836194\",\n \"title\": \"The Universal Protein Resource (UniProt) 2009.\",\n \"abstract\": \"The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information that is essential for modern biological research. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute, the Protein Information Resource and the Swiss Institute of Bioinformatics. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, a user-friendly UniProt website and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. One of the key achievements of the UniProt consortium in 2008 is the completion of the first draft of the complete human proteome in UniProtKB/Swiss-Prot. This manually annotated representation of all currently known human protein-coding genes was made available in UniProt release 14.0 with 20 325 entries. UniProt is updated and distributed every three weeks and can be accessed online for searches or downloaded at www.uniprot.org.\",\n \"corpus_id\": 14202205,\n \"score\": 2\n },\n {\n \"doc_id\": \"18849571\",\n \"title\": \"HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.\",\n \"abstract\": \"The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap).\",\n \"corpus_id\": 1626367,\n \"score\": 2\n },\n {\n \"doc_id\": \"19457249\",\n \"title\": \"EDGAR: a software framework for the comparative analysis of prokaryotic genomes.\",\n \"abstract\": \"BACKGROUND: The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. RESULTS: To support these studies EDGAR - \\\"Efficient Database framework for comparative Genome Analyses using BLAST score Ratios\\\" - was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. CONCLUSION: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de, where the precomputed data sets can be browsed.\",\n \"corpus_id\": 1041880,\n \"score\": 2\n },\n {\n \"doc_id\": \"19892825\",\n \"title\": \"The comprehensive microbial resource.\",\n \"abstract\": \"The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. At the gene level users can view the gene annotation and underlying evidence. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available. The data and tools on the CMR aid genomic research and analysis, and the CMR is included in over 200 scientific publications. The code underlying the CMR website and the CMR database are freely available for download with no license restrictions.\",\n \"corpus_id\": 331367,\n \"score\": 2\n },\n {\n \"doc_id\": \"21556138\",\n \"title\": \"Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.\",\n \"abstract\": \"The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs), each selected from a Representative Proteome Group (RPG) containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT) are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55) most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains) and annotation information (93% of experimentally characterized proteins). All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.\",\n \"corpus_id\": 18017470,\n \"score\": 2\n },\n {\n \"doc_id\": \"21584191\",\n \"title\": \"MTB-PCDB: Mycobacterium tuberculosis proteome comparison database.\",\n \"abstract\": \"UNLABELLED: The Mycobacterium tuberculosis Proteome Comparison Database (MTB-PCDB) is an online database providing integrated access to proteome sequence comparison data for five strains of Mycobacterium tuberculosis (H37Rv, H37Ra, CDC 1551, F11 and KZN 1435) sequenced completely so far. MTB-PCDB currently hosts 40252 protein sequence comparison data obtained through inter-strain proteome comparison of five different strains of MTB. 2373 proteins were found to be identical in all 5 strains using MTB H(37)Rv as reference strain. To enable wide use of this data, MTB-PCDB provides a set of tools for searching, browsing, analyzing and downloading the data. By bringing together, M. tuberculosis proteome comparison among virulent & avirulent strains and also drug susceptible & drug resistance strains MTB-PCDB provides a unique discovery platform for comparative proteomics among these strains which may give insights into the discovery & development of TB drugs, vaccines and biomarkers. AVAILABILITY: The database is available for free at http://www.bicjbtdrc-mgims.in/MTB-PCDB/\",\n \"corpus_id\": 6143443,\n \"score\": 2\n },\n {\n \"doc_id\": \"21901743\",\n \"title\": \"Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.\",\n \"abstract\": \"OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that were pre-computed using the OrthoMCL algorithm. Version 4 of this database contained 116,536 ortholog groups clustered from 1,270,853 proteins obtained from 88 eukaryotic genomes, 16 archaean genomes, and 34 bacterial genomes. Future versions of OrthoMCL-DB will include more proteomes as more genomes are sequenced. Here, we describe how you can group your proteins of interest into ortholog clusters using two different means provided by the OrthoMCL system. The OrthoMCL-DB Web site has a tool for uploading and grouping a set of protein sequences, typically representing a proteome. This method maps the uploaded proteins to existing groups in OrthoMCL-DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install, and run the stand-alone OrthoMCL software.\",\n \"corpus_id\": 31516519,\n \"score\": 2\n },\n {\n \"doc_id\": \"22180819\",\n \"title\": \"Solving the Problem: Genome Annotation Standards before the Data Deluge.\",\n \"abstract\": \"The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.\",\n \"corpus_id\": 6814002,\n \"score\": 2\n },\n {\n \"doc_id\": \"23193269\",\n \"title\": \"MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.\",\n \"abstract\": \"MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.\",\n \"corpus_id\": 18494847,\n \"score\": 2\n },\n {\n \"doc_id\": \"24163254\",\n \"title\": \"Ensembl Genomes 2013: scaling up access to genome-wide data.\",\n \"abstract\": \"Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.\",\n \"corpus_id\": 137549,\n \"score\": 2\n },\n {\n \"doc_id\": \"24460813\",\n \"title\": \"CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.\",\n \"abstract\": \"BACKGROUND: The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult. RESULTS: We have developed CodaChrome (http://www.sourceforge.com/p/codachrome), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori. CONCLUSION: CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes.\",\n \"corpus_id\": 6395529,\n \"score\": 2\n },\n {\n \"doc_id\": \"24723423\",\n \"title\": \"OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.\",\n \"abstract\": \"Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://www.orthomam.univ-montp2.fr/.\",\n \"corpus_id\": 15030916,\n \"score\": 2\n },\n {\n \"doc_id\": \"25348405\",\n \"title\": \"UniProt: a hub for protein information.\",\n \"abstract\": \"UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.\",\n \"corpus_id\": 16082970,\n \"score\": 2\n },\n {\n \"doc_id\": \"25378341\",\n \"title\": \"diArk--the database for eukaryotic genome and transcriptome assemblies in 2014.\",\n \"abstract\": \"Eukaryotic genomes are the basis for understanding the complexity of life from populations to the molecular level. Recent technological innovations have revolutionized the speed of data generation enabling the sequencing of eukaryotic genomes and transcriptomes within days. The database diArk (http://www.diark.org) has been developed with the aim to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes. In this new version of the database we have also integrated species, for which transcriptome assemblies are available, and we provide more analyses of assemblies.\",\n \"corpus_id\": 15098268,\n \"score\": 2\n },\n {\n \"doc_id\": \"25429972\",\n \"title\": \"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.\",\n \"abstract\": \"The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.\",\n \"corpus_id\": 1983307,\n \"score\": 2\n },\n {\n \"doc_id\": \"25435546\",\n \"title\": \"Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.\",\n \"abstract\": \"Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. The amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant genomics studies. The acquisition of information on protein structure can help elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. In this study, we calculated multiple physicochemical and secondary structural parameters of protein sequences, including length, hydrophobicity, the amount of secondary structure, the number of intrinsically disordered regions (IDRs) and the predicted presence of transmembrane helices and signal peptides, using a total of 208,333 protein sequences from the genomes of six representative plant species, Arabidopsis thaliana, Glycine max (soybean), Populus trichocarpa (poplar), Oryza sativa (rice), Physcomitrella patens (moss) and Cyanidioschyzon merolae (alga). Using the PASS tool and the Rosetta Stone method, we annotated the presence of novel functional regions in 1,732 protein sequences that included unannotated sequences from the Arabidopsis and rice proteomes. These results were organized into the Plant Protein Annotation Suite database (Plant-PrAS), which can be freely accessed online at http://plant-pras.riken.jp/.\",\n \"corpus_id\": 11116254,\n \"score\": 2\n },\n {\n \"doc_id\": \"26673716\",\n \"title\": \"The Pfam protein families database: towards a more sustainable future.\",\n \"abstract\": \"In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.\",\n \"corpus_id\": 9574721,\n \"score\": 2\n },\n {\n \"doc_id\": \"27153665\",\n \"title\": \"DOGMA: domain-based transcriptome and proteome quality assessment.\",\n \"abstract\": \"MOTIVATION: Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. RESULTS: We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. AVAILABILITY AND IMPLEMENTATION: DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3187987,\n \"score\": 2\n },\n {\n \"doc_id\": \"18637161\",\n \"title\": \"WildSilkbase: an EST database of wild silkmoths.\",\n \"abstract\": \"BACKGROUND: Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed. DESCRIPTION: WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, Antheraea assama, an Indian tropical tasar silkmoth, A. mylitta and eri silkmoth, Samia cynthia ricini. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from http://www.cdfd.org.in/wildsilkbase/. CONCLUSION: A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.\",\n \"corpus_id\": 13755501,\n \"score\": 1\n },\n {\n \"doc_id\": \"22524279\",\n \"title\": \"Methods for visual mining of genomic and proteomic data atlases.\",\n \"abstract\": \"BACKGROUND: As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. RESULTS: This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. CONCLUSIONS: The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations. Providing linked task specific views that allow a user to start from points of interest (from diseases to single genes) enables targeted exploration of thousands of spectra and genomes. As the composition of the atlases changes, and our understanding of the biology increase, new tasks will continually arise. It is therefore important to provide the means to make the data available in a suitable manner in as short a time as possible. We have done this through the use of common visualization workflows, into which we rapidly deploy visual tools. These visualizations follow common metaphors where possible to assist users in understanding the displayed data. Rapid development of tools and task specific views allows researchers to mine large-scale data almost as quickly as it is produced. Ultimately these visual tools enable new inferences, new analyses and further refinement of the large scale data being provided in atlases such as PeptideAtlas and The Cancer Genome Atlas.\",\n \"corpus_id\": 16114676,\n \"score\": 1\n },\n {\n \"doc_id\": \"23203878\",\n \"title\": \"D²P²: database of disordered protein predictions.\",\n \"abstract\": \"We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D(2)P(2) will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life.\",\n \"corpus_id\": 6164727,\n \"score\": 1\n },\n {\n \"doc_id\": \"23262288\",\n \"title\": \"LepChorionDB, a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes.\",\n \"abstract\": \"Chorion proteins of Lepidoptera have a tripartite structure, which consists of a central domain and two, more variable, flanking arms. The central domain is highly conserved and it is used for the classification of chorion proteins into two major classes, A and B. Annotated and unreviewed Lepidopteran chorion protein sequences are available in various databases. A database, named LepChorionDB, was constructed by searching 5 different protein databases using class A and B central domain-specific profile Hidden Markov Models (pHMMs), developed in this work. A total of 413 Lepidopteran chorion proteins from 9 moths and 1 butterfly species were retrieved. These data were enriched and organised in order to populate LepChorionDB, the first relational database, available on the web, containing Lepidopteran chorion proteins grouped in A and B classes. LepChorionDB may provide insights in future functional and evolutionary studies of Lepidopteran chorion proteins and thus, it will be a useful tool for the Lepidopteran scientific community and Lepidopteran genome annotators, since it also provides access to the two pHMMs developed in this work, which may be used to discriminate A and B class chorion proteins. LepChorionDB is freely available at http://bioinformatics.biol.uoa.gr/LepChorionDB.\",\n \"corpus_id\": 23547009,\n \"score\": 1\n },\n {\n \"doc_id\": \"23409217\",\n \"title\": \"The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.\",\n \"abstract\": \"Variability in the extent of the descriptions of data ('metadata') held in public repositories forces users to assess the quality of records individually, which rapidly becomes impractical. The scoring of records on the richness of their description provides a simple, objective proxy measure for quality that enables filtering that supports downstream analysis. Pivotally, such descriptions should spur on improvements. Here, we introduce such a measure - the 'Metadata Coverage Index' (MCI): the percentage of available fields actually filled in a record or description. MCI scores can be calculated across a database, for individual records or for their component parts (e.g., fields of interest). There are many potential uses for this simple metric: for example; to filter, rank or search for records; to assess the metadata availability of an ad hoc collection; to determine the frequency with which fields in a particular record type are filled, especially with respect to standards compliance; to assess the utility of specific tools and resources, and of data capture practice more generally; to prioritize records for further curation; to serve as performance metrics of funded projects; or to quantify the value added by curation. Here we demonstrate the utility of MCI scores using metadata from the Genomes Online Database (GOLD), including records compliant with the 'Minimum Information about a Genome Sequence' (MIGS) standard developed by the Genomic Standards Consortium. We discuss challenges and address the further application of MCI scores; to show improvements in annotation quality over time, to inform the work of standards bodies and repository providers on the usability and popularity of their products, and to assess and credit the work of curators. Such an index provides a step towards putting metadata capture practices and in the future, standards compliance, into a quantitative and objective framework.\",\n \"corpus_id\": 30896675,\n \"score\": 1\n },\n {\n \"doc_id\": \"24150944\",\n \"title\": \"HRaP: database of occurrence of HomoRepeats and patterns in proteomes.\",\n \"abstract\": \"We focus our attention on multiple repeats of one amino acid (homorepeats) and create a new database (named HRaP, at http://bioinfo.protres.ru/hrap/) of occurrence of homorepeats and disordered patterns in different proteomes. HRaP is aimed at understanding the amino acid tandem repeat function in different proteomes. Therefore, the database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kingdoms and 5 phyla of bacteria. The database includes 1,449,561 protein sequences and 771,786 sequences of proteins with GO annotations. We have determined homorepeats and patterns that are associated with some function. Through our web server, the user can do the following: (i) search for proteins with the given homorepeat in 122 proteomes, including GO annotation for these proteins; (ii) search for proteins with the given disordered pattern from the library of disordered patterns constructed on the clustered Protein Data Bank in 122 proteomes, including GO annotations for these proteins; (iii) analyze lengths of homorepeats in different proteomes; (iv) investigate disordered regions in the chosen proteins in 122 proteomes; (v) study the coupling of different homorepeats in one protein; (vi) determine longest runs for each amino acid inside each proteome; and (vii) download the full list of proteins with the given length of a homorepeat.\",\n \"corpus_id\": 18523541,\n \"score\": 1\n },\n {\n \"doc_id\": \"24304897\",\n \"title\": \"Plasma Proteome Database as a resource for proteomics research: 2014 update.\",\n \"abstract\": \"Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.\",\n \"corpus_id\": 11646204,\n \"score\": 1\n },\n {\n \"doc_id\": \"24498877\",\n \"title\": \"PrionScan: an online database of predicted prion domains in complete proteomes.\",\n \"abstract\": \"BACKGROUND: Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. DESCRIPTION: Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. CONCLUSIONS: It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.\",\n \"corpus_id\": 14127536,\n \"score\": 1\n },\n {\n \"doc_id\": \"27153712\",\n \"title\": \"Computational clustering for viral reference proteomes.\",\n \"abstract\": \"MOTIVATION: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies. RESULTS: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt's curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs. AVAILABILITY AND IMPLEMENTATION: http://proteininformationresource.org/rps/viruses/ CONTACT: chenc@udel.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 18086674,\n \"score\": 1\n },\n {\n \"doc_id\": \"28317029\",\n \"title\": \"Listeriomics: an Interactive Web Platform for Systems Biology of Listeria.\",\n \"abstract\": \"As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach.\",\n \"corpus_id\": 17356251,\n \"score\": 1\n },\n {\n \"doc_id\": \"18281347\",\n \"title\": \"Information quality in proteomics.\",\n \"abstract\": \"Proteomics, the study of the protein complement of a biological system, is generating increasing quantities of data from rapidly developing technologies employed in a variety of different experimental workflows. Experimental processes, e.g. for comparative 2D gel studies or LC-MS/MS analyses of complex protein mixtures, involve a number of steps: from experimental design, through wet and dry lab operations, to publication of data in repositories and finally to data annotation and maintenance. The presence of inaccuracies throughout the processing pipeline, however, results in data that can be untrustworthy, thus offsetting the benefits of high-throughput technology. While researchers and practitioners are generally aware of some of the information quality issues associated with public proteomics data, there are few accepted criteria and guidelines for dealing with them. In this article, we highlight factors that impact on the quality of experimental data and review current approaches to information quality management in proteomics. Data quality issues are considered throughout the lifecycle of a proteomics experiment, from experiment design and technique selection, through data analysis, to archiving and sharing.\",\n \"corpus_id\": 11262766,\n \"score\": 0\n },\n {\n \"doc_id\": \"18314066\",\n \"title\": \"Proteomics: methodologies and applications in oncology.\",\n \"abstract\": \"Few technological developments have created as much excitement and skepticism as proteomics over their potential to change clinical diagnostic and prognostic procedures. Proteomics concerns itself with the characterization and function of all cellular proteins, the ultimate determinants of cellular function. As such, it represents the end result of all mechanisms of gene regulation and thus offers tremendous potential for characterizing biology. In much the same way as what has occurred with the genome, the scientific community is coming to grips with the fact that the proteome, although enormously complex, is finite. It is conceivable that we will learn the identity of all possible proteins, including all posttranslational modifications. The rate of protein discovery continues to accelerate in large part because of improvements in mass spectrometry-based technologies coupled with improved genomic databases and bioinformatic tools. In addition, there is reason to believe that proteomics is on the verge of moving from a methodology that requires repeated proteome \\\"discovery\\\" to one that can more systematically profile proteomes. This review discusses current proteomic-based technologies and the efforts of scientists to move them into the clinic for use in patients treated with radiotherapy and other modalities.\",\n \"corpus_id\": 24486625,\n \"score\": 0\n },\n {\n \"doc_id\": \"18592171\",\n \"title\": \"Plant proteomics.\",\n \"abstract\": \"An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.\",\n \"corpus_id\": 32604142,\n \"score\": 0\n },\n {\n \"doc_id\": \"18978022\",\n \"title\": \"Sys-BodyFluid: a systematical database for human body fluid proteome research.\",\n \"abstract\": \"Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.\",\n \"corpus_id\": 694240,\n \"score\": 0\n },\n {\n \"doc_id\": \"19129418\",\n \"title\": \"The proteome of seed development in the model legume Lotus japonicus.\",\n \"abstract\": \"We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family.\",\n \"corpus_id\": 7992872,\n \"score\": 0\n },\n {\n \"doc_id\": \"19541297\",\n \"title\": \"PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison.\",\n \"abstract\": \"Mitochondrial proteins associated with a wide spectrum of human diseases and currently large amounts of tissue or organ specific human mitochondrial proteome datasets are generated. However, high-throughput comparative proteomic methods have yet to be applied to extract subtle differences among mitochondria from different tissues or muscle types. The aim of this work was to provide an integrated way to identify and compare huge mitochondrial protein or peptide mass spectral data sets acquired from expert mitochondrial proteome or biomarker discovery community. Proteome comparison of human mitochondria (PCHM) is a web-based analysis environment for manual or automatic analysis of individual peptide mass fingerprints alongside a database of proteins and peptides identified in various organs for human mitochondrial proteins. PCHM provides a suite of graphical tools that allow the virtual plot of peptide mass fingerprinting (PMF) spectra and a fully automatic protein function classification based on gene ontology (GO) annotation system. The new virtual PMF plot is very useful to validate fragmented ion loses of any identical proteins and to remove unwanted foreign ion peaks. Fully automatic protein function classifier provides an easier way to compare the subtle differences of compositionally biased mitochondrial protein functions. PCHM also provides a variety of query algorithms aid in browsing, searching, and accessing complete annotations of data relevant to each mitochondrial protein of interest, which link external databases and users. PCHM will be a useful tool for the systematic and functional characterization of the mitochondrial proteins in relation to human diseases or biological research applications. PCHM can be accessed freely via a web interface http://pchm.inje.ac.kr.\",\n \"corpus_id\": 31902462,\n \"score\": 0\n },\n {\n \"doc_id\": \"20837570\",\n \"title\": \"A unified index of sequence quality and contig overlap for DNA barcoding.\",\n \"abstract\": \"SUMMARY: Barcode quality index (B) is a novel, unified measure of sequence quality and contig overlap tailored to the needs of DNA barcoding. Re-analysis of published data demonstrates the utility of B. AVAILABILITY AND IMPLEMENTATION: A GPL PERL script is available for download (http://www.nybg.org/files/scientists/dlittle/B.html).\",\n \"corpus_id\": 17620650,\n \"score\": 0\n },\n {\n \"doc_id\": \"21107258\",\n \"title\": \"Proteomics beyond proteomics: toward clinical applications.\",\n \"abstract\": \"PURPOSE OF REVIEW: There is an increasing interest in the application of proteomics in all areas of the life sciences, especially in the area of biomedical research wherein the analysis of biological fluids is very promising for biomarker discovery. The rapid development of proteomics as a field has depended upon substantial advances in instrumentation, methodologies, software and the availability of comprehensive sequence databases. However, progress has been slower than anticipated with respect to application in the realm of biomedicine. RECENT FINDINGS: We review some of the areas of importance for the development of proteomics and its applications to biomedical research. SUMMARY: One of the factors explaining the slow progress of candidate proteomics biomarkers through the translational pipeline has been the difficulty to develop validation and standardization of procedures to improve reproducibility, sensitivity and specificity. This challenge has now largely been met by large, consortium efforts, leading to the discovery of drug-specific protein biomarkers. The need for integrating complex protein patterns is now recognized in a new test classification by the US Food and Drug Administration termed 'in-vitro diagnostic multivariate index assays'. Further progress in clinical proteomics will depend upon continued collaborative efforts and infrastructure development by the proteomics community.\",\n \"corpus_id\": 11110793,\n \"score\": 0\n },\n {\n \"doc_id\": \"21264403\",\n \"title\": \"pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.\",\n \"abstract\": \"pep2pro is a comprehensive proteome analysis database specifically suitable for flexible proteome data analysis. The pep2pro database schema offers solutions to the various challenges of developing a proteome data analysis database and because data integrated in pep2pro are in relational format, it enables flexible and detailed data analysis. The information provided here will facilitate building proteome data analysis databases for other organisms or applications. The capacity of the pep2pro database for the integration and analysis of large proteome datasets was demonstrated by creating the pep2pro dataset, which is an organ-specific characterisation of the Arabidopsis thaliana proteome containing 14 522 identified proteins based on 2.6 million peptide spectrum assignments. This dataset provides evidence of protein expression and reveals organ-specific processes. The high coverage and density of the dataset are essential for protein quantification by normalised spectral counting and allowed us to extract information that is usually not accessible in low-coverage datasets. With this quantitative protein information we analysed organ- and organelle-specific sub-proteomes. In addition we matched spectra to regions in the genome that were not predicted to have protein coding capacity and provide PCR validation for selected revised gene models. Furthermore, we analysed the peptide features that distinguish detected from non-detected peptides and found substantial disagreement between predicted and detected proteotypic peptides, suggesting that large-scale proteomics data are essential for efficient selection of proteotypic peptides in targeted proteomics surveys. The pep2pro dataset is available as a resource for plant systems biology at www.pep2pro.ethz.ch.\",\n \"corpus_id\": 1044388,\n \"score\": 0\n },\n {\n \"doc_id\": \"21466708\",\n \"title\": \"dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.\",\n \"abstract\": \"BACKGROUND: Protein O-GlcNAcylation (or O-GlcNAc-ylation) is an O-linked glycosylation involving the transfer of β-N-acetylglucosamine to the hydroxyl group of serine or threonine residues of proteins. Growing evidences suggest that protein O-GlcNAcylation is common and is analogous to phosphorylation in modulating broad ranges of biological processes. However, compared to phosphorylation, the amount of protein O-GlcNAcylation data is relatively limited and its annotation in databases is scarce. Furthermore, a bioinformatics resource for O-GlcNAcylation is lacking, and an O-GlcNAcylation site prediction tool is much needed. DESCRIPTION: We developed a database of O-GlcNAcylated proteins and sites, dbOGAP, primarily based on literature published since O-GlcNAcylation was first described in 1984. The database currently contains ~800 proteins with experimental O-GlcNAcylation information, of which ~61% are of humans, and 172 proteins have a total of ~400 O-GlcNAcylation sites identified. The O-GlcNAcylated proteins are primarily nucleocytoplasmic, including membrane- and non-membrane bounded organelle-associated proteins. The known O-GlcNAcylated proteins exert a broad range of functions including transcriptional regulation, macromolecular complex assembly, intracellular transport, translation, and regulation of cell growth or death. The database also contains ~365 potential O-GlcNAcylated proteins inferred from known O-GlcNAcylated orthologs. Additional annotations, including other protein posttranslational modifications, biological pathways and disease information are integrated into the database. We developed an O-GlcNAcylation site prediction system, OGlcNAcScan, based on Support Vector Machine and trained using protein sequences with known O-GlcNAcylation sites from dbOGAP. The site prediction system achieved an area under ROC curve of 74.3% in five-fold cross-validation. The dbOGAP website was developed to allow for performing search and query on O-GlcNAcylated proteins and associated literature, as well as for browsing by gene names, organisms or pathways, and downloading of the database. Also available from the website, the OGlcNAcScan tool presents a list of predicted O-GlcNAcylation sites for given protein sequences. CONCLUSIONS: dbOGAP is the first public bioinformatics resource to allow systematic access to the O-GlcNAcylated proteins, and related functional information and bibliography, as well as to an O-GlcNAcylation site prediction tool. The resource will facilitate research on O-GlcNAcylation and its proteomic identification.\",\n \"corpus_id\": 14550239,\n \"score\": 0\n },\n {\n \"doc_id\": \"21518215\",\n \"title\": \"Proteomics of extremophiles.\",\n \"abstract\": \"Functional genomic approaches, such as proteomics, greatly enhance the value of genome sequences by providing a global level assessment of which genes are expressed, when genes are expressed and at what cellular levels gene products are synthesized. With over 1000 complete genome sequences of different microorganisms available, and DNA sequencing for environmental samples (metagenomes) producing vast amounts of gene sequence data, there is a real opportunity and a clear need to generate associated functional genomic data to learn about the source microorganisms. In contrast to the technological advances that have led to the accelerated rate and ease at which DNA sequence data can be generated, mass spectrometry based proteomics remains a technically sophisticated and exacting science. In recognition of the need to make proteomics more accessible to a growing number of environmental microbiologists so that the 'functional genomics gap' may be bridged, this review strives to demystify proteomic technologies and describe ways in which they have been applied, and more importantly, can be applied to study the physiology and ecology of extremophiles.\",\n \"corpus_id\": 27992723,\n \"score\": 0\n },\n {\n \"doc_id\": \"21538885\",\n \"title\": \"A posteriori quality control for the curation and reuse of public proteomics data.\",\n \"abstract\": \"Proteomics is a rapidly expanding field encompassing a multitude of complex techniques and data types. To date much effort has been devoted to achieving the highest possible coverage of proteomes with the aim to inform future developments in basic biology as well as in clinical settings. As a result, growing amounts of data have been deposited in publicly available proteomics databases. These data are in turn increasingly reused for orthogonal downstream purposes such as data mining and machine learning. These downstream uses however, need ways to a posteriori validate whether a particular data set is suitable for the envisioned purpose. Furthermore, the (semi-)automatic curation of repository data is dependent on analyses that can highlight misannotation and edge conditions for data sets. Such curation is an important prerequisite for efficient proteomics data reuse in the life sciences in general. We therefore present here a selection of quality control metrics and approaches for the a posteriori detection of potential issues encountered in typical proteomics data sets. We illustrate our metrics by relying on publicly available data from the Proteomics Identifications Database (PRIDE), and simultaneously show the usefulness of the large body of PRIDE data as a means to derive empirical background distributions for relevant metrics.\",\n \"corpus_id\": 5224565,\n \"score\": 0\n },\n {\n \"doc_id\": \"22522798\",\n \"title\": \"A proteomics performance standard to support measurement quality in proteomics.\",\n \"abstract\": \"The emergence of MS-based proteomic platforms as a prominent technology utilized in biochemical and biomedical research has increased the need for high-quality MS measurements. To address this need, National Institute of Standards and Technology (NIST) reference material (RM) 8323 yeast protein extract is introduced as a proteomics quality control material for benchmarking the preanalytical and analytical performance of proteomics-based experimental workflows. RM 8323 yeast protein extract is based upon the well-characterized eukaryote Saccharomyces cerevisiae and can be utilized in the design and optimization of proteomics-based methodologies from sample preparation to data analysis. To demonstrate its utility as a proteomics quality control material, we coupled LC-MS/MS measurements of RM 8323 with the NIST MS Quality Control (MSQC) performance metrics to quantitatively assess the LC-MS/MS instrumentation parameters that influence measurement accuracy, repeatability, and reproducibility. Due to the complexity of the yeast proteome, we also demonstrate how NIST RM 8323, along with the NIST MSQC performance metrics, can be used in the evaluation and optimization of proteomics-based sample preparation methods.\",\n \"corpus_id\": 31435450,\n \"score\": 0\n },\n {\n \"doc_id\": \"22682516\",\n \"title\": \"ROCS: a reproducibility index and confidence score for interaction proteomics studies.\",\n \"abstract\": \"BACKGROUND: Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. METHODS: To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. RESULTS: We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. CONCLUSIONS: Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called \\\"ROCS\\\", freely available from the CRAN repository http://cran.r-project.org/.\",\n \"corpus_id\": 309294,\n \"score\": 0\n },\n {\n \"doc_id\": \"23153078\",\n \"title\": \"P2TF: a comprehensive resource for analysis of prokaryotic transcription factors.\",\n \"abstract\": \"BACKGROUND: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families according to their domain organisation. There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences. DESCRIPTION: P2TF (Predicted Prokaryotic Transcription Factors) is an integrated and comprehensive database relating to transcription factor proteins. The current version of the database contains 372,877 TFs from 1,987 completely sequenced prokaryotic genomes and 43 metagenomes. The database provides annotation, classification and visualisation of TF genes and their genetic context, providing researchers with a one-stop shop in which to investigate TFs. The P2TF database analyses TFs in both predicted proteomes and reconstituted ORFeomes, recovering approximately 3% more TF proteins than just screening predicted proteomes. Users are able to search the database with sequence or domain architecture queries, and resulting hits can be aligned to investigate evolutionary relationships and conservation of residues. To increase utility, all searches can be filtered by taxonomy, TF genes can be added to the P2TF cart, and gene lists can be exported for external analysis in a variety of formats. CONCLUSIONS: P2TF is an open resource for biologists, allowing exploration of all TFs within prokaryotic genomes and metagenomes. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access and download the data. The database is freely available at http://www.p2tf.org/.\",\n \"corpus_id\": 5497004,\n \"score\": 0\n },\n {\n \"doc_id\": \"23246537\",\n \"title\": \"Quality assessment for clinical proteomics.\",\n \"abstract\": \"Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a quality by design paradigm, the variability of individual steps in experimental pipelines will be reduced, regularizing overall outcomes. This review discusses the evolution of quality assessment in 2D gel electrophoresis, mass spectrometry-based proteomic profiling, tandem mass spectrometry-based protein inventories, and proteomic quantitation. Taken together, the advances in each of these technologies are establishing databases that will be increasingly useful for decision-making in clinical experimentation.\",\n \"corpus_id\": 25403695,\n \"score\": 0\n },\n {\n \"doc_id\": \"23256906\",\n \"title\": \"CAPER: a chromosome-assembled human proteome browsER.\",\n \"abstract\": \"High-throughput mass spectrometry and antibody-based experiments have begun to produce a large amount of proteomic data sets. Chromosome-based visualization of these data sets and their annotations can help effectively integrate, organize, and analyze them. Therefore, we developed a web-based, user-friendly Chromosome-Assembled human Proteome browsER (CAPER). To display proteomic data sets and related annotations comprehensively, CAPER employs two distinct visualization strategies: track-view for the sequence/site information and the correspondence between proteome, transcriptome, genome, and chromosome and heatmap-view for the qualitative and quantitative functional annotations. CAPER supports data browsing at multiple scales through Google Map-like smooth navigation, zooming, and positioning with chromosomes as the reference coordinate. Both track-view and heatmap-view can mutually switch, providing a high-quality user interface. Taken together, CAPER will greatly facilitate the complete annotation and functional interpretation of the human genome by proteomic approaches, thereby making a significant contribution to the Chromosome-Centric Human Proteome Project and even the human physiology/pathology research. CAPER can be accessed at http://www.bprc.ac.cn/CAPE .\",\n \"corpus_id\": 38216842,\n \"score\": 0\n },\n {\n \"doc_id\": \"24105449\",\n \"title\": \"Proteomics in radiation research: present status and future perspectives.\",\n \"abstract\": \"Rapidly developing postgenome research has made proteins an attractive target for biological analysis. The well-established term of proteome is defined as the complete set of proteins expressed in a given cell, tissue or organism. Unlike the genome, a proteome is rapidly changing as it tends to adapt to microenvironmental signals. The systematic analysis of the proteome at a given time and state is referred to as proteomics. This technique provides information on the molecular and cellular mechanisms that regulate physiology and pathophysiology of the cell. Applications of proteome profiling in radiation research are increasing. However, the large-scale proteomics data sets generated need to be integrated into other fields of radiation biology to facilitate the interpretation of radiation-induced cellular and tissue effects. The aim of this review is to introduce the most recent developments in the field of radiation proteomics.\",\n \"corpus_id\": 45488511,\n \"score\": 0\n },\n {\n \"doc_id\": \"24316359\",\n \"title\": \"Proteomics quality and standard: from a regulatory perspective.\",\n \"abstract\": \"Proteomics has emerged as a rapidly expanding field dealing with large-scale protein analyses. It is anticipated that proteomics data will be increasingly submitted to the U.S. Food and Drug Administration (FDA) for biomarker qualification or in conjunction with applications for the approval of drugs, medical devices, and other FDA-regulated consumer products. To date, however, no established guideline has been available regarding the generation, submission and assessment of the quality of proteomics data that will be reviewed by regulatory agencies for decision making. Therefore, this commentary is aimed at provoking some thoughts and debates towards developing a framework which can guide future proteomics data submission. The ultimate goal is to establish quality control standards for proteomics data generation and evaluation, and to prepare government agencies such as the FDA to meet future obligations utilizing proteomics data to support regulatory decision.\",\n \"corpus_id\": 8789892,\n \"score\": 0\n },\n {\n \"doc_id\": \"24467687\",\n \"title\": \"Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.\",\n \"abstract\": \"BACKGROUND: Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. RESULTS: To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). CONCLUSIONS: Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.\",\n \"corpus_id\": 1592784,\n \"score\": 0\n },\n {\n \"doc_id\": \"24648354\",\n \"title\": \"Proteomics made more accessible.\",\n \"abstract\": \"MS-based proteomics is a bioinformatic-intensive field. Additionally, the instruments and instrument-related and analytic software are expensive. Some free Internet-based proteomics tools have gained wide usage, but there have not been any single bioinformatic framework that in an easy and intuitive way guided the user through the whole process from analyses to submission. Together, these factors may have limited the expansion of proteomics analyses, and also the secondary use (reanalyses) of proteomic data. Vaudel et al. (Proteomics 2014, 14, 1001-1005) are now describing their Compomics framework that guides the user through all the main steps, from the database generation, via the analyses and validation, and through the submission process to PRIDE, a proteomic data bank. Vaudel et al. partly base the framework on tools that they have developed themselves, and partly they are integrating other freeware tools into the workflow. One of the most interesting aspects with the Compomics framework is the possibility of extending MS-based proteomics outside the MS laboratory itself. With the Compomics framework, any laboratory can handle large amounts of proteomic data, thereby facilitating collaboration and in-depth data analyses. The described software also opens the potential for any laboratory to reanalyze data deposited in PRIDE.\",\n \"corpus_id\": 416164,\n \"score\": 0\n },\n {\n \"doc_id\": \"24833567\",\n \"title\": \"Practice quality improvement during residency: where do we stand and where can we improve?\",\n \"abstract\": \"RATIONALE AND OBJECTIVES: Completing a systems-based practice project, equivalent to a practice quality improvement project (PQI), is a residency requirement by the Accreditation Council for Graduate Medical Education and an American Board of Radiology milestone. The aim of this study was to assess the residents' perspectives on quality improvement projects in radiology. MATERIALS AND METHODS: Survey data were collected from 154 trainee members of the Association of University Radiologists to evaluate the residents' views on PQI. RESULTS: Most residents were aware of the requirement of completing a PQI project and had faculty mentors for their projects. Residents who thought it was difficult to find a mentor were more likely to start their project later in residency (P < .0001). Publication rates were low overall, and lack of time was considered the greatest obstacle. Having dedicated time for a PQI project was associated with increased likelihood of publishing or presenting the data (P = .0091). Residents who rated the five surveyed PQI steps (coming up with an idea, finding a mentor, designing a project, finding resources, and finding time) as difficult steps were more likely to not have initiated a PQI project (P < .0001 for the first four and P = .0046 for time). CONCLUSION: We present five practical areas of improvement to make PQI a valuable learning experience: 1) Increasing awareness of PQI and providing ideas for projects, 2) encouraging faculty mentorship and publication, 3) educating residents about project design and implementation, 4) providing resources such as books and funds, and 5) allowing dedicated time.\",\n \"corpus_id\": 9490938,\n \"score\": 0\n },\n {\n \"doc_id\": \"25416467\",\n \"title\": \"The quality/safety medical index: implementation and analysis.\",\n \"abstract\": \"Medical analytics relating to quality and safety measures have become particularly timely and of high importance in contemporary medical practice. In medical imaging, the dynamic relationship between medical imaging quality and radiation safety creates challenges in quantifying quality or safety independently. By creating a standardized measurement which simultaneously accounts for quality and safety measures (i.e., quality safety index), one can in theory create a standardized method for combined quality and safety analysis, which in turn can be analyzed in the context of individual patient, exam, and clinical profiles. The derived index measures can be entered into a centralized database, which in turn can be used for comparative performance of individual and institutional service providers. In addition, data analytics can be used to create customizable educational resources for providers and patients, clinical decision support tools, technology performance analysis, and clinical/economic outcomes research.\",\n \"corpus_id\": 23427235,\n \"score\": 0\n },\n {\n \"doc_id\": \"26590258\",\n \"title\": \"MitoAge: a database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity.\",\n \"abstract\": \"Mitochondria are the only organelles in the animal cells that have their own genome. Due to a key role in energy production, generation of damaging factors (ROS, heat), and apoptosis, mitochondria and mtDNA in particular have long been considered one of the major players in the mechanisms of aging, longevity and age-related diseases. The rapidly increasing number of species with fully sequenced mtDNA, together with accumulated data on longevity records, provides a new fascinating basis for comparative analysis of the links between mtDNA features and animal longevity. To facilitate such analyses and to support the scientific community in carrying these out, we developed the MitoAge database containing calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop) regions, and codon usage/amino acids frequency for each protein-coding gene. MitoAge includes 922 species with fully sequenced mtDNA and maximum lifespan records. The database is available through the MitoAge website (www.mitoage.org or www.mitoage.info), which provides the necessary tools for searching, browsing, comparing and downloading the data sets of interest for selected taxonomic groups across the Kingdom Animalia. The MitoAge website assists in statistical analysis of different features of the mtDNA and their correlative links to longevity.\",\n \"corpus_id\": 21237600,\n \"score\": 0\n },\n {\n \"doc_id\": \"26974716\",\n \"title\": \"Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics.\",\n \"abstract\": \"Despite many technological and computational advances, the results of a mass spectrometry proteomics experiment are still subject to a large variability. For the understanding and evaluation of how technical variability affects the results of an experiment, several computationally derived quality control metrics have been introduced. However, despite the availability of these metrics, a systematic approach to quality control is often still lacking because the metrics are not fully understood and are hard to interpret. Here, we present a toolkit of powerful techniques to analyze and interpret multivariate quality control metrics to assess the quality of mass spectrometry proteomics experiments. We show how unsupervised techniques applied to these quality control metrics can provide an initial discrimination between low-quality experiments and high-quality experiments prior to manual investigation. Furthermore, we provide a technique to obtain detailed information on the quality control metrics that are related to the decreased performance, which can be used as actionable information to improve the experimental setup. Our toolkit is released as open-source and can be downloaded from https://bitbucket.org/proteinspector/qc_analysis/ .\",\n \"corpus_id\": 20294295,\n \"score\": 0\n },\n {\n \"doc_id\": \"27577934\",\n \"title\": \"Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.\",\n \"abstract\": \"The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .\",\n \"corpus_id\": 4572904,\n \"score\": 0\n },\n {\n \"doc_id\": \"27794554\",\n \"title\": \"RNAcentral: a comprehensive database of non-coding RNA sequences.\",\n \"abstract\": \"RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.\",\n \"corpus_id\": 36012271,\n \"score\": 0\n },\n {\n \"doc_id\": \"27899569\",\n \"title\": \"MEGARes: an antimicrobial resistance database for high throughput sequencing.\",\n \"abstract\": \"Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.\",\n \"corpus_id\": 17753684,\n \"score\": 0\n },\n {\n \"doc_id\": \"28025334\",\n \"title\": \"Minimizing proteome redundancy in the UniProt Knowledgebase.\",\n \"abstract\": \"Advances in high-throughput sequencing have led to an unprecedented growth in genome sequences being submitted to biological databases. In particular, the sequencing of large numbers of nearly identical bacterial genomes during infection outbreaks and for other large-scale studies has resulted in a high level of redundancy in nucleotide databases and consequently in the UniProt Knowledgebase (UniProtKB). Redundancy negatively impacts on database searches by causing slower searches, an increase in statistical bias and cumbersome result analysis. The redundancy combined with the large data volume increases the computational costs for most reuses of UniProtKB data. All of this poses challenges for effective discovery in this wealth of data. With the continuing development of sequencing technologies, it is clear that finding ways to minimize redundancy is crucial to maintaining UniProt's essential contribution to data interpretation by our users. We have developed a methodology to identify and remove highly redundant proteomes from UniProtKB. The procedure identifies redundant proteomes by performing pairwise alignments of sets of sequences for pairs of proteomes and subsequently, applies graph theory to find dominating sets that provide a set of non-redundant proteomes with a minimal loss of information. This method was implemented for bacteria in mid-2015, resulting in a removal of 50 million proteins in UniProtKB. With every new release, this procedure is used to filter new incoming proteomes, resulting in a more scalable and scientifically valuable growth of UniProtKB.Database URL: http://www.uniprot.org/proteomes/.\",\n \"corpus_id\": 2231658,\n \"score\": 0\n },\n {\n \"doc_id\": \"28676234\",\n \"title\": \"Computational proteomics tools for identification and quality control.\",\n \"abstract\": \"Computational proteomics is a constantly growing field to support end users with powerful and reliable tools for performing several computational steps within an analytics workflow for proteomics experiments. Typically, after capturing with a mass spectrometer, the proteins have to be identified and quantified. After certain follow-up analyses, an optional targeted approach is suitable for validating the results. The de. NBI (German network for bioinformatics infrastructure) service center in Dortmund provides several software applications and platforms as services to meet these demands. In this work, we present our tools and services, which is the combination of SearchGUI and PeptideShaker. SearchGUI is a managing tool for several search engines to find peptide spectra matches for one or more complex MS(2) measurements. PeptideShaker combines all matches and creates a consensus list of identified proteins providing statistical confidence measures. In a next step, we are planning to release a web service for protein identification containing both tools. This system will be designed for high scalability and distributed computing using solutions like the Docker container system among others. As an additional service, we offer a web service oriented database providing all necessary high-quality and high-resolution data for starting targeted proteomics analyses. The user can easily select proteins of interest, review the according spectra and download both protein sequences and spectral library. All systems are designed to be intuitively and user-friendly operable.\",\n \"corpus_id\": 10712225,\n \"score\": 0\n },\n {\n \"doc_id\": \"29124938\",\n \"title\": \"Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.\",\n \"abstract\": \"Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. We evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating six 2D LC-MS/MS data sets for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we derived a quantification confidence score based on the quality of each peptide-spectrum match to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS data sets collected over a 7-month period. This study provides the first quality assessment on long-term stability and technical considerations for study design of a large-scale clinical proteomics project.\",\n \"corpus_id\": 3952058,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":87,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28652896\",\n \"title\": \"Resurrecting the Dead (Molecules).\",\n \"abstract\": \"Biological molecules, like organisms themselves, are subject to genetic drift and may even become \\\"extinct\\\". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of \\\"molecular resurrection\\\" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began.\",\n \"corpus_id\": 28341922\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18493600","title":"Resurrection of DNA function in vivo from an extinct genome.","abstract":"There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.","corpus_id":12566859,"score":2},{"doc_id":"19760276","title":"Darwin's warm little pond revisited: from molecules to the origin of life.","abstract":"All known cosmic and geological conditions and laws of chemistry and thermodynamics allow that complex organic matter could have formed spontaneously on pristine planet Earth about 4,000 mya. Simple gasses and minerals on the surface and in oceans of the early Earth reacted and were eventually organized in supramolecular aggregates and enveloped cells that evolved into primitive forms of life. Chemical evolution, which preceded all species of extant organisms, is a fact. In this review, we have concentrated on experimental and theoretical research published over the last two decades, which has added a wealth of new details and helped to close gaps in our previous understanding of this multifaceted field. Recent exciting progress in the molecular and genetic analyses of existing life, in particular microorganisms of ancient origin, even supports the possibility that a cellular, self-reproducing common ancestor might be assembled and resurrected in anaerobic cultures at some time in the future. Charles Darwin did not, and indeed, could not, address and specify the earliest phases of life which preceded the Origin of Species. However, in a famous letter, he sketched \"a warm little pond with all sorts of... (chemicals, in which) ...a protein was chemically formed.\" We try to trace the impact of his charming clear-sighted metaphor up to the present time.","corpus_id":23259886,"score":2},{"doc_id":"21460845","title":"Single-molecule paleoenzymology probes the chemistry of resurrected enzymes.","abstract":"It is possible to travel back in time at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx) dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32 °C more stable than modern enzymes, and the oldest show markedly higher activity than extant ones at pH 5. We probed the mechanisms of reduction of these enzymes using single-molecule force spectroscopy. From the force dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs use chemical mechanisms of reduction similar to those of modern enzymes. Although Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over 4 Gyr to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth.","corpus_id":2002600,"score":2},{"doc_id":"21703277","title":"RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems.","abstract":"The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical DRT systems. Beyond covalent molecular assembly, an extension of the DRT concept can include RNA molecules acting as dynamic structural template guides for the specific non-covalent assembly of multi-subunit complexes, equivalent to structural assembly chaperones. However, despite numerous precedents for RNA molecules acting as scaffolds for protein complexes, true RNA-mediated assembly chaperoning appears to be absent in modern biosystems. Another level of function with parallels to a DRT system is possible if RNA structural motifs dynamically guided specific patterns of catalytic modifications within multiple target sites in a pre-formed polymer or macromolecular complex. It is suggested that this type of structural RNA templating could logically play a functional role in certain areas of biology, one of which is the glycome of complex organisms. If any such RNA templating processes are shown to exist, they would share no necessary evolutionary relationships with events during early molecular evolution, but may promote understanding of the practical limits of biological RNA functions now and in the ancient RNA World. Awareness of these formal possibilities may also assist in the current search for functions of extensive non-coding RNAs in complex organisms, or for efforts towards artificial rendering of DRT systems.","corpus_id":510563,"score":2},{"doc_id":"21781330","title":"Resurrection of an ancestral 5S rRNA.","abstract":"BACKGROUND: In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences can be used to understand early events in evolution. In the case of RNA, the nature of parsimony is such that when applied to multiple RNA sequences it typically predicts ancestral sequences that satisfy the base pairing constraints associated with secondary structure. The case for such sequences being actual ancestors is greatly improved, if they can be shown to be biologically functional. RESULTS: A unique common ancestral sequence of 28 Vibrio 5S ribosomal RNA sequences predicted by parsimony was resurrected and found to be functional in the context of the E. coli cellular environment. The functionality of various point variants and intermediates that were constructed as part of the resurrection were examined in detail. When separately introduced the changes at single stranded positions and individual double variants at base-paired positions were also viable. An additional double variant was examined at a different base-paired position and it was also valid. CONCLUSIONS: The results show that at least in the case of the 5S rRNAs considered here, ancestors predicted by parsimony are likely to be realistic when the prediction is not overly influenced by single outliers. It is especially noteworthy that the phenotype of the predicted ancestors could be anticipated as a cumulative consequence of the phenotypes of the individual variants that comprised them. Thus, point mutation data is potentially useful in evaluating the reasonableness of ancestral sequences predicted by parsimony or other methods. The results also suggest that in the absence of significant tertiary structure constraints double variants that preserve pairing in stem regions will typically be accepted. Overall, the results suggest that it will be feasible to resurrect additional meaningful 5S rRNA ancestors as well as ancestral sequences of many different types of RNA.","corpus_id":7971821,"score":2},{"doc_id":"22330132","title":"Aqueous phase separation as a possible route to compartmentalization of biological molecules.","abstract":"How could the incredible complexity of modern cells evolve from something simple enough to have appeared in a primordial soup? This enduring question has sparked the interest of researchers since Darwin first considered his theory of natural selection. Organic molecules, even potentially functional molecules including peptides and nucleotides, can be produced abiotically. Amphiphiles such as surfactants and lipids display remarkable self-assembly processes including the spontaneous formation of vesicles resembling the membranes of living cells. Nonetheless, numerous questions remain. Given the presumably dilute concentrations of macromolecules in the prebiotic pools where the earliest cells are thought to have appeared, how could the necessary components become concentrated and encapsulated within a semipermeable membrane? What would drive the further structural complexity that is a hallmark of modern living systems? The interior of modern cells is subdivided into microcompartments such as the nucleoid of bacteria or the organelles of eukaryotic cells. Even within what at first appears to be a single compartment, for example, the cytoplasm or nucleus, chemical composition is often nonuniform, containing gradients, macromolecular assemblies, and/or liquid droplets. What might the internal structure of intermediate evolutionary forms have looked like? The nonideal aqueous solution chemistry of macromolecules offers an attractive possible answer to these questions. Aqueous polymer solutions will form multiple coexisting thermodynamic phases under a variety of readily accessible conditions. In this Account, we describe aqueous phase separation as a model system for biological compartmentalization in both early and modern cells, with an emphasis on systems that have been encapsulated within a lipid bilayer. We begin with an introduction to aqueous phase separation and discuss how this phenomenon can lead to microcompartmentalization and could facilitate biopolymer encapsulation by partitioning of solutes between the phases. We then describe primitive model cells based on phase separation inside lipid vesicles, which mimic several basic properties of biological cells: microcompartmentation, protein relocalization in response to stimulus, loss of symmetry, and asymmetric vesicle division. We observe these seemingly complex phenomena in the absence of genetic molecules, enzymes, or cellular machinery, and as a result these processes could provide clues to possible intermediates in the early evolution of cell-like assemblies.","corpus_id":10586980,"score":2},{"doc_id":"22674514","title":"Resurrecting ancient animal genomes: the extinct moa and more.","abstract":"Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.","corpus_id":40330531,"score":2},{"doc_id":"23355531","title":"Lateral gene transfer from the dead.","abstract":"In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.","corpus_id":6080655,"score":2},{"doc_id":"23394108","title":"Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases.","abstract":"We report a sequence reconstruction analysis targeting several Precambrian nodes in the evolution of class-A β-lactamases and the preparation and experimental characterization of their encoded proteins. Despite extensive sequence differences with the modern enzymes (~100 amino acid differences), the proteins resurrected in the laboratory properly fold into the canonical lactamase structure. The encoded proteins from 2-3 billion years (Gyr)-old β-lactamase sequences undergo cooperative two-state thermal denaturation and display very large denaturation temperature enhancements (~35 °C) relative to modern β-lactamases. They degrade different antibiotics in vitro with catalytic efficiencies comparable to that of an average modern enzyme. This enhanced substrate promiscuity is not accompanied by significant changes in the active-site region as seen in static X-ray structures, suggesting a plausible role for dynamics in the evolution of function in these proteins. Laboratory resurrections of 2-3 Gyr-old β-lactamases also endowed modern microorganisms with significant levels of resistance toward a variety of antibiotics, opening up the possibility of performing laboratory replays of the molecular tape of lactamase evolution. Overall, these results support the notions that Precambrian life was thermophilic and that proteins can evolve from substrate-promiscuous generalists into specialists during the course of natural evolution. They also highlight the biotechnological potential of laboratory resurrection of Precambrian proteins, as both high stability and enhanced promiscuity (likely contributors to high evolvability) are advantageous features in protein scaffolds for molecular design and laboratory evolution.","corpus_id":207092445,"score":2},{"doc_id":"24356963","title":"Tracing primordial protein evolution through structurally guided stepwise segment elongation.","abstract":"The understanding of how primordial proteins emerged has been a fundamental and longstanding issue in biology and biochemistry. For a better understanding of primordial protein evolution, we synthesized an artificial protein on the basis of an evolutionary hypothesis, segment-based elongation starting from an autonomously foldable short peptide. A 10-residue protein, chignolin, the smallest foldable polypeptide ever reported, was used as a structural support to facilitate higher structural organization and gain-of-function in the development of an artificial protein. Repetitive cycles of segment elongation and subsequent phage display selection successfully produced a 25-residue protein, termed AF.2A1, with nanomolar affinity against the Fc region of immunoglobulin G. AF.2A1 shows exquisite molecular recognition ability such that it can distinguish conformational differences of the same molecule. The structure determined by NMR measurements demonstrated that AF.2A1 forms a globular protein-like conformation with the chignolin-derived β-hairpin and a tryptophan-mediated hydrophobic core. Using sequence analysis and a mutation study, we discovered that the structural organization and gain-of-function emerged from the vicinity of the chignolin segment, revealing that the structural support served as the core in both structural and functional development. Here, we propose an evolutionary model for primordial proteins in which a foldable segment serves as the evolving core to facilitate structural and functional evolution. This study provides insights into primordial protein evolution and also presents a novel methodology for designing small sized proteins useful for industrial and pharmaceutical applications.","corpus_id":38728521,"score":2},{"doc_id":"24606140","title":"Progress toward synthetic cells.","abstract":"The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems.","corpus_id":24175504,"score":2},{"doc_id":"25809963","title":"Protocells: at the interface of life and non-life.","abstract":"The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one \"correct\" structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form-\"protocells\". At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called \"pseudo-protocells\". Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to \"true-protocells\". The emergence of a \"chromosome\" (with genes linked together)-thus avoiding \"gene-loss\" during the protocell division, was another key event in the evolution of protocells. Such \"unitary-protocells\", containing a central genetic molecule, may have appeared as a milestone-in principle, since then life could evolve endlessly, \"gaining\" more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life.","corpus_id":14784602,"score":2},{"doc_id":"26530525","title":"Mammoth 2.0: will genome engineering resurrect extinct species?","abstract":"It is impossible to 'clone' species for which no living cells exist. Genome editing may therefore provide the only means to bring extinct species--or, more accurately, extinct traits--back to life.","corpus_id":14722203,"score":2},{"doc_id":"26763705","title":"Experimental macroevolution.","abstract":"The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.","corpus_id":1298118,"score":2},{"doc_id":"27863072","title":"When directed evolution met ancestral enzyme resurrection.","abstract":"The directed evolution of ancestral -resurrected- enzymes can give a new twist in protein engineering approaches towards more versatile and robust biocatalysts.","corpus_id":17506710,"score":2},{"doc_id":"28008088","title":"Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering.","abstract":"A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes. Recently, however, ASR has developed from a tool for testing hypotheses about protein evolution to a useful means for designing novel proteins. The strength of this approach lies in the ability to infer ancestral sequences encoding proteins that have desirable properties compared with contemporary forms, particularly thermostability and broad substrate range, making them good starting points for laboratory evolution. Developments in technologies for DNA sequencing and synthesis and computational phylogenetic analysis have led to an escalation in the number of ancient proteins resurrected in the last decade and greatly facilitated the use of ASR in the burgeoning field of synthetic biology. However, the primary challenge of ASR remains in accurately inferring ancestral states, despite the uncertainty arising from evolutionary models, incomplete sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering.","corpus_id":28416897,"score":2},{"doc_id":"28094501","title":"Artificial Cells: Synthetic Compartments with Life-like Functionality and Adaptivity.","abstract":"Cells are highly advanced microreactors that form the basis of all life. Their fascinating complexity has inspired scientists to create analogs from synthetic and natural components using a bottom-up approach. The ultimate goal here is to assemble a fully man-made cell that displays functionality and adaptivity as advanced as that found in nature, which will not only provide insight into the fundamental processes in natural cells but also pave the way for new applications of such artificial cells. In this Account, we highlight our recent work and that of others on the construction of artificial cells. First, we will introduce the key features that characterize a living system; next, we will discuss how these have been imitated in artificial cells. First, compartmentalization is crucial to separate the inner chemical milieu from the external environment. Current state-of-the-art artificial cells comprise subcompartments to mimic the hierarchical architecture of eukaryotic cells and tissue. Furthermore, synthetic gene circuits have been used to encode genetic information that creates complex behavior like pulses or feedback. Additionally, artificial cells have to reproduce to maintain a population. Controlled growth and fission of synthetic compartments have been demonstrated, but the extensive regulation of cell division in nature is still unmatched. Here, we also point out important challenges the field needs to overcome to realize its full potential. As artificial cells integrate increasing orders of functionality, maintaining a supporting metabolism that can regenerate key metabolites becomes crucial. Furthermore, life does not operate in isolation. Natural cells constantly sense their environment, exchange (chemical) signals, and can move toward a chemoattractant. Here, we specifically explore recent efforts to reproduce such adaptivity in artificial cells. For instance, synthetic compartments have been produced that can recruit proteins to the membrane upon an external stimulus or modulate their membrane composition and permeability to control their interaction with the environment. A next step would be the communication of artificial cells with either bacteria or another artificial cell. Indeed, examples of such primitive chemical signaling are presented. Finally, motility is important for many organisms and has, therefore, also been pursued in synthetic systems. Synthetic compartments that were designed to move in a directed, controlled manner have been assembled, and directed movement toward a chemical attractant is among one of the most life-like directions currently under research. Although the bottom-up construction of an artificial cell that can be truly considered \"alive\" is still an ambitious goal, the recent work discussed in this Account shows that this is an active field with contributions from diverse disciplines like materials chemistry and biochemistry. Notably, research during the past decade has already provided valuable insights into complex synthetic systems with life-like properties. In the future, artificial cells are thought to contribute to an increased understanding of processes in natural cells and provide opportunities to create smart, autonomous, cell-like materials.","corpus_id":18934065,"score":2},{"doc_id":"28316883","title":"Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.","abstract":"BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. METHODS: ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. RESULTS: Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. DISCUSSION: The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.","corpus_id":23977880,"score":2},{"doc_id":"28671667","title":"Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins.","abstract":"The sarcomere-based structure of muscles is conserved among vertebrates; however, vertebrate muscle physiology is extremely diverse. A molecular explanation for this diversity and its evolution has not been proposed. We use phylogenetic analyses and single-molecule force spectroscopy (smFS) to investigate the mechanochemical evolution of titin, a giant protein responsible for the elasticity of muscle filaments. We resurrect eight-domain fragments of titin corresponding to the common ancestors to mammals, sauropsids, and tetrapods, which lived 105-356 Myr ago, and compare them with titin fragments from some of their modern descendants. We demonstrate that the resurrected titin molecules are rich in disulfide bonds and display high mechanical stability. These mechanochemical elements have changed over time, creating a paleomechanical trend that seems to correlate with animal body size, allowing us to estimate the sizes of extinct species. We hypothesize that mechanical adjustments in titin contributed to physiological changes that allowed the muscular development and diversity of modern tetrapods.","corpus_id":54482436,"score":2},{"doc_id":"28719578","title":"De novo active sites for resurrected Precambrian enzymes.","abstract":"Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.","corpus_id":36345380,"score":2},{"doc_id":"28915003","title":"The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery.","abstract":"Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify \"successful\" structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous \"DNA robots\" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.","corpus_id":-1,"score":2},{"doc_id":"28916155","title":"Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection.","abstract":"Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator. We tested hypotheses of adaptive evolution in the protein coding sequences of ESR2, and determined that ESR2 evolved via episodic positive selection on the NWM stem lineage. We separately co-transfected ESR2 constructs for human, NWM, and the anthropoid ancestor along with reporter gene vectors and performed hormone binding dose response experiments that measure transactivation activity. We found the transactivation potentials of the ancestral and human sequences to be significantly lower (p<0.0001 in each comparison) than that of the NWM when treated with estradiol, the most prevalent estrogen. We conclude the difference in fold activation is due to positive selection in the NWM ERβ ligand binding domain. Our study validates inferential methods for detecting adaptive evolution that predict functional consequences of nucleotide substitutions and points a way toward examining the functional consequences of positive Darwinian selection.","corpus_id":205842572,"score":2},{"doc_id":"29133450","title":"Resurrecting ancestral genes in bacteria to interpret ancient biosignatures.","abstract":"Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction. This article is part of the themed issue 'Reconceptualizing the origins of life'.","corpus_id":27456937,"score":2},{"doc_id":"29660672","title":"Biotechnological and protein-engineering implications of ancestral protein resurrection.","abstract":"Approximations to the sequences of ancestral proteins can be derived from the sequences of their modern descendants. Proteins encoded by such reconstructed sequences can be prepared in the laboratory and subjected to experimental scrutiny. These 'resurrected' ancestral proteins often display remarkable properties, reflecting ancestral adaptations to intra-cellular and extra-cellular environments that differed from the environments hosting modern/extant proteins. Recent experimental and computational work has specifically discussed high stability, substrate and catalytic promiscuity, conformational flexibility/diversity and altered patterns of interaction with other sub-cellular components. In this review, we discuss these remarkable properties as well as recent attempts to explore their biotechnological and protein-engineering potential.","corpus_id":4936466,"score":2},{"doc_id":"19033463","title":"Extinction and resurrection in gene networks.","abstract":"When gene regulatory networks operate in regimes where the number of protein molecules is so small that the molecular species are on the verge of extinction, the death and resurrection of the species greatly modifies the attractor landscape. Deterministic models and the diffusion approximation to the master equation break down at the limits of protein populations in a way very analogous to the breakdown of geometrical optics that occurs at distances <1 wavelength of light from edges. Stable stochastic attractors arise from extinction and resurrection events that are not predicted by the deterministic description. With this view, we explore the attractors of the regular toggle switch and the exclusive switch, focusing on the effects of cooperative binding and the production of protein in bursts. Our arguments suggest that the stability of lysogeny in the lambda-phage may be influenced by such extinction phenomena.","corpus_id":2077265,"score":1},{"doc_id":"19108768","title":"Convergent evolution: raising a family from the dead.","abstract":"New molecular evidence shows that Hawaiian honeyeaters did not evolve from the similar looking Australasian honeyeaters, but instead represent a striking case of convergent evolution. These now extinct birds form their own family, representing the only complete extinction of an entire avian family in modern times.","corpus_id":6410048,"score":1},{"doc_id":"19198773","title":"Paleoclimate and evolution: emergence of sponges during the neoproterozoic.","abstract":"In the last 15 years, we had to cope with many technological and conceptual obstacles. The major hindrance was the view that sponges are primitive and exist separated from the other metazoan organisms. After answering these problems, the painful scientific process to position the most enigmatic metazoan phylum, the Porifera, into the correct phylogenetic place among the eukaryotes in general and the multicellular animals in particular came to an end. The well-studied taxon Porifera (sponges) was first grouped to the animal-plants or plant-animals, then to the Zoophyta or Mesozoa, and finally to the Parazoa. Only by the application of molecular biological techniques was it possible to place the Porifera monophyletically with the other metazoan phyla, justifying a unification of all multicellular animals to only one kingdom, the Metazoa. The first strong support came from the discovery that cell-cell and cell-matrix adhesion molecules, that were cloned from sponges (mainly the demosponges Suberites domuncula and Geodia cydonium) and that were subsequently expressed, share high DNA sequence and protein function similarity with the corresponding molecules of other metazoans. Together with the molecular biological studies and with the use of the cell culture technologies (primmorphs), which allowed an insight into the stem cell system of these simple organisms, it was possible to stethoscope back in the paleontological history of animals. These studies confirmed the view that the sponges evolved between two epochal ice times, 710-680 Ma (Sturtian glaciation) and 605-585 Ma (Varanger-Marinoan ice age), a period which allowed evolution to proceed but resulted also in a mass extinction of most animal taxa, with the exception of the Porifera. These animals could develop in the aqueous milieu which was rich in silica, due also to their ability to live in a symbiosis with unicellular organisms (prokaryotic and also eukaryotic). Those organisms provided the sponges with the nutrition to survive and to overcome the food deprivation in cold water and even in an environment under the ice. Based on the diverse genetic toolkit, the sponges could also resist the adverse temperature and sunlight climatic influences. It is fortunate that the sponges survived the last 800 million years with their basic body plan. This fact might qualify the sponges to become model organisms not only in biology and molecular biology but also to be used - as living fossils - as reference organisms to deduce important and new insights in the understanding of fossil records explored from the Neoproterozoic. Taken together, these data caused a paradigmatic change; the Porifera are complex and simple, but by far not primitive, and they contribute to the understanding of the deep evolution of animals in molecular biological and paleontological views.","corpus_id":35941341,"score":1},{"doc_id":"19254178","title":"A new model for investigating the evolution of transcription control networks.","abstract":"Biological systems show unbounded capacity for complex behaviors and responses to their environments. This principally arises from their genetic networks. The processes governing transcription, translation, and gene regulation are well understood, as are the mechanisms of network evolution, such as gene duplication and horizontal gene transfer. However, the evolved networks arising from these simple processes are much more difficult to understand, and it is difficult to perform experiments on the evolution of these networks in living organisms because of the timescales involved. We propose a new framework for modeling and investigating the evolution of transcription networks in realistic, varied environments. The model we introduce contains novel, important, and lifelike features that allow the evolution of arbitrarily complex transcription networks. Molecular interactions are not specified; instead they are determined dynamically based on shape, allowing protein function to freely evolve. Transcriptional logic provides a flexible mechanism for defining genetic regulatory activity. Simulations demonstrate a realistic life cycle as an emergent property, and that even in simple environments lifelike and complex regulation mechanisms are evolved, including stable proteins, unstable mRNA, and repressor activity. This study also highlights the importance of using in silico genetics techniques to investigate evolved model robustness.","corpus_id":30705728,"score":1},{"doc_id":"19614583","title":"The fine details of evolution.","abstract":"Charles Darwin's theory of evolution was based on studies of biology at the species level. In the time since his death, studies at the molecular level have confirmed his ideas about the kinship of all life on Earth and have provided a wealth of detail about the evolutionary relationships between different species and a deeper understanding of the finer workings of natural selection. We now have a wealth of data, including the genome sequences of a wide range of organisms, an even larger number of protein sequences, a significant knowledge of the three-dimensional structures of proteins, DNA and other biological molecules, and a huge body of information about the operation of these molecules as systems in the molecular machinery of all living things. This issue of Biochemical Society Transactions contains papers from oral presentations given at a Biochemical Society Focused Meeting to commemorate the 200th Anniversary of Charles Darwin's birth, held on 26-27 January 2009 at the Wellcome Trust Conference Centre, Cambridge. The talks reported on some of the insights into evolution which have been obtained from the study of protein sequences, structures and systems.","corpus_id":9276603,"score":1},{"doc_id":"20195774","title":"The resurrection of life.","abstract":"The question of life was progressively put aside in the second half of the 20th century with the rise of molecular biology, but has recently re-emerged. Many scientists and philosophers consider that there is no place for this question within biology; that the distinction between living and non-living is arbitrary; and that progress in synthetic biology will finally put this question out of people's minds. I will argue that there is something wrong with the arguments supporting these statements. There are no reasons to exclude the question \"What is life?\" from biology. But the nature of the question has dramatically changed recently. Instead of being a search for the principles of life, the answer is now sought in the description of the historical process that has coupled the now well-established characteristics of organisms.","corpus_id":13077344,"score":1},{"doc_id":"21046016","title":"The ancestry and cumulative evolution of immune reactions.","abstract":"The last two decades of study enriched greatly our knowledge of how the immune system originated and the sophisticated immune mechanisms of today's vertebrates and invertebrates developed. Even unicellular organisms possess mechanisms for pathogen destruction and self recognition. The ability to distinguish self from non-self is a prerequisite for recognition of sexual compatibility and ensuring survival. Molecules involved in these processes resemble those found in the phagocytic cells of higher organisms. Recognition of bacteria by scavenger receptors induces phagocytosis or endocytosis. The phagocytic mechanisms characterizing the amoeboid protozoans developed further during the evolution towards innate immunity. The scavenger receptor cysteine-rich domain SRCR is encoded in the genomes from the most primitive sponges to mammals. The immune system of sponges comprises signal transduction molecules which occur in higher metazoans as well. Sponges already possess recognition systems for pathogenic bacteria and fungi, based on membrane receptors (a lipopolysaccharide-interacting protein, a cell surface receptor recognizing β(1 → 3)-d-glucans of fungi). Perforin-like molecules and lysozymes are involved, among others, in defense in sponges. Reactive oxygen and nitrogen species function in the immunity of early metazoan. Genes encoding the family of reactive oxygen-generating NADPH oxidases (Noxes) are found in a variety of protists and plants. The NO synthases of cnidarians, mollusks, and chordates are conserved with respect to the mammalian NOS. The antimicrobial peptides of protozoans, amoebapores, are structural and functional analogs of the natural killer cell peptide, NK-lysin, of vertebrates. An ancestral S-type lectin has been found in sponges. Opsonizing properties of lectins and the ability to agglutinate cells justify their classification as primitive recognition molecules. Invertebrate cytokines are not homologous to those of vertebrate, and their functional convergence was presumably enabled by the general similarity of the lectin-like recognition domain three-dimensional structure. Sponges contain molecules with SCR/CCP domains that show high homology to the mammalian regulators of complement activation (RCA family). A multi-component complement system comprising at least the central molecule of the complement system, C3, Factor B, and MASP developed in the cnidarians and evolved into the multilevel cascade engaged in innate and acquired immunity of vertebrates. The adaptive immune system of mammals is also deeply rooted in the metazoan evolution. Some its precursors have been traced as deep as in sponges, namely, two classes of receptors that comprise Ig-like domains, the receptor tyrosine kinases (RTK), and the non-enzymic sponge adhesion molecules (SAM). The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T-cell receptor (TCR), B-cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes. However, genes closely resembling RAG1 and RAG2 have been uncovered in the genome of a see urchin. The ancestry of MHC gene remains unknown. Similarly, no homologue of the protein binding domain (PBD) in MHC molecules has been found in invertebrates. The pathway by which endogenous peptides are degraded for presentation with class I MHC molecules utilizes mechanisms similar to those involved in the normal turnover of intracellular proteins, apparently recruited to work also for the immune system. Several cDNAs coding for lysosomal enzymes, e.g., cathepsin, have been isolated from sponges. All chromosomal duplication events in the MHC region occurred after the origin of the agnathans but before the gnathostomes split from them. The V-domains of the subtype found in the receptors of T and B-cells are known from both agnathans and cephalochordates, although they do not rearrange. The rearrangement mechanism of the lymphocyte V-domains suggests its origin from a common ancestral domain existing before the divergence of the extant gnathostome classes. Activation-induced deaminase (AID) - homologous proteins have been found only in the gnathostomes. It appears thus that the adaptive immunity of vertebrates is a result of stepwise accumulation of small changes in molecules, cells and organs over almost half a billion years.","corpus_id":12607648,"score":1},{"doc_id":"22098061","title":"Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises.","abstract":"In isolated oceanic islands, colonization patterns are often interpreted as resulting from dispersal rather than vicariant events. Such inferences may not be appropriate when island associations change over time and new islands do not form in a simple linear trend. Further complexity in the phylogeography of ocean islands arises when dealing with endangered taxa as extinctions, uncertainty on the number of evolutionary 'units', and human activities can obscure the progression of colonization events. Here, we address these issues through a reconstruction of the evolutionary history of giant Galápagos tortoises, integrating DNA data from extinct and extant species with information on recent human activities and newly available geological data. Our results show that only three of the five extinct or nearly extinct species should be considered independent evolutionary units. Dispersal from mainland South America started at approximately 3.2 Ma after the emergence of the two oldest islands of San Cristobal and Española. Dispersal from older to younger islands began approximately 1.74 Ma and was followed by multiple colonizations from different sources within the archipelago. Vicariant events, spurred by island formation, coalescence, and separation, contributed to lineage diversifications on Pinzón and Floreana dating from 1.26 and 0.85 Ma. This work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human-mediated dispersal events and highlights the need to take into account both vicariance and dispersal when dealing with organisms from islands whose associations are not simply explained by a linear emergence model.","corpus_id":32620164,"score":1},{"doc_id":"22750993","title":"A possible molecular metric for biological evolvability.","abstract":"Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring 'evolvability' of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.","corpus_id":15015178,"score":1},{"doc_id":"24333920","title":"Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?","abstract":"Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a \"molecular scaffold\" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a \"Paraná Portal\" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.","corpus_id":15030118,"score":1},{"doc_id":"24641285","title":"Evolutionary insights into the origin of innate and adaptive immune systems: different shades of grey.","abstract":"To struggle for survival, all living organisms, from protists to humans, must defend themselves from attack by predators. From the time when life began around 3,500 million years ago, all living cells have evolved mechanisms and strategies to optimally defend themselves, while the invaders also need to survive by evading these immune defenses. The end results would be healthy co-evolution of both parties. Classically, immune host defense is divided into two main categories, namely, innate and adaptive systems. It is well documented that while vertebrates possess both systems, invertebrates and prokaryotes like bacteria and archaea depend almost exclusively on the innate immune functions. Although the adaptive immune system like antibodies and cellular immunity or their equivalents are believed to have evolved at the time when the vertebrates first appeared about 550 million years ago, more recent information from molecular and genomic studies suggest that different forms of adaptive immune system may also be present in the invertebrates as well. These forms of \"adaptive\" immune system exhibit, for instance, limited degrees of memory, diversity and similarities of their immune receptors with the immunoglobulin domains of the conventional adaptive immune system of vertebrates. Organized lymphoid tissues have been identified in all vertebrates. Very recent molecular and genetic data further suggest that a special type of adaptive system functioning like RNAi of vertebrates is also present in the very ancient form of life like the bacteria and archaea. In this review, I provide some insights, based on recent information gathering from evolutionary data of innate and adaptive immune receptors of invertebrate and vertebrate animals that should convince the readers that our current view on the innate and adaptive immunity may need to be modified. The distinction between the two systems should not be thought of in terms of a \"black and white\" phenomenon anymore, as recent molecular and genomic information points to the fact that a line of distinction is not as sharp as it was once thought to be, but it is blurred by different shades of grey.","corpus_id":402533,"score":1},{"doc_id":"24799958","title":"Quantum entanglement in photoactive prebiotic systems.","abstract":"This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modelled photoactive prebiotic kernel systems. We define our modelled self-assembled supramolecular photoactive centres, composed of one or more sensitizer molecules, precursors of fatty acids and a number of water molecules, as a photoactive prebiotic kernel systems. We propose that life first emerged in the form of such minimal photoactive prebiotic kernel systems and later in the process of evolution these photoactive prebiotic kernel systems would have produced fatty acids and covered themselves with fatty acid envelopes to become the minimal cells of the Fatty Acid World. Specifically, we model self-assembling of photoactive prebiotic systems with observed quantum entanglement phenomena. We address the idea that quantum entanglement was important in the first stages of origins of life and evolution of the biospheres because simultaneously excite two prebiotic kernels in the system by appearance of two additional quantum entangled excited states, leading to faster growth and self-replication of minimal living cells. The quantum mechanically modelled possibility of synthesizing artificial self-reproducing quantum entangled prebiotic kernel systems and minimal cells also impacts the possibility of the most probable path of emergence of protocells on the Earth or elsewhere. We also examine the quantum entangled logic gates discovered in the modelled systems composed of two prebiotic kernels. Such logic gates may have application in the destruction of cancer cells or becoming building blocks of new forms of artificial cells including magnetically active ones.","corpus_id":1910925,"score":1},{"doc_id":"25204387","title":"Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae.","abstract":"BACKGROUND AND AIMS: The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS: Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions. KEY RESULTS: Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. CONCLUSIONS: The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.","corpus_id":-1,"score":1},{"doc_id":"26149747","title":"Towards self-assembled hybrid artificial cells: novel bottom-up approaches to functional synthetic membranes.","abstract":"There has been increasing interest in utilizing bottom-up approaches to develop synthetic cells. A popular methodology is the integration of functionalized synthetic membranes with biological systems, producing \"hybrid\" artificial cells. This Concept article covers recent advances and the current state-of-the-art of such hybrid systems. Specifically, we describe minimal supramolecular constructs that faithfully mimic the structure and/or function of living cells, often by controlling the assembly of highly ordered membrane architectures with defined functionality. These studies give us a deeper understanding of the nature of living systems, bring new insights into the origin of cellular life, and provide novel synthetic chassis for advancing synthetic biology.","corpus_id":37968455,"score":1},{"doc_id":"26423359","title":"Alternative adaptive immunity strategies: coelacanth, cod and shark immunity.","abstract":"The advent of high throughput sequencing has permitted to investigate the genome and the transcriptome of novel non-model species with unprecedented depth. This technological advance provided a better understanding of the evolution of adaptive immune genes in gnathostomes, revealing several unexpected features in different fish species which are of particular interest. In the present paper, we review the current understanding of the adaptive immune system of the coelacanth, the elephant shark and the Atlantic cod. The study of coelacanth, the only living extant of the long thought to be extinct Sarcopterygian lineage, is fundamental to bring new insights on the evolution of the immune system in higher vertebrates. Surprisingly, coelacanths are the only known jawed vertebrates to lack IgM, whereas two IgD/W loci are present. Cartilaginous fish are of great interest due to their basal position in the vertebrate tree of life; the genome of the elephant shark revealed the lack of several important immune genes related to T cell functions, which suggest the existence of a primordial set of TH1-like cells. Finally, the Atlantic cod lacks a functional major histocompatibility II complex, but balances this evolutionary loss with the expansion of specific gene families, including MHC I, Toll-like receptors and antimicrobial peptides. Overall, these data point out that several fish species present an unconventional adaptive immune system, but the loss of important immune genes is balanced by adaptive evolutionary strategies which still guarantee the establishment of an efficient immune response against the pathogens they have to fight during their life.","corpus_id":207009133,"score":1},{"doc_id":"28812662","title":"Spending limited resources on de-extinction could lead to net biodiversity loss.","abstract":"There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing and maintaining populations of these species on conservation of extant threatened species. Even using the optimistic assumptions that resurrection of species is externally sponsored, and that actions for resurrected species can share costs with extant analogue species, public funding for conservation of resurrected species would lead to fewer extant species that could be conserved, suggesting net biodiversity loss. If full costs of establishment and maintenance for resurrected species populations were publicly funded, there could be substantial sacrifices in extant species conservation. If conservation of resurrected species populations could be fully externally sponsored, there could be benefits to extant threatened species. However, such benefits would be outweighed by opportunity costs, assuming such discretionary money could directly fund conservation of extant species. Potential sacrifices in conservation of extant species should be a crucial consideration in deciding whether to invest in de-extinction or focus our efforts on extant species.","corpus_id":19887264,"score":1},{"doc_id":"19435181","title":"Love letters to the dead: resurrecting an epistolary art.","abstract":"This article explores the art of letter-writing, specifically to our beloved dead, as a form of autoethnographic research, pedagogy, and care work. As university teachers and qualitative researchers in palliative and end-of-life care, we review the literature and history of epistolary communications with the deceased, as a prelude to writing our own letters. John writes to his long-dead mother and Dorothy to her recently deceased spouse Patrick, each letter followed by a reflective dialogue between us. Through this dialogue, we highlight the potential application of this art, or handcraft, to formal and informal palliative care, and the implications for practice, pedagogy, policy, and research. We propose that such direct, non-mediated, communications can offer a valuable form of healing for bereaved people. The therapeutic potential of letter writing and the abundance of literary and popular culture exemplars of responses from the dead are also largely unexplored in death education and research.","corpus_id":46600881,"score":0},{"doc_id":"19774069","title":"Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.","abstract":"BACKGROUND: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. METHODOLOGY/PRINCIPAL FINDINGS: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. CONCLUSIONS/SIGNIFICANCE: Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.","corpus_id":12514252,"score":0},{"doc_id":"20072108","title":"The 2009 Lindau Nobel Laureate Meeting: Roger Y. Tsien, Chemistry 2008.","abstract":"American biochemist Roger Tsien shared the 2008 Nobel Prize in Chemistry with Martin Chalfie and Osamu Shimomura for their discovery and development of the Green Fluorescent Protein (GFP). Tsien, who was born in New York in 1952 and grew up in Livingston New Jersey, began to experiment in the basement of the family home at a young age. From growing silica gardens of colorful crystallized metal salts to attempting to synthesize aspirin, these early experiments fueled what would become Tsien's lifelong interest in chemistry and colors. Tsien's first official laboratory experience was an NSF-supported summer research program in which he used infrared spectroscopy to examine how metals bind to thiocyanate, for which he was awarded a $10,000 scholarship in the Westinghouse Science Talent Search. Following graduation from Harvard in 1972, Tsien attended Cambridge University in England under a Marshall Scholarship. There he learned organic chemistry --a subject he'd hated as an undergraduate-- and looked for a way to synthesize dyes for imaging neuronal activity, generating BAPTA based optical calcium indicator dyes. Following the completion of his postdoctoral training at Cambridge in 1982, Tsien accepted a faculty position at the University of California, Berkeley. There he and colleagues developed and improved numerous small molecule indicators, including indicators fura-2 and indo-1. In 1989, Tsien moved his laboratory to the University of California at San Diego, where he and his colleagues developed the enhanced mutant of GFP as a way to devise a cyclic AMP (cAMP) sensor for use in live cells. They initially engineered molecules to take advantage of the conformational change that occurs when cAMP binds to protein kinase A (PKA). By labeling one part of PKA with fluoroscein and another with a rhodamine, they hoped to detect Fluorescence Resonance Energy Transfer (FRET), which would occur when the two molecules were in close proximity. The initial experiments presented numerous difficulties due to the challenges of expressing PKA subunits in E. coli, labeling the protein without destroying its function, and delivering the protein to cells via microinjection. Eventually, Tsien sought a more elegant approach, hoping to use and modify a naturally fluorescent protein that could be expressed in the cell. GFP originally described by Davenport in 1955, extracted and purified by Shimomura in 1965, and cloned by Prasher in 1992 was an appealing candidate. To make the protein more useful for their FRET studies, Tsien and colleagues modified the amino acid structure of the protein (S65T). The improved protein had an excitation peak near that of fluoroscein, and was photostable. Tsien and colleagues also solved the protein's crystal structure, enabling them to generate additional colors with spectral properties suitable for FRET. However, when they attempted to use the GFP proteins in the detection of cAMP, they experienced further difficulties with PKA. Instead, their first successful use of GFP derivatives for FRET was in the detection of intracellular calcium using their engineered calmodulin-based calcium indicator, Cameleon. In a short time, Tsien's work has led to further technological developments and important scientific findings. GFP and its derivatives have been used in a wide range of biological applications, from the study of protein localization to understanding how HIV spreads from cell to cell. The need for such probes is highlighted by the abundance of research conducted using these fluorescent proteins, as well as the continued development of similar fluorescent proteins, such as the coral-derived dsRED. Tsien is currently developing genetically encoded Infrared Fluorescent Proteins (IFPs), which with their long emission wavelengths of >700 nm, have the ability to pass through living tissue and improve imaging in living organisms. He is also building synthetic molecules for use in humans. He cites team effort and the contributions of students and post-docs as key components of progress and success: \"Even if I had the time, I couldn't have done the experiments, because I don't know how. It's very much a team effort.\"","corpus_id":13072590,"score":0},{"doc_id":"20396881","title":"Synthetic biology approaches in drug discovery and pharmaceutical biotechnology.","abstract":"Synthetic biology is the attempt to apply the concepts of engineering to biological systems with the aim to create organisms with new emergent properties. These organisms might have desirable novel biosynthetic capabilities, act as biosensors or help us to understand the intricacies of living systems. This approach has the potential to assist the discovery and production of pharmaceutical compounds at various stages. New sources of bioactive compounds can be created in the form of genetically encoded small molecule libraries. The recombination of individual parts has been employed to design proteins that act as biosensors, which could be used to identify and quantify molecules of interest. New biosynthetic pathways may be designed by stitching together enzymes with desired activities, and genetic code expansion can be used to introduce new functionalities into peptides and proteins to increase their chemical scope and biological stability. This review aims to give an insight into recently developed individual components and modules that might serve as parts in a synthetic biology approach to pharmaceutical biotechnology.","corpus_id":10381795,"score":0},{"doc_id":"21507096","title":"Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture.","abstract":"Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.","corpus_id":14711450,"score":0},{"doc_id":"21951575","title":"The properties of bio-energy transport and influence of structure nonuniformity and temperature of systems on energy transport along polypeptide chains.","abstract":"A new theory of bio-energy transport along protein molecules in living systems, where the energy is released by hydrolysis of adenosine triphosphate (ATP), is proposed based on some physical and biological reasons. In the new theory, the Davydov's Hamiltonian and wave function of the systems are simultaneously modified and extended. A new interaction has been added into Davydov's Hamiltonian. The wave function of the excitation state of single particles for the excitons in the Davydov model is replaced by a new wave function of two-quanta quasicoherent state. In such a case, the bio-energy is transported by the new soliton, which differs from the Davydov's soliton. The soliton is formed through self- trapping of two excitons interacting amino acid residues. The exciton is generated by vibrations of amide-I (CO stretching) arising from the energy of hydrolysis of ATP. The properties of the new soliton are extensively studied by analytical method and its lifetime is calculated using the nonlinear quantum perturbation theory and a wide ranges of parameter values relevant to protein molecules. The lifetime of the new soliton at the biological temperature 300 K is enough large and belongs to the order of 10⁻¹⁰ s, or τ/τ₀≥700, in which the soliton can transports over several hundreds amino acid residues. These studied results show clearly that the new soliton is thermally stable and has so larger lifetime that it can play an important role in biological processes. Thus the new model is a candidate of the bio-energy transport mechanism in protein molecules. In the meanwhile, the influences of structure nonuniformity in protein molecules and temperature of the systems on the states and properties of the soliton transport of bio-energy are numerically simulated and studied by the fourth-order Runge-Kutta method. The structure nonuniformity arises from the disorder distributions of masses of amino acid residues, side groups and impurities, which results also in the fluctuations of the spring constant of protein molecules, dipole-dipole interaction between the neighboring amides, exciton-phonon (vibration of amino acids)interaction, chain-chain interaction among the three channels and ground state energy of the systems. We investigated the behaviors and states of the new solitons in a single protein molecular chain and α-Helix protein molecules with three channels under influences of the structure nonuniformity. We prove first that the bio-energy is transported by a soliton, which can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. When the structure nonuniformity exists, although the fluctuations of the spring constant, dipole-dipole interaction constant, exciton-phonon coupling constant and ground state energy and the nonuniformity distributions of masses of amino acid residues can change the states and properties of motion of new soliton, they are still quite stable and very robust against these structure nonuniformities, i.e., even there are a larger structure nonuniformity in the protein molecules, the new solitons cannot be still dispersed. If the effects of thermal perturbation of medium on the soliton in nonuniform proteins is considered again, the new soliton can transport also over a larger spacing of 400 amino acids and has a longer time period of 300 ps, it is still thermally stable up to 320 K under the influence of the above structure nonuniformities. However, the new soliton disperses in the case of a higher temperature of 325 K and in more large structure nonuniformity. Thus, we determine that the new soliton's lifetime and critical temperature are 300 ps and 320 K, respectively. These results are also consistent with analytical data obtained via quantum perturbed theory. For α-Helix protein molecules with three channels, the results obtained show that the structure nonuniformity and quantum fluctuation can change the states and features of the new solitons, for example, the amplitudes, energies and velocities of the new soliton are decreased, but the solitons have been not destroyed, they can still transport steadily along the molecular chains retaining energy and momentum. When the quantum fluctuations are larger, such as, structure disorders and quantum fluctuations of 0.67<α(K)<2, ΔW=±8%W¯, ΔJ=±1%J¯, Δ(χ₁+χ₂)=±3%(χ¯₁+χ¯₂) and ΔL=±1%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.1 meV, |β(n)|<0.5, the new soliton is still stable. Therefore, the new solitons are quite robust against these nonuniform effects. However, they will be dispersed or disrupted in cases of very large structure nonuniformity. When the influence of temperature on solitons is considered, we find that the new solitons can transport steadily over 333 amino acid residues in the case of a long time period of 120 ps, in which the soliton can retain its shape and energy to travel forward along protein molecules after their mutual collision at the biological temperature of 300 K. However, the soliton disperses in cases of higher temperatures 325 K under action of a larger structure disorder. Thus, its critical temperature is about 320 K. When the effects of structure nonuniformity and temperature are considered simultaneously, then the new soliton has still high thermal stability and can transport also along the protein molecular chains retaining its amplitude, energy and velocity, they will disperses in the larger fluctuations, for example, 0.67 M¯<M(k)<2M¯, ΔW=±6%W¯, ΔJ=±1.3%J¯, Δ(χ₁+χ₂)=±2%(χ¯₁+χ¯₂), ΔL=±1.5%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.82 meV, |β(n)|≤0.5 at T=300 K, or at higher temperatures 320 K and the fluctuations of 0.67M¯<M(k)<2M¯, Δ(χ₁+χ₂=±1%(χ¯₁+χ¯₂), ΔJ=±0.7%J¯, ΔW=±7%W¯, ΔL=±0.8%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.4 meV, |β(n)|≤0.5. These results mean that the critical temperature of the new soliton is 315K in this condition. Thus, we can conclude from these investigations that the new soliton is quite robust against the structure nonuniformities and thermal perturbation of proteins at 300 K in α-helix protein molecules, then it is a carrier of bio-energy transport and the improved model is a candidate for the mechanism of the bio-energy transport in the protein molecules. Finally we gave some experimental evidences for real existence of the soliton and validity of the theory of bio-energy transport in proteins.","corpus_id":9537702,"score":0},{"doc_id":"22304966","title":"From extant to extinct: locomotor ontogeny and the evolution of avian flight.","abstract":"Evolutionary transformations are recorded by fossils with transitional morphologies, and are key to understanding the history of life. Reconstructing these transformations requires interpreting functional attributes of extinct forms by exploring how similar features function in extant organisms. However, extinct-extant comparisons are often difficult, because extant adult forms frequently differ substantially from fossil material. Here, we illustrate how postnatal developmental transitions in extant birds can provide rich and novel insights into evolutionary transformations in theropod dinosaurs. Although juveniles have not been a focus of extinct-extant comparisons, developing juveniles in many groups transition through intermediate morphological, functional and behavioral stages that anatomically and conceptually parallel evolutionary transformations. Exploring developmental transitions may thus disclose observable, ecologically relevant answers to long puzzling evolutionary questions.","corpus_id":14775936,"score":0},{"doc_id":"22368802","title":"[Autopsies of the real: resurrecting the dead].","abstract":"Autopsias de lo real: resucitando a los muertos. The sense of the real, or the material - the dead body - as an inextricable part of the sacred does not disappear in the secular environment of the nineteenth and twentieth centuries. This article analyzes specific humanitarian narratives centered on the practice of autopsy and mummification, in which the traces of Catholicism act as a kind of spectral discourse of the imagination, where the real is configured in forms of the uncanny, the monstrous or the sacred.","corpus_id":40330528,"score":0},{"doc_id":"23062450","title":"[Posttraumatic stress disorder (PTSD) as a consequence of the interaction between an individual genetic susceptibility, a traumatogenic event and a social context].","abstract":"L'état de stress post-traumatique comme conséquence de l'interaction entre une susceptibilité génétique individuelle, un évènement traumatogène et un contexte social. INTRODUCTION: Why are some individuals more likely than others to develop a posttraumatic stress disorder (PTSD) in the face of similar levels of trauma exposure? Monitoring the traumatic process combining the antecedents, the determinants of the psychic trauma and the acute symptoms can clarify the causes of the final onset of a chronic repetition syndrome. Epidemiologic research has clarified risk factors that increase the likelihood of PTSD after exposure to a potentially traumatic event. PTSD is an interaction between a subject, a traumatogenic factor and a social context. With each epidemiological, psychopathological and more particularly neurogenetic study, we will expand on the impact of these interactions on the therapeutic treatment of psycho-traumatised persons. LITERATURE FINDINGS: Most studies have shown that unrelated to the traumatic event, additional risk factors for developing PTSD include younger age at the time of the trauma, female gender, lower social economic statuts, lack of social support, premorbid personality characteristics and preexisting anxiety or depressive disorders increase the risk of PTSD. The psychic trauma is firmly attached to the repetition and the previous traumas are as many risks of developing a subsequent PTSD in the wake of a new trauma: PTSD in adults may represent a prolonged symptomatic reaction to prior traumatic assault, child abuse and childhood adversities. Related to the traumatic event, the organic pain, the traumatic brain injury, but also the sight of blood can lead to a trauma being considered as more serious or more harmful to life. It is useful to recognize the acute reactions of exhaustion stress as they can guide both the pharmacotherapeutic and the psychotherapeutic treatment thanks to debriefings. Even though the majority of people with acute stress disorder subsequently develop PTSD, the current data indicate that too many people can develop PTSD without initially displaying acute stress disorder. Though peritraumatic dissociation and peritraumatic distress have emerged as the strongest predictors for PTSD and have to be treated as soon as possible with the debriefing or the pharmacology; initial evidence suggests the potential benefits of early intervention, shortly after the trauma, and psychological debriefing has received increasing interest from the scientific community. However the Anglo-Saxon techniques (such as Critical Incident Stress Debriefing also known as the Mitchell model) are in total contrast with the French approach. In the first case the emotional response is controlled to ensure the pursuit of the group action, whilst in the second case the debriefing concerns patients with acute symptoms in order to prevent the development of a PTSD structuring of the latter. The facts, emotions and thoughts are not partitioned but inter-linked, thus enabling a fragmentation of the traumatic experience. In the face of the annihilation experienced, speech production by the subject is restored linking the person to the human community, once abandoned. However, debate continues on the efficacy of single session debriefing in the prevention of PTSD. At the time of the acute stress reactions, benzodiazepines are contraindicated at this stage as they promote dissociation and ulterior revivals. On the other hand, treatment with propranolol could be proposed: a two or three week course of propranolol begun in the aftermath of a traumatic event can reduce subsequent PTSD symptoms. DISCUSSION: A genetic polymorphism is evidently at work in the development of a PTSD via the regulation of the expression of genes of interest to the serotoninergic system and the adrenocorticotropic axis. The 5-HTTLPR (promoter region of SLC6A4 witch encodes the serotonin transporter) constitutes a genetic candidate region that may modulate emotional responses to traumatic events. The interaction between variation at the 5HTTLPR and stressful life events could predict depression and PTSD. Considering the dopaminergic pathway, the A1 allele coding the type 2 dopaminergic receptor is associated with a severe comorbidity of PTSD with the presence of somatic disorders, anxiety, social change and depression. For noradrenergic neuromodulation, an interaction between the polymorphism of gene GABRA2 and the occurrence of PTSD is described whereas an interaction between the number of traumatic events and Val(158)Met polymorphism of the gene coding for catecholamine-o-methyltransferase has also been found. The role of polymorphisms in FKBP5 (a co-chaperone of hsp 90 which binds to the glucocorticoid receptor) in predicting PTSD too, with a gene-by-environment point of view. These gene-by-environment studies are needed to focus more on distinct endophenotypes and influences from environmental factors. If several candidate genes are involved, a weighting of susceptibility to such and such a neurological regulation system will imply various endophenotypes. According to the monoamine predominantly incriminated, PTSD can take on a more hyper-vegetative clinical expression linked with noradrenergic overuse. Differently, avoidance behaviour and the depressive aspect invoke more a modification of the serotoninergic modulation whilst posttraumatic psychotic reactions question the role of dopaminergic pathways. Neuroscientific discoveries interesting the biological support of PTSD can thus modify our view of the conception of the disorder in relation to different therapeutic prospects. CONCLUSION: Chronic PTSD can manifest itself in different clinical forms. The repetition syndrome can appear a long time after the traumatic event, following a paucisymptomatic latency period, which can last several years or even decades. The absence of complaints from the patient is common, the latter suffering in silence. Often other comorbid disorders and other complaints arise sooner than the clinical picture. Thus a depressive episode characterised as drug-seeking behaviour is frequently encountered. The therapeutic accompaniment traditionally combines a pharmacological and a psychotherapeutic treatment even if recommendations are rare. A posttraumatic stress disorder is never just a coincidence. The different stages of the evolution and the establishment of a PTSD are the expression of an interaction between the outside and the inner self. Despite a known progression of the posttraumatic stress disorder, this deleterious evolution is far from being a foregone conclusion. On the contrary, several levels of prevention are possible at each stage of its structuration to propose treatments to subjects who are vulnerable and/or present symptoms. No neurobiological study has yet found a biological marker, which would apparently and inevitably destine a subject to structure, a posttraumatic stress disorder in reaction to a stress. Conversely, the psychopathological study finds afterwards that a particular subject has necessarily built a traumatic repetition syndrome according to the concordance of significant data relative to his/her history. The event strikes a repression or an anterior biographical deadlock and of which the thematic questions the fundamentals of human culture in its emancipation with nature, like the question of death and its consequences: bereavement, parentality, transgenerational transmission and organicity often linked to the illness. A therapeutic proposal constitutes an environmental factor par excellence which can be either protective or deleterious. If the traumatic repetition syndrome has been known since Antiquity, the birth of PTSD has followed the chronology of the DSM according to the sociopolitical contexts encountered. A PTSD does not occur by chance: the conditions of possibility of the trauma are established by genetic and psychological determinants interactively integrated at the heart of a social context. After the increase in a psychotraumatic interest in international publications since the 1980s, a fight against over-victimisation seems to be setting in. The advances in genetic and neuroimaging techniques are in the process of superseding psychometric studies in terms of reliability and validity; maybe we should see in this social evolution the changes of tomorrow concerning the clinical of PTSD and its treatment. The healing of the psycho-traumatised subject cannot just be established on the passive status of victim, which would be detrimental to reflection and ultimately reconstruction: the rebirth of the subject will require active commitment, which could distract from the deadly repetition. Whilst the confrontation with death resembled nonsense, the subject will question the psychotraumatic determinants of his/her life history to reinstate this tragic event within a search for meaning. Such restructuring is built on the intersubjectivity of the clinical relationship, which occurs within a social context. PTSD is a pathology which interacts with the societal context: on the one hand the trauma is established on the brutal reconsideration of social values which seem immutable and on the other hand, the clinical and nosographical concept of PTSD is changing with the evolution of society.","corpus_id":25554857,"score":0},{"doc_id":"23103915","title":"Reliable predictions of unusual molecules.","abstract":"Quantum chemistry can today be employed to invent new molecules and investigate their properties and chemical bonding. However, the predicted species must be viable in order to be synthesized by experimentalists. In this perspective article we describe the technology of reliable theoretical predictions and show how understanding of chemical bonding in studied chemical systems could help to design new molecular structures. We also provide a short overview of successfully predicted and already produced (in some cases) planar hypercoordinate species to demonstrate that the consistent theoretical prediction of viable molecules with unusual structures and properties is now a reliable tool for exploring new, yet unknown molecules, clusters, nanomaterials and solids.","corpus_id":7169897,"score":0},{"doc_id":"24124192","title":"Is EM dead?","abstract":"Since electron microscopy (EM) first appeared in the 1930s, it has held centre stage as the primary tool for the exploration of biological structure. Yet, with the recent developments of light microscopy techniques that overcome the limitations imposed by the diffraction boundary, the question arises as to whether the importance of EM in on the wane. This Commentary describes some of the pioneering studies that have shaped our understanding of cell structure. These include the development of cryo-EM techniques that have given researchers the ability to capture images of native structures and at the molecular level. It also describes how a number of recent developments significantly increase the ability of EM to visualise biological systems across a range of length scales, and in 3D, ensuring that EM will remain at the forefront of biology research for the foreseeable future.","corpus_id":12747549,"score":0},{"doc_id":"24588263","title":"Physical and biochemical insights on DNA structures in artificial and living systems.","abstract":"CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.","corpus_id":206824830,"score":0},{"doc_id":"24681091","title":"Natural products from resurrection plants: potential for medical applications.","abstract":"Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly - often within hours - regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications.","corpus_id":206182000,"score":0},{"doc_id":"24921467","title":"Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators.","abstract":"This article deals with artificial vesicles and their membranes as reaction promoters and regulators. Among the various molecular assemblies which can form in an aqueous medium from amphiphilic molecules, vesicle systems are unique. Vesicles compartmentalize the aqueous solution in which they exist, independent on whether the vesicles are biological vesicles (existing in living systems) or whether they are artificial vesicles (formed in vitro from natural or synthetic amphiphiles). After the formation of artificial vesicles, their aqueous interior (the endovesicular volume) may become - or may be made - chemically different from the external medium (the exovesicular solution), depending on how the vesicles are prepared. The existence of differences between endo- and exovesicular composition is one of the features on the basis of which biological vesicles contribute to the complex functioning of living organisms. Furthermore, artificial vesicles can be formed from mixtures of amphiphiles in such a way that the vesicle membranes become molecularly, compositionally and organizationally highly complex, similarly to the lipidic matrix of biological membranes. All the various properties of artificial vesicles as membranous compartment systems emerge from molecular assembly as these properties are not present in the individual molecules the system is composed of. One particular emergent property of vesicle membranes is their possible functioning as promoters and regulators of chemical reactions caused by the localization of reaction components, and possibly catalysts, within or on the surface of the membranes. This specific feature is reviewed and highlighted with a few selected examples which range from the promotion of decarboxylation reactions, the selective binding of DNA or RNA to suitable vesicle membranes, and the reactivation of fragmented enzymes to the regulation of the enzymatic synthesis of polymers. Such type of emergent properties of vesicle membranes may have been important for the prebiological evolution of protocells, the hypothetical compartment systems preceding the first cells in those chemical and physico-chemical processes that led to the origin of life.","corpus_id":32585856,"score":0},{"doc_id":"26002527","title":"What can we learn from the transcriptome of the resurrection plant Craterostigma plantagineum?","abstract":"MAIN CONCLUSION: The desiccation transcriptome of the resurrection plant C. plantagineum is composed of conserved protein coding transcripts, taxonomically restricted transcripts and recently evolved non-protein coding transcripts. Research in resurrection plants has been hampered by the lack of genome sequence information, but recently introduced sequencing technologies overcome this limitation partially and provide access to the transcriptome of these plants. Transcriptome studies showed that mechanisms involved in desiccation tolerance are conserved in resurrection plants, seeds and pollen. The accumulation of protective molecules such as sugars and LEA proteins are major components in desiccation tolerance. Leaf folding, chloroplast protection and protection during rehydration must involve specific molecular mechanisms, but the basis of such mechanisms is mainly unknown. The study of regulatory regions of a desiccation-induced C. plantagineum gene suggests that cis-regulatory elements may be responsible for expression variations in desiccation tolerant and non-desiccation-tolerant plants. The analysis of the C. plantagineum transcriptome also revealed that part of it is composed of taxonomically restricted genes (TRGs) and non-protein coding RNAs (ncRNAs). TRGs are known to code for new traits required for the adaptation of organisms to particular environmental conditions. Thus the study of TRGs from resurrection plants should reveal species-specific functions related to the desiccation tolerance phenotype. Non-protein coding RNAs can regulate gene expression at epigenetic, transcriptional and post-transcriptional level and thus these RNAs may be key players in the rewiring of regulatory networks of desiccation-related genes in C. plantagineum.","corpus_id":16084932,"score":0},{"doc_id":"26691665","title":"Karyotype is not dead (yet)!","abstract":"BACKGROUND: While array-comparative genomic hybridization (a-CGH) and next-generation sequencing (NGS or exome) technologies have swiftly spread throughout the medical field, karyotype has gradually lost its leading role among genetic tests. Several international guidelines recommend starting with a-CGH screening then going on with exome analysis when investigating a patient with intellectual disability (ID) and no precise clinical diagnosis. A-CGH and whole exome sequencing increase etiologic diagnoses rate up to 30% in case of ID. However, physicians have to deal with the lack of qualitative information of the genome. Especially, exome and a-CGH analysis fail to detect chromosomal rearrangements because breakpoints are either located in introns or not associated with a gain or loss of genetic material. If these technologies cannot easily identify chromosomal translocations or inversions which sometimes split a gene, karyotype can. DISCUSSION: For the 5 cases described, karyotype provided the right diagnosis for a Mendelian disease while molecular analysis remained unsuccessful. We conclude that when a Mendelian disease is strongly suggested clinically, if molecular analysis is normal, it could be very useful to carry out a karyotype in order to demonstrate a chromosomal rearrangement involving the targeted gene. If this gene is disrupted, the physician can confirm the suspected disease and give appropriate genetic counseling. SUMMARY: This article aims at keeping in mind that karyotype, this old-fashioned genetic tool, can still remain powerful and useful within some genetic issues. Even in this modern period of whole exome sequencing, young geneticists should know that karyotype remains a powerful and cheap technology, available throughout the world and can still do a lot for families.","corpus_id":37373234,"score":0},{"doc_id":"27499678","title":"Enhancement of Plant Productivity in the Post-Genomics Era.","abstract":"Obtaining high plant yield is not always achievable in agricultural activity as it is determined by various factors, including cultivar quality, nutrient and water supplies, degree of infection by pathogens, natural calamities and soil conditions, which affect plant growth and development. More noticeably, sustainable plant productivity to provide sufficient food for the increasing human population has become a thorny issue to scientists in the era of unpredictable global climatic changes, appearance of more tremendous or multiple stresses, and land restriction for cultivation. Well-established agricultural management by agrotechnological means has shown no longer to be effective enough to confront with this challenge. Instead, in order to maximize the production, it is advisable to implement such practices in combination with biological applications. Nowadays, high technologies are widely adopted into agricultural production, biological diversity conservation and crop improvement. Wang et al. has nicely outlined the utilization of DNA-based technologies in this field. Among these are the applications of (i) DNA markers into cultivar identification, seed purity analysis, germplasm resource evaluation, heterosis prediction, genetic mapping, cloning and breeding; and (ii) gene expression data in supporting the description of crop phenology, the analytic comparison of crop growth under stress versus non-stress conditions, or the study of fertilizer effects. Besides, various purposes of using transgenic technologies in agriculture, such as generating cultivars with better product quality, better tolerance to biotic or abiotic stress, are also discussed in the review. One of the important highlights in this issue is the review of the benefits brought by high-throughput sequencing technology, which is also known as next-generation sequencing (NGS). It is not so difficult to recognize that its application has allowed us to carry out biological studies at much deeper level and larger scale. In their article, Onda and Mochida detailed how to use these technologies in fully characterizing the genetic diversity or multigenecity within a particular plant species. The authors discussed the constant innovation of sequencing platforms which has made sequencing technologies become more superior and more powerful than ever before. Additionally, the efforts result in not only further cut down of the sequencing cost and increase in the sequencing speed, but also improvement in sequencing accuracy and extended sequencing application to studies at both DNA and RNA levels. Such knowledge will help the scientists interpret, at least partially, how plants can adapt to various environmental conditions, or how different cultivars can respond differently to the same stress. Another article by Ong et al. also laid emphasis on the importance of various high-throughput sequencing platforms, thanks to which a large number of genomic databases supplied with detailed annotation and useful bioinformatics tools have been established to assist geneticists. Readers can find in this review the summary of available plant-specific genomic databases up-to-date and popular web-based resources that are relevant for comparative genomics, plant evolution and phylogenomics studies. These, along with other approaches, such as quantitative trait locus and genome-wide association study, will lay foundation for prediction and identification of genes or alleles responsible for valuable agronomic traits, contributing to the enhancement of plant productivity by genetic engineering approach. In this thematic issue, specific examples for crop improvement are also demonstrated. The first showcase is given by Nongpiur et al. who provided evidence that synergistic employment of genomics approaches and high-throughput gene expression methods have aided in dissecting the salinity-responsive signaling pathway, identifying genes involved in the stress response and selecting candidate genes for further characterization aimed at generating new cultivars with better salinity stress tolerance. This paper is also a good reference source for readers who wish to get an overview about the general process from gene prediction to validation by experiments, including the details on techniques and approaches used. Another demonstration is provided by Khan et al. whose interest is enhancement of drought tolerance in crops. The focus of this article is to overview our current understanding of mechanisms regulating plants responses to drought. Evaluation of plant performance to drought and production of new elite varieties with better drought tolerance on the basis of using phenotyping and genomics-assisted breeding are also well discussed. In addition to the topics of environmental stress tolerance in plants, current knowledge on improving biotic stress tolerance is also summarized in our issue. Current picture on crosstalk of signaling mechanisms in rice between its immune system and symbiosis with microorganisms is presented by Akamatsu et al. Rice responses to bacteria and fungi via interactions between the plant pattern recognition receptors and the molecular microbe-associated molecular patterns are described in detail and suggested as targets for manipulation in order to increase disease resistance in crops. On the other hand, Bouain et al. are concerned about nutrient deficiency; specifically, how plant root system develops under growing conditions with inadequate phosphate. The authors overviewed our current understanding of the low phosphate-responsive mechanisms in Arabidopsis model plant, which was gained by using a combination of various advanced methods, including high-througput phenotyping, system biology analysis and \"omics\" technologies. Stress management in plants is proposed to be also achievable by regulating activities of cyclic nucleotide-gated ion channels. As emphasized in the paper of Jha et al., the application of such channels is important in mediating cellular ion homeostasis and plant tolerance to both biotic and abiotic stresses. In summary, with recent progresses in biological and biotechnological areas, especially rapid development of advanced technologies in biological system modeling, functional genomics, computer-based analyzing tools, genetic engineering and molecular breeding, biological control and biotechnological applications in agriculture have brought about an extraordinary revolution and have been considered the most powerful approaches in maintaining or even increasing crop yield. Therefore, in this issue, we would like to introduce to the audience a collection of various strategies used for enhancing crop productivity, with the focus on advanced biological-biotechnological platforms in the post-genomics era.","corpus_id":9605718,"score":0},{"doc_id":"27734746","title":"Why STAN might not be dead.","abstract":"Recently, a meta-analysis, including 26 526 laboring vertex singletons at term, summarized all available level-1 data from six high-quality randomized clinical trials (RCTs) on the use of ST analysis (STAN) during labor as an adjunct to conventional intrapartum fetal heart rate monitoring. The meta-analysis showed that STAN did not improve perinatal outcomes or decrease cesarean deliveries. Nonetheless, there are still reasons to believe STAN may have a role in the future research on intrapartum fetal monitoring. Out of six trials included in the meta-analysis, two included all cephalic singletons in labor, and four enrolled only high-risk pregnant women. This combination of both low- and high-risk populations may have distorted the potential impact of STAN. The test for heterogeneity between both subgroups was found to be statistically significant, indicating that the effect of STAN was different in high-risk women compared to a combination of both low- and high-risk women. Furthermore, the classifications of the fetal heart rate patterns used in the included randomized trials were different. Last but not least, despite >26 000 women with singleton gestations were included in the meta-analysis, the evidence still suffers from a lack of power, especially for subgroup analyses. In summary, while the level-1 data so far indicate overall no perinatal benefit of adding STAN to conventional intrapartum fetal heart rate monitoring for the outcomes most of interest, several issues point to the fact that more research is needed before the STAN technology can be deemed of no value for fetal monitoring in labor.","corpus_id":25857762,"score":0},{"doc_id":"28241039","title":"The genotype-phenotype map of an evolving digital organism.","abstract":"To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.","corpus_id":3744243,"score":0},{"doc_id":"29302273","title":"Resurrection ecology in Artemia.","abstract":"Resurrection ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this study, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well-documented phylogeography, and ecology) for a good RE model. We show in detail with a case study how cysts can be recovered from sediments to document the history and dynamics of a biological invasion. We finally discuss with precise examples the many RE possibilities with this model system: adaptation to climate change, to pollution, to parasites, to invaders and evolution of reproductive systems.","corpus_id":31993561,"score":0}],"string":"[\n {\n \"doc_id\": \"18493600\",\n \"title\": \"Resurrection of DNA function in vivo from an extinct genome.\",\n \"abstract\": \"There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.\",\n \"corpus_id\": 12566859,\n \"score\": 2\n },\n {\n \"doc_id\": \"19760276\",\n \"title\": \"Darwin's warm little pond revisited: from molecules to the origin of life.\",\n \"abstract\": \"All known cosmic and geological conditions and laws of chemistry and thermodynamics allow that complex organic matter could have formed spontaneously on pristine planet Earth about 4,000 mya. Simple gasses and minerals on the surface and in oceans of the early Earth reacted and were eventually organized in supramolecular aggregates and enveloped cells that evolved into primitive forms of life. Chemical evolution, which preceded all species of extant organisms, is a fact. In this review, we have concentrated on experimental and theoretical research published over the last two decades, which has added a wealth of new details and helped to close gaps in our previous understanding of this multifaceted field. Recent exciting progress in the molecular and genetic analyses of existing life, in particular microorganisms of ancient origin, even supports the possibility that a cellular, self-reproducing common ancestor might be assembled and resurrected in anaerobic cultures at some time in the future. Charles Darwin did not, and indeed, could not, address and specify the earliest phases of life which preceded the Origin of Species. However, in a famous letter, he sketched \\\"a warm little pond with all sorts of... (chemicals, in which) ...a protein was chemically formed.\\\" We try to trace the impact of his charming clear-sighted metaphor up to the present time.\",\n \"corpus_id\": 23259886,\n \"score\": 2\n },\n {\n \"doc_id\": \"21460845\",\n \"title\": \"Single-molecule paleoenzymology probes the chemistry of resurrected enzymes.\",\n \"abstract\": \"It is possible to travel back in time at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx) dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32 °C more stable than modern enzymes, and the oldest show markedly higher activity than extant ones at pH 5. We probed the mechanisms of reduction of these enzymes using single-molecule force spectroscopy. From the force dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs use chemical mechanisms of reduction similar to those of modern enzymes. Although Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over 4 Gyr to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth.\",\n \"corpus_id\": 2002600,\n \"score\": 2\n },\n {\n \"doc_id\": \"21703277\",\n \"title\": \"RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems.\",\n \"abstract\": \"The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical DRT systems. Beyond covalent molecular assembly, an extension of the DRT concept can include RNA molecules acting as dynamic structural template guides for the specific non-covalent assembly of multi-subunit complexes, equivalent to structural assembly chaperones. However, despite numerous precedents for RNA molecules acting as scaffolds for protein complexes, true RNA-mediated assembly chaperoning appears to be absent in modern biosystems. Another level of function with parallels to a DRT system is possible if RNA structural motifs dynamically guided specific patterns of catalytic modifications within multiple target sites in a pre-formed polymer or macromolecular complex. It is suggested that this type of structural RNA templating could logically play a functional role in certain areas of biology, one of which is the glycome of complex organisms. If any such RNA templating processes are shown to exist, they would share no necessary evolutionary relationships with events during early molecular evolution, but may promote understanding of the practical limits of biological RNA functions now and in the ancient RNA World. Awareness of these formal possibilities may also assist in the current search for functions of extensive non-coding RNAs in complex organisms, or for efforts towards artificial rendering of DRT systems.\",\n \"corpus_id\": 510563,\n \"score\": 2\n },\n {\n \"doc_id\": \"21781330\",\n \"title\": \"Resurrection of an ancestral 5S rRNA.\",\n \"abstract\": \"BACKGROUND: In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences can be used to understand early events in evolution. In the case of RNA, the nature of parsimony is such that when applied to multiple RNA sequences it typically predicts ancestral sequences that satisfy the base pairing constraints associated with secondary structure. The case for such sequences being actual ancestors is greatly improved, if they can be shown to be biologically functional. RESULTS: A unique common ancestral sequence of 28 Vibrio 5S ribosomal RNA sequences predicted by parsimony was resurrected and found to be functional in the context of the E. coli cellular environment. The functionality of various point variants and intermediates that were constructed as part of the resurrection were examined in detail. When separately introduced the changes at single stranded positions and individual double variants at base-paired positions were also viable. An additional double variant was examined at a different base-paired position and it was also valid. CONCLUSIONS: The results show that at least in the case of the 5S rRNAs considered here, ancestors predicted by parsimony are likely to be realistic when the prediction is not overly influenced by single outliers. It is especially noteworthy that the phenotype of the predicted ancestors could be anticipated as a cumulative consequence of the phenotypes of the individual variants that comprised them. Thus, point mutation data is potentially useful in evaluating the reasonableness of ancestral sequences predicted by parsimony or other methods. The results also suggest that in the absence of significant tertiary structure constraints double variants that preserve pairing in stem regions will typically be accepted. Overall, the results suggest that it will be feasible to resurrect additional meaningful 5S rRNA ancestors as well as ancestral sequences of many different types of RNA.\",\n \"corpus_id\": 7971821,\n \"score\": 2\n },\n {\n \"doc_id\": \"22330132\",\n \"title\": \"Aqueous phase separation as a possible route to compartmentalization of biological molecules.\",\n \"abstract\": \"How could the incredible complexity of modern cells evolve from something simple enough to have appeared in a primordial soup? This enduring question has sparked the interest of researchers since Darwin first considered his theory of natural selection. Organic molecules, even potentially functional molecules including peptides and nucleotides, can be produced abiotically. Amphiphiles such as surfactants and lipids display remarkable self-assembly processes including the spontaneous formation of vesicles resembling the membranes of living cells. Nonetheless, numerous questions remain. Given the presumably dilute concentrations of macromolecules in the prebiotic pools where the earliest cells are thought to have appeared, how could the necessary components become concentrated and encapsulated within a semipermeable membrane? What would drive the further structural complexity that is a hallmark of modern living systems? The interior of modern cells is subdivided into microcompartments such as the nucleoid of bacteria or the organelles of eukaryotic cells. Even within what at first appears to be a single compartment, for example, the cytoplasm or nucleus, chemical composition is often nonuniform, containing gradients, macromolecular assemblies, and/or liquid droplets. What might the internal structure of intermediate evolutionary forms have looked like? The nonideal aqueous solution chemistry of macromolecules offers an attractive possible answer to these questions. Aqueous polymer solutions will form multiple coexisting thermodynamic phases under a variety of readily accessible conditions. In this Account, we describe aqueous phase separation as a model system for biological compartmentalization in both early and modern cells, with an emphasis on systems that have been encapsulated within a lipid bilayer. We begin with an introduction to aqueous phase separation and discuss how this phenomenon can lead to microcompartmentalization and could facilitate biopolymer encapsulation by partitioning of solutes between the phases. We then describe primitive model cells based on phase separation inside lipid vesicles, which mimic several basic properties of biological cells: microcompartmentation, protein relocalization in response to stimulus, loss of symmetry, and asymmetric vesicle division. We observe these seemingly complex phenomena in the absence of genetic molecules, enzymes, or cellular machinery, and as a result these processes could provide clues to possible intermediates in the early evolution of cell-like assemblies.\",\n \"corpus_id\": 10586980,\n \"score\": 2\n },\n {\n \"doc_id\": \"22674514\",\n \"title\": \"Resurrecting ancient animal genomes: the extinct moa and more.\",\n \"abstract\": \"Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.\",\n \"corpus_id\": 40330531,\n \"score\": 2\n },\n {\n \"doc_id\": \"23355531\",\n \"title\": \"Lateral gene transfer from the dead.\",\n \"abstract\": \"In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.\",\n \"corpus_id\": 6080655,\n \"score\": 2\n },\n {\n \"doc_id\": \"23394108\",\n \"title\": \"Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases.\",\n \"abstract\": \"We report a sequence reconstruction analysis targeting several Precambrian nodes in the evolution of class-A β-lactamases and the preparation and experimental characterization of their encoded proteins. Despite extensive sequence differences with the modern enzymes (~100 amino acid differences), the proteins resurrected in the laboratory properly fold into the canonical lactamase structure. The encoded proteins from 2-3 billion years (Gyr)-old β-lactamase sequences undergo cooperative two-state thermal denaturation and display very large denaturation temperature enhancements (~35 °C) relative to modern β-lactamases. They degrade different antibiotics in vitro with catalytic efficiencies comparable to that of an average modern enzyme. This enhanced substrate promiscuity is not accompanied by significant changes in the active-site region as seen in static X-ray structures, suggesting a plausible role for dynamics in the evolution of function in these proteins. Laboratory resurrections of 2-3 Gyr-old β-lactamases also endowed modern microorganisms with significant levels of resistance toward a variety of antibiotics, opening up the possibility of performing laboratory replays of the molecular tape of lactamase evolution. Overall, these results support the notions that Precambrian life was thermophilic and that proteins can evolve from substrate-promiscuous generalists into specialists during the course of natural evolution. They also highlight the biotechnological potential of laboratory resurrection of Precambrian proteins, as both high stability and enhanced promiscuity (likely contributors to high evolvability) are advantageous features in protein scaffolds for molecular design and laboratory evolution.\",\n \"corpus_id\": 207092445,\n \"score\": 2\n },\n {\n \"doc_id\": \"24356963\",\n \"title\": \"Tracing primordial protein evolution through structurally guided stepwise segment elongation.\",\n \"abstract\": \"The understanding of how primordial proteins emerged has been a fundamental and longstanding issue in biology and biochemistry. For a better understanding of primordial protein evolution, we synthesized an artificial protein on the basis of an evolutionary hypothesis, segment-based elongation starting from an autonomously foldable short peptide. A 10-residue protein, chignolin, the smallest foldable polypeptide ever reported, was used as a structural support to facilitate higher structural organization and gain-of-function in the development of an artificial protein. Repetitive cycles of segment elongation and subsequent phage display selection successfully produced a 25-residue protein, termed AF.2A1, with nanomolar affinity against the Fc region of immunoglobulin G. AF.2A1 shows exquisite molecular recognition ability such that it can distinguish conformational differences of the same molecule. The structure determined by NMR measurements demonstrated that AF.2A1 forms a globular protein-like conformation with the chignolin-derived β-hairpin and a tryptophan-mediated hydrophobic core. Using sequence analysis and a mutation study, we discovered that the structural organization and gain-of-function emerged from the vicinity of the chignolin segment, revealing that the structural support served as the core in both structural and functional development. Here, we propose an evolutionary model for primordial proteins in which a foldable segment serves as the evolving core to facilitate structural and functional evolution. This study provides insights into primordial protein evolution and also presents a novel methodology for designing small sized proteins useful for industrial and pharmaceutical applications.\",\n \"corpus_id\": 38728521,\n \"score\": 2\n },\n {\n \"doc_id\": \"24606140\",\n \"title\": \"Progress toward synthetic cells.\",\n \"abstract\": \"The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems.\",\n \"corpus_id\": 24175504,\n \"score\": 2\n },\n {\n \"doc_id\": \"25809963\",\n \"title\": \"Protocells: at the interface of life and non-life.\",\n \"abstract\": \"The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one \\\"correct\\\" structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form-\\\"protocells\\\". At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called \\\"pseudo-protocells\\\". Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to \\\"true-protocells\\\". The emergence of a \\\"chromosome\\\" (with genes linked together)-thus avoiding \\\"gene-loss\\\" during the protocell division, was another key event in the evolution of protocells. Such \\\"unitary-protocells\\\", containing a central genetic molecule, may have appeared as a milestone-in principle, since then life could evolve endlessly, \\\"gaining\\\" more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life.\",\n \"corpus_id\": 14784602,\n \"score\": 2\n },\n {\n \"doc_id\": \"26530525\",\n \"title\": \"Mammoth 2.0: will genome engineering resurrect extinct species?\",\n \"abstract\": \"It is impossible to 'clone' species for which no living cells exist. Genome editing may therefore provide the only means to bring extinct species--or, more accurately, extinct traits--back to life.\",\n \"corpus_id\": 14722203,\n \"score\": 2\n },\n {\n \"doc_id\": \"26763705\",\n \"title\": \"Experimental macroevolution.\",\n \"abstract\": \"The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.\",\n \"corpus_id\": 1298118,\n \"score\": 2\n },\n {\n \"doc_id\": \"27863072\",\n \"title\": \"When directed evolution met ancestral enzyme resurrection.\",\n \"abstract\": \"The directed evolution of ancestral -resurrected- enzymes can give a new twist in protein engineering approaches towards more versatile and robust biocatalysts.\",\n \"corpus_id\": 17506710,\n \"score\": 2\n },\n {\n \"doc_id\": \"28008088\",\n \"title\": \"Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering.\",\n \"abstract\": \"A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes. Recently, however, ASR has developed from a tool for testing hypotheses about protein evolution to a useful means for designing novel proteins. The strength of this approach lies in the ability to infer ancestral sequences encoding proteins that have desirable properties compared with contemporary forms, particularly thermostability and broad substrate range, making them good starting points for laboratory evolution. Developments in technologies for DNA sequencing and synthesis and computational phylogenetic analysis have led to an escalation in the number of ancient proteins resurrected in the last decade and greatly facilitated the use of ASR in the burgeoning field of synthetic biology. However, the primary challenge of ASR remains in accurately inferring ancestral states, despite the uncertainty arising from evolutionary models, incomplete sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering.\",\n \"corpus_id\": 28416897,\n \"score\": 2\n },\n {\n \"doc_id\": \"28094501\",\n \"title\": \"Artificial Cells: Synthetic Compartments with Life-like Functionality and Adaptivity.\",\n \"abstract\": \"Cells are highly advanced microreactors that form the basis of all life. Their fascinating complexity has inspired scientists to create analogs from synthetic and natural components using a bottom-up approach. The ultimate goal here is to assemble a fully man-made cell that displays functionality and adaptivity as advanced as that found in nature, which will not only provide insight into the fundamental processes in natural cells but also pave the way for new applications of such artificial cells. In this Account, we highlight our recent work and that of others on the construction of artificial cells. First, we will introduce the key features that characterize a living system; next, we will discuss how these have been imitated in artificial cells. First, compartmentalization is crucial to separate the inner chemical milieu from the external environment. Current state-of-the-art artificial cells comprise subcompartments to mimic the hierarchical architecture of eukaryotic cells and tissue. Furthermore, synthetic gene circuits have been used to encode genetic information that creates complex behavior like pulses or feedback. Additionally, artificial cells have to reproduce to maintain a population. Controlled growth and fission of synthetic compartments have been demonstrated, but the extensive regulation of cell division in nature is still unmatched. Here, we also point out important challenges the field needs to overcome to realize its full potential. As artificial cells integrate increasing orders of functionality, maintaining a supporting metabolism that can regenerate key metabolites becomes crucial. Furthermore, life does not operate in isolation. Natural cells constantly sense their environment, exchange (chemical) signals, and can move toward a chemoattractant. Here, we specifically explore recent efforts to reproduce such adaptivity in artificial cells. For instance, synthetic compartments have been produced that can recruit proteins to the membrane upon an external stimulus or modulate their membrane composition and permeability to control their interaction with the environment. A next step would be the communication of artificial cells with either bacteria or another artificial cell. Indeed, examples of such primitive chemical signaling are presented. Finally, motility is important for many organisms and has, therefore, also been pursued in synthetic systems. Synthetic compartments that were designed to move in a directed, controlled manner have been assembled, and directed movement toward a chemical attractant is among one of the most life-like directions currently under research. Although the bottom-up construction of an artificial cell that can be truly considered \\\"alive\\\" is still an ambitious goal, the recent work discussed in this Account shows that this is an active field with contributions from diverse disciplines like materials chemistry and biochemistry. Notably, research during the past decade has already provided valuable insights into complex synthetic systems with life-like properties. In the future, artificial cells are thought to contribute to an increased understanding of processes in natural cells and provide opportunities to create smart, autonomous, cell-like materials.\",\n \"corpus_id\": 18934065,\n \"score\": 2\n },\n {\n \"doc_id\": \"28316883\",\n \"title\": \"Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.\",\n \"abstract\": \"BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. METHODS: ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. RESULTS: Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. DISCUSSION: The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.\",\n \"corpus_id\": 23977880,\n \"score\": 2\n },\n {\n \"doc_id\": \"28671667\",\n \"title\": \"Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins.\",\n \"abstract\": \"The sarcomere-based structure of muscles is conserved among vertebrates; however, vertebrate muscle physiology is extremely diverse. A molecular explanation for this diversity and its evolution has not been proposed. We use phylogenetic analyses and single-molecule force spectroscopy (smFS) to investigate the mechanochemical evolution of titin, a giant protein responsible for the elasticity of muscle filaments. We resurrect eight-domain fragments of titin corresponding to the common ancestors to mammals, sauropsids, and tetrapods, which lived 105-356 Myr ago, and compare them with titin fragments from some of their modern descendants. We demonstrate that the resurrected titin molecules are rich in disulfide bonds and display high mechanical stability. These mechanochemical elements have changed over time, creating a paleomechanical trend that seems to correlate with animal body size, allowing us to estimate the sizes of extinct species. We hypothesize that mechanical adjustments in titin contributed to physiological changes that allowed the muscular development and diversity of modern tetrapods.\",\n \"corpus_id\": 54482436,\n \"score\": 2\n },\n {\n \"doc_id\": \"28719578\",\n \"title\": \"De novo active sites for resurrected Precambrian enzymes.\",\n \"abstract\": \"Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.\",\n \"corpus_id\": 36345380,\n \"score\": 2\n },\n {\n \"doc_id\": \"28915003\",\n \"title\": \"The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery.\",\n \"abstract\": \"Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify \\\"successful\\\" structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous \\\"DNA robots\\\" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28916155\",\n \"title\": \"Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection.\",\n \"abstract\": \"Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator. We tested hypotheses of adaptive evolution in the protein coding sequences of ESR2, and determined that ESR2 evolved via episodic positive selection on the NWM stem lineage. We separately co-transfected ESR2 constructs for human, NWM, and the anthropoid ancestor along with reporter gene vectors and performed hormone binding dose response experiments that measure transactivation activity. We found the transactivation potentials of the ancestral and human sequences to be significantly lower (p<0.0001 in each comparison) than that of the NWM when treated with estradiol, the most prevalent estrogen. We conclude the difference in fold activation is due to positive selection in the NWM ERβ ligand binding domain. Our study validates inferential methods for detecting adaptive evolution that predict functional consequences of nucleotide substitutions and points a way toward examining the functional consequences of positive Darwinian selection.\",\n \"corpus_id\": 205842572,\n \"score\": 2\n },\n {\n \"doc_id\": \"29133450\",\n \"title\": \"Resurrecting ancestral genes in bacteria to interpret ancient biosignatures.\",\n \"abstract\": \"Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction. This article is part of the themed issue 'Reconceptualizing the origins of life'.\",\n \"corpus_id\": 27456937,\n \"score\": 2\n },\n {\n \"doc_id\": \"29660672\",\n \"title\": \"Biotechnological and protein-engineering implications of ancestral protein resurrection.\",\n \"abstract\": \"Approximations to the sequences of ancestral proteins can be derived from the sequences of their modern descendants. Proteins encoded by such reconstructed sequences can be prepared in the laboratory and subjected to experimental scrutiny. These 'resurrected' ancestral proteins often display remarkable properties, reflecting ancestral adaptations to intra-cellular and extra-cellular environments that differed from the environments hosting modern/extant proteins. Recent experimental and computational work has specifically discussed high stability, substrate and catalytic promiscuity, conformational flexibility/diversity and altered patterns of interaction with other sub-cellular components. In this review, we discuss these remarkable properties as well as recent attempts to explore their biotechnological and protein-engineering potential.\",\n \"corpus_id\": 4936466,\n \"score\": 2\n },\n {\n \"doc_id\": \"19033463\",\n \"title\": \"Extinction and resurrection in gene networks.\",\n \"abstract\": \"When gene regulatory networks operate in regimes where the number of protein molecules is so small that the molecular species are on the verge of extinction, the death and resurrection of the species greatly modifies the attractor landscape. Deterministic models and the diffusion approximation to the master equation break down at the limits of protein populations in a way very analogous to the breakdown of geometrical optics that occurs at distances <1 wavelength of light from edges. Stable stochastic attractors arise from extinction and resurrection events that are not predicted by the deterministic description. With this view, we explore the attractors of the regular toggle switch and the exclusive switch, focusing on the effects of cooperative binding and the production of protein in bursts. Our arguments suggest that the stability of lysogeny in the lambda-phage may be influenced by such extinction phenomena.\",\n \"corpus_id\": 2077265,\n \"score\": 1\n },\n {\n \"doc_id\": \"19108768\",\n \"title\": \"Convergent evolution: raising a family from the dead.\",\n \"abstract\": \"New molecular evidence shows that Hawaiian honeyeaters did not evolve from the similar looking Australasian honeyeaters, but instead represent a striking case of convergent evolution. These now extinct birds form their own family, representing the only complete extinction of an entire avian family in modern times.\",\n \"corpus_id\": 6410048,\n \"score\": 1\n },\n {\n \"doc_id\": \"19198773\",\n \"title\": \"Paleoclimate and evolution: emergence of sponges during the neoproterozoic.\",\n \"abstract\": \"In the last 15 years, we had to cope with many technological and conceptual obstacles. The major hindrance was the view that sponges are primitive and exist separated from the other metazoan organisms. After answering these problems, the painful scientific process to position the most enigmatic metazoan phylum, the Porifera, into the correct phylogenetic place among the eukaryotes in general and the multicellular animals in particular came to an end. The well-studied taxon Porifera (sponges) was first grouped to the animal-plants or plant-animals, then to the Zoophyta or Mesozoa, and finally to the Parazoa. Only by the application of molecular biological techniques was it possible to place the Porifera monophyletically with the other metazoan phyla, justifying a unification of all multicellular animals to only one kingdom, the Metazoa. The first strong support came from the discovery that cell-cell and cell-matrix adhesion molecules, that were cloned from sponges (mainly the demosponges Suberites domuncula and Geodia cydonium) and that were subsequently expressed, share high DNA sequence and protein function similarity with the corresponding molecules of other metazoans. Together with the molecular biological studies and with the use of the cell culture technologies (primmorphs), which allowed an insight into the stem cell system of these simple organisms, it was possible to stethoscope back in the paleontological history of animals. These studies confirmed the view that the sponges evolved between two epochal ice times, 710-680 Ma (Sturtian glaciation) and 605-585 Ma (Varanger-Marinoan ice age), a period which allowed evolution to proceed but resulted also in a mass extinction of most animal taxa, with the exception of the Porifera. These animals could develop in the aqueous milieu which was rich in silica, due also to their ability to live in a symbiosis with unicellular organisms (prokaryotic and also eukaryotic). Those organisms provided the sponges with the nutrition to survive and to overcome the food deprivation in cold water and even in an environment under the ice. Based on the diverse genetic toolkit, the sponges could also resist the adverse temperature and sunlight climatic influences. It is fortunate that the sponges survived the last 800 million years with their basic body plan. This fact might qualify the sponges to become model organisms not only in biology and molecular biology but also to be used - as living fossils - as reference organisms to deduce important and new insights in the understanding of fossil records explored from the Neoproterozoic. Taken together, these data caused a paradigmatic change; the Porifera are complex and simple, but by far not primitive, and they contribute to the understanding of the deep evolution of animals in molecular biological and paleontological views.\",\n \"corpus_id\": 35941341,\n \"score\": 1\n },\n {\n \"doc_id\": \"19254178\",\n \"title\": \"A new model for investigating the evolution of transcription control networks.\",\n \"abstract\": \"Biological systems show unbounded capacity for complex behaviors and responses to their environments. This principally arises from their genetic networks. The processes governing transcription, translation, and gene regulation are well understood, as are the mechanisms of network evolution, such as gene duplication and horizontal gene transfer. However, the evolved networks arising from these simple processes are much more difficult to understand, and it is difficult to perform experiments on the evolution of these networks in living organisms because of the timescales involved. We propose a new framework for modeling and investigating the evolution of transcription networks in realistic, varied environments. The model we introduce contains novel, important, and lifelike features that allow the evolution of arbitrarily complex transcription networks. Molecular interactions are not specified; instead they are determined dynamically based on shape, allowing protein function to freely evolve. Transcriptional logic provides a flexible mechanism for defining genetic regulatory activity. Simulations demonstrate a realistic life cycle as an emergent property, and that even in simple environments lifelike and complex regulation mechanisms are evolved, including stable proteins, unstable mRNA, and repressor activity. This study also highlights the importance of using in silico genetics techniques to investigate evolved model robustness.\",\n \"corpus_id\": 30705728,\n \"score\": 1\n },\n {\n \"doc_id\": \"19614583\",\n \"title\": \"The fine details of evolution.\",\n \"abstract\": \"Charles Darwin's theory of evolution was based on studies of biology at the species level. In the time since his death, studies at the molecular level have confirmed his ideas about the kinship of all life on Earth and have provided a wealth of detail about the evolutionary relationships between different species and a deeper understanding of the finer workings of natural selection. We now have a wealth of data, including the genome sequences of a wide range of organisms, an even larger number of protein sequences, a significant knowledge of the three-dimensional structures of proteins, DNA and other biological molecules, and a huge body of information about the operation of these molecules as systems in the molecular machinery of all living things. This issue of Biochemical Society Transactions contains papers from oral presentations given at a Biochemical Society Focused Meeting to commemorate the 200th Anniversary of Charles Darwin's birth, held on 26-27 January 2009 at the Wellcome Trust Conference Centre, Cambridge. The talks reported on some of the insights into evolution which have been obtained from the study of protein sequences, structures and systems.\",\n \"corpus_id\": 9276603,\n \"score\": 1\n },\n {\n \"doc_id\": \"20195774\",\n \"title\": \"The resurrection of life.\",\n \"abstract\": \"The question of life was progressively put aside in the second half of the 20th century with the rise of molecular biology, but has recently re-emerged. Many scientists and philosophers consider that there is no place for this question within biology; that the distinction between living and non-living is arbitrary; and that progress in synthetic biology will finally put this question out of people's minds. I will argue that there is something wrong with the arguments supporting these statements. There are no reasons to exclude the question \\\"What is life?\\\" from biology. But the nature of the question has dramatically changed recently. Instead of being a search for the principles of life, the answer is now sought in the description of the historical process that has coupled the now well-established characteristics of organisms.\",\n \"corpus_id\": 13077344,\n \"score\": 1\n },\n {\n \"doc_id\": \"21046016\",\n \"title\": \"The ancestry and cumulative evolution of immune reactions.\",\n \"abstract\": \"The last two decades of study enriched greatly our knowledge of how the immune system originated and the sophisticated immune mechanisms of today's vertebrates and invertebrates developed. Even unicellular organisms possess mechanisms for pathogen destruction and self recognition. The ability to distinguish self from non-self is a prerequisite for recognition of sexual compatibility and ensuring survival. Molecules involved in these processes resemble those found in the phagocytic cells of higher organisms. Recognition of bacteria by scavenger receptors induces phagocytosis or endocytosis. The phagocytic mechanisms characterizing the amoeboid protozoans developed further during the evolution towards innate immunity. The scavenger receptor cysteine-rich domain SRCR is encoded in the genomes from the most primitive sponges to mammals. The immune system of sponges comprises signal transduction molecules which occur in higher metazoans as well. Sponges already possess recognition systems for pathogenic bacteria and fungi, based on membrane receptors (a lipopolysaccharide-interacting protein, a cell surface receptor recognizing β(1 → 3)-d-glucans of fungi). Perforin-like molecules and lysozymes are involved, among others, in defense in sponges. Reactive oxygen and nitrogen species function in the immunity of early metazoan. Genes encoding the family of reactive oxygen-generating NADPH oxidases (Noxes) are found in a variety of protists and plants. The NO synthases of cnidarians, mollusks, and chordates are conserved with respect to the mammalian NOS. The antimicrobial peptides of protozoans, amoebapores, are structural and functional analogs of the natural killer cell peptide, NK-lysin, of vertebrates. An ancestral S-type lectin has been found in sponges. Opsonizing properties of lectins and the ability to agglutinate cells justify their classification as primitive recognition molecules. Invertebrate cytokines are not homologous to those of vertebrate, and their functional convergence was presumably enabled by the general similarity of the lectin-like recognition domain three-dimensional structure. Sponges contain molecules with SCR/CCP domains that show high homology to the mammalian regulators of complement activation (RCA family). A multi-component complement system comprising at least the central molecule of the complement system, C3, Factor B, and MASP developed in the cnidarians and evolved into the multilevel cascade engaged in innate and acquired immunity of vertebrates. The adaptive immune system of mammals is also deeply rooted in the metazoan evolution. Some its precursors have been traced as deep as in sponges, namely, two classes of receptors that comprise Ig-like domains, the receptor tyrosine kinases (RTK), and the non-enzymic sponge adhesion molecules (SAM). The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T-cell receptor (TCR), B-cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes. However, genes closely resembling RAG1 and RAG2 have been uncovered in the genome of a see urchin. The ancestry of MHC gene remains unknown. Similarly, no homologue of the protein binding domain (PBD) in MHC molecules has been found in invertebrates. The pathway by which endogenous peptides are degraded for presentation with class I MHC molecules utilizes mechanisms similar to those involved in the normal turnover of intracellular proteins, apparently recruited to work also for the immune system. Several cDNAs coding for lysosomal enzymes, e.g., cathepsin, have been isolated from sponges. All chromosomal duplication events in the MHC region occurred after the origin of the agnathans but before the gnathostomes split from them. The V-domains of the subtype found in the receptors of T and B-cells are known from both agnathans and cephalochordates, although they do not rearrange. The rearrangement mechanism of the lymphocyte V-domains suggests its origin from a common ancestral domain existing before the divergence of the extant gnathostome classes. Activation-induced deaminase (AID) - homologous proteins have been found only in the gnathostomes. It appears thus that the adaptive immunity of vertebrates is a result of stepwise accumulation of small changes in molecules, cells and organs over almost half a billion years.\",\n \"corpus_id\": 12607648,\n \"score\": 1\n },\n {\n \"doc_id\": \"22098061\",\n \"title\": \"Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises.\",\n \"abstract\": \"In isolated oceanic islands, colonization patterns are often interpreted as resulting from dispersal rather than vicariant events. Such inferences may not be appropriate when island associations change over time and new islands do not form in a simple linear trend. Further complexity in the phylogeography of ocean islands arises when dealing with endangered taxa as extinctions, uncertainty on the number of evolutionary 'units', and human activities can obscure the progression of colonization events. Here, we address these issues through a reconstruction of the evolutionary history of giant Galápagos tortoises, integrating DNA data from extinct and extant species with information on recent human activities and newly available geological data. Our results show that only three of the five extinct or nearly extinct species should be considered independent evolutionary units. Dispersal from mainland South America started at approximately 3.2 Ma after the emergence of the two oldest islands of San Cristobal and Española. Dispersal from older to younger islands began approximately 1.74 Ma and was followed by multiple colonizations from different sources within the archipelago. Vicariant events, spurred by island formation, coalescence, and separation, contributed to lineage diversifications on Pinzón and Floreana dating from 1.26 and 0.85 Ma. This work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human-mediated dispersal events and highlights the need to take into account both vicariance and dispersal when dealing with organisms from islands whose associations are not simply explained by a linear emergence model.\",\n \"corpus_id\": 32620164,\n \"score\": 1\n },\n {\n \"doc_id\": \"22750993\",\n \"title\": \"A possible molecular metric for biological evolvability.\",\n \"abstract\": \"Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring 'evolvability' of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.\",\n \"corpus_id\": 15015178,\n \"score\": 1\n },\n {\n \"doc_id\": \"24333920\",\n \"title\": \"Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?\",\n \"abstract\": \"Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a \\\"molecular scaffold\\\" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a \\\"Paraná Portal\\\" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.\",\n \"corpus_id\": 15030118,\n \"score\": 1\n },\n {\n \"doc_id\": \"24641285\",\n \"title\": \"Evolutionary insights into the origin of innate and adaptive immune systems: different shades of grey.\",\n \"abstract\": \"To struggle for survival, all living organisms, from protists to humans, must defend themselves from attack by predators. From the time when life began around 3,500 million years ago, all living cells have evolved mechanisms and strategies to optimally defend themselves, while the invaders also need to survive by evading these immune defenses. The end results would be healthy co-evolution of both parties. Classically, immune host defense is divided into two main categories, namely, innate and adaptive systems. It is well documented that while vertebrates possess both systems, invertebrates and prokaryotes like bacteria and archaea depend almost exclusively on the innate immune functions. Although the adaptive immune system like antibodies and cellular immunity or their equivalents are believed to have evolved at the time when the vertebrates first appeared about 550 million years ago, more recent information from molecular and genomic studies suggest that different forms of adaptive immune system may also be present in the invertebrates as well. These forms of \\\"adaptive\\\" immune system exhibit, for instance, limited degrees of memory, diversity and similarities of their immune receptors with the immunoglobulin domains of the conventional adaptive immune system of vertebrates. Organized lymphoid tissues have been identified in all vertebrates. Very recent molecular and genetic data further suggest that a special type of adaptive system functioning like RNAi of vertebrates is also present in the very ancient form of life like the bacteria and archaea. In this review, I provide some insights, based on recent information gathering from evolutionary data of innate and adaptive immune receptors of invertebrate and vertebrate animals that should convince the readers that our current view on the innate and adaptive immunity may need to be modified. The distinction between the two systems should not be thought of in terms of a \\\"black and white\\\" phenomenon anymore, as recent molecular and genomic information points to the fact that a line of distinction is not as sharp as it was once thought to be, but it is blurred by different shades of grey.\",\n \"corpus_id\": 402533,\n \"score\": 1\n },\n {\n \"doc_id\": \"24799958\",\n \"title\": \"Quantum entanglement in photoactive prebiotic systems.\",\n \"abstract\": \"This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modelled photoactive prebiotic kernel systems. We define our modelled self-assembled supramolecular photoactive centres, composed of one or more sensitizer molecules, precursors of fatty acids and a number of water molecules, as a photoactive prebiotic kernel systems. We propose that life first emerged in the form of such minimal photoactive prebiotic kernel systems and later in the process of evolution these photoactive prebiotic kernel systems would have produced fatty acids and covered themselves with fatty acid envelopes to become the minimal cells of the Fatty Acid World. Specifically, we model self-assembling of photoactive prebiotic systems with observed quantum entanglement phenomena. We address the idea that quantum entanglement was important in the first stages of origins of life and evolution of the biospheres because simultaneously excite two prebiotic kernels in the system by appearance of two additional quantum entangled excited states, leading to faster growth and self-replication of minimal living cells. The quantum mechanically modelled possibility of synthesizing artificial self-reproducing quantum entangled prebiotic kernel systems and minimal cells also impacts the possibility of the most probable path of emergence of protocells on the Earth or elsewhere. We also examine the quantum entangled logic gates discovered in the modelled systems composed of two prebiotic kernels. Such logic gates may have application in the destruction of cancer cells or becoming building blocks of new forms of artificial cells including magnetically active ones.\",\n \"corpus_id\": 1910925,\n \"score\": 1\n },\n {\n \"doc_id\": \"25204387\",\n \"title\": \"Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae.\",\n \"abstract\": \"BACKGROUND AND AIMS: The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS: Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions. KEY RESULTS: Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. CONCLUSIONS: The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26149747\",\n \"title\": \"Towards self-assembled hybrid artificial cells: novel bottom-up approaches to functional synthetic membranes.\",\n \"abstract\": \"There has been increasing interest in utilizing bottom-up approaches to develop synthetic cells. A popular methodology is the integration of functionalized synthetic membranes with biological systems, producing \\\"hybrid\\\" artificial cells. This Concept article covers recent advances and the current state-of-the-art of such hybrid systems. Specifically, we describe minimal supramolecular constructs that faithfully mimic the structure and/or function of living cells, often by controlling the assembly of highly ordered membrane architectures with defined functionality. These studies give us a deeper understanding of the nature of living systems, bring new insights into the origin of cellular life, and provide novel synthetic chassis for advancing synthetic biology.\",\n \"corpus_id\": 37968455,\n \"score\": 1\n },\n {\n \"doc_id\": \"26423359\",\n \"title\": \"Alternative adaptive immunity strategies: coelacanth, cod and shark immunity.\",\n \"abstract\": \"The advent of high throughput sequencing has permitted to investigate the genome and the transcriptome of novel non-model species with unprecedented depth. This technological advance provided a better understanding of the evolution of adaptive immune genes in gnathostomes, revealing several unexpected features in different fish species which are of particular interest. In the present paper, we review the current understanding of the adaptive immune system of the coelacanth, the elephant shark and the Atlantic cod. The study of coelacanth, the only living extant of the long thought to be extinct Sarcopterygian lineage, is fundamental to bring new insights on the evolution of the immune system in higher vertebrates. Surprisingly, coelacanths are the only known jawed vertebrates to lack IgM, whereas two IgD/W loci are present. Cartilaginous fish are of great interest due to their basal position in the vertebrate tree of life; the genome of the elephant shark revealed the lack of several important immune genes related to T cell functions, which suggest the existence of a primordial set of TH1-like cells. Finally, the Atlantic cod lacks a functional major histocompatibility II complex, but balances this evolutionary loss with the expansion of specific gene families, including MHC I, Toll-like receptors and antimicrobial peptides. Overall, these data point out that several fish species present an unconventional adaptive immune system, but the loss of important immune genes is balanced by adaptive evolutionary strategies which still guarantee the establishment of an efficient immune response against the pathogens they have to fight during their life.\",\n \"corpus_id\": 207009133,\n \"score\": 1\n },\n {\n \"doc_id\": \"28812662\",\n \"title\": \"Spending limited resources on de-extinction could lead to net biodiversity loss.\",\n \"abstract\": \"There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing and maintaining populations of these species on conservation of extant threatened species. Even using the optimistic assumptions that resurrection of species is externally sponsored, and that actions for resurrected species can share costs with extant analogue species, public funding for conservation of resurrected species would lead to fewer extant species that could be conserved, suggesting net biodiversity loss. If full costs of establishment and maintenance for resurrected species populations were publicly funded, there could be substantial sacrifices in extant species conservation. If conservation of resurrected species populations could be fully externally sponsored, there could be benefits to extant threatened species. However, such benefits would be outweighed by opportunity costs, assuming such discretionary money could directly fund conservation of extant species. Potential sacrifices in conservation of extant species should be a crucial consideration in deciding whether to invest in de-extinction or focus our efforts on extant species.\",\n \"corpus_id\": 19887264,\n \"score\": 1\n },\n {\n \"doc_id\": \"19435181\",\n \"title\": \"Love letters to the dead: resurrecting an epistolary art.\",\n \"abstract\": \"This article explores the art of letter-writing, specifically to our beloved dead, as a form of autoethnographic research, pedagogy, and care work. As university teachers and qualitative researchers in palliative and end-of-life care, we review the literature and history of epistolary communications with the deceased, as a prelude to writing our own letters. John writes to his long-dead mother and Dorothy to her recently deceased spouse Patrick, each letter followed by a reflective dialogue between us. Through this dialogue, we highlight the potential application of this art, or handcraft, to formal and informal palliative care, and the implications for practice, pedagogy, policy, and research. We propose that such direct, non-mediated, communications can offer a valuable form of healing for bereaved people. The therapeutic potential of letter writing and the abundance of literary and popular culture exemplars of responses from the dead are also largely unexplored in death education and research.\",\n \"corpus_id\": 46600881,\n \"score\": 0\n },\n {\n \"doc_id\": \"19774069\",\n \"title\": \"Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.\",\n \"abstract\": \"BACKGROUND: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. METHODOLOGY/PRINCIPAL FINDINGS: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. CONCLUSIONS/SIGNIFICANCE: Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.\",\n \"corpus_id\": 12514252,\n \"score\": 0\n },\n {\n \"doc_id\": \"20072108\",\n \"title\": \"The 2009 Lindau Nobel Laureate Meeting: Roger Y. Tsien, Chemistry 2008.\",\n \"abstract\": \"American biochemist Roger Tsien shared the 2008 Nobel Prize in Chemistry with Martin Chalfie and Osamu Shimomura for their discovery and development of the Green Fluorescent Protein (GFP). Tsien, who was born in New York in 1952 and grew up in Livingston New Jersey, began to experiment in the basement of the family home at a young age. From growing silica gardens of colorful crystallized metal salts to attempting to synthesize aspirin, these early experiments fueled what would become Tsien's lifelong interest in chemistry and colors. Tsien's first official laboratory experience was an NSF-supported summer research program in which he used infrared spectroscopy to examine how metals bind to thiocyanate, for which he was awarded a $10,000 scholarship in the Westinghouse Science Talent Search. Following graduation from Harvard in 1972, Tsien attended Cambridge University in England under a Marshall Scholarship. There he learned organic chemistry --a subject he'd hated as an undergraduate-- and looked for a way to synthesize dyes for imaging neuronal activity, generating BAPTA based optical calcium indicator dyes. Following the completion of his postdoctoral training at Cambridge in 1982, Tsien accepted a faculty position at the University of California, Berkeley. There he and colleagues developed and improved numerous small molecule indicators, including indicators fura-2 and indo-1. In 1989, Tsien moved his laboratory to the University of California at San Diego, where he and his colleagues developed the enhanced mutant of GFP as a way to devise a cyclic AMP (cAMP) sensor for use in live cells. They initially engineered molecules to take advantage of the conformational change that occurs when cAMP binds to protein kinase A (PKA). By labeling one part of PKA with fluoroscein and another with a rhodamine, they hoped to detect Fluorescence Resonance Energy Transfer (FRET), which would occur when the two molecules were in close proximity. The initial experiments presented numerous difficulties due to the challenges of expressing PKA subunits in E. coli, labeling the protein without destroying its function, and delivering the protein to cells via microinjection. Eventually, Tsien sought a more elegant approach, hoping to use and modify a naturally fluorescent protein that could be expressed in the cell. GFP originally described by Davenport in 1955, extracted and purified by Shimomura in 1965, and cloned by Prasher in 1992 was an appealing candidate. To make the protein more useful for their FRET studies, Tsien and colleagues modified the amino acid structure of the protein (S65T). The improved protein had an excitation peak near that of fluoroscein, and was photostable. Tsien and colleagues also solved the protein's crystal structure, enabling them to generate additional colors with spectral properties suitable for FRET. However, when they attempted to use the GFP proteins in the detection of cAMP, they experienced further difficulties with PKA. Instead, their first successful use of GFP derivatives for FRET was in the detection of intracellular calcium using their engineered calmodulin-based calcium indicator, Cameleon. In a short time, Tsien's work has led to further technological developments and important scientific findings. GFP and its derivatives have been used in a wide range of biological applications, from the study of protein localization to understanding how HIV spreads from cell to cell. The need for such probes is highlighted by the abundance of research conducted using these fluorescent proteins, as well as the continued development of similar fluorescent proteins, such as the coral-derived dsRED. Tsien is currently developing genetically encoded Infrared Fluorescent Proteins (IFPs), which with their long emission wavelengths of >700 nm, have the ability to pass through living tissue and improve imaging in living organisms. He is also building synthetic molecules for use in humans. He cites team effort and the contributions of students and post-docs as key components of progress and success: \\\"Even if I had the time, I couldn't have done the experiments, because I don't know how. It's very much a team effort.\\\"\",\n \"corpus_id\": 13072590,\n \"score\": 0\n },\n {\n \"doc_id\": \"20396881\",\n \"title\": \"Synthetic biology approaches in drug discovery and pharmaceutical biotechnology.\",\n \"abstract\": \"Synthetic biology is the attempt to apply the concepts of engineering to biological systems with the aim to create organisms with new emergent properties. These organisms might have desirable novel biosynthetic capabilities, act as biosensors or help us to understand the intricacies of living systems. This approach has the potential to assist the discovery and production of pharmaceutical compounds at various stages. New sources of bioactive compounds can be created in the form of genetically encoded small molecule libraries. The recombination of individual parts has been employed to design proteins that act as biosensors, which could be used to identify and quantify molecules of interest. New biosynthetic pathways may be designed by stitching together enzymes with desired activities, and genetic code expansion can be used to introduce new functionalities into peptides and proteins to increase their chemical scope and biological stability. This review aims to give an insight into recently developed individual components and modules that might serve as parts in a synthetic biology approach to pharmaceutical biotechnology.\",\n \"corpus_id\": 10381795,\n \"score\": 0\n },\n {\n \"doc_id\": \"21507096\",\n \"title\": \"Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture.\",\n \"abstract\": \"Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.\",\n \"corpus_id\": 14711450,\n \"score\": 0\n },\n {\n \"doc_id\": \"21951575\",\n \"title\": \"The properties of bio-energy transport and influence of structure nonuniformity and temperature of systems on energy transport along polypeptide chains.\",\n \"abstract\": \"A new theory of bio-energy transport along protein molecules in living systems, where the energy is released by hydrolysis of adenosine triphosphate (ATP), is proposed based on some physical and biological reasons. In the new theory, the Davydov's Hamiltonian and wave function of the systems are simultaneously modified and extended. A new interaction has been added into Davydov's Hamiltonian. The wave function of the excitation state of single particles for the excitons in the Davydov model is replaced by a new wave function of two-quanta quasicoherent state. In such a case, the bio-energy is transported by the new soliton, which differs from the Davydov's soliton. The soliton is formed through self- trapping of two excitons interacting amino acid residues. The exciton is generated by vibrations of amide-I (CO stretching) arising from the energy of hydrolysis of ATP. The properties of the new soliton are extensively studied by analytical method and its lifetime is calculated using the nonlinear quantum perturbation theory and a wide ranges of parameter values relevant to protein molecules. The lifetime of the new soliton at the biological temperature 300 K is enough large and belongs to the order of 10⁻¹⁰ s, or τ/τ₀≥700, in which the soliton can transports over several hundreds amino acid residues. These studied results show clearly that the new soliton is thermally stable and has so larger lifetime that it can play an important role in biological processes. Thus the new model is a candidate of the bio-energy transport mechanism in protein molecules. In the meanwhile, the influences of structure nonuniformity in protein molecules and temperature of the systems on the states and properties of the soliton transport of bio-energy are numerically simulated and studied by the fourth-order Runge-Kutta method. The structure nonuniformity arises from the disorder distributions of masses of amino acid residues, side groups and impurities, which results also in the fluctuations of the spring constant of protein molecules, dipole-dipole interaction between the neighboring amides, exciton-phonon (vibration of amino acids)interaction, chain-chain interaction among the three channels and ground state energy of the systems. We investigated the behaviors and states of the new solitons in a single protein molecular chain and α-Helix protein molecules with three channels under influences of the structure nonuniformity. We prove first that the bio-energy is transported by a soliton, which can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. When the structure nonuniformity exists, although the fluctuations of the spring constant, dipole-dipole interaction constant, exciton-phonon coupling constant and ground state energy and the nonuniformity distributions of masses of amino acid residues can change the states and properties of motion of new soliton, they are still quite stable and very robust against these structure nonuniformities, i.e., even there are a larger structure nonuniformity in the protein molecules, the new solitons cannot be still dispersed. If the effects of thermal perturbation of medium on the soliton in nonuniform proteins is considered again, the new soliton can transport also over a larger spacing of 400 amino acids and has a longer time period of 300 ps, it is still thermally stable up to 320 K under the influence of the above structure nonuniformities. However, the new soliton disperses in the case of a higher temperature of 325 K and in more large structure nonuniformity. Thus, we determine that the new soliton's lifetime and critical temperature are 300 ps and 320 K, respectively. These results are also consistent with analytical data obtained via quantum perturbed theory. For α-Helix protein molecules with three channels, the results obtained show that the structure nonuniformity and quantum fluctuation can change the states and features of the new solitons, for example, the amplitudes, energies and velocities of the new soliton are decreased, but the solitons have been not destroyed, they can still transport steadily along the molecular chains retaining energy and momentum. When the quantum fluctuations are larger, such as, structure disorders and quantum fluctuations of 0.67<α(K)<2, ΔW=±8%W¯, ΔJ=±1%J¯, Δ(χ₁+χ₂)=±3%(χ¯₁+χ¯₂) and ΔL=±1%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.1 meV, |β(n)|<0.5, the new soliton is still stable. Therefore, the new solitons are quite robust against these nonuniform effects. However, they will be dispersed or disrupted in cases of very large structure nonuniformity. When the influence of temperature on solitons is considered, we find that the new solitons can transport steadily over 333 amino acid residues in the case of a long time period of 120 ps, in which the soliton can retain its shape and energy to travel forward along protein molecules after their mutual collision at the biological temperature of 300 K. However, the soliton disperses in cases of higher temperatures 325 K under action of a larger structure disorder. Thus, its critical temperature is about 320 K. When the effects of structure nonuniformity and temperature are considered simultaneously, then the new soliton has still high thermal stability and can transport also along the protein molecular chains retaining its amplitude, energy and velocity, they will disperses in the larger fluctuations, for example, 0.67 M¯<M(k)<2M¯, ΔW=±6%W¯, ΔJ=±1.3%J¯, Δ(χ₁+χ₂)=±2%(χ¯₁+χ¯₂), ΔL=±1.5%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.82 meV, |β(n)|≤0.5 at T=300 K, or at higher temperatures 320 K and the fluctuations of 0.67M¯<M(k)<2M¯, Δ(χ₁+χ₂=±1%(χ¯₁+χ¯₂), ΔJ=±0.7%J¯, ΔW=±7%W¯, ΔL=±0.8%L¯ and Δɛ₀=ɛ|β(n)|, ɛ=0.4 meV, |β(n)|≤0.5. These results mean that the critical temperature of the new soliton is 315K in this condition. Thus, we can conclude from these investigations that the new soliton is quite robust against the structure nonuniformities and thermal perturbation of proteins at 300 K in α-helix protein molecules, then it is a carrier of bio-energy transport and the improved model is a candidate for the mechanism of the bio-energy transport in the protein molecules. Finally we gave some experimental evidences for real existence of the soliton and validity of the theory of bio-energy transport in proteins.\",\n \"corpus_id\": 9537702,\n \"score\": 0\n },\n {\n \"doc_id\": \"22304966\",\n \"title\": \"From extant to extinct: locomotor ontogeny and the evolution of avian flight.\",\n \"abstract\": \"Evolutionary transformations are recorded by fossils with transitional morphologies, and are key to understanding the history of life. Reconstructing these transformations requires interpreting functional attributes of extinct forms by exploring how similar features function in extant organisms. However, extinct-extant comparisons are often difficult, because extant adult forms frequently differ substantially from fossil material. Here, we illustrate how postnatal developmental transitions in extant birds can provide rich and novel insights into evolutionary transformations in theropod dinosaurs. Although juveniles have not been a focus of extinct-extant comparisons, developing juveniles in many groups transition through intermediate morphological, functional and behavioral stages that anatomically and conceptually parallel evolutionary transformations. Exploring developmental transitions may thus disclose observable, ecologically relevant answers to long puzzling evolutionary questions.\",\n \"corpus_id\": 14775936,\n \"score\": 0\n },\n {\n \"doc_id\": \"22368802\",\n \"title\": \"[Autopsies of the real: resurrecting the dead].\",\n \"abstract\": \"Autopsias de lo real: resucitando a los muertos. The sense of the real, or the material - the dead body - as an inextricable part of the sacred does not disappear in the secular environment of the nineteenth and twentieth centuries. This article analyzes specific humanitarian narratives centered on the practice of autopsy and mummification, in which the traces of Catholicism act as a kind of spectral discourse of the imagination, where the real is configured in forms of the uncanny, the monstrous or the sacred.\",\n \"corpus_id\": 40330528,\n \"score\": 0\n },\n {\n \"doc_id\": \"23062450\",\n \"title\": \"[Posttraumatic stress disorder (PTSD) as a consequence of the interaction between an individual genetic susceptibility, a traumatogenic event and a social context].\",\n \"abstract\": \"L'état de stress post-traumatique comme conséquence de l'interaction entre une susceptibilité génétique individuelle, un évènement traumatogène et un contexte social. INTRODUCTION: Why are some individuals more likely than others to develop a posttraumatic stress disorder (PTSD) in the face of similar levels of trauma exposure? Monitoring the traumatic process combining the antecedents, the determinants of the psychic trauma and the acute symptoms can clarify the causes of the final onset of a chronic repetition syndrome. Epidemiologic research has clarified risk factors that increase the likelihood of PTSD after exposure to a potentially traumatic event. PTSD is an interaction between a subject, a traumatogenic factor and a social context. With each epidemiological, psychopathological and more particularly neurogenetic study, we will expand on the impact of these interactions on the therapeutic treatment of psycho-traumatised persons. LITERATURE FINDINGS: Most studies have shown that unrelated to the traumatic event, additional risk factors for developing PTSD include younger age at the time of the trauma, female gender, lower social economic statuts, lack of social support, premorbid personality characteristics and preexisting anxiety or depressive disorders increase the risk of PTSD. The psychic trauma is firmly attached to the repetition and the previous traumas are as many risks of developing a subsequent PTSD in the wake of a new trauma: PTSD in adults may represent a prolonged symptomatic reaction to prior traumatic assault, child abuse and childhood adversities. Related to the traumatic event, the organic pain, the traumatic brain injury, but also the sight of blood can lead to a trauma being considered as more serious or more harmful to life. It is useful to recognize the acute reactions of exhaustion stress as they can guide both the pharmacotherapeutic and the psychotherapeutic treatment thanks to debriefings. Even though the majority of people with acute stress disorder subsequently develop PTSD, the current data indicate that too many people can develop PTSD without initially displaying acute stress disorder. Though peritraumatic dissociation and peritraumatic distress have emerged as the strongest predictors for PTSD and have to be treated as soon as possible with the debriefing or the pharmacology; initial evidence suggests the potential benefits of early intervention, shortly after the trauma, and psychological debriefing has received increasing interest from the scientific community. However the Anglo-Saxon techniques (such as Critical Incident Stress Debriefing also known as the Mitchell model) are in total contrast with the French approach. In the first case the emotional response is controlled to ensure the pursuit of the group action, whilst in the second case the debriefing concerns patients with acute symptoms in order to prevent the development of a PTSD structuring of the latter. The facts, emotions and thoughts are not partitioned but inter-linked, thus enabling a fragmentation of the traumatic experience. In the face of the annihilation experienced, speech production by the subject is restored linking the person to the human community, once abandoned. However, debate continues on the efficacy of single session debriefing in the prevention of PTSD. At the time of the acute stress reactions, benzodiazepines are contraindicated at this stage as they promote dissociation and ulterior revivals. On the other hand, treatment with propranolol could be proposed: a two or three week course of propranolol begun in the aftermath of a traumatic event can reduce subsequent PTSD symptoms. DISCUSSION: A genetic polymorphism is evidently at work in the development of a PTSD via the regulation of the expression of genes of interest to the serotoninergic system and the adrenocorticotropic axis. The 5-HTTLPR (promoter region of SLC6A4 witch encodes the serotonin transporter) constitutes a genetic candidate region that may modulate emotional responses to traumatic events. The interaction between variation at the 5HTTLPR and stressful life events could predict depression and PTSD. Considering the dopaminergic pathway, the A1 allele coding the type 2 dopaminergic receptor is associated with a severe comorbidity of PTSD with the presence of somatic disorders, anxiety, social change and depression. For noradrenergic neuromodulation, an interaction between the polymorphism of gene GABRA2 and the occurrence of PTSD is described whereas an interaction between the number of traumatic events and Val(158)Met polymorphism of the gene coding for catecholamine-o-methyltransferase has also been found. The role of polymorphisms in FKBP5 (a co-chaperone of hsp 90 which binds to the glucocorticoid receptor) in predicting PTSD too, with a gene-by-environment point of view. These gene-by-environment studies are needed to focus more on distinct endophenotypes and influences from environmental factors. If several candidate genes are involved, a weighting of susceptibility to such and such a neurological regulation system will imply various endophenotypes. According to the monoamine predominantly incriminated, PTSD can take on a more hyper-vegetative clinical expression linked with noradrenergic overuse. Differently, avoidance behaviour and the depressive aspect invoke more a modification of the serotoninergic modulation whilst posttraumatic psychotic reactions question the role of dopaminergic pathways. Neuroscientific discoveries interesting the biological support of PTSD can thus modify our view of the conception of the disorder in relation to different therapeutic prospects. CONCLUSION: Chronic PTSD can manifest itself in different clinical forms. The repetition syndrome can appear a long time after the traumatic event, following a paucisymptomatic latency period, which can last several years or even decades. The absence of complaints from the patient is common, the latter suffering in silence. Often other comorbid disorders and other complaints arise sooner than the clinical picture. Thus a depressive episode characterised as drug-seeking behaviour is frequently encountered. The therapeutic accompaniment traditionally combines a pharmacological and a psychotherapeutic treatment even if recommendations are rare. A posttraumatic stress disorder is never just a coincidence. The different stages of the evolution and the establishment of a PTSD are the expression of an interaction between the outside and the inner self. Despite a known progression of the posttraumatic stress disorder, this deleterious evolution is far from being a foregone conclusion. On the contrary, several levels of prevention are possible at each stage of its structuration to propose treatments to subjects who are vulnerable and/or present symptoms. No neurobiological study has yet found a biological marker, which would apparently and inevitably destine a subject to structure, a posttraumatic stress disorder in reaction to a stress. Conversely, the psychopathological study finds afterwards that a particular subject has necessarily built a traumatic repetition syndrome according to the concordance of significant data relative to his/her history. The event strikes a repression or an anterior biographical deadlock and of which the thematic questions the fundamentals of human culture in its emancipation with nature, like the question of death and its consequences: bereavement, parentality, transgenerational transmission and organicity often linked to the illness. A therapeutic proposal constitutes an environmental factor par excellence which can be either protective or deleterious. If the traumatic repetition syndrome has been known since Antiquity, the birth of PTSD has followed the chronology of the DSM according to the sociopolitical contexts encountered. A PTSD does not occur by chance: the conditions of possibility of the trauma are established by genetic and psychological determinants interactively integrated at the heart of a social context. After the increase in a psychotraumatic interest in international publications since the 1980s, a fight against over-victimisation seems to be setting in. The advances in genetic and neuroimaging techniques are in the process of superseding psychometric studies in terms of reliability and validity; maybe we should see in this social evolution the changes of tomorrow concerning the clinical of PTSD and its treatment. The healing of the psycho-traumatised subject cannot just be established on the passive status of victim, which would be detrimental to reflection and ultimately reconstruction: the rebirth of the subject will require active commitment, which could distract from the deadly repetition. Whilst the confrontation with death resembled nonsense, the subject will question the psychotraumatic determinants of his/her life history to reinstate this tragic event within a search for meaning. Such restructuring is built on the intersubjectivity of the clinical relationship, which occurs within a social context. PTSD is a pathology which interacts with the societal context: on the one hand the trauma is established on the brutal reconsideration of social values which seem immutable and on the other hand, the clinical and nosographical concept of PTSD is changing with the evolution of society.\",\n \"corpus_id\": 25554857,\n \"score\": 0\n },\n {\n \"doc_id\": \"23103915\",\n \"title\": \"Reliable predictions of unusual molecules.\",\n \"abstract\": \"Quantum chemistry can today be employed to invent new molecules and investigate their properties and chemical bonding. However, the predicted species must be viable in order to be synthesized by experimentalists. In this perspective article we describe the technology of reliable theoretical predictions and show how understanding of chemical bonding in studied chemical systems could help to design new molecular structures. We also provide a short overview of successfully predicted and already produced (in some cases) planar hypercoordinate species to demonstrate that the consistent theoretical prediction of viable molecules with unusual structures and properties is now a reliable tool for exploring new, yet unknown molecules, clusters, nanomaterials and solids.\",\n \"corpus_id\": 7169897,\n \"score\": 0\n },\n {\n \"doc_id\": \"24124192\",\n \"title\": \"Is EM dead?\",\n \"abstract\": \"Since electron microscopy (EM) first appeared in the 1930s, it has held centre stage as the primary tool for the exploration of biological structure. Yet, with the recent developments of light microscopy techniques that overcome the limitations imposed by the diffraction boundary, the question arises as to whether the importance of EM in on the wane. This Commentary describes some of the pioneering studies that have shaped our understanding of cell structure. These include the development of cryo-EM techniques that have given researchers the ability to capture images of native structures and at the molecular level. It also describes how a number of recent developments significantly increase the ability of EM to visualise biological systems across a range of length scales, and in 3D, ensuring that EM will remain at the forefront of biology research for the foreseeable future.\",\n \"corpus_id\": 12747549,\n \"score\": 0\n },\n {\n \"doc_id\": \"24588263\",\n \"title\": \"Physical and biochemical insights on DNA structures in artificial and living systems.\",\n \"abstract\": \"CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.\",\n \"corpus_id\": 206824830,\n \"score\": 0\n },\n {\n \"doc_id\": \"24681091\",\n \"title\": \"Natural products from resurrection plants: potential for medical applications.\",\n \"abstract\": \"Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly - often within hours - regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications.\",\n \"corpus_id\": 206182000,\n \"score\": 0\n },\n {\n \"doc_id\": \"24921467\",\n \"title\": \"Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators.\",\n \"abstract\": \"This article deals with artificial vesicles and their membranes as reaction promoters and regulators. Among the various molecular assemblies which can form in an aqueous medium from amphiphilic molecules, vesicle systems are unique. Vesicles compartmentalize the aqueous solution in which they exist, independent on whether the vesicles are biological vesicles (existing in living systems) or whether they are artificial vesicles (formed in vitro from natural or synthetic amphiphiles). After the formation of artificial vesicles, their aqueous interior (the endovesicular volume) may become - or may be made - chemically different from the external medium (the exovesicular solution), depending on how the vesicles are prepared. The existence of differences between endo- and exovesicular composition is one of the features on the basis of which biological vesicles contribute to the complex functioning of living organisms. Furthermore, artificial vesicles can be formed from mixtures of amphiphiles in such a way that the vesicle membranes become molecularly, compositionally and organizationally highly complex, similarly to the lipidic matrix of biological membranes. All the various properties of artificial vesicles as membranous compartment systems emerge from molecular assembly as these properties are not present in the individual molecules the system is composed of. One particular emergent property of vesicle membranes is their possible functioning as promoters and regulators of chemical reactions caused by the localization of reaction components, and possibly catalysts, within or on the surface of the membranes. This specific feature is reviewed and highlighted with a few selected examples which range from the promotion of decarboxylation reactions, the selective binding of DNA or RNA to suitable vesicle membranes, and the reactivation of fragmented enzymes to the regulation of the enzymatic synthesis of polymers. Such type of emergent properties of vesicle membranes may have been important for the prebiological evolution of protocells, the hypothetical compartment systems preceding the first cells in those chemical and physico-chemical processes that led to the origin of life.\",\n \"corpus_id\": 32585856,\n \"score\": 0\n },\n {\n \"doc_id\": \"26002527\",\n \"title\": \"What can we learn from the transcriptome of the resurrection plant Craterostigma plantagineum?\",\n \"abstract\": \"MAIN CONCLUSION: The desiccation transcriptome of the resurrection plant C. plantagineum is composed of conserved protein coding transcripts, taxonomically restricted transcripts and recently evolved non-protein coding transcripts. Research in resurrection plants has been hampered by the lack of genome sequence information, but recently introduced sequencing technologies overcome this limitation partially and provide access to the transcriptome of these plants. Transcriptome studies showed that mechanisms involved in desiccation tolerance are conserved in resurrection plants, seeds and pollen. The accumulation of protective molecules such as sugars and LEA proteins are major components in desiccation tolerance. Leaf folding, chloroplast protection and protection during rehydration must involve specific molecular mechanisms, but the basis of such mechanisms is mainly unknown. The study of regulatory regions of a desiccation-induced C. plantagineum gene suggests that cis-regulatory elements may be responsible for expression variations in desiccation tolerant and non-desiccation-tolerant plants. The analysis of the C. plantagineum transcriptome also revealed that part of it is composed of taxonomically restricted genes (TRGs) and non-protein coding RNAs (ncRNAs). TRGs are known to code for new traits required for the adaptation of organisms to particular environmental conditions. Thus the study of TRGs from resurrection plants should reveal species-specific functions related to the desiccation tolerance phenotype. Non-protein coding RNAs can regulate gene expression at epigenetic, transcriptional and post-transcriptional level and thus these RNAs may be key players in the rewiring of regulatory networks of desiccation-related genes in C. plantagineum.\",\n \"corpus_id\": 16084932,\n \"score\": 0\n },\n {\n \"doc_id\": \"26691665\",\n \"title\": \"Karyotype is not dead (yet)!\",\n \"abstract\": \"BACKGROUND: While array-comparative genomic hybridization (a-CGH) and next-generation sequencing (NGS or exome) technologies have swiftly spread throughout the medical field, karyotype has gradually lost its leading role among genetic tests. Several international guidelines recommend starting with a-CGH screening then going on with exome analysis when investigating a patient with intellectual disability (ID) and no precise clinical diagnosis. A-CGH and whole exome sequencing increase etiologic diagnoses rate up to 30% in case of ID. However, physicians have to deal with the lack of qualitative information of the genome. Especially, exome and a-CGH analysis fail to detect chromosomal rearrangements because breakpoints are either located in introns or not associated with a gain or loss of genetic material. If these technologies cannot easily identify chromosomal translocations or inversions which sometimes split a gene, karyotype can. DISCUSSION: For the 5 cases described, karyotype provided the right diagnosis for a Mendelian disease while molecular analysis remained unsuccessful. We conclude that when a Mendelian disease is strongly suggested clinically, if molecular analysis is normal, it could be very useful to carry out a karyotype in order to demonstrate a chromosomal rearrangement involving the targeted gene. If this gene is disrupted, the physician can confirm the suspected disease and give appropriate genetic counseling. SUMMARY: This article aims at keeping in mind that karyotype, this old-fashioned genetic tool, can still remain powerful and useful within some genetic issues. Even in this modern period of whole exome sequencing, young geneticists should know that karyotype remains a powerful and cheap technology, available throughout the world and can still do a lot for families.\",\n \"corpus_id\": 37373234,\n \"score\": 0\n },\n {\n \"doc_id\": \"27499678\",\n \"title\": \"Enhancement of Plant Productivity in the Post-Genomics Era.\",\n \"abstract\": \"Obtaining high plant yield is not always achievable in agricultural activity as it is determined by various factors, including cultivar quality, nutrient and water supplies, degree of infection by pathogens, natural calamities and soil conditions, which affect plant growth and development. More noticeably, sustainable plant productivity to provide sufficient food for the increasing human population has become a thorny issue to scientists in the era of unpredictable global climatic changes, appearance of more tremendous or multiple stresses, and land restriction for cultivation. Well-established agricultural management by agrotechnological means has shown no longer to be effective enough to confront with this challenge. Instead, in order to maximize the production, it is advisable to implement such practices in combination with biological applications. Nowadays, high technologies are widely adopted into agricultural production, biological diversity conservation and crop improvement. Wang et al. has nicely outlined the utilization of DNA-based technologies in this field. Among these are the applications of (i) DNA markers into cultivar identification, seed purity analysis, germplasm resource evaluation, heterosis prediction, genetic mapping, cloning and breeding; and (ii) gene expression data in supporting the description of crop phenology, the analytic comparison of crop growth under stress versus non-stress conditions, or the study of fertilizer effects. Besides, various purposes of using transgenic technologies in agriculture, such as generating cultivars with better product quality, better tolerance to biotic or abiotic stress, are also discussed in the review. One of the important highlights in this issue is the review of the benefits brought by high-throughput sequencing technology, which is also known as next-generation sequencing (NGS). It is not so difficult to recognize that its application has allowed us to carry out biological studies at much deeper level and larger scale. In their article, Onda and Mochida detailed how to use these technologies in fully characterizing the genetic diversity or multigenecity within a particular plant species. The authors discussed the constant innovation of sequencing platforms which has made sequencing technologies become more superior and more powerful than ever before. Additionally, the efforts result in not only further cut down of the sequencing cost and increase in the sequencing speed, but also improvement in sequencing accuracy and extended sequencing application to studies at both DNA and RNA levels. Such knowledge will help the scientists interpret, at least partially, how plants can adapt to various environmental conditions, or how different cultivars can respond differently to the same stress. Another article by Ong et al. also laid emphasis on the importance of various high-throughput sequencing platforms, thanks to which a large number of genomic databases supplied with detailed annotation and useful bioinformatics tools have been established to assist geneticists. Readers can find in this review the summary of available plant-specific genomic databases up-to-date and popular web-based resources that are relevant for comparative genomics, plant evolution and phylogenomics studies. These, along with other approaches, such as quantitative trait locus and genome-wide association study, will lay foundation for prediction and identification of genes or alleles responsible for valuable agronomic traits, contributing to the enhancement of plant productivity by genetic engineering approach. In this thematic issue, specific examples for crop improvement are also demonstrated. The first showcase is given by Nongpiur et al. who provided evidence that synergistic employment of genomics approaches and high-throughput gene expression methods have aided in dissecting the salinity-responsive signaling pathway, identifying genes involved in the stress response and selecting candidate genes for further characterization aimed at generating new cultivars with better salinity stress tolerance. This paper is also a good reference source for readers who wish to get an overview about the general process from gene prediction to validation by experiments, including the details on techniques and approaches used. Another demonstration is provided by Khan et al. whose interest is enhancement of drought tolerance in crops. The focus of this article is to overview our current understanding of mechanisms regulating plants responses to drought. Evaluation of plant performance to drought and production of new elite varieties with better drought tolerance on the basis of using phenotyping and genomics-assisted breeding are also well discussed. In addition to the topics of environmental stress tolerance in plants, current knowledge on improving biotic stress tolerance is also summarized in our issue. Current picture on crosstalk of signaling mechanisms in rice between its immune system and symbiosis with microorganisms is presented by Akamatsu et al. Rice responses to bacteria and fungi via interactions between the plant pattern recognition receptors and the molecular microbe-associated molecular patterns are described in detail and suggested as targets for manipulation in order to increase disease resistance in crops. On the other hand, Bouain et al. are concerned about nutrient deficiency; specifically, how plant root system develops under growing conditions with inadequate phosphate. The authors overviewed our current understanding of the low phosphate-responsive mechanisms in Arabidopsis model plant, which was gained by using a combination of various advanced methods, including high-througput phenotyping, system biology analysis and \\\"omics\\\" technologies. Stress management in plants is proposed to be also achievable by regulating activities of cyclic nucleotide-gated ion channels. As emphasized in the paper of Jha et al., the application of such channels is important in mediating cellular ion homeostasis and plant tolerance to both biotic and abiotic stresses. In summary, with recent progresses in biological and biotechnological areas, especially rapid development of advanced technologies in biological system modeling, functional genomics, computer-based analyzing tools, genetic engineering and molecular breeding, biological control and biotechnological applications in agriculture have brought about an extraordinary revolution and have been considered the most powerful approaches in maintaining or even increasing crop yield. Therefore, in this issue, we would like to introduce to the audience a collection of various strategies used for enhancing crop productivity, with the focus on advanced biological-biotechnological platforms in the post-genomics era.\",\n \"corpus_id\": 9605718,\n \"score\": 0\n },\n {\n \"doc_id\": \"27734746\",\n \"title\": \"Why STAN might not be dead.\",\n \"abstract\": \"Recently, a meta-analysis, including 26 526 laboring vertex singletons at term, summarized all available level-1 data from six high-quality randomized clinical trials (RCTs) on the use of ST analysis (STAN) during labor as an adjunct to conventional intrapartum fetal heart rate monitoring. The meta-analysis showed that STAN did not improve perinatal outcomes or decrease cesarean deliveries. Nonetheless, there are still reasons to believe STAN may have a role in the future research on intrapartum fetal monitoring. Out of six trials included in the meta-analysis, two included all cephalic singletons in labor, and four enrolled only high-risk pregnant women. This combination of both low- and high-risk populations may have distorted the potential impact of STAN. The test for heterogeneity between both subgroups was found to be statistically significant, indicating that the effect of STAN was different in high-risk women compared to a combination of both low- and high-risk women. Furthermore, the classifications of the fetal heart rate patterns used in the included randomized trials were different. Last but not least, despite >26 000 women with singleton gestations were included in the meta-analysis, the evidence still suffers from a lack of power, especially for subgroup analyses. In summary, while the level-1 data so far indicate overall no perinatal benefit of adding STAN to conventional intrapartum fetal heart rate monitoring for the outcomes most of interest, several issues point to the fact that more research is needed before the STAN technology can be deemed of no value for fetal monitoring in labor.\",\n \"corpus_id\": 25857762,\n \"score\": 0\n },\n {\n \"doc_id\": \"28241039\",\n \"title\": \"The genotype-phenotype map of an evolving digital organism.\",\n \"abstract\": \"To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.\",\n \"corpus_id\": 3744243,\n \"score\": 0\n },\n {\n \"doc_id\": \"29302273\",\n \"title\": \"Resurrection ecology in Artemia.\",\n \"abstract\": \"Resurrection ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this study, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well-documented phylogeography, and ecology) for a good RE model. We show in detail with a case study how cysts can be recovered from sediments to document the history and dynamics of a biological invasion. We finally discuss with precise examples the many RE possibilities with this model system: adaptation to climate change, to pollution, to parasites, to invaders and evolution of reproductive systems.\",\n \"corpus_id\": 31993561,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":88,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"23255122\",\n \"title\": \"Identification of a cation transport pathway in Neisseria meningitidis PorB.\",\n \"abstract\": \"Neisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion-selective, cation translocation through nucleotide-bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs(+), which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs(+) form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis.\",\n \"corpus_id\": -1\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18191311","title":"The PorB porin from commensal Neisseria lactamica induces Th1 and Th2 immune responses to ovalbumin in mice and is a potential immune adjuvant.","abstract":"Porins from pathogenic Neisseriae are among several bacterial products with immune adjuvant activity. Neisseria meningitidis (Nme) PorB, has been shown to induce immune cells activation in a TLR2-dependent manner and acts as a vaccine immune adjuvant. The PorB porin from Neisseria lactamica (Nlac), a common nasopharyngeal commensal, shares significant structural and functional similarities with Nme PorB. In this work we ask whether the immune adjuvant ability of porins from pathogenic Neisserial strains is a characteristic shared with porins from non-pathogenic Neisserial species or whether it is unique for bacterial products derived from microorganisms capable of inducing inflammation and disease. We evaluated the potential immune adjuvant effect of Nlac PorB in mice using ovalbumin (OVA) as a prototype antigen. Immunization with Nlac PorB/OVA induced high OVA-specific IgG and IgM titers compared to OVA alone, similar to other adjuvants such as Nme PorB and alum. High titers of IgG1 and IgG2b were detected as well as production of IL-4, IL-10, IL-12 and INF-gamma in response to Nlac PorB, consistent with induction of both a Th1-type and a Th2-type immune response. OVA-specific proliferation was also determined in splenocytes from Nlac PorB/OVA-immunized mice. In addition, B cell activation in vitro and cytokine production in response to Nlac PorB was found to be mediated by TLR2, in a similar manner to Nme PorB.","corpus_id":-1,"score":2},{"doc_id":"18287580","title":"Role of protein tyrosine kinase and Erk1/2 activities in the Toll-like receptor 2-induced cellular activation of murine B cells by neisserial porin.","abstract":"Neisserial porins are potent immune adjuvants and have been demonstrated to stimulate and induce the activation of human and murine B lymphocytes. Their immunopotentiating ability is due largely to the upregulation of the surface expression of the costimulatory ligand CD86 (B7-2) on B cells and other antigen-presenting cells. Porin-induced activation is dependent on the innate immune pattern recognition receptor Toll-like receptor 2 (TLR2). These data have led us to investigate the signal transduction events induced by PorB from Neisseria meningitidis and then, using inhibitors of these pathways, to establish the mechanism by which this bacterial major outer membrane protein induces CD86 upregulation and the proliferation of murine B cells. PorB was able to induce (i) protein tyrosine kinase (PTK) activity, (ii) the phosphorylation of Erk1 and Erk2, and (iii) IkappaB-alpha phosphorylation, leading to NF-kappaB nuclear translocation in B cells in a TLR2-dependent manner. PorB-induced NF-kappaB nuclear translocation was not dependent on either PTK or Erk1/2 activities. However, B-cell proliferation and the induction of increased surface expression of CD86 by PorB were dependent on PTK activity and not Erk1/2 activation. In conclusion, PorB acts through TLR2 as a B-cell mitogen, triggering tyrosine phosphorylation of various cellular proteins that are involved in proliferation and CD86 expression, as well as the phosphorylation of Erk1/2, which is not necessary for CD86 upregulation or the proliferation of B cells.","corpus_id":-1,"score":2},{"doc_id":"18451061","title":"Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.","abstract":"One potential vaccine strategy in the fight against meningococcal disease involves the exploitation of outer-membrane components of Neisseria lactamica, a commensal bacterium closely related to the meningococcus, Neisseria meningitidis. Although N. lactamica shares many surface structures with the meningococcus, little is known about the antigenic diversity of this commensal bacterium or the antigenic relationships between N. lactamica and N. meningitidis. Here, the N. lactamica porin protein (Por) was examined and compared to the related PorB antigens of N. meningitidis, to investigate potential involvement in anti-meningococcal immunity. Relationships among porin sequences were determined using distance-based methods and F(ST), and maximum-likelihood analyses were used to compare the selection pressures acting on the encoded proteins. These analyses demonstrated that the N. lactamica porin was less diverse than meningococcal PorB and although it was subject to positive selection, this was not as strong as the positive selection pressures acting on the meningococcal porin. In addition, the N. lactamica porin gene sequences and the protein sequences of the loop regions predicted to be exposed to the human immune system were dissimilar to the corresponding sequences in the meningococcus. This suggests that N. lactamica Por, contrary to previous suggestions, may have limited involvement in the development of natural immunity to meningococcal disease and might not be effective as a meningococcal vaccine component.","corpus_id":-1,"score":2},{"doc_id":"18614668","title":"Neisseria meningitidis PorB, a Toll-like receptor 2 ligand, improves the capacity of Francisella tularensis lipopolysaccharide to protect mice against experimental tularemia.","abstract":"Francisella tularensis causes severe pneumonia that can be fatal if it is left untreated. Due to its potential use as a biological weapon, research is being conducted to develop an effective vaccine and to select and study adjuvant molecules able to generate a better and long-lasting protective effect. PorB, a porin from Neisseria meningitidis, is a well-established Toll-like receptor 2 ligand and has been shown to be a promising vaccine adjuvant candidate due to its ability to enhance the T-cell costimulatory activity of antigen-presenting cells both in vitro and in vivo. BALB/c mice were immunized with lipopolysaccharide (LPS) isolated from the F. tularensis subsp. holarctica live vaccine strain (LVS), with or without PorB from N. meningitidis, and the antibody levels induced during the vaccination regimen and the level of protection against intranasal challenge with LVS were determined. Antigen administered alone induced a specific F. tularensis LPS immunoglobulin M (IgM) response that was not maintained over the weeks and that conferred protection to only 25% of the mice. In contrast, F. tularensis LPS given in combination with neisserial PorB induced consistent levels of specific IgM throughout the immunization and increased the proportion of surviving mice to 70%. Postchallenge cytokine analysis showed that interleukin-6 (IL-6), monocyte chemoattractant protein 1, and gamma interferon were markers of mortality and that IL-1beta was a correlate of survival, independent of the presence of PorB as an adjuvant. These data indicate that neisserial PorB might be an optimal candidate adjuvant for improving the protective effect of F. tularensis LPS and other subunit vaccines against tularemia, but there is still a need to test its efficacy against virulent type A and type B F. tularensis strains.","corpus_id":-1,"score":2},{"doc_id":"18722761","title":"Functional characterization of PorB class II porin from Neisseria meningitidis using a tethered bilayer lipid membrane.","abstract":"PorB class II from Neisseria meningitidis is a pore-forming, outer-membrane protein that can translocate to the host-cell membrane during Neisserial infections. This report describes development of tethered bilayer lipid membrane (tBLM) system to measure PorB conductance properties. The tBLM was fabricated by depositing a self-assembled monolayer of 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) tethering lipid on a gold electrode and then using 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes to deposit the upper tBLM leaflet. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were used to monitor tBLM formation and subsequent PorB incorporation. The highly insulating tBLM exhibited a membrane resistance and capacitance of 2.5MOmegacm(2) and 0.7 microF/cm(2), respectively. PorB was incorporated into the tBLM in an active conformation, as evidenced by its mediation of ion passage and the decrease in membrane impedance. After PorB incorporation, the membrane resistance decreased to 0.6MOmegacm(2). As expected, the PorB channel was found to be non-selective, allowing the transport of both cations and anions. Cyclic voltammetry indicated that ferricyanide ions can also pass through the pores. The PorB-containing biomimetic interface developed in this study could potentially be used to screen for compounds that modulate PorB activity.","corpus_id":-1,"score":2},{"doc_id":"19137557","title":"Analysis of outer membrane porin complexes of Neisseria meningitidis in wild-type and specific knock-out mutant strains.","abstract":"The structure of the porin complexes of Neisseria meningitidis was assessed in the vaccine strain H44/76 and its homologous mutants lacking the main porins (PorA and PorB) and other outer membrane (OM) components (RmpM and FetA). The analysis using 1-D blue native (BN) electrophoresis, 2-D BN/SDS-PAGE and 2-D diagonal electrophoresis, followed by LC/MS-MS (for 1-D gels) or MALDI-TOF (for 2-D gels) revealed at least six porin complexes in the wild-type strain with molecular masses (MW) ranging from 145 to 195 kDa and variable composition: The two higher MW complexes are formed by PorA, PorB and RmpM, the following three are formed by PorA and PorB, and the lower MW one is formed by only PorB. Complexes in the mutants lacking either PorA, PorB or RmpM, but not those in the mutant lacking FetA, were alterered respect to those in the wild-type strain. The most evident alteration was seen in the mutant lacking PorB, in which PorA formed only a high MW complex (approximately 800 kDa). Our results suggest that PorA and PorB could form a 'basic' template for the transportation systems in the OM of the meningococci. Other proteins (such as RmpM) could be transiently associated to the porin complexes, depending on the specific tranport needs at different stages of the meningococcal life cycle, resulting in a dynamic net of pores of variable composition.","corpus_id":-1,"score":2},{"doc_id":"19607954","title":"Characterisation and immune responses to meningococcal recombinant porin complexes incorporated into liposomes.","abstract":"We have analysed the structure of meningococcal outer membrane complexes and found that the main complexes are formed by different combinations of PorA and/or PorB molecules, associated to other proteins such as RmpM. In view of the growing knowledge of the importance of conformational epitopes in the immune responses to many pathogens, our aim in this study was to analyse the interactions of PorA and PorB by reconstitution of both recombinant porins into liposomes and determine the relevance of these interactions for the immune response. Recombinant PorA and PorB incorporated into liposomes associate forming complexes that are homomeric when only one of the porins is present, but heteromeric when both neisserial porins are present, mimicking those found previously in native outer membrane vesicles (OMVs). Association of PorA and PorB to form heterocomplexes modifies the immunogenicity of at least PorB, allowing the production of antibodies that recognise conformational epitopes, and produces new epitopes that react with a 50 kDa outer membrane protein not yet identified.","corpus_id":-1,"score":2},{"doc_id":"19851005","title":"Expression, purification and preliminary X-ray analysis of the Neisseria meningitidis outer membrane protein PorB.","abstract":"The Neisseria meningitidis outer membrane protein PorB was expressed in Escherichia coli and purified from inclusion bodies by denaturation in urea followed by refolding in buffered LDAO on a size-exclusion column. PorB has been crystallized in three different crystal forms: C222, R32 and P6(3). The C222 crystal form may contain either one or two PorB monomers in the asymmetric unit, while both the R32 and P6(3) crystal forms contained one PorB monomer in the asymmetric unit. Of the three, the P6(3) crystal form had the best diffraction quality, yielding data extending to 2.3 A resolution.","corpus_id":-1,"score":2},{"doc_id":"19851451","title":"Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis.","abstract":"The bacterial PorB porin, an ATP-binding beta-barrel protein of pathogenic Neisseria gonorrhoeae, triggers host cell apoptosis by an unknown mechanism. PorB is targeted to and imported by host cell mitochondria, causing the breakdown of the mitochondrial membrane potential (DeltaPsi(m)). Here, we show that PorB induces the condensation of the mitochondrial matrix and the loss of cristae structures, sensitizing cells to the induction of apoptosis via signaling pathways activated by BH3-only proteins. PorB is imported into mitochondria through the general translocase TOM but, unexpectedly, is not recognized by the SAM sorting machinery, usually required for the assembly of beta-barrel proteins in the mitochondrial outer membrane. PorB integrates into the mitochondrial inner membrane, leading to the breakdown of DeltaPsi(m). The PorB channel is regulated by nucleotides and an isogenic PorB mutant defective in ATP-binding failed to induce DeltaPsi(m) loss and apoptosis, demonstrating that dissipation of DeltaPsi(m) is a requirement for cell death caused by neisserial infection.","corpus_id":-1,"score":2},{"doc_id":"20028813","title":"Meningococcal porin PorB prevents cellular apoptosis in a toll-like receptor 2- and NF-kappaB-independent manner.","abstract":"Meningococcal porin PorB is an inhibitor of apoptosis induced via the intrinsic pathway in various cell types. This effect is attributed to prevention of mitochondrial depolarization and of subsequent release of proapoptotic mitochondrial factors. To determine whether apoptosis is globally inhibited by PorB, we compared the intrinsic and extrinsic pathways in HeLa cells. Interestingly, PorB does not prevent extrinsic apoptosis induced by tumor necrosis factor alpha plus cycloheximide, suggesting a unique mitochondrial pathway specificity. Several intracellular factors regulated by NF-kappaB, including members of the Bcl-2 family and of the inhibitor of apoptosis (IAP) family, play major roles in controlling apoptosis, and some of them are thought to contribute to the antiapoptotic effect of the gonococcal porin, PIB. However, most of the members of the Bcl-2 family and the IAP family are not induced by meningococcal PorB in HeLa cells, with the exception of Bfl-1/A1. Interestingly, PorB does not induce NF-kappaB activation in HeLa cells, likely due to a lack of Toll-like receptor 2 (TLR2) expression in these cells. Bfl-1/A1 expression is also regulated by CBF1, a nuclear component of the Notch signaling pathway, independent of NF-kappaB activation. Since HeLa cells are protected by PorB from intrinsic apoptosis events, regardless of TLR2 and NF-kappaB expression, the possibility of a contribution of alternative signaling pathways to this effect cannot be excluded. In this paper, we describe an initial dissection of the cascade of cellular events involved in the antiapoptotic effect of PorB in the absence of TLR2.","corpus_id":-1,"score":2},{"doc_id":"20351243","title":"Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.","abstract":"PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 A resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.","corpus_id":-1,"score":2},{"doc_id":"20937766","title":"Human airway epithelial cell responses to Neisseria lactamica and purified porin via Toll-like receptor 2-dependent signaling.","abstract":"The human airway epithelium is constantly exposed to microbial products from colonizing organisms. Regulation of Toll-like receptor (TLR) expression and specific interactions with bacterial ligands is thought to mitigate exacerbation of inflammatory processes induced by the commensal flora in these cells. The genus Neisseria comprises pathogenic and commensal organisms that colonize the human nasopharynx. Neisseria lactamica is not associated with disease, but N. meningitidis occasionally invades the host, causing meningococcal disease and septicemia. Upon colonization of the airway epithelium, specific host cell receptors interact with numerous Neisseria components, including the PorB porin, at the immediate bacterial-host cell interface. This major outer membrane protein is expressed by all Neisseria strains, regardless of pathogenicity, but its amino acid sequence varies among strains, particularly in the surface-exposed regions. The interaction of Neisseria PorB with TLR2 is essential for driving TLR2/TLR1-dependent cellular responses and is thought to occur via the porin's surface-exposed loop regions. Our studies show that N. lactamica PorB is a TLR2 ligand but its binding specificity for TLR2 is different from that of meningococcal PorB. Furthermore, N. lactamica PorB is a poor inducer of proinflammatory mediators and of TLR2 expression in human airway epithelial cells. These effects are reproduced by whole N. lactamica organisms. Since the responsiveness of human airway epithelial cells to colonizing bacteria is in part regulated via TLR2 expression and signaling, commensal organisms such as N. lactamica would benefit from expressing a product that induces low TLR2-dependent local inflammation, likely delaying or avoiding clearance by the host.","corpus_id":-1,"score":2},{"doc_id":"21354102","title":"Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study.","abstract":"Members of the gram-positive mycolata bacteria have unusual cell envelopes which help them to avoid the immune system and the effects of most antibiotics, whilst rendering them permeable to solutes of importance in industrial bioconversion. It is therefore of interest to understand the molecular mechanisms for this selective permeability. PorB is an unusual porin from the outer membrane (OM) of Corynebacterium glutamicum. It has been proposed as an atypical α-helical, symmetrical homo-pentameric architecture, with an unusual distribution of polar amino acids on its surface. The proposed structure is too short to traverse a typical phospholipid bilayer, in contrast with the β-barrel porins of Gram-negative bacteria. Nevertheless, it has been shown to form small anion-selective channels in membranes typical of Escherichia coli. To further understand its function, we have performed ~400 ns of all-atom and ~270 μs of coarse-grained simulations of PorB in a range of membrane mimetic and phospholipid milieus. Our results suggest that PorB can undergo spontaneous conformational rearrangements that allow it to adapt to its local lipid environment. We speculate that the increased flexibility of this α-helical porin in comparison with rigid β-barrels may be an adaptation for the heterogeneous mycolic OM, and explains its demonstrated ability to form measurable pores with phospholipid membranes.","corpus_id":-1,"score":2},{"doc_id":"21843471","title":"Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail.","abstract":"Presently, most simulations of ion channel function rely upon nonatomistic Brownian dynamics calculations, indirect interpretation of energy maps, or application of external electric fields. We present a computational method to directly simulate ion flux through membrane channels based on biologically realistic electrochemical gradients. In close analogy to single-channel electrophysiology, physiologically and experimentally relevant timescales are achieved. We apply our method to the bacterial channel PorB from pathogenic Neisseria meningitidis, which, during Neisserial infection, inserts into the mitochondrial membrane of target cells and elicits apoptosis by dissipating the membrane potential. We show that our method accurately predicts ion conductance and selectivity and elucidates ion conduction mechanisms in great detail. Handles for overcoming channel-related antibiotic resistance are identified.","corpus_id":-1,"score":2},{"doc_id":"22032638","title":"Targeting of Neisserial PorB to the mitochondrial outer membrane: an insight on the evolution of β-barrel protein assembly machines.","abstract":"Mitochondria originated from Gram-negative bacteria through endosymbiosis. In modern day mitochondria, the Sorting and Assembly Machinery (SAM) is responsible for eukaryotic β-barrel protein assembly in the mitochondrial outer membrane. The SAM is the functional equivalent of the β-barrel assembly machinery found in the outer membrane of Gram-negative bacteria. In this study we examined the import pathway of a pathogenic bacterial protein, PorB, which is targeted from pathogenic Neisseria to the host mitochondria. We have developed a new method for measurement of PorB assembly into mitochondria that relies on the mobility shift exhibited by bacterial β-barrel proteins once folded and separated under semi-native electrophoretic conditions. We show that PorB is targeted to the outer mitochondrial membrane with a dependence on the intermembrane space shuttling chaperones and the core component of the SAM, Sam50, which is a functional homologue of BamA that is required for PorB assembly in bacteria. The peripheral subunits of the SAM, Sam35 and Sam37, which are essential for eukaryotic β-barrel protein assembly but do not have distinguishable functional homologues in bacteria, are not required for PorB assembly in eukaryotes. This shows that PorB uses an evolutionary conserved 'bacterial like' mechanism to infiltrate the host mitochondrial outer membrane.","corpus_id":-1,"score":2},{"doc_id":"22825445","title":"The amino acid sequence of Neisseria lactamica PorB surface-exposed loops influences Toll-like receptor 2-dependent cell activation.","abstract":"Toll-like receptors (TLRs) play a major role in host mucosal and systemic defense mechanisms by recognizing a diverse array of conserved pathogen-associated molecular patterns (PAMPs). TLR2, with TLR1 and TLR6, recognizes structurally diverse bacterial products such as lipidated factors (lipoproteins and peptidoglycans) and nonlipidated proteins, i.e., bacterial porins. PorB is a pan-neisserial porin expressed regardless of organisms' pathogenicity. However, commensal Neisseria lactamica organisms and purified N. lactamica PorB (published elsewhere as Nlac PorB) induce TLR2-dependent proinflammatory responses of lower magnitude than N. meningitidis organisms and N. meningitidis PorB (published elsewhere as Nme PorB). Both PorB types bind to TLR2 in vitro but with different apparent specificities. The structural and molecular details of PorB-TLR2 interaction are only beginning to be unraveled and may be due to electrostatic attraction. PorB molecules have significant strain-specific sequence variability within surface-exposed regions (loops) putatively involved in TLR2 interaction. By constructing chimeric recombinant PorB loop mutants in which surface-exposed loop residues have been switched between N. lactamica PorB and N. meningitidis PorB, we identified residues in loop 5 and loop 7 that influence TLR2-dependent cell activation using HEK cells and BEAS-2B cells. These loops are not uniquely responsible for PorB interaction with TLR2, but NF-κB and MAP kinases signaling downstream of TLR2 recognition are likely influenced by a hypothetical \"TLR2-binding signature\" within the sequence of PorB surface-exposed loops. Consistent with the effect of purified PorB in vitro, a chimeric N. meningitidis strain expressing N. lactamica PorB induces lower levels of interleukin 8 (IL-8) secretion than wild-type N. meningitidis, suggesting a role for PorB in induction of host cell activation by whole bacteria.","corpus_id":-1,"score":2},{"doc_id":"23083768","title":"Voltage dependent closure of PorB class II porin from Neisseria meningitidis investigated using impedance spectroscopy in a tethered bilayer lipid membrane interface.","abstract":"Electrochemical impedance spectroscopy (EIS) was used to characterize voltage-dependent closure of PorB class II (PorBII) porin from Neisseria meningitidis incorporated in a tethered bilayer lipid membrane (tBLM). The tBLM's lower leaflet was fabricated by depositing a self assembled monolayer (SAM) of 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) on a gold electrode, and the upper leaflet was formed by depositing1,2-dioleoyl-sn-glycero-3-phoshocholine (DOPC) liposomes. At 0mV bias DC potential, incorporation of PorBII decreased the membrane resistance (R(m)) from 2.5 MΩc m(2) to 0.6 MΩ cm(2), giving a ΔR(m) of 1.9 MΩ cm(2) and a normalized ΔR(m) (ΔR(m) divided by the R(m) of the tBLM without PorBII) of 76%. When the bias DC potential was increased to 200 mV, the normalized ΔR(m) value decreased to 20%. The effect of applied voltage on ΔR(m) was completely reversible, suggesting voltage-dependent closure of PorBII. The voltage dependence of PorBII was further studied in a planar bilayer lipid membrane made from 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhytPC). Following a single insertion event, PorBII exhibited multiple conductance states, with reversible, voltage-dependent closure of PorBII porin occurring at high transmembrane potentials. The trimetric porin closed in three discrete steps, each step corresponding to closure of one conducting monomer unit. The most probable single channel conductance was 4.2 nS. The agreement between results obtained with the tBLM and pBLM platforms demonstrates the utility of EIS to screen channel proteins immobilized in tBLM for voltage-gated behavior.","corpus_id":-1,"score":2},{"doc_id":"23095086","title":"Structure and function of the PorB porin from disseminating Neisseria gonorrhoeae.","abstract":"The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and mediate a rapid bacterial invasion into host cells in a phosphate-sensitive manner. To gain insights into this structure-function relationship we analysed PorBIA by X-ray crystallography in the presence of phosphate and ATP. The structure of PorBIA in the complex solved at a resolution of 3.3 Å (1 Å=0.1 nm) displays a surplus of positive charges inside the channel. ATP ligand-binding in the channel is co-ordinated by the positively charged residues of the channel interior. These residues ligate the aromatic, sugar and pyrophosphate moieties of the ligand. Two phosphate ions were observed in the structure, one of which clamped by two arginine residues (Arg92 and Arg124) localized at the extraplasmic channel exit. A short β-bulge in β2-strand together with the long L3 loop narrow the barrel diameter significantly and further support substrate specificity through hydrogen bond interactions. Interestingly the structure also comprised a small peptide as a remnant of a periplasmic protein which physically links porin molecules to the peptidoglycan network. To test the importance of Arg92 on bacterial invasion the residue was mutated. In vivo assays of bacteria carrying a R92S mutation confirmed the importance of this residue for host-cell invasion. Furthermore systematic sequence and structure comparisons of PorBIA from Neisseriaceae indicated Arg92 to be unique in disseminating N. gonorrhoeae thereby possibly distinguishing invasion-promoting porins from other neisserial porins.","corpus_id":-1,"score":2},{"doc_id":"23259616","title":"High resolution clear native electrophoresis (hrCNE) allows a detailed analysis of the heterotrimeric structure of recombinant Neisseria meningitidis porins inserted into liposomes.","abstract":"Three recombinant proteins of Neisseria meningitidis, rPorB, rPorA, and rRmpM, were purified and incorporated into liposomes prepared by dialysis-extrusion. The protein complexes formed using different combinations of recombinant proteins were studied by high resolution clear native electrophoresis (hrCNE) and 2-D hrCNE/SDS-PAGE, analyzing the influence of the stoichiometry of the two porins in the formation of complexes and comparing them with native porin complexes present in OMVs from five different N. meningitidis strains. Insertion of the recombinant proteins into liposomes allowed a complete refolding of porin complexes, and the electrophoretic analyses showed that, when the three recombinant proteins are present, the pattern of porin complexes obtained is similar to that observed in native OMVs. We could show homocomplexes of each individual porin and PorA/PorB, RmpM/PorB, and PorA/PorB/RmpM heterocomplexes. Our results suggest that RmpM binds only to PorB, confirm the trimeric structure of N. meningitidis pores, and demonstrate that insertion into liposomes restores the native structure of porin complexes.","corpus_id":-1,"score":2},{"doc_id":"23305865","title":"Study of the stability of proteoliposomes as vehicles for vaccines against Neisseria meningitidis based on recombinant porin complexes.","abstract":"Although effective against epidemic serogroup B Neisseria meningitidis strains, vaccines based on outer membrane vesicles continue to present important limitations, and great efforts are currently being focused in the development of a variety of new vaccine candidates and in the reformulation of currently existing ones. In this work, three N. meningitidis proteins, the PorA and PorB porins and the RmpM protein, were cloned, purified and incorporated into liposomes to build defined systems. The ability of proteoliposomes to allow the refolding porin complexes, and their stability during storage at 4°C and after lyophilization in presence of two cryoprotection agents, glucose and trehalose, were evaluated. This approach allowed to mimic the porin complexes present in natural OMVs, reducing the content of hypervariable protein PorA. During storage at 4°C, our systems showed some changes in the morphology and aggregation after three months, while after lyophilization the systems maintained their properties during the whole nine months of storage checked, with glucose allowing the best preservation of the antigenic properties of the proteins in the proteoliposomes.","corpus_id":-1,"score":2},{"doc_id":"24244002","title":"Saturating mutagenesis of an essential gene: a majority of the Neisseria gonorrhoeae major outer membrane porin (PorB) is mutable.","abstract":"The major outer membrane porin (PorB) of Neisseria gonorrhoeae is an essential protein that mediates ion exchange between the organism and its environment and also plays multiple roles in human host pathogenesis. To facilitate structure-function studies of porin's multiple roles, we performed saturating mutagenesis at the porB locus and used deep sequencing to identify essential versus mutable residues. Random mutations in porB were generated in a plasmid vector, and mutant gene pools were transformed into N. gonorrhoeae to select for alleles that maintained bacterial viability. Deep sequencing of the input plasmid pools and the output N. gonorrhoeae genomic DNA pools identified mutations present in each, and the mutations in both pools were compared to determine which changes could be tolerated by the organism. We examined the mutability of 328 amino acids in the mature PorB protein and found that 308 of them were likely to be mutable and that 20 amino acids were likely to be nonmutable. A subset of these predictions was validated experimentally. This approach to identifying essential amino acids in a protein of interest introduces an additional application for next-generation sequencing technology and provides a template for future studies of both porin and other essential bacterial genes.","corpus_id":-1,"score":2},{"doc_id":"24361688","title":"Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition.","abstract":"Among all Neisseriae species, Neisseria meningitidis and Neisseria gonorrhoeae are the only human pathogens, causative agents of bacterial meningitis and gonorrhoea, respectively. PorB, a pan-Neisseriae trimeric porin that mediates diffusive transport of essential molecules across the bacterial outer membrane, is also known to activate host innate immunity via Toll-like receptor 2 (TLR2)-mediated signaling. The molecular mechanism of PorB binding to TLR2 is not known, but it has been hypothesized that electrostatic interactions contribute to ligand/receptor binding. Strain-specific sequence variability in the surface-exposed loops of PorB which are potentially implicated in TLR2 binding, may explain the difference in TLR2-mediated cell activation in vitro by PorB homologs from the commensal Neisseriae lactamica and the pathogen N. meningitidis. Here, we report a comparative structural analysis of PorB from N. meningitidis serogroup B strain 8765 (63% sequence homology with PorB from N. meningitidis serogroup W135) and a mutant in which amino acid substitutions in the extracellular loop 7 lead to significantly reduced TLR2-dependent activity in vitro. We observe that this mutation both alters the loop conformation and causes dramatic changes of electrostatic surface charge, both of which may affect TLR2 recognition and signaling.","corpus_id":-1,"score":2},{"doc_id":"25575589","title":"One-step purification and porin transport activity of the major outer membrane proteins P2 from Haemophilus influenzae, FomA from Fusobacterium nucleatum and PorB from Neisseria meningitidis.","abstract":"Bacterial porins are major outer membrane proteins that function as essential solute transporters between the bacteria and the extracellular environment. Structural features of porins are also recognized by eukaryotic cell receptors involved in innate and adaptive immunity. To better investigate the function of porins, proper refolding is necessary following purification from inclusion bodies [1, 2]. Using a single-step size exclusion chromatographic method, we have purified three major porins from pathogenic bacteria, the OmpP2 (P2) from Haemophilus influenzae, FomA from Fusobacterium nucleatum and PorB from Neisseria meningitidis, at high yield and report their unique solute transport activity with size exclusion limit. Furthermore, we have optimized their purification method and achieved improvement of their thermostability for facilitating functional and structural analyses.","corpus_id":-1,"score":2},{"doc_id":"26091047","title":"Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations.","abstract":"The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.","corpus_id":-1,"score":2},{"doc_id":"26562068","title":"Neisseria meningitidis lacking the major porins PorA and PorB are viable and modulate apoptosis and the oxidative burst of neutrophils.","abstract":"The bacterial pathogen Neisseria meningitidis expresses two major outer-membrane porins. PorA expression is subject to phase-variation (high frequency, random, on-off switching) and both PorA and PorB are antigenically variable between strains. PorA expression is variable and not correlated with meningococcal colonisation or invasive disease, whereas all naturally-occurring strains express PorB suggesting strong selection for expression. We have generated N. meningitidis strains lacking expression of both major porins, demonstrating that they are dispensable for bacterial growth in vitro. The porAB mutant strain has an exponential growth rate similar to the parental strain, as do the single porA or porB mutants, but the porAB mutant strain does not reach the same cell density in stationary phase. Proteomic analysis suggests that the double mutant strain exhibits compensatory expression changes in proteins associated with cellular redox state, energy/nutrient metabolism, and membrane stability. On solid media, there is obvious growth impairment that is rescued by addition of blood or serum from mammalian species, particularly heme. These porin mutants are not impaired in their capacity to inhibit both staurosporine-induced apoptosis and a phorbol 12-myristate 13-acetate -induced oxidative burst in human neutrophils suggesting that the porins are not the only bacterial factors that can modulate these processes in host cells.","corpus_id":-1,"score":2},{"doc_id":"27156582","title":"Typing and surface charges of the variable loop regions of PorB from Neisseria meningitidis.","abstract":"PorB is a pan-Neisserial major outer membrane protein with a trimeric β-barrel structure. Each monomer presents eight periplasmic turns and eight surface exposed loop regions with sequence variability. PorB induces activation of host cell responses via a TLR2-dependent mechanism likely mediated by electrostatic interactions between TLR2 and PorB surface exposed loops. Variability in the loop amino acid sequence is known to influence cell responses to PorB in vitro, particularly for the residues in L5 and L7. In this work, the sequence of the porB gene and the electrostatic surface charges of PorB from 35 invasive meningococcal isolates belonging to the main clonal complexes identified in Italy and from five carriage genomes available on the website http://pubmlst.org/neisseria/ were examined. Analysis of the porB encoding regions from the invasive meningococci has identified four new alleles and a potential association between porB alleles, serogroup, and clonal complexes. Through computer-based modeling and analysis of the electrostatic surface charges of PorB from these strains, loop charge segregation between PorB from invasive serogroups B and C was observed. Specifically, loops 1, 4, and 7 were negatively charged and L2 and L8 were mostly neutral in serogroup B isolates, while an overall homogeneous positive surface charge was present in PorB from invasive serogroup C strains. A higher PorB sequence variability was observed among carriage genomes, and a general prevalence of negative loop surface charges. The surface charge differences in PorB from serogroups B and C invasive and carriage strains may, in part, influence the outcomes of Neisseriae interactions with host cells. © 2016 IUBMB Life, 68(6):488-495, 2016.","corpus_id":-1,"score":2},{"doc_id":"27488811","title":"An epitope-imprinted piezoelectric diagnostic tool for Neisseria meningitidis detection.","abstract":"Neisseria meningitidis, a human-specific bacterial pathogen causes bacterial meningitis by invading the meninges (outer lining) of central nervous system. It is the polysaccharide present on the bacterial capsid that distinguishes various serogroups of N. meningitidis and can be utilized as antigens to elicit immune response. A computational approach identified candidate T-cell epitopes from outer membrane proteins Por B of N. meningitidis (MC58): ((273) KGLVDDADI(282) in loop VII and (170) GRHNSESYH(179) in loop IV) present on the exposed surface of immunogenic loops of class 3 outer membrane proteins allele of N. meningitidis. One of them, KGLVDDADI is used here for designing a diagnostic tool via molecularly imprinted piezoelectric sensor (molecularly imprinted polymer-quartz crystal microbalance) for N. meningitidis strain MC58. Methacrylic acid, ethylene glycol dimethacrylate and azoisobutyronitrile were used as functional monomer, cross-linker and initiator, respectively. The epitope can be simultaneously bound to methacrylic acid and fitted into the shape-selective cavities. On extraction of epitope sequence from thus grafted polymeric film, shape-selective and sensitive sites were generated on electrochemical quartz crystal microbalance crystal, ie, known as epitope imprinted polymers. Imprinting was characterized by atomic force microscopy images. The epitope-imprinted sensor was able to selectively bind N. meningitidis proteins present in blood serum of patients suffering from brain fever. Thus, fabricated sensor can be used as a diagnostic tool for meningitis disease.","corpus_id":-1,"score":2},{"doc_id":"27934398","title":"Energetic and Dynamic Analysis of Transport of Na(+) and K(+) through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers.","abstract":"Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na(+) and K(+) are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na(+) and K(+) reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na(+) and K(+) ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.","corpus_id":-1,"score":2},{"doc_id":"28708335","title":"Heterogeneity in non-epitope loop sequence and outer membrane protein complexes alters antibody binding to the major porin protein PorB in serogroup B Neisseria meningitidis.","abstract":"PorB is a well-characterized outer membrane protein that is common among Neisseria species and is required for survival. A vaccine candidate, PorB induces antibody responses that are directed against six variable surface-exposed loops that differ in sequence depending on serotype. Although Neisseria meningitidis is naturally competent and porB genetic mosaicism provides evidence for strong positive selection, the sequences of PorB serotypes commonly associated with invasive disease are often conserved, calling into question the interaction of specific PorB loop sequences in immune engagement. In this report, we provide evidence that antibody binding to a PorB epitope can be altered by sequence mutations in non-epitope loops. Through the construction of hybrid PorB types and PorB molecular dynamics simulations, we demonstrate that loops both adjacent and non-adjacent to the epitope loop can enhance or diminish antibody binding, a phenotype that correlates with serum bactericidal activity. We further examine the interaction of PorB with outer membrane-associated proteins, including PorA and RmpM. Deletion of these proteins alters the composition of PorB-containing native complexes and reduces antibody binding and serum killing relative to the parental strain, suggesting that both intramolecular and intermolecular PorB interactions contribute to host adaptive immune evasion.","corpus_id":-1,"score":2},{"doc_id":"29601598","title":"Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.","abstract":"Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhoea by evading innate immunity. Colonizing the mucosa of the reproductive tract depends on the bacterial outer membrane porin, PorB, which is essential for ion and nutrient uptake. PorB is also targeted to host mitochondria and regulates apoptosis pathways to promote infections. How PorB traffics from the outer membrane of N. gonorrhoeae to mitochondria and whether it modulates innate immune cells, such as macrophages, remains unclear. Here, we show that N. gonorrhoeae secretes PorB via outer membrane vesicles (OMVs). Purified OMVs contained primarily outer membrane proteins including oligomeric PorB. The porin was targeted to mitochondria of macrophages after exposure to purified OMVs and wild type N. gonorrhoeae. This was associated with loss of mitochondrial membrane potential, release of cytochrome c, activation of apoptotic caspases and cell death in a time-dependent manner. Consistent with this, OMV-induced macrophage death was prevented with the pan-caspase inhibitor, Q-VD-PH. This shows that N. gonorrhoeae utilizes OMVs to target PorB to mitochondria and to induce apoptosis in macrophages, thus affecting innate immunity.","corpus_id":-1,"score":2},{"doc_id":"19529772","title":"Towards the immunoproteome of Neisseria meningitidis.","abstract":"Despite the introduction of conjugated polysaccharide vaccines for many of the Neisseria meningitidis serogroups, neisserial infections continue to cause septicaemia and meningitis across the world. This is in part due to the difficulties in developing a, cross-protective vaccine that is effective against all serogroups, including serogroup B meningococci. Although convalescent N. meningitidis patients develop a natural long-lasting cross-protective immunity, the antigens that mediate this response remain unknown. To help define the target of this protective immunity we identified the proteins recognized by IgG in sera from meningococcal patients by a combination of 2D protein gels, western blots and mass spectrometry. Although a number of outer membrane antigens were identified the majority of the antigens were cytoplasmic, with roles in cellular processes and metabolism. When recombinant proteins were expressed and used to raise sera in mice, none of the antigens elicited a positive SBA result, however flow cytometry did demonstrate that some, including the ribosomal protein, RplY were localised to the neisserial cell surface.","corpus_id":2901003,"score":1},{"doc_id":"19932117","title":"Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.","abstract":"The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow \"constriction zone\". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets were obtained at 2.6 A and 3.0 A resolution with K(+) and Rb(+), respectively. The Rb(+)-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 A and cation positions were determined. A PEG molecule was observed in the pore region for both the K(+) and Rb(+)-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.","corpus_id":-1,"score":1},{"doc_id":"20441547","title":"Innate immune function of the neisserial porins and the relationship to vaccine adjuvant activity.","abstract":"Neisseria meningitidis is a Gram-negative pathogenic bacteria responsible for bacterial meningitis and septicemia. Porins are the most represented outer membrane proteins in the pathogenic Neisseria species, functioning as pores for the exchange of ions, and are characterized by a trimeric beta-barrel structure. Neisserial porins have been shown to act as adjuvants in the immune response via activation of B cells and other antigen-presenting cells. Their effect on the immune response is mediated by upregulation of the costimulatory molecule B7-2 (CD86) on the surface of antigen-presenting cells, an effect that is dependent on Toll-like receptor (TLR)2 and MyD88, through a cascade of signal transduction events mediated by direct binding of the porin to the TLR2-TLR1 heterodimer. This article summarizes work carried out investigating the mechanisms of the immune stimulating capacity of the neisserial porins (specifically meningococcal PorB), emphasizing cellular events involved in antigen-presenting cell activation and induction of expression of cell surface molecules involved in the immune response.","corpus_id":-1,"score":1},{"doc_id":"21281574","title":"Molecular dynamics studies of ion permeation in VDAC.","abstract":"The voltage-dependent anion channel (VDAC) in the outer membrane of mitochondria serves an essential role in the transport of metabolites and electrolytes between the cell matrix and mitochondria. To examine its structure, dynamics, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 μs molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 mV. The calculated conductance and ion selectivity are in good agreement with the experimental measurements. In addition, ion density distributions inside the channel reveal possible pathways for different ion species. Based on these observations, a mechanism underlying the anion selectivity is proposed; both ion species are transported across the channel, but the rate for K(+) is smaller than that for Cl(-) because of the attractive interactions between K(+) and residues on the channel wall. This difference leads to the anion selectivity of VDAC.","corpus_id":-1,"score":1},{"doc_id":"21296967","title":"Role of the periplasmic chaperones Skp, SurA, and DegQ in outer membrane protein biogenesis in Neisseria meningitidis.","abstract":"The periplasmic chaperones Skp, SurA, and DegP are implicated in the biogenesis of outer membrane proteins (OMPs) in Escherichia coli. Here, we investigated whether these chaperones exert similar functions in Neisseria meningitidis. Although N. meningitidis does not contain a homolog of the protease/chaperone DegP, it does possess a homolog of another E. coli protein, DegQ, which can functionally replace DegP when overproduced. Hence, we examined whether in N. meningitidis, DegQ acts as a functional homolog of DegP. Single skp, surA, and degQ mutants were easily obtained, showing that none of these chaperones is essential in N. meningitidis. Furthermore, all combinations of double mutants were generated and no synthetic lethality was observed. The absence of SurA or DegQ did not affect OMP biogenesis. In contrast, the absence of Skp resulted in severely lower levels of the porins PorA and PorB but not of other OMPs. These decreased levels were not due to proteolytic activity of DegQ, since porin levels remained low in a skp degQ double mutant, indicating that neisserial DegQ is not a functional homolog of E. coli DegP. The absence of Skp resulted in lower expression of the porB gene, as shown by using a P(porB)-lacZ fusion. We found no cross-species complementation when Skp of E. coli or N. meningitidis was heterologously expressed in skp mutants, indicating that Skp functions in a species-specific manner. Our results demonstrate an important role for Skp but not for SurA or DegQ in OMP biogenesis in N. meningitidis.","corpus_id":-1,"score":1},{"doc_id":"22298007","title":"Refolding, purification and crystallization of the FrpB outer membrane iron transporter from Neisseria meningitidis.","abstract":"FrpB is an integral outer membrane protein from the human pathogen Neisseria meningitidis. It is a member of the TonB-dependent transporter family and promotes the uptake of iron across the outer membrane. There is also evidence that FrpB is an antigen and hence a potential component of a vaccine against meningococcal meningitis. FrpB incorporating a polyhistidine tag was overexpressed in Escherichia coli into inclusion bodies. The protein was then solubilized in urea, refolded and purified to homogeneity. Two separate antigenic variants of FrpB were crystallized by sitting-drop vapour diffusion. Crystals of the F5-1 variant diffracted to 2.4 Å resolution and belonged to space group C2, with unit-cell parameters a = 176.5, b = 79.4, c = 75.9 Å, β = 98.3°. Crystal-packing calculations suggested the presence of a monomer in the asymmetric unit. Crystals of the F3-3 variant also diffracted to 2.4 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 85.3, b = 104.6, c = 269.1 Å. Preliminary analysis suggested the presence of an FrpB trimer in the asymmetric unit.","corpus_id":-1,"score":1},{"doc_id":"22509000","title":"Designing biomimetic pores based on carbon nanotubes.","abstract":"Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca(2+) ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels.","corpus_id":-1,"score":1},{"doc_id":"23457610","title":"Use of a molecular decoy to segregate transport from antigenicity in the FrpB iron transporter from Neisseria meningitidis.","abstract":"FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT) family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe(3+) with high affinity. EPR spectra of the bound Fe(3+) ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe(3+) binding was reduced or abolished on mutation of the Fe(3+)-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe(3+). The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a 'molecular decoy' to distract immune surveillance.","corpus_id":-1,"score":1},{"doc_id":"23542377","title":"Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.","abstract":"The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel's full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate.","corpus_id":-1,"score":1},{"doc_id":"23545639","title":"Structure of Neisseria meningitidis lipoprotein GNA1162.","abstract":"GNA1162, a predicted lipoprotein from Neisseria meningitidis, is a potential candidate for a universal vaccine against meningococcal disease caused by N. meningitidis serogroup B. Here, the crystal structure of GNA1162 at 1.89 Å resolution determined by single-wavelength anomalous dispersion (SAD) is reported. The structure of GNA1162 appears to be a dimer in the crystallographic asymmetric unit as well as in solution. The overall structure of the dimer indicates that each monomer inserts its C-terminal α5 helix into the hydrophobic groove of the other molecule. Moreover, the β4 strands of each monomer lie antiparallel to each other and interact through multiple main-chain hydrogen bonds. Through structural comparisons and operon predictions, it is hypothesized that GNA1162 is part of a transport system and assists in transport and reassembly. The crystal structure of GNA1162 sheds light on its possible function and provides potentially valuable information for the design of a vaccine against meningococcal disease.","corpus_id":-1,"score":1},{"doc_id":"23817612","title":"Identification of genes involved in Neisseria meningitidis colonization.","abstract":"Neisseria meningitidis is a worldwide cause of meningitis and septicemia leading at least to 50,000 deaths every year. Nevertheless, N. meningitidis is also a commensal bacterium that asymptomatically colonizes the epithelial cells of the nasopharynx of 10 to 30% of healthy individuals. Occasionally, N. meningitidis crosses the nasopharyngeal barrier and enters the bloodstream. During bacteremia, N. meningitidis may adhere to endothelial cells of brain vessels and invade meninges. To identify the genes required for meningococcal host colonization, we screened a signature-tagged transposon mutagenesis library using an innovative in vitro colonization model in order to identify mutants displaying decreased capacity to colonize human epithelial cells. Approximately 1,600 defined insertion mutants of invasive serogroup C strain NEM8013 were screened. Candidate mutants were tested individually for quantification of bacterial biomass with confocal microscope and COMSTAT software. Five mutants were demonstrated to exhibit significantly decreased colonization ability. The identified genes, including narP and estD, appeared to be involved in adaptation to hypoxic conditions and stress resistance. Interestingly, the genes fadD1, nnrS, and NMV_2034 (encoding a putative thioredoxin), prior to this study, had not been shown to be involved in colonization. Therefore, we provide here insights into the meningococcal functions necessary for the bacterium to adapt to growth on host cells.","corpus_id":-1,"score":1},{"doc_id":"24106986","title":"A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.","abstract":"OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.","corpus_id":-1,"score":1},{"doc_id":"24147565","title":"Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations.","abstract":"Using the X-ray structure of a recently discovered bacterial protein, the N-acetylneuraminic acid-inducible channel (NanC), we investigate computationally K(+) and Cl(-) ions' permeation. We identify ion permeation pathways that are likely to be populated using coarse-grain Monte Carlo simulations. Next, we use these pathways as reaction coordinates for umbrella sampling-based free energy simulations. We find distinct tubelike pathways connecting specific binding sites for K(+) and, more pronounced, for Cl(-) ions. Both ions permeate the porin preserving almost all of their first hydration shell. The calculated free energy barriers are G(#) ≈ 4 kJ/mol and G(#) ≈ 8 kJ/mol for Cl(-) and K(+), respectively. Within the approximations associated with these values, discussed in detail in this work, we suggest that the porin is slightly selective for Cl(-) versus K(+). Our suggestion is consistent with the experimentally observed weak Cl(-) over K(+) selectivity. A rationale for the latter is suggested by a comparison with previous calculations on strongly anion selective porins.","corpus_id":-1,"score":1},{"doc_id":"24161028","title":"Simulation of ion transport through an N-acetylneuraminic acid-inducible membrane channel: from understanding to engineering.","abstract":"N-acetylneuraminic acid-inducible channel (NanC) is an outer membrane channel of Escherichia coli . This porin folds as a 12-stranded β-barrel leading to a tubular shape. Electrophysiological experiments have revealed an asymmetric conductance with respect to the direction of the applied voltage and a weak anion selectivity of the channel. To this end, we performed all-atom molecular dynamics (MD) simulations to decipher the ion transport properties of the NanC channel. Concentration-dependent applied-field MD simulations recover the asymmetric conductance property and the anion selectivity of the channel in agreement with experiments. Further molecular analysis revealed the role of the asymmetric charge distribution inside the channel as the basis of the asymmetry in conductance. In addition, the particular distribution of charged residues at the inner channel walls leads to a faster permeation of Cl(-) ions compared to K(+) ions resulting in the anion selectivity of NanC. These findings are well supported by position-dependent diffusion coefficients and potential of mean force profiles derived from unbiased MD simulations. Taking one step further, we were able to engineer the NanC channel in silico by mutations leading to enhanced asymmetric conductances and anion selectivities. The E186Q mutant, for example, changes NanC into a decent molecular diode with an ionic current ratio of about 3:1 for opposite bias voltages.","corpus_id":-1,"score":1},{"doc_id":"24204275","title":"Zinc piracy as a mechanism of Neisseria meningitidis for evasion of nutritional immunity.","abstract":"The outer membrane of Gram-negative bacteria functions as a permeability barrier that protects these bacteria against harmful compounds in the environment. Most nutrients pass the outer membrane by passive diffusion via pore-forming proteins known as porins. However, diffusion can only satisfy the growth requirements if the extracellular concentration of the nutrients is high. In the vertebrate host, the sequestration of essential nutrient metals is an important defense mechanism that limits the growth of invading pathogens, a process known as \"nutritional immunity.\" The acquisition of scarce nutrients from the environment is mediated by receptors in the outer membrane in an energy-requiring process. Most characterized receptors are involved in the acquisition of iron. In this study, we characterized a hitherto unknown receptor from Neisseria meningitidis, a causative agent of sepsis and meningitis. Expression of this receptor, designated CbpA, is induced when the bacteria are grown under zinc limitation. We demonstrate that CbpA functions as a receptor for calprotectin, a protein that is massively produced by neutrophils and other cells and that has been shown to limit bacterial growth by chelating Zn²⁺ and Mn²⁺ ions. Expression of CbpA enables N. meningitidis to survive and propagate in the presence of calprotectin and to use calprotectin as a zinc source. Besides CbpA, also the TonB protein, which couples energy of the proton gradient across the inner membrane to receptor-mediated transport across the outer membrane, is required for the process. CbpA was found to be expressed in all N. meningitidis strains examined, consistent with a vital role for the protein when the bacteria reside in the host. Together, our results demonstrate that N. meningitidis is able to subvert an important defense mechanism of the human host and to utilize calprotectin to promote its growth.","corpus_id":-1,"score":1},{"doc_id":"25462170","title":"VCA1008: An Anion-Selective Porin of Vibrio Cholerae.","abstract":"A putative porin function has been assigned to VCA1008 of Vibrio cholerae. Its coding gene, vca1008, is expressed upon colonization of the small intestine in infant mice and human volunteers, and is essential for infection. In vitro, vca1008 is expressed under inorganic phosphate limitation and, in this condition, VCA1008 is the major outer membrane protein of the bacterium. Here, we provide the first functional characterization of VCA1008 reconstituted into planar lipid bilayers. Our main findings were: 1) VCA1008 forms an ion channel that, at high voltage (~±100 mV), presents a voltage-dependent activity and displays closures typical of trimeric porins, with a conductance of 4.28±0.04 nS (n=164) in 1M KCl; 2) It has a preferred selectivity for anions over cations; 3) Its conductance saturates with increasing inorganic phosphate concentration, suggesting VCA1008 contains binding site(s) for this anion; 4) Its ion selectivity is controlled by both fixed charged residues within the channel and diffusion along the pore; 5) Partitioning of poly (ethylene glycol)s (PEGs) of different molecular mass suggests that VCA1008 channel has a pore exclusion limit of 0.9 nm.","corpus_id":-1,"score":1},{"doc_id":"25860993","title":"Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.","abstract":"In the exchange of metabolites and ions between the mitochondrion and the cytosol, the voltage-dependent anion channel (VDAC) is a key element, as it forms the major transport pathway for these compounds through the mitochondrial outer membrane. Numerous experimental studies have promoted the idea that VDAC acts as a regulator of essential mitochondrial functions. In this study, using a combination of molecular dynamics simulations, free-energy calculations, and electrophysiological measurements, we investigated the transport of ions through VDAC, with a focus on phosphate ions and metabolites. We showed that selectivity of VDAC towards small anions including monovalent phosphates arises from short-lived interactions with positively charged residues scattered throughout the pore. In dramatic contrast, permeation of divalent phosphate ions and phosphate metabolites (AMP and ATP) involves binding sites along a specific translocation pathway. This permeation mechanism offers an explanation for the decrease in VDAC conductance measured in the presence of ATP or AMP at physiological salt concentration. The binding sites occur at similar locations for the divalent phosphate ions, AMP and ATP, and contain identical basic residues. ATP features a marked affinity for a central region of the pore lined by two lysines and one arginine of the N-terminal helix. This cluster of residues together with a few other basic amino acids forms a \"charged brush\" which facilitates the passage of the anionic metabolites through the pore. All of this reveals that VDAC controls the transport of the inorganic phosphates and phosphate metabolites studied here through two different mechanisms.","corpus_id":-1,"score":1},{"doc_id":"25955156","title":"Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level.","abstract":"Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane. They feature a constriction zone, contributed by the plunging of extracellular loop 3 (L3) into the channel lumen. Porins are generally in the open state, but undergo gating in response to external voltages. To date the underlying mechanism is unclear. Here we report results from molecular dynamics simulations on the two porins of Providenica stuartii, Omp-Pst1 and Omp-Pst2, which display distinct voltage sensitivities. Voltage gating was observed in Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 and Omp-Pst2 structures and trajectories suggests that their sensitivity to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall, as we observed that it is the strength of this network that governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel furthermore suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis.","corpus_id":-1,"score":1},{"doc_id":"26190347","title":"Neisseria meningitidis infection: who, when and where?","abstract":"Neisseria meningitidis is a Gram-negative β-proteobacterium responsible for an endemic worldwide infection. The epidemiology and serogroup distribution can change very quickly. The incidence of meningitis infection varies from very rare to more than 1000 cases per 100,000 of the population yearly. The carriage of N. meningitidis, which represents an exclusive human commensal, is asymptomatic, but in rare cases bacteria proliferate in the CNS and rapidly lead to the death of the affected subjects. Host genetic factors, such as single nucleotide polymorphisms, can promote meningococcal disease, being able to influence the individual predisposition to the pathology. Although a reduction in meningococcal disease has been observed in Europe, a continuous surveillance is necessary to control any possible outbreaks of new hypervirulent clones into populations that could modify the epidemiology of meningococcal infections and the clinical spectrum of affected subjects.","corpus_id":-1,"score":1},{"doc_id":"26651735","title":"Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane.","abstract":"We have applied a combined fluorescence microscopy and single-ion-channel electric current recording approach, correlating with molecular dynamics (MD) simulations, to study the mechanism of voltage-sensor domain translocation across a lipid bilayer. We use the colicin Ia ion channel as a model system, and our experimental and simulation results show the following: (1) The open-close activity of an activated colicin Ia is not necessarily sensitive to the amplitude of the applied cross-membrane voltage when the cross-membrane voltage is around the resting potential of excitable membranes; and (2) there is a significant probability that the activation of colicin Ia occurs by forming a transient and fluctuating water pore of ∼15 Å diameter in the lipid bilayer membrane. The location of the water-pore formation is nonrandom and highly specific, right at the insertion site of colicin Ia charged residues in the lipid bilayer membrane, and the formation is intrinsically associated with the polypeptide conformational fluctuations and solvation dynamics. Our results suggest an interesting mechanistic pathway for voltage-sensitive ion channel activation, and specifically for translocation of charged polypeptide chains across the lipid membrane under a transmembrane electric field: the charged polypeptide domain facilitates the formation of hydrophilic water pore in the membrane and diffuses through the hydrophilic pathway across the membrane; i.e., the charged polypeptide chain can cross a lipid membrane without entering into the hydrophobic core of the lipid membrane but entirely through the aqueous and hydrophilic environment to achieve a cross-membrane translocation. This mechanism sheds light on the intensive and fundamental debate on how a hydrophilic and charged peptide domain diffuses across the biologically inaccessible high-energy barrier of the hydrophobic core of a lipid bilayer: The peptide domain does not need to cross the hydrophobic core to move across a lipid bilayer.","corpus_id":32835839,"score":1},{"doc_id":"26826035","title":"The VDAC channel: Molecular basis for selectivity.","abstract":"The voltage dependent anion-selective channel, VDAC, is the major permeability pathway by which molecules and ion cross the mitochondrial outer membrane. This pathway has evolved to optimize the flow of these substances and to control this flow by a gating process that is influenced by a variety of factors including transmembrane voltage. The permeation pathway formed through the membrane by VDAC is complex. Small ion flow is primarily influenced by the charged surface of the inner walls of the channel. Channel closure changes this landscape resulting in a change from a channel that favors anions to one that favors cations. Molecular ions interact more intimately with the inner walls of the channel and are selected by their 3-dimensional structure, not merely by their size and charge. Molecular ions typically found in cells are greatly favored over those that are not. For these larger structures the channel may form a low-energy translocation path that complements the structure of the permeant. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.","corpus_id":-1,"score":1},{"doc_id":"26895142","title":"Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies.","abstract":"Porins are water-filled protein channels across the outer membrane of gram-negative bacteria. They facilitate the uptake of nutrients and essential ions. Solutes are filtered by a constriction loop L3 at the mid of a pore. Porins are heat-stable and resistant to toxic agents and detergents. Most porins are trimer, but no clear explanation why trimeric form is preferable. In this work, we thus studied effects of oligomerization on porin structure and function in microscopic detail. A well-studied OmpF (general porin from Escherichia coli) and well-characterised OprP (phosphate-specific pore from Pseudomonas aeruginosa) are used as samples from 2 types of porins found in gram-negative bacteria. MD simulations of trimeric and monomeric pores in pure water and 1M NaCl solution were performed. With a salt solution, the external electric field was applied to mimic a transmembrane potential. Expectedly, OprP is more stable than OmpF. Interestingly, being a monomer turns OmpF into an anion-selective pore. The dislocation of D113's side chain on L3 in OmpF causes the disruption of cation pathway resulting in the reduction of cation influx. In contrast, OprP's structure and function are less dependent on oligomeric states. Both monomeric and trimeric OprP can maintain their anion selectivity. Our findings suggest that trimerization is crucial for both structure and function of general porin OmpF, whereas being trimer in substrate-specific channel OprP supports a pore function.","corpus_id":-1,"score":1},{"doc_id":"26913282","title":"Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations.","abstract":"Sucrose-specific porin (ScrY) is a transmembrane protein that allows for the uptake of sucrose under growth-limiting conditions. The crystal structure of ScrY was resolved before by X-ray crystallography, both in its uncomplexed form and with bound sucrose. However, little is known about the molecular characteristics of the transport mechanism of ScrY. To date, there has not yet been any clear demonstration for sucrose transport through the ScrY. Here, the dynamics of the ScrY trimer embedded in a phospholipid bilayer as well as the characteristics of sucrose translocation were investigated by means of atomistic molecular dynamics (MD) simulations. The potential of mean force (PMF) for sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Energy decomposition allowed to pinpoint three aspartic acids as key residues opposing the passage of sucrose, all located within the L3 loop. Mutation of two aspartic acids to uncharged residues resulted in an accordingly modified electrostatics and decreased PMF barrier. The chosen methodology and results will aid in the design of porins with modified transport specificities.","corpus_id":-1,"score":1},{"doc_id":"27454890","title":"Transport and Catabolism of Carbohydrates by Neisseria meningitidis.","abstract":"We identified the genes encoding the proteins for the transport of glucose and maltose in Neisseria meningitidis strain 2C4-3. A mutant deleted for NMV_1892(glcP) no longer grew on glucose and deletion of NMV_0424(malY) prevented the utilization of maltose. We also purified and characterized glucokinase and α-phosphoglucomutase, which catalyze early catabolic steps of the two carbohydrates. N. meningitidis catabolizes the two carbohydrates either via the Entner-Doudoroff (ED) pathway or the pentose phosphate pathway, thereby forming glyceraldehyde-3-P and either pyruvate or fructose-6-P, respectively. We purified and characterized several key enzymes of the two pathways. The genes required for the transformation of glucose into gluconate-6-P and its further catabolism via the ED pathway are organized in two adjacent operons. N. meningitidis also contains genes encoding proteins which exhibit similarity to the gluconate transporter (NMV_2230) and gluconate kinase (NMV_2231) of Enterobacteriaceae and Firmicutes. However, gluconate might not be the real substrate of NMV_2230 because N. meningitidis was not able to grow on gluconate as the sole carbon source. Surprisingly, deletion of NMV_2230 stimulated growth in minimal medium in the presence and absence of glucose and drastically slowed the clearance of N. meningitidis cells from transgenic mice after intraperitoneal challenge.","corpus_id":-1,"score":1},{"doc_id":"18076035","title":"In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.","abstract":"OpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)-containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10-stranded beta-barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the beta-barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA.","corpus_id":-1,"score":0},{"doc_id":"19273554","title":"Functional comparison of the binding of factor H short consensus repeat 6 (SCR 6) to factor H binding protein from Neisseria meningitidis and the binding of factor H SCR 18 to 20 to Neisseria gonorrhoeae porin.","abstract":"Both Neisseria meningitidis and Neisseria gonorrhoeae recruit the alternative pathway complement inhibitory protein factor H (fH) to their surfaces to evade complement-dependent killing. Meningococci bind fH via fH binding protein (fHbp), a surface-exposed lipoprotein that is subdivided into three variant families based on one classification scheme. Chimeric proteins that comprise contiguous domains of fH fused to murine Fc were used to localize the binding site for all three fHbp variants on fH to short consensus repeat 6 (SCR 6). As expected, fH-like protein 1 (FHL-1), which contains fH SCR 6, also bound to fHbp-expressing meningococci. Using site-directed mutagenesis, we identified histidine 337 and histidine 371 in SCR 6 as important for binding to fHbp. These findings may provide the molecular basis for recent observations that demonstrated human-specific fH binding to meningococci. Differences in the interactions of fHbp variants with SCR 6 were evident. Gonococci bind fH via their porin (Por) molecules (PorB.1A or PorB.1B); sialylation of lipooligosaccharide enhances fH binding. Both sialylated PorB.1B- and (unsialylated) PorB.1A-bearing gonococci bind fH through SCR 18 to 20; PorB.1A can also bind SCR 6, but only weakly, as evidenced by a low level of binding of FHL-1 relative to that of fH. Using isogenic strains expressing either meningococcal fHbp or gonococcal PorB.1B, we discovered that strains expressing gonococcal PorB.1B in the presence of sialylated lipooligosaccharide bound more fH, more effectively limited C3 deposition, and were more serum resistant than their isogenic counterparts expressing fHbp. Differences in fH binding to these two related pathogens may be important for modulating their individual responses to host immune attack.","corpus_id":-1,"score":0},{"doc_id":"21476783","title":"Neisseria meningitidis endocarditis: a case report and review of the literature.","abstract":"Neisseria meningitidis is the leading cause of bacterial meningitis in children and young adults, with an overall mortality rate of up to 25%, but it is a rare cause of infective endocarditis. We present herein a case of N. meningitidis meningitis complicated with infective endocarditis.","corpus_id":-1,"score":0},{"doc_id":"22185907","title":"Vascular colonization by Neisseria meningitidis.","abstract":"Bacterial infection of human vasculature can lead to unregulated systemic activation of coagulation and innate immunity and rapidly becomes life threatening. Neisseria meningitidis is a vascular pathogen that causes fatal sepsis and meningitis. Post-mortem histological analysis of tissues from individuals infected with N. meningitidis show large bacterial aggregates in close association with the vascular wall of small vessels. The ability of this bacterium to colonize blood vessel endothelium is likely to impact its capacity to both multiply in the blood stream and reach the brain. This process will be referred to as vascular colonization. Recent work has described a number of early steps in N. meningitidis vascular colonization, from attachment to proliferation and dissemination, focusing on the bacterial-host interaction.","corpus_id":-1,"score":0},{"doc_id":"23875754","title":"Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation.","abstract":"The outer membrane porin OprP of Pseudomonas aeruginosa forms a highly specific phosphate selective channel. This channel is responsible for the high-affinity uptake of phosphate ions into the periplasmic space of the bacteria. A detailed investigation of the structure-function relationship of OprP is inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, in terms of its effects in selectivity and ion transport properties of the pore. Electrophysiological bilayer measurements and free-energy molecular dynamics simulations were carried out to probe the transport of different ions through various R133 mutants. For these mutants, the change in phosphate binding specificity, ion conduction, and anion selectivity was determined and compared to previous molecular dynamic calculations and electrophysiological measurements with wild-type OprP. Molecular analysis revealed a rather particular role of arginine 133 and its charge, while at the same time this residue together with the network of other residues, namely, D94 and Y114, has the ability to dehydrate the permeating ion. These very specific features govern the ion selectivity of OprP.","corpus_id":-1,"score":0},{"doc_id":"25191646","title":"Metabolism and virulence in Neisseria meningitidis.","abstract":"A longstanding question in infection biology addresses the genetic basis for invasive behavior in commensal pathogens. A prime example for such a pathogen is Neisseria meningitidis. On the one hand it is a harmless commensal bacterium exquisitely adapted to humans, and on the other hand it sometimes behaves like a ferocious pathogen causing potentially lethal disease such as sepsis and acute bacterial meningitis. Despite the lack of a classical repertoire of virulence genes in N. meningitidis separating commensal from invasive strains, molecular epidemiology suggests that carriage and invasive strains belong to genetically distinct populations. In recent years, it has become increasingly clear that metabolic adaptation enables meningococci to exploit host resources, supporting the concept of nutritional virulence as a crucial determinant of invasive capability. Here, we discuss the contribution of core metabolic pathways in the context of colonization and invasion with special emphasis on results from genome-wide surveys. The metabolism of lactate, the oxidative stress response, and, in particular, glutathione metabolism as well as the denitrification pathway provide examples of how meningococcal metabolism is intimately linked to pathogenesis. We further discuss evidence from genome-wide approaches regarding potential metabolic differences between strains from hyperinvasive and carriage lineages and present new data assessing in vitro growth differences of strains from these two populations. We hypothesize that strains from carriage and hyperinvasive lineages differ in the expression of regulatory genes involved particularly in stress responses and amino acid metabolism under infection conditions.","corpus_id":-1,"score":0}],"string":"[\n {\n \"doc_id\": \"18191311\",\n \"title\": \"The PorB porin from commensal Neisseria lactamica induces Th1 and Th2 immune responses to ovalbumin in mice and is a potential immune adjuvant.\",\n \"abstract\": \"Porins from pathogenic Neisseriae are among several bacterial products with immune adjuvant activity. Neisseria meningitidis (Nme) PorB, has been shown to induce immune cells activation in a TLR2-dependent manner and acts as a vaccine immune adjuvant. The PorB porin from Neisseria lactamica (Nlac), a common nasopharyngeal commensal, shares significant structural and functional similarities with Nme PorB. In this work we ask whether the immune adjuvant ability of porins from pathogenic Neisserial strains is a characteristic shared with porins from non-pathogenic Neisserial species or whether it is unique for bacterial products derived from microorganisms capable of inducing inflammation and disease. We evaluated the potential immune adjuvant effect of Nlac PorB in mice using ovalbumin (OVA) as a prototype antigen. Immunization with Nlac PorB/OVA induced high OVA-specific IgG and IgM titers compared to OVA alone, similar to other adjuvants such as Nme PorB and alum. High titers of IgG1 and IgG2b were detected as well as production of IL-4, IL-10, IL-12 and INF-gamma in response to Nlac PorB, consistent with induction of both a Th1-type and a Th2-type immune response. OVA-specific proliferation was also determined in splenocytes from Nlac PorB/OVA-immunized mice. In addition, B cell activation in vitro and cytokine production in response to Nlac PorB was found to be mediated by TLR2, in a similar manner to Nme PorB.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"18287580\",\n \"title\": \"Role of protein tyrosine kinase and Erk1/2 activities in the Toll-like receptor 2-induced cellular activation of murine B cells by neisserial porin.\",\n \"abstract\": \"Neisserial porins are potent immune adjuvants and have been demonstrated to stimulate and induce the activation of human and murine B lymphocytes. Their immunopotentiating ability is due largely to the upregulation of the surface expression of the costimulatory ligand CD86 (B7-2) on B cells and other antigen-presenting cells. Porin-induced activation is dependent on the innate immune pattern recognition receptor Toll-like receptor 2 (TLR2). These data have led us to investigate the signal transduction events induced by PorB from Neisseria meningitidis and then, using inhibitors of these pathways, to establish the mechanism by which this bacterial major outer membrane protein induces CD86 upregulation and the proliferation of murine B cells. PorB was able to induce (i) protein tyrosine kinase (PTK) activity, (ii) the phosphorylation of Erk1 and Erk2, and (iii) IkappaB-alpha phosphorylation, leading to NF-kappaB nuclear translocation in B cells in a TLR2-dependent manner. PorB-induced NF-kappaB nuclear translocation was not dependent on either PTK or Erk1/2 activities. However, B-cell proliferation and the induction of increased surface expression of CD86 by PorB were dependent on PTK activity and not Erk1/2 activation. In conclusion, PorB acts through TLR2 as a B-cell mitogen, triggering tyrosine phosphorylation of various cellular proteins that are involved in proliferation and CD86 expression, as well as the phosphorylation of Erk1/2, which is not necessary for CD86 upregulation or the proliferation of B cells.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"18451061\",\n \"title\": \"Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.\",\n \"abstract\": \"One potential vaccine strategy in the fight against meningococcal disease involves the exploitation of outer-membrane components of Neisseria lactamica, a commensal bacterium closely related to the meningococcus, Neisseria meningitidis. Although N. lactamica shares many surface structures with the meningococcus, little is known about the antigenic diversity of this commensal bacterium or the antigenic relationships between N. lactamica and N. meningitidis. Here, the N. lactamica porin protein (Por) was examined and compared to the related PorB antigens of N. meningitidis, to investigate potential involvement in anti-meningococcal immunity. Relationships among porin sequences were determined using distance-based methods and F(ST), and maximum-likelihood analyses were used to compare the selection pressures acting on the encoded proteins. These analyses demonstrated that the N. lactamica porin was less diverse than meningococcal PorB and although it was subject to positive selection, this was not as strong as the positive selection pressures acting on the meningococcal porin. In addition, the N. lactamica porin gene sequences and the protein sequences of the loop regions predicted to be exposed to the human immune system were dissimilar to the corresponding sequences in the meningococcus. This suggests that N. lactamica Por, contrary to previous suggestions, may have limited involvement in the development of natural immunity to meningococcal disease and might not be effective as a meningococcal vaccine component.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"18614668\",\n \"title\": \"Neisseria meningitidis PorB, a Toll-like receptor 2 ligand, improves the capacity of Francisella tularensis lipopolysaccharide to protect mice against experimental tularemia.\",\n \"abstract\": \"Francisella tularensis causes severe pneumonia that can be fatal if it is left untreated. Due to its potential use as a biological weapon, research is being conducted to develop an effective vaccine and to select and study adjuvant molecules able to generate a better and long-lasting protective effect. PorB, a porin from Neisseria meningitidis, is a well-established Toll-like receptor 2 ligand and has been shown to be a promising vaccine adjuvant candidate due to its ability to enhance the T-cell costimulatory activity of antigen-presenting cells both in vitro and in vivo. BALB/c mice were immunized with lipopolysaccharide (LPS) isolated from the F. tularensis subsp. holarctica live vaccine strain (LVS), with or without PorB from N. meningitidis, and the antibody levels induced during the vaccination regimen and the level of protection against intranasal challenge with LVS were determined. Antigen administered alone induced a specific F. tularensis LPS immunoglobulin M (IgM) response that was not maintained over the weeks and that conferred protection to only 25% of the mice. In contrast, F. tularensis LPS given in combination with neisserial PorB induced consistent levels of specific IgM throughout the immunization and increased the proportion of surviving mice to 70%. Postchallenge cytokine analysis showed that interleukin-6 (IL-6), monocyte chemoattractant protein 1, and gamma interferon were markers of mortality and that IL-1beta was a correlate of survival, independent of the presence of PorB as an adjuvant. These data indicate that neisserial PorB might be an optimal candidate adjuvant for improving the protective effect of F. tularensis LPS and other subunit vaccines against tularemia, but there is still a need to test its efficacy against virulent type A and type B F. tularensis strains.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"18722761\",\n \"title\": \"Functional characterization of PorB class II porin from Neisseria meningitidis using a tethered bilayer lipid membrane.\",\n \"abstract\": \"PorB class II from Neisseria meningitidis is a pore-forming, outer-membrane protein that can translocate to the host-cell membrane during Neisserial infections. This report describes development of tethered bilayer lipid membrane (tBLM) system to measure PorB conductance properties. The tBLM was fabricated by depositing a self-assembled monolayer of 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) tethering lipid on a gold electrode and then using 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes to deposit the upper tBLM leaflet. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were used to monitor tBLM formation and subsequent PorB incorporation. The highly insulating tBLM exhibited a membrane resistance and capacitance of 2.5MOmegacm(2) and 0.7 microF/cm(2), respectively. PorB was incorporated into the tBLM in an active conformation, as evidenced by its mediation of ion passage and the decrease in membrane impedance. After PorB incorporation, the membrane resistance decreased to 0.6MOmegacm(2). As expected, the PorB channel was found to be non-selective, allowing the transport of both cations and anions. Cyclic voltammetry indicated that ferricyanide ions can also pass through the pores. The PorB-containing biomimetic interface developed in this study could potentially be used to screen for compounds that modulate PorB activity.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19137557\",\n \"title\": \"Analysis of outer membrane porin complexes of Neisseria meningitidis in wild-type and specific knock-out mutant strains.\",\n \"abstract\": \"The structure of the porin complexes of Neisseria meningitidis was assessed in the vaccine strain H44/76 and its homologous mutants lacking the main porins (PorA and PorB) and other outer membrane (OM) components (RmpM and FetA). The analysis using 1-D blue native (BN) electrophoresis, 2-D BN/SDS-PAGE and 2-D diagonal electrophoresis, followed by LC/MS-MS (for 1-D gels) or MALDI-TOF (for 2-D gels) revealed at least six porin complexes in the wild-type strain with molecular masses (MW) ranging from 145 to 195 kDa and variable composition: The two higher MW complexes are formed by PorA, PorB and RmpM, the following three are formed by PorA and PorB, and the lower MW one is formed by only PorB. Complexes in the mutants lacking either PorA, PorB or RmpM, but not those in the mutant lacking FetA, were alterered respect to those in the wild-type strain. The most evident alteration was seen in the mutant lacking PorB, in which PorA formed only a high MW complex (approximately 800 kDa). Our results suggest that PorA and PorB could form a 'basic' template for the transportation systems in the OM of the meningococci. Other proteins (such as RmpM) could be transiently associated to the porin complexes, depending on the specific tranport needs at different stages of the meningococcal life cycle, resulting in a dynamic net of pores of variable composition.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19607954\",\n \"title\": \"Characterisation and immune responses to meningococcal recombinant porin complexes incorporated into liposomes.\",\n \"abstract\": \"We have analysed the structure of meningococcal outer membrane complexes and found that the main complexes are formed by different combinations of PorA and/or PorB molecules, associated to other proteins such as RmpM. In view of the growing knowledge of the importance of conformational epitopes in the immune responses to many pathogens, our aim in this study was to analyse the interactions of PorA and PorB by reconstitution of both recombinant porins into liposomes and determine the relevance of these interactions for the immune response. Recombinant PorA and PorB incorporated into liposomes associate forming complexes that are homomeric when only one of the porins is present, but heteromeric when both neisserial porins are present, mimicking those found previously in native outer membrane vesicles (OMVs). Association of PorA and PorB to form heterocomplexes modifies the immunogenicity of at least PorB, allowing the production of antibodies that recognise conformational epitopes, and produces new epitopes that react with a 50 kDa outer membrane protein not yet identified.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19851005\",\n \"title\": \"Expression, purification and preliminary X-ray analysis of the Neisseria meningitidis outer membrane protein PorB.\",\n \"abstract\": \"The Neisseria meningitidis outer membrane protein PorB was expressed in Escherichia coli and purified from inclusion bodies by denaturation in urea followed by refolding in buffered LDAO on a size-exclusion column. PorB has been crystallized in three different crystal forms: C222, R32 and P6(3). The C222 crystal form may contain either one or two PorB monomers in the asymmetric unit, while both the R32 and P6(3) crystal forms contained one PorB monomer in the asymmetric unit. Of the three, the P6(3) crystal form had the best diffraction quality, yielding data extending to 2.3 A resolution.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19851451\",\n \"title\": \"Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis.\",\n \"abstract\": \"The bacterial PorB porin, an ATP-binding beta-barrel protein of pathogenic Neisseria gonorrhoeae, triggers host cell apoptosis by an unknown mechanism. PorB is targeted to and imported by host cell mitochondria, causing the breakdown of the mitochondrial membrane potential (DeltaPsi(m)). Here, we show that PorB induces the condensation of the mitochondrial matrix and the loss of cristae structures, sensitizing cells to the induction of apoptosis via signaling pathways activated by BH3-only proteins. PorB is imported into mitochondria through the general translocase TOM but, unexpectedly, is not recognized by the SAM sorting machinery, usually required for the assembly of beta-barrel proteins in the mitochondrial outer membrane. PorB integrates into the mitochondrial inner membrane, leading to the breakdown of DeltaPsi(m). The PorB channel is regulated by nucleotides and an isogenic PorB mutant defective in ATP-binding failed to induce DeltaPsi(m) loss and apoptosis, demonstrating that dissipation of DeltaPsi(m) is a requirement for cell death caused by neisserial infection.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"20028813\",\n \"title\": \"Meningococcal porin PorB prevents cellular apoptosis in a toll-like receptor 2- and NF-kappaB-independent manner.\",\n \"abstract\": \"Meningococcal porin PorB is an inhibitor of apoptosis induced via the intrinsic pathway in various cell types. This effect is attributed to prevention of mitochondrial depolarization and of subsequent release of proapoptotic mitochondrial factors. To determine whether apoptosis is globally inhibited by PorB, we compared the intrinsic and extrinsic pathways in HeLa cells. Interestingly, PorB does not prevent extrinsic apoptosis induced by tumor necrosis factor alpha plus cycloheximide, suggesting a unique mitochondrial pathway specificity. Several intracellular factors regulated by NF-kappaB, including members of the Bcl-2 family and of the inhibitor of apoptosis (IAP) family, play major roles in controlling apoptosis, and some of them are thought to contribute to the antiapoptotic effect of the gonococcal porin, PIB. However, most of the members of the Bcl-2 family and the IAP family are not induced by meningococcal PorB in HeLa cells, with the exception of Bfl-1/A1. Interestingly, PorB does not induce NF-kappaB activation in HeLa cells, likely due to a lack of Toll-like receptor 2 (TLR2) expression in these cells. Bfl-1/A1 expression is also regulated by CBF1, a nuclear component of the Notch signaling pathway, independent of NF-kappaB activation. Since HeLa cells are protected by PorB from intrinsic apoptosis events, regardless of TLR2 and NF-kappaB expression, the possibility of a contribution of alternative signaling pathways to this effect cannot be excluded. In this paper, we describe an initial dissection of the cascade of cellular events involved in the antiapoptotic effect of PorB in the absence of TLR2.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"20351243\",\n \"title\": \"Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.\",\n \"abstract\": \"PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 A resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"20937766\",\n \"title\": \"Human airway epithelial cell responses to Neisseria lactamica and purified porin via Toll-like receptor 2-dependent signaling.\",\n \"abstract\": \"The human airway epithelium is constantly exposed to microbial products from colonizing organisms. Regulation of Toll-like receptor (TLR) expression and specific interactions with bacterial ligands is thought to mitigate exacerbation of inflammatory processes induced by the commensal flora in these cells. The genus Neisseria comprises pathogenic and commensal organisms that colonize the human nasopharynx. Neisseria lactamica is not associated with disease, but N. meningitidis occasionally invades the host, causing meningococcal disease and septicemia. Upon colonization of the airway epithelium, specific host cell receptors interact with numerous Neisseria components, including the PorB porin, at the immediate bacterial-host cell interface. This major outer membrane protein is expressed by all Neisseria strains, regardless of pathogenicity, but its amino acid sequence varies among strains, particularly in the surface-exposed regions. The interaction of Neisseria PorB with TLR2 is essential for driving TLR2/TLR1-dependent cellular responses and is thought to occur via the porin's surface-exposed loop regions. Our studies show that N. lactamica PorB is a TLR2 ligand but its binding specificity for TLR2 is different from that of meningococcal PorB. Furthermore, N. lactamica PorB is a poor inducer of proinflammatory mediators and of TLR2 expression in human airway epithelial cells. These effects are reproduced by whole N. lactamica organisms. Since the responsiveness of human airway epithelial cells to colonizing bacteria is in part regulated via TLR2 expression and signaling, commensal organisms such as N. lactamica would benefit from expressing a product that induces low TLR2-dependent local inflammation, likely delaying or avoiding clearance by the host.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"21354102\",\n \"title\": \"Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study.\",\n \"abstract\": \"Members of the gram-positive mycolata bacteria have unusual cell envelopes which help them to avoid the immune system and the effects of most antibiotics, whilst rendering them permeable to solutes of importance in industrial bioconversion. It is therefore of interest to understand the molecular mechanisms for this selective permeability. PorB is an unusual porin from the outer membrane (OM) of Corynebacterium glutamicum. It has been proposed as an atypical α-helical, symmetrical homo-pentameric architecture, with an unusual distribution of polar amino acids on its surface. The proposed structure is too short to traverse a typical phospholipid bilayer, in contrast with the β-barrel porins of Gram-negative bacteria. Nevertheless, it has been shown to form small anion-selective channels in membranes typical of Escherichia coli. To further understand its function, we have performed ~400 ns of all-atom and ~270 μs of coarse-grained simulations of PorB in a range of membrane mimetic and phospholipid milieus. Our results suggest that PorB can undergo spontaneous conformational rearrangements that allow it to adapt to its local lipid environment. We speculate that the increased flexibility of this α-helical porin in comparison with rigid β-barrels may be an adaptation for the heterogeneous mycolic OM, and explains its demonstrated ability to form measurable pores with phospholipid membranes.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"21843471\",\n \"title\": \"Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail.\",\n \"abstract\": \"Presently, most simulations of ion channel function rely upon nonatomistic Brownian dynamics calculations, indirect interpretation of energy maps, or application of external electric fields. We present a computational method to directly simulate ion flux through membrane channels based on biologically realistic electrochemical gradients. In close analogy to single-channel electrophysiology, physiologically and experimentally relevant timescales are achieved. We apply our method to the bacterial channel PorB from pathogenic Neisseria meningitidis, which, during Neisserial infection, inserts into the mitochondrial membrane of target cells and elicits apoptosis by dissipating the membrane potential. We show that our method accurately predicts ion conductance and selectivity and elucidates ion conduction mechanisms in great detail. Handles for overcoming channel-related antibiotic resistance are identified.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"22032638\",\n \"title\": \"Targeting of Neisserial PorB to the mitochondrial outer membrane: an insight on the evolution of β-barrel protein assembly machines.\",\n \"abstract\": \"Mitochondria originated from Gram-negative bacteria through endosymbiosis. In modern day mitochondria, the Sorting and Assembly Machinery (SAM) is responsible for eukaryotic β-barrel protein assembly in the mitochondrial outer membrane. The SAM is the functional equivalent of the β-barrel assembly machinery found in the outer membrane of Gram-negative bacteria. In this study we examined the import pathway of a pathogenic bacterial protein, PorB, which is targeted from pathogenic Neisseria to the host mitochondria. We have developed a new method for measurement of PorB assembly into mitochondria that relies on the mobility shift exhibited by bacterial β-barrel proteins once folded and separated under semi-native electrophoretic conditions. We show that PorB is targeted to the outer mitochondrial membrane with a dependence on the intermembrane space shuttling chaperones and the core component of the SAM, Sam50, which is a functional homologue of BamA that is required for PorB assembly in bacteria. The peripheral subunits of the SAM, Sam35 and Sam37, which are essential for eukaryotic β-barrel protein assembly but do not have distinguishable functional homologues in bacteria, are not required for PorB assembly in eukaryotes. This shows that PorB uses an evolutionary conserved 'bacterial like' mechanism to infiltrate the host mitochondrial outer membrane.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"22825445\",\n \"title\": \"The amino acid sequence of Neisseria lactamica PorB surface-exposed loops influences Toll-like receptor 2-dependent cell activation.\",\n \"abstract\": \"Toll-like receptors (TLRs) play a major role in host mucosal and systemic defense mechanisms by recognizing a diverse array of conserved pathogen-associated molecular patterns (PAMPs). TLR2, with TLR1 and TLR6, recognizes structurally diverse bacterial products such as lipidated factors (lipoproteins and peptidoglycans) and nonlipidated proteins, i.e., bacterial porins. PorB is a pan-neisserial porin expressed regardless of organisms' pathogenicity. However, commensal Neisseria lactamica organisms and purified N. lactamica PorB (published elsewhere as Nlac PorB) induce TLR2-dependent proinflammatory responses of lower magnitude than N. meningitidis organisms and N. meningitidis PorB (published elsewhere as Nme PorB). Both PorB types bind to TLR2 in vitro but with different apparent specificities. The structural and molecular details of PorB-TLR2 interaction are only beginning to be unraveled and may be due to electrostatic attraction. PorB molecules have significant strain-specific sequence variability within surface-exposed regions (loops) putatively involved in TLR2 interaction. By constructing chimeric recombinant PorB loop mutants in which surface-exposed loop residues have been switched between N. lactamica PorB and N. meningitidis PorB, we identified residues in loop 5 and loop 7 that influence TLR2-dependent cell activation using HEK cells and BEAS-2B cells. These loops are not uniquely responsible for PorB interaction with TLR2, but NF-κB and MAP kinases signaling downstream of TLR2 recognition are likely influenced by a hypothetical \\\"TLR2-binding signature\\\" within the sequence of PorB surface-exposed loops. Consistent with the effect of purified PorB in vitro, a chimeric N. meningitidis strain expressing N. lactamica PorB induces lower levels of interleukin 8 (IL-8) secretion than wild-type N. meningitidis, suggesting a role for PorB in induction of host cell activation by whole bacteria.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23083768\",\n \"title\": \"Voltage dependent closure of PorB class II porin from Neisseria meningitidis investigated using impedance spectroscopy in a tethered bilayer lipid membrane interface.\",\n \"abstract\": \"Electrochemical impedance spectroscopy (EIS) was used to characterize voltage-dependent closure of PorB class II (PorBII) porin from Neisseria meningitidis incorporated in a tethered bilayer lipid membrane (tBLM). The tBLM's lower leaflet was fabricated by depositing a self assembled monolayer (SAM) of 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) on a gold electrode, and the upper leaflet was formed by depositing1,2-dioleoyl-sn-glycero-3-phoshocholine (DOPC) liposomes. At 0mV bias DC potential, incorporation of PorBII decreased the membrane resistance (R(m)) from 2.5 MΩc m(2) to 0.6 MΩ cm(2), giving a ΔR(m) of 1.9 MΩ cm(2) and a normalized ΔR(m) (ΔR(m) divided by the R(m) of the tBLM without PorBII) of 76%. When the bias DC potential was increased to 200 mV, the normalized ΔR(m) value decreased to 20%. The effect of applied voltage on ΔR(m) was completely reversible, suggesting voltage-dependent closure of PorBII. The voltage dependence of PorBII was further studied in a planar bilayer lipid membrane made from 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhytPC). Following a single insertion event, PorBII exhibited multiple conductance states, with reversible, voltage-dependent closure of PorBII porin occurring at high transmembrane potentials. The trimetric porin closed in three discrete steps, each step corresponding to closure of one conducting monomer unit. The most probable single channel conductance was 4.2 nS. The agreement between results obtained with the tBLM and pBLM platforms demonstrates the utility of EIS to screen channel proteins immobilized in tBLM for voltage-gated behavior.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23095086\",\n \"title\": \"Structure and function of the PorB porin from disseminating Neisseria gonorrhoeae.\",\n \"abstract\": \"The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and mediate a rapid bacterial invasion into host cells in a phosphate-sensitive manner. To gain insights into this structure-function relationship we analysed PorBIA by X-ray crystallography in the presence of phosphate and ATP. The structure of PorBIA in the complex solved at a resolution of 3.3 Å (1 Å=0.1 nm) displays a surplus of positive charges inside the channel. ATP ligand-binding in the channel is co-ordinated by the positively charged residues of the channel interior. These residues ligate the aromatic, sugar and pyrophosphate moieties of the ligand. Two phosphate ions were observed in the structure, one of which clamped by two arginine residues (Arg92 and Arg124) localized at the extraplasmic channel exit. A short β-bulge in β2-strand together with the long L3 loop narrow the barrel diameter significantly and further support substrate specificity through hydrogen bond interactions. Interestingly the structure also comprised a small peptide as a remnant of a periplasmic protein which physically links porin molecules to the peptidoglycan network. To test the importance of Arg92 on bacterial invasion the residue was mutated. In vivo assays of bacteria carrying a R92S mutation confirmed the importance of this residue for host-cell invasion. Furthermore systematic sequence and structure comparisons of PorBIA from Neisseriaceae indicated Arg92 to be unique in disseminating N. gonorrhoeae thereby possibly distinguishing invasion-promoting porins from other neisserial porins.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23259616\",\n \"title\": \"High resolution clear native electrophoresis (hrCNE) allows a detailed analysis of the heterotrimeric structure of recombinant Neisseria meningitidis porins inserted into liposomes.\",\n \"abstract\": \"Three recombinant proteins of Neisseria meningitidis, rPorB, rPorA, and rRmpM, were purified and incorporated into liposomes prepared by dialysis-extrusion. The protein complexes formed using different combinations of recombinant proteins were studied by high resolution clear native electrophoresis (hrCNE) and 2-D hrCNE/SDS-PAGE, analyzing the influence of the stoichiometry of the two porins in the formation of complexes and comparing them with native porin complexes present in OMVs from five different N. meningitidis strains. Insertion of the recombinant proteins into liposomes allowed a complete refolding of porin complexes, and the electrophoretic analyses showed that, when the three recombinant proteins are present, the pattern of porin complexes obtained is similar to that observed in native OMVs. We could show homocomplexes of each individual porin and PorA/PorB, RmpM/PorB, and PorA/PorB/RmpM heterocomplexes. Our results suggest that RmpM binds only to PorB, confirm the trimeric structure of N. meningitidis pores, and demonstrate that insertion into liposomes restores the native structure of porin complexes.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23305865\",\n \"title\": \"Study of the stability of proteoliposomes as vehicles for vaccines against Neisseria meningitidis based on recombinant porin complexes.\",\n \"abstract\": \"Although effective against epidemic serogroup B Neisseria meningitidis strains, vaccines based on outer membrane vesicles continue to present important limitations, and great efforts are currently being focused in the development of a variety of new vaccine candidates and in the reformulation of currently existing ones. In this work, three N. meningitidis proteins, the PorA and PorB porins and the RmpM protein, were cloned, purified and incorporated into liposomes to build defined systems. The ability of proteoliposomes to allow the refolding porin complexes, and their stability during storage at 4°C and after lyophilization in presence of two cryoprotection agents, glucose and trehalose, were evaluated. This approach allowed to mimic the porin complexes present in natural OMVs, reducing the content of hypervariable protein PorA. During storage at 4°C, our systems showed some changes in the morphology and aggregation after three months, while after lyophilization the systems maintained their properties during the whole nine months of storage checked, with glucose allowing the best preservation of the antigenic properties of the proteins in the proteoliposomes.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"24244002\",\n \"title\": \"Saturating mutagenesis of an essential gene: a majority of the Neisseria gonorrhoeae major outer membrane porin (PorB) is mutable.\",\n \"abstract\": \"The major outer membrane porin (PorB) of Neisseria gonorrhoeae is an essential protein that mediates ion exchange between the organism and its environment and also plays multiple roles in human host pathogenesis. To facilitate structure-function studies of porin's multiple roles, we performed saturating mutagenesis at the porB locus and used deep sequencing to identify essential versus mutable residues. Random mutations in porB were generated in a plasmid vector, and mutant gene pools were transformed into N. gonorrhoeae to select for alleles that maintained bacterial viability. Deep sequencing of the input plasmid pools and the output N. gonorrhoeae genomic DNA pools identified mutations present in each, and the mutations in both pools were compared to determine which changes could be tolerated by the organism. We examined the mutability of 328 amino acids in the mature PorB protein and found that 308 of them were likely to be mutable and that 20 amino acids were likely to be nonmutable. A subset of these predictions was validated experimentally. This approach to identifying essential amino acids in a protein of interest introduces an additional application for next-generation sequencing technology and provides a template for future studies of both porin and other essential bacterial genes.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"24361688\",\n \"title\": \"Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition.\",\n \"abstract\": \"Among all Neisseriae species, Neisseria meningitidis and Neisseria gonorrhoeae are the only human pathogens, causative agents of bacterial meningitis and gonorrhoea, respectively. PorB, a pan-Neisseriae trimeric porin that mediates diffusive transport of essential molecules across the bacterial outer membrane, is also known to activate host innate immunity via Toll-like receptor 2 (TLR2)-mediated signaling. The molecular mechanism of PorB binding to TLR2 is not known, but it has been hypothesized that electrostatic interactions contribute to ligand/receptor binding. Strain-specific sequence variability in the surface-exposed loops of PorB which are potentially implicated in TLR2 binding, may explain the difference in TLR2-mediated cell activation in vitro by PorB homologs from the commensal Neisseriae lactamica and the pathogen N. meningitidis. Here, we report a comparative structural analysis of PorB from N. meningitidis serogroup B strain 8765 (63% sequence homology with PorB from N. meningitidis serogroup W135) and a mutant in which amino acid substitutions in the extracellular loop 7 lead to significantly reduced TLR2-dependent activity in vitro. We observe that this mutation both alters the loop conformation and causes dramatic changes of electrostatic surface charge, both of which may affect TLR2 recognition and signaling.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"25575589\",\n \"title\": \"One-step purification and porin transport activity of the major outer membrane proteins P2 from Haemophilus influenzae, FomA from Fusobacterium nucleatum and PorB from Neisseria meningitidis.\",\n \"abstract\": \"Bacterial porins are major outer membrane proteins that function as essential solute transporters between the bacteria and the extracellular environment. Structural features of porins are also recognized by eukaryotic cell receptors involved in innate and adaptive immunity. To better investigate the function of porins, proper refolding is necessary following purification from inclusion bodies [1, 2]. Using a single-step size exclusion chromatographic method, we have purified three major porins from pathogenic bacteria, the OmpP2 (P2) from Haemophilus influenzae, FomA from Fusobacterium nucleatum and PorB from Neisseria meningitidis, at high yield and report their unique solute transport activity with size exclusion limit. Furthermore, we have optimized their purification method and achieved improvement of their thermostability for facilitating functional and structural analyses.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"26091047\",\n \"title\": \"Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations.\",\n \"abstract\": \"The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"26562068\",\n \"title\": \"Neisseria meningitidis lacking the major porins PorA and PorB are viable and modulate apoptosis and the oxidative burst of neutrophils.\",\n \"abstract\": \"The bacterial pathogen Neisseria meningitidis expresses two major outer-membrane porins. PorA expression is subject to phase-variation (high frequency, random, on-off switching) and both PorA and PorB are antigenically variable between strains. PorA expression is variable and not correlated with meningococcal colonisation or invasive disease, whereas all naturally-occurring strains express PorB suggesting strong selection for expression. We have generated N. meningitidis strains lacking expression of both major porins, demonstrating that they are dispensable for bacterial growth in vitro. The porAB mutant strain has an exponential growth rate similar to the parental strain, as do the single porA or porB mutants, but the porAB mutant strain does not reach the same cell density in stationary phase. Proteomic analysis suggests that the double mutant strain exhibits compensatory expression changes in proteins associated with cellular redox state, energy/nutrient metabolism, and membrane stability. On solid media, there is obvious growth impairment that is rescued by addition of blood or serum from mammalian species, particularly heme. These porin mutants are not impaired in their capacity to inhibit both staurosporine-induced apoptosis and a phorbol 12-myristate 13-acetate -induced oxidative burst in human neutrophils suggesting that the porins are not the only bacterial factors that can modulate these processes in host cells.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"27156582\",\n \"title\": \"Typing and surface charges of the variable loop regions of PorB from Neisseria meningitidis.\",\n \"abstract\": \"PorB is a pan-Neisserial major outer membrane protein with a trimeric β-barrel structure. Each monomer presents eight periplasmic turns and eight surface exposed loop regions with sequence variability. PorB induces activation of host cell responses via a TLR2-dependent mechanism likely mediated by electrostatic interactions between TLR2 and PorB surface exposed loops. Variability in the loop amino acid sequence is known to influence cell responses to PorB in vitro, particularly for the residues in L5 and L7. In this work, the sequence of the porB gene and the electrostatic surface charges of PorB from 35 invasive meningococcal isolates belonging to the main clonal complexes identified in Italy and from five carriage genomes available on the website http://pubmlst.org/neisseria/ were examined. Analysis of the porB encoding regions from the invasive meningococci has identified four new alleles and a potential association between porB alleles, serogroup, and clonal complexes. Through computer-based modeling and analysis of the electrostatic surface charges of PorB from these strains, loop charge segregation between PorB from invasive serogroups B and C was observed. Specifically, loops 1, 4, and 7 were negatively charged and L2 and L8 were mostly neutral in serogroup B isolates, while an overall homogeneous positive surface charge was present in PorB from invasive serogroup C strains. A higher PorB sequence variability was observed among carriage genomes, and a general prevalence of negative loop surface charges. The surface charge differences in PorB from serogroups B and C invasive and carriage strains may, in part, influence the outcomes of Neisseriae interactions with host cells. © 2016 IUBMB Life, 68(6):488-495, 2016.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"27488811\",\n \"title\": \"An epitope-imprinted piezoelectric diagnostic tool for Neisseria meningitidis detection.\",\n \"abstract\": \"Neisseria meningitidis, a human-specific bacterial pathogen causes bacterial meningitis by invading the meninges (outer lining) of central nervous system. It is the polysaccharide present on the bacterial capsid that distinguishes various serogroups of N. meningitidis and can be utilized as antigens to elicit immune response. A computational approach identified candidate T-cell epitopes from outer membrane proteins Por B of N. meningitidis (MC58): ((273) KGLVDDADI(282) in loop VII and (170) GRHNSESYH(179) in loop IV) present on the exposed surface of immunogenic loops of class 3 outer membrane proteins allele of N. meningitidis. One of them, KGLVDDADI is used here for designing a diagnostic tool via molecularly imprinted piezoelectric sensor (molecularly imprinted polymer-quartz crystal microbalance) for N. meningitidis strain MC58. Methacrylic acid, ethylene glycol dimethacrylate and azoisobutyronitrile were used as functional monomer, cross-linker and initiator, respectively. The epitope can be simultaneously bound to methacrylic acid and fitted into the shape-selective cavities. On extraction of epitope sequence from thus grafted polymeric film, shape-selective and sensitive sites were generated on electrochemical quartz crystal microbalance crystal, ie, known as epitope imprinted polymers. Imprinting was characterized by atomic force microscopy images. The epitope-imprinted sensor was able to selectively bind N. meningitidis proteins present in blood serum of patients suffering from brain fever. Thus, fabricated sensor can be used as a diagnostic tool for meningitis disease.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"27934398\",\n \"title\": \"Energetic and Dynamic Analysis of Transport of Na(+) and K(+) through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers.\",\n \"abstract\": \"Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na(+) and K(+) are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na(+) and K(+) reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na(+) and K(+) ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28708335\",\n \"title\": \"Heterogeneity in non-epitope loop sequence and outer membrane protein complexes alters antibody binding to the major porin protein PorB in serogroup B Neisseria meningitidis.\",\n \"abstract\": \"PorB is a well-characterized outer membrane protein that is common among Neisseria species and is required for survival. A vaccine candidate, PorB induces antibody responses that are directed against six variable surface-exposed loops that differ in sequence depending on serotype. Although Neisseria meningitidis is naturally competent and porB genetic mosaicism provides evidence for strong positive selection, the sequences of PorB serotypes commonly associated with invasive disease are often conserved, calling into question the interaction of specific PorB loop sequences in immune engagement. In this report, we provide evidence that antibody binding to a PorB epitope can be altered by sequence mutations in non-epitope loops. Through the construction of hybrid PorB types and PorB molecular dynamics simulations, we demonstrate that loops both adjacent and non-adjacent to the epitope loop can enhance or diminish antibody binding, a phenotype that correlates with serum bactericidal activity. We further examine the interaction of PorB with outer membrane-associated proteins, including PorA and RmpM. Deletion of these proteins alters the composition of PorB-containing native complexes and reduces antibody binding and serum killing relative to the parental strain, suggesting that both intramolecular and intermolecular PorB interactions contribute to host adaptive immune evasion.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"29601598\",\n \"title\": \"Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.\",\n \"abstract\": \"Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhoea by evading innate immunity. Colonizing the mucosa of the reproductive tract depends on the bacterial outer membrane porin, PorB, which is essential for ion and nutrient uptake. PorB is also targeted to host mitochondria and regulates apoptosis pathways to promote infections. How PorB traffics from the outer membrane of N. gonorrhoeae to mitochondria and whether it modulates innate immune cells, such as macrophages, remains unclear. Here, we show that N. gonorrhoeae secretes PorB via outer membrane vesicles (OMVs). Purified OMVs contained primarily outer membrane proteins including oligomeric PorB. The porin was targeted to mitochondria of macrophages after exposure to purified OMVs and wild type N. gonorrhoeae. This was associated with loss of mitochondrial membrane potential, release of cytochrome c, activation of apoptotic caspases and cell death in a time-dependent manner. Consistent with this, OMV-induced macrophage death was prevented with the pan-caspase inhibitor, Q-VD-PH. This shows that N. gonorrhoeae utilizes OMVs to target PorB to mitochondria and to induce apoptosis in macrophages, thus affecting innate immunity.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19529772\",\n \"title\": \"Towards the immunoproteome of Neisseria meningitidis.\",\n \"abstract\": \"Despite the introduction of conjugated polysaccharide vaccines for many of the Neisseria meningitidis serogroups, neisserial infections continue to cause septicaemia and meningitis across the world. This is in part due to the difficulties in developing a, cross-protective vaccine that is effective against all serogroups, including serogroup B meningococci. Although convalescent N. meningitidis patients develop a natural long-lasting cross-protective immunity, the antigens that mediate this response remain unknown. To help define the target of this protective immunity we identified the proteins recognized by IgG in sera from meningococcal patients by a combination of 2D protein gels, western blots and mass spectrometry. Although a number of outer membrane antigens were identified the majority of the antigens were cytoplasmic, with roles in cellular processes and metabolism. When recombinant proteins were expressed and used to raise sera in mice, none of the antigens elicited a positive SBA result, however flow cytometry did demonstrate that some, including the ribosomal protein, RplY were localised to the neisserial cell surface.\",\n \"corpus_id\": 2901003,\n \"score\": 1\n },\n {\n \"doc_id\": \"19932117\",\n \"title\": \"Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.\",\n \"abstract\": \"The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow \\\"constriction zone\\\". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets were obtained at 2.6 A and 3.0 A resolution with K(+) and Rb(+), respectively. The Rb(+)-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 A and cation positions were determined. A PEG molecule was observed in the pore region for both the K(+) and Rb(+)-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"20441547\",\n \"title\": \"Innate immune function of the neisserial porins and the relationship to vaccine adjuvant activity.\",\n \"abstract\": \"Neisseria meningitidis is a Gram-negative pathogenic bacteria responsible for bacterial meningitis and septicemia. Porins are the most represented outer membrane proteins in the pathogenic Neisseria species, functioning as pores for the exchange of ions, and are characterized by a trimeric beta-barrel structure. Neisserial porins have been shown to act as adjuvants in the immune response via activation of B cells and other antigen-presenting cells. Their effect on the immune response is mediated by upregulation of the costimulatory molecule B7-2 (CD86) on the surface of antigen-presenting cells, an effect that is dependent on Toll-like receptor (TLR)2 and MyD88, through a cascade of signal transduction events mediated by direct binding of the porin to the TLR2-TLR1 heterodimer. This article summarizes work carried out investigating the mechanisms of the immune stimulating capacity of the neisserial porins (specifically meningococcal PorB), emphasizing cellular events involved in antigen-presenting cell activation and induction of expression of cell surface molecules involved in the immune response.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"21281574\",\n \"title\": \"Molecular dynamics studies of ion permeation in VDAC.\",\n \"abstract\": \"The voltage-dependent anion channel (VDAC) in the outer membrane of mitochondria serves an essential role in the transport of metabolites and electrolytes between the cell matrix and mitochondria. To examine its structure, dynamics, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 μs molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 mV. The calculated conductance and ion selectivity are in good agreement with the experimental measurements. In addition, ion density distributions inside the channel reveal possible pathways for different ion species. Based on these observations, a mechanism underlying the anion selectivity is proposed; both ion species are transported across the channel, but the rate for K(+) is smaller than that for Cl(-) because of the attractive interactions between K(+) and residues on the channel wall. This difference leads to the anion selectivity of VDAC.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"21296967\",\n \"title\": \"Role of the periplasmic chaperones Skp, SurA, and DegQ in outer membrane protein biogenesis in Neisseria meningitidis.\",\n \"abstract\": \"The periplasmic chaperones Skp, SurA, and DegP are implicated in the biogenesis of outer membrane proteins (OMPs) in Escherichia coli. Here, we investigated whether these chaperones exert similar functions in Neisseria meningitidis. Although N. meningitidis does not contain a homolog of the protease/chaperone DegP, it does possess a homolog of another E. coli protein, DegQ, which can functionally replace DegP when overproduced. Hence, we examined whether in N. meningitidis, DegQ acts as a functional homolog of DegP. Single skp, surA, and degQ mutants were easily obtained, showing that none of these chaperones is essential in N. meningitidis. Furthermore, all combinations of double mutants were generated and no synthetic lethality was observed. The absence of SurA or DegQ did not affect OMP biogenesis. In contrast, the absence of Skp resulted in severely lower levels of the porins PorA and PorB but not of other OMPs. These decreased levels were not due to proteolytic activity of DegQ, since porin levels remained low in a skp degQ double mutant, indicating that neisserial DegQ is not a functional homolog of E. coli DegP. The absence of Skp resulted in lower expression of the porB gene, as shown by using a P(porB)-lacZ fusion. We found no cross-species complementation when Skp of E. coli or N. meningitidis was heterologously expressed in skp mutants, indicating that Skp functions in a species-specific manner. Our results demonstrate an important role for Skp but not for SurA or DegQ in OMP biogenesis in N. meningitidis.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"22298007\",\n \"title\": \"Refolding, purification and crystallization of the FrpB outer membrane iron transporter from Neisseria meningitidis.\",\n \"abstract\": \"FrpB is an integral outer membrane protein from the human pathogen Neisseria meningitidis. It is a member of the TonB-dependent transporter family and promotes the uptake of iron across the outer membrane. There is also evidence that FrpB is an antigen and hence a potential component of a vaccine against meningococcal meningitis. FrpB incorporating a polyhistidine tag was overexpressed in Escherichia coli into inclusion bodies. The protein was then solubilized in urea, refolded and purified to homogeneity. Two separate antigenic variants of FrpB were crystallized by sitting-drop vapour diffusion. Crystals of the F5-1 variant diffracted to 2.4 Å resolution and belonged to space group C2, with unit-cell parameters a = 176.5, b = 79.4, c = 75.9 Å, β = 98.3°. Crystal-packing calculations suggested the presence of a monomer in the asymmetric unit. Crystals of the F3-3 variant also diffracted to 2.4 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 85.3, b = 104.6, c = 269.1 Å. Preliminary analysis suggested the presence of an FrpB trimer in the asymmetric unit.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"22509000\",\n \"title\": \"Designing biomimetic pores based on carbon nanotubes.\",\n \"abstract\": \"Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca(2+) ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23457610\",\n \"title\": \"Use of a molecular decoy to segregate transport from antigenicity in the FrpB iron transporter from Neisseria meningitidis.\",\n \"abstract\": \"FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT) family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe(3+) with high affinity. EPR spectra of the bound Fe(3+) ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe(3+) binding was reduced or abolished on mutation of the Fe(3+)-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe(3+). The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a 'molecular decoy' to distract immune surveillance.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23542377\",\n \"title\": \"Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.\",\n \"abstract\": \"The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel's full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23545639\",\n \"title\": \"Structure of Neisseria meningitidis lipoprotein GNA1162.\",\n \"abstract\": \"GNA1162, a predicted lipoprotein from Neisseria meningitidis, is a potential candidate for a universal vaccine against meningococcal disease caused by N. meningitidis serogroup B. Here, the crystal structure of GNA1162 at 1.89 Å resolution determined by single-wavelength anomalous dispersion (SAD) is reported. The structure of GNA1162 appears to be a dimer in the crystallographic asymmetric unit as well as in solution. The overall structure of the dimer indicates that each monomer inserts its C-terminal α5 helix into the hydrophobic groove of the other molecule. Moreover, the β4 strands of each monomer lie antiparallel to each other and interact through multiple main-chain hydrogen bonds. Through structural comparisons and operon predictions, it is hypothesized that GNA1162 is part of a transport system and assists in transport and reassembly. The crystal structure of GNA1162 sheds light on its possible function and provides potentially valuable information for the design of a vaccine against meningococcal disease.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"23817612\",\n \"title\": \"Identification of genes involved in Neisseria meningitidis colonization.\",\n \"abstract\": \"Neisseria meningitidis is a worldwide cause of meningitis and septicemia leading at least to 50,000 deaths every year. Nevertheless, N. meningitidis is also a commensal bacterium that asymptomatically colonizes the epithelial cells of the nasopharynx of 10 to 30% of healthy individuals. Occasionally, N. meningitidis crosses the nasopharyngeal barrier and enters the bloodstream. During bacteremia, N. meningitidis may adhere to endothelial cells of brain vessels and invade meninges. To identify the genes required for meningococcal host colonization, we screened a signature-tagged transposon mutagenesis library using an innovative in vitro colonization model in order to identify mutants displaying decreased capacity to colonize human epithelial cells. Approximately 1,600 defined insertion mutants of invasive serogroup C strain NEM8013 were screened. Candidate mutants were tested individually for quantification of bacterial biomass with confocal microscope and COMSTAT software. Five mutants were demonstrated to exhibit significantly decreased colonization ability. The identified genes, including narP and estD, appeared to be involved in adaptation to hypoxic conditions and stress resistance. Interestingly, the genes fadD1, nnrS, and NMV_2034 (encoding a putative thioredoxin), prior to this study, had not been shown to be involved in colonization. Therefore, we provide here insights into the meningococcal functions necessary for the bacterium to adapt to growth on host cells.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24106986\",\n \"title\": \"A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.\",\n \"abstract\": \"OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24147565\",\n \"title\": \"Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations.\",\n \"abstract\": \"Using the X-ray structure of a recently discovered bacterial protein, the N-acetylneuraminic acid-inducible channel (NanC), we investigate computationally K(+) and Cl(-) ions' permeation. We identify ion permeation pathways that are likely to be populated using coarse-grain Monte Carlo simulations. Next, we use these pathways as reaction coordinates for umbrella sampling-based free energy simulations. We find distinct tubelike pathways connecting specific binding sites for K(+) and, more pronounced, for Cl(-) ions. Both ions permeate the porin preserving almost all of their first hydration shell. The calculated free energy barriers are G(#) ≈ 4 kJ/mol and G(#) ≈ 8 kJ/mol for Cl(-) and K(+), respectively. Within the approximations associated with these values, discussed in detail in this work, we suggest that the porin is slightly selective for Cl(-) versus K(+). Our suggestion is consistent with the experimentally observed weak Cl(-) over K(+) selectivity. A rationale for the latter is suggested by a comparison with previous calculations on strongly anion selective porins.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24161028\",\n \"title\": \"Simulation of ion transport through an N-acetylneuraminic acid-inducible membrane channel: from understanding to engineering.\",\n \"abstract\": \"N-acetylneuraminic acid-inducible channel (NanC) is an outer membrane channel of Escherichia coli . This porin folds as a 12-stranded β-barrel leading to a tubular shape. Electrophysiological experiments have revealed an asymmetric conductance with respect to the direction of the applied voltage and a weak anion selectivity of the channel. To this end, we performed all-atom molecular dynamics (MD) simulations to decipher the ion transport properties of the NanC channel. Concentration-dependent applied-field MD simulations recover the asymmetric conductance property and the anion selectivity of the channel in agreement with experiments. Further molecular analysis revealed the role of the asymmetric charge distribution inside the channel as the basis of the asymmetry in conductance. In addition, the particular distribution of charged residues at the inner channel walls leads to a faster permeation of Cl(-) ions compared to K(+) ions resulting in the anion selectivity of NanC. These findings are well supported by position-dependent diffusion coefficients and potential of mean force profiles derived from unbiased MD simulations. Taking one step further, we were able to engineer the NanC channel in silico by mutations leading to enhanced asymmetric conductances and anion selectivities. The E186Q mutant, for example, changes NanC into a decent molecular diode with an ionic current ratio of about 3:1 for opposite bias voltages.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"24204275\",\n \"title\": \"Zinc piracy as a mechanism of Neisseria meningitidis for evasion of nutritional immunity.\",\n \"abstract\": \"The outer membrane of Gram-negative bacteria functions as a permeability barrier that protects these bacteria against harmful compounds in the environment. Most nutrients pass the outer membrane by passive diffusion via pore-forming proteins known as porins. However, diffusion can only satisfy the growth requirements if the extracellular concentration of the nutrients is high. In the vertebrate host, the sequestration of essential nutrient metals is an important defense mechanism that limits the growth of invading pathogens, a process known as \\\"nutritional immunity.\\\" The acquisition of scarce nutrients from the environment is mediated by receptors in the outer membrane in an energy-requiring process. Most characterized receptors are involved in the acquisition of iron. In this study, we characterized a hitherto unknown receptor from Neisseria meningitidis, a causative agent of sepsis and meningitis. Expression of this receptor, designated CbpA, is induced when the bacteria are grown under zinc limitation. We demonstrate that CbpA functions as a receptor for calprotectin, a protein that is massively produced by neutrophils and other cells and that has been shown to limit bacterial growth by chelating Zn²⁺ and Mn²⁺ ions. Expression of CbpA enables N. meningitidis to survive and propagate in the presence of calprotectin and to use calprotectin as a zinc source. Besides CbpA, also the TonB protein, which couples energy of the proton gradient across the inner membrane to receptor-mediated transport across the outer membrane, is required for the process. CbpA was found to be expressed in all N. meningitidis strains examined, consistent with a vital role for the protein when the bacteria reside in the host. Together, our results demonstrate that N. meningitidis is able to subvert an important defense mechanism of the human host and to utilize calprotectin to promote its growth.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25462170\",\n \"title\": \"VCA1008: An Anion-Selective Porin of Vibrio Cholerae.\",\n \"abstract\": \"A putative porin function has been assigned to VCA1008 of Vibrio cholerae. Its coding gene, vca1008, is expressed upon colonization of the small intestine in infant mice and human volunteers, and is essential for infection. In vitro, vca1008 is expressed under inorganic phosphate limitation and, in this condition, VCA1008 is the major outer membrane protein of the bacterium. Here, we provide the first functional characterization of VCA1008 reconstituted into planar lipid bilayers. Our main findings were: 1) VCA1008 forms an ion channel that, at high voltage (~±100 mV), presents a voltage-dependent activity and displays closures typical of trimeric porins, with a conductance of 4.28±0.04 nS (n=164) in 1M KCl; 2) It has a preferred selectivity for anions over cations; 3) Its conductance saturates with increasing inorganic phosphate concentration, suggesting VCA1008 contains binding site(s) for this anion; 4) Its ion selectivity is controlled by both fixed charged residues within the channel and diffusion along the pore; 5) Partitioning of poly (ethylene glycol)s (PEGs) of different molecular mass suggests that VCA1008 channel has a pore exclusion limit of 0.9 nm.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25860993\",\n \"title\": \"Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.\",\n \"abstract\": \"In the exchange of metabolites and ions between the mitochondrion and the cytosol, the voltage-dependent anion channel (VDAC) is a key element, as it forms the major transport pathway for these compounds through the mitochondrial outer membrane. Numerous experimental studies have promoted the idea that VDAC acts as a regulator of essential mitochondrial functions. In this study, using a combination of molecular dynamics simulations, free-energy calculations, and electrophysiological measurements, we investigated the transport of ions through VDAC, with a focus on phosphate ions and metabolites. We showed that selectivity of VDAC towards small anions including monovalent phosphates arises from short-lived interactions with positively charged residues scattered throughout the pore. In dramatic contrast, permeation of divalent phosphate ions and phosphate metabolites (AMP and ATP) involves binding sites along a specific translocation pathway. This permeation mechanism offers an explanation for the decrease in VDAC conductance measured in the presence of ATP or AMP at physiological salt concentration. The binding sites occur at similar locations for the divalent phosphate ions, AMP and ATP, and contain identical basic residues. ATP features a marked affinity for a central region of the pore lined by two lysines and one arginine of the N-terminal helix. This cluster of residues together with a few other basic amino acids forms a \\\"charged brush\\\" which facilitates the passage of the anionic metabolites through the pore. All of this reveals that VDAC controls the transport of the inorganic phosphates and phosphate metabolites studied here through two different mechanisms.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25955156\",\n \"title\": \"Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level.\",\n \"abstract\": \"Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane. They feature a constriction zone, contributed by the plunging of extracellular loop 3 (L3) into the channel lumen. Porins are generally in the open state, but undergo gating in response to external voltages. To date the underlying mechanism is unclear. Here we report results from molecular dynamics simulations on the two porins of Providenica stuartii, Omp-Pst1 and Omp-Pst2, which display distinct voltage sensitivities. Voltage gating was observed in Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 and Omp-Pst2 structures and trajectories suggests that their sensitivity to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall, as we observed that it is the strength of this network that governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel furthermore suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26190347\",\n \"title\": \"Neisseria meningitidis infection: who, when and where?\",\n \"abstract\": \"Neisseria meningitidis is a Gram-negative β-proteobacterium responsible for an endemic worldwide infection. The epidemiology and serogroup distribution can change very quickly. The incidence of meningitis infection varies from very rare to more than 1000 cases per 100,000 of the population yearly. The carriage of N. meningitidis, which represents an exclusive human commensal, is asymptomatic, but in rare cases bacteria proliferate in the CNS and rapidly lead to the death of the affected subjects. Host genetic factors, such as single nucleotide polymorphisms, can promote meningococcal disease, being able to influence the individual predisposition to the pathology. Although a reduction in meningococcal disease has been observed in Europe, a continuous surveillance is necessary to control any possible outbreaks of new hypervirulent clones into populations that could modify the epidemiology of meningococcal infections and the clinical spectrum of affected subjects.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26651735\",\n \"title\": \"Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane.\",\n \"abstract\": \"We have applied a combined fluorescence microscopy and single-ion-channel electric current recording approach, correlating with molecular dynamics (MD) simulations, to study the mechanism of voltage-sensor domain translocation across a lipid bilayer. We use the colicin Ia ion channel as a model system, and our experimental and simulation results show the following: (1) The open-close activity of an activated colicin Ia is not necessarily sensitive to the amplitude of the applied cross-membrane voltage when the cross-membrane voltage is around the resting potential of excitable membranes; and (2) there is a significant probability that the activation of colicin Ia occurs by forming a transient and fluctuating water pore of ∼15 Å diameter in the lipid bilayer membrane. The location of the water-pore formation is nonrandom and highly specific, right at the insertion site of colicin Ia charged residues in the lipid bilayer membrane, and the formation is intrinsically associated with the polypeptide conformational fluctuations and solvation dynamics. Our results suggest an interesting mechanistic pathway for voltage-sensitive ion channel activation, and specifically for translocation of charged polypeptide chains across the lipid membrane under a transmembrane electric field: the charged polypeptide domain facilitates the formation of hydrophilic water pore in the membrane and diffuses through the hydrophilic pathway across the membrane; i.e., the charged polypeptide chain can cross a lipid membrane without entering into the hydrophobic core of the lipid membrane but entirely through the aqueous and hydrophilic environment to achieve a cross-membrane translocation. This mechanism sheds light on the intensive and fundamental debate on how a hydrophilic and charged peptide domain diffuses across the biologically inaccessible high-energy barrier of the hydrophobic core of a lipid bilayer: The peptide domain does not need to cross the hydrophobic core to move across a lipid bilayer.\",\n \"corpus_id\": 32835839,\n \"score\": 1\n },\n {\n \"doc_id\": \"26826035\",\n \"title\": \"The VDAC channel: Molecular basis for selectivity.\",\n \"abstract\": \"The voltage dependent anion-selective channel, VDAC, is the major permeability pathway by which molecules and ion cross the mitochondrial outer membrane. This pathway has evolved to optimize the flow of these substances and to control this flow by a gating process that is influenced by a variety of factors including transmembrane voltage. The permeation pathway formed through the membrane by VDAC is complex. Small ion flow is primarily influenced by the charged surface of the inner walls of the channel. Channel closure changes this landscape resulting in a change from a channel that favors anions to one that favors cations. Molecular ions interact more intimately with the inner walls of the channel and are selected by their 3-dimensional structure, not merely by their size and charge. Molecular ions typically found in cells are greatly favored over those that are not. For these larger structures the channel may form a low-energy translocation path that complements the structure of the permeant. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26895142\",\n \"title\": \"Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies.\",\n \"abstract\": \"Porins are water-filled protein channels across the outer membrane of gram-negative bacteria. They facilitate the uptake of nutrients and essential ions. Solutes are filtered by a constriction loop L3 at the mid of a pore. Porins are heat-stable and resistant to toxic agents and detergents. Most porins are trimer, but no clear explanation why trimeric form is preferable. In this work, we thus studied effects of oligomerization on porin structure and function in microscopic detail. A well-studied OmpF (general porin from Escherichia coli) and well-characterised OprP (phosphate-specific pore from Pseudomonas aeruginosa) are used as samples from 2 types of porins found in gram-negative bacteria. MD simulations of trimeric and monomeric pores in pure water and 1M NaCl solution were performed. With a salt solution, the external electric field was applied to mimic a transmembrane potential. Expectedly, OprP is more stable than OmpF. Interestingly, being a monomer turns OmpF into an anion-selective pore. The dislocation of D113's side chain on L3 in OmpF causes the disruption of cation pathway resulting in the reduction of cation influx. In contrast, OprP's structure and function are less dependent on oligomeric states. Both monomeric and trimeric OprP can maintain their anion selectivity. Our findings suggest that trimerization is crucial for both structure and function of general porin OmpF, whereas being trimer in substrate-specific channel OprP supports a pore function.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26913282\",\n \"title\": \"Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations.\",\n \"abstract\": \"Sucrose-specific porin (ScrY) is a transmembrane protein that allows for the uptake of sucrose under growth-limiting conditions. The crystal structure of ScrY was resolved before by X-ray crystallography, both in its uncomplexed form and with bound sucrose. However, little is known about the molecular characteristics of the transport mechanism of ScrY. To date, there has not yet been any clear demonstration for sucrose transport through the ScrY. Here, the dynamics of the ScrY trimer embedded in a phospholipid bilayer as well as the characteristics of sucrose translocation were investigated by means of atomistic molecular dynamics (MD) simulations. The potential of mean force (PMF) for sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Energy decomposition allowed to pinpoint three aspartic acids as key residues opposing the passage of sucrose, all located within the L3 loop. Mutation of two aspartic acids to uncharged residues resulted in an accordingly modified electrostatics and decreased PMF barrier. The chosen methodology and results will aid in the design of porins with modified transport specificities.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"27454890\",\n \"title\": \"Transport and Catabolism of Carbohydrates by Neisseria meningitidis.\",\n \"abstract\": \"We identified the genes encoding the proteins for the transport of glucose and maltose in Neisseria meningitidis strain 2C4-3. A mutant deleted for NMV_1892(glcP) no longer grew on glucose and deletion of NMV_0424(malY) prevented the utilization of maltose. We also purified and characterized glucokinase and α-phosphoglucomutase, which catalyze early catabolic steps of the two carbohydrates. N. meningitidis catabolizes the two carbohydrates either via the Entner-Doudoroff (ED) pathway or the pentose phosphate pathway, thereby forming glyceraldehyde-3-P and either pyruvate or fructose-6-P, respectively. We purified and characterized several key enzymes of the two pathways. The genes required for the transformation of glucose into gluconate-6-P and its further catabolism via the ED pathway are organized in two adjacent operons. N. meningitidis also contains genes encoding proteins which exhibit similarity to the gluconate transporter (NMV_2230) and gluconate kinase (NMV_2231) of Enterobacteriaceae and Firmicutes. However, gluconate might not be the real substrate of NMV_2230 because N. meningitidis was not able to grow on gluconate as the sole carbon source. Surprisingly, deletion of NMV_2230 stimulated growth in minimal medium in the presence and absence of glucose and drastically slowed the clearance of N. meningitidis cells from transgenic mice after intraperitoneal challenge.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"18076035\",\n \"title\": \"In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.\",\n \"abstract\": \"OpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)-containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10-stranded beta-barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the beta-barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"19273554\",\n \"title\": \"Functional comparison of the binding of factor H short consensus repeat 6 (SCR 6) to factor H binding protein from Neisseria meningitidis and the binding of factor H SCR 18 to 20 to Neisseria gonorrhoeae porin.\",\n \"abstract\": \"Both Neisseria meningitidis and Neisseria gonorrhoeae recruit the alternative pathway complement inhibitory protein factor H (fH) to their surfaces to evade complement-dependent killing. Meningococci bind fH via fH binding protein (fHbp), a surface-exposed lipoprotein that is subdivided into three variant families based on one classification scheme. Chimeric proteins that comprise contiguous domains of fH fused to murine Fc were used to localize the binding site for all three fHbp variants on fH to short consensus repeat 6 (SCR 6). As expected, fH-like protein 1 (FHL-1), which contains fH SCR 6, also bound to fHbp-expressing meningococci. Using site-directed mutagenesis, we identified histidine 337 and histidine 371 in SCR 6 as important for binding to fHbp. These findings may provide the molecular basis for recent observations that demonstrated human-specific fH binding to meningococci. Differences in the interactions of fHbp variants with SCR 6 were evident. Gonococci bind fH via their porin (Por) molecules (PorB.1A or PorB.1B); sialylation of lipooligosaccharide enhances fH binding. Both sialylated PorB.1B- and (unsialylated) PorB.1A-bearing gonococci bind fH through SCR 18 to 20; PorB.1A can also bind SCR 6, but only weakly, as evidenced by a low level of binding of FHL-1 relative to that of fH. Using isogenic strains expressing either meningococcal fHbp or gonococcal PorB.1B, we discovered that strains expressing gonococcal PorB.1B in the presence of sialylated lipooligosaccharide bound more fH, more effectively limited C3 deposition, and were more serum resistant than their isogenic counterparts expressing fHbp. Differences in fH binding to these two related pathogens may be important for modulating their individual responses to host immune attack.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"21476783\",\n \"title\": \"Neisseria meningitidis endocarditis: a case report and review of the literature.\",\n \"abstract\": \"Neisseria meningitidis is the leading cause of bacterial meningitis in children and young adults, with an overall mortality rate of up to 25%, but it is a rare cause of infective endocarditis. We present herein a case of N. meningitidis meningitis complicated with infective endocarditis.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"22185907\",\n \"title\": \"Vascular colonization by Neisseria meningitidis.\",\n \"abstract\": \"Bacterial infection of human vasculature can lead to unregulated systemic activation of coagulation and innate immunity and rapidly becomes life threatening. Neisseria meningitidis is a vascular pathogen that causes fatal sepsis and meningitis. Post-mortem histological analysis of tissues from individuals infected with N. meningitidis show large bacterial aggregates in close association with the vascular wall of small vessels. The ability of this bacterium to colonize blood vessel endothelium is likely to impact its capacity to both multiply in the blood stream and reach the brain. This process will be referred to as vascular colonization. Recent work has described a number of early steps in N. meningitidis vascular colonization, from attachment to proliferation and dissemination, focusing on the bacterial-host interaction.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"23875754\",\n \"title\": \"Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation.\",\n \"abstract\": \"The outer membrane porin OprP of Pseudomonas aeruginosa forms a highly specific phosphate selective channel. This channel is responsible for the high-affinity uptake of phosphate ions into the periplasmic space of the bacteria. A detailed investigation of the structure-function relationship of OprP is inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, in terms of its effects in selectivity and ion transport properties of the pore. Electrophysiological bilayer measurements and free-energy molecular dynamics simulations were carried out to probe the transport of different ions through various R133 mutants. For these mutants, the change in phosphate binding specificity, ion conduction, and anion selectivity was determined and compared to previous molecular dynamic calculations and electrophysiological measurements with wild-type OprP. Molecular analysis revealed a rather particular role of arginine 133 and its charge, while at the same time this residue together with the network of other residues, namely, D94 and Y114, has the ability to dehydrate the permeating ion. These very specific features govern the ion selectivity of OprP.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"25191646\",\n \"title\": \"Metabolism and virulence in Neisseria meningitidis.\",\n \"abstract\": \"A longstanding question in infection biology addresses the genetic basis for invasive behavior in commensal pathogens. A prime example for such a pathogen is Neisseria meningitidis. On the one hand it is a harmless commensal bacterium exquisitely adapted to humans, and on the other hand it sometimes behaves like a ferocious pathogen causing potentially lethal disease such as sepsis and acute bacterial meningitis. Despite the lack of a classical repertoire of virulence genes in N. meningitidis separating commensal from invasive strains, molecular epidemiology suggests that carriage and invasive strains belong to genetically distinct populations. In recent years, it has become increasingly clear that metabolic adaptation enables meningococci to exploit host resources, supporting the concept of nutritional virulence as a crucial determinant of invasive capability. Here, we discuss the contribution of core metabolic pathways in the context of colonization and invasion with special emphasis on results from genome-wide surveys. The metabolism of lactate, the oxidative stress response, and, in particular, glutathione metabolism as well as the denitrification pathway provide examples of how meningococcal metabolism is intimately linked to pathogenesis. We further discuss evidence from genome-wide approaches regarding potential metabolic differences between strains from hyperinvasive and carriage lineages and present new data assessing in vitro growth differences of strains from these two populations. We hypothesize that strains from carriage and hyperinvasive lineages differ in the expression of regulatory genes involved particularly in stress responses and amino acid metabolism under infection conditions.\",\n \"corpus_id\": -1,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":89,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28800436\",\n \"title\": \"Tactile acuity testing at the neck: A comparison of methods.\",\n \"abstract\": \"BACKGROUND: Interest in measurement of tactile acuity in musculoskeletal practice has emerged following its link to functional reorganization of the somatosensory cortex in ongoing pain states. Several tactile acuity measurement methods have been described but have not been thoroughly investigated in the cervical region. OBJECTIVE: This study examined reliability, concurrent validity and responsiveness of four tests of tactile acuity-Two-point discrimination, Point-to-point, Graphesthesia, and Localisation tests-at the cervical region. METHOD: Forty-two healthy participants were included. In Part 1 (n = 22), participants' tactile acuity was assessed at two time points, 30 min apart, to determine the test-retest reliability and concurrent validity of each of the tests. In Part 2 (n = 20), participants received five daily tactile training sessions, delivered via a vibro-tactile device. Tactile acuity was assessed pre- and post-training to examine responsiveness of each test. RESULTS: Two-point discrimination demonstrated excellent test-retest reliability (ICC = 0.85, SEM = 3.7 mm), Point-to-point and Localisation tests demonstrated good reliability (ICC = 0.60, SEM = 2.8 mm; ICC = 0.60, SEM = 8.8%), and Graphesthesia demonstrated fair reliability (ICC = 0.48, SEM = 1.9/20). There was no significant correlation among measures. Only Graphesthesia failed to show responsiveness to change following training. CONCLUSION: The reliability of Two-point discrimination appears superior to other examined tests of tactile acuity, however measurement variability should be considered. Two-point discrimination, Point-to-point, and Localisation tests appear responsive to change, although testing in clinical samples is needed. The lack of concurrent validity among tests suggests that they cannot be used interchangeably.\",\n \"corpus_id\": 8153527\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18054437","title":"Tactile discrimination, but not tactile stimulation alone, reduces chronic limb pain.","abstract":"Chronic pain is often associated with reduced tactile acuity. A relationship exists between pain intensity, tactile acuity and cortical reorganisation. When pain resolves, tactile function improves and cortical organisation normalises. Tactile acuity can be improved in healthy controls when tactile stimulation is associated with a behavioural objective. We hypothesised that, in patients with chronic limb pain and decreased tactile acuity, discriminating between tactile stimuli would decrease pain and increase tactile acuity, but tactile stimulation alone would not. Thirteen patients with complex regional pain syndrome (CRPS) of one limb underwent a waiting period and then approximately 2 weeks of tactile stimulation under two conditions: stimulation alone or discrimination between stimuli according to their diameter and location. There was no change in pain (100 mm VAS) or two-point discrimination (TPD) during a no-treatment waiting period, nor during the stimulation phase (p > 0.32 for both). Pain and TPD were lower after the discrimination phase [mean (95% CI) effect size for pain VAS = 27 mm (14-40 mm) and for TPD = 5.7 mm (2.9-8. ), p < 0.015 for both]. These gains were maintained at three-month follow-up. We conclude that tactile stimulation can decrease pain and increase tactile acuity when patients are required to discriminate between the type and location of tactile stimuli.","corpus_id":2757963,"score":2},{"doc_id":"19553222","title":"Tactile acuity and lumbopelvic motor control in patients with back pain and healthy controls.","abstract":"BACKGROUND: Voluntary lumbopelvic control is compromised in patients with back pain. Loss of proprioceptive acuity is one contributor to decreased control. Several reasons for decreased proprioceptive acuity have been proposed, but the integrity of cortical body maps has been overlooked. We investigated whether tactile acuity, a clear clinical signature of primary sensory cortex organisation, relates to lumbopelvic control in people with back pain. METHODS: Forty-five patients with back pain and 45 age- and sex-matched healthy controls participated in this cross-sectional study. Tactile acuity at the back was assessed using two-point discrimination (TPD) threshold in vertical and horizontal directions. Voluntary motor control was assessed using an established battery of clinical tests. RESULTS: Patients performed worse on the voluntary lumbopelvic tasks than healthy controls did (p<0.001). TPD threshold was larger in patients (mean (SD)=61 (13) mm) than in healthy controls (44 (10) mm). Moreover, larger TPD threshold was positively related to worse performance on the voluntary lumbopelvic tasks (Pearson's r=0.49; p<0.001). DISCUSSION: Tactile acuity, a clear clinical signature of primary sensory cortex organisation, relates to voluntary lumbopelvic control. This relationship raises the possibility that the former contributes to the latter, in which case training tactile acuity may aid recovery and assist in achieving normal motor performance after back injury.","corpus_id":22933101,"score":2},{"doc_id":"22309074","title":"Reproducibility of tactile assessments for children with unilateral cerebral palsy.","abstract":"A systematic review identified tactile assessments used in children with cerebral palsy (CP), but their reproducibility is unknown. Sixteen children with unilateral CP and 31 typically developing children (TDC) were assessed 2-4 weeks apart. Test-retest percent agreements within one point for children with unilateral CP (and TDC) were Semmes-Weinstein monofilaments: 75% (90%); single-point localization: 69% (97%); static two-point discrimination: 93% (97%); and moving two-point discrimination: 87% (97%). Test-retest reliability for registration and unilateral spatial tactile perception tests was high in children with CP (intraclass correlation coefficient [ICC] = 0.79-0.96). Two tests demonstrated a learning effect for children with CP, double simultaneous and tactile texture perception. Stereognosis had a ceiling effect for TDC (ICC = 0) and variability for children with CP (% exact agreement = 47%-50%). The Semmes-Weinstein monofilaments, single-point localization, and both static and moving two-point discrimination are recommended for use in practice and research. Although recommended to provide a comprehensive assessment, the measures of double simultaneous, stereognosis, and tactile texture perception may not be responsive to change over time in children with unilateral CP.","corpus_id":18713889,"score":2},{"doc_id":"23611918","title":"Assessing tactile acuity in rheumatology and musculoskeletal medicine--how reliable are two-point discrimination tests at the neck, hand, back and foot?","abstract":"OBJECTIVE: Chronic pain from rheumatic and musculoskeletal conditions is associated with cortical changes and altered tactile acuity. Tactile acuity is considered a clinical signature of primary somatosensory representation. The two-point discrimination (TPD) threshold is increasingly used both clinically and in research. Remarkably, the reliability and precision of the measure at commonly used sites has not been determined. This study aimed to determine the utility, intra- and inter-rater reliability, bias and variability of TPD threshold assessment at the neck, back, hand and foot using mechanical callipers. METHODS: Intra- and inter-rater reliability of TPD was assessed at the back, neck, hand and foot of 28 healthy young adults by 28 clinicians. Each clinician received training in the assessment of TPD using mechanical callipers and following a standardized protocol. Intraclass correlation coefficients (ICCs) and Bland-Altman plots were used to assess reliability, bias and variability. RESULTS: Intra-rater assessments in all four regions and inter-rater assessments at the neck and foot were reliable (ICC range 0.79-0.86), but large variability was seen in all assessments. Inter-rater assessment of the back (ICC = 0.66) and hand (ICC = 0.62) was deemed unreliable. Negligible systematic bias suggested learning did not affect reliability. CONCLUSION: Individual clinicians are able to reliably assess TPD threshold at the neck, back, hand and foot using mechanical callipers. Measures obtained by different clinicians were only reliable for the neck and foot. Large variability was observed in all assessments, which suggests clinicians should be cautious when interpreting changes in tactile acuity in individual patients.","corpus_id":2260754,"score":2},{"doc_id":"23661429","title":"Tactile acuity is disrupted in osteoarthritis but is unrelated to disruptions in motor imagery performance.","abstract":"OBJECTIVE: To determine whether tactile acuity is disrupted in people with knee OA and to determine whether tactile acuity, a clinical signature of primary sensory cortex representation, is related to motor imagery performance (MIP; evaluates working body schema) and pain. METHODS: Experiment 1: two-point discrimination (TPD) threshold at the knee was compared between 20 participants with painful knee OA, 20 participants with arm pain and 20 healthy controls. Experiment 2: TPD threshold, MIP (left/right judgements of body parts) and usual pain were assessed in 20 people with painful knee OA, 17 people with back pain and 38 healthy controls (20 knee TPD; 18 back TPD). RESULTS: People with painful knee OA had larger TPD thresholds than those with arm pain and healthy controls (P < 0.05). TPD and MIP were not related in people with knee OA (P = 0.88) but were related in people with back pain and in healthy controls (P < 0.001). Pain did not relate to TPD threshold or to MIP (P > 0.15 for all). CONCLUSION: In painful knee OA, tactile acuity at the knee is decreased, implying disrupted representation of the knee in primary sensory cortex. That TPD and MIP were unrelated in knee OA, but related in back pain, suggests that the relationship between them may vary between chronic pain conditions. That pain was not related to TPD threshold nor MIP suggests against the idea that disrupted cortical representations contribute to the pain of either condition.","corpus_id":2585669,"score":2},{"doc_id":"24062677","title":"Two-point orientation discrimination versus the traditional two-point test for tactile spatial acuity assessment.","abstract":"Two-point discrimination is widely used to measure tactile spatial acuity. The validity of the two-point threshold as a spatial acuity measure rests on the assumption that two points can be distinguished from one only when the two points are sufficiently separated to evoke spatially distinguishable foci of neural activity. However, some previous research has challenged this view, suggesting instead that two-point task performance benefits from an unintended non-spatial cue, allowing spuriously good performance at small tip separations. We compared the traditional two-point task to an equally convenient alternative task in which participants attempt to discern the orientation (vertical or horizontal) of two points of contact. We used precision digital readout calipers to administer two-interval forced-choice versions of both tasks to 24 neurologically healthy adults, on the fingertip, finger base, palm, and forearm. We used Bayesian adaptive testing to estimate the participants' psychometric functions on the two tasks. Traditional two-point performance remained significantly above chance levels even at zero point separation. In contrast, two-point orientation discrimination approached chance as point separation approached zero, as expected for a valid measure of tactile spatial acuity. Traditional two-point performance was so inflated at small point separations that 75%-correct thresholds could be determined on all tested sites for fewer than half of participants. The 95%-correct thresholds on the two tasks were similar, and correlated with receptive field spacing. In keeping with previous critiques, we conclude that the traditional two-point task provides an unintended non-spatial cue, resulting in spuriously good performance at small spatial separations. Unlike two-point discrimination, two-point orientation discrimination rigorously measures tactile spatial acuity. We recommend the use of two-point orientation discrimination for neurological assessment.","corpus_id":248215,"score":2},{"doc_id":"24484671","title":"Lumbar tactile acuity is near identical between sides in healthy pain-free participants.","abstract":"A growing body of literature suggests that alterations in brain structure and function are a feature of chronic back pain. Tactile acuity is considered a clinical signature of primary somatosensory representation and offers a simple measure of cortical reorganisation. Clinical interpretation of test scores from an individual patient is hampered by variance in published normative values and less than ideal inter-rater reliability. These problems might be mitigated in people with unilateral back pain by using the patient as their own control and comparing tactile acuity at the painful site to performance at the corresponding position on the non-painful side. The first step in exploring this approach is to quantify the normal side-to-side difference in healthy populations. We pooled data from three previous studies that measured lumbar tactile acuity bilaterally in healthy controls using similar protocols. We calculated the mean and variance of the absolute error between sides, the standard error of measurement and the reliable change index (RCI). The mean difference between sides was 3.2 mm (±5.2) when assessed vertically and 1.9 mm (±3.2) when assessed horizontally. The standard error of measurement was 4.2 mm when assessed vertically and 2.7 mm when assessed horizontally. The RCI suggests that differences of greater than 13 mm when assessed horizontally and 17 mm when assessed vertically equate to 95% confidence that a difference truly exists. Several assumptions related to the application of this approach need to be investigated further.","corpus_id":10112626,"score":2},{"doc_id":"24504346","title":"Tactile acuity charts: a reliable measure of spatial acuity.","abstract":"For assessing tactile spatial resolution it has recently been recommended to use tactile acuity charts which follow the design principles of the Snellen letter charts for visual acuity and involve active touch. However, it is currently unknown whether acuity thresholds obtained with this newly developed psychophysical procedure are in accordance with established measures of tactile acuity that involve passive contact with fixed duration and control of contact force. Here we directly compared tactile acuity thresholds obtained with the acuity charts to traditional two-point and grating orientation thresholds in a group of young healthy adults. For this purpose, two types of charts, using either Braille-like dot patterns or embossed Landolt rings with different orientations, were adapted from previous studies. Measurements with the two types of charts were equivalent, but generally more reliable with the dot pattern chart. A comparison with the two-point and grating orientation task data showed that the test-retest reliability of the acuity chart measurements after one week was superior to that of the passive methods. Individual thresholds obtained with the acuity charts agreed reasonably with the grating orientation threshold, but less so with the two-point threshold that yielded relatively distinct acuity estimates compared to the other methods. This potentially considerable amount of mismatch between different measures of tactile acuity suggests that tactile spatial resolution is a complex entity that should ideally be measured with different methods in parallel. The simple test procedure and high reliability of the acuity charts makes them a promising complement and alternative to the traditional two-point and grating orientation thresholds.","corpus_id":1727869,"score":2},{"doc_id":"24571855","title":"Tactile acuity training for patients with chronic low back pain: a pilot randomised controlled trial.","abstract":"BACKGROUND: Chronic pain can disrupt the cortical representation of a painful body part. This disruption may play a role in maintaining the individual's pain. Tactile acuity training has been used to normalise cortical representation and reduce pain in certain pain conditions. However, there is little evidence for the effectiveness of this intervention for chronic low back pain (CLBP). The primary aim of this study was to inform the development of a fully powered randomised controlled trial (RCT) by providing preliminary data on the effect of tactile acuity training on pain and function in individuals with CLBP. The secondary aim was to obtain qualitative feedback about the intervention. METHODS: In this mixed-methods pilot RCT 15 individuals were randomised to either an intervention (tactile acuity training) or a placebo group (sham tactile acuity training). All participants received 3 sessions of acuity training (intervention or sham) from a physiotherapist and were requested to undertake daily acuity home training facilitated by an informal carer (friend/relative). All participants also received usual care physiotherapy. The primary outcome measures were pain (0-100visual analogue scale (VAS)) and function (Roland Morris Disability Questionnaire (RMDQ)). Participants and their informal carers were invited to a focus group to provide feedback on the intervention. RESULTS: The placebo group improved by the greatest magnitude for both outcome measures, but there was no statistically significant difference (Mean difference (95%CI), p-value) between groups for change in pain (25.6 (-0.7 to 51.9), p = 0.056) or function (2.2 (-1.6 to 6.0), p = 0.237). Comparing the number of individuals achieving a minimally clinically significant improvement, the placebo group had better outcomes for pain with all participants achieving ≥30% improvement compared to only a third of the intervention group (6/6 vs. 3/9, p = 0.036). Qualitatively, participants reported that needing an informal carer was a considerable barrier to the home training component of the study. CONCLUSIONS: This pilot RCT found tactile acuity training to be no more effective than sham tactile acuity training for function and less effective for pain in individuals with CLBP. That the intervention could not be self-applied was a considerable barrier to its use. TRIAL REGISTRATION ISRCTN: ISRCTN98118082.","corpus_id":7456543,"score":2},{"doc_id":"24870716","title":"Show me the skin! Does seeing the back enhance tactile acuity at the back?","abstract":"A growing body of literature associates musculoskeletal disorders with cortical reorganisation. One condition in which reorganisation is established and treatments that 'train the brain' are being widely used is chronic back pain. Recent evidence suggests that treatments that involve tactile training are more effective if they incorporate multisensory mechanisms, most obviously vision. With regard to back pain however, we must first determine if tactile function is enhanced by incorporating other modalities. A series of three cross-over experiments were conducted in healthy pain-free subjects to determine whether tactile acuity is enhanced when participants can see the skin of their back during testing. An initial randomised cross-over experiment suggested tactile acuity was significantly enhanced when participants could see their backs (t(25) = -4.226, p < 0.001, r = 0.65). However, a second replication experiment was not corroborative. Both the second (F(3,66) = 1.00, p = 0.398) and third (t(9) = 0.969, p = 0.358) experiments suggested that seeing the back did not significantly affect tactile acuity, confirming that our initial results were likely due to chance. The principle that visual feedback improves tactile acuity at the hand does not apply to the back. These results strongly suggest that attempts to enhance tactile training by incorporating vision will not offer the benefit to treatment of back pain that has been observed for treatment of hand pain.","corpus_id":3072753,"score":2},{"doc_id":"24983492","title":"Is tactile acuity altered in people with chronic pain? a systematic review and meta-analysis.","abstract":"UNLABELLED: Impaired tactile acuity in people with chronic pain conditions has been suggested to reflect altered cortical representation of the painful body part, and treatments that aim to improve tactile acuity in these conditions have shown clinical benefit. Whether abnormalities in tactile acuity are a consistent feature of chronic pain remains largely unknown. The aim of this review was to systematically evaluate the literature and use meta-analysis to establish whether tactile acuity is altered in people with chronic non-neuropathic pain. We systematically searched the literature for studies that investigated tactile acuity in people with chronic non-neuropathic pain and compared it to an appropriate control group. Sixteen studies, reporting data from 5 chronic pain conditions, were included. Data were available for 18 chronic pain populations (n = 484) and 15 control populations (n = 378). Our results suggest that tactile acuity is diminished in arthritis, complex regional pain syndrome, and chronic low back pain but not in burning mouth syndrome. The strength of the available evidence is weakened by somewhat inconsistent results and the high risk of bias observed in all of the included studies. PERSPECTIVE: This systematic review synthesizes the evidence for tactile acuity deficits in people with chronic non-neuropathic pain. The findings suggest that tactile acuity deficits may be characteristic of chronic pain. That tactile acuity training may benefit those with chronic pain disorders suggests that clinical trials may be warranted.","corpus_id":3962142,"score":2},{"doc_id":"25610384","title":"Pain sensitivity and tactile spatial acuity are altered in healthy musicians as in chronic pain patients.","abstract":"Extensive training of repetitive and highly skilled movements, as it occurs in professional classical musicians, may lead to changes in tactile sensitivity and corresponding cortical reorganization of somatosensory cortices. It is also known that professional musicians frequently experience musculoskeletal pain and pain-related symptoms during their careers. The present study aimed at understanding the complex interaction between chronic pain and music training with respect to somatosensory processing. For this purpose, tactile thresholds (mechanical detection, grating orientation, two-point discrimination) and subjective ratings to thermal and pressure pain stimuli were assessed in 17 professional musicians with chronic pain, 30 pain-free musicians, 20 non-musicians with chronic pain, and 18 pain-free non-musicians. We found that pain-free musicians displayed greater touch sensitivity (i.e., lower mechanical detection thresholds), lower tactile spatial acuity (i.e., higher grating orientation thresholds) and increased pain sensitivity to pressure and heat compared to pain-free non-musicians. Moreover, we also found that musicians and non-musicians with chronic pain presented lower tactile spatial acuity and increased pain sensitivity to pressure and heat compared to pain-free non-musicians. The significant increment of pain sensitivity together with decreased spatial discrimination in pain-free musicians and the similarity of results found in chronic pain patients, suggests that the extensive training of repetitive and highly skilled movements in classical musicians could be considered as a risk factor for developing chronic pain, probably due to use-dependent plastic changes elicited in somatosensory pathways.","corpus_id":10903921,"score":2},{"doc_id":"25858650","title":"A preliminary investigation of lumbar tactile acuity in yoga practitioners.","abstract":"BACKGROUND: Tactile acuity in the back relates to voluntary lumbo-pelvic control and is lower in chronic low back pain (CLBP) patients. Two-point discrimination (TPD) thresholds are higher, indicating decreased tactile acuity in patients with CLBP. Yoga has been shown to help relieve CLBP. OBJECTIVES: This study investigated the hypothesis that regular practitioners of yoga have increased tactile acuity (i.e., lower TPD thresholds) when compared to matched controls who regularly perform gym-based (resistance training or aerobic-type) exercise. METHOD: Tactile acuity in the low back was assessed using TPD in 16 long-term practitioners of yoga (5 Ashtanga, 5 Bikram, and 6 Iyengar practitioners) and 16 age- and gender-matched healthy controls who exercise (with weights and aerobic exercise). RESULTS: The yoga practitioners' TPD was lower than that of the exercisers, indicating greater tactile acuity in the low back. While there was no difference between the TPD of the practitioners of different yoga styles, the TPD of the Ashtanga yoga participants were significantly lower than those of the exercisers. The yogis whose main reasons to practice yoga were for \"meditation or increased mindfulness\" and for \"well-being\" showed a nonsignificant trend of higher tactile acuity than those who did yoga for \"physical exercise.\" There was no association between TPD threshold and cumulative amount of yoga practice in terms of hours per week and years of experience. However, increased hours of exercise per week correlated with higher TPD. CONCLUSION: The findings suggest that there may be a relationship between yoga practice and enhanced tactile acuity in the low back.","corpus_id":25886977,"score":2},{"doc_id":"26592230","title":"The effect of motor control and tactile acuity training on patients with non-specific low back pain and movement control impairment.","abstract":"BACKGROUND: Movement control impairment is a clinical subgroup of non-specific low back pain which can be assessed reliably. There is a strong correlation between tactile acuity and movement control suggesting these two treatments might have additive effects. The first research aim was to determine if patients with a motor control impairment demonstrated improvement in outcome with combined tactile acuity and motor control training. The second aim was to determine if tactile acuity training enhanced the effect of motor control training. METHOD: The primary study was a single-arm cohort study conducted in three physiotherapy practices in the German-speaking part of Switzerland. 40 patients (23 males and 17 females) suffering from non-specific low back pain (NSLBP) and movement control impairment were treated. Patients were assessed at baseline and immediately post treatment. Treatment included exercises to lumbopelvic control and graphesthesia training to improve tactile acuity. Treatment effects were evaluated using the Roland Morris disability questionnaire (RMQ) and the patient-specific functional scale (PSFS). The performance on a set of six movement control tests and lumbar two-point discrimination were also assessed. The results of this cohort study were compared with a historic control group which was comparable with the primary study but included only motor control exercises. RESULTS: All the outcomes improved significantly with the combined training (RMQ - 2.2 pts., PSFS - 2.8 pts.; MCTB - 2.02 pts. & TPD - 17.07 mm; all p < 0.05). In comparison to the outcomes of the historic control, there was no significant differences in movement control, patient-specific functional complaints or disability between the groups. CONCLUSIONS: The results of this study, based on a before and after intervention comparison, showed that outcome improved significantly following combined tactile acuity and motor control training. However, compared to an earlier study, the tactile acuity training did not have an additional effect to the results. The use of historical controls does not control for allocation bias and the results obtained here require verification in a randomized controlled trial.","corpus_id":42378384,"score":2},{"doc_id":"26797175","title":"The point-to-point test: A new diagnostic tool for measuring lumbar tactile acuity? Inter and intra-examiner reliability study of pain-free subjects.","abstract":"A two-point discrimination test (TPD) is commonly used to investigate lumbar tactile acuity. However, low inter-examiner reliability and difficulties in execution significantly limit its application. Therefore the aim of this study was to compare the inter- and intra-examiner reliability of a new approach, the point-to-point test (PTP), with the TPD. Twenty-one pain-free subjects attended the inter-examiner stage of the study. Eighteen of them were further recruited into an intra-examiner (reproducibility and repeatability) reliability study. PTP was performed on the three points plotted at the L3 spinal level. Point '0' overlapped with the L3 spinous process, from which points '1' and '2' were horizontally separated by 5 and 10 cm, respectively. Participants manually indicated a point previously touched by the examiner, while the distance (error) was measured. Reliability was determined with the intraclass correlation coefficient (ICC2,3). The results revealed good and moderate inter- and intra-examiner reliability at point '1' (ICC2,3 = 0.68-0.84) and good reliability at point '2' (ICC2,3 = 0.84-0.86). At point '0', reliability was moderate to poor (ICC2,3 = 0.13-0.63). TPD was characterised by a poor to moderate level of inter- (ICC2,1 = 0.51; ICC2,3 = 0.56) and intra-examiner reliability (ICC(2,1) = 0.50; ICC2,3 = 0.74). Our findings suggest that PTP is more reliable than TPD at two investigated points at the L3 spinal level. However, further research on PTP validity data is strongly warranted.","corpus_id":27046581,"score":2},{"doc_id":"27495743","title":"Short-term test-retest-reliability of conditioned pain modulation using the cold-heat-pain method in healthy subjects and its correlation to parameters of standardized quantitative sensory testing.","abstract":"BACKGROUND: Conditioned Pain Modulation (CPM) is often used to assess human descending pain inhibition. Nine different studies on the test-retest-reliability of different CPM paradigms have been published, but none of them has investigated the commonly used heat-cold-pain method. The results vary widely and therefore, reliability measures cannot be extrapolated from one CPM paradigm to another. Aim of the present study was to analyse the test-retest-reliability of the common heat-cold-pain method and its correlation to pain thresholds. METHODS: We tested the short-term test-retest-reliability within 40 ± 19.9 h using a cold-water immersion (10 °C, left hand) as conditioning stimulus (CS) and heat pain (43-49 °C, pain intensity 60 ± 5 on the 101-point numeric rating scale, right forearm) as test stimulus (TS) in 25 healthy right-handed subjects (12females, 31.6 ± 14.1 years). The TS was applied 30s before (TSbefore), during (TSduring) and after (TSafter) the 60s CS. The difference between the pain ratings for TSbefore and TSduring represents the early CPM-effect, between TSbefore and TSafter the late CPM-effect. Quantitative sensory testing (QST, DFNS protocol) was performed on both sessions before the CPM assessment. STATISTICS: paired t-tests, Intraclass correlation coefficient (ICC), standard error of measurement (SEM), smallest real difference (SRD), Pearson's correlation, Bland-Altman analysis, significance level p < 0.05 with Bonferroni correction for multiple comparisons, when necessary. RESULTS: Pain ratings during CPM correlated significantly (ICC: 0.411…0.962) between both days, though ratings for TSafter were lower on day 2 (p < 0.005). The early (day 1: 16.7 ± 11.7; day 2: 19.5 ± 11.9; ICC: 0.618, SRD: 20.2) and late (day 1: 1.7 ± 9.2; day 2: 7.6 ± 11.5; ICC: 0.178, SRD: 27.0) CPM effect did not differ significantly between both days. Both early and late CPM-effects did not correlate with the pain thresholds. CONCLUSIONS: The short-term test-retest-reliability of the early CPM-effect using the heat-cold-pain method in healthy subjects achieved satisfying results in terms of the ICC. The SRD of the early CPM effect showed that an individual change of > 20 NRS can be attributed to a real change rather than chance. The late CPM-effect was weaker and not reliable.","corpus_id":13907272,"score":2},{"doc_id":"29140929","title":"Tactile acuity (dys)function in acute nociceptive low back pain: a double-blind experiment.","abstract":"Research shows that chronic pain is related to cortical alterations that can be reflected in reduced tactile acuity, but whether acute pain perception influences tactile acuity has not been tested. Considering the biological role of nociception, it was hypothesized that nociceptive pain will lead to a rapid improvement in tactile acuity and that this effect is correlated with pain intensity and pain distribution. In this randomised double-blind controlled experiment (trial no. NCT03021278), healthy participants were exposed to 1 of 3 experimental conditions: acute, nociceptive low back pain induced by saline injection, a sham injection (without piercing the skin) potentially inducing nocebo pain, or no intervention. Tactile acuity was measured by a battery of tests, including two-point discrimination threshold (TPD), before, during the pain experience, and after it subsided. We found that TPD did not improve but deteriorated during pain induction in the experimental group compared with the control group (P < 0.001; η = 0.20) and changed from 56.94 mm (95% confidence interval: 53.43-60.44) at baseline to 64.22 mm (95% confidence interval: 60.42-68.02) during the pain experience. Maximum reported pain was a significant predictor (β = 0.55, P = 0.01) and accounted for 26% of the variance in TPD (P < 0.05). Other tests, point-to-point test and two-point estimation task, changed with a similar trend but did not reach significance. We concluded that acute, nociceptive pain does not improve but deteriorates tactile acuity linearly. The biological role of the observed phenomenon is unknown, and therefore, future studies should address this question.","corpus_id":3652320,"score":2},{"doc_id":"29180111","title":"Tactile acuity is reduced in people with chronic neck pain.","abstract":"BACKGROUND: Tactile acuity deficits have been demonstrated in a range of persistent pain conditions and may reflect underlying cortical re-organisation. OBJECTIVE: This study aimed to determine whether tactile acuity is impaired in people with chronic neck pain relative to controls, and whether deficits relate to pain location, duration and intensity. METHODS: In this cross-sectional study, 20 people with chronic neck pain (5 idiopathic neck pain; 15 whiplash-associated disorder) and 20 pain-free controls underwent two-point discrimination (TPD) testing at the neck, back and arm, and point-to-point (PTP) and graphesthesia tests of tactile acuity at the neck and arm. RESULTS: Linear mixed effects models demonstrated a significant group*body region interaction for TPD, Graphesthesia and PTP tests (Ps < 0.001), with post hoc tests showing impaired TPD in people with neck pain relative to controls at the neck, low back, and arm (P ≤ 0.001). Graphesthesia and PTP was also impaired at the neck (P < 0.001) but not the arm (P ≥ 0.48). TPD correlated with intensity and duration of pain (Pearson's r = 0.48, P < 0.05; Pearson's r = 0.77, P < 0.01). There was no sig difference between the two neck pain groups for any tactile acuity measure (TPD: P = 0.054; Graphesthesia; P = 0.67; Point to Point: P = 0.77), however, low power limited confidence in this comparison. CONCLUSION: People with chronic neck pain demonstrated tactile acuity deficits in painful and non-painful regions when measured using the TPD test, with the magnitude of deficits appearing greatest at the neck. The study also revealed a positive relationship between TPD and pain intensity/duration, further supporting the main study finding.","corpus_id":46750111,"score":2},{"doc_id":"29681809","title":"Tactile-STAR: A Novel Tactile STimulator And Recorder System for Evaluating and Improving Tactile Perception.","abstract":"Many neurological diseases impair the motor and somatosensory systems. While several different technologies are used in clinical practice to assess and improve motor functions, somatosensation is evaluated subjectively with qualitative clinical scales. Treatment of somatosensory deficits has received limited attention. To bridge the gap between the assessment and training of motor vs. somatosensory abilities, we designed, developed, and tested a novel, low-cost, two-component (bimanual) mechatronic system targeting tactile somatosensation: the Tactile-STAR-a tactile stimulator and recorder. The stimulator is an actuated pantograph structure driven by two servomotors, with an end-effector covered by a rubber material that can apply two different types of skin stimulation: brush and stretch. The stimulator has a modular design, and can be used to test the tactile perception in different parts of the body such as the hand, arm, leg, big toe, etc. The recorder is a passive pantograph that can measure hand motion using two potentiometers. The recorder can serve multiple purposes: participants can move its handle to match the direction and amplitude of the tactile stimulator, or they can use it as a master manipulator to control the tactile stimulator as a slave. Our ultimate goal is to assess and affect tactile acuity and somatosensory deficits. To demonstrate the feasibility of our novel system, we tested the Tactile-STAR with 16 healthy individuals and with three stroke survivors using the skin-brush stimulation. We verified that the system enables the mapping of tactile perception on the hand in both populations. We also tested the extent to which 30 min of training in healthy individuals led to an improvement of tactile perception. The results provide a first demonstration of the ability of this new system to characterize tactile perception in healthy individuals, as well as a quantification of the magnitude and pattern of tactile impairment in a small cohort of stroke survivors. The finding that short-term training with Tactile-STAR can improve the acuity of tactile perception in healthy individuals suggests that Tactile-STAR may have utility as a therapeutic intervention for somatosensory deficits.","corpus_id":4615636,"score":2},{"doc_id":"19501965","title":"The effect of tactile discrimination training is enhanced when patients watch the reflected image of their unaffected limb during training.","abstract":"In patients with phantom limb pain or complex regional pain syndrome (CRPS), sensory discrimination training increases tactile acuity, normalises cortical reorganisation and decreases pain. In healthy people, sensory cortical response, and tactile acuity, are greater if the participant looks towards the body part being stimulated. Does this effect enhance tactile training in CRPS patients? Ten patients underwent a 30-min tactile discrimination training session under four conditions (order randomised) in a 2 x 2 design: looking towards or away from the stimulated limb and seeing or not seeing skin. Tactile training imparted long-term improvement in tactile acuity when patients watched the reflected image of their unaffected limb in a mirror during training (that is, they looked towards the stimulated body part and could see the skin of the opposite body part in the mirror): two-point discrimination threshold (TPD) was 8mm less 2 days after training than it was before training ([95% CI=1.5-14.3mm], p<0.001). Although this condition also imparted a greater reduction in resting pain at post-treatment than the other conditions, and change in pain and change in TPD over the session were strongly related (r=0.83, p<0.001), there was no residual effect on pain at 2-day follow-up. In the other conditions, tactile acuity had returned to pre-training levels at 2-day follow-up. The results should directly improve management of CRPS, and have implications for rehabilitation of other conditions associated with nervous system injury or disease, for example stroke, in which tactile recovery is a major objective of rehabilitation.","corpus_id":8155362,"score":1},{"doc_id":"24299621","title":"The intra- and inter-rater reliability of five clinical muscle performance tests in patients with and without neck pain.","abstract":"BACKGROUND: This study investigates the reliability of muscle performance tests using cost- and time-effective methods similar to those used in clinical practice. When conducting reliability studies, great effort goes into standardising test procedures to facilitate a stable outcome. Therefore, several test trials are often performed. However, when muscle performance tests are applied in the clinical setting, clinicians often only conduct a muscle performance test once as repeated testing may produce fatigue and pain, thus variation in test results. We aimed to investigate whether cervical muscle performance tests, which have shown promising psychometric properties, would remain reliable when examined under conditions similar to those of daily clinical practice. METHODS: The intra-rater (between-day) and inter-rater (within-day) reliability was assessed for five cervical muscle performance tests in patients with (n = 33) and without neck pain (n = 30). The five tests were joint position error, the cranio-cervical flexion test, the neck flexor muscle endurance test performed in supine and in a 45°-upright position and a new neck extensor test. RESULTS: Intra-rater reliability ranged from moderate to almost perfect agreement for joint position error (ICC ≥ 0.48-0.82), the cranio-cervical flexion test (ICC ≥ 0.69), the neck flexor muscle endurance test performed in supine (ICC ≥ 0.68) and in a 45°-upright position (ICC ≥ 0.41) with the exception of a new test (neck extensor test), which ranged from slight to moderate agreement (ICC = 0.14-0.41). Likewise, inter-rater reliability ranged from moderate to almost perfect agreement for joint position error (ICC ≥ 0.51-0.75), the cranio-cervical flexion test (ICC ≥ 0.85), the neck flexor muscle endurance test performed in supine (ICC ≥ 0.70) and in a 45°-upright position (ICC ≥ 0.56). However, only slight to fair agreement was found for the neck extensor test (ICC = 0.19-0.25). CONCLUSIONS: Intra- and inter-rater reliability ranged from moderate to almost perfect agreement with the exception of a new test (neck extensor test), which ranged from slight to moderate agreement. The significant variability observed suggests that tests like the neck extensor test and the neck flexor muscle endurance test performed in a 45°-upright position are too unstable to be used when evaluating neck muscle performance.","corpus_id":1931582,"score":1},{"doc_id":"24945099","title":"Reliability study of thermal quantitative sensory testing in healthy Chinese.","abstract":"BACKGROUND: Test-retest reliability is important to establish for any diagnostic tool. The reliability of quantitative sensory testing (QST) in the trigeminal region has recently been described in Caucasians as well as differences in absolute thresholds and responses between Caucasians and Chinese. However, the test-retest reliability has not been determined in a Chinese population. OBJECTIVE: To provide novel information on the test-retest reliability of thermal QST in the trigeminal and spinal system in healthy Chinese. METHODS: Twenty healthy volunteers (10 women and 10 men) participated. Cold detection threshold (CDT), warm detection threshold (WDT), cold pain threshold (CPT), and heat pain threshold (HPT) were measured at two sites: the surface of the left hand and the left masseter. The testing was performed over three consecutive stimuli trials, three sessions conducted on one day and repeated one week later. Data were analyzed with intra-tester reliability test and four-way analysis of variance (ANOVA) for repeated measures. RESULTS: There was a tendency for the first trial in CDT (p = 0.005), CPT (p = 0.02), and HPT (p < 0.001) to reflect higher sensitivity than the subsequent two trials. Most variables showed acceptable to excellent reliability and non-significant difference across different trials (ICC: 0.912-0.989), sessions (ICC: 0.791-0.977), and days (ICC: 0.415-0.837). Between-site differences were significant for CDT (p = 0.003) and HPT (p = 0.045) with higher sensitivity at the masseter muscle. There were significant gender differences with higher sensitivity in women for CPT (p = 0.001) and HPT (p = 0.001). CONCLUSION: Test site and gender affect thermal thresholds substantially. The test-retest reliability of most thermal threshold measures were acceptable for assessing somatosensory function, however, innocuous thresholds appear to be associated with larger variability than noxious thresholds in a Chinese population.","corpus_id":36671079,"score":1},{"doc_id":"25161897","title":"Intersession reliability of fMRI activation for heat pain and motor tasks.","abstract":"As the practice of conducting longitudinal fMRI studies to assess mechanisms of pain-reducing interventions becomes more common, there is a great need to assess the test-retest reliability of the pain-related BOLD fMRI signal across repeated sessions. This study quantitatively evaluated the reliability of heat pain-related BOLD fMRI brain responses in healthy volunteers across 3 sessions conducted on separate days using two measures: (1) intraclass correlation coefficients (ICC) calculated based on signal amplitude and (2) spatial overlap. The ICC analysis of pain-related BOLD fMRI responses showed fair-to-moderate intersession reliability in brain areas regarded as part of the cortical pain network. Areas with the highest intersession reliability based on the ICC analysis included the anterior midcingulate cortex, anterior insula, and second somatosensory cortex. Areas with the lowest intersession reliability based on the ICC analysis also showed low spatial reliability; these regions included pregenual anterior cingulate cortex, primary somatosensory cortex, and posterior insula. Thus, this study found regional differences in pain-related BOLD fMRI response reliability, which may provide useful information to guide longitudinal pain studies. A simple motor task (finger-thumb opposition) was performed by the same subjects in the same sessions as the painful heat stimuli were delivered. Intersession reliability of fMRI activation in cortical motor areas was comparable to previously published findings for both spatial overlap and ICC measures, providing support for the validity of the analytical approach used to assess intersession reliability of pain-related fMRI activation. A secondary finding of this study is that the use of standard ICC alone as a measure of reliability may not be sufficient, as the underlying variance structure of an fMRI dataset can result in inappropriately high ICC values; a method to eliminate these false positive results was used in this study and is recommended for future studies of test-retest reliability.","corpus_id":16090306,"score":1},{"doc_id":"25477032","title":"Reliability, construct and discriminative validity of clinical testing in subjects with and without chronic neck pain.","abstract":"BACKGROUND: The reliability of clinical tests for the cervical spine has not been adequately evaluated. Six cervical clinical tests, which are low cost and easy to perform in clinical settings, were tested for intra- and inter-examiner reliability, and two performance tests were assessed for test-retest reliability in people with and without chronic neck pain. Moreover, construct and between-group discriminative validity of the tests were examined. METHODS: Twenty-one participants with chronic neck pain and 21 asymptomatic participants were included. Intra- and inter-reliability were evaluated for the Cranio-Cervical Flexion Test (CCFT), Range of Movement (ROM), Joint Position Error (JPE), Gaze Stability (GS), Smooth Pursuit Neck Torsion Test (SPNTT), and neuromuscular control of the Deep Cervical Extensors (DCE). Test-retest reliability was assessed for Postural Control (SWAY) and Pressure Pain Threshold (PPT) over tibialis anterior, infraspinatus and the C3-C4 segment. RESULTS: Intraclass Correlation Coefficient (ICC) for intra- and inter-examiner reliability was highest for ROM (range: 0.80 to 0.94), DCE (0.75 to 0.90) and CCFT (0.63 to 0.86). JPE had the lowest ICC (0.02 to 0.66). Intra- and inter-reliability for GS and SPNTT showed kappa ranging from 0.66 to 0.92, and 0.57 to 0.78 (prevalence adjusted), respectively. For the test-retest study, ICC was 0.83 to 0.89 for PPT and 0.39 to 0.79 for SWAY. Construct validity was satisfactory for all tests, except JPE. Significant between group discriminative validity was found for CCFT, ROM, GS, SPNTT and PPT, however, differences were within the limits of the minimal detectable change. CONCLUSIONS: The majority of the tests evaluated showed satisfactory reliability and construct validity supporting their use in the clinical evaluation of patients with chronic neck pain.","corpus_id":7681661,"score":1},{"doc_id":"27796191","title":"Disrupted Tactile Acuity in People With Achilles Tendinopathy: A Preliminary Case-Control Investigation.","abstract":"Study Design Controlled laboratory study, preliminary case-control design. Background The mechanisms that contribute to Achilles tendinopathy remain poorly understood. The disparity between pain experience and peripheral pathology demonstrated in patients with Achilles tendinopathy suggests that changes in central nervous system function may be involved. Objectives To investigate whether lower-limb tactile acuity is impaired in people with nonacute Achilles tendinopathy. Methods Thirteen consecutive participants with nonacute midportion Achilles tendinopathy and 13 healthy controls were enrolled. Two-point discrimination thresholds over the affected Achilles tendon, unaffected tendon, and tendon of healthy controls were evaluated. Independent and dependent t tests were used to compare group means. Results Two-point discrimination distance over the affected limb in participants with Achilles tendinopathy was significantly increased when compared to the unaffected limb (mean difference, 11.7 mm; 95% confidence interval [CI]: 1.9, 21.5; P = .02) and to healthy controls (mean difference, 13.1 mm; 95% CI: 1.6, 24.6; P = .03). There was no significant difference between the healthy controls and the unaffected side in people with Achilles tendinopathy (mean difference, 1.4 mm; 95% CI: -7.9, 5.1; P = .66). Conclusion These data provide the first evidence of reduced 2-point discrimination over the affected tendon in patients with Achilles tendinopathy. Further research is needed to determine the cause for the change in tactile acuity. J Orthop Sports Phys Ther 2016;46(12):1061-1064. Epub 30 Oct 2016. doi:10.2519/jospt.2016.6514.","corpus_id":22168443,"score":1},{"doc_id":"28008644","title":"Test-retest reliability of quantitative sensory testing for mechanical somatosensory and pain modulation assessment of masticatory structures.","abstract":"Assessing the reliability of medical measurements is a crucial step towards the elaboration of an applicable clinical instrument. There are few studies that evaluate the reliability of somatosensory assessment and pain modulation of masticatory structures. This study estimated the test-retest reliability, that is over time, of the mechanical somatosensory assessment of anterior temporalis, masseter and temporomandibular joint (TMJ) and the conditioned pain modulation (CPM) using the anterior temporalis as the test site. Twenty healthy women were evaluated in two sessions (1 week apart) by the same examiner. Mechanical detection threshold (MDT), mechanical pain threshold (MPT), wind-up ratio (WUR) and pressure pain threshold (PPT) were assessed on the skin overlying the anterior temporalis, masseter and TMJ of the dominant side. CPM was tested by comparing PPT before and during the hand immersion in a hot water bath. anova and intra-class correlation coefficients (ICCs) were applied to the data (α = 5%). The overall ICCs showed acceptable values for the test-retest reliability of mechanical somatosensory assessment of masticatory structures. The ICC values of 75% of all quantitative sensory measurements were considered fair to excellent (fair = 8·4%, good = 33·3% and excellent = 33·3%). However, the CPM paradigm presented poor reliability (ICC = 0·25). The mechanical somatosensory assessment of the masticatory structures, but not the proposed CPM protocol, can be considered sufficiently reliable over time to evaluate the trigeminal sensory function.","corpus_id":206123658,"score":1},{"doc_id":"28558952","title":"Intra- and inter-rater reliability of neutral head position and target head position tests in patients with and without neck pain.","abstract":"BACKGROUND: Cervical proprioception is a common term used in neck rehabilitation, and it is examined using neutral head position (NHP) and target head position (THP) tests. OBJECTIVE: To investigate intra- and inter-rater reliability of the NHP and THP tests in patients with neck pain and in healthy controls. METHODS: The intra-rater (between-day) and inter-rater (within-day) reliability of the NHP and THP tests were assessed in 36 patients with neck pain and 33 healthy subjects. NHP testing was evaluated in cervical extension, while THP testing was evaluated in six directions of cervical motion: cervical flexion, extension, side bending right, side bending left, rotation right, and rotation left. RESULTS: The intra-rater reliability for the NHP tests had intraclass correlation coefficient (ICC) values of 0.74-0.78 and a standard error of measurement (SEM) of 1.78-1.88; the THP tests had ICC values of 0.70-0.83 and SEM of 1.45-2.45. Likewise, inter-rater reliability for NHP had ICC values of 0.74-0.79 and SEM of 1.79-1.87. For the THP test, the inter-rater reliability had ICC values of 0.62-0.84 and SEM of 1.50-2.23. CONCLUSION: Intra- and inter-rater reliability ranged from good to very good agreement both for NHP and for THP tests of cervical proprioception.","corpus_id":10899571,"score":1},{"doc_id":"29174222","title":"Inter- and intrarater reliability of two proprioception tests using clinical applicable measurement tools in subjects with and without knee osteoarthritis.","abstract":"BACKGROUND: The therapeutic value of proprioceptive-based exercises in knee osteoarthritis (KOA) management warrants investigation of proprioceptive testing methods easily accessible in clinical practice. OBJECTIVE: To estimate inter- and intrarater reliability of the knee joint position sense (KJPS) test and knee force sense (KFS) test in subjects with and without KOA. DESIGN: Cross-sectional test-retest design. METHOD: Two blinded raters performed independently repeated measures of the KJPS and KFS test, using an analogue inclinometer and handheld dynamometer, respectively, in eight KOA patients (12 symptomatic knees) and 26 healthy controls (52 asymptomatic knees). Intraclass correlation coefficients (ICCs; model 2,1), standard error of measurement (SEM) and minimal detectable change with 95% confidence bounds (MDC95) were calculated. RESULTS: For KJPS, results showed good to excellent test-retest agreement (ICCs 0.70-0.95 in KOA patients; ICCs 0.65-0.85 in healthy controls). A 2° measurement error (SEM 1°) was reported when measuring KJPS in multiple test positions and calculating mean repositioning error. Testing KOA patients pre and post therapy a repositioning error larger than 4° (MDC95) is needed to consider true change. Measuring KFS using handheld dynamometry showed poor to fair interrater and poor to excellent intrarater reliability in subjects with and without KOA. CONCLUSIONS: Measuring KJPS in multiple test positions using an analogue inclinometer and calculating mean repositioning error is reliable and can be used in clinical practice. We do not recommend the use of the KFS test to clinicians. Further research is required to establish diagnostic accuracy and validity of our KJPS test in larger knee pain populations.","corpus_id":37957780,"score":1},{"doc_id":"29282073","title":"Responsiveness of clinical tests for people with neck pain.","abstract":"BACKGROUND: Responsiveness of a clinical test is highly relevant in order to evaluate the effect of a given intervention. However, the responsiveness of clinical tests for people with neck pain has not been adequately evaluated. The objective of the present study was to examine the responsiveness of four clinical tests which are low cost and easy to perform in a clinical setting, including the craniocervical flexion test, cervical active range of movement, test for the cervical extensors and pressure pain threshold testing. METHODS: This study is a secondary analysis of data collected in a previously published randomised controlled trial. Participants were randomized to either physical training, exercises and pain education combined or pain education only. Participants were tested on the clinical tests at baseline and at 4-month follow-up. An anchor-based approach using Receiver Operator Characteristics (ROC) curves was used to evaluate responsiveness of the clinical tests. The Neck Disability Index was used to discriminate between those who had improved and those who were unchanged at the 4-month follow-up. Minimum Clinically Important Difference (MCID), together with sensitivity, specificity, positive and negative predictive values, in addition to positive and negative likelihood ratios were calculated. RESULTS: In total, 164 participants completed the 4 month follow up. One-hundred forty four participants were classified as unchanged whereas 20 patients were considered to be improved. Twenty-six participants didn't complete all of the clinical tests, leaving a total of 138 to be included for analyses. Area Under Curve (AUC) ranged from 0.50-0.62 for the clinical tests, and were all below an acceptable level. MCID was generally large, and the corresponding sensitivity and specificity was low with sensitivity ranging from 20 to 60%, and specificity from 54 to 86%. LR+ (0.8-2.07) and LR- (0.7-1.1) showed low diagnostic value for all variables, with PPV ranging from 12.1 to 26.1 and NPV ranging from 84.7 to 89.2. CONCLUSION: Responsiveness of the included clinical tests was generally low when using change in NDI score as the anchor from baseline to the 4-month follow up. Further investigations of responsiveness are warranted, possibly using other anchors, which to a higher degree resemble similar dimensions as the clinical tests.","corpus_id":25302890,"score":1},{"doc_id":"20671244","title":"Psychometric comparisons of 3 functional ambulation measures for patients with stroke.","abstract":"BACKGROUND AND PURPOSE: We compared the test-retest reliability, validity, and responsiveness of the Dynamic Gait Index, the 4-item Dynamic Gait Index, and the Functional Gait Assessment for assessment of walking in patients with stroke. METHODS: Forty-five outpatients participating in the validity and responsiveness study were tested using the 3 walking measures as well as the 10-m walk test, Barthel Index, and Postural Assessment Scale for Stroke Patients. We tested them during the first week, then again after 2 months and 5 months of therapy. Another 48 chronic patients completed the 3 measures twice, 1 week apart, in the test-retest reliability study. RESULTS: Thirty-five participants completed 3 time-point assessments. The Functional Gait Assessment showed the least floor and ceiling effects, indicating it has the best discriminative ability for patients with stroke with high walking function. We found the 3 measures were highly correlated with each other, indicating excellent concurrent validity, and all measures at the first week of therapy were moderately to highly correlated with the Barthel Index scores at 5 months, indicating good predictive validity. Responsiveness of the 3 measures was moderate during a 5-month period, and all showed good test-retest reliability. The minimal detectable changes between tests indicate acceptable random error. CONCLUSIONS: All 3 measures showed sufficient validity, responsiveness, and reliability for assessment of walking function in patients with stroke undergoing rehabilitation, but the Functional Gait Assessment is recommended for its psychometric properties.","corpus_id":2664925,"score":0},{"doc_id":"22152048","title":"Test-retest reliability and construct validity of the ENERGY-child questionnaire on energy balance-related behaviours and their potential determinants: the ENERGY-project.","abstract":"BACKGROUND: Insight in children's energy balance-related behaviours (EBRBs) and their determinants is important to inform obesity prevention research. Therefore, reliable and valid tools to measure these variables in large-scale population research are needed. OBJECTIVE: To examine the test-retest reliability and construct validity of the child questionnaire used in the ENERGY-project, measuring EBRBs and their potential determinants among 10-12 year old children. METHODS: We collected data among 10-12 year old children (n = 730 in the test-retest reliability study; n = 96 in the construct validity study) in six European countries, i.e. Belgium, Greece, Hungary, the Netherlands, Norway, and Spain. Test-retest reliability was assessed using the intra-class correlation coefficient (ICC) and percentage agreement comparing scores from two measurements, administered one week apart. To assess construct validity, the agreement between questionnaire responses and a subsequent face-to-face interview was assessed using ICC and percentage agreement. RESULTS: Of the 150 questionnaire items, 115 (77%) showed good to excellent test-retest reliability as indicated by ICCs > .60 or percentage agreement ≥ 75%. Test-retest reliability was moderate for 34 items (23%) and poor for one item. Construct validity appeared to be good to excellent for 70 (47%) of the 150 items, as indicated by ICCs > .60 or percentage agreement ≥ 75%. From the other 80 items, construct validity was moderate for 39 (26%) and poor for 41 items (27%). CONCLUSIONS: Our results demonstrate that the ENERGY-child questionnaire, assessing EBRBs of the child as well as personal, family, and school-environmental determinants related to these EBRBs, has good test-retest reliability and moderate to good construct validity for the large majority of items.","corpus_id":16154288,"score":0},{"doc_id":"22415358","title":"Assessing the reliability and validity of a shorter walk test compared with the 10-Meter Walk Test for measurements of gait speed in healthy, older adults.","abstract":"BACKGROUND AND PURPOSE: Walking speed is associated with several health-related outcomes. Research examining how differences in test walking distance affect walking speed reliability and validity is limited. The primary purpose of this study was to examine the reliability and concurrent validity of gait speed measurements obtained from a 4-Meter Walk Test compared with the commonly used 10-Meter Walk Test. A second objective was to similarly examine 2 different timing methods: stopwatch and automatic timers. METHODS: Forty-three healthy, older adults (mean age = 84.3 ± 6.9 years) performed 3 consecutive walking trials on the 4- and 10-Meter Walk Tests at their self-selected walking speed. RESULTS: Gait speed measurements for both tests were shown to have excellent test-retest reliability (ICC values of 0.96-0.98), with similar results for stopwatch and automatic timer assessments (ICC values of 0.99-1.00). Standard error of the measurement (SEM) values were small (0.004-0.008 m/s) across measurement methods. While the ICC value for gait speed measurements between the 2 walk tests was 0.93, the Bland-Altman analysis revealed a discrepancy of ±0.15 to ±0.17 m/s between measurement methods. DISCUSSION: Both 4- and 10-m gait speed assessments had excellent test-retest reliability with similar SEM and minimal detectable change values. There was little difference in SEM values between the 2 timing methods. While the mean difference in gait speed between the 4- and 10-Meter Walk Tests was small, the range of the measurement differences was large enough to potentially mask meaningful changes in gait speed over time if both methods were used interchangeably. CONCLUSIONS: While the reliability of both walking tests is excellent, the 4-Meter Walk Test does not exhibit a high enough degree of concurrent validity with the 10-Meter Walk Test to be used interchangeably for gait speed assessments in healthy, older adults. We therefore recommend using the 10-Meter Walk Test to obtain the most valid clinical assessment of walking speed when using it as a 1-time indicator of health status.","corpus_id":44406711,"score":0},{"doc_id":"22888983","title":"Test-retest reliability and construct validity of the ENERGY-parent questionnaire on parenting practices, energy balance-related behaviours and their potential behavioural determinants: the ENERGY-project.","abstract":"BACKGROUND: Insight in parental energy balance-related behaviours, their determinants and parenting practices are important to inform childhood obesity prevention. Therefore, reliable and valid tools to measure these variables in large-scale population research are needed. The objective of the current study was to examine the test-retest reliability and construct validity of the parent questionnaire used in the ENERGY-project, assessing parental energy balance-related behaviours, their determinants, and parenting practices among parents of 10-12 year old children. FINDINGS: We collected data among parents (n = 316 in the test-retest reliability study; n = 109 in the construct validity study) of 10-12 year-old children in six European countries, i.e. Belgium, Greece, Hungary, the Netherlands, Norway, and Spain. Test-retest reliability was assessed using the intra-class correlation coefficient (ICC) and percentage agreement comparing scores from two measurements, administered one week apart. To assess construct validity, the agreement between questionnaire responses and a subsequent interview was assessed using ICC and percentage agreement. All but one item showed good to excellent test-retest reliability as indicated by ICCs > .60 or percentage agreement ≥ 75%. Construct validity appeared to be good to excellent for 92 out of 121 items, as indicated by ICCs > .60 or percentage agreement ≥ 75%. From the other 29 items, construct validity was moderate for 24 and poor for 5 items. CONCLUSIONS: The reliability and construct validity of the items of the ENERGY-parent questionnaire on multiple energy balance-related behaviours, their potential determinants, and parenting practices appears to be good. Based on the results of the validity study, we strongly recommend adapting parts of the ENERGY-parent questionnaire if used in future research.","corpus_id":48561,"score":0},{"doc_id":"23153836","title":"The assessment of cervical sensory motor control: a systematic review focusing on measuring methods and their clinimetric characteristics.","abstract":"BACKGROUND: Cervical sensorimotor control (CSMC) becomes increasingly important in the assessment and treatment of patients with neck pain. This review aims to compare commonly used CSMC measuring methods in terms of required tasks, measuring device and clinimetric properties. SEARCH METHODS: A systematic review of two databases, followed by methodological quality assessment (CBO guidelines). RESULTS: The methodological quality of 34 included articles was generally good (five to seven out of eight), the inter-rater agreement was excellent (κw=0.966, p<0.01). Following tasks were found: head repositioning accuracy to the neutral head position (HRA-to-NHP) and to a target position (HRA-to-target), a virtual reality test, a continuous linear movement technique (CLMT) and an object following non-linear movement technique (NLMT) (The Fly™). Test-retest reliability was fair to excellent (ICC 0.35-0.87) for the HRA-to-NHP, very bad to excellent (ICC 0.01-0.90) for the HRA-to-target, fair to good (ICC 0.25-0.77) for the virtual reality test and moderate to excellent (ICC: 0.60-0.86) for The Fly™. The reliability of the CLMT was not documented. The HRA-to-NHP, The Fly™ and the CLMT can discriminate between patients with neck complaints and controls (discriminant validity). Currently, only The Fly™ can discriminate between different patient populations (post-traumatic and non-traumatic neck pain). The sensitivity, specificity and responsiveness of the methods have to be assessed in future research. CONCLUSIONS: The dynamic method The Fly™ appears to be more reliable than the HRA-to-NHP and is able to discriminate between different patient populations. The diagnostic potential is to be confirmed in future research.","corpus_id":9754556,"score":0},{"doc_id":"23362555","title":"The oncology acuity tool: a reliable, valid method for measuring patient acuity for nurse assignment decisions.","abstract":"BACKGROUND AND PURPOSE: Matching nurse assignments with patient acuity has critical implications for providing safe, effective, and efficient care. Despite this, we lack well-established methods for accurate assessment of acuity. This study aimed to evaluate the reliability and validity of the Oncology Acuity Tool (OAT), which is used for determining nurse assignments. METHODS: Inter-rater reliability and concurrent validity were assessed via surveys of current users of the tool. Content validity data were collected from expert oncology nurses. Predictive validity was assessed by tracking patients who sustained either of two acute events. RESULTS: Findings included high inter-rater reliability, moderately strong concurrent validity, and moderate content validity. Acuity significantly predicted rapid response team consults but not falls. CONCLUSIONS: The OAT demonstrated sufficient reliability and validity for measuring acuity prospectively in this population.","corpus_id":19628927,"score":0},{"doc_id":"23522388","title":"The Swedish version of OMAS is a reliable and valid outcome measure for patients with ankle fractures.","abstract":"BACKGROUND: The aim of this study was to evaluate the test-retest reliability and the validity of the self-reported questionnaire Olerud-Molander Ankle Score (OMAS) in subjects after an ankle fracture. METHODS: When evaluating the test-retest reliability of the OMAS, 42 subjects surgically treated due to an ankle fracture participated 12 months after injury. OMAS was completed by the patients on two occasions at one to two weeks' interval. Concurrent criterion validity was evaluated using the five subscales of the Foot and Ankle Outcome Score (FAOS) and global self-rating function (GSRF), which is a five-grade Likert scale with the alternatives: \"very good\", \"good\", \"fair\", \"poor\", \"very poor\". Forty-six patients participated in the validation against FAOS, and for GSRF 105 patients participated at 6 months and 99 at 12 months. Uni-, bi- and trimalleolar fractures were all included and both non-rigid and rigid surgical techniques were used. All fractures healed without complications. Before analysis of the results the five groups according to GSRF were reduced to three: \"good\", \"fair\" and \"poor\". Test-retest reliability was assessed using Spearman's rank correlation, the intraclass correlation coefficient (ICC), the standard error of measurement (SEM and SEM%) and the smallest real difference (SRD and SRD%). The Cronbach's alpha score and validity versus FAOS was assessed using Spearman's rank correlation and validity versus GSRF using the Kruskal-Wallis Test and the Mann-Whitney U-Test as ad hoc analyses. RESULTS: The test-retest reliability correlation coefficient obtained was rho = 0.95 and ICC = 0.94. The SEM was 4.4 points and SEM% 5.8% and should be interpreted as the smallest change that indicates a real change of clinical interest for a group of subjects. The SRD was 12 points and SRD% 15.8% and should be interpreted as the smallest change that indicates a real change of clinical interest for a single subject. The correlation coefficients versus the five subscales of FAOS ranged from rho = 0.80 to 0.86. There were significant differences between GSRF groups \"good\", \"fair\" and \"poor\" (p < 0.001) at both the six-month and the 12-month follow-up. The internal consistency for the OMAS was 0.76. The effect size between results from 6-month and 12-month follow-up turned out be 0.44 and should be considered as medium. CONCLUSION: The results showed that the test-retest reliability of the Swedish version of OMAS was very high in subjects after an ankle fracture and the standard error of measurement was low. Furthermore the OMAS was found to be valid using both the five subscales of FAOS and the GSRF. The OMAS can thus be used as an outcome measure after an ankle fracture.","corpus_id":2677831,"score":0},{"doc_id":"23561578","title":"Reliability and validity of the weight status and dietary intake measures in the COMPASS questionnaire: are the self-reported measures of body mass index (BMI) and Canada's food guide servings robust?","abstract":"BACKGROUND: The COMPASS study is designed to follow a cohort of ~30,000 grade 9 to 12 students attending ~60 secondary schools for four years to understand how changes in school characteristics (policies, programs, built environment) are associated with changes in youth health behaviours. Since the student-level questionnaire for COMPASS (Cq) is designed to facilitate multiple large-scale school-based data collections using passive consent procedures, the Cq is only comprised of self-reported measures. The present study assesses the 1-week (1 wk) test-retest reliability and the concurrent validity of the Cq measures for weight status and dietary intake. METHODS: Validation study data were collected from 178 grade 9 students in Ontario (Canada). At time 1 (T1), participants completed the Cq and daily recoding of their dietary intake using the web-based eaTracker tool. After one week, (T2), students completed the Cq again, participants submitted their daily eaTracker logs and staff measured their height and weight. Test-retest reliability of the self-reported (SR) weight status and dietary intake measures at T1 and T2, and the concurrent validity of the objectively measured and SR weight status and dietary intake measures at T2 were examined using intraclass correlation coefficients (ICC). RESULTS: Test-retest reliability for SR height (ICC 0.96), weight (ICC 0.99), and BMI (ICC 0.95) are considered substantial. The concurrent validity for SR height (ICC 0.88), weight (ICC 0.95), and BMI (ICC 0.84) are also considered substantial. The test-retest reliability for SR dietary intake for fruits and vegetables (ICC 0.68) and milk and alternatives (ICC 0.69) are considered moderate, whereas meat and alternatives (ICC 0.41), and grain products (ICC 0.56) are considered fair. The concurrent validity for SR dietary intake identified that fruits and vegetables (ICC 0.53), milk and alternatives (ICC 0.60), and grain products (ICC 0.41) are considered fair, whereas meat and alternatives (ICC 0.34) was considered slight. CONCLUSIONS: While the test-retest reliability of the measures used in this study were all high, the concurrent validity of the measures was considered acceptable. The results support the use of the self-reported COMPASS weight status and dietary intake measures for use in research where objective measures are not possible.","corpus_id":3534949,"score":0},{"doc_id":"24168373","title":"Observer ratings of neighborhoods: comparison of two methods.","abstract":"BACKGROUND: Although neighborhood characteristics have important relationships with health outcomes, direct observation involves imperfect measurement. The African American Health (AAH) study included two observer neighborhood rating systems (5-item Krause and 18-item AAH Neighborhood Assessment Scale [NAS]), initially fielded at two different waves. Good measurement characteristics were previously shown for both, but there was more rater variability than desired. In 2010 both measures were re-fielded together, with enhanced training and field methods implemented to decrease rater variability while maintaining psychometric properties. METHODS: AAH included a poor inner city and more heterogeneous suburban areas. Four interviewers rated 483 blocks, with 120 randomly-selected blocks rated by two interviewers. We conducted confirmatory factor analysis of scales and tested the Krause (5-20 points), AAH 18-item NAS (0-28 points), and a previous 7-item and new 5-item versions of the NAS (0-17 points, 0-11 points). Retest reliability for items (kappa) and scales (Intraclass Correlation Coefficient [ICC]) were calculated overall and among pre-specified subgroups. Linear regression assessed interviewer effects on total scale scores and assessed concurrent validity on lung and lower body functions. Mismeasurement effects on self-rated health were also assessed. RESULTS: Scale scores were better in the suburbs than in the inner city. ICC was poor for the Krause scale (ICC=0.19), but improved if the retests occurred within 10 days (ICC=0.49). The 7- and 5-item NAS scales had better ICCs (0.56 and 0.62, respectively), and were higher (0.71 and 0.73) within 10 days. Rater variability for the Kraus and 5- and 7-item NAS scales was 1-3 points (compared to the supervising rater). Concurrent validity was modest, with residents living in worse neighborhood conditions having worse function. Unadjusted estimates were biased towards the null compared with measurement-error corrected estimates. CONCLUSIONS: Enhanced field protocols and rater training did not improve measurement quality. Specifically, retest reliability and interviewer variability remained problematic. Measurement error partially reduced, but did not eliminate concurrent validity, suggesting there are robust associations between neighborhood characteristics and health outcomes. We conclude that the 5-item AAH NAS has sufficient reliability and validity for further use. Additional research on the measurement properties of environmental rating methods is encouraged.","corpus_id":2867997,"score":0},{"doc_id":"24423109","title":"Head-eye movement control tests in patients with chronic neck pain; inter-observer reliability and discriminative validity.","abstract":"BACKGROUND: Head-eye movement control deficit is an identified problem in patients with chronic neck pain, particularly in cases of whiplash associated disorders (WAD). To date, there is no evidence concerning the reliability and validity of visually assessed active head-eye movement control tests. Therefore, the objectives of the present cross-sectional study were, a) to develop a test battery; and b) to investigate inter-observer reliability and discriminative validity in patients with chronic neck pain compared to healthy controls. METHODS: The study was conducted at two physiotherapy clinics in Switzerland. Ethics Committee approval was obtained. Ten active head-eye coordination tests, on 23 patients with chronic neck pain and associated symptoms and 19 healthy controls, were videotaped. The tests included eye movements in the neutral head position and 45° relative neck rotation, gaze stability and sequential head-eye movements. All tests were performed in the sitting and standing positions. Two blinded physiotherapists independently rated the randomized videos. Performance was rated as \"negative\", \"moderately positive\" or \"clearly positive\". Weighted kappa (wK) and 95% confidence intervals (CI) were calculated to investigate inter-observer reliability. Good reliability was defined as wK >0.5 with a lower boundary of 95% CI >0.2. Odds ratios (to define cut-off points) and the distribution of the classificator, numbers of positive tests, were calculated. RESULTS: Three out of ten tests showed \"excellent\" (wK 0.82 to 0.86), five out of ten tests showed \"substantial\" (wK 0.69 to 0.79) and two out of ten tests showed \"moderate\" (wK 0.54 to 0.59) reliability. Results were comparable in the sitting and standing positions. On average, three out of five tests were rated positive in patients and one out of five tests was rated positive in healthy controls. An odds ratio of 13.3 to 18.6 was obtained using ≥2/5 tests as a cut-off point. CONCLUSION: Visual assessment by physiotherapists of head-eye movement control tests is reliable. The test battery is able to discriminate between patients with chronic neck pain and healthy controls. There were no differences in performance between the sitting and standing positions. The test battery can therefore be reduced to five tests. Further research is needed to identify the test-retest stability and responsiveness.","corpus_id":6098885,"score":0},{"doc_id":"24452650","title":"Craniofacial pain and disability inventory (CF-PDI): development and psychometric validation of a new questionnaire.","abstract":"BACKGROUND: Orofacial pain, headaches, and neck pain are very common pain conditions in the general population and might be associated in their pathophysiology, although this is not yet clarified. The development and validation of a prediction inventory is important to minimize risks. Most recent questionnaires have not focused on pain, but pain is the common symptom in temporomandibular disorders, headaches, and neck pain. It is necessary to provide tools for these conditions. OBJECTIVES: The purpose of this study is to present the development and analysis of the factorial structure and psychometric properties of a new self-administered questionnaire (Craniofacial Pain and Disability Inventory [CF-PDI]) designed to measure pain, disability, and functional status of the mandibular and craniofacial regions. STUDY DESIGN: Multicenter, prospective, cross-sectional, descriptive survey design. A secondary analysis of the reliability of the measures was a longitudinal, observational study. SETTING: A convenience sample was recruited from a hospital and 2 specialty clinics in Madrid, Spain. METHODS: The study sample consisted of 192 heterogeneous chronic craniofacial pain patients. A sub-sample of 106 patients was asked to answer the questionnaire a second time, to assess the test-retest reliability. The development and validation of the CF-PDI were conducted using the standard methodology, which included item development, cognitive debriefing, and psychometric validation. The questionnaire was assessed for the following psychometric properties: internal consistency (Cronbach's α); floor and ceiling effects; test-retest reliability (Intraclass Correlation Coefficient [ICC]; Bland and Altman method); construct validity (exploratory factor analysis); responsiveness (standard error of measurement [SEM] and minimal detectable change [MDC]); and convergent validity (Pearson correlation coefficient), by comparing visual analog scale (VAS), the Tampa Scale for Kinesiophobia (TSK-11), the Pain Catastrophizing Scale (PCS), the Neck Disability Index (NDI), and the Headache Impact Test-6 (HIT-6). Multiple linear regression analysis was used to estimate the strength of the associations with theoretically similar constructs. RESULTS: The final version of the CF-PDI consists of 21 items. Exploratory factor analysis revealed 2 factors (\"pain and disability\" and \"jaw functional status\"), both with an eigenvalue greater than one, explaining 44.77% of the variance. Floor or ceiling effects were not observed. High internal consistency of the CF-PDI (Cronbach's α: 0.88) and also of the 2 subscales (Cronbach's α: 0.80 - 0.86) was confirmed. ICC was found to be 0.90 (95% confidence interval [CI] 0.86 - 0.93), which was considered to be excellent test-retest reliability. The SEM and MDC were 2.4 and 7 points, respectively. The total CF-PDI score showed a moderate correlation with most of the assessed questionnaires (r = 0.36 - 0.52) and a strong correlation with the NDI (r = 0.65; P < 0.001). The NDI, VAS, and TSK-11 were predictors of CF-PDI. LIMITATIONS: Only self-reported measures were considered for convergent validity. Future research should use physical tests to explore the clinical signs relating to pain and disability. CONCLUSION: The CF-PDI showed good psychometric properties. Based on the findings of this study, the CF-PDI can be used in research and clinical practice for the assessment of patients with craniofacial pain.","corpus_id":35392251,"score":0},{"doc_id":"24871639","title":"Repeatability of visual acuity testing using a psychometric function.","abstract":"PURPOSE: To evaluate the repeatability of a new method of measurement of visual acuity by use of a psychometric function. METHODS: The visual acuity of 15 healthy adults was measured by use of a psychometric function (PFVA) and by use of a conventional method using a decimal visual acuity chart (DeVA). We performed two tests. To evaluate intra-rater reliability, a tester measured the visual acuity three times for each subject, and the intraclass correlation coefficients, ICC (1,1), were calculated for PFVA and DeVA. Next, to evaluate inter-rater reliability, three testers measured the visual acuity for one subject, and the ICC (2,1) were calculated for PFVA and DeVA. The PFVA and DeVA of five subjects with ocular diseases were also measured. RESULTS: In the evaluation of intra-rater reliability, the ICC (1,1) of the DeVA was 0.83 and the ICC (1,1) of the PFVA was 0.95. In the evaluation of inter-rater reliability, the ICC (2,1) of the DeVA was 0.88 and the ICC (2,1) of the PFVA was 0.93. In both tests the standard deviations of the PFVA were significantly lower than those of the DeVA. For four of the five subjects with ocular diseases, the PFVA was significantly improved by treatment. CONCLUSION: The repeatability of our method is better than that of the conventional method using a decimal visual acuity chart.","corpus_id":36943520,"score":0},{"doc_id":"25151998","title":"Establishing the reliability and concurrent validity of physical performance tests using virtual reality equipment for community-dwelling healthy elders.","abstract":"PURPOSE: The aim of this study was to determine the reliability and concurrent validity of commonly used physical performance tests using the OmniVR Virtual Rehabilitation System for healthy community-dwelling elders. METHOD: Participants (N = 40) were recruited by the authors and were screened for eligibility. The initial method of measurement was randomized to either virtual reality (VR) or clinically based measures (CM). Physical performance tests included the five times sit to stand, Timed Up and Go (TUG), Forward Functional Reach (FFR) and 30-s stand test. A random number generator determined the testing order. The test-re-test reliability for the VR and CM was determined. Furthermore, concurrent validity was determined using a Pearson product moment correlation (Pearson r). RESULTS: The VR demonstrated excellent reliability for 5 × STS intraclass correlation coefficient (ICC) = 0.931(3,1), FFR ICC = 0.846(3,1) and the TUG ICC = 0.944(3,1). The concurrent validity data for the VR and CM (ICC 3, k) were moderate for FFR ICC = 0.682, excellent 5 × STS ICC = 0.889 and excellent for the TUG ICC = 0.878. The concurrent validity of the 30-s stand test was good ICC = 0.735(3,1). CONCLUSIONS: This study supports the use of VR equipment for measuring physical performance tests in the clinic for healthy community-dwelling elders. IMPLICATIONS FOR REHABILITATION: Virtual reality equipment is not only used to treat balance impairments but it is also used to measure and determine physical impairments through the use of physical performance tests. Virtual reality equipment is a reliable and valid tool for collecting physical performance data for the 5 × STS, FFR, TUG and 30-s stand test for healthy community-dwelling elders.","corpus_id":30801168,"score":0},{"doc_id":"25306061","title":"Cardiopulmonary exercise testing early after stroke using feedback-controlled robotics-assisted treadmill exercise: test-retest reliability and repeatability.","abstract":"BACKGROUND: Exercise capacity is seriously reduced after stroke. While cardiopulmonary assessment and intervention strategies have been validated for the mildly and moderately impaired populations post-stroke, there is a lack of effective concepts for stroke survivors suffering from severe motor limitations. This study investigated the test-retest reliability and repeatability of cardiopulmonary exercise testing (CPET) using feedback-controlled robotics-assisted treadmill exercise (FC-RATE) in severely motor impaired individuals early after stroke. METHODS: 20 subjects (age 44-84 years, <6 month post-stroke) with severe motor limitations (Functional Ambulatory Classification 0-2) were selected for consecutive constant load testing (CLT) and incremental exercise testing (IET) within a powered exoskeleton, synchronised with a treadmill and a body weight support system. A manual human-in-the-loop feedback system was used to guide individual work rate levels. Outcome variables focussed on standard cardiopulmonary performance parameters. Relative and absolute test-retest reliability were assessed by intraclass correlation coefficients (ICC), standard error of the measurement (SEM), and minimal detectable change (MDC). Mean difference, limits of agreement, and coefficient of variation (CoV) were estimated to assess repeatability. RESULTS: Peak performance parameters during IET yielded good to excellent relative reliability: absolute peak oxygen uptake (ICC =0.82), relative peak oxygen uptake (ICC =0.72), peak work rate (ICC =0.91), peak heart rate (ICC =0.80), absolute gas exchange threshold (ICC =0.91), relative gas exchange threshold (ICC =0.88), oxygen cost of work (ICC =0.87), oxygen pulse at peak oxygen uptake (ICC =0.92), ventilation rate versus carbon dioxide output slope (ICC =0.78). For these variables, SEM was 4-13%, MDC 12-36%, and CoV 0.10-0.36. CLT revealed high mean differences and insufficient test-retest reliability for all variables studied. CONCLUSIONS: This study presents first evidence on reliability and repeatability for CPET in severely motor impaired individuals early after stroke using a feedback-controlled robotics-assisted treadmill. The results demonstrate good to excellent test-retest reliability and appropriate repeatability for the most important peak cardiopulmonary performance parameters. These findings have important implications for the design and implementation of cardiovascular exercise interventions in severely impaired populations. Future research needs to develop advanced control strategies to enable the true limit of functional exercise capacity to be reached and to further assess test-retest reliability and repeatability in larger samples.","corpus_id":15549488,"score":0},{"doc_id":"25491137","title":"Reliability of the Timed Up and Go test and Ten-Metre Timed Walk Test in Pregnant Women with Pelvic Girdle Pain.","abstract":"BACKGROUND AND PURPOSE: There is a lack of functional objective tests available to measure functional status in women with pelvic girdle pain (PGP). The purpose of this study was to establish test-retest and intertester reliability of the Timed Up and Go (TUG) test and Ten-metre Timed Walk Test (10mTWT) in pregnant women with PGP. METHODS: A convenience sample of women was recruited over a 4-month period and tested on two occasions, 1 week apart to determine test-retest reliability. Intertester reliability was established between two assessors at the first testing session. Subjects were instructed to undertake the TUG and 10mTWT at maximum speed. One practise trial and two timed trials for each walking test was undertaken on Day 1 and one practise trial and one timed trial on Day 2. RESULTS: Seventeen women with PGP aged 31.1 years (SD [standard deviation] = 2.3) and 28.7 weeks pregnant (SD = 7.4) completed gait testing. Test-retest reliability using the intraclass correlation coefficient (ICC) was excellent for the TUG (0.88) and good for the 10mTWT (0.74). Intertester reliability was determined in the first 13 participants with excellent ICC values being found for both walking tests (TUG: 0.95; 10mTWT: 0.94). CONCLUSION: This study demonstrated that the TUG and 10mTWT undertaken at fast pace are reliable, objective functional tests in pregnant women with PGP. While both tests are suitable for use in the clinical and research settings, we would recommend the TUG given the findings of higher test-retest reliability and as this test requires less space and time to set up and score. Future studies in a larger sample size are warranted to confirm the results of this study.","corpus_id":44691675,"score":0},{"doc_id":"25585517","title":"Reliability of the chin tuck neck flexion test for assessing endurance of short neck flexors in healthy individuals.","abstract":"OBJECTIVES: The aim of the study was to examine of the intra-rater reliability of the chin tuck neck flexion (CTNF) test for assessing the endurance of neck flexors. MATERIALS AND METHODS: The study was performed at the Cardiorespiratory laboratory of the Physiotherapy Department, School of Health and Caring Professions, TEI Lamia, Greece. Twenty healthy volunteers (males/females: 9/11, age: 22.2 ± 1.7 y ears) with no known musculoskeletal, cardiovascular, pulmonary, neurological, or psychiatric disorder were recruited. The participants were positioned in a supine position and were asked to raise their head 2.5 cm above the plinth and to maintain this position for as long as possible without losing craniocervical or cervical flexion. This test was repeated three times with 5-min intervals between the trials. RESULTS: The results showed that this test could discriminate between neck flexor endurance in men and women. However, although the test seems to be highly reliable (ICC: 0.81-0.88), it presents unsatisfactory standard error of measurement (SEM: 10.7-14.7 s) and smallest detectable differences (SDD: 80.5-110.9%). Furthermore, subgroup analysis showed the test seems to be more reliable for women (ICC: 0.93-0.94) than for men (ICC: 0.68-0.8), but the SEM and SDD values for them remain unsatisfactory (SEM: 4.4-5.3 s, SDD: 57.5-63.99%). CONCLUSIONS: Due to high reproducibility and discriminant validity, clinicians and researchers might want to consider using the CTNF test for the assessment of neck flexor endurance. However, they should seek alternative measurement tools when they want to avoid a large measurement error.","corpus_id":42925517,"score":0},{"doc_id":"25663715","title":"Age and strength influences on lingual tactile acuity.","abstract":"Sensory function during the oral processing of liquids is thought to play a key role in informing the tailoring of swallowing motor behaviours to the flow characteristics of the bolus. In addition to taste receptors, the mouth and tongue house trigeminal nerve receptors that support the sensory detection of bolus size, shape (stereognosis), mass, temperature and movement. Recent studies suggest that healthy adults lose tongue strength with advancing age. However, little is known about changes in the sensory function of the tongue attributable to age, or associated with reductions in strength. In this study, we explored lingual tactile acuity in healthy young and older adults, and measured the relationship between tactile acuity and measures of tongue strength. The results showed an age-related reduction in lingual tactile acuity that was not explained by variations in tongue strength. PRACTICAL APPLICATIONS: Sensory motor interactions are a topic of interest in understanding the processing activities that take place in the mouth during eating and swallowing. In this paper, we explore a test of sensory acuity in the mouth, in which the tongue is used to \"read\" embossed letters on Teflon strips. Our questions were to determine whether sensory acuity for this task declines with age, or with age-related reductions in tongue strength. We determined that older people perform this task with less accuracy, suggesting some changes in oral sensory function with age. However, these changes were not related to tongue strength. The findings suggest that strength does not play a major role in the kind of sensory discrimination task tested in this study.","corpus_id":45574226,"score":0},{"doc_id":"25690522","title":"Contribution of sVEP visual acuity testing in comparison with subjective visual acuity.","abstract":"AIMS: Visual acuity determination is an important task in ophthalmology and optometry practices. Visual acuity can be examined objectively or subjectively. The objective examination method, sVEP, allows for quick objective measurements of patient's visual acuity. Previous studies have not demonstrated the repeatability of this objective sVEP method. This study aims to evaluate the sVEP method and compare it to a subjective method. METHODS AND RESULTS: The sample was divided into two groups. For the first group, visual acuity was measured with sVEP and Snellen methods on only one patient twelve times. In the second group, visual acuity was measured twice with sVEP followed twice with the Snellen method with Landolt's rings and logMAR modification on 32 non-pathological patients. Results showed significant differences between average values of visual acuity obtained with both methods (sVEP and Snellen) in both samples (T-test, P < 0.01; Wilcoxon test, P = 0.02 in second group). In the second group, significant correlations between repeated sVEP measurements (Spearman test, P < 0.05, r = 0.69) were found but no significant correlation between average sVEP measurement and average Snellen measurement (Spearman test, P > 0.05, r = 0.15) was found. CONCLUSION: Objective measurement of visual acuity with sVEP is a valid and reliable method, but is recommended only when it is not possible to use a subjective method for measuring visual acuity, e.g. children, patients with mental retardation or simulating/dissimulating patients.","corpus_id":2986550,"score":0},{"doc_id":"26200616","title":"The Development and Validation of Hundred Paisa Pain Scale for Measuring Musculoskeletal Pain: A Prospective Observational Study.","abstract":"The reduction in the pain intensity is one of the most important outcome measures in musculoskeletal disorders. The assessment of pain required reliable and valid scale. The aims of this prospective observational study were to develop and evaluate concurrent validity and test-retest reliability of hundred paisa pain scale (HPPS) for measuring musculoskeletal pain. A consecutive 74 patients with musculoskeletal pain with a wide variety of diagnoses were enrolled. Patients reported their intensity of pain on the following scale: HPPS, \"visual analog scale (VAS),\" and \"numerical rating scale (NRS).\" Patients were asked to complete another HPPS, VAS, and NRS after 2 days to determine the reproducibility of the scales. Spearman rank correlation coefficients between the HPPS and the NRS, and VAS were used to determine the validity of the scales. The correlation between the change score of HPPS, VAS, and NRS was used to determine the responsiveness of HPPS. Results of test-retest indicate that the reproducibility of HPPS was good to excellent with the intraclass correlation coefficient (ICC) value of 0.85 (95% confidence interval [CI], 0.76-0.91). The standard error of measurement (SEM) was 5.24. The minimum detectable change based on the SEM for test-retest was 14.52. The reproducibility of VAS is moderate to good with the ICC value of 0.82 (95% CI, 0.72-0.88). The reproducibility of NRS is good to excellent with the ICC value of 0.88 (95% CI, 0.81-0.92). There was a strong correlation between the HPPS and the VAS, and NRS (P < 0.01), which confirm the validity. The HPPS was responsive as the correlation of the change score of HPPS with the change score of VAS, and NRS were good (0.80 and 0.86, respectively). The HPPS is a valid and reliable scale to assess musculoskeletal pain, with psychometric properties in agreement with other comparable scale.","corpus_id":278529,"score":0},{"doc_id":"27002314","title":"Reliability and Normative Data for the Dynamic Visual Acuity Test for Vestibular Screening.","abstract":"HYPOTHESIS: The purpose of this study was to determine reliability of computerized dynamic visual acuity (DVA) testing and to determine reference values for younger and older adults. BACKGROUND: A primary function of the vestibular system is to maintain gaze stability during head motion. The DVA test quantifies gaze stabilization with the head moving versus stationary. Commercially available computerized systems allow clinicians to incorporate DVA into their assessment; however, information regarding reliability and normative values of these systems is sparse. METHODS: Forty-six healthy adults, grouped by age, with normal vestibular function were recruited. Each participant completed computerized DVA testing including static visual acuity, minimum perception time, and DVA using the NeuroCom inVision System. Testing was performed by two examiners in the same session and then repeated at a follow-up session 3 to 14 days later. Intraclass correlation coefficients (ICCs) were used to determine inter-rater and test-retest reliability. RESULTS: ICCs for inter-rater reliability ranged from 0.323 to 0.937 and from 0.434 to 0.909 for horizontal and vertical head movements, respectively. ICCs for test-retest reliability ranged from 0.154 to 0.856 and from 0.377 to 0.9062 for horizontal and vertical head movements, respectively. Overall, raw scores (left/right DVA and up/down DVA) were more reliable than DVA loss scores. CONCLUSION: Reliability of a commercially available DVA system has poor-to-fair reliability for DVA loss scores. The use of a convergence paradigm and not incorporating the forced choice paradigm may contribute to poor reliability.","corpus_id":8831894,"score":0},{"doc_id":"27338815","title":"Concurrent validity of different functional and neuroproteomic pain assessment methods in the rat osteoarthritis monosodium iodoacetate (MIA) model.","abstract":"BACKGROUND: Lack of validity in osteoarthritis pain models and assessment methods is suspected. Our goal was to 1) assess the repeatability and reproducibility of measurement and the influence of environment, and acclimatization, to different pain assessment outcomes in normal rats, and 2) test the concurrent validity of the most reliable methods in relation to the expression of different spinal neuropeptides in a chemical model of osteoarthritic pain. METHODS: Repeatability and inter-rater reliability of reflexive nociceptive mechanical thresholds, spontaneous static weight-bearing, treadmill, rotarod, and operant place escape/avoidance paradigm (PEAP) were assessed by the intraclass correlation coefficient (ICC). The most reliable acclimatization protocol was determined by comparing coefficients of variation. In a pilot comparative study, the sensitivity and responsiveness to treatment of the most reliable methods were tested in the monosodium iodoacetate (MIA) model over 21 days. Two MIA (2 mg) groups (including one lidocaine treatment group) and one sham group (0.9 % saline) received an intra-articular (50 μL) injection. RESULTS: No effect of environment (observer, inverted circadian cycle, or exercise) was observed; all tested methods except mechanical sensitivity (ICC <0.3), offered good repeatability (ICC ≥0.7). The most reliable acclimatization protocol included five assessments over two weeks. MIA-related osteoarthritic change in pain was demonstrated with static weight-bearing, punctate tactile allodynia evaluation, treadmill exercise and operant PEAP, the latter being the most responsive to analgesic intra-articular lidocaine. Substance P and calcitonin gene-related peptide were higher in MIA groups compared to naive (adjusted P (adj-P) = 0.016) or sham-treated (adj-P = 0.029) rats. Repeated post-MIA lidocaine injection resulted in 34 times lower downregulation for spinal substance P compared to MIA alone (adj-P = 0.029), with a concomitant increase of 17 % in time spent on the PEAP dark side (indicative of increased comfort). CONCLUSION: This study of normal rats and rats with pain established the most reliable and sensitive pain assessment methods and an optimized acclimatization protocol. Operant PEAP testing was more responsive to lidocaine analgesia than other tests used, while neuropeptide spinal concentration is an objective quantification method attractive to support and validate different centralized pain functional assessment methods.","corpus_id":18188204,"score":0},{"doc_id":"27418890","title":"Reliability of the Handgrip Strength Test in Elderly Subjects With Parkinson Disease.","abstract":"BACKGROUND: The handgrip strength test is widely used by clinicians; however, little has been investigated about its reliability when used in subjects with Parkinson disease (PD). The purpose of this study was to investigate the test-retest reliability of the handgrip strength test for subjects with PD. METHODS: The PD group consisted of 15 patients, and the control group consisted of 15 healthy subjects. Each patient performed 3 pain-free maximal isometric contractions on each hand on 2 occasions, 1 week apart. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), and 95% limits of agreement (LOA) were calculated. The 2-way analysis of variance (ANOVA) was conducted to determine the differences between sides and groups. RESULTS: Test-retest reliability of measurements of grip strength was excellent for dominant (ICC = 0.97; P = .001) and non-dominant (ICC = 0.98; P = .001) hand of participant with PD and (ICC = 0.99; P = .001) and (ICC = 0.99; P = .001) respectively, of healthy group. CONCLUSIONS: The Jamar hand dynamometer had fair to excellent test-retest reliability to test grip strength in participants with PD.","corpus_id":31903041,"score":0},{"doc_id":"28074292","title":"Reliability of the nociceptive blink reflex evoked by electrical stimulation of the trigeminal nerve in humans.","abstract":"OBJECTIVE: The nociceptive blink reflex (nBR) can be useful to investigate trigeminal nociceptive function. The aim of this study was to estimate the reliability of the nBR evoked by electrical stimulation of the three branches of the trigeminal nerve under the following conditions: over time (test-retest and intrarater reliability) and by two examiners (interrater reliability). MATERIALS AND METHODS: Twenty-one healthy participants were evaluated in two sessions (24 h apart). The nBR was elicited by a so-called \"nociceptive-specific\" electrode placed over the entry zone of the right supraorbital (V1R), infraorbital (V2R), mental (V3R), and left infraorbital (V2L) nerve. The outcomes were individual electrical sensory (I 0) and pain thresholds (I P); root mean square (RMS), area-under-the-curve (AUC), and onset latencies of R2 responses (determined twice after a recalibration session); and stimulus-evoked pain on a 0-10 numerical rating scale. Intraclass correlation coefficients (ICCs) and Kappa statistics were computed (α = 5%). RESULTS: ICCs were fair to excellent in 82% of the psychophysical measures (fair 21%, good 31%, excellent 30%) and in 86% of V1R, V2R, and V2L nBR parameters, whereas 52% of V3R showed poor reliability. ICCs for intrarater reliability were fair to good in 70% of measurements (fair 20%, good 50%) and in 75% of interrater measurements after the recalibration (fair 55%, good 20%). All kappa values showed at least fair agreement and the majority of the nBR measures (93%) presented moderate to excellent reliability. CONCLUSION: The nBR and its associated psychophysical measures can be considered a sufficiently reliable test. CLINICAL SIGNIFICANCE: The nBR can be recommended as an electrophysiological technique to assess trigeminal nociceptive function.","corpus_id":11132779,"score":0},{"doc_id":"28262642","title":"Gaze stabilization and dynamic visual acuity in people with multiple sclerosis.","abstract":"BACKGROUND: The functional capacity of the vestibulo-ocular reflex (VOR) is not well understood in people with multiple sclerosis (MS). OBJECTIVE: To determine the psychometric properties of computerized Gaze Stabilization Test (GST) and Dynamic Visual Acuity Test (DVAT) in people with MS. METHODS: This cross-sectional study determined discriminant validity of the GST and DVAT between 15 healthy controls and 30 participants with MS, and between participants with MS who had higher versus lower disability. This study also determined same-day and between-session test-retest reliability, and concurrent validity with patient-reported outcomes (PROs) of balance, dizziness, and fatigue. RESULTS: GST (p < 0.001) and DVAT (p = 0.001) scores were lower in participants with MS compared to controls. GST (p = 0.035) but not DVAT (p = 0.313) scores were lower in those with higher compared to lower disability. Test-retest reliability intraclass correlation coefficients (ICC (2,1)) were fair-to-good for the GST (0.48 to 0.74) and DVAT (0.47 to 0.60). PROs correlated significantly with GST, but not DVAT scores. CONCLUSIONS: This study provides initial evidence that the functional capacity of the VOR is impaired in people with MS as measured by the GST and DVAT. Further investigation is warranted to determine usefulness of both measures as outcomes for people with MS.","corpus_id":5959101,"score":0},{"doc_id":"28451614","title":"The Functional Arm Scale for Throwers (FAST)-Part II: Reliability and Validity of an Upper Extremity Region-Specific and Population-Specific Patient-Reported Outcome Scale for Throwing Athletes.","abstract":"BACKGROUND: The Functional Arm Scale for Throwers (FAST) is an upper extremity (UE) region-specific and population-specific patient-reported outcome (PRO) scale developed to measure health-related quality of life in throwers with UE injuries. Stages I and II, described in a companion paper, of FAST development produced a 22-item scale and a 9-item pitcher module. Stage III of scale development, establishing reliability and validity of the FAST, is reported herein. PURPOSE: To describe stage III of scale development: reliability and validity of the FAST. STUDY DESIGN: Cohort study (diagnosis); Level of evidence, 2. METHODS: Data from throwing athletes collected over 5 studies were pooled to assess reliability and validity of the FAST. Reliability was estimated using FAST scores from 162 throwing athletes who were injured (n = 23) and uninjured (n = 139). Concurrent validity was estimated using FAST scores and Disabilities of the Arm, Shoulder, and Hand (DASH) and Kerlan-Jobe Orthopaedic Clinic (KJOC) scores from 106 healthy, uninjured throwing athletes. Known-groups validity was estimated using FAST scores from 557 throwing athletes who were injured (n = 142) and uninjured (n = 415). Reliability and validity were assessed using intraclass correlation coefficients (ICCs), and measurement error was assessed using standard error of measurement (SEM) and minimum detectable change (MDC). Receiver operating characteristic curves and sensitivity/specificity values were estimated for known-groups validity. Data from a separate group (n = 18) of postsurgical and nonoperative/conservative rehabilitation patients were analyzed to report responsiveness of the FAST. RESULTS: The FAST total, subscales, and pitcher module scores demonstrated excellent test-retest reliability (ICC, 0.91-0.98). The SEM95 and MDC95 for the FAST total score were 3.8 and 10.5 points, respectively. The SEM95 and MDC95 for the pitcher module score were 5.7 and 15.7 points, respectively. The FAST scores showed acceptable correlation with DASH (ICC, 0.49-0.82) and KJOC (ICC, 0.62-0.81) scores. The FAST total score classified 85.1% of players into the correct injury group. For predicting UE injury status, a FAST total cutoff score of 10.0 out of 100.0 was 91% sensitive and 75% specific, and a pitcher module score of 10.0 out of 100.0 was 87% sensitive and 78% specific. The FAST total score demonstrated responsiveness on several indices between intake and discharge time points. CONCLUSION: The FAST is a reliable, valid, and responsive UE region-specific and population-specific PRO scale for measuring patient-reported health care outcomes in throwing athletes with injury.","corpus_id":10924574,"score":0},{"doc_id":"28728465","title":"Evaluating the test-retest reliability of symptom indices associated with the ImPACT post-concussion symptom scale (PCSS).","abstract":"OBJECTIVE: The Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) is a commonly used tool in sports concussion assessment. While test-retest reliabilities have been established for the ImPACT cognitive composites, few studies have evaluated the psychometric properties of the ImPACT's Post-Concussion Symptom Scale (PCSS). The purpose of this study was to establish the test-retest reliability of symptom indices associated with the PCSS. PARTICIPANTS AND METHODS: Participants included 38 undergraduate students (50.0% male) who underwent neuropsychological testing as part of their participation in their psychology department's research subject pool. The majority of the participants were Caucasian (94.7%) and had no history of concussion (73.7%). All participants completed the ImPACT at two time points, approximately 6 weeks apart. The PCSS was the main outcome measure, and eight symptom indices were calculated (a total symptom score, three symptom summary indices, and four symptom clusters). RESULTS: Pearson correlations (r) and intraclass correlation coefficients (ICCs) were computed as measures of test-retest reliability. Overall, reliabilities ranged from low to high (r = .44 to .80; ICC = .44 to .77). The cognitive symptom cluster exhibited the highest test-retest reliability (r = .80, ICC = .77), followed by the positive symptom total (PST) index, an indicator of the total number of symptoms endorsed (r = .71, ICC = .69). In contrast, the commonly used total symptom score showed lower test-retest reliability (r = .67, ICC = .62). Paired-samples t tests revealed no significant differences between test and retest for any of the symptom variables (all p > .01). Finally, reliable change indices (RCI) were computed to determine whether differences observed between test and retest represented clinically significant change. RCI values were provided for each symptom index at the 80%, 90%, and 95% confidence intervals. CONCLUSION: These results suggest that evaluating additional symptom indices beyond the total symptom score from the PCSS is beneficial. Findings from this study can be applied to athlete samples to assess reliable change in symptoms following concussion.","corpus_id":4001296,"score":0},{"doc_id":"28888770","title":"Test-retest reliability of cerebral blood flow in healthy individuals using arterial spin labeling: Findings from the EMBARC study.","abstract":"INTRODUCTION: Previous investigations of test-retest reliability of cerebral blood flow (CBF) at rest measured with pseudo-continuous Arterial Spin Labeling (pCASL) demonstrated good reliability, but are limited by the use of similar scanner platforms. In the present study we examined test-retest reliability of CBF in regions implicated in emotion and the default mode network. MATERIAL AND METHODS: We measured absolute and relative CBF at rest in thirty-one healthy subjects in two scan sessions, one week apart, at four different sites and three different scan platforms. We derived CBF from pCASL images with an automated algorithm and calculated intra-class correlation coefficients (ICCs) across sessions for regions of interest. In addition, we investigated site effects. RESULTS: For both absolute and relative CBF measures, ICCs were good to excellent (i.e. >0.6) in most brain regions, with highest values observed for the subgenual anterior cingulate cortex and ventral striatum. A leave-one-site-out cross validation analysis did not show a significant effect for site on whole brain CBF and there was no proportional bias across sites. However, a significant site effect was present in the repeated measures ANOVA. CONCLUSIONS: The high test-retest reliability of CBF measured with pCASL in a range of brain regions implicated in emotion and salience processing, emotion regulation, and the default mode network, which have been previously linked to depression symptomatology supports its use in studies that aim to identify neuroimaging biomarkers of treatment response.","corpus_id":22313148,"score":0},{"doc_id":"28890223","title":"A new iPhone application for measuring active craniocervical range of motion in patients with non-specific neck pain: a reliability and validity study.","abstract":"BACKGROUND CONTEXT: Measurement of cervical spine range of motion (ROM) is often considered to be an essential component of cervical spine physiotherapy assessment. PURPOSE: This study aimed to investigate the reliability and validity of an iPhone application (app) (Goniometer Pro) for measuring active craniocervical ROM (ACCROM) in patients with non-specific neck pain. STUDY DESIGN/SETTING: A cross-sectional study was conducted at the musculoskeletal biomechanics laboratory located at Iran University of Medical Sciences. PATIENT SAMPLE: Forty non-specific neck pain patients participated in this study. OUTCOME MEASURES: The outcome measure was the ACCROM, including flexion, extension, lateral flexion, and rotation. METHOD: Following the recruitment process, ACCROM was measured using a universal goniometer (UG) and iPhone 7 app. Two blinded examiners each used the UG and iPhone to measure ACCROM in the following sequences: flexion, extension, lateral flexion, and rotation. The second (2 hours later) and third (48 hours later) sessions were carried out in the same manner as the first session. Intraclass correlation coefficient (ICC) models were used to determine the intra-rater and inter-rater reliability. The Pearson correlation coefficients were used to establish concurrent validity of the iPhone app. Minimum detectable change at the 95% confidence level (MDC95) was also computed. RESULTS: Good intra-rater and inter-rater reliability was demonstrated for the goniometer with ICC values of ≥0.66 and ≥0.70 and the iPhone app with ICC values of ≥0.62 and ≥0.65, respectively. The MDC95 ranged from 2.21° to 12.50° for the intra-rater analysis and from 3.40° to 12.61° for the inter-rater analysis. The concurrent validity between the two instruments was high, with r valuesof ≥0.63. The magnitude of the differences between the UG and iPhone app values (effect sizes) was small, with Cohen d values of ≤0.17. CONCLUSIONS: The iPhone app possesses good reliability and high validity. It seems that this app can be used for measuring ACCROM.","corpus_id":3931425,"score":0},{"doc_id":"28893312","title":"The validity and reliability of the four square step test in different adult populations: a systematic review.","abstract":"BACKGROUND: The four square step test (FSST) was first validated in healthy older adults to provide a measure of dynamic standing balance and mobility. The FSST has since been used in a variety of patient populations. The purpose of this systematic review is to determine the validity and reliability of the FSST in these different adult patient populations. METHODS: The literature search was conducted to highlight all the studies that measured validity and reliability of the FSST. Six electronic databases were searched including AMED, CINAHL, MEDLINE, PEDro, Web of Science and Google Scholar. Grey literature was also searched for any documents relevant to the review. Two independent reviewers carried out study selection and quality assessment. The methodological quality was assessed using the QUADAS-2 tool, which is a validated tool for the quality assessment of diagnostic accuracy studies, and the COSMIN four-point checklist, which contains standards for evaluating reliability studies on the measurement properties of health instruments. RESULTS: Fifteen studies were reviewed studying community-dwelling older adults, Parkinson's disease, Huntington's disease, multiple sclerosis, vestibular disorders, post stroke, post unilateral transtibial amputation, knee pain and hip osteoarthritis. Three of the studies were of moderate methodological quality scoring low in risk of bias and applicability for all domains in the QUADAS-2 tool. Three studies scored \"fair\" on the COSMIN four-point checklist for the reliability components. The concurrent validity of the FSST was measured in nine of the studies with moderate to strong correlations being found. Excellent Intraclass Correlation Coefficients were found between physiotherapists carrying out the tests (ICC = .99) with good to excellent test-retest reliability shown in nine of the studies (ICC = .73-.98). CONCLUSIONS: The FSST may be an effective and valid tool for measuring dynamic balance and a participants' falls risk. It has been shown to have strong correlations with other measures of balance and mobility with good reliability shown in a number of populations. However, the quality of the papers reviewed was variable with key factors, such as sample size and test set up, needing to be addressed before the tool can be confidently used in these specified populations.","corpus_id":24727140,"score":0},{"doc_id":"29280180","title":"Comparison of the outcomes of dynamic/static tests and palpation tests in TMD-pain patients.","abstract":"In addition to palpation tests, dynamic/static tests have been proposed to complement temporomandibular disorders (TMD) patients' evaluation in the clinical setting. The aim of this study was to assess the intra- and inter-observer reliability of the palpation tests and of the dynamic/static tests, and to determine whether those tests would yield comparable outcomes in terms of pain diagnoses. Ninety-eight (N = 98) consecutive adult patients were examined during 2 clinical sessions by 2 independent examiners, based on muscle and joint palpation techniques described in the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD). They also underwent dynamic/static tests. The intra-observer reliability of palpation tests was generally poor, with fair-to-good to excellent ICC values only for the superior masseter and intra-oral sites. The inter-observer reliability of palpation was fair-to-good for muscles, but it was poor for the TMJ lateral pole. Both intra- and inter-observer reliability for the dynamic/static tests varied from fair-to-good to excellent. The intra-observer reliability for muscle pain diagnoses based on palpation tests was between poor and fair-to-good, whereas the inter-observer reliability was excellent. The intra-observer reliability for pain diagnoses based on dynamic/static tests was fair-to-good, and the inter-observer reliability varied from fair-to-good to excellent. CONCLUSIONS: Some features of the dynamic/static tests make them potentially more useful than palpation tests for selected clinical purposes, such as discriminating between joint and muscle pain as well as monitoring symptoms course. Thus, findings from this investigation suggest that both tests should be included in the TMD diagnostic algorithms.","corpus_id":3276081,"score":0},{"doc_id":"29328979","title":"Concurrent validity and interrater reliability of a new smartphone application to assess 3D active cervical range of motion in patients with neck pain.","abstract":"BACKGROUND: There is a lack of valid, reliable, and feasible instruments for measuring planar active cervical range of motion (aCROM) and associated 3D coupling motions in patients with neck pain. Smartphones have advanced sensors and appear to be suitable for these measurements. OBJECTIVES: To estimate the concurrent validity and interrater reliability of a new iPhone application for assessing planar aCROM and associated 3D coupling motions in patients with neck pain, using an electromagnetic tracking device as a reference test. DESIGN: Cross-sectional study. METHODS: Two samples of neck pain patients were recruited; 30 patients for the validity study and 26 patients for the reliability study. Validity was estimated using intraclass correlation coefficients (ICCs), and by calculating 95% limits of agreement (LoA). To estimate interrater reliability, ICCs were calculated. Cervical 3D coupling motions were analyzed by calculating the cross-correlation coefficients and ratio between the main motions and coupled motions for both instruments. RESULTS: ICCs for concurrent validity and interrater reliability ranged from 0.90 to 0.99. The width of the 95% LoA ranged from about 5° for right lateral bending to 11° for total rotation. No significant differences were found between both devices for associated coupling motion analysis. CONCLUSIONS: The iPhone application appears to be a useful discriminative tool for the measurement of planar aCROM and associated coupling motions in patients with neck pain. It fulfills the need for a valid, reliable, and feasible instrument in clinical practice and research. Therapists and researchers should consider measurement error when interpreting scores.","corpus_id":3804287,"score":0}],"string":"[\n {\n \"doc_id\": \"18054437\",\n \"title\": \"Tactile discrimination, but not tactile stimulation alone, reduces chronic limb pain.\",\n \"abstract\": \"Chronic pain is often associated with reduced tactile acuity. A relationship exists between pain intensity, tactile acuity and cortical reorganisation. When pain resolves, tactile function improves and cortical organisation normalises. Tactile acuity can be improved in healthy controls when tactile stimulation is associated with a behavioural objective. We hypothesised that, in patients with chronic limb pain and decreased tactile acuity, discriminating between tactile stimuli would decrease pain and increase tactile acuity, but tactile stimulation alone would not. Thirteen patients with complex regional pain syndrome (CRPS) of one limb underwent a waiting period and then approximately 2 weeks of tactile stimulation under two conditions: stimulation alone or discrimination between stimuli according to their diameter and location. There was no change in pain (100 mm VAS) or two-point discrimination (TPD) during a no-treatment waiting period, nor during the stimulation phase (p > 0.32 for both). Pain and TPD were lower after the discrimination phase [mean (95% CI) effect size for pain VAS = 27 mm (14-40 mm) and for TPD = 5.7 mm (2.9-8. ), p < 0.015 for both]. These gains were maintained at three-month follow-up. We conclude that tactile stimulation can decrease pain and increase tactile acuity when patients are required to discriminate between the type and location of tactile stimuli.\",\n \"corpus_id\": 2757963,\n \"score\": 2\n },\n {\n \"doc_id\": \"19553222\",\n \"title\": \"Tactile acuity and lumbopelvic motor control in patients with back pain and healthy controls.\",\n \"abstract\": \"BACKGROUND: Voluntary lumbopelvic control is compromised in patients with back pain. Loss of proprioceptive acuity is one contributor to decreased control. Several reasons for decreased proprioceptive acuity have been proposed, but the integrity of cortical body maps has been overlooked. We investigated whether tactile acuity, a clear clinical signature of primary sensory cortex organisation, relates to lumbopelvic control in people with back pain. METHODS: Forty-five patients with back pain and 45 age- and sex-matched healthy controls participated in this cross-sectional study. Tactile acuity at the back was assessed using two-point discrimination (TPD) threshold in vertical and horizontal directions. Voluntary motor control was assessed using an established battery of clinical tests. RESULTS: Patients performed worse on the voluntary lumbopelvic tasks than healthy controls did (p<0.001). TPD threshold was larger in patients (mean (SD)=61 (13) mm) than in healthy controls (44 (10) mm). Moreover, larger TPD threshold was positively related to worse performance on the voluntary lumbopelvic tasks (Pearson's r=0.49; p<0.001). DISCUSSION: Tactile acuity, a clear clinical signature of primary sensory cortex organisation, relates to voluntary lumbopelvic control. This relationship raises the possibility that the former contributes to the latter, in which case training tactile acuity may aid recovery and assist in achieving normal motor performance after back injury.\",\n \"corpus_id\": 22933101,\n \"score\": 2\n },\n {\n \"doc_id\": \"22309074\",\n \"title\": \"Reproducibility of tactile assessments for children with unilateral cerebral palsy.\",\n \"abstract\": \"A systematic review identified tactile assessments used in children with cerebral palsy (CP), but their reproducibility is unknown. Sixteen children with unilateral CP and 31 typically developing children (TDC) were assessed 2-4 weeks apart. Test-retest percent agreements within one point for children with unilateral CP (and TDC) were Semmes-Weinstein monofilaments: 75% (90%); single-point localization: 69% (97%); static two-point discrimination: 93% (97%); and moving two-point discrimination: 87% (97%). Test-retest reliability for registration and unilateral spatial tactile perception tests was high in children with CP (intraclass correlation coefficient [ICC] = 0.79-0.96). Two tests demonstrated a learning effect for children with CP, double simultaneous and tactile texture perception. Stereognosis had a ceiling effect for TDC (ICC = 0) and variability for children with CP (% exact agreement = 47%-50%). The Semmes-Weinstein monofilaments, single-point localization, and both static and moving two-point discrimination are recommended for use in practice and research. Although recommended to provide a comprehensive assessment, the measures of double simultaneous, stereognosis, and tactile texture perception may not be responsive to change over time in children with unilateral CP.\",\n \"corpus_id\": 18713889,\n \"score\": 2\n },\n {\n \"doc_id\": \"23611918\",\n \"title\": \"Assessing tactile acuity in rheumatology and musculoskeletal medicine--how reliable are two-point discrimination tests at the neck, hand, back and foot?\",\n \"abstract\": \"OBJECTIVE: Chronic pain from rheumatic and musculoskeletal conditions is associated with cortical changes and altered tactile acuity. Tactile acuity is considered a clinical signature of primary somatosensory representation. The two-point discrimination (TPD) threshold is increasingly used both clinically and in research. Remarkably, the reliability and precision of the measure at commonly used sites has not been determined. This study aimed to determine the utility, intra- and inter-rater reliability, bias and variability of TPD threshold assessment at the neck, back, hand and foot using mechanical callipers. METHODS: Intra- and inter-rater reliability of TPD was assessed at the back, neck, hand and foot of 28 healthy young adults by 28 clinicians. Each clinician received training in the assessment of TPD using mechanical callipers and following a standardized protocol. Intraclass correlation coefficients (ICCs) and Bland-Altman plots were used to assess reliability, bias and variability. RESULTS: Intra-rater assessments in all four regions and inter-rater assessments at the neck and foot were reliable (ICC range 0.79-0.86), but large variability was seen in all assessments. Inter-rater assessment of the back (ICC = 0.66) and hand (ICC = 0.62) was deemed unreliable. Negligible systematic bias suggested learning did not affect reliability. CONCLUSION: Individual clinicians are able to reliably assess TPD threshold at the neck, back, hand and foot using mechanical callipers. Measures obtained by different clinicians were only reliable for the neck and foot. Large variability was observed in all assessments, which suggests clinicians should be cautious when interpreting changes in tactile acuity in individual patients.\",\n \"corpus_id\": 2260754,\n \"score\": 2\n },\n {\n \"doc_id\": \"23661429\",\n \"title\": \"Tactile acuity is disrupted in osteoarthritis but is unrelated to disruptions in motor imagery performance.\",\n \"abstract\": \"OBJECTIVE: To determine whether tactile acuity is disrupted in people with knee OA and to determine whether tactile acuity, a clinical signature of primary sensory cortex representation, is related to motor imagery performance (MIP; evaluates working body schema) and pain. METHODS: Experiment 1: two-point discrimination (TPD) threshold at the knee was compared between 20 participants with painful knee OA, 20 participants with arm pain and 20 healthy controls. Experiment 2: TPD threshold, MIP (left/right judgements of body parts) and usual pain were assessed in 20 people with painful knee OA, 17 people with back pain and 38 healthy controls (20 knee TPD; 18 back TPD). RESULTS: People with painful knee OA had larger TPD thresholds than those with arm pain and healthy controls (P < 0.05). TPD and MIP were not related in people with knee OA (P = 0.88) but were related in people with back pain and in healthy controls (P < 0.001). Pain did not relate to TPD threshold or to MIP (P > 0.15 for all). CONCLUSION: In painful knee OA, tactile acuity at the knee is decreased, implying disrupted representation of the knee in primary sensory cortex. That TPD and MIP were unrelated in knee OA, but related in back pain, suggests that the relationship between them may vary between chronic pain conditions. That pain was not related to TPD threshold nor MIP suggests against the idea that disrupted cortical representations contribute to the pain of either condition.\",\n \"corpus_id\": 2585669,\n \"score\": 2\n },\n {\n \"doc_id\": \"24062677\",\n \"title\": \"Two-point orientation discrimination versus the traditional two-point test for tactile spatial acuity assessment.\",\n \"abstract\": \"Two-point discrimination is widely used to measure tactile spatial acuity. The validity of the two-point threshold as a spatial acuity measure rests on the assumption that two points can be distinguished from one only when the two points are sufficiently separated to evoke spatially distinguishable foci of neural activity. However, some previous research has challenged this view, suggesting instead that two-point task performance benefits from an unintended non-spatial cue, allowing spuriously good performance at small tip separations. We compared the traditional two-point task to an equally convenient alternative task in which participants attempt to discern the orientation (vertical or horizontal) of two points of contact. We used precision digital readout calipers to administer two-interval forced-choice versions of both tasks to 24 neurologically healthy adults, on the fingertip, finger base, palm, and forearm. We used Bayesian adaptive testing to estimate the participants' psychometric functions on the two tasks. Traditional two-point performance remained significantly above chance levels even at zero point separation. In contrast, two-point orientation discrimination approached chance as point separation approached zero, as expected for a valid measure of tactile spatial acuity. Traditional two-point performance was so inflated at small point separations that 75%-correct thresholds could be determined on all tested sites for fewer than half of participants. The 95%-correct thresholds on the two tasks were similar, and correlated with receptive field spacing. In keeping with previous critiques, we conclude that the traditional two-point task provides an unintended non-spatial cue, resulting in spuriously good performance at small spatial separations. Unlike two-point discrimination, two-point orientation discrimination rigorously measures tactile spatial acuity. We recommend the use of two-point orientation discrimination for neurological assessment.\",\n \"corpus_id\": 248215,\n \"score\": 2\n },\n {\n \"doc_id\": \"24484671\",\n \"title\": \"Lumbar tactile acuity is near identical between sides in healthy pain-free participants.\",\n \"abstract\": \"A growing body of literature suggests that alterations in brain structure and function are a feature of chronic back pain. Tactile acuity is considered a clinical signature of primary somatosensory representation and offers a simple measure of cortical reorganisation. Clinical interpretation of test scores from an individual patient is hampered by variance in published normative values and less than ideal inter-rater reliability. These problems might be mitigated in people with unilateral back pain by using the patient as their own control and comparing tactile acuity at the painful site to performance at the corresponding position on the non-painful side. The first step in exploring this approach is to quantify the normal side-to-side difference in healthy populations. We pooled data from three previous studies that measured lumbar tactile acuity bilaterally in healthy controls using similar protocols. We calculated the mean and variance of the absolute error between sides, the standard error of measurement and the reliable change index (RCI). The mean difference between sides was 3.2 mm (±5.2) when assessed vertically and 1.9 mm (±3.2) when assessed horizontally. The standard error of measurement was 4.2 mm when assessed vertically and 2.7 mm when assessed horizontally. The RCI suggests that differences of greater than 13 mm when assessed horizontally and 17 mm when assessed vertically equate to 95% confidence that a difference truly exists. Several assumptions related to the application of this approach need to be investigated further.\",\n \"corpus_id\": 10112626,\n \"score\": 2\n },\n {\n \"doc_id\": \"24504346\",\n \"title\": \"Tactile acuity charts: a reliable measure of spatial acuity.\",\n \"abstract\": \"For assessing tactile spatial resolution it has recently been recommended to use tactile acuity charts which follow the design principles of the Snellen letter charts for visual acuity and involve active touch. However, it is currently unknown whether acuity thresholds obtained with this newly developed psychophysical procedure are in accordance with established measures of tactile acuity that involve passive contact with fixed duration and control of contact force. Here we directly compared tactile acuity thresholds obtained with the acuity charts to traditional two-point and grating orientation thresholds in a group of young healthy adults. For this purpose, two types of charts, using either Braille-like dot patterns or embossed Landolt rings with different orientations, were adapted from previous studies. Measurements with the two types of charts were equivalent, but generally more reliable with the dot pattern chart. A comparison with the two-point and grating orientation task data showed that the test-retest reliability of the acuity chart measurements after one week was superior to that of the passive methods. Individual thresholds obtained with the acuity charts agreed reasonably with the grating orientation threshold, but less so with the two-point threshold that yielded relatively distinct acuity estimates compared to the other methods. This potentially considerable amount of mismatch between different measures of tactile acuity suggests that tactile spatial resolution is a complex entity that should ideally be measured with different methods in parallel. The simple test procedure and high reliability of the acuity charts makes them a promising complement and alternative to the traditional two-point and grating orientation thresholds.\",\n \"corpus_id\": 1727869,\n \"score\": 2\n },\n {\n \"doc_id\": \"24571855\",\n \"title\": \"Tactile acuity training for patients with chronic low back pain: a pilot randomised controlled trial.\",\n \"abstract\": \"BACKGROUND: Chronic pain can disrupt the cortical representation of a painful body part. This disruption may play a role in maintaining the individual's pain. Tactile acuity training has been used to normalise cortical representation and reduce pain in certain pain conditions. However, there is little evidence for the effectiveness of this intervention for chronic low back pain (CLBP). The primary aim of this study was to inform the development of a fully powered randomised controlled trial (RCT) by providing preliminary data on the effect of tactile acuity training on pain and function in individuals with CLBP. The secondary aim was to obtain qualitative feedback about the intervention. METHODS: In this mixed-methods pilot RCT 15 individuals were randomised to either an intervention (tactile acuity training) or a placebo group (sham tactile acuity training). All participants received 3 sessions of acuity training (intervention or sham) from a physiotherapist and were requested to undertake daily acuity home training facilitated by an informal carer (friend/relative). All participants also received usual care physiotherapy. The primary outcome measures were pain (0-100visual analogue scale (VAS)) and function (Roland Morris Disability Questionnaire (RMDQ)). Participants and their informal carers were invited to a focus group to provide feedback on the intervention. RESULTS: The placebo group improved by the greatest magnitude for both outcome measures, but there was no statistically significant difference (Mean difference (95%CI), p-value) between groups for change in pain (25.6 (-0.7 to 51.9), p = 0.056) or function (2.2 (-1.6 to 6.0), p = 0.237). Comparing the number of individuals achieving a minimally clinically significant improvement, the placebo group had better outcomes for pain with all participants achieving ≥30% improvement compared to only a third of the intervention group (6/6 vs. 3/9, p = 0.036). Qualitatively, participants reported that needing an informal carer was a considerable barrier to the home training component of the study. CONCLUSIONS: This pilot RCT found tactile acuity training to be no more effective than sham tactile acuity training for function and less effective for pain in individuals with CLBP. That the intervention could not be self-applied was a considerable barrier to its use. TRIAL REGISTRATION ISRCTN: ISRCTN98118082.\",\n \"corpus_id\": 7456543,\n \"score\": 2\n },\n {\n \"doc_id\": \"24870716\",\n \"title\": \"Show me the skin! Does seeing the back enhance tactile acuity at the back?\",\n \"abstract\": \"A growing body of literature associates musculoskeletal disorders with cortical reorganisation. One condition in which reorganisation is established and treatments that 'train the brain' are being widely used is chronic back pain. Recent evidence suggests that treatments that involve tactile training are more effective if they incorporate multisensory mechanisms, most obviously vision. With regard to back pain however, we must first determine if tactile function is enhanced by incorporating other modalities. A series of three cross-over experiments were conducted in healthy pain-free subjects to determine whether tactile acuity is enhanced when participants can see the skin of their back during testing. An initial randomised cross-over experiment suggested tactile acuity was significantly enhanced when participants could see their backs (t(25) = -4.226, p < 0.001, r = 0.65). However, a second replication experiment was not corroborative. Both the second (F(3,66) = 1.00, p = 0.398) and third (t(9) = 0.969, p = 0.358) experiments suggested that seeing the back did not significantly affect tactile acuity, confirming that our initial results were likely due to chance. The principle that visual feedback improves tactile acuity at the hand does not apply to the back. These results strongly suggest that attempts to enhance tactile training by incorporating vision will not offer the benefit to treatment of back pain that has been observed for treatment of hand pain.\",\n \"corpus_id\": 3072753,\n \"score\": 2\n },\n {\n \"doc_id\": \"24983492\",\n \"title\": \"Is tactile acuity altered in people with chronic pain? a systematic review and meta-analysis.\",\n \"abstract\": \"UNLABELLED: Impaired tactile acuity in people with chronic pain conditions has been suggested to reflect altered cortical representation of the painful body part, and treatments that aim to improve tactile acuity in these conditions have shown clinical benefit. Whether abnormalities in tactile acuity are a consistent feature of chronic pain remains largely unknown. The aim of this review was to systematically evaluate the literature and use meta-analysis to establish whether tactile acuity is altered in people with chronic non-neuropathic pain. We systematically searched the literature for studies that investigated tactile acuity in people with chronic non-neuropathic pain and compared it to an appropriate control group. Sixteen studies, reporting data from 5 chronic pain conditions, were included. Data were available for 18 chronic pain populations (n = 484) and 15 control populations (n = 378). Our results suggest that tactile acuity is diminished in arthritis, complex regional pain syndrome, and chronic low back pain but not in burning mouth syndrome. The strength of the available evidence is weakened by somewhat inconsistent results and the high risk of bias observed in all of the included studies. PERSPECTIVE: This systematic review synthesizes the evidence for tactile acuity deficits in people with chronic non-neuropathic pain. The findings suggest that tactile acuity deficits may be characteristic of chronic pain. That tactile acuity training may benefit those with chronic pain disorders suggests that clinical trials may be warranted.\",\n \"corpus_id\": 3962142,\n \"score\": 2\n },\n {\n \"doc_id\": \"25610384\",\n \"title\": \"Pain sensitivity and tactile spatial acuity are altered in healthy musicians as in chronic pain patients.\",\n \"abstract\": \"Extensive training of repetitive and highly skilled movements, as it occurs in professional classical musicians, may lead to changes in tactile sensitivity and corresponding cortical reorganization of somatosensory cortices. It is also known that professional musicians frequently experience musculoskeletal pain and pain-related symptoms during their careers. The present study aimed at understanding the complex interaction between chronic pain and music training with respect to somatosensory processing. For this purpose, tactile thresholds (mechanical detection, grating orientation, two-point discrimination) and subjective ratings to thermal and pressure pain stimuli were assessed in 17 professional musicians with chronic pain, 30 pain-free musicians, 20 non-musicians with chronic pain, and 18 pain-free non-musicians. We found that pain-free musicians displayed greater touch sensitivity (i.e., lower mechanical detection thresholds), lower tactile spatial acuity (i.e., higher grating orientation thresholds) and increased pain sensitivity to pressure and heat compared to pain-free non-musicians. Moreover, we also found that musicians and non-musicians with chronic pain presented lower tactile spatial acuity and increased pain sensitivity to pressure and heat compared to pain-free non-musicians. The significant increment of pain sensitivity together with decreased spatial discrimination in pain-free musicians and the similarity of results found in chronic pain patients, suggests that the extensive training of repetitive and highly skilled movements in classical musicians could be considered as a risk factor for developing chronic pain, probably due to use-dependent plastic changes elicited in somatosensory pathways.\",\n \"corpus_id\": 10903921,\n \"score\": 2\n },\n {\n \"doc_id\": \"25858650\",\n \"title\": \"A preliminary investigation of lumbar tactile acuity in yoga practitioners.\",\n \"abstract\": \"BACKGROUND: Tactile acuity in the back relates to voluntary lumbo-pelvic control and is lower in chronic low back pain (CLBP) patients. Two-point discrimination (TPD) thresholds are higher, indicating decreased tactile acuity in patients with CLBP. Yoga has been shown to help relieve CLBP. OBJECTIVES: This study investigated the hypothesis that regular practitioners of yoga have increased tactile acuity (i.e., lower TPD thresholds) when compared to matched controls who regularly perform gym-based (resistance training or aerobic-type) exercise. METHOD: Tactile acuity in the low back was assessed using TPD in 16 long-term practitioners of yoga (5 Ashtanga, 5 Bikram, and 6 Iyengar practitioners) and 16 age- and gender-matched healthy controls who exercise (with weights and aerobic exercise). RESULTS: The yoga practitioners' TPD was lower than that of the exercisers, indicating greater tactile acuity in the low back. While there was no difference between the TPD of the practitioners of different yoga styles, the TPD of the Ashtanga yoga participants were significantly lower than those of the exercisers. The yogis whose main reasons to practice yoga were for \\\"meditation or increased mindfulness\\\" and for \\\"well-being\\\" showed a nonsignificant trend of higher tactile acuity than those who did yoga for \\\"physical exercise.\\\" There was no association between TPD threshold and cumulative amount of yoga practice in terms of hours per week and years of experience. However, increased hours of exercise per week correlated with higher TPD. CONCLUSION: The findings suggest that there may be a relationship between yoga practice and enhanced tactile acuity in the low back.\",\n \"corpus_id\": 25886977,\n \"score\": 2\n },\n {\n \"doc_id\": \"26592230\",\n \"title\": \"The effect of motor control and tactile acuity training on patients with non-specific low back pain and movement control impairment.\",\n \"abstract\": \"BACKGROUND: Movement control impairment is a clinical subgroup of non-specific low back pain which can be assessed reliably. There is a strong correlation between tactile acuity and movement control suggesting these two treatments might have additive effects. The first research aim was to determine if patients with a motor control impairment demonstrated improvement in outcome with combined tactile acuity and motor control training. The second aim was to determine if tactile acuity training enhanced the effect of motor control training. METHOD: The primary study was a single-arm cohort study conducted in three physiotherapy practices in the German-speaking part of Switzerland. 40 patients (23 males and 17 females) suffering from non-specific low back pain (NSLBP) and movement control impairment were treated. Patients were assessed at baseline and immediately post treatment. Treatment included exercises to lumbopelvic control and graphesthesia training to improve tactile acuity. Treatment effects were evaluated using the Roland Morris disability questionnaire (RMQ) and the patient-specific functional scale (PSFS). The performance on a set of six movement control tests and lumbar two-point discrimination were also assessed. The results of this cohort study were compared with a historic control group which was comparable with the primary study but included only motor control exercises. RESULTS: All the outcomes improved significantly with the combined training (RMQ - 2.2 pts., PSFS - 2.8 pts.; MCTB - 2.02 pts. & TPD - 17.07 mm; all p < 0.05). In comparison to the outcomes of the historic control, there was no significant differences in movement control, patient-specific functional complaints or disability between the groups. CONCLUSIONS: The results of this study, based on a before and after intervention comparison, showed that outcome improved significantly following combined tactile acuity and motor control training. However, compared to an earlier study, the tactile acuity training did not have an additional effect to the results. The use of historical controls does not control for allocation bias and the results obtained here require verification in a randomized controlled trial.\",\n \"corpus_id\": 42378384,\n \"score\": 2\n },\n {\n \"doc_id\": \"26797175\",\n \"title\": \"The point-to-point test: A new diagnostic tool for measuring lumbar tactile acuity? Inter and intra-examiner reliability study of pain-free subjects.\",\n \"abstract\": \"A two-point discrimination test (TPD) is commonly used to investigate lumbar tactile acuity. However, low inter-examiner reliability and difficulties in execution significantly limit its application. Therefore the aim of this study was to compare the inter- and intra-examiner reliability of a new approach, the point-to-point test (PTP), with the TPD. Twenty-one pain-free subjects attended the inter-examiner stage of the study. Eighteen of them were further recruited into an intra-examiner (reproducibility and repeatability) reliability study. PTP was performed on the three points plotted at the L3 spinal level. Point '0' overlapped with the L3 spinous process, from which points '1' and '2' were horizontally separated by 5 and 10 cm, respectively. Participants manually indicated a point previously touched by the examiner, while the distance (error) was measured. Reliability was determined with the intraclass correlation coefficient (ICC2,3). The results revealed good and moderate inter- and intra-examiner reliability at point '1' (ICC2,3 = 0.68-0.84) and good reliability at point '2' (ICC2,3 = 0.84-0.86). At point '0', reliability was moderate to poor (ICC2,3 = 0.13-0.63). TPD was characterised by a poor to moderate level of inter- (ICC2,1 = 0.51; ICC2,3 = 0.56) and intra-examiner reliability (ICC(2,1) = 0.50; ICC2,3 = 0.74). Our findings suggest that PTP is more reliable than TPD at two investigated points at the L3 spinal level. However, further research on PTP validity data is strongly warranted.\",\n \"corpus_id\": 27046581,\n \"score\": 2\n },\n {\n \"doc_id\": \"27495743\",\n \"title\": \"Short-term test-retest-reliability of conditioned pain modulation using the cold-heat-pain method in healthy subjects and its correlation to parameters of standardized quantitative sensory testing.\",\n \"abstract\": \"BACKGROUND: Conditioned Pain Modulation (CPM) is often used to assess human descending pain inhibition. Nine different studies on the test-retest-reliability of different CPM paradigms have been published, but none of them has investigated the commonly used heat-cold-pain method. The results vary widely and therefore, reliability measures cannot be extrapolated from one CPM paradigm to another. Aim of the present study was to analyse the test-retest-reliability of the common heat-cold-pain method and its correlation to pain thresholds. METHODS: We tested the short-term test-retest-reliability within 40 ± 19.9 h using a cold-water immersion (10 °C, left hand) as conditioning stimulus (CS) and heat pain (43-49 °C, pain intensity 60 ± 5 on the 101-point numeric rating scale, right forearm) as test stimulus (TS) in 25 healthy right-handed subjects (12females, 31.6 ± 14.1 years). The TS was applied 30s before (TSbefore), during (TSduring) and after (TSafter) the 60s CS. The difference between the pain ratings for TSbefore and TSduring represents the early CPM-effect, between TSbefore and TSafter the late CPM-effect. Quantitative sensory testing (QST, DFNS protocol) was performed on both sessions before the CPM assessment. STATISTICS: paired t-tests, Intraclass correlation coefficient (ICC), standard error of measurement (SEM), smallest real difference (SRD), Pearson's correlation, Bland-Altman analysis, significance level p < 0.05 with Bonferroni correction for multiple comparisons, when necessary. RESULTS: Pain ratings during CPM correlated significantly (ICC: 0.411…0.962) between both days, though ratings for TSafter were lower on day 2 (p < 0.005). The early (day 1: 16.7 ± 11.7; day 2: 19.5 ± 11.9; ICC: 0.618, SRD: 20.2) and late (day 1: 1.7 ± 9.2; day 2: 7.6 ± 11.5; ICC: 0.178, SRD: 27.0) CPM effect did not differ significantly between both days. Both early and late CPM-effects did not correlate with the pain thresholds. CONCLUSIONS: The short-term test-retest-reliability of the early CPM-effect using the heat-cold-pain method in healthy subjects achieved satisfying results in terms of the ICC. The SRD of the early CPM effect showed that an individual change of > 20 NRS can be attributed to a real change rather than chance. The late CPM-effect was weaker and not reliable.\",\n \"corpus_id\": 13907272,\n \"score\": 2\n },\n {\n \"doc_id\": \"29140929\",\n \"title\": \"Tactile acuity (dys)function in acute nociceptive low back pain: a double-blind experiment.\",\n \"abstract\": \"Research shows that chronic pain is related to cortical alterations that can be reflected in reduced tactile acuity, but whether acute pain perception influences tactile acuity has not been tested. Considering the biological role of nociception, it was hypothesized that nociceptive pain will lead to a rapid improvement in tactile acuity and that this effect is correlated with pain intensity and pain distribution. In this randomised double-blind controlled experiment (trial no. NCT03021278), healthy participants were exposed to 1 of 3 experimental conditions: acute, nociceptive low back pain induced by saline injection, a sham injection (without piercing the skin) potentially inducing nocebo pain, or no intervention. Tactile acuity was measured by a battery of tests, including two-point discrimination threshold (TPD), before, during the pain experience, and after it subsided. We found that TPD did not improve but deteriorated during pain induction in the experimental group compared with the control group (P < 0.001; η = 0.20) and changed from 56.94 mm (95% confidence interval: 53.43-60.44) at baseline to 64.22 mm (95% confidence interval: 60.42-68.02) during the pain experience. Maximum reported pain was a significant predictor (β = 0.55, P = 0.01) and accounted for 26% of the variance in TPD (P < 0.05). Other tests, point-to-point test and two-point estimation task, changed with a similar trend but did not reach significance. We concluded that acute, nociceptive pain does not improve but deteriorates tactile acuity linearly. The biological role of the observed phenomenon is unknown, and therefore, future studies should address this question.\",\n \"corpus_id\": 3652320,\n \"score\": 2\n },\n {\n \"doc_id\": \"29180111\",\n \"title\": \"Tactile acuity is reduced in people with chronic neck pain.\",\n \"abstract\": \"BACKGROUND: Tactile acuity deficits have been demonstrated in a range of persistent pain conditions and may reflect underlying cortical re-organisation. OBJECTIVE: This study aimed to determine whether tactile acuity is impaired in people with chronic neck pain relative to controls, and whether deficits relate to pain location, duration and intensity. METHODS: In this cross-sectional study, 20 people with chronic neck pain (5 idiopathic neck pain; 15 whiplash-associated disorder) and 20 pain-free controls underwent two-point discrimination (TPD) testing at the neck, back and arm, and point-to-point (PTP) and graphesthesia tests of tactile acuity at the neck and arm. RESULTS: Linear mixed effects models demonstrated a significant group*body region interaction for TPD, Graphesthesia and PTP tests (Ps < 0.001), with post hoc tests showing impaired TPD in people with neck pain relative to controls at the neck, low back, and arm (P ≤ 0.001). Graphesthesia and PTP was also impaired at the neck (P < 0.001) but not the arm (P ≥ 0.48). TPD correlated with intensity and duration of pain (Pearson's r = 0.48, P < 0.05; Pearson's r = 0.77, P < 0.01). There was no sig difference between the two neck pain groups for any tactile acuity measure (TPD: P = 0.054; Graphesthesia; P = 0.67; Point to Point: P = 0.77), however, low power limited confidence in this comparison. CONCLUSION: People with chronic neck pain demonstrated tactile acuity deficits in painful and non-painful regions when measured using the TPD test, with the magnitude of deficits appearing greatest at the neck. The study also revealed a positive relationship between TPD and pain intensity/duration, further supporting the main study finding.\",\n \"corpus_id\": 46750111,\n \"score\": 2\n },\n {\n \"doc_id\": \"29681809\",\n \"title\": \"Tactile-STAR: A Novel Tactile STimulator And Recorder System for Evaluating and Improving Tactile Perception.\",\n \"abstract\": \"Many neurological diseases impair the motor and somatosensory systems. While several different technologies are used in clinical practice to assess and improve motor functions, somatosensation is evaluated subjectively with qualitative clinical scales. Treatment of somatosensory deficits has received limited attention. To bridge the gap between the assessment and training of motor vs. somatosensory abilities, we designed, developed, and tested a novel, low-cost, two-component (bimanual) mechatronic system targeting tactile somatosensation: the Tactile-STAR-a tactile stimulator and recorder. The stimulator is an actuated pantograph structure driven by two servomotors, with an end-effector covered by a rubber material that can apply two different types of skin stimulation: brush and stretch. The stimulator has a modular design, and can be used to test the tactile perception in different parts of the body such as the hand, arm, leg, big toe, etc. The recorder is a passive pantograph that can measure hand motion using two potentiometers. The recorder can serve multiple purposes: participants can move its handle to match the direction and amplitude of the tactile stimulator, or they can use it as a master manipulator to control the tactile stimulator as a slave. Our ultimate goal is to assess and affect tactile acuity and somatosensory deficits. To demonstrate the feasibility of our novel system, we tested the Tactile-STAR with 16 healthy individuals and with three stroke survivors using the skin-brush stimulation. We verified that the system enables the mapping of tactile perception on the hand in both populations. We also tested the extent to which 30 min of training in healthy individuals led to an improvement of tactile perception. The results provide a first demonstration of the ability of this new system to characterize tactile perception in healthy individuals, as well as a quantification of the magnitude and pattern of tactile impairment in a small cohort of stroke survivors. The finding that short-term training with Tactile-STAR can improve the acuity of tactile perception in healthy individuals suggests that Tactile-STAR may have utility as a therapeutic intervention for somatosensory deficits.\",\n \"corpus_id\": 4615636,\n \"score\": 2\n },\n {\n \"doc_id\": \"19501965\",\n \"title\": \"The effect of tactile discrimination training is enhanced when patients watch the reflected image of their unaffected limb during training.\",\n \"abstract\": \"In patients with phantom limb pain or complex regional pain syndrome (CRPS), sensory discrimination training increases tactile acuity, normalises cortical reorganisation and decreases pain. In healthy people, sensory cortical response, and tactile acuity, are greater if the participant looks towards the body part being stimulated. Does this effect enhance tactile training in CRPS patients? Ten patients underwent a 30-min tactile discrimination training session under four conditions (order randomised) in a 2 x 2 design: looking towards or away from the stimulated limb and seeing or not seeing skin. Tactile training imparted long-term improvement in tactile acuity when patients watched the reflected image of their unaffected limb in a mirror during training (that is, they looked towards the stimulated body part and could see the skin of the opposite body part in the mirror): two-point discrimination threshold (TPD) was 8mm less 2 days after training than it was before training ([95% CI=1.5-14.3mm], p<0.001). Although this condition also imparted a greater reduction in resting pain at post-treatment than the other conditions, and change in pain and change in TPD over the session were strongly related (r=0.83, p<0.001), there was no residual effect on pain at 2-day follow-up. In the other conditions, tactile acuity had returned to pre-training levels at 2-day follow-up. The results should directly improve management of CRPS, and have implications for rehabilitation of other conditions associated with nervous system injury or disease, for example stroke, in which tactile recovery is a major objective of rehabilitation.\",\n \"corpus_id\": 8155362,\n \"score\": 1\n },\n {\n \"doc_id\": \"24299621\",\n \"title\": \"The intra- and inter-rater reliability of five clinical muscle performance tests in patients with and without neck pain.\",\n \"abstract\": \"BACKGROUND: This study investigates the reliability of muscle performance tests using cost- and time-effective methods similar to those used in clinical practice. When conducting reliability studies, great effort goes into standardising test procedures to facilitate a stable outcome. Therefore, several test trials are often performed. However, when muscle performance tests are applied in the clinical setting, clinicians often only conduct a muscle performance test once as repeated testing may produce fatigue and pain, thus variation in test results. We aimed to investigate whether cervical muscle performance tests, which have shown promising psychometric properties, would remain reliable when examined under conditions similar to those of daily clinical practice. METHODS: The intra-rater (between-day) and inter-rater (within-day) reliability was assessed for five cervical muscle performance tests in patients with (n = 33) and without neck pain (n = 30). The five tests were joint position error, the cranio-cervical flexion test, the neck flexor muscle endurance test performed in supine and in a 45°-upright position and a new neck extensor test. RESULTS: Intra-rater reliability ranged from moderate to almost perfect agreement for joint position error (ICC ≥ 0.48-0.82), the cranio-cervical flexion test (ICC ≥ 0.69), the neck flexor muscle endurance test performed in supine (ICC ≥ 0.68) and in a 45°-upright position (ICC ≥ 0.41) with the exception of a new test (neck extensor test), which ranged from slight to moderate agreement (ICC = 0.14-0.41). Likewise, inter-rater reliability ranged from moderate to almost perfect agreement for joint position error (ICC ≥ 0.51-0.75), the cranio-cervical flexion test (ICC ≥ 0.85), the neck flexor muscle endurance test performed in supine (ICC ≥ 0.70) and in a 45°-upright position (ICC ≥ 0.56). However, only slight to fair agreement was found for the neck extensor test (ICC = 0.19-0.25). CONCLUSIONS: Intra- and inter-rater reliability ranged from moderate to almost perfect agreement with the exception of a new test (neck extensor test), which ranged from slight to moderate agreement. The significant variability observed suggests that tests like the neck extensor test and the neck flexor muscle endurance test performed in a 45°-upright position are too unstable to be used when evaluating neck muscle performance.\",\n \"corpus_id\": 1931582,\n \"score\": 1\n },\n {\n \"doc_id\": \"24945099\",\n \"title\": \"Reliability study of thermal quantitative sensory testing in healthy Chinese.\",\n \"abstract\": \"BACKGROUND: Test-retest reliability is important to establish for any diagnostic tool. The reliability of quantitative sensory testing (QST) in the trigeminal region has recently been described in Caucasians as well as differences in absolute thresholds and responses between Caucasians and Chinese. However, the test-retest reliability has not been determined in a Chinese population. OBJECTIVE: To provide novel information on the test-retest reliability of thermal QST in the trigeminal and spinal system in healthy Chinese. METHODS: Twenty healthy volunteers (10 women and 10 men) participated. Cold detection threshold (CDT), warm detection threshold (WDT), cold pain threshold (CPT), and heat pain threshold (HPT) were measured at two sites: the surface of the left hand and the left masseter. The testing was performed over three consecutive stimuli trials, three sessions conducted on one day and repeated one week later. Data were analyzed with intra-tester reliability test and four-way analysis of variance (ANOVA) for repeated measures. RESULTS: There was a tendency for the first trial in CDT (p = 0.005), CPT (p = 0.02), and HPT (p < 0.001) to reflect higher sensitivity than the subsequent two trials. Most variables showed acceptable to excellent reliability and non-significant difference across different trials (ICC: 0.912-0.989), sessions (ICC: 0.791-0.977), and days (ICC: 0.415-0.837). Between-site differences were significant for CDT (p = 0.003) and HPT (p = 0.045) with higher sensitivity at the masseter muscle. There were significant gender differences with higher sensitivity in women for CPT (p = 0.001) and HPT (p = 0.001). CONCLUSION: Test site and gender affect thermal thresholds substantially. The test-retest reliability of most thermal threshold measures were acceptable for assessing somatosensory function, however, innocuous thresholds appear to be associated with larger variability than noxious thresholds in a Chinese population.\",\n \"corpus_id\": 36671079,\n \"score\": 1\n },\n {\n \"doc_id\": \"25161897\",\n \"title\": \"Intersession reliability of fMRI activation for heat pain and motor tasks.\",\n \"abstract\": \"As the practice of conducting longitudinal fMRI studies to assess mechanisms of pain-reducing interventions becomes more common, there is a great need to assess the test-retest reliability of the pain-related BOLD fMRI signal across repeated sessions. This study quantitatively evaluated the reliability of heat pain-related BOLD fMRI brain responses in healthy volunteers across 3 sessions conducted on separate days using two measures: (1) intraclass correlation coefficients (ICC) calculated based on signal amplitude and (2) spatial overlap. The ICC analysis of pain-related BOLD fMRI responses showed fair-to-moderate intersession reliability in brain areas regarded as part of the cortical pain network. Areas with the highest intersession reliability based on the ICC analysis included the anterior midcingulate cortex, anterior insula, and second somatosensory cortex. Areas with the lowest intersession reliability based on the ICC analysis also showed low spatial reliability; these regions included pregenual anterior cingulate cortex, primary somatosensory cortex, and posterior insula. Thus, this study found regional differences in pain-related BOLD fMRI response reliability, which may provide useful information to guide longitudinal pain studies. A simple motor task (finger-thumb opposition) was performed by the same subjects in the same sessions as the painful heat stimuli were delivered. Intersession reliability of fMRI activation in cortical motor areas was comparable to previously published findings for both spatial overlap and ICC measures, providing support for the validity of the analytical approach used to assess intersession reliability of pain-related fMRI activation. A secondary finding of this study is that the use of standard ICC alone as a measure of reliability may not be sufficient, as the underlying variance structure of an fMRI dataset can result in inappropriately high ICC values; a method to eliminate these false positive results was used in this study and is recommended for future studies of test-retest reliability.\",\n \"corpus_id\": 16090306,\n \"score\": 1\n },\n {\n \"doc_id\": \"25477032\",\n \"title\": \"Reliability, construct and discriminative validity of clinical testing in subjects with and without chronic neck pain.\",\n \"abstract\": \"BACKGROUND: The reliability of clinical tests for the cervical spine has not been adequately evaluated. Six cervical clinical tests, which are low cost and easy to perform in clinical settings, were tested for intra- and inter-examiner reliability, and two performance tests were assessed for test-retest reliability in people with and without chronic neck pain. Moreover, construct and between-group discriminative validity of the tests were examined. METHODS: Twenty-one participants with chronic neck pain and 21 asymptomatic participants were included. Intra- and inter-reliability were evaluated for the Cranio-Cervical Flexion Test (CCFT), Range of Movement (ROM), Joint Position Error (JPE), Gaze Stability (GS), Smooth Pursuit Neck Torsion Test (SPNTT), and neuromuscular control of the Deep Cervical Extensors (DCE). Test-retest reliability was assessed for Postural Control (SWAY) and Pressure Pain Threshold (PPT) over tibialis anterior, infraspinatus and the C3-C4 segment. RESULTS: Intraclass Correlation Coefficient (ICC) for intra- and inter-examiner reliability was highest for ROM (range: 0.80 to 0.94), DCE (0.75 to 0.90) and CCFT (0.63 to 0.86). JPE had the lowest ICC (0.02 to 0.66). Intra- and inter-reliability for GS and SPNTT showed kappa ranging from 0.66 to 0.92, and 0.57 to 0.78 (prevalence adjusted), respectively. For the test-retest study, ICC was 0.83 to 0.89 for PPT and 0.39 to 0.79 for SWAY. Construct validity was satisfactory for all tests, except JPE. Significant between group discriminative validity was found for CCFT, ROM, GS, SPNTT and PPT, however, differences were within the limits of the minimal detectable change. CONCLUSIONS: The majority of the tests evaluated showed satisfactory reliability and construct validity supporting their use in the clinical evaluation of patients with chronic neck pain.\",\n \"corpus_id\": 7681661,\n \"score\": 1\n },\n {\n \"doc_id\": \"27796191\",\n \"title\": \"Disrupted Tactile Acuity in People With Achilles Tendinopathy: A Preliminary Case-Control Investigation.\",\n \"abstract\": \"Study Design Controlled laboratory study, preliminary case-control design. Background The mechanisms that contribute to Achilles tendinopathy remain poorly understood. The disparity between pain experience and peripheral pathology demonstrated in patients with Achilles tendinopathy suggests that changes in central nervous system function may be involved. Objectives To investigate whether lower-limb tactile acuity is impaired in people with nonacute Achilles tendinopathy. Methods Thirteen consecutive participants with nonacute midportion Achilles tendinopathy and 13 healthy controls were enrolled. Two-point discrimination thresholds over the affected Achilles tendon, unaffected tendon, and tendon of healthy controls were evaluated. Independent and dependent t tests were used to compare group means. Results Two-point discrimination distance over the affected limb in participants with Achilles tendinopathy was significantly increased when compared to the unaffected limb (mean difference, 11.7 mm; 95% confidence interval [CI]: 1.9, 21.5; P = .02) and to healthy controls (mean difference, 13.1 mm; 95% CI: 1.6, 24.6; P = .03). There was no significant difference between the healthy controls and the unaffected side in people with Achilles tendinopathy (mean difference, 1.4 mm; 95% CI: -7.9, 5.1; P = .66). Conclusion These data provide the first evidence of reduced 2-point discrimination over the affected tendon in patients with Achilles tendinopathy. Further research is needed to determine the cause for the change in tactile acuity. J Orthop Sports Phys Ther 2016;46(12):1061-1064. Epub 30 Oct 2016. doi:10.2519/jospt.2016.6514.\",\n \"corpus_id\": 22168443,\n \"score\": 1\n },\n {\n \"doc_id\": \"28008644\",\n \"title\": \"Test-retest reliability of quantitative sensory testing for mechanical somatosensory and pain modulation assessment of masticatory structures.\",\n \"abstract\": \"Assessing the reliability of medical measurements is a crucial step towards the elaboration of an applicable clinical instrument. There are few studies that evaluate the reliability of somatosensory assessment and pain modulation of masticatory structures. This study estimated the test-retest reliability, that is over time, of the mechanical somatosensory assessment of anterior temporalis, masseter and temporomandibular joint (TMJ) and the conditioned pain modulation (CPM) using the anterior temporalis as the test site. Twenty healthy women were evaluated in two sessions (1 week apart) by the same examiner. Mechanical detection threshold (MDT), mechanical pain threshold (MPT), wind-up ratio (WUR) and pressure pain threshold (PPT) were assessed on the skin overlying the anterior temporalis, masseter and TMJ of the dominant side. CPM was tested by comparing PPT before and during the hand immersion in a hot water bath. anova and intra-class correlation coefficients (ICCs) were applied to the data (α = 5%). The overall ICCs showed acceptable values for the test-retest reliability of mechanical somatosensory assessment of masticatory structures. The ICC values of 75% of all quantitative sensory measurements were considered fair to excellent (fair = 8·4%, good = 33·3% and excellent = 33·3%). However, the CPM paradigm presented poor reliability (ICC = 0·25). The mechanical somatosensory assessment of the masticatory structures, but not the proposed CPM protocol, can be considered sufficiently reliable over time to evaluate the trigeminal sensory function.\",\n \"corpus_id\": 206123658,\n \"score\": 1\n },\n {\n \"doc_id\": \"28558952\",\n \"title\": \"Intra- and inter-rater reliability of neutral head position and target head position tests in patients with and without neck pain.\",\n \"abstract\": \"BACKGROUND: Cervical proprioception is a common term used in neck rehabilitation, and it is examined using neutral head position (NHP) and target head position (THP) tests. OBJECTIVE: To investigate intra- and inter-rater reliability of the NHP and THP tests in patients with neck pain and in healthy controls. METHODS: The intra-rater (between-day) and inter-rater (within-day) reliability of the NHP and THP tests were assessed in 36 patients with neck pain and 33 healthy subjects. NHP testing was evaluated in cervical extension, while THP testing was evaluated in six directions of cervical motion: cervical flexion, extension, side bending right, side bending left, rotation right, and rotation left. RESULTS: The intra-rater reliability for the NHP tests had intraclass correlation coefficient (ICC) values of 0.74-0.78 and a standard error of measurement (SEM) of 1.78-1.88; the THP tests had ICC values of 0.70-0.83 and SEM of 1.45-2.45. Likewise, inter-rater reliability for NHP had ICC values of 0.74-0.79 and SEM of 1.79-1.87. For the THP test, the inter-rater reliability had ICC values of 0.62-0.84 and SEM of 1.50-2.23. CONCLUSION: Intra- and inter-rater reliability ranged from good to very good agreement both for NHP and for THP tests of cervical proprioception.\",\n \"corpus_id\": 10899571,\n \"score\": 1\n },\n {\n \"doc_id\": \"29174222\",\n \"title\": \"Inter- and intrarater reliability of two proprioception tests using clinical applicable measurement tools in subjects with and without knee osteoarthritis.\",\n \"abstract\": \"BACKGROUND: The therapeutic value of proprioceptive-based exercises in knee osteoarthritis (KOA) management warrants investigation of proprioceptive testing methods easily accessible in clinical practice. OBJECTIVE: To estimate inter- and intrarater reliability of the knee joint position sense (KJPS) test and knee force sense (KFS) test in subjects with and without KOA. DESIGN: Cross-sectional test-retest design. METHOD: Two blinded raters performed independently repeated measures of the KJPS and KFS test, using an analogue inclinometer and handheld dynamometer, respectively, in eight KOA patients (12 symptomatic knees) and 26 healthy controls (52 asymptomatic knees). Intraclass correlation coefficients (ICCs; model 2,1), standard error of measurement (SEM) and minimal detectable change with 95% confidence bounds (MDC95) were calculated. RESULTS: For KJPS, results showed good to excellent test-retest agreement (ICCs 0.70-0.95 in KOA patients; ICCs 0.65-0.85 in healthy controls). A 2° measurement error (SEM 1°) was reported when measuring KJPS in multiple test positions and calculating mean repositioning error. Testing KOA patients pre and post therapy a repositioning error larger than 4° (MDC95) is needed to consider true change. Measuring KFS using handheld dynamometry showed poor to fair interrater and poor to excellent intrarater reliability in subjects with and without KOA. CONCLUSIONS: Measuring KJPS in multiple test positions using an analogue inclinometer and calculating mean repositioning error is reliable and can be used in clinical practice. We do not recommend the use of the KFS test to clinicians. Further research is required to establish diagnostic accuracy and validity of our KJPS test in larger knee pain populations.\",\n \"corpus_id\": 37957780,\n \"score\": 1\n },\n {\n \"doc_id\": \"29282073\",\n \"title\": \"Responsiveness of clinical tests for people with neck pain.\",\n \"abstract\": \"BACKGROUND: Responsiveness of a clinical test is highly relevant in order to evaluate the effect of a given intervention. However, the responsiveness of clinical tests for people with neck pain has not been adequately evaluated. The objective of the present study was to examine the responsiveness of four clinical tests which are low cost and easy to perform in a clinical setting, including the craniocervical flexion test, cervical active range of movement, test for the cervical extensors and pressure pain threshold testing. METHODS: This study is a secondary analysis of data collected in a previously published randomised controlled trial. Participants were randomized to either physical training, exercises and pain education combined or pain education only. Participants were tested on the clinical tests at baseline and at 4-month follow-up. An anchor-based approach using Receiver Operator Characteristics (ROC) curves was used to evaluate responsiveness of the clinical tests. The Neck Disability Index was used to discriminate between those who had improved and those who were unchanged at the 4-month follow-up. Minimum Clinically Important Difference (MCID), together with sensitivity, specificity, positive and negative predictive values, in addition to positive and negative likelihood ratios were calculated. RESULTS: In total, 164 participants completed the 4 month follow up. One-hundred forty four participants were classified as unchanged whereas 20 patients were considered to be improved. Twenty-six participants didn't complete all of the clinical tests, leaving a total of 138 to be included for analyses. Area Under Curve (AUC) ranged from 0.50-0.62 for the clinical tests, and were all below an acceptable level. MCID was generally large, and the corresponding sensitivity and specificity was low with sensitivity ranging from 20 to 60%, and specificity from 54 to 86%. LR+ (0.8-2.07) and LR- (0.7-1.1) showed low diagnostic value for all variables, with PPV ranging from 12.1 to 26.1 and NPV ranging from 84.7 to 89.2. CONCLUSION: Responsiveness of the included clinical tests was generally low when using change in NDI score as the anchor from baseline to the 4-month follow up. Further investigations of responsiveness are warranted, possibly using other anchors, which to a higher degree resemble similar dimensions as the clinical tests.\",\n \"corpus_id\": 25302890,\n \"score\": 1\n },\n {\n \"doc_id\": \"20671244\",\n \"title\": \"Psychometric comparisons of 3 functional ambulation measures for patients with stroke.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: We compared the test-retest reliability, validity, and responsiveness of the Dynamic Gait Index, the 4-item Dynamic Gait Index, and the Functional Gait Assessment for assessment of walking in patients with stroke. METHODS: Forty-five outpatients participating in the validity and responsiveness study were tested using the 3 walking measures as well as the 10-m walk test, Barthel Index, and Postural Assessment Scale for Stroke Patients. We tested them during the first week, then again after 2 months and 5 months of therapy. Another 48 chronic patients completed the 3 measures twice, 1 week apart, in the test-retest reliability study. RESULTS: Thirty-five participants completed 3 time-point assessments. The Functional Gait Assessment showed the least floor and ceiling effects, indicating it has the best discriminative ability for patients with stroke with high walking function. We found the 3 measures were highly correlated with each other, indicating excellent concurrent validity, and all measures at the first week of therapy were moderately to highly correlated with the Barthel Index scores at 5 months, indicating good predictive validity. Responsiveness of the 3 measures was moderate during a 5-month period, and all showed good test-retest reliability. The minimal detectable changes between tests indicate acceptable random error. CONCLUSIONS: All 3 measures showed sufficient validity, responsiveness, and reliability for assessment of walking function in patients with stroke undergoing rehabilitation, but the Functional Gait Assessment is recommended for its psychometric properties.\",\n \"corpus_id\": 2664925,\n \"score\": 0\n },\n {\n \"doc_id\": \"22152048\",\n \"title\": \"Test-retest reliability and construct validity of the ENERGY-child questionnaire on energy balance-related behaviours and their potential determinants: the ENERGY-project.\",\n \"abstract\": \"BACKGROUND: Insight in children's energy balance-related behaviours (EBRBs) and their determinants is important to inform obesity prevention research. Therefore, reliable and valid tools to measure these variables in large-scale population research are needed. OBJECTIVE: To examine the test-retest reliability and construct validity of the child questionnaire used in the ENERGY-project, measuring EBRBs and their potential determinants among 10-12 year old children. METHODS: We collected data among 10-12 year old children (n = 730 in the test-retest reliability study; n = 96 in the construct validity study) in six European countries, i.e. Belgium, Greece, Hungary, the Netherlands, Norway, and Spain. Test-retest reliability was assessed using the intra-class correlation coefficient (ICC) and percentage agreement comparing scores from two measurements, administered one week apart. To assess construct validity, the agreement between questionnaire responses and a subsequent face-to-face interview was assessed using ICC and percentage agreement. RESULTS: Of the 150 questionnaire items, 115 (77%) showed good to excellent test-retest reliability as indicated by ICCs > .60 or percentage agreement ≥ 75%. Test-retest reliability was moderate for 34 items (23%) and poor for one item. Construct validity appeared to be good to excellent for 70 (47%) of the 150 items, as indicated by ICCs > .60 or percentage agreement ≥ 75%. From the other 80 items, construct validity was moderate for 39 (26%) and poor for 41 items (27%). CONCLUSIONS: Our results demonstrate that the ENERGY-child questionnaire, assessing EBRBs of the child as well as personal, family, and school-environmental determinants related to these EBRBs, has good test-retest reliability and moderate to good construct validity for the large majority of items.\",\n \"corpus_id\": 16154288,\n \"score\": 0\n },\n {\n \"doc_id\": \"22415358\",\n \"title\": \"Assessing the reliability and validity of a shorter walk test compared with the 10-Meter Walk Test for measurements of gait speed in healthy, older adults.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: Walking speed is associated with several health-related outcomes. Research examining how differences in test walking distance affect walking speed reliability and validity is limited. The primary purpose of this study was to examine the reliability and concurrent validity of gait speed measurements obtained from a 4-Meter Walk Test compared with the commonly used 10-Meter Walk Test. A second objective was to similarly examine 2 different timing methods: stopwatch and automatic timers. METHODS: Forty-three healthy, older adults (mean age = 84.3 ± 6.9 years) performed 3 consecutive walking trials on the 4- and 10-Meter Walk Tests at their self-selected walking speed. RESULTS: Gait speed measurements for both tests were shown to have excellent test-retest reliability (ICC values of 0.96-0.98), with similar results for stopwatch and automatic timer assessments (ICC values of 0.99-1.00). Standard error of the measurement (SEM) values were small (0.004-0.008 m/s) across measurement methods. While the ICC value for gait speed measurements between the 2 walk tests was 0.93, the Bland-Altman analysis revealed a discrepancy of ±0.15 to ±0.17 m/s between measurement methods. DISCUSSION: Both 4- and 10-m gait speed assessments had excellent test-retest reliability with similar SEM and minimal detectable change values. There was little difference in SEM values between the 2 timing methods. While the mean difference in gait speed between the 4- and 10-Meter Walk Tests was small, the range of the measurement differences was large enough to potentially mask meaningful changes in gait speed over time if both methods were used interchangeably. CONCLUSIONS: While the reliability of both walking tests is excellent, the 4-Meter Walk Test does not exhibit a high enough degree of concurrent validity with the 10-Meter Walk Test to be used interchangeably for gait speed assessments in healthy, older adults. We therefore recommend using the 10-Meter Walk Test to obtain the most valid clinical assessment of walking speed when using it as a 1-time indicator of health status.\",\n \"corpus_id\": 44406711,\n \"score\": 0\n },\n {\n \"doc_id\": \"22888983\",\n \"title\": \"Test-retest reliability and construct validity of the ENERGY-parent questionnaire on parenting practices, energy balance-related behaviours and their potential behavioural determinants: the ENERGY-project.\",\n \"abstract\": \"BACKGROUND: Insight in parental energy balance-related behaviours, their determinants and parenting practices are important to inform childhood obesity prevention. Therefore, reliable and valid tools to measure these variables in large-scale population research are needed. The objective of the current study was to examine the test-retest reliability and construct validity of the parent questionnaire used in the ENERGY-project, assessing parental energy balance-related behaviours, their determinants, and parenting practices among parents of 10-12 year old children. FINDINGS: We collected data among parents (n = 316 in the test-retest reliability study; n = 109 in the construct validity study) of 10-12 year-old children in six European countries, i.e. Belgium, Greece, Hungary, the Netherlands, Norway, and Spain. Test-retest reliability was assessed using the intra-class correlation coefficient (ICC) and percentage agreement comparing scores from two measurements, administered one week apart. To assess construct validity, the agreement between questionnaire responses and a subsequent interview was assessed using ICC and percentage agreement. All but one item showed good to excellent test-retest reliability as indicated by ICCs > .60 or percentage agreement ≥ 75%. Construct validity appeared to be good to excellent for 92 out of 121 items, as indicated by ICCs > .60 or percentage agreement ≥ 75%. From the other 29 items, construct validity was moderate for 24 and poor for 5 items. CONCLUSIONS: The reliability and construct validity of the items of the ENERGY-parent questionnaire on multiple energy balance-related behaviours, their potential determinants, and parenting practices appears to be good. Based on the results of the validity study, we strongly recommend adapting parts of the ENERGY-parent questionnaire if used in future research.\",\n \"corpus_id\": 48561,\n \"score\": 0\n },\n {\n \"doc_id\": \"23153836\",\n \"title\": \"The assessment of cervical sensory motor control: a systematic review focusing on measuring methods and their clinimetric characteristics.\",\n \"abstract\": \"BACKGROUND: Cervical sensorimotor control (CSMC) becomes increasingly important in the assessment and treatment of patients with neck pain. This review aims to compare commonly used CSMC measuring methods in terms of required tasks, measuring device and clinimetric properties. SEARCH METHODS: A systematic review of two databases, followed by methodological quality assessment (CBO guidelines). RESULTS: The methodological quality of 34 included articles was generally good (five to seven out of eight), the inter-rater agreement was excellent (κw=0.966, p<0.01). Following tasks were found: head repositioning accuracy to the neutral head position (HRA-to-NHP) and to a target position (HRA-to-target), a virtual reality test, a continuous linear movement technique (CLMT) and an object following non-linear movement technique (NLMT) (The Fly™). Test-retest reliability was fair to excellent (ICC 0.35-0.87) for the HRA-to-NHP, very bad to excellent (ICC 0.01-0.90) for the HRA-to-target, fair to good (ICC 0.25-0.77) for the virtual reality test and moderate to excellent (ICC: 0.60-0.86) for The Fly™. The reliability of the CLMT was not documented. The HRA-to-NHP, The Fly™ and the CLMT can discriminate between patients with neck complaints and controls (discriminant validity). Currently, only The Fly™ can discriminate between different patient populations (post-traumatic and non-traumatic neck pain). The sensitivity, specificity and responsiveness of the methods have to be assessed in future research. CONCLUSIONS: The dynamic method The Fly™ appears to be more reliable than the HRA-to-NHP and is able to discriminate between different patient populations. The diagnostic potential is to be confirmed in future research.\",\n \"corpus_id\": 9754556,\n \"score\": 0\n },\n {\n \"doc_id\": \"23362555\",\n \"title\": \"The oncology acuity tool: a reliable, valid method for measuring patient acuity for nurse assignment decisions.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: Matching nurse assignments with patient acuity has critical implications for providing safe, effective, and efficient care. Despite this, we lack well-established methods for accurate assessment of acuity. This study aimed to evaluate the reliability and validity of the Oncology Acuity Tool (OAT), which is used for determining nurse assignments. METHODS: Inter-rater reliability and concurrent validity were assessed via surveys of current users of the tool. Content validity data were collected from expert oncology nurses. Predictive validity was assessed by tracking patients who sustained either of two acute events. RESULTS: Findings included high inter-rater reliability, moderately strong concurrent validity, and moderate content validity. Acuity significantly predicted rapid response team consults but not falls. CONCLUSIONS: The OAT demonstrated sufficient reliability and validity for measuring acuity prospectively in this population.\",\n \"corpus_id\": 19628927,\n \"score\": 0\n },\n {\n \"doc_id\": \"23522388\",\n \"title\": \"The Swedish version of OMAS is a reliable and valid outcome measure for patients with ankle fractures.\",\n \"abstract\": \"BACKGROUND: The aim of this study was to evaluate the test-retest reliability and the validity of the self-reported questionnaire Olerud-Molander Ankle Score (OMAS) in subjects after an ankle fracture. METHODS: When evaluating the test-retest reliability of the OMAS, 42 subjects surgically treated due to an ankle fracture participated 12 months after injury. OMAS was completed by the patients on two occasions at one to two weeks' interval. Concurrent criterion validity was evaluated using the five subscales of the Foot and Ankle Outcome Score (FAOS) and global self-rating function (GSRF), which is a five-grade Likert scale with the alternatives: \\\"very good\\\", \\\"good\\\", \\\"fair\\\", \\\"poor\\\", \\\"very poor\\\". Forty-six patients participated in the validation against FAOS, and for GSRF 105 patients participated at 6 months and 99 at 12 months. Uni-, bi- and trimalleolar fractures were all included and both non-rigid and rigid surgical techniques were used. All fractures healed without complications. Before analysis of the results the five groups according to GSRF were reduced to three: \\\"good\\\", \\\"fair\\\" and \\\"poor\\\". Test-retest reliability was assessed using Spearman's rank correlation, the intraclass correlation coefficient (ICC), the standard error of measurement (SEM and SEM%) and the smallest real difference (SRD and SRD%). The Cronbach's alpha score and validity versus FAOS was assessed using Spearman's rank correlation and validity versus GSRF using the Kruskal-Wallis Test and the Mann-Whitney U-Test as ad hoc analyses. RESULTS: The test-retest reliability correlation coefficient obtained was rho = 0.95 and ICC = 0.94. The SEM was 4.4 points and SEM% 5.8% and should be interpreted as the smallest change that indicates a real change of clinical interest for a group of subjects. The SRD was 12 points and SRD% 15.8% and should be interpreted as the smallest change that indicates a real change of clinical interest for a single subject. The correlation coefficients versus the five subscales of FAOS ranged from rho = 0.80 to 0.86. There were significant differences between GSRF groups \\\"good\\\", \\\"fair\\\" and \\\"poor\\\" (p < 0.001) at both the six-month and the 12-month follow-up. The internal consistency for the OMAS was 0.76. The effect size between results from 6-month and 12-month follow-up turned out be 0.44 and should be considered as medium. CONCLUSION: The results showed that the test-retest reliability of the Swedish version of OMAS was very high in subjects after an ankle fracture and the standard error of measurement was low. Furthermore the OMAS was found to be valid using both the five subscales of FAOS and the GSRF. The OMAS can thus be used as an outcome measure after an ankle fracture.\",\n \"corpus_id\": 2677831,\n \"score\": 0\n },\n {\n \"doc_id\": \"23561578\",\n \"title\": \"Reliability and validity of the weight status and dietary intake measures in the COMPASS questionnaire: are the self-reported measures of body mass index (BMI) and Canada's food guide servings robust?\",\n \"abstract\": \"BACKGROUND: The COMPASS study is designed to follow a cohort of ~30,000 grade 9 to 12 students attending ~60 secondary schools for four years to understand how changes in school characteristics (policies, programs, built environment) are associated with changes in youth health behaviours. Since the student-level questionnaire for COMPASS (Cq) is designed to facilitate multiple large-scale school-based data collections using passive consent procedures, the Cq is only comprised of self-reported measures. The present study assesses the 1-week (1 wk) test-retest reliability and the concurrent validity of the Cq measures for weight status and dietary intake. METHODS: Validation study data were collected from 178 grade 9 students in Ontario (Canada). At time 1 (T1), participants completed the Cq and daily recoding of their dietary intake using the web-based eaTracker tool. After one week, (T2), students completed the Cq again, participants submitted their daily eaTracker logs and staff measured their height and weight. Test-retest reliability of the self-reported (SR) weight status and dietary intake measures at T1 and T2, and the concurrent validity of the objectively measured and SR weight status and dietary intake measures at T2 were examined using intraclass correlation coefficients (ICC). RESULTS: Test-retest reliability for SR height (ICC 0.96), weight (ICC 0.99), and BMI (ICC 0.95) are considered substantial. The concurrent validity for SR height (ICC 0.88), weight (ICC 0.95), and BMI (ICC 0.84) are also considered substantial. The test-retest reliability for SR dietary intake for fruits and vegetables (ICC 0.68) and milk and alternatives (ICC 0.69) are considered moderate, whereas meat and alternatives (ICC 0.41), and grain products (ICC 0.56) are considered fair. The concurrent validity for SR dietary intake identified that fruits and vegetables (ICC 0.53), milk and alternatives (ICC 0.60), and grain products (ICC 0.41) are considered fair, whereas meat and alternatives (ICC 0.34) was considered slight. CONCLUSIONS: While the test-retest reliability of the measures used in this study were all high, the concurrent validity of the measures was considered acceptable. The results support the use of the self-reported COMPASS weight status and dietary intake measures for use in research where objective measures are not possible.\",\n \"corpus_id\": 3534949,\n \"score\": 0\n },\n {\n \"doc_id\": \"24168373\",\n \"title\": \"Observer ratings of neighborhoods: comparison of two methods.\",\n \"abstract\": \"BACKGROUND: Although neighborhood characteristics have important relationships with health outcomes, direct observation involves imperfect measurement. The African American Health (AAH) study included two observer neighborhood rating systems (5-item Krause and 18-item AAH Neighborhood Assessment Scale [NAS]), initially fielded at two different waves. Good measurement characteristics were previously shown for both, but there was more rater variability than desired. In 2010 both measures were re-fielded together, with enhanced training and field methods implemented to decrease rater variability while maintaining psychometric properties. METHODS: AAH included a poor inner city and more heterogeneous suburban areas. Four interviewers rated 483 blocks, with 120 randomly-selected blocks rated by two interviewers. We conducted confirmatory factor analysis of scales and tested the Krause (5-20 points), AAH 18-item NAS (0-28 points), and a previous 7-item and new 5-item versions of the NAS (0-17 points, 0-11 points). Retest reliability for items (kappa) and scales (Intraclass Correlation Coefficient [ICC]) were calculated overall and among pre-specified subgroups. Linear regression assessed interviewer effects on total scale scores and assessed concurrent validity on lung and lower body functions. Mismeasurement effects on self-rated health were also assessed. RESULTS: Scale scores were better in the suburbs than in the inner city. ICC was poor for the Krause scale (ICC=0.19), but improved if the retests occurred within 10 days (ICC=0.49). The 7- and 5-item NAS scales had better ICCs (0.56 and 0.62, respectively), and were higher (0.71 and 0.73) within 10 days. Rater variability for the Kraus and 5- and 7-item NAS scales was 1-3 points (compared to the supervising rater). Concurrent validity was modest, with residents living in worse neighborhood conditions having worse function. Unadjusted estimates were biased towards the null compared with measurement-error corrected estimates. CONCLUSIONS: Enhanced field protocols and rater training did not improve measurement quality. Specifically, retest reliability and interviewer variability remained problematic. Measurement error partially reduced, but did not eliminate concurrent validity, suggesting there are robust associations between neighborhood characteristics and health outcomes. We conclude that the 5-item AAH NAS has sufficient reliability and validity for further use. Additional research on the measurement properties of environmental rating methods is encouraged.\",\n \"corpus_id\": 2867997,\n \"score\": 0\n },\n {\n \"doc_id\": \"24423109\",\n \"title\": \"Head-eye movement control tests in patients with chronic neck pain; inter-observer reliability and discriminative validity.\",\n \"abstract\": \"BACKGROUND: Head-eye movement control deficit is an identified problem in patients with chronic neck pain, particularly in cases of whiplash associated disorders (WAD). To date, there is no evidence concerning the reliability and validity of visually assessed active head-eye movement control tests. Therefore, the objectives of the present cross-sectional study were, a) to develop a test battery; and b) to investigate inter-observer reliability and discriminative validity in patients with chronic neck pain compared to healthy controls. METHODS: The study was conducted at two physiotherapy clinics in Switzerland. Ethics Committee approval was obtained. Ten active head-eye coordination tests, on 23 patients with chronic neck pain and associated symptoms and 19 healthy controls, were videotaped. The tests included eye movements in the neutral head position and 45° relative neck rotation, gaze stability and sequential head-eye movements. All tests were performed in the sitting and standing positions. Two blinded physiotherapists independently rated the randomized videos. Performance was rated as \\\"negative\\\", \\\"moderately positive\\\" or \\\"clearly positive\\\". Weighted kappa (wK) and 95% confidence intervals (CI) were calculated to investigate inter-observer reliability. Good reliability was defined as wK >0.5 with a lower boundary of 95% CI >0.2. Odds ratios (to define cut-off points) and the distribution of the classificator, numbers of positive tests, were calculated. RESULTS: Three out of ten tests showed \\\"excellent\\\" (wK 0.82 to 0.86), five out of ten tests showed \\\"substantial\\\" (wK 0.69 to 0.79) and two out of ten tests showed \\\"moderate\\\" (wK 0.54 to 0.59) reliability. Results were comparable in the sitting and standing positions. On average, three out of five tests were rated positive in patients and one out of five tests was rated positive in healthy controls. An odds ratio of 13.3 to 18.6 was obtained using ≥2/5 tests as a cut-off point. CONCLUSION: Visual assessment by physiotherapists of head-eye movement control tests is reliable. The test battery is able to discriminate between patients with chronic neck pain and healthy controls. There were no differences in performance between the sitting and standing positions. The test battery can therefore be reduced to five tests. Further research is needed to identify the test-retest stability and responsiveness.\",\n \"corpus_id\": 6098885,\n \"score\": 0\n },\n {\n \"doc_id\": \"24452650\",\n \"title\": \"Craniofacial pain and disability inventory (CF-PDI): development and psychometric validation of a new questionnaire.\",\n \"abstract\": \"BACKGROUND: Orofacial pain, headaches, and neck pain are very common pain conditions in the general population and might be associated in their pathophysiology, although this is not yet clarified. The development and validation of a prediction inventory is important to minimize risks. Most recent questionnaires have not focused on pain, but pain is the common symptom in temporomandibular disorders, headaches, and neck pain. It is necessary to provide tools for these conditions. OBJECTIVES: The purpose of this study is to present the development and analysis of the factorial structure and psychometric properties of a new self-administered questionnaire (Craniofacial Pain and Disability Inventory [CF-PDI]) designed to measure pain, disability, and functional status of the mandibular and craniofacial regions. STUDY DESIGN: Multicenter, prospective, cross-sectional, descriptive survey design. A secondary analysis of the reliability of the measures was a longitudinal, observational study. SETTING: A convenience sample was recruited from a hospital and 2 specialty clinics in Madrid, Spain. METHODS: The study sample consisted of 192 heterogeneous chronic craniofacial pain patients. A sub-sample of 106 patients was asked to answer the questionnaire a second time, to assess the test-retest reliability. The development and validation of the CF-PDI were conducted using the standard methodology, which included item development, cognitive debriefing, and psychometric validation. The questionnaire was assessed for the following psychometric properties: internal consistency (Cronbach's α); floor and ceiling effects; test-retest reliability (Intraclass Correlation Coefficient [ICC]; Bland and Altman method); construct validity (exploratory factor analysis); responsiveness (standard error of measurement [SEM] and minimal detectable change [MDC]); and convergent validity (Pearson correlation coefficient), by comparing visual analog scale (VAS), the Tampa Scale for Kinesiophobia (TSK-11), the Pain Catastrophizing Scale (PCS), the Neck Disability Index (NDI), and the Headache Impact Test-6 (HIT-6). Multiple linear regression analysis was used to estimate the strength of the associations with theoretically similar constructs. RESULTS: The final version of the CF-PDI consists of 21 items. Exploratory factor analysis revealed 2 factors (\\\"pain and disability\\\" and \\\"jaw functional status\\\"), both with an eigenvalue greater than one, explaining 44.77% of the variance. Floor or ceiling effects were not observed. High internal consistency of the CF-PDI (Cronbach's α: 0.88) and also of the 2 subscales (Cronbach's α: 0.80 - 0.86) was confirmed. ICC was found to be 0.90 (95% confidence interval [CI] 0.86 - 0.93), which was considered to be excellent test-retest reliability. The SEM and MDC were 2.4 and 7 points, respectively. The total CF-PDI score showed a moderate correlation with most of the assessed questionnaires (r = 0.36 - 0.52) and a strong correlation with the NDI (r = 0.65; P < 0.001). The NDI, VAS, and TSK-11 were predictors of CF-PDI. LIMITATIONS: Only self-reported measures were considered for convergent validity. Future research should use physical tests to explore the clinical signs relating to pain and disability. CONCLUSION: The CF-PDI showed good psychometric properties. Based on the findings of this study, the CF-PDI can be used in research and clinical practice for the assessment of patients with craniofacial pain.\",\n \"corpus_id\": 35392251,\n \"score\": 0\n },\n {\n \"doc_id\": \"24871639\",\n \"title\": \"Repeatability of visual acuity testing using a psychometric function.\",\n \"abstract\": \"PURPOSE: To evaluate the repeatability of a new method of measurement of visual acuity by use of a psychometric function. METHODS: The visual acuity of 15 healthy adults was measured by use of a psychometric function (PFVA) and by use of a conventional method using a decimal visual acuity chart (DeVA). We performed two tests. To evaluate intra-rater reliability, a tester measured the visual acuity three times for each subject, and the intraclass correlation coefficients, ICC (1,1), were calculated for PFVA and DeVA. Next, to evaluate inter-rater reliability, three testers measured the visual acuity for one subject, and the ICC (2,1) were calculated for PFVA and DeVA. The PFVA and DeVA of five subjects with ocular diseases were also measured. RESULTS: In the evaluation of intra-rater reliability, the ICC (1,1) of the DeVA was 0.83 and the ICC (1,1) of the PFVA was 0.95. In the evaluation of inter-rater reliability, the ICC (2,1) of the DeVA was 0.88 and the ICC (2,1) of the PFVA was 0.93. In both tests the standard deviations of the PFVA were significantly lower than those of the DeVA. For four of the five subjects with ocular diseases, the PFVA was significantly improved by treatment. CONCLUSION: The repeatability of our method is better than that of the conventional method using a decimal visual acuity chart.\",\n \"corpus_id\": 36943520,\n \"score\": 0\n },\n {\n \"doc_id\": \"25151998\",\n \"title\": \"Establishing the reliability and concurrent validity of physical performance tests using virtual reality equipment for community-dwelling healthy elders.\",\n \"abstract\": \"PURPOSE: The aim of this study was to determine the reliability and concurrent validity of commonly used physical performance tests using the OmniVR Virtual Rehabilitation System for healthy community-dwelling elders. METHOD: Participants (N = 40) were recruited by the authors and were screened for eligibility. The initial method of measurement was randomized to either virtual reality (VR) or clinically based measures (CM). Physical performance tests included the five times sit to stand, Timed Up and Go (TUG), Forward Functional Reach (FFR) and 30-s stand test. A random number generator determined the testing order. The test-re-test reliability for the VR and CM was determined. Furthermore, concurrent validity was determined using a Pearson product moment correlation (Pearson r). RESULTS: The VR demonstrated excellent reliability for 5 × STS intraclass correlation coefficient (ICC) = 0.931(3,1), FFR ICC = 0.846(3,1) and the TUG ICC = 0.944(3,1). The concurrent validity data for the VR and CM (ICC 3, k) were moderate for FFR ICC = 0.682, excellent 5 × STS ICC = 0.889 and excellent for the TUG ICC = 0.878. The concurrent validity of the 30-s stand test was good ICC = 0.735(3,1). CONCLUSIONS: This study supports the use of VR equipment for measuring physical performance tests in the clinic for healthy community-dwelling elders. IMPLICATIONS FOR REHABILITATION: Virtual reality equipment is not only used to treat balance impairments but it is also used to measure and determine physical impairments through the use of physical performance tests. Virtual reality equipment is a reliable and valid tool for collecting physical performance data for the 5 × STS, FFR, TUG and 30-s stand test for healthy community-dwelling elders.\",\n \"corpus_id\": 30801168,\n \"score\": 0\n },\n {\n \"doc_id\": \"25306061\",\n \"title\": \"Cardiopulmonary exercise testing early after stroke using feedback-controlled robotics-assisted treadmill exercise: test-retest reliability and repeatability.\",\n \"abstract\": \"BACKGROUND: Exercise capacity is seriously reduced after stroke. While cardiopulmonary assessment and intervention strategies have been validated for the mildly and moderately impaired populations post-stroke, there is a lack of effective concepts for stroke survivors suffering from severe motor limitations. This study investigated the test-retest reliability and repeatability of cardiopulmonary exercise testing (CPET) using feedback-controlled robotics-assisted treadmill exercise (FC-RATE) in severely motor impaired individuals early after stroke. METHODS: 20 subjects (age 44-84 years, <6 month post-stroke) with severe motor limitations (Functional Ambulatory Classification 0-2) were selected for consecutive constant load testing (CLT) and incremental exercise testing (IET) within a powered exoskeleton, synchronised with a treadmill and a body weight support system. A manual human-in-the-loop feedback system was used to guide individual work rate levels. Outcome variables focussed on standard cardiopulmonary performance parameters. Relative and absolute test-retest reliability were assessed by intraclass correlation coefficients (ICC), standard error of the measurement (SEM), and minimal detectable change (MDC). Mean difference, limits of agreement, and coefficient of variation (CoV) were estimated to assess repeatability. RESULTS: Peak performance parameters during IET yielded good to excellent relative reliability: absolute peak oxygen uptake (ICC =0.82), relative peak oxygen uptake (ICC =0.72), peak work rate (ICC =0.91), peak heart rate (ICC =0.80), absolute gas exchange threshold (ICC =0.91), relative gas exchange threshold (ICC =0.88), oxygen cost of work (ICC =0.87), oxygen pulse at peak oxygen uptake (ICC =0.92), ventilation rate versus carbon dioxide output slope (ICC =0.78). For these variables, SEM was 4-13%, MDC 12-36%, and CoV 0.10-0.36. CLT revealed high mean differences and insufficient test-retest reliability for all variables studied. CONCLUSIONS: This study presents first evidence on reliability and repeatability for CPET in severely motor impaired individuals early after stroke using a feedback-controlled robotics-assisted treadmill. The results demonstrate good to excellent test-retest reliability and appropriate repeatability for the most important peak cardiopulmonary performance parameters. These findings have important implications for the design and implementation of cardiovascular exercise interventions in severely impaired populations. Future research needs to develop advanced control strategies to enable the true limit of functional exercise capacity to be reached and to further assess test-retest reliability and repeatability in larger samples.\",\n \"corpus_id\": 15549488,\n \"score\": 0\n },\n {\n \"doc_id\": \"25491137\",\n \"title\": \"Reliability of the Timed Up and Go test and Ten-Metre Timed Walk Test in Pregnant Women with Pelvic Girdle Pain.\",\n \"abstract\": \"BACKGROUND AND PURPOSE: There is a lack of functional objective tests available to measure functional status in women with pelvic girdle pain (PGP). The purpose of this study was to establish test-retest and intertester reliability of the Timed Up and Go (TUG) test and Ten-metre Timed Walk Test (10mTWT) in pregnant women with PGP. METHODS: A convenience sample of women was recruited over a 4-month period and tested on two occasions, 1 week apart to determine test-retest reliability. Intertester reliability was established between two assessors at the first testing session. Subjects were instructed to undertake the TUG and 10mTWT at maximum speed. One practise trial and two timed trials for each walking test was undertaken on Day 1 and one practise trial and one timed trial on Day 2. RESULTS: Seventeen women with PGP aged 31.1 years (SD [standard deviation] = 2.3) and 28.7 weeks pregnant (SD = 7.4) completed gait testing. Test-retest reliability using the intraclass correlation coefficient (ICC) was excellent for the TUG (0.88) and good for the 10mTWT (0.74). Intertester reliability was determined in the first 13 participants with excellent ICC values being found for both walking tests (TUG: 0.95; 10mTWT: 0.94). CONCLUSION: This study demonstrated that the TUG and 10mTWT undertaken at fast pace are reliable, objective functional tests in pregnant women with PGP. While both tests are suitable for use in the clinical and research settings, we would recommend the TUG given the findings of higher test-retest reliability and as this test requires less space and time to set up and score. Future studies in a larger sample size are warranted to confirm the results of this study.\",\n \"corpus_id\": 44691675,\n \"score\": 0\n },\n {\n \"doc_id\": \"25585517\",\n \"title\": \"Reliability of the chin tuck neck flexion test for assessing endurance of short neck flexors in healthy individuals.\",\n \"abstract\": \"OBJECTIVES: The aim of the study was to examine of the intra-rater reliability of the chin tuck neck flexion (CTNF) test for assessing the endurance of neck flexors. MATERIALS AND METHODS: The study was performed at the Cardiorespiratory laboratory of the Physiotherapy Department, School of Health and Caring Professions, TEI Lamia, Greece. Twenty healthy volunteers (males/females: 9/11, age: 22.2 ± 1.7 y ears) with no known musculoskeletal, cardiovascular, pulmonary, neurological, or psychiatric disorder were recruited. The participants were positioned in a supine position and were asked to raise their head 2.5 cm above the plinth and to maintain this position for as long as possible without losing craniocervical or cervical flexion. This test was repeated three times with 5-min intervals between the trials. RESULTS: The results showed that this test could discriminate between neck flexor endurance in men and women. However, although the test seems to be highly reliable (ICC: 0.81-0.88), it presents unsatisfactory standard error of measurement (SEM: 10.7-14.7 s) and smallest detectable differences (SDD: 80.5-110.9%). Furthermore, subgroup analysis showed the test seems to be more reliable for women (ICC: 0.93-0.94) than for men (ICC: 0.68-0.8), but the SEM and SDD values for them remain unsatisfactory (SEM: 4.4-5.3 s, SDD: 57.5-63.99%). CONCLUSIONS: Due to high reproducibility and discriminant validity, clinicians and researchers might want to consider using the CTNF test for the assessment of neck flexor endurance. However, they should seek alternative measurement tools when they want to avoid a large measurement error.\",\n \"corpus_id\": 42925517,\n \"score\": 0\n },\n {\n \"doc_id\": \"25663715\",\n \"title\": \"Age and strength influences on lingual tactile acuity.\",\n \"abstract\": \"Sensory function during the oral processing of liquids is thought to play a key role in informing the tailoring of swallowing motor behaviours to the flow characteristics of the bolus. In addition to taste receptors, the mouth and tongue house trigeminal nerve receptors that support the sensory detection of bolus size, shape (stereognosis), mass, temperature and movement. Recent studies suggest that healthy adults lose tongue strength with advancing age. However, little is known about changes in the sensory function of the tongue attributable to age, or associated with reductions in strength. In this study, we explored lingual tactile acuity in healthy young and older adults, and measured the relationship between tactile acuity and measures of tongue strength. The results showed an age-related reduction in lingual tactile acuity that was not explained by variations in tongue strength. PRACTICAL APPLICATIONS: Sensory motor interactions are a topic of interest in understanding the processing activities that take place in the mouth during eating and swallowing. In this paper, we explore a test of sensory acuity in the mouth, in which the tongue is used to \\\"read\\\" embossed letters on Teflon strips. Our questions were to determine whether sensory acuity for this task declines with age, or with age-related reductions in tongue strength. We determined that older people perform this task with less accuracy, suggesting some changes in oral sensory function with age. However, these changes were not related to tongue strength. The findings suggest that strength does not play a major role in the kind of sensory discrimination task tested in this study.\",\n \"corpus_id\": 45574226,\n \"score\": 0\n },\n {\n \"doc_id\": \"25690522\",\n \"title\": \"Contribution of sVEP visual acuity testing in comparison with subjective visual acuity.\",\n \"abstract\": \"AIMS: Visual acuity determination is an important task in ophthalmology and optometry practices. Visual acuity can be examined objectively or subjectively. The objective examination method, sVEP, allows for quick objective measurements of patient's visual acuity. Previous studies have not demonstrated the repeatability of this objective sVEP method. This study aims to evaluate the sVEP method and compare it to a subjective method. METHODS AND RESULTS: The sample was divided into two groups. For the first group, visual acuity was measured with sVEP and Snellen methods on only one patient twelve times. In the second group, visual acuity was measured twice with sVEP followed twice with the Snellen method with Landolt's rings and logMAR modification on 32 non-pathological patients. Results showed significant differences between average values of visual acuity obtained with both methods (sVEP and Snellen) in both samples (T-test, P < 0.01; Wilcoxon test, P = 0.02 in second group). In the second group, significant correlations between repeated sVEP measurements (Spearman test, P < 0.05, r = 0.69) were found but no significant correlation between average sVEP measurement and average Snellen measurement (Spearman test, P > 0.05, r = 0.15) was found. CONCLUSION: Objective measurement of visual acuity with sVEP is a valid and reliable method, but is recommended only when it is not possible to use a subjective method for measuring visual acuity, e.g. children, patients with mental retardation or simulating/dissimulating patients.\",\n \"corpus_id\": 2986550,\n \"score\": 0\n },\n {\n \"doc_id\": \"26200616\",\n \"title\": \"The Development and Validation of Hundred Paisa Pain Scale for Measuring Musculoskeletal Pain: A Prospective Observational Study.\",\n \"abstract\": \"The reduction in the pain intensity is one of the most important outcome measures in musculoskeletal disorders. The assessment of pain required reliable and valid scale. The aims of this prospective observational study were to develop and evaluate concurrent validity and test-retest reliability of hundred paisa pain scale (HPPS) for measuring musculoskeletal pain. A consecutive 74 patients with musculoskeletal pain with a wide variety of diagnoses were enrolled. Patients reported their intensity of pain on the following scale: HPPS, \\\"visual analog scale (VAS),\\\" and \\\"numerical rating scale (NRS).\\\" Patients were asked to complete another HPPS, VAS, and NRS after 2 days to determine the reproducibility of the scales. Spearman rank correlation coefficients between the HPPS and the NRS, and VAS were used to determine the validity of the scales. The correlation between the change score of HPPS, VAS, and NRS was used to determine the responsiveness of HPPS. Results of test-retest indicate that the reproducibility of HPPS was good to excellent with the intraclass correlation coefficient (ICC) value of 0.85 (95% confidence interval [CI], 0.76-0.91). The standard error of measurement (SEM) was 5.24. The minimum detectable change based on the SEM for test-retest was 14.52. The reproducibility of VAS is moderate to good with the ICC value of 0.82 (95% CI, 0.72-0.88). The reproducibility of NRS is good to excellent with the ICC value of 0.88 (95% CI, 0.81-0.92). There was a strong correlation between the HPPS and the VAS, and NRS (P < 0.01), which confirm the validity. The HPPS was responsive as the correlation of the change score of HPPS with the change score of VAS, and NRS were good (0.80 and 0.86, respectively). The HPPS is a valid and reliable scale to assess musculoskeletal pain, with psychometric properties in agreement with other comparable scale.\",\n \"corpus_id\": 278529,\n \"score\": 0\n },\n {\n \"doc_id\": \"27002314\",\n \"title\": \"Reliability and Normative Data for the Dynamic Visual Acuity Test for Vestibular Screening.\",\n \"abstract\": \"HYPOTHESIS: The purpose of this study was to determine reliability of computerized dynamic visual acuity (DVA) testing and to determine reference values for younger and older adults. BACKGROUND: A primary function of the vestibular system is to maintain gaze stability during head motion. The DVA test quantifies gaze stabilization with the head moving versus stationary. Commercially available computerized systems allow clinicians to incorporate DVA into their assessment; however, information regarding reliability and normative values of these systems is sparse. METHODS: Forty-six healthy adults, grouped by age, with normal vestibular function were recruited. Each participant completed computerized DVA testing including static visual acuity, minimum perception time, and DVA using the NeuroCom inVision System. Testing was performed by two examiners in the same session and then repeated at a follow-up session 3 to 14 days later. Intraclass correlation coefficients (ICCs) were used to determine inter-rater and test-retest reliability. RESULTS: ICCs for inter-rater reliability ranged from 0.323 to 0.937 and from 0.434 to 0.909 for horizontal and vertical head movements, respectively. ICCs for test-retest reliability ranged from 0.154 to 0.856 and from 0.377 to 0.9062 for horizontal and vertical head movements, respectively. Overall, raw scores (left/right DVA and up/down DVA) were more reliable than DVA loss scores. CONCLUSION: Reliability of a commercially available DVA system has poor-to-fair reliability for DVA loss scores. The use of a convergence paradigm and not incorporating the forced choice paradigm may contribute to poor reliability.\",\n \"corpus_id\": 8831894,\n \"score\": 0\n },\n {\n \"doc_id\": \"27338815\",\n \"title\": \"Concurrent validity of different functional and neuroproteomic pain assessment methods in the rat osteoarthritis monosodium iodoacetate (MIA) model.\",\n \"abstract\": \"BACKGROUND: Lack of validity in osteoarthritis pain models and assessment methods is suspected. Our goal was to 1) assess the repeatability and reproducibility of measurement and the influence of environment, and acclimatization, to different pain assessment outcomes in normal rats, and 2) test the concurrent validity of the most reliable methods in relation to the expression of different spinal neuropeptides in a chemical model of osteoarthritic pain. METHODS: Repeatability and inter-rater reliability of reflexive nociceptive mechanical thresholds, spontaneous static weight-bearing, treadmill, rotarod, and operant place escape/avoidance paradigm (PEAP) were assessed by the intraclass correlation coefficient (ICC). The most reliable acclimatization protocol was determined by comparing coefficients of variation. In a pilot comparative study, the sensitivity and responsiveness to treatment of the most reliable methods were tested in the monosodium iodoacetate (MIA) model over 21 days. Two MIA (2 mg) groups (including one lidocaine treatment group) and one sham group (0.9 % saline) received an intra-articular (50 μL) injection. RESULTS: No effect of environment (observer, inverted circadian cycle, or exercise) was observed; all tested methods except mechanical sensitivity (ICC <0.3), offered good repeatability (ICC ≥0.7). The most reliable acclimatization protocol included five assessments over two weeks. MIA-related osteoarthritic change in pain was demonstrated with static weight-bearing, punctate tactile allodynia evaluation, treadmill exercise and operant PEAP, the latter being the most responsive to analgesic intra-articular lidocaine. Substance P and calcitonin gene-related peptide were higher in MIA groups compared to naive (adjusted P (adj-P) = 0.016) or sham-treated (adj-P = 0.029) rats. Repeated post-MIA lidocaine injection resulted in 34 times lower downregulation for spinal substance P compared to MIA alone (adj-P = 0.029), with a concomitant increase of 17 % in time spent on the PEAP dark side (indicative of increased comfort). CONCLUSION: This study of normal rats and rats with pain established the most reliable and sensitive pain assessment methods and an optimized acclimatization protocol. Operant PEAP testing was more responsive to lidocaine analgesia than other tests used, while neuropeptide spinal concentration is an objective quantification method attractive to support and validate different centralized pain functional assessment methods.\",\n \"corpus_id\": 18188204,\n \"score\": 0\n },\n {\n \"doc_id\": \"27418890\",\n \"title\": \"Reliability of the Handgrip Strength Test in Elderly Subjects With Parkinson Disease.\",\n \"abstract\": \"BACKGROUND: The handgrip strength test is widely used by clinicians; however, little has been investigated about its reliability when used in subjects with Parkinson disease (PD). The purpose of this study was to investigate the test-retest reliability of the handgrip strength test for subjects with PD. METHODS: The PD group consisted of 15 patients, and the control group consisted of 15 healthy subjects. Each patient performed 3 pain-free maximal isometric contractions on each hand on 2 occasions, 1 week apart. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), and 95% limits of agreement (LOA) were calculated. The 2-way analysis of variance (ANOVA) was conducted to determine the differences between sides and groups. RESULTS: Test-retest reliability of measurements of grip strength was excellent for dominant (ICC = 0.97; P = .001) and non-dominant (ICC = 0.98; P = .001) hand of participant with PD and (ICC = 0.99; P = .001) and (ICC = 0.99; P = .001) respectively, of healthy group. CONCLUSIONS: The Jamar hand dynamometer had fair to excellent test-retest reliability to test grip strength in participants with PD.\",\n \"corpus_id\": 31903041,\n \"score\": 0\n },\n {\n \"doc_id\": \"28074292\",\n \"title\": \"Reliability of the nociceptive blink reflex evoked by electrical stimulation of the trigeminal nerve in humans.\",\n \"abstract\": \"OBJECTIVE: The nociceptive blink reflex (nBR) can be useful to investigate trigeminal nociceptive function. The aim of this study was to estimate the reliability of the nBR evoked by electrical stimulation of the three branches of the trigeminal nerve under the following conditions: over time (test-retest and intrarater reliability) and by two examiners (interrater reliability). MATERIALS AND METHODS: Twenty-one healthy participants were evaluated in two sessions (24 h apart). The nBR was elicited by a so-called \\\"nociceptive-specific\\\" electrode placed over the entry zone of the right supraorbital (V1R), infraorbital (V2R), mental (V3R), and left infraorbital (V2L) nerve. The outcomes were individual electrical sensory (I 0) and pain thresholds (I P); root mean square (RMS), area-under-the-curve (AUC), and onset latencies of R2 responses (determined twice after a recalibration session); and stimulus-evoked pain on a 0-10 numerical rating scale. Intraclass correlation coefficients (ICCs) and Kappa statistics were computed (α = 5%). RESULTS: ICCs were fair to excellent in 82% of the psychophysical measures (fair 21%, good 31%, excellent 30%) and in 86% of V1R, V2R, and V2L nBR parameters, whereas 52% of V3R showed poor reliability. ICCs for intrarater reliability were fair to good in 70% of measurements (fair 20%, good 50%) and in 75% of interrater measurements after the recalibration (fair 55%, good 20%). All kappa values showed at least fair agreement and the majority of the nBR measures (93%) presented moderate to excellent reliability. CONCLUSION: The nBR and its associated psychophysical measures can be considered a sufficiently reliable test. CLINICAL SIGNIFICANCE: The nBR can be recommended as an electrophysiological technique to assess trigeminal nociceptive function.\",\n \"corpus_id\": 11132779,\n \"score\": 0\n },\n {\n \"doc_id\": \"28262642\",\n \"title\": \"Gaze stabilization and dynamic visual acuity in people with multiple sclerosis.\",\n \"abstract\": \"BACKGROUND: The functional capacity of the vestibulo-ocular reflex (VOR) is not well understood in people with multiple sclerosis (MS). OBJECTIVE: To determine the psychometric properties of computerized Gaze Stabilization Test (GST) and Dynamic Visual Acuity Test (DVAT) in people with MS. METHODS: This cross-sectional study determined discriminant validity of the GST and DVAT between 15 healthy controls and 30 participants with MS, and between participants with MS who had higher versus lower disability. This study also determined same-day and between-session test-retest reliability, and concurrent validity with patient-reported outcomes (PROs) of balance, dizziness, and fatigue. RESULTS: GST (p < 0.001) and DVAT (p = 0.001) scores were lower in participants with MS compared to controls. GST (p = 0.035) but not DVAT (p = 0.313) scores were lower in those with higher compared to lower disability. Test-retest reliability intraclass correlation coefficients (ICC (2,1)) were fair-to-good for the GST (0.48 to 0.74) and DVAT (0.47 to 0.60). PROs correlated significantly with GST, but not DVAT scores. CONCLUSIONS: This study provides initial evidence that the functional capacity of the VOR is impaired in people with MS as measured by the GST and DVAT. Further investigation is warranted to determine usefulness of both measures as outcomes for people with MS.\",\n \"corpus_id\": 5959101,\n \"score\": 0\n },\n {\n \"doc_id\": \"28451614\",\n \"title\": \"The Functional Arm Scale for Throwers (FAST)-Part II: Reliability and Validity of an Upper Extremity Region-Specific and Population-Specific Patient-Reported Outcome Scale for Throwing Athletes.\",\n \"abstract\": \"BACKGROUND: The Functional Arm Scale for Throwers (FAST) is an upper extremity (UE) region-specific and population-specific patient-reported outcome (PRO) scale developed to measure health-related quality of life in throwers with UE injuries. Stages I and II, described in a companion paper, of FAST development produced a 22-item scale and a 9-item pitcher module. Stage III of scale development, establishing reliability and validity of the FAST, is reported herein. PURPOSE: To describe stage III of scale development: reliability and validity of the FAST. STUDY DESIGN: Cohort study (diagnosis); Level of evidence, 2. METHODS: Data from throwing athletes collected over 5 studies were pooled to assess reliability and validity of the FAST. Reliability was estimated using FAST scores from 162 throwing athletes who were injured (n = 23) and uninjured (n = 139). Concurrent validity was estimated using FAST scores and Disabilities of the Arm, Shoulder, and Hand (DASH) and Kerlan-Jobe Orthopaedic Clinic (KJOC) scores from 106 healthy, uninjured throwing athletes. Known-groups validity was estimated using FAST scores from 557 throwing athletes who were injured (n = 142) and uninjured (n = 415). Reliability and validity were assessed using intraclass correlation coefficients (ICCs), and measurement error was assessed using standard error of measurement (SEM) and minimum detectable change (MDC). Receiver operating characteristic curves and sensitivity/specificity values were estimated for known-groups validity. Data from a separate group (n = 18) of postsurgical and nonoperative/conservative rehabilitation patients were analyzed to report responsiveness of the FAST. RESULTS: The FAST total, subscales, and pitcher module scores demonstrated excellent test-retest reliability (ICC, 0.91-0.98). The SEM95 and MDC95 for the FAST total score were 3.8 and 10.5 points, respectively. The SEM95 and MDC95 for the pitcher module score were 5.7 and 15.7 points, respectively. The FAST scores showed acceptable correlation with DASH (ICC, 0.49-0.82) and KJOC (ICC, 0.62-0.81) scores. The FAST total score classified 85.1% of players into the correct injury group. For predicting UE injury status, a FAST total cutoff score of 10.0 out of 100.0 was 91% sensitive and 75% specific, and a pitcher module score of 10.0 out of 100.0 was 87% sensitive and 78% specific. The FAST total score demonstrated responsiveness on several indices between intake and discharge time points. CONCLUSION: The FAST is a reliable, valid, and responsive UE region-specific and population-specific PRO scale for measuring patient-reported health care outcomes in throwing athletes with injury.\",\n \"corpus_id\": 10924574,\n \"score\": 0\n },\n {\n \"doc_id\": \"28728465\",\n \"title\": \"Evaluating the test-retest reliability of symptom indices associated with the ImPACT post-concussion symptom scale (PCSS).\",\n \"abstract\": \"OBJECTIVE: The Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) is a commonly used tool in sports concussion assessment. While test-retest reliabilities have been established for the ImPACT cognitive composites, few studies have evaluated the psychometric properties of the ImPACT's Post-Concussion Symptom Scale (PCSS). The purpose of this study was to establish the test-retest reliability of symptom indices associated with the PCSS. PARTICIPANTS AND METHODS: Participants included 38 undergraduate students (50.0% male) who underwent neuropsychological testing as part of their participation in their psychology department's research subject pool. The majority of the participants were Caucasian (94.7%) and had no history of concussion (73.7%). All participants completed the ImPACT at two time points, approximately 6 weeks apart. The PCSS was the main outcome measure, and eight symptom indices were calculated (a total symptom score, three symptom summary indices, and four symptom clusters). RESULTS: Pearson correlations (r) and intraclass correlation coefficients (ICCs) were computed as measures of test-retest reliability. Overall, reliabilities ranged from low to high (r = .44 to .80; ICC = .44 to .77). The cognitive symptom cluster exhibited the highest test-retest reliability (r = .80, ICC = .77), followed by the positive symptom total (PST) index, an indicator of the total number of symptoms endorsed (r = .71, ICC = .69). In contrast, the commonly used total symptom score showed lower test-retest reliability (r = .67, ICC = .62). Paired-samples t tests revealed no significant differences between test and retest for any of the symptom variables (all p > .01). Finally, reliable change indices (RCI) were computed to determine whether differences observed between test and retest represented clinically significant change. RCI values were provided for each symptom index at the 80%, 90%, and 95% confidence intervals. CONCLUSION: These results suggest that evaluating additional symptom indices beyond the total symptom score from the PCSS is beneficial. Findings from this study can be applied to athlete samples to assess reliable change in symptoms following concussion.\",\n \"corpus_id\": 4001296,\n \"score\": 0\n },\n {\n \"doc_id\": \"28888770\",\n \"title\": \"Test-retest reliability of cerebral blood flow in healthy individuals using arterial spin labeling: Findings from the EMBARC study.\",\n \"abstract\": \"INTRODUCTION: Previous investigations of test-retest reliability of cerebral blood flow (CBF) at rest measured with pseudo-continuous Arterial Spin Labeling (pCASL) demonstrated good reliability, but are limited by the use of similar scanner platforms. In the present study we examined test-retest reliability of CBF in regions implicated in emotion and the default mode network. MATERIAL AND METHODS: We measured absolute and relative CBF at rest in thirty-one healthy subjects in two scan sessions, one week apart, at four different sites and three different scan platforms. We derived CBF from pCASL images with an automated algorithm and calculated intra-class correlation coefficients (ICCs) across sessions for regions of interest. In addition, we investigated site effects. RESULTS: For both absolute and relative CBF measures, ICCs were good to excellent (i.e. >0.6) in most brain regions, with highest values observed for the subgenual anterior cingulate cortex and ventral striatum. A leave-one-site-out cross validation analysis did not show a significant effect for site on whole brain CBF and there was no proportional bias across sites. However, a significant site effect was present in the repeated measures ANOVA. CONCLUSIONS: The high test-retest reliability of CBF measured with pCASL in a range of brain regions implicated in emotion and salience processing, emotion regulation, and the default mode network, which have been previously linked to depression symptomatology supports its use in studies that aim to identify neuroimaging biomarkers of treatment response.\",\n \"corpus_id\": 22313148,\n \"score\": 0\n },\n {\n \"doc_id\": \"28890223\",\n \"title\": \"A new iPhone application for measuring active craniocervical range of motion in patients with non-specific neck pain: a reliability and validity study.\",\n \"abstract\": \"BACKGROUND CONTEXT: Measurement of cervical spine range of motion (ROM) is often considered to be an essential component of cervical spine physiotherapy assessment. PURPOSE: This study aimed to investigate the reliability and validity of an iPhone application (app) (Goniometer Pro) for measuring active craniocervical ROM (ACCROM) in patients with non-specific neck pain. STUDY DESIGN/SETTING: A cross-sectional study was conducted at the musculoskeletal biomechanics laboratory located at Iran University of Medical Sciences. PATIENT SAMPLE: Forty non-specific neck pain patients participated in this study. OUTCOME MEASURES: The outcome measure was the ACCROM, including flexion, extension, lateral flexion, and rotation. METHOD: Following the recruitment process, ACCROM was measured using a universal goniometer (UG) and iPhone 7 app. Two blinded examiners each used the UG and iPhone to measure ACCROM in the following sequences: flexion, extension, lateral flexion, and rotation. The second (2 hours later) and third (48 hours later) sessions were carried out in the same manner as the first session. Intraclass correlation coefficient (ICC) models were used to determine the intra-rater and inter-rater reliability. The Pearson correlation coefficients were used to establish concurrent validity of the iPhone app. Minimum detectable change at the 95% confidence level (MDC95) was also computed. RESULTS: Good intra-rater and inter-rater reliability was demonstrated for the goniometer with ICC values of ≥0.66 and ≥0.70 and the iPhone app with ICC values of ≥0.62 and ≥0.65, respectively. The MDC95 ranged from 2.21° to 12.50° for the intra-rater analysis and from 3.40° to 12.61° for the inter-rater analysis. The concurrent validity between the two instruments was high, with r valuesof ≥0.63. The magnitude of the differences between the UG and iPhone app values (effect sizes) was small, with Cohen d values of ≤0.17. CONCLUSIONS: The iPhone app possesses good reliability and high validity. It seems that this app can be used for measuring ACCROM.\",\n \"corpus_id\": 3931425,\n \"score\": 0\n },\n {\n \"doc_id\": \"28893312\",\n \"title\": \"The validity and reliability of the four square step test in different adult populations: a systematic review.\",\n \"abstract\": \"BACKGROUND: The four square step test (FSST) was first validated in healthy older adults to provide a measure of dynamic standing balance and mobility. The FSST has since been used in a variety of patient populations. The purpose of this systematic review is to determine the validity and reliability of the FSST in these different adult patient populations. METHODS: The literature search was conducted to highlight all the studies that measured validity and reliability of the FSST. Six electronic databases were searched including AMED, CINAHL, MEDLINE, PEDro, Web of Science and Google Scholar. Grey literature was also searched for any documents relevant to the review. Two independent reviewers carried out study selection and quality assessment. The methodological quality was assessed using the QUADAS-2 tool, which is a validated tool for the quality assessment of diagnostic accuracy studies, and the COSMIN four-point checklist, which contains standards for evaluating reliability studies on the measurement properties of health instruments. RESULTS: Fifteen studies were reviewed studying community-dwelling older adults, Parkinson's disease, Huntington's disease, multiple sclerosis, vestibular disorders, post stroke, post unilateral transtibial amputation, knee pain and hip osteoarthritis. Three of the studies were of moderate methodological quality scoring low in risk of bias and applicability for all domains in the QUADAS-2 tool. Three studies scored \\\"fair\\\" on the COSMIN four-point checklist for the reliability components. The concurrent validity of the FSST was measured in nine of the studies with moderate to strong correlations being found. Excellent Intraclass Correlation Coefficients were found between physiotherapists carrying out the tests (ICC = .99) with good to excellent test-retest reliability shown in nine of the studies (ICC = .73-.98). CONCLUSIONS: The FSST may be an effective and valid tool for measuring dynamic balance and a participants' falls risk. It has been shown to have strong correlations with other measures of balance and mobility with good reliability shown in a number of populations. However, the quality of the papers reviewed was variable with key factors, such as sample size and test set up, needing to be addressed before the tool can be confidently used in these specified populations.\",\n \"corpus_id\": 24727140,\n \"score\": 0\n },\n {\n \"doc_id\": \"29280180\",\n \"title\": \"Comparison of the outcomes of dynamic/static tests and palpation tests in TMD-pain patients.\",\n \"abstract\": \"In addition to palpation tests, dynamic/static tests have been proposed to complement temporomandibular disorders (TMD) patients' evaluation in the clinical setting. The aim of this study was to assess the intra- and inter-observer reliability of the palpation tests and of the dynamic/static tests, and to determine whether those tests would yield comparable outcomes in terms of pain diagnoses. Ninety-eight (N = 98) consecutive adult patients were examined during 2 clinical sessions by 2 independent examiners, based on muscle and joint palpation techniques described in the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD). They also underwent dynamic/static tests. The intra-observer reliability of palpation tests was generally poor, with fair-to-good to excellent ICC values only for the superior masseter and intra-oral sites. The inter-observer reliability of palpation was fair-to-good for muscles, but it was poor for the TMJ lateral pole. Both intra- and inter-observer reliability for the dynamic/static tests varied from fair-to-good to excellent. The intra-observer reliability for muscle pain diagnoses based on palpation tests was between poor and fair-to-good, whereas the inter-observer reliability was excellent. The intra-observer reliability for pain diagnoses based on dynamic/static tests was fair-to-good, and the inter-observer reliability varied from fair-to-good to excellent. CONCLUSIONS: Some features of the dynamic/static tests make them potentially more useful than palpation tests for selected clinical purposes, such as discriminating between joint and muscle pain as well as monitoring symptoms course. Thus, findings from this investigation suggest that both tests should be included in the TMD diagnostic algorithms.\",\n \"corpus_id\": 3276081,\n \"score\": 0\n },\n {\n \"doc_id\": \"29328979\",\n \"title\": \"Concurrent validity and interrater reliability of a new smartphone application to assess 3D active cervical range of motion in patients with neck pain.\",\n \"abstract\": \"BACKGROUND: There is a lack of valid, reliable, and feasible instruments for measuring planar active cervical range of motion (aCROM) and associated 3D coupling motions in patients with neck pain. Smartphones have advanced sensors and appear to be suitable for these measurements. OBJECTIVES: To estimate the concurrent validity and interrater reliability of a new iPhone application for assessing planar aCROM and associated 3D coupling motions in patients with neck pain, using an electromagnetic tracking device as a reference test. DESIGN: Cross-sectional study. METHODS: Two samples of neck pain patients were recruited; 30 patients for the validity study and 26 patients for the reliability study. Validity was estimated using intraclass correlation coefficients (ICCs), and by calculating 95% limits of agreement (LoA). To estimate interrater reliability, ICCs were calculated. Cervical 3D coupling motions were analyzed by calculating the cross-correlation coefficients and ratio between the main motions and coupled motions for both instruments. RESULTS: ICCs for concurrent validity and interrater reliability ranged from 0.90 to 0.99. The width of the 95% LoA ranged from about 5° for right lateral bending to 11° for total rotation. No significant differences were found between both devices for associated coupling motion analysis. CONCLUSIONS: The iPhone application appears to be a useful discriminative tool for the measurement of planar aCROM and associated coupling motions in patients with neck pain. It fulfills the need for a valid, reliable, and feasible instrument in clinical practice and research. Therapists and researchers should consider measurement error when interpreting scores.\",\n \"corpus_id\": 3804287,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":90,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"19539124\",\n \"title\": \"Is it reasonable to use an individual patient's progress after treatment as a guide to ongoing clinical reasoning?\",\n \"abstract\": \"Systematic assessment of a patient's progress after an intervention is frequently used to inform decision making in ongoing conservative management of patients with musculoskeletal symptoms. Although reassessment of impairments immediately after treatment is commonplace in clinical practice, relatively little research has considered whether this method is reasonable. The history of, rationale behind, and evidence for the use of patient responses to inform clinical reasoning are explored in this commentary. Although the evidence is not conclusive, an argument is presented suggesting it is more reasonable to use a patient's response to treatment to inform ongoing clinical reasoning than to follow predetermined protocols. A methodical approach that considers change in parameters such as patient impairments is likely to be a useful guide for decision making during ongoing patient management but only when the change being reassessed can be directly linked to functional goals. Changes in active range of movement or centralization of pain appear to be better indicators of treatment effectiveness than changes in either pain intensity or assessment of joint position. There is limited evidence to support the use of changes in segmental stiffness to guide ongoing management. Although reassessment of some impairments has been found to be useful, the author suggests that care is required in the selection of reassessments used to guide ongoing management. The usefulness of any reassessment is considered to rely on how well a change in the selected impairment predicts that individual patient's ability to achieve their goals.\",\n \"corpus_id\": 16510630\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18427230","title":"Are we measuring what we need to measure?","abstract":"Optimal treatment for patients with chronic pain remains elusive. A growing international consensus advocates evidence-based practice with assessment of clinical outcomes to improve the process and outcome of care. Clinical decision making about treatment options for an individual patient should include the patient's clinical presentation, available evidence, and patient preferences. Treatment should then be monitored and outcomes of treatment assessed. Although the placement of clinical decision making on a scientific, often quantitative basis as opposed to a subjective, impressionistic approach makes intuitive sense, the question is whether we have been measuring what we need to measure to practice evidence-based practice when we consider the current available evidence on pain management? The methods of synthesis of available evidence are still in development. Much of the evidence, although having internal validity, has limited external validity and is difficult to apply to the individual patient. Patients with chronic pain are a heterogeneous group, and different interventions may be indicated for different subgroups of patients. Various methods are being developed to better match patients with treatment. Little information exists on patient preferences, or how best to measure these. Information on how health care providers make clinical decisions is also scarce. Outcome measurement has come a long way and core domains to be measured have been established. Establishing normative data is a next main goal. Important methodologic and practical challenges remain to formulate evidence that can be applied to the individual patient with chronic pain.","corpus_id":205454058,"score":2},{"doc_id":"19117231","title":"Philosophy of science and physiotherapy: an insight into practice.","abstract":"This article presents an overview of the philosophy of science and applies such philosophical theory to clinical practice within physiotherapy. A brief history of science is followed by the theories of the four most commonly acknowledged philosophers, introduced in the context of examples from clinical practice. By providing direct links to practical examples, it demonstrates the possibilities of relating the logical basis of this field of study to the clinical setting. The relevance to physiotherapy is that, by relating this theory, clinicians can better understand and analyse the fundamental logic behind their practice. The insight this provides can benefit professional development in several ways. For the clinician, it permits more comprehensive and coherent reasoning and helps to relate evidence with respect to individual patients. On a larger scale, it encourages reflective discussion between peers around the virtues of alternative treatment approaches. Thus, this topic has the potential to guide clinical practice toward being more scientific and may help raise the credibility of the profession as a whole.","corpus_id":205654531,"score":2},{"doc_id":"23925525","title":"Integrating patient-reported outcomes into orthopaedic clinical practice: proof of concept from FORCE-TJR.","abstract":"BACKGROUND: Good orthopaedic care requires a knowledge of the patient's history of musculoskeletal pain and associated limitations in daily function. Standardized measures of patient-reported outcomes (PROs) can provide this information. Integrating PROs into routine orthopaedic patient visits can provide key information to monitor changes in symptom severity over time, support shared clinical care decisions, and assess treatment effectiveness for quality initiatives and value-based reimbursement. WHERE ARE WE NOW?: Although standardized, validated PRO surveys are routinely used in clinical and comparative effectiveness research, they are not consistently or efficiently collected in clinical practice. WHERE DO WE NEED TO GO?: Ideally, PROs need to be collected directly from patients before their surgeon visit so the data are readily available to the surgeon and patient at the time of the office visit. In addition, PROs should be integrated in the electronic health record to monitor patient status over time. HOW DO WE GET THERE?: PRO integration in clinical practice requires minor modifications to the office flow, some additional staff to facilitate collection, and the technical infrastructure to score, process, and store the responses. We document successful office procedures for collecting PROs in one busy orthopaedic clinic and some suggested methods to extend this model to the Function and Outcomes Research for Comparative Effectiveness in Total Joint Replacement (FORCE-TJR) consortium of 121 surgeons where the process is centralized and staff obtained consent to send the PRO directly to the patient's home. Both methods are options for the broader adoption of office-based PROs.","corpus_id":42267876,"score":2},{"doc_id":"24372846","title":"Learning clinical reasoning.","abstract":"Errors in clinical reasoning continue to account for significant morbidity and mortality, despite evidence-based guidelines and improved technology. Experts in clinical reasoning often use unconscious cognitive processes that they are not aware of unless they explain how they are thinking. Understanding the intuitive and analytical thinking processes provides a guide for instruction. How knowledge is stored is critical to expertise in clinical reasoning. Curricula should be designed so that trainees store knowledge in a way that is clinically relevant. Competence in clinical reasoning is acquired by supervised practice with effective feedback. Clinicians must recognise the common errors in clinical reasoning and how to avoid them. Trainees can learn clinical reasoning effectively in everyday practice if teachers provide guidance on the cognitive processes involved in making diagnostic decisions.","corpus_id":37979636,"score":2},{"doc_id":"26486941","title":"A Bayesian perspective on constructing a written assessment of probabilistic clinical reasoning in experienced clinicians.","abstract":"RATIONALE: Decision-making performance assessments have proven problematic for assessing clinical reasoning. AIMS AND OBJECTIVES: A Bayesian approach to designing an advanced clinical reasoning assessment is well grounded in mathematical and cognitive theory and may offer significant psychometric advantages. Probabilistic logic plays an important role in medical problem solving, and performances on Bayesian-type tasks appear to be causally-related to the ability to make sound clinical decisions. METHODS: A validity argument is used to guide the design of an assessment of medical reasoning using clinical probabilities. RESULTS/CONCLUSIONS: The practical advantage of using a Bayesian approach to item design relates to the fact that probability theory provides a rationally optimal method for managing uncertain information and provides the criteria for objective correct answer scoring. Potential item formats are discussed.","corpus_id":24403018,"score":2},{"doc_id":"26988928","title":"Identification of predicted individual treatment effects in randomized clinical trials.","abstract":"In most medical research, treatment effectiveness is assessed using the average treatment effect or some version of subgroup analysis. The practice of individualized or precision medicine, however, requires new approaches that predict how an individual will respond to treatment, rather than relying on aggregate measures of effect. In this study, we present a conceptual framework for estimating individual treatment effects, referred to as predicted individual treatment effects. We first apply the predicted individual treatment effect approach to a randomized controlled trial designed to improve behavioral and physical symptoms. Despite trivial average effects of the intervention, we show substantial heterogeneity in predicted individual treatment response using the predicted individual treatment effect approach. The predicted individual treatment effects can be used to predict individuals for whom the intervention may be most effective (or harmful). Next, we conduct a Monte Carlo simulation study to evaluate the accuracy of predicted individual treatment effects. We compare the performance of two methods used to obtain predictions: multiple imputation and non-parametric random decision trees. Results showed that, on average, both predictive methods produced accurate estimates at the individual level; however, the random decision trees tended to underestimate the predicted individual treatment effect for people at the extreme and showed more variability in predictions across repetitions compared to the imputation approach. Limitations and future directions are discussed.","corpus_id":4781711,"score":2},{"doc_id":"29708632","title":"A concise guide to clinical reasoning.","abstract":"What constitutes clinical reasoning is a disputed subject regarding the processes underlying accurate diagnosis, the importance of patient-specific versus population-based data, and the relation between virtue and expertise in clinical practice. In this paper, I present a model of clinical reasoning that identifies and integrates the processes of diagnosis, prognosis, and therapeutic decision making. The model is based on the generalized empirical method of Bernard Lonergan, which approaches inquiry with equal attention to the subject who investigates and the object under investigation. After identifying the structured operations of knowing and doing and relating these to a self-correcting cycle of learning, I correlate levels of inquiry regarding what-is-going-on and what-to-do to the practical and theoretical elements of clinical reasoning. I conclude that this model provides a methodical way to study questions regarding the operations of clinical reasoning as well as what constitute significant clinical data, clinical expertise, and virtuous health care practice.","corpus_id":14034747,"score":2},{"doc_id":"18519094","title":"How to manage musculoskeletal conditions.","abstract":"Musculoskeletal conditions are becoming more prevalent in the aging and increasingly overweight Western population. Many such conditions are chronic, and most people concerned have problems with more than one anatomical joint region, resulting in cumulatively increased problems with performing daily tasks. Management is complex because of the chronic nature of many of these conditions, the need for regular assessment of disease impact, the individual's responses to the disease and its treatment, the presence of co-morbidities, and the lack of well-designed studies of long-term outcome to guide treatment. There are significant issues about how to monitor outcomes in routine practice, and many outcome measures have been developed for use in clinical trials. Principles of modern management include involvement of people in their own care, early intervention, and the need to consider a multidisciplinary approach. Most conditions will require combinations of one or more non-pharmacological therapies (especially muscle strengthening and aerobic exercise) and pharmacological agents, with attention given to appropriate timing of surgical interventions.","corpus_id":42708604,"score":1},{"doc_id":"18569855","title":"Clinical reasoning and population health: decision making for an emerging paradigm of health care.","abstract":"Chronic conditions now provide the major disease and disability burden facing humanity. This development has necessitated a reorientation in the practice skills of health care professions away from hospital-based inpatient and outpatient care toward community-based management of patients with chronic conditions. Part of this reorientation toward community-based management of chronic conditions involves practitioners' understanding and adoption of a concept of population health management based on appropriate theoretical models of health care. Drawing on recent studies of expertise in physiotherapy, this article proposes a clinical reasoning and decision-making framework to meet these challenges. The challenge of population and community-based management of chronic conditions also provides an opportunity for physiotherapists to further clarify a professional epistemology of practice that embraces the kinds of knowledge and clinical reasoning processes used in physiotherapy practice. Three case studies related to the management of chronic musculoskeletal pain in different populations are used to exemplify the range of epistemological perspectives that underpin community-based practice. They illustrate the link between conceptualizations of practice problems and knowledge sources that are used as a basis for clinical reasoning and decision making as practitioners are increasingly required to move between the clinic and the community.","corpus_id":24249615,"score":1},{"doc_id":"18638679","title":"The assessment of musculoskeletal pain in the clinical setting.","abstract":"Pain is a primary symptom in musculoskeletal conditions, and aspects of the pain experience (eg, severity) are key considerations in clinical decision-making and in the outcome of trials and interventions. Consequently, appropriate assessment of pain is essential. This article reviews the measures most commonly used in rheumatology practice, arguing that many are significantly limited in their ability to reflect the complexity of the patient's experience. The authors provide examples of alternative approaches, concluding that there is real scope for improving assessment and measurement of musculoskeletal pain in the clinical setting.","corpus_id":13535690,"score":1},{"doc_id":"19202161","title":"Chronic musculoskeletal pain in children: assessment and management.","abstract":"Paediatricians and paediatric rheumatologists review a large number of children with ongoing pain (disease and non-disease related). A small number of these develop chronic pain conditions that are complex and distressing. Over recent years studies of the epidemiology, aetiology and rehabilitation of pain and pain-associated disability in children have revealed a large prevalence of clinically relevant pain, and have emphasized the need for early recognition and intervention. Medication has a role when part of a multidisciplinary framework, although there is little evidence for or against the effectiveness of most pharmacotherapy. There is strong evidence to support early targeted psychological and physical intervention, and an understanding that parental education and involvement is essential if progress is to be maintained. In this review, an overview of the assessment is presented and management of childhood chronic musculoskeletal pain conditions with reference to main research findings to date.","corpus_id":17934101,"score":1},{"doc_id":"19232911","title":"An introduction to evidence-based practice for hand surgeons and therapists.","abstract":"Evidence-based practice is a methodical approach to clinical practice where experience, best research evidence, and patient goals and values are integrated to make optimal decisions when making a diagnosis, selecting a diagnostic test, picking an intervention or determining prognosis. There are five steps in this process. Hand surgeons and therapists can use the evidence-based process to attain optimal management of individual patients, manage their overall practice, guide the ongoing professional development, and deal with funding and policy makers.","corpus_id":11173059,"score":1},{"doc_id":"19411769","title":"Sensorimotor function and dizziness in neck pain: implications for assessment and management.","abstract":"SYNOPSIS: The term sensorimotor describes all the afferent, efferent, and central integration and processing components involved in maintaining stability in the postural control system through intrinsic motor-control properties. The scope of this paper is to highlight the sensorimotor deficits that can arise from altered cervical afferent input. From a clinical orthopaedic perspective, the peripheral mechanoreceptors are the most important in functional joint stability; but in the cervical region they are also important for postural stability, as well as head and eye movement control. Consequently, conventional musculoskeletal intervention approaches may be sufficient only for patients with neck pain and minimal sensorimotor proprioceptive disturbances. Clinical experience and research indicates that significant sensorimotor cervical proprioceptive disturbances might be an important factor in the maintenance, recurrence, or progression of various symptoms in some patients with neck pain. In these cases, more specific and novel treatment methods are needed which progressively address neck position and movement sense, as well as cervicogenic oculomotor disturbances, postural stability, and cervicogenic dizziness. In this commentary we review the most relevant theoretical and practical knowledge on this matter and implications for clinical assessment and management, and we propose future directions for research. LEVEL OF EVIDENCE: Level 5.","corpus_id":36677967,"score":1},{"doc_id":"19583554","title":"Evidence-based medicine and the Cochrane Collaboration.","abstract":"Providing evidence-based care to patients involves turning a clinical problem into an answerable question, systematically searching for the best evidence relevant to the question, critically appraising that evidence, and, finally, using the evidence as the basis for clinical decisions to solve the problem. While the overload of medical information today presents a demanding challenge to physicians to sort and identify relevant and valid evidence, it is vitally important to translate that evidence into clinically useful terms. To apply evidence to patient clinical management, it is critical to discuss with patients the evidence, the benefits and the harms, and the alternative treatments, such that they understand and can fully participate in the decision-making process. The framework of evidenced-based medicine provides a concrete methodology to address these issues, here, framed and detailed in five steps. The Cochrane Collaboration has been at the forefront of applying the methods of evidence-based medicine (EBM) in the treatment and management of musculoskeletal and other disorders.","corpus_id":38090726,"score":1},{"doc_id":"19583560","title":"Monitoring response to therapy in rheumatoid arthritis - perspectives from the clinic.","abstract":"The major objectives in treating patients with rheumatoid arthritis are managing the symptoms of disease and preserving joint structure, with the ultimate goal of disease remission. Several independent studies have shown that treatment decisions driven by quantitative rather than subjective monitoring of disease activity result in significantly improved patient outcomes. Various assessment tools are available that measure both clinical and patient-reported outcomes. While some measurement tools may be more appropriate for use in clinical trials, several have been developed that are simple and practical to use, even in a busy clinic. As pivotal members of the multidisciplinary rheumatology healthcare provider team, the nurse and the rheumatologist play key roles in managing a patient's progress by closely monitoring their response to treatment. Here, we discuss optimal disease management founded on a multidisciplinary approach and provide an overview of some key measures for assessing patient response to treatment.","corpus_id":23734693,"score":1},{"doc_id":"19638766","title":"A universal model of diagnostic reasoning.","abstract":"Clinical judgment is a critical aspect of physician performance in medicine. It is essential in the formulation of a diagnosis and key to the effective and safe management of patients. Yet, the overall diagnostic error rate remains unacceptably high. In more than four decades of research, a variety of approaches have been taken, but a consensus approach toward diagnostic decision making has not emerged. In the last 20 years, important gains have been made in psychological research on human judgment. Dual-process theory has emerged as the predominant approach, positing two systems of decision making, System 1 (heuristic, intuitive) and System 2 (systematic, analytical). The author proposes a schematic model that uses the theory to develop a universal approach toward clinical decision making. Properties of the model explain many of the observed characteristics of physicians' performance. Yet the author cautions that not all medical reasoning and decision making falls neatly into one or the other of the model's systems, even though they provide a basic framework incorporating the recognized diverse approaches. He also emphasizes the complexity of decision making in actual clinical situations and the urgent need for more research to help clinicians gain additional insight and understanding regarding their decision making.","corpus_id":8805552,"score":1},{"doc_id":"19643835","title":"Strategies to promote evidence-based practice in pediatric physical therapy: a formative evaluation pilot project.","abstract":"BACKGROUND: The physical therapy profession has been perceived as one that bases its practice largely on anecdotal evidence and that uses treatment techniques for which there is little scientific support. Physical therapists have been urged to increase evidence-based practice behaviors as a means to address this perception and to enhance the translation of knowledge from research evidence into clinical practice. However, little attention has been paid to the best ways in which to support clinicians' efforts toward improving evidence-based practice. OBJECTIVES: The purpose of this study was to identify, implement, and evaluate the effectiveness of strategies aimed at enhancing the ability of 5 pediatric physical therapists to integrate scientific research evidence into clinical decision making. DESIGN: This study was a formative evaluation pilot project. METHODS: The participants in this study collaborated with the first author to identify and implement strategies and outcomes aimed at enhancing their ability to use research evidence during clinical decision making. Outcome data were analyzed with qualitative methods. RESULTS: The participants were able to implement several, but not all, of the strategies and made modest self-reported improvements in evidence-based practice behaviors, such as reading journal articles and completing database searches. They identified several barriers, including a lack of time, other influences on clinical decision making, and a lack of incentives for evidence-based practice activities. CONCLUSIONS: The pediatric physical therapists who took part in this project had positive attitudes toward evidence-based practice and made modest improvements in this area. It is critical for the profession to continue to investigate optimal strategies to aid practicing clinicians in applying research evidence to clinical decision making.","corpus_id":9327241,"score":1},{"doc_id":"19668280","title":"An introduction to an evidence-based approach to interventional techniques in the management of chronic spinal pain.","abstract":"Practice guidelines are systematically developed statements to assist practitioners and patients in making decisions about appropriate health care for specific clinical circumstances. Clinical practice guidelines present statements of best practice based on a thorough evaluation of the evidence from published studies on the outcomes of treatment. In November 1989, Congress mandated the creation of the Agency for Healthcare Policy and Research (AHCPR). AHCPR was given broad responsibility for supporting research, data development, and related activities. Associated with this mandate, the National Academy of Sciences published a document indicating that guidelines are expected to enhance the quality, appropriateness, and effectiveness of health care services. Guidelines as a whole have been characterized by multiple conflicts in terminology and technique. These conflicts are notable for the confusion they create and for what they reflect about differences in values, experiences, and interest among different parties. Despite this confusion, public and private development of guidelines is growing exponentially. There are only limited means to coordinate these guidelines in order to resolve inconsistencies, fill in gaps, track applications and results, and assess the soundness of individual guidelines. Significant diversity exists in clinical practice guidelines. The inconsistency amongst guidelines arises from variations in values, tolerance for risks, preferences, expertise, and conflicts of interest. In 2000, the American Society of Interventional Pain Physicians (ASIPP) first created treatment guidelines to help practitioners. There have been 4 subsequent updates. These guidelines address the issues of systematic evaluation and ongoing care of chronic or persistent pain, and provide information about the scientific basis of recommended procedures. These guidelines are expected to increase patient compliance, dispel misconceptions among providers and patients, manage patient expectations reasonably, and form the basis of a therapeutic partnership between the patient, the provider, and payors. The ASIPP guidelines are based on evidence-based medicine (EBM). EBM is in turn based on 4 basic contingencies: the recognition of the patient's problem and the construction of a structured clinical question; the ability to efficiently and effectively search the medical literature to retrieve the best available evidence to answer the clinical question; clinical appraisal of the evidence; and integration of the evidence with all aspects of the individual patient's decision-making to determine the best clinical care of the patient. Evidence synthesis for guidelines includes the review of all relevant systematic reviews and individual articles, grading them for relevance, methodologic quality, consistency, and recommendations.","corpus_id":39722772,"score":1},{"doc_id":"19669915","title":"Reducing diagnostic error with computer-based clinical decision support.","abstract":"Information technology approaches to delivering diagnostic clinical decision support (CDS) are the subject of the papers to follow in the proceedings. These will address the history of CDS and present day approaches (Miller), evaluation of diagnostic CDS methods (Friedman), and the role of clinical documentation in supporting diagnostic decision making (Schiff). In addition, several other considerations relating to this topic are interesting to ponder. We are moving toward increased understanding of gene regulation and gene expression, identification of biomarkers, and the ability to predict patient response to disease and to tailor treatments to these individual variations-referred to as \"personalized\" or, more recently, \"predictive\" medicine. Consequently, diagnostic decision making is more and more linked to management decision making, and generic diagnostic labels like \"diabetes\" or \"colon cancer\" will no longer be sufficient, because they don't tell us what to do. Ultimately, if we have more complete data including more structured capture of phenomic data as well as the characterization of the patient's genome, direct prediction from responses of highly refined subsets of similar patients in a database can be used to select appropriate management, the effectiveness of which was demonstrated in projects in selected limited domains as early as the 1970s. In general, there are six classes of methodologies, including the above, which can be applied to delivering CDS. In addition, patients are becoming more knowledgeable and should be regarded as active participants, not only in helping to obtain data but also in their own status assessment and as recipients of decision support. With the above advances, this is a very promising time to be engaged in pursuit of methods of CDS.","corpus_id":43063083,"score":1},{"doc_id":"19753425","title":"Factors that influence the clinical decision-making of rehabilitation professionals in long-term care settings.","abstract":"The purpose of this qualitative research was to evaluate the reasoning of clinicians practicing in long-term care facilities and to explore factors influencing their professional development. Eighteen participants were recruited from eight clinical sites and included seven occupational therapists, eight physical therapists, and three speech therapists distributed across three groups relative to experience. Nonparticipant observation and videotape of therapist-patient interactions were used in semi-structured interviews with each participant. Qualitative data analysis software was used during a process of open and axial coding, followed by thematic analysis. The facilitory and inhibitory factors that affect clinical reasoning and professional development were identified. Rehabilitation professionals in long-term care demonstrated clinical reasoning within the context of patient-centered goals. Well-developed and explicit programs for mentorship, professional development, and continuing education fostered their clinical reasoning abilities. Participants perceived that these factors were vital to achieving optimal patient outcomes.","corpus_id":32655820,"score":1},{"doc_id":"19787009","title":"Evidence-based medicine, systematic reviews, and guidelines in interventional pain management: part 6. Systematic reviews and meta-analyses of observational studies.","abstract":"Observational studies provide an important source of information when randomized controlled trials (RCTs) cannot or should not be undertaken, provided that the data are analyzed and interpreted with special attention to bias. Evidence-based medicine (EBM) stresses the examination of evidence from clinical research and describes it as a shift in medical paradigm, in contrast to intuition, unsystematic clinical experience, and pathophysiologic rationale. While the importance of randomized trials has been created by the concept of the hierarchy of evidence in guiding therapy, much of the medical research is observational. The reporting of observational research is often not detailed and clear enough with insufficient quality and poor reporting, which hampers the assessment of strengths and weaknesses of the study and the generalizability of the mixed results. Thus, in recent years, progress and innovations in health care are measured by systematic reviews and meta-analyses. A systematic review is defined as, \"the application of scientific strategies that limit bias by the systematic assembly, clinical appraisal, and synthesis of all relevant studies on a specific topic.\" Meta-analysis usually is the final step in a systematic review. Systematic reviews and meta-analyses are labor intensive, requiring expertise in both the subject matter and review methodology, and also must follow the rules of EBM which suggests that a formal set of rules must complement medical training and common sense for clinicians to integrate the results of clinical research effectively. While expertise in the review methods is important, the expertise in the subject matter and technical components is also crucial. Even though, systematic reviews and meta-analyses, specifically of RCTs, have exploded, the quality of the systematic reviews is highly variable and consequently, the opinions reached of the same studies are quite divergent. Numerous deficiencies have been described in methodologic assessment of the quality of the individual articles. Consequently, observational studies can provide an important complementary source of information, provided that the data are analyzed and interpreted in the context of confounding bias to which they are prone. Appropriate systematic reviews of observational studies, in conjunction with RCTs, may provide the basis for elimination of a dangerous discrepancy between the experts and the evidence. Steps in conducting systematic reviews of observational studies include planning, conducting, reporting, and disseminating the results. MOOSE, or Meta-analysis of Observational Studies in Epidemiology, a proposal for reporting contains specifications including background, search strategy, methods, results, discussion, and conclusion. Use of the MOOSE checklist should improve the usefulness of meta-analysis for authors, reviewers, editors, readers, and decision-makers. This manuscript describes systematic reviews and meta-analyses of observational studies. Authors frequently utilize RCTs and observational studies in one systematic review; thus, they should also follow the reporting standards of the Quality of Reporting of Meta-analysis (QUOROM) statement, which also provides a checklist. A combined approach of QUOROM and MOOSE will improve reporting of systematic reviews and lead to progress and innovations in health care.","corpus_id":-1,"score":1},{"doc_id":"20205815","title":"How to integrate individual patient values and preferences in clinical practice guidelines? A research protocol.","abstract":"BACKGROUND: Clinical practice guidelines are largely conceived as tools that will inform health professionals' decisions rather than foster patient involvement in decision making. The time now seems right to adapt clinical practice guidelines in such a way that both the professional's perspective as care provider and the patients' preferences and characteristics are being weighed equally in the decision-making process. We hypothesise that clinical practice guidelines can be adapted to facilitate the integration of individual patients' preferences in clinical decision making. This research protocol asks two questions: How should clinical practice guidelines be adapted to elicit patient preferences and to support shared decision making? What type of clinical decisions are perceived as most requiring consideration of individual patients' preferences rather than promoting a single best choice? METHODS: Stakeholders' opinions and ideas will be explored through an 18-month qualitative study. Data will be collected from in-depth individual interviews. A purposive sample of 20 to 25 key-informants will be selected among three groups of stakeholders: health professionals using guidelines (e.g., physicians, nurses); experts at the macro- and meso-level, including guideline and decision aids developers, policy makers, and researchers; and patient representatives. Ideas and recommendations expressed by stakeholders will be prioritized by nominal group technique in expert meetings. DISCUSSION: One-for-all guidelines do not account for differences in patients' characteristics and for their preferences for medical interventions and health outcomes, suggesting a need for flexible guidelines that facilitate patient involvement in clinical decision making. The question is how this can be achieved. This study is not about patient participation in guideline development, a closely related and important issue that does not however substitute for, or guarantee individual patient involvement in clinical decisions. The study results will provide the needed background for recommendations about potential effective and feasible strategies to ensure greater responsiveness of clinical practice guidelines to individual patient's preferences in clinical decision-making.","corpus_id":449228,"score":1},{"doc_id":"21817012","title":"Building the rationale and structure for a complex physical therapy intervention within the context of a clinical trial: a multimodal individualized treatment for patients with hip osteoarthritis.","abstract":"Evaluating the efficacy of complex interventions such as multimodal, impairment-based physical therapy treatments in randomized controlled trials is essential to inform practice and compare relative benefits of available treatment options. Studies of physical therapy interventions using highly standardized intervention protocols, although methodologically rigorous, do not necessarily reflect \"real-world\" clinical practice, and in many cases results have been disappointing. Development of a complex intervention that includes multiple treatment modalities and individualized treatment technique selection requires a systematic approach to designing all aspects of the intervention based on theory, evidence, and practical constraints. This perspective article outlines the development of the rationale and structure of a multimodal physical therapy program for painful hip osteoarthritis to be assessed in a clinical trial. The resulting intervention protocol comprises a semi-structured program of exercises and manual therapy, advice, physical activity, and optional prescription of a gait aid that is standardized, yet can be individualized according to physical assessment and radiographic findings. The program is evidence based and reflects contemporary physical therapist practice, while also being reproducible and reportable. This perspective article aims to encourage physical therapy researchers involved in evaluation of complex interventions to better document their own intervention development, as well as the outcomes, thus generating a body of knowledge about the development processes and protocols that is generalizable to the real-world complexity of providing physical therapy to individual patients.","corpus_id":25128343,"score":1},{"doc_id":"25716151","title":"The 'Best Practice Guide to Conservative Management of Patellofemoral Pain': incorporating level 1 evidence with expert clinical reasoning.","abstract":"IMPORTANCE: Patellofemoral pain (PFP) is both chronic and prevalent; it has complex aetiology and many conservative treatment options. OBJECTIVE: Develop a comprehensive contemporary guide to conservative management of PFP outlining key considerations for clinicians to follow. DESIGN: Mixed methods. METHODS: We synthesised the findings from six high-quality systematic reviews to September 2013 with the opinions of 17 experts obtained via semistructured interviews. Experts had at least 5 years clinical experience with PFP as a specialist focus, were actively involved in PFP research and contributed to specialist international meetings. The interviews covered clinical reasoning, perception of current evidence and research priorities. RESULTS: Multimodal intervention including exercise to strengthen the gluteal and quadriceps musculature, manual therapy and taping possessed the strongest evidence. Evidence also supports use of foot orthoses and acupuncture. Interview transcript analysis identified 23 themes and 58 subthemes. Four key over-arching principles to ensure effective management included-(1) PFP is a multifactorial condition requiring an individually tailored multimodal approach. ( 2) Immediate pain relief should be a priority to gain patient trust. ( 3) Patient empowerment by emphasising active over passive interventions is important. ( 4) Good patient education and activity modification is essential. Future research priorities include identifying risk factors, testing effective prevention, developing education strategies, evaluating the influence of psychosocial factors on treatment outcomes and how to address them, evaluating the efficacy of movement pattern retraining and improving clinicians' assessment skills to facilitate optimal individual prescription. CONCLUSIONS AND RELEVANCE: Effective management of PFP requires consideration of a number of proven conservative interventions. An individually tailored multimodal intervention programme including gluteal and quadriceps strengthening, patellar taping and an emphasis on education and activity modification should be prescribed for patients with PFP. We provide a 'Best Practice Guide to Conservative Management of Patellofemoral Pain' outlining key considerations.","corpus_id":24463210,"score":1},{"doc_id":"26482401","title":"Assessing progression of clinical reasoning through virtual patients: An exploratory study.","abstract":"To avoid test-driven learning, there have been discussions regarding the use of more formative assessments in health care education to promote students' deep learning. Feedback is important in formative assessment, but many students ignore it; therefore, interventions should be introduced which stimulate them to reflect on the new knowledge. The aim for this study was to explore if Virtual Patient (VP)-based formative assessments, in connection with self-evaluations, had an impact on postgraduate pediatric nursing students' development of clinical reasoning abilities. Students' self-evaluations served as the basis for measuring progress. Data was analysed using deductive content analysis. The findings showed a clear progression of the clinical reasoning ability of the students. After the first assessment, the students described feelings of uncertainty and that their knowledge gaps were exposed. At the mid-course assessment the awareness of improved clinical reasoning was obvious and the students were more certain of knowing how to solve the VP cases. In the final assessment, self-efficacy was expressed. VP-based assessments, in connection with self-evaluations, early in the education resulted in a gain of students' own identification of the concept of clinical reasoning, awareness of what to focus on during clinical practice and visualised expected clinical competence.","corpus_id":9335460,"score":1},{"doc_id":"27815820","title":"The impact of patient-reported outcome measures in clinical practice for pain: a systematic review.","abstract":"PURPOSE: Patient-reported outcome measures (PROMs) have increasingly been incorporated into clinical practice. Research suggests that PROMs could be viewed as active components of complex interventions and may affect the process and outcome of care. This systematic review examines PROMs in the context of treatment for non-malignant pain. METHODS: An electronic search on: MEDLINE, EMBASE, PsycINFO, PsycARTICLES, Cochrane Library and Web of Science identified relevant papers (February 2015). The inclusion criteria were: focused on implementing PROMs into clinical practice, adults, and primary data studies. Critical interpretive synthesis was used to synthesise qualitative and quantitative findings into a theoretical argument. RESULTS: Thirteen eligible studies were identified. Synthesis suggested that PROMs may be included in the initial consultation to assess patients and for shared decision-making regarding patient care. During the course of treatment, PROMs can be used to track progress, evaluate treatment, and change the course of care; using PROMs may also influence the therapeutic relationship. Post-treatment, using PROMs might directly influence other outcomes such as pain and patient satisfaction. However, although studies have investigated these areas, evidence is weak and inconclusive. CONCLUSION: Due to the poor quality, lack of generalisability and heterogeneity of these studies, it is not possible to provide a comprehensive understanding of how PROMs may impact clinical treatment of non-malignant pain. The literature suggests that PROMs enable pain assessment, decision-making, the therapeutic relationship, evaluation of treatment and may influence outcomes. Further research is needed to provide better evidence as to whether PROMs do indeed have any effects on these domains.","corpus_id":7126091,"score":1},{"doc_id":"28694677","title":"Does shared decision making results in better health related outcomes for individuals with painful musculoskeletal disorders? A systematic review.","abstract":"Background: Shared Decision-Making (SDM) is a dynamic process by which the health care professional and the patient influence each other in making health-related choices or decisions. SDM is strongly embedded in today's health care approaches, and is advocated as an ideal model since it renders individuals more control towards the health care they choose to receive, and has been shown to improve patient outcomes. Objectives: The goal of this systematic review was to investigate the added-value of SDM on clinical health-related outcomes in patients with a variety of musculoskeletal conditions. Data sources: PubMed and CINAHL. Study selection: PRISMA guidelines were followed for this review. To be considered for review, the study had to meet all the following criteria: (1) prospective studies that involved treatment decision-making; (2) randomized controlled trial design; (3) involving patients faced with having to make a treatment decision; (4) comparing SDM with a control intervention and (5) including one or more of the following outcome measures: well-being, costs, health-related pain or disability measures, or quality of life. Study appraisal: A priori, we determined to perform methodological quality assessment using the Cochrane Risk of Bias tool for randomized controlled trials. Results: We did not find a single study that looked at the true effect of SDM on patient reported outcomes in a population with musculoskeletal pain. Conclusion: For the management of painful musculoskeletal conditions, in the light of the current evidence (none), we estimate that it would be wise to explore the effectiveness of SDM before forcing its large-scale implementation in rehabilitation.","corpus_id":33055615,"score":1},{"doc_id":"29259567","title":"Using Functional Analysis as a Framework to Guide Individualized Treatment for Negative Symptoms.","abstract":"Although numerous interventions are available for negative symptoms, outcomes have been unsatisfactory with pharmacological and psychological interventions producing changes of only limited clinical significance. Here, we argue that because negative symptoms occur as a complex syndrome caused and maintained by numerous factors that vary between individuals they are unlikely to be treated effectively by the present \"one size fits all\" approaches. Instead, a well-founded selection of those interventions relevant to each individual is needed to optimize both the efficiency and the efficacy of existing approaches. The concept of functional analysis (FA) can be used to structure existing knowledge so that it can guide individualized treatment planning. FA is based on stimulus-response learning mechanisms taking into account the characteristics of the organism that contribute to the responses, their consequences and the contingency with which consequences are tied to the response. FA can thus be flexibly applied to the level of individual patients to understand the factors causing and maintaining negative symptoms and derive suitable interventions. In this article we will briefly introduce the concept of FA and demonstrate-exemplarily-how known psychological and biological correlates of negative symptoms can be incorporated into its framework. We then outline the framework's implications for individual assessment and treatment. Following the logic of FA, we argue that a detailed assessment is needed to identify the key factors causing or maintaining negative symptoms for each individual patient. Interventions can then be selected according to their likelihood of changing these key factors and need to take interactions between different factors into account. Supplementary case vignettes exemplify the usefulness of functional analysis for individual treatment planning. Finally, we discuss and point to avenues for future research guided by this model.","corpus_id":25979763,"score":1},{"doc_id":"29473563","title":"Are randomized, blind clinical trials enough to guide individualized decisions for patients with neurologic diseases?","abstract":"The practice of medicine relies on the patient-physician relationship, knowledge, and clinical judgment. Randomized controlled trials (RCTs) remain the least biased method for studying the effects of interventions in selected populations and are the only method to control adequately for unknown confounders. However, physicians face the limitations of RCTs on a daily basis as they treat relatively unselected populations and individual patients. We explore the benefits and limitations of RCTs for some neurologic disorders, and discuss the difficulties of predicting individualized outcomes and anticipating treatment responses in those heterogeneous conditions. Observational studies and advances in understanding neurologic diseases complement RCTs in decision-making. Considerable challenges remain for personalized medicine; for now, clinicians must rely on their ability to integrate evidence and clinical judgment.","corpus_id":3680642,"score":1},{"doc_id":"29564549","title":"Call for action: how to improve use of patient-reported outcomes to guide clinical decision making in rheumatoid arthritis.","abstract":"Current guidelines for the management of rheumatoid arthritis (RA) recommend early treatment and a treat-to-target goal of remission or low disease activity. Over the past decade, this approach has been extremely successful in reducing disease activity and joint damage in patients with RA. At the same time, however, overall patient perception of well-being appears to have decreased with respect to outcome measures considered important by patients themselves, such as pain, fatigue, physical function and quality of life. The timely and effective use of patient-reported outcomes (PROs) could encourage physicians to focus more on the impact of RA on patients and how patients are feeling. This in turn would facilitate shared decision making between patients and physicians, ultimately leading to a more patient-centered approach and improved patient care. Indeed, PROs provide information about individual patients that complements information provided by physical assessment and composite scores, and can also be used to guide patient care, such as determining whether a clinic visit is needed or whether treatment modifications are necessary. This is particularly important for patients who do not achieve the aspirational target of remission or low disease activity with pharmacological treatment. A number of validated PRO questionnaires are available, but how and which PROs should be incorporated into rheumatology clinical practice as part of the decision-making process is still controversial. Combining PROs with technology, such as computer adaptive tests, electronic PRO systems, web-based platforms and patient dashboards, could further aid PRO integration into daily rheumatology clinical practice.","corpus_id":4106315,"score":1},{"doc_id":"19083686","title":"A system of performance intervention zones for use during student evaluation in the clinical environment.","abstract":"In order to support decision making during comprehensive clinical examinations involving patient care, a system of performance intervention zones was developed and implemented. The aims of the system were to assist examiners in deciding when to intervene during a clinical examination, to facilitate consistency in decision making, and to create the basis and language for shared understanding of examinee performance. The system was recently utilized in Ontario during assessment of internationally educated massage therapists in relation to provincially set competency standards. Feedback from examiners suggested that the system of intervention zones was effective in achieving the specified aims, and on the basis of this preliminary field test, further work is being planned in order to establish the reliability of the system.","corpus_id":26046747,"score":0},{"doc_id":"19230220","title":"Community ambulation: influences on therapists and clients reasoning and decision making.","abstract":"BACKGROUND: Community ambulation is an important element of a rehabilitation training programme and its achievement is a goal shared by rehabilitation professionals and clients. The factors that influence a physiotherapist's or health professionals decision making around the preparation of a client for community ambulation and the factors that influence a client's decision to return to walking in their community are unclear. OBJECTIVE: To review the available literature about the factors that have influenced the reasoning and decision making of rehabilitation therapists and clients around the topic of ambulation in the community. METHOD: Three separate searches of the available literature were undertaken using Ovid, Cinahl, ProQuest, Medline and Ebscohost databases. Databases were searched from 1966 to October 2006.The first search explored the literature for factors that influence the clinical reasoning of rehabilitation therapists. The second search explored the literature for factors that influence client's decision to ambulate in the community. A third search was undertaken to explore the literature for the demands of community ambulation in rural communities. RESULTS: Very few studies were found that explored community ambulation in the context of clinical reasoning and decision making, the facilitators and barriers to a clients return to ambulation in their community or the demands of ambulation in a rural community. CONCLUSION: Consideration of the environment is key to the successful return to walking in the community of clients with mobility problems yet little literature has been found to guide physiotherapist's decision making about preparing a clients to return to walking in the community. An individual's participation in their society is also a result of the interaction between their personal characteristics and his or her environment. The influence of these characteristics may vary from one individual to another yet the factors that influence a person's decision to return to walking in their community after stroke remain unclear.","corpus_id":19105577,"score":0},{"doc_id":"19252261","title":"The physical therapist as a musculoskeletal specialist in the emergency department.","abstract":"Because patients with musculoskeletal injuries commonly seek intervention in the emergency department (ED), it has been proposed that practitioners with expertise in musculoskeletal practice can be of benefit in this setting. This clinical commentary describes the rationale for utilizing physical therapists as musculoskeletal specialists in the ED. Evidence indicates that physical therapists have the knowledge and skills to provide such expertise. Literature describing ED practice suggests that the management of patients with musculoskeletal conditions would be improved through the consistent integration of evaluation and treatment principles associated with physical therapy practice. Furthermore, early access to physical therapy, as can be provided in the ED setting, has the potential to positively influence patient recovery. Based on prior research and recent evolution of practice, further consideration of physical therapists as consultants in the ED is warranted, and, therefore, additional dialogue on the subject should be encouraged.","corpus_id":5910513,"score":0},{"doc_id":"19397820","title":"A description of a knowledge broker role implemented as part of a randomized controlled trial evaluating three knowledge translation strategies.","abstract":"BACKGROUND: A knowledge broker (KB) is a popular knowledge translation and exchange (KTE) strategy emerging in Canada to promote interaction between researchers and end users, as well as to develop capacity for evidence-informed decision making. A KB provides a link between research producers and end users by developing a mutual understanding of goals and cultures, collaborates with end users to identify issues and problems for which solutions are required, and facilitates the identification, access, assessment, interpretation, and translation of research evidence into local policy and practice. Knowledge-brokering can be carried out by individuals, groups and/or organizations, as well as entire countries. In each case, the KB is linked with a group of end users and focuses on promoting the integration of the best available evidence into policy and practice-related decisions. METHODS: A KB intervention comprised one of three KTE interventions evaluated in a randomized controlled trial. RESULTS: KB activities were classified into the following categories: initial and ongoing needs assessments; scanning the horizon; knowledge management; KTE; network development, maintenance, and facilitation; facilitation of individual capacity development in evidence informed decision making; and g) facilitation of and support for organizational change. CONCLUSION: As the KB role developed during this study, central themes that emerged as particularly important included relationship development, ongoing support, customized approaches, and opportunities for individual and organizational capacity development. The novelty of the KB role in public health provides a unique opportunity to assess the need for and reaction to the role and its associated activities. Future research should include studies to evaluate the effectiveness of KBs in different settings and among different health care professionals, and to explore the optimal preparation and training of KBs, as well as the identification of the personality characteristics most closely associated with KB effectiveness. Studies should also seek to better understand which combination of KB activities are associated with optimal evidence-informed decision making outcomes, and whether the combination changes in different settings and among different health care decision makers.","corpus_id":-1,"score":0},{"doc_id":"19540406","title":"[Addiction and brief-systemic therapy: working with compulsion].","abstract":"Addictions et thérapie systémique brève : un travail sous contrainte. In our daily practice in public hospitals, we are regularly confronted with the paradox of helping patients, who do not ask for help. Although the French law is clearly defined to allow us to treat patients suffering from psychiatric conditions, who are unable to give their consent, it is not the case for those with addictive disorders. In fact, their disorder does not always (or does not yet) justify treatment without their consent, according to the 1990 law (psychiatric treatment without the patient's consent). However, many of them are referred to us because a third party has forced them (spouse, general practitioner, treatment order) and even though some patients consult spontaneously, they often do so more \"for others\" than for themselves. Because of this, the therapist (doctor, psychologist or nurse), in addition to the paradox of treating patients who do not ask for treatment, find themselves in a situation with two-fold compulsion, fixed by the social (or family) setting, both as a helper and as a coercive agent, thus, putting the fundamental concepts of treatment into question. A therapeutic agreement, free-will and motivation are in jeopardy when the pressure is strong, which removes the therapist from his mission of treating. Although we would not question the necessity for psychiatric treatment in patients who do not ask for it (addictions are a major public-health problem), we should not forget that motivation is one of the essential elements for making any changes in behavior. Although compulsion (external or internal) is recognized by everyone as a limiting factor, we would like to show here how much it can be a lever for change, as long as this compulsion is identified right from the first meeting with the patient, who consults in an addiction centre. Brief systemic therapy may be of interest for these patients, since it reinforces the motivating approach, which is recommended today and since the compulsive nature of the request for treatment is not an obstacle for such treatment to be started. We try to outline here how the therapist can get out of this two-fold compulsion and help the patient to become the instigator of this change, often imposed on him. Two elements are fundamental to understand the function of brief systemic therapy. First of all, \"systemic\" means \"interaction\". A systemic approach to treatment requires working in clinical situations, particular attention being paid to interactions. Second, brief therapy does not mean short therapy, but rather therapy with an objective in view. The objective is determined by the patient together with the therapist and they work out together how to reach it, with or without the family's help. Because of this, we use a five-point assessment to offer a concrete response to the patients in these psychotherapeutic consultations. Firstly, is the patient the one who has asked for treatment? We know that in addictive behavior, it is not always the one with symptoms who asks for help (many couples consult who are persuaded that the other one needs to change). Once we know who has asked for treatment, we clarify (with the patient's help) that his/her objectives are not the same as someone who asks for treatment and we can then redefine them (first step in the therapeutic agreement). Once the request for treatment is clarified, we can clearly define what the problem is, the objectives that the patient fixes for him/herself and how to reach them. A large proportion of therapeutic failures result from the request for treatment being unclear. In this way, we define the problem in concrete terms, without using classifications and the previous attempts to solve it (third point). In fact, we often find that the problem itself is the solution, which is chosen to try to resolve it. Knowing which solutions have been tried (and failed) allows the patient to realize what is effective and what is not. The role of the therapist is to help the family and the patient to find other types of solution to their problem. The therapist only offers concrete tasks, which can be done in the near future (minimal changes). Finally, the therapist takes into account the patient's beliefs, values and personal priorities, to which they are attached and which have determined up to now, how they react to the problem. To work with a patient suffering from addiction, it is important, first of all, to find the elements of compulsion, which are hiding behind each request for treatment. This is because, if the patient does not follow the initial therapeutic objectives, there is always the underlying complaint, which should motivate the patient to improve the situation. An individual patient only has a few possibilities for adapting to this type of situation (agreeing, refusal or negotiation) and the role of the therapist is first of all to help him to realize this. This helps to avoid resistance developing, by underlying the compulsive aspect, which originates from the family's request for treatment. We offer a way for setting up the first meeting: working on the role of the patient in the treatment. Three types of patients consult: patients who are \"not concerned\" (sent by a third party; their main problem is with the person who asked for them to be treated), \"victims\" (they complain and consult because they put the responsibility of their problem on someone else) and \"clients\" (they consult because they consider that their problem depends on themselves and they want help to solve it actively). In fact, changing is not easy and does not happen without making an effort. Change comes from a complex cycle of interactions, for which it is often impossible to find a single origin for the situation in question. The psychological world tends towards homeostasis, just like all human systems, and so, suggesting making changes can only be experienced as an intrusion. Pathology begins when an individual can no longer choose what he/she needs to do. We do not consider that a brief-concrete approach is better than any other approach, but its pragmatic nature seems to fit in with the new conception of addiction therapy, with earlier intervention. However, is it possible to make changes outside of a crisis situation? We are unable to answer this question, except to say that the best time for change is that chosen by the patient.","corpus_id":29322440,"score":0},{"doc_id":"19595419","title":"A retrospective analysis of self-reported symptoms from 761 consecutive new patients presenting to a Neuro Emotional Technique chiropractic clinic.","abstract":"PURPOSE: To describe the profile of patients presenting to a private chiropractic clinic specialising in Neuro Emotional Technique (NET) and to identify trends in the presentation of symptoms from these patients. METHODS: 761 consecutive new patients presented to a large, multi-doctor chiropractic clinic in which practitioners all adopt a similar philosophical paradigm and practice NET From January 2005 to December 2005, self-referred patients completed a new patient questionnaire, in which they self-reported one primary complaint for why they were visiting the practitioner. Predetermined patient information was entered manually into a database and basic descriptive statistics extracted. RESULTS: 67.3% of participants were female and 32.6% of the participants were between the ages of 31 and 40. 54.8% of patients presented with a primary musculoskeletal complaint and 36.0% a non-musculoskeletal complaint. Of the musculoskeletal complaints, 40.8% of patients presented with back pain, 20.9% with neck pain and 11.5% with shoulder pain. The most common form of non-musculoskeletal complaint was immune and recurrent infections (13.9%), stress and anxiety (12.8%) and depression (10.9%). 41.4% of participants reported a first time complaint, however, of the patients who had had the presenting complaint before 60.7% reported as having the complaint for greater than 1 year. Musculoskeletal and non-musculoskeletal participants had similar pain profiles. CONCLUSION: This retrospective analysis is the first comprehensive description of the scope of NET patients and their presenting complaints. The patient profile of this NET clinic has a higher degree of non-musculoskeletal patients than that usually reported in non-NET chiropractic offices, and other forms of chiropractic previously described in the literature. Further cross sectional research is required to determine if this particular clinic is indicative of all NET practices and whether the presenting symptoms, especially the non-musculoskeletal, are resolved with NET.","corpus_id":1388270,"score":0},{"doc_id":"19674225","title":"Do physical therapists change their beliefs, attitudes, knowledge, skills and behaviour after a biopsychosocially orientated university course?","abstract":"AIM: The aim of this study is to examine the effects of an 8-day university-based training course, aimed at identifying and addressing psychosocial prognostic factors during physiotherapy treatment, in shifting therapists towards a more biopsychosocial orientation as measured by changes in beliefs/attitudes, knowledge, skills and behaviour. METHOD: We combined a randomized controlled trail with a pre-post design. Forty-two physiotherapists applied for a university-accredited training course designed to enhance knowledge and management of psychosocial factors in their practice with patients suffering from musculoskeletal pain. The course participants were randomized either to receiving the course or to a waiting list for training. Attitudes and beliefs towards, and knowledge of psychosocial factors, patient vignettes and a video of an imaginary patient were tested before and after training. The patients of the course participants were asked to fill out a questionnaire with background questions at treatment start. The patients also received a questionnaire about the physical therapists' behaviour and patient satisfaction 6 weeks after treatment start. RESULTS: The results show that physical therapists' attitudes and believes became more biopsychosocially and less biomedically orientated, they were less convinced that pain justifies disability and limitation of activities, and their knowledge and skills on psychosocial risk factors increased after a university-accredited training course. Yet despite these changes their patients perceived their practice behaviour before and after the course as similar and were equally satisfied with their treatment and treatment result. CONCLUSION: A course, which enhanced biopsychosocial attitudes and beliefs, as well as increased such knowledge and skills did not change the way patients perceived their physical therapists. A future question is whether it improves patient outcome.","corpus_id":26542164,"score":0},{"doc_id":"19922741","title":"Tools and strategies for ongoing assessment of depression: a measurement-based approach to remission.","abstract":"The goal of treatment for major depressive disorder is remission, but many patients do not achieve complete remission, and few reach sustained remission (ie, recovery). However, systematically using clinical strategies such as implementing measurement-based care tactics and following treatment algorithms can improve the accuracy of ongoing assessment of depressive symptoms, better inform treatment decisions, and make sustained remission more likely. Measurement-based care tactics include using assessment tools to measure medication adherence, side effects, depressive symptoms, and suicide risk. Particularly useful in clinical practice are the Frequency, Intensity, and Burden of Side Effects-Rating (FIBSER) questionnaire; the 9-item Patient Health Questionnaire (PHQ-9); and the 16-item Quick Inventory of Depressive Symptomatology (Clinician-Rated or Self-Report versions; QIDS-C or QIDS-SR). The use of these measurements at regular patient visits can be combined with the use of treatment algorithms so that appropriate treatment selections are made on the basis of assessment tool results at critical decision points in follow-up. This article includes an example of how, at each treatment step, assessments can be made and results used to monitor progress toward remission, efficacy of dosage, and tolerability and to make informed, evidence-based treatment decisions.","corpus_id":25581885,"score":0},{"doc_id":"20797938","title":"Challenges in pain assessment in cognitively intact and cognitively impaired older adults with cancer.","abstract":"PURPOSE/OBJECTIVES: To describe approaches to pain assessment in cognitively intact and cognitively impaired older adults with cancer. DATA SOURCES: MEDLINE literature search, personal reference collection, and clinical experience. DATA SYNTHESIS: A systematic and comprehensive pain assessment is the cornerstone of effective treatment strategies. Determining the effect of pain on older adults' ability to function is as important as rating pain intensity. Evidence-based recommendations exist to guide practice. CONCLUSIONS: The undertreatment of pain in older adults persists despite a plethora of published guidelines addressing pain assessment and management. Unrelieved pain affects recovery from illness and all aspects of life. Systematic and ongoing assessment is elementary to effective pain management, yet assessments frequently are neither completed nor documented. Because pain is subjective and individual responses to pain interventions vary widely and are unpredictable, assessment is vital to comprehensive pain care in all clinical settings. Reliable and validated pain assessment tools for cognitively intact and cognitively impaired older adults are available to guide practice. IMPLICATIONS FOR NURSING: Pain assessment is a core competency for nurses in all clinical settings. Comprehensive, individualized, and ongoing assessment provides the information necessary so that clinicians can develop interventions to relieve patients' pain and improve their quality of life. Nurses have the knowledge, skills, and tools to adequately screen and comprehensively assess pain in older adult patients, including those with cognitive impairment. By using this knowledge, nurses can change systems and practices, have a significant effect on improving pain care, and increase quality of life and function of older adults with pain.","corpus_id":206990248,"score":0},{"doc_id":"20862210","title":"Treatment for lexical retrieval in progressive aphasia.","abstract":"BACKGROUND: Treatment for lexical retrieval impairment has been shown to yield positive outcomes in individuals with aphasia due to focal lesions, but there has been little research regarding the treatment of such impairments in individuals with progressive aphasia. AIMS: The purpose of this study was to examine the therapeutic effects of a semantic treatment for anomia in progressive aphasia relative to the outcome in an individual with stroke-induced aphasia. METHODS #ENTITYSTARTX00026; PROCEDURES: Two individuals with progressive aphasia and one with aphasia resulting from stroke participated in the study. Each participant presented with fluent, anomic aphasia; however, one of the patients with progressive aphasia demonstrated characteristics indicating a likely progression towards non-fluency. Each participant received a brief, intensive treatment intended to improve lexical retrieval in the context of generative naming for selected semantic categories. Treatment tasks included guided lexical retrieval prompted by the identification and elaboration of items within semantic subcategories, as well as other semantic tasks. Treatment outcomes were quantified using standard effects sizes as well as nonparametric tests comparing pre- versus post-treatment performance. OUTCOMES #ENTITYSTARTX00026; RESULTS: One of the individuals with progressive aphasia showed large treatment effects for lexical retrieval of items from targeted semantic categories. The other progressive aphasia patient showed very small effects overall for treated categories. The individual with the focal lesion due to stroke showed medium-sized effects for trained categories as well as significant improvement on a standardised measure of naming. CONCLUSIONS: Findings indicate that intensive, semantically based treatment for lexical retrieval can result in positive outcomes in individuals with progressive as well as stroke-induced aphasia. Examination of individual differences suggests that the status of semantic and episodic memory may provide predictive information regarding responsiveness to treatment.","corpus_id":28626660,"score":0},{"doc_id":"20944656","title":"Focusing on glaucoma progression and the clinical importance of progression rate measurement: a review.","abstract":"PURPOSE: This review aims to provide guidance in managing glaucoma patients more effectively. It focuses on the importance of detecting progression and measuring its rate within the management of primary open-angle glaucoma today. Recent findings strongly indicate that continued monitoring of visual fields (VFs) and reassessment of target intraocular pressures (IOPs) depending on VF progression rates are mandatory in the management of glaucoma. METHODS: Data on glaucoma progression from older as well as most recent literature findings are summarized in this article. In addition, the article elaborates on the scientific content from a series of lectures given by experts in the field during several international symposia on 'rate of progression' in 2008. RESULTS: This review summarizes key findings on the natural history of glaucoma and known factors for disease progression. It highlights the visual function changes observed as glaucoma progresses and discusses disease impact on patients' quality of life. Findings support the need to obtain information on rate of progression and its importance for clinical management. Practical ways to measure rate of progression are given by new software options to help measure major parameters. Finally, on the basis of a patient's individual rate of progression therapeutic options are assessed, such as maximum medical therapy with fixed combinations. CONCLUSIONS: Estimating a patient's individual rate of VF progression by using newly developed analyses will be helpful to forecast the potential future development of the glaucoma. An individualized treatment approach then requires that in patients in whom the risk of becoming visually impaired or blind during their lifetime is higher, a more intensive medical IOP-lowering therapy such as fixed combinations can be considered as treatment option.","corpus_id":36487873,"score":0},{"doc_id":"21332991","title":"Effects of rehabilitative interventions on pain, function and physical impairments in people with hand osteoarthritis: a systematic review.","abstract":"INTRODUCTION: Hand osteoarthritis (OA) is associated with pain, reduced grip strength, loss of range of motion and joint stiffness leading to impaired hand function and difficulty with daily activities. The effectiveness of different rehabilitation interventions on specific treatment goals has not yet been fully explored. The objective of this systematic review is to provide evidence based knowledge on the treatment effects of different rehabilitation interventions for specific treatment goals for hand OA. METHODS: A computerized literature search of Medline, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), ISI Web of Science, the Physiotherapy Evidence Database (PEDro) and SCOPUS was performed. Studies that had an evidence level of 2b or higher and that compared a rehabilitation intervention with a control group and assessed at least one of the following outcome measures - pain, physical hand function or other measures of hand impairment - were included. The eligibility and methodological quality of trials were systematically assessed by two independent reviewers using the PEDro scale. Treatment effects were calculated using standardized mean difference and 95% confidence intervals. RESULTS: Ten studies, of which six were of higher quality (PEDro score >6), were included. The rehabilitation techniques reviewed included three studies on exercise, two studies each on laser and heat, and one study each on splints, massage and acupuncture. One higher quality trial showed a large positive effect of 12-month use of a night splint on hand pain, function, strength and range of motion. Exercise had no effect on hand pain or function although it may be able to improve hand strength. Low level laser therapy may be useful for improving range of motion. No rehabilitation interventions were found to improve stiffness. CONCLUSIONS: There is emerging high quality evidence to support that rehabilitation interventions can offer significant benefits to individuals with hand OA. A summary of the higher quality evidence is provided to assist with clinical decision making based on current evidence. Further high-quality research is needed concerning the effects of rehabilitation interventions on specific treatment goals for hand OA.","corpus_id":14933735,"score":0},{"doc_id":"22331537","title":"[The use of HoNOS in the treatment of patients].","abstract":"Gebruik van de HoNOS bij de behandeling van patiënten. BACKGROUND: In order to use outcome scores for making decisions about treatment, practitioners need to know the course of scores of several groups of patients. AIM: To test the applicability of methods for computing cut-off scores and individual changes. METHOD: Using Health of the Nation Outcome Scales (HoNOS), we analysed repeated assessments of 699 adults and 414 elderly patients in different treatment settings. RESULTS: Mean HoNOS scores and cut-off scores differentiated between patient groups reasonably well. Scores and threshold values for elderly patients were relatively high. The reliable change index showed few individual changes even for groups where change was expected. The effect size and the standard error of measurement were found to be more sensitive to change. CONCLUSION: More research is needed before the findings can be generalised.","corpus_id":34913519,"score":0},{"doc_id":"22497751","title":"The science and art of pain management in older persons: case study and discussion.","abstract":"INTRODUCTION: Evidence-based medicine has been adopted as a means of achieving optimal medical care and to reduce variations in clinical practice. Randomised controlled trials are considered the highest level of scientific evidence. Older individuals are either excluded or underrepresented in these studies, and those who are included are often atypical of patients seen in clinical practice. OBJECTIVE: To examine the approach to clinical decision making in frail older persons when there is little or no scientific evidence to guide management. METHODS: A case study is presented of refractory post herpetic neuralgia in a frail older person. Management plans were developed combining the scientific evidence from the pain literature with the practice known as Comprehensive Geriatric Assessment. The rationale and evidence for clinical decision making is explored. RESULTS: Standard therapies for post herpetic neuralgia had been ineffective or limited by side effects in this patient. By a process of trial and error a combination of treatments was found that improved pain and mood but adversely affected cognition. Adjustment in treatments over time resulted in improved pain, mood, and cognition. CONCLUSIONS: The art of medicine is not the antithesis of the scientific approach. The art of medicine involves balancing the scientific evidence with the circumstances and the preferences of the patient. Combining the practices of Pain Medicine and Comprehensive Geriatric Assessment may result in a better outcome. When treating older people, clinicians not only need to take into consideration the severity of pain, but also the impact of pain and its treatment on cognition, mood and functional status.","corpus_id":5483536,"score":0},{"doc_id":"22641763","title":"Treatment of maladaptive aggression in youth: CERT guidelines II. Treatments and ongoing management.","abstract":"OBJECTIVE: To develop guidelines for management and treatment of maladaptive aggression in youth in the areas of psychosocial interventions, medication treatments, and side-effect management. METHODS: Evidence was assembled and evaluated in a multistep process, including systematic reviews of published literature; an expert survey of recommended practices; a consensus conference of researchers, policymakers, clinicians, and family advocates; and review by the steering committee of successive drafts of the recommendations. The Center for Education and Research on Mental Health Therapeutics Treatment of Maladaptive Aggression in Youth guidelines reflect a synthesis of the available evidence, based on this multistep process. RESULTS: This article describes the content, rationale, and evidence for 11 recommendations. Key treatment principles include considering psychosocial interventions, such as evidence-based parent and child skills training as the first line of treatment; targeting the underlying disorder first following evidence-based guidelines; considering individual psychosocial and medical factors, including cardiovascular risk in the selection of agents if medication treatment (ideally with the best evidence base) is initiated; avoiding the use of multiple psychotropic medications simultaneously; and careful monitoring of treatment response, by using structured rating scales, as well as close medical monitoring for side effects, including metabolic changes. CONCLUSIONS: Treatment of children with maladaptive aggression is a \"moving target\" requiring ongoing assimilation of new evidence as it emerges. Based on the existing evidence, the Treatment of Maladaptive Aggression in Youth guidelines provide a framework for management of maladaptive aggression in youth, appropriate for use by primary care clinicians and mental health providers.","corpus_id":13976294,"score":0},{"doc_id":"23121530","title":"Survey of UK speech and language therapists' assessment and treatment practices for people with progressive dysarthria.","abstract":"BACKGROUND: Dysarthria knowledge is predominantly impairment-based. As a result, speech and language therapists (SLTs) have traditionally adopted impairment-focused management practices. However, guidance for best practice suggests that SLTs should consider the client holistically, including the impact of dysarthria beyond the impairment. AIMS: To investigate the current assessment and treatment practices used by UK SLTs with clients with progressive dysarthria and to identify whether these satisfy the needs of SLTs in their everyday practice. To investigate the extent to which they consider oromotor abilities, intelligibility, functional communication, participation and interaction to be important regarding assessment and treatment decisions. To explore whether management decisions are affected by level of clinical experience or settings in which SLTs work. METHODS & PROCEDURES: An online survey of UK SLTs working with adults with progressive dysarthria. OUTCOMES & RESULTS: A total of 119 SLTs completed the survey. Respondents considered that targeting the levels of impairment, activity and participation are important in the management of clients with progressive dysarthria, as recommended by clinical guidelines and recent research. However a particularly high proportion of respondents reported the use of impairment-based assessments. Respondents reported lacking the necessary tools to target interaction in assessment and intervention. The intervention that respondents use with clients varies according to the progressive disorder and dysarthria severity. There is evidence for a trend that less experienced SLTs and those working predominantly in hospital-based settings focus on the impairment, whereas more SLTs with more experience and those based in predominantly community-based settings look beyond the impairment. CONCLUSIONS & IMPLICATIONS: The values held by SLTs match guideline recommendations for best practice, however the clinical reality is that the assessment of progressive dysarthria remains predominantly impairment-focused. New tools need to be developed and integrated into practice to target interaction in assessment and intervention, to reduce the gap between best practice recommendations and clinical reality. Ongoing research into the effectiveness of SLT intervention with clients with progressive dysarthria is required to guide clinical management decisions.","corpus_id":28352192,"score":0},{"doc_id":"23409541","title":"[Clinical reasoning in nursing, concept analysis].","abstract":"Le raisonnement clinique des infirmières, analyse de concept. BACKGROUND: Nurses work in situations of complex care requiring great clinical reasoning abilities. In literature, clinical reasoning is often confused with other concepts and it has no consensual definition. AIM: To conduct a concept analysis of a nurse's clinical reasoning in order to clarify, define and distinguish it from the other concepts as well as to better understand clinical reasoning. METHOD: Rodgers's method of concept analysis was used, after literature was retrieved with the use of clinical reasoning, concept analysis, nurse, intensive care and decision making as key-words. RESULTS: The use of cognition, cognitive strategies, a systematic approach of analysis and data interpretation, generating hypothesis and alternatives are attributes of clinical reasoning. The antecedents are experience, knowledge, memory, cues, intuition and data collection. The consequences are decision making, action, clues and problem resolution. CONCLUSION: This concept analysis helped to define clinical reasoning, to distinguish it from other concepts used synonymously and to guide future research.","corpus_id":11770699,"score":0},{"doc_id":"24123615","title":"The hippocampus uses information just encountered to guide efficient ongoing behavior.","abstract":"Adaptive ongoing behavior requires using immediate sensory input to guide upcoming actions. Using a novel paradigm with volitional exploration of visuo-spatial scenes, we revealed novel deficits among hippocampal amnesic patients in effective spatial exploration of scenes, indicated by less-systematic exploration patterns than those of healthy comparison subjects. The disorganized exploration by amnesic patients occurred despite successful retention of individual object locations across the entire exploration period, indicating that exploration impairments were not secondary to rapid decay of scene information. These exploration deficits suggest that amnesic patients are impaired in integrating memory for recent actions, which may include information such as locations just visited and scene content, to plan immediately forthcoming actions. Using a novel task that measured the on-line links between sensory input and behavior, we observed the critical role of the hippocampus in modulating ongoing behavior.","corpus_id":1745397,"score":0},{"doc_id":"24204133","title":"Pain management in patients with dementia.","abstract":"There are an estimated 35 million people with dementia across the world, of whom 50% experience regular pain. Despite this, current assessment and treatment of pain in this patient group are inadequate. In addition to the discomfort and distress caused by pain, it is frequently the underlying cause of behavioral symptoms, which can lead to inappropriate treatment with antipsychotic medications. Pain also contributes to further complications in treatment and care. This review explores four key perspectives of pain management in dementia and makes recommendations for practice and research. The first perspective discussed is the considerable uncertainty within the literature on the impact of dementia neuropathology on pain perception and processing in Alzheimer's disease and other dementias, where white matter lesions and brain atrophy appear to influence the neurobiology of pain. The second perspective considers the assessment of pain in dementia. This is challenging, particularly because of the limited capacity of self-report by these individuals, which means that assessment relies in large part on observational methods. A number of tools are available but the psychometric quality and clinical utility of these are uncertain. The evidence for efficient treatment (the third perspective) with analgesics is also limited, with few statistically well-powered trials. The most promising evidence supports the use of stepped treatment approaches, and indicates the benefit of pain and behavioral interventions on both these important symptoms. The fourth perspective debates further difficulties in pain management due to the lack of sufficient training and education for health care professionals at all levels, where evidence-based guidance is urgently needed. To address the current inadequate management of pain in dementia, a comprehensive approach is needed. This would include an accurate, validated assessment tool that is sensitive to different types of pain and therapeutic effects, supported by better training and support for care staff across all settings.","corpus_id":8418621,"score":0},{"doc_id":"24467960","title":"[Treatment of patients with osteoarthritis].","abstract":"Tratamiento del paciente con artrosis. The therapeutic management of patients with osteoarthritis aims to decrease pain and inflammation, improve physical function, and to apply safe and effective treatments. A patient-centered approach implies the active participation of the patient in the design of the treatment plan and in timely and informed decision-making at all stages of the disease. The nucleus of treatment is patient education, physical activity and therapeutic exercise, together with weight control in overweight or obese patients. Self-care by the individual and by the family is fundamental in day-to-day patient management. The use of physical therapies, technical aids (walking sticks, etc.) and simple analgesics, opium alkaloids, and antiinflammatory drugs have demonstrated effectiveness in controlling pain, improving physical function and quality of life and their use is clearly indicated in the treatment of osteoarthritis. Conservative surgery and joint replacement is indicated when treatment goals are not achieved in specific patients.","corpus_id":206049492,"score":0},{"doc_id":"25209421","title":"Deepening the quality of clinical reasoning and decision-making in rural hospital nursing practice.","abstract":"INTRODUCTION: Rural acute care nursing requires an extensive breadth and depth of knowledge as well as the ability to quickly reason through problems in order to make sound clinical decisions. This reasoning often occurs within an environment that has minimal medical or ancillary support. Registered nurses (RN) new to rural nursing, and employers, have raised concerns about patient safety while new nurses make the transition into rural practice. In addition, feeling unprepared for the rigors of rural hospital nursing practice is a central issue influencing RN recruitment and retention. Understanding how rural RNs reason is a key element for identifying professional development needs and may support recruitment and retention of skilled rural nurses. The purpose of this study was to explore how rural RNs reason through clinical problems as well as to assess the quality of such reasoning. METHODS: This study used a non-traditional approach for data collection. Fifteen rural acute care nurses with varying years of experience working in southern Alberta, Canada, were observed while they provided care to patients of varying acuity within a simulated rural setting. Following the simulation, semi-structured interviews were conducted using a substantive approach to critical thinking. RESULTS: Findings revealed that the ability to engage in deep clinical reasoning varied considerably among participants despite being given the same information under the same circumstances. Furthermore, the number of years of experience did not seem to be directly linked to the ability to engage in sound clinical reasoning. Novice nurses, however, did rely heavily on others in their decision making in order to ensure they were making the right decision. Hence, their relationships with other staff members influenced their ability to engage in clinical reasoning and decision making. In situations where the patient's condition was deteriorating quickly, regardless of years of experience, all of the participants depended on their colleagues when making decisions and reasoning throughout the simulation. CONCLUSIONS: Deep clinical reasoning and decision making is a function of reflection and self-correction that requires a critical self-awareness and is more about how nurses think than what they think. The degree of sophistication in reasoning of experts and novices is at times equivalent in that the reasoning of experts and novices can be somewhat limited and focused primarily on human physicality and less on conceptual knowledge. To become proficient in clinical reasoning, practice is necessary. The study supports the accumulating evidence that using clinical simulation and reflective interviewing that emphasize how clinical decisions are made enhances reasoning skills and confidence.","corpus_id":44807253,"score":0},{"doc_id":"25547621","title":"Evaluating the guideline enhancement tool (GET): an innovative clinical training tool to enhance the use of hypertension guidelines in general practice.","abstract":"BACKGROUND: This project aims to evaluate the effectiveness of an innovative educational intervention in enhancing clinical decision making related to the management of hypertension in general practice. The relatively low level of uptake of clinical practice guidelines by clinicians is widely recognised as a problem that impacts on clinical outcomes. This project addresses this problem with a focus on hypertension guidelines. Hypertension is the most frequently managed problem in general practice but evidence suggests that management of Hypertension in general practice is sub-optimal. METHODS/DESIGN: This study will explore the effectiveness of an educational intervention named the 'Guideline Enhancement Tool (GET)'. The intervention is designed to guide clinicians through a systematic process of considering key decision points related to the management of hypertension and provides a mechanism for clinicians to engage with the hypertension clinical guidelines. The intervention will be administered within the Australian General Practice Training program, via one of the regional training providers. Two cohorts of trainees will participate as the intervention and delayed intervention groups. This process is expected to improve clinicians' engagement with the hypertension guidelines in particular, and enhance their clinical reasoning abilities in general. The effectiveness of the intervention in improving clinical reasoning will be evaluated using the 'Script Concordance Test'. DISCUSSION: The study design presented in this protocol aims to achieve two major outcomes. Firstly, the trial and evaluation of the educational intervention can lead to the development of a validated clinical education strategy that can be used in GP training to enhance the decision-making processes related to the management of hypertension. This has the potential to be adapted to other clinical conditions and training programs and can benefit clinicians in their clinical decision-making. Secondly, the study explores features that influence the effective use of clinical practice guidelines. The study thus addresses a significant problem in clinical education.","corpus_id":13089267,"score":0},{"doc_id":"25929534","title":"Direct and Indirect Benefits Reported by Users of Transcutaneous Electrical Nerve Stimulation for Chronic Musculoskeletal Pain: Qualitative Exploration Using Patient Interviews.","abstract":"BACKGROUND: There is no consensus regarding the effectiveness of transcutaneous electrical nerve stimulation (TENS) for management of chronic musculoskeletal pain or chronic low back pain. A recent review of previous trial methodology identified significant problems with low treatment fidelity. There is little information available to guide selection of patient-reported outcome measures appropriate for TENS evaluation. OBJECTIVES: The purpose of this study was to explore the experiences of patients at a secondary care pain clinic who successfully used TENS to help manage chronic musculoskeletal pain. These key informants were selected because they had the potential to generate knowledge that could inform research design and clinical practice. DESIGN: A qualitative method using individual semistructured interviews with open questions was selected for its capacity to generate rich data. METHODS: A mini focus group informed the development of a discussion guide for semistructured interviews with 9 patients (6 women, 3 men). Thematic analysis was used as the primary data analysis method, and this analysis was enhanced by a case-level analysis of the context and processes of TENS use of each individual. RESULTS: Data analysis indicated that distraction from pain and a reduction in the sensations associated with muscle tension or spasm should be considered as separate outcomes from pain relief. These direct benefits led to a wide range of indirect benefits dependent on patient decision making, including medication reduction, enhanced function, psychological benefits, and enhanced ability to rest. CONCLUSIONS: The findings indicate that evaluating TENS using a unidimensional pain scale is likely to overlook potential benefits. The complex pattern of TENS usage, as well as multiple direct and indirect outcomes, indicates that TENS could be considered as a complex intervention.","corpus_id":44602849,"score":0},{"doc_id":"25991108","title":"Use of eye-tracking technology in clinical reasoning: a systematic review.","abstract":"Achieving a better understanding of the clinical reasoning process is an important approach to improve patient management and patient safety. Although clinical psychologists have used talk-aloud or stimulated recall approaches, these methods have biases. Recently, researchers have been exploring eye-tracking technology to gain \"live\" insight into clinicians' reasoning processes in certain fields of medicine (radiology, dermatology, etc.). We present a systematic review of eye-tracking literature used for clinical reasoning. We performed a literature search using the terms \"eye\" or \"gaze tracking\", \"clinical\" or \"diagnostic reasoning\", and \"physician\" in Pubmed, Embase, Psychinfo, Web of Science and ACM databases. Two investigators screened the abstracts, then full-text articles to select 10 pertinent studies. The studies evaluated medical decision making in four different medical domains using mostly experimental, observational approaches. A total of 208 participants were enrolled for the selected experiments. Paths for further studies are discussed that may extend the use of eye trackers in order to improve understanding of medical decision making.","corpus_id":16300898,"score":0},{"doc_id":"26309382","title":"Imaging in conjunction with physical therapy in management of a patient with history of thoracic tumour.","abstract":"BACKGROUND: Physical therapy care for musculoskeletal conditions includes an ongoing process that systematically considers and prioritises diagnostic hypotheses. These diagnostic hypotheses include those that are typical for common musculoskeletal conditions, and must also include more rare conditions that would require care outside the scope of practice of the physical therapist. When additional screening is required, physical therapists collaborate with other providers or directly order the appropriate tests to rule out suspected pathology. CASE DESCRIPTION: This article illustrates the use of musculoskeletal imaging ordered by a physical therapist to guide ongoing management of a patient with back pain and a history of cancer. OUTCOMES: The patient successfully returned to moderate-intensity sport activities after a course of physical therapy. DISCUSSION: This case provides an example of how clinical diagnostic reasoning combined with clinical privileges to order musculoskeletal imaging can facilitate diagnostic accuracy in a timely and cost-efficient manner.","corpus_id":37436583,"score":0},{"doc_id":"26792832","title":"Predicting the onset of psychosis in patients at clinical high risk: practical guide to probabilistic prognostic reasoning.","abstract":"Prediction of psychosis in patients at clinical high risk (CHR) has become a mainstream focus of clinical and research interest worldwide. When using CHR instruments for clinical purposes, the predicted outcome is but only a probability; and, consequently, any therapeutic action following the assessment is based on probabilistic prognostic reasoning. Yet, probabilistic reasoning makes considerable demands on the clinicians. We provide here a scholarly practical guide summarising the key concepts to support clinicians with probabilistic prognostic reasoning in the CHR state. We review risk or cumulative incidence of psychosis in, person-time rate of psychosis, Kaplan-Meier estimates of psychosis risk, measures of prognostic accuracy, sensitivity and specificity in receiver operator characteristic curves, positive and negative predictive values, Bayes' theorem, likelihood ratios, potentials and limits of real-life applications of prognostic probabilistic reasoning in the CHR state. Understanding basic measures used for prognostic probabilistic reasoning is a prerequisite for successfully implementing the early detection and prevention of psychosis in clinical practice. Future refinement of these measures for CHR patients may actually influence risk management, especially as regards initiating or withholding treatment.","corpus_id":19758818,"score":0},{"doc_id":"28148616","title":"Beneficial Effects of Guided Imagery or Clinical Massage on the Status of Patients in a Progressive Care Unit.","abstract":"BACKGROUND: Patients in the progressive care unit typically experience high levels of pain and anxiety and exhibit difficulty sleeping. OBJECTIVE: To determine whether either clinical massage or guided imagery could reduce pain and anxiety and improve sleep. METHODS: This study included 288 inpatients on 2 floors of a progressive care unit. On 1 floor, each patient was offered daily a 15-minute complimentary clinical massage, whereas the patients on the other floor were provided access to a 30-minute guided-imagery recording. Patients were asked to rate their pain and anxiety levels immediately before and after the massage intervention or were asked whether the guided-imagery intervention was helpful for pain, anxiety, or insomnia. RESULTS: The massage intervention showed an immediate and significant reduction in self-reported pain and anxiety (P < .001); likewise, a significant number of patients self-reported that guided imagery helped alleviate pain, anxiety, and insomnia (P < .001). CONCLUSION: The results of this study indicate that clinical massage and guided imagery can benefit patients in the progressive care unit.","corpus_id":25225181,"score":0},{"doc_id":"29028765","title":"Preventing clinical progression and need for treatment in patients on active surveillance for prostate cancer.","abstract":"PURPOSE OF REVIEW: Active surveillance is an established treatment option for men with localized, low-risk prostate cancer (CaP). It entails the postponement of immediate therapy with the option of delayed intervention upon disease progression. The rate of clinical progression and need for treatment on active surveillance is approximately 50% over 15 years. The present review summarizes recent data on current methods, attempting to prevent clinical progression. RECENT FINDINGS: Patient selection for active surveillance is the first mandatory step required to lower progression. Adherence to active surveillance protocols is critical in making sure patients are monitored well and treated early when progression occurs. Before active surveillance allocation and during active surveillance follow-up, methods involving multiparametric MRI, prostate specific antigen derivatives, biopsy factors, urinary, tissue and genetic markers can be used to prevent clinical progression and/or identify those at risk for progression. Medications such as 5α-reductase inhibitors and others might inhibit disease progression in patients on active surveillance. SUMMARY: Active surveillance is required because of overdiagnosis, along with our inability to accurately predict individual CaP behavior. Several methods can potentially reduce the risk of CaP progression in patients with active surveillance. However, a measure of uncertainty and fear of progression will always accompany patients with active surveillance and the physicians treating them.","corpus_id":763507,"score":0},{"doc_id":"29433500","title":"Effects of local treatment with and without sensorimotor and balance exercise in individuals with neck pain: protocol for a randomized controlled trial.","abstract":"BACKGROUND: Impaired cervical joint position sense and balance are associated with neck pain. Specific therapeutic exercise and manual therapy are effective for improving neck pain and functional ability but their effects on joint position sense and balance impairments remain uncertain. Changes in the joint position sense and balance may need to be addressed specifically. The primary objective is to investigate the most effective interventions to improve impaired cervical joint position sense and balance in individuals with neck pain. The secondary objective is to assess the effectiveness of the interventions on pain intensity and disability, pain location, dizziness symptoms, cervical range of motion, gait speed, functional ability, treatment satisfaction and quality of life. METHODS: A 2 × 2 factorial, single blind RCT with immediate, short- and long-term follow-ups. One hundred and sixty eight participants with neck pain with impaired joint position sense and balance will be recruited into the trial. Participants will be randomly allocated to one of four intervention groups: i) local neck treatment, ii) local treatment plus tailored sensorimotor exercises, iii) local treatment plus balance exercises, and iv) local treatment plus sensorimotor and balance exercises. Participants receive two treatments for 6 weeks. Primary outcomes are postural sway and cervical joint position error. Secondary outcomes include gait speed, dizziness intensity, neck pain intensity, neck disability, pain extent and location, cervical range of motion, functional ability, perceived benefit, and quality of life. Assessment will be measured at baseline, immediately after treatment and at 3, 6, 12 month-follow ups. DISCUSSION: Neck pain is one of the major causes of disability. Effective treatment must address not only the symptoms but the dysfunctions associated with neck pain. This trial will evaluate the effectiveness of interventions for individuals with neck pain with impaired cervical joint position sense and balance. This trial will impact on clinical practice by providing evidence towards optimal and efficient management. TRIAL REGISTRATION: ClinicalTrials.gov ( NCT03149302 ). May 10, 2017.","corpus_id":3366991,"score":0},{"doc_id":"29535047","title":"Design and rational for the precision medicine guided treatment for cancer pain pragmatic clinical trial.","abstract":"INTRODUCTION: Pain is one of the most burdensome symptoms associated with cancer and its treatment, and opioids are the cornerstone of pain management. Opioid therapy is empirically selected, and patients often require adjustments in therapy to effectively alleviate pain or ameliorate adverse drug effects that interfere with quality of life. There are data suggesting CYP2D6 genotype may contribute to inter-patient variability in response to opioids through its effects on opioid metabolism. Therefore, we aim to determine if CYP2D6 genotype-guided opioid prescribing results in greater reductions in pain and symptom severity and interference with daily living compared to a conventional prescribing approach in patients with cancer. METHODS: Patients with solid tumors with metastasis and a self-reported pain score ≥ 4/10 are eligible for enrollment and randomized to a genotype-guided or conventional pain management strategy. For patients in the genotype-guided arm, CYP2D6 genotype information is integrated into opioid prescribing decisions. Patients are asked to complete questionnaires regarding their pain, symptoms, and quality of life at baseline and 2, 4, 6, and 8 weeks after enrollment. The primary endpoint is differential change in pain severity by treatment strategy (genotype-guided versus conventional pain management). Secondary endpoints include change in pain and symptom interference with daily living. CONCLUSION: Pharmacogenetic-guided opioid selection for cancer pain management has potential clinical utility, but current evidence is limited to retrospective and observational studies. Precision Medicine Guided Treatment for Cancer Pain is a pragmatic clinical trial that seeks to determine the utility of CYP2D6 genotype-guided opioid prescribing in patients with cancer.","corpus_id":4911724,"score":0}],"string":"[\n {\n \"doc_id\": \"18427230\",\n \"title\": \"Are we measuring what we need to measure?\",\n \"abstract\": \"Optimal treatment for patients with chronic pain remains elusive. A growing international consensus advocates evidence-based practice with assessment of clinical outcomes to improve the process and outcome of care. Clinical decision making about treatment options for an individual patient should include the patient's clinical presentation, available evidence, and patient preferences. Treatment should then be monitored and outcomes of treatment assessed. Although the placement of clinical decision making on a scientific, often quantitative basis as opposed to a subjective, impressionistic approach makes intuitive sense, the question is whether we have been measuring what we need to measure to practice evidence-based practice when we consider the current available evidence on pain management? The methods of synthesis of available evidence are still in development. Much of the evidence, although having internal validity, has limited external validity and is difficult to apply to the individual patient. Patients with chronic pain are a heterogeneous group, and different interventions may be indicated for different subgroups of patients. Various methods are being developed to better match patients with treatment. Little information exists on patient preferences, or how best to measure these. Information on how health care providers make clinical decisions is also scarce. Outcome measurement has come a long way and core domains to be measured have been established. Establishing normative data is a next main goal. Important methodologic and practical challenges remain to formulate evidence that can be applied to the individual patient with chronic pain.\",\n \"corpus_id\": 205454058,\n \"score\": 2\n },\n {\n \"doc_id\": \"19117231\",\n \"title\": \"Philosophy of science and physiotherapy: an insight into practice.\",\n \"abstract\": \"This article presents an overview of the philosophy of science and applies such philosophical theory to clinical practice within physiotherapy. A brief history of science is followed by the theories of the four most commonly acknowledged philosophers, introduced in the context of examples from clinical practice. By providing direct links to practical examples, it demonstrates the possibilities of relating the logical basis of this field of study to the clinical setting. The relevance to physiotherapy is that, by relating this theory, clinicians can better understand and analyse the fundamental logic behind their practice. The insight this provides can benefit professional development in several ways. For the clinician, it permits more comprehensive and coherent reasoning and helps to relate evidence with respect to individual patients. On a larger scale, it encourages reflective discussion between peers around the virtues of alternative treatment approaches. Thus, this topic has the potential to guide clinical practice toward being more scientific and may help raise the credibility of the profession as a whole.\",\n \"corpus_id\": 205654531,\n \"score\": 2\n },\n {\n \"doc_id\": \"23925525\",\n \"title\": \"Integrating patient-reported outcomes into orthopaedic clinical practice: proof of concept from FORCE-TJR.\",\n \"abstract\": \"BACKGROUND: Good orthopaedic care requires a knowledge of the patient's history of musculoskeletal pain and associated limitations in daily function. Standardized measures of patient-reported outcomes (PROs) can provide this information. Integrating PROs into routine orthopaedic patient visits can provide key information to monitor changes in symptom severity over time, support shared clinical care decisions, and assess treatment effectiveness for quality initiatives and value-based reimbursement. WHERE ARE WE NOW?: Although standardized, validated PRO surveys are routinely used in clinical and comparative effectiveness research, they are not consistently or efficiently collected in clinical practice. WHERE DO WE NEED TO GO?: Ideally, PROs need to be collected directly from patients before their surgeon visit so the data are readily available to the surgeon and patient at the time of the office visit. In addition, PROs should be integrated in the electronic health record to monitor patient status over time. HOW DO WE GET THERE?: PRO integration in clinical practice requires minor modifications to the office flow, some additional staff to facilitate collection, and the technical infrastructure to score, process, and store the responses. We document successful office procedures for collecting PROs in one busy orthopaedic clinic and some suggested methods to extend this model to the Function and Outcomes Research for Comparative Effectiveness in Total Joint Replacement (FORCE-TJR) consortium of 121 surgeons where the process is centralized and staff obtained consent to send the PRO directly to the patient's home. Both methods are options for the broader adoption of office-based PROs.\",\n \"corpus_id\": 42267876,\n \"score\": 2\n },\n {\n \"doc_id\": \"24372846\",\n \"title\": \"Learning clinical reasoning.\",\n \"abstract\": \"Errors in clinical reasoning continue to account for significant morbidity and mortality, despite evidence-based guidelines and improved technology. Experts in clinical reasoning often use unconscious cognitive processes that they are not aware of unless they explain how they are thinking. Understanding the intuitive and analytical thinking processes provides a guide for instruction. How knowledge is stored is critical to expertise in clinical reasoning. Curricula should be designed so that trainees store knowledge in a way that is clinically relevant. Competence in clinical reasoning is acquired by supervised practice with effective feedback. Clinicians must recognise the common errors in clinical reasoning and how to avoid them. Trainees can learn clinical reasoning effectively in everyday practice if teachers provide guidance on the cognitive processes involved in making diagnostic decisions.\",\n \"corpus_id\": 37979636,\n \"score\": 2\n },\n {\n \"doc_id\": \"26486941\",\n \"title\": \"A Bayesian perspective on constructing a written assessment of probabilistic clinical reasoning in experienced clinicians.\",\n \"abstract\": \"RATIONALE: Decision-making performance assessments have proven problematic for assessing clinical reasoning. AIMS AND OBJECTIVES: A Bayesian approach to designing an advanced clinical reasoning assessment is well grounded in mathematical and cognitive theory and may offer significant psychometric advantages. Probabilistic logic plays an important role in medical problem solving, and performances on Bayesian-type tasks appear to be causally-related to the ability to make sound clinical decisions. METHODS: A validity argument is used to guide the design of an assessment of medical reasoning using clinical probabilities. RESULTS/CONCLUSIONS: The practical advantage of using a Bayesian approach to item design relates to the fact that probability theory provides a rationally optimal method for managing uncertain information and provides the criteria for objective correct answer scoring. Potential item formats are discussed.\",\n \"corpus_id\": 24403018,\n \"score\": 2\n },\n {\n \"doc_id\": \"26988928\",\n \"title\": \"Identification of predicted individual treatment effects in randomized clinical trials.\",\n \"abstract\": \"In most medical research, treatment effectiveness is assessed using the average treatment effect or some version of subgroup analysis. The practice of individualized or precision medicine, however, requires new approaches that predict how an individual will respond to treatment, rather than relying on aggregate measures of effect. In this study, we present a conceptual framework for estimating individual treatment effects, referred to as predicted individual treatment effects. We first apply the predicted individual treatment effect approach to a randomized controlled trial designed to improve behavioral and physical symptoms. Despite trivial average effects of the intervention, we show substantial heterogeneity in predicted individual treatment response using the predicted individual treatment effect approach. The predicted individual treatment effects can be used to predict individuals for whom the intervention may be most effective (or harmful). Next, we conduct a Monte Carlo simulation study to evaluate the accuracy of predicted individual treatment effects. We compare the performance of two methods used to obtain predictions: multiple imputation and non-parametric random decision trees. Results showed that, on average, both predictive methods produced accurate estimates at the individual level; however, the random decision trees tended to underestimate the predicted individual treatment effect for people at the extreme and showed more variability in predictions across repetitions compared to the imputation approach. Limitations and future directions are discussed.\",\n \"corpus_id\": 4781711,\n \"score\": 2\n },\n {\n \"doc_id\": \"29708632\",\n \"title\": \"A concise guide to clinical reasoning.\",\n \"abstract\": \"What constitutes clinical reasoning is a disputed subject regarding the processes underlying accurate diagnosis, the importance of patient-specific versus population-based data, and the relation between virtue and expertise in clinical practice. In this paper, I present a model of clinical reasoning that identifies and integrates the processes of diagnosis, prognosis, and therapeutic decision making. The model is based on the generalized empirical method of Bernard Lonergan, which approaches inquiry with equal attention to the subject who investigates and the object under investigation. After identifying the structured operations of knowing and doing and relating these to a self-correcting cycle of learning, I correlate levels of inquiry regarding what-is-going-on and what-to-do to the practical and theoretical elements of clinical reasoning. I conclude that this model provides a methodical way to study questions regarding the operations of clinical reasoning as well as what constitute significant clinical data, clinical expertise, and virtuous health care practice.\",\n \"corpus_id\": 14034747,\n \"score\": 2\n },\n {\n \"doc_id\": \"18519094\",\n \"title\": \"How to manage musculoskeletal conditions.\",\n \"abstract\": \"Musculoskeletal conditions are becoming more prevalent in the aging and increasingly overweight Western population. Many such conditions are chronic, and most people concerned have problems with more than one anatomical joint region, resulting in cumulatively increased problems with performing daily tasks. Management is complex because of the chronic nature of many of these conditions, the need for regular assessment of disease impact, the individual's responses to the disease and its treatment, the presence of co-morbidities, and the lack of well-designed studies of long-term outcome to guide treatment. There are significant issues about how to monitor outcomes in routine practice, and many outcome measures have been developed for use in clinical trials. Principles of modern management include involvement of people in their own care, early intervention, and the need to consider a multidisciplinary approach. Most conditions will require combinations of one or more non-pharmacological therapies (especially muscle strengthening and aerobic exercise) and pharmacological agents, with attention given to appropriate timing of surgical interventions.\",\n \"corpus_id\": 42708604,\n \"score\": 1\n },\n {\n \"doc_id\": \"18569855\",\n \"title\": \"Clinical reasoning and population health: decision making for an emerging paradigm of health care.\",\n \"abstract\": \"Chronic conditions now provide the major disease and disability burden facing humanity. This development has necessitated a reorientation in the practice skills of health care professions away from hospital-based inpatient and outpatient care toward community-based management of patients with chronic conditions. Part of this reorientation toward community-based management of chronic conditions involves practitioners' understanding and adoption of a concept of population health management based on appropriate theoretical models of health care. Drawing on recent studies of expertise in physiotherapy, this article proposes a clinical reasoning and decision-making framework to meet these challenges. The challenge of population and community-based management of chronic conditions also provides an opportunity for physiotherapists to further clarify a professional epistemology of practice that embraces the kinds of knowledge and clinical reasoning processes used in physiotherapy practice. Three case studies related to the management of chronic musculoskeletal pain in different populations are used to exemplify the range of epistemological perspectives that underpin community-based practice. They illustrate the link between conceptualizations of practice problems and knowledge sources that are used as a basis for clinical reasoning and decision making as practitioners are increasingly required to move between the clinic and the community.\",\n \"corpus_id\": 24249615,\n \"score\": 1\n },\n {\n \"doc_id\": \"18638679\",\n \"title\": \"The assessment of musculoskeletal pain in the clinical setting.\",\n \"abstract\": \"Pain is a primary symptom in musculoskeletal conditions, and aspects of the pain experience (eg, severity) are key considerations in clinical decision-making and in the outcome of trials and interventions. Consequently, appropriate assessment of pain is essential. This article reviews the measures most commonly used in rheumatology practice, arguing that many are significantly limited in their ability to reflect the complexity of the patient's experience. The authors provide examples of alternative approaches, concluding that there is real scope for improving assessment and measurement of musculoskeletal pain in the clinical setting.\",\n \"corpus_id\": 13535690,\n \"score\": 1\n },\n {\n \"doc_id\": \"19202161\",\n \"title\": \"Chronic musculoskeletal pain in children: assessment and management.\",\n \"abstract\": \"Paediatricians and paediatric rheumatologists review a large number of children with ongoing pain (disease and non-disease related). A small number of these develop chronic pain conditions that are complex and distressing. Over recent years studies of the epidemiology, aetiology and rehabilitation of pain and pain-associated disability in children have revealed a large prevalence of clinically relevant pain, and have emphasized the need for early recognition and intervention. Medication has a role when part of a multidisciplinary framework, although there is little evidence for or against the effectiveness of most pharmacotherapy. There is strong evidence to support early targeted psychological and physical intervention, and an understanding that parental education and involvement is essential if progress is to be maintained. In this review, an overview of the assessment is presented and management of childhood chronic musculoskeletal pain conditions with reference to main research findings to date.\",\n \"corpus_id\": 17934101,\n \"score\": 1\n },\n {\n \"doc_id\": \"19232911\",\n \"title\": \"An introduction to evidence-based practice for hand surgeons and therapists.\",\n \"abstract\": \"Evidence-based practice is a methodical approach to clinical practice where experience, best research evidence, and patient goals and values are integrated to make optimal decisions when making a diagnosis, selecting a diagnostic test, picking an intervention or determining prognosis. There are five steps in this process. Hand surgeons and therapists can use the evidence-based process to attain optimal management of individual patients, manage their overall practice, guide the ongoing professional development, and deal with funding and policy makers.\",\n \"corpus_id\": 11173059,\n \"score\": 1\n },\n {\n \"doc_id\": \"19411769\",\n \"title\": \"Sensorimotor function and dizziness in neck pain: implications for assessment and management.\",\n \"abstract\": \"SYNOPSIS: The term sensorimotor describes all the afferent, efferent, and central integration and processing components involved in maintaining stability in the postural control system through intrinsic motor-control properties. The scope of this paper is to highlight the sensorimotor deficits that can arise from altered cervical afferent input. From a clinical orthopaedic perspective, the peripheral mechanoreceptors are the most important in functional joint stability; but in the cervical region they are also important for postural stability, as well as head and eye movement control. Consequently, conventional musculoskeletal intervention approaches may be sufficient only for patients with neck pain and minimal sensorimotor proprioceptive disturbances. Clinical experience and research indicates that significant sensorimotor cervical proprioceptive disturbances might be an important factor in the maintenance, recurrence, or progression of various symptoms in some patients with neck pain. In these cases, more specific and novel treatment methods are needed which progressively address neck position and movement sense, as well as cervicogenic oculomotor disturbances, postural stability, and cervicogenic dizziness. In this commentary we review the most relevant theoretical and practical knowledge on this matter and implications for clinical assessment and management, and we propose future directions for research. LEVEL OF EVIDENCE: Level 5.\",\n \"corpus_id\": 36677967,\n \"score\": 1\n },\n {\n \"doc_id\": \"19583554\",\n \"title\": \"Evidence-based medicine and the Cochrane Collaboration.\",\n \"abstract\": \"Providing evidence-based care to patients involves turning a clinical problem into an answerable question, systematically searching for the best evidence relevant to the question, critically appraising that evidence, and, finally, using the evidence as the basis for clinical decisions to solve the problem. While the overload of medical information today presents a demanding challenge to physicians to sort and identify relevant and valid evidence, it is vitally important to translate that evidence into clinically useful terms. To apply evidence to patient clinical management, it is critical to discuss with patients the evidence, the benefits and the harms, and the alternative treatments, such that they understand and can fully participate in the decision-making process. The framework of evidenced-based medicine provides a concrete methodology to address these issues, here, framed and detailed in five steps. The Cochrane Collaboration has been at the forefront of applying the methods of evidence-based medicine (EBM) in the treatment and management of musculoskeletal and other disorders.\",\n \"corpus_id\": 38090726,\n \"score\": 1\n },\n {\n \"doc_id\": \"19583560\",\n \"title\": \"Monitoring response to therapy in rheumatoid arthritis - perspectives from the clinic.\",\n \"abstract\": \"The major objectives in treating patients with rheumatoid arthritis are managing the symptoms of disease and preserving joint structure, with the ultimate goal of disease remission. Several independent studies have shown that treatment decisions driven by quantitative rather than subjective monitoring of disease activity result in significantly improved patient outcomes. Various assessment tools are available that measure both clinical and patient-reported outcomes. While some measurement tools may be more appropriate for use in clinical trials, several have been developed that are simple and practical to use, even in a busy clinic. As pivotal members of the multidisciplinary rheumatology healthcare provider team, the nurse and the rheumatologist play key roles in managing a patient's progress by closely monitoring their response to treatment. Here, we discuss optimal disease management founded on a multidisciplinary approach and provide an overview of some key measures for assessing patient response to treatment.\",\n \"corpus_id\": 23734693,\n \"score\": 1\n },\n {\n \"doc_id\": \"19638766\",\n \"title\": \"A universal model of diagnostic reasoning.\",\n \"abstract\": \"Clinical judgment is a critical aspect of physician performance in medicine. It is essential in the formulation of a diagnosis and key to the effective and safe management of patients. Yet, the overall diagnostic error rate remains unacceptably high. In more than four decades of research, a variety of approaches have been taken, but a consensus approach toward diagnostic decision making has not emerged. In the last 20 years, important gains have been made in psychological research on human judgment. Dual-process theory has emerged as the predominant approach, positing two systems of decision making, System 1 (heuristic, intuitive) and System 2 (systematic, analytical). The author proposes a schematic model that uses the theory to develop a universal approach toward clinical decision making. Properties of the model explain many of the observed characteristics of physicians' performance. Yet the author cautions that not all medical reasoning and decision making falls neatly into one or the other of the model's systems, even though they provide a basic framework incorporating the recognized diverse approaches. He also emphasizes the complexity of decision making in actual clinical situations and the urgent need for more research to help clinicians gain additional insight and understanding regarding their decision making.\",\n \"corpus_id\": 8805552,\n \"score\": 1\n },\n {\n \"doc_id\": \"19643835\",\n \"title\": \"Strategies to promote evidence-based practice in pediatric physical therapy: a formative evaluation pilot project.\",\n \"abstract\": \"BACKGROUND: The physical therapy profession has been perceived as one that bases its practice largely on anecdotal evidence and that uses treatment techniques for which there is little scientific support. Physical therapists have been urged to increase evidence-based practice behaviors as a means to address this perception and to enhance the translation of knowledge from research evidence into clinical practice. However, little attention has been paid to the best ways in which to support clinicians' efforts toward improving evidence-based practice. OBJECTIVES: The purpose of this study was to identify, implement, and evaluate the effectiveness of strategies aimed at enhancing the ability of 5 pediatric physical therapists to integrate scientific research evidence into clinical decision making. DESIGN: This study was a formative evaluation pilot project. METHODS: The participants in this study collaborated with the first author to identify and implement strategies and outcomes aimed at enhancing their ability to use research evidence during clinical decision making. Outcome data were analyzed with qualitative methods. RESULTS: The participants were able to implement several, but not all, of the strategies and made modest self-reported improvements in evidence-based practice behaviors, such as reading journal articles and completing database searches. They identified several barriers, including a lack of time, other influences on clinical decision making, and a lack of incentives for evidence-based practice activities. CONCLUSIONS: The pediatric physical therapists who took part in this project had positive attitudes toward evidence-based practice and made modest improvements in this area. It is critical for the profession to continue to investigate optimal strategies to aid practicing clinicians in applying research evidence to clinical decision making.\",\n \"corpus_id\": 9327241,\n \"score\": 1\n },\n {\n \"doc_id\": \"19668280\",\n \"title\": \"An introduction to an evidence-based approach to interventional techniques in the management of chronic spinal pain.\",\n \"abstract\": \"Practice guidelines are systematically developed statements to assist practitioners and patients in making decisions about appropriate health care for specific clinical circumstances. Clinical practice guidelines present statements of best practice based on a thorough evaluation of the evidence from published studies on the outcomes of treatment. In November 1989, Congress mandated the creation of the Agency for Healthcare Policy and Research (AHCPR). AHCPR was given broad responsibility for supporting research, data development, and related activities. Associated with this mandate, the National Academy of Sciences published a document indicating that guidelines are expected to enhance the quality, appropriateness, and effectiveness of health care services. Guidelines as a whole have been characterized by multiple conflicts in terminology and technique. These conflicts are notable for the confusion they create and for what they reflect about differences in values, experiences, and interest among different parties. Despite this confusion, public and private development of guidelines is growing exponentially. There are only limited means to coordinate these guidelines in order to resolve inconsistencies, fill in gaps, track applications and results, and assess the soundness of individual guidelines. Significant diversity exists in clinical practice guidelines. The inconsistency amongst guidelines arises from variations in values, tolerance for risks, preferences, expertise, and conflicts of interest. In 2000, the American Society of Interventional Pain Physicians (ASIPP) first created treatment guidelines to help practitioners. There have been 4 subsequent updates. These guidelines address the issues of systematic evaluation and ongoing care of chronic or persistent pain, and provide information about the scientific basis of recommended procedures. These guidelines are expected to increase patient compliance, dispel misconceptions among providers and patients, manage patient expectations reasonably, and form the basis of a therapeutic partnership between the patient, the provider, and payors. The ASIPP guidelines are based on evidence-based medicine (EBM). EBM is in turn based on 4 basic contingencies: the recognition of the patient's problem and the construction of a structured clinical question; the ability to efficiently and effectively search the medical literature to retrieve the best available evidence to answer the clinical question; clinical appraisal of the evidence; and integration of the evidence with all aspects of the individual patient's decision-making to determine the best clinical care of the patient. Evidence synthesis for guidelines includes the review of all relevant systematic reviews and individual articles, grading them for relevance, methodologic quality, consistency, and recommendations.\",\n \"corpus_id\": 39722772,\n \"score\": 1\n },\n {\n \"doc_id\": \"19669915\",\n \"title\": \"Reducing diagnostic error with computer-based clinical decision support.\",\n \"abstract\": \"Information technology approaches to delivering diagnostic clinical decision support (CDS) are the subject of the papers to follow in the proceedings. These will address the history of CDS and present day approaches (Miller), evaluation of diagnostic CDS methods (Friedman), and the role of clinical documentation in supporting diagnostic decision making (Schiff). In addition, several other considerations relating to this topic are interesting to ponder. We are moving toward increased understanding of gene regulation and gene expression, identification of biomarkers, and the ability to predict patient response to disease and to tailor treatments to these individual variations-referred to as \\\"personalized\\\" or, more recently, \\\"predictive\\\" medicine. Consequently, diagnostic decision making is more and more linked to management decision making, and generic diagnostic labels like \\\"diabetes\\\" or \\\"colon cancer\\\" will no longer be sufficient, because they don't tell us what to do. Ultimately, if we have more complete data including more structured capture of phenomic data as well as the characterization of the patient's genome, direct prediction from responses of highly refined subsets of similar patients in a database can be used to select appropriate management, the effectiveness of which was demonstrated in projects in selected limited domains as early as the 1970s. In general, there are six classes of methodologies, including the above, which can be applied to delivering CDS. In addition, patients are becoming more knowledgeable and should be regarded as active participants, not only in helping to obtain data but also in their own status assessment and as recipients of decision support. With the above advances, this is a very promising time to be engaged in pursuit of methods of CDS.\",\n \"corpus_id\": 43063083,\n \"score\": 1\n },\n {\n \"doc_id\": \"19753425\",\n \"title\": \"Factors that influence the clinical decision-making of rehabilitation professionals in long-term care settings.\",\n \"abstract\": \"The purpose of this qualitative research was to evaluate the reasoning of clinicians practicing in long-term care facilities and to explore factors influencing their professional development. Eighteen participants were recruited from eight clinical sites and included seven occupational therapists, eight physical therapists, and three speech therapists distributed across three groups relative to experience. Nonparticipant observation and videotape of therapist-patient interactions were used in semi-structured interviews with each participant. Qualitative data analysis software was used during a process of open and axial coding, followed by thematic analysis. The facilitory and inhibitory factors that affect clinical reasoning and professional development were identified. Rehabilitation professionals in long-term care demonstrated clinical reasoning within the context of patient-centered goals. Well-developed and explicit programs for mentorship, professional development, and continuing education fostered their clinical reasoning abilities. Participants perceived that these factors were vital to achieving optimal patient outcomes.\",\n \"corpus_id\": 32655820,\n \"score\": 1\n },\n {\n \"doc_id\": \"19787009\",\n \"title\": \"Evidence-based medicine, systematic reviews, and guidelines in interventional pain management: part 6. Systematic reviews and meta-analyses of observational studies.\",\n \"abstract\": \"Observational studies provide an important source of information when randomized controlled trials (RCTs) cannot or should not be undertaken, provided that the data are analyzed and interpreted with special attention to bias. Evidence-based medicine (EBM) stresses the examination of evidence from clinical research and describes it as a shift in medical paradigm, in contrast to intuition, unsystematic clinical experience, and pathophysiologic rationale. While the importance of randomized trials has been created by the concept of the hierarchy of evidence in guiding therapy, much of the medical research is observational. The reporting of observational research is often not detailed and clear enough with insufficient quality and poor reporting, which hampers the assessment of strengths and weaknesses of the study and the generalizability of the mixed results. Thus, in recent years, progress and innovations in health care are measured by systematic reviews and meta-analyses. A systematic review is defined as, \\\"the application of scientific strategies that limit bias by the systematic assembly, clinical appraisal, and synthesis of all relevant studies on a specific topic.\\\" Meta-analysis usually is the final step in a systematic review. Systematic reviews and meta-analyses are labor intensive, requiring expertise in both the subject matter and review methodology, and also must follow the rules of EBM which suggests that a formal set of rules must complement medical training and common sense for clinicians to integrate the results of clinical research effectively. While expertise in the review methods is important, the expertise in the subject matter and technical components is also crucial. Even though, systematic reviews and meta-analyses, specifically of RCTs, have exploded, the quality of the systematic reviews is highly variable and consequently, the opinions reached of the same studies are quite divergent. Numerous deficiencies have been described in methodologic assessment of the quality of the individual articles. Consequently, observational studies can provide an important complementary source of information, provided that the data are analyzed and interpreted in the context of confounding bias to which they are prone. Appropriate systematic reviews of observational studies, in conjunction with RCTs, may provide the basis for elimination of a dangerous discrepancy between the experts and the evidence. Steps in conducting systematic reviews of observational studies include planning, conducting, reporting, and disseminating the results. MOOSE, or Meta-analysis of Observational Studies in Epidemiology, a proposal for reporting contains specifications including background, search strategy, methods, results, discussion, and conclusion. Use of the MOOSE checklist should improve the usefulness of meta-analysis for authors, reviewers, editors, readers, and decision-makers. This manuscript describes systematic reviews and meta-analyses of observational studies. Authors frequently utilize RCTs and observational studies in one systematic review; thus, they should also follow the reporting standards of the Quality of Reporting of Meta-analysis (QUOROM) statement, which also provides a checklist. A combined approach of QUOROM and MOOSE will improve reporting of systematic reviews and lead to progress and innovations in health care.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"20205815\",\n \"title\": \"How to integrate individual patient values and preferences in clinical practice guidelines? A research protocol.\",\n \"abstract\": \"BACKGROUND: Clinical practice guidelines are largely conceived as tools that will inform health professionals' decisions rather than foster patient involvement in decision making. The time now seems right to adapt clinical practice guidelines in such a way that both the professional's perspective as care provider and the patients' preferences and characteristics are being weighed equally in the decision-making process. We hypothesise that clinical practice guidelines can be adapted to facilitate the integration of individual patients' preferences in clinical decision making. This research protocol asks two questions: How should clinical practice guidelines be adapted to elicit patient preferences and to support shared decision making? What type of clinical decisions are perceived as most requiring consideration of individual patients' preferences rather than promoting a single best choice? METHODS: Stakeholders' opinions and ideas will be explored through an 18-month qualitative study. Data will be collected from in-depth individual interviews. A purposive sample of 20 to 25 key-informants will be selected among three groups of stakeholders: health professionals using guidelines (e.g., physicians, nurses); experts at the macro- and meso-level, including guideline and decision aids developers, policy makers, and researchers; and patient representatives. Ideas and recommendations expressed by stakeholders will be prioritized by nominal group technique in expert meetings. DISCUSSION: One-for-all guidelines do not account for differences in patients' characteristics and for their preferences for medical interventions and health outcomes, suggesting a need for flexible guidelines that facilitate patient involvement in clinical decision making. The question is how this can be achieved. This study is not about patient participation in guideline development, a closely related and important issue that does not however substitute for, or guarantee individual patient involvement in clinical decisions. The study results will provide the needed background for recommendations about potential effective and feasible strategies to ensure greater responsiveness of clinical practice guidelines to individual patient's preferences in clinical decision-making.\",\n \"corpus_id\": 449228,\n \"score\": 1\n },\n {\n \"doc_id\": \"21817012\",\n \"title\": \"Building the rationale and structure for a complex physical therapy intervention within the context of a clinical trial: a multimodal individualized treatment for patients with hip osteoarthritis.\",\n \"abstract\": \"Evaluating the efficacy of complex interventions such as multimodal, impairment-based physical therapy treatments in randomized controlled trials is essential to inform practice and compare relative benefits of available treatment options. Studies of physical therapy interventions using highly standardized intervention protocols, although methodologically rigorous, do not necessarily reflect \\\"real-world\\\" clinical practice, and in many cases results have been disappointing. Development of a complex intervention that includes multiple treatment modalities and individualized treatment technique selection requires a systematic approach to designing all aspects of the intervention based on theory, evidence, and practical constraints. This perspective article outlines the development of the rationale and structure of a multimodal physical therapy program for painful hip osteoarthritis to be assessed in a clinical trial. The resulting intervention protocol comprises a semi-structured program of exercises and manual therapy, advice, physical activity, and optional prescription of a gait aid that is standardized, yet can be individualized according to physical assessment and radiographic findings. The program is evidence based and reflects contemporary physical therapist practice, while also being reproducible and reportable. This perspective article aims to encourage physical therapy researchers involved in evaluation of complex interventions to better document their own intervention development, as well as the outcomes, thus generating a body of knowledge about the development processes and protocols that is generalizable to the real-world complexity of providing physical therapy to individual patients.\",\n \"corpus_id\": 25128343,\n \"score\": 1\n },\n {\n \"doc_id\": \"25716151\",\n \"title\": \"The 'Best Practice Guide to Conservative Management of Patellofemoral Pain': incorporating level 1 evidence with expert clinical reasoning.\",\n \"abstract\": \"IMPORTANCE: Patellofemoral pain (PFP) is both chronic and prevalent; it has complex aetiology and many conservative treatment options. OBJECTIVE: Develop a comprehensive contemporary guide to conservative management of PFP outlining key considerations for clinicians to follow. DESIGN: Mixed methods. METHODS: We synthesised the findings from six high-quality systematic reviews to September 2013 with the opinions of 17 experts obtained via semistructured interviews. Experts had at least 5 years clinical experience with PFP as a specialist focus, were actively involved in PFP research and contributed to specialist international meetings. The interviews covered clinical reasoning, perception of current evidence and research priorities. RESULTS: Multimodal intervention including exercise to strengthen the gluteal and quadriceps musculature, manual therapy and taping possessed the strongest evidence. Evidence also supports use of foot orthoses and acupuncture. Interview transcript analysis identified 23 themes and 58 subthemes. Four key over-arching principles to ensure effective management included-(1) PFP is a multifactorial condition requiring an individually tailored multimodal approach. ( 2) Immediate pain relief should be a priority to gain patient trust. ( 3) Patient empowerment by emphasising active over passive interventions is important. ( 4) Good patient education and activity modification is essential. Future research priorities include identifying risk factors, testing effective prevention, developing education strategies, evaluating the influence of psychosocial factors on treatment outcomes and how to address them, evaluating the efficacy of movement pattern retraining and improving clinicians' assessment skills to facilitate optimal individual prescription. CONCLUSIONS AND RELEVANCE: Effective management of PFP requires consideration of a number of proven conservative interventions. An individually tailored multimodal intervention programme including gluteal and quadriceps strengthening, patellar taping and an emphasis on education and activity modification should be prescribed for patients with PFP. We provide a 'Best Practice Guide to Conservative Management of Patellofemoral Pain' outlining key considerations.\",\n \"corpus_id\": 24463210,\n \"score\": 1\n },\n {\n \"doc_id\": \"26482401\",\n \"title\": \"Assessing progression of clinical reasoning through virtual patients: An exploratory study.\",\n \"abstract\": \"To avoid test-driven learning, there have been discussions regarding the use of more formative assessments in health care education to promote students' deep learning. Feedback is important in formative assessment, but many students ignore it; therefore, interventions should be introduced which stimulate them to reflect on the new knowledge. The aim for this study was to explore if Virtual Patient (VP)-based formative assessments, in connection with self-evaluations, had an impact on postgraduate pediatric nursing students' development of clinical reasoning abilities. Students' self-evaluations served as the basis for measuring progress. Data was analysed using deductive content analysis. The findings showed a clear progression of the clinical reasoning ability of the students. After the first assessment, the students described feelings of uncertainty and that their knowledge gaps were exposed. At the mid-course assessment the awareness of improved clinical reasoning was obvious and the students were more certain of knowing how to solve the VP cases. In the final assessment, self-efficacy was expressed. VP-based assessments, in connection with self-evaluations, early in the education resulted in a gain of students' own identification of the concept of clinical reasoning, awareness of what to focus on during clinical practice and visualised expected clinical competence.\",\n \"corpus_id\": 9335460,\n \"score\": 1\n },\n {\n \"doc_id\": \"27815820\",\n \"title\": \"The impact of patient-reported outcome measures in clinical practice for pain: a systematic review.\",\n \"abstract\": \"PURPOSE: Patient-reported outcome measures (PROMs) have increasingly been incorporated into clinical practice. Research suggests that PROMs could be viewed as active components of complex interventions and may affect the process and outcome of care. This systematic review examines PROMs in the context of treatment for non-malignant pain. METHODS: An electronic search on: MEDLINE, EMBASE, PsycINFO, PsycARTICLES, Cochrane Library and Web of Science identified relevant papers (February 2015). The inclusion criteria were: focused on implementing PROMs into clinical practice, adults, and primary data studies. Critical interpretive synthesis was used to synthesise qualitative and quantitative findings into a theoretical argument. RESULTS: Thirteen eligible studies were identified. Synthesis suggested that PROMs may be included in the initial consultation to assess patients and for shared decision-making regarding patient care. During the course of treatment, PROMs can be used to track progress, evaluate treatment, and change the course of care; using PROMs may also influence the therapeutic relationship. Post-treatment, using PROMs might directly influence other outcomes such as pain and patient satisfaction. However, although studies have investigated these areas, evidence is weak and inconclusive. CONCLUSION: Due to the poor quality, lack of generalisability and heterogeneity of these studies, it is not possible to provide a comprehensive understanding of how PROMs may impact clinical treatment of non-malignant pain. The literature suggests that PROMs enable pain assessment, decision-making, the therapeutic relationship, evaluation of treatment and may influence outcomes. Further research is needed to provide better evidence as to whether PROMs do indeed have any effects on these domains.\",\n \"corpus_id\": 7126091,\n \"score\": 1\n },\n {\n \"doc_id\": \"28694677\",\n \"title\": \"Does shared decision making results in better health related outcomes for individuals with painful musculoskeletal disorders? A systematic review.\",\n \"abstract\": \"Background: Shared Decision-Making (SDM) is a dynamic process by which the health care professional and the patient influence each other in making health-related choices or decisions. SDM is strongly embedded in today's health care approaches, and is advocated as an ideal model since it renders individuals more control towards the health care they choose to receive, and has been shown to improve patient outcomes. Objectives: The goal of this systematic review was to investigate the added-value of SDM on clinical health-related outcomes in patients with a variety of musculoskeletal conditions. Data sources: PubMed and CINAHL. Study selection: PRISMA guidelines were followed for this review. To be considered for review, the study had to meet all the following criteria: (1) prospective studies that involved treatment decision-making; (2) randomized controlled trial design; (3) involving patients faced with having to make a treatment decision; (4) comparing SDM with a control intervention and (5) including one or more of the following outcome measures: well-being, costs, health-related pain or disability measures, or quality of life. Study appraisal: A priori, we determined to perform methodological quality assessment using the Cochrane Risk of Bias tool for randomized controlled trials. Results: We did not find a single study that looked at the true effect of SDM on patient reported outcomes in a population with musculoskeletal pain. Conclusion: For the management of painful musculoskeletal conditions, in the light of the current evidence (none), we estimate that it would be wise to explore the effectiveness of SDM before forcing its large-scale implementation in rehabilitation.\",\n \"corpus_id\": 33055615,\n \"score\": 1\n },\n {\n \"doc_id\": \"29259567\",\n \"title\": \"Using Functional Analysis as a Framework to Guide Individualized Treatment for Negative Symptoms.\",\n \"abstract\": \"Although numerous interventions are available for negative symptoms, outcomes have been unsatisfactory with pharmacological and psychological interventions producing changes of only limited clinical significance. Here, we argue that because negative symptoms occur as a complex syndrome caused and maintained by numerous factors that vary between individuals they are unlikely to be treated effectively by the present \\\"one size fits all\\\" approaches. Instead, a well-founded selection of those interventions relevant to each individual is needed to optimize both the efficiency and the efficacy of existing approaches. The concept of functional analysis (FA) can be used to structure existing knowledge so that it can guide individualized treatment planning. FA is based on stimulus-response learning mechanisms taking into account the characteristics of the organism that contribute to the responses, their consequences and the contingency with which consequences are tied to the response. FA can thus be flexibly applied to the level of individual patients to understand the factors causing and maintaining negative symptoms and derive suitable interventions. In this article we will briefly introduce the concept of FA and demonstrate-exemplarily-how known psychological and biological correlates of negative symptoms can be incorporated into its framework. We then outline the framework's implications for individual assessment and treatment. Following the logic of FA, we argue that a detailed assessment is needed to identify the key factors causing or maintaining negative symptoms for each individual patient. Interventions can then be selected according to their likelihood of changing these key factors and need to take interactions between different factors into account. Supplementary case vignettes exemplify the usefulness of functional analysis for individual treatment planning. Finally, we discuss and point to avenues for future research guided by this model.\",\n \"corpus_id\": 25979763,\n \"score\": 1\n },\n {\n \"doc_id\": \"29473563\",\n \"title\": \"Are randomized, blind clinical trials enough to guide individualized decisions for patients with neurologic diseases?\",\n \"abstract\": \"The practice of medicine relies on the patient-physician relationship, knowledge, and clinical judgment. Randomized controlled trials (RCTs) remain the least biased method for studying the effects of interventions in selected populations and are the only method to control adequately for unknown confounders. However, physicians face the limitations of RCTs on a daily basis as they treat relatively unselected populations and individual patients. We explore the benefits and limitations of RCTs for some neurologic disorders, and discuss the difficulties of predicting individualized outcomes and anticipating treatment responses in those heterogeneous conditions. Observational studies and advances in understanding neurologic diseases complement RCTs in decision-making. Considerable challenges remain for personalized medicine; for now, clinicians must rely on their ability to integrate evidence and clinical judgment.\",\n \"corpus_id\": 3680642,\n \"score\": 1\n },\n {\n \"doc_id\": \"29564549\",\n \"title\": \"Call for action: how to improve use of patient-reported outcomes to guide clinical decision making in rheumatoid arthritis.\",\n \"abstract\": \"Current guidelines for the management of rheumatoid arthritis (RA) recommend early treatment and a treat-to-target goal of remission or low disease activity. Over the past decade, this approach has been extremely successful in reducing disease activity and joint damage in patients with RA. At the same time, however, overall patient perception of well-being appears to have decreased with respect to outcome measures considered important by patients themselves, such as pain, fatigue, physical function and quality of life. The timely and effective use of patient-reported outcomes (PROs) could encourage physicians to focus more on the impact of RA on patients and how patients are feeling. This in turn would facilitate shared decision making between patients and physicians, ultimately leading to a more patient-centered approach and improved patient care. Indeed, PROs provide information about individual patients that complements information provided by physical assessment and composite scores, and can also be used to guide patient care, such as determining whether a clinic visit is needed or whether treatment modifications are necessary. This is particularly important for patients who do not achieve the aspirational target of remission or low disease activity with pharmacological treatment. A number of validated PRO questionnaires are available, but how and which PROs should be incorporated into rheumatology clinical practice as part of the decision-making process is still controversial. Combining PROs with technology, such as computer adaptive tests, electronic PRO systems, web-based platforms and patient dashboards, could further aid PRO integration into daily rheumatology clinical practice.\",\n \"corpus_id\": 4106315,\n \"score\": 1\n },\n {\n \"doc_id\": \"19083686\",\n \"title\": \"A system of performance intervention zones for use during student evaluation in the clinical environment.\",\n \"abstract\": \"In order to support decision making during comprehensive clinical examinations involving patient care, a system of performance intervention zones was developed and implemented. The aims of the system were to assist examiners in deciding when to intervene during a clinical examination, to facilitate consistency in decision making, and to create the basis and language for shared understanding of examinee performance. The system was recently utilized in Ontario during assessment of internationally educated massage therapists in relation to provincially set competency standards. Feedback from examiners suggested that the system of intervention zones was effective in achieving the specified aims, and on the basis of this preliminary field test, further work is being planned in order to establish the reliability of the system.\",\n \"corpus_id\": 26046747,\n \"score\": 0\n },\n {\n \"doc_id\": \"19230220\",\n \"title\": \"Community ambulation: influences on therapists and clients reasoning and decision making.\",\n \"abstract\": \"BACKGROUND: Community ambulation is an important element of a rehabilitation training programme and its achievement is a goal shared by rehabilitation professionals and clients. The factors that influence a physiotherapist's or health professionals decision making around the preparation of a client for community ambulation and the factors that influence a client's decision to return to walking in their community are unclear. OBJECTIVE: To review the available literature about the factors that have influenced the reasoning and decision making of rehabilitation therapists and clients around the topic of ambulation in the community. METHOD: Three separate searches of the available literature were undertaken using Ovid, Cinahl, ProQuest, Medline and Ebscohost databases. Databases were searched from 1966 to October 2006.The first search explored the literature for factors that influence the clinical reasoning of rehabilitation therapists. The second search explored the literature for factors that influence client's decision to ambulate in the community. A third search was undertaken to explore the literature for the demands of community ambulation in rural communities. RESULTS: Very few studies were found that explored community ambulation in the context of clinical reasoning and decision making, the facilitators and barriers to a clients return to ambulation in their community or the demands of ambulation in a rural community. CONCLUSION: Consideration of the environment is key to the successful return to walking in the community of clients with mobility problems yet little literature has been found to guide physiotherapist's decision making about preparing a clients to return to walking in the community. An individual's participation in their society is also a result of the interaction between their personal characteristics and his or her environment. The influence of these characteristics may vary from one individual to another yet the factors that influence a person's decision to return to walking in their community after stroke remain unclear.\",\n \"corpus_id\": 19105577,\n \"score\": 0\n },\n {\n \"doc_id\": \"19252261\",\n \"title\": \"The physical therapist as a musculoskeletal specialist in the emergency department.\",\n \"abstract\": \"Because patients with musculoskeletal injuries commonly seek intervention in the emergency department (ED), it has been proposed that practitioners with expertise in musculoskeletal practice can be of benefit in this setting. This clinical commentary describes the rationale for utilizing physical therapists as musculoskeletal specialists in the ED. Evidence indicates that physical therapists have the knowledge and skills to provide such expertise. Literature describing ED practice suggests that the management of patients with musculoskeletal conditions would be improved through the consistent integration of evaluation and treatment principles associated with physical therapy practice. Furthermore, early access to physical therapy, as can be provided in the ED setting, has the potential to positively influence patient recovery. Based on prior research and recent evolution of practice, further consideration of physical therapists as consultants in the ED is warranted, and, therefore, additional dialogue on the subject should be encouraged.\",\n \"corpus_id\": 5910513,\n \"score\": 0\n },\n {\n \"doc_id\": \"19397820\",\n \"title\": \"A description of a knowledge broker role implemented as part of a randomized controlled trial evaluating three knowledge translation strategies.\",\n \"abstract\": \"BACKGROUND: A knowledge broker (KB) is a popular knowledge translation and exchange (KTE) strategy emerging in Canada to promote interaction between researchers and end users, as well as to develop capacity for evidence-informed decision making. A KB provides a link between research producers and end users by developing a mutual understanding of goals and cultures, collaborates with end users to identify issues and problems for which solutions are required, and facilitates the identification, access, assessment, interpretation, and translation of research evidence into local policy and practice. Knowledge-brokering can be carried out by individuals, groups and/or organizations, as well as entire countries. In each case, the KB is linked with a group of end users and focuses on promoting the integration of the best available evidence into policy and practice-related decisions. METHODS: A KB intervention comprised one of three KTE interventions evaluated in a randomized controlled trial. RESULTS: KB activities were classified into the following categories: initial and ongoing needs assessments; scanning the horizon; knowledge management; KTE; network development, maintenance, and facilitation; facilitation of individual capacity development in evidence informed decision making; and g) facilitation of and support for organizational change. CONCLUSION: As the KB role developed during this study, central themes that emerged as particularly important included relationship development, ongoing support, customized approaches, and opportunities for individual and organizational capacity development. The novelty of the KB role in public health provides a unique opportunity to assess the need for and reaction to the role and its associated activities. Future research should include studies to evaluate the effectiveness of KBs in different settings and among different health care professionals, and to explore the optimal preparation and training of KBs, as well as the identification of the personality characteristics most closely associated with KB effectiveness. Studies should also seek to better understand which combination of KB activities are associated with optimal evidence-informed decision making outcomes, and whether the combination changes in different settings and among different health care decision makers.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"19540406\",\n \"title\": \"[Addiction and brief-systemic therapy: working with compulsion].\",\n \"abstract\": \"Addictions et thérapie systémique brève : un travail sous contrainte. In our daily practice in public hospitals, we are regularly confronted with the paradox of helping patients, who do not ask for help. Although the French law is clearly defined to allow us to treat patients suffering from psychiatric conditions, who are unable to give their consent, it is not the case for those with addictive disorders. In fact, their disorder does not always (or does not yet) justify treatment without their consent, according to the 1990 law (psychiatric treatment without the patient's consent). However, many of them are referred to us because a third party has forced them (spouse, general practitioner, treatment order) and even though some patients consult spontaneously, they often do so more \\\"for others\\\" than for themselves. Because of this, the therapist (doctor, psychologist or nurse), in addition to the paradox of treating patients who do not ask for treatment, find themselves in a situation with two-fold compulsion, fixed by the social (or family) setting, both as a helper and as a coercive agent, thus, putting the fundamental concepts of treatment into question. A therapeutic agreement, free-will and motivation are in jeopardy when the pressure is strong, which removes the therapist from his mission of treating. Although we would not question the necessity for psychiatric treatment in patients who do not ask for it (addictions are a major public-health problem), we should not forget that motivation is one of the essential elements for making any changes in behavior. Although compulsion (external or internal) is recognized by everyone as a limiting factor, we would like to show here how much it can be a lever for change, as long as this compulsion is identified right from the first meeting with the patient, who consults in an addiction centre. Brief systemic therapy may be of interest for these patients, since it reinforces the motivating approach, which is recommended today and since the compulsive nature of the request for treatment is not an obstacle for such treatment to be started. We try to outline here how the therapist can get out of this two-fold compulsion and help the patient to become the instigator of this change, often imposed on him. Two elements are fundamental to understand the function of brief systemic therapy. First of all, \\\"systemic\\\" means \\\"interaction\\\". A systemic approach to treatment requires working in clinical situations, particular attention being paid to interactions. Second, brief therapy does not mean short therapy, but rather therapy with an objective in view. The objective is determined by the patient together with the therapist and they work out together how to reach it, with or without the family's help. Because of this, we use a five-point assessment to offer a concrete response to the patients in these psychotherapeutic consultations. Firstly, is the patient the one who has asked for treatment? We know that in addictive behavior, it is not always the one with symptoms who asks for help (many couples consult who are persuaded that the other one needs to change). Once we know who has asked for treatment, we clarify (with the patient's help) that his/her objectives are not the same as someone who asks for treatment and we can then redefine them (first step in the therapeutic agreement). Once the request for treatment is clarified, we can clearly define what the problem is, the objectives that the patient fixes for him/herself and how to reach them. A large proportion of therapeutic failures result from the request for treatment being unclear. In this way, we define the problem in concrete terms, without using classifications and the previous attempts to solve it (third point). In fact, we often find that the problem itself is the solution, which is chosen to try to resolve it. Knowing which solutions have been tried (and failed) allows the patient to realize what is effective and what is not. The role of the therapist is to help the family and the patient to find other types of solution to their problem. The therapist only offers concrete tasks, which can be done in the near future (minimal changes). Finally, the therapist takes into account the patient's beliefs, values and personal priorities, to which they are attached and which have determined up to now, how they react to the problem. To work with a patient suffering from addiction, it is important, first of all, to find the elements of compulsion, which are hiding behind each request for treatment. This is because, if the patient does not follow the initial therapeutic objectives, there is always the underlying complaint, which should motivate the patient to improve the situation. An individual patient only has a few possibilities for adapting to this type of situation (agreeing, refusal or negotiation) and the role of the therapist is first of all to help him to realize this. This helps to avoid resistance developing, by underlying the compulsive aspect, which originates from the family's request for treatment. We offer a way for setting up the first meeting: working on the role of the patient in the treatment. Three types of patients consult: patients who are \\\"not concerned\\\" (sent by a third party; their main problem is with the person who asked for them to be treated), \\\"victims\\\" (they complain and consult because they put the responsibility of their problem on someone else) and \\\"clients\\\" (they consult because they consider that their problem depends on themselves and they want help to solve it actively). In fact, changing is not easy and does not happen without making an effort. Change comes from a complex cycle of interactions, for which it is often impossible to find a single origin for the situation in question. The psychological world tends towards homeostasis, just like all human systems, and so, suggesting making changes can only be experienced as an intrusion. Pathology begins when an individual can no longer choose what he/she needs to do. We do not consider that a brief-concrete approach is better than any other approach, but its pragmatic nature seems to fit in with the new conception of addiction therapy, with earlier intervention. However, is it possible to make changes outside of a crisis situation? We are unable to answer this question, except to say that the best time for change is that chosen by the patient.\",\n \"corpus_id\": 29322440,\n \"score\": 0\n },\n {\n \"doc_id\": \"19595419\",\n \"title\": \"A retrospective analysis of self-reported symptoms from 761 consecutive new patients presenting to a Neuro Emotional Technique chiropractic clinic.\",\n \"abstract\": \"PURPOSE: To describe the profile of patients presenting to a private chiropractic clinic specialising in Neuro Emotional Technique (NET) and to identify trends in the presentation of symptoms from these patients. METHODS: 761 consecutive new patients presented to a large, multi-doctor chiropractic clinic in which practitioners all adopt a similar philosophical paradigm and practice NET From January 2005 to December 2005, self-referred patients completed a new patient questionnaire, in which they self-reported one primary complaint for why they were visiting the practitioner. Predetermined patient information was entered manually into a database and basic descriptive statistics extracted. RESULTS: 67.3% of participants were female and 32.6% of the participants were between the ages of 31 and 40. 54.8% of patients presented with a primary musculoskeletal complaint and 36.0% a non-musculoskeletal complaint. Of the musculoskeletal complaints, 40.8% of patients presented with back pain, 20.9% with neck pain and 11.5% with shoulder pain. The most common form of non-musculoskeletal complaint was immune and recurrent infections (13.9%), stress and anxiety (12.8%) and depression (10.9%). 41.4% of participants reported a first time complaint, however, of the patients who had had the presenting complaint before 60.7% reported as having the complaint for greater than 1 year. Musculoskeletal and non-musculoskeletal participants had similar pain profiles. CONCLUSION: This retrospective analysis is the first comprehensive description of the scope of NET patients and their presenting complaints. The patient profile of this NET clinic has a higher degree of non-musculoskeletal patients than that usually reported in non-NET chiropractic offices, and other forms of chiropractic previously described in the literature. Further cross sectional research is required to determine if this particular clinic is indicative of all NET practices and whether the presenting symptoms, especially the non-musculoskeletal, are resolved with NET.\",\n \"corpus_id\": 1388270,\n \"score\": 0\n },\n {\n \"doc_id\": \"19674225\",\n \"title\": \"Do physical therapists change their beliefs, attitudes, knowledge, skills and behaviour after a biopsychosocially orientated university course?\",\n \"abstract\": \"AIM: The aim of this study is to examine the effects of an 8-day university-based training course, aimed at identifying and addressing psychosocial prognostic factors during physiotherapy treatment, in shifting therapists towards a more biopsychosocial orientation as measured by changes in beliefs/attitudes, knowledge, skills and behaviour. METHOD: We combined a randomized controlled trail with a pre-post design. Forty-two physiotherapists applied for a university-accredited training course designed to enhance knowledge and management of psychosocial factors in their practice with patients suffering from musculoskeletal pain. The course participants were randomized either to receiving the course or to a waiting list for training. Attitudes and beliefs towards, and knowledge of psychosocial factors, patient vignettes and a video of an imaginary patient were tested before and after training. The patients of the course participants were asked to fill out a questionnaire with background questions at treatment start. The patients also received a questionnaire about the physical therapists' behaviour and patient satisfaction 6 weeks after treatment start. RESULTS: The results show that physical therapists' attitudes and believes became more biopsychosocially and less biomedically orientated, they were less convinced that pain justifies disability and limitation of activities, and their knowledge and skills on psychosocial risk factors increased after a university-accredited training course. Yet despite these changes their patients perceived their practice behaviour before and after the course as similar and were equally satisfied with their treatment and treatment result. CONCLUSION: A course, which enhanced biopsychosocial attitudes and beliefs, as well as increased such knowledge and skills did not change the way patients perceived their physical therapists. A future question is whether it improves patient outcome.\",\n \"corpus_id\": 26542164,\n \"score\": 0\n },\n {\n \"doc_id\": \"19922741\",\n \"title\": \"Tools and strategies for ongoing assessment of depression: a measurement-based approach to remission.\",\n \"abstract\": \"The goal of treatment for major depressive disorder is remission, but many patients do not achieve complete remission, and few reach sustained remission (ie, recovery). However, systematically using clinical strategies such as implementing measurement-based care tactics and following treatment algorithms can improve the accuracy of ongoing assessment of depressive symptoms, better inform treatment decisions, and make sustained remission more likely. Measurement-based care tactics include using assessment tools to measure medication adherence, side effects, depressive symptoms, and suicide risk. Particularly useful in clinical practice are the Frequency, Intensity, and Burden of Side Effects-Rating (FIBSER) questionnaire; the 9-item Patient Health Questionnaire (PHQ-9); and the 16-item Quick Inventory of Depressive Symptomatology (Clinician-Rated or Self-Report versions; QIDS-C or QIDS-SR). The use of these measurements at regular patient visits can be combined with the use of treatment algorithms so that appropriate treatment selections are made on the basis of assessment tool results at critical decision points in follow-up. This article includes an example of how, at each treatment step, assessments can be made and results used to monitor progress toward remission, efficacy of dosage, and tolerability and to make informed, evidence-based treatment decisions.\",\n \"corpus_id\": 25581885,\n \"score\": 0\n },\n {\n \"doc_id\": \"20797938\",\n \"title\": \"Challenges in pain assessment in cognitively intact and cognitively impaired older adults with cancer.\",\n \"abstract\": \"PURPOSE/OBJECTIVES: To describe approaches to pain assessment in cognitively intact and cognitively impaired older adults with cancer. DATA SOURCES: MEDLINE literature search, personal reference collection, and clinical experience. DATA SYNTHESIS: A systematic and comprehensive pain assessment is the cornerstone of effective treatment strategies. Determining the effect of pain on older adults' ability to function is as important as rating pain intensity. Evidence-based recommendations exist to guide practice. CONCLUSIONS: The undertreatment of pain in older adults persists despite a plethora of published guidelines addressing pain assessment and management. Unrelieved pain affects recovery from illness and all aspects of life. Systematic and ongoing assessment is elementary to effective pain management, yet assessments frequently are neither completed nor documented. Because pain is subjective and individual responses to pain interventions vary widely and are unpredictable, assessment is vital to comprehensive pain care in all clinical settings. Reliable and validated pain assessment tools for cognitively intact and cognitively impaired older adults are available to guide practice. IMPLICATIONS FOR NURSING: Pain assessment is a core competency for nurses in all clinical settings. Comprehensive, individualized, and ongoing assessment provides the information necessary so that clinicians can develop interventions to relieve patients' pain and improve their quality of life. Nurses have the knowledge, skills, and tools to adequately screen and comprehensively assess pain in older adult patients, including those with cognitive impairment. By using this knowledge, nurses can change systems and practices, have a significant effect on improving pain care, and increase quality of life and function of older adults with pain.\",\n \"corpus_id\": 206990248,\n \"score\": 0\n },\n {\n \"doc_id\": \"20862210\",\n \"title\": \"Treatment for lexical retrieval in progressive aphasia.\",\n \"abstract\": \"BACKGROUND: Treatment for lexical retrieval impairment has been shown to yield positive outcomes in individuals with aphasia due to focal lesions, but there has been little research regarding the treatment of such impairments in individuals with progressive aphasia. AIMS: The purpose of this study was to examine the therapeutic effects of a semantic treatment for anomia in progressive aphasia relative to the outcome in an individual with stroke-induced aphasia. METHODS #ENTITYSTARTX00026; PROCEDURES: Two individuals with progressive aphasia and one with aphasia resulting from stroke participated in the study. Each participant presented with fluent, anomic aphasia; however, one of the patients with progressive aphasia demonstrated characteristics indicating a likely progression towards non-fluency. Each participant received a brief, intensive treatment intended to improve lexical retrieval in the context of generative naming for selected semantic categories. Treatment tasks included guided lexical retrieval prompted by the identification and elaboration of items within semantic subcategories, as well as other semantic tasks. Treatment outcomes were quantified using standard effects sizes as well as nonparametric tests comparing pre- versus post-treatment performance. OUTCOMES #ENTITYSTARTX00026; RESULTS: One of the individuals with progressive aphasia showed large treatment effects for lexical retrieval of items from targeted semantic categories. The other progressive aphasia patient showed very small effects overall for treated categories. The individual with the focal lesion due to stroke showed medium-sized effects for trained categories as well as significant improvement on a standardised measure of naming. CONCLUSIONS: Findings indicate that intensive, semantically based treatment for lexical retrieval can result in positive outcomes in individuals with progressive as well as stroke-induced aphasia. Examination of individual differences suggests that the status of semantic and episodic memory may provide predictive information regarding responsiveness to treatment.\",\n \"corpus_id\": 28626660,\n \"score\": 0\n },\n {\n \"doc_id\": \"20944656\",\n \"title\": \"Focusing on glaucoma progression and the clinical importance of progression rate measurement: a review.\",\n \"abstract\": \"PURPOSE: This review aims to provide guidance in managing glaucoma patients more effectively. It focuses on the importance of detecting progression and measuring its rate within the management of primary open-angle glaucoma today. Recent findings strongly indicate that continued monitoring of visual fields (VFs) and reassessment of target intraocular pressures (IOPs) depending on VF progression rates are mandatory in the management of glaucoma. METHODS: Data on glaucoma progression from older as well as most recent literature findings are summarized in this article. In addition, the article elaborates on the scientific content from a series of lectures given by experts in the field during several international symposia on 'rate of progression' in 2008. RESULTS: This review summarizes key findings on the natural history of glaucoma and known factors for disease progression. It highlights the visual function changes observed as glaucoma progresses and discusses disease impact on patients' quality of life. Findings support the need to obtain information on rate of progression and its importance for clinical management. Practical ways to measure rate of progression are given by new software options to help measure major parameters. Finally, on the basis of a patient's individual rate of progression therapeutic options are assessed, such as maximum medical therapy with fixed combinations. CONCLUSIONS: Estimating a patient's individual rate of VF progression by using newly developed analyses will be helpful to forecast the potential future development of the glaucoma. An individualized treatment approach then requires that in patients in whom the risk of becoming visually impaired or blind during their lifetime is higher, a more intensive medical IOP-lowering therapy such as fixed combinations can be considered as treatment option.\",\n \"corpus_id\": 36487873,\n \"score\": 0\n },\n {\n \"doc_id\": \"21332991\",\n \"title\": \"Effects of rehabilitative interventions on pain, function and physical impairments in people with hand osteoarthritis: a systematic review.\",\n \"abstract\": \"INTRODUCTION: Hand osteoarthritis (OA) is associated with pain, reduced grip strength, loss of range of motion and joint stiffness leading to impaired hand function and difficulty with daily activities. The effectiveness of different rehabilitation interventions on specific treatment goals has not yet been fully explored. The objective of this systematic review is to provide evidence based knowledge on the treatment effects of different rehabilitation interventions for specific treatment goals for hand OA. METHODS: A computerized literature search of Medline, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), ISI Web of Science, the Physiotherapy Evidence Database (PEDro) and SCOPUS was performed. Studies that had an evidence level of 2b or higher and that compared a rehabilitation intervention with a control group and assessed at least one of the following outcome measures - pain, physical hand function or other measures of hand impairment - were included. The eligibility and methodological quality of trials were systematically assessed by two independent reviewers using the PEDro scale. Treatment effects were calculated using standardized mean difference and 95% confidence intervals. RESULTS: Ten studies, of which six were of higher quality (PEDro score >6), were included. The rehabilitation techniques reviewed included three studies on exercise, two studies each on laser and heat, and one study each on splints, massage and acupuncture. One higher quality trial showed a large positive effect of 12-month use of a night splint on hand pain, function, strength and range of motion. Exercise had no effect on hand pain or function although it may be able to improve hand strength. Low level laser therapy may be useful for improving range of motion. No rehabilitation interventions were found to improve stiffness. CONCLUSIONS: There is emerging high quality evidence to support that rehabilitation interventions can offer significant benefits to individuals with hand OA. A summary of the higher quality evidence is provided to assist with clinical decision making based on current evidence. Further high-quality research is needed concerning the effects of rehabilitation interventions on specific treatment goals for hand OA.\",\n \"corpus_id\": 14933735,\n \"score\": 0\n },\n {\n \"doc_id\": \"22331537\",\n \"title\": \"[The use of HoNOS in the treatment of patients].\",\n \"abstract\": \"Gebruik van de HoNOS bij de behandeling van patiënten. BACKGROUND: In order to use outcome scores for making decisions about treatment, practitioners need to know the course of scores of several groups of patients. AIM: To test the applicability of methods for computing cut-off scores and individual changes. METHOD: Using Health of the Nation Outcome Scales (HoNOS), we analysed repeated assessments of 699 adults and 414 elderly patients in different treatment settings. RESULTS: Mean HoNOS scores and cut-off scores differentiated between patient groups reasonably well. Scores and threshold values for elderly patients were relatively high. The reliable change index showed few individual changes even for groups where change was expected. The effect size and the standard error of measurement were found to be more sensitive to change. CONCLUSION: More research is needed before the findings can be generalised.\",\n \"corpus_id\": 34913519,\n \"score\": 0\n },\n {\n \"doc_id\": \"22497751\",\n \"title\": \"The science and art of pain management in older persons: case study and discussion.\",\n \"abstract\": \"INTRODUCTION: Evidence-based medicine has been adopted as a means of achieving optimal medical care and to reduce variations in clinical practice. Randomised controlled trials are considered the highest level of scientific evidence. Older individuals are either excluded or underrepresented in these studies, and those who are included are often atypical of patients seen in clinical practice. OBJECTIVE: To examine the approach to clinical decision making in frail older persons when there is little or no scientific evidence to guide management. METHODS: A case study is presented of refractory post herpetic neuralgia in a frail older person. Management plans were developed combining the scientific evidence from the pain literature with the practice known as Comprehensive Geriatric Assessment. The rationale and evidence for clinical decision making is explored. RESULTS: Standard therapies for post herpetic neuralgia had been ineffective or limited by side effects in this patient. By a process of trial and error a combination of treatments was found that improved pain and mood but adversely affected cognition. Adjustment in treatments over time resulted in improved pain, mood, and cognition. CONCLUSIONS: The art of medicine is not the antithesis of the scientific approach. The art of medicine involves balancing the scientific evidence with the circumstances and the preferences of the patient. Combining the practices of Pain Medicine and Comprehensive Geriatric Assessment may result in a better outcome. When treating older people, clinicians not only need to take into consideration the severity of pain, but also the impact of pain and its treatment on cognition, mood and functional status.\",\n \"corpus_id\": 5483536,\n \"score\": 0\n },\n {\n \"doc_id\": \"22641763\",\n \"title\": \"Treatment of maladaptive aggression in youth: CERT guidelines II. Treatments and ongoing management.\",\n \"abstract\": \"OBJECTIVE: To develop guidelines for management and treatment of maladaptive aggression in youth in the areas of psychosocial interventions, medication treatments, and side-effect management. METHODS: Evidence was assembled and evaluated in a multistep process, including systematic reviews of published literature; an expert survey of recommended practices; a consensus conference of researchers, policymakers, clinicians, and family advocates; and review by the steering committee of successive drafts of the recommendations. The Center for Education and Research on Mental Health Therapeutics Treatment of Maladaptive Aggression in Youth guidelines reflect a synthesis of the available evidence, based on this multistep process. RESULTS: This article describes the content, rationale, and evidence for 11 recommendations. Key treatment principles include considering psychosocial interventions, such as evidence-based parent and child skills training as the first line of treatment; targeting the underlying disorder first following evidence-based guidelines; considering individual psychosocial and medical factors, including cardiovascular risk in the selection of agents if medication treatment (ideally with the best evidence base) is initiated; avoiding the use of multiple psychotropic medications simultaneously; and careful monitoring of treatment response, by using structured rating scales, as well as close medical monitoring for side effects, including metabolic changes. CONCLUSIONS: Treatment of children with maladaptive aggression is a \\\"moving target\\\" requiring ongoing assimilation of new evidence as it emerges. Based on the existing evidence, the Treatment of Maladaptive Aggression in Youth guidelines provide a framework for management of maladaptive aggression in youth, appropriate for use by primary care clinicians and mental health providers.\",\n \"corpus_id\": 13976294,\n \"score\": 0\n },\n {\n \"doc_id\": \"23121530\",\n \"title\": \"Survey of UK speech and language therapists' assessment and treatment practices for people with progressive dysarthria.\",\n \"abstract\": \"BACKGROUND: Dysarthria knowledge is predominantly impairment-based. As a result, speech and language therapists (SLTs) have traditionally adopted impairment-focused management practices. However, guidance for best practice suggests that SLTs should consider the client holistically, including the impact of dysarthria beyond the impairment. AIMS: To investigate the current assessment and treatment practices used by UK SLTs with clients with progressive dysarthria and to identify whether these satisfy the needs of SLTs in their everyday practice. To investigate the extent to which they consider oromotor abilities, intelligibility, functional communication, participation and interaction to be important regarding assessment and treatment decisions. To explore whether management decisions are affected by level of clinical experience or settings in which SLTs work. METHODS & PROCEDURES: An online survey of UK SLTs working with adults with progressive dysarthria. OUTCOMES & RESULTS: A total of 119 SLTs completed the survey. Respondents considered that targeting the levels of impairment, activity and participation are important in the management of clients with progressive dysarthria, as recommended by clinical guidelines and recent research. However a particularly high proportion of respondents reported the use of impairment-based assessments. Respondents reported lacking the necessary tools to target interaction in assessment and intervention. The intervention that respondents use with clients varies according to the progressive disorder and dysarthria severity. There is evidence for a trend that less experienced SLTs and those working predominantly in hospital-based settings focus on the impairment, whereas more SLTs with more experience and those based in predominantly community-based settings look beyond the impairment. CONCLUSIONS & IMPLICATIONS: The values held by SLTs match guideline recommendations for best practice, however the clinical reality is that the assessment of progressive dysarthria remains predominantly impairment-focused. New tools need to be developed and integrated into practice to target interaction in assessment and intervention, to reduce the gap between best practice recommendations and clinical reality. Ongoing research into the effectiveness of SLT intervention with clients with progressive dysarthria is required to guide clinical management decisions.\",\n \"corpus_id\": 28352192,\n \"score\": 0\n },\n {\n \"doc_id\": \"23409541\",\n \"title\": \"[Clinical reasoning in nursing, concept analysis].\",\n \"abstract\": \"Le raisonnement clinique des infirmières, analyse de concept. BACKGROUND: Nurses work in situations of complex care requiring great clinical reasoning abilities. In literature, clinical reasoning is often confused with other concepts and it has no consensual definition. AIM: To conduct a concept analysis of a nurse's clinical reasoning in order to clarify, define and distinguish it from the other concepts as well as to better understand clinical reasoning. METHOD: Rodgers's method of concept analysis was used, after literature was retrieved with the use of clinical reasoning, concept analysis, nurse, intensive care and decision making as key-words. RESULTS: The use of cognition, cognitive strategies, a systematic approach of analysis and data interpretation, generating hypothesis and alternatives are attributes of clinical reasoning. The antecedents are experience, knowledge, memory, cues, intuition and data collection. The consequences are decision making, action, clues and problem resolution. CONCLUSION: This concept analysis helped to define clinical reasoning, to distinguish it from other concepts used synonymously and to guide future research.\",\n \"corpus_id\": 11770699,\n \"score\": 0\n },\n {\n \"doc_id\": \"24123615\",\n \"title\": \"The hippocampus uses information just encountered to guide efficient ongoing behavior.\",\n \"abstract\": \"Adaptive ongoing behavior requires using immediate sensory input to guide upcoming actions. Using a novel paradigm with volitional exploration of visuo-spatial scenes, we revealed novel deficits among hippocampal amnesic patients in effective spatial exploration of scenes, indicated by less-systematic exploration patterns than those of healthy comparison subjects. The disorganized exploration by amnesic patients occurred despite successful retention of individual object locations across the entire exploration period, indicating that exploration impairments were not secondary to rapid decay of scene information. These exploration deficits suggest that amnesic patients are impaired in integrating memory for recent actions, which may include information such as locations just visited and scene content, to plan immediately forthcoming actions. Using a novel task that measured the on-line links between sensory input and behavior, we observed the critical role of the hippocampus in modulating ongoing behavior.\",\n \"corpus_id\": 1745397,\n \"score\": 0\n },\n {\n \"doc_id\": \"24204133\",\n \"title\": \"Pain management in patients with dementia.\",\n \"abstract\": \"There are an estimated 35 million people with dementia across the world, of whom 50% experience regular pain. Despite this, current assessment and treatment of pain in this patient group are inadequate. In addition to the discomfort and distress caused by pain, it is frequently the underlying cause of behavioral symptoms, which can lead to inappropriate treatment with antipsychotic medications. Pain also contributes to further complications in treatment and care. This review explores four key perspectives of pain management in dementia and makes recommendations for practice and research. The first perspective discussed is the considerable uncertainty within the literature on the impact of dementia neuropathology on pain perception and processing in Alzheimer's disease and other dementias, where white matter lesions and brain atrophy appear to influence the neurobiology of pain. The second perspective considers the assessment of pain in dementia. This is challenging, particularly because of the limited capacity of self-report by these individuals, which means that assessment relies in large part on observational methods. A number of tools are available but the psychometric quality and clinical utility of these are uncertain. The evidence for efficient treatment (the third perspective) with analgesics is also limited, with few statistically well-powered trials. The most promising evidence supports the use of stepped treatment approaches, and indicates the benefit of pain and behavioral interventions on both these important symptoms. The fourth perspective debates further difficulties in pain management due to the lack of sufficient training and education for health care professionals at all levels, where evidence-based guidance is urgently needed. To address the current inadequate management of pain in dementia, a comprehensive approach is needed. This would include an accurate, validated assessment tool that is sensitive to different types of pain and therapeutic effects, supported by better training and support for care staff across all settings.\",\n \"corpus_id\": 8418621,\n \"score\": 0\n },\n {\n \"doc_id\": \"24467960\",\n \"title\": \"[Treatment of patients with osteoarthritis].\",\n \"abstract\": \"Tratamiento del paciente con artrosis. The therapeutic management of patients with osteoarthritis aims to decrease pain and inflammation, improve physical function, and to apply safe and effective treatments. A patient-centered approach implies the active participation of the patient in the design of the treatment plan and in timely and informed decision-making at all stages of the disease. The nucleus of treatment is patient education, physical activity and therapeutic exercise, together with weight control in overweight or obese patients. Self-care by the individual and by the family is fundamental in day-to-day patient management. The use of physical therapies, technical aids (walking sticks, etc.) and simple analgesics, opium alkaloids, and antiinflammatory drugs have demonstrated effectiveness in controlling pain, improving physical function and quality of life and their use is clearly indicated in the treatment of osteoarthritis. Conservative surgery and joint replacement is indicated when treatment goals are not achieved in specific patients.\",\n \"corpus_id\": 206049492,\n \"score\": 0\n },\n {\n \"doc_id\": \"25209421\",\n \"title\": \"Deepening the quality of clinical reasoning and decision-making in rural hospital nursing practice.\",\n \"abstract\": \"INTRODUCTION: Rural acute care nursing requires an extensive breadth and depth of knowledge as well as the ability to quickly reason through problems in order to make sound clinical decisions. This reasoning often occurs within an environment that has minimal medical or ancillary support. Registered nurses (RN) new to rural nursing, and employers, have raised concerns about patient safety while new nurses make the transition into rural practice. In addition, feeling unprepared for the rigors of rural hospital nursing practice is a central issue influencing RN recruitment and retention. Understanding how rural RNs reason is a key element for identifying professional development needs and may support recruitment and retention of skilled rural nurses. The purpose of this study was to explore how rural RNs reason through clinical problems as well as to assess the quality of such reasoning. METHODS: This study used a non-traditional approach for data collection. Fifteen rural acute care nurses with varying years of experience working in southern Alberta, Canada, were observed while they provided care to patients of varying acuity within a simulated rural setting. Following the simulation, semi-structured interviews were conducted using a substantive approach to critical thinking. RESULTS: Findings revealed that the ability to engage in deep clinical reasoning varied considerably among participants despite being given the same information under the same circumstances. Furthermore, the number of years of experience did not seem to be directly linked to the ability to engage in sound clinical reasoning. Novice nurses, however, did rely heavily on others in their decision making in order to ensure they were making the right decision. Hence, their relationships with other staff members influenced their ability to engage in clinical reasoning and decision making. In situations where the patient's condition was deteriorating quickly, regardless of years of experience, all of the participants depended on their colleagues when making decisions and reasoning throughout the simulation. CONCLUSIONS: Deep clinical reasoning and decision making is a function of reflection and self-correction that requires a critical self-awareness and is more about how nurses think than what they think. The degree of sophistication in reasoning of experts and novices is at times equivalent in that the reasoning of experts and novices can be somewhat limited and focused primarily on human physicality and less on conceptual knowledge. To become proficient in clinical reasoning, practice is necessary. The study supports the accumulating evidence that using clinical simulation and reflective interviewing that emphasize how clinical decisions are made enhances reasoning skills and confidence.\",\n \"corpus_id\": 44807253,\n \"score\": 0\n },\n {\n \"doc_id\": \"25547621\",\n \"title\": \"Evaluating the guideline enhancement tool (GET): an innovative clinical training tool to enhance the use of hypertension guidelines in general practice.\",\n \"abstract\": \"BACKGROUND: This project aims to evaluate the effectiveness of an innovative educational intervention in enhancing clinical decision making related to the management of hypertension in general practice. The relatively low level of uptake of clinical practice guidelines by clinicians is widely recognised as a problem that impacts on clinical outcomes. This project addresses this problem with a focus on hypertension guidelines. Hypertension is the most frequently managed problem in general practice but evidence suggests that management of Hypertension in general practice is sub-optimal. METHODS/DESIGN: This study will explore the effectiveness of an educational intervention named the 'Guideline Enhancement Tool (GET)'. The intervention is designed to guide clinicians through a systematic process of considering key decision points related to the management of hypertension and provides a mechanism for clinicians to engage with the hypertension clinical guidelines. The intervention will be administered within the Australian General Practice Training program, via one of the regional training providers. Two cohorts of trainees will participate as the intervention and delayed intervention groups. This process is expected to improve clinicians' engagement with the hypertension guidelines in particular, and enhance their clinical reasoning abilities in general. The effectiveness of the intervention in improving clinical reasoning will be evaluated using the 'Script Concordance Test'. DISCUSSION: The study design presented in this protocol aims to achieve two major outcomes. Firstly, the trial and evaluation of the educational intervention can lead to the development of a validated clinical education strategy that can be used in GP training to enhance the decision-making processes related to the management of hypertension. This has the potential to be adapted to other clinical conditions and training programs and can benefit clinicians in their clinical decision-making. Secondly, the study explores features that influence the effective use of clinical practice guidelines. The study thus addresses a significant problem in clinical education.\",\n \"corpus_id\": 13089267,\n \"score\": 0\n },\n {\n \"doc_id\": \"25929534\",\n \"title\": \"Direct and Indirect Benefits Reported by Users of Transcutaneous Electrical Nerve Stimulation for Chronic Musculoskeletal Pain: Qualitative Exploration Using Patient Interviews.\",\n \"abstract\": \"BACKGROUND: There is no consensus regarding the effectiveness of transcutaneous electrical nerve stimulation (TENS) for management of chronic musculoskeletal pain or chronic low back pain. A recent review of previous trial methodology identified significant problems with low treatment fidelity. There is little information available to guide selection of patient-reported outcome measures appropriate for TENS evaluation. OBJECTIVES: The purpose of this study was to explore the experiences of patients at a secondary care pain clinic who successfully used TENS to help manage chronic musculoskeletal pain. These key informants were selected because they had the potential to generate knowledge that could inform research design and clinical practice. DESIGN: A qualitative method using individual semistructured interviews with open questions was selected for its capacity to generate rich data. METHODS: A mini focus group informed the development of a discussion guide for semistructured interviews with 9 patients (6 women, 3 men). Thematic analysis was used as the primary data analysis method, and this analysis was enhanced by a case-level analysis of the context and processes of TENS use of each individual. RESULTS: Data analysis indicated that distraction from pain and a reduction in the sensations associated with muscle tension or spasm should be considered as separate outcomes from pain relief. These direct benefits led to a wide range of indirect benefits dependent on patient decision making, including medication reduction, enhanced function, psychological benefits, and enhanced ability to rest. CONCLUSIONS: The findings indicate that evaluating TENS using a unidimensional pain scale is likely to overlook potential benefits. The complex pattern of TENS usage, as well as multiple direct and indirect outcomes, indicates that TENS could be considered as a complex intervention.\",\n \"corpus_id\": 44602849,\n \"score\": 0\n },\n {\n \"doc_id\": \"25991108\",\n \"title\": \"Use of eye-tracking technology in clinical reasoning: a systematic review.\",\n \"abstract\": \"Achieving a better understanding of the clinical reasoning process is an important approach to improve patient management and patient safety. Although clinical psychologists have used talk-aloud or stimulated recall approaches, these methods have biases. Recently, researchers have been exploring eye-tracking technology to gain \\\"live\\\" insight into clinicians' reasoning processes in certain fields of medicine (radiology, dermatology, etc.). We present a systematic review of eye-tracking literature used for clinical reasoning. We performed a literature search using the terms \\\"eye\\\" or \\\"gaze tracking\\\", \\\"clinical\\\" or \\\"diagnostic reasoning\\\", and \\\"physician\\\" in Pubmed, Embase, Psychinfo, Web of Science and ACM databases. Two investigators screened the abstracts, then full-text articles to select 10 pertinent studies. The studies evaluated medical decision making in four different medical domains using mostly experimental, observational approaches. A total of 208 participants were enrolled for the selected experiments. Paths for further studies are discussed that may extend the use of eye trackers in order to improve understanding of medical decision making.\",\n \"corpus_id\": 16300898,\n \"score\": 0\n },\n {\n \"doc_id\": \"26309382\",\n \"title\": \"Imaging in conjunction with physical therapy in management of a patient with history of thoracic tumour.\",\n \"abstract\": \"BACKGROUND: Physical therapy care for musculoskeletal conditions includes an ongoing process that systematically considers and prioritises diagnostic hypotheses. These diagnostic hypotheses include those that are typical for common musculoskeletal conditions, and must also include more rare conditions that would require care outside the scope of practice of the physical therapist. When additional screening is required, physical therapists collaborate with other providers or directly order the appropriate tests to rule out suspected pathology. CASE DESCRIPTION: This article illustrates the use of musculoskeletal imaging ordered by a physical therapist to guide ongoing management of a patient with back pain and a history of cancer. OUTCOMES: The patient successfully returned to moderate-intensity sport activities after a course of physical therapy. DISCUSSION: This case provides an example of how clinical diagnostic reasoning combined with clinical privileges to order musculoskeletal imaging can facilitate diagnostic accuracy in a timely and cost-efficient manner.\",\n \"corpus_id\": 37436583,\n \"score\": 0\n },\n {\n \"doc_id\": \"26792832\",\n \"title\": \"Predicting the onset of psychosis in patients at clinical high risk: practical guide to probabilistic prognostic reasoning.\",\n \"abstract\": \"Prediction of psychosis in patients at clinical high risk (CHR) has become a mainstream focus of clinical and research interest worldwide. When using CHR instruments for clinical purposes, the predicted outcome is but only a probability; and, consequently, any therapeutic action following the assessment is based on probabilistic prognostic reasoning. Yet, probabilistic reasoning makes considerable demands on the clinicians. We provide here a scholarly practical guide summarising the key concepts to support clinicians with probabilistic prognostic reasoning in the CHR state. We review risk or cumulative incidence of psychosis in, person-time rate of psychosis, Kaplan-Meier estimates of psychosis risk, measures of prognostic accuracy, sensitivity and specificity in receiver operator characteristic curves, positive and negative predictive values, Bayes' theorem, likelihood ratios, potentials and limits of real-life applications of prognostic probabilistic reasoning in the CHR state. Understanding basic measures used for prognostic probabilistic reasoning is a prerequisite for successfully implementing the early detection and prevention of psychosis in clinical practice. Future refinement of these measures for CHR patients may actually influence risk management, especially as regards initiating or withholding treatment.\",\n \"corpus_id\": 19758818,\n \"score\": 0\n },\n {\n \"doc_id\": \"28148616\",\n \"title\": \"Beneficial Effects of Guided Imagery or Clinical Massage on the Status of Patients in a Progressive Care Unit.\",\n \"abstract\": \"BACKGROUND: Patients in the progressive care unit typically experience high levels of pain and anxiety and exhibit difficulty sleeping. OBJECTIVE: To determine whether either clinical massage or guided imagery could reduce pain and anxiety and improve sleep. METHODS: This study included 288 inpatients on 2 floors of a progressive care unit. On 1 floor, each patient was offered daily a 15-minute complimentary clinical massage, whereas the patients on the other floor were provided access to a 30-minute guided-imagery recording. Patients were asked to rate their pain and anxiety levels immediately before and after the massage intervention or were asked whether the guided-imagery intervention was helpful for pain, anxiety, or insomnia. RESULTS: The massage intervention showed an immediate and significant reduction in self-reported pain and anxiety (P < .001); likewise, a significant number of patients self-reported that guided imagery helped alleviate pain, anxiety, and insomnia (P < .001). CONCLUSION: The results of this study indicate that clinical massage and guided imagery can benefit patients in the progressive care unit.\",\n \"corpus_id\": 25225181,\n \"score\": 0\n },\n {\n \"doc_id\": \"29028765\",\n \"title\": \"Preventing clinical progression and need for treatment in patients on active surveillance for prostate cancer.\",\n \"abstract\": \"PURPOSE OF REVIEW: Active surveillance is an established treatment option for men with localized, low-risk prostate cancer (CaP). It entails the postponement of immediate therapy with the option of delayed intervention upon disease progression. The rate of clinical progression and need for treatment on active surveillance is approximately 50% over 15 years. The present review summarizes recent data on current methods, attempting to prevent clinical progression. RECENT FINDINGS: Patient selection for active surveillance is the first mandatory step required to lower progression. Adherence to active surveillance protocols is critical in making sure patients are monitored well and treated early when progression occurs. Before active surveillance allocation and during active surveillance follow-up, methods involving multiparametric MRI, prostate specific antigen derivatives, biopsy factors, urinary, tissue and genetic markers can be used to prevent clinical progression and/or identify those at risk for progression. Medications such as 5α-reductase inhibitors and others might inhibit disease progression in patients on active surveillance. SUMMARY: Active surveillance is required because of overdiagnosis, along with our inability to accurately predict individual CaP behavior. Several methods can potentially reduce the risk of CaP progression in patients with active surveillance. However, a measure of uncertainty and fear of progression will always accompany patients with active surveillance and the physicians treating them.\",\n \"corpus_id\": 763507,\n \"score\": 0\n },\n {\n \"doc_id\": \"29433500\",\n \"title\": \"Effects of local treatment with and without sensorimotor and balance exercise in individuals with neck pain: protocol for a randomized controlled trial.\",\n \"abstract\": \"BACKGROUND: Impaired cervical joint position sense and balance are associated with neck pain. Specific therapeutic exercise and manual therapy are effective for improving neck pain and functional ability but their effects on joint position sense and balance impairments remain uncertain. Changes in the joint position sense and balance may need to be addressed specifically. The primary objective is to investigate the most effective interventions to improve impaired cervical joint position sense and balance in individuals with neck pain. The secondary objective is to assess the effectiveness of the interventions on pain intensity and disability, pain location, dizziness symptoms, cervical range of motion, gait speed, functional ability, treatment satisfaction and quality of life. METHODS: A 2 × 2 factorial, single blind RCT with immediate, short- and long-term follow-ups. One hundred and sixty eight participants with neck pain with impaired joint position sense and balance will be recruited into the trial. Participants will be randomly allocated to one of four intervention groups: i) local neck treatment, ii) local treatment plus tailored sensorimotor exercises, iii) local treatment plus balance exercises, and iv) local treatment plus sensorimotor and balance exercises. Participants receive two treatments for 6 weeks. Primary outcomes are postural sway and cervical joint position error. Secondary outcomes include gait speed, dizziness intensity, neck pain intensity, neck disability, pain extent and location, cervical range of motion, functional ability, perceived benefit, and quality of life. Assessment will be measured at baseline, immediately after treatment and at 3, 6, 12 month-follow ups. DISCUSSION: Neck pain is one of the major causes of disability. Effective treatment must address not only the symptoms but the dysfunctions associated with neck pain. This trial will evaluate the effectiveness of interventions for individuals with neck pain with impaired cervical joint position sense and balance. This trial will impact on clinical practice by providing evidence towards optimal and efficient management. TRIAL REGISTRATION: ClinicalTrials.gov ( NCT03149302 ). May 10, 2017.\",\n \"corpus_id\": 3366991,\n \"score\": 0\n },\n {\n \"doc_id\": \"29535047\",\n \"title\": \"Design and rational for the precision medicine guided treatment for cancer pain pragmatic clinical trial.\",\n \"abstract\": \"INTRODUCTION: Pain is one of the most burdensome symptoms associated with cancer and its treatment, and opioids are the cornerstone of pain management. Opioid therapy is empirically selected, and patients often require adjustments in therapy to effectively alleviate pain or ameliorate adverse drug effects that interfere with quality of life. There are data suggesting CYP2D6 genotype may contribute to inter-patient variability in response to opioids through its effects on opioid metabolism. Therefore, we aim to determine if CYP2D6 genotype-guided opioid prescribing results in greater reductions in pain and symptom severity and interference with daily living compared to a conventional prescribing approach in patients with cancer. METHODS: Patients with solid tumors with metastasis and a self-reported pain score ≥ 4/10 are eligible for enrollment and randomized to a genotype-guided or conventional pain management strategy. For patients in the genotype-guided arm, CYP2D6 genotype information is integrated into opioid prescribing decisions. Patients are asked to complete questionnaires regarding their pain, symptoms, and quality of life at baseline and 2, 4, 6, and 8 weeks after enrollment. The primary endpoint is differential change in pain severity by treatment strategy (genotype-guided versus conventional pain management). Secondary endpoints include change in pain and symptom interference with daily living. CONCLUSION: Pharmacogenetic-guided opioid selection for cancer pain management has potential clinical utility, but current evidence is limited to retrospective and observational studies. Precision Medicine Guided Treatment for Cancer Pain is a pragmatic clinical trial that seeks to determine the utility of CYP2D6 genotype-guided opioid prescribing in patients with cancer.\",\n \"corpus_id\": 4911724,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":91,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28544481\",\n \"title\": \"Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.\",\n \"abstract\": \"The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.\",\n \"corpus_id\": 3625713\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19223933","title":"Predicting human height by Victorian and genomic methods.","abstract":"In the Victorian era, Sir Francis Galton showed that 'when dealing with the transmission of stature from parents to children, the average height of the two parents, ... is all we need care to know about them' (1886). One hundred and twenty-two years after Galton's work was published, 54 loci showing strong statistical evidence for association to human height were described, providing us with potential genomic means of human height prediction. In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4-6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance, and showed high discriminative accuracy. We have also explored how much variance a genomic profile should explain to reach certain AUC values. For highly heritable traits such as height, we conclude that in applications in which parental phenotypic information is available (eg, medicine), the Victorian Galton's method will long stay unsurpassed, in terms of both discriminative accuracy and costs. For less heritable traits, and in situations in which parental information is not available (eg, forensics), genomic methods may provide an alternative, given that the variants determining an essential proportion of the trait's variation can be identified.","corpus_id":21845780,"score":2},{"doc_id":"21151957","title":"A unifying framework for evaluating the predictive power of genetic variants based on the level of heritability explained.","abstract":"An increasing number of genetic variants have been identified for many complex diseases. However, it is controversial whether risk prediction based on genomic profiles will be useful clinically. Appropriate statistical measures to evaluate the performance of genetic risk prediction models are required. Previous studies have mainly focused on the use of the area under the receiver operating characteristic (ROC) curve, or AUC, to judge the predictive value of genetic tests. However, AUC has its limitations and should be complemented by other measures. In this study, we develop a novel unifying statistical framework that connects a large variety of predictive indices together. We showed that, given the overall disease probability and the level of variance in total liability (or heritability) explained by the genetic variants, we can estimate analytically a large variety of prediction metrics, for example the AUC, the mean risk difference between cases and non-cases, the net reclassification improvement (ability to reclassify people into high- and low-risk categories), the proportion of cases explained by a specific percentile of population at the highest risk, the variance of predicted risks, and the risk at any percentile. We also demonstrate how to construct graphs to visualize the performance of risk models, such as the ROC curve, the density of risks, and the predictiveness curve (disease risk plotted against risk percentile). The results from simulations match very well with our theoretical estimates. Finally we apply the methodology to nine complex diseases, evaluating the predictive power of genetic tests based on known susceptibility variants for each trait.","corpus_id":25977515,"score":2},{"doc_id":"22247263","title":"Bioinformatics for personal genome interpretation.","abstract":"An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship between genotype and phenotype. Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes. Some of these use intra-species genetic variability as a means for better understanding this relationship. In addition, several online resources are now dedicated to collecting single nucleotide variants and other types of variants, and annotating their functional effects and associations with phenotypic traits. This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants. In this work, we review the most important developments in the field--the databases and bioinformatics tools that will be of utmost importance in our concerted effort to interpret the human variome.","corpus_id":1691561,"score":2},{"doc_id":"22549284","title":"Whole-genome sequencing in personalized therapeutics.","abstract":"Eleven years since the initial drafts of the human genome were published, we have begun to see the first examples of the application of whole-genome sequencing to personalized diagnosis and therapeutics. The exponential decline in sequencing costs and the constant improvement in these technologies promise to further advance the use of a patient's full genetic profile in the clinic. However, realizing the potential benefit of such sequencing will require a concerted effort by science, medicine, law, and management. In this review, we discuss current approaches to decoding the 6 billion-letter genetic code of a whole genome in a clinical context, give current examples of translating this information into therapy-guiding knowledge, and list the challenges that will need to be surmounted before these powerful data can be fully exploited to forward the goals of personalized medicine.","corpus_id":4381014,"score":2},{"doc_id":"22847385","title":"Whole-genome and whole-exome sequencing in neurological diseases.","abstract":"Genetic risk factors that underlie many rare and common neurological disorders remain poorly understood because of the multifactorial and heterogeneous nature of these complex traits. With the decreasing cost of massively parallel sequencing technologies, whole-genome and whole-exome sequencing will soon allow the characterization of the full spectrum of sequence and structural variants present in each individual. Methods are being developed to parse the huge amount of genomic data and to sift out which variants are associated with diseases. Numerous challenges are inherent in the identification of rare and common variants that have a role in complex neurological diseases, and tools are being developed to overcome these challenges. Given that genomic data will soon be the main driver towards the goal of personalized medicine, future developments in the production and interpretation of data, as well as in ethics and counselling, will be needed for whole-genome and whole-exome sequencing to be used as informative tools in a clinical setting.","corpus_id":2585584,"score":2},{"doc_id":"22962312","title":"DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.","abstract":"Patients with developmental disorders often harbour sub-microscopic deletions or duplications that lead to a disruption of normal gene expression or perturbation in the copy number of dosage-sensitive genes. Clinical interpretation for such patients in isolation is hindered by the rarity and novelty of such disorders. The DECIPHER project (https://decipher.sanger.ac.uk) was established in 2004 as an accessible online repository of genomic and associated phenotypic data with the primary goal of aiding the clinical interpretation of rare copy-number variants (CNVs). DECIPHER integrates information from a variety of bioinformatics resources and uses visualization tools to identify potential disease genes within a CNV. A two-tier access system permits clinicians and clinical scientists to maintain confidential linked anonymous records of phenotypes and CNVs for their patients that, with informed consent, can subsequently be shared with the wider clinical genetics and research communities. Advances in next-generation sequencing technologies are making it practical and affordable to sequence the whole exome/genome of patients who display features suggestive of a genetic disorder. This approach enables the identification of smaller intragenic mutations including single-nucleotide variants that are not accessible even with high-resolution genomic array analysis. This article briefly summarizes the current status and achievements of the DECIPHER project and looks ahead to the opportunities and challenges of jointly analysing structural and sequence variation in the human genome.","corpus_id":10645012,"score":2},{"doc_id":"23164068","title":"Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.","abstract":"UNLABELLED: BACKGROUND: Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection. In addition the use of platform related sequencing error models can help in the recovery of ambiguous genotypes from lower coverage data. DESCRIPTION: We have developed a whole genome database of human genetic variations, Huvariome, determined by whole genome deep sequencing data with high coverage and low error rates. The database was designed to be sequencing technology independent but is currently populated with 165 individual whole genomes consisting of small pedigrees and matched tumor/normal samples sequenced with the Complete Genomics sequencing platform. Common variants have been determined for a Benelux population cohort and represented as genotypes alongside the results of two sets of control data (73 of the 165 genomes), Huvariome Core which comprises 31 healthy individuals from the Benelux region, and Diversity Panel consisting of 46 healthy individuals representing 10 different populations and 21 samples in three Pedigrees. Users can query the database by gene or position via a web interface and the results are displayed as the frequency of the variations as detected in the datasets. We demonstrate that Huvariome can provide accurate reference allele frequencies to disambiguate sequencing inconsistencies produced in resequencing experiments. Huvariome has been used to support the selection of candidate cardiomyopathy related genes which have a homozygous genotype in the reference cohorts. This database allows the users to see which selected variants are common variants (> 5% minor allele frequency) in the Huvariome core samples, thus aiding in the selection of potentially pathogenic variants by filtering out common variants that are not listed in one of the other public genomic variation databases. The no-call rate and the accuracy of allele calling in Huvariome provides the user with the possibility of identifying platform dependent errors associated with specific regions of the human genome. CONCLUSION: Huvariome is a simple to use resource for validation of resequencing results obtained by NGS experiments. The high sequence coverage and low error rates provide scientists with the ability to remove false positive results from pedigree studies. Results are returned via a web interface that displays location-based genetic variation frequency, impact on protein function, association with known genetic variations and a quality score of the variation base derived from Huvariome Core and the Diversity Panel data. These results may be used to identify and prioritize rare variants that, for example, might be disease relevant. In testing the accuracy of the Huvariome database, alleles of a selection of ambiguously called coding single nucleotide variants were successfully predicted in all cases. Data protection of individuals is ensured by restricted access to patient derived genomes from the host institution which is relevant for future molecular diagnostics.","corpus_id":8245048,"score":2},{"doc_id":"23962656","title":"Towards precision medicine: advances in computational approaches for the analysis of human variants.","abstract":"Variations and similarities in our individual genomes are part of our history, our heritage, and our identity. Some human genomic variants are associated with common traits such as hair and eye color, while others are associated with susceptibility to disease or response to drug treatment. Identifying the human variations producing clinically relevant phenotypic changes is critical for providing accurate and personalized diagnosis, prognosis, and treatment for diseases. Furthermore, a better understanding of the molecular underpinning of disease can lead to development of new drug targets for precision medicine. Several resources have been designed for collecting and storing human genomic variations in highly structured, easily accessible databases. Unfortunately, a vast amount of information about these genetic variants and their functional and phenotypic associations is currently buried in the literature, only accessible by manual curation or sophisticated text text-mining technology to extract the relevant information. In addition, the low cost of sequencing technologies coupled with increasing computational power has enabled the development of numerous computational methodologies to predict the pathogenicity of human variants. This review provides a detailed comparison of current human variant resources, including HGMD, OMIM, ClinVar, and UniProt/Swiss-Prot, followed by an overview of the computational methods and techniques used to leverage the available data to predict novel deleterious variants. We expect these resources and tools to become the foundation for understanding the molecular details of genomic variants leading to disease, which in turn will enable the promise of precision medicine.","corpus_id":13169513,"score":2},{"doc_id":"24150940","title":"DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.","abstract":"The DECIPHER database (https://decipher.sanger.ac.uk/) is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype-phenotype characteristics and highlights potentially pathogenic genes. In a significant development, we have extended DECIPHER from a database of just copy-number variants to allow upload, annotation and analysis of sequence variants such as single nucleotide variants (SNVs) and InDels. Other notable developments in DECIPHER include a purpose-built, customizable and interactive genome browser to aid combined visualization and interpretation of sequence and copy-number variation against informative datasets of pathogenic and population variation. We have also introduced several new features to our deposition and analysis interface. This article provides an update to the DECIPHER database, an earlier instance of which has been described elsewhere [Swaminathan et al. (2012) DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet., 21, R37-R44].","corpus_id":123692,"score":2},{"doc_id":"24162188","title":"Improved exome prioritization of disease genes through cross-species phenotype comparison.","abstract":"Numerous new disease-gene associations have been identified by whole-exome sequencing studies in the last few years. However, many cases remain unsolved due to the sheer number of candidate variants remaining after common filtering strategies such as removing low quality and common variants and those deemed unlikely to be pathogenic. The observation that each of our genomes contains about 100 genuine loss-of-function variants makes identification of the causative mutation problematic when using these strategies alone. We propose using the wealth of genotype to phenotype data that already exists from model organism studies to assess the potential impact of these exome variants. Here, we introduce PHenotypic Interpretation of Variants in Exomes (PHIVE), an algorithm that integrates the calculation of phenotype similarity between human diseases and genetically modified mouse models with evaluation of the variants according to allele frequency, pathogenicity, and mode of inheritance approaches in our Exomiser tool. Large-scale validation of PHIVE analysis using 100,000 exomes containing known mutations demonstrated a substantial improvement (up to 54.1-fold) over purely variant-based (frequency and pathogenicity) methods with the correct gene recalled as the top hit in up to 83% of samples, corresponding to an area under the ROC curve of >95%. We conclude that incorporation of phenotype data can play a vital role in translational bioinformatics and propose that exome sequencing projects should systematically capture clinical phenotypes to take advantage of the strategy presented here.","corpus_id":20782582,"score":2},{"doc_id":"24510652","title":"Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis.","abstract":"Over the last several years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test under particular circumstances in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing but rather the analysis and interpretation. Interpretation of genetic findings in a clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires the development of novel or repositioned analysis tools, methodologies, and processes. This unit provides an overview of these items. Specific challenges related to implementation in a clinical setting are discussed.","corpus_id":38226022,"score":2},{"doc_id":"25188385","title":"A probabilistic model to predict clinical phenotypic traits from genome sequencing.","abstract":"Genetic screening is becoming possible on an unprecedented scale. However, its utility remains controversial. Although most variant genotypes cannot be easily interpreted, many individuals nevertheless attempt to interpret their genetic information. Initiatives such as the Personal Genome Project (PGP) and Illumina's Understand Your Genome are sequencing thousands of adults, collecting phenotypic information and developing computational pipelines to identify the most important variant genotypes harbored by each individual. These pipelines consider database and allele frequency annotations and bioinformatics classifications. We propose that the next step will be to integrate these different sources of information to estimate the probability that a given individual has specific phenotypes of clinical interest. To this end, we have designed a Bayesian probabilistic model to predict the probability of dichotomous phenotypes. When applied to a cohort from PGP, predictions of Gilbert syndrome, Graves' disease, non-Hodgkin lymphoma, and various blood groups were accurate, as individuals manifesting the phenotype in question exhibited the highest, or among the highest, predicted probabilities. Thirty-eight PGP phenotypes (26%) were predicted with area-under-the-ROC curve (AUC)>0.7, and 23 (15.8%) of these were statistically significant, based on permutation tests. Moreover, in a Critical Assessment of Genome Interpretation (CAGI) blinded prediction experiment, the models were used to match 77 PGP genomes to phenotypic profiles, generating the most accurate prediction of 16 submissions, according to an independent assessor. Although the models are currently insufficiently accurate for diagnostic utility, we expect their performance to improve with growth of publicly available genomics data and model refinement by domain experts.","corpus_id":18960629,"score":2},{"doc_id":"25519328","title":"A dual-clustering framework for association screening with whole genome sequencing data and longitudinal traits.","abstract":"Current sequencing technology enables generation of whole genome sequencing data sets that contain a high density of rare variants, each of which is carried by, at most, 5% of the sampled subjects. Such variants are involved in the etiology of most common diseases in humans. These diseases can be studied by relevant longitudinal phenotype traits. Tests for association between such genotype information and longitudinal traits allow the study of the function of rare variants in complex human disorders. In this paper, we propose an association-screening framework that highlights the genotypic differences observed on rare variants and the longitudinal nature of phenotypes. In particular, both variants within a gene and longitudinal phenotypes are used to create partitions of subjects. Association between the 2 sets of constructed partitions is then evaluated. We apply the proposed strategy to the simulated data from the Genetic Analysis Workshop 18 and compare the obtained results with those from sequence kernel association test using the receiver operating characteristic curves.","corpus_id":54631532,"score":2},{"doc_id":"25519339","title":"Prediction of genetic contributions to complex traits using whole genome sequencing data.","abstract":"Although markers identified by genome-wide association studies have individually strong statistical significance, their performance in prediction remains limited. Our goal was to use animal breeding genomic prediction models to predict additive genetic contributions for systolic blood pressure (SBP) using whole genome sequencing data with different validation designs. The additive genetic contributions of SBP were estimated via linear mixed model. Rare variants (MAF<0.05) were collapsed through the k-means method to create a \"collapsed single-nucleotide polymorphisms.\" Prediction of the additive genomic contributions of SBP was conducted using genomic Best Linear Unbiased Predictor (GBLUP) and BayesCπ. Estimates of predictive accuracy were compared using common single-nucleotide polymorphisms (SNPs) versus common and collapsed SNPs, and for prediction within and across families. The additive genetic variance of SBP contributed to 18% of the phenotypic variance (h(2) = 0.18). BayesCπ had slightly better prediction accuracies than GBLUP. In both models, within-family predictions had higher accuracies both in the training and testing set than didacross-family design. Collapsing rare variants via the k-means method and adding to the common SNPs did not improve prediction accuracies. The prediction model, including both pedigree and genomic information, achieved a slightly higher accuracy than using either source of information alone. Prediction of genetic contributions to complex traits is feasible using whole genome sequencing and statistical methods borrowed from animal breeding. The relatedness of individuals between the training and testing set strongly affected the performance of prediction models. Methods for inclusion of rare variants in these models need more development.","corpus_id":17397555,"score":2},{"doc_id":"25733939","title":"The Human Genome Project, and recent advances in personalized genomics.","abstract":"The language of \"personalized medicine\" and \"personal genomics\" has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient's health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the \"technological imperative\", due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding.","corpus_id":-1,"score":2},{"doc_id":"26046366","title":"Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.","abstract":"Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.","corpus_id":22813281,"score":2},{"doc_id":"26448358","title":"Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.","abstract":"High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing, prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies. There are significant barriers to realizing this goal that are related to the difficult task of interpreting personal genetic variation. A comprehensive, widely accessible application for interpretation of whole genome sequence data is needed. Here, we present a series of methods for identification of genetic variants and genotypes with clinical associations, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios. We demonstrate application of these methods for disease and drug response prognostication in whole genome sequence data from twelve unrelated adults, and for disease gene discovery in one father-mother-child trio with apparently simplex congenital ventricular arrhythmia. In doing so we identify clinically actionable inherited disease risk and drug response genotypes in pre-symptomatic individuals. We also nominate a new candidate gene in congenital arrhythmia, ATP2B4, and provide experimental evidence of a regulatory role for variants discovered using this framework.","corpus_id":18200967,"score":2},{"doc_id":"27666372","title":"Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project.","abstract":"Massively parallel whole-genome sequencing (WGS) data have ushered in a new era in human genetics. These data are now being used to understand the role of rare variants in complex traits and to advance the goals of precision medicine. The technological and computing advances that have enabled us to generate WGS data on thousands of individuals have also outpaced our ability to perform analyses in scientifically and statistically rigorous and thoughtful ways. The past several years have witnessed the application of whole-exome sequencing (WES) to complex traits and diseases. From our analysis of NHLBI Exome Sequencing Project (ESP) data, not only have a number of important disease and complex trait association findings emerged, but our collective experience offers some valuable lessons for WGS initiatives. These include caveats associated with generating automated pipelines for quality control and analysis of rare variants; the importance of studying minority populations; sample size requirements and efficient study designs for identifying rare-variant associations; and the significance of incidental findings in population-based genetic research. With the ESP as an example, we offer guidance and a framework on how to conduct a large-scale association study in the era of WGS.","corpus_id":42260652,"score":2},{"doc_id":"27725664","title":"Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.","abstract":"To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=-0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations.","corpus_id":1065990,"score":2},{"doc_id":"28039885","title":"Rare variant association test with multiple phenotypes.","abstract":"Although genome-wide association studies (GWAS) have now discovered thousands of genetic variants associated with common traits, such variants cannot explain the large degree of \"missing heritability,\" likely due to rare variants. The advent of next generation sequencing technology has allowed rare variant detection and association with common traits, often by investigating specific genomic regions for rare variant effects on a trait. Although multiple correlated phenotypes are often concurrently observed in GWAS, most studies analyze only single phenotypes, which may lessen statistical power. To increase power, multivariate analyses, which consider correlations between multiple phenotypes, can be used. However, few existing multivariant analyses can identify rare variants for assessing multiple phenotypes. Here, we propose Multivariate Association Analysis using Score Statistics (MAAUSS), to identify rare variants associated with multiple phenotypes, based on the widely used sequence kernel association test (SKAT) for a single phenotype. We applied MAAUSS to whole exome sequencing (WES) data from a Korean population of 1,058 subjects to discover genes associated with multiple traits of liver function. We then assessed validation of those genes by a replication study, using an independent dataset of 3,445 individuals. Notably, we detected the gene ZNF620 among five significant genes. We then performed a simulation study to compare MAAUSS's performance with existing methods. Overall, MAAUSS successfully conserved type 1 error rates and in many cases had a higher power than the existing methods. This study illustrates a feasible and straightforward approach for identifying rare variants correlated with multiple phenotypes, with likely relevance to missing heritability.","corpus_id":4525299,"score":2},{"doc_id":"29704323","title":"Machine learning in schizophrenia genomics, a case-control study using 5,090 exomes.","abstract":"Our hypothesis is that machine learning (ML) analysis of whole exome sequencing (WES) data can be used to identify individuals at high risk for schizophrenia (SCZ). This study applies ML to WES data from 2,545 individuals with SCZ and 2,545 unaffected individuals, accessed via the database of genotypes and phenotypes (dbGaP). Single nucleotide variants and small insertions and deletions were annotated by ANNOVAR using the reference genome hg19/GRCh37. Rare (predicted functional) variants with a minor allele frequency ≤1% and genotype quality ≥90 including missense, frameshift, stop gain, stop loss, intronic, and exonic splicing variants were selected. A file containing all cases and controls, the names of genes with variants meeting our criteria, and the number of variants per gene for each individual, was used for ML analysis. The supervised machine-learning algorithm used the patterns of variants observed in the different genes to determine which subset of genes can best predict that an individual is affected. Seventy percent of the data was used to train the algorithm and the remaining 30% of data (n = 1,526) was used to evaluate its efficiency. The supervised ML algorithm, gradient boosted trees with regularization (eXtreme Gradient Boosting implementation) was the best performing algorithm yielding promising results (accuracy: 85.7%, specificity: 86.6%, sensitivity: 84.9%, area under the receiver-operator characteristic curve: 0.95). The top 50 features (genes) of the algorithm were analyzed using bioinformatics resources for new insights about the pathophysiology of SCZ. This manuscript presents a novel predictor which could potentially enable studies exploring disease-modifying intervention in the early stages of the disease.","corpus_id":13809018,"score":2},{"doc_id":"20193048","title":"The 1000 Genomes Project: new opportunities for research and social challenges.","abstract":"The 1000 Genomes Project, an international collaboration, is sequencing the whole genome of approximately 2,000 individuals from different worldwide populations. The central goal of this project is to describe most of the genetic variation that occurs at a population frequency greater than 1%. The results of this project will allow scientists to identify genetic variation at an unprecedented degree of resolution and will also help improve the imputation methods for determining unobserved genetic variants that are not represented on current genotyping arrays. By identifying novel or rare functional genetic variants, researchers will be able to pinpoint disease-causing genes in genomic regions initially identified by association studies. This level of detailed sequence information will also improve our knowledge of the evolutionary processes and the genomic patterns that have shaped the human species as we know it today. The new data will also lay the foundation for future clinical applications, such as prediction of disease susceptibility and drug response. However, the forthcoming availability of whole genome sequences at affordable prices will raise ethical concerns and pose potential threats to individual privacy. Nevertheless, we believe that these potential risks are outweighed by the benefits in terms of diagnosis and research, so long as rigorous safeguards are kept in place through legislation that prevents discrimination on the basis of the results of genetic testing.","corpus_id":14555018,"score":1},{"doc_id":"20373666","title":"Personal genomes in progress: from the human genome project to the personal genome project.","abstract":"The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007--even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polylmorphisms, this has caused a significant rise in interest in correlating genome sequences with comprehensive environmental and trait data (GET). The cost of electronic health records, imaging, and microbial, immunological, and behavioral data are also dropping quickly. Sharing such integrated GET datasets and their interpretations with a diversity of researchers and research subjects highlights the need for informed-consent models capable of addressing novel privacy and other issues, as well as for flexible data-sharing resources that make materials and data available with minimum restrictions on use. This article examines the Personal Genome Project's effort to develop a GET database as a public genomics resource broadly accessible to both researchers and research participants, while pursuing the highest standards in research ethics.","corpus_id":263624552,"score":1},{"doc_id":"21121034","title":"GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROM POPULATION GENOMICS TO PERSONALIZED MEDICINE - Session Introduction.","abstract":"Genome-wide associations studies (GWAS) have been very successful in identifying common genetic variation associated to numerous complex diseases [1]. However, most of the identified common genetic variants appear to confer modest risk and few causal alleles have been identified [2]. Furthermore, these associations account for a small portion of the total heritability of inherited disease variation [1]. This has led to the reexamination of the contribution of environment, gene-gene and gene-environment interactions, and rare genetic variants in complex diseases [1, 3, 4]. There is strong evidence that rare variants play an important role in complex disease etiology and may have larger genetic effects than common variants [2]. Currently, much of what we know regarding the contribution of rare genetic variants to disease risk is based on a limited number of phenotypes and candidate genes. However, rapid advancement of second generation sequencing technologies will invariably lead to widespread association studies comparing whole exome and eventually whole genome sequencing of cases and controls. A tremendous challenge for enabling these \"next generation\" medical genomic studies is developing statistical approaches for correlating rare genetic variants with disease outcome. The analysis of rare variants is challenging since methods used for common variants are woefully underpowered. Therefore, methods that can deal with genetic heterogeneity at the trait-associated locus have been developed to analyze rare variants. These methods instead analyzing individual variants analyze variants within a region/gene as a group and usually rely on collapsing. They can be applied to both in cases vs. controls and quantitative trait studies are needed. The paper of Bansal et al. in this volume describes the application of a number of statistical methods for testing associations between rare variants in two genes to obesity. The authors considered the relative merits of the different methods as well as important implementation details, such as the leveraging of genomic annotations and determining p-values. Knowledge of haplotypes can increase the power of GWAS studies and also highlight associations that are impossible to detect without haplotype phase (e.g. loss of heterozygosity). Even more complicated phase-dependent interactions of variants in linkage equilibrium have also been suggested as possible causes of missing heritability. In their work, Hallsorsson et al. formulate algorithmic strategies for haplotype phasing by multi-assembly of shared haplotypes from next-generation sequencing data. These methods would allow testing haplotypes harboring rare variants for association and potentially increase their explanatory power. Since single SNP tests are often underpowered in rare variant association analysis, Zeggini and Asimit propose a locus-based method that has high power in the presence of rare variants and that incorporate base quality scores available for sequencing data. Their results suggest that this multi-marker approach may be best suited for smaller regions, or after some filtering to reduce the number of SNPs that are jointly tested to reduce loss of power due to multiple-testing adjustments. Finally, the paper of Zhou et al., presents a penalized regression framework for association testing on sequence data, in the presence of both common and rare variants. This method also introduces the use of weights to incorporate available biological information on the variants. Although these tactics improve both false positive and false negative rates, they represent an incremental development and there is still significant room for improvement. With the development of sequencing technologies and methods to detect complex trait rare variant associations many new and exciting discovery are imminent. The analysis of rare variants is still in its infancy and the next few years promises to produce many new methods to meet the special demands of analyzing this type of data. Note from Publisher: This article contains the abstract and references.","corpus_id":42856307,"score":1},{"doc_id":"21811411","title":"Rare and common regulatory variation in population-scale sequenced human genomes.","abstract":"Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs) when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs) discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.","corpus_id":17801771,"score":1},{"doc_id":"21881504","title":"Whole exome and whole genome sequencing.","abstract":"PURPOSE OF REVIEW: The purpose of this review is to describe the new DNA sequencing technologies referred to as next-generation sequencing (NGS). These new methods are becoming central to research in human disease and are starting to be used in routine clinical care. RECENT FINDINGS: Advances in instrumentation have dramatically reduced the cost of DNA sequencing. An individual's entire genome can now be sequenced for $7500. In addition, the software needed to analyze and help interpret this data is rapidly improving. This technology has been used by researchers to discover new genetic disorders and new disease associations. In the clinic, it can define the etiology in patients with undiagnosed genetic disorders and identify mutations in a cancer to help guide chemotherapy. SUMMARY: Here we discuss how whole-exome sequencing and whole-genome sequencing are used in basic research and clinical care. These new techniques promise to speed research and affect how healthcare is delivered.","corpus_id":263623356,"score":1},{"doc_id":"22128050","title":"Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.","abstract":"Genetic Analysis Workshop 17 (GAW17) focused on the transition from genome-wide association study designs and methods to the study designs and statistical genetic methods that will be required for the analysis of next-generation sequence data including both common and rare sequence variants. In the 166 contributions to GAW17, a wide variety of statistical methods were applied to simulated traits in population- and family-based samples, and results from these analyses were compared to the known generating model. In general, many of the statistical genetic methods used in the population-based sample identified causal sequence variants (SVs) when the estimated locus-specific heritability, as measured in the population-based sample, was greater than about 0.08. However, SVs with locus-specific heritabilities less than 0.03 were rarely identified consistently. In the family-based samples, many of the methods detected SVs that were rarer than those detected in the population-based sample, but the estimated locus-specific heritabilities for these rare SVs, as measured in the family-based samples, were substantially higher (>0.2) than their corresponding heritabilities in the population-based samples. Substantial inflation of the type I error rate was observed across a wide variety of statistical methods. Although many of the contributions found little inflation in type I error for Q4, a trait with no causal SVs, type I error rates for Q1 and Q2 were well above their nominal levels with the inflation for Q1 being higher than that for Q2. It seems likely that this inflation in type I error is due to correlations among SVs.","corpus_id":24792051,"score":1},{"doc_id":"22344227","title":"Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.","abstract":"PURPOSE: The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. METHODS: These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. RESULTS: The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. CONCLUSION: There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.","corpus_id":13771383,"score":1},{"doc_id":"22403585","title":"Bioinformatic Resources of microRNA Sequences, Gene Targets, and Genetic Variation.","abstract":"Variation in quantitative gene expression has been observed in natural populations and associated with various complex traits/phenotypes such as risks for common diseases and drug response. MicroRNAs (miRNAs), a family of small, non-coding RNA molecules, have been demonstrated to be an important class of gene regulators that mostly downregulate gene expression at the post-transcriptional level. A comprehensive and reliable catalogue of miRNAs and miRNA gene targets is critical to understanding the gene regulatory networks. Though experimental approaches have been used to identify many miRNAs and their gene targets, due to cost and efficiency, currently miRNA and target identification still largely relies on computational algorithms. We reviewed several widely used bioinformatic resources of miRNA sequences and gene targets that take advantage of the unique characteristics of miRNA-mRNA interactions, experimental validation, as well as the integration of sequence-based evidence and microarray expression data. Furthermore, given the importance of miRNAs in regulating gene expression, elucidating expression quantitative trait loci involved with miRSNPs or miR-polymorphisms will help improve our understanding of complex traits. We reviewed the available resources of miRNA genetic variation, and the current progress (e.g., the 1000 Genomes Project) in detailing the genetic variation in miRNA-related single nucleotide polymorphisms (SNPs). We also provided our perspectives of the potential impact of next-generation sequencing on the research of miRNAs, gene targets, and miRSNPs. These bioinformatic resources may help interpret experimental and association study results, thus enhancing our knowledge of the dynamic gene regulatory networks and the physiological pathways for complex traits/phenotypes. Prospectively, these bioinformatic resources of miRNAs will need to address the challenges raised by the application of next-generation sequencing in miRNA research.","corpus_id":13039940,"score":1},{"doc_id":"22811759","title":"Limitations of the human reference genome for personalized genomics.","abstract":"Data from the 1000 genomes project (1KGP) and Complete Genomics (CG) have dramatically increased the numbers of known genetic variants and challenge several assumptions about the reference genome and its uses in both clinical and research settings. Specifically, 34% of published array-based GWAS studies for a variety of diseases utilize probes that overlap unanticipated single nucleotide polymorphisms (SNPs), indels, or structural variants. Linkage disequilibrium (LD) block length depends on the numbers of markers used, and the mean LD block size decreases from 16 kb to 7 kb,when HapMap-based calculations are compared to blocks computed from1KGP data. Additionally, when 1KGP and CG variants are compared, 19% of the single nucleotide variants (SNVs) reported from common genomes are unique to one dataset; likely a result of differences in data collection methodology, alignment of reads to the reference genome, and variant-calling algorithms. Together these observations indicate that current research resources and informatics methods do not adequately account for the high level of variation that already exists in the human population and significant efforts are needed to create resources that can accurately assess personal genomics for health, disease, and predict treatment outcomes.","corpus_id":18325651,"score":1},{"doc_id":"23097404","title":"Breeding and Genetics Symposium: networks and pathways to guide genomic selection.","abstract":"Many traits affecting profitability and sustainability of meat, milk, and fiber production are polygenic, with no single gene having an overwhelming influence on observed variation. No knowledge of the specific genes controlling these traits has been needed to make substantial improvement through selection. Significant gains have been made through phenotypic selection enhanced by pedigree relationships and continually improving statistical methodology. Genomic selection, recently enabled by assays for dense SNP located throughout the genome, promises to increase selection accuracy and accelerate genetic improvement by emphasizing the SNP most strongly correlated to phenotype although the genes and sequence variants affecting phenotype remain largely unknown. These genomic predictions theoretically rely on linkage disequilibrium (LD) between genotyped SNP and unknown functional variants, but familial linkage may increase effectiveness when predicting individuals related to those in the training data. Genomic selection with functional SNP genotypes should be less reliant on LD patterns shared by training and target populations, possibly allowing robust prediction across unrelated populations. Although the specific variants causing polygenic variation may never be known with certainty, a number of tools and resources can be used to identify those most likely to affect phenotype. Associations of dense SNP genotypes with phenotype provide a 1-dimensional approach for identifying genes affecting specific traits; in contrast, associations with multiple traits allow defining networks of genes interacting to affect correlated traits. Such networks are especially compelling when corroborated by existing functional annotation and established molecular pathways. The SNP occurring within network genes, obtained from public databases or derived from genome and transcriptome sequences, may be classified according to expected effects on gene products. As illustrated by functionally informed genomic predictions being more accurate than naive whole-genome predictions of beef tenderness, coupling evidence from livestock genotypes, phenotypes, gene expression, and genomic variants with existing knowledge of gene functions and interactions may provide greater insight into the genes and genomic mechanisms affecting polygenic traits and facilitate functional genomic selection for economically important traits.","corpus_id":5743933,"score":1},{"doc_id":"23166519","title":"A unified method for detecting secondary trait associations with rare variants: application to sequence data.","abstract":"Next-generation sequencing has made possible the detection of rare variant (RV) associations with quantitative traits (QT). Due to high sequencing cost, many studies can only sequence a modest number of selected samples with extreme QT. Therefore association testing in individual studies can be underpowered. Besides the primary trait, many clinically important secondary traits are often measured. It is highly beneficial if multiple studies can be jointly analyzed for detecting associations with commonly measured traits. However, analyzing secondary traits in selected samples can be biased if sample ascertainment is not properly modeled. Some methods exist for analyzing secondary traits in selected samples, where some burden tests can be implemented. However p-values can only be evaluated analytically via asymptotic approximations, which may not be accurate. Additionally, potentially more powerful sequence kernel association tests, variable selection-based methods, and burden tests that require permutations cannot be incorporated. To overcome these limitations, we developed a unified method for analyzing secondary trait associations with RVs (STAR) in selected samples, incorporating all RV tests. Statistical significance can be evaluated either through permutations or analytically. STAR makes it possible to apply more powerful RV tests to analyze secondary trait associations. It also enables jointly analyzing multiple cohorts ascertained under different study designs, which greatly boosts power. The performance of STAR and commonly used RV association tests were comprehensively evaluated using simulation studies. STAR was also implemented to analyze a dataset from the SardiNIA project where samples with extreme low-density lipoprotein levels were sequenced. A significant association between LDLR and systolic blood pressure was identified, which is supported by pharmacogenetic studies. In summary, for sequencing studies, STAR is an important tool for detecting secondary-trait RV associations.","corpus_id":846238,"score":1},{"doc_id":"23714750","title":"The Genome of the Netherlands: design, and project goals.","abstract":"Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.","corpus_id":15265934,"score":1},{"doc_id":"24297551","title":"Imputation-based assessment of next generation rare exome variant arrays.","abstract":"A striking finding from recent large-scale sequencing efforts is that the vast majority of variants in the human genome are rare and found within single populations or lineages. These observations hold important implications for the design of the next round of disease variant discovery efforts-if genetic variants that influence disease risk follow the same trend, then we expect to see population-specific disease associations that require large sample sizes for detection. To address this challenge, and due to the still prohibitive cost of sequencing large cohorts, researchers have developed a new generation of low-cost genotyping arrays that assay rare variation previously identified from large exome sequencing studies. Genotyping approaches rely not only on directly observing variants, but also on phasing and imputation methods that use publicly available reference panels to infer unobserved variants in a study cohort. Rare variant exome arrays are intentionally enriched for variants likely to be disease causing, and here we assay the ability of the first commercially available rare exome variant array (the Illumina Infinium HumanExome BeadChip) to also tag other potentially damaging variants not molecularly assayed. Using full sequence data from chromosome 22 from the phase I 1000 Genomes Project, we evaluate three methods for imputation (BEAGLE, MaCH-Admix, and SHAPEIT2/IMPUTE2) with the rare exome variant array under varied study panel sizes, reference panel sizes, and LD structures via population differences. We find that imputation is more accurate across both the genome and exome for common variant arrays than the next generation array for all allele frequencies, including rare alleles. We also find that imputation is the least accurate in African populations, and accuracy is substantially improved for rare variants when the same population is included in the reference panel. Depending on the goals of GWAS researchers, our results will aid budget decisions by helping determine whether money is best spent sequencing the genomes of smaller sample sizes, genotyping larger sample sizes with rare and/or common variant arrays and imputing SNPs, or some combination of the two.","corpus_id":6211724,"score":1},{"doc_id":"25152847","title":"Genomic Variation: Lessons Learned from Whole-Genome CNV Analysis.","abstract":"One of the most fundamental goals of the study of human genetics was to determine the relationship between genomic variation and human disease. The effects of large-scale structural variation, such as aneuploidy and other cytogenetically visible imbalances, as well as sequence-level variation, have been studied for several decades. However, compared to these, the impact of submicroscopic copy number variants (CNV) has only recently been appreciated. Despite this, lessons learned from the study of CNVs have already proven significant and broadly applicable. From expanding the concept of normal human variation to providing concrete examples of the utility of genomics in clinical care and challenging notions of the genetic architecture of complex disease, CNVs have provided valuable insights into the genomics of human health and development.","corpus_id":16847333,"score":1},{"doc_id":"25378555","title":"Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes.","abstract":"Initial results from sequencing studies suggest that there are relatively few low-frequency (<5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency-large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant-common phenotype associations-11 132 cis-gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (<5%), respectively, low frequency-large effect associations comprised 7% of detectable cis-gene expression traits [89 of 1314 cis-eQTLs at P < 1 × 10(-06) (false discovery rate ∼5%)] and one of eight biomarker associations at P < 8 × 10(-10). Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect.","corpus_id":15487729,"score":1},{"doc_id":"25765185","title":"Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry.","abstract":"BACKGROUND: The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; \"tent-dwelling\" Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage. RESULTS: We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 'loss-of-function' and 2,314 'deleterious' coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant's family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays. CONCLUSIONS: We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity.","corpus_id":1621508,"score":1},{"doc_id":"26927186","title":"Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine.","abstract":"Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.","corpus_id":2695531,"score":1},{"doc_id":"27184599","title":"Coming of age: ten years of next-generation sequencing technologies.","abstract":"Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. An astonishing complexity of genome architecture has been revealed, bringing these sequencing technologies to even greater advancements. Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.","corpus_id":8295541,"score":1},{"doc_id":"27436001","title":"Applications of the 1000 Genomes Project resources.","abstract":"The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci, filtering non-pathogenic variants from exome, whole genome and cancer genome sequencing projects, and genetic analysis of population structure and molecular evolution. In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies.","corpus_id":3621791,"score":1},{"doc_id":"27724973","title":"The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.","abstract":"BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. CONCLUSIONS: These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.","corpus_id":15722345,"score":1},{"doc_id":"27822964","title":"Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies.","abstract":"Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.","corpus_id":3730453,"score":1},{"doc_id":"27905878","title":"Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein-Friesian cattle.","abstract":"BACKGROUND: Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic prediction by using imputed sequence data or preselected SNPs from a genome-wide association study (GWAS) with imputed whole-genome sequence data. METHODS: Phenotypes were available for 5503 Holstein-Friesian bulls. Genotypes were imputed up to whole-genome sequence (13,789,029 segregating DNA variants) by using run 4 of the 1000 bull genomes project. The program GCTA was used to perform GWAS for protein yield (PY), somatic cell score (SCS) and interval from first to last insemination (IFL). From the GWAS, subsets of variants were selected and genomic relationship matrices (GRM) were used to estimate the variance explained in 2087 validation animals and to evaluate the genomic prediction ability. Finally, two GRM were fitted together in several models to evaluate the effect of selected variants that were in competition with all the other variants. RESULTS: The GRM based on full sequence data explained only marginally more genetic variation than that based on common SNP panels: for PY, SCS and IFL, genomic heritability improved from 0.81 to 0.83, 0.83 to 0.87 and 0.69 to 0.72, respectively. Sequence data also helped to identify more variants linked to quantitative trait loci and resulted in clearer GWAS peaks across the genome. The proportion of total variance explained by the selected variants combined in a GRM was considerably smaller than that explained by all variants (less than 0.31 for all traits). When selected variants were used, accuracy of genomic predictions decreased and bias increased. CONCLUSIONS: Although 35 to 42 variants were detected that together explained 13 to 19% of the total variance (18 to 23% of the genetic variance) when fitted alone, there was no advantage in using dense sequence information for genomic prediction in the Holstein data used in our study. Detection and selection of variants within a single breed are difficult due to long-range linkage disequilibrium. Stringent selection of variants resulted in more biased genomic predictions, although this might be due to the training population being the same dataset from which the selected variants were identified.","corpus_id":879270,"score":1},{"doc_id":"27917525","title":"A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next-generation sequencing.","abstract":"In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F-distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high-dimensional genotype data. It is shown that approximate F-distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i.e., scenarios in which some genetic variants have relatively large effects on the phenotypes); GAMuT has higher power and is more appropriate for analyzing polygenic effects (i.e., effects from a large number of genetic variants each of which contributes a small amount to the phenotypes). MFLM and MANOVA are very flexible and can be used to perform association analysis for (i) rare variants, (ii) common variants, and (iii) a combination of rare and common variants. Although GAMuT was designed to analyze rare variants, it can be applied to analyze a combination of rare and common variants and it performs well when (1) the number of genetic variants is large and (2) each variant contributes a small amount to the phenotypes (i.e., polygenes). MFLM and MANOVA are fixed effect models that perform well for major gene association analysis. GAMuT can be viewed as an extension of sequence kernel association tests (SKAT). Both GAMuT and SKAT are more appropriate for analyzing polygenic effects and they perform well not only in the rare variant case, but also in the case of a combination of rare and common variants. Data analyses of European cohorts and the Trinity Students Study are presented to compare the performance of the two methods.","corpus_id":13757678,"score":1},{"doc_id":"28035032","title":"Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.","abstract":"MOTIVATION: Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X). RESULTS: We have applied our classifier to compare call sets generated with different calling methods, including both single-sample and multi-sample callers. At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illuminas single-sample caller CASAVA, Real Time Genomics multisample variant caller, and the GATK UnifiedGenotyper, respectively. Since NGS sequencing data may be accompanied by genotype data for the same samples, either collected concurrent to sequencing or from a previous study, our method can be trained on each dataset to provide a more accurate computational validation of site calls compared to generic methods. Moreover, our method allows for adjustment based on allele frequency (e.g. a different set of criteria to determine quality for rare versus common variants) and thereby provides insight into sequencing characteristics that indicate call quality for variants of different frequencies. AVAILABILITY AND IMPLEMENTATION: Code is available on Github at: https://github.com/suyashss/variant_validation CONTACTS: : suyashs@stanford.edu or mtaub@jhsph.eduSupplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":3799989,"score":1},{"doc_id":"28051073","title":"Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project.","abstract":"Providing ostensibly healthy individuals with personal results from whole-genome sequencing could lead to improved health and well-being via enhanced disease risk prediction, prevention, and diagnosis, but also poses practical and ethical challenges. Understanding how individuals react psychologically and behaviourally will be key in assessing the potential utility of personal whole-genome sequencing. We conducted an exploratory longitudinal cohort study in which quantitative surveys and in-depth qualitative interviews were conducted before and after personal results were returned to individuals who underwent whole-genome sequencing. The participants were offered a range of interpreted results, including Alzheimer's disease, type 2 diabetes, pharmacogenomics, rare disease-associated variants, and ancestry. They were also offered their raw data. Of the 35 participants at baseline, 29 (82.9%) completed the 6-month follow-up. In the quantitative surveys, test-related distress was low, although it was higher at 1-week than 6-month follow-up (Z=2.68, P=0.007). In the 6-month qualitative interviews, most participants felt happy or relieved about their results. A few were concerned, particularly about rare disease-associated variants and Alzheimer's disease results. Two of the 29 participants had sought clinical follow-up as a direct or indirect consequence of rare disease-associated variants results. Several had mentioned their results to their doctors. Some participants felt having their raw data might be medically useful to them in the future. The majority reported positive reactions to having their genomes sequenced, but there were notable exceptions to this. The impact and value of returning personal results from whole-genome sequencing when implemented on a larger scale remains to be seen.","corpus_id":10313269,"score":1},{"doc_id":"28224672","title":"PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.","abstract":"Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed toward the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools. These areas include collection and distribution of benchmark datasets, their use for systematic large-scale method assessment, and the development of guidelines for reporting methods and their performance. For us, CAGI has provided a chance to experiment with new ideas, test the application areas of our methods, and network with other prediction method developers. In this article, we discuss our experiences and lessons learned from the various CAGI challenges. We describe our approaches, their performance, and impact of CAGI on our research. Finally, we discuss some of the possibilities that CAGI experiments have opened up and make some suggestions for future experiments.","corpus_id":43059185,"score":1},{"doc_id":"28440912","title":"Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.","abstract":"Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of 10 variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene. Twenty-two pathogenicity predictors were assessed with a variety of accuracy measures for reliability in a medical context. Different assessment measures were combined in an overall ranking to provide more robust results. The R scripts used for assessment are publicly available from a GitHub repository for future use in similar assessment exercises. Despite a limited test-set size, our findings show a variety of results, with some methods performing significantly better. Methods combining different strategies frequently outperform simpler approaches. The best predictor, Yang&Zhou lab, uses a machine learning method combining an empirical energy function measuring protein stability with an evolutionary conservation term. The p16INK4a challenge highlights how subtle structural effects can neutralize otherwise deleterious variants.","corpus_id":46850510,"score":1},{"doc_id":"28634997","title":"Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.","abstract":"Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.","corpus_id":571850,"score":1},{"doc_id":"28938720","title":"Deep whole-genome sequencing of 90 Han Chinese genomes.","abstract":"Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency < 5%), including 5 813 503 single nucleotide polymorphisms, 1 169 199 InDels, and 17 927 structural variants. Using deep sequencing data, we have built a greatly expanded spectrum of genetic variation for the Han Chinese genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000 Genomes Project, as well as to other human genome projects.","corpus_id":35588592,"score":1},{"doc_id":"28961785","title":"FIRE: functional inference of genetic variants that regulate gene expression.","abstract":"Motivation: Interpreting genetic variation in noncoding regions of the genome is an important challenge for personal genome analysis. One mechanism by which noncoding single nucleotide variants (SNVs) influence downstream phenotypes is through the regulation of gene expression. Methods to predict whether or not individual SNVs are likely to regulate gene expression would aid interpretation of variants of unknown significance identified in whole-genome sequencing studies. Results: We developed FIRE (Functional Inference of Regulators of Expression), a tool to score both noncoding and coding SNVs based on their potential to regulate the expression levels of nearby genes. FIRE consists of 23 random forests trained to recognize SNVs in cis-expression quantitative trait loci (cis-eQTLs) using a set of 92 genomic annotations as predictive features. FIRE scores discriminate cis-eQTL SNVs from non-eQTL SNVs in the training set with a cross-validated area under the receiver operating characteristic curve (AUC) of 0.807, and discriminate cis-eQTL SNVs shared across six populations of different ancestry from non-eQTL SNVs with an AUC of 0.939. FIRE scores are also predictive of cis-eQTL SNVs across a variety of tissue types. Availability and implementation: FIRE scores for genome-wide SNVs in hg19/GRCh37 are available for download at https://sites.google.com/site/fireregulatoryvariation/. Contact: nilah@stanford.edu. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4441565,"score":1},{"doc_id":"28984185","title":"STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data.","abstract":"BACKGROUND: Short tandem repeats (STRs) are found in many prokaryotic and eukaryotic genomes, and are commonly used as genetic markers, in particular for identity and parental testing in DNA forensics. The unstable expansion of some STRs was associated with various genetic disorders (e.g., the Huntington disease), and thus was used in genetic testing for screening individuals at high risk. Traditional STR analyses were based on the PCR amplification of STR loci followed by gel electrophoresis. With the availability of massive whole genome sequencing data, it becomes practical to mine STR profiles in silico from genome sequences. Software tools such as lobSTR and STR-FM have been developed to address these demands, which are, however, built upon whole genome reads mapping tools, and thus may not be sensitive enough. RESULTS: In this paper, we present a standalone software tool STRScan that uses a greedy algorithm for targeted STR profiling in next-generation sequencing (NGS) data. STRScan was tested on the whole genome sequencing data from Venter genome sequencing and 1000 Genomes Project. The results showed that STRScan can profile 20% more STRs in the target set that are missed by lobSTR. CONCLUSION: STRScan is particularly useful for the NGS-based targeted STR profiling, e.g., in genetic and human identity testing. STRScan is available as open-source software at http://darwin.informatics.indiana.edu/str/ .","corpus_id":5110156,"score":1},{"doc_id":"29258987","title":"The application of MutMap in forward genetic studies based on whole-genome sequencing.","abstract":"Classical forward genetic analysis relies on construction of complicated progeny populations and development of many molecular markers for linkage analysis in genetic mapping, which is both time- and cost-consuming. The recently developed MutMap is a new forward genetic approach based on high-throughput next-generation sequencing technologies. It is more efficient and affordable than traditional methods. Moreover, new extended methods based on MutMap have been developed: MutMap+, which is based on self-crossing; MutMap-Gap, which is used to recognize the causative variations occurring in genome gap regions; QTL-seq, a method similar to MutMap for mapping quantitative trait loci. These methods are free from constructing complicated mapping population, genetic hybridization and linkage information. They have greatly accelerated the identification of genetic elements associated with interested phenotypic variation. Here, we review the basic principles of MutMap, and discuss their future applications in next generation sequencing-based forward genetic mapping and crop improvement.","corpus_id":3872054,"score":1},{"doc_id":"29431110","title":"The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.","abstract":"BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.","corpus_id":46753806,"score":1},{"doc_id":"20238084","title":"Whole genome sequencing.","abstract":"Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences. The reference-based assembly approach involves mapping each read to a reference genome sequence. We discuss methods for identifying genetic variation (single nucleotide polymorphisms, small indels, and copy number variants) and building haplotypes from genome assemblies, and discuss potential pitfalls. We expect methodologies to evolve rapidly as sequencing technologies improve and more human genomes are sequenced.","corpus_id":260566168,"score":0},{"doc_id":"20946837","title":"The fungal genome initiative and lessons learned from genome sequencing.","abstract":"The sequence of Saccharomyces cerevisiae enabled systematic genome-wide experimental approaches, demonstrating the power of having the complete genome of an organism. The rapid impact of these methods on research in yeast mobilized an effort to expand genomic resources for other fungi. The \"fungal genome initiative\" represents an organized genome sequencing effort to promote comparative and evolutionary studies across the fungal kingdom. Through such an approach, scientists can not only better understand specific organisms but also illuminate the shared and unique aspects of fungal biology that underlie the importance of fungi in biomedical research, health, food production, and industry. To date, assembled genomes for over 100 fungi are available in public databases, and many more sequencing projects are underway. Here, we discuss both examples of findings from comparative analysis of fungal sequences, with a specific emphasis on yeast genomes, and on the analytical approaches taken to mine fungal genomes. New sequencing methods are accelerating comparative studies of fungi by reducing the cost and difficulty of sequencing. This has driven more common use of sequencing applications, such as to study genome-wide variation in populations or to deeply profile RNA transcripts. These and further technological innovations will continue to be piloted in yeasts and other fungi, and will expand the applications of sequencing to study fungal biology.","corpus_id":10486841,"score":0},{"doc_id":"24599000","title":"Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.","abstract":"Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.","corpus_id":18993255,"score":0},{"doc_id":"27067834","title":"Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).","abstract":"BACKGROUND: Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS: In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS: This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.","corpus_id":12594090,"score":0},{"doc_id":"27068766","title":"Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges.","abstract":"Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.","corpus_id":576744,"score":0},{"doc_id":"29345757","title":"Whole genome sequencing analysis for cancer genomics and precision medicine.","abstract":"Explosive advances in next-generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein-altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non-coding regions, including introns, regulatory elements and non-coding RNA. Structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can be used to comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signatures in cancer genomes and elucidate the functional or clinical implications of these unexplored genomic regions and mutational signatures. This review describes recently developed technical approaches for cancer WGS and the future direction of cancer WGS, and discusses its utility and limitations as an analysis platform and for mutation interpretation for cancer genomics and cancer precision medicine. Taking into account the diversity of cancer genomes and phenotypes, interpretation of abundant mutation information from WGS, especially non-coding and structure variants, requires the analysis of large-scale WGS data integrated with RNA-Seq, epigenomics, immuno-genomic and clinic-pathological information.","corpus_id":3741533,"score":0}],"string":"[\n {\n \"doc_id\": \"19223933\",\n \"title\": \"Predicting human height by Victorian and genomic methods.\",\n \"abstract\": \"In the Victorian era, Sir Francis Galton showed that 'when dealing with the transmission of stature from parents to children, the average height of the two parents, ... is all we need care to know about them' (1886). One hundred and twenty-two years after Galton's work was published, 54 loci showing strong statistical evidence for association to human height were described, providing us with potential genomic means of human height prediction. In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4-6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance, and showed high discriminative accuracy. We have also explored how much variance a genomic profile should explain to reach certain AUC values. For highly heritable traits such as height, we conclude that in applications in which parental phenotypic information is available (eg, medicine), the Victorian Galton's method will long stay unsurpassed, in terms of both discriminative accuracy and costs. For less heritable traits, and in situations in which parental information is not available (eg, forensics), genomic methods may provide an alternative, given that the variants determining an essential proportion of the trait's variation can be identified.\",\n \"corpus_id\": 21845780,\n \"score\": 2\n },\n {\n \"doc_id\": \"21151957\",\n \"title\": \"A unifying framework for evaluating the predictive power of genetic variants based on the level of heritability explained.\",\n \"abstract\": \"An increasing number of genetic variants have been identified for many complex diseases. However, it is controversial whether risk prediction based on genomic profiles will be useful clinically. Appropriate statistical measures to evaluate the performance of genetic risk prediction models are required. Previous studies have mainly focused on the use of the area under the receiver operating characteristic (ROC) curve, or AUC, to judge the predictive value of genetic tests. However, AUC has its limitations and should be complemented by other measures. In this study, we develop a novel unifying statistical framework that connects a large variety of predictive indices together. We showed that, given the overall disease probability and the level of variance in total liability (or heritability) explained by the genetic variants, we can estimate analytically a large variety of prediction metrics, for example the AUC, the mean risk difference between cases and non-cases, the net reclassification improvement (ability to reclassify people into high- and low-risk categories), the proportion of cases explained by a specific percentile of population at the highest risk, the variance of predicted risks, and the risk at any percentile. We also demonstrate how to construct graphs to visualize the performance of risk models, such as the ROC curve, the density of risks, and the predictiveness curve (disease risk plotted against risk percentile). The results from simulations match very well with our theoretical estimates. Finally we apply the methodology to nine complex diseases, evaluating the predictive power of genetic tests based on known susceptibility variants for each trait.\",\n \"corpus_id\": 25977515,\n \"score\": 2\n },\n {\n \"doc_id\": \"22247263\",\n \"title\": \"Bioinformatics for personal genome interpretation.\",\n \"abstract\": \"An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship between genotype and phenotype. Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes. Some of these use intra-species genetic variability as a means for better understanding this relationship. In addition, several online resources are now dedicated to collecting single nucleotide variants and other types of variants, and annotating their functional effects and associations with phenotypic traits. This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants. In this work, we review the most important developments in the field--the databases and bioinformatics tools that will be of utmost importance in our concerted effort to interpret the human variome.\",\n \"corpus_id\": 1691561,\n \"score\": 2\n },\n {\n \"doc_id\": \"22549284\",\n \"title\": \"Whole-genome sequencing in personalized therapeutics.\",\n \"abstract\": \"Eleven years since the initial drafts of the human genome were published, we have begun to see the first examples of the application of whole-genome sequencing to personalized diagnosis and therapeutics. The exponential decline in sequencing costs and the constant improvement in these technologies promise to further advance the use of a patient's full genetic profile in the clinic. However, realizing the potential benefit of such sequencing will require a concerted effort by science, medicine, law, and management. In this review, we discuss current approaches to decoding the 6 billion-letter genetic code of a whole genome in a clinical context, give current examples of translating this information into therapy-guiding knowledge, and list the challenges that will need to be surmounted before these powerful data can be fully exploited to forward the goals of personalized medicine.\",\n \"corpus_id\": 4381014,\n \"score\": 2\n },\n {\n \"doc_id\": \"22847385\",\n \"title\": \"Whole-genome and whole-exome sequencing in neurological diseases.\",\n \"abstract\": \"Genetic risk factors that underlie many rare and common neurological disorders remain poorly understood because of the multifactorial and heterogeneous nature of these complex traits. With the decreasing cost of massively parallel sequencing technologies, whole-genome and whole-exome sequencing will soon allow the characterization of the full spectrum of sequence and structural variants present in each individual. Methods are being developed to parse the huge amount of genomic data and to sift out which variants are associated with diseases. Numerous challenges are inherent in the identification of rare and common variants that have a role in complex neurological diseases, and tools are being developed to overcome these challenges. Given that genomic data will soon be the main driver towards the goal of personalized medicine, future developments in the production and interpretation of data, as well as in ethics and counselling, will be needed for whole-genome and whole-exome sequencing to be used as informative tools in a clinical setting.\",\n \"corpus_id\": 2585584,\n \"score\": 2\n },\n {\n \"doc_id\": \"22962312\",\n \"title\": \"DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.\",\n \"abstract\": \"Patients with developmental disorders often harbour sub-microscopic deletions or duplications that lead to a disruption of normal gene expression or perturbation in the copy number of dosage-sensitive genes. Clinical interpretation for such patients in isolation is hindered by the rarity and novelty of such disorders. The DECIPHER project (https://decipher.sanger.ac.uk) was established in 2004 as an accessible online repository of genomic and associated phenotypic data with the primary goal of aiding the clinical interpretation of rare copy-number variants (CNVs). DECIPHER integrates information from a variety of bioinformatics resources and uses visualization tools to identify potential disease genes within a CNV. A two-tier access system permits clinicians and clinical scientists to maintain confidential linked anonymous records of phenotypes and CNVs for their patients that, with informed consent, can subsequently be shared with the wider clinical genetics and research communities. Advances in next-generation sequencing technologies are making it practical and affordable to sequence the whole exome/genome of patients who display features suggestive of a genetic disorder. This approach enables the identification of smaller intragenic mutations including single-nucleotide variants that are not accessible even with high-resolution genomic array analysis. This article briefly summarizes the current status and achievements of the DECIPHER project and looks ahead to the opportunities and challenges of jointly analysing structural and sequence variation in the human genome.\",\n \"corpus_id\": 10645012,\n \"score\": 2\n },\n {\n \"doc_id\": \"23164068\",\n \"title\": \"Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.\",\n \"abstract\": \"UNLABELLED: BACKGROUND: Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection. In addition the use of platform related sequencing error models can help in the recovery of ambiguous genotypes from lower coverage data. DESCRIPTION: We have developed a whole genome database of human genetic variations, Huvariome, determined by whole genome deep sequencing data with high coverage and low error rates. The database was designed to be sequencing technology independent but is currently populated with 165 individual whole genomes consisting of small pedigrees and matched tumor/normal samples sequenced with the Complete Genomics sequencing platform. Common variants have been determined for a Benelux population cohort and represented as genotypes alongside the results of two sets of control data (73 of the 165 genomes), Huvariome Core which comprises 31 healthy individuals from the Benelux region, and Diversity Panel consisting of 46 healthy individuals representing 10 different populations and 21 samples in three Pedigrees. Users can query the database by gene or position via a web interface and the results are displayed as the frequency of the variations as detected in the datasets. We demonstrate that Huvariome can provide accurate reference allele frequencies to disambiguate sequencing inconsistencies produced in resequencing experiments. Huvariome has been used to support the selection of candidate cardiomyopathy related genes which have a homozygous genotype in the reference cohorts. This database allows the users to see which selected variants are common variants (> 5% minor allele frequency) in the Huvariome core samples, thus aiding in the selection of potentially pathogenic variants by filtering out common variants that are not listed in one of the other public genomic variation databases. The no-call rate and the accuracy of allele calling in Huvariome provides the user with the possibility of identifying platform dependent errors associated with specific regions of the human genome. CONCLUSION: Huvariome is a simple to use resource for validation of resequencing results obtained by NGS experiments. The high sequence coverage and low error rates provide scientists with the ability to remove false positive results from pedigree studies. Results are returned via a web interface that displays location-based genetic variation frequency, impact on protein function, association with known genetic variations and a quality score of the variation base derived from Huvariome Core and the Diversity Panel data. These results may be used to identify and prioritize rare variants that, for example, might be disease relevant. In testing the accuracy of the Huvariome database, alleles of a selection of ambiguously called coding single nucleotide variants were successfully predicted in all cases. Data protection of individuals is ensured by restricted access to patient derived genomes from the host institution which is relevant for future molecular diagnostics.\",\n \"corpus_id\": 8245048,\n \"score\": 2\n },\n {\n \"doc_id\": \"23962656\",\n \"title\": \"Towards precision medicine: advances in computational approaches for the analysis of human variants.\",\n \"abstract\": \"Variations and similarities in our individual genomes are part of our history, our heritage, and our identity. Some human genomic variants are associated with common traits such as hair and eye color, while others are associated with susceptibility to disease or response to drug treatment. Identifying the human variations producing clinically relevant phenotypic changes is critical for providing accurate and personalized diagnosis, prognosis, and treatment for diseases. Furthermore, a better understanding of the molecular underpinning of disease can lead to development of new drug targets for precision medicine. Several resources have been designed for collecting and storing human genomic variations in highly structured, easily accessible databases. Unfortunately, a vast amount of information about these genetic variants and their functional and phenotypic associations is currently buried in the literature, only accessible by manual curation or sophisticated text text-mining technology to extract the relevant information. In addition, the low cost of sequencing technologies coupled with increasing computational power has enabled the development of numerous computational methodologies to predict the pathogenicity of human variants. This review provides a detailed comparison of current human variant resources, including HGMD, OMIM, ClinVar, and UniProt/Swiss-Prot, followed by an overview of the computational methods and techniques used to leverage the available data to predict novel deleterious variants. We expect these resources and tools to become the foundation for understanding the molecular details of genomic variants leading to disease, which in turn will enable the promise of precision medicine.\",\n \"corpus_id\": 13169513,\n \"score\": 2\n },\n {\n \"doc_id\": \"24150940\",\n \"title\": \"DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.\",\n \"abstract\": \"The DECIPHER database (https://decipher.sanger.ac.uk/) is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype-phenotype characteristics and highlights potentially pathogenic genes. In a significant development, we have extended DECIPHER from a database of just copy-number variants to allow upload, annotation and analysis of sequence variants such as single nucleotide variants (SNVs) and InDels. Other notable developments in DECIPHER include a purpose-built, customizable and interactive genome browser to aid combined visualization and interpretation of sequence and copy-number variation against informative datasets of pathogenic and population variation. We have also introduced several new features to our deposition and analysis interface. This article provides an update to the DECIPHER database, an earlier instance of which has been described elsewhere [Swaminathan et al. (2012) DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet., 21, R37-R44].\",\n \"corpus_id\": 123692,\n \"score\": 2\n },\n {\n \"doc_id\": \"24162188\",\n \"title\": \"Improved exome prioritization of disease genes through cross-species phenotype comparison.\",\n \"abstract\": \"Numerous new disease-gene associations have been identified by whole-exome sequencing studies in the last few years. However, many cases remain unsolved due to the sheer number of candidate variants remaining after common filtering strategies such as removing low quality and common variants and those deemed unlikely to be pathogenic. The observation that each of our genomes contains about 100 genuine loss-of-function variants makes identification of the causative mutation problematic when using these strategies alone. We propose using the wealth of genotype to phenotype data that already exists from model organism studies to assess the potential impact of these exome variants. Here, we introduce PHenotypic Interpretation of Variants in Exomes (PHIVE), an algorithm that integrates the calculation of phenotype similarity between human diseases and genetically modified mouse models with evaluation of the variants according to allele frequency, pathogenicity, and mode of inheritance approaches in our Exomiser tool. Large-scale validation of PHIVE analysis using 100,000 exomes containing known mutations demonstrated a substantial improvement (up to 54.1-fold) over purely variant-based (frequency and pathogenicity) methods with the correct gene recalled as the top hit in up to 83% of samples, corresponding to an area under the ROC curve of >95%. We conclude that incorporation of phenotype data can play a vital role in translational bioinformatics and propose that exome sequencing projects should systematically capture clinical phenotypes to take advantage of the strategy presented here.\",\n \"corpus_id\": 20782582,\n \"score\": 2\n },\n {\n \"doc_id\": \"24510652\",\n \"title\": \"Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis.\",\n \"abstract\": \"Over the last several years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test under particular circumstances in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing but rather the analysis and interpretation. Interpretation of genetic findings in a clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires the development of novel or repositioned analysis tools, methodologies, and processes. This unit provides an overview of these items. Specific challenges related to implementation in a clinical setting are discussed.\",\n \"corpus_id\": 38226022,\n \"score\": 2\n },\n {\n \"doc_id\": \"25188385\",\n \"title\": \"A probabilistic model to predict clinical phenotypic traits from genome sequencing.\",\n \"abstract\": \"Genetic screening is becoming possible on an unprecedented scale. However, its utility remains controversial. Although most variant genotypes cannot be easily interpreted, many individuals nevertheless attempt to interpret their genetic information. Initiatives such as the Personal Genome Project (PGP) and Illumina's Understand Your Genome are sequencing thousands of adults, collecting phenotypic information and developing computational pipelines to identify the most important variant genotypes harbored by each individual. These pipelines consider database and allele frequency annotations and bioinformatics classifications. We propose that the next step will be to integrate these different sources of information to estimate the probability that a given individual has specific phenotypes of clinical interest. To this end, we have designed a Bayesian probabilistic model to predict the probability of dichotomous phenotypes. When applied to a cohort from PGP, predictions of Gilbert syndrome, Graves' disease, non-Hodgkin lymphoma, and various blood groups were accurate, as individuals manifesting the phenotype in question exhibited the highest, or among the highest, predicted probabilities. Thirty-eight PGP phenotypes (26%) were predicted with area-under-the-ROC curve (AUC)>0.7, and 23 (15.8%) of these were statistically significant, based on permutation tests. Moreover, in a Critical Assessment of Genome Interpretation (CAGI) blinded prediction experiment, the models were used to match 77 PGP genomes to phenotypic profiles, generating the most accurate prediction of 16 submissions, according to an independent assessor. Although the models are currently insufficiently accurate for diagnostic utility, we expect their performance to improve with growth of publicly available genomics data and model refinement by domain experts.\",\n \"corpus_id\": 18960629,\n \"score\": 2\n },\n {\n \"doc_id\": \"25519328\",\n \"title\": \"A dual-clustering framework for association screening with whole genome sequencing data and longitudinal traits.\",\n \"abstract\": \"Current sequencing technology enables generation of whole genome sequencing data sets that contain a high density of rare variants, each of which is carried by, at most, 5% of the sampled subjects. Such variants are involved in the etiology of most common diseases in humans. These diseases can be studied by relevant longitudinal phenotype traits. Tests for association between such genotype information and longitudinal traits allow the study of the function of rare variants in complex human disorders. In this paper, we propose an association-screening framework that highlights the genotypic differences observed on rare variants and the longitudinal nature of phenotypes. In particular, both variants within a gene and longitudinal phenotypes are used to create partitions of subjects. Association between the 2 sets of constructed partitions is then evaluated. We apply the proposed strategy to the simulated data from the Genetic Analysis Workshop 18 and compare the obtained results with those from sequence kernel association test using the receiver operating characteristic curves.\",\n \"corpus_id\": 54631532,\n \"score\": 2\n },\n {\n \"doc_id\": \"25519339\",\n \"title\": \"Prediction of genetic contributions to complex traits using whole genome sequencing data.\",\n \"abstract\": \"Although markers identified by genome-wide association studies have individually strong statistical significance, their performance in prediction remains limited. Our goal was to use animal breeding genomic prediction models to predict additive genetic contributions for systolic blood pressure (SBP) using whole genome sequencing data with different validation designs. The additive genetic contributions of SBP were estimated via linear mixed model. Rare variants (MAF<0.05) were collapsed through the k-means method to create a \\\"collapsed single-nucleotide polymorphisms.\\\" Prediction of the additive genomic contributions of SBP was conducted using genomic Best Linear Unbiased Predictor (GBLUP) and BayesCπ. Estimates of predictive accuracy were compared using common single-nucleotide polymorphisms (SNPs) versus common and collapsed SNPs, and for prediction within and across families. The additive genetic variance of SBP contributed to 18% of the phenotypic variance (h(2) = 0.18). BayesCπ had slightly better prediction accuracies than GBLUP. In both models, within-family predictions had higher accuracies both in the training and testing set than didacross-family design. Collapsing rare variants via the k-means method and adding to the common SNPs did not improve prediction accuracies. The prediction model, including both pedigree and genomic information, achieved a slightly higher accuracy than using either source of information alone. Prediction of genetic contributions to complex traits is feasible using whole genome sequencing and statistical methods borrowed from animal breeding. The relatedness of individuals between the training and testing set strongly affected the performance of prediction models. Methods for inclusion of rare variants in these models need more development.\",\n \"corpus_id\": 17397555,\n \"score\": 2\n },\n {\n \"doc_id\": \"25733939\",\n \"title\": \"The Human Genome Project, and recent advances in personalized genomics.\",\n \"abstract\": \"The language of \\\"personalized medicine\\\" and \\\"personal genomics\\\" has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient's health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the \\\"technological imperative\\\", due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"26046366\",\n \"title\": \"Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.\",\n \"abstract\": \"Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.\",\n \"corpus_id\": 22813281,\n \"score\": 2\n },\n {\n \"doc_id\": \"26448358\",\n \"title\": \"Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.\",\n \"abstract\": \"High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing, prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies. There are significant barriers to realizing this goal that are related to the difficult task of interpreting personal genetic variation. A comprehensive, widely accessible application for interpretation of whole genome sequence data is needed. Here, we present a series of methods for identification of genetic variants and genotypes with clinical associations, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios. We demonstrate application of these methods for disease and drug response prognostication in whole genome sequence data from twelve unrelated adults, and for disease gene discovery in one father-mother-child trio with apparently simplex congenital ventricular arrhythmia. In doing so we identify clinically actionable inherited disease risk and drug response genotypes in pre-symptomatic individuals. We also nominate a new candidate gene in congenital arrhythmia, ATP2B4, and provide experimental evidence of a regulatory role for variants discovered using this framework.\",\n \"corpus_id\": 18200967,\n \"score\": 2\n },\n {\n \"doc_id\": \"27666372\",\n \"title\": \"Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project.\",\n \"abstract\": \"Massively parallel whole-genome sequencing (WGS) data have ushered in a new era in human genetics. These data are now being used to understand the role of rare variants in complex traits and to advance the goals of precision medicine. The technological and computing advances that have enabled us to generate WGS data on thousands of individuals have also outpaced our ability to perform analyses in scientifically and statistically rigorous and thoughtful ways. The past several years have witnessed the application of whole-exome sequencing (WES) to complex traits and diseases. From our analysis of NHLBI Exome Sequencing Project (ESP) data, not only have a number of important disease and complex trait association findings emerged, but our collective experience offers some valuable lessons for WGS initiatives. These include caveats associated with generating automated pipelines for quality control and analysis of rare variants; the importance of studying minority populations; sample size requirements and efficient study designs for identifying rare-variant associations; and the significance of incidental findings in population-based genetic research. With the ESP as an example, we offer guidance and a framework on how to conduct a large-scale association study in the era of WGS.\",\n \"corpus_id\": 42260652,\n \"score\": 2\n },\n {\n \"doc_id\": \"27725664\",\n \"title\": \"Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.\",\n \"abstract\": \"To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=-0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations.\",\n \"corpus_id\": 1065990,\n \"score\": 2\n },\n {\n \"doc_id\": \"28039885\",\n \"title\": \"Rare variant association test with multiple phenotypes.\",\n \"abstract\": \"Although genome-wide association studies (GWAS) have now discovered thousands of genetic variants associated with common traits, such variants cannot explain the large degree of \\\"missing heritability,\\\" likely due to rare variants. The advent of next generation sequencing technology has allowed rare variant detection and association with common traits, often by investigating specific genomic regions for rare variant effects on a trait. Although multiple correlated phenotypes are often concurrently observed in GWAS, most studies analyze only single phenotypes, which may lessen statistical power. To increase power, multivariate analyses, which consider correlations between multiple phenotypes, can be used. However, few existing multivariant analyses can identify rare variants for assessing multiple phenotypes. Here, we propose Multivariate Association Analysis using Score Statistics (MAAUSS), to identify rare variants associated with multiple phenotypes, based on the widely used sequence kernel association test (SKAT) for a single phenotype. We applied MAAUSS to whole exome sequencing (WES) data from a Korean population of 1,058 subjects to discover genes associated with multiple traits of liver function. We then assessed validation of those genes by a replication study, using an independent dataset of 3,445 individuals. Notably, we detected the gene ZNF620 among five significant genes. We then performed a simulation study to compare MAAUSS's performance with existing methods. Overall, MAAUSS successfully conserved type 1 error rates and in many cases had a higher power than the existing methods. This study illustrates a feasible and straightforward approach for identifying rare variants correlated with multiple phenotypes, with likely relevance to missing heritability.\",\n \"corpus_id\": 4525299,\n \"score\": 2\n },\n {\n \"doc_id\": \"29704323\",\n \"title\": \"Machine learning in schizophrenia genomics, a case-control study using 5,090 exomes.\",\n \"abstract\": \"Our hypothesis is that machine learning (ML) analysis of whole exome sequencing (WES) data can be used to identify individuals at high risk for schizophrenia (SCZ). This study applies ML to WES data from 2,545 individuals with SCZ and 2,545 unaffected individuals, accessed via the database of genotypes and phenotypes (dbGaP). Single nucleotide variants and small insertions and deletions were annotated by ANNOVAR using the reference genome hg19/GRCh37. Rare (predicted functional) variants with a minor allele frequency ≤1% and genotype quality ≥90 including missense, frameshift, stop gain, stop loss, intronic, and exonic splicing variants were selected. A file containing all cases and controls, the names of genes with variants meeting our criteria, and the number of variants per gene for each individual, was used for ML analysis. The supervised machine-learning algorithm used the patterns of variants observed in the different genes to determine which subset of genes can best predict that an individual is affected. Seventy percent of the data was used to train the algorithm and the remaining 30% of data (n = 1,526) was used to evaluate its efficiency. The supervised ML algorithm, gradient boosted trees with regularization (eXtreme Gradient Boosting implementation) was the best performing algorithm yielding promising results (accuracy: 85.7%, specificity: 86.6%, sensitivity: 84.9%, area under the receiver-operator characteristic curve: 0.95). The top 50 features (genes) of the algorithm were analyzed using bioinformatics resources for new insights about the pathophysiology of SCZ. This manuscript presents a novel predictor which could potentially enable studies exploring disease-modifying intervention in the early stages of the disease.\",\n \"corpus_id\": 13809018,\n \"score\": 2\n },\n {\n \"doc_id\": \"20193048\",\n \"title\": \"The 1000 Genomes Project: new opportunities for research and social challenges.\",\n \"abstract\": \"The 1000 Genomes Project, an international collaboration, is sequencing the whole genome of approximately 2,000 individuals from different worldwide populations. The central goal of this project is to describe most of the genetic variation that occurs at a population frequency greater than 1%. The results of this project will allow scientists to identify genetic variation at an unprecedented degree of resolution and will also help improve the imputation methods for determining unobserved genetic variants that are not represented on current genotyping arrays. By identifying novel or rare functional genetic variants, researchers will be able to pinpoint disease-causing genes in genomic regions initially identified by association studies. This level of detailed sequence information will also improve our knowledge of the evolutionary processes and the genomic patterns that have shaped the human species as we know it today. The new data will also lay the foundation for future clinical applications, such as prediction of disease susceptibility and drug response. However, the forthcoming availability of whole genome sequences at affordable prices will raise ethical concerns and pose potential threats to individual privacy. Nevertheless, we believe that these potential risks are outweighed by the benefits in terms of diagnosis and research, so long as rigorous safeguards are kept in place through legislation that prevents discrimination on the basis of the results of genetic testing.\",\n \"corpus_id\": 14555018,\n \"score\": 1\n },\n {\n \"doc_id\": \"20373666\",\n \"title\": \"Personal genomes in progress: from the human genome project to the personal genome project.\",\n \"abstract\": \"The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007--even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polylmorphisms, this has caused a significant rise in interest in correlating genome sequences with comprehensive environmental and trait data (GET). The cost of electronic health records, imaging, and microbial, immunological, and behavioral data are also dropping quickly. Sharing such integrated GET datasets and their interpretations with a diversity of researchers and research subjects highlights the need for informed-consent models capable of addressing novel privacy and other issues, as well as for flexible data-sharing resources that make materials and data available with minimum restrictions on use. This article examines the Personal Genome Project's effort to develop a GET database as a public genomics resource broadly accessible to both researchers and research participants, while pursuing the highest standards in research ethics.\",\n \"corpus_id\": 263624552,\n \"score\": 1\n },\n {\n \"doc_id\": \"21121034\",\n \"title\": \"GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROM POPULATION GENOMICS TO PERSONALIZED MEDICINE - Session Introduction.\",\n \"abstract\": \"Genome-wide associations studies (GWAS) have been very successful in identifying common genetic variation associated to numerous complex diseases [1]. However, most of the identified common genetic variants appear to confer modest risk and few causal alleles have been identified [2]. Furthermore, these associations account for a small portion of the total heritability of inherited disease variation [1]. This has led to the reexamination of the contribution of environment, gene-gene and gene-environment interactions, and rare genetic variants in complex diseases [1, 3, 4]. There is strong evidence that rare variants play an important role in complex disease etiology and may have larger genetic effects than common variants [2]. Currently, much of what we know regarding the contribution of rare genetic variants to disease risk is based on a limited number of phenotypes and candidate genes. However, rapid advancement of second generation sequencing technologies will invariably lead to widespread association studies comparing whole exome and eventually whole genome sequencing of cases and controls. A tremendous challenge for enabling these \\\"next generation\\\" medical genomic studies is developing statistical approaches for correlating rare genetic variants with disease outcome. The analysis of rare variants is challenging since methods used for common variants are woefully underpowered. Therefore, methods that can deal with genetic heterogeneity at the trait-associated locus have been developed to analyze rare variants. These methods instead analyzing individual variants analyze variants within a region/gene as a group and usually rely on collapsing. They can be applied to both in cases vs. controls and quantitative trait studies are needed. The paper of Bansal et al. in this volume describes the application of a number of statistical methods for testing associations between rare variants in two genes to obesity. The authors considered the relative merits of the different methods as well as important implementation details, such as the leveraging of genomic annotations and determining p-values. Knowledge of haplotypes can increase the power of GWAS studies and also highlight associations that are impossible to detect without haplotype phase (e.g. loss of heterozygosity). Even more complicated phase-dependent interactions of variants in linkage equilibrium have also been suggested as possible causes of missing heritability. In their work, Hallsorsson et al. formulate algorithmic strategies for haplotype phasing by multi-assembly of shared haplotypes from next-generation sequencing data. These methods would allow testing haplotypes harboring rare variants for association and potentially increase their explanatory power. Since single SNP tests are often underpowered in rare variant association analysis, Zeggini and Asimit propose a locus-based method that has high power in the presence of rare variants and that incorporate base quality scores available for sequencing data. Their results suggest that this multi-marker approach may be best suited for smaller regions, or after some filtering to reduce the number of SNPs that are jointly tested to reduce loss of power due to multiple-testing adjustments. Finally, the paper of Zhou et al., presents a penalized regression framework for association testing on sequence data, in the presence of both common and rare variants. This method also introduces the use of weights to incorporate available biological information on the variants. Although these tactics improve both false positive and false negative rates, they represent an incremental development and there is still significant room for improvement. With the development of sequencing technologies and methods to detect complex trait rare variant associations many new and exciting discovery are imminent. The analysis of rare variants is still in its infancy and the next few years promises to produce many new methods to meet the special demands of analyzing this type of data. Note from Publisher: This article contains the abstract and references.\",\n \"corpus_id\": 42856307,\n \"score\": 1\n },\n {\n \"doc_id\": \"21811411\",\n \"title\": \"Rare and common regulatory variation in population-scale sequenced human genomes.\",\n \"abstract\": \"Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs) when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs) discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.\",\n \"corpus_id\": 17801771,\n \"score\": 1\n },\n {\n \"doc_id\": \"21881504\",\n \"title\": \"Whole exome and whole genome sequencing.\",\n \"abstract\": \"PURPOSE OF REVIEW: The purpose of this review is to describe the new DNA sequencing technologies referred to as next-generation sequencing (NGS). These new methods are becoming central to research in human disease and are starting to be used in routine clinical care. RECENT FINDINGS: Advances in instrumentation have dramatically reduced the cost of DNA sequencing. An individual's entire genome can now be sequenced for $7500. In addition, the software needed to analyze and help interpret this data is rapidly improving. This technology has been used by researchers to discover new genetic disorders and new disease associations. In the clinic, it can define the etiology in patients with undiagnosed genetic disorders and identify mutations in a cancer to help guide chemotherapy. SUMMARY: Here we discuss how whole-exome sequencing and whole-genome sequencing are used in basic research and clinical care. These new techniques promise to speed research and affect how healthcare is delivered.\",\n \"corpus_id\": 263623356,\n \"score\": 1\n },\n {\n \"doc_id\": \"22128050\",\n \"title\": \"Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.\",\n \"abstract\": \"Genetic Analysis Workshop 17 (GAW17) focused on the transition from genome-wide association study designs and methods to the study designs and statistical genetic methods that will be required for the analysis of next-generation sequence data including both common and rare sequence variants. In the 166 contributions to GAW17, a wide variety of statistical methods were applied to simulated traits in population- and family-based samples, and results from these analyses were compared to the known generating model. In general, many of the statistical genetic methods used in the population-based sample identified causal sequence variants (SVs) when the estimated locus-specific heritability, as measured in the population-based sample, was greater than about 0.08. However, SVs with locus-specific heritabilities less than 0.03 were rarely identified consistently. In the family-based samples, many of the methods detected SVs that were rarer than those detected in the population-based sample, but the estimated locus-specific heritabilities for these rare SVs, as measured in the family-based samples, were substantially higher (>0.2) than their corresponding heritabilities in the population-based samples. Substantial inflation of the type I error rate was observed across a wide variety of statistical methods. Although many of the contributions found little inflation in type I error for Q4, a trait with no causal SVs, type I error rates for Q1 and Q2 were well above their nominal levels with the inflation for Q1 being higher than that for Q2. It seems likely that this inflation in type I error is due to correlations among SVs.\",\n \"corpus_id\": 24792051,\n \"score\": 1\n },\n {\n \"doc_id\": \"22344227\",\n \"title\": \"Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.\",\n \"abstract\": \"PURPOSE: The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. METHODS: These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. RESULTS: The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. CONCLUSION: There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.\",\n \"corpus_id\": 13771383,\n \"score\": 1\n },\n {\n \"doc_id\": \"22403585\",\n \"title\": \"Bioinformatic Resources of microRNA Sequences, Gene Targets, and Genetic Variation.\",\n \"abstract\": \"Variation in quantitative gene expression has been observed in natural populations and associated with various complex traits/phenotypes such as risks for common diseases and drug response. MicroRNAs (miRNAs), a family of small, non-coding RNA molecules, have been demonstrated to be an important class of gene regulators that mostly downregulate gene expression at the post-transcriptional level. A comprehensive and reliable catalogue of miRNAs and miRNA gene targets is critical to understanding the gene regulatory networks. Though experimental approaches have been used to identify many miRNAs and their gene targets, due to cost and efficiency, currently miRNA and target identification still largely relies on computational algorithms. We reviewed several widely used bioinformatic resources of miRNA sequences and gene targets that take advantage of the unique characteristics of miRNA-mRNA interactions, experimental validation, as well as the integration of sequence-based evidence and microarray expression data. Furthermore, given the importance of miRNAs in regulating gene expression, elucidating expression quantitative trait loci involved with miRSNPs or miR-polymorphisms will help improve our understanding of complex traits. We reviewed the available resources of miRNA genetic variation, and the current progress (e.g., the 1000 Genomes Project) in detailing the genetic variation in miRNA-related single nucleotide polymorphisms (SNPs). We also provided our perspectives of the potential impact of next-generation sequencing on the research of miRNAs, gene targets, and miRSNPs. These bioinformatic resources may help interpret experimental and association study results, thus enhancing our knowledge of the dynamic gene regulatory networks and the physiological pathways for complex traits/phenotypes. Prospectively, these bioinformatic resources of miRNAs will need to address the challenges raised by the application of next-generation sequencing in miRNA research.\",\n \"corpus_id\": 13039940,\n \"score\": 1\n },\n {\n \"doc_id\": \"22811759\",\n \"title\": \"Limitations of the human reference genome for personalized genomics.\",\n \"abstract\": \"Data from the 1000 genomes project (1KGP) and Complete Genomics (CG) have dramatically increased the numbers of known genetic variants and challenge several assumptions about the reference genome and its uses in both clinical and research settings. Specifically, 34% of published array-based GWAS studies for a variety of diseases utilize probes that overlap unanticipated single nucleotide polymorphisms (SNPs), indels, or structural variants. Linkage disequilibrium (LD) block length depends on the numbers of markers used, and the mean LD block size decreases from 16 kb to 7 kb,when HapMap-based calculations are compared to blocks computed from1KGP data. Additionally, when 1KGP and CG variants are compared, 19% of the single nucleotide variants (SNVs) reported from common genomes are unique to one dataset; likely a result of differences in data collection methodology, alignment of reads to the reference genome, and variant-calling algorithms. Together these observations indicate that current research resources and informatics methods do not adequately account for the high level of variation that already exists in the human population and significant efforts are needed to create resources that can accurately assess personal genomics for health, disease, and predict treatment outcomes.\",\n \"corpus_id\": 18325651,\n \"score\": 1\n },\n {\n \"doc_id\": \"23097404\",\n \"title\": \"Breeding and Genetics Symposium: networks and pathways to guide genomic selection.\",\n \"abstract\": \"Many traits affecting profitability and sustainability of meat, milk, and fiber production are polygenic, with no single gene having an overwhelming influence on observed variation. No knowledge of the specific genes controlling these traits has been needed to make substantial improvement through selection. Significant gains have been made through phenotypic selection enhanced by pedigree relationships and continually improving statistical methodology. Genomic selection, recently enabled by assays for dense SNP located throughout the genome, promises to increase selection accuracy and accelerate genetic improvement by emphasizing the SNP most strongly correlated to phenotype although the genes and sequence variants affecting phenotype remain largely unknown. These genomic predictions theoretically rely on linkage disequilibrium (LD) between genotyped SNP and unknown functional variants, but familial linkage may increase effectiveness when predicting individuals related to those in the training data. Genomic selection with functional SNP genotypes should be less reliant on LD patterns shared by training and target populations, possibly allowing robust prediction across unrelated populations. Although the specific variants causing polygenic variation may never be known with certainty, a number of tools and resources can be used to identify those most likely to affect phenotype. Associations of dense SNP genotypes with phenotype provide a 1-dimensional approach for identifying genes affecting specific traits; in contrast, associations with multiple traits allow defining networks of genes interacting to affect correlated traits. Such networks are especially compelling when corroborated by existing functional annotation and established molecular pathways. The SNP occurring within network genes, obtained from public databases or derived from genome and transcriptome sequences, may be classified according to expected effects on gene products. As illustrated by functionally informed genomic predictions being more accurate than naive whole-genome predictions of beef tenderness, coupling evidence from livestock genotypes, phenotypes, gene expression, and genomic variants with existing knowledge of gene functions and interactions may provide greater insight into the genes and genomic mechanisms affecting polygenic traits and facilitate functional genomic selection for economically important traits.\",\n \"corpus_id\": 5743933,\n \"score\": 1\n },\n {\n \"doc_id\": \"23166519\",\n \"title\": \"A unified method for detecting secondary trait associations with rare variants: application to sequence data.\",\n \"abstract\": \"Next-generation sequencing has made possible the detection of rare variant (RV) associations with quantitative traits (QT). Due to high sequencing cost, many studies can only sequence a modest number of selected samples with extreme QT. Therefore association testing in individual studies can be underpowered. Besides the primary trait, many clinically important secondary traits are often measured. It is highly beneficial if multiple studies can be jointly analyzed for detecting associations with commonly measured traits. However, analyzing secondary traits in selected samples can be biased if sample ascertainment is not properly modeled. Some methods exist for analyzing secondary traits in selected samples, where some burden tests can be implemented. However p-values can only be evaluated analytically via asymptotic approximations, which may not be accurate. Additionally, potentially more powerful sequence kernel association tests, variable selection-based methods, and burden tests that require permutations cannot be incorporated. To overcome these limitations, we developed a unified method for analyzing secondary trait associations with RVs (STAR) in selected samples, incorporating all RV tests. Statistical significance can be evaluated either through permutations or analytically. STAR makes it possible to apply more powerful RV tests to analyze secondary trait associations. It also enables jointly analyzing multiple cohorts ascertained under different study designs, which greatly boosts power. The performance of STAR and commonly used RV association tests were comprehensively evaluated using simulation studies. STAR was also implemented to analyze a dataset from the SardiNIA project where samples with extreme low-density lipoprotein levels were sequenced. A significant association between LDLR and systolic blood pressure was identified, which is supported by pharmacogenetic studies. In summary, for sequencing studies, STAR is an important tool for detecting secondary-trait RV associations.\",\n \"corpus_id\": 846238,\n \"score\": 1\n },\n {\n \"doc_id\": \"23714750\",\n \"title\": \"The Genome of the Netherlands: design, and project goals.\",\n \"abstract\": \"Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.\",\n \"corpus_id\": 15265934,\n \"score\": 1\n },\n {\n \"doc_id\": \"24297551\",\n \"title\": \"Imputation-based assessment of next generation rare exome variant arrays.\",\n \"abstract\": \"A striking finding from recent large-scale sequencing efforts is that the vast majority of variants in the human genome are rare and found within single populations or lineages. These observations hold important implications for the design of the next round of disease variant discovery efforts-if genetic variants that influence disease risk follow the same trend, then we expect to see population-specific disease associations that require large sample sizes for detection. To address this challenge, and due to the still prohibitive cost of sequencing large cohorts, researchers have developed a new generation of low-cost genotyping arrays that assay rare variation previously identified from large exome sequencing studies. Genotyping approaches rely not only on directly observing variants, but also on phasing and imputation methods that use publicly available reference panels to infer unobserved variants in a study cohort. Rare variant exome arrays are intentionally enriched for variants likely to be disease causing, and here we assay the ability of the first commercially available rare exome variant array (the Illumina Infinium HumanExome BeadChip) to also tag other potentially damaging variants not molecularly assayed. Using full sequence data from chromosome 22 from the phase I 1000 Genomes Project, we evaluate three methods for imputation (BEAGLE, MaCH-Admix, and SHAPEIT2/IMPUTE2) with the rare exome variant array under varied study panel sizes, reference panel sizes, and LD structures via population differences. We find that imputation is more accurate across both the genome and exome for common variant arrays than the next generation array for all allele frequencies, including rare alleles. We also find that imputation is the least accurate in African populations, and accuracy is substantially improved for rare variants when the same population is included in the reference panel. Depending on the goals of GWAS researchers, our results will aid budget decisions by helping determine whether money is best spent sequencing the genomes of smaller sample sizes, genotyping larger sample sizes with rare and/or common variant arrays and imputing SNPs, or some combination of the two.\",\n \"corpus_id\": 6211724,\n \"score\": 1\n },\n {\n \"doc_id\": \"25152847\",\n \"title\": \"Genomic Variation: Lessons Learned from Whole-Genome CNV Analysis.\",\n \"abstract\": \"One of the most fundamental goals of the study of human genetics was to determine the relationship between genomic variation and human disease. The effects of large-scale structural variation, such as aneuploidy and other cytogenetically visible imbalances, as well as sequence-level variation, have been studied for several decades. However, compared to these, the impact of submicroscopic copy number variants (CNV) has only recently been appreciated. Despite this, lessons learned from the study of CNVs have already proven significant and broadly applicable. From expanding the concept of normal human variation to providing concrete examples of the utility of genomics in clinical care and challenging notions of the genetic architecture of complex disease, CNVs have provided valuable insights into the genomics of human health and development.\",\n \"corpus_id\": 16847333,\n \"score\": 1\n },\n {\n \"doc_id\": \"25378555\",\n \"title\": \"Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes.\",\n \"abstract\": \"Initial results from sequencing studies suggest that there are relatively few low-frequency (<5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency-large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant-common phenotype associations-11 132 cis-gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (<5%), respectively, low frequency-large effect associations comprised 7% of detectable cis-gene expression traits [89 of 1314 cis-eQTLs at P < 1 × 10(-06) (false discovery rate ∼5%)] and one of eight biomarker associations at P < 8 × 10(-10). Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect.\",\n \"corpus_id\": 15487729,\n \"score\": 1\n },\n {\n \"doc_id\": \"25765185\",\n \"title\": \"Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry.\",\n \"abstract\": \"BACKGROUND: The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; \\\"tent-dwelling\\\" Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage. RESULTS: We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 'loss-of-function' and 2,314 'deleterious' coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant's family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays. CONCLUSIONS: We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity.\",\n \"corpus_id\": 1621508,\n \"score\": 1\n },\n {\n \"doc_id\": \"26927186\",\n \"title\": \"Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine.\",\n \"abstract\": \"Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.\",\n \"corpus_id\": 2695531,\n \"score\": 1\n },\n {\n \"doc_id\": \"27184599\",\n \"title\": \"Coming of age: ten years of next-generation sequencing technologies.\",\n \"abstract\": \"Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. An astonishing complexity of genome architecture has been revealed, bringing these sequencing technologies to even greater advancements. Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.\",\n \"corpus_id\": 8295541,\n \"score\": 1\n },\n {\n \"doc_id\": \"27436001\",\n \"title\": \"Applications of the 1000 Genomes Project resources.\",\n \"abstract\": \"The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci, filtering non-pathogenic variants from exome, whole genome and cancer genome sequencing projects, and genetic analysis of population structure and molecular evolution. In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies.\",\n \"corpus_id\": 3621791,\n \"score\": 1\n },\n {\n \"doc_id\": \"27724973\",\n \"title\": \"The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.\",\n \"abstract\": \"BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. CONCLUSIONS: These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.\",\n \"corpus_id\": 15722345,\n \"score\": 1\n },\n {\n \"doc_id\": \"27822964\",\n \"title\": \"Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies.\",\n \"abstract\": \"Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.\",\n \"corpus_id\": 3730453,\n \"score\": 1\n },\n {\n \"doc_id\": \"27905878\",\n \"title\": \"Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein-Friesian cattle.\",\n \"abstract\": \"BACKGROUND: Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic prediction by using imputed sequence data or preselected SNPs from a genome-wide association study (GWAS) with imputed whole-genome sequence data. METHODS: Phenotypes were available for 5503 Holstein-Friesian bulls. Genotypes were imputed up to whole-genome sequence (13,789,029 segregating DNA variants) by using run 4 of the 1000 bull genomes project. The program GCTA was used to perform GWAS for protein yield (PY), somatic cell score (SCS) and interval from first to last insemination (IFL). From the GWAS, subsets of variants were selected and genomic relationship matrices (GRM) were used to estimate the variance explained in 2087 validation animals and to evaluate the genomic prediction ability. Finally, two GRM were fitted together in several models to evaluate the effect of selected variants that were in competition with all the other variants. RESULTS: The GRM based on full sequence data explained only marginally more genetic variation than that based on common SNP panels: for PY, SCS and IFL, genomic heritability improved from 0.81 to 0.83, 0.83 to 0.87 and 0.69 to 0.72, respectively. Sequence data also helped to identify more variants linked to quantitative trait loci and resulted in clearer GWAS peaks across the genome. The proportion of total variance explained by the selected variants combined in a GRM was considerably smaller than that explained by all variants (less than 0.31 for all traits). When selected variants were used, accuracy of genomic predictions decreased and bias increased. CONCLUSIONS: Although 35 to 42 variants were detected that together explained 13 to 19% of the total variance (18 to 23% of the genetic variance) when fitted alone, there was no advantage in using dense sequence information for genomic prediction in the Holstein data used in our study. Detection and selection of variants within a single breed are difficult due to long-range linkage disequilibrium. Stringent selection of variants resulted in more biased genomic predictions, although this might be due to the training population being the same dataset from which the selected variants were identified.\",\n \"corpus_id\": 879270,\n \"score\": 1\n },\n {\n \"doc_id\": \"27917525\",\n \"title\": \"A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next-generation sequencing.\",\n \"abstract\": \"In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F-distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high-dimensional genotype data. It is shown that approximate F-distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i.e., scenarios in which some genetic variants have relatively large effects on the phenotypes); GAMuT has higher power and is more appropriate for analyzing polygenic effects (i.e., effects from a large number of genetic variants each of which contributes a small amount to the phenotypes). MFLM and MANOVA are very flexible and can be used to perform association analysis for (i) rare variants, (ii) common variants, and (iii) a combination of rare and common variants. Although GAMuT was designed to analyze rare variants, it can be applied to analyze a combination of rare and common variants and it performs well when (1) the number of genetic variants is large and (2) each variant contributes a small amount to the phenotypes (i.e., polygenes). MFLM and MANOVA are fixed effect models that perform well for major gene association analysis. GAMuT can be viewed as an extension of sequence kernel association tests (SKAT). Both GAMuT and SKAT are more appropriate for analyzing polygenic effects and they perform well not only in the rare variant case, but also in the case of a combination of rare and common variants. Data analyses of European cohorts and the Trinity Students Study are presented to compare the performance of the two methods.\",\n \"corpus_id\": 13757678,\n \"score\": 1\n },\n {\n \"doc_id\": \"28035032\",\n \"title\": \"Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.\",\n \"abstract\": \"MOTIVATION: Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X). RESULTS: We have applied our classifier to compare call sets generated with different calling methods, including both single-sample and multi-sample callers. At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illuminas single-sample caller CASAVA, Real Time Genomics multisample variant caller, and the GATK UnifiedGenotyper, respectively. Since NGS sequencing data may be accompanied by genotype data for the same samples, either collected concurrent to sequencing or from a previous study, our method can be trained on each dataset to provide a more accurate computational validation of site calls compared to generic methods. Moreover, our method allows for adjustment based on allele frequency (e.g. a different set of criteria to determine quality for rare versus common variants) and thereby provides insight into sequencing characteristics that indicate call quality for variants of different frequencies. AVAILABILITY AND IMPLEMENTATION: Code is available on Github at: https://github.com/suyashss/variant_validation CONTACTS: : suyashs@stanford.edu or mtaub@jhsph.eduSupplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3799989,\n \"score\": 1\n },\n {\n \"doc_id\": \"28051073\",\n \"title\": \"Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project.\",\n \"abstract\": \"Providing ostensibly healthy individuals with personal results from whole-genome sequencing could lead to improved health and well-being via enhanced disease risk prediction, prevention, and diagnosis, but also poses practical and ethical challenges. Understanding how individuals react psychologically and behaviourally will be key in assessing the potential utility of personal whole-genome sequencing. We conducted an exploratory longitudinal cohort study in which quantitative surveys and in-depth qualitative interviews were conducted before and after personal results were returned to individuals who underwent whole-genome sequencing. The participants were offered a range of interpreted results, including Alzheimer's disease, type 2 diabetes, pharmacogenomics, rare disease-associated variants, and ancestry. They were also offered their raw data. Of the 35 participants at baseline, 29 (82.9%) completed the 6-month follow-up. In the quantitative surveys, test-related distress was low, although it was higher at 1-week than 6-month follow-up (Z=2.68, P=0.007). In the 6-month qualitative interviews, most participants felt happy or relieved about their results. A few were concerned, particularly about rare disease-associated variants and Alzheimer's disease results. Two of the 29 participants had sought clinical follow-up as a direct or indirect consequence of rare disease-associated variants results. Several had mentioned their results to their doctors. Some participants felt having their raw data might be medically useful to them in the future. The majority reported positive reactions to having their genomes sequenced, but there were notable exceptions to this. The impact and value of returning personal results from whole-genome sequencing when implemented on a larger scale remains to be seen.\",\n \"corpus_id\": 10313269,\n \"score\": 1\n },\n {\n \"doc_id\": \"28224672\",\n \"title\": \"PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.\",\n \"abstract\": \"Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed toward the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools. These areas include collection and distribution of benchmark datasets, their use for systematic large-scale method assessment, and the development of guidelines for reporting methods and their performance. For us, CAGI has provided a chance to experiment with new ideas, test the application areas of our methods, and network with other prediction method developers. In this article, we discuss our experiences and lessons learned from the various CAGI challenges. We describe our approaches, their performance, and impact of CAGI on our research. Finally, we discuss some of the possibilities that CAGI experiments have opened up and make some suggestions for future experiments.\",\n \"corpus_id\": 43059185,\n \"score\": 1\n },\n {\n \"doc_id\": \"28440912\",\n \"title\": \"Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.\",\n \"abstract\": \"Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of 10 variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene. Twenty-two pathogenicity predictors were assessed with a variety of accuracy measures for reliability in a medical context. Different assessment measures were combined in an overall ranking to provide more robust results. The R scripts used for assessment are publicly available from a GitHub repository for future use in similar assessment exercises. Despite a limited test-set size, our findings show a variety of results, with some methods performing significantly better. Methods combining different strategies frequently outperform simpler approaches. The best predictor, Yang&Zhou lab, uses a machine learning method combining an empirical energy function measuring protein stability with an evolutionary conservation term. The p16INK4a challenge highlights how subtle structural effects can neutralize otherwise deleterious variants.\",\n \"corpus_id\": 46850510,\n \"score\": 1\n },\n {\n \"doc_id\": \"28634997\",\n \"title\": \"Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.\",\n \"abstract\": \"Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.\",\n \"corpus_id\": 571850,\n \"score\": 1\n },\n {\n \"doc_id\": \"28938720\",\n \"title\": \"Deep whole-genome sequencing of 90 Han Chinese genomes.\",\n \"abstract\": \"Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency < 5%), including 5 813 503 single nucleotide polymorphisms, 1 169 199 InDels, and 17 927 structural variants. Using deep sequencing data, we have built a greatly expanded spectrum of genetic variation for the Han Chinese genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000 Genomes Project, as well as to other human genome projects.\",\n \"corpus_id\": 35588592,\n \"score\": 1\n },\n {\n \"doc_id\": \"28961785\",\n \"title\": \"FIRE: functional inference of genetic variants that regulate gene expression.\",\n \"abstract\": \"Motivation: Interpreting genetic variation in noncoding regions of the genome is an important challenge for personal genome analysis. One mechanism by which noncoding single nucleotide variants (SNVs) influence downstream phenotypes is through the regulation of gene expression. Methods to predict whether or not individual SNVs are likely to regulate gene expression would aid interpretation of variants of unknown significance identified in whole-genome sequencing studies. Results: We developed FIRE (Functional Inference of Regulators of Expression), a tool to score both noncoding and coding SNVs based on their potential to regulate the expression levels of nearby genes. FIRE consists of 23 random forests trained to recognize SNVs in cis-expression quantitative trait loci (cis-eQTLs) using a set of 92 genomic annotations as predictive features. FIRE scores discriminate cis-eQTL SNVs from non-eQTL SNVs in the training set with a cross-validated area under the receiver operating characteristic curve (AUC) of 0.807, and discriminate cis-eQTL SNVs shared across six populations of different ancestry from non-eQTL SNVs with an AUC of 0.939. FIRE scores are also predictive of cis-eQTL SNVs across a variety of tissue types. Availability and implementation: FIRE scores for genome-wide SNVs in hg19/GRCh37 are available for download at https://sites.google.com/site/fireregulatoryvariation/. Contact: nilah@stanford.edu. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4441565,\n \"score\": 1\n },\n {\n \"doc_id\": \"28984185\",\n \"title\": \"STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data.\",\n \"abstract\": \"BACKGROUND: Short tandem repeats (STRs) are found in many prokaryotic and eukaryotic genomes, and are commonly used as genetic markers, in particular for identity and parental testing in DNA forensics. The unstable expansion of some STRs was associated with various genetic disorders (e.g., the Huntington disease), and thus was used in genetic testing for screening individuals at high risk. Traditional STR analyses were based on the PCR amplification of STR loci followed by gel electrophoresis. With the availability of massive whole genome sequencing data, it becomes practical to mine STR profiles in silico from genome sequences. Software tools such as lobSTR and STR-FM have been developed to address these demands, which are, however, built upon whole genome reads mapping tools, and thus may not be sensitive enough. RESULTS: In this paper, we present a standalone software tool STRScan that uses a greedy algorithm for targeted STR profiling in next-generation sequencing (NGS) data. STRScan was tested on the whole genome sequencing data from Venter genome sequencing and 1000 Genomes Project. The results showed that STRScan can profile 20% more STRs in the target set that are missed by lobSTR. CONCLUSION: STRScan is particularly useful for the NGS-based targeted STR profiling, e.g., in genetic and human identity testing. STRScan is available as open-source software at http://darwin.informatics.indiana.edu/str/ .\",\n \"corpus_id\": 5110156,\n \"score\": 1\n },\n {\n \"doc_id\": \"29258987\",\n \"title\": \"The application of MutMap in forward genetic studies based on whole-genome sequencing.\",\n \"abstract\": \"Classical forward genetic analysis relies on construction of complicated progeny populations and development of many molecular markers for linkage analysis in genetic mapping, which is both time- and cost-consuming. The recently developed MutMap is a new forward genetic approach based on high-throughput next-generation sequencing technologies. It is more efficient and affordable than traditional methods. Moreover, new extended methods based on MutMap have been developed: MutMap+, which is based on self-crossing; MutMap-Gap, which is used to recognize the causative variations occurring in genome gap regions; QTL-seq, a method similar to MutMap for mapping quantitative trait loci. These methods are free from constructing complicated mapping population, genetic hybridization and linkage information. They have greatly accelerated the identification of genetic elements associated with interested phenotypic variation. Here, we review the basic principles of MutMap, and discuss their future applications in next generation sequencing-based forward genetic mapping and crop improvement.\",\n \"corpus_id\": 3872054,\n \"score\": 1\n },\n {\n \"doc_id\": \"29431110\",\n \"title\": \"The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.\",\n \"abstract\": \"BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.\",\n \"corpus_id\": 46753806,\n \"score\": 1\n },\n {\n \"doc_id\": \"20238084\",\n \"title\": \"Whole genome sequencing.\",\n \"abstract\": \"Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences. The reference-based assembly approach involves mapping each read to a reference genome sequence. We discuss methods for identifying genetic variation (single nucleotide polymorphisms, small indels, and copy number variants) and building haplotypes from genome assemblies, and discuss potential pitfalls. We expect methodologies to evolve rapidly as sequencing technologies improve and more human genomes are sequenced.\",\n \"corpus_id\": 260566168,\n \"score\": 0\n },\n {\n \"doc_id\": \"20946837\",\n \"title\": \"The fungal genome initiative and lessons learned from genome sequencing.\",\n \"abstract\": \"The sequence of Saccharomyces cerevisiae enabled systematic genome-wide experimental approaches, demonstrating the power of having the complete genome of an organism. The rapid impact of these methods on research in yeast mobilized an effort to expand genomic resources for other fungi. The \\\"fungal genome initiative\\\" represents an organized genome sequencing effort to promote comparative and evolutionary studies across the fungal kingdom. Through such an approach, scientists can not only better understand specific organisms but also illuminate the shared and unique aspects of fungal biology that underlie the importance of fungi in biomedical research, health, food production, and industry. To date, assembled genomes for over 100 fungi are available in public databases, and many more sequencing projects are underway. Here, we discuss both examples of findings from comparative analysis of fungal sequences, with a specific emphasis on yeast genomes, and on the analytical approaches taken to mine fungal genomes. New sequencing methods are accelerating comparative studies of fungi by reducing the cost and difficulty of sequencing. This has driven more common use of sequencing applications, such as to study genome-wide variation in populations or to deeply profile RNA transcripts. These and further technological innovations will continue to be piloted in yeasts and other fungi, and will expand the applications of sequencing to study fungal biology.\",\n \"corpus_id\": 10486841,\n \"score\": 0\n },\n {\n \"doc_id\": \"24599000\",\n \"title\": \"Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.\",\n \"abstract\": \"Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.\",\n \"corpus_id\": 18993255,\n \"score\": 0\n },\n {\n \"doc_id\": \"27067834\",\n \"title\": \"Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).\",\n \"abstract\": \"BACKGROUND: Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS: In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS: This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.\",\n \"corpus_id\": 12594090,\n \"score\": 0\n },\n {\n \"doc_id\": \"27068766\",\n \"title\": \"Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges.\",\n \"abstract\": \"Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.\",\n \"corpus_id\": 576744,\n \"score\": 0\n },\n {\n \"doc_id\": \"29345757\",\n \"title\": \"Whole genome sequencing analysis for cancer genomics and precision medicine.\",\n \"abstract\": \"Explosive advances in next-generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein-altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non-coding regions, including introns, regulatory elements and non-coding RNA. Structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can be used to comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signatures in cancer genomes and elucidate the functional or clinical implications of these unexplored genomic regions and mutational signatures. This review describes recently developed technical approaches for cancer WGS and the future direction of cancer WGS, and discusses its utility and limitations as an analysis platform and for mutation interpretation for cancer genomics and cancer precision medicine. Taking into account the diversity of cancer genomes and phenotypes, interpretation of abundant mutation information from WGS, especially non-coding and structure variants, requires the analysis of large-scale WGS data integrated with RNA-Seq, epigenomics, immuno-genomic and clinic-pathological information.\",\n \"corpus_id\": 3741533,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":92,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25111182\",\n \"title\": \"SpyAvidin hubs enable precise and ultrastable orthogonal nanoassembly.\",\n \"abstract\": \"The capture of biotin by streptavidin is an inspiration for supramolecular chemistry and a central tool for biological chemistry and nanotechnology, because of the rapid and exceptionally stable interaction. However, there is no robust orthogonal interaction to this hub, limiting the size and complexity of molecular assemblies that can be created. Here we combined traptavidin (a streptavidin variant maximizing biotin binding strength) with an orthogonal irreversible interaction. SpyTag is a peptide engineered to form a spontaneous isopeptide bond to its protein partner SpyCatcher. SpyTag or SpyCatcher was successfully fused to the C-terminus of Dead streptavidin subunits. We were able to generate chimeric tetramers with n (0 ≤ n ≤ 4) biotin binding sites and 4-n SpyTag or SpyCatcher binding sites. Chimeric SpyAvidin tetramers bound precise numbers of ligands fused to biotin or SpyTag/SpyCatcher. Mixing chimeric tetramers enabled assembly of SpyAvidin octamers (8 subunits) or eicosamers (20 subunits). We validated assemblies using electrophoresis and native mass spectrometry. Eicosameric SpyAvidin was used to cluster trimeric major histocompatibility complex (MHC) class I:β2-microglobulin:peptide complexes, generating an assembly with up to 56 components. MHC eicosamers surpassed the conventional MHC tetramers in acting as a powerful stimulus to T cell signaling. Combining ultrastable noncovalent with irreversible covalent interaction, SpyAvidins enable a simple route to create robust nanoarchitectures.\",\n \"corpus_id\": 13376591\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"22366317","title":"Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin.","abstract":"Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.","corpus_id":13927823,"score":2},{"doc_id":"24056174","title":"Plug-and-play pairing via defined divalent streptavidins.","abstract":"Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.","corpus_id":9595969,"score":2},{"doc_id":"24873508","title":"Dynamic supramolecular complexes constructed by orthogonal self-assembly.","abstract":"CONSPECTUS: Supramolecular complexes, including various low-molecular-mass structures and large molecular aggregates that are assembled by reversible and highly directional noncovalent interactions, have attracted more and more attention due to their fascinating and unconventional chemical and physical properties that are different from those of traditional architectures encountered by covalently linked backbones. Supramolecular complexes are by nature dynamic architectures considering the reversibility of noncovalent interactions by which small molecular monomers can assemble into specific architectures that are able to be repeatably reorganized through the assembly/disassembly processes under certain environmental factors such as temperature, concentration, and solvent conditions. The construction of supramolecular complexes by orthogonal self-assembly with different types of highly specific, noninterfering interactions is currently attracting considerable interest since they not only can dynamically self-assemble, but also can be tuned by various external stimuli through addressing each type of noncovalent interaction separately. Therefore, these dynamic supramolecular complexes, especially with external responsiveness, represent the most outstanding candidates for the future development of functional and smart materials, and even mimic the assembling process of natural systems. In this Account, we will summarize the recent advances of dynamic supramolecular complexes constructed by orthogonal self-assembly in soluiton in two sections: (1) Construction strategies for supramolecular complexes based on orthogonal self-assembly, whose dynamic behaviors with external responsiveness were not experimentally investigated but potentially existed due to the intrinsic reversibility of noncovalent bonds; (2) dynamic behaviors of multiresponsive supramolecular complexes, which were experimentally reported to exhibit reversible multi-responsiveness to external stimuli. Dynamic nature is one of intrinsic properties of supramolecular complexes constructed by self-assembly. Therefore, in the first section, we will describe the dynamic self-assembly in the construction of supramolecular complexes, but will focus on their external responsive dynamic behaviors in the second section. In addition, considering that an increasing number of supramolecular complexes constructed by biological building blocks through bio-orthogonal assembly as mimics of biological systems have been reported in recent years, in the second section we will also present some typical examples on such special dynamic biological supramolecular complexes. The final part of this Account is devoted to foreseeing the rapid development of dynamic supramolecular complexes toward applications in functional and smart materials and fundamental questions facing dynamic supramolecular complexes in the future.","corpus_id":5283533,"score":2},{"doc_id":"26787909","title":"Programmable polyproteams built using twin peptide superglues.","abstract":"Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable \"polyproteams\" should enable exploration of a new area of biological space.","corpus_id":4687927,"score":2},{"doc_id":"28989685","title":"Tuning SpyTag-SpyCatcher mutant pairs toward orthogonal reactivity encryption.","abstract":"Genetically encoded covalent peptide tagging technology, such as the SpyTag-SpyCatcher reaction, has emerged as a unique way to do chemistry with proteins. Herein, we report the reactivity engineering of SpyTag-SpyCatcher mutant pairs and show that distinct reactivity can be encrypted for the same reaction based on protein sequences of high similarity. Valuable features, including high selectivity, inverse temperature dependence and (nearly) orthogonal reactivity, could be achieved based on as few as three mutations. This demonstrates the robustness of the SpyTag-SpyCatcher reaction and the plasticity of its sequence specificity, pointing to a family of engineered protein chemistry tools.","corpus_id":23949264,"score":2},{"doc_id":"29662234","title":"Modular assembly of proteins on nanoparticles.","abstract":"Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.","corpus_id":4901820,"score":2},{"doc_id":"19259577","title":"Supramolecular self-assembly of dendrimers containing orthogonal binding motifs.","abstract":"Two orthogonal non-covalent binding sites, namely metal-ligand complexation of Ru and bipyridine and intermolecular hydrogen bonding, facilitate the self-assembly of a new type of supramolecular dendrimers.","corpus_id":262929368,"score":1},{"doc_id":"19425108","title":"Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction.","abstract":"Natural tetrameric streptavidin captures and immobilizes biotinylated molecules with ultra-tight binding (K(d) approximately 10(-13) to 10(-14) M). In contrast, engineered monomeric streptavidin offers reversible binding (K(d) approximately 10(-7) M). To develop an ideal engineered streptavidin which possesses both the immobilization capability of the natural streptavidin and the reversible interaction reactivity of the monomeric streptavidin, a pair of engineered biomaterials was designed through molecular modeling. This system consists of two recombinant components: an engineered monomeric streptavidin M6, which has a cysteine residue (C118) near the biotin binding site, and a cysteine containing biotinylation tag. Interactions between M6 and the biotinylated peptide tag go through a two-stage process (capture and immobilization) to generate a covalently linked complex. Biotinylation is essential in the capture stage. Once the biotin moiety in the biotinylated tag is captured by M6, the biotinylated tag can fold back and rotate on the surface of the complex with the biotinylated lysine in the peptide tag as the axis until the formationof a disulfide bond. Consequently, cysteine residue in different positions flanking the biotin residue in the biotinylation tag can successfully form a disulfide bond with M6. Intermolecular disulfide bond formation between M6 and the tag containing protein offers the immobilization capability to M6. In the presence of reducing agent and biotin, bound ligands can be dissociated. This system has the potential to extend the biotin-streptavidin technology to develop reusable biosensor/protein chips and bioreactors.","corpus_id":26377763,"score":1},{"doc_id":"20383133","title":"A streptavidin variant with slower biotin dissociation and increased mechanostability.","abstract":"Streptavidin binds biotin conjugates with exceptional stability but dissociation does occur, limiting its use in imaging, DNA amplification and nanotechnology. We identified a mutant streptavidin, traptavidin, with more than tenfold slower biotin dissociation, increased mechanical strength and improved thermostability; this resilience should enable diverse applications. FtsK, a motor protein important in chromosome segregation, rapidly displaced streptavidin from biotinylated DNA, whereas traptavidin resisted displacement, indicating the force generated by Ftsk translocation.","corpus_id":2988461,"score":1},{"doc_id":"20462407","title":"Binary polypeptide system for permanent and oriented protein immobilization.","abstract":"BACKGROUND: Many techniques in molecular biology, clinical diagnostics and biotechnology rely on binary affinity tags. The existing tags are based on either small molecules (e.g., biotin/streptavidin or glutathione/GST) or peptide tags (FLAG, Myc, HA, Strep-tag and His-tag). Among these, the biotin-streptavidin system is most popular due to the nearly irreversible interaction of biotin with the tetrameric protein, streptavidin. The major drawback of the stable biotin-streptavidin system, however, is that neither of the two tags can be added to a protein of interest via recombinant means (except for the Strep-tag case) leading to the requirement for chemical coupling. RESULTS: Here we report a new immobilization system which utilizes two monomeric polypeptides which self-assemble to produce non-covalent yet nearly irreversible complex which is stable in strong detergents, chaotropic agents, as well as in acids and alkali. Our system is based on the core region of the tetra-helical bundle known as the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex. This irreversible protein attachment system (IPAS) uses either a shortened syntaxin helix and fused SNAP25-synaptobrevin or a fused syntaxin-synaptobrevin and SNAP25 allowing a two-component system suitable for recombinant protein tagging, capture and immobilization. We also show that IPAS is suitable for use with traditional beads and chromatography, planar surfaces and Biacore, gold nanoparticles and for protein-protein interaction in solution. CONCLUSIONS: IPAS offers an alternative to chemical cross-linking, streptavidin-biotin system and to traditional peptide affinity tags and can be used for a wide range of applications in nanotechnology and molecular sciences.","corpus_id":3040277,"score":1},{"doc_id":"21241253","title":"How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer.","abstract":"The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein-ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin-Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin-Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin-Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.","corpus_id":28492457,"score":1},{"doc_id":"21551057","title":"Scaffold proteins: hubs for controlling the flow of cellular information.","abstract":"The spatial and temporal organization of molecules within a cell is critical for coordinating the many distinct activities carried out by the cell. In an increasing number of biological signaling processes, scaffold proteins have been found to play a central role in physically assembling the relevant molecular components. Although most scaffolds use a simple tethering mechanism to increase the efficiency of interaction between individual partner molecules, these proteins can also exert complex allosteric control over their partners and are themselves the target of regulation. Scaffold proteins offer a simple, flexible strategy for regulating selectivity in pathways, shaping output behaviors, and achieving new responses from preexisting signaling components. As a result, scaffold proteins have been exploited by evolution, pathogens, and cellular engineers to reshape cellular behavior.","corpus_id":6512196,"score":1},{"doc_id":"22102445","title":"Nanomechanics of streptavidin hubs for molecular materials.","abstract":"A new strategy is reported for creating protein-based nanomaterials by genetically fusing large polypeptides to monomeric streptavidin and exploiting the propensity of streptavidin monomers(SM) to self-assemble into stable tetramers. We have characterized the mechanical properties of streptavidin-linked structures and measured, for the first time, the mechanical strength of streptavidin tetramers themselves. Using streptavidin tetramers as molecular hubs offers a unique opportunity to create a variety of well-defined, self-assembled protein-based (nano)materials with unusual mechanical properties.","corpus_id":205242517,"score":1},{"doc_id":"22170585","title":"Advances in switchable supramolecular nanoassemblies.","abstract":"Supramolecular nanoassemblies are gaining increasing importance as promising new materials with considerable potential for novel and promising applications. Within supramolecular nanoassemblies the connectivity of the monomeric units is based on reversible noncovalent interactions, like van der Waals interactions, hydrogen bonding, or ionic interactions. As the strength of these interactions depends on the molecular surrounding, the formation of nanoassemblies in principle can be controlled externally by changing the environment and/or the molecular shape of the underlying monomer. This way it is not only possible to switch the self-assembly on or off, but also to change between different aggregation states. In this minireview we present some recent selected approaches to supramolecular stimuli-responsive nanoassemblies.","corpus_id":205595932,"score":1},{"doc_id":"22806584","title":"Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection.","abstract":"The coupling between the quaternary structure, stability and function of streptavidin makes it difficult to engineer a stable, high affinity monomer for biotechnology applications. For example, the binding pocket of streptavidin tetramer is comprised of residues from multiple subunits, which cannot be replicated in a single domain protein. However, rhizavidin from Rhizobium etli was recently shown to bind biotin with high affinity as a dimer without the hydrophobic tryptophan lid donated by an adjacent subunit. In particular, the binding site of rhizavidin uses residues from a single subunit to interact with bound biotin. We therefore postulated that replacing the binding site residues of streptavidin monomer with corresponding rhizavidin residues would lead to the design of a high affinity monomer useful for biotechnology applications. Here, we report the construction and characterization of a structural monomer, mSA, which combines the streptavidin and rhizavidin sequences to achieve optimized biophysical properties. First, the biotin affinity of mSA (K(d) = 2.8 nM) is the highest among nontetrameric streptavidin, allowing sensitive monovalent detection of biotinylated ligands. The monomer also has significantly higher stability (T(m) = 59.8 °C) and solubility than all other previously engineered monomers to ensure the molecule remains folded and functional during its application. Using fluorescence correlation spectroscopy, we show that mSA binds biotinylated targets as a monomer. We also show that the molecule can be used as a genetic tag to introduce biotin binding capability to a heterologous protein. For example, recombinantly fusing the monomer to a cell surface receptor allows direct labeling and imaging of transfected cells using biotinylated fluorophores. A stable and functional streptavidin monomer, such as mSA, should be a useful reagent for designing novel detection systems based on monovalent biotin interaction.","corpus_id":5140258,"score":1},{"doc_id":"22984964","title":"Kinetic stability of the streptavidin-biotin interaction enhanced in the gas phase.","abstract":"Results of the first detailed study of the structure and kinetic stability of the model high-affinity protein-ligand interaction between biotin (B) and the homotetrameric protein complex streptavidin (S(4)) in the gas phase are described. Collision cross sections (Ω) measured for protonated gaseous ions of free and ligand-bound truncated (residues 13-139) wild-type (WT) streptavidin, i.e., S(4)(n+) and (S(4)+4B)(n+) at charge states n = 12-16, were found to be independent of charge state and in agreement (within 10%) with values estimated for crystal structures reported for S(4) and (S(4)+4B). These results suggest that significant structural changes do not occur upon transfer of the complexes from solution to the gas phase by electrospray ionization. Temperature-dependent rate constants were measured for the loss of B from the protonated (S(4)+4B)(n+) ions. Over the temperature range investigated, the kinetic stability increases with decreasing charge state, from n = 16 to 13, but is indistinguishable for n = 12 and 13. A comparison of the activation energies (E(a)) measured for the loss of B from the (S(4)+4B)(13+) ions composed of WT streptavidin and five binding site mutants (Trp79Phe, Trp108Phe, Trp120Phe, Ser27Ala, and Tyr43Ala) suggests that at least some of the specific intermolecular interactions are preserved in the gas phase. The results of molecular dynamics simulations performed on WT (S(4)+4B)(12+) ions with different charge configurations support this conclusion. The most significant finding of this study is that the gaseous WT (S(4)+4B)(n+) ions at n = 12-14, owing to a much larger E(a) (by as much as 13 kcal mol(-1)) for the loss of B, are dramatically more stable kinetically at 25 °C than the (S(4)+4B) complex in aqueous neutral solution. The differences in E(a) values measured for the gaseous (S(4)+4B)(n+) ions and solvated (S(4)+4B) complex can be largely accounted for by a late dissociative transition state and the rehydration of B and the protein binding cavity in solution.","corpus_id":207085543,"score":1},{"doc_id":"22989197","title":"A new modular approach to nanoassembly: stable and addressable DNA nanoconstructs via orthogonal click chemistries.","abstract":"Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures.","corpus_id":10768662,"score":1},{"doc_id":"23282586","title":"Orthogonality in organic, polymer, and supramolecular chemistry: from Merrifield to click chemistry.","abstract":"The concept of orthogonality has been applied to many areas of chemistry, ranging from wave functions to chromatography. But it was Barany and Merrifield's orthogonal protecting group strategy that paved the way for solid phase peptide syntheses, other important classes of biomaterials such as oligosaccharides and oligonucleotides, and ultimately to a term in widespread usage that is focused on chemical reactivity and binding selectivity. The orthogonal protection strategy has been extended to the development of orthogonal activation, and recently the click reaction, for streamlining organic synthesis. The click reaction and its variants are considered orthogonal as the components react together in high yield and in the presence of many other functional groups. Likewise, supramolecular building blocks can also be orthogonal, thereby enabling programmed self-assembly, a superb strategy to create complex architectures. Overall, orthogonal reactions and supramolecular interactions have dramatically improved the syntheses, the preparation of functional materials, and the self-assembly of nanoscale structures.","corpus_id":3027284,"score":1},{"doc_id":"23670729","title":"Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate.","abstract":"We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.","corpus_id":206407422,"score":1},{"doc_id":"23964715","title":"Controlling macromolecular topology with genetically encoded SpyTag-SpyCatcher chemistry.","abstract":"Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag-SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyTag and SpyCatcher can be strategically placed into ELP genes to direct post-translational topological modification in situ. Placement of SpyTag at the N-terminus and SpyCatcher at the C-terminus directs formation of circular ELPs. Induction of expression at 16 °C with 10 μM IPTG yields 80% monomeric cyclic protein. When SpyTag is placed in the middle of the chain, it exhibits an even stronger tendency toward cyclization, yielding up to 94% monomeric tadpole proteins. Telechelic ELPs containing either SpyTag or SpyCatcher can be expressed, purified, and then coupled spontaneously upon mixing in vitro. Block proteins, 3-arm or 4-arm star proteins, and H-shaped proteins have been prepared, with the folded CnaB2 domain that results from the SpyTag-SpyCatcher reaction as the molecular core or branch junction. The modular character of the SpyTag-SpyCatcher strategy should make it useful for preparing nonlinear macromolecules of diverse sequence and structure.","corpus_id":262965573,"score":1},{"doc_id":"24161952","title":"Structural analysis and optimization of the covalent association between SpyCatcher and a peptide Tag.","abstract":"Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.","corpus_id":42121602,"score":1},{"doc_id":"24639550","title":"SpyLigase peptide-peptide ligation polymerizes affibodies to enhance magnetic cancer cell capture.","abstract":"Individual proteins can now often be modified with atomic precision, but there are still major obstacles to connecting proteins into larger assemblies. To direct protein assembly, ideally, peptide tags would be used, providing the minimal perturbation to protein function. However, binding to peptides is generally weak, so assemblies are unstable over time and disassemble with force or harsh conditions. We have recently developed an irreversible protein-peptide interaction (SpyTag/SpyCatcher), based on a protein domain from Streptococcus pyogenes, that locks itself together via spontaneous isopeptide bond formation. Here we develop irreversible peptide-peptide interaction, through redesign of this domain and genetic dissection into three parts: a protein domain termed SpyLigase, which now ligates two peptide tags to each other. All components expressed efficiently in Escherichia coli and peptide tags were reactive at the N terminus, at the C terminus, or at internal sites. Peptide-peptide ligation enabled covalent and site-specific polymerization of affibodies or antibodies against the tumor markers epidermal growth factor receptor (EGFR) and HER2. Magnetic capture of circulating tumor cells (CTCs) is one of the most promising approaches to improve cancer prognosis and management, but CTC capture is limited by inefficient recovery of cells expressing low levels of tumor antigen. SpyLigase-assembled protein polymers made possible the isolation of cancerous cells expressing lower levels of tumor antigen and should have general application in enhancing molecular capture.","corpus_id":7349100,"score":1},{"doc_id":"24817566","title":"SpyTag/SpyCatcher cyclization confers resilience to boiling on a mesophilic enzyme.","abstract":"SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β-lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild-type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β-lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.","corpus_id":205380547,"score":1},{"doc_id":"24905869","title":"Engineering orthogonality in supramolecular polymers: from simple scaffolds to complex materials.","abstract":"Owing to the mastery exhibited by Nature in integrating both covalent and noncovalent interactions in a highly efficient manner, the quest to construct polymeric systems that rival not only the precision and fidelity but also the structure of natural systems has remained a daunting challenge. Supramolecular chemists have long endeavored to control the interplay between covalent and noncovalent bond formation, so as to examine and fully comprehend how function is predicated on self-assembly. The ability to reliably control polymer self-assembly is essential to generate \"smart\" materials and has the potential to tailor polymer properties (i.e., viscosity, electronic properties) through fine-tuning the noncovalent interactions that comprise the polymer architecture. In this context, supramolecular polymers have a distinct advantage over fully covalent systems in that they are dynamically modular, since noncovalent recognition motifs can be engineered to either impart a desired functionality within the overall architecture or provide a designed bias for the self-assembly process. In this Account, we describe engineering principles being developed and pursued by our group that exploit the orthogonal nature of noncovalent interactions, such as hydrogen bonding, metal coordination, and Coulombic interactions, to direct the self-assembly of functionalized macromolecules, resulting in the formation of supramolecular polymers. To begin, we describe our efforts to fabricate a modular poly(norbornene)-based scaffold via ring-opening metathesis polymerization (ROMP), wherein pendant molecular recognition elements based upon nucleobase-mimicking elements (e.g., thymine, diaminotriazine) or SCS-Pd(II) pincer were integrated within covalent monofunctional or symmetrically functionalized polymers. The simple polymer backbones exhibited reliable self-assembly with complementary polymers or small molecules. Within these systems, we applied successful protecting group strategies and template polymerizations to enhance the control afforded by ROMP. Main-chain-functionalized alternating block polymers based upon SCS-Pd(II) pincer-pyridine motifs were achieved through the combined exploitation of bimetallic initiators and supramolecularly functionalized terminators. Our initial design principles led to the successful fabrication of both main-chain- and side-chain-functionalized poly(norbornenes) via ROMP. Utilizing all of these techniques in concert led to engineering orthogonality while achieving complexity through the installation of multiple supramolecular motifs within the side chain, main chain, or both in our polymer systems. The exploitation and modification of design principles based upon functional ROMP initiators and terminators has resulted in the first synthesis of main-chain heterotelechelic polymers that self-assemble into A/B/C supramolecular triblock polymers composed of orthogonal cyanuric acid-Hamilton wedge and SCS-Pd(II) pincer-pyridine motifs. Furthermore, supramolecular A/B/A triblock copolymers were realized through the amalgamation of functionalized monomers, ROMP initiators, and terminators. To date, this ROMP-fabricated system represents the only known method to afford polymer main chains and side chains studded with orthogonal motifs. We end by discussing the impetus to attain functional materials via orthogonal self-assembly. Collectively, our studies suggest that combining covalent and noncovalent bonds in a well-defined and precise manner is an essential design element to achieve complex architectures. The results discussed in this Account illustrate the finesse associated with engineering orthogonal interactions within supramolecular systems and are considered essential steps toward developing complex biomimetic materials with high precision and fidelity.","corpus_id":37347553,"score":1},{"doc_id":"25082796","title":"\"Plug-and-go\" strategy to manipulate streptavidin valencies.","abstract":"The streptavidin-biotin set is one of the most widely utilized conjugation pairs in biotechnological applications. The tetravalent nature of streptavidin and its homologues, however, tends to result in such undesirable complications as cross-linking or ill-defined stoichiometry. Here, we describe a mutagenesis-free strategy to manipulate the valencies of wild-type streptavidin that only requires commercially available reagents. The basic idea is simple: one obtains the desired streptavidin valency by blocking off unwanted binding sites using ancillary biotin (\"plug\"); this way, the extraordinary fM-biotin-binding affinity is fully retained for the remaining sites in streptavidin. In the present implementation, the ancillary biotin is attached to an auxiliary separation handle, negatively charged DNA or His-tagged protein, via a photochemically or enzymatically cleavable linker. Mixing streptavidin with the ancillary biotin construct produces a distribution of streptavidin valencies. The subsequent chromatographic separation readily isolates the construct of desired streptavidin valency, and the auxiliary handles are easily removed afterward (\"go\"). We demonstrate how this \"plug-and-go\" strategy allows a precise control for the compositions of streptavidin-biotin conjugates at the single-molecule level. This low-entry-barrier protocol could further expand the application scope of the streptavidin technology.","corpus_id":31997189,"score":1},{"doc_id":"25168413","title":"Superglue from bacteria: unbreakable bridges for protein nanotechnology.","abstract":"Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.","corpus_id":22873894,"score":1},{"doc_id":"25357135","title":"Programming supramolecular biohybrids as precision therapeutics.","abstract":"CONSPECTUS: Chemical programming of macromolecular structures to instill a set of defined chemical properties designed to behave in a sequential and precise manner is a characteristic vision for creating next generation nanomaterials. In this context, biopolymers such as proteins and nucleic acids provide an attractive platform for the integration of complex chemical design due to their sequence specificity and geometric definition, which allows accurate translation of chemical functionalities to biological activity. Coupled with the advent of amino acid specific modification techniques, \"programmable\" areas of a protein chain become exclusively available for any synthetic customization. We envision that chemically reprogrammed hybrid proteins will bridge the vital link to overcome the limitations of synthetic and biological materials, providing a unique strategy for tailoring precision therapeutics. In this Account, we present our work toward the chemical design of protein- derived hybrid polymers and their supramolecular responsiveness, while summarizing their impact and the advancement in biomedicine. Proteins, in their native form, represent the central framework of all biological processes and are an unrivaled class of macromolecular drugs with immense specificity. Nonetheless, the route of administration of protein therapeutics is often vastly different from Nature's biosynthesis. Therefore, it is imperative to chemically reprogram these biopolymers to direct their entry and activity toward the designated target. As a consequence of the innate structural regularity of proteins, we show that supramolecular interactions facilitated by stimulus responsive chemistry can be intricately designed as a powerful tool to customize their functions, stability, activity profiles, and transportation capabilities. From another perspective, a protein in its denatured, unfolded form serves as a monodispersed, biodegradable polymer scaffold decorated with functional side chains available for grafting with molecules of interest. Additionally, we are equipped with analytical tools to map the fingerprint of the protein chain, directly elucidating the structure at the molecular level. Contrary to conventional polymers, these biopolymers facilitate a more systematic avenue to investigate engineered macromolecules, with greater detail and accuracy. In this regard, we focus on denaturing serum albumin, an abundant blood protein, and exploit its peptidic array of functionalities to program supramolecular architectures for bioimaging, drug and gene delivery. Ultimately, we seek to assimilate the evolutionary advantage of these protein based biopolymers with the limitless versatility of synthetic chemistry to merge the best of both worlds.","corpus_id":5073559,"score":1},{"doc_id":"26020143","title":"Protein-induced supramolecular disassembly of amphiphilic polypeptide nanoassemblies.","abstract":"Mimicking noncovalent interaction based processes in nature has been an important goal of supramolecular chemistry. Here, we report on amphiphilic polypeptides that self-assemble to form nanoscale supramolecular assemblies and are programmed to disassemble in response to a specific protein. Benzenesulfonamide and carbonic anhydrase have been chosen as the ligand and protein, respectively, to demonstrate this possibility. Since the amphiphilic nanoassembly sequesters hydrophobic guest molecules, the protein-specific disassembly event provides a protein-sensitive molecular release as well. We envision that the binding induced disassembly and guest release might open up new opportunities for the next generation of supramolecular assemblies for protein-specific delivery and diagnostics.","corpus_id":207156156,"score":1},{"doc_id":"26278701","title":"Synthetic Biology: A New Tool for the Trade.","abstract":"Protein-protein interactions are fundamental to many biological processes. Yet, the weak and transient noncovalent bonds that characterize most protein-protein interactions found in nature impose limits on many bioengineering experiments. Here, a new class of genetically encodable peptide-protein pairs--isopeptag-N/pilin-N, isopeptag/pilin-C, and SpyTag/SpyCatcher--that interact through autocatalytic intermolecular isopeptide bond formation is described. Reactions between peptide-protein pairs are specific, robust, orthogonal, and able to proceed under most biologically relevant conditions both in vitro and in vivo. As fusion constructs, they provide a handle on molecules of interest, both organic and inorganic, that can be grasped with an iron grip. Such stable interactions provide robust post-translational control over biological processes and open new opportunities in synthetic biology for engineering programmable and self-assembling protein nanoarchitectures.","corpus_id":44982914,"score":1},{"doc_id":"26517567","title":"Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher.","abstract":"SpyTag is a short peptide that forms an isopeptide bond upon encountering its protein partner SpyCatcher. This covalent peptide interaction is a simple and powerful tool for bioconjugation and extending what protein architectures are accessible. Here we review the origin and mechanism of SpyTag/SpyCatcher, focusing on recent innovative applications. Ligation of targeting-antibody with antigen provided a simple route to vaccine generation. SpyRings, from head-to-tail cyclisation, gave major enhancements in enzyme resilience. Linking multiple SpyCatchers gave dendrimers for T-cell activation or Spy networks forming hydrogels for stem cell culture. Synthetic biology applications include integrating amyloid biomaterials with living bacteria, for irreversible derivatisation of biofilms with enzymes or nanoparticles. We also discuss further opportunities to apply and enhance SpyTag/SpyCatcher technology.","corpus_id":9799436,"score":1},{"doc_id":"26781591","title":"Plug-and-Display: decoration of Virus-Like Particles via isopeptide bonds for modular immunization.","abstract":"Virus-like particles (VLPs) are non-infectious self-assembling nanoparticles, useful in medicine and nanotechnology. Their repetitive molecularly-defined architecture is attractive for engineering multivalency, notably for vaccination. However, decorating VLPs with target-antigens by genetic fusion or chemical modification is time-consuming and often leads to capsid misassembly or antigen misfolding, hindering generation of protective immunity. Here we establish a platform for irreversibly decorating VLPs simply by mixing with protein antigen. SpyCatcher is a genetically-encoded protein designed to spontaneously form a covalent bond to its peptide-partner SpyTag. We expressed in E. coli VLPs from the bacteriophage AP205 genetically fused to SpyCatcher. We demonstrated quantitative covalent coupling to SpyCatcher-VLPs after mixing with SpyTag-linked to malaria antigens, including CIDR and Pfs25. In addition, we showed coupling to the VLPs for peptides relevant to cancer from epidermal growth factor receptor and telomerase. Injecting SpyCatcher-VLPs decorated with a malarial antigen efficiently induced antibody responses after only a single immunization. This simple, efficient and modular decoration of nanoparticles should accelerate vaccine development, as well as other applications of nanoparticle devices.","corpus_id":1730573,"score":1},{"doc_id":"27034717","title":"Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization.","abstract":"BACKGROUND: SpyTag is a peptide that can form an irreversible covalent linkage to its 12 kDa partner SpyCatcher via a spontaneous isopeptide bond. Herein, we fused SpyTag at the N-terminal of lichenase and SpyCatcher at C-terminal so that the termini of lichenase were locked together by the covalent interaction between the partners. In addition, an elastin-like polypeptides tag was subsequently attached to the C-terminus of SpyCatcher, thereby facilitating the non-chromatographic purification of cyclized lichenase. RESULTS: The study showed that the optimum temperature of the cyclized lichenase was about 5 °C higher in comparison to its linear counterpart. Moreover, nearly 80 % of the cyclized lichenase activities were retained after 100 °C exposure, whereas the linear form lost almost all of its activities. Therefore, the cyclized variant displayed a significantly higher thermal stability as temperature elevated and was resistant to hyperthermal denaturation. Besides, the Km value of the cyclized lichenase (7.58 ± 0.92 mg/mL) was approximately 1.7-fold lower than that of the linear one (12.96 ± 1.93 mg/mL), indicating a higher affinity with substrates. CONCLUSIONS: This new SpyTag/SpyCatcher cyclization strategy is deemed as a generalized reference for enhancing enzyme stability and can be effectively customized to the cyclization of various enzymes, hence a tremendous potential for successful application in the biocatalytic conversion of biomass to produce fuels and chemicals.","corpus_id":15396810,"score":1},{"doc_id":"27117585","title":"Bacterial superglue enables easy development of efficient virus-like particle based vaccines.","abstract":"BACKGROUND: Virus-like particles (VLPs) represent a significant advance in the development of subunit vaccines, combining high safety and efficacy. Their particulate nature and dense repetitive subunit organization makes them ideal scaffolds for display of vaccine antigens. Traditional approaches for VLP-based antigen display require labor-intensive trial-and-error optimization, and often fail to generate dense antigen display. Here we utilize the split-intein (SpyTag/SpyCatcher) conjugation system to generate stable isopeptide bound antigen-VLP complexes by simply mixing of the antigen and VLP components. RESULTS: Genetic fusion of SpyTag or SpyCatcher to the N-terminus and/or C-terminus of the Acinetobacter phage AP205 capsid protein resulted in formation of stable, nonaggregated VLPs expressing one SpyCatcher, one SpyTag or two SpyTags per capsid protein. Mixing of spy-VLPs with eleven different vaccine antigens fused to SpyCatcher or SpyTag resulted in formation of antigen-VLP complexes with coupling efficiencies (% occupancy of total VLP binding sites) ranging from 22-88 %. In mice, spy-VLP vaccines presenting the malaria proteins Pfs25 or VAR2CSA markedly increased antibody titer, affinity, longevity and functional efficacy compared to corresponding vaccines employing monomeric proteins. The spy-VLP vaccines also effectively broke B cell self-tolerance and induced potent and durable antibody responses upon vaccination with cancer or allergy-associated self-antigens (PD-L1, CTLA-4 and IL-5). CONCLUSIONS: The spy-VLP system constitutes a versatile and rapid method to develop highly immunogenic VLP-based vaccines. Our data provide proof-of-concept for the technology's ability to present complex vaccine antigens to the immune system and elicit robust functional antibody responses as well as to efficiently break B cell self-tolerance. The spy-VLP-system may serve as a generic tool for the cost-effective development of effective VLP-vaccines against both infectious- and non-communicable diseases and could facilitate rapid and unbiased screening of vaccine candidate antigens.","corpus_id":217519352,"score":1},{"doc_id":"27249579","title":"Geometrical assembly of ultrastable protein templates for nanomaterials.","abstract":"The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein-protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.","corpus_id":5664344,"score":1},{"doc_id":"27477779","title":"Engineering Protein Hydrogels Using SpyCatcher-SpyTag Chemistry.","abstract":"Constructing hydrogels from engineered proteins has attracted significant attention within the material sciences, owing to their myriad potential applications in biomedical engineering. Developing efficient methods to cross-link tailored protein building blocks into hydrogels with desirable mechanical, physical, and functional properties is of paramount importance. By making use of the recently developed SpyCatcher-SpyTag chemistry, we successfully engineered protein hydrogels on the basis of engineered tandem modular elastomeric proteins. Our resultant protein hydrogels are soft but stable, and show excellent biocompatibility. As the first step, we tested the use of these hydrogels as a drug carrier, as well as in encapsulating human lung fibroblast cells. Our results demonstrate the robustness of the SpyCatcher-SpyTag chemistry, even when the SpyTag (or SpyCatcher) is flanked by folded globular domains. These results demonstrate that SpyCatcher-SpyTag chemistry can be used to engineer protein hydrogels from tandem modular elastomeric proteins that can find applications in tissue engineering, in fundamental mechano-biological studies, and as a controlled drug release vehicle.","corpus_id":2616636,"score":1},{"doc_id":"27503402","title":"Protein-like Nanoparticles Based on Orthogonal Self-Assembly of Chimeric Peptides.","abstract":"A novel two-component self-assembling chimeric peptide is designed where two orthogonal protein folding motifs are linked side by side with precisely defined position relative to one another. The self-assembly is driven by a combination of symmetry controlled molecular packing, intermolecular interactions, and geometric constraint to limit the assembly into compact dodecameric protein nanoparticles.","corpus_id":46851353,"score":1},{"doc_id":"27658030","title":"SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase.","abstract":"SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.","corpus_id":8477179,"score":1},{"doc_id":"27783674","title":"Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly.","abstract":"Over the last few years, a number of different protein assembly strategies have been developed, greatly expanding the toolbox for controlling macromolecular assembly. One of the most promising developments is a rapid protein ligation approach using a short polypeptide SpyTag and its partner, SpyCatcher derived from Streptococcus pyogenes fibronectin-binding protein, FbaB. To extend this technology, we have engineered and characterized a new Tag-Catcher pair from a related fibronectin-binding protein in Streptococcus dysgalactiae. The polypeptide Tag, named SdyTag, was constructed based on the native Cna protein B-type (CnaB) domain and was found to be highly unreactive to SpyCatcher. SpyCatcher has 320-fold specificity for its native SpyTag compared to SdyTag. Similarly, SdyTag has a 75-fold specificity for its optimized Catcher, named SdyCatcherDANG short, compared to SpyCatcher. These Tag-Catcher pairs were used in combination to demonstrate specific sequential assembly of tagged proteins in vitro. We also demonstrated that the in vivo generation of circularized proteins in a Tag-Catcher specific manner where specific Tags can be left unreacted for use in subsequent ligation reactions. From the success of these experiments, we foresee the application of SdyTags and SpyTags, not only, for multiplexed control of protein assembly but also for the construction of novel protein architectures.","corpus_id":1537692,"score":1},{"doc_id":"27982100","title":"Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates.","abstract":"Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.","corpus_id":18992987,"score":1},{"doc_id":"28105787","title":"Orthogonal Surface Tags for Whole-Cell Biocatalysis.","abstract":"We herein describe the engineering of E. coli strains that display orthogonal tags for immobilization on their surface and overexpress a functional heterologous \"protein content\" in their cytosol at the same time. Using the outer membrane protein Lpp-ompA, cell-surface display of the streptavidin-binding peptide, the SpyTag/SpyCatcher system, or a HaloTag variant allowed us to generate bacterial strains that can selectively bind to solid substrates, as demonstrated with magnetic microbeads. The simultaneous cytosolic expression of functional content was demonstrated for fluorescent proteins or stereoselective ketoreductase enzymes. The latter strains gave high selectivities for specific immobilization onto complementary surfaces and also in the whole-cell stereospecific transformation of a prochiral CS -symmetric nitrodiketone.","corpus_id":205398168,"score":1},{"doc_id":"28437083","title":"Dual Plug-and-Display Synthetic Assembly Using Orthogonal Reactive Proteins for Twin Antigen Immunization.","abstract":"Engineering modular platforms to control biomolecular architecture can advance both the understanding and the manipulation of biological systems. Icosahedral particles uniformly displaying single antigens stimulate potent immune activation and have been successful in various licensed vaccines. However, it remains challenging to display multiple antigens on a single particle and to induce broader immunity protective across strains or even against distinct diseases. Here, we design a dually addressable synthetic nanoparticle by engineering the multimerizing coiled-coil IMX313 and two orthogonally reactive split proteins. SpyCatcher protein forms an isopeptide bond with SpyTag peptide through spontaneous amidation. SnoopCatcher forms an isopeptide bond with SnoopTag peptide through transamidation. SpyCatcher-IMX-SnoopCatcher provides a modular platform, whereby SpyTag-antigen and SnoopTag-antigen can be multimerized on opposite faces of the particle simply upon mixing. We demonstrate efficient derivatization of the platform with model proteins and complex pathogen-derived antigens. SpyCatcher-IMX-SnoopCatcher was expressed in Escherichia coli and was resilient to lyophilization or extreme temperatures. For the next generation of malaria vaccines, blocking the transmission of the parasite from human to mosquito is an important goal. SpyCatcher-IMX-SnoopCatcher multimerization of the leading transmission-blocking antigens Pfs25 and Pfs28 greatly enhanced the antibody response to both antigens in comparison to the monomeric proteins. This dual plug-and-display architecture should help to accelerate vaccine development for malaria and other diseases.","corpus_id":206520806,"score":1},{"doc_id":"28757182","title":"Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction.","abstract":"Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1-6 amines per subunit: \"amine landscaping.\" Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe.","corpus_id":20816884,"score":1},{"doc_id":"29024296","title":"Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics.","abstract":"SpyTag is a peptide that forms a spontaneous amide bond with its protein partner SpyCatcher. This protein superglue is a broadly useful tool for molecular assembly, locking together biological building blocks efficiently and irreversibly in diverse architectures. We initially developed SpyTag and SpyCatcher by rational design, through splitting a domain from a Gram-positive bacterial adhesin. In this work, we established a phage-display platform to select for specific amidation, leading to an order of magnitude acceleration for interaction of the SpyTag002 variant with the SpyCatcher002 variant. We show that the 002 pair bonds rapidly under a wide range of conditions and at either protein terminus. SpyCatcher002 was fused to an intimin derived from enterohemorrhagic Escherichia coli. SpyTag002 reaction enabled specific and covalent decoration of intimin for live cell fluorescent imaging of the dynamics of the bacterial outer membrane as cells divide.","corpus_id":3598641,"score":1},{"doc_id":"29039416","title":"Antibodies to biotin enable large-scale detection of biotinylation sites on proteins.","abstract":"Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.","corpus_id":21738454,"score":1},{"doc_id":"29625006","title":"SpyCatcher-NTEV: A Circularly Permuted, Disordered SpyCatcher Variant for Less Trace Ligation.","abstract":"The SpyTag/SpyCatcher reaction has emerged as a powerful way for bioconjugation, but it leaves a folded complex in the product after the formation of the isopeptide bond. To vary the location of the reactive residue and reduce the size of the complex and its potential immunogenicity, we engineer two circularly permuted SpyCatcher variants, SpyCatcher-N and SpyCatcher-NTEV, the latter of which possesses a TEV-recognition site for removal of the fragment containing the catalytic site. Surprisingly, both variants are found to be disordered in solution, yet still retain the ability to form an ordered complex upon reaction with SpyTag with second-order rate constants of ∼10 M-1 s-1. Cellular expression of a telechelic protein bearing SpyCatcher-NTEV at the N-terminus and SpyTag at the C-terminus gives both cyclized and chain-extended products. Notably, the monomers exist almost exclusively in the cyclic form owing to its high reactivity in vivo. The fragment containing the catalytic site of SpyCatcher-NTEV can then be removed by TEV digestion, giving a circular protein with minimal trace from the ligation reaction. The plasticity of SpyTag/SpyCatcher reactive pair has promised an ever-expanding toolbox of genetically encoded peptide-protein reaction with versatile features.","corpus_id":4645665,"score":1},{"doc_id":"18668104","title":"Functionalizing hydrogen-bonded surface networks with self-assembled monolayers.","abstract":"One of the central challenges in nanotechnology is the development of flexible and efficient methods for creating ordered structures with nanometre precision over an extended length scale. Supramolecular self-assembly on surfaces offers attractive features in this regard: it is a 'bottom-up' approach and thus allows the simple and rapid creation of surface assemblies, which are readily tuned through the choice of molecular building blocks used and stabilized by hydrogen bonding, van der Waals interactions, pi-pi bonding or metal coordination between the blocks. Assemblies in the form of two-dimensional open networks are of particular interest for possible applications because well-defined pores can be used for the precise localization and confinement of guest entities such as molecules or clusters, which can add functionality to the supramolecular network. Another widely used method for producing surface structures involves self-assembled monolayers (SAMs), which have introduced unprecedented flexibility in our ability to tailor interfaces and generate patterned surfaces. But SAMs are part of a top-down technology that is limited in terms of the spatial resolution that can be achieved. We therefore rationalized that a particularly powerful fabrication platform might be realized by combining non-covalent self-assembly of porous networks and SAMs, with the former providing nanometre-scale precision and the latter allowing versatile functionalization. Here we show that the two strategies can indeed be combined to create integrated network-SAM hybrid systems that are sufficiently robust for further processing. We show that the supramolecular network and the SAM can both be deposited from solution, which should enable the widespread and flexible use of this combined fabrication method.","corpus_id":205213948,"score":0},{"doc_id":"19374419","title":"Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.","abstract":"We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of chi1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic chi1 angles. We observe changes in the chi1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution-phase simulations is predominantly broken in this much longer solution-phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution-phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.","corpus_id":8825566,"score":0},{"doc_id":"20462252","title":"A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?","abstract":"We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.","corpus_id":22733513,"score":0},{"doc_id":"21892837","title":"Engineered streptavidin monomer and dimer with improved stability and function.","abstract":"Although streptavidin's high affinity for biotin has made it a widely used and studied binding protein and labeling tool, its tetrameric structure may interfere with some assays. A streptavidin mutant with a simpler quaternary structure would demonstrate a molecular-level understanding of its structural organization and lead to the development of a novel molecular reagent. However, modulating the tetrameric structure without disrupting biotin binding has been extremely difficult. In this study, we describe the design of a stable monomer that binds biotin both in vitro and in vivo. To this end, we constructed and characterized monomers containing rationally designed mutations. The mutations improved the stability of the monomer (increase in T(m) from 31 to 47 °C) as well as its affinity (increase in K(d) from 123 to 38 nM). We also used the stability-improved monomer to construct a dimer consisting of two streptavidin subunits that interact across the dimer-dimer interface, which we call the A/D dimer. The biotin binding pocket is conserved between the tetramer and the A/D dimer, and therefore, the dimer is expected to have a significantly higher affinity than the monomer. The affinity of the dimer (K(d) = 17 nM) is higher than that of the monomer but is still many orders of magnitude lower than that of the wild-type tetramer, which suggests there are other factors important for high-affinity biotin binding. We show that the engineered streptavidin monomer and dimer can selectively bind biotinylated targets in vivo by labeling the cells displaying biotinylated receptors. Therefore, the designed mutants may be useful in novel applications as well as in future studies in elucidating the role of oligomerization in streptavidin function.","corpus_id":21622029,"score":0},{"doc_id":"22802499","title":"Ultra-precision: enabling our future.","abstract":"This paper provides a perspective on the development of ultra-precision technologies: What drove their evolution and what do they now promise for the future as we face the consequences of consumption of the Earth's finite resources? Improved application of measurement is introduced as a major enabler of mass production, and its resultant impact on wealth generation is considered. This paper identifies the ambitions of the defence, automotive and microelectronics sectors as important drivers of improved manufacturing accuracy capability and ever smaller feature creation. It then describes how science fields such as astronomy have presented significant precision engineering challenges, illustrating how these fields of science have achieved unprecedented levels of accuracy, sensitivity and sheer scale. Notwithstanding their importance to science understanding, many science-driven ultra-precision technologies became key enablers for wealth generation and other well-being issues. Specific ultra-precision machine tools important to major astronomy programmes are discussed, as well as the way in which subsequently evolved machine tools made at the beginning of the twenty-first century, now provide much wider benefits.","corpus_id":6059560,"score":0},{"doc_id":"23534402","title":"Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes.","abstract":"Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.","corpus_id":27269560,"score":0},{"doc_id":"24790550","title":"Fluorescence enhancement of fluorescent unnatural streptavidin by binding of a biotin analogue with spacer tail and its application to biotin sensing.","abstract":"We designed a novel molecular biosensing system for the detection of biotin, an important vitamin by the combination of fluorescent unnatural streptavidin with a commercialized biotin-(AC5)2-hydrazide. A fluorescent unnatural amino acid, BODIPY-FL-aminophenylalanine (BFLAF), was position-specifically incorporated into Trp120 of streptavidin by four-base codon method. Fluorescence of the Trp120BFLAF mutant streptavidin was enhanced by the addition of biotin-(AC5)2-hydrazide with the concentration dependent, whereas fluorescence enhancement was not observed at all by the addition of natural biotin. It was considered that the spacer tail of biotin-(AC5)2-hydrazide may disturb the fluorescence quenching of the Trp120BFLAF by Trp79 and Trp108 of the neighbor subunit. Therefore, biotin sensing was carried out by the competitive binding reaction of biotin-(AC5)2-hydrazide and natural biotin to the fluorescent mutant streptavidin. The fluorescence intensity decreased by increasing free biotin concentration. The result suggested that molecular biosensor for small ligand could be successfully designed by the pair of fluorescent mutant binding protein and ligand analogue.","corpus_id":15608490,"score":0},{"doc_id":"25049400","title":"Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry.","abstract":"Protein-based hydrogels have emerged as promising alternatives to synthetic hydrogels for biomedical applications, owing to the precise control of structure and function enabled by protein engineering. Nevertheless, strategies for assembling 3D molecular networks that carry the biological information encoded in full-length proteins remain underdeveloped. Here we present a robust protein gelation strategy based on a pair of genetically encoded reactive partners, SpyTag and SpyCatcher, that spontaneously form covalent isopeptide linkages under physiological conditions. The resulting \"network of Spies\" may be designed to include cell-adhesion ligands, matrix metalloproteinase-1 cleavage sites, and full-length globular proteins [mCherry and leukemia inhibitory factor (LIF)]. The LIF network was used to encapsulate mouse embryonic stem cells; the encapsulated cells remained pluripotent in the absence of added LIF. These results illustrate a versatile strategy for the creation of information-rich biomaterials.","corpus_id":16197967,"score":0},{"doc_id":"25119814","title":"Increasing and decreasing the ultrastability of bacterial chemotaxis core signaling complexes by modifying protein-protein contacts.","abstract":"The chemosensory signaling array of bacterial chemotaxis is composed of functional core units containing two receptor trimers of dimers, a homodimeric CheA kinase, and two CheW adaptor proteins. In vitro reconstitutions generate individual, functional core units and larger functional assemblies, including dimers, hexagons, and hexagonal arrays. Such reconstituted complexes have been shown to have both quasi-stable and ultrastable populations that decay with lifetimes of 1-2 days and ∼3 weeks at 22 °C, respectively, where decay results primarily from proteolysis of the bound kinase [Erbse, A. H., and Falke, J. J. (2009) Biochemistry 48, 6975-6987; Slivka, P. F., and Falke, J. J. (2012) Biochemistry 51, 10218-10228]. In this work, we show that the ultrastable population can be destabilized to the quasi-stable level via the introduction of a bulky tryptophan residue at either one of two essential protein-protein interfaces within the core unit: the receptor-kinase contact or kinase-adaptor interface 1. Moreover, we demonstrate that the quasi-stable population can be made ultrastable via the introduction of a disulfide bond that covalently stabilizes the latter interface. The resulting disulfide at least doubles the functional lifetime of the ultrastable population, to ≥5.9 weeks at 22 °C, by protecting the kinase from endogenous and exogenous proteases. Together, these results indicate that the ultrastability of reconstituted core complexes requires well-formed contacts among the receptor, kinase, and adaptor proteins, whereas quasi-stability arises from less perfect contacts that allow slow proteolysis of the bound kinase. Furthermore, the results reveal that ultrastability, and perhaps the size or order of chemosensory complexes and arrays, can be increased by an engineered disulfide bond that covalently cross-links a key interface. Overall, it appears that native ultrastability has evolved to provide an optimal rather than maximal level of kinetic durability, suggesting that altered selective pressure could either increase or decrease the functional lifetime of core complexes.","corpus_id":8321829,"score":0},{"doc_id":"25482395","title":"Ultrastable cellulosome-adhesion complex tightens under load.","abstract":"Challenging environments have guided nature in the development of ultrastable protein complexes. Specialized bacteria produce discrete multi-component protein networks called cellulosomes to effectively digest lignocellulosic biomass. While network assembly is enabled by protein interactions with commonplace affinities, we show that certain cellulosomal ligand-receptor interactions exhibit extreme resistance to applied force. Here, we characterize the ligand-receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome using single-molecule force spectroscopy and steered molecular dynamics simulations. The complex withstands forces of 600-750 pN, making it one of the strongest bimolecular interactions reported, equivalent to half the mechanical strength of a covalent bond. Our findings demonstrate force activation and inter-domain stabilization of the complex, and suggest that certain network components serve as mechanical effectors for maintaining network integrity. This detailed understanding of cellulosomal network components may help in the development of biocatalysts for production of fuels and chemicals from renewable plant-derived biomass.","corpus_id":465374,"score":0},{"doc_id":"25560523","title":"SWATH enables precise label-free quantification on proteome scale.","abstract":"MS-based proteomics has emerged as a powerful tool in biological studies. The shotgun proteomics strategy, in which proteolytic peptides are analyzed in data-dependent mode, enables a detection of the most comprehensive proteome (>10 000 proteins from whole-cell lysate). The quantitative proteomics uses stable isotopes or label-free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label-free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. Sequential window acquisition of all theoretical mass spectra (SWATH) is a recently developed technique, in which data-independent acquisition is coupled with peptide spectral library match. In principle SWATH method is able to do label-free quantification in an MRM-like manner, which has higher quantification accuracy and precision. Previous data have demonstrated that SWATH can be used to quantify less complex systems, such as spiked-in peptide mixture or protein complex. Our study first time assessed the quantification performance of SWATH method on proteome scale using a complex mouse-cell lysate sample. In total 3600 proteins got identified and quantified without sample prefractionation. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly. However, this inaccuracy does not prevent discovering biological correlates, because the measured signal intensities had linear relationship to the sample loading amounts; thus the SWATH method can predict precisely the significance of a protein. Our results prove that SWATH can provide precise label-free quantification on proteome scale.","corpus_id":5498735,"score":0},{"doc_id":"26709829","title":"Chemotactic Signaling by Single-Chain Chemoreceptors.","abstract":"Bacterial chemoreceptors of the methyl-accepting chemotaxis protein (MCP) family operate in commingled clusters that enable cells to detect and track environmental chemical gradients with high sensitivity and precision. MCP homodimers of different detection specificities form mixed trimers of dimers that facilitate inter-receptor communication in core signaling complexes, which in turn assemble into a large signaling network. The two subunits of each homodimeric receptor molecule occupy different locations in the core complexes. One subunit participates in trimer-stabilizing interactions at the trimer axis, the other lies on the periphery of the trimer, where it can interact with two cytoplasmic proteins: CheA, a signaling autokinase, and CheW, which couples CheA activity to receptor control. As a possible tool for independently manipulating receptor subunits in these two structural environments, we constructed and characterized fused genes for the E. coli serine chemoreceptor Tsr that encoded single-chain receptor molecules in which the C-terminus of the first Tsr subunit was covalently connected to the N-terminus of the second with a polypeptide linker. We showed with soft agar assays and with a FRET-based in vivo CheA kinase assay that single-chain Tsr~Tsr molecules could promote serine sensing and chemotaxis responses. The length of the connection between the joined subunits was critical. Linkers nine residues or shorter locked the receptor in a kinase-on state, most likely by distorting the native structure of the receptor HAMP domain. Linkers 22 or more residues in length permitted near-normal Tsr function. Few single-chain molecules were found as monomer-sized proteolytic fragments in cells, indicating that covalently joined receptor subunits were responsible for mediating the signaling responses we observed. However, cysteine-directed crosslinking, spoiling by dominant-negative Tsr subunits, and rearrangement of ligand-binding site lesions revealed subunit swapping interactions that will need to be taken into account in experimental applications of single-chain chemoreceptors.","corpus_id":13263204,"score":0},{"doc_id":"28551501","title":"The role of CH/π interactions in the high affinity binding of streptavidin and biotin.","abstract":"The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10(15)mol(-1)) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.","corpus_id":5472834,"score":0},{"doc_id":"29206886","title":"Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry.","abstract":"The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.","corpus_id":13408524,"score":0},{"doc_id":"29233896","title":"Retargeting Lentiviruses via SpyCatcher-SpyTag Chemistry for Gene Delivery into Specific Cell Types.","abstract":"We report a simple strategy for the creation of lentiviral vectors specific to any desired target cells. SpyTag is inserted into an engineered Sindbis virus envelope protein and displayed on the lentivirus surface to create Sindbis virus-SpyTag pseudoparticles (Sind-SpyTag-pp). The SpyTag serves as the covalent anchoring site for a target-cell-specific cell-binding protein (CBP) that is fused to a truncated SpyCatcher (SpyCatcherΔ). Target-cell-specific lentiviruses are created by mixing the Sind-SpyTag-pp and CBP-SpyCatcherΔ in vitro We first used a HER2-binding designed ankyrin repeat protein (DARPin.9.26) as the model CBP. The DARPin-conjugated lentivirus transduced HER2+ SKOV3 cells with an infectious titer of 5.2 × 106 IU/ml, >500-fold higher than the unfunctionalized \"naked\" virions (<104 IU/ml). The ability of the DARPin-conjugated lentivirus to transduce HER2+ cells correlated with the surface expression level of HER2. Furthermore, these lentiviruses preferentially transduced HER2+ cells in cocultures containing HER2+ and HER2- cells. To enable the use of commercially available monoclonal antibodies (MAbs) as the CBP, we developed a convenient click chemistry-based approach to conjugate MAb-derived Fab fragments to a variant SpyCatcherΔ protein containing a nonnatural amino acid, 4-azido-l-phenylalanine (AzF). Using the HER2-binding trastuzumab as a model cell-specific MAb, we created Fab-conjugated lentiviral vectors that transduced HER2+ SKOV3 cells with an infectious titer of 2.8 × 106 IU/ml, on par with the result achieved using the DARPin-SpyCatcherΔ fusion protein. The ability to create cell-specific lentiviral vectors through chemical conjugation of a CBP should make this approach generalizable to any antibody, giving it broad utility for a wide range of research and clinical applications. IMPORTANCE Lentiviral vectors hold great potential in gene therapy. However, it remains a major hurdle to robustly engineer cell-specific lentiviral vectors. This article reports a simple and effective strategy to functionalize lentiviral vectors with cell-binding proteins, thus retargeting these viruses to cells expressing the binding partner of the CBP. The CBP is genetically or chemically linked to the SpyCatcher. The SpyTag is displayed on the virion surface as a fusion to an engineered Sindbis virus envelope protein and is used as the anchorage site for SpyCatcher-linked CBP. Using this strategy, we created lentiviral vectors highly infectious toward HER2+ cancer cells. The ability to rapidly create cell-specific lentiviral vectors targeting a wide range of cell types should accelerate the development of custom lentiviral vectors for many research and clinical applications.","corpus_id":23106579,"score":0}],"string":"[\n {\n \"doc_id\": \"22366317\",\n \"title\": \"Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin.\",\n \"abstract\": \"Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.\",\n \"corpus_id\": 13927823,\n \"score\": 2\n },\n {\n \"doc_id\": \"24056174\",\n \"title\": \"Plug-and-play pairing via defined divalent streptavidins.\",\n \"abstract\": \"Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.\",\n \"corpus_id\": 9595969,\n \"score\": 2\n },\n {\n \"doc_id\": \"24873508\",\n \"title\": \"Dynamic supramolecular complexes constructed by orthogonal self-assembly.\",\n \"abstract\": \"CONSPECTUS: Supramolecular complexes, including various low-molecular-mass structures and large molecular aggregates that are assembled by reversible and highly directional noncovalent interactions, have attracted more and more attention due to their fascinating and unconventional chemical and physical properties that are different from those of traditional architectures encountered by covalently linked backbones. Supramolecular complexes are by nature dynamic architectures considering the reversibility of noncovalent interactions by which small molecular monomers can assemble into specific architectures that are able to be repeatably reorganized through the assembly/disassembly processes under certain environmental factors such as temperature, concentration, and solvent conditions. The construction of supramolecular complexes by orthogonal self-assembly with different types of highly specific, noninterfering interactions is currently attracting considerable interest since they not only can dynamically self-assemble, but also can be tuned by various external stimuli through addressing each type of noncovalent interaction separately. Therefore, these dynamic supramolecular complexes, especially with external responsiveness, represent the most outstanding candidates for the future development of functional and smart materials, and even mimic the assembling process of natural systems. In this Account, we will summarize the recent advances of dynamic supramolecular complexes constructed by orthogonal self-assembly in soluiton in two sections: (1) Construction strategies for supramolecular complexes based on orthogonal self-assembly, whose dynamic behaviors with external responsiveness were not experimentally investigated but potentially existed due to the intrinsic reversibility of noncovalent bonds; (2) dynamic behaviors of multiresponsive supramolecular complexes, which were experimentally reported to exhibit reversible multi-responsiveness to external stimuli. Dynamic nature is one of intrinsic properties of supramolecular complexes constructed by self-assembly. Therefore, in the first section, we will describe the dynamic self-assembly in the construction of supramolecular complexes, but will focus on their external responsive dynamic behaviors in the second section. In addition, considering that an increasing number of supramolecular complexes constructed by biological building blocks through bio-orthogonal assembly as mimics of biological systems have been reported in recent years, in the second section we will also present some typical examples on such special dynamic biological supramolecular complexes. The final part of this Account is devoted to foreseeing the rapid development of dynamic supramolecular complexes toward applications in functional and smart materials and fundamental questions facing dynamic supramolecular complexes in the future.\",\n \"corpus_id\": 5283533,\n \"score\": 2\n },\n {\n \"doc_id\": \"26787909\",\n \"title\": \"Programmable polyproteams built using twin peptide superglues.\",\n \"abstract\": \"Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable \\\"polyproteams\\\" should enable exploration of a new area of biological space.\",\n \"corpus_id\": 4687927,\n \"score\": 2\n },\n {\n \"doc_id\": \"28989685\",\n \"title\": \"Tuning SpyTag-SpyCatcher mutant pairs toward orthogonal reactivity encryption.\",\n \"abstract\": \"Genetically encoded covalent peptide tagging technology, such as the SpyTag-SpyCatcher reaction, has emerged as a unique way to do chemistry with proteins. Herein, we report the reactivity engineering of SpyTag-SpyCatcher mutant pairs and show that distinct reactivity can be encrypted for the same reaction based on protein sequences of high similarity. Valuable features, including high selectivity, inverse temperature dependence and (nearly) orthogonal reactivity, could be achieved based on as few as three mutations. This demonstrates the robustness of the SpyTag-SpyCatcher reaction and the plasticity of its sequence specificity, pointing to a family of engineered protein chemistry tools.\",\n \"corpus_id\": 23949264,\n \"score\": 2\n },\n {\n \"doc_id\": \"29662234\",\n \"title\": \"Modular assembly of proteins on nanoparticles.\",\n \"abstract\": \"Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.\",\n \"corpus_id\": 4901820,\n \"score\": 2\n },\n {\n \"doc_id\": \"19259577\",\n \"title\": \"Supramolecular self-assembly of dendrimers containing orthogonal binding motifs.\",\n \"abstract\": \"Two orthogonal non-covalent binding sites, namely metal-ligand complexation of Ru and bipyridine and intermolecular hydrogen bonding, facilitate the self-assembly of a new type of supramolecular dendrimers.\",\n \"corpus_id\": 262929368,\n \"score\": 1\n },\n {\n \"doc_id\": \"19425108\",\n \"title\": \"Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction.\",\n \"abstract\": \"Natural tetrameric streptavidin captures and immobilizes biotinylated molecules with ultra-tight binding (K(d) approximately 10(-13) to 10(-14) M). In contrast, engineered monomeric streptavidin offers reversible binding (K(d) approximately 10(-7) M). To develop an ideal engineered streptavidin which possesses both the immobilization capability of the natural streptavidin and the reversible interaction reactivity of the monomeric streptavidin, a pair of engineered biomaterials was designed through molecular modeling. This system consists of two recombinant components: an engineered monomeric streptavidin M6, which has a cysteine residue (C118) near the biotin binding site, and a cysteine containing biotinylation tag. Interactions between M6 and the biotinylated peptide tag go through a two-stage process (capture and immobilization) to generate a covalently linked complex. Biotinylation is essential in the capture stage. Once the biotin moiety in the biotinylated tag is captured by M6, the biotinylated tag can fold back and rotate on the surface of the complex with the biotinylated lysine in the peptide tag as the axis until the formationof a disulfide bond. Consequently, cysteine residue in different positions flanking the biotin residue in the biotinylation tag can successfully form a disulfide bond with M6. Intermolecular disulfide bond formation between M6 and the tag containing protein offers the immobilization capability to M6. In the presence of reducing agent and biotin, bound ligands can be dissociated. This system has the potential to extend the biotin-streptavidin technology to develop reusable biosensor/protein chips and bioreactors.\",\n \"corpus_id\": 26377763,\n \"score\": 1\n },\n {\n \"doc_id\": \"20383133\",\n \"title\": \"A streptavidin variant with slower biotin dissociation and increased mechanostability.\",\n \"abstract\": \"Streptavidin binds biotin conjugates with exceptional stability but dissociation does occur, limiting its use in imaging, DNA amplification and nanotechnology. We identified a mutant streptavidin, traptavidin, with more than tenfold slower biotin dissociation, increased mechanical strength and improved thermostability; this resilience should enable diverse applications. FtsK, a motor protein important in chromosome segregation, rapidly displaced streptavidin from biotinylated DNA, whereas traptavidin resisted displacement, indicating the force generated by Ftsk translocation.\",\n \"corpus_id\": 2988461,\n \"score\": 1\n },\n {\n \"doc_id\": \"20462407\",\n \"title\": \"Binary polypeptide system for permanent and oriented protein immobilization.\",\n \"abstract\": \"BACKGROUND: Many techniques in molecular biology, clinical diagnostics and biotechnology rely on binary affinity tags. The existing tags are based on either small molecules (e.g., biotin/streptavidin or glutathione/GST) or peptide tags (FLAG, Myc, HA, Strep-tag and His-tag). Among these, the biotin-streptavidin system is most popular due to the nearly irreversible interaction of biotin with the tetrameric protein, streptavidin. The major drawback of the stable biotin-streptavidin system, however, is that neither of the two tags can be added to a protein of interest via recombinant means (except for the Strep-tag case) leading to the requirement for chemical coupling. RESULTS: Here we report a new immobilization system which utilizes two monomeric polypeptides which self-assemble to produce non-covalent yet nearly irreversible complex which is stable in strong detergents, chaotropic agents, as well as in acids and alkali. Our system is based on the core region of the tetra-helical bundle known as the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex. This irreversible protein attachment system (IPAS) uses either a shortened syntaxin helix and fused SNAP25-synaptobrevin or a fused syntaxin-synaptobrevin and SNAP25 allowing a two-component system suitable for recombinant protein tagging, capture and immobilization. We also show that IPAS is suitable for use with traditional beads and chromatography, planar surfaces and Biacore, gold nanoparticles and for protein-protein interaction in solution. CONCLUSIONS: IPAS offers an alternative to chemical cross-linking, streptavidin-biotin system and to traditional peptide affinity tags and can be used for a wide range of applications in nanotechnology and molecular sciences.\",\n \"corpus_id\": 3040277,\n \"score\": 1\n },\n {\n \"doc_id\": \"21241253\",\n \"title\": \"How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer.\",\n \"abstract\": \"The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein-ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin-Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin-Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin-Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.\",\n \"corpus_id\": 28492457,\n \"score\": 1\n },\n {\n \"doc_id\": \"21551057\",\n \"title\": \"Scaffold proteins: hubs for controlling the flow of cellular information.\",\n \"abstract\": \"The spatial and temporal organization of molecules within a cell is critical for coordinating the many distinct activities carried out by the cell. In an increasing number of biological signaling processes, scaffold proteins have been found to play a central role in physically assembling the relevant molecular components. Although most scaffolds use a simple tethering mechanism to increase the efficiency of interaction between individual partner molecules, these proteins can also exert complex allosteric control over their partners and are themselves the target of regulation. Scaffold proteins offer a simple, flexible strategy for regulating selectivity in pathways, shaping output behaviors, and achieving new responses from preexisting signaling components. As a result, scaffold proteins have been exploited by evolution, pathogens, and cellular engineers to reshape cellular behavior.\",\n \"corpus_id\": 6512196,\n \"score\": 1\n },\n {\n \"doc_id\": \"22102445\",\n \"title\": \"Nanomechanics of streptavidin hubs for molecular materials.\",\n \"abstract\": \"A new strategy is reported for creating protein-based nanomaterials by genetically fusing large polypeptides to monomeric streptavidin and exploiting the propensity of streptavidin monomers(SM) to self-assemble into stable tetramers. We have characterized the mechanical properties of streptavidin-linked structures and measured, for the first time, the mechanical strength of streptavidin tetramers themselves. Using streptavidin tetramers as molecular hubs offers a unique opportunity to create a variety of well-defined, self-assembled protein-based (nano)materials with unusual mechanical properties.\",\n \"corpus_id\": 205242517,\n \"score\": 1\n },\n {\n \"doc_id\": \"22170585\",\n \"title\": \"Advances in switchable supramolecular nanoassemblies.\",\n \"abstract\": \"Supramolecular nanoassemblies are gaining increasing importance as promising new materials with considerable potential for novel and promising applications. Within supramolecular nanoassemblies the connectivity of the monomeric units is based on reversible noncovalent interactions, like van der Waals interactions, hydrogen bonding, or ionic interactions. As the strength of these interactions depends on the molecular surrounding, the formation of nanoassemblies in principle can be controlled externally by changing the environment and/or the molecular shape of the underlying monomer. This way it is not only possible to switch the self-assembly on or off, but also to change between different aggregation states. In this minireview we present some recent selected approaches to supramolecular stimuli-responsive nanoassemblies.\",\n \"corpus_id\": 205595932,\n \"score\": 1\n },\n {\n \"doc_id\": \"22806584\",\n \"title\": \"Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection.\",\n \"abstract\": \"The coupling between the quaternary structure, stability and function of streptavidin makes it difficult to engineer a stable, high affinity monomer for biotechnology applications. For example, the binding pocket of streptavidin tetramer is comprised of residues from multiple subunits, which cannot be replicated in a single domain protein. However, rhizavidin from Rhizobium etli was recently shown to bind biotin with high affinity as a dimer without the hydrophobic tryptophan lid donated by an adjacent subunit. In particular, the binding site of rhizavidin uses residues from a single subunit to interact with bound biotin. We therefore postulated that replacing the binding site residues of streptavidin monomer with corresponding rhizavidin residues would lead to the design of a high affinity monomer useful for biotechnology applications. Here, we report the construction and characterization of a structural monomer, mSA, which combines the streptavidin and rhizavidin sequences to achieve optimized biophysical properties. First, the biotin affinity of mSA (K(d) = 2.8 nM) is the highest among nontetrameric streptavidin, allowing sensitive monovalent detection of biotinylated ligands. The monomer also has significantly higher stability (T(m) = 59.8 °C) and solubility than all other previously engineered monomers to ensure the molecule remains folded and functional during its application. Using fluorescence correlation spectroscopy, we show that mSA binds biotinylated targets as a monomer. We also show that the molecule can be used as a genetic tag to introduce biotin binding capability to a heterologous protein. For example, recombinantly fusing the monomer to a cell surface receptor allows direct labeling and imaging of transfected cells using biotinylated fluorophores. A stable and functional streptavidin monomer, such as mSA, should be a useful reagent for designing novel detection systems based on monovalent biotin interaction.\",\n \"corpus_id\": 5140258,\n \"score\": 1\n },\n {\n \"doc_id\": \"22984964\",\n \"title\": \"Kinetic stability of the streptavidin-biotin interaction enhanced in the gas phase.\",\n \"abstract\": \"Results of the first detailed study of the structure and kinetic stability of the model high-affinity protein-ligand interaction between biotin (B) and the homotetrameric protein complex streptavidin (S(4)) in the gas phase are described. Collision cross sections (Ω) measured for protonated gaseous ions of free and ligand-bound truncated (residues 13-139) wild-type (WT) streptavidin, i.e., S(4)(n+) and (S(4)+4B)(n+) at charge states n = 12-16, were found to be independent of charge state and in agreement (within 10%) with values estimated for crystal structures reported for S(4) and (S(4)+4B). These results suggest that significant structural changes do not occur upon transfer of the complexes from solution to the gas phase by electrospray ionization. Temperature-dependent rate constants were measured for the loss of B from the protonated (S(4)+4B)(n+) ions. Over the temperature range investigated, the kinetic stability increases with decreasing charge state, from n = 16 to 13, but is indistinguishable for n = 12 and 13. A comparison of the activation energies (E(a)) measured for the loss of B from the (S(4)+4B)(13+) ions composed of WT streptavidin and five binding site mutants (Trp79Phe, Trp108Phe, Trp120Phe, Ser27Ala, and Tyr43Ala) suggests that at least some of the specific intermolecular interactions are preserved in the gas phase. The results of molecular dynamics simulations performed on WT (S(4)+4B)(12+) ions with different charge configurations support this conclusion. The most significant finding of this study is that the gaseous WT (S(4)+4B)(n+) ions at n = 12-14, owing to a much larger E(a) (by as much as 13 kcal mol(-1)) for the loss of B, are dramatically more stable kinetically at 25 °C than the (S(4)+4B) complex in aqueous neutral solution. The differences in E(a) values measured for the gaseous (S(4)+4B)(n+) ions and solvated (S(4)+4B) complex can be largely accounted for by a late dissociative transition state and the rehydration of B and the protein binding cavity in solution.\",\n \"corpus_id\": 207085543,\n \"score\": 1\n },\n {\n \"doc_id\": \"22989197\",\n \"title\": \"A new modular approach to nanoassembly: stable and addressable DNA nanoconstructs via orthogonal click chemistries.\",\n \"abstract\": \"Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures.\",\n \"corpus_id\": 10768662,\n \"score\": 1\n },\n {\n \"doc_id\": \"23282586\",\n \"title\": \"Orthogonality in organic, polymer, and supramolecular chemistry: from Merrifield to click chemistry.\",\n \"abstract\": \"The concept of orthogonality has been applied to many areas of chemistry, ranging from wave functions to chromatography. But it was Barany and Merrifield's orthogonal protecting group strategy that paved the way for solid phase peptide syntheses, other important classes of biomaterials such as oligosaccharides and oligonucleotides, and ultimately to a term in widespread usage that is focused on chemical reactivity and binding selectivity. The orthogonal protection strategy has been extended to the development of orthogonal activation, and recently the click reaction, for streamlining organic synthesis. The click reaction and its variants are considered orthogonal as the components react together in high yield and in the presence of many other functional groups. Likewise, supramolecular building blocks can also be orthogonal, thereby enabling programmed self-assembly, a superb strategy to create complex architectures. Overall, orthogonal reactions and supramolecular interactions have dramatically improved the syntheses, the preparation of functional materials, and the self-assembly of nanoscale structures.\",\n \"corpus_id\": 3027284,\n \"score\": 1\n },\n {\n \"doc_id\": \"23670729\",\n \"title\": \"Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate.\",\n \"abstract\": \"We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.\",\n \"corpus_id\": 206407422,\n \"score\": 1\n },\n {\n \"doc_id\": \"23964715\",\n \"title\": \"Controlling macromolecular topology with genetically encoded SpyTag-SpyCatcher chemistry.\",\n \"abstract\": \"Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag-SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyTag and SpyCatcher can be strategically placed into ELP genes to direct post-translational topological modification in situ. Placement of SpyTag at the N-terminus and SpyCatcher at the C-terminus directs formation of circular ELPs. Induction of expression at 16 °C with 10 μM IPTG yields 80% monomeric cyclic protein. When SpyTag is placed in the middle of the chain, it exhibits an even stronger tendency toward cyclization, yielding up to 94% monomeric tadpole proteins. Telechelic ELPs containing either SpyTag or SpyCatcher can be expressed, purified, and then coupled spontaneously upon mixing in vitro. Block proteins, 3-arm or 4-arm star proteins, and H-shaped proteins have been prepared, with the folded CnaB2 domain that results from the SpyTag-SpyCatcher reaction as the molecular core or branch junction. The modular character of the SpyTag-SpyCatcher strategy should make it useful for preparing nonlinear macromolecules of diverse sequence and structure.\",\n \"corpus_id\": 262965573,\n \"score\": 1\n },\n {\n \"doc_id\": \"24161952\",\n \"title\": \"Structural analysis and optimization of the covalent association between SpyCatcher and a peptide Tag.\",\n \"abstract\": \"Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.\",\n \"corpus_id\": 42121602,\n \"score\": 1\n },\n {\n \"doc_id\": \"24639550\",\n \"title\": \"SpyLigase peptide-peptide ligation polymerizes affibodies to enhance magnetic cancer cell capture.\",\n \"abstract\": \"Individual proteins can now often be modified with atomic precision, but there are still major obstacles to connecting proteins into larger assemblies. To direct protein assembly, ideally, peptide tags would be used, providing the minimal perturbation to protein function. However, binding to peptides is generally weak, so assemblies are unstable over time and disassemble with force or harsh conditions. We have recently developed an irreversible protein-peptide interaction (SpyTag/SpyCatcher), based on a protein domain from Streptococcus pyogenes, that locks itself together via spontaneous isopeptide bond formation. Here we develop irreversible peptide-peptide interaction, through redesign of this domain and genetic dissection into three parts: a protein domain termed SpyLigase, which now ligates two peptide tags to each other. All components expressed efficiently in Escherichia coli and peptide tags were reactive at the N terminus, at the C terminus, or at internal sites. Peptide-peptide ligation enabled covalent and site-specific polymerization of affibodies or antibodies against the tumor markers epidermal growth factor receptor (EGFR) and HER2. Magnetic capture of circulating tumor cells (CTCs) is one of the most promising approaches to improve cancer prognosis and management, but CTC capture is limited by inefficient recovery of cells expressing low levels of tumor antigen. SpyLigase-assembled protein polymers made possible the isolation of cancerous cells expressing lower levels of tumor antigen and should have general application in enhancing molecular capture.\",\n \"corpus_id\": 7349100,\n \"score\": 1\n },\n {\n \"doc_id\": \"24817566\",\n \"title\": \"SpyTag/SpyCatcher cyclization confers resilience to boiling on a mesophilic enzyme.\",\n \"abstract\": \"SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β-lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild-type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β-lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.\",\n \"corpus_id\": 205380547,\n \"score\": 1\n },\n {\n \"doc_id\": \"24905869\",\n \"title\": \"Engineering orthogonality in supramolecular polymers: from simple scaffolds to complex materials.\",\n \"abstract\": \"Owing to the mastery exhibited by Nature in integrating both covalent and noncovalent interactions in a highly efficient manner, the quest to construct polymeric systems that rival not only the precision and fidelity but also the structure of natural systems has remained a daunting challenge. Supramolecular chemists have long endeavored to control the interplay between covalent and noncovalent bond formation, so as to examine and fully comprehend how function is predicated on self-assembly. The ability to reliably control polymer self-assembly is essential to generate \\\"smart\\\" materials and has the potential to tailor polymer properties (i.e., viscosity, electronic properties) through fine-tuning the noncovalent interactions that comprise the polymer architecture. In this context, supramolecular polymers have a distinct advantage over fully covalent systems in that they are dynamically modular, since noncovalent recognition motifs can be engineered to either impart a desired functionality within the overall architecture or provide a designed bias for the self-assembly process. In this Account, we describe engineering principles being developed and pursued by our group that exploit the orthogonal nature of noncovalent interactions, such as hydrogen bonding, metal coordination, and Coulombic interactions, to direct the self-assembly of functionalized macromolecules, resulting in the formation of supramolecular polymers. To begin, we describe our efforts to fabricate a modular poly(norbornene)-based scaffold via ring-opening metathesis polymerization (ROMP), wherein pendant molecular recognition elements based upon nucleobase-mimicking elements (e.g., thymine, diaminotriazine) or SCS-Pd(II) pincer were integrated within covalent monofunctional or symmetrically functionalized polymers. The simple polymer backbones exhibited reliable self-assembly with complementary polymers or small molecules. Within these systems, we applied successful protecting group strategies and template polymerizations to enhance the control afforded by ROMP. Main-chain-functionalized alternating block polymers based upon SCS-Pd(II) pincer-pyridine motifs were achieved through the combined exploitation of bimetallic initiators and supramolecularly functionalized terminators. Our initial design principles led to the successful fabrication of both main-chain- and side-chain-functionalized poly(norbornenes) via ROMP. Utilizing all of these techniques in concert led to engineering orthogonality while achieving complexity through the installation of multiple supramolecular motifs within the side chain, main chain, or both in our polymer systems. The exploitation and modification of design principles based upon functional ROMP initiators and terminators has resulted in the first synthesis of main-chain heterotelechelic polymers that self-assemble into A/B/C supramolecular triblock polymers composed of orthogonal cyanuric acid-Hamilton wedge and SCS-Pd(II) pincer-pyridine motifs. Furthermore, supramolecular A/B/A triblock copolymers were realized through the amalgamation of functionalized monomers, ROMP initiators, and terminators. To date, this ROMP-fabricated system represents the only known method to afford polymer main chains and side chains studded with orthogonal motifs. We end by discussing the impetus to attain functional materials via orthogonal self-assembly. Collectively, our studies suggest that combining covalent and noncovalent bonds in a well-defined and precise manner is an essential design element to achieve complex architectures. The results discussed in this Account illustrate the finesse associated with engineering orthogonal interactions within supramolecular systems and are considered essential steps toward developing complex biomimetic materials with high precision and fidelity.\",\n \"corpus_id\": 37347553,\n \"score\": 1\n },\n {\n \"doc_id\": \"25082796\",\n \"title\": \"\\\"Plug-and-go\\\" strategy to manipulate streptavidin valencies.\",\n \"abstract\": \"The streptavidin-biotin set is one of the most widely utilized conjugation pairs in biotechnological applications. The tetravalent nature of streptavidin and its homologues, however, tends to result in such undesirable complications as cross-linking or ill-defined stoichiometry. Here, we describe a mutagenesis-free strategy to manipulate the valencies of wild-type streptavidin that only requires commercially available reagents. The basic idea is simple: one obtains the desired streptavidin valency by blocking off unwanted binding sites using ancillary biotin (\\\"plug\\\"); this way, the extraordinary fM-biotin-binding affinity is fully retained for the remaining sites in streptavidin. In the present implementation, the ancillary biotin is attached to an auxiliary separation handle, negatively charged DNA or His-tagged protein, via a photochemically or enzymatically cleavable linker. Mixing streptavidin with the ancillary biotin construct produces a distribution of streptavidin valencies. The subsequent chromatographic separation readily isolates the construct of desired streptavidin valency, and the auxiliary handles are easily removed afterward (\\\"go\\\"). We demonstrate how this \\\"plug-and-go\\\" strategy allows a precise control for the compositions of streptavidin-biotin conjugates at the single-molecule level. This low-entry-barrier protocol could further expand the application scope of the streptavidin technology.\",\n \"corpus_id\": 31997189,\n \"score\": 1\n },\n {\n \"doc_id\": \"25168413\",\n \"title\": \"Superglue from bacteria: unbreakable bridges for protein nanotechnology.\",\n \"abstract\": \"Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.\",\n \"corpus_id\": 22873894,\n \"score\": 1\n },\n {\n \"doc_id\": \"25357135\",\n \"title\": \"Programming supramolecular biohybrids as precision therapeutics.\",\n \"abstract\": \"CONSPECTUS: Chemical programming of macromolecular structures to instill a set of defined chemical properties designed to behave in a sequential and precise manner is a characteristic vision for creating next generation nanomaterials. In this context, biopolymers such as proteins and nucleic acids provide an attractive platform for the integration of complex chemical design due to their sequence specificity and geometric definition, which allows accurate translation of chemical functionalities to biological activity. Coupled with the advent of amino acid specific modification techniques, \\\"programmable\\\" areas of a protein chain become exclusively available for any synthetic customization. We envision that chemically reprogrammed hybrid proteins will bridge the vital link to overcome the limitations of synthetic and biological materials, providing a unique strategy for tailoring precision therapeutics. In this Account, we present our work toward the chemical design of protein- derived hybrid polymers and their supramolecular responsiveness, while summarizing their impact and the advancement in biomedicine. Proteins, in their native form, represent the central framework of all biological processes and are an unrivaled class of macromolecular drugs with immense specificity. Nonetheless, the route of administration of protein therapeutics is often vastly different from Nature's biosynthesis. Therefore, it is imperative to chemically reprogram these biopolymers to direct their entry and activity toward the designated target. As a consequence of the innate structural regularity of proteins, we show that supramolecular interactions facilitated by stimulus responsive chemistry can be intricately designed as a powerful tool to customize their functions, stability, activity profiles, and transportation capabilities. From another perspective, a protein in its denatured, unfolded form serves as a monodispersed, biodegradable polymer scaffold decorated with functional side chains available for grafting with molecules of interest. Additionally, we are equipped with analytical tools to map the fingerprint of the protein chain, directly elucidating the structure at the molecular level. Contrary to conventional polymers, these biopolymers facilitate a more systematic avenue to investigate engineered macromolecules, with greater detail and accuracy. In this regard, we focus on denaturing serum albumin, an abundant blood protein, and exploit its peptidic array of functionalities to program supramolecular architectures for bioimaging, drug and gene delivery. Ultimately, we seek to assimilate the evolutionary advantage of these protein based biopolymers with the limitless versatility of synthetic chemistry to merge the best of both worlds.\",\n \"corpus_id\": 5073559,\n \"score\": 1\n },\n {\n \"doc_id\": \"26020143\",\n \"title\": \"Protein-induced supramolecular disassembly of amphiphilic polypeptide nanoassemblies.\",\n \"abstract\": \"Mimicking noncovalent interaction based processes in nature has been an important goal of supramolecular chemistry. Here, we report on amphiphilic polypeptides that self-assemble to form nanoscale supramolecular assemblies and are programmed to disassemble in response to a specific protein. Benzenesulfonamide and carbonic anhydrase have been chosen as the ligand and protein, respectively, to demonstrate this possibility. Since the amphiphilic nanoassembly sequesters hydrophobic guest molecules, the protein-specific disassembly event provides a protein-sensitive molecular release as well. We envision that the binding induced disassembly and guest release might open up new opportunities for the next generation of supramolecular assemblies for protein-specific delivery and diagnostics.\",\n \"corpus_id\": 207156156,\n \"score\": 1\n },\n {\n \"doc_id\": \"26278701\",\n \"title\": \"Synthetic Biology: A New Tool for the Trade.\",\n \"abstract\": \"Protein-protein interactions are fundamental to many biological processes. Yet, the weak and transient noncovalent bonds that characterize most protein-protein interactions found in nature impose limits on many bioengineering experiments. Here, a new class of genetically encodable peptide-protein pairs--isopeptag-N/pilin-N, isopeptag/pilin-C, and SpyTag/SpyCatcher--that interact through autocatalytic intermolecular isopeptide bond formation is described. Reactions between peptide-protein pairs are specific, robust, orthogonal, and able to proceed under most biologically relevant conditions both in vitro and in vivo. As fusion constructs, they provide a handle on molecules of interest, both organic and inorganic, that can be grasped with an iron grip. Such stable interactions provide robust post-translational control over biological processes and open new opportunities in synthetic biology for engineering programmable and self-assembling protein nanoarchitectures.\",\n \"corpus_id\": 44982914,\n \"score\": 1\n },\n {\n \"doc_id\": \"26517567\",\n \"title\": \"Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher.\",\n \"abstract\": \"SpyTag is a short peptide that forms an isopeptide bond upon encountering its protein partner SpyCatcher. This covalent peptide interaction is a simple and powerful tool for bioconjugation and extending what protein architectures are accessible. Here we review the origin and mechanism of SpyTag/SpyCatcher, focusing on recent innovative applications. Ligation of targeting-antibody with antigen provided a simple route to vaccine generation. SpyRings, from head-to-tail cyclisation, gave major enhancements in enzyme resilience. Linking multiple SpyCatchers gave dendrimers for T-cell activation or Spy networks forming hydrogels for stem cell culture. Synthetic biology applications include integrating amyloid biomaterials with living bacteria, for irreversible derivatisation of biofilms with enzymes or nanoparticles. We also discuss further opportunities to apply and enhance SpyTag/SpyCatcher technology.\",\n \"corpus_id\": 9799436,\n \"score\": 1\n },\n {\n \"doc_id\": \"26781591\",\n \"title\": \"Plug-and-Display: decoration of Virus-Like Particles via isopeptide bonds for modular immunization.\",\n \"abstract\": \"Virus-like particles (VLPs) are non-infectious self-assembling nanoparticles, useful in medicine and nanotechnology. Their repetitive molecularly-defined architecture is attractive for engineering multivalency, notably for vaccination. However, decorating VLPs with target-antigens by genetic fusion or chemical modification is time-consuming and often leads to capsid misassembly or antigen misfolding, hindering generation of protective immunity. Here we establish a platform for irreversibly decorating VLPs simply by mixing with protein antigen. SpyCatcher is a genetically-encoded protein designed to spontaneously form a covalent bond to its peptide-partner SpyTag. We expressed in E. coli VLPs from the bacteriophage AP205 genetically fused to SpyCatcher. We demonstrated quantitative covalent coupling to SpyCatcher-VLPs after mixing with SpyTag-linked to malaria antigens, including CIDR and Pfs25. In addition, we showed coupling to the VLPs for peptides relevant to cancer from epidermal growth factor receptor and telomerase. Injecting SpyCatcher-VLPs decorated with a malarial antigen efficiently induced antibody responses after only a single immunization. This simple, efficient and modular decoration of nanoparticles should accelerate vaccine development, as well as other applications of nanoparticle devices.\",\n \"corpus_id\": 1730573,\n \"score\": 1\n },\n {\n \"doc_id\": \"27034717\",\n \"title\": \"Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization.\",\n \"abstract\": \"BACKGROUND: SpyTag is a peptide that can form an irreversible covalent linkage to its 12 kDa partner SpyCatcher via a spontaneous isopeptide bond. Herein, we fused SpyTag at the N-terminal of lichenase and SpyCatcher at C-terminal so that the termini of lichenase were locked together by the covalent interaction between the partners. In addition, an elastin-like polypeptides tag was subsequently attached to the C-terminus of SpyCatcher, thereby facilitating the non-chromatographic purification of cyclized lichenase. RESULTS: The study showed that the optimum temperature of the cyclized lichenase was about 5 °C higher in comparison to its linear counterpart. Moreover, nearly 80 % of the cyclized lichenase activities were retained after 100 °C exposure, whereas the linear form lost almost all of its activities. Therefore, the cyclized variant displayed a significantly higher thermal stability as temperature elevated and was resistant to hyperthermal denaturation. Besides, the Km value of the cyclized lichenase (7.58 ± 0.92 mg/mL) was approximately 1.7-fold lower than that of the linear one (12.96 ± 1.93 mg/mL), indicating a higher affinity with substrates. CONCLUSIONS: This new SpyTag/SpyCatcher cyclization strategy is deemed as a generalized reference for enhancing enzyme stability and can be effectively customized to the cyclization of various enzymes, hence a tremendous potential for successful application in the biocatalytic conversion of biomass to produce fuels and chemicals.\",\n \"corpus_id\": 15396810,\n \"score\": 1\n },\n {\n \"doc_id\": \"27117585\",\n \"title\": \"Bacterial superglue enables easy development of efficient virus-like particle based vaccines.\",\n \"abstract\": \"BACKGROUND: Virus-like particles (VLPs) represent a significant advance in the development of subunit vaccines, combining high safety and efficacy. Their particulate nature and dense repetitive subunit organization makes them ideal scaffolds for display of vaccine antigens. Traditional approaches for VLP-based antigen display require labor-intensive trial-and-error optimization, and often fail to generate dense antigen display. Here we utilize the split-intein (SpyTag/SpyCatcher) conjugation system to generate stable isopeptide bound antigen-VLP complexes by simply mixing of the antigen and VLP components. RESULTS: Genetic fusion of SpyTag or SpyCatcher to the N-terminus and/or C-terminus of the Acinetobacter phage AP205 capsid protein resulted in formation of stable, nonaggregated VLPs expressing one SpyCatcher, one SpyTag or two SpyTags per capsid protein. Mixing of spy-VLPs with eleven different vaccine antigens fused to SpyCatcher or SpyTag resulted in formation of antigen-VLP complexes with coupling efficiencies (% occupancy of total VLP binding sites) ranging from 22-88 %. In mice, spy-VLP vaccines presenting the malaria proteins Pfs25 or VAR2CSA markedly increased antibody titer, affinity, longevity and functional efficacy compared to corresponding vaccines employing monomeric proteins. The spy-VLP vaccines also effectively broke B cell self-tolerance and induced potent and durable antibody responses upon vaccination with cancer or allergy-associated self-antigens (PD-L1, CTLA-4 and IL-5). CONCLUSIONS: The spy-VLP system constitutes a versatile and rapid method to develop highly immunogenic VLP-based vaccines. Our data provide proof-of-concept for the technology's ability to present complex vaccine antigens to the immune system and elicit robust functional antibody responses as well as to efficiently break B cell self-tolerance. The spy-VLP-system may serve as a generic tool for the cost-effective development of effective VLP-vaccines against both infectious- and non-communicable diseases and could facilitate rapid and unbiased screening of vaccine candidate antigens.\",\n \"corpus_id\": 217519352,\n \"score\": 1\n },\n {\n \"doc_id\": \"27249579\",\n \"title\": \"Geometrical assembly of ultrastable protein templates for nanomaterials.\",\n \"abstract\": \"The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein-protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.\",\n \"corpus_id\": 5664344,\n \"score\": 1\n },\n {\n \"doc_id\": \"27477779\",\n \"title\": \"Engineering Protein Hydrogels Using SpyCatcher-SpyTag Chemistry.\",\n \"abstract\": \"Constructing hydrogels from engineered proteins has attracted significant attention within the material sciences, owing to their myriad potential applications in biomedical engineering. Developing efficient methods to cross-link tailored protein building blocks into hydrogels with desirable mechanical, physical, and functional properties is of paramount importance. By making use of the recently developed SpyCatcher-SpyTag chemistry, we successfully engineered protein hydrogels on the basis of engineered tandem modular elastomeric proteins. Our resultant protein hydrogels are soft but stable, and show excellent biocompatibility. As the first step, we tested the use of these hydrogels as a drug carrier, as well as in encapsulating human lung fibroblast cells. Our results demonstrate the robustness of the SpyCatcher-SpyTag chemistry, even when the SpyTag (or SpyCatcher) is flanked by folded globular domains. These results demonstrate that SpyCatcher-SpyTag chemistry can be used to engineer protein hydrogels from tandem modular elastomeric proteins that can find applications in tissue engineering, in fundamental mechano-biological studies, and as a controlled drug release vehicle.\",\n \"corpus_id\": 2616636,\n \"score\": 1\n },\n {\n \"doc_id\": \"27503402\",\n \"title\": \"Protein-like Nanoparticles Based on Orthogonal Self-Assembly of Chimeric Peptides.\",\n \"abstract\": \"A novel two-component self-assembling chimeric peptide is designed where two orthogonal protein folding motifs are linked side by side with precisely defined position relative to one another. The self-assembly is driven by a combination of symmetry controlled molecular packing, intermolecular interactions, and geometric constraint to limit the assembly into compact dodecameric protein nanoparticles.\",\n \"corpus_id\": 46851353,\n \"score\": 1\n },\n {\n \"doc_id\": \"27658030\",\n \"title\": \"SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase.\",\n \"abstract\": \"SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.\",\n \"corpus_id\": 8477179,\n \"score\": 1\n },\n {\n \"doc_id\": \"27783674\",\n \"title\": \"Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly.\",\n \"abstract\": \"Over the last few years, a number of different protein assembly strategies have been developed, greatly expanding the toolbox for controlling macromolecular assembly. One of the most promising developments is a rapid protein ligation approach using a short polypeptide SpyTag and its partner, SpyCatcher derived from Streptococcus pyogenes fibronectin-binding protein, FbaB. To extend this technology, we have engineered and characterized a new Tag-Catcher pair from a related fibronectin-binding protein in Streptococcus dysgalactiae. The polypeptide Tag, named SdyTag, was constructed based on the native Cna protein B-type (CnaB) domain and was found to be highly unreactive to SpyCatcher. SpyCatcher has 320-fold specificity for its native SpyTag compared to SdyTag. Similarly, SdyTag has a 75-fold specificity for its optimized Catcher, named SdyCatcherDANG short, compared to SpyCatcher. These Tag-Catcher pairs were used in combination to demonstrate specific sequential assembly of tagged proteins in vitro. We also demonstrated that the in vivo generation of circularized proteins in a Tag-Catcher specific manner where specific Tags can be left unreacted for use in subsequent ligation reactions. From the success of these experiments, we foresee the application of SdyTags and SpyTags, not only, for multiplexed control of protein assembly but also for the construction of novel protein architectures.\",\n \"corpus_id\": 1537692,\n \"score\": 1\n },\n {\n \"doc_id\": \"27982100\",\n \"title\": \"Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates.\",\n \"abstract\": \"Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.\",\n \"corpus_id\": 18992987,\n \"score\": 1\n },\n {\n \"doc_id\": \"28105787\",\n \"title\": \"Orthogonal Surface Tags for Whole-Cell Biocatalysis.\",\n \"abstract\": \"We herein describe the engineering of E. coli strains that display orthogonal tags for immobilization on their surface and overexpress a functional heterologous \\\"protein content\\\" in their cytosol at the same time. Using the outer membrane protein Lpp-ompA, cell-surface display of the streptavidin-binding peptide, the SpyTag/SpyCatcher system, or a HaloTag variant allowed us to generate bacterial strains that can selectively bind to solid substrates, as demonstrated with magnetic microbeads. The simultaneous cytosolic expression of functional content was demonstrated for fluorescent proteins or stereoselective ketoreductase enzymes. The latter strains gave high selectivities for specific immobilization onto complementary surfaces and also in the whole-cell stereospecific transformation of a prochiral CS -symmetric nitrodiketone.\",\n \"corpus_id\": 205398168,\n \"score\": 1\n },\n {\n \"doc_id\": \"28437083\",\n \"title\": \"Dual Plug-and-Display Synthetic Assembly Using Orthogonal Reactive Proteins for Twin Antigen Immunization.\",\n \"abstract\": \"Engineering modular platforms to control biomolecular architecture can advance both the understanding and the manipulation of biological systems. Icosahedral particles uniformly displaying single antigens stimulate potent immune activation and have been successful in various licensed vaccines. However, it remains challenging to display multiple antigens on a single particle and to induce broader immunity protective across strains or even against distinct diseases. Here, we design a dually addressable synthetic nanoparticle by engineering the multimerizing coiled-coil IMX313 and two orthogonally reactive split proteins. SpyCatcher protein forms an isopeptide bond with SpyTag peptide through spontaneous amidation. SnoopCatcher forms an isopeptide bond with SnoopTag peptide through transamidation. SpyCatcher-IMX-SnoopCatcher provides a modular platform, whereby SpyTag-antigen and SnoopTag-antigen can be multimerized on opposite faces of the particle simply upon mixing. We demonstrate efficient derivatization of the platform with model proteins and complex pathogen-derived antigens. SpyCatcher-IMX-SnoopCatcher was expressed in Escherichia coli and was resilient to lyophilization or extreme temperatures. For the next generation of malaria vaccines, blocking the transmission of the parasite from human to mosquito is an important goal. SpyCatcher-IMX-SnoopCatcher multimerization of the leading transmission-blocking antigens Pfs25 and Pfs28 greatly enhanced the antibody response to both antigens in comparison to the monomeric proteins. This dual plug-and-display architecture should help to accelerate vaccine development for malaria and other diseases.\",\n \"corpus_id\": 206520806,\n \"score\": 1\n },\n {\n \"doc_id\": \"28757182\",\n \"title\": \"Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction.\",\n \"abstract\": \"Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1-6 amines per subunit: \\\"amine landscaping.\\\" Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe.\",\n \"corpus_id\": 20816884,\n \"score\": 1\n },\n {\n \"doc_id\": \"29024296\",\n \"title\": \"Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics.\",\n \"abstract\": \"SpyTag is a peptide that forms a spontaneous amide bond with its protein partner SpyCatcher. This protein superglue is a broadly useful tool for molecular assembly, locking together biological building blocks efficiently and irreversibly in diverse architectures. We initially developed SpyTag and SpyCatcher by rational design, through splitting a domain from a Gram-positive bacterial adhesin. In this work, we established a phage-display platform to select for specific amidation, leading to an order of magnitude acceleration for interaction of the SpyTag002 variant with the SpyCatcher002 variant. We show that the 002 pair bonds rapidly under a wide range of conditions and at either protein terminus. SpyCatcher002 was fused to an intimin derived from enterohemorrhagic Escherichia coli. SpyTag002 reaction enabled specific and covalent decoration of intimin for live cell fluorescent imaging of the dynamics of the bacterial outer membrane as cells divide.\",\n \"corpus_id\": 3598641,\n \"score\": 1\n },\n {\n \"doc_id\": \"29039416\",\n \"title\": \"Antibodies to biotin enable large-scale detection of biotinylation sites on proteins.\",\n \"abstract\": \"Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.\",\n \"corpus_id\": 21738454,\n \"score\": 1\n },\n {\n \"doc_id\": \"29625006\",\n \"title\": \"SpyCatcher-NTEV: A Circularly Permuted, Disordered SpyCatcher Variant for Less Trace Ligation.\",\n \"abstract\": \"The SpyTag/SpyCatcher reaction has emerged as a powerful way for bioconjugation, but it leaves a folded complex in the product after the formation of the isopeptide bond. To vary the location of the reactive residue and reduce the size of the complex and its potential immunogenicity, we engineer two circularly permuted SpyCatcher variants, SpyCatcher-N and SpyCatcher-NTEV, the latter of which possesses a TEV-recognition site for removal of the fragment containing the catalytic site. Surprisingly, both variants are found to be disordered in solution, yet still retain the ability to form an ordered complex upon reaction with SpyTag with second-order rate constants of ∼10 M-1 s-1. Cellular expression of a telechelic protein bearing SpyCatcher-NTEV at the N-terminus and SpyTag at the C-terminus gives both cyclized and chain-extended products. Notably, the monomers exist almost exclusively in the cyclic form owing to its high reactivity in vivo. The fragment containing the catalytic site of SpyCatcher-NTEV can then be removed by TEV digestion, giving a circular protein with minimal trace from the ligation reaction. The plasticity of SpyTag/SpyCatcher reactive pair has promised an ever-expanding toolbox of genetically encoded peptide-protein reaction with versatile features.\",\n \"corpus_id\": 4645665,\n \"score\": 1\n },\n {\n \"doc_id\": \"18668104\",\n \"title\": \"Functionalizing hydrogen-bonded surface networks with self-assembled monolayers.\",\n \"abstract\": \"One of the central challenges in nanotechnology is the development of flexible and efficient methods for creating ordered structures with nanometre precision over an extended length scale. Supramolecular self-assembly on surfaces offers attractive features in this regard: it is a 'bottom-up' approach and thus allows the simple and rapid creation of surface assemblies, which are readily tuned through the choice of molecular building blocks used and stabilized by hydrogen bonding, van der Waals interactions, pi-pi bonding or metal coordination between the blocks. Assemblies in the form of two-dimensional open networks are of particular interest for possible applications because well-defined pores can be used for the precise localization and confinement of guest entities such as molecules or clusters, which can add functionality to the supramolecular network. Another widely used method for producing surface structures involves self-assembled monolayers (SAMs), which have introduced unprecedented flexibility in our ability to tailor interfaces and generate patterned surfaces. But SAMs are part of a top-down technology that is limited in terms of the spatial resolution that can be achieved. We therefore rationalized that a particularly powerful fabrication platform might be realized by combining non-covalent self-assembly of porous networks and SAMs, with the former providing nanometre-scale precision and the latter allowing versatile functionalization. Here we show that the two strategies can indeed be combined to create integrated network-SAM hybrid systems that are sufficiently robust for further processing. We show that the supramolecular network and the SAM can both be deposited from solution, which should enable the widespread and flexible use of this combined fabrication method.\",\n \"corpus_id\": 205213948,\n \"score\": 0\n },\n {\n \"doc_id\": \"19374419\",\n \"title\": \"Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.\",\n \"abstract\": \"We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of chi1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic chi1 angles. We observe changes in the chi1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution-phase simulations is predominantly broken in this much longer solution-phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution-phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.\",\n \"corpus_id\": 8825566,\n \"score\": 0\n },\n {\n \"doc_id\": \"20462252\",\n \"title\": \"A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?\",\n \"abstract\": \"We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.\",\n \"corpus_id\": 22733513,\n \"score\": 0\n },\n {\n \"doc_id\": \"21892837\",\n \"title\": \"Engineered streptavidin monomer and dimer with improved stability and function.\",\n \"abstract\": \"Although streptavidin's high affinity for biotin has made it a widely used and studied binding protein and labeling tool, its tetrameric structure may interfere with some assays. A streptavidin mutant with a simpler quaternary structure would demonstrate a molecular-level understanding of its structural organization and lead to the development of a novel molecular reagent. However, modulating the tetrameric structure without disrupting biotin binding has been extremely difficult. In this study, we describe the design of a stable monomer that binds biotin both in vitro and in vivo. To this end, we constructed and characterized monomers containing rationally designed mutations. The mutations improved the stability of the monomer (increase in T(m) from 31 to 47 °C) as well as its affinity (increase in K(d) from 123 to 38 nM). We also used the stability-improved monomer to construct a dimer consisting of two streptavidin subunits that interact across the dimer-dimer interface, which we call the A/D dimer. The biotin binding pocket is conserved between the tetramer and the A/D dimer, and therefore, the dimer is expected to have a significantly higher affinity than the monomer. The affinity of the dimer (K(d) = 17 nM) is higher than that of the monomer but is still many orders of magnitude lower than that of the wild-type tetramer, which suggests there are other factors important for high-affinity biotin binding. We show that the engineered streptavidin monomer and dimer can selectively bind biotinylated targets in vivo by labeling the cells displaying biotinylated receptors. Therefore, the designed mutants may be useful in novel applications as well as in future studies in elucidating the role of oligomerization in streptavidin function.\",\n \"corpus_id\": 21622029,\n \"score\": 0\n },\n {\n \"doc_id\": \"22802499\",\n \"title\": \"Ultra-precision: enabling our future.\",\n \"abstract\": \"This paper provides a perspective on the development of ultra-precision technologies: What drove their evolution and what do they now promise for the future as we face the consequences of consumption of the Earth's finite resources? Improved application of measurement is introduced as a major enabler of mass production, and its resultant impact on wealth generation is considered. This paper identifies the ambitions of the defence, automotive and microelectronics sectors as important drivers of improved manufacturing accuracy capability and ever smaller feature creation. It then describes how science fields such as astronomy have presented significant precision engineering challenges, illustrating how these fields of science have achieved unprecedented levels of accuracy, sensitivity and sheer scale. Notwithstanding their importance to science understanding, many science-driven ultra-precision technologies became key enablers for wealth generation and other well-being issues. Specific ultra-precision machine tools important to major astronomy programmes are discussed, as well as the way in which subsequently evolved machine tools made at the beginning of the twenty-first century, now provide much wider benefits.\",\n \"corpus_id\": 6059560,\n \"score\": 0\n },\n {\n \"doc_id\": \"23534402\",\n \"title\": \"Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes.\",\n \"abstract\": \"Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.\",\n \"corpus_id\": 27269560,\n \"score\": 0\n },\n {\n \"doc_id\": \"24790550\",\n \"title\": \"Fluorescence enhancement of fluorescent unnatural streptavidin by binding of a biotin analogue with spacer tail and its application to biotin sensing.\",\n \"abstract\": \"We designed a novel molecular biosensing system for the detection of biotin, an important vitamin by the combination of fluorescent unnatural streptavidin with a commercialized biotin-(AC5)2-hydrazide. A fluorescent unnatural amino acid, BODIPY-FL-aminophenylalanine (BFLAF), was position-specifically incorporated into Trp120 of streptavidin by four-base codon method. Fluorescence of the Trp120BFLAF mutant streptavidin was enhanced by the addition of biotin-(AC5)2-hydrazide with the concentration dependent, whereas fluorescence enhancement was not observed at all by the addition of natural biotin. It was considered that the spacer tail of biotin-(AC5)2-hydrazide may disturb the fluorescence quenching of the Trp120BFLAF by Trp79 and Trp108 of the neighbor subunit. Therefore, biotin sensing was carried out by the competitive binding reaction of biotin-(AC5)2-hydrazide and natural biotin to the fluorescent mutant streptavidin. The fluorescence intensity decreased by increasing free biotin concentration. The result suggested that molecular biosensor for small ligand could be successfully designed by the pair of fluorescent mutant binding protein and ligand analogue.\",\n \"corpus_id\": 15608490,\n \"score\": 0\n },\n {\n \"doc_id\": \"25049400\",\n \"title\": \"Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry.\",\n \"abstract\": \"Protein-based hydrogels have emerged as promising alternatives to synthetic hydrogels for biomedical applications, owing to the precise control of structure and function enabled by protein engineering. Nevertheless, strategies for assembling 3D molecular networks that carry the biological information encoded in full-length proteins remain underdeveloped. Here we present a robust protein gelation strategy based on a pair of genetically encoded reactive partners, SpyTag and SpyCatcher, that spontaneously form covalent isopeptide linkages under physiological conditions. The resulting \\\"network of Spies\\\" may be designed to include cell-adhesion ligands, matrix metalloproteinase-1 cleavage sites, and full-length globular proteins [mCherry and leukemia inhibitory factor (LIF)]. The LIF network was used to encapsulate mouse embryonic stem cells; the encapsulated cells remained pluripotent in the absence of added LIF. These results illustrate a versatile strategy for the creation of information-rich biomaterials.\",\n \"corpus_id\": 16197967,\n \"score\": 0\n },\n {\n \"doc_id\": \"25119814\",\n \"title\": \"Increasing and decreasing the ultrastability of bacterial chemotaxis core signaling complexes by modifying protein-protein contacts.\",\n \"abstract\": \"The chemosensory signaling array of bacterial chemotaxis is composed of functional core units containing two receptor trimers of dimers, a homodimeric CheA kinase, and two CheW adaptor proteins. In vitro reconstitutions generate individual, functional core units and larger functional assemblies, including dimers, hexagons, and hexagonal arrays. Such reconstituted complexes have been shown to have both quasi-stable and ultrastable populations that decay with lifetimes of 1-2 days and ∼3 weeks at 22 °C, respectively, where decay results primarily from proteolysis of the bound kinase [Erbse, A. H., and Falke, J. J. (2009) Biochemistry 48, 6975-6987; Slivka, P. F., and Falke, J. J. (2012) Biochemistry 51, 10218-10228]. In this work, we show that the ultrastable population can be destabilized to the quasi-stable level via the introduction of a bulky tryptophan residue at either one of two essential protein-protein interfaces within the core unit: the receptor-kinase contact or kinase-adaptor interface 1. Moreover, we demonstrate that the quasi-stable population can be made ultrastable via the introduction of a disulfide bond that covalently stabilizes the latter interface. The resulting disulfide at least doubles the functional lifetime of the ultrastable population, to ≥5.9 weeks at 22 °C, by protecting the kinase from endogenous and exogenous proteases. Together, these results indicate that the ultrastability of reconstituted core complexes requires well-formed contacts among the receptor, kinase, and adaptor proteins, whereas quasi-stability arises from less perfect contacts that allow slow proteolysis of the bound kinase. Furthermore, the results reveal that ultrastability, and perhaps the size or order of chemosensory complexes and arrays, can be increased by an engineered disulfide bond that covalently cross-links a key interface. Overall, it appears that native ultrastability has evolved to provide an optimal rather than maximal level of kinetic durability, suggesting that altered selective pressure could either increase or decrease the functional lifetime of core complexes.\",\n \"corpus_id\": 8321829,\n \"score\": 0\n },\n {\n \"doc_id\": \"25482395\",\n \"title\": \"Ultrastable cellulosome-adhesion complex tightens under load.\",\n \"abstract\": \"Challenging environments have guided nature in the development of ultrastable protein complexes. Specialized bacteria produce discrete multi-component protein networks called cellulosomes to effectively digest lignocellulosic biomass. While network assembly is enabled by protein interactions with commonplace affinities, we show that certain cellulosomal ligand-receptor interactions exhibit extreme resistance to applied force. Here, we characterize the ligand-receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome using single-molecule force spectroscopy and steered molecular dynamics simulations. The complex withstands forces of 600-750 pN, making it one of the strongest bimolecular interactions reported, equivalent to half the mechanical strength of a covalent bond. Our findings demonstrate force activation and inter-domain stabilization of the complex, and suggest that certain network components serve as mechanical effectors for maintaining network integrity. This detailed understanding of cellulosomal network components may help in the development of biocatalysts for production of fuels and chemicals from renewable plant-derived biomass.\",\n \"corpus_id\": 465374,\n \"score\": 0\n },\n {\n \"doc_id\": \"25560523\",\n \"title\": \"SWATH enables precise label-free quantification on proteome scale.\",\n \"abstract\": \"MS-based proteomics has emerged as a powerful tool in biological studies. The shotgun proteomics strategy, in which proteolytic peptides are analyzed in data-dependent mode, enables a detection of the most comprehensive proteome (>10 000 proteins from whole-cell lysate). The quantitative proteomics uses stable isotopes or label-free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label-free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. Sequential window acquisition of all theoretical mass spectra (SWATH) is a recently developed technique, in which data-independent acquisition is coupled with peptide spectral library match. In principle SWATH method is able to do label-free quantification in an MRM-like manner, which has higher quantification accuracy and precision. Previous data have demonstrated that SWATH can be used to quantify less complex systems, such as spiked-in peptide mixture or protein complex. Our study first time assessed the quantification performance of SWATH method on proteome scale using a complex mouse-cell lysate sample. In total 3600 proteins got identified and quantified without sample prefractionation. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly. However, this inaccuracy does not prevent discovering biological correlates, because the measured signal intensities had linear relationship to the sample loading amounts; thus the SWATH method can predict precisely the significance of a protein. Our results prove that SWATH can provide precise label-free quantification on proteome scale.\",\n \"corpus_id\": 5498735,\n \"score\": 0\n },\n {\n \"doc_id\": \"26709829\",\n \"title\": \"Chemotactic Signaling by Single-Chain Chemoreceptors.\",\n \"abstract\": \"Bacterial chemoreceptors of the methyl-accepting chemotaxis protein (MCP) family operate in commingled clusters that enable cells to detect and track environmental chemical gradients with high sensitivity and precision. MCP homodimers of different detection specificities form mixed trimers of dimers that facilitate inter-receptor communication in core signaling complexes, which in turn assemble into a large signaling network. The two subunits of each homodimeric receptor molecule occupy different locations in the core complexes. One subunit participates in trimer-stabilizing interactions at the trimer axis, the other lies on the periphery of the trimer, where it can interact with two cytoplasmic proteins: CheA, a signaling autokinase, and CheW, which couples CheA activity to receptor control. As a possible tool for independently manipulating receptor subunits in these two structural environments, we constructed and characterized fused genes for the E. coli serine chemoreceptor Tsr that encoded single-chain receptor molecules in which the C-terminus of the first Tsr subunit was covalently connected to the N-terminus of the second with a polypeptide linker. We showed with soft agar assays and with a FRET-based in vivo CheA kinase assay that single-chain Tsr~Tsr molecules could promote serine sensing and chemotaxis responses. The length of the connection between the joined subunits was critical. Linkers nine residues or shorter locked the receptor in a kinase-on state, most likely by distorting the native structure of the receptor HAMP domain. Linkers 22 or more residues in length permitted near-normal Tsr function. Few single-chain molecules were found as monomer-sized proteolytic fragments in cells, indicating that covalently joined receptor subunits were responsible for mediating the signaling responses we observed. However, cysteine-directed crosslinking, spoiling by dominant-negative Tsr subunits, and rearrangement of ligand-binding site lesions revealed subunit swapping interactions that will need to be taken into account in experimental applications of single-chain chemoreceptors.\",\n \"corpus_id\": 13263204,\n \"score\": 0\n },\n {\n \"doc_id\": \"28551501\",\n \"title\": \"The role of CH/π interactions in the high affinity binding of streptavidin and biotin.\",\n \"abstract\": \"The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10(15)mol(-1)) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.\",\n \"corpus_id\": 5472834,\n \"score\": 0\n },\n {\n \"doc_id\": \"29206886\",\n \"title\": \"Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry.\",\n \"abstract\": \"The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.\",\n \"corpus_id\": 13408524,\n \"score\": 0\n },\n {\n \"doc_id\": \"29233896\",\n \"title\": \"Retargeting Lentiviruses via SpyCatcher-SpyTag Chemistry for Gene Delivery into Specific Cell Types.\",\n \"abstract\": \"We report a simple strategy for the creation of lentiviral vectors specific to any desired target cells. SpyTag is inserted into an engineered Sindbis virus envelope protein and displayed on the lentivirus surface to create Sindbis virus-SpyTag pseudoparticles (Sind-SpyTag-pp). The SpyTag serves as the covalent anchoring site for a target-cell-specific cell-binding protein (CBP) that is fused to a truncated SpyCatcher (SpyCatcherΔ). Target-cell-specific lentiviruses are created by mixing the Sind-SpyTag-pp and CBP-SpyCatcherΔ in vitro We first used a HER2-binding designed ankyrin repeat protein (DARPin.9.26) as the model CBP. The DARPin-conjugated lentivirus transduced HER2+ SKOV3 cells with an infectious titer of 5.2 × 106 IU/ml, >500-fold higher than the unfunctionalized \\\"naked\\\" virions (<104 IU/ml). The ability of the DARPin-conjugated lentivirus to transduce HER2+ cells correlated with the surface expression level of HER2. Furthermore, these lentiviruses preferentially transduced HER2+ cells in cocultures containing HER2+ and HER2- cells. To enable the use of commercially available monoclonal antibodies (MAbs) as the CBP, we developed a convenient click chemistry-based approach to conjugate MAb-derived Fab fragments to a variant SpyCatcherΔ protein containing a nonnatural amino acid, 4-azido-l-phenylalanine (AzF). Using the HER2-binding trastuzumab as a model cell-specific MAb, we created Fab-conjugated lentiviral vectors that transduced HER2+ SKOV3 cells with an infectious titer of 2.8 × 106 IU/ml, on par with the result achieved using the DARPin-SpyCatcherΔ fusion protein. The ability to create cell-specific lentiviral vectors through chemical conjugation of a CBP should make this approach generalizable to any antibody, giving it broad utility for a wide range of research and clinical applications. IMPORTANCE Lentiviral vectors hold great potential in gene therapy. However, it remains a major hurdle to robustly engineer cell-specific lentiviral vectors. This article reports a simple and effective strategy to functionalize lentiviral vectors with cell-binding proteins, thus retargeting these viruses to cells expressing the binding partner of the CBP. The CBP is genetically or chemically linked to the SpyCatcher. The SpyTag is displayed on the virion surface as a fusion to an engineered Sindbis virus envelope protein and is used as the anchorage site for SpyCatcher-linked CBP. Using this strategy, we created lentiviral vectors highly infectious toward HER2+ cancer cells. The ability to rapidly create cell-specific lentiviral vectors targeting a wide range of cell types should accelerate the development of custom lentiviral vectors for many research and clinical applications.\",\n \"corpus_id\": 23106579,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":93,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26670244\",\n \"title\": \"Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.\",\n \"abstract\": \"Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970-1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263-1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition.\",\n \"corpus_id\": 14888611\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18077713","title":"Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus.","abstract":"A new Salmonella enterica phage, Det7, was isolated from sewage and shown by electron microscopy to belong to the Myoviridae morphogroup of bacteriophages. Det7 contains a 75-kDa protein with 50% overall sequence identity to the tail spike endorhamnosidase of podovirus P22. Adsorption of myoviruses to their bacterial hosts is normally mediated by long and short tail fibers attached to a contractile tail, whereas podoviruses do not contain fibers but attach to host cells through stubby tail spikes attached to a very short, noncontractile tail. The amino-terminal 150 residues of the Det7 protein lack homology to the P22 tail spike and are probably responsible for binding to the base plate of the myoviral tail. Det7 tail spike lacking this putative particle-binding domain was purified from Escherichia coli, and well-diffracting crystals of the protein were obtained. The structure, determined by molecular replacement and refined at a 1.6-A resolution, is very similar to that of bacteriophage P22 tail spike. Fluorescence titrations with an octasaccharide suggest Det7 tail spike to bind its receptor lipopolysaccharide somewhat less tightly than the P22 tail spike. The Det7 tail spike is even more resistant to thermal unfolding than the already exceptionally stable homologue from P22. Folding and assembly of both trimeric proteins are equally temperature sensitive and equally slow. Despite the close structural, biochemical, and sequence similarities between both proteins, the Det7 tail spike lacks both carboxy-terminal cysteines previously proposed to form a transient disulfide during P22 tail spike assembly. Our data suggest receptor-binding module exchange between podoviruses and myoviruses in the course of bacteriophage evolution.","corpus_id":22593104,"score":2},{"doc_id":"18160394","title":"Structure of the bacteriophage phi KZ lytic transglycosylase gp144.","abstract":"Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage phi KZ has been determined to 2.5-A resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. phi KZ gp144 is a 260-residue alpha-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G D-Ala-D-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu 115 in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the phi KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine)(4) has been determined to 2.6-A resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.","corpus_id":37782816,"score":2},{"doc_id":"18462681","title":"An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.","abstract":"Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect gram-negative bacteria by insertion of their double-stranded DNA. They attach to their hosts specifically via their tailspike proteins. The 1.25 A crystal structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved architecture with a central, right-handed beta helix. In the trimer of Sf6 TSP, the parallel beta helices form a left-handed, coiled-beta coil with a pitch of 340 A. The C-terminal domain consists of a beta sandwich reminiscent of viral capsid proteins. Further crystallographic and biochemical analyses show a Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site located between two beta-helix subunits each anchoring one catalytic carboxylate. The functionally and structurally related bacteriophage, P22 TSP, lacks sequence identity with Sf6 TSP and has its active sites on single subunits. Sf6 TSP may serve as an example for the evolution of different host specificities on a similar general architecture.","corpus_id":205258558,"score":2},{"doc_id":"19189967","title":"Proteolytic release of the intramolecular chaperone domain confers processivity to endosialidase F.","abstract":"Endosialidases (endoNs), as identified so far, are tailspike proteins of bacteriophages that specifically bind and degrade the alpha2,8-linked polysialic acid (polySia) capsules of their hosts. The crystal structure solved for the catalytic domain of endoN from coliphage K1F (endoNF) revealed a functional trimer. Folding of the catalytic trimer is mediated by an intramolecular C-terminal chaperone domain. Release of the chaperone from the folded protein confers kinetic stability to endoNF. In mutant c(S), the replacement of serine 911 by alanine prevents proteolysis and generates an enzyme that varies in activity from wild type. Using soluble polySia as substrate a 3-times higher activity was detected while evaluation with immobilized polySia revealed a 190-fold reduced activity. Importantly, activity of c(S) did not differ from wild type with tetrameric sialic acid, the minimal endoNF substrate. Furthermore, we show that the presence of the chaperone domain in c(S) destabilizes binding to polySia in a similar way as did selective disruption of a polySia binding site in the stalk domain. The improved catalytic efficiency toward soluble polySia observed in these mutants can be explained by higher dissociation and association probabilities, whereas inversely, an impaired processivity was found. The fact that endoNF is a processive enzyme introduces a new molecular basis to explain capsule degradation by bacteriophages, which until now has been regarded as a result of cooperative interaction of tailspike proteins. Moreover, knowing that release of the chaperone domain confers kinetic stability and processivity, conservation of the proteolytic process can be explained by its importance in phage evolution.","corpus_id":205377694,"score":2},{"doc_id":"19780551","title":"Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2.","abstract":"The P2 phage virion has tail spike proteins beneath the baseplate and uses them to adsorb to the outer membrane of Escherichia coli during the infection process. Previous immunoelectron microscopic studies suggested that the tail spikes are composed of the gene V product (gpV); however, experimental evidence of its membrane binding activity has yet to be reported. In this study, we purified and characterized recombinant full-length gpV and its C-terminal domain. Limited chymotrypsin proteolysis of gpV produced a C-terminal domain composed of Ser86-Leu211. Our experiments demonstrated that the N- and C-terminal domains have very different melting temperatures: 50 and 74 degrees C, respectively. We also found that gpV binds the E. coli membrane via its C-terminal domain. We conclude that the C-terminal domain of gpV is a stable trimer and serves as the receptor-binding domain for the second step in the phage adsorption process.","corpus_id":14722,"score":2},{"doc_id":"19913618","title":"Two-chaperone assisted soluble expression and purification of the bacteriophage T4 long tail fibre protein gp37.","abstract":"Bacteriophage T4 recognises its host cells through its long tail fibre protein gene product (gp) 37. Gp37 is a protein containing 1026 amino acids per monomer, forming a fibrous parallel homotrimer at the distal end of the long tail fibres. The other distal half-fibre protein, gp36, is much smaller, forming a trimer of 221 amino acids per monomer. Functional and structural studies of gp37 have been hampered by the inability to produce suitable amounts of it. We produced soluble gp37 by co-expression with two bacteriophage T4-encoded chaperones in a two-vector system; co-expression with each chaperone separately did not lead to good amounts of correctly folded, trimeric protein. An expression vector for the bacteriophage T4 fibrous protein chaperone gp57 was co-transformed into bacteria with a compatible bi-cistronic expression vector containing bacteriophage T4 genes 37 and 38. A six-histidine tag is encoded amino-terminal to the gp37 gene. Recombinant trimeric gp37, containing the histidine tag and residues 12-1026 of gp37, was purified from lysed bacteria by subsequent nickel-affinity, size exclusion and strong anion exchange column chromatography. Yields of approximately 4 mg of purified protein per litre of bacterial culture were achieved. Electron microscopy confirmed the protein to form fibres around 63 nm long, presumably gp36 makes up the remaining 11 nm in the intact distal half-fibre. Purified, correctly folded, gp37 will be useful for receptor-binding studies, high-resolution structural studies and for specific binding and detection of bacteria.","corpus_id":38077951,"score":2},{"doc_id":"20478417","title":"The C-terminal domain is sufficient for host-binding activity of the Mu phage tail-spike protein.","abstract":"The Mu phage virion contains tail-spike proteins beneath the baseplate, which it uses to adsorb to the outer membrane of Escherichia coli during the infection process. The tail spikes are composed of gene product 45 (gp45), which contains 197 amino acid residues. In this study, we purified and characterized both the full-length and the C-terminal domains of recombinant gp45 to identify the functional and structural domains. Limited proteolysis resulted in a Ser64-Gln197 sequence, which was composed of a stable C-terminal domain. Analytical ultracentrifugation of the recombinant C-terminal domain (gp45-C) indicated that the molecular weight of gp45-C was about 58 kDa and formed a trimeric protomer in solution. Coprecipitation experiments and a quartz crystal microbalance (QCM) demonstrated that gp45-C irreversibly binds to the E. coli membrane. These results indicate that gp45 shows behaviors similar to tail-spike proteins of other phages; however, gp45 did not show significant sequence homology with the other phage tail-spike structures that have been identified.","corpus_id":5160019,"score":2},{"doc_id":"20531477","title":"[The beta-helical domain of bacteriophage T4 controls the folding of the fragment of long tail fibers in a chimeric protein].","abstract":"The key stage of the infection of the Escherichia coli cell with bacteriophage T4, the binding to the surface of the host cell, is determined by the specificity of the long tail fiber proteins of the phage, in particular, gp37. The assembly and oligomerization of this protein under natural conditions requires the participation of at least two additional protein factors, gp57A and gp38, which strongly hinders the production of the recombinant form of gp37. To overcome this problem, a modern protein engineering strategy was used, which involves the construction of a chimeric protein containing a carrier protein that drives the correct folding of the target protein. For this purpose, the trimeric beta-helical domain of another protein of phage T4, gp5, was used. It was shown that this domain, represented as a rigid trimeric polypeptide prism, has properties favorable for use as a protein carrier. A fragment of protein gp37 containing five pentapeptides repeats, Gly-X-His-X-His, which determine the binding to the receptors on the bacterial cell surface, was fused in a continuous reading frame to the C-terminus of the domain of gp5. The resulting chimeric protein forms a trimer that has the native conformation of gp37 and exhibits biological activity.","corpus_id":36456702,"score":2},{"doc_id":"20843802","title":"Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages.","abstract":"Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.","corpus_id":21515226,"score":2},{"doc_id":"21041684","title":"Structure of the bacteriophage T4 long tail fiber receptor-binding tip.","abstract":"Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity.","corpus_id":11209758,"score":2},{"doc_id":"21705802","title":"Atomic structure of bacteriophage Sf6 tail needle knob.","abstract":"Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the \"tail needle\" likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.","corpus_id":19334689,"score":2},{"doc_id":"21821878","title":"The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure.","abstract":"The adsorption and infection of bacteriophage P2 is mediated by tail fibres and tail spikes. The tail spikes on the tail baseplate are used to irreversibly adsorb to the host cells. Recently, a P2 phage tail-spike protein, gpV, was purified and it was shown that a C-terminal domain, Ser87-Leu211, is sufficient for the binding of gpV to host Escherichia coli membranes [Kageyama et al. (2009), Biochemistry, 48, 10129-10135]. In this paper, the crystal structure of the C-terminal domain of P2 gpV is reported. The structure is a triangular pyramid and looks like a spearhead composed of an intertwined β-sheet, a triple β-helix and a metal-binding region containing iron, calcium and chloride ions.","corpus_id":5282916,"score":2},{"doc_id":"21885679","title":"A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries.","abstract":"Bacteriophages belonging to the order Caudovirales possess a tail acting as a molecular nanomachine used during infection to recognize the host cell wall, attach to it, pierce it, and ensure the high-efficiency delivery of the genomic DNA to the host cytoplasm. In this review, we provide a comprehensive analysis of the various proteins constituting tailed bacteriophages from a structural viewpoint. To this end, we had in mind to pinpoint the resemblances within and between functional modules such as capsid/tail connectors, the tails themselves, or the tail distal host recognition devices, termed baseplates. This comparison has been extended to bacterial machineries embedded in the cell wall, for which shared molecular homology with phages has been recently revealed. This is the case for the type VI secretion system (T6SS), an inverted phage tail at the bacterial surface, or bacteriocins. Gathering all these data, we propose that a unique ancestral protein fold may have given rise to a large number of bacteriophage modules as well as to some related bacterial machinery components.","corpus_id":9299498,"score":2},{"doc_id":"22297990","title":"Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17.","abstract":"Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371-553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space group P2(1)2(1)2(1) (unit-cell parameters a = 61.2, b = 86.0, c = 118.4 Å) and space group C222(1) (unit-cell parameters a = 68.3, b = 145.6, c = 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress.","corpus_id":9817331,"score":2},{"doc_id":"22303017","title":"Structural basis for antifreeze activity of ice-binding protein from arctic yeast.","abstract":"Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of ∼25 kDa, which can lower the freezing point below the melting point once it binds to ice. LeIBP is a member of a large class of ice-binding proteins, the structures of which are unknown. Here, we report the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57- and 2.43-Å resolution, respectively. Structural analysis of the LeIBPs revealed a dimeric right-handed β-helix fold, which is composed of three parts: a large coiled structural domain, a long helix region (residues 96-115 form a long α-helix that packs along one face of the β-helix), and a C-terminal hydrophobic loop region ((243)PFVPAPEVV(251)). Unexpectedly, the C-terminal hydrophobic loop region has an extended conformation pointing away from the body of the coiled structural domain and forms intertwined dimer interactions. In addition, structural analysis of glycosylated LeIBP with sugar moieties attached to Asn(185) provides a basis for interpreting previous biochemical analyses as well as the increased stability and secretion of glycosylated LeIBP. We also determined that the aligned Thr/Ser/Ala residues are critical for ice binding within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a common β-helical fold similar to that of canonical hyperactive antifreeze proteins, the ice-binding site is more complex and does not have a simple ice-binding motif. In conclusion, we could identify the ice-binding site of LeIBP and discuss differences in the ice-binding modes compared with other known antifreeze proteins and ice-binding proteins.","corpus_id":26030063,"score":2},{"doc_id":"22611190","title":"Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.","abstract":"Phages of the Caudovirales order possess a tail that recognizes the host and ensures genome delivery upon infection. The X-ray structure of the approximately 1.8 MDa host adsorption device (baseplate) from the lactococcal phage TP901-1 shows that the receptor-binding proteins are pointing in the direction of the host, suggesting that this organelle is in a conformation ready for host adhesion. This result is in marked contrast with the lactococcal phage p2 situation, whose baseplate is known to undergo huge conformational changes in the presence of Ca(2+) to reach its active state. In vivo infection experiments confirmed these structural observations by demonstrating that Ca(2+) ions are required for host adhesion among p2-like phages (936-species) but have no influence on TP901-1-like phages (P335-species). These data suggest that these two families rely on diverse adhesion strategies which may lead to different signaling for genome release.","corpus_id":863683,"score":2},{"doc_id":"22645347","title":"Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers.","abstract":"The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.","corpus_id":22597494,"score":2},{"doc_id":"22659573","title":"New insights into pb5, the receptor binding protein of bacteriophage T5, and its interaction with its Escherichia coli receptor FhuA.","abstract":"The majority of bacterial viruses are bacteriophages bearing a tail that serves to recognise the bacterial surface and deliver the genome into the host cell. Infection is initiated by the irreversible interaction between the viral receptor binding protein (RBP) and a receptor at the surface of the bacterium. This interaction results ultimately in the phage DNA release in the host cytoplasm. Phage T5 infects Escherichia coli after binding of its RBP pb5 to the outer membrane ferrichrome transporter FhuA. Here, we have studied the complex formed by pb5 and FhuA by a variety of biophysical and biochemical techniques. We show that unlike RBPs of known structures, pb5 probably folds as a unique domain fulfilling both functions of binding to the host receptor and interaction with the rest of the phage. Pb5 likely binds to the domain occluding the β-barrel of FhuA as well as to external loops of the barrel. Furthermore, upon binding to FhuA, pb5 undergoes conformational changes, at the secondary and tertiary structure level that would be the key to the transmission of the signal through the tail to the capsid, triggering DNA release. This is the first structural information regarding the binding of a RBP to a proteic receptor.","corpus_id":20354844,"score":2},{"doc_id":"22666655","title":"The C-terminal cysteine annulus participates in auto-chaperone function for Salmonella phage P22 tailspike folding and assembly.","abstract":"Elongated trimeric adhesins are a distinct class of proteins employed by phages and viruses to recognize and bind to their host cells, and by bacteria to bind to their target cells and tissues. The tailspikes of E. coli phage K1F and Bacillus phage Ø29 exhibit auto-chaperone activity in their trimeric C-terminal domains. The P22 tailspike is structurally homologous to those adhesins. Though there are no disulfide bonds or reactive cysteines in the native P22 tailspikes, a set of C-terminal cysteines are very reactive in partially folded intermediates, implying an unusual local conformation in the domain. This is likely to be involved in the auto-chaperone function. We examined the unusual reactivity of C-terminal tailspike cysteines during folding and assembly as a potential reporter of auto-chaperone function. Reaction with IAA blocked productive refolding in vitro, but not off-pathway aggregation. Two-dimensional PAGE revealed that the predominant intermediate exhibiting reactive cysteine side chains was a partially folded monomer. Treatment with reducing reagent promoted native trimer formation from these species, consistent with transient disulfide bonds in the auto-chaperone domain. Limited enzymatic digestion and mass spectrometry of folding and assembly intermediates indicated that the C-terminal domain was compact in the protrimer species. These results indicate that the C-terminal domain of the P22 tailspike folds itself and associates prior to formation of the protrimer intermediate, and not after, as previously proposed. The C-terminal cysteines and triple β-helix domains apparently provide the staging for the correct auto-chaperone domain formation, needed for alignment of P22 tailspike native trimer.","corpus_id":17799096,"score":2},{"doc_id":"24155371","title":"Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages.","abstract":"The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process that is initiated from the proteins forming the distal tail tip complex. In Gram-positive-bacterium-infecting siphophages, the distal tail (Dit) protein has been structurally characterized and is proposed to represent a baseplate hub docking structure. It is organized as a hexameric ring that connects the tail tube and the adsorption device. In this study, we report the characterization of pb9, a tail tip protein of Escherichia coli bacteriophage T5. By immunolocalization, we show that pb9 is located in the upper part of the cone of the T5 tail tip, at the end of the tail tube. The crystal structure of pb9 reveals a two-domain protein. Domain A exhibits remarkable structural similarity with the N-terminal domain of known Dit proteins, while domain B adopts an oligosaccharide/oligonucleotide-binding fold (OB-fold) that is not shared by these proteins. We thus propose that pb9 is the Dit protein of T5, making it the first Dit protein described for a Gram-negative-bacterium-infecting siphophage. Multiple sequence alignments suggest that pb9 is a paradigm for a large family of Dit proteins of siphophages infecting mostly Gram-negative hosts. The modular structure of the Dit protein maintains the basic building block that would be conserved among all siphophages, combining it with a more divergent domain that might serve specific host adhesion properties.","corpus_id":25872618,"score":2},{"doc_id":"24316831","title":"Crystallization of the C-terminal domain of the bacteriophage T5 L-shaped fibre.","abstract":"Tails of bacteriophage T5 (a member of the Siphoviridae family) were studied by electron microscopy. For the distal parts of the L-shaped tail fibres, which are involved in host cell receptor binding, a low-resolution volume was calculated. Several C-terminal fragments of the fibre were expressed and purified. Crystals of two of them were obtained that belonged to space groups P63 and R32 and diffracted synchrotron radiation to 2.3 and 2.9 Å resolution, respectively. A single-wavelength anomalous dispersion data set to 2.5 Å resolution was also collected from a selenomethionine-derivatized crystal of one of the fragments, which belonged to space group C2.","corpus_id":22403299,"score":2},{"doc_id":"24816102","title":"Bacteriophage P22 tailspike: structure of the complete protein and function of the interdomain linker.","abstract":"Attachment of phages to host cells, followed by phage DNA ejection, represents the first stage of viral infection of bacteria. Salmonella phage P22 has been extensively studied, serving as an experimental model for bacterial infection by phages. P22 engages bacteria by binding to the sugar moiety of lipopolysaccharides using the viral tailspike protein for attachment. While the structures of the N-terminal particle-binding domain and the major receptor-binding domain of the tailspike have been analyzed individually, the three-dimensional organization of the intact protein, including the highly conserved linker region between the two domains, remained unknown. A single amino-acid exchange in the linker sequence made it possible to crystallize the full-length protein. Two crystal structures of the linker region are presented: one attached to the N-terminal domain and the other present within the complete tailspike protein. Both retain their biological function, but the mutated full-length tailspike displays a retarded folding pathway. Fitting of the full-length tailspike into a published cryo-electron microscopy map of the P22 virion requires an elastic distortion of the crystal structure. The conservation of the linker suggests a role in signal transmission from the distal tip of the molecule to the phage head, eventually leading to DNA ejection.","corpus_id":19300673,"score":2},{"doc_id":"25005101","title":"Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34.","abstract":"The phage-proximal part of the long tail fibres of bacteriophage T4 consists of a trimer of the 1289 amino-acid gene product 34 (gp34). Different carboxy-terminal parts of gp34 have been produced and crystallized. Crystals of gp34(726-1289) diffracting X-rays to 2.9 Å resolution, crystals of gp34(781-1289) diffracting to 1.9 Å resolution and crystals of gp34(894-1289) diffracting to 3.0 and 2.0 Å resolution and belonging to different crystal forms were obtained. Native data were collected for gp34(726-1289) and gp34(894-1289), while single-wavelength anomalous diffraction data were collected for selenomethionine-containing gp34(781-1289) and gp34(894-1289). For the latter, high-quality anomalous signal was obtained.","corpus_id":26376710,"score":2},{"doc_id":"26805872","title":"Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis.","abstract":"The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host's O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.","corpus_id":334754,"score":2},{"doc_id":"28510021","title":"Molecular assembly and structure of the bacteriophage T4 tail.","abstract":"The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8 Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.","corpus_id":9922995,"score":2},{"doc_id":"28665339","title":"Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.","abstract":"Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900-1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146-1238), while the C-terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.","corpus_id":2193886,"score":2},{"doc_id":"29204885","title":"Bacteriophage T4 long tail fiber domains.","abstract":"Bacteriophage T4 initially recognizes its host cells using its long tail fibers. Long tail fibers consist of a phage-proximal and a phage-distal rod, each around 80 nm long and attached to each other at a slight angle. The phage-proximal rod is formed by a homo-trimer of gene product 34 (gp34) and is attached to the phage-distal rod by a monomer of gp35. The phage-distal rod consists of two protein trimers: a trimer of gp36, attached to gp35, although most of the phage-distal rod, including the receptor-binding domain, is formed by a trimer of gp37. In this review, we discuss what is known about the detailed structure and function of the different long tail fiber domains. Partial crystal structures of gp34 and gp37 have revealed the presence of new protein folds, some of which are present in several repeats, while others are apparently unique. Gp38, a phage chaperone protein necessary for folding of gp37, is thought to act on an α-helical coiled-coil region in gp37. Future studies should reveal the remaining structure of the long tail fibers, how they assemble into a functional unit, and how the long tail fibers trigger the infection process after successful recognition of a suitable host bacterium.","corpus_id":4871689,"score":2},{"doc_id":"29209037","title":"Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.","abstract":"The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.","corpus_id":21264668,"score":2},{"doc_id":"18189419","title":"Crystal structure of a novel bacterial cell-surface flagellin binding to a polysaccharide.","abstract":"Bacterial flagellins are generally self-assembled into extracellular flagella for cell motility. However, the flagellin homologue p5 is found on the cell surface of Sphingomonas sp. A1 (strain A1) and binds tightly to the alginate polysaccharide. To assimilate alginate, strain A1 forms a mouthlike pit on the cell surface and concentrates the polymer in the pit. p5 is a candidate receptor that recognizes extracellular alginate and controls pit formation. To improve our understanding of the structure and function of p5, we determined the crystal structure of truncated p5 (p5DeltaN53C45) at 2.0 A resolution. This, to our knowledge, is the first structure of flagellin_IN motif-containing flagellin. p5DeltaN53C45 consists of two domains: an alpha-domain rich in alpha-helices that forms the N- and C-terminal regions and a beta-domain rich in beta-strands that constitutes the central region. The alpha-domain is structurally similar to the D1 domain of Salmonella typhimurium flagellin, while the beta-domain is structurally similar to the finger domain of the bacteriophage T4 baseplate protein that is important for intermolecular interactions between baseplate and a long or short tail fiber. Results from the deletion mutant analysis suggest that residues 20-40 and 353-363 are responsible for alginate binding. Truncated N- and C-terminal regions are thought to constitute alpha-helices extending from the alpha-domain. On the basis of the size and surface charge, the cleft in extended alpha-helices is proposed as an alginate binding site of p5. Structural similarity in the beta-domain suggests that the beta-domain is involved in the proper localization and/or orientation of p5 on the cell surface.","corpus_id":11163721,"score":1},{"doc_id":"18201719","title":"Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.","abstract":"Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.","corpus_id":43335465,"score":1},{"doc_id":"19218213","title":"Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre.","abstract":"Avian reovirus fibre, a homo-trimer of the sigmaC protein, is a minor component of the avian reovirus outer capsid. It is anchored via a short N-terminal sequence to the inner capsid lambdaC pentamer, and its protruding globular C-terminal domain is responsible for primary host cell attachment. We have previously solved the structure of a receptor-binding fragment in which residues 160-191 form a triple beta-spiral and 196-326 a beta-barrel head domain. Here we have expressed, purified and crystallized a major sigmaC fragment comprising residues 117-326. Its structure, which was solved by molecular replacement using the previously determined receptor-binding domain structure and refined to 1.75 A (0.175 nm) resolution, reveals an alpha-helical triple coiled-coil connected to the previously solved structure by a zinc-ion-containing linker. The coiled-coil domain contains two chloride ion binding sites, as well as specific trimerization and registration sequences. The linker may act as a functionally important hinge.","corpus_id":206211556,"score":1},{"doc_id":"19241380","title":"Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.","abstract":"The tail needle, gp26, is a highly stable homo-trimeric fiber found in the tail apparatus of bacteriophage P22. In the mature virion, gp26 is responsible for plugging the DNA exit channel, and likely plays an important role in penetrating the host cell envelope. In this article, we have determined the 1.98 A resolution crystal structure of gp26 bound to xenon gas. The structure led us to identify a calcium and a chloride ion intimately bound at the interior of alpha-helical core, as well as seven small cavities occupied by xenon atoms. The two ions engage in buried polar interactions with gp26 side chains that provide specificity and register to gp26 helical core, thus enhancing its stability. Conversely, the distribution of xenon accessible cavities correlates well with the flexibility of the fiber observed in solution and in the crystal structure. We suggest that small internal cavities in gp26 between the helical core and the C-terminal tip allow for flexible swinging of the latter, without affecting the overall stability of the protein. The C-terminal tip may be important in scanning the bacterial surface in search of a cell-envelope penetration site, or for recognition of a yet unidentified receptor on the surface of the host.","corpus_id":25594438,"score":1},{"doc_id":"19482036","title":"An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil.","abstract":"Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated alpha-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 A. gp26 tail needles display a high level of structural stability in solution, with T(m) (temperature of melting) between 85 and 95 degrees C. To determine how the structural stability of these phage fibers correlates with the length of the alpha-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the alpha-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the alpha-helical core.","corpus_id":27199806,"score":1},{"doc_id":"19895817","title":"The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins.","abstract":"The final step in the morphogenesis of long-tailed double-stranded DNA bacteriophages is the joining of the DNA-filled head to the tail. The connector is a specialized structure of the head that serves as the interface for tail attachment and the point of egress for DNA from the head during infection. Here, we report the determination of a 2.1 A crystal structure of gp6 of bacteriophage HK97. Through structural comparisons, functional studies, and bioinformatic analysis, gp6 has been determined to be a component of the connector of phage HK97 that is evolutionarily related to gp15, a well-characterized connector component of bacteriophage SPP1. Whereas the structure of gp15 was solved in a monomeric form, gp6 crystallized as an oligomeric ring with the dimensions expected for a connector protein. Although this ring is composed of 13 subunits, which does not match the symmetry of the connector within the phage, sequence conservation and modeling of this structure into the cryo-electron microscopy density of the SPP1 connector indicate that this oligomeric structure represents the arrangement of gp6 subunits within the mature phage particle. Through sequence searches and genomic position analysis, we determined that gp6 is a member of a large family of connector proteins that are present in long-tailed phages. We have also identified gp7 of HK97 as a homologue of gp16 of phage SPP1, which is the second component of the connector of this phage. These proteins are members of another large protein family involved in connector assembly.","corpus_id":6534193,"score":1},{"doc_id":"20693685","title":"Structure of the N-terminal fragment of Escherichia coli Lon protease.","abstract":"The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.","corpus_id":10466829,"score":1},{"doc_id":"20826161","title":"The solution structure of the C-terminal Ig-like domain of the bacteriophage λ tail tube protein.","abstract":"Immunoglobulin (Ig)-like domains are found frequently on the surface of tailed double-stranded DNA bacteriophages, yet their functional role remains obscure. Here, we have investigated the structure and function of the C-terminal Ig-like domain of gpV (gpV(C)), the tail tube protein of phage λ. This domain has been predicted through sequence similarity to be a member of the bacterial Ig-like domain 2 (Big_2) family, which is composed of more than 1300 phage and bacterial sequences. Using trypsin proteolysis, we have delineated the boundaries of gpV(C) and have shown that its removal reduces the biological activity of gpV by 100-fold; thus providing a definitive demonstration of a functional role for this domain. Determination of the solution structure of gpV(C) by NMR spectroscopy showed that it adopts a canonical Ig-like fold of the I-set class. This represents the first structure of a phage-encoded Ig-like domain and only the second structure of a Big_2 domain. Structural and sequence comparisons indicate that the gpV(C) structure is more representative of both the phage-encoded Big_2 domains and Big_2 domains in general than the other available Big_2 structure. Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV(C) that may be important in mediating the function of this domain.","corpus_id":45685977,"score":1},{"doc_id":"21646642","title":"Unraveling lactococcal phage baseplate assembly by mass spectrometry.","abstract":"Bacteriophages belonging to the Caudovirales order possess a tail acting as a molecular machine used during infection to recognize the host and ensure high-efficiency genome delivery to the cell cytoplasm. They bear a large and sophisticated multiprotein organelle at their distal tail end, either a baseplate or a tail-tip, which is the control center for infectivity. We report here insights into the baseplate assembly pathways of two lactoccocal phages (p2 and TP901-1) using electrospray ionization-mass spectrometry. Based on our \"block cloning\" strategy we have expressed large complexes of their baseplates as well as several significant structural subcomplexes. Previous biophysical characterization using size-exclusion chromatography coupled with on-line light scattering and refractometry demonstrated that the overproduced recombinant proteins interact with each other to form large (up to 1.9 MDa) and stable assemblies. The structures of several of these complexes have been determined by x-ray diffraction or by electron microscopy. In this contribution, we demonstrate that electrospray ionization-mass spectrometry yields accurate mass measurements for the different baseplate complexes studied from which their stoichiometries can be discerned, and that the subspecies observed in the spectra provide valuable information on the assembly mechanisms of these large organelles.","corpus_id":20813814,"score":1},{"doc_id":"21805520","title":"Crystal structure of the read-through domain from bacteriophage Qβ A1 protein.","abstract":"Bacteriophage Qβ is a small RNA virus that infects Escherichia coli. The virus particle contains a few copies of the minor coat protein A1, a C-terminally prolonged version of the coat protein, which is formed when ribosomes occasionally read-through the leaky stop codon of the coat protein. The crystal structure of the read-through domain from bacteriophage Qβ A1 protein was determined at a resolution of 1.8 Å. The domain consists of a heavily deformed five-stranded β-barrel on one side of the protein and a β-hairpin and a three-stranded β-sheet on the other. Several short helices and well-ordered loops are also present throughout the protein. The N-terminal part of the read-through domain contains a prominent polyproline type II helix. The overall fold of the domain is not similar to any published structure in the Protein Data Bank.","corpus_id":3418824,"score":1},{"doc_id":"22153511","title":"Structural conservation of the myoviridae phage tail sheath protein fold.","abstract":"Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.","corpus_id":5103216,"score":1},{"doc_id":"23530214","title":"Viral infection modulation and neutralization by camelid nanobodies.","abstract":"Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides covering the entire bacterium. The phage TP901-1 baseplate, located at the tip of the tail, harbors 18 trimeric receptor binding proteins (RBPs) promoting adhesion to a specific lactococcal strain. Phage TP901-1 adhesion does not require major conformational changes or Ca(2+), which contrasts other lactococcal phages. Here, we produced and characterized llama nanobodies raised against the purified baseplate and the Tal protein of phage TP901-1 as tools to dissect the molecular determinants of phage TP901-1 infection. Using a set of complementary techniques, surface plasmon resonance, EM, and X-ray crystallography in a hybrid approach, we identified binders to the three components of the baseplate, analyzed their affinity for their targets, and determined their epitopes as well as their functional impact on TP901-1 phage infectivity. We determined the X-ray structures of three nanobodies in complex with the RBP. Two of them bind to the saccharide binding site of the RBP and are able to fully neutralize TP901-1 phage infectivity, even after 15 passages. These results provide clear evidence for a practical use of nanobodies in circumventing lactococcal phages viral infection in dairy fermentation.","corpus_id":33331946,"score":1},{"doc_id":"24100566","title":"Crystallization of the C-terminal head domain of the fibre protein from a siadenovirus, turkey adenovirus 3.","abstract":"Turkey adenovirus 3 belongs to the genus Siadenovirus. Its predicted fibre protein consists of an N-terminal virus-attachment domain, a central shaft domain and a head domain at the C-terminus. The head domain has little sequence identity to known adenovirus fibre head structures. Crystals of the fibre head domain consisting of amino acids 304-454 with an N-terminal purification tag were produced. Crystals of native and selenomethionine-derivatized protein belonged to space group I23 (unit-cell parameter 99 Å). They diffracted synchrotron radiation to 2.0 and 2.14 Å resolution, respectively, and are expected to contain one monomer in the asymmetric unit.","corpus_id":6477287,"score":1},{"doc_id":"24316834","title":"Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.","abstract":"Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.","corpus_id":35326870,"score":1},{"doc_id":"24336205","title":"Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.","abstract":"Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host.","corpus_id":205236687,"score":1},{"doc_id":"24531468","title":"Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.","abstract":"Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.","corpus_id":22279907,"score":1},{"doc_id":"24598932","title":"Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion.","abstract":"In X-ray crystallographic analysis, the single-wavelength and multi-wavelength anomalous diffraction (SAD and MAD) methods have been widely used in order to solve the phase problem. Selenium-labelled methionine has been shown to be very effective for anomalous dispersion phasing, and at least one selenomethionine is required for every 100 amino acids. Some proteins, such as the Arabidopsis thaliana thylakoid lumen protein AtTLP18.3, can be overexpressed in an Escherichia coli system and high-quality protein crystals can be obtained. However, AtTLP18.3 contains no methionine residues, and site-directed mutagenesis was required in order to introduce methionine residues into the protein. A criterion for the mutated residues is that they should avoid affecting the structure and function. In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159) of AtTLP18.3 were mutated to methionine residues. After overexpression and purification, only two single-mutant lines, L128M and I159M, could be crystallized. Finally, a double-mutation line of truncated AtTLP18.3 with L128M and I159M mutations was constructed. The structure of the double mutant AtTLP18.3 protein was resolved using the single-wavelength anomalous diffraction method at 2.6 Å resolution. The results indicated that a combination of secondary-structure and solvent-accessibility prediction for methionine substitution is a useful method in SAD and MAD phasing.","corpus_id":22549296,"score":1},{"doc_id":"25064136","title":"Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.","abstract":"BACKGROUND: Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge. METHODS: The CHAP(K) domain of LysK was crystallized and high-resolution diffraction data was collected both from a native protein crystal and a methylmercury chloride derivatized crystal. The anomalous signal contained in the derivative data allowed the location of heavy atom sites and phase determination. The resulting structures were completed, refined and analyzed. The presence of calcium and zinc ions in the structure was confirmed by X-ray fluorescence emission spectroscopy. Zymogram analysis was performed on the enzyme and selected site-directed mutants. RESULTS: The structure of CHAP(K) revealed a papain-like topology with a hydrophobic cleft, where the catalytic triad is located. Ordered buffer molecules present in this groove may mimic the peptidoglycan substrate. When compared to previously solved CHAP domains, CHAP(K) contains an additional lobe in its N-terminal domain, with a structural calcium ion, coordinated by residues Asp45, Asp47, Tyr49, His51 and Asp56. The presence of a zinc ion in the active site was also apparent, coordinated by the catalytic residue Cys54 and a possible substrate analogue. Site-directed mutagenesis was used to demonstrate that residues involved in calcium binding and of the proposed active site were important for enzyme activity. CONCLUSIONS: The high-resolution structure of the CHAP(K) domain of LysK was determined, suggesting the location of the active site, the substrate-binding groove and revealing the presence of a structurally important calcium ion. A zinc ion was found more loosely bound. Based on the structure, we propose a possible reaction mechanism. Future studies will be aimed at co-crystallizing CHAP(K) with substrate analogues and elucidating its role in the complete LysK protein. This, in turn, may lead to the design of site-directed mutants with altered activity or substrate specificity.","corpus_id":1380517,"score":1},{"doc_id":"25994880","title":"Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.","abstract":"BACKGROUND: In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus. METHODS: We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414-535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution. RESULTS: Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed. CONCLUSIONS: Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.","corpus_id":8568594,"score":1},{"doc_id":"26418008","title":"Structure and Sialyllactose Binding of the Carboxy-Terminal Head Domain of the Fibre from a Siadenovirus, Turkey Adenovirus 3.","abstract":"The virulent form of turkey adenovirus 3 (TAdV-3), also known as turkey hemorrhagic enteritis virus (THEV), is an economically important poultry pathogen, while the avirulent form is used as a vaccine. TAdV-3 belongs to the genus Siadenovirus. The carboxy-terminal region of its fibre does not have significant sequence similarity to any other adenovirus fibre heads of known structure. Two amino acid sequence differences between virulent and avirulent TAdV-3 map on the fibre head: where virulent TAdV-3 contains Ile354 and Thr376, avirulent TAdV-3 contains Met354 and Met376. We determined the crystal structures of the trimeric virulent and avirulent TAdV-3 fibre head domains at 2.2 Å resolution. Each monomer contains a beta-sandwich, which, surprisingly, resembles reovirus fibre head more than other adenovirus fibres, although the ABCJ-GHID topology is conserved in all. A beta-hairpin insertion in the C-strand of each trimer subunit embraces its neighbouring monomer. The avirulent and virulent TAdV-3 fibre heads are identical apart from the exact orientation of the beta-hairpin insertion. In vitro, sialyllactose was identified as a ligand by glycan microarray analysis, nuclear magnetic resonance spectroscopy, and crystallography. Its dissociation constant was measured to be in the mM range by isothermal titration calorimetry. The ligand binds to the side of the fibre head, involving amino acids Glu392, Thr419, Val420, Lys421, Asn422, and Gly423 binding to the sialic acid group. It binds slightly more strongly to the avirulent form. We propose that, in vivo, the TAdV-3 fibre may bind a sialic acid-containing cell surface component.","corpus_id":23279362,"score":1},{"doc_id":"26574546","title":"Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.","abstract":"Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal \"trimer of hairpins\" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.","corpus_id":34346428,"score":1},{"doc_id":"26814179","title":"The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.","abstract":"UNLABELLED: The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages. Lactococcal phage Tuc2009 possesses extensive genomic homology to phage TP901-1. However, striking differences in the baseplate-encoding genes stimulated our interest in solving the structure of this host's adhesion device. We report here the X-ray structures of phage Tuc2009 receptor binding protein (RBP) and of a \"tripod\" assembly of three baseplate components, BppU, BppA, and BppL (the RBP). These structures made it possible to generate a realistic atomic model of the complete Tuc2009 baseplate that consists of an 84-protein complex: 18 BppU, 12 BppA, and 54 BppL proteins. The RBP head domain possesses a different fold than those of phages p2, TP901-1, and 1358, while the so-called \"stem\" and \"neck\" domains share structural features with their equivalents in phage TP901-1. The BppA module interacts strongly with the BppU N-terminal domain. Unlike other characterized lactococcal phages, Tuc2009 baseplate harbors two different carbohydrate recognition sites: one in the bona fide RBP head domain and the other in BppA. These findings represent a major step forward in deciphering the molecular mechanism by which Tuc2009 recognizes its saccharidic receptor(s) on its host. IMPORTANCE: Understanding how siphophages infect Lactococcus lactis is of commercial importance as they cause milk fermentation failures in the dairy industry. In addition, such knowledge is crucial in a general sense in order to understand how viruses recognize their host through protein-glycan interactions. We report here the lactococcal phage Tuc2009 receptor binding protein (RBP) structure as well as that of its baseplate. The RBP head domain has a different fold than those of phages p2, TP901-1, and 1358, while the so-called \"stem\" and \"neck\" share the fold characteristics also found in the equivalent baseplate proteins of phage TP901-1. The baseplate structure contains, in contrast to other characterized lactococcal phages, two different carbohydrate binding modules that may bind different motifs of the host's surface polysaccharide.","corpus_id":15144214,"score":1},{"doc_id":"27334597","title":"Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains.","abstract":"BACKGROUND: Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose. METHODS: Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay. RESULTS: The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly. CONCLUSIONS: The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge suggest that RAdV-1 uses a different natural receptor for cell attachment than TAdV-3. Deletion of the beta-hairpin arm shows little impact on the structure and stability of the siadenovirus fibre heads.","corpus_id":11335559,"score":1},{"doc_id":"29695426","title":"Structural and Functional Features of the Reovirus σ1 Tail.","abstract":"Mammalian orthoreovirus attachment to target cells is mediated by the outer capsid protein σ1, which projects from the virion surface. The σ1 protein is a homotrimer consisting of a filamentous tail, which is partly inserted into the virion; a body domain constructed from β-spiral repeats; and a globular head with receptor-binding properties. The σ1 tail is predicted to form an α-helical coiled coil. Although σ1 undergoes a conformational change during cell entry, the nature of this change and its contributions to viral replication are unknown. Electron micrographs of σ1 molecules released from virions identified three regions of flexibility, including one at the midpoint of the molecule, that may be involved in its structural rearrangement. To enable a detailed understanding of essential σ1 tail organization and properties, we determined high-resolution structures of the reovirus type 1 Lang (T1L) and type 3 Dearing (T3D) σ1 tail domains. Both molecules feature extended α-helical coiled coils, with T1L σ1 harboring central chloride ions. Each molecule displays a discontinuity (stutter) within the coiled coil and an unexpectedly seamless transition to the body domain. The transition region features conserved interdomain interactions and appears rigid rather than highly flexible. Functional analyses of reoviruses containing engineered σ1 mutations suggest that conserved residues predicted to stabilize the coiled-coil-to-body junction are essential for σ1 folding and encapsidation, whereas central chloride ion coordination and the stutter are dispensable for efficient replication. Together, these findings enable modeling of full-length reovirus σ1 and provide insight into the stabilization of a multidomain virus attachment protein. IMPORTANCE While it is established that different conformational states of attachment proteins of enveloped viruses mediate receptor binding and membrane fusion, less is understood about how such proteins mediate attachment and entry of nonenveloped viruses. The filamentous reovirus attachment protein σ1 binds cellular receptors; contains regions of predicted flexibility, including one at the fiber midpoint; and undergoes a conformational change during cell entry. Neither the nature of the structural change nor its contribution to viral infection is understood. We determined crystal structures of large σ1 fragments for two different reovirus serotypes. We observed an unexpectedly tight transition between two domains spanning the fiber midpoint, which allows for little flexibility. Studies of reoviruses with engineered changes near the σ1 midpoint suggest that the stabilization of this region is critical for function. Together with a previously determined structure, we now have a complete model of the full-length, elongated reovirus σ1 attachment protein.","corpus_id":25113018,"score":1},{"doc_id":"18096638","title":"Solution structure of the C-terminal domain of Ole e 9, a major allergen of olive pollen.","abstract":"Ole e 9 is an olive pollen allergen belonging to group 2 of pathogenesis-related proteins. The protein is composed of two immunological independent domains: an N-terminal domain (NtD) with 1,3-beta-glucanase activity, and a C-terminal domain (CtD) that binds 1,3-beta-glucans. We have determined the three-dimensional structure of CtD-Ole e 9 (101 amino acids), which consists of two parallel alpha-helices forming an angle of approximately 55 degrees , a small antiparallel beta-sheet with two short strands, and a 3-10 helix turn, all connected by long coil segments, resembling a novel type of folding among allergens. Two regions surrounded by aromatic residues (F49, Y60, F96, Y91 and Y31, H68, Y65, F78) have been localized on the protein surface, and a role for sugar binding is suggested. The epitope mapping of CtD-Ole e 9 shows that B-cell epitopes are mainly located on loops, although some of them are contained in secondary structural elements. Interestingly, the IgG and IgE epitopes are contiguous or overlapped, rather than coincident. The three-dimensional structure of CtD-Ole e 9 might help to understand the underlying mechanism of its biochemical function and to determine possible structure-allergenicity relationships.","corpus_id":23733055,"score":0},{"doc_id":"18373550","title":"Structural models and binding site prediction of the C-terminal domain of human Hsp90: a new target for anticancer drugs.","abstract":"Heat shock protein 90 is a valuable target for anticancer drugs because of its role in the activation and stabilization of multiple oncogenic signalling proteins. While several compounds inhibit heat shock protein 90 by binding the N-terminal domain, recent studies have proved that the C-terminal domain is important for dimerization of the chaperone and contains an additional binding site for inhibitors. Heat shock protein 90 inhibition achieved with molecules binding to the C-terminal domain provides an additional and novel opportunity to design and develop drugs. Therefore, for the first time, we have investigated the structure and the dynamic behaviour of the C-terminal domain of human heat shock protein 90 with and without the small-middle domain, using homology modelling and molecular dynamics simulations. In addition, secondary structure predictions and peptide folding simulations proved useful to investigate a putative additional alpha-helix located between H18 and beta20 of the C-terminal domain. Finally, we used the structural information to infer the location of the binding site located in the C-terminal domain by using a number of computational tools. The predicted pocket is formed by two grooves located between helix H18, the loop downstream of H18 and the loop connecting helices H20 and H21 of each monomer of the C-terminal domain, with only two amino acids contributing from each middle domain.","corpus_id":31018983,"score":0},{"doc_id":"18552768","title":"Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail.","abstract":"ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.","corpus_id":19426181,"score":0},{"doc_id":"19324050","title":"NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.","abstract":"The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the \"unstructured\" amino terminus is required for recombination.","corpus_id":25344386,"score":0},{"doc_id":"19447113","title":"Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding.","abstract":"Several crystal structures of AFL, a novel lipase from the archaeon Archaeoglobus fulgidus, complexed with various ligands, have been determined at about 1.8 A resolution. This enzyme has optimal activity in the temperature range of 70-90 degrees C and pH 10-11. AFL consists of an N-terminal alpha/beta-hydrolase fold domain, a small lid domain, and a C-terminal beta-barrel domain. The N-terminal catalytic domain consists of a 6-stranded beta-sheet flanked by seven alpha-helices, four on one side and three on the other side. The C-terminal lipid binding domain consists of a beta-sheet of 14 strands and a substrate covering motif on top of the highly hydrophobic substrate binding site. The catalytic triad residues (Ser136, Asp163, and His210) and the residues forming the oxyanion hole (Leu31 and Met137) are in positions similar to those of other lipases. Long-chain lipid is located across the two domains in the AFL-substrate complex. Structural comparison of the catalytic domain of AFL with a homologous lipase from Bacillus subtilis reveals an opposite substrate binding orientation in the two enzymes. AFL has a higher preference toward long-chain substrates whose binding site is provided by a hydrophobic tunnel in the C-terminal domain. The unusually large interacting surface area between the two domains may contribute to thermostability of the enzyme. Two amino acids, Asp61 and Lys101, are identified as hinge residues regulating movement of the lid domain. The hydrogen-bonding pattern associated with these two residues is pH dependent, which may account for the optimal enzyme activity at high pH. Further engineering of this novel lipase with high temperature and alkaline stability will find its use in industrial applications.","corpus_id":5604880,"score":0},{"doc_id":"22708907","title":"Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD.","abstract":"BACKGROUND: Type III secretion systems are used by Gram-negative bacteria as \"macromolecular syringes\" to inject effector proteins into eukaryotic cells. Two hydrophobic proteins called translocators form the necessary pore in the host cell membrane. Both translocators depend on binding to a single chaperone in the bacterial cytoplasm to ensure their stability and efficient transport through the secretion needle. It was suggested that the conserved chaperones bind the more divergent translocators via a hexapeptide motif that is found in both translocators and conserved between species. RESULTS: We crystallized a synthetic decapeptide from the Yersinia enterocolitica minor type III secretion translocator YopD bound to its cognate chaperone SycD and determined the complex structure at 2.5 Å resolution. The structure of peptide-bound SycD is almost identical to that of apo SycD with an all helical fold consisting of three tetratricopeptide repeats (TPRs) and an additional C-terminal helix. Peptide-bound SycD formed a kinked head-to-head dimer that had previously been observed for the apo form of SycD. The homodimer interface comprises both helices of the first tetratricopeptide repeat. The YopD peptide bound in extended conformation into a mainly hydrophobic groove on the concave side of SycD. TPRs 1 and 2 of SycD form three hydrophobic pockets that accommodated the conserved hydrophobic residues at position 1, 3 and 6 of the translocator hexapeptide sequence. Two tyrosines that are highly conserved among translocator chaperones contribute to the hydrophobic patches but also form hydrogen bonds to the peptide backbone. CONCLUSIONS: The interaction between SycD and YopD is very similar to the binding of the Pseudomonas minor translocator PopD to its chaperone PcrH and the Shigella major translocator IpaB to its chaperone IpgC. This confirms the prediction made by Kolbe and co-workers that a hexapeptide with hydrophobic residues at three positions is a conserved chaperone binding motif. Because the hydrophobic groove on the concave side of translocator chaperones is involved in binding of the major and the minor translocator, simultaneous binding of both translocators to a single type III secretion class II chaperone appears unlikely.","corpus_id":15764038,"score":0},{"doc_id":"25982270","title":"Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major.","abstract":"Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.","corpus_id":7615194,"score":0},{"doc_id":"29223729","title":"Structure-Function Analysis of the C-Terminal Domain of the Type VI Secretion TssB Tail Sheath Subunit.","abstract":"